Publications

Eggleton, BJ, Steel, MJ & Poulton, CG 2022, Preface, Elsevier.
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Aganetti, MA, Cruz, CS, Galvão, I, Engels, DF, Ricci, MF & Vieira, AT 2022, 'The Gut Microbiota and Immunopathophysiology' in Comprehensive Pharmacology, Elsevier, pp. 492-514.
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Ben-Nissan, B, Choi, G, Choi, AH, Karacan, I & Evans, L 2022, 'Natural and Synthetic Intelligent Self-healing and Adaptive Materials for Medical and Engineering Applications' in Innovative Bioceramics in Translational Medicine I, Springer Singapore, pp. 89-124.
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Blumenthal, DJ, Kabakova, I, Rakich, PT & Vahala, K 2022, 'Integrated Brillouin lasers and their applications' in Brillouin Scattering Part 2, Elsevier, pp. 107-180.
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In this chapter we give a brief history of the Brillouin gain process in optical waveguides and SBLs realized with integrated Brillouin resonators. A brief discussion on the laser fundamental and integral linewidths, the fractional frequency noise, and drift is provided. We discuss progress to date on Brillouin processes in integrated silica, silicon nitride, silicon, and chalcogenide platforms. The underlying Brillouin physics in waveguide materials and the range of waveguide structures and related requirements for photon–phonon phase matching are covered as well as research efforts to implement SBS gain and lasing in these waveguide material systems. Cascaded Brillouin lasing is discussed, including mode engineering approaches to inhibit cascading to enable further linewidth narrowing and higher output powers. Finally, several applications using these integrated Brillouin technologies are presented.

Bourke, JE, Ammit, AJ, Burgess, JK, Gosens, R, Halayko, AJ, Seow, C & Hirst, SJ 2022, 'Smooth Muscle Cells' in Encyclopedia of Respiratory Medicine, Elsevier, pp. 37-51.
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Chowdhury, PR, Stokes, HW & Labbate, M 2022, 'Intégrons: Antibiotic resistance evolution and beyond' in Roberts, AP & Mullany, P (eds), Bacterial Integrative Mobile Genetic Elements, Landes Bioscience, Austin, Texas USA, pp. 53-69.
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Intégrons include a site-specific recombination system that can capture gene cassettes. Gene cassettes are the smallest known mobilizable units of DNA and normally only comprise a single gene and a recombination site essential for the site-specific recombination event to occur. Although the site specific recombination reaction is catalyzed by an integrase protein that is a member of the tyrosine family of site specific recombinases, the biology and biochemistry of the system is unusual in a number of respects. Most notably, gene cassettes comprise a family of elements that are highly diverse both with respect to the genes and the recombination sites within them. Intégrons first came to prominence as a consequence of their infiltrating pathogenic Gram negative bacteria. In this context intégrons commonly possess multiple cassettes with the associated genes conferring, collectively, resistance to a wide range of clinically important antibiotics. As a consequence they are one of the single biggest contributors to the evolution of antibiotic resistant bacteria. Intégrons however are ancient structures that are widely distributed among the Proteobacteria. In the broader context, cassette associated genes are remarkably diverse and highly novel. This mobile cassette 'metagenome' includes a pool of novel gene cassettes potentially available to whole microbial communities. While the function of most cassette genes in this pool remains unknown, it is clear that they are rich source of innovation and novelty.

Clerc, EE, Raina, J-B, Peaudecerf, FJ, Seymour, JR & Stocker, R 2022, 'Survival in a Sea of Gradients: Bacterial and Archaeal Foraging in a Heterogeneous Ocean' in The Microbiomes of Humans, Animals, Plants, and the Environment, Springer International Publishing, pp. 47-102.
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Devkota, HP, Adhikari-Devkota, A, Paudel, KR, Panth, N, Gupta, G, Chellappan, DK, Hansbro, PM & Dua, K 2022, 'Phytochemicals and their Nanoformulations Targeted for Pulmonary Diseases' in Chellappan, DK, Pabreja, K & Faiyazuddin, M (eds), Advanced Drug Delivery Strategies for Targeting Chronic Inflammatory Lung Diseases, Springer Singapore, Singapore, pp. 95-106.
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Plant-derived natural products, also known as phytochemicals, are one of the most important sources of drug discovery. Due to their wide abundance in nature and structural diversity, various phytochemicals are gaining research interest for the discovery and development of effective therapeutic agents for various diseases, including lung diseases. Bioavailability and metabolism have been the main limiting factors for the effective use of these phytochemicals. In recent years, various novel drug delivery systems, including nanoformulations, have been evaluated for the effective delivery of these phytochemicals. This chapter will cover research related to the potential use of phytochemicals (e.g., polyphenols, alkaloids, steroids) and their nanoformulations in lung diseases.

Elbeltagi, A, Kushwaha, NL, Srivastava, A & Zoof, AT 2022, 'Artificial intelligent-based water and soil management' in Deep Learning for Sustainable Agriculture, Elsevier, pp. 129-142.
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Artificial intelligence (AI) has revolutionized information technology and shaped the way we live. AI is a computational model that allows computers to learn from data and approximate solutions for complex functions. Due to their flexibility and robustness, AI has been widely applied in large scale fields ranging from robotics to airplane flight control. This chapter discusses the advances in all aspect of AI applied in several issues, such as hydrology, agronomy, meteorology, education, healthcare, action, and more. It focuses specifically on various AI applications related to water and soil management and states that AI achieves high performance, accuracy, and correlation with low statistical errors as a rapid decision tool under changing climate conditions. Brief introductions of AI with their adaptability to agricultural water and soil management are also interpreted. Furthermore, this chapter illustrates how the AI tool will help agricultural decision makers and water and soil managers achieve agricultural sustainability.

Hossain, SI, Islam, MZ, Saha, SC & Deplazes, E 2022, 'Drug Meets Monolayer: Understanding the Interactions of Sterol Drugs with Models of the Lung Surfactant Monolayer Using Molecular Dynamics Simulations' in Methods in Molecular Biology, Springer US, Switzerland, pp. 103-121.
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The lung surfactant monolayer (LSM) is a thin layer of lipids and proteins that forms the air/water interface of the alveoli. The primary function of the LSM is to reduce the surface tension at the air/water interface during breathing. The LSM also forms the main biological barrier for any inhaled particles, including drugs, to treat lung diseases. Elucidating the mechanism by which these drugs bind to and absorb into the LSM requires a molecular-level understanding of any drug-induced changes to the morphology, structure, and phase changes of the LSM.Molecular dynamics simulations have been used extensively to study the structure and dynamics of the LSM. The monolayer is usually simulated in at least two states: the compressed state, mimicking exhalation, and the expanded state, mimicking inhalation. In this chapter, we provide detailed instructions on how to set up, run, and analyze coarse-grained MD simulations to study the concentration-dependent effect of a sterol drug on the LSM, both in the expanded and compressed state.

Ikram, M, Raza, A, Ikram, M & Mahmood, A 2022, 'Carbon Nanocomposite-Based SCs as Wearable Energy Storage' in Nanostructured Materials for Supercapacitors, Springer International Publishing, pp. 451-483.
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Irga, P & Torpy, F 2022, 'Understanding the impacts of air pollution on human experience: Two case studies' in Grau, U & Fernandez-Abascal, G (eds), Folk Costumes, Indo-Pacific Air, Art Paper Editions, Ghent, Begium, pp. 128-135.
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It has long been known that substances in the air can have adverse effects on human health. Today, with the impacts of climate change and human activity changing the world in untold ways, air pollution represents a considerable and global threat to our health. Between 2005 and 2010, the death rate associated with exposure to outdoor air pollution increased globally by 4 per cent, by 5 per cent in China and by a staggering 12 per cent in India (Kumar et al., 2019). The Organisation for Economic Co-operation and Development (OECD) has stated thatoutdoor air pollution exposure is predicted to become the leading environmental cause of premature death by 2050 (WHO Regional Office for Europe, 2015). In 2012 alone, it was estimated that approximately 7 million deaths were related to outdoor air pollution (World Health Organization, 2016). Pollution exposure also has a negative impact on economies, with a reported ~USD$ 1.7 trillion spent on health-related costs in 2010 (Kitamori et al., 2012).Whilst a proportion of air pollution results from natural processes such as bushfire smoke, pollen release and surface dust, in cities large quantities of pollutants are produced from fossil fuel emissions, which comprise a mixture of solid particulate matter (PM) and gases, including oxides of sulphur (SOx), oxides of nitrogen (NOx), carbon monoxide (CO), carbon dioxide (CO2), and ozone (Bai et al., 2018).By examining industrial pollution in China and the pollution resulting from the recent Australian bushfires, we can see how our changing planet is influencing both manmade and biomass generated sources of air pollution. But first, it is important to have an understanding of the pollutants and their risk profiles.

Kabakova, I, Scarcelli, G & Yun, S-H 2022, 'Brillouin light scattering in biological systems' in Brillouin Scattering Part 2, Elsevier, pp. 313-348.
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The past 20 years have seen new application of the physics of Brillouin light scattering to the fields of biology, bioengineering, and biomedicine. Mapping of the 3D micromechanical properties of biological systems with the focused beam of light holds great potential to provide new insights in the range of fundamental biology questions related to cell–matrix interactions, cell differentiation, and pathogenesis. In this chapter we introduce the main principles on which the field of BioBrillouin imaging stands, discuss major technological developments in the instrumentations of Brillouin microscopy, and provide a brief overview of key applications of this technology to various fields of biology and medicine.

Karacan, I, Milthorpe, B, Ben-Nissan, B & Santos, J 2022, 'Stem Cells and Proteomics in Biomaterials and Biomedical Applications' in Innovative Bioceramics in Translational Medicine I, Springer Singapore, pp. 125-157.
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Kuzhiumparambil, U, Kumar, M, Nizio, KD, Alonso, D, Gorst-Allman, P, Kelly, C, MacLeod, B, Forbes, S & Ralph, P 2022, 'Metabolomic profiling of anthropogenically threatened Australian seagrass Zostera muelleri using one- and two-dimensional gas chromatography' in Applied Environmental Metabolomics, Elsevier, pp. 135-151.
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The global decline of seagrass meadows due to sustained pressure from anthropogenic activities and the ongoing threat from climate change has weakened their capacity for supporting coastal productivity and fisheries habitats, while also increasing sediment erosion. The ongoing efforts to prevent seagrass decline require novel tools to monitor seagrass health and assess the effects of habitat management. Such monitoring tools require the use of sensitive indicators to assess the intensity of environmental stressors and to monitor the corresponding responses of seagrass. Environmental metabolomics has proven valuable in identifying such phenotypic traits of abiotic and biotic stress in plants. The identification of metabolite changes in seagrass linked to an environmental stress response may lead to the development of a molecular diagnostic tool that could be used to give an early warning of seagrass stress. Therefore, we explore the potential of one- and two-dimensional gas chromatography coupled with time-of-flight mass spectrometry (1D and 2D GC-TOFMS) in Australia’s most threatened seagrass species—Zostera muelleri. Overall, GC×GC-TOFMS outperformed GC-TOFMS and offered a robust, comprehensive, and superior analytical sensitivity and resolution with a total of 156 metabolites compared to 93 identified in GC-TOFMS. Among these metabolites, >  50% were identified exclusively in GC×GC-TOFMS and include secondary metabolites of the phenylpropenoid class, phytohormones, and various sugar and amino acid derivatives. Therefore, GC×GC-TOFMS represents a comprehensive metabolomics platform for both discovery and targeted studies in seagrass that may aid diagnostic tool development for more targeted seagrass management.

Lawson, CA, Camp, E, Davy, SK, Ferrier-Pagès, C, Matthews, J & Suggett, DJ 2022, 'Informing Coral Reef Conservation Through Metabolomic Approaches' in Coral Reefs of the World, Springer International Publishing, pp. 179-202.
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Macha, IJ & Ben-Nissan, B 2022, 'Past and Future of Wound Dressing in Soft and Hard Tissue Surgery' in Springer Series in Biomaterials Science and Engineering, Springer Singapore, pp. 1-14.
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Mahmud, MAP & Tasmin, N 2022, 'Environmental impact assessment of hydropower stations' in Environmental Assessment of Renewable Energy Conversion Technologies, Elsevier, pp. 213-230.
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McCauley, JI, Ortega, JS, Gentile, C & Ralph, PJ 2022, 'Chapter 7 Microalgal applications in biomedicine and healthcare' in Algae-Based Biomaterials for Sustainable Development, Elsevier, pp. 133-156.
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McCauley, JI, Ortega, JS, Gentile, C & Ralph, PJ 2022, 'Microalgal applications in biomedicine and healthcare' in Algae-Based Biomaterials for Sustainable Development, Elsevier, pp. 133-156.
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The field of research that explores the use of microalgae in biomedicine and health is complex and diverse. Numerous research avenues currently explore the use of microalgae in biomedicine and heath such as: focusing on establishing and boosting nutritional profiles for food applications; identification, characterisation and utilisation of microalgal metabolites with biological activity as functional ingredients and/or drugs; utilisation of recombinant technology to genetically modify the algae for use as production systems for enzymes, antibodies, growth factors, drugs, and vaccines; or the use of microalgae as a source of “biomaterial” for use in applications such as drug carriers or cellular scaffolds for tissue engineering. To illustrate the diversity of microalgae and its potential for utilisation in a wide variety of biomedical and heath care applications, this chapter will present a concise overview of this broad applicability of microalgae in biomedicine and health, while highlighting research that is also occurring into the production and biorefinery of these compounds to facilitate a viable transition from laboratory to commercial production. Thus, this chapter aims to bridge the knowledge gap between both existing and potentially new algae applications, in particular, the use of microalgae as a source of “biomaterials” for biomedicine and health applications.

Mirakhorli, F, Mohseni, SS, Bazaz, SR, Mehrizi, AA, Ralph, PJ & Warkiani, ME 2022, 'Microfluidic Platforms for Cell Sorting' in Sustainable Separation Engineering: Materials, Techniques and Process Development, Wiley, pp. 653-695.
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Microfluidic platforms have evolved in recent years to assist researchers and biologists in performing biological and medical assays for cell separation and sorting. These microfluidic systems are competitive alternatives to conventional methods in terms of cost, sample volume reduction, high sensitivity, portability, fast processing, and elimination of chemical labels required for detection. In this chapter, these techniques have been classified into two major groups, active and passive, based on their energy intake and operating standards. Each separation technique was described briefly, and their operational principles were explained in detail. To specify the applications of each technique, the most recent popular examples have been explained along with common metrics used for the evolution of microfluidic system, including efficiency, accuracy, and throughput. This chapter is designed to be helpful for researchers who aim to develop unique microfluidic separator systems with further innovative designs in microfluidic platforms.

Ngo, HH, Vo, HNP, Guo, W, Lee, D-J & Zhang, S 2022, 'Carbon dioxide fixation and phycoremediation by algae-based technologies for biofuels and biomaterials' in Biomass, Biofuels, Biochemicals, Elsevier, pp. 253-277.
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Nguyen, LN, Vu, MT, Vu, HP, Zdarta, J, Mohammed, JAH, Pathak, N, Ralph, PJ & Nghiem, LD 2022, 'Chapter 4 Seaweed carrageenans: Productions and applications' in Algae-Based Biomaterials for Sustainable Development, pp. 67-80.
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Nguyen, LN, Vu, MT, Vu, HP, Zdarta, J, Mohammed, JAH, Pathak, N, Ralph, PJ & Nghiem, LD 2022, 'Seaweed carrageenans: Productions and applications' in Algae-Based Biomaterials for Sustainable Development, Elsevier, pp. 67-80.
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Nucera, F, Hansbro, PM, Paudel, KR, Casolaro, V, Appanna, R, Kirkham, P, Adcock, IM & Caramori, G 2022, 'Role of autoimmunity in the pathogenesis of chronic obstructive pulmonary disease and pulmonary emphysema' in Translational Autoimmunity, Elsevier, pp. 311-331.
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Poulton, CG, Steel, MJ, Wiederhecker, G & Thévenaz, L 2022, 'Historical perspective and basic principles' in Brillouin Scattering Part 1, Elsevier, pp. 1-25.
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We give a broad overview of the historical development and physics of Brillouin scattering. We discuss the seminal papers of Brillouin and Mandelstam and give the historical context of their research. We discuss the development of experiments and observations from the early, prelaser work to the present day. We then give a broad, nonmathematical explanation of Brillouin scattering as it is currently understood, and outline the different types of scattering as well as the conditions under which it occurs.

Prasher, P, Sharma, M, Kapoor, DN, Negi, P, Gupta, G, Zacconi, FC, Tambuwala, MM, Mehta, M, Satija, S, Dureja, H, Chellappan, DK & Dua, K 2022, 'Chemical Moieties as Advanced Therapeutics for Targeting Respiratory Disorders' in Advanced Drug Delivery Strategies for Targeting Chronic Inflammatory Lung Diseases, Springer Singapore, pp. 75-93.
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Ragu Nandhakumar, S, Rajeshkumar, S, Anand, RS, Malyla, V, Dua, K, Ezhilarasan, D & Lakshmi, T 2022, 'Biogenic metal sulfide nanoparticles synthesis and applications for biomedical and environmental technology' in Agri-Waste and Microbes for Production of Sustainable Nanomaterials, Elsevier, pp. 495-506.
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Roux, C 2022, 'Foreword', pp. xvii-xviii.

Sadaqat, M, Tabassum, H, Tianjie, Q, Mahmood, A, Nisar, L & Naeem Ashiq, M 2022, 'Hierarchical porous carbon-incorporated metal-based nanocomposites for secondary metal-ion batteries' in Metal Oxide-Carbon Hybrid Materials, Elsevier, pp. 179-216.
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Sahoo, JP, Tripathy, AK, Mohanty, M, Li, KC & Nayak, AK 2022, 'Preface', pp. xiii-xiv.

Satija, S, Dhanjal, DS, Sharma, P, Hussain, MS, Chan, Y, Ng, SW, Prasher, P, Dureja, H, Chopra, C, Singh, R, Gupta, G, Chellappan, DK, Dua, K & Mehta, M 2022, 'Vesicular Drug Delivery Systems in Respiratory Diseases' in Advanced Drug Delivery Strategies for Targeting Chronic Inflammatory Lung Diseases, Springer Singapore, pp. 125-141.
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Schotsmans, EMJ, Georges-Zimmermann, P, Ueland, M & Dent, BB 2022, 'From Flesh to Bone' in The Routledge Handbook of Archaeothanatology, Routledge, pp. 500-541.
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Stadler, F, Johnston, NP, Butterworth, NJ & Wallman, JF 2022, '13. Fly Colony Establishment, Quality Control and Improvement' in A Complete Guide to Maggot Therapy, Open Book Publishers, pp. 257-288.
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Sunkara, K, Mehta, M, Satija, S, Dhanjal, DS, Sharma, P, Shukla, SD, Shastri, M, Zacconi, FC, Dua, K & Allam, VSRR 2022, 'An Introduction to Respiratory Diseases and an Emerging Need for Efficient Drug Delivery Systems' in Advanced Drug Delivery Strategies for Targeting Chronic Inflammatory Lung Diseases, Springer Singapore, pp. 1-24.
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Szabo, EA, Arundell, EJ, Farrell, H, Imlay, A, King, T, Shadbolt, C & Taylor, MD 2022, 'Responding to incidents of low-level chemical contamination and deliberate contamination in food' in Ensuring Global Food Safety, Elsevier, pp. 359-377.
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Vo, HNP, Chaiwong, C, Zheng, L, Nguyen, TMH, Koottatep, T & Nguyen, TT 2022, 'Algae-based biomaterials in 3D printing for applications in medical, environmental remediation, and commercial products' in Algae-Based Biomaterials for Sustainable Development, Elsevier, pp. 185-202.
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Wadhwa, R, Paudel, KR, Shukla, S, Shastri, M, Gupta, G, Devkota, HP, Bebawy, M, Chellappan, DK, Hansbro, PM & Dua, K 2022, 'Epigenetic Therapy as a Potential Approach for Targeting Oxidative Stress–Induced Non-small-Cell Lung Cancer' in Handbook of Oxidative Stress in Cancer: Mechanistic Aspects, Springer Nature Singapore, pp. 1545-1560.
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Wadhwa, R, Paudel, KR, Shukla, S, Shastri, M, Gupta, G, Devkota, HP, Chellappan, DK, Hansbro, PM & Dua, K 2022, 'Epigenetic Therapy as a Potential Approach for Targeting Oxidative Stress–Induced Non-Small-Cell Lung Cancer' in Handbook of Oxidative Stress in Cancer: Mechanistic Aspects, Springer Singapore, pp. 1-16.
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Waqas Hakim, M, Fatima, S, Rizwan, S & Mahmood, A 2022, 'Pseudo-capacitors: Introduction, Controlling Factors and Future' in Nanostructured Materials for Supercapacitors, Springer International Publishing, pp. 53-70.
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Wolff, C, Poulton, CG, Steel, MJ & Wiederhecker, G 2022, 'Theoretical formalisms for stimulated Brillouin scattering' in Brillouin Scattering Part 1, Elsevier, pp. 27-91.
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We present the theoretical formalism for Brillouin scattering, beginning with the equations for linear elasticity together with Maxwells equations, and ending with the equations of motion for the optical and acoustic envelope fields. The treatment presented here is based on the Hamiltonian for the opto-acoustic interaction, but we discuss other possible derivations, as well as alternate formulations that describe Brillouin phenomena. We cover the theory of Brillouin scattering in both waveguides and resonators, and present the equations for several typical settings in each case. An Appendix gives a brief introduction to linear elasticity theory for optical physicists.

Aamidor, SE, Cardoso-Júnior, CAM, Harianto, J, Nowell, CJ, Cole, L, Oldroyd, BP & Ronai, I 2022, 'Reproductive plasticity and oogenesis in the queen honey bee (Apis mellifera)', Journal of Insect Physiology, vol. 136, pp. 104347-104347.
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In the honey bee (Apis mellifera), queen and worker castes originate from identical genetic templates but develop into different phenotypes. Queens lay up to 2000 eggs daily whereas workers are sterile in the queen's presence. Periodically queens stop laying: during swarming, when resources are scarce in winter, and when they are confined to a cage by beekeepers. We used confocal microscopy and gene expression assays to investigate the control of oogenesis in the ovaries of honey bee queens that were caged inside and outside the colony. We find evidence that queens use a different combination of 'checkpoints' to regulate oogenesis compared to honey bee workers and other insect species. However, both queen and worker castes likely use the same programmed cell death pathways to terminate oocyte development at their caste-specific checkpoints. Our results also suggest that a key factor driving the termination of oogenesis in queens is nutritional stress. Thus, queens may regulate oogenesis via the same regulatory pathways that were utilised by ancestral solitary species but likely have adjusted physiological checkpoints to suit their highly-derived life history.

Abdollahi, A, Liu, Y, Pradhan, B, Huete, A, Dikshit, A & Nguyen Tran, N 2022, 'Short-time-series grassland mapping using Sentinel-2 imagery and deep learning-based architecture', The Egyptian Journal of Remote Sensing and Space Science, vol. 25, no. 3, pp. 673-685.
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In the present work, a deep learning-based network called LeNet is applied for accurate grassland map production from Sentinel-2 data for the Greater Sydney region, Australia. First, we apply the technique to the base date Sentinel-2 data (non-seasonal) to make the vegetation maps. Then, we combine short time-series (seasonal) data and enhanced vegetation index (EVI) information to the base date imagery to improve the classification results and generate high-resolution grassland maps. The proposed model obtained an overall accuracy (OA) of 88.36% for the mono-temporal data, and 92.74% for the multi-temporal data. The experimental products proved that, by combining the short time-series images and EVI information to the base date, the classification maps' accuracy is increased by 4.38%. Moreover, the Sentinel-2 produced grassland maps are compared with the pre-existing maps such as Australian Land Use and Management (ALUM) 50 m resolution and Dynamic Land Cover Dataset (DLCD) with 250 m resolution as well as some traditional machine learning methods such as Support Vector Machine (SVM) and Random Forest (RF). The results show the effect of the LeNet network's performance and efficiency for grassland map production from short time-series data. As a result, decision-makers and urban planners can benefit from this work in terms of grassland change identification, monitoring, and planning assessment.

Abell-King, C, Costas, A, Duggin, IG & Söderström, B 2022, 'Bacterial filamentation during urinary tract infections', PLOS Pathogens, vol. 18, no. 12, pp. e1010950-e1010950.
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Abiero, AR, Ali, Z, Vissel, B & Bradfield, LA 2022, 'Outcome-selective reinstatement is predominantly context-independent, and associated with c-Fos activation in the posterior dorsomedial striatum', Neurobiology of Learning and Memory, vol. 187, pp. 107556-107556.
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Research from human and animal studies has found that after responding has been successfully reduced following treatment it can return upon exposure to certain contexts. An individual in recovery from alcohol use disorder, for example, might relapse to drinking upon visiting their favourite bar. However, most of these data have been derived from experiments involving a single (active) response, and the context-dependence of returned responding in situations involving choice between multiple actions and outcomes is less well-understood. We thus investigated how outcome-selective reinstatement - a procedure involving choice between two actions and outcomes - was affected by altering the physical context in rats. In Experiment 1, rats were trained over 6 days to press a left lever for one food outcome (pellets or sucrose) and a right lever for the other outcome. Then, rats received an extinction session in either the same context (A) as lever press training, or in a different context (B). Rats were tested immediately (5 min) after extinction in Context A or B such that there were four groups in total: AAA, ABB, ABA, and AAB. Reinstatement testing consisted of one food outcome being delivered 'freely' (i.e. unearned by lever pressing and unsignalled by cues) to the food magazine every 4 min in the following order: Sucrose, Pellet, Pellet, Sucrose. Selective reinstatement was considered intact if pellet delivery increased pressing selectively on the pellet lever, and sucrose delivery selectively increased pressing on the sucrose lever. This result (Reinstated > Nonreinstated) was observed for rats in group AAA and ABB, but not rats in groups ABA and AAB. Experiment 2 was conducted identically, except that rats received two extinction sessions over two days and tested one day later. This time, all groups demonstrated intact outcome-selective reinstatement regardless of context. Analysis of c-Fos expression in several brain regions revealed that only c-Fos exp...

Abolpour Moshizi, S, Pastras, CJ, Sharma, R, Parvez Mahmud, MA, Ryan, R, Razmjou, A & Asadnia, M 2022, 'Recent advancements in bioelectronic devices to interface with the peripheral vestibular system', Biosensors and Bioelectronics, vol. 214, pp. 114521-114521.
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Adhikari, S, Timms, W & Mahmud, MAP 2022, 'Optimising water holding capacity and hydrophobicity of biochar for soil amendment – A review', Science of The Total Environment, vol. 851, pp. 158043-158043.
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Adhikary, P, Mahmud, MAP, Solaiman, T & Wang, ZL 2022, 'Recent advances on biomechanical motion-driven triboelectric nanogenerators for drug delivery', Nano Today, vol. 45, pp. 101513-101513.
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Afrose, D, Chen, H, Ranashinghe, A, Liu, C-C, Henessy, A, Hansbro, PM & McClements, L 2022, 'The diagnostic potential of oxidative stress biomarkers for preeclampsia: systematic review and meta-analysis', Biology of Sex Differences, vol. 13, no. 1, p. 26.
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Abstract Background Preeclampsia is a multifactorial cardiovascular disorder of pregnancy. If left untreated, it can lead to severe maternal and fetal outcomes. Hence, timely diagnosis and management of preeclampsia are extremely important. Biomarkers of oxidative stress are associated with the pathogenesis of preeclampsia and therefore could be indicative of evolving preeclampsia and utilized for timely diagnosis. In this study, we conducted a systematic review and meta-analysis to determine the most reliable oxidative stress biomarkers in preeclampsia, based on their diagnostic sensitivities and specificities as well as their positive and negative predictive values. Methods A systematic search using PubMed, ScienceDirect, ResearchGate, and PLOS databases (1900 to March 2021) identified nine relevant studies including a total of 343 women with preeclampsia and 354 normotensive controls. Results Ischemia-modified albumin (IMA), uric acid (UA), and malondialdehyde (MDA) were associated with 3.38 (95% CI 2.23, 4.53), 3.05 (95% CI 2.39, 3.71), and 2.37 (95% CI 1.03, 3.70) odds ratios for preeclampsia diagnosis, respectively. The IMA showed the most promising diagnostic potential with the positive predictive ratio (PPV) of 0.852 (95% CI 0.728, 0.929) and negative predictive ratio (NPV) of 0.811 (95% CI 0.683, 0.890) for preeclampsia. Minor between-study heterogeneity was reported for these biomarkers (Higgins’ I2 = 0–15.879%). Conclusions This systematic review and meta-analysis identifie...

Aharonovich, I, Tetienne, J-P & Toth, M 2022, 'Quantum Emitters in Hexagonal Boron Nitride', Nano Letters, vol. 22, no. 23, pp. 9227-9235.
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Hexagonal boron nitride (hBN) has emerged as a fascinating platform to explore quantum emitters and their applications. Beyond being a wide-bandgap material, it is also a van der Waals crystal, enabling direct exfoliation of atomically thin layers─a combination which offers unique advantages over bulk, 3D crystals. In this Mini Review we discuss the unique properties of hBN quantum emitters and highlight progress toward their future implementation in practical devices. We focus on engineering and integration of the emitters with scalable photonic resonators. We also highlight recently discovered spin defects in hBN and discuss their potential utility for quantum sensing. All in all, hBN has become a front runner in explorations of solid-state quantum science with promising future prospects.

Aili, SR, De Silva, R, Wilhelm, K, Jha, SR, Fritis-Lamora, R, Montgomery, E, Pierce, R, Lam, F, Brennan, X, Gorrie, N, Schnegg, B, Jabbour, A, Kotlyar, E, Muthiah, K, Keogh, AM, Jansz, PC, Hayward, C & Macdonald, PS 2022, 'Validation of Cognitive Impairment in Combination With Physical Frailty as a Predictor of Mortality in Patients With Advanced Heart Failure Referred for Heart Transplantation', Transplantation, vol. 106, no. 1, pp. 200-209.
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Background. The aim of this study was to validate our previous finding that frailty predicts early mortality in patients with advanced heart failure (AHF) and that including cognition in the frailty assessment enhances the prediction of mortality. Methods. Patients with AHF referred to our Transplant Unit between November 2015 and April 2020 underwent physical frailty assessment using the modified Fried physical frailty (PF) phenotype as well as cognitive assessment using the Montreal Cognitive Assessment to identify patients who were cognitively frail (CogF). We assessed the predictive value of the 2 frailty measures (PF ≥ 3 of 5 = frail; CogF ≥ 3 of 6 = frail) for pretransplant mortality. Results. Three hundred thirteen patients (233 male and 80 female; age 53 ± 13 y) were assessed. Of these, 224 patients (72%) were nonfrail and 89 (28%) were frail using the PF. The CogF assessment identified an additional 30 patients as frail: 119 (38%). Frail patients had significantly increased mortality as compared to nonfrail patients. Ventricular assist device and heart transplant-censored survival at 12 mo was 92 ± 2 % for nonfrail and 69 ± 5% for frail patients (P < 0.0001) using the CogF instrument. Conclusions. This study validates our previously published findings that frailty is prevalent in patients with AHF referred for heart transplantation. PF predicts early mortality. The addition of cognitive assessment to the physical assessment of frailty identifies an additional cohort of patients with a similarly poor prognosis.

Ajani, PA, Henriquez-Nunez, HF, Verma, A, Nagai, S, Uchida, H, Tesoriero, MJ, Farrell, H, Zammit, A, Brett, S & Murray, SA 2022, 'Mapping the development of a Dinophysis bloom in a shellfish aquaculture area using a novel molecular qPCR assay', Harmful Algae, vol. 116, pp. 102253-102253.
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Alderdice, R, Hume, BCC, Kühl, M, Pernice, M, Suggett, DJ & Voolstra, CR 2022, 'Disparate Inventories of Hypoxia Gene Sets Across Corals Align With Inferred Environmental Resilience', Frontiers in Marine Science, vol. 9, pp. 1-14.
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Aquatic deoxygenation has been flagged as an overlooked but key factor contributing to mass bleaching-induced coral mortality. During deoxygenation events triggered by coastal nutrient pollution and ocean warming, oxygen supplies lower to concentrations that can elicit an aerobic metabolic crisis i.e., hypoxia. Surprisingly little is known of the fundamental hypoxia gene set inventory that corals possess to respond to lowered oxygen (i.e., deoxygenation). For instance, it is unclear whether gene copy number differences exist across species that may affect the efficacy of a measured transcriptomic stress response. Therefore, we conducted an ortholog-based meta-analysis to investigate how hypoxia gene inventories differ amongst coral species to assess putative copy number variations (CNVs). We specifically elucidated CNVs for a compiled list of 32 hypoxia genes across 24 protein sets from species with a sequenced genome spanning corals from the robust and complex clade. We found approximately a third of the investigated genes exhibited copy number differences, and these differences were species-specific rather than attributable to the robust-complex split. Interestingly, we consistently found the highest gene expansion present in Porites lutea, which is considered to exhibit inherently greater stress tolerance than other species. Consequently, our analysis suggests that hypoxia stress gene expansion may coincide with increased stress tolerance. As such, the unevenly expanded (or reduced) hypoxia genes presented here provide key genes of interest to target in examining (or diagnosing) coral stress responses. Important next steps will involve determining to what extent such gene copy differences align with certain coral traits.

Alderdice, R, Perna, G, Cárdenas, A, Hume, BCC, Wolf, M, Kühl, M, Pernice, M, Suggett, DJ & Voolstra, CR 2022, 'Deoxygenation lowers the thermal threshold of coral bleaching', Scientific Reports, vol. 12, no. 1, pp. 1-14.
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AbstractExposure to deoxygenation from climate warming and pollution is emerging as a contributing factor of coral bleaching and mortality. However, the combined effects of heating and deoxygenation on bleaching susceptibility remain unknown. Here, we employed short-term thermal stress assays to show that deoxygenated seawater can lower the thermal limit of an Acropora coral by as much as 1 °C or 0.4 °C based on bleaching index scores or dark-acclimated photosynthetic efficiencies, respectively. Using RNA-Seq, we show similar stress responses to heat with and without deoxygenated seawater, both activating putative key genes of the hypoxia-inducible factor response system indicative of cellular hypoxia. We also detect distinct deoxygenation responses, including a disruption of O2-dependent photo-reception/-protection, redox status, and activation of an immune response prior to the onset of bleaching. Thus, corals are even more vulnerable when faced with heat stress in deoxygenated waters. This highlights the need to integrate dissolved O2 measurements into global monitoring programs of coral reefs.

Alderdice, R, Pernice, M, Cárdenas, A, Hughes, DJ, Harrison, PL, Boulotte, N, Chartrand, K, Kühl, M, Suggett, DJ & Voolstra, CR 2022, 'Hypoxia as a physiological cue and pathological stress for coral larvae', Molecular Ecology, vol. 31, no. 2, pp. 571-587.
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AbstractOcean deoxygenation events are intensifying worldwide and can rapidly drive adult corals into a state of metabolic crisis and bleaching‐induced mortality, but whether coral larvae are subject to similar stress remains untested. We experimentally exposed apo‐symbiotic coral larvae of Acropora selago to deoxygenation stress with subsequent reoxygenation aligned to their night‐day light cycle, and followed their gene expression using RNA‐Seq. After 12 h of deoxygenation stress (~2 mg O2/L), coral planulae demonstrated a low expression of HIF‐targeted hypoxia response genes concomitant with a significantly high expression of PHD2 (a promoter of HIFα proteasomal degradation), similar to corresponding adult corals. Despite exhibiting a consistent swimming phenotype compared to control samples, the differential gene expression observed in planulae exposed to deoxygenation‐reoxygenation suggests a disruption of pathways involved in developmental regulation, mitochondrial activity, lipid metabolism, and O2‐sensitive epigenetic regulators. Importantly, we found that treated larvae exhibited a disruption in the expression of conserved HIF‐targeted developmental regulators, for example, Homeobox (HOX) genes, corroborating how changes in external oxygen levels can affect animal development. We discuss how the observed deoxygenation responses may be indicative of a possible acclimation response or alternatively may imply negative latent impacts for coral larval fitness.

Alghalayini, A, Cranfield, CG, Cornell, BA & Valenzuela, SM 2022, 'Preparing Ion Channel Switch Membrane-Based Biosensors', Methods in Molecular Biology, vol. 2402, pp. 13-20.
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Monitoring the changes in membrane conductance using electrical impedance spectroscopy is the platform of membrane-based biosensors in order to detect a specific target molecule. These biosensors represent the amalgamation of an electrical conductor such as gold and a chemically tethered bilayer lipid membrane with specific incorporated ion channels such as gramicidin-A that is further functionalized with detector molecules of interest.

Alharbi, KS, Afzal, O, almalki, WH, Kazmi, I, Javed Shaikh, MA, Thangavelu, L, Gulati, M, Singh, SK, Jha, NK, Gupta, PK, Chellappan, DK, Oliver, BG, Dua, K & Gupta, G 2022, 'Nuclear factor-kappa B (NF-κB) inhibition as a therapeutic target for plant nutraceuticals in mitigating inflammatory lung diseases', Chemico-Biological Interactions, vol. 354, pp. 109842-109842.
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Alharbi, KS, Shaikh, MAJ, Almalki, WH, Kazmi, I, Al-Abbasi, FA, Alzarea, SI, Imam, SS, Alshehri, S, Ghoneim, MM, Singh, SK, Chellappan, DK, Oliver, BG, Dua, K & Gupta, G 2022, 'PI3K/Akt/mTOR Pathways Inhibitors with Potential Prospects in Non-Small-Cell Lung Cancer', Journal of Environmental Pathology, Toxicology and Oncology, vol. 41, no. 4, pp. 85-102.
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Lung cancer is the leading cause of cancer-related mortality across the globe. The most prevalent pathological form of lung cancer is non-small-cell lung cancer (NSCLC). Elevated stimulation of the PI3K/Akt/mTOR pathway causes a slew of cancer-related symptoms, making it a promising target for new anticancer drugs. The PI3K/Akt/mTOR path is involved extensively in carcinogenesis and disease advancement in NSCLC. Several new inhibitors targeting this pathway have been discovered in preclinical investigations and clinical trials. The etiology and epidemiology of NSCLC and biology of the PI3K/Akt/mTOR cascade and its role in NSCLC pathogenesis have all been discussed in this article. In this article, we've reviewed PI3K/Akt/mTOR cascade inhibitors that have been proven in vitro and in preclinical trials to be effective in NSCLC. Drugs targeting the PI3K/Akt/mTOR path in the treatment of NSCLC were also addressed. A better knowledge of the underlying molecular biology, including epigenetic changes, is also critical to detecting relevant biomarkers and guiding combination methods. Additionally, improved clinical trial designs will increase the capacity to test novel drugs and combinations for accounting for genomic variation and eventually improve patient outcomes.

Ali, S, Jameel, MA, Gupta, A, Shafiei, M & Langford, SJ 2022, 'A room temperature functioning ammonia sensor utilising a bis-phenylalanine naphthalene diimide', Sensors and Actuators A: Physical, vol. 348, pp. 114008-114008.
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Ali, S, Jameel, MA, Harrison, CJ, Gupta, A, Shafiei, M & Langford, SJ 2022, 'Nanoporous naphthalene diimide surface enhances humidity and ammonia sensing at room temperature', Sensors and Actuators B: Chemical, vol. 351, pp. 130972-130972.
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Ali, SMN, Hossain, MJ, Wang, D, Mahmud, MAP, Sharma, V, Kashif, M & Kouzani, AZ 2022, 'Thermally degraded speed estimation of traction machine drive in electric vehicle', IET Electric Power Applications, vol. 16, no. 12, pp. 1464-1475.
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The speed of an induction machine drive (IMD) in the electrified powertrain of an electric vehicle (EV) suffers from thermal degradation caused by EV loading, driving cycle schedules, EV operating conditions, traffic state and temperature. It is necessary to estimate this thermal degradation in order to design appropriate control methodologies to address this significant issue that directly affects the EV performance. This study proposes a robust linear parameter varying (LPV) observer to estimate this degradation in IMD as well as EV speed under various thermal and loading conditions in steady state and during large transients. The stability and robustness of LPV methodology is ensured by optimal gains of (Formula presented.) control and linear matrix inequalities using convex optimisation techniques. The weighting functions in LPV design are optimised by genetic algorithms. The proposed observer performance is compared with that of conventional sensorless field-oriented control and sliding mode observer. An improved speed performance during EV operation is also presented to validate the robustness of the proposed LPV observer against New European Driving Cycle. The performance analysis is conducted through NI myRIO 1900 controller-based electrical drive set-up.

Aliee, H, Massip, F, Qi, C, Stella de Biase, M, van Nijnatten, J, Kersten, ETG, Kermani, NZ, Khuder, B, Vonk, JM, Vermeulen, RCH, Neighbors, M, Tew, GW, Grimbaldeston, MA, ten Hacken, NHT, Hu, S, Guo, Y, Zhang, X, Sun, K, Hiemstra, PS, Ponder, BA, Mäkelä, MJ, Malmström, K, Rintoul, RC, Reyfman, PA, Theis, FJ, Brandsma, C, Adcock, IM, Timens, W, Xu, C, van den Berge, M, Schwarz, RF, Koppelman, GH, Nawijn, MC & Faiz, A 2022, 'Determinants of expression of SARS‐CoV‐2 entry‐related genes in upper and lower airways', Allergy, vol. 77, no. 2, pp. 690-694.
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Allam, VSRR, Chellappan, DK, Jha, NK, Shastri, MD, Gupta, G, Shukla, SD, Singh, SK, Sunkara, K, Chitranshi, N, Gupta, V, Wich, PR, MacLoughlin, R, Oliver, BGG, Wernersson, S, Pejler, G & Dua, K 2022, 'Treatment of chronic airway diseases using nutraceuticals: Mechanistic insight', Critical Reviews in Food Science and Nutrition, vol. 62, no. 27, pp. 7576-7590.
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Respiratory diseases, both acute and chronic, are reported to be the leading cause of morbidity and mortality, affecting millions of people globally, leading to high socio-economic burden for the society in the recent decades. Chronic inflammation and decline in lung function are the common symptoms of respiratory diseases. The current treatment strategies revolve around using appropriate anti-inflammatory agents and bronchodilators. A range of anti-inflammatory agents and bronchodilators are currently available in the market; however, the usage of such medications is limited due to the potential for various adverse effects. To cope with this issue, researchers have been exploring various novel, alternative therapeutic strategies that are safe and effective to treat respiratory diseases. Several studies have been reported on the possible links between food and food-derived products in combating various chronic inflammatory diseases. Nutraceuticals are examples of such food-derived products which are gaining much interest in terms of its usage for the well-being and better human health. As a consequence, intensive research is currently aimed at identifying novel nutraceuticals, and there is an emerging notion that nutraceuticals can have a positive impact in various respiratory diseases. In this review, we discuss the efficacy of nutraceuticals in altering the various cellular and molecular mechanisms involved in mitigating the symptoms of respiratory diseases.

Allam, VSRR, Paudel, KR, Gupta, G, Singh, SK, Vishwas, S, Gulati, M, Gupta, S, Chaitanya, MVNL, Jha, NK, Gupta, PK, Patel, VK, Liu, G, Kamal, MA, Hansbro, PM, Oliver, BGG, Chellappan, DK & Dua, K 2022, 'Nutraceuticals and mitochondrial oxidative stress: bridging the gap in the management of bronchial asthma', Environmental Science and Pollution Research, vol. 29, no. 42, pp. 62733-62754.
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AbstractAsthma is a chronic inflammatory disease primarily characterized by inflammation and reversible bronchoconstriction. It is currently one of the leading causes of morbidity and mortality in the world. Oxidative stress further complicates the pathology of the disease. The current treatment strategies for asthma mainly involve the use of anti-inflammatory agents and bronchodilators. However, long-term usage of such medications is associated with severe adverse effects and complications. Hence, there is an urgent need to develop newer, novel, and safe treatment modalities for the management of asthma. This has therefore prompted further investigations and detailed research to identify and develop novel therapeutic interventions from potent untapped resources. This review focuses on the significance of oxidative stressors that are primarily derived from both mitochondrial and non-mitochondrial sources in initiating the clinical features of asthma. The review also discusses the biological scavenging system of the body and factors that may lead to its malfunction which could result in altered states. Furthermore, the review provides a detailed insight into the therapeutic role of nutraceuticals as an effective strategy to attenuate the deleterious effects of oxidative stress and may be used in the mitigation of the cardinal features of bronchial asthma.

Allan, SJ, O'Connell, MJ, Harasti, D, Klanten, OS & Booth, DJ 2022, 'Searching for seadragons: predicting micro‐habitat use for the common (weedy) seadragon (Phyllopteryx taeniolatus) based on habitat and prey', Journal of Fish Biology, vol. 100, no. 4, pp. 935-943.
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AbstractHabitat associations can be critical predictors of larger‐scale organism distributions and range shifts. Here the authors consider how a critical habitat, kelp (Ecklonia radiata) and prey (mysid crustacean swarms), can influence small‐ and large‐scale distribution on the iconic common (weedy) seadragon (Phyllopteryx taeniolatus:Syngnathidae). P. taeniolatus are charismatic fish endemic to the temperate reefs of southern Australia, reported to range from Geraldton, Western Australia (28.7667°S, 114.6167°E) around southern Australia to Port Stephens, New South Wales (32.614369°S, 152.325676°E). The authors test a previously developed model of seadragon habitat preferences to predict P. taeniolatus occurrence within four sites from Sydney to the northern limit of their range in eastern Australia. They determined that P. taeniolatus associations with Ecklonia and mysid shrimp can be extrapolated across multiple sites to predict the occurrence of individual P. taeniolatus within a location/site. For instance, the authors demonstrated a significant positive relationship between the density of mysid swarms and the density of P. taeniolatus, evident across all sites despite large differences in the density of mysid swarms among sites. The findings are the first to model P. taeniolatus habitat associations across multiple sites to the northern limit of their range and have applications in protecting P. taeniolatus populations and how they may respond under climate change scenarios, such as poleward kelp retractions.

Allan, SJ, O'Connell, MJ, Harasti, D, Klanten, OS & Booth, DJ 2022, 'Space use by the endemic common (weedy) seadragon (Phyllopteryx taeniolatus): influence of habitat and prey', Journal of Fish Biology, vol. 100, no. 1, pp. 175-183.
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AbstractThe weedy seadragon (Phyllopteryx taeniolatus: Syngnathidae) is an iconic fish endemic to the southern coastal waters of Australia. The authors of this study analysed the habitat preferences and factors influencing microhabitat selection by P. taeniolatus in a population from Kurnell, NSW, Australia. Using field surveys and the resource selection probability function, the authors determined that P. taeniolatus significantly preferred kelp (Ecklonia radiata)–dominated habitat and avoided rock‐dominated habitat. They showed P. taeniolatus preferred habitat of between 40% and 80% coverage of Ecklonia, while avoiding areas of <20% cover. Furthermore, across all habitats, mysid prey availability significantly influenced P. taeniolatus habitat selection. The strong dependence of P. taeniolatus on Ecklonia habitat shown in this study was previously untested and highlights that reductions in Ecklonia cover under climate change, or impacts from increasing urbanisation, may render seadragon populations vulnerable to declines.

Allison, MC, Wurmehl, S, Büchner, B, Vella, JL, Söhnel, T, Bräuninger, SA, Klauss, H-H, Avdeev, M, Marlton, FP, Schmid, S & Ling, CD 2022, 'FeMn₃Ge₂Sn₇O₁₆: A Perfectly Isotropic 2-D Kagomé Lattice that Breaks Magnetic Symmetry with Partial Spin Order', Chemistry of Materials, vol. 34, no. 3, pp. 1369-1375.
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Alonzo, M, Alder, R, Clancy, L & Fu, S 2022, 'Portable testing techniques for the analysis of drug materials', WIREs Forensic Science, vol. 4, no. 6.
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AbstractThe analysis of drug material in the field is an important function of law enforcement agencies, forensic drug laboratories, and drug checking services. Portable testing techniques employed by these different groups range from inexpensive screening tools with low discriminating power, such as presumptive chemical color tests, to more sophisticated portable analytical techniques that behave as miniaturized versions of their laboratory counterparts, such as gas chromatography–mass spectrometry (GC–MS). Rapid non‐destructive analysis in the field and non‐laboratory environments is afforded by portable and handheld Fourier transform infrared (FTIR) spectrometers with little to no sample preparation, while handheld Raman analyzers have the added potential for drug material identification through sealed packaging using spatially offset Raman spectroscopy (SORS). Utilization of the most suitable testing technique for the given environment is demonstrated at international borders and airports wherein ion mobility spectroscopy (IMS) is frequently employed for the detection of drug (and explosive) residues owing to its ease of operation and rapid analysis. Advances in technology and materials have provided analysts with new portable testing techniques, including paper spray ionization–MS (PSI‐MS), an ambient MS technique that provides sensitive, rapid, and reliable analysis without the need for sample preparation steps. A growing area of research and interest in the development of sensitive and selective optical and electrochemical portable (bio)sensors for in‐field analysis of drug material indicates that new commercial sensors for drug detection will be available in the foreseeable future.This article is categorized under:Forensic Chemistry and Trace Evidence > Controlled and Emerging Drug Compounds

Alquethamy, S, Ganio, K, Luo, Z, Hossain, SI, Hayes, AJ, Ve, T, Davies, MR, Deplazes, E, Kobe, B & McDevitt, CA 2022, 'Structural and biochemical characterization of Acinetobacter baumannii ZnuA', Journal of Inorganic Biochemistry, vol. 231, pp. 111787-111787.
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Alsarraf, HMAB, Ung, KL, Johansen, MD, Dimon, J, Olieric, V, Kremer, L & Blaise, M 2022, 'Biochemical, structural, and functional studies reveal that MAB_4324c from Mycobacterium abscessus is an active tandem repeat N‐acetyltransferase', FEBS Letters, vol. 596, no. 12, pp. 1516-1532.
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Mycobacterium abscessus is a pathogenic non‐tuberculous mycobacterium that possesses an intrinsic drug resistance profile. Several N‐acetyltransferases mediate drug resistance and/or participate in M. abscessus virulence. Mining the M. abscessus genome has revealed genes encoding additional N‐acetyltransferases whose functions remain uncharacterized, among them MAB_4324c. Here, we showed that the purified MAB_4324c protein is a N‐acetyltransferase able to acetylate small polyamine substrates. The crystal structure of MAB_4324c was solved at high resolution in complex with its cofactor, revealing the presence of two GCN5‐related N‐acetyltransferase domains and a cryptic binding site for NADPH. Genetic studies demonstrate that MAB_4324c is not essential for in vitro growth of M. abscessus; however, overexpression of the protein enhanced the uptake and survival of M. abscessus in THP‐1 macrophages.

Alves, FM, Kysenius, K, Caldow, MK, Hardee, JP, Chung, JD, Trieu, J, Hare, DJ, Crouch, PJ, Ayton, S, Bush, AI, Lynch, GS & Koopman, R 2022, 'Iron overload and impaired iron handling contribute to the dystrophic pathology in models of Duchenne muscular dystrophy', Journal of Cachexia, Sarcopenia and Muscle, vol. 13, no. 3, pp. 1541-1553.
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AbstractBackgroundOxidative stress is implicated in the pathophysiology of Duchenne muscular dystrophy (DMD, caused by mutations in the dystrophin gene), which is the most common and severe of the muscular dystrophies. To our knowledge, the distribution of iron, an important modulator of oxidative stress, has not been assessed in DMD. We tested the hypotheses that iron accumulation occurs in mouse models of DMD and that modulation of iron through the diet or chelation could modify disease severity.MethodsWe assessed iron distribution and total elemental iron using LA‐ICP‐MS on skeletal muscle cross‐sections of 8‐week‐old Bl10 control mice and dystrophic mdx mice (with moderate dystrophy) and dystrophin/utrophin‐null mice (dko, with severe dystrophy). In addition, mdx mice (4 weeks) were treated with either an iron chelator (deferiprone 150 mg/kg/day) or iron‐enriched feed (containing 1% added iron as carbonyl iron). Immunoblotting was used to determine the abundance of iron‐ and mitochondria‐related proteins. (Immuno)histochemical and mRNA assessments of fibrosis and inflammation were also performed.ResultsWe observed a significant increase in total elemental iron in hindlimb muscles of dko mice (+50%, P < 0.05) and in the diaphragm of mdx mice (+80%, P < 0.05), with both tissues exhibiting severe pathology. Iron dyshomeostasis was further evidenced by an increase in the storage protein ferritin (dko: +39%, P < 0.05) and ferroportin compared with Bl10 control mice (mdx: +152% and

Ambrose, SJ, Hamidian, M & Hall, RM 2022, 'Extensively resistant Acinetobacter baumannii isolate RCH52 carries several resistance genes derived from an IncC plasmid', Journal of Antimicrobial Chemotherapy, vol. 77, no. 4, pp. 930-933.
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Abstract Objectives To identify the origins of resistance in a sporadic extensively resistant Acinetobacter baumannii isolate. Methods The complete genome of RCH52 was determined by combining available Illumina short reads with MinION (Oxford Nanopore) long reads using Unicycler. Bioinformatic searches were used to identify features of interest. Results The complete genome of RCH52 revealed an unusual chromosomal region containing all of the antibiotic resistance genes, except tet39, which is in a plasmid. A 129 585 bp segment was bounded by inversely oriented copies of ISAba1 and included two groups of resistance genes separated by the large segment of the backbone of type 1 IncC plasmids that lies between the ARI-A and ARI-B resistance islands but does not include the replication region. The ISAba1-bounded segment was located in a novel integrative element that had integrated into the chromosomal thyA gene but provided a replacement thyA gene. Several resistance genes are derived from either the ARI-A or the ARI-B resistance islands found in IncC plasmids that have been brought together by an IS26-mediated deletion of the original plasmid. This non-replicating circular molecule (or translocatable unit) has been incorporated into a smaller ISAba1-bounded unit that includes oxa23 in Tn2008B via homologous recombination between sul2-CR2-floR segments found in both. Conclusions The plasmids shared by most Gram-negative pathogens, including the broad ho...

Anantanawat, K, Papanicolaou, A, Hill, K & Xu, W 2022, 'Mediterranean fruit fly genes exhibit different expression patterns between heat and cold treatments', Bulletin of Entomological Research, vol. 112, no. 2, pp. 236-242.
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AbstractInvasive Tephritid fruit flies are a global threat to both agriculture and horticulture industries. Biosecurity has played a critical role in reducing their damage but becomes more and more challenging after several key chemical pesticides were banned or withdrawn for health or environmental reasons. This has led to non-chemical approaches including heat and cold treatments being broadly utilized to get rid of fruit fly infestation. However, the molecular mechanisms to kill the flies underlying these stressors are not clear yet. This knowledge will certainly help refine current post-harvest treatment strategies and develop more efficient, cost-effective and environmentally friendly approaches for fruit fly management. Previously, the molecular response of the Mediterranean fruit fly,Ceratitis capitata(Wiedemann) to heat was examined thoroughly, in which 31 key genes were identified with significant changes in expression levels and their high-resolution expression timeline was constructed across 11 timepoints. However, whether these candidate genes respond to cold in the same way was unknown. Here, a temperature bioassay was conducted and the expression profiles of these genes were investigated across the same 11 timepoints using cold treatment. The results showed that most of candidate genes exhibited divergent expression profiles compared to heat treatment, suggesting that the fly molecular response to cold may be different from those to heat. This study provides new knowledge of Tephritid fruit fly response to cold at a molecular level, which could aid in improving current fruit fly management and facilitate the development of new strategies to control this serious horticultural insect pest.

Angeloski, A, Price, JR, Ennis, C, Smith, K, McDonagh, AM, Dowd, A, Thomas, P, Cortie, M, Appadoo, D & Bhadbhade, M 2022, 'Thermosalience Revealed on the Atomic Scale: Rapid Synchrotron Techniques Uncover Molecular Motion Preceding Crystal Jumping', Crystal Growth & Design, vol. 22, no. 3, pp. 1951-1959.
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The solid-state phase transformation in nickel(II) bis(diisopropyldithiocarbonate) is analyzed using a combination of high-speed in situ single-crystal diffraction, terahertz spectroscopy, optical microscopy, thermal analysis, and density functional theory. We show that the monoclinic P21/c structure of this compound undergoes a displacive phase change at about 3 °C. The monoclinic angles and unit cell volumes change reversibly between 110.3°/2265 Å3 and 103.8°/2168 Å3. An analysis of atomic positions using high-resolution in situ synchrotron X-ray diffraction data revealed details of the atomic displacements that show a change in order that precedes and accompanies the change in structure. The structural changes are rapid and are manifested as reversible macroscale crystal movement and jumping (thermosalience) and represent the first case of thermosalience in dithiocarbamate complexes.

Armstrong, E, Rai, T, Hersh, D, Thompson, S, Coffin, J, Ciccone, N, Flicker, L, Cadilhac, D, Godecke, E, Woods, D, Hayward, C, Hankey, GJ, McAllister, M & Katzenellenbogen, J 2022, 'Statistical analysis plan for the stepped wedge clinical trial Healing Right Way—enhancing rehabilitation services for Aboriginal Australians after brain injury', Trials, vol. 23, no. 1, p. 886.
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Abstract Background Aboriginal Australians are known to suffer high levels of acquired brain injury (stroke and traumatic brain injury) yet experience significant barriers in accessing rehabilitation services. The aim of the Healing Right Way trial is to evaluate a culturally secure intervention for Aboriginal people with newly acquired brain injury to improve their rehabilitation experience and quality of life. Following publication of the trial protocol, this paper outlines the statistical analysis plan prior to locking the database.  Methods The trial involves a stepped wedge design with four steps over 3 years. Participants were 108 adult Aboriginal Australians admitted to one of eight hospitals (four rural, four urban) in Western Australia within 6 weeks of onset of a new stroke or traumatic brain injury who consented to follow-up for 26 weeks. All hospital sites started in a control phase, with the intervention assigned to pairs of sites (one metropolitan, one rural) every 26 weeks until all sites received the intervention. The two-component intervention involves training in culturally safe care for hospital sites and enhanced support provided to participants by Aboriginal Brain Injury Coordinators during their hospital stay and after discharge. The primary outcome is quality of life as measured by the Euro QOL–5D-3L VAS. A mixed effects linear regression model will be used to assess the between-group difference at 26 weeks post-injury. The model will control for injury type and severity, age at recruitment and time since commencement of the trial, as fixed effects. Recruitment site and participant will be included as random effects. Secondary outcomes include measurements of function, independence, anxiety and depression, carer strain, alli...

Arora, P, Nainwal, LM, Gupta, G, Singh, SK, Chellappan, DK, Oliver, BG & Dua, K 2022, 'Orally administered solasodine, a steroidal glycoalkaloid, suppresses ovalbumin-induced exaggerated Th2-immune response in rat model of bronchial asthma', Chemico-Biological Interactions, vol. 366, pp. 110138-110138.
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Asfour, L, Smyth, D, Whitchurch, CB, Cavaliere, R & Roland, JT 2022, 'Fluorescence in situ hybridization and microbial community profiling analysis of explanted cochlear implants', Acta Oto-Laryngologica, vol. 142, no. 5, pp. 395-401.
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Ashhurst, AS, Johansen, MD, Maxwell, JWC, Stockdale, S, Ashley, CL, Aggarwal, A, Siddiquee, R, Miemczyk, S, Nguyen, DH, Mackay, JP, Counoupas, C, Byrne, SN, Turville, S, Steain, M, Triccas, JA, Hansbro, PM, Payne, RJ & Britton, WJ 2022, 'Mucosal TLR2-activating protein-based vaccination induces potent pulmonary immunity and protection against SARS-CoV-2 in mice', Nature Communications, vol. 13, no. 1, p. 6972.
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AbstractCurrent vaccines against SARS-CoV-2 substantially reduce mortality, but protection against infection is less effective. Enhancing immunity in the respiratory tract, via mucosal vaccination, may provide protection against infection and minimise viral spread. Here, we report testing of a subunit vaccine in mice, consisting of SARS-CoV-2 Spike protein with a TLR2-stimulating adjuvant (Pam2Cys), delivered to mice parenterally or mucosally. Both routes of vaccination induce substantial neutralising antibody (nAb) titres, however, mucosal vaccination uniquely generates anti-Spike IgA, increases nAb in the serum and airways, and increases lung CD4+ T-cell responses. TLR2 is expressed by respiratory epithelia and immune cells. Using TLR2 deficient chimeric mice, we determine that TLR2 expression in either compartment facilitates early innate responses to mucosal vaccination. By contrast, TLR2 on hematopoietic cells is essential for optimal lung-localised, antigen-specific responses. In K18-hACE2 mice, vaccination provides complete protection against disease and sterilising lung immunity against SARS-CoV-2, with a short-term non-specific protective effect from mucosal Pam2Cys alone. These data support mucosal vaccination as a strategy to improve protection in the respiratory tract against SARS-CoV-2 and other respiratory viruses.

Ashique, S, De Rubis, G, Sirohi, E, Mishra, N, Rihan, M, Garg, A, Reyes, R-J, Manandhar, B, Bhatt, S, Jha, NK, Singh, TG, Gupta, G, Singh, SK, Chellappan, DK, Paudel, KR, Hansbro, PM, Oliver, BG & Dua, K 2022, 'Short Chain Fatty Acids: Fundamental mediators of the gut-lung axis and their involvement in pulmonary diseases', Chemico-Biological Interactions, vol. 368, pp. 110231-110231.
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Ashourloo, D, Nematollahi, H, Huete, A, Aghighi, H, Azadbakht, M, Shahrabi, HS & Goodarzdashti, S 2022, 'A new phenology-based method for mapping wheat and barley using time-series of Sentinel-2 images', Remote Sensing of Environment, vol. 280, pp. 113206-113206.
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In recent years, various techniques have been developed to generate crop-type maps based on remote sensing data. Wheat and barley are two major cereal crops cultivated as the first and fourth largest grain crops across the globe. The variations in spectral temporal profile of both crops are generally insignificant at small scales and therefore the two crops are phenologically fairly clearly separated; however, at large scale areas the variance of phenological parameters increases for both crops due to the effects of various climatic and orographic factors which adversely influences discrimination of wheat and barley. Additionally, wheat and barley are usually cultivated as both spring and winter or early and late season crops in some areas, making it more difficult to distinguish them. Therefore, developing a new method based on remote sensing data for effective discrimination of wheat and barley is an important necessity in the field of precision agriculture. To this end, this research presents a new phenology-based method to discriminate barley from wheat. In this study, Sentinel-2 (S2) time-series data of a study site in Iran (Markazi) and two sites in the USA (Idaho and North California), are employed. Spectral reflectance values of wheat and barley are examined during the growing season and a new spectral-temporal feature is successfully developed for automatic identification of the barley heading date. The Relief-f algorithm is then employed to select appropriate spectral features of S2 to distinguish wheat from barley at the heading date. Finally, generated spectral features at the heading date are used as input to Support Vector Machine (SVM) and Random Forest (RF) to produce barley and wheat maps. The Kappa coefficient and overall accuracy (OA) obtained for the three study sites are more than 0.67 and 76%, respectively. The findings of this study demonstrate the potential of remote sensing data to identify the phenological growth stages of barl...

Asrani, P, Tiwari, K, Eapen, MS, McAlinden, KD, Haug, G, Johansen, MD, Hansbro, PM, Flanagan, KL, Hassan, MI & Sohal, SS 2022, 'Clinical features and mechanistic insights into drug repurposing for combating COVID-19', The International Journal of Biochemistry & Cell Biology, vol. 142, pp. 106114-106114.
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Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) emerged from Wuhan in China before it spread to the entire globe. It causes coronavirus disease of 2019 (COVID-19) where mostly individuals present mild symptoms, some remain asymptomatic and some show severe lung inflammation and pneumonia in the host through the induction of a marked inflammatory 'cytokine storm'. New and efficacious vaccines have been developed and put into clinical practice in record time, however, there is a still a need for effective treatments for those who are not vaccinated or remain susceptible to emerging SARS-CoV-2 variant strains. Despite this, effective therapeutic interventions against COVID-19 remain elusive. Here, we have reviewed potential drugs for COVID-19 classified on the basis of their mode of action. The mechanisms of action of each are discussed in detail to highlight the therapeutic targets that may help in reducing the global pandemic. The review was done up to July 2021 and the data was assessed through the official websites of WHO and CDC for collecting the information on the clinical trials. Moreover, the recent research papers were also assessed for the relevant data. The search was mainly based on keywords like Coronavirus, SARS-CoV-2, drugs (specific name of the drugs), COVID-19, clinical efficiency, safety profile, side-effects etc.This review outlines potential areas for future research into COVID-19 treatment strategies.

Augustine, R, S, A, Nayeem, A, Salam, SA, Augustine, P, Dan, P, Maureira, P, Mraiche, F, Gentile, C, Hansbro, PM, McClements, L & Hasan, A 2022, 'Increased complications of COVID-19 in people with cardiovascular disease: Role of the renin–angiotensin-aldosterone system (RAAS) dysregulation', Chemico-Biological Interactions, vol. 351, pp. 109738-109738.
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The rapid spread of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) that causes coronavirus disease 2019 (COVID-19), has had a dramatic negative impact on public health and economies worldwide. Recent studies on COVID-19 complications and mortality rates suggest that there is a higher prevalence in cardiovascular diseases (CVD) patients. Past investigations on the associations between pre-existing CVDs and susceptibility to coronavirus infections including SARS-CoV and the Middle East Respiratory Syndrome coronavirus (MERS-CoV), have demonstrated similar results. However, the underlying mechanisms are poorly understood. This has impeded adequate risk stratification and treatment strategies for CVD patients with SARS-CoV-2 infections. Generally, dysregulation of the expression of angiotensin-converting enzyme (ACE) and the counter regulator, angiotensin-converting enzyme 2 (ACE2) is a hallmark of cardiovascular risk and CVD. ACE2 is the main host receptor for SARS-CoV-2. Although further studies are required, dysfunction of ACE2 after virus binding and dysregulation of the renin-angiotensin-aldosterone system (RAAS) signaling may worsen the outcomes of people affected by COVID-19 and with preexisting CVD. Here, we review the current knowledge and outline the gaps related to the relationship between CVD and COVID-19 with a focus on the RAAS. Improved understanding of the mechanisms regulating viral entry and the role RAAS may direct future research with the potential to improve the prevention and management of COVID-19.

Bai, L, Song, A, Lei, X, Zhang, T, Song, S, Tian, H, Liu, H, Qin, X, Wang, G & Shao, G 2022, 'Hierarchical construction of hollow NiCo2S4 nanotube@NiCo2S4 nanosheet arrays on Ni foam as an efficient and durable electrocatalyst for hydrogen evolution reaction', International Journal of Hydrogen Energy, vol. 47, no. 91, pp. 38524-38532.
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Ternary transition metal chalcogenide (TTMC) with multicomponent, different phases and unique electronic structures have been studied in electrocatalytic hydrogen evolution reaction (HER). However, the strong interaction between adsorbed H (H∗) and sulfur leads to the unfavorable hydrogen desorption properties of considerable TTMC. Herein, we constructed the hierarchical hollow NiCo2S4 nanotube@NiCo2S4 nanosheet arrays on Ni foam substrate (NT-NiCo2S4@NS-NiCo2S4/NF) by ion-exchange method. Homogeneous anion diffusion facilitates the formation of regular ultrathin nanosheets on hollow NiCo2S4 nanotube arrays, which presents hierarchical architecture with more surface area and channels to active site exposure, electrolyte diffusion, and gas desorption for HER. As-synthesized optimal NT-NiCo2S4@NS-NiCo2S4/NF electrode demonstrates an excellent HER activity, especially an overpotential of 221 mV, a Tafel slope of 108 mV dec−1, and remarkable stability at current densities of 100 mA cm−2 in 1.0 M NaOH electrolyte.

Bai, X, Chen, H & Oliver, BG 2022, 'miRNAs-mediated overexpression of Periostin is correlated with poor prognosis and immune infiltration in lung squamous cell carcinoma', Aging, vol. 14, no. 9, pp. 3757-3781.
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Lung cancer is one of the most common malignancies with a high mortality rate worldwide. POSTN has been shown to be strongly correlated with the poor prognosis of lung cancer patients. However, the function and mechanism of action of POSTN in lung cancer remain unclear. Here, we carried out a pan-cancer analysis to assess the clinical prognostic value of POSTN based on the TCGA, TIMER, Oncomine, Kaplan-Meier, and UALCAN databases. We found that upregulated POSTN can be a promising biomarker to predict the prognosis of patients with lung cancer. High levels of POSTN correlated with immune cell infiltration in lung cancer, especially lung squamous cell carcinoma (LUSC), which was further confirmed based on the results from the TISIDB database. Moreover, the expression analysis, correlation analysis, and survival analysis revealed that POSTN-targeted miRNAs, downregulation of has-miR-144-3p and has-miR-30e-3p, were significantly linked to poor prognosis in patients with LUSC. Taken together, we identified that POSTN can act as a novel biomarker for determining the prognosis related to immune infiltration in patients with LUSC and deserves further research.

Bai, X, Chen, H & Oliver, BG 2022, 'The health effects of traffic-related air pollution: A review focused the health effects of going green', Chemosphere, vol. 289, pp. 133082-133082.
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Bake, A, Rahman, MR, Evans, PJ, Cortie, M, Nancarrow, M, Abrudan, R, Radu, F, Khaydukov, Y, Causer, G, Livesey, KL, Callori, S, Mitchell, DRG, Pastuovic, Z, Wang, X & Cortie, D 2022, 'Ultra-small cobalt particles embedded in titania by ion beam synthesis: Additional datasets including electron microscopy, neutron reflectometry, modelling outputs and particle size analysis', Data in Brief, vol. 40, pp. 107674-107674.
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Barolo, L, Commault, AS, Abbriano, RM, Padula, MP, Kim, M, Kuzhiumparambil, U, Ralph, PJ & Pernice, M 2022, 'Unassembled cell wall proteins form aggregates in the extracellular space of Chlamydomonas reinhardtii strain UVM4', Applied Microbiology and Biotechnology, vol. 106, no. 11, pp. 4145-4156.
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Abstract The green microalga Chlamydomonas reinhardtii is emerging as a promising cell biofactory for secreted recombinant protein (RP) production. In recent years, the generation of the broadly used cell wall–deficient mutant strain UVM4 has allowed for a drastic increase in secreted RP yields. However, purification of secreted RPs from the extracellular space of C. reinhardtii strain UVM4 is challenging. Previous studies suggest that secreted RPs are trapped in a matrix of cell wall protein aggregates populating the secretome of strain UVM4, making it difficult to isolate and purify the RPs. To better understand the nature and behaviour of these extracellular protein aggregates, we analysed and compared the extracellular proteome of the strain UVM4 to its cell-walled ancestor, C. reinhardtii strain 137c. When grown under the same conditions, strain UVM4 produced a unique extracellular proteomic profile, including a higher abundance of secreted cell wall glycoproteins. Further characterization of high molecular weight extracellular protein aggregates in strain UVM4 revealed that they are largely comprised of pherophorins, a specific class of cell wall glycoproteins. Our results offer important new insights into the extracellular space of strain UVM4, including strain-specific secreted cell wall proteins and the composition of the aggregates possibly related to impaired RP purification. The discovery of pherophorins as a major component of extracellular protein aggregates will inform future strategies to remove or prevent aggregate formation, enhance purification of secreted RPs, and improve yields of recombinant biopharmaceuticals in this emerging cell biofactory. Key points •

Barone-Adesi, G, Platen, E & Sala, C 2022, 'Managing the Shortfall Risk of Target Date Funds by Overfunding', Swiss Finance Institute Research Paper, no. 20.

Becchi, S, Hood, J, Kendig, MD, Mohammadkhani, A, Shipman, ML, Balleine, BW, Borgland, SL & Corbit, LH 2022, 'Food for thought: diet-induced impairments to decision-making and amelioration by N-acetylcysteine in male rats', Psychopharmacology, vol. 239, no. 11, pp. 3495-3506.
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RATIONALE: Attempts to lose weight often fail despite knowledge of the health risks associated with obesity and determined efforts. We previously showed that rodents fed an obesogenic diet displayed premature habitual behavioural control and weakened flexible decision-making based on the current value of outcomes produced by their behaviour. Thus, habitual control may contribute to failed attempts to modify eating behaviours. OBJECTIVES: To examine the effects of an obesogenic diet on behavioural control and glutamate transmission in dorsal striatum regions and to assess the ability of N-acetylcysteine (NAC) to reverse deficits. METHODS: Here, we examined diet-induced changes to decision-making and used in vitro electrophysiology to investigate the effects of diet on glutamate transmission within the dorsomedial (DMS) and dorsolateral (DLS) striatum, areas that control goal-directed and habitual behaviours, respectively. We administered NAC in order to normalize glutamate release and tested whether this would restore goal-directed performance following an obesogenic diet. RESULTS: We found that an obesogenic diet reduced sensitivity to outcome devaluation and increased glutamate release in the DMS, but not DLS. Administration of NAC restored goal-directed control and normalized mEPSCs in the DMS. Finally, NAC administered directly to the DMS was sufficient to reinstate sensitivity to outcome devaluation following an obesogenic diet. CONCLUSIONS: These data indicate that obesogenic diets alter neural activity in the basal ganglia circuit responsible for goal-directed learning and control which leads to premature habitual control. While the effects of diet are numerous and widespread, normalization of glutamatergic activity in this circuit is sufficient for restoring goal-directed behaviour.

Becker, EJ, Faiz, A, van den Berge, M, Timens, W, Hiemstra, PS, Clark, K, Liu, G, Xiao, X, Alekseyev, YO, O'Connor, G, Lam, S, Spira, A, Lenburg, ME & Steiling, K 2022, 'Bronchial gene expression signature associated with rate of subsequent FEV₁ decline in individuals with and at risk of COPD', Thorax, vol. 77, no. 1, pp. 31-39.
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BackgroundCOPD is characterised by progressive lung function decline. Leveraging prior work demonstrating bronchial airway COPD-associated gene expression alterations, we sought to determine if there are alterations associated with differences in the rate of FEV1 decline.MethodsWe examined gene expression among ever smokers with and without COPD who at baseline had bronchial brushings profiled by Affymetrix microarrays and had longitudinal lung function measurements (n=134; mean follow-up=6.38±2.48 years). Gene expression profiles associated with the rate of FEV1 decline were identified by linear modelling.ResultsExpression differences in 171 genes were associated with rate of FEV1 decline (false discovery rate <0.05). The FEV1 decline signature was replicated in an independent dataset of bronchial biopsies from patients with COPD (n=46; p=0.018; mean follow-up=6.76±1.32 years). Genes elevated in individuals with more rapid FEV1 decline are significantly enriched among the genes altered by modulation of XBP1 in two independent datasets (Gene Set Enrichment Analysis (GSEA) p<0.05) and are enriched in mucin-related genes (GSEA p<0.05).ConclusionWe have identified and replicated an airway gene expression signature associated with the rate of FEV1 decline. Aspects of this signature are related to increased expression of XBP1-regulated genes, a transcription factor involved in the unfolded protein response, and genes related to mucin production. Collectively, these data suggest that molecular processes related to the rate of FEV1 decline can be detected in airway epithelium, id...

Belay, Y, Muller, A & Williams, DBG 2022, 'Lanthanum-1,2,3-Triazole-Based 2D Coordination Polymer is an Efficient Catalyst for the Oxidation of Olefins', Inorganic Chemistry, vol. 61, no. 21, pp. 8226-8232.
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Bell, KJ, Saad, S, Tillett, BJ, McGuire, HM, Bordbar, S, Yap, YA, Nguyen, LT, Wilkins, MR, Corley, S, Brodie, S, Duong, S, Wright, CJ, Twigg, S, de St Groth, BF, Harrison, LC, Mackay, CR, Gurzov, EN, Hamilton-Williams, EE & Mariño, E 2022, 'Metabolite-based dietary supplementation in human type 1 diabetes is associated with microbiota and immune modulation', Microbiome, vol. 10, no. 1.
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Abstract Background Short-chain fatty acids (SCFAs) produced by the gut microbiota have beneficial anti-inflammatory and gut homeostasis effects and prevent type 1 diabetes (T1D) in mice. Reduced SCFA production indicates a loss of beneficial bacteria, commonly associated with chronic autoimmune and inflammatory diseases, including T1D and type 2 diabetes. Here, we addressed whether a metabolite-based dietary supplement has an impact on humans with T1D. We conducted a single-arm pilot-and-feasibility trial with high-amylose maize-resistant starch modified with acetate and butyrate (HAMSAB) to assess safety, while monitoring changes in the gut microbiota in alignment with modulation of the immune system status. Results HAMSAB supplement was administered for 6 weeks with follow-up at 12 weeks in adults with long-standing T1D. Increased concentrations of SCFA acetate, propionate, and butyrate in stools and plasma were in concert with a shift in the composition and function of the gut microbiota. While glucose control and insulin requirements did not change, subjects with the highest SCFA concentrations exhibited the best glycemic control. Bifidobacterium longum, Bifidobacterium adolescentis, and vitamin B7 production correlated with lower HbA1c and basal insulin requirements. Circulating B and T cells developed a more regulatory phenotype post-intervention. Conclusion Changes in gut microbiota composition, function, and immune profile following 6 weeks of HAMSAB supplementation were associated with increased SCFAs in stools and plasma. The persistence of these effects suggests that targeti...

Bendall, ER, Bedward, M, Boer, M, Clarke, H, Collins, L, Leigh, A & Bradstock, RA 2022, 'Changes in the resilience of resprouting juvenile tree populations in temperate forests due to coupled severe drought and fire', Plant Ecology, vol. 223, no. 7, pp. 907-923.
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AbstractElevated tree mortality and reduced recruitment of new trees linked to drought and fires has been reported across a range of forests over the last few decades. Forests that resprout new foliage epicormically from buds beneath the bark are considered highly resilient to disturbance, but are potentially at risk of elevated mortality, demographic shifts and changes to species composition due to synergistic effects of drought and fire. Despite this, the effects of drought-fire interactions on such forests remain largely unknown. We assessed the effects of drought severity and fire frequency on juvenile mortality, post-fire seedling recruitment and replacement of juvenile trees (balance of recruitment minus mortality) following fire. We compared dry ridgetops and wet gullies (i.e. two forest types that inhabit different topographic positions in the landscape) across a temperate forest in southern Australia. Both forest types experienced higher rates of fire-induced juvenile mortality in areas that had experienced severe drought compared to moderate drought, though mortality rates were generally low across all drought and fire combinations (e.g. < 15%). This result indicated that topographic position did little to reduce juvenile mortality when exposed to severe drought plus fire. In wet forest, severe drought also reduced recruitment and replacement of dead juveniles by post-fire seedlings compared to moderate drought. In dry forest net-negative replacement increased with the severity of drought. Across both forest types, the total pool of juveniles was reduced under severe drought (by 16–79 in DSF; 5–11 in WSF). Future increases in the frequency of coupled severe drought and fire could potentially increase the susceptibility of resilient temperate forests to major changes in structure and function.

Bendall, ER, Bedward, M, Boer, M, Clarke, H, Collins, L, Leigh, A & Bradstock, RA 2022, 'Growth enhancements of elevated atmospheric [CO₂] are reduced under drought‐like conditions in temperate eucalypts', Functional Ecology, vol. 36, no. 7, pp. 1542-1558.
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AbstractElevated atmospheric [CO2] (‘eCO2’) may alter species composition within vegetation types by favouring the growth of some species over others. However, other related changes in climate conditions, such as increased frequency and severity of drought, may reduce eCO2 fertilisation effects on plant growth. For many species, it is not known if responses will reflect variability in trait adaptations due to environment.We grew seedlings of nine species of eucalypts indicative of three regional vegetation types (representing a mesic–xeric ecosystem gradient) under two CO2 concentrations (400 parts per million; 640 ppm, i.e. eCO2) and two watering regimes (well‐watered; drought‐like conditions).Elevated CO2 increased biomass accumulation but drought reduced this effect, with mesic species experiencing larger relative reductions. Elevated CO2 increased the size of storage organs used during resprouting, in the absence of drought. Typical drought responses, such as increased leaf mass per unit area and root mass ratio, were more pronounced in xeric species and were reduced under eCO2.Seedling growth and resprouting may be enhanced by eCO2, suggesting continued dominance of resprouting species in disturbance‐prone ecosystems, although severe drought is likely to offset eCO2 fertilisation. Xeric species may cope with drought more effectively under eCO2 than mesic species due to resource acquisition and storage traits that are more responsive.Read the f...

Bendall, ER, Bedward, M, Boer, M, Clarke, H, Collins, L, Leigh, A & Bradstock, RA 2022, 'Mortality and resprouting responses in forest trees driven more by tree and ecosystem characteristics than drought severity and fire frequency', Forest Ecology and Management, vol. 509, pp. 120070-120070.
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Bennett, B, Urzúa‐Encina, C, Pardo‐Roa, C, Ariyama, N, Lecocq, C, Rivera, C, Badía, C, Suárez, P, Agredo, M, Aguayo, C, Ávila, C, Araya, H, Pérez, P, Berrios, F, Agüero, B, Mendieta, V, Pituco, EM, de Almeida, IG, Medina, R, Brito, B, Johow, M & Ramirez, VN 2022, 'First report and genetic characterization of Seneca Valley virus (SVV) in Chile', Transboundary and Emerging Diseases, vol. 69, no. 6.
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Berdinsky, D, Elder, M & Kruengthomya, P 2022, 'Cayley polynomial–time computable groups', Information and Computation, vol. 288, pp. 104768-104768.
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Beringer, J, Moore, CE, Cleverly, J, Campbell, DI, Cleugh, H, De Kauwe, MG, Kirschbaum, MUF, Griebel, A, Grover, S, Huete, A, Hutley, LB, Laubach, J, Van Niel, T, Arndt, SK, Bennett, AC, Cernusak, LA, Eamus, D, Ewenz, CM, Goodrich, JP, Jiang, M, Hinko‐Najera, N, Isaac, P, Hobeichi, S, Knauer, J, Koerber, GR, Liddell, M, Ma, X, Macfarlane, C, McHugh, ID, Medlyn, BE, Meyer, WS, Norton, AJ, Owens, J, Pitman, A, Pendall, E, Prober, SM, Ray, RL, Restrepo‐Coupe, N, Rifai, SW, Rowlings, D, Schipper, L, Silberstein, RP, Teckentrup, L, Thompson, SE, Ukkola, AM, Wall, A, Wang, Y, Wardlaw, TJ & Woodgate, W 2022, 'Bridge to the future: Important lessons from 20 years of ecosystem observations made by the OzFlux network', Global Change Biology, vol. 28, no. 11, pp. 3489-3514.
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AbstractIn 2020, the Australian and New Zealand flux research and monitoring network, OzFlux, celebrated its 20th anniversary by reflecting on the lessons learned through two decades of ecosystem studies on global change biology. OzFlux is a network not only for ecosystem researchers, but also for those ‘next users’ of the knowledge, information and data that such networks provide. Here, we focus on eight lessons across topics of climate change and variability, disturbance and resilience, drought and heat stress and synergies with remote sensing and modelling. In distilling the key lessons learned, we also identify where further research is needed to fill knowledge gaps and improve the utility and relevance of the outputs from OzFlux. Extreme climate variability across Australia and New Zealand (droughts and flooding rains) provides a natural laboratory for a global understanding of ecosystems in this time of accelerating climate change. As evidence of worsening global fire risk emerges, the natural ability of these ecosystems to recover from disturbances, such as fire and cyclones, provides lessons on adaptation and resilience to disturbance. Drought and heatwaves are common occurrences across large parts of the region and can tip an ecosystem's carbon budget from a net CO2 sink to a net CO2 source. Despite such responses to stress, ecosystems at OzFlux sites show their resilience to climate variability by rapidly pivoting back to a strong carbon sink upon the return of favourable conditions. Located in under‐represented areas, OzFlux data have the potential for reducing uncertainties in global remote sensing products, and these data provide several opportunities to develop new theories and improve our ecosystem models. The accumulated impacts of these lessons over the last 20 years highlights the value of long‐term flux observations for natural and managed ...

Bernardini, A, Brown, J, Chipperfield, J, Bycroft, C, Chieppa, A, Cibella, N, Dunnet, G, Hawkes, MF, Hleihel, A, Law, EC, Ward, D & Zhang, L-C 2022, 'Evolution of the person census and the estimation of population counts in New Zealand, United Kingdom, Italy and Israel', Statistical Journal of the IAOS, vol. 38, no. 4, pp. 1221-1237.
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A Census of a nation’s people and housing provides statistics about its health, income and social structures at a local level. While the demand for these statistics is unchanged the way they are collected is changing in many nations because of common drivers: cost pressure, web-based collection, decreasing response rates, environmental shocks and the availability of administrative data. Within this context, this paper gives an overview of the evolution of the Census in Israel, Italy, New Zealand, and the United Kingdom and thereby provides an insight of the challenges and solutions of the modern Census.

Bhat, AA, Gupta, G, Alharbi, KS, Afzal, O, Altamimi, ASA, Almalki, WH, Kazmi, I, Al-Abbasi, FA, Alzarea, SI, Chellappan, DK, Singh, SK, MacLoughlin, R, Oliver, BG & Dua, K 2022, 'Polysaccharide-Based Nanomedicines Targeting Lung Cancer', Pharmaceutics, vol. 14, no. 12, pp. 2788-2788.
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A primary illness that accounts for a significant portion of fatalities worldwide is cancer. Among the main malignancies, lung cancer is recognised as the most chronic kind of cancer around the globe. Radiation treatment, surgery, and chemotherapy are some medical procedures used in the traditional care of lung cancer. However, these methods lack selectivity and damage nearby healthy cells. Several polysaccharide-based nanomaterials have been created to transport chemotherapeutics to reduce harmful and adverse side effects and improve response during anti-tumour reactions. To address these drawbacks, a class of naturally occurring polymers called polysaccharides have special physical, chemical, and biological characteristics. They can interact with the immune system to induce a better immunological response. Furthermore, because of the flexibility of their structures, it is possible to create multifunctional nanocomposites with excellent stability and bioavailability for the delivery of medicines to tumour tissues. This study seeks to present new views on the use of polysaccharide-based chemotherapeutics and to highlight current developments in polysaccharide-based nanomedicines for lung cancer.

Bhattacharyya, A, Ahmed, M, Wadhwa, R, Aggarwal, S, Mustafiz, A & Rajagopalan, G 2022, 'High Production of Trametes cinnabarina Laccase (lac1) by Suspended and Immobilized Cells of Recombinant Pichia pastoris from Crude Glycerol', Waste and Biomass Valorization, vol. 13, no. 4, pp. 2149-2168.
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Bittleston, H, Hocking, JS, Goller, JL, Coombe, J, Bateson, D, Sweeney, S, Fleming, K & Huston, WM 2022, 'Is there a place for a molecular diagnostic test for pelvic inflammatory disease in primary care? An exploratory qualitative study', PLOS ONE, vol. 17, no. 9, pp. e0274666-e0274666.
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IntroductionThere is currently no test for pelvic inflammatory disease (PID) that is non-invasive and sufficiently sensitive and specific. Clinicians must therefore diagnose PID clinically, ruling out medical emergencies and conducting pelvic examinations where possible. While guidelines state that clinicians should be prepared to over-diagnose PID, it remains an under-diagnosed condition, with severe reproductive health impacts when left untreated. This research is the first to consider the perspectives of end-users on the development of a diagnostic test for PID.MethodsSemi-structured live video feed online (Zoom) interviews were conducted with 11 clinicians and nine women (aged 18–30 years) in Australia to understand how a diagnostic test might be used, and what characteristics a test would need for it to be acceptable to clinicians and young women. Participants were recruited via researcher and university student networks. Reflexive thematic analysis was used to identify key themes relating to the acceptability and characteristics of a diagnostic test for PID.ResultsSeven general practitioners, four clinicians working in sexual health clinics, and nine young women (aged 21–27 years) were interviewed. Clinicians were aged between 31–58 years and were predominantly female. Clinicians recognised that the development of an accurate test to diagnose PID would be valuable to themselves and other clinicians, particularly those who lack experience diagnosing PID, and those working in certain settings, including emergency departments. They discussed how they might use a test to enhance their clinical assessment but highlighted that it would not replace clinical judgement. Clinicians also considered how a test would impact the patient experience and time to ...

Bohaud, C, Johansen, MD, Varga, B, Contreras-Lopez, R, Barthelaix, A, Hamela, C, Sapède, D, Cloitre, T, Gergely, C, Jorgensen, C, Kremer, L & Djouad, F 2022, 'Exploring Macrophage-Dependent Wound Regeneration During Mycobacterial Infection in Zebrafish', Frontiers in Immunology, vol. 13, pp. 1-16.
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The molecular and cellular mechanisms associated with tissue degradation or regeneration in an infectious context are poorly defined. Herein, we explored the role of macrophages in orchestrating either tissue regeneration or degradation in zebrafish embryos pre-infected with the fish pathogen Mycobacterium marinum. Zebrafish were inoculated with different infectious doses of M. marinum prior to fin resection. While mild infection accelerated fin regeneration, moderate or severe infection delayed this process by reducing blastemal cell proliferation and impeding tissue morphogenesis. This was correlated with impaired macrophage recruitment at the wound of the larvae receiving high infectious doses. Macrophage activation characterized, in part, by a high expression level of tnfa was exacerbated in severely infected fish during the early phase of the regeneration process, leading to macrophage necrosis and their complete absence in the later phase. Our results demonstrate how a mycobacterial infection influences the macrophage response and tissue regenerative processes.

Bordhan, P, Razavi Bazaz, S, Jin, D & Ebrahimi Warkiani, M 2022, 'Advances and enabling technologies for phase-specific cell cycle synchronisation', Lab on a Chip, vol. 22, no. 3, pp. 445-462.
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Schematic illustration of conventional (left) and microfluidics-based (right) phase-specific cell cycle synchronization strategies.

Bradbury, P, Cidem, A, Mahmodi, H, Davies, JM, Spicer, PT, Prescott, SW, Kabakova, I, Ong, HX & Traini, D 2022, 'Timothy Grass Pollen Induces Spatial Reorganisation of F-Actin and Loss of Junctional Integrity in Respiratory Cells', Inflammation, vol. 45, no. 3, pp. 1209-1223.
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Grass pollens have been identified as mediators of respiratory distress, capable of exacerbating respiratory diseases including epidemic thunderstorm asthma (ETSA). It is hypothesised that during thunderstorms, grass pollen grains swell to absorb atmospheric water, rupture, and release internal protein content to the atmosphere. The inhalation of atmospheric grass pollen proteins results in deadly ETSA events. We sought to identify the underlying cellular mechanisms that may contribute towards the severity of ETSA in temperate climates using Timothy grass (Phleum pratense). Respiratory cells exposed to Timothy grass pollen protein extract (PPE) caused cells to undergo hypoxia ultimately triggering the subcellular re-organisation of F-actin from the peri junctional belt to cytoplasmic fibre assembly traversing the cell body. This change in actin configuration coincided with the spatial reorganisation of microtubules and importantly, decreased cell compressibility specifically at the cell centre. Further to this, we find that the pollen-induced reorganisation of the actin cytoskeleton prompting secretion of the pro-inflammatory cytokine, interleukin-8. In addition, the loss of peri-junctional actin following exposure to pollen proteins was accompanied by the release of epithelial transmembrane protein, E-cadherin from cell-cell junctions resulting in a decrease in epithelial barrier integrity. We demonstrate that Timothy grass pollen regulates F-actin dynamics and E-cadherin localisation in respiratory cells to mediate cell-cell junctional integrity highlighting a possible molecular pathway underpinning ETSA events.

Brito, BP, Koong, J, Wozniak, A, Opazo-Capurro, A, To, J, Garcia, P & Hamidian, M 2022, 'Genomic Analysis of Carbapenem-Resistant Acinetobacter baumannii Strains Recovered from Chilean Hospitals Reveals Lineages Specific to South America and Multiple Routes for Acquisition of Antibiotic Resistance Genes', Microbiology Spectrum, vol. 10, no. 5, p. e0246322.
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Treating infections caused by carbapenem-resistant A. baumannii (CR Ab ) has become a global challenge given that CR Ab strains are also often resistant to a wide range of antibiotics. Analysis of whole-genome sequence data is now a standard approach for studying the genomic context of antibiotic resistance genes; however, genome sequence data from South American countries are scarce.

Broome, ST, Musumeci, G & Castorina, A 2022, 'PACAP and VIP Mitigate Rotenone-Induced Inflammation in BV-2 Microglial Cells', Journal of Molecular Neuroscience, vol. 72, no. 11, pp. 2163-2175.
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AbstractRotenone is a commercial pesticide commonly used to model Parkinson’s disease (PD) due to its ability to induce dopaminergic degeneration. Studies have confirmed that rotenone causes microglial activation, which seems to contribute to the toxic effects seen in rodent models. Pituitary adenylate cyclase–activating polypeptide (PACAP) and vasoactive intestinal peptide (VIP) are two structurally related neuropeptides that have robust neuroprotective and anti-inflammatory properties. However, their ability to regulate microglial activity in response to rotenone is not fully understood. Using rotenone as an inflammatory stimulus, we tested whether PACAP or VIP could mitigate microglial activation in BV2 microglial cells. Rotenone dose-dependently reduced cell viability and the percentage of apoptotic cells. It also increased the release of nitric oxide (NO) in culture media and the expression of microglial activation markers and pro-inflammatory markers, including CD11b, MMP-9 and IL-6, and heightened the endogenous levels of PACAP and its preferring receptor PAC1. Co-treatment with PACAP or VIP prevented rotenone-induced increase of NO, CD11b, MMP-9 and IL-6. These results indicate that both PACAP and VIP are able to prevent the pro-inflammatory effects of rotenone in BV2 cells, supporting the idea that these molecules can have therapeutic value in slowing down PD progression. Graphical Abstract

Brunet, M, Le Duff, N, Barbeyron, T & Thomas, F 2022, 'Consuming fresh macroalgae induces specific catabolic pathways, stress reactions and Type IX secretion in marine flavobacterial pioneer degraders', The ISME Journal, vol. 16, no. 8, pp. 2027-2039.
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Abstract Macroalgae represent huge amounts of biomass worldwide, largely recycled by marine heterotrophic bacteria. We investigated the strategies of bacteria within the flavobacterial genus Zobellia to initiate the degradation of whole algal tissues, which has received little attention compared to the degradation of isolated polysaccharides. Zobellia galactanivorans DsijT has the capacity to use fresh brown macroalgae as a sole carbon source and extensively degrades algal tissues via the secretion of extracellular enzymes, even in the absence of physical contact with the algae. Co-cultures experiments with the non-degrading strain Tenacibaculum aestuarii SMK-4T showed that Z. galactanivorans can act as a pioneer that initiates algal breakdown and shares public goods with other bacteria. A comparison of eight Zobellia strains, and strong transcriptomic shifts in Z. galactanivorans cells using fresh macroalgae vs. isolated polysaccharides, revealed potential overlooked traits of pioneer bacteria. Besides brown algal polysaccharide degradation, they notably include oxidative stress resistance proteins, type IX secretion system proteins and novel uncharacterized polysaccharide utilization loci. Overall, this work highlights the relevance of studying fresh macroalga degradation to fully understand the metabolic and ecological strategies of pioneer microbial degraders, key players in macroalgal biomass remineralization.

Butt, N, Halpern, BS, O'Hara, CC, Allcock, AL, Polidoro, B, Sherman, S, Byrne, M, Birkeland, C, Dwyer, RG, Frazier, M, Woodworth, BK, Arango, CP, Kingsford, MJ, Udyawer, V, Hutchings, P, Scanes, E, McClaren, EJ, Maxwell, SM, Diaz‐Pulido, G, Dugan, E, Simmons, BA, Wenger, AS, Linardich, C & Klein, CJ 2022, 'A trait‐based framework for assessing the vulnerability of marine species to human impacts', Ecosphere, vol. 13, no. 2.
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AbstractMarine species and ecosystems are widely affected by anthropogenic stressors, ranging from pollution and fishing to climate change. Comprehensive assessments of how species and ecosystems are impacted by anthropogenic stressors are critical for guiding conservation and management investments. Previous global risk or vulnerability assessments have focused on marine habitats, or on limited taxa or specific regions. However, information about the susceptibility of marine species across a range of taxa to different stressors everywhere is required to predict how marine biodiversity will respond to human pressures. We present a novel framework that uses life‐history traits to assess species' vulnerability to a stressor, which we compare across more than 44,000 species from 12 taxonomic groups (classes). Using expert elicitation and literature review, we assessed every combination of each of 42 traits and 22 anthropogenic stressors to calculate each species' or representative species group's sensitivity and adaptive capacity to stressors, and then used these assessments to derive their overall relative vulnerability. The stressors with the greatest potential impact were related to biomass removal (e.g., fisheries), pollution, and climate change. The taxa with the highest vulnerabilities across the range of stressors were mollusks, corals, and echinoderms, while elasmobranchs had the highest vulnerability to fishing‐related stressors. Traits likely to confer vulnerability to climate change stressors were related to the presence of calcium carbonate structures, and whether a species exists across the interface of marine, terrestrial, and atmospheric realms. Traits likely to confer vulnerability to pollution stressors were related to planktonic state, organism size, and respiration. Such a replicable, broadly applicable method is useful for informing ocean conservation and management decisions at a range of scales, and th...

Butterworth, NJ & Wallman, JF 2022, 'Flies getting filthy: The precopulatory mating behaviours of three mud‐dwelling species of Australian Lispe (Diptera: Muscidae)', Ethology, vol. 128, no. 4, pp. 369-377.
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AbstractLispe (Diptera: Muscidae) is a cosmopolitan genus of predatory flies that inhabit the muddy and sandy surrounds of water bodies. There are more than 163 described species worldwide, many of which are known to exhibit cursorial courtship displays which involve complex visual and vibratory signals. Despite the widespread distribution of these flies and their remarkable courtship displays, the biology and behaviour of most species are entirely unknown. Here, for the first time, we describe the precopulatory mating behaviours of three widespread and common Australian species: Lispe sydneyensis, Lispe albimaculata and Lispe xenochaeta. We demonstrate that all three species exhibit entirely unique courtship displays, consisting of complex behavioural repertoires. Importantly, we highlight intra‐sexual competition in L. sydneyensis, where males engage in competitive dances and combat. We also report female–male aggression in L. albimaculata and L. xenochaeta where females charge and display towards males. These novel mating systems provide unique opportunities to test ecological and evolutionary hypotheses.

Buzova, D, Braghini, MR, Bianco, SD, Lo Re, O, Raffaele, M, Frohlich, J, Kisheva, A, Crudele, A, Mosca, A, Sartorelli, MR, Balsano, C, Cerveny, J, Mazza, T, Alisi, A & Vinciguerra, M 2022, 'Profiling of cell‐free DNA methylation and histone signatures in pediatric NAFLD: A pilot study', Hepatology Communications, vol. 6, no. 12, pp. 3311-3323.
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Abstract Nonalcoholic fatty liver disease (NAFLD) has become the most common chronic liver disease in children and adolescents, increasing the risk of its progression toward nonalcoholic steatohepatitis (NASH), cirrhosis, and cancer. There is an urgent need for noninvasive early diagnostic and prognostic tools such as epigenetic marks (epimarks), which would replace liver biopsy in the future. We used plasma samples from 67 children with biopsy‐proven NAFLD, and as controls we used samples from 20 children negative for steatosis by ultrasound. All patients were genotyped for patatin‐like phospholipase domain containing 3 (PNPLA3), transmembrane 6 superfamily member 2 (TM6SF2), membrane bound O‐acyltransferase domain containing 7 (MBOAT7), and klotho‐β (KLB) gene variants, and data on anthropometric and biochemical parameters were collected. Furthermore, plasma cell‐free DNA (cfDNA) methylation was quantified using a commercially available kit, and ImageStream(X) was used for the detection of free circulating histone complexes and variants. We found a significant enrichment of the levels of histone macroH2A1.2 in the plasma of children with NAFLD compared to controls, and a strong correlation between cfDNA methylation levels and NASH. Receiver operating characteristic curve analysis demonstrated that combination of cfDNA methylation, PNPLA3 rs738409 variant, coupled with either high‐density lipoprotein cholesterol or alanine aminotransferase levels can strongly predict the progression of pediatric NAFLD to NASH with area under the curve >0.87. Conclusion: Our pilot study combined epimarks and genetic and metabolic markers for a robust risk assessment of NAFLD development and progression in children, offering a promising noninvasive tool for the consistent diagnosis and prognosis of pediatric NAFLD. Further studies are necessary to identify their pathogenic origin and fu...

Camaya, I, Donnelly, S & O'Brien, B 2022, 'Targeting the PI3K/Akt signaling pathway in pancreatic β‐cells to enhance their survival and function: An emerging therapeutic strategy for type 1 diabetes', Journal of Diabetes, vol. 14, no. 4, pp. 247-260.
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AbstractType 1 diabetes (T1D) is an autoimmune disease caused by the destruction of the insulin‐producing β‐cells within the pancreas. Islet transplantation represents one cure; however, during islet preparation and post transplantation significant amounts of β‐cell death occur. Therefore, prevention and cure of T1D is dependent upon the preservation of β‐cell function and the prevention of β‐cell death. Phosphoinositide 3‐kinase (PI3K)/Akt signaling represents a promising therapeutic target for T1D due to its pronounced effects on cellular survival, proliferation, and metabolism. A growing amount of evidence indicates that PI3K/Akt signaling is a critical determinant of β‐cell mass and function. Modulation of the PI3K/Akt pathway, directly (via the use of highly specific protein and peptide‐based biologics, excretory/secretory products of parasitic worms, and complex constituents of plant extracts) or indirectly (through microRNA interactions) can regulate the β‐cell processes to ultimately determine the fate of β‐cell mass. An important consideration is the identification of the specific PI3K/Akt pathway modulators that enhance β‐cell function and prevent β‐cell death without inducing excessive β‐cell proliferation, which may carry carcinogenic side effects. Among potential PI3K/Akt pathway agonists, we have identified a novel parasite‐derived protein, termed FhHDM‐1 (Fasciola hepatica helminth defense molecule 1), which efficiently stimulates the PI3K/Akt pathway in β‐cells to enhance function and prevent death without concomitantly inducing proliferation unlike several other identified stimulators of PI3K/Akt signaling . As such, FhHDM‐1 will inform the design of biologics aimed at targeting the PI3K/Akt pathway to prevent/ameliorate not only T1D but also T2D, which is now widely recognized as an inflammatory disease characterized by β‐cell dysfunction and death. This review will explore th...

Camirand Lemyre, F, Carroll, RJ & Delaigle, A 2022, 'Semiparametric Estimation of the Distribution of Episodically Consumed Foods Measured With Error', Journal of the American Statistical Association, vol. 117, no. 537, pp. 469-481.
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© 2020 American Statistical Association. Dietary data collected from 24-hour dietary recalls are observed with significant measurement errors. In the nonparametric curve estimation literature, much of the effort has been devoted to designing methods that are consistent under contamination by noise, and which have been traditionally applied for analyzing those data. However, some foods such as alcohol or fruits are consumed only episodically, and may not be consumed during the day when the 24-hour recall is administered. These so-called excess zeros make existing nonparametric estimators break down, and new techniques need to be developed for such data. We develop two new consistent semiparametric estimators of the distribution of such episodically consumed food data, making parametric assumptions only on some less important parts of the model. We establish its theoretical properties and illustrate the good performance of our fully data-driven method in simulated and real data. Supplementary materials for this article are available online.

Camp, EF, Kahlke, T, Signal, B, Oakley, CA, Lutz, A, Davy, SK, Suggett, DJ & Leggat, WP 2022, 'Proteome metabolome and transcriptome data for three Symbiodiniaceae under ambient and heat stress conditions', Scientific Data, vol. 9, no. 1, pp. 1-10.
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AbstractThe Symbiodiniaceae are a taxonomically and functionally diverse family of marine dinoflagellates. Their symbiotic relationship with invertebrates such as scleractinian corals has made them the focus of decades of research to resolve the underlying biology regulating their sensitivity to stressors, particularly thermal stress. Research to-date suggests that Symbiodiniaceae stress sensitivity is governed by a complex interplay between phylogenetic dependent and independent traits (diversity of characteristics of a species). Consequently, there is a need for datasets that simultaneously broadly resolve molecular and physiological processes under stressed and non-stressed conditions. Therefore, we provide a dataset simultaneously generating transcriptome, metabolome, and proteome data for three ecologically important Symbiodiniaceae isolates under nutrient replete growth conditions and two temperature treatments (ca. 26 °C and 32 °C). Elevated sea surface temperature is primarily responsible for coral bleaching events that occur when the coral-Symbiodiniaceae relationship has been disrupted. Symbiodiniaceae can strongly influence their host’s response to thermal stress and consequently it is necessary to resolve drivers of Symbiodiniaceae heat stress tolerance. We anticipate these datasets to expand our understanding on the key genotypic and functional properties that influence the sensitivities of Symbiodiniaceae to thermal stress.

Camp, EF, Nitschke, MR, Clases, D, Gonzalez de Vega, R, Reich, HG, Goyen, S & Suggett, DJ 2022, 'Micronutrient content drives elementome variability amongst the Symbiodiniaceae', BMC Plant Biology, vol. 22, no. 1, pp. 1-14.
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AbstractBackgroundElements are the basis of life on Earth, whereby organisms are essentially evolved chemical substances that dynamically interact with each other and their environment. Determining species elemental quotas (their elementome) is a key indicator for their success across environments with different resource availabilities. Elementomes remain undescribed for functionally diverse dinoflagellates within the family Symbiodiniaceae that includes coral endosymbionts. We used dry combustion and ICP-MS to assess whether Symbiodiniaceae (ten isolates spanning five generaBreviolum, Cladocopium, Durusdinium, Effrenium, Symbiodinium) maintained under long-term nutrient replete conditions have unique elementomes (six key macronutrients and nine micronutrients) that would reflect evolutionarily conserved preferential elemental acquisition. For three isolates we assessed how elevated temperature impacted their elementomes. Further, we tested whether Symbiodiniaceae conform to common stoichiometric hypotheses (e.g., the growth rate hypothesis) documented in other marine algae. This study considers whether Symbiodiniaceae isolates possess unique elementomes reflective of their natural ecologies, evolutionary histories, and resistance to environmental change.ResultsSymbiodiniaceae isolates maintained under long-term luxury uptake conditions, all exhibited highly divergent elementomes from one another, driven primarily by differential content of micronutrients. All N:P and C:P ratios were below the Redfield ratio values, whereas C:N was close to the Redfield value. Elevated temperature resulted in a more homogenised elementome across isolates. The Family-level elementome was (C19.8N2.6P1.0S18.8K0.7Ca...

Cao, X, Huo, J, Li, L, Qu, J, Zhao, Y, Chen, W, Liu, C, Liu, H & Wang, G 2022, 'Recent Advances in Engineered Ru‐Based Electrocatalysts for the Hydrogen/Oxygen Conversion Reactions', Advanced Energy Materials, vol. 12, no. 41, pp. 2202119-2202119.
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AbstractThe application of renewable energy conversion devices is considered as one of the effective ways to alleviate the energy shortage and environmental pollution. Designing electrocatalysts with excellent performance and affordable price is promising to accelerate the reaction process and large‐scale application. At present, ruthenium (Ru)‐based nanomaterials have shown similar catalytic activity but superior price demand compared to commercial Pt/C. This undoubtedly makes Ru‐based nanomaterials a perfect candidate to replace advanced Pt catalysts. Significant progress is made in the rational design of Ru‐based electrocatalysts, but an in‐depth understanding of the engineering strategies and induced effects is still at an early stage. This review summarizes the modification strategies for enhancing the catalytic activity of Ru, including surface structure, metal element, nonmetal element, size, bimetallic oxides, and heterostructure engineering strategies. Then the induced electronic modulation effects generated by the intramolecular and intermolecular of the Ru‐based nanomaterials are elucidated. Further, the application progress of engineered Ru‐based nanomaterials for hydrogen and oxygen conversion reactions is highlighted, and the correlations of engineering strategies, catalytic activity, and reaction pathways are elaborated. Finally, challenges and prospects are presented for the future development and practical application of Ru‐based nanomaterials.

Cao, Y, Xie, Z, Woodgate, W, Ma, X, Cleverly, J, Pang, Y, Qin, F & Huete, A 2022, 'Ecohydrological decoupling of water storage and vegetation attributed to China’s large-scale ecological restoration programs', Journal of Hydrology, vol. 615, pp. 128651-128651.
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China has implemented some of the world's most ambitious ecological restoration (ER) programs over the past two decades. These large-scale multi-billion-dollar projects have achieved widespread greening across the country. However, the impacts of different ER-driven land cover modifications on total water resources remain largely unknown, particularly over areas characterized by complex environments of coupled human and natural systems. Here we quantified ecohydrological impacts of multiple ER programs applied over various parts of China's Yellow River Basin (YRB), with their lumped effects being partitioned into individual ones. ER-related drivers were disentangled, leading in individual attribution of inter-annual climatic variability and agricultural activity with cross-sensor satellite observations and statistical modelling. Our results showed an ecohydrological decoupling of water storage and vegetation greenness attributed to ER programs. Increases in natural land cover types (e.g. forest and grassland) were found at the expense of human intensive land use, such as farmland, with the combined changes resulting in a concurrent dramatic water storage loss of 3.70 billion tons/year from 2002 to 2021. ER was the dominant driver of water loss (>66 %) among all factors considered, commensurate with areal land-cover change and ER program cost. The entire basin was divided into two regions with opposite water trends by the ER activities with different restoration strategies. This study's framework is applicable to substantial part of the globe like YRB and is encouraged to be applied for more wholistic ER impact evaluations.

Cárdenas, A, Raina, J-B, Pogoreutz, C, Rädecker, N, Bougoure, J, Guagliardo, P, Pernice, M & Voolstra, CR 2022, 'Greater functional diversity and redundancy of coral endolithic microbiomes align with lower coral bleaching susceptibility', The ISME Journal, vol. 16, no. 10, pp. 2406-2420.
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Abstract The skeleton of reef-building coral harbors diverse microbial communities that could compensate for metabolic deficiencies caused by the loss of algal endosymbionts, i.e., coral bleaching. However, it is unknown to what extent endolith taxonomic diversity and functional potential might contribute to thermal resilience. Here we exposed Goniastrea edwardsi and Porites lutea, two common reef-building corals from the central Red Sea to a 17-day long heat stress. Using hyperspectral imaging, marker gene/metagenomic sequencing, and NanoSIMS, we characterized their endolithic microbiomes together with 15N and 13C assimilation of two skeletal compartments: the endolithic band directly below the coral tissue and the deep skeleton. The bleaching-resistant G. edwardsi was associated with endolithic microbiomes of greater functional diversity and redundancy that exhibited lower N and C assimilation than endoliths in the bleaching-sensitive P. lutea. We propose that the lower endolithic primary productivity in G. edwardsi can be attributed to the dominance of chemolithotrophs. Lower primary production within the skeleton may prevent unbalanced nutrient fluxes to coral tissues under heat stress, thereby preserving nutrient-limiting conditions characteristic of a stable coral-algal symbiosis. Our findings link coral endolithic microbiome structure and function to bleaching susceptibility, providing new avenues for understanding and eventually mitigating reef loss.

Carter, DJ, Rahmani, A & Brown, JJ 2022, 'Regulating Health Care Safety: Enforcement and Responsibility Attribution in Response to Iatrogenic Harm.', J Law Med, vol. 29, no. 3, pp. 847-865.
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The regulation of health care safety is undertaken in the name of the public and is motivated and justified by their protection. This regulatory action generates debate concerning the proper limits of responsibility attribution and enforcement, while the actions and opinion - both imagined and real - of the public loom large in this field. However, there exists limited knowledge of public opinion on key aspects of health care safety enforcement and responsibility attribution following iatrogenic harm. This article reports on the results of a survey-administered experimental study to determine how the Australian general public attributes responsibility, moral censure and enforcement actions in the event of health care safety failures in hospital and outpatient settings. The study provide evidence that the general public are sensitive to corporate and individual sources of error; attribute responsibility in a pluralistic manner; differentiate between recklessness and negligence; and will attempt both formal and social enforcement actions in response to harm.

Castorina, A, Mandwie, M, Piper, J, Gorrie, C, Keay, K, Musumeci, G & Al-Badri, G 2022, 'Rapid GFAP and Iba1 expression changes in the female rat brain following spinal cord injury', Neural Regeneration Research, vol. 17, no. 2, pp. 378-378.
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Spinal cord injury (SCI) is a devastating condition often associated with sleep disorders, mood change and depression. Evidence suggests that rapid changes to supporting glia may predispose individuals with SCI to such comorbidities. Here, we interrogated the expression of astrocyte- and microglial-specific markers glial fibrillary acidic protein (GFAP) and ionized calcium binding adaptor molecule 1 (Iba1) in the rat brain in the first 24 hours following spinal cord injury (SCI). Female Sprague Dawley rats underwent thoracic laminectomy; half of the rats received a mild contusion injury at the level of the T10 vertebral body (SCI group), the other half did not (Sham group). Twenty-four hours post-surgery the rats were sacrificed, and the amygdala, periaqueductal grey, prefrontal cortex, hypothalamus, lateral thalamus, hippocampus (dorsal and ventral) were collected. GFAP and Iba1 mRNA and protein levels were measured by real-time qPCR and Western blot. In SCI rats, GFAP mRNA and protein expression increased in the amygdala and hypothalamus (*p<0.05). In contrast, gene and protein expression decreased in the thalamus (**p<0.01) and dorsal hippocampus (*p<0.05 and **p<0.01, respectively). Interestingly, Iba1 transcripts and proteins were significantly diminished only in the dorsal (*p<0.05 and **p<0.01, respectively) and ventral hippocampus, where gene expression diminished (*p<0.05 for both mRNA and protein). Considered together, these findings demonstrate that as early as 24 hours post-SCI there are region-specific disruptions of GFAP and Iba1 transcript and protein levels in higher brain regions.

Cawley, A, Keen, B, Tou, K, Elbourne, M & Keledjian, J 2022, 'Biomarker ratios', Drug Testing and Analysis, vol. 14, no. 5, pp. 983-990.
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AbstractThe concept of biomarker measurements in the form of a ratio has not been explored in detail. This is surprising considering the current and future potential for biomarkers incorporating endogenous reference compounds (ERCs) in a range of fields. A selection of these relating to clinical and forensic applications, human antidoping, equine antidoping and veterinary residues are discussed.

Chalmers, T, Hickey, BA, Newton, P, Lin, C-T, Sibbritt, D, McLachlan, CS, Clifton-Bligh, R, Morley, J & Lal, S 2022, 'Stress Watch: The Use of Heart Rate and Heart Rate Variability to Detect Stress: A Pilot Study Using Smart Watch Wearables', Sensors, vol. 22, no. 1, pp. 151-151.
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Stress is an inherent part of the normal human experience. Although, for the most part, this stress response is advantageous, chronic, heightened, or inappropriate stress responses can have deleterious effects on the human body. It has been suggested that individuals who experience repeated or prolonged stress exhibit blunted biological stress responses when compared to the general population. Thus, when assessing whether a ubiquitous stress response exists, it is important to stratify based on resting levels in the absence of stress. Research has shown that stress that causes symptomatic responses requires early intervention in order to mitigate possible associated mental health decline and personal risks. Given this, real-time monitoring of stress may provide immediate biofeedback to the individual and allow for early self-intervention. This study aimed to determine if the change in heart rate variability could predict, in two different cohorts, the quality of response to acute stress when exposed to an acute stressor and, in turn, contribute to the development of a physiological algorithm for stress which could be utilized in future smartwatch technologies. This study also aimed to assess whether baseline stress levels may affect the changes seen in heart rate variability at baseline and following stress tasks. A total of 30 student doctor participants and 30 participants from the general population were recruited for the study. The Trier Stress Test was utilized to induce stress, with resting and stress phase ECGs recorded, as well as inter-second heart rate (recorded using a FitBit). Although the present study failed to identify ubiquitous patterns of HRV and HR changes during stress, it did identify novel changes in these parameters between resting and stress states. This study has shown that the utilization of HRV as a measure of stress should be calculated with consideration of resting (baseline) anxiety and stress states in order to ens...

Chalmers, T, Hickey, BA, Newton, P, Lin, C-T, Sibbritt, D, McLachlan, CS, Clifton-Bligh, R, Morley, JW & Lal, S 2022, 'Associations between Sleep Quality and Heart Rate Variability: Implications for a Biological Model of Stress Detection Using Wearable Technology', International Journal of Environmental Research and Public Health, vol. 19, no. 9, pp. 5770-5770.
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Introduction: The autonomic nervous system plays a vital role in the modulation of many vital bodily functions, one of which is sleep and wakefulness. Many studies have investigated the link between autonomic dysfunction and sleep cycles; however, few studies have investigated the links between short-term sleep health, as determined by the Pittsburgh Quality of Sleep Index (PSQI), such as subjective sleep quality, sleep latency, sleep duration, habitual sleep efficiency, sleep disturbances, use of sleeping medication, and daytime dysfunction, and autonomic functioning in healthy individuals. Aim: In this cross-sectional study, the aim was to investigate the links between short-term sleep quality and duration, and heart rate variability in 60 healthy individuals, in order to provide useful information about the effects of stress and sleep on heart rate variability (HRV) indices, which in turn could be integrated into biological models for wearable devices. Methods: Sleep parameters were collected from participants on commencement of the study, and HRV was derived using an electrocardiogram (ECG) during a resting and stress task (Trier Stress Test). Result: Low-frequency to high-frequency (LF:HF) ratio was significantly higher during the stress task than during the baseline resting phase, and very-low-frequency and high-frequency HRV were inversely related to impaired sleep during stress tasks. Conclusion: Given the ubiquitous nature of wearable technologies for monitoring health states, in particular HRV, it is important to consider the impacts of sleep states when using these technologies to interpret data. Very-low-frequency HRV during the stress task was found to be inversely related to three negative sleep indices: sleep quality, daytime dysfunction, and global sleep score.

Chan, LLY, Anderson, DE, Cheng, HS, Ivan, FX, Chen, S, Kang, AEZ, Foo, R, Gamage, AM, Tiew, PY, Koh, MS, Lee, KCH, Nichol, K, Pathinayake, PS, Chan, YL, Yeo, TW, Oliver, BG, Wark, PAB, Liu, L, Tan, NS, Wang, L-F & Chotirmall, SH 2022, 'The establishment of COPD organoids to study host-pathogen interaction reveals enhanced viral fitness of SARS-CoV-2 in bronchi', Nature Communications, vol. 13, no. 1, p. 7635.
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AbstractChronic obstructive pulmonary disease (COPD) is characterised by airflow limitation and infective exacerbations, however, in-vitro model systems for the study of host-pathogen interaction at the individual level are lacking. Here, we describe the establishment of nasopharyngeal and bronchial organoids from healthy individuals and COPD that recapitulate disease at the individual level. In contrast to healthy organoids, goblet cell hyperplasia and reduced ciliary beat frequency were observed in COPD organoids, hallmark features of the disease. Single-cell transcriptomics uncovered evidence for altered cellular differentiation trajectories in COPD organoids. SARS-CoV-2 infection of COPD organoids revealed more productive replication in bronchi, the key site of infection in severe COVID-19. Viral and bacterial exposure of organoids induced greater pro-inflammatory responses in COPD organoids. In summary, we present an organoid model that recapitulates the in vivo physiological lung microenvironment at the individual level and is amenable to the study of host-pathogen interaction and emerging infectious disease.

Chan, Y, Singh, SK, Gulati, M, Wadhwa, S, Prasher, P, Kumar, D, Kumar, AP, Gupta, G, Kuppusamy, G, Haghi, M, George Oliver, BG, Adams, J, Chellappan, DK & Dua, K 2022, 'Advances and applications of monoolein as a novel nanomaterial in mitigating chronic lung diseases', Journal of Drug Delivery Science and Technology, vol. 74, pp. 103541-103541.
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Chronic lung diseases such as asthma, chronic obstructive pulmonary disease, lung cancer, and the recently emerged COVID-19, are a huge threat to human health, and among the leading causes of global morbidity and mortality every year. Despite availability of various conventional therapeutics, many patients remain poorly controlled and have a poor quality of life. Furthermore, the treatment and diagnosis of these diseases are becoming increasingly challenging. In the recent years, the application of nanomedicine has become increasingly popular as a novel strategy for diagnosis, treatment, prevention, as well as follow-up of chronic lung diseases. This is attributed to the ability of nanoscale drug carriers to achieve targeted delivery of therapeutic moieties with specificity to diseased site within the lung, thereby enhancing therapeutic outcomes of conventional therapies whilst minimizing the risks of adverse reactions. For this instance, monoolein is a polar lipid nanomaterial best known for its versatility, thermodynamic stability, biocompatibility, and biodegradability. As such, it is commonly employed in liquid crystalline systems for various drug delivery applications. In this review, we present the applications of monoolein as a novel nanomaterial-based strategy for targeted drug delivery with the potential to revolutionize therapeutic approaches in chronic lung diseases.

Charbe, NB, Castillo, F, Tambuwala, MM, Prasher, P, Chellappan, DK, Carreño, A, Satija, S, Singh, SK, Gulati, M, Dua, K, González-Aramundiz, JV & Zacconi, FC 2022, 'A new era in oxygen therapeutics? From perfluorocarbon systems to haemoglobin-based oxygen carriers', Blood Reviews, vol. 54, pp. 100927-100927.
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Charon, J, Kahlke, T, Larsson, ME, Abbriano, R, Commault, A, Burke, J, Ralph, P & Holmes, EC 2022, 'Diverse RNA Viruses Associated with Diatom, Eustigmatophyte, Dinoflagellate, and Rhodophyte Microalgae Cultures', Journal of Virology, vol. 96, no. 20, p. e0078322.
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Our knowledge of the diversity of RNA viruses infecting microbial algae—the microalgae—is minimal. However, describing the RNA viruses infecting these organisms is of primary importance at both the ecological and economic scales because of the fundamental roles these organisms play in aquatic environments and their growing value across a range of industrial fields.

Chau, CV, Sen, S, Sedgwick, AC, Gale, PA, Pantos, GD, Kim, SK, Park, JS, Tomat, E, Arambula, JF, Gorden, AEV & Furuta, H 2022, 'Solving world problems with pyrrole: 65th birthday tribute to Prof. Jonathan L. Sessler', Chem, vol. 8, no. 3, pp. 587-598.
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Che, S, Zhang, L, Wang, T, Su, D & Wang, C 2022, 'Graphitic Carbon Nitride‐Based Photocatalysts for Biological Applications', Advanced Sustainable Systems, vol. 6, no. 1, pp. 2100294-2100294.
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AbstractMetal‐free graphitic carbon nitride (g‐C3N4) as a newly emerging nanomaterial has been employed in the biomedical field because of its special optical and electrical characterizations. This review summarizes diverse methods for preparing g‐C3N4‐based materials, and discusses contemporary advancements in biosensors, photocatalytic sterilization, photodynamic therapy, drug carrier, and biological imaging. The biosafety and toxicity evaluations of g‐C3N4‐based materials are discussed as well. The review ends with an overview and several insights on the challenges and opportunities of g‐C3N4‐based nanomaterials in this burgeoning field. This review is expected to provide inspiration for developing future g‐C3N4‐based materials for the biomedical applications.

Che, S, Zhou, X, Zhang, L, Su, D, Wang, T & Wang, C 2022, 'Construction of a 2D Layered Phosphorus‐doped Graphitic Carbon Nitride/BiOBr Heterojunction for Highly Efficient Photocatalytic Disinfection', Chemistry – An Asian Journal, vol. 17, no. 11, p. e202200095.
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AbstractInfectious diseases caused by bacteria intimidate the health of human beings all over the world. Although many avenues have been tried, various operating conditions limit their actual applications. Photocatalytic nanomaterials are becoming candidates to be competent for water purification. Here, a novel and more efficient S‐scheme has been engineered between two dimensional (2D) layered phosphorus‐doped graphitic carbon nitride (P‐g‐C3N4) and BiOBr via hydrothermal polymerization to inhibit the recombination of charge and broaden light absorption. The as‐prepared P‐g‐C3N4/BiOBr hybrids exhibits significantly improved photocatalytic disinfection contrast to g‐C3N4/BiOBr in visible wavelengths, suggesting phosphorus doping which adjusts the band structure plays a significant role in the S‐scheme system. And the sterilization rate of multidrug‐resistant Acinetobacter baumannii 28 (AB 28) was 99.9999% within 80 min and Staphylococcus aureus (S. aureus) was 99.9%.

Chellappan, DK, Paudel, KR, Tan, NW, Cheong, KS, Khoo, SSQ, Seow, SM, Chellian, J, Candasamy, M, Patel, VK, Arora, P, Singh, PK, Singh, SK, Gupta, G, Oliver, BG, Hansbro, PM & Dua, K 2022, 'Targeting the mitochondria in chronic respiratory diseases', Mitochondrion, vol. 67, pp. 15-37.
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Chellappan, DK, Prasher, P, Saravanan, V, Vern Yee, VS, Wen Chi, WC, Wong, JW, Wong, JK, Wong, JT, Wan, W, Chellian, J, Molugulu, N, Prabu, SL, Ibrahim, R, Darmarajan, T, Candasamy, M, Singh, PK, Mishra, V, Shastri, MD, Zacconi, FC, Chakraborty, A, Mehta, M, Gupta, PK, Dureja, H, Gulati, M, Singh, SK, Gupta, G, Jha, NK, George Oliver, BG & Dua, K 2022, 'Protein and peptide delivery to lungs by using advanced targeted drug delivery', Chemico-Biological Interactions, vol. 351, pp. 109706-109706.
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The challenges and difficulties associated with conventional drug delivery systems have led to the emergence of novel, advanced targeted drug delivery systems. Therapeutic drug delivery of proteins and peptides to the lungs is complicated owing to the large size and polar characteristics of the latter. Nevertheless, the pulmonary route has attracted great interest today among formulation scientists, as it has evolved into one of the important targeted drug delivery platforms for the delivery of peptides, and related compounds effectively to the lungs, primarily for the management and treatment of chronic lung diseases. In this review, we have discussed and summarized the current scenario and recent developments in targeted delivery of proteins and peptide-based drugs to the lungs. Moreover, we have also highlighted the advantages of pulmonary drug delivery over conventional drug delivery approaches for peptide-based drugs, in terms of efficacy, retention time and other important pharmacokinetic parameters. The review also highlights the future perspectives and the impact of targeted drug delivery on peptide-based drugs in the coming decade.

Chen, C & Jin, D 2022, 'Giant nonlinearity in upconversion nanoparticles', Nature Photonics, vol. 16, no. 8, pp. 553-554.
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Chen, H & van Reyk, D 2022, 'Reply to Duric', Advances in Physiology Education, vol. 46, no. 3, pp. 508-508.
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Chen, H, Aneman, I, Nikolic, V, Karadzov Orlic, N, Mikovic, Z, Stefanovic, M, Cakic, Z, Jovanovic, H, Town, SEL, Padula, MP & McClements, L 2022, 'Maternal plasma proteome profiling of biomarkers and pathogenic mechanisms of early-onset and late-onset preeclampsia', Scientific Reports, vol. 12, no. 1, p. 19099.
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AbstractPreeclampsia is still the leading cause of morbidity and mortality in pregnancy without a cure. There are two phenotypes of preeclampsia, early-onset (EOPE) and late-onset (LOPE) with poorly defined pathogenic differences. This study aimed to facilitate better understanding of the mechanisms of pathophysiology of EOPE and LOPE, and identify specific biomarkers or therapeutic targets. In this study, we conducted an untargeted, label-free quantitative proteomic analyses of plasma samples from pregnant women with EOPE (n = 17) and LOPE (n = 11), and age, BMI-matched normotensive controls (n = 18). Targeted proteomics approach was also employed to validate a subset of proteins (n = 17). In total, there were 26 and 20 differentially abundant proteins between EOPE or LOPE, and normotensive controls, respectively. A series of angiogenic and inflammatory proteins, including insulin-like growth factor-binding protein 4 (IGFBP4; EOPE: FDR = 0.0030 and LOPE: FDR = 0.00396) and inter-alpha-trypsin inhibitor heavy chain H2-4 (ITIH2-4), were significantly altered in abundance in both phenotypes. Through validation we confirmed that ITIH2 was perturbed only in LOPE (p = 0.005) whereas ITIH3 and ITIH4 were perturbed in both phenotypes (p < 0.05). Overall, lipid metabolism/transport proteins associated with atherosclerosis were highly abundant in LOPE, however, ECM proteins had a more pronounced role in EOPE. The complement cascade and binding and uptake of ligands by scavenger receptors, pathways, were associated with both EOPE and LOPE.

Chen, H, Haddadi, N, Zhu, X, Hatoum, D, Chen, S, Nassif, NT, Lin, Y & McGowan, EM 2022, 'Expression Profile of Sphingosine Kinase 1 Isoforms in Human Cancer Tissues and Cells: Importance and Clinical Relevance of the Neglected 1b-Isoform', Journal of Oncology, vol. 2022, pp. 1-12.
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Background.Overexpression of sphingosine kinase 1 (SphK1) is casually associated with many types of cancer, and inhibitors of SphK1 sensitize tumors to chemotherapy. SphK1 is expressed as two major isoforms, SphK1a and SphK1b. To date, no information has been reported on the SphK1 isoform expression profile and its clinical relevance. Objective. The objective is to examine the expression profile of the SphK1a and SPhK1b isoforms in human cancer and noncancer tissues and cell lines and explore their clinical relevance. Methods. We used PCR to qualitatively examine the expression profile of these two isoforms in breast, liver, and prostate cancer tissues plus paired adjacent tissues and in 11 cancer and normal cell lines (breast, cervical, bone, prostate, colon, brain, mesothelioma tumor and benign, and human kidney cells). Results. We found that SphK1a was ubiquitously expressed in all cancer cells and tissues tested; in contrast, SphK1b was only expressed in selective cell types in breast, prostate, and lung cancer. Conclusions. Our data suggest that SphK1a is important for generic SphK1/S1P functions, and SphK1b mediates specialized and/or unique pathways in a specific type of tissue and could be a biomarker for cancer. This discovery is important for future SphK1-related cancer research and may have clinical implications in drug development associated with SphK1-directed cancer treatment.

Chen, H, Kimyon, Ö, Ramandi, HL, Craig, P, Gunawan, C, Wu, S, Manefield, M, Crosky, A & Saydam, S 2022, 'Microbiologically influenced stress corrosion cracking responsible for catastrophic failure of cable bolts', Engineering Failure Analysis, vol. 131, pp. 105884-105884.
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In the past two decades, reports of the premature failure of cable bolts used in the mining and civil industries have been increasing. Previous studies have established that failure occurs through hydrogen-induced stress corrosion cracking (HISCC), which is a type of environmentally assisted hydrogen cracking. However, to date, the cause of HISCC has been unclear. For the first time, we studied the role of microorganisms in the failure of cable bolts using components present in SCC-affected mines. Stressed coupons were prepared from the cable bolt wires and tested in groundwater with additions of sulphate-reducing bacteria, coal, clay, pyrite and lactate. It was found that hydrogen sulphide (H2S) produced by sulphate- and sulphur-reducing bacteria promoted hydrogen diffusion into the steel and, in the presence of stress, caused HISCC. This suggests that control of H2S production should be a priority for mining and civil industries to avoid premature failure of anchoring systems.

Chen, H, Oliver, BG, Pant, A, Olivera, A, Poronnik, P, Pollock, CA & Saad, S 2022, 'Effects of air pollution on human health – Mechanistic evidence suggested by in vitro and in vivo modelling', Environmental Research, vol. 212, pp. 113378-113378.
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Chen, H, Tesic, M, Nikolic, VN, Pavlovic, M, Vucic, RM, Spasic, A, Jovanovic, H, Jovanovic, I, Town, SEL, Padula, MP & McClements, L 2022, 'Systemic Biomarkers and Unique Pathways in Different Phenotypes of Heart Failure with Preserved Ejection Fraction', Biomolecules, vol. 12, no. 10, pp. 1419-1419.
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Heart failure with preserved ejection fraction (HFpEF) accounts for around 50% of all heart failure cases. It is a heterogeneous condition with poorly understood pathogenesis. Here, we aimed to identify unique pathogenic mechanisms in acute and chronic HFpEF and hypertrophic cardiomyopathy (HCM). We performed unbiased, comprehensive proteomic analyses of plasma samples from gender- and BMI-matched patients with acute HFpEF (n = 8), chronic HFpEF (n = 9) and HCM (n = 14) using liquid chromatography–mass spectrometry. Distinct molecular signatures were observed in different HFpEF forms. Clusters of biomarkers differentially abundant between HFpEF forms were predominantly associated with microvascular inflammation. New candidate protein markers were also identified, including leucine-rich alpha-2-glycoprotein 1 (LRG1), serum amyloid A1 (SAA1) and inter-alpha-trypsin inhibitor heavy chain 3 (ITIH3). Our study is the first to apply systematic, quantitative proteomic screening of plasma samples from patients with different subtypes of HFpEF and identify candidate biomarkers for improved management of acute and chronic HFpEF and HCM.

Chen, H, Van Reyk, D, Oliveira, A, Chan, YL, Town, SEL, Rayner, B, Pollock, CA, Saad, S, George, J, Padula, MP & Oliver, BG 2022, 'Sex-Dependent Responses to Maternal Exposure to PM2.5 in the Offspring', Antioxidants, vol. 11, no. 11, pp. 2255-2255.
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Objective: Particulate matter (PM) with a diameter of 2.5 μm or less (PM2.5) can cross the blood-placental barrier causing adverse foetal outcomes. However, the impact of maternal exposure to low-levels of PM2.5 on liver health and the metabolic profile is unclear. This study aimed to investigate hepatic responses to long-term gestational low-dose PM2.5 exposure, and whether the removal of PM after conception can prevent such effects. Method: Female Balb/c mice (8 weeks) were exposed to PM2.5 (5 μg/day) for 6 weeks prior to mating, during gestation and lactation to model living in a polluted environment (PM group). In a sub-group, PM2.5 exposure was stopped post-conception to model mothers moving to areas with clean air (pre-gestation, Pre) group. Livers were studied in 13-week old offspring. Results: Female offspring in both PM and Pre groups had increased liver triglyceride and glycogen levels, glucose intolerance, but reduced serum insulin and insulin resistance. Male offspring from only the Pre group had increased liver and serum triglycerides, increased liver glycogen, glucose intolerance and higher fasting glucose level. Markers of oxidative stress and inflammation were increased in females from PM and Pre groups. There was also a significant sex difference in the hepatic response to PM2.5 with differential changes in several metabolic markers identified by proteomic analysis. Conclusions: Maternal PM exposure exerted sex-dependent effects on liver health with more severe impacts on females. The removal of PM2.5 during gestation provided limited protection in the offspring’s metabolism regardless of sex.

Chen, H, van Reyk, D, Reyna, J & Oliver, BG 2022, 'A comparison of attitudes toward remote learning during the COVID-19 pandemic between students attending a Chinese and an Australian campus', Advances in Physiology Education, vol. 46, no. 2, pp. 297-308.
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The COVID-19 pandemic has been a strong driver for moving more teaching and learning activities online. Border restrictions have had a severe impact on international students either hoping to enroll in courses offered in Australia or continue with such courses if they are already enrolled. The online learning experience is likely different between students onshore and offshore. This study took a unique opportunity to investigate any such differences in students’ attitudes toward remote learning, necessitated by the pandemic, by comparing two cohorts of students, Australia versus China based. An anonymous survey using the Likert Scale and open-ended questions was available for student feedback on subject delivery. The students based in Australia expressed a preference for remote learning due to the convenience of attendance and availability of the video recordings. However, students in China had a strong preference for face-to-face sessions, with the lack of prior experience in an English-speaking learning environment and hesitance to speak with the lecturers and engage in the learning activities possible reasons for this. In quizzes, students in Australia performed better than those in China regardless of local or international student status. This difference may be due to the Australian-based students’ prior experience of English-speaking environments and open-book quizzes. In conclusion, remote learning in a familiar language and learning environment is accepted by students, whereas if the teaching is delivered in a second language using unfamiliar teaching methods, remote learning will require additional scaffolding to enhance their learning experience.

Chen, H, Yang, Y, Miyai, H, Yi, C & Oliver, BG 2022, 'The effects of exercise with nicotine replacement therapy for smoking cessation in adults: A systematic review', Frontiers in Psychiatry, vol. 13, p. 1053937.
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ObjectiveThis systematic review aimed to evaluate the efficacy of exercise programmes with nicotine replacement therapy (NRT) for smoking cessation in adults.IntroductionNicotine addiction is mediated by dopamine. Exercise can also activate the dopamine reward system. Therefore, exercise may effectively facilitate NRT to reduce cigarette cravings and withdrawal symptoms.Inclusion criteriaClinical trials between 2000 and 2022 used exercise protocols of any intensity for smoking cessation, in current smokers or recent quitters of both genders, aged 18–70, without severe diseases and pregnancy. Mental disorders were not excluded, as exercise can improve mental health status. Therefore, it may be as effective among people with mental health issues as the general population in preventing nicotine cravings and supporting abstinence.MethodsFour databases (PubMed, Embase, Cochrane, and Medline) were searched for papers in English using the terms “nicotine replacement therapy’, “exercise,” and “smoking cessation.” Titles and abstracts were screened for potentially eligibility before full texts were reviewed. Sample size, gender, study duration, and age was then extracted. The certainty of the evidence was assessed using Joanna Briggs Institute’s (JBI’s) GRADE approach.ResultsSeventeen studies were identified with a total of 3,191 participants. Three studies are not a randomised control study. There was moderate-high quality evidence that exercise can aid NRT in promoting smoking cessation in the short term. Several studies reported temporary reductions in cravings; however, only one trial reported a decrease in cigarette consumption due to exercise intervention and one dem...

Chen, J, Yao, B, Yang, Z, Shi, W, Luo, T, Xi, P, Jin, D & Li, Y 2022, 'Ratiometric 4Pi single-molecule localization with optimal resolution and color assignment', Optics Letters, vol. 47, no. 2, pp. 325-325.
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4Pi single-molecule localization microscopy (4Pi-SMLM) with two opposing objectives achieves sub-10 nm isotropic 3D resolution when as few as 250 photons are collected by each objective. Here, we develop a new ratiometric multi-color imaging strategy for 4Pi-SMLM that employs the intrinsic multi-phase interference intensity without increasing the complexity of the system and achieves both optimal 3D resolution and color separation. By partially linking the photon parameters between channels with an interference difference of π during global fitting of the multi-channel 4Pi single-molecule data, we show via simulated data that the loss of localization precision is minimal compared with the theoretical minimum uncertainty, the Cramer–Rao lower bound.

Chen, L, Wu, X, Gilchrist, AM & Gale, PA 2022, 'Organoplatinum Compounds as Anion‐Tuneable Uphill Hydroxide Transporters', Angewandte Chemie International Edition, vol. 61, no. 19, p. e202116355.
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AbstractActive transport of ions uphill, creating a concentration gradient across a cell membrane, is essential for life. It remains a significant challenge to develop synthetic systems that allow active uphill transport. Here, a transport process fuelled by organometallic compounds is reported that creates a pH gradient. The hydrolysis reaction of PtII complexes results in the formation of aqua complexes that established rapid transmembrane movement (“flip‐flop”) of neutral Pt−OH species, leading to protonation of the OH group in the inner leaflet, generating OH− ions, and so increasing the pH in the intravesicular solution. The organoplatinum complex effectively transports bound hydroxide ions across the membrane in a neutral complex. The initial net flow of the PtII complex into the vesicles generates a positive electric potential that can further drive uphill transport because the electric potential is opposed to the chemical potential of OH−. The OH− ions equilibrate with this transmembrane electric potential but cannot remove it due to the relatively low permeability of the charged species. As a result, effective hydroxide transport against its concentration gradient can be achieved, and multiple additions can continuously drive the generation of OH− against its concentration gradient up to ΔpH>2. Moreover, the external addition of different anions can control the generation of OH− depending on their anion binding affinity. When anions displayed very high binding affinities towards PtII compounds, such as halides, the external anions could dissipate the pH gradient. In contrast, a further pH increase was observed for weak binding anions, such as sulfate, due to the increase of positive electric potential.

Chen, X, Gu, Y, Chai, Y, Wu, N, Wen, C, Ke, J, Sun, Y, Li, F & Feng, W 2022, 'An Optical Multiplexing Method Using Upconversion Nanoparticles with Tunable P–I Relationship', Advanced Optical Materials, vol. 10, no. 22.
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AbstractOptical multiplexing is of great value in information acquisition due to its excellent signal encoding ability. However, the number of encoding channels is often limited by instruments or luminescent materials used as information carriers in practical applications. To provide a new option, an optical multiplexing method based on the tunable relationship between excitation power density and emission intensity of upconversion nanoparticles (UCNPs; P–I relationship), which can be regulated by the co‐doping ratio of sensitizer ions and activator ions, is developed. This method can be implemented on commonly used optical imaging equipment. Since the P–I relationship is only related to the energy transfer process of lanthanide ions in UCNPs, it has the potential to be combined with other dimensions of optical multiplexing such as wavelength and intensity to provide more robust encoding ability.

Chen, Y, Shimoni, O, Huang, G, Wen, S, Liao, J, Duong, HTT, Maddahfar, M, Su, QP, Ortega, DG, Lu, Y, Campbell, DH, Walsh, BJ & Jin, D 2022, 'Upconversion nanoparticle‐assisted single‐molecule assay for detecting circulating antigens of aggressive prostate cancer', Cytometry Part A, vol. 101, no. 5, pp. 400-410.
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AbstractSensitive and quantitative detection of molecular biomarkers is crucial for the early diagnosis of diseases like metabolic syndrome and cancer. Here we present a single‐molecule sandwich immunoassay by imaging the number of single nanoparticles to diagnose aggressive prostate cancer. Our assay employed the photo‐stable upconversion nanoparticles (UCNPs) as labels to detect the four types of circulating antigens in blood circulation, including glypican‐1 (GPC‐1), leptin, osteopontin (OPN), and vascular endothelial growth factor (VEGF), as their serum concentrations indicate aggressive prostate cancer. Under a wide‐field microscope, a single UCNP doped with thousands of lanthanide ions can emit sufficiently bright anti‐Stokes' luminescence to become quantitatively detectable. By counting every single streptavidin‐functionalized UCNP which specifically labeled on each sandwich immune complex across multiple fields of views, we achieved the Limit of Detection (LOD) of 0.0123 ng/ml, 0.2711 ng/ml, 0.1238 ng/ml, and 0.0158 ng/ml for GPC‐1, leptin, OPN and VEGF, respectively. The serum circulating level of GPC‐1, leptin, OPN, and VEGF in a mixture of 10 healthy normal human serum was 25.17 ng/ml, 18.04 ng/ml, 11.34 ng/ml, and 1.55 ng/ml, which was within the assay dynamic detection range for each analyte. Moreover, a 20% increase of GPC‐1 and OPN was observed by spiking the normal human serum with recombinant antigens to confirm the accuracy of the assay. We observed no cross‐reactivity among the four biomarker analytes, which eliminates the false positives and enhances the detection accuracy. The developed single upconversion nanoparticle‐assisted single‐molecule assay suggests its potential in clinical usage for prostate cancer detection by monitoring tiny concentration differences in a panel of serum biomarkers.

Cheng, J, Li, C, Ying, Y, Lv, J, Qu, X, McGowan, E, Lin, Y & Zhu, X 2022, 'Metformin Alleviates Endometriosis and Potentiates Endometrial Receptivity via Decreasing VEGF and MMP9 and Increasing Leukemia Inhibitor Factor and HOXA10', Frontiers in Pharmacology, vol. 13, p. 750208.
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Background: Endometriosis affects endometrial receptivity, a key factor for successful embryo implantation. Metformin treatment is associated with alleviating the symptoms of endometriosis; however the mechanism of metformin action is unclear. Neoangiogenesis plays an important role in the development and recurrence of endometriosis. In addition, the leukemia inhibitor factor (LIF) and HOXA10 genes are also distinguishing markers of endometriosis (decrease) and endometrial receptivity (increase). This study investigated the therapeutic potentials of metformin and the underlying mechanism using an in vivo rat endometriosis model.Methods: Female Wistar albino mature rats with experimentally induced endometriosis were used in this study. Metformin was administered at doses of 100 mg/kg/d and 200 mg/kg/d. The volume of endometriotic implants was assessed. The protein and mRNA expression of the vascular endothelial growth factor (VEGF), matrix metalloproteinase-9 (MMP-9), the endometrial receptivity markers, LIF and HOXA10, were measured in the endometrium of rats with endometriosis.Results: Metformin treatment significantly suppressed the growth of endometriotic implants. Further, the expression of VEGF and MMP-9 protein and mRNA in endometriotic implants were significantly reduced. Metformin also significantly upregulated LIF and HOXA10 expression in endometrium from rats with endometriosis. The inhibitory effect of metformin on the growth of endometriotic implants, VEGF and MMP-9, and upregulating effect on LIF and HOXA10, was optimal at a dose of 100 mg/kg/d.Conclusion: Our in vivo data demonstrates that metformin treatment alleviates endometriosis and potentiates endometrial receptivity. The underlying mechanisms are associated with decreased expressio...

Chew, AW, Oo, CZ, Wong, ALH & Gladding, J 2022, 'An initial evaluation of research data management online training at the University of New South Wales', IFLA Journal, vol. 48, no. 4, pp. 510-522.
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In response to low research data management engagement at the University of New South Wales, Australia, an introductory research data management online training was developed and rolled out to all newly enrolled Higher Degree Research candidates. This article outlines the development process of the research data management online training and provides an initial evaluation of the training from the perspectives of the candidates and the university. As such, this article joins up with existing literature on research data management training to assist institutions and research data management stakeholders with the development of research data management training to help researchers and research students enact research data management best practices. Overall, the majority of the candidates ( n = 643) were satisfied with the quality of the training and found it helpful. The benefits the training brought to the university are mapped out by linking institutional research data management problems, the research data management online training’s design and findings into a coherent narrative.

Chong, H, Fang, S, Yang, D, Tan, C, Wei, J, Chang, S-H, Fan, H, Yao, H, Qin, A, Shao, H, Zhang, Y, Leng, J, Su, D, Wang, C & Li, H 2022, 'Toxicity assessments and transcriptional effects of monofunctionalized Pt(II) complex under dark and light irradiation condition in Caenorhabditis elegans', Journal of Inorganic Biochemistry, vol. 230, pp. 111720-111720.
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In vivo toxicity of aromatic ring (BODIPY, 1,3,5,7,8-pentamethyl dipyrrin borondifluoride) attached monofunctional Pt(II) complexes mCBP {[cis-Pt(NH3)2Cl] 8-(para-pyridine-methylene),1,3,5,7-tetramethyl dipyrrin borondifluoride}+ Nitrate- and dCBP {[cis-Pt(NH3)2Cl]28-(1,3-pyrimidine-5-methylene),1,3,5,7-tetramethyl dipyrrin borondifluoride}2+ diNitrate2- were tested in Caenorhabditis elegans (C. elegans). dCBP showed promising reactive oxygen ROS (reactive oxygen species) generating capability. This complex resulted reduction of lifespan, body length and egg laying rate under dark and light irradiation in both N2 (wild-type, cisplatin resistant) and ok938 (asna-1, cisplatin sensitive) C. elegans. Expressional change of several key cancer related pathway (JNK (c-Jun N-terminal kinase) and Wnt/β-catenin (Wingless/Integrated/β-catenin)) related genes (for instance, jnk-1, wrm-1 and gst-4) were confirmed by RNA sequencing experiments. These transcriptional alternations could explain physiological parameters change in nematode and partially revealed how both Pt(II) based complexes influence cancer related pathways. Furthermore, these associated genes exhibited the function of apoptosis, reduced chemoresistance of cancer cells and most of those expressional changes were linked to extended survival of cancer patients.

Chotirmall, SH, Bogaert, D, Chalmers, JD, Cox, MJ, Hansbro, PM, Huang, YJ, Molyneaux, PL, O’Dwyer, DN, Pragman, AA, Rogers, GB, Segal, LN & Dickson, RP 2022, 'Therapeutic Targeting of the Respiratory Microbiome', American Journal of Respiratory and Critical Care Medicine, vol. 206, no. 5, pp. 535-544.
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Choucair, H, Rahman, MK, Umashankar, B, Al-Zubaidi, Y, Bourget, K, Chen, Y, Dunstan, C, Rawling, T & Murray, M 2022, 'The aryl-ureido fatty acid CTU activates endoplasmic reticulum stress and PERK/NOXA-mediated apoptosis in tumor cells by a dual mitochondrial-targeting mechanism', Cancer Letters, vol. 526, pp. 131-141.
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The cancer cell mitochondrion is functionally different from that in normal cells and could be targeted to develop novel experimental therapeutics. The aryl-ureido fatty acid CTU (16({[4-chloro-3-(trifluoromethyl)phenyl]-carbamoyl}amino)hexadecanoic acid) is the prototype of a new class of mitochondrion-targeted agents that kill cancer cells. Here we show that CTU rapidly depolarized the inner mitochondrial membrane, selectively inhibited complex III of the electron transport chain and increased reactive oxygen species (ROS) production. From RNA-seq analysis, endoplasmic reticulum (ER)-stress was a major activated pathway in CTU-treated cells and in MDA-MB-231 tumor xenografts from CTU-treated nu/nu mice. Mitochondrion-derived ROS activated the PERK-linked ER-stress pathway and induced the BH3-only protein NOXA leading to outer mitochondrial membrane (OMM) disruption. The lipid peroxyl scavenger α-tocopherol attenuated CTU-dependent ER-stress and apoptosis which confirmed the critical role of ROS. Oleic acid protected against CTU-mediated apoptosis by activating Mcl-1 expression, which increased NOXA sequestration and prevented OMM disruption. Taken together, CTU both uncouples mitochondrial electron transport and activates ROS production which promotes ER-stress-dependent OMM disruption and tumor cell death. Dual-mitochondrial targeting agents like CTU offer a novel approach for development of new anti-cancer therapeutics.

Clark, SR, Pagendam, D & Ryan, L 2022, 'Forecasting Multiple Groundwater Time Series with Local and Global Deep Learning Networks', International Journal of Environmental Research and Public Health, vol. 19, no. 9, pp. 5091-5091.
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Time series data from environmental monitoring stations are often analysed with machine learning methods on an individual basis, however recent advances in the machine learning field point to the advantages of incorporating multiple related time series from the same monitoring network within a ‘global’ model. This approach provides the opportunity for larger training data sets, allows information to be shared across the network, leading to greater generalisability, and can overcome issues encountered in the individual time series, such as small datasets or missing data. We present a case study involving the analysis of 165 time series from groundwater monitoring wells in the Namoi region of Australia. Analyses of the multiple time series using a variety of different aggregations are compared and contrasted (with single time series, subsets, and all of the time series together), using variations of the multilayer perceptron (MLP), self-organizing map (SOM), long short-term memory (LSTM), and a recently developed LSTM extension (DeepAR) that incorporates autoregressive terms and handles multiple time series. The benefits, in terms of prediction performance, of these various approaches are investigated, and challenges such as differing measurement frequencies and variations in temporal patterns between the time series are discussed. We conclude with some discussion regarding recommendations and opportunities associated with using networks of environmental data to help inform future resource-related decision making.

Clarke, H, Nolan, RH, De Dios, VR, Bradstock, R, Griebel, A, Khanal, S & Boer, MM 2022, 'Forest fire threatens global carbon sinks and population centres under rising atmospheric water demand', Nature Communications, vol. 13, no. 1, p. 7161.
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AbstractLevels of fire activity and severity that are unprecedented in the instrumental record have recently been observed in forested regions around the world. Using a large sample of daily fire events and hourly climate data, here we show that fire activity in all global forest biomes responds strongly and predictably to exceedance of thresholds in atmospheric water demand, as measured by maximum daily vapour pressure deficit. The climatology of vapour pressure deficit can therefore be reliably used to predict forest fire risk under projected future climates. We find that climate change is projected to lead to widespread increases in risk, with at least 30 additional days above critical thresholds for fire activity in forest biomes on every continent by 2100 under rising emissions scenarios. Escalating forest fire risk threatens catastrophic carbon losses in the Amazon and major population health impacts from wildfire smoke in south Asia and east Africa.

Colarusso, C, Terlizzi, M, Maglio, A, Molino, A, Candia, C, Vitale, C, Hansbro, PM, Vatrella, A, Pinto, A & Sorrentino, R 2022, 'Activation of the AIM2 Receptor in Circulating Cells of Post-COVID-19 Patients With Signs of Lung Fibrosis Is Associated With the Release of IL-1α, IFN-α and TGF-β', Frontiers in Immunology, vol. 13, p. 934264.
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Severe acute respiratory syndrome-coronavirus-2 (SARS‐CoV‐2), responsible for COVID-19, has caused a global pandemic. Observational studies revealed a condition, herein called as Long-COVID syndrome (PC), that affects both moderately and severely infected patients, reducing quality-of-life. The mechanism/s underlying the onset of fibrotic-like changes in PC are still not well defined. The goal of this study was to understand the involvement of the Absent in melanoma-2 (AIM2) inflammasome in PC-associated lung fibrosis-like changes revealed by chest CT scans. Peripheral blood mononuclear cells (PBMCs) obtained from PC patients who did not develop signs of lung fibrosis were not responsive to AIM2 activation by Poly dA:dT. In sharp contrast, PBMCs from PC patients with signs of lung fibrosis were highly responsive to AIM2 activation, which induced the release of IL-1α, IFN-α and TGF-β. The recognition of Poly dA:dT was not due to the activation of cyclic GMP-AMP (cGAMP) synthase, a stimulator of interferon response (cGAS-STING) pathways, implying a role for AIM2 in PC conditions. The release of IFN-α was caspase-1- and caspase-4-dependent when AIM2 was triggered. Instead, the release of pro-inflammatory IL-1α and pro-fibrogenic TGF-β were inflammasome independent because the inhibition of caspase-1 and caspase-4 did not alter the levels of the two cytokines. Moreover, the responsiveness of AIM2 correlated with higher expression of the receptor in circulating CD14+ cells in PBMCs from patients with signs of lung fibrosis.

Collins, S, Maestrini, L, Ueland, M & Stuart, B 2022, 'A preliminary investigation to determine the suitability of pigs as human analogues for post-mortem lipid analysis', Talanta Open, vol. 5, pp. 100100-100100.
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The determination of time since death is a major challenge to law enforcement when faced with the discovery of human remains. This is due to the fact that decomposition is a complex, dynamic process influenced by several abiotic and biotic factors. For decades, post-mortem decomposition studies have used pigs as human analogues due to ethical and legal restrictions surrounding the use of human cadavers for such research. However, few comparative studies have been conducted to assess the suitability of these analogues. Recent forensic studies have successfully demonstrated the use of post-mortem lipids in textiles as a method to obtain vital information about decomposition process. The current investigation involved two studies: Trial 1 (summer) and Trial 2 (winter). Each trial with n = 1 human cadaver and n = 2 pigs. Samples were collected over a timeline of 105 days post-placement and analyzed using attenuated total reflectance (ATR-) Fourier-transform infrared (FTIR) spectroscopy. The data was then statistically assessed using functional principal component analysis, semi-parametric regression modeling and analysis of variance. The results demonstrated a clear statistically significant interspecies difference between pigs and humans in both trials. The preliminary implications of this study suggest that pigs are not suitable analogues for humans in decomposition research and have broader implications that caution the direct translation of decomposition data obtained from pigs to real human casework, particularly with respect to time since death estimations.

Coni, EOC, Booth, DJ & Nagelkerken, I 2022, 'Coral-reef fishes can become more risk-averse at their poleward range limits', Proceedings of the Royal Society B: Biological Sciences, vol. 289, no. 1971, pp. 1-8.
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As climate warms, tropical species are expanding their distribution to temperate ecosystems where they are confronted with novel predators and habitats. Predation strongly regulates ecological communities, and range-extending species that adopt an effective antipredator strategy have a higher likelihood to persist in non-native environments. Here, we test this hypothesis by comparing various proxies of antipredator and other fitness-related behaviours between range-extending tropical fishes and native-temperate fishes at multiple sites across a 730 km latitudinal range. Although some behavioural proxies of risk aversion remained unaltered for individual tropical fish species, in general they became more risk-averse (increased sheltering and/or flight initiation distance), and their activity level decreased poleward. Nevertheless, they did not experience a decline in body condition or feeding rate in their temperate ranges. Temperate fishes did not show a consistently altered pattern in their behaviours across range locations, even though one species increased its flight initiation distance at the warm-temperate location and another one had lowest activity levels at the coldest range location. The maintenance of feeding and bite rate combined with a decreased activity level and increased sheltering may be behavioural strategies adopted by range-extending tropical fishes, to preserve energy and maintain fitness in their novel temperate ecosystems.

Coni, EOC, Booth, DJ, Ferreira, CM & Nagelkerken, I 2022, 'Behavioural generalism could facilitate coexistence of tropical and temperate fishes under climate change', Journal of Animal Ecology, vol. 91, no. 1, pp. 86-100.
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AbstractCoral‐reef fishes are shifting their distributions poleward in response to human‐mediated ocean warming; yet, the consequences for recipient temperate fish communities remain poorly understood. Behavioural modification is often the first response of species to environmental change, but we know little about how this might shape the ongoing colonisation by tropical fishes of temperate‐latitude ecosystems under climate change.In a global hotspot of ocean warming (southeast Australia), we quantified 14 behavioural traits of invading tropical and local co‐occurring temperate fishes at 10 sites across a 730 km latitudinal gradient as a proxy of species behavioural niche space in different climate ranges (subtropical, warm‐temperate and cold‐temperate).We found that tropical fishes (four species) modified their behavioural niches as well as increased their overall behavioural niche breadth in their novel temperate ranges where temperate species predominate, but maintained a moderate to high niche segregation with native temperate species across latitudinal range position. Temperate species (three co‐occurring species) also modified their niches, but in contrast to tropical species, experienced an increased niche breadth towards subtropical ranges. Alterations to feeding and shoaling behaviours contributed most to niche modifications in tropical and temperate species, while behaviours related to alertness and escape from potential threats contributed least.We here show that at warmer and colder range edges where community structures are being reshuffled due to climate change, behavioural generalism and niche modification are potential mechanisms adopted by tropical range extenders and native temperate fishes to adjust to novel spe...

Coupland, M 2022, 'Thirteen things about eyes and mathematics, and why I feel lucky to be able to see at all.', Reflections, vol. 47, no. 3, pp. 6-14.
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Some time ago, in 2013 in fact, I was unlucky enough to endure a retinal detachment. Along the way to recovery I found that there were many things about eyes, vision, and surgery that mathematics helps to understand. This paper addresses some of these interesting things.

Cowan, AE, Bailey, RL, Jun, S, Dodd, KW, Gahche, JJ, Eicher-Miller, HA, Guenther, PM, Dwyer, JT, Potischman, N, Bhadra, A, Carroll, RJ & Tooze, JA 2022, 'The Total Nutrient Index is a Useful Measure for Assessing Total Micronutrient Exposures Among US Adults', The Journal of Nutrition, vol. 152, no. 3, pp. 863-871.
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BACKGROUND: Most dietary indices reflect foods and beverages and do not include exposures from dietary supplements (DS) that provide substantial amounts of micronutrients. A nutrient-based approach that captures total intake inclusive of DS can strengthen exposure assessment. OBJECTIVE: To examine the construct and criterion validity of the Total Nutrient Index (TNI) among U.S. adults (≥19y; non-pregnant or lactating). METHODS: The TNI includes eight under-consumed micronutrients identified by the Dietary Guidelines for Americans: calcium; magnesium; potassium; choline; and vitamins A, C, D, and E. The TNI is expressed as a percentage of the Recommended Dietary Allowance or Adequate Intake to compute micronutrient component scores; the mean of the component scores yields the TNI score, ranging from 0-100. Data from exemplary menus and the 2003-2006 (≥19y; n = 8,861) and 2011-2014 NHANES (≥19y; n = 9,954) were employed. Exemplary menus were used to determine if the TNI yielded high scores from dietary sources (women 31-50y; men ≥70y). TNI scores were correlated with Healthy Eating Index (HEI)-2015 overall and component scores for dairy, fruits, and vegetables; TNI component scores for vitamins A, C, D, and E were correlated with respective biomarker data. TNI scores were compared between groups with known differences in nutrient intake based on the literature. RESULTS: The TNI yielded high scores on exemplary menus (84.8-93.3/100) and was moderately correlated (r = 0.48) with the HEI-2015. Mean TNI scores were significantly different for DS users (83.5) vs. non-users (67.1), non-smokers (76.8) vs. smokers (70.3), and those living with food security (76.6) vs. food insecurity (69.1). Correlations of TNI vitamin component scores with available biomarkers ranged from r = 0.12 (α-tocopherol) to r = 0.36 (serum 25(OH)D), and were significantly higher than correlations obtained from the diet alone. CONCLUSION: The evaluation of validity supports that the TNI i...

Cowan, AE, Tooze, JA, Gahche, JJ, Eicher-Miller, HA, Guenther, PM, Dwyer, JT, Potischman, N, Bhadra, A, Carroll, RJ & Bailey, RL 2022, 'Trends in Overall and Micronutrient-Containing Dietary Supplement Use in US Adults and Children, NHANES 2007–2018', The Journal of Nutrition, vol. 152, no. 12, pp. 2789-2801.
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ABSTRACT Background Dietary supplement (DS) use is widespread in the United States and contributes large amounts of micronutrients to users. Most studies have relied on data from 1 assessment method to characterize the prevalence of DS use. Combining multiple methods enhances the ability to capture nutrient exposures from DSs and examine trends over time. Objectives The objective of this study was to characterize DS use and examine trends in any DS as well as micronutrient-containing (MN) DS use in a nationally representative sample of the US population (≥1 y) from the 2007–2018 NHANES using a combined approach. Methods NHANES obtains an in-home inventory with a frequency-based dietary supplement and prescription medicine questionnaire (DSMQ), and two 24-h dietary recalls (24HRs). Trends in the prevalence of use and selected types of products used were estimated for the population and by sex, age, race/Hispanic origin, family income [poverty-to-income ratio (PIR)], and household food security (food-secure vs. food-insecure) using the DSMQ or ≥ 1 24HR. Linear trends were tested using orthogonal polynomials (significance set at P &lt; 0.05). Results DS use increased from 50% in 2007 to 56% in 2018 (P = 0.001); use of MN products increased from 46% to 49% (P = 0.03), and single-nutrient DS (e.g., magnesium, vitamins B-12 and D) use also increased (all P &lt; 0.001). In contrast, multivitamin-mineral use decreased (70% to 56%; P &lt; 0.001). In adults ...

Cramer, A, Galvão, I, Venturini de Sá, N, Gaio, P, Fernanda de Melo Oliveira, N, Rates Gonzaga Santos, M, Henrique Campolina-Silva, G, Vinicius Santos Valiate, B, Rezende Souza, F, Dantas Cassali, G, Martins Teixeira, M, Almeida Amaral, F & Simão Machado, F 2022, 'Role of Suppressor of cytokine signaling 2 during the development and resolution of an experimental arthritis', Cellular Immunology, vol. 372, pp. 104476-104476.
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Cranfield, CG, Le Brun, AP, Garcia, A, Cornell, BA & Holt, SA 2022, 'Langmuir-Schaefer Deposition to Create an Asymmetrical Lipopolysaccharide Sparsely Tethered Lipid Bilayer', Methods in Molecular Biology, vol. 2402, pp. 21-30.
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Because they are firmly anchored to a noble metal substrate, tethered bilayer lipid membranes (tBLMs) are considerably more robust than supported lipid bilayers such as black lipid membranes (BLMs) (Cranfield et al. Biophys J 106:182-189, 2014). The challenge to rapidly create asymmetrical tBLMs that include a lipopolysaccharide outer leaflet for bacterial model membrane research can be overcome by the use of a Langmuir-Schaefer deposition protocol. Here, we describe the procedures required to assemble and test asymmetric lipopolysaccharide (LPS) tethered lipid bilayers.

Crispino, F, Weyermann, C, Delémont, O, Roux, C & Ribaux, O 2022, 'Towards another paradigm for forensic science?', WIREs Forensic Science, vol. 4, no. 3.
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AbstractDaubert skews the contribution of forensic science because it only took into account its Galilean dimension (construction of general predictive models). However, forensic science should better be classified in the historical sciences (clinical approach to reconstruct a past event of presence or activity). We therefore need a complementary approach that integrates the necessarily “clinical” part in the resolution of forensic issues. Such an evolution involves semiotics. While recognizing that the Bayesian way of thinking is the only prescriptive available model for interpretation fitting well in the Galilean paradigm, the complexity of the reconstruction of a past‐uncontrolled singular case and the robustness of available relevant data to it, invites consideration of its implementation in a semiotic line of arguments. Indeed, Bayes makes it possible to remain in a single harmonized model integrating both the clinical and Galilean dimensions, but rapidly the complexity of the modeling and its mathematization come up against more qualitative natural and legal reasoning. Two different systems of reasoning at stake are inevitably creating a “bug” that could explain the current forensic crisis and miscarriages of justice. This anomaly is reflected in the issue of transparency (misunderstandings by and between interlocutors on the nature of the expertise, if not science). Peirce offers a path to address the tension between complementary reasoning systems.This article is categorized under:Crime Scene Investigation > Epistemology and MethodCrime Scene Investigation > From Traces to Intelligence and EvidenceCrime Scene Investigation > Education and Formation

Crowley, J, Withana, M & Deplazes, E 2022, 'The interaction of steroids with phospholipid bilayers and membranes', Biophysical Reviews, vol. 14, no. 1, pp. 163-179.
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Steroids are critical for various physiological processes and used to treat inflammatory conditions. Steroids act by two distinct pathways. The genomic pathway is initiated by the steroid binding to nuclear receptors while the non-genomic pathway involves plasma membrane receptors. It has been proposed that steroids might also act in a more indirect mechanism by altering biophysical properties of membranes. Yet, little is known about the effect of steroids on membranes, and steroid-membrane interactions are complex and challenging to characterise. The focus of this review is to outline what is currently known about the interactions of steroids with phospholipid bilayers and illustrate the complexity of these systems using cortisone and progesterone as the main examples. The combined findings from current work demonstrate that the hydrophobicity and planarity of the steroid core does not provide a consensus for steroid-membrane interactions. Even small differences in the substituents on the steroid core can result in significant changes in steroid-membrane interactions. Furthermore, steroid-induced changes in phospholipid bilayer properties are often dependent on steroid concentration and lipid composition. This complexity means that currently there is insufficient information to establish a reliable structure–activity relationship to describe the effect of steroids on membrane properties. Future work should address the challenge of connecting the findings from studying the effect of steroids on phospholipid bilayers to cell membranes. Insights from steroid-membrane interactions will benefit our understanding of normal physiology and assist drug development.

Cui, E, Thompson, EC, Carroll, RJ & Ruppert, D 2022, 'A semiparametric risk score for physical activity', Statistics in Medicine, vol. 41, no. 7, pp. 1191-1204.
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We develop a generalized partially additive model to build a single semiparametric risk scoring system for physical activity across multiple populations. A score comprised of distinct and objective physical activity measures is a new concept that offers challenges due to the nonlinear relationship between physical behaviors and various health outcomes. We overcome these challenges by modeling each score component as a smooth term, an extension of generalized partially linear single‐index models. We use penalized splines and propose two inferential methods, one using profile likelihood and a nonparametric bootstrap, the other using a full Bayesian model, to solve additional computational problems. Both methods exhibit similar and accurate performance in simulations. These models are applied to the National Health and Nutrition Examination Survey and quantify nonlinear and interpretable shapes of score components for all‐cause mortality.

Cui, L, Wang, Z, Kang, S, Fang, Y, Chen, Y, Gao, W, Zhang, Z, Gao, X, Song, C, Chen, X, Wang, Y & Wang, G 2022, 'N, P Codoped Hollow Carbon Nanospheres Decorated with MoSe₂ Ultrathin Nanosheets for Efficient Potassium-Ion Storage', ACS Applied Materials & Interfaces, vol. 14, no. 10, pp. 12551-12561.
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Potassium-ion batteries (KIBs) are gradually being considered as an alternative for lithium-ion batteries because of their non-negligible advantages such as abundance and low expenditure of K, as well as higher electrochemical potential than another alternative─sodium-ion batteries. Nevertheless, when the electrode materials are inserted and extracted with large-sized K+ ions, the tremendous volume change will cause the collapse of the microstructures of electrodes and make the charging/discharging process irreversible, thus disapproving their extended application. In response to this, we put forward a feasible strategy to realize the in situ assembly of layered MoSe2 nanosheets onto N, P codoped hollow carbon nanospheres (MoSe2/NP-HCNSs) through thermal annealing and heteroatom doping strategies, and the resulting nanoengineered material can function well as an anode for KIBs. This cleverly designed nanostructure of MoSe2/NP-HCNS can broaden the interlayer spacing of MoSe2 to boost the efficiency of the insertion/extraction of K ions and also can accommodate large volume change-caused mechanical strain, facilitate electrolyte penetration, and prevent the aggregation of MoSe2 nanosheets. This synthetic method generates abundant defects to increase the amounts of active sites, as well as conductivity. The hierarchical nanostructure can effectively increase the proportion of pseudo-capacitance and promote interfacial electronic transfer and K+ diffusion, thus imparting great electrochemical performance. The MoSe2/NP-HCNS anode exhibits a high reversible capacity of 239.9 mA h g-1 at 0.1 A g-1 after 200 cycles and an ultralong cycling life of 161.1 mA h g-1 at 1 A g-1 for a long period of 1000 cycles. This nanoengineering method opens up new insights into the development of promising anode materials for KIBs.

Cummins, ML, Reid, CJ & Djordjevic, SP 2022, 'Erratum for Cummins et al., “F Plasmid Lineages in Escherichia coli ST95: Implications for Host Range, Antibiotic Resistance, and Zoonoses”', mSystems, vol. 7, no. 2, p. e0021022.
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Cummins, ML, Reid, CJ & Djordjevic, SP 2022, 'F Plasmid Lineages in Escherichia coli ST95: Implications for Host Range, Antibiotic Resistance, and Zoonoses', mSystems, vol. 7, no. 1.
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E. coli ST95 is one of five dominant ExPEC lineages globally and noted for causing urinary tract and bloodstream infections and neonatal meningitis in humans and colibacillosis in poultry. Using high-resolution phylogenomics, we show that F replicon sequence type is linked to ST95 clade structure and zoonotic potential.

Cunliffe, AM, Anderson, K, Boschetti, F, Brazier, RE, Graham, HA, Myers‐Smith, IH, Astor, T, Boer, MM, Calvo, LG, Clark, PE, Cramer, MD, Encinas‐Lara, MS, Escarzaga, SM, Fernández‐Guisuraga, JM, Fisher, AG, Gdulová, K, Gillespie, BM, Griebel, A, Hanan, NP, Hanggito, MS, Haselberger, S, Havrilla, CA, Heilman, P, Ji, W, Karl, JW, Kirchhoff, M, Kraushaar, S, Lyons, MB, Marzolff, I, Mauritz, ME, McIntire, CD, Metzen, D, Méndez‐Barroso, LA, Power, SC, Prošek, J, Sanz‐Ablanedo, E, Sauer, KJ, Schulze‐Brüninghoff, D, Šímová, P, Sitch, S, Smit, JL, Steele, CM, Suárez‐Seoane, S, Vargas, SA, Villarreal, M, Visser, F, Wachendorf, M, Wirnsberger, H & Wojcikiewicz, R 2022, 'Global application of an unoccupied aerial vehicle photogrammetry protocol for predicting aboveground biomass in non‐forest ecosystems', Remote Sensing in Ecology and Conservation, vol. 8, no. 1, pp. 57-71.
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AbstractNon‐forest ecosystems, dominated by shrubs, grasses and herbaceous plants, provide ecosystem services including carbon sequestration and forage for grazing, and are highly sensitive to climatic changes. Yet these ecosystems are poorly represented in remotely sensed biomass products and are undersampled by in situ monitoring. Current global change threats emphasize the need for new tools to capture biomass change in non‐forest ecosystems at appropriate scales. Here we developed and deployed a new protocol for photogrammetric height using unoccupied aerial vehicle (UAV) images to test its capability for delivering standardized measurements of biomass across a globally distributed field experiment. We assessed whether canopy height inferred from UAV photogrammetry allows the prediction of aboveground biomass (AGB) across low‐stature plant species by conducting 38 photogrammetric surveys over 741 harvested plots to sample 50 species. We found mean canopy height was strongly predictive of AGB across species, with a median adjusted R2 of 0.87 (ranging from 0.46 to 0.99) and median prediction error from leave‐one‐out cross‐validation of 3.9%. Biomass per‐unit‐of‐height was similar within but different among, plant functional types. We found that photogrammetric reconstructions of canopy height were sensitive to wind speed but not sun elevation during surveys. We demonstrated that our photogrammetric approach produced generalizable measurements across growth forms and environmental settings and yielded accuracies as good as those obtained from in situ approaches. We demonstrate that using a standardized approach for UAV photogrammetry can deliver accurate AGB estimates across a wide range of dynamic and heterogeneous ecosystems. Many academic and land management institutions have the technical capacity to deploy these ap...

Daher, W, Leclercq, L-D, Johansen, MD, Hamela, C, Karam, J, Trivelli, X, Nigou, J, Guérardel, Y & Kremer, L 2022, 'Glycopeptidolipid glycosylation controls surface properties and pathogenicity in Mycobacterium abscessus', Cell Chemical Biology, vol. 29, no. 5, pp. 910-924.e7.
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Mycobacterium abscessus is an emerging and difficult-to-manage mycobacterial species that exhibits smooth (S) or rough (R) morphotypes. Disruption of glycopeptidolipid (GPL) production results in transition from S to R and severe lung disease. A structure-activity relationship study was undertaken to decipher the role of GPL glycosylation in morphotype transition and pathogenesis. Deletion of gtf3 uncovered the prominent role of the extra rhamnose in enhancing mannose receptor-mediated internalization of M. abscessus by macrophages. In contrast, the absence of the 6-deoxy-talose and the first rhamnose in mutants lacking gtf1 and gtf2, respectively, affected M abscessus phagocytosis but also resulted in the S-to-R transition. Strikingly, gtf1 and gtf2 mutants displayed a strong propensity to form cords and abscesses in zebrafish, leading to robust and lethal infection. Together, these results underscore the importance and differential contribution of GPL monosaccharides in promoting virulence and infection outcomes.

Dang, HP, Chen, H, Dargaville, TR & Tuch, BE 2022, 'Cell delivery systems: Toward the next generation of cell therapies for type 1 diabetes', Journal of Cellular and Molecular Medicine, vol. 26, no. 18, pp. 4756-4767.
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AbstractImmunoprotection and oxygen supply are vital in implementing a cell therapy for type 1 diabetes (T1D). Without these features, the transplanted islet cell clusters will be rejected by the host immune system, and necrosis will occur due to hypoxia. The use of anti‐rejection drugs can help protect the transplanted cells from the immune system; yet, they also may have severe side effects. Cell delivery systems (CDS) have been developed for islet transplantation to avoid using immunosuppressants. CDS provide physical barriers to reduce the immune response and chemical coatings to reduce host fibrotic reaction. In some CDS, there is architecture to support vascularization, which enhances oxygen exchange. In this review, we discuss the current clinical and preclinical studies using CDS without immunosuppression as a cell therapy for T1D. We find that though CDS have been demonstrated for their ability to support immunoisolation of the grafted cells, their functionality has not been fully optimized. Current advanced methods in clinical trials demonstrate the systems are partly functional, physically complicated to implement or inefficient. However, modifications are being made to overcome these issues.

Daniels, RK, Mallinson, JB, Heywood, ZE, Bones, PJ, Arnold, MD & Brown, SA 2022, 'Reservoir computing with 3D nanowire networks', Neural Networks, vol. 154, pp. 122-130.
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Darmarajan, T, Paudel, KR, Candasamy, M, Chellian, J, Madheswaran, T, Sakthivel, LP, Goh, BH, Gupta, PK, Jha, NK, Devkota, HP, Gupta, G, Gulati, M, Singh, SK, Hansbro, PM, Oliver, BGG, Dua, K & Chellappan, DK 2022, 'Autoantibodies and autoimmune disorders in SARS-CoV-2 infection: pathogenicity and immune regulation', Environmental Science and Pollution Research, vol. 29, no. 36, pp. 54072-54087.
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Davies, JM, Smith, BA, Milic, A, Campbell, B, Van Haeften, S, Burton, P, Keaney, B, Lampugnani, ER, Vicendese, D, Medek, D, Huete, A, Erbas, B, Newbigin, E, Katelaris, CH, Haberle, SG & Beggs, PJ 2022, 'The AusPollen partnership project: Allergenic airborne grass pollen seasonality and magnitude across temperate and subtropical eastern Australia, 2016–2020', Environmental Research, vol. 214, no. Pt 1, pp. 113762-113762.
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BACKGROUND: Allergic rhinitis affects half a billion people globally, including a fifth of the Australian population. As the foremost outdoor allergen source, ambient grass pollen exposure is likely to be altered by climate change. The AusPollen Partnership aimed to standardize pollen monitoring and examine broad-scale biogeographical and meteorological factors influencing interannual variation in seasonality of grass pollen aerobiology in Australia. METHODS: Daily airborne grass and other pollen concentrations in four eastern Australian cities separated by over 1700 km, were simultaneously monitored using Hirst-style samplers following the Australian Interim Pollen and Spore Monitoring Standard and Protocols over four seasons from 2016 to 2020. The grass seasonal pollen integral was determined. Gridded rainfall, temperature, and satellite-derived grassland sources up to 100 km from the monitoring site were analysed. RESULTS: The complexity of grass pollen seasons was related to latitude with multiple major summer-autumn peaks in Brisbane, major spring and minor summer peaks in Sydney and Canberra, and single major spring peaks occurring in Melbourne. The subtropical site of Brisbane showed a higher proportion of grass out of total pollen than more temperate sites. The magnitude of the grass seasonal pollen integral was correlated with pasture greenness, rainfall and number of days over 30 °C, preceding and within the season, up to 100 km radii from monitoring sites. CONCLUSIONS: Interannual fluctuations in Australian grass pollen season magnitude are strongly influenced by regional biogeography and both pre- and in-season weather. This first continental scale, Southern Hemisphere standardized aerobiology dataset forms the basis to track shifts in pollen seasonality, biodiversity and impacts on allergic respiratory diseases.

Dawson, BM, Wallman, JF & Barton, PS 2022, 'How does mass loss compare with total body score when assessing decomposition of human and pig cadavers?', Forensic Science, Medicine and Pathology, vol. 18, no. 3, pp. 343-351.
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AbstractProviding accurate and reliable measures of decomposition is paramount for forensic research where decomposition progress is used to estimate time of death. Mass loss is routinely used as a direct measure of biomass decomposition in ecological studies, yet few studies have analysed mass loss in a forensic context on human cadavers to determine its usefulness for modelling the decomposition process. Mass loss was examined in decomposing human and pig cadavers, and compared with other common decomposition metrics, such as total body score (TBS). One summer and one winter field decomposition experiment was conducted using human and pig cadavers, as pigs are often used as proxies for human cadavers in forensic research. The two measures of decomposition revealed two contrasting patterns of decomposition on pigs and humans, particularly in winter where TBS stabilised at similar values, but mass loss differed greatly. Mass loss was found to be faster in pigs than humans during early decomposition. Pigs lost 75% of their mass in winter, while humans lost less than 50%; however, in summer, both lost around 80% of their mass. TBS displayed similar patterns in both experiments, with TBS increasing more rapidly in pigs compared with humans but both eventually reaching similar TBS values in late decomposition. Measuring mass loss can provide additional information about decomposition progress that is missed if using TBS only. Key differences in decomposition progress between cadaver types were also observed, suggesting caution when extrapolating data from pigs to humans for forensic research and decomposition modelling.

Dawson, BM, Wallman, JF, Evans, MJ & Barton, PS 2022, 'Insect abundance patterns on vertebrate remains reveal carrion resource quality variation', Oecologia, vol. 198, no. 4, pp. 1043-1056.
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AbstractResource quality is a key driver of species abundance and community structure. Carrion is unique among resources due to its high nutritional quality, rapidly changing nature, and the diverse community of organisms it supports. Yet the role resource quality plays in driving variation in abundance patterns of carrion-associated species remains poorly studied. Here we investigate how species abundances change with a measure of resource change, and interpret these findings to determine how species differ in their association with carrion that changes in quality over time. We conducted field succession experiments using pigs and humans over two winters and one summer. We quantified the effect of total body score, an objective measure of resource change, on adult insect abundance using generalised additive models. For each species, phases of increasing abundance likely indicated attraction to a high-quality resource, and length of abundance maxima indicated optimal oviposition and feeding time. Some species such as the beetle Necrobia rufipes had a rapid spike in abundance, suggesting a narrow window of opportunity for carrion resource exploitation, while species like the wasp Nasonia vitripennis had a gradual change in abundance, indicating a wide window of resource exploitation. Different abundance patterns were also observed between species occurring on pigs and humans, suggesting cadaver type is an important aspect of resource quality. Our findings show that species abundances, unlike species occurrences, can reveal additional detail about species exploitation of carrion and provide information about how resource quality may drive competition and variation in insect community succession.

de Vries, M, Nwozor, KO, Muizer, K, Wisman, M, Timens, W, van den Berge, M, Faiz, A, Hackett, T-L, Heijink, IH & Brandsma, CA 2022, 'The relation between age and airway epithelial barrier function', Respiratory Research, vol. 23, no. 1.
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Abstract Background The prevalence of age-associated diseases, such as chronic obstructive pulmonary disease (COPD), is increasing as the average life expectancy increases around the world. We previously identified a gene signature for ageing in the human lung which included genes involved in apical and tight junction assembly, suggesting a role for airway epithelial barrier dysfunction with ageing. Aim To investigate the association between genes involved in epithelial barrier function and age both in silico and in vitro in the airway epithelium. Methods We curated a gene signature of 274 genes for epithelial barrier function and tested the association with age in two independent cohorts of bronchial brushings from healthy individuals with no respiratory disease, using linear regression analysis (FDR < 0.05). Protein–protein interactions were identified using STRING©. The barrier function of primary bronchial epithelial cells at air–liquid interface and CRISPR–Cas9-induced knock-down of target genes in human bronchial 16HBE14o-cells was assessed using Trans epithelial resistance (TER) measurement and Electric cell-surface impedance sensing (ECIS) respectively. Results In bronchial brushings, we found 55 genes involved in barrier function to be significantly associated with age (FDR < 0.05). EPCAM was most significantly associated with increasing age and TRPV4 with decreasing age. Protein interaction analysis identified CDH1, that was negatively ...

Dedousis-Wallace, A, Drysdale, SAO, McAloon, J, Murrihy, RC, Greene, RW & Ollendick, TH 2022, 'Predictors and Moderators Two Treatments of Oppositional Defiant Disorder in Children', Journal of Clinical Child & Adolescent Psychology, pp. 1-16.
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OBJECTIVE: The aim of this study was to examine predictors and moderators of behavioral improvement in children with Oppositional Defiant Disorder (ODD) following treatment with Parent Management Training (PMT) and Collaborative and Proactive Solutions (CPS). Initial problem severity, inconsistent discipline, parental attributions of child misbehavior, and child lagging cognitive skills were examined. METHOD: One hundred and forty-five children aged between 7 and 14 (103 males, M = 8.88 years, ethnicity representative of the wider Australian population) were randomly assigned to PMT and CPS. Assessment was conducted at baseline, post-intervention, and at 6-month follow-up, using independently rated semi-structured diagnostic interviews and parent-ratings of ODD symptoms. Using an intent-to-treat sample in this secondary analysis (Murrihy et al., 2022), linear regressions and PROCESS (Hayes, 2017) were used to examine these predictors and possible moderators of treatment. RESULTS: Higher pre-treatment levels of conduct problems, lagging skills, and inconsistent discipline predicted poorer behavioral outcomes following both treatments. The only characteristic that moderated treatment outcome was child-responsible attributions - mothers who were more likely to attribute their child's problematic behaviors to factors in the child had significantly poorer outcomes in PMT than CPS at 6-month follow-up. CONCLUSIONS: CPS may be a more beneficial treatment than PMT for families who have been identified as having higher levels of child-responsible attributions before commencing treatment for ODD. While tentative, this provides promising insights as to how treatment outcomes for children with ODD may be improved.

Degani, E, Maestrini, L, Toczydłowska, D & Wand, MP 2022, 'Sparse linear mixed model selection via streamlined variational Bayes', Electronic Journal of Statistics, vol. 16, no. 2, pp. 5182-5225.
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Linear mixed models are a versatile statistical tool to study data by accounting for fixed effects and random effects from multiple sources of variability. In many situations, a large number of candidate fixed effects is available and it is of interest to select a parsimonious subset of those being effectively relevant for predicting the response variable. Variational approximations facilitate fast approximate Bayesian inference for the parameters of a variety of statistical models, including linear mixed models. However, for models having a high number of fixed or random effects, simple application of standard variational inference principles does not lead to fast approximate inference algorithms, due to the size of model design matrices and inefficient treatment of sparse matrix problems arising from the required approximating density parameters updates. We illustrate how recently developed streamlined variational inference procedures can be generalized to make fast and accurate inference for the parameters of linear mixed models with nested random effects and global-local priors for Bayesian fixed effects selection. Our variational inference algorithms achieve convergence to the same optima of their standard imple-mentations, although with significantly lower computational effort, mem-ory usage and time, especially for large numbers of random effects. Using simulated and real data examples, we assess the quality of automated procedures for fixed effects selection that are free from hyperparameters tuning and only rely upon variational posterior approximations. Moreover, we show high accuracy of variational approximations against model fitting via Markov Chain Monte Carlo sampling.

Deignan, LK & McDougald, D 2022, 'Differential Response of the Microbiome of Pocillopora acuta to Reciprocal Transplantation Within Singapore', Microbial Ecology, vol. 83, no. 3, pp. 608-618.
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AbstractAs corals continue to decline globally, particularly due to climate change, it is vital to understand the extent to which their microbiome may confer an adaptive resilience against environmental stress. Corals that survive on the urban reefs of Singapore are ideal candidates to study the association of scleractinians with their microbiome, which in turn can inform reef conservation and management. In this study, we monitored differences in the microbiome of Pocillopora acuta colonies reciprocally transplanted between two reefs, Raffles and Kusu, within the Port of Singapore, where corals face intense anthropogenic impacts. Pocillopora acuta had previously been shown to host distinct microbial communities between these two reefs. Amplicon sequencing (16S rRNA) was used to assess the coral microbiomes at 1, 2, 4, and 10 days post-transplantation. Coral microbiomes responded rapidly to transplantation, becoming similar to those of the local corals at the destination reef within one day at Raffles and within two days at Kusu. Elevated nitrate concentrations were detected at Raffles for the duration of the study, potentially influencing the microbiome’s response to transplantation. The persistence of corals within the port of Singapore highlights the ability of corals to adapt to stressful environments. Further, coral resilience appears to coincide with a dynamic microbiome which can undergo shifts in composition without succumbing to dysbiosis.

Dennis, J, Tyrer, JP, Walker, LC, Michailidou, K, Dorling, L, Bolla, MK, Wang, Q, Ahearn, TU, Andrulis, IL, Anton-Culver, H, Antonenkova, NN, Arndt, V, Aronson, KJ, Freeman, LEB, Beckmann, MW, Behrens, S, Benitez, J, Bermisheva, M, Bogdanova, NV, Bojesen, SE, Brenner, H, Castelao, JE, Chang-Claude, J, Chenevix-Trench, G, Clarke, CL, Kristensen, VN, Sahlberg, KK, Børresen-Dale, A-L, Gram, IT, Engebråten, O, Naume, B, Geisler, J, Alnæs, GIG, Collée, JM, Lacey, J, Martinez, E, Couch, FJ, Cox, A, Cross, SS, Czene, K, Devilee, P, Dörk, T, Dossus, L, Eliassen, AH, Eriksson, M, Evans, DG, Fasching, PA, Figueroa, J, Fletcher, O, Flyger, H, Fritschi, L, Gabrielson, M, Gago-Dominguez, M, García-Closas, M, Giles, GG, González-Neira, A, Guénel, P, Hahnen, E, Haiman, CA, Hall, P, Hollestelle, A, Hoppe, R, Hopper, JL, Howell, A, Clarke, C, Carpenter, J, Marsh, D, Scott, R, Baxter, R, Yip, D, Davis, A, Pathmanathan, N, Simpson, P, Graham, D, Sachchithananthan, M, Campbell, I, de Fazio, A, Fox, S, Kirk, J, Lindeman, G, Milne, R, Southey, M, Spurdle, A, Thorne, H, Jager, A, Jakubowska, A, John, EM, Johnson, N, Jones, ME, Jung, A, Kaaks, R, Keeman, R, Khusnutdinova, E, Kitahara, CM, Ko, Y-D, Kosma, V-M, Koutros, S, Kraft, P, Kristensen, VN, Kubelka-Sabit, K, Kurian, AW, Lacey, JV, Lambrechts, D, Larson, NL, Linet, M, Ogrodniczak, A, Mannermaa, A, Manoukian, S, Margolin, S, Mavroudis, D, Milne, RL, Muranen, TA, Murphy, RA, Nevanlinna, H, Olson, JE, Olsson, H, Park-Simon, T-W, Perou, CM, Peterlongo, P, Plaseska-Karanfilska, D, Pylkäs, K, Rennert, G, Saloustros, E, Sandler, DP, Sawyer, EJ, Schmidt, MK, Schmutzler, RK, Shibli, R, Smeets, A, Soucy, P, Southey, MC, Swerdlow, AJ, Tamimi, RM, Taylor, JA, Teras, LR, Terry, MB, Tomlinson, I, Troester, MA, Truong, T, Vachon, CM, Wendt, C, Winqvist, R, Wolk, A, Yang, XR, Zheng, W, Ziogas, A, Simard, J, Dunning, AM, Pharoah, PDP & Easton, DF 2022, 'Rare germline copy number variants (CNVs) and breast cancer risk', Communications Biology, vol. 5, no. 1, p. 65.
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AbstractGermline copy number variants (CNVs) are pervasive in the human genome but potential disease associations with rare CNVs have not been comprehensively assessed in large datasets. We analysed rare CNVs in genes and non-coding regions for 86,788 breast cancer cases and 76,122 controls of European ancestry with genome-wide array data. Gene burden tests detected the strongest association for deletions in BRCA1 (P = 3.7E−18). Nine other genes were associated with a p-value < 0.01 including known susceptibility genes CHEK2 (P = 0.0008), ATM (P = 0.002) and BRCA2 (P = 0.008). Outside the known genes we detected associations with p-values < 0.001 for either overall or subtype-specific breast cancer at nine deletion regions and four duplication regions. Three of the deletion regions were in established common susceptibility loci. To the best of our knowledge, this is the first genome-wide analysis of rare CNVs in a large breast cancer case-control dataset. We detected associations with exonic deletions in established breast cancer susceptibility genes. We also detected suggestive associations with non-coding CNVs in known and novel loci with large effects sizes. Larger sample sizes will be required to reach robust levels of statistical significance.

Dhanjal, DS, Sharma, P, Mehta, M, Tambuwala, MM, Prasher, P, Paudel, KR, Liu, G, Shukla, SD, Hansbro, PM, Chellappan, DK, Dua, K & Satija, S 2022, 'Concepts of advanced therapeutic delivery systems for the management of remodeling and inflammation in airway diseases', Future Medicinal Chemistry, vol. 14, no. 4, pp. 271-288.
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Chronic respiratory disorders affect millions of people worldwide. Pathophysiological changes to the normal airway wall structure, including changes in the composition and organization of its cellular and molecular constituents, are referred to as airway remodeling. The inadequacy of effective treatment strategies and scarcity of novel therapies available for the treatment and management of chronic respiratory diseases have given rise to a serious impediment in the clinical management of such diseases. The progress made in advanced drug delivery, has offered additional advantages to fight against the emerging complications of airway remodeling. This review aims to address the gaps in current knowledge about airway remodeling, the relationships between remodeling, inflammation, clinical phenotypes and the significance of using novel drug delivery methods.

Di, X, Wang, D, Su, QP, Liu, Y, Liao, J, Maddahfar, M, Zhou, J & Jin, D 2022, 'Spatiotemporally mapping temperature dynamics of lysosomes and mitochondria using cascade organelle-targeting upconversion nanoparticles', Proceedings of the National Academy of Sciences, vol. 119, no. 45, p. e2207402119.
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The intracellular metabolism of organelles, like lysosomes and mitochondria, is highly coordinated spatiotemporally and functionally. The activities of lysosomal enzymes significantly rely on the cytoplasmic temperature, and heat is constantly released by mitochondria as the byproduct of adenosine triphosphate (ATP) generation during active metabolism. Here, we developed temperature-sensitive LysoDots and MitoDots to monitor the in situ thermal dynamics of lysosomes and mitochondria. The design is based on upconversion nanoparticles (UCNPs) with high-density surface modifications to achieve the exceptionally high sensitivity of 2.7% K −1 and low uncertainty of 0.8 K for nanothermometry to be used in living cells. We show the measurement is independent of the ion concentrations and pH values. With Ca 2+ ion shock, the temperatures of both lysosomes and mitochondria increased by ∼2 to 4 °C. Intriguingly, with chloroquine (CQ) treatment, the lysosomal temperature was observed to decrease by up to ∼3 °C, while mitochondria remained relatively stable. Lastly, with oxidative phosphorylation inhibitor treatment, we observed an ∼3 to 7 °C temperature increase and a thermal transition from mitochondria to lysosomes. These observations indicate different metabolic pathways and thermal transitions between lysosomes and mitochondria inside HeLa cells. The nanothermometry probes provide a powerful tool for multimodality functional imaging of subcellular organelles and interactions with high spatial, temporal, and thermal dynamics resolutions.

DiBattista, JD, Fowler, AM, Riley, IJ, Reader, S, Hay, A, Parkinson, K & Hobbs, J-PA 2022, 'The use of environmental DNA to monitor impacted coastal estuaries', Marine Pollution Bulletin, vol. 181, pp. 113860-113860.
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Environmental DNA (eDNA) metabarcoding is increasingly being used to assess community composition in coastal ecosystems. In this study, we chose to examine temporal and spatial changes in the aquatic community of Manly Lagoon - one of the most heavily developed and polluted estuaries in eastern Australia. Based on metabarcoding of the 16S mitochondrial gene (for fish) and the 18S nuclear gene (for macroinvertebrates), we identified seasonal differences in fish and macroinvertebrate community composition as well as species richness, which correlated, in some cases, with the environmental parameters of sea surface temperature and freshwater input. Moreover, given the greater taxonomic resolution of fish versus macroinvertebrate assignments, we identified several known migratory fish species of management importance that contributed significantly to the overall patterns observed. Overall, our data support the use of eDNA metabarcoding to track fish assemblages shifting in response to environmental drivers in polluted estuaries with increased sampling and consultation with historical data.

Dikshit, A, Pradhan, B, Huete, A & Park, H-J 2022, 'Spatial based drought assessment: Where are we heading? A review on the current status and future', Science of The Total Environment, vol. 844, pp. 157239-157239.
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Droughts are the most spatially complex natural hazards that exert global impacts and are further aggravated by climate change. The investigation of drought events is challenging as it involves numerous factors ranging from detection and assessment to modelling, management and mitigation. The analysis of these factors and their quantitative assessments have significantly evolved in recent times. In this paper, we review recent methods used to examine and model droughts from a spatial viewpoint. Our analysis was conducted at three spatial scales (point-wise, regional and global) and we evaluated how recent spatial methods have advanced our understanding of drought through case study examples. Further, we also examine and provide a broad overview of relevant case studies related to future drought occurrences under climate change. This study is a comprehensive synthesis of the various quantitative techniques used to assess the spatial characteristics of droughts at different spatial scales, and not an exhaustive review of all drought aspects. However, this serves as a basis for understanding the key milestones and advances accomplished through new spatial concepts relative to the traditional approaches to study drought. This work also aims to address the gaps in knowledge that are in need of further attention and provides recommendations to improve our understanding of droughts.

Ding, L, Razavi Bazaz, S, Asadniaye Fardjahromi, M, McKinnirey, F, Saputro, B, Banerjee, B, Vesey, G & Ebrahimi Warkiani, M 2022, 'A modular 3D printed microfluidic system: a potential solution for continuous cell harvesting in large-scale bioprocessing', Bioresources and Bioprocessing, vol. 9, no. 1.
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AbstractMicrofluidic devices have shown promising applications in the bioprocessing industry. However, the lack of modularity and high cost of testing and error limit their implementation in the industry. Advances in 3D printing technologies have facilitated the conversion of microfluidic devices from research output to applicable industrial systems. Here, for the first time, we presented a 3D printed modular microfluidic system consisting of two micromixers, one spiral microfluidic separator, and one microfluidic concentrator. We showed that this system can detach and separate mesenchymal stem cells (MSCs) from microcarriers (MCs) in a short time while maintaining the cell’s viability and functionality. The system can be multiplexed and scaled up to process large volumes of the industry. Importantly, this system is a closed system with no human intervention and is promising for current good manufacturing practices. Graphical Abstract

Ding, L, Razavi Bazaz, S, Hall, T, Vesey, G & Ebrahimi Warkiani, M 2022, 'Giardia purification from fecal samples using rigid spiral inertial microfluidics', Biomicrofluidics, vol. 16, no. 1, pp. 014105-014105.
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Giardia is one of the most common waterborne pathogens causing around 200 × 106 diarrheal infections annually. It is of great interest to microbiological research as it is among the oldest known eukaryotic cells. Purifying Giardia from fecal samples for both research and diagnostic purposes presents one of the most difficult challenges. Traditional purification methods rely on density gradient centrifugation, membrane-based filtration, and sedimentation methods, which suffer from low recovery rates, high costs, and poor efficiency. Here, we report on the use of microfluidics to purify Giardia cysts from mouse feces. We propose a rigid spiral microfluidic device with a trapezoidal cross section to effectively separate Giardia from surrounding debris. Our characterizations reveal that the recovery rate is concentration-dependent, and our proposed device can achieve recovery rates as high as 75% with 0.75 ml/min throughput. Moreover, this device can purify Giardia from extremely turbid samples to a level where cysts are visually distinguishable with just one round of purification. This highly scalable and versatile 3D printed microfluidic device is then capable of further purifying or enhancing the recovery rate of the samples by recirculation. This device also has the potential to purify other gastrointestinal pathogens of similar size, and throughput can be significantly increased by parallelization.

Ding, L, Razavi Bazaz, S, Shrestha, J, A. Amiri, H, Mas-hafi, S, Banerjee, B, Vesey, G, Miansari, M & Ebrahimi Warkiani, M 2022, 'Rapid and Continuous Cryopreservation of Stem Cells with a 3D Micromixer', Micromachines, vol. 13, no. 9, pp. 1516-1516.
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Cryopreservation is the final step of stem cell production before the cryostorage of the product. Conventional methods of adding cryoprotecting agents (CPA) into the cells can be manual or automated with robotic arms. However, challenging issues with these methods at industrial-scale production are the insufficient mixing of cells and CPA, leading to damage of cells, discontinuous feeding, the batch-to-batch difference in products, and, occasionally, cross-contamination. Therefore, the current study proposes an alternative way to overcome the abovementioned challenges; a highly efficient micromixer for low-cost, continuous, labour-free, and automated mixing of stem cells with CPA solutions. Our results show that our micromixer provides a more homogenous mixing of cells and CPA compared to the manual mixing method, while the cell properties, including surface markers, differentiation potential, proliferation, morphology, and therapeutic potential, are well preserved.

Ding, L, Shan, X, Wang, D, Liu, B, Du, Z, Di, X, Chen, C, Maddahfar, M, Zhang, L, Shi, Y, Reece, P, Halkon, B, Aharonovich, I, Xu, X & Wang, F 2022, 'Lanthanide Ion Resonance‐Driven Rayleigh Scattering of Nanoparticles for Dual‐Modality Interferometric Scattering Microscopy', Advanced Science, vol. 9, no. 32, pp. e2203354-2203354.
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AbstractLight scattering from nanoparticles is significant in nanoscale imaging, photon confinement. and biosensing. However, engineering the scattering spectrum, traditionally by modifying the geometric feature of particles, requires synthesis and fabrication with nanometre accuracy. Here it is reported that doping lanthanide ions can engineer the scattering properties of low‐refractive‐index nanoparticles. When the excitation wavelength matches the ion resonance frequency of lanthanide ions, the polarizability and the resulted scattering cross‐section of nanoparticles are dramatically enhanced. It is demonstrated that these purposely engineered nanoparticles can be used for interferometric scattering (iSCAT) microscopy. Conceptually, a dual‐modality iSCAT microscopy is further developed to identify different nanoparticle types in living HeLa cells. The work provides insight into engineering the scattering features by doping elements in nanomaterials, further inspiring exploration of the geometry‐independent scattering modulation strategy.

Ditz, B, Boekhoudt, J, Couto, N, Brandsma, CA, Hiemstra, PS, Tew, GW, Neighbors, M, Grimbaldeston, MA, Timens, W, Kerstjens, HAM, Rossen, JWA, Guryev, V, van den Berge, M & Faiz, A 2022, 'The Microbiome in Bronchial Biopsies from Smokers and Ex-Smokers with Stable COPD - A Metatranscriptomic Approach', COPD: Journal of Chronic Obstructive Pulmonary Disease, vol. 19, no. 1, pp. 81-87.
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Don Wai Luu, L, Kaakoush, NO & Castaño-Rodríguez, N 2022, 'The role of ATG16L2 in autophagy and disease', Autophagy, vol. 18, no. 11, pp. 2537-2546.
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Donovan, C, Kim, RY, Galvao, I, Jarnicki, AG, Brown, AC, Jones‐Freeman, B, Gomez, HM, Wadhwa, R, Hortle, E, Jayaraman, R, Khan, H, Pickles, S, Sahu, P, Chimankar, V, Tu, X, Ali, MK, Mayall, JR, Nguyen, DH, Budden, KF, Kumar, V, Schroder, K, Robertson, AAB, Cooper, MA, Wark, PAB, Oliver, BG, Horvat, JC & Hansbro, PM 2022, 'Aim2 suppresses cigarette smoke‐induced neutrophil recruitment, neutrophil caspase‐1 activation and anti‐Ly6G‐mediated neutrophil depletion', Immunology & Cell Biology, vol. 100, no. 4, pp. 235-249.
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AbstractIncreased inflammasome responses are strongly implicated in inflammatory diseases; however, their specific roles are incompletely understood. Therefore, we sought to examine the roles of nucleotide‐binding oligomerization domain–like receptor (NLR) family, pyrin domain–containing 3 (NLRP3) and absent in melanoma‐2 (AIM2) inflammasomes in cigarette smoke–induced inflammation in a model of experimental chronic obstructive pulmonary disease (COPD). We targeted NLRP3 with the inhibitor MCC950 given prophylactically or therapeutically and examined Aim2−/− mice in cigarette smoke–induced experimental COPD. MCC950 treatment had minimal effects on disease development and/or progression. Aim2−/− mice had increased airway neutrophils with decreased caspase‐1 levels, independent of changes in lung neutrophil chemokines. Suppressing neutrophils with anti‐Ly6G in experimental COPD in wild‐type mice reduced neutrophils in bone marrow, blood and lung. By contrast, anti‐Ly6G treatment in Aim2−/− mice with experimental COPD had no effect on neutrophils in bone marrow, partially reduced neutrophils in the blood and had no effect on neutrophils or neutrophil caspase‐1 levels in the lungs. These findings identify that following cigarette smoke exposure, Aim2 is important for anti‐Ly6G–mediated depletion of neutrophils, suppression of neutrophil recruitment and mediates activation of caspase‐1 in neutrophils.

Doré, H, Leconte, J, Guyet, U, Breton, S, Farrant, GK, Demory, D, Ratin, M, Hoebeke, M, Corre, E, Pitt, FD, Ostrowski, M, Scanlan, DJ, Partensky, F, Six, C & Garczarek, L 2022, 'Global Phylogeography of Marine Synechococcus in Coastal Areas Reveals Strong Community Shifts', mSystems, vol. 7, no. 6, p. e0065622.
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Synechococcus is the second most abundant phytoplanktonic organism on Earth, and its wide genetic diversity allowed it to colonize all the oceans except for polar waters, with different clades colonizing distinct oceanic niches. In recent years, the use of global metagenomics data sets has greatly improved our knowledge of “who is where” by describing the distribution of Synechococcus clades or ecotypes in the open ocean.

dos Remedios, C, Cranfield, C, Whelan, D, Cox, C, Shearwin, K, Ho, J, Allen, T, Shibuya, R, Hibino, E, Hayashi, K & Li, A 2022, 'A special issue of the Australian society for Biophysics', Biophysical Reviews, vol. 14, no. 1, pp. 1-2.
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Douglas, ANJ, Morgan, AL, Irga, PJ & Torpy, FR 2022, 'The need for multifaceted approaches when dealing with the differing impacts of natural disasters and anthropocentric events on air quality', Atmospheric Pollution Research, vol. 13, no. 11, pp. 101570-101570.
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Dower, A, Mulcahy, M, Maharaj, M, Chen, H, Lim, CED, Li, Y & Sheridan, M 2022, 'Surgical decompression for malignant cerebral oedema after ischaemic stroke', Cochrane Database of Systematic Reviews, vol. 2022, no. 11, p. CD014989.
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BACKGROUND: Large territory middle cerebral artery (MCA) ischaemic strokes account for around 10% of all ischaemic strokes and have a particularly devastating prognosis when associated with malignant oedema. Progressive cerebral oedema starts developing in the first 24 to 48 hours of stroke ictus with an associated rise in intracranial pressure. The rise in intracranial pressure may eventually overwhelm compensatory mechanisms leading to a cascading secondary damage to surrounding unaffected parenchyma. This downward spiral can rapidly progress to death or severe neurological disability. Early decompressive craniectomy to relieve intracranial pressure and associated tissue shift can help ameliorate this secondary damage and improve outcomes. Evidence has been accumulating of the benefit of early surgical decompression in stroke patients. Earlier studies have excluded people above the age of 60 due to associated poor outcomes; however, newer trials have included this patient subgroup. This review follows a Cochrane Review published in 2012. OBJECTIVES: To assess the effectiveness of surgical decompression in people with malignant oedema after ischaemic stroke with regard to reduction in mortality and improved functional outcome. We also aimed to examine the adverse effects of surgical decompression in this patient cohort. SEARCH METHODS: We searched the Cochrane Stroke Group Trials Register, the Cochrane Central Register of Controlled Trials (CENTRAL; 2022, Issue 7 of 12), MEDLINE Ovid, Embase Ovid, Web of Science Core Collection, Scopus databases, ClinicalTrials.gov, and the WHO ICTRP to July 2022. We also reviewed the reference lists of relevant articles. SELECTION CRITERIA: We included randomised controlled trials (RCTs) comparing decompressive craniectomy with medical management to best medical management alone for people with malignant cerebral oedema after MCA ischaemic stroke. DATA COLLECTION AND ANALYSIS: Two review authors independently screened...

Duncan, RJ & Petrou, K 2022, 'Biomolecular Composition of Sea Ice Microalgae and Its Influence on Marine Biogeochemical Cycling and Carbon Transfer through Polar Marine Food Webs', Geosciences, vol. 12, no. 1, pp. 38-38.
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Microalgae growing on the underside of sea ice are key primary producers in polar marine environments. Their nutritional status, determined by their macromolecular composition, contributes to the region’s biochemistry and the unique temporal and spatial characteristics of their growth makes them essential for sustaining polar marine food webs. Here, we review the plasticity and taxonomic diversity of sea ice microalgae macromolecular composition, with a focus on how different environmental conditions influence macromolecular production and partitioning within cells and communities. The advantages and disadvantages of methodologies for assessing macromolecular composition are presented, including techniques that provide high throughput, whole macromolecular profile and/or species-specific resolution, which are particularly recommended for future studies. The directions of environmentally driven macromolecular changes are discussed, alongside anticipated consequences on nutrients supplied to the polar marine ecosystem. Given that polar regions are facing accelerated rates of environmental change, it is argued that a climate change signature will become evident in the biochemical composition of sea ice microalgal communities, highlighting the need for further research to understand the synergistic effects of multiple environmental stressors. The importance of sea ice microalgae as primary producers in polar marine ecosystems means that ongoing research into climate-change driven macromolecular phenotyping is critical to understanding the implications for the regions biochemical cycling and carbon transfer.

Duncan, RJ, Nielsen, DA, Sheehan, CE, Deppeler, S, Hancock, AM, Schulz, KG, Davidson, AT & Petrou, K 2022, 'Ocean acidification alters the nutritional value of Antarctic diatoms', New Phytologist, vol. 233, no. 4, pp. 1813-1827.
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SummaryPrimary production in the Southern Ocean is dominated by diatom‐rich phytoplankton assemblages, whose individual physiological characteristics and community composition are strongly shaped by the environment, yet knowledge on how diatoms allocate cellular energy in response to ocean acidification (OA) is limited. Understanding such changes in allocation is integral to determining the nutritional quality of diatoms and the subsequent impacts on the trophic transfer of energy and nutrients.Using synchrotron‐based Fourier transform infrared microspectroscopy, we analysed the macromolecular content of selected individual diatom taxa from a natural Antarctic phytoplankton community exposed to a gradient of fCO2 levels (288–1263 µatm).Strong species‐specific differences in macromolecular partitioning were observed under OA. Large taxa showed preferential energy allocation towards proteins, while smaller taxa increased both lipid and protein stores at high fCO2.If these changes are representative of future Antarctic diatom physiology, we may expect a shift away from lipid‐rich large diatoms towards a community dominated by smaller taxa, but with higher lipid and protein stores than their present‐day contemporaries, a response that could have cascading effects on food web dynamics in the Antarctic marine ecosystem.

Edla, M, Mikio, D, Izadgoshasb, I, Mahmud, MAP & Kouzani, AZ 2022, 'Self-powered boost-converter for power optimisation and piezo garden lights', Smart Materials and Structures, vol. 31, no. 4, pp. 045021-045021.
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Abstract This study gives a thorough model for a small vibration powered piezoelectric device (PD) and analysis modes of operation and control of a self-powered boost converter circuit (SPBC) for the goal of tracking the PD’s finest functioning points. The concept defines the power dependency of the PD on mechanical excitation and frequency, and it aids in the design of load behaviour for power optimisation. With a fundamental control circuit, the electrical nature of the input (i.e. PD) of an SPBC circuit in the discontinuous current mode is found to be in perfect configuration with the studied optimisation requirements. The performance of the proposed SPBC circuit is studied in terms of both simulation and experiment. Firstly, the performance of the SPBC on optimisation of the PD is investigated using a mechanical shaker. Then, the proposed circuit’s ability to charge a battery, which can be used in piezo garden lights with low-frequency applicability, is also investigated. The proposed circuit and control can also be utilised to optimise electromagnetic applications.

Eggleton, BJ, Steel, MJ & Poulton, CG 2022, 'Preface', pp. xiii-xviii.
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Eilers, K, Kuok Hoong Yam, J, Morton, R, Mei Hui Yong, A, Brizuela, J, Hadjicharalambous, C, Liu, X, Givskov, M, Rice, SA & Filloux, A 2022, 'Phenotypic and integrated analysis of a comprehensive Pseudomonas aeruginosa PAO1 library of mutants lacking cyclic-di-GMP-related genes', Frontiers in Microbiology, vol. 13, pp. 1-21.
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Pseudomonas aeruginosa is a Gram-negative bacterium that is able to survive and adapt in a multitude of niches as well as thrive within many different hosts. This versatility lies within its large genome of ca. 6 Mbp and a tight control in the expression of thousands of genes. Among the regulatory mechanisms widespread in bacteria, cyclic-di-GMP signaling is one which influences all levels of control. c-di-GMP is made by diguanylate cyclases and degraded by phosphodiesterases, while the intracellular level of this molecule drives phenotypic responses. Signaling involves the modification of enzymes’ or proteins’ function upon c-di-GMP binding, including modifying the activity of regulators which in turn will impact the transcriptome. In P. aeruginosa, there are ca. 40 genes encoding putative DGCs or PDEs. The combined activity of those enzymes should reflect the overall c-di-GMP concentration, while specific phenotypic outputs could be correlated to a given set of dgc/pde. This notion of specificity has been addressed in several studies and different strains of P. aeruginosa. Here, we engineered a mutant library for the 41 individual dgc/pde genes in P. aeruginosa PAO1. In most cases, we observed a significant to slight variation in the global c-di-GMP pool of cells grown planktonically, while several mutants display a phenotypic impact on biofilm including initial attachment and maturation. If this observation of minor changes in c-di-GMP level correlating with significant phenotypic impact appears to be true, it further supports the idea of a local vs global c-di-GMP pool. In contrast, there was little to no effect on motility, which differs from previous studies. Our RNA-seq analysis indicated that all PA...

Elankumaran, P, Browning, GF, Marenda, MS, Reid, CJ & Djordjevic, SP 2022, 'Close genetic linkage between human and companion animal extraintestinal pathogenic Escherichia coli ST127', Current Research in Microbial Sciences, vol. 3, pp. 100106-100106.
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Elankumaran, P, Cummins, ML, Browning, GF, Marenda, MS, Reid, CJ & Djordjevic, SP 2022, 'Genomic and Temporal Trends in Canine ExPEC Reflect Those of Human ExPEC', Microbiology Spectrum, vol. 10, no. 3.
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Pathogenic E. coli that causes extraintestinal infections (ExPEC) in humans and canines represents a significant burden in hospital and veterinary settings. Despite the obvious interrelationship between dogs and humans favoring both zoonotic and anthropozoonotic infections, whole-genome sequencing projects examining large numbers of canine-origin ExPEC are lacking.

Elbadawi, C, Kianinia, M, Bendavid, A & Lobo, CJ 2022, 'Charged Particle Induced Etching and Functionalization of Two-Dimensional Materials', ECS Journal of Solid State Science and Technology, vol. 11, no. 3, pp. 035011-035011.
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Focused electron beam induced deposition and etching (FEBID and FEBIE) are direct-write nanofabrication techniques in which an electron beam is used to achieve nanostructure functionalization, etching or deposition. Either alone or in combination with in situ plasmas, these techniques can also be used to accelerate reactions that occur in ambient environment, with simultaneous high-resolution imaging. Here, we describe our recent work on etching, functionalization and directed assembly of a range of nano- and two-dimensional materials using temperature-dependent FEBIE experiments in an environmental scanning electron microscope (ESEM). As examples of the application of these techniques, we demonstrate processes for assembling arrays of nanodiamonds that can be used as magnetic field sensors, as well as for controlled etching of hexagonal boron nitride (hBN) and black phosphorus (BP).

Elbourne, LDH, Sutcliffe, B, Humphreys, W, Focardi, A, Saccò, M, Campbell, MA, Paulsen, IT & Tetu, SG 2022, 'Unravelling Stratified Microbial Assemblages in Australia’s Only Deep Anchialine System, The Bundera Sinkhole', Frontiers in Marine Science, vol. 9.
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Bundera sinkhole, located in north-western Australia, is the only known continental anchialine system in the Southern Hemisphere. Anchialine environments are characterised by stratified water columns with complex physicochemical profiles spanning hypoxic and anoxic regions, often displaying high levels of endemism. Research on these systems has focused on eukaryotic fauna, however interest in the microbial diversity of these environments is growing, enabled by next-generation DNA sequencing. Here we report detailed analyses of the microbial communities across a depth profile within Bundera sinkhole (from 2 to 28 m), involving parallel physicochemical measurements, cell population counts and 16S rRNA amplicon analyses. We observed clear shifts in microbial cell counts, community diversity, structure and membership across the depth profile, reflecting changing levels of light, organic and inorganic energy sources as well as shifts in pH and salinity. While Proteobacteria were the most abundant phylum found, there was a high degree of taxonomic novelty within these microbial communities, with 13,028 unique amplicon sequence variants (ASVs) identified, belonging to 67 identifiable bacterial and archaeal phyla. Of these ~4,600, more than one third of the total, were unclassified below family level. A small number of ASVs were highly abundant at select depths, all of which were part of the set not classified below family level. The 2 m and 6 m samples had in common two highly abundant ASVs, belonging to the Ectothiorhodospiraceae and Thiotrichaceae families, while the 8 m community contained a single predominant ASV belonging to family Thioglobaceae. At lower depths a different Ectothiorhodospiraceae ASV comprised up to 68% relative abundance, peaking at 26 and 28 m. Canonical correspondence analyses indicated that community structure was strongly influenced by differences in key physicochemical parameters, particularly salinity, dissolved organic and...

Elbourne, M, Cawley, A, Stanley, S, Bowen, C & Fu, S 2022, 'Intelligence benefit of the 3‐methoxytyramine to tyramine ratio in equine urine', Drug Testing and Analysis, vol. 14, no. 5, pp. 936-942.
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AbstractEquine urine analysis has evolved over time to detect thousands of urinary compounds for doping control in the horse racing industry. The longitudinal assessment of 3‐methoxytyramine to tyramine ratio (3‐MT/T) values in equine urine by GC–MS profiling was investigated to support the Racing NSW Equine Biological Passport (EBP) for detection of dopaminergic manipulation in racehorses. This involved comparison of routine urine samples to administration studies of Sinemet, a common Parkinson's disease medication containing levodopa. Using an endogenous reference compound (ERC) in a urinary ratio enabled greater confidence to provide intelligence of pharmaceutical manipulation as distinct from physiological variation. Population reference limits (PRLs) of 776 ng/ml for urinary 3‐MT and 5.3 for 3‐MT/T, together with the use of individual reference limits (IRLs), are proposed.

Elbourne, M, Fu, S, Cawley, A, Bowen, C & Gupta, A 2022, 'Metabolomic analysis of equine urine to determine route of altrenogest administration', Toxicologie Analytique et Clinique, vol. 34, no. 3, pp. S55-S56.
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Emmerson, KM, Addison-Smith, E, Ebert, E, Milic, A, Vicendese, D, Lampugnani, ER, Erbas, B, Medek, DE, Huete, A, Beggs, P, Katelaris, CH, Haberle, SG, Newbigin, E & Davies, JM 2022, 'Evaluation of the performance of short-term curated daily airborne grass pollen forecasts in diverse biogeographical regions during the AusPollen Partnership project 2016–2020', Atmospheric Environment: X, vol. 15, pp. 100183-100183.
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When providing pollen forecasts to the community, there is a need to verify the accuracy of curated forecasts, but evaluation is not routinely reported. This study of the AusPollen Partnership compared multi-category grass pollen forecasts for up to six days ahead with daily airborne grass pollen concentrations measured in Brisbane, Canberra, Melbourne, and Sydney, Australia during four pollen seasons from 2016 to 2020. The accuracy of categorical grass pollen forecasts predicting grass pollen concentrations in the high and greater, or moderate and greater categories, were assessed as often applied in meteorology using Gerrity scores, equitable threat scores, false alarm ratios, success ratios, and probability of detection of correct category. The skill of grass pollen forecasts curated by aerobiologists were compared with two retrospectively calculated naïve reference forecast methods; climatology and persistence. For Brisbane and Melbourne, high or greater grass pollen levels occurred on average 32% and 22% of days, whereas for Canberra and Sydney, there were few high days, but moderate or greater pollen levels occurred on average 26% and 19% of days, respectively. Average annual Gerrity scores for curated forecasts of high or greater improved with experience from 0.20 to 0.66 in Brisbane, and from 0.39 to 0.55 in Melbourne between 2016 and 2019. Average Gerrity Scores for moderate or greater categories in Sydney were 0.45 and 0.43 in 2016 and 2018 respectively, and in Canberra were 0.34 and 0.41, in the same years. The skill of curated forecasts was usually better than persistence forecasts, but the accuracy of the curated forecasts decreased with longer lead times. Although persistence grass pollen forecasts consistently performed better than climatologies, persistence depends on previous day pollen concentrations being available. Short-term curated daily grass pollen forecasts of the AusPollen Partnership offer useful information for people with al...

Etchart, MG, Anderson, LL, Ametovski, A, Jones, PM, George, AM, Banister, SD & Arnold, JC 2022, 'In vitro evaluation of the interaction of the cannabis constituents cannabichromene and cannabichromenic acid with ABCG2 and ABCB1 transporters', European Journal of Pharmacology, vol. 922, pp. 174836-174836.
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Etminaniesfahani, A, Gu, H & Salehipour, A 2022, 'ABFIA: A hybrid algorithm based on artificial bee colony and Fibonacci indicator algorithm', Journal of Computational Science, vol. 61, pp. 101651-101651.
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Facey, JA, King, JJ, Apte, SC & Mitrovic, SM 2022, 'Assessing the importance of cobalt as a micronutrient for freshwater cyanobacteria', Journal of Phycology, vol. 58, no. 1, pp. 71-79.
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Micronutrients play key roles in numerous metabolic processes in cyanobacteria. However, our understanding of whether the micronutrient cobalt influences the productivity of freshwater systems or the occurrence of cyanobacterial blooms is limited. This study aimed to quantify the concentration of Co necessary for optimal cyanobacterial growth by exposing Microcystis aeruginosa to a range of Co concentrations under culture conditions. Extended exposure to concentrations below ˜0.06 μg · L−1 resulted in notable inhibition of M. aeruginosa growth. A clear negative relationship was observed between Co concentration in solution and intracellular Fe quota of M. aeruginosa, possibly due to decreased transport of Fe at higher Co concentrations. Cyanocobalamin and any Co within the structure of cyanocobalamin appears to be non‐bioavailable to M. aeruginosa, instead they likely rely on the synthesis of a structural variant – pseudocobalamin, which may have implications for the wider algal community as the variants of cobalamin are not necessarily functionally exchangeable. To evaluate the likelihood of Co limitation of cyanobacterial growth under field conditions, a survey of 10 freshwater reservoirs in South‐Eastern Australia was conducted. Four of the ten sites had dissolved Co concentrations below the 0.06 μg · L−1 threshold value. All four of these sites rarely undergo cyanobacterial blooms, strengthening evidence of the potential for Co to limit growth, perhaps either alone or in combination with phosphorus.

Facey, JA, Michie, LE, King, JJ, Hitchcock, JN, Apte, SC & Mitrovic, SM 2022, 'Severe cyanobacterial blooms in an Australian lake; causes and factors controlling succession patterns', Harmful Algae, vol. 117, pp. 102284-102284.
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Cyanobacterial blooms have major impacts on the ecological integrity and anthropogenic value of freshwater systems. Chrysosporum ovalisporum, a potentially toxic cyanobacteria has been rare in Australian waters until recently when is has bloomed in a number of lake and river systems. The aim of this study was to determine drivers of its growth and growing dominance. We performed regular monitoring of Mannus Lake, a small freshwater reservoir in South-Eastern Australia that has recently undergone extremely dense bloom events. Blooms of the diazotrophic Chrysosporum ovalisporum occurred in both summers of the 19 month study during periods of persistent thermal stratification. Following the C. ovalisporum blooms, non-diazotrophic taxa (Microcystis aeruginosa and Woronichinia sp.) dominated the phytoplankton community under less stratified conditions. Thermal stratification and nitrogen availability appeared to be the primary drivers of changes in cyanobacterial community structure. We propose that the observed transition from C. ovalisporum to M. aeruginosa and/or Woronichinia sp. may be a result of nitrogen limitation in early summer, which combined with persistent thermal stratification led to an ecological advantage for the nitrogen-fixing C. ovalisporum. Mixing events caused the senescence of the C. ovalisporum bloom, likely supplementing the nutrient budget of the lake with atmospherically derived N and alleviating N limitation to non-diazotrophic taxa. Non-diazotrophic cyanobacterial growth then increased, albeit at much lower biovolumes compared to the initial bloom. Overall, the results demonstrate the role of thermal stratification and nutrient cycling in structuring the cyanobacterial community and provide insights into the environmental factors driving the proliferation of the relatively new, potentially toxic cyanobacterium C. ovalisporum in Australian waters.

Facey, JA, Violi, JP, King, JJ, Sarowar, C, Apte, SC & Mitrovic, SM 2022, 'The Influence of Micronutrient Trace Metals on Microcystis aeruginosa Growth and Toxin Production', Toxins, vol. 14, no. 11, pp. 812-812.
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Microcystis aeruginosa is a widespread cyanobacteria capable of producing hepatotoxic microcystins. Understanding the environmental factors that influence its growth and toxin production is essential to managing the negative effects on freshwater systems. Some micronutrients are important cofactors in cyanobacterial proteins and can influence cyanobacterial growth when availability is limited. However, micronutrient requirements are often species specific, and can be influenced by substitution between metals or by luxury uptake. In this study, M. aeruginosa was grown in modified growth media that individually excluded some micronutrients (cobalt, copper, iron, manganese, molybdenum) to assess the effect on growth, toxin production, cell morphology and iron accumulation. M. aeruginosa growth was limited when iron, cobalt and manganese were excluded from the growth media, whereas the exclusion of copper and molybdenum had no effect on growth. Intracellular microcystin-LR concentrations were variable and were at times elevated in treatments undergoing growth limitation by cobalt. Intracellular iron was notably higher in treatments grown in cobalt-deplete media compared to other treatments possibly due to inhibition or competition for transporters, or due to irons role in detoxifying reactive oxygen species (ROS).

Fairley, LH, Grimm, A & Eckert, A 2022, 'Mitochondria Transfer in Brain Injury and Disease', Cells, vol. 11, no. 22, pp. 3603-3603.
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Intercellular mitochondria transfer is a novel form of cell signalling in which whole mitochondria are transferred between cells in order to enhance cellular functions or aid in the degradation of dysfunctional mitochondria. Recent studies have observed intercellular mitochondria transfer between glia and neurons in the brain, and mitochondrial transfer has emerged as a key neuroprotective mechanism in a range of neurological conditions. In particular, artificial mitochondria transfer has sparked widespread interest as a potential therapeutic strategy for brain disorders. In this review, we discuss the mechanisms and effects of intercellular mitochondria transfer in the brain. The role of mitochondrial transfer in neurological conditions, including neurodegenerative disease, brain injury, and neurodevelopmental disorders, is discussed as well as therapeutic strategies targeting mitochondria transfer in the brain.

Faiz, A & van den Berge, M 2022, 'Quality over quantity: the importance of collecting relevant samples to understand complex diseases', European Respiratory Journal, vol. 59, no. 5, pp. 2200418-2200418.
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Faiz, A, Boedijono, FS, Timens, W, Nawijn, M, Hansbro, PM, Mahbub, R, Johansen, MD, Brandsma, C, Heijink, IH, Massip, F, De Biase, MS, Schwarz, RF, Adcock, IM, Chung, KF, Hiemstra, PS, Goulaouic, H, Xing, H, Abdulai, R, De Rinaldis, E, Cunoosamy, D, Harel, S, Lederer, DJ, Nivens, C, Kerstjens, H, Hylkema, M & Van Den Berge, M 2022, 'The regulation of IL33 following smoking cessation', 03.01 - Molecular pathology and functional genomics.
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Fam, J, Clemens, KJ, Westbrook, RF, Morris, MJ & Kendig, MD 2022, 'Chronic exposure to cafeteria-style diet in rats alters sweet taste preference and reduces motivation for, but not ‘liking’ of sucrose', Appetite, vol. 168, pp. 105742-105742.
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Obesity is associated with changes to taste perception and brain reward circuitry. It is important to understand how these effects alter the preference for palatable foods and drinks, given that these are widely consumed, and leading risk factors for obesity. This study examined the effects of diet-induced obesity on sweet taste preference by analysing the microstructure of licking for sugar solutions and assessing pERK expression in the nucleus accumbens shell and insula. Adult male Sprague-Dawley rats were fed standard chow (Control; n = 16) or a varied, palatable cafeteria diet (Caf; n = 16) for 12 weeks. Two-choice preference tests between 2%, 8% and 32% sucrose solutions were conducted at baseline and in weeks 11-12 of the diet. Rats in the Caf group trebled energy intake and doubled weight gain relative to controls. In tests held under water restriction after 11 weeks of diet, the Control group reliably preferred higher sucrose concentrations (i.e., 32% > 8% > 2%). Relative to controls, the Caf group showed a stronger preference for 32% vs. 2% sucrose, lower preference for 32% vs. 8% sucrose, and were indifferent to 8% vs. 2% sucrose. Testing without water restriction increased preference for higher sucrose concentrations in both groups. Chronic Caf diet increased the latency to lick, decreased total licks and reduced alternations between spouts, but did not alter lick cluster size, a measure of hedonic appraisal, on any test. Following a final exposure to a novel sucrose concentration, neuronal activity (pERK) in the insula and nucleus accumbens shell was significantly reduced in the Caf group. Results indicate that differences in 'liking' do not underlie obesity-induced changes to sweet taste preference.

Fang, G, Lu, H, Al-Nakashli, R, Chapman, R, Zhang, Y, Ju, LA, Lin, G, Stenzel, MH & Jin, D 2022, 'Enabling peristalsis of human colon tumor organoids on microfluidic chips', Biofabrication, vol. 14, no. 1, pp. 015006-015006.
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Abstract Peristalsis in the digestive tract is crucial to maintain physiological functions. It remains challenging to mimic the peristaltic microenvironment in gastrointestinal organoid culture. Here, we present a method to model the peristalsis for human colon tumor organoids on a microfluidic chip. The chip contains hundreds of lateral microwells and a surrounding pressure channel. Human colon tumor organoids growing in the microwell were cyclically contracted by pressure channel, mimicking the in vivo mechano-stimulus by intestinal muscles. The chip allows the control of peristalsis amplitude and rhythm and the high throughput culture of organoids simultaneously. By applying 8% amplitude with 8 ∼ 10 times min−1, we observed the enhanced expression of Lgr5 and Ki67. Moreover, ellipticine-loaded polymeric micelles showed reduced uptake in the organoids under peristalsis and resulted in compromised anti-tumor efficacy. The results indicate the importance of mechanical stimuli mimicking the physiological environment when using in vitro models to evaluate nanoparticles. This work provides a method for attaining more reliable and representative organoids models in nanomedicine.

Fang, XM, Liu, Y, Wang, J, Zhang, X, Wang, L, Zhang, L, Zhang, HP, Liu, L, Huang, D, Liu, D, Deng, K, Luo, FM, Wan, HJ, Li, WM, Wang, G & Oliver, BG 2022, 'Endogenous Adenosine 5′-Monophosphate, But Not Acetylcholine or Histamine, is Associated with Asthma Control, Quality of Life, and Exacerbations', Lung, vol. 200, no. 5, pp. 579-589.
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OBJECTIVE: Endogenous adenosine 5'-monophosphate (AMP), acetylcholine (ACh), and histamine (HA) are known to be important in bronchial contraction, but their clinical relevance to asthma is poorly understood. We aimed to quantify endogenous AMP, ACh, and HA in induced sputum samples and explore their relationships with asthma control and exacerbations. METHODS: 20 healthy subjects and 112 asthmatics underwent clinical assessment, sputum induction, and blood sampling. The level of asthma control was determined by the asthma control test (ACT) questionnaire. Asthma exacerbation was evaluated according to the criteria of the American Thoracic Society/European Respiratory Society. Levels of AMP, ACh, and HA in sputum were measured by liquid chromatography coupled to tandem mass spectrometry. IL-β, IL-4, IL-5, IL-6, IL-8, IL-13, IL-17A, TNF-α, IFN-γ, and macrophage-derived chemokine (MDC) were also measured. RESULTS: Compared to healthy controls, asthmatics had higher levels of HA, lower levels of ACh, and similar levels of AMP in induced sputum samples. Compared to controlled asthma (n = 54), uncontrolled asthma (n = 58) showed higher AMP levels (P = 0.002), but similar HA and ACh levels. AMP was negatively correlated with ACT scores (r = - 0.348) and asthma quality of life questionnaire scores (r = - 0.188) and positively correlated with blood monocytes percentage (r = 0.195), sputum MDC (r = 0.214), and IL-6 levels (r = 0.196). Furthermore, AMP was associated with an increased risk of exacerbations in the preceding year. CONCLUSION: Endogenous AMP, but not ACh or HA, was associated with asthma control, quality of life, and exacerbations in the previous year, which indicates that AMP could be a clinically useful biomarker of asthma.

Farabi, L, Rehn, S & Boakes, RA 2022, 'Caffeine-based flavor preference conditioning in the rat', Learning & Behavior, vol. 50, no. 2, pp. 222-232.
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Farahmandjou, M, Zhao, S, Lai, W-H, Sun, B, Notten, PHL & Wang, G 2022, 'Oxygen redox chemistry in lithium-rich cathode materials for Li-ion batteries: Understanding from atomic structure to nano-engineering', Nano Materials Science, vol. 4, no. 4, pp. 322-338.
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Fares, M, Canfield, P, Alsherbiny, MA, Lewis, W, Willis, AC, Guang Li, C, Neyts, J, Jochmans, D, Gale, PA & Keller, PA 2022, 'Synthesis, X-ray crystallographic analysis, DFT studies and biological evaluation of triazolopyrimidines and 2-anilinopyrimidines', Journal of Molecular Structure, vol. 1252, pp. 132092-132092.
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Favaloro, J, Bryant, C, Abadir, E, Yang, S, Gardiner, S, Nassif, N, Sedger, L, Joshua, D & Ho, PJ 2022, 'OAB-023: Single-cell analysis reveals disease induced perturbations of CD8+T-cell subsets in the bone marrow and peripheral blood of newly diagnosed multiple myeloma patients', Clinical Lymphoma Myeloma and Leukemia, vol. 22, pp. S14-S14.
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Feng, OY, Chen, Y, Han, Q, Carroll, RJ & Samworth, RJ 2022, 'Nonparametric, Tuning-Free Estimation of S-Shaped Functions', Journal of the Royal Statistical Society Series B: Statistical Methodology, vol. 84, no. 4, pp. 1324-1352.
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AbstractWe consider the nonparametric estimation of an S-shaped regression function. The least squares estimator provides a very natural, tuning-free approach, but results in a non-convex optimization problem, since the inflection point is unknown. We show that the estimator may nevertheless be regarded as a projection onto a finite union of convex cones, which allows us to propose a mixed primal-dual bases algorithm for its efficient, sequential computation. After developing a projection framework that demonstrates the consistency and robustness to misspecification of the estimator, our main theoretical results provide sharp oracle inequalities that yield worst-case and adaptive risk bounds for the estimation of the regression function, as well as a rate of convergence for the estimation of the inflection point. These results reveal not only that the estimator achieves the minimax optimal rate of convergence for both the estimation of the regression function and its inflection point (up to a logarithmic factor in the latter case), but also that it is able to achieve an almost-parametric rate when the true regression function is piecewise affine with not too many affine pieces. Simulations and a real data application to air pollution modelling also confirm the desirable finite-sample properties of the estimator, and our algorithm is implemented in the R package Sshaped.

Feng, S, Ngo, HH, Guo, W, Chang, SW, Nguyen, DD, Liu, Y, Zhang, S, Phong Vo, HN, Bui, XT & Ngoc Hoang, B 2022, 'Volatile fatty acids production from waste streams by anaerobic digestion: A critical review of the roles and application of enzymes', Bioresource Technology, vol. 359, pp. 127420-127420.
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Volatile fatty acids (VFAs) produced from organic-rich wastewater by anaerobic digestion attract attention due to the increasing volatile fatty acids market, sustainability and environmentally friendly characteristics. This review aims to give an overview of the roles and applications of enzymes, a biocatalyst which plays a significant role in anaerobic digestion, to enhance volatile fatty acids production. This paper systematically overviewed: (i) the enzymatic pathways of VFAs formation, competition, and consumption; (ii) the applications of enzymes in VFAs production; and (iii) feasible measures to boost the enzymatic processes. Furthermore, this review presents a critical evaluation on the major obstacles and feasible future research directions for the better applications of enzymatic processes to promote VFAs production from wastewater.

Fernandes, KE, Frost, EA, Remnant, EJ, Schell, KR, Cokcetin, NN & Carter, DA 2022, 'The role of honey in the ecology of the hive: Nutrition, detoxification, longevity, and protection against hive pathogens', Frontiers in Nutrition, vol. 9, p. 954170.
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Honey is the source of energy for the European honey bee, Apis mellifera. Beyond simple nutrition and a hedge against the seasonal, geographic, and chemical unpredictability of nectar, honey has properties that protect the hive against various stresses. Enzyme-mediated detoxification during honey ripening neutralizes potentially toxic phytochemicals, and bees that consume honey have enhanced tolerance to other ingested toxins. Catalase and antioxidant phenolics protect honey bees from oxidative damage caused by reactive oxygen species, promoting their longevity. Phytochemical components of honey and microRNAs have the potential to influence developmental pathways, with diet playing a large role in honey bee caste determination. Components of honey mediate stress response and promote cold tolerance during overwintering. Honey has a suite of antimicrobial mechanisms including osmotic pressure, low water activity, low pH, hydrogen peroxide, and plant-, honey bee-, and microbiota-derived compounds such as phytochemicals and antimicrobial peptides. Certain types of honey, particularly polyfloral honeys, have been shown to inhibit important honey bee pathogens including the bacteria responsible for American and European Foulbrood, the microsporidian Nosema ceranae, and the fungi responsible for Stonebrood. Understanding the diverse functional properties of honey has far-ranging implications for honey bee and hive health and management by beekeepers.

Fernandez, E, Seymour, JR & Petrou, K 2022, 'Phytoplankton Sources and Sinks of Dimethylsulphoniopropionate (DMSP) in Temperate Coastal Waters of Australia', Microorganisms, vol. 10, no. 8, pp. 1539-1539.
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The ecologically important organic sulfur compound, dimethylsulfoniopropionate (DMSP), is ubiquitous in marine environments. Produced by some species of phytoplankton and bacteria, it plays a key role in cellular responses to environmental change. Recently, uptake of DMSP by non-DMSP-producing phytoplankton species has been demonstrated, highlighting knowledge gaps concerning DMSP distribution through the marine microbial food web. In this study, we traced the uptake and distribution of DMSP through a natural marine microbial community collected from off the eastern coastline Australia. We found a diverse phytoplankton community representing six major taxonomic groups and conducted DMSP-enrichment experiments both on the whole community, and the community separated into large (≥8.0 µm), medium (3.0–8.0 µm), and small (0.2–3.0 µm) size fractions. Our results revealed active uptake of DMSP in all three size fractions of the community, with the largest fraction (>8 µm) forming the major DMSP sink, where enrichment resulted in an increase of DMSPp by 144%. We observed evidence for DMSP catabolism in all size fractions with DMSP enrichment, highlighting loss from the system via MeSH or DMS production. Based on taxonomic diversity, we postulate the sources of DMSP were the dinoflagellates, Phaeocystis sp., and Trichodesmium sp., which were present in a relatively high abundance, and the sinks for DMSP were the diatoms and picoeucaryotes in this temperate community. These findings corroborate the role of hitherto disregarded phytoplankton taxa as potentially important players in the cycling of DMSP in coastal waters of Australia and emphasize the need to better understand the fate of accumulated DMSP and its significance in cellular metabolism of non-DMSP producers.

Fernandez, TT, Johnston, B, Gross, S, Cozic, S, Poulain, M, Mahmodi, H, Kabakova, I, Withford, M & Fuerbach, A 2022, 'Ultrafast laser inscribed waveguides in tailored fluoride glasses: an enabling technology for mid-infrared integrated photonics devices', Scientific Reports, vol. 12, no. 1, p. 14674.
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AbstractZirconium fluoride (ZBLAN) glass, the standard material used in fiber-based mid-infrared photonics, has been re-designed to enable the fabrication of high index-contrast low-loss waveguides via femtosecond laser direct writing. We demonstrate that in contrast to pure ZBLAN, a positive index change of close to 10−2 can be induced in hybrid zirconium/hafnium (Z/HBLAN) glasses during ultrafast laser inscription and show that this can be explained by an electron cloud distortion effect that is driven by the existence of two glass formers with contrasting polarizability. High numerical aperture (NA) type-I waveguides that support a well confined 3.1 μm wavelength mode with a mode-field diameter (MFD) as small as 12 μm have successfully been fabricated. These findings open the door for the fabrication of mid-infrared integrated photonic devices that can readily be pigtailed to existing ZBLAN fibers.

Fernandez, TT, Johnston, B, Mahmodi, H, Privat, K, Kabakova, I, Gross, S, Withford, M & Fuerbach, A 2022, 'Thermally stable high numerical aperture integrated waveguides and couplers for the 3 μm wavelength range', APL Photonics, vol. 7, no. 12, pp. 126106-126106.
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The femtosecond laser direct write technique was used to fabricate mid-infrared compatible waveguide couplers into Suprasil 3001, a fused silica glass with an OH content of as low as ≤1 ppm. Smooth positive step-index change multi-scan waveguides were produced with a high index contrast of 1 × 10−2, measured directly using quadriwave lateral shearing interferometry. Waveguides were annealed at 400 °C for 15 h and found to be highly stable, with only &lt;5% reduction in positive index change. Brillouin microscopy and cathodoluminescence are introduced as novel tools that complement Raman mapping and electron microscopy for the investigation of the laser-induced structural changes within the glass matrix, and it was found that although a uniform step index profile is observed across the entire guiding region, different physical mechanisms underpin the index change in the upper and lower sections of the waveguide cross-section, respectively. Waveguides were optimized for mode-matching with optical fibers for the 3.2 μm wavelength range, and evanescent four-port directional couplers with coupling ratios ranging from 5:95 to 50:50 were designed and fabricated. This demonstration opens the door to the development of fully integrated and temperature-stable hybrid chip/fiber systems for the important mid-infrared spectral range.

Ferrell, KC, Johansen, MD, Triccas, JA & Counoupas, C 2022, 'Virulence Mechanisms of Mycobacterium abscessus: Current Knowledge and Implications for Vaccine Design', Frontiers in Microbiology, vol. 13, pp. 1-21.
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Mycobacterium abscessus is a member of the non-tuberculous mycobacteria (NTM) group, responsible for chronic infections in individuals with cystic fibrosis (CF) or those otherwise immunocompromised. While viewed traditionally as an opportunistic pathogen, increasing research into M. abscessus in recent years has highlighted its continued evolution into a true pathogen. This is demonstrated through an extensive collection of virulence factors (VFs) possessed by this organism which facilitate survival within the host, particularly in the harsh environment of the CF lung. These include VFs resembling those of other Mycobacteria, and non-mycobacterial VFs, both of which make a notable contribution in shaping M. abscessus interaction with the host. Mycobacterium abscessus continued acquisition of VFs is cause for concern and highlights the need for novel vaccination strategies to combat this pathogen. An effective M. abscessus vaccine must be suitably designed for target populations (i.e., individuals with CF) and incorporate current knowledge on immune correlates of protection against M. abscessus infection. Vaccination strategies must also build upon lessons learned from ongoing efforts to develop novel vaccines for other pathogens, particularly Mycobacterium tuberculosis (M. tb); decades of research into M. tb has provided insight into unconventional and innovative vaccine approaches that may be applied to M. abscessus. Continued research into M. abscessus pathogenesis will be critical for the future development of safe and effective vaccines and therapeutics to reduce global incidence of this emerging pathogen.

Fitzgerald, CCJ, Bowen, C, Elbourne, M, Cawley, A & McLeod, MD 2022, 'Energy-Resolved Fragmentation Aiding the Structure Elucidation of Steroid Biomarkers', Journal of the American Society for Mass Spectrometry, vol. 33, no. 7, pp. 1276-1281.
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Fleck, R, Gill, R, Pettit, TJ, Torpy, FR & Irga, PJ 2022, 'Bio-solar green roofs increase solar energy output: The sunny side of integrating sustainable technologies', Building and Environment, vol. 226, pp. 109703-109703.
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In urban spaces, localised energy generation through rooftop solar has become increasingly popular, and green roofs are often used for a range of services such as thermal insulation. In recent years, the adoption of Bio-solar green roofs (BSGR) for both thermal insulation and increased solar energy outputs has increased. Here we present two buildings of the same dimensions and location, similar age and construction material, where one hosts a BSGR, and the other a conventional solar roof (CSR) in Sydney, Australia. Each solar array hosted a range of environmental sensors, including ambient temperature and global horizontal irradiance (GHI). The modelled BSGR average hourly energy output was 4.5% higher than the CSR (seasonal trends observed Spring; 4.14%, Summer; 4.16%, and Autumn; 5.21%) with BSGR producing 14.26 MWh more than the CSR, valued at $4526.22 AUD, and equal to 11.55 t e-CO2 greenhouse gas mitigation. Further potential for up to 1.55 t of CO2 could be mitigated by the plant material on the roof, provided the trimming of plant material during maintenance is conducted responsibly. In this instance, the implementation of a BSGR increased the system's solar output by 23.88 kWh per m2 of panel coverage, as well as reducing the e-CO2 emissions by 0.019 t per m2 over the CSR. When compared to the results of previously reported pilot studies and some simulations, it is evident that the implementation of a BSGR is favourable for maximising energy production and the mitigation of GHGs.

Fleck, R, Gill, RL, Saadeh, S, Pettit, T, Wooster, E, Torpy, F & Irga, P 2022, 'Urban green roofs to manage rooftop microclimates: A case study from Sydney, Australia', Building and Environment, vol. 209, pp. 108673-108673.
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Urbanisation has led to a growing need for sustainable development leading to climate resilient cities. As the urban heat burden increases in severity, technologies to improve the thermal comfort of cities are increasingly required. Green roofs are one such technology that can provide increased building thermal performance. In this study, we investigate two identical buildings, except, one was equipped with a green roof, and the other without. We present the longest-term assessment conducted on an Australian green roof with in-situ thermal monitoring coupled with surface temperature assessments. Field measurements were utilised to calculate the thermal buffer potential of the green roof compared to a near-identical conventional roof, over three seasons. Our findings indicated a reduction in rooftop surface temperatures up to 20 °C when ambient temperatures exceeded 40 °C, as well as improvements to heat flow of up to 55.54%. These results indicate that green roofs may contribute to the much-needed reduction in ambient city temperature to alleviate overheating and the costs associated with the urban heat island effect.

Fleck, R, Westerhausen, MT, Killingsworth, N, Ball, J, Torpy, FR & Irga, PJ 2022, 'The hydrological performance of a green roof in Sydney, Australia: A tale of two towers', Building and Environment, vol. 221, pp. 109274-109274.
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This study describes the sister buildings Daramu house and International house in Barangaroo, Sydney (Australia's largest metropolitan city), with and without a green roof, respectively. Trace metal samples were collected from both roofs and analysed using ICP-MS to determine the bioretention potential of the green roof to remediate soluble and particulate stormwater trace metal contamination. Retention of ambient trace metal contamination by the green roof substrate was deemed significant for soluble copper and particulate zinc, chromium and copper. In addition, hydrological models (DRAINS and SWMM) were applied to predict the performance of the green roof to identify its ability to manage stormwater runoff and frequency, as well as to analyse the green roof's performance in complex surface flooding situations where storage or backwater effects occur in overflow routes and surface flows. Our results demonstrate a reduction in peak stormwater flow by 18.29 L/s (∼50%) for storms as infrequent as 1 in 5 years, and peak flow reductions up to 90% storms of lower intensities. These results are significant as it demonstrates that a green roof could remediating trace metals contamination, thus reducing the impact on aquatic environments through stormwater runoff. It also highlights their potential to reduce stormwater flow, and utilise this additional water for evapotranspiration, leading to cooler ambient temperatures. Future works should aim to quantify the remediation effect of various planted species on in-situ green roofs, as well as determine the specific retention capabilities of various substrate compositions.

Flood, RL, Danzenbaker, M, Hansbro, PM, Rogers, C, Tanoi, H & Tanoi, S 2022, 'More New Zealand Storm Petrels Fregetta maoriana off Gau Island, Fiji, in May 2022', Bulletin of the British Ornithologists’ Club, vol. 142, no. 3, pp. 380-382.
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Focardi, A, Moore, LR, Raina, J-B, Seymour, JR, Paulsen, IT & Tetu, SG 2022, 'Plastic leachates impair picophytoplankton and dramatically reshape the marine microbiome', Microbiome, vol. 10, no. 1, p. 179.
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Abstract Background Each year, approximately 9.5 million metric tons of plastic waste enter the ocean with the potential to adversely impact all trophic levels. Until now, our understanding of the impact of plastic pollution on marine microorganisms has been largely restricted to the microbial assemblages that colonize plastic particles. However, plastic debris also leaches considerable amounts of chemical additives into the water, and this has the potential to impact key groups of planktonic marine microbes, not just those organisms attached to plastic surfaces. Results To investigate this, we explored the population and genetic level responses of a marine microbial community following exposure to leachate from a common plastic (polyvinyl chloride) or zinc, a specific plastic additive. Both the full mix of substances leached from polyvinyl chloride (PVC) and zinc alone had profound impacts on the taxonomic and functional diversity of our natural planktonic community. Microbial primary producers, both prokaryotic and eukaryotic, which comprise the base of the marine food web, were strongly impaired by exposure to plastic leachates, showing significant declines in photosynthetic efficiency, diversity, and abundance. Key heterotrophic taxa, such as SAR11, which are the most abundant planktonic organisms in the ocean, also exhibited significant declines in relative abundance when exposed to higher levels of PVC leachate. In contrast, many copiotrophic bacteria, including members of the Alteromonadales, dramatically increased in relative abundance under both exposure treatments. Moreover, functional gene and genome analyses, derived from metagenomes, revealed that PVC leachate exposure selects for fast-adapting, motile organisms, along with enrichmen...

Foley, PB, Hare, DJ & Double, KL 2022, 'A brief history of brain iron accumulation in Parkinson disease and related disorders', Journal of Neural Transmission, vol. 129, no. 5-6, pp. 505-520.
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AbstractIron has a long and storied history in Parkinson disease and related disorders. This essential micronutrient is critical for normal brain function, but abnormal brain iron accumulation has been associated with extrapyramidal disease for a century. Precisely why, how, and when iron is implicated in neuronal death remains the subject of investigation. In this article, we review the history of iron in movement disorders, from the first observations in the early twentieth century to recent efforts that view extrapyramidal iron as a novel therapeutic target and diagnostic indicator.

Foster, PS, Tay, HL & Oliver, BG 2022, 'Deficiency in the zinc transporter ZIP8 impairs epithelia renewal and enhances lung fibrosis', Journal of Clinical Investigation, vol. 132, no. 11, p. e160595.
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Although aging and lung injury are linked to the development of idiopathic pulmonary fibrosis (IPF), the underlying pathognomonic processes predisposing to fibrotic lesions remain largely unknown. A deficiency in the ability of type 2 alveolar epithelial cell (AEC2) progenitors to regenerate and repair the epithelia has been proposed as a critical factor. In this issue of the JCI, Liang et al. identify a deficiency in the zinc transporter SLC39A8 (ZIP8) in AEC2s and in the subsequent activation of the sirtuin SIRT1 that predisposes to decreased AEC2 renewal capacity and enhanced lung fibrosis in both IPF and aging lungs. Interestingly, the authors demonstrate the efficacy of modulating dietary zinc levels, suggesting the need for clinical trials to evaluate the therapeutic potential of dietary supplementation and the development of pharmacological modulation of the Zn/ZIP8/SIRT1 axis for treatment.

Fowler, AM, Ochwada-Doyle, FA, Dowling, NA, Folpp, H, Hughes, JM, Lowry, MB, Lyle, JM, Lynch, TP, Miles, NG & Chick, RC 2022, 'Integrating recreational fishing into harvest strategies: linking data with objectives', ICES Journal of Marine Science, vol. 79, no. 2, pp. 285-307.
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AbstractRecreational fishing (RF) is a popular pastime resulting in substantial fish mortality in many regions. Yet inclusion of RF in fishery harvest strategies is limited, because the sector's objectives are poorly understood, as are the data required to track their performance. To address this, we reviewed RF data sources available from a region of globally high participation (New South Wales [NSW], Australia) and evaluated their utility for RF-specific performance indicators within harvest strategies. We then linked these data sources to RF objectives they may be used to monitor. A total of 21 RF data sources were identified in NSW over the past two decades, spanning all major aquatic environments and 146 fished species. Numerous data sources were available to monitor ecological objectives, providing time-series and potential reference points for key indicators such as catch-per-unit-effort. Few data sources were available for social, economic, and institutional objectives, consistent with a global paucity of these data. We found that most social objectives of RF lie outside the scope of traditional harvest strategies, although some are linked to underlying ecological performance. Harvest strategy performance for RF will depend on the relative importance of social objectives and whether these can be achieved by controlling harvest.

Fowler, K, Peel, M, Saft, M, Peterson, TJ, Western, A, Band, L, Petheram, C, Dharmadi, S, Tan, KS, Zhang, L, Lane, P, Kiem, A, Marshall, L, Griebel, A, Medlyn, BE, Ryu, D, Bonotto, G, Wasko, C, Ukkola, A, Stephens, C, Frost, A, Gardiya Weligamage, H, Saco, P, Zheng, H, Chiew, F, Daly, E, Walker, G, Vervoort, RW, Hughes, J, Trotter, L, Neal, B, Cartwright, I & Nathan, R 2022, 'Explaining changes in rainfall–runoff relationships during and after Australia's Millennium Drought: a community perspective', Hydrology and Earth System Sciences, vol. 26, no. 23, pp. 6073-6120.
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Abstract. The Millennium Drought lasted more than a decade and is notable for causing persistent shifts in the relationship between rainfall and runoff in many southeastern Australian catchments. Research to date has successfully characterised where and when shifts occurred and explored relationships with potential drivers, but a convincing physical explanation for observed changes in catchment behaviour is still lacking. Originating from a large multi-disciplinary workshop, this paper presents and evaluates a range of hypothesised process explanations of flow response to the Millennium Drought. The hypotheses consider climatic forcing, vegetation, soil moisture dynamics, groundwater, and anthropogenic influence. The hypotheses are assessed against evidence both temporally (e.g. why was the Millennium Drought different to previous droughts?) and spatially (e.g. why did rainfall–runoff relationships shift in some catchments but not in others?). Thus, the strength of this work is a large-scale assessment of hydrologic changes and potential drivers. Of 24 hypotheses, 3 are considered plausible, 10 are considered inconsistent with evidence, and 11 are in a category in between, whereby they are plausible yet with reservations (e.g. applicable in some catchments but not others). The results point to the unprecedented length of the drought as the primary climatic driver, paired with interrelated groundwater processes, including declines in groundwater storage, altered recharge associated with vadose zone expansion, and reduced connection between subsurface and surface waterprocesses. Other causes include increased evaporative demand and harvestingof runoff by small private dams. Finally, we discuss the need for long-termfield monitoring, particularly targeting internal catchment processes andsubsurface dynamics. We recommend continued investment in the understanding of hydrological shifts, particularly given their relevance to water planning under ...

Francis, I, Shrestha, J, Paudel, KR, Hansbro, PM, Warkiani, ME & Saha, SC 2022, 'Recent advances in lung-on-a-chip models', Drug Discovery Today, vol. 27, no. 9, pp. 2593-2602.
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Fröch, JE, Li, C, Chen, Y, Toth, M, Kianinia, M, Kim, S & Aharonovich, I 2022, 'Purcell Enhancement of a Cavity‐Coupled Emitter in Hexagonal Boron Nitride', Small, vol. 18, no. 2, pp. 1-6.
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AbstractIntegration of solid‐state quantum emitters into nanophotonic circuits is a critical step towards fully on‐chip quantum photonic‐based technologies. Among potential materials platforms, quantum emitters in hexagonal boron nitride (hBN) have emerged as a viable candidate over the last years. While the fundamental physical properties have been intensively studied, only a few works have focused on the emitter integration into photonic resonators. Yet, for a potential quantum photonic material platform, the integration with nanophotonic cavities is an important cornerstone, as it enables the deliberate tuning of the spontaneous emission and the improved readout of distinct transitions for a quantum emitter. In this work, the resonant tuning of a monolithic cavity integrated hBN quantum emitter is demonstrated through gas condensation at cryogenic temperature. In resonance, an emission enhancement and lifetime reduction are observed, with an estimate for the Purcell factor of ≈15.

Froehlich, CYM, Heatwole, SJ, Klanten, OS & Wong, MYL 2022, 'Habitat health, size and saturation do not alter movement decisions in a social coral reef fish', Animal Behaviour, vol. 191, pp. 125-133.
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Fu, F, Tschitschko, B, Hutchins, DA, Larsson, ME, Baker, KG, McInnes, A, Kahlke, T, Verma, A, Murray, SA & Doblin, MA 2022, 'Temperature variability interacts with mean temperature to influence the predictability of microbial phenotypes', Global Change Biology, vol. 28, no. 19, pp. 5741-5754.
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AbstractDespite their relatively high thermal optima (Topt), tropical taxa may be particularly vulnerable to a rising baseline and increased temperature variation because they live in relatively stable temperatures closer to their Topt. We examined how microbial eukaryotes with differing thermal histories responded to temperature fluctuations of different amplitudes (0 control, ±2, ±4°C) around mean temperatures below or above their Topt. Cosmopolitan dinoflagellates were selected based on their distinct thermal traits and included two species of the same genus (tropical and temperate Coolia spp.), and two strains of the same species maintained at different temperatures for >500 generations (tropical Amphidinium massartii control temperature and high temperature, CT and HT, respectively). There was a universal decline in population growth rate under temperature fluctuations, but strains with narrower thermal niche breadth (temperate Coolia and HT) showed ~10% greater reduction in growth. At suboptimal mean temperatures, cells in the cool phase of the fluctuation stopped dividing, fixed less carbon (C) and had enlarged cell volumes that scaled positively with elemental C, N, and P and C:Chlorophyll‐a. However, at a supra‐optimal mean temperature, fixed C was directed away from cell division and novel trait combinations developed, leading to greater phenotypic diversity. At the molecular level, heat‐shock proteins, and chaperones, in addition to transcripts involving genome rearrangements, were upregulated in CT and HT during the warm phase of the supra‐optimal fluctuation (30 ± 4°C), a stress response indicating protection. In contrast, the tropical Coolia

Fu, L, Shi, B, Wen, S, Morsch, M, Wang, G, Zhou, Z, Mi, C, Sadraeian, M, Lin, G, Lu, Y, Jin, D & Chung, R 2022, 'Aspect Ratio of PEGylated Upconversion Nanocrystals Affects the Cellular Uptake In Vitro and In Vivo', Acta Biomaterialia, vol. 147, pp. 403-413.
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The central nervous system (CNS) is protected by the blood-brain barrier (BBB), which acts as a physical barrier to regulate and prevent the uptake of endogenous metabolites and xenobiotics. However, the BBB prevents most non-lipophilic drugs from reaching the CNS following systematic administration. Therefore, there is considerable interest in identifying drug carriers that can maintain the biostability of therapeutic molecules and target their transport across the BBB. In this regard, upconversion nanoparticles (UCNPs) have become popular as a nanoparticle-based solution to this problem, with the additional benefit that they display unique properties for in vivo visualization. The majority of studies to date have explored basic spherical UCNPs for drug delivery applications. However, the biophysical properties of UCNPs, cell uptake and BBB transport have not been thoroughly investigated. In this study, we described a one-pot seed-mediated approach to precisely control longitudinal growth to produce bright UCNPs with various aspect ratios. We have systematically evaluated the effects of the physical aspect ratios and PEGylation of UCNPs on cellular uptake in different cell lines and an in vivo zebrafish model. We found that PEGylated the original UCNPs can enhance their biostability and cell uptake capacity. We identify an optimal aspect ratio for UCNP uptake into several different types of cultured cells, finding that this is generally in the ratio of 2 (length/width). This data provides a crucial clue for further optimizing UCNPs as a drug carrier to deliver therapeutic agents into the CNS. STATEMENT OF SIGNIFICANCE: The central nervous system (CNS) is protected by the blood-brain barrier (BBB), which acts as a highly selective semipermeable barrier of endothelial cells to regulate and prevent the uptake of toxins and pathogens. However, the BBB prevents most non-lipophilic drugs from reaching the CNS following systematic administration. The proposed...

Gaiani, G, Cucchi, F, Toldrà, A, Andree, KB, Rey, M, Tsumuraya, T, O'Sullivan, CK, Diogène, J & Campàs, M 2022, 'Electrochemical biosensor for the dual detection of Gambierdiscus australes and Gambierdiscus excentricus in field samples. First report of G. excentricus in the Balearic Islands', Science of The Total Environment, vol. 806, no. Pt 4, pp. 150915-150915.
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Several genera of marine dinoflagellates are known to produce bioactive compounds that affect human health. Among them, Gambierdiscus and Fukuyoa stand out for their ability to produce several toxins, including the potent neurotoxic ciguatoxins (CTXs), which accumulate through the food web. Once fishes contaminated with CTXs are ingested by humans, it can result in an intoxication named ciguatera. Within the two genera, only some species are able to produce toxins, and G. australes and G. excentricus have been highlighted to be the most abundant and toxic. Although the genera Gambierdiscus and Fukuyoa are endemic to tropical areas, their presence in subtropical and temperate regions has been recently recorded. In this work, the combined use of species-specific PCR primers for G. australes and G. excentricus modified with short oligonucleotide tails allowed the development of a multiplex detection system for these two toxin-producing species. Simultaneous detection was achieved using capture probes specific for G. australes and G. excentricus immobilized on maleimide-coated magnetic beads (MBs), separately placed on the working electrodes of a dual electrode array. Additionally, a rapid DNA extraction technique based on a portable bead beater system and MBs was developed, significantly reducing the extraction time (from several hours to 30 min). The developed technique was able to detect as low as 10 cells of both Gambierdiscus species and allowed the first detection of G. excentricus in the Balearic Islands in 8 out of the 12 samples analyzed. Finally, field samples were screened for CTXs with an immunosensor, successfully reporting 13.35 ± 0.5 pg CTX1B equiv. cell-1 in one sample and traces of toxins in 3 out of the 9 samples analyzed. These developments provide rapid and cost-effective strategies for ciguatera risk assessment, with the aim of guaranteeing seafood safety.

Gaiani, G, Rey, M, Tudó, À, Rambla, M, Diogène, J, Campàs, M & Alcaraz, C 2022, 'New information about the toxicological profile of Prorocentrum panamense (Prorocentrales, Dinophyceae) and its global distribution', Phycological Research, vol. 70, no. 2, pp. 81-88.
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SUMMARYDinoflagellates of the genera Prorocentrum and Dinophysis are known producers of toxic compounds belonging to the okadaic acid (OA) group. The ingestion of shellfish contaminated with these toxins causes a human disease named diarrheic shellfish poisoning (DSP). In this study, the first record of Prorocentrum panamense, a potential toxin‐producer species, was reported in the Canary Islands together with its toxicological characterization. Prorocentrum panamense cells were collected during April 2017 from natural pools located in the Northeastern part of Gran Canaria. This new record represents an expansion of P. panamense distribution area, previously restricted to the Pacific Ocean, Indian Ocean, Arabian Gulf and the Caribbean, and its introduction mechanisms are discussed. Laboratory cultures of P. panamense were settled and toxin production was assessed in both cell pellets and culture media at four different growth phases (latency, exponential, early stationary and late stationary) implementing LC‐MS/MS and neuro‐2a cell‐based assay (CBA). LC‐MS/MS allowed the identification of OA in the fraction corresponding to the late stationary phase, and tests performed on neuro‐2a cells showed, for most of the fractions, OA‐like activity observable by both cell morphology changes and cell mortality. This information is fundamental for a better understanding of the genus Prorocentrum global distribution, its ecology, and risks associated to toxic producing species.

Gaio, D, Anantanawat, K, To, J, Liu, M, Monahan, L & Darling, AE 2022, 'Hackflex: low-cost, high-throughput, Illumina Nextera Flex library construction', Microbial Genomics, vol. 8, no. 1.
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We developed a low-cost method for the production of Illumina-compatible sequencing libraries that allows up to 14 times more libraries for high-throughput Illumina sequencing to be generated for the same cost. We call this new method Hackflex. The quality of library preparation was tested by constructing libraries from Escherichia coli MG1655 genomic DNA using either Hackflex, standard Nextera Flex (recently renamed as Illumina DNA Prep) or a variation of standard Nextera Flex in which the bead-linked transposase is diluted prior to use. In order to test the library quality for genomes with a higher and a lower G+C content, library construction methods were also tested on Pseudomonas aeruginosa PAO1 and Staphylococcus aureus ATCC 25923, respectively. We demonstrated that Hackflex can produce high-quality libraries and yields a highly uniform coverage, equivalent to the standard Nextera Flex kit. We show that strongly size-sel...

Gaio, D, DeMaere, MZ, Anantanawat, K, Eamens, GJ, Falconer, L, Chapman, TA, Djordjevic, S & Darling, AE 2022, 'Phylogenetic diversity analysis of shotgun metagenomic reads describes gut microbiome development and treatment effects in the post-weaned pig', PLOS ONE, vol. 17, no. 6, pp. e0270372-e0270372.
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Intensive farming practices can increase exposure of animals to infectious agents against which antibiotics are used. Orally administered antibiotics are well known to cause dysbiosis. To counteract dysbiotic effects, numerous studies in the past two decades sought to understand whether probiotics are a valid tool to help re-establish a healthy gut microbial community after antibiotic treatment. Although dysbiotic effects of antibiotics are well investigated, little is known about the effects of intramuscular antibiotic treatment on the gut microbiome and a few studies attempted to study treatment effects using phylogenetic diversity analysis techniques. In this study we sought to determine the effects of two probiotic- and one intramuscularly administered antibiotic treatment on the developing gut microbiome of post-weaning piglets between their 3rdand 9thweek of life. Shotgun metagenomic sequences from over 800 faecal time-series samples derived from 126 post-weaning piglets and 42 sows were analysed in a phylogenetic framework. Differences between individual hosts such as breed, litter, and age, were found to be important contributors to variation in the community composition. Host age was the dominant factor in shaping the gut microbiota of piglets after weaning. The post-weaning pig gut microbiome appeared to follow a highly structured developmental program with characteristic post-weaning changes that can distinguish hosts that were born as little as two days apart in the second month of life. Treatment effects of the antibiotic and probiotic treatments were found but were subtle and included a higher representation ofMollicutesassociated with intramuscular antibiotic treatment, and an increase ofLactobacillusassociated with probiotic treatment. The discovery of correlations between experimental factors and microbial community composition is mor...

Gale, A, Li, C, Chen, Y, Watanabe, K, Taniguchi, T, Aharonovich, I & Toth, M 2022, 'Site-Specific Fabrication of Blue Quantum Emitters in Hexagonal Boron Nitride', ACS Photonics, vol. 9, no. 6, pp. 2170-2177.
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Hexagonal boron nitride (hBN) is gaining considerable attention as a solid-state host of quantum emitters from the ultraviolet to the near-infrared spectral ranges. However, the atomic structures of most of the emitters are speculative or unknown, and emitter fabrication methods typically suffer from poor reproducibility, spatial accuracy, or spectral specificity. Here, we present a robust, electron beam technique for site-specific fabrication of blue quantum emitters with a zero-phonon line at 436 nm (2.8 eV). We show that the emission intensity is proportional to electron dose and that the efficacy of the fabrication method correlates with a defect emission at 305 nm (4.1 eV). We attribute blue emitter generation to the fragmentation of carbon clusters by electron impact and show that the robustness and universality of the emitter fabrication technique are enhanced by a pre-irradiation annealing treatment. Our results provide important insights into photophysical properties and structure of defects in hBN and a framework for site-specific fabrication of quantum emitters in hBN.

Ganbat, N, Altaee, A, Zhou, JL, Lockwood, T, Al-Juboori, RA, Hamdi, FM, Karbassiyazdi, E, Samal, AK, Hawari, A & Khabbaz, H 2022, 'Investigation of the effect of surfactant on the electrokinetic treatment of PFOA contaminated soil', Environmental Technology & Innovation, vol. 28, pp. 102938-102938.
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Gao, S, Huete, A, Kobayashi, H, Doody, TM, Liu, W, Wang, Y, Zhang, Y & Lu, X 2022, 'Simulation of solar-induced chlorophyll fluorescence in a heterogeneous forest using 3-D radiative transfer modelling and airborne LiDAR', ISPRS Journal of Photogrammetry and Remote Sensing, vol. 191, pp. 1-17.
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Solar-induced chlorophyll fluorescence (SIF) provides a means to estimate plant photosynthetic activities and to detect early plant stress. The accurate quantification of SIF emitted by various scene components (tree crowns and background) may significantly improve the interpretation of top-of-canopy SIF (SIFtoc) measurements made over heterogeneous canopies. To do so, a three-dimensional (3-D) canopy SIF model (FluorFLiES) was introduced by coupling the excitation-fluorescence matrices (EF-matrices) with a 3-D Monte Carlo canopy radiative transfer model (Forest Light Environmental Simulator, FLiES). A tool was developed to construct forest canopy scene components from LiDAR data and enable their simulated contributions in structurally complex forest scenes. FluorFLiES is able to quantify SIF measurements with good accuracy at both half-hourly (R2 = 0.72, RMSE = 0.26 mW m−2 sr−1 nm−1) and daily (R2 = 0.83, RMSE = 0.19 mW m−2 sr−1 nm−1) scales. This study showed that non-photosynthetic elements in tree crowns, the fractional vegetation cover (FVC), and the background (including understory vegetation and soils) had a strong influence on SIFtoc intensity. Non-photosynthetic woody material suppressed the propagation of photons within crowns, thereby decreasing SIFtoc by around 10%. The canopy background made a significant contribution to SIFtoc in the NIR region by scattering downward SIF photons upward, and the background contribution increased rapidly with decreasing FVC: SIFtoc increased two-fold from 0.15 to 0.3 mW m−2 sr−1 nm−1 when ground leaf area index increased from 0.5 to 1.5 m2/m2. The results showed that the fluorescence escape ratio (fesc), a key variable relating observed SIFtoc to photosynthesis CO2 rate, contained a contribution from the background with a magnitude of 42%, even for relatively dense forest canopies. Assuming fesc simulated by the FluorFLiES model as a reference value, this study demonstrated that the current reflectance-based...

García, P, Brito, B, Alcalde-Rico, M, Munita, JM, Martínez, JRW, Olivares-Pacheco, J, Quiroz, V & Wozniak, A 2022, 'Acquisition of resistance to ceftazidime-avibactam during infection treatment in Pseudomonas aeruginosa through D179Y mutation in one of two blaKPC-2 gene copies without losing carbapenem resistance', Frontiers in Cellular and Infection Microbiology, vol. 12, p. 981792.
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Ceftazidime/Avibactam (CAZ/AVI) is frequently used to treat KPC-producing Pseudomonas aeruginosa (KPC-PA) and Enterobacterales. CAZ/AVI resistance is driven by several mechanisms. In P. aeruginosa this mainly occurs through alteration of AmpC, porins, and/or efflux pump overexpression, whereas in Enterobacterales it frequently occurs through D179Y substitution in the active site of KPC enzyme. This aminoacid change abolishes AVI binding to the KPC active site, hence inhibition is impaired. However, this substitution also decreases KPC-mediated resistance to carbapenems (“see-saw” effect). The goal of this work was to characterize the in vivo acquisition of CAZ/AVI resistance through D179Y substitution in a KPC-PA isolated from a hospitalized patient after CAZ/AVI treatment. Two KPC-PA isolates were obtained. The first isolate, PA-1, was obtained before CAZ/AVI treatment and was susceptible to CAZ/AVI. The second isolate, PA-2, was obtained after CAZ/AVI treatment and exhibited high-level CAZ/AVI resistance. Characterization of isolates PA-1 and PA-2 was performed through short and long-read whole genome sequencing analysis. The hybrid assembly showed that PA-1 and PA-2A had a single plasmid of 54,030 bp, named pPA-1 and pPA-2 respectively. Each plasmid harbored two copies of the blaKPC-containing Tn4401b transposon. However, while pPA-1 carried two copies of blaKPC-2, pPA-2 had one copy of blaKPC-2 and one copy of blaKPC-33, the allele with the D179Y substitution. Interestingly, isolate PA-2 did not exhibit the “see-saw” effect. The blaKPC-33 allele w...

Gardner, SG, Nitschke, MR, O’Brien, J, Motti, CA, Seymour, JR, Ralph, PJ, Petrou, K & Raina, J-B 2022, 'Increased DMSP availability during thermal stress influences DMSP-degrading bacteria in coral mucus', Frontiers in Marine Science, vol. 9.
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Reef-building corals are among the largest producers of dimethylsulfoniopropionate (DMSP), an essential compound in marine biogeochemical cycles. DMSP can be catabolised in coral mucus by a wide diversity of coral-associated bacteria, where it can either be demethylated, leading to the incorporation of sulfur and carbon into bacterial biomass – or cleaved by lyases, releasing the climatically-active gas dimethyl sulfide (DMS). It has been demonstrated that thermal stress increases DMSP concentrations in many coral species, however the effect of increased DMSP availability on coral-associated bacteria has not been explored. Here we performed thermal stress experiments to examine how changes in DMSP availability impact bacterial degradation pathways in the mucus of Acropora millepora. DMSP concentrations increased with temperature, reaching a maximum of 177.3 μM after 10 days of heat stress, which represents the highest concentration of DMSP recorded in any environment to date. Bacterial communities in coral mucus were significantly different from the surrounding seawater, yet they did not vary significantly between temperature or time. However, during thermal stress, when DMSP concentrations increased, a significant increase in the abundance of both the demethylation gene dmdA and the cleavage gene dddP were recorded. Importantly, our results show that for the highest DMSP concentrations recorded (above 30 μM), the cleavage pathway became more abundant than the demethylation pathway. This suggests that under high DMSP concentrations characteristic of heat stress, a larger fraction of the DMSP pool in the coral mucus is likely catabolised through the DMS-producing cleavage pathway.

Garner, N, Ross, PM, Falkenberg, LJ, Seymour, JR, Siboni, N & Scanes, E 2022, 'Can seagrass modify the effects of ocean acidification on oysters?', Marine Pollution Bulletin, vol. 177, pp. 113438-113438.
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Solutions are being sought to ameliorate the impacts of anthropogenic climate change. Seagrass may be a solution to provide refugia from climate change for marine organisms. This study aimed to determine if the seagrass Zostera muelleri sub spp. capricorni benefits the Sydney rock oyster Saccostrea glomerata, and if these benefits can modify any anticipated negative impacts of ocean acidification. Future and ambient ocean acidification conditions were simulated in 52 L mesocosms at control (381 μatm) and elevated (848 μatm) CO2 with and without Z. muelleri. Oyster growth, physiology and microbiomes of oysters and seagrass were measured. Seagrass was beneficial to oyster growth at ambient pCO2, but did not positively modify the impacts of ocean acidification on oysters at elevated pCO2. Oyster microbiomes were altered by the presence of seagrass but not by elevated pCO2. Our results indicate seagrasses may not be a panacea for the impacts of climate change.

Gill, RL, Collins, S, Argyle, PA, Larsson, ME, Fleck, R & Doblin, MA 2022, 'Predictability of thermal fluctuations influences functional traits of a cosmopolitan marine diatom', Proceedings of the Royal Society B: Biological Sciences, vol. 289, no. 1973, p. 20212581.
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Evolutionary theory predicts that organismal plasticity should evolve in environments that fluctuate regularly. However, in environments that fluctuate less predictably, plasticity may be constrained because environmental cues become less reliable for expressing the optimum phenotype. Here, we examine how the predictability of +5°C temperature fluctuations impacts the phenotype of the marine diatom Thalassiosira pseudonana . Thermal regimes were informed by temperatures experienced by microbes in an ocean simulation and featured regular or irregular temporal sequences of fluctuations that induced mild physiological stress. Physiological traits (growth, cell size, complexity and pigmentation) were quantified at the individual cell level using flow cytometry. Changes in cellular complexity emerged as the first impact of predictability after only 8–11 days, followed by deleterious impacts on growth on days 13–16. Specifically, cells with a history of irregular fluctuation exposure exhibited a 50% reduction in growth compared with the stable reference environment, while growth was 3–18 times higher when fluctuations were regular. We observed no evidence of heat hardening (increasingly positive growth) with recurrent fluctuations. This study demonstrates that unpredictable temperature fluctuations impact this cosmopolitan diatom under ecologically relevant time frames, suggesting shifts in environmental stochasticity under a changing climate could have widespread consequences among ocean primary producers.

Gnoatto, A, Grasselli, M & Platen, E 2022, 'Calibration to FX triangles of the 4/2 model under the benchmark approach', Decisions in Economics and Finance, vol. 45, no. 1, pp. 1-34.
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AbstractWe calibrate a novel multifactor stochastic volatility model that includes as special cases the Heston-based model of De Col et al. (J Bank Finance 37(10):3799–3818, 2013) and the 3/2-based model of Baldeaux et al. (J Bank Finance 53:34–48, 2015). Using a dataset on vanilla option quotes in a triangle of currencies, we find that the risk neutral approach typically fails for the calibrated model, in line with the results of Baldeaux et al. (2015).

Goddard, BK, Becker, A, Harasti, D, Smith, JA, Subramaniam, RC & Suthers, IM 2022, 'The trophic basis of fish assemblages in temperate estuarine and coastal ecosystems', Marine Biology, vol. 169, no. 2.
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Godecke, E, Brogan, E, Ciccone, N, Rose, ML, Armstrong, E, Whitworth, A, Ellery, F, Holland, A, Middleton, S, Rai, T, Hankey, GJ, Cadilhac, D & Bernhardt, J 2022, 'Treatment fidelity monitoring, reporting and findings in a complex aphasia intervention trial: a substudy of the Very Early Rehabilitation in SpEech (VERSE) trial', Trials, vol. 23, no. 1, p. 501.
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Abstract Background Treatment fidelity is inconsistently reported in aphasia research, contributing to uncertainty about the effectiveness of types of aphasia therapy following stroke. We outline the processes and outcomes of treatment fidelity monitoring in a pre-specified secondary analysis of the VERSE trial. Methods VERSE was a 3-arm, single-blinded RCT with a 12-week primary endpoint comparing Usual Care (UC) to two higher intensity treatments: Usual Care-Plus (UC-Plus) and VERSE, a prescribed intervention. Primary outcome results were previously reported. This secondary analysis focused on treatment fidelity. Video-recorded treatment sessions in the higher intensity study arms were evaluated for treatment adherence and treatment differentiation. Treatment components were evaluated using a pre-determined fidelity checklist. Primary outcome: prescribed amount of therapy time (minutes); secondary outcomes: (i) adherence to therapy protocol (%) and (ii) treatment differentiation between control and high intensity groups. Results Two hundred forty-six participants were randomised to Usual Care (n=81), Usual Care-Plus (n=82), and VERSE (n=83). One hundred thirty-five (82%) participants in higher intensity intervention arms received the minimum prescribed therapy minutes. From 10,805 (UC 7787; UC-Plus 1450; VERSE 1568) service events, 431 treatment protocol deviations were noted in 114 participants. Four hundred thirty-seven videos were evaluated. The VERSE therapists achieved over 84% adherence to key protocol elements. Higher stroke and aphasia severity, olde...

Gonzalez de Vega, R, Lockwood, TE, Xu, X, Gonzalez de Vega, C, Scholz, J, Horstmann, M, Doble, PA & Clases, D 2022, 'Analysis of Ti- and Pb-based particles in the aqueous environment of Melbourne (Australia) via single particle ICP-MS', Analytical and Bioanalytical Chemistry, vol. 414, no. 18, pp. 5671-5681.
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AbstractThe analysis of natural and anthropogenic nanomaterials (NMs) in the environment is challenging and requires methods capable to identify and characterise structures on the nanoscale regarding particle number concentrations (PNCs), elemental composition, size, and mass distributions. In this study, we employed single particle inductively coupled plasma-mass spectrometry (SP ICP-MS) to investigate the occurrence of NMs in the Melbourne area (Australia) across 63 locations. Poisson statistics were used to discriminate between signals from nanoparticulate matter and ionic background. TiO2-based NMs were frequently detected and corresponding NM signals were calibated with an automated data processing platform. Additionally, a method utilising a larger mass bandpass was developed to screen for particulate high-mass elements. This procedure identified Pb-based NMs in various samples. The effects of different environmental matrices consisting of fresh, brackish, or seawater were mitigated with an aerosol dilution method reducing the introduction of salt into the plasma and avoiding signal drift. Signals from TiO2- and Pb-based NMs were counted, integrated, and subsequently calibrated to determine PNCs as well as mass and size distributions. PNCs, mean sizes, particulate masses, and ionic background levels were compared across different locations and environments. Graphical abstract

González-Pech, RA, Hughes, DJ, Strudwick, P, Lewis, BM, Booth, DJ, Figueira, WF, Sommer, B, Suggett, DJ & Matthews, J 2022, 'Physiological factors facilitating the persistence of Pocillopora aliciae and Plesiastrea versipora in temperate reefs of south-eastern Australia under ocean warming', Coral Reefs, vol. 41, no. 4, pp. 1239-1253.
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AbstractHigh-latitude reefs are suboptimal coral habitats, but such habitats are increasingly considered to be potential refugia from climate change for range-shifting coral reef species. Notably, tropical reef fish have been observed along the south-east coast of Australia, but their establishment on temperate rocky reefs is currently limited by winter minimum temperatures and other resource needs, such as structurally complex habitats typical of tropical reefs. Recent expansion of the branching subtropical coral Pocillopora aliciae in rocky reefs near Sydney (34° S) could diversify the architectural structure of temperate marine environments, thereby providing potential shelter for tropical reef taxa in warming seas. Here, we investigated whether future environmental conditions (i.e. temperature increase) can influence the dominance of the subtropical branching coral P. aliciae over the resident encrusting coral Plesiastrea versipora in coastal Sydney by characterising physiological (e.g. metabolic stability) and behavioural (e.g. interspecific competitive hierarchy) traits that contribute to their competitive fitness. Our results suggest that a metabolic response, mediated by sterol and lipid metabolic pathways and provision of antioxidants, allows P. aliciae to reduce cellular stress and withstand exposure to short-term increased temperature. Conversely, P. versipora was more susceptible to heat exposure with no metabolic mediation observed. While P. versipora displayed greater aggressive behaviour when in direct contact with P. aliciae under all temperature conditions, the superior physiological and metabolic flexibility under increased temperatures o...

Goodman, EK, Mitchell, CS, Teo, JD, Gladding, JM, Abbott, KN, Rafiei, N, Zhang, L, Herzog, H & Begg, DP 2022, 'The effect of insulin receptor deletion in neuropeptide Y neurons on hippocampal dependent cognitive function in aging mice', Journal of Integrative Neuroscience, vol. 21, no. 1, pp. 006-006.
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Goodswen, SJ, Kennedy, PJ & Ellis, JT 2022, 'Compilation of parasitic immunogenic proteins from 30 years of published research using machine learning and natural language processing', Scientific Reports, vol. 12, no. 1.
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AbstractThe World Health Organisation reported in 2020 that six of the top 10 sources of death in low-income countries are parasites. Parasites are microorganisms in a relationship with a larger organism, the host. They acquire all benefits at the host’s expense. A disease develops if the parasitic infection disrupts normal functioning of the host. This disruption can range from mild to severe, including death. Humans and livestock continue to be challenged by established and emerging infectious disease threats. Vaccination is the most efficient tool for preventing current and future threats. Immunogenic proteins sourced from the disease-causing parasite are worthwhile vaccine components (subunits) due to reliable safety and manufacturing capacity. Publications with ‘subunit vaccine’ in their title have accumulated to thousands over the last three decades. However, there are possibly thousands more reporting immunogenicity results without mentioning ‘subunit’ and/or ‘vaccine’. The exact number is unclear given the non-standardised keywords in publications. The study aim is to identify parasite proteins that induce a protective response in an animal model as reported in the scientific literature within the last 30 years using machine learning and natural language processing. Source code to fulfil this aim and the vaccine candidate list obtained is made available.

Gow, I, Smith, NC, Stark, D & Ellis, J 2022, 'Laboratory diagnostics for human Leishmania infections: a polymerase chain reaction-focussed review of detection and identification methods', Parasites & Vectors, vol. 15, no. 1, p. 412.
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AbstractLeishmania infections span a range of clinical syndromes and impact humans from many geographic foci, but primarily the world’s poorest regions. Transmitted by the bite of a female sand fly, Leishmania infections are increasing with human movement (due to international travel and war) as well as with shifts in vector habitat (due to climate change). Accurate diagnosis of the 20 or so species of Leishmania that infect humans can lead to the successful treatment of infections and, importantly, their prevention through modelling and intervention programs. A multitude of laboratory techniques for the detection of Leishmania have been developed over the past few decades, and although many have drawbacks, several of them show promise, particularly molecular methods like polymerase chain reaction. This review provides an overview of the methods available to diagnostic laboratories, from traditional techniques to the now-preferred molecular techniques, with an emphasis on polymerase chain reaction-based detection and typing methods. Graphical abstract

Grant, SJ, Spiegel, G, Brand, A, Kwon, KK, Heller, G, Choi, V, Wong, EK, Randle, L & Lacey, J 2022, 'Acupuncture and Reflexology for Patients Undergoing Chemotherapy: A Cohort Study', Integrative Cancer Therapies, vol. 21, pp. 153473542211230-153473542211230.
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Purpose: Around three quarters of individuals undergoing chemotherapy self-report multiple symptoms. There is clinical trial evidence of effectiveness for acupuncture for commonly experienced symptoms, and emerging evidence for reflexology, but little is known about the effects of these therapies on multiple symptoms when implemented in a real world setting during active chemotherapy treatment. Methods: This was a cohort study of participants receiving reflexology and/or acupuncture while attending chemotherapy. Participants received a 20 minute reflexology treatment or a 20 minute acupuncture treatment or a combination of both. Patient reported outcome measures were administered before and after the treatment using the Edmonton Symptom Assessment Scale (ESAS). Results: During the study period, 330 unique patients received a total of 809 acupuncture and/or reflexology treatments. Participants had, on average, 5.3 symptoms each which they reported as moderate to severe (≥4/10) using the ESAS at baseline. Following treatment, participants reported 3.2 symptoms as moderate to severe. The symptom change for all participant encounters receiving any therapy was statistically significant for all symptoms, and clinically significant (a reduction of more than 1) for all symptoms except financial distress, appetite, and memory. Clinically significant levels of global distress (<3) were reduced in 72% of all participants receiving either therapy. No adverse events were recorded. Conclusions: The results indicate that acupuncture and reflexology administered alongside chemotherapy may reduce patient reported symptom burden and patient global symptom related distress. Future research would include an active control group, and consider ...

Griebel, A, Metzen, D, Pendall, E, Nolan, RH, Clarke, H, Renchon, AA & Boer, MM 2022, 'Recovery from Severe Mistletoe Infection After Heat- and Drought-Induced Mistletoe Death', Ecosystems, vol. 25, no. 1, pp. 1-16.
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Mistletoes are emerging as important co-contributors to tree mortality across terrestrial ecosystems, particularly when infected trees are stressed by water limitations during drought. While the mechanistic effects of mistletoe infection on host physiology are reasonably well understood, quantifying the effects of mistletoe infection on stand productivity, canopy turnover and ecosystem structure remains challenging. Moreover, the potential devastating effect of mistletoe infection on host survival has distracted from the challenges that mistletoe populations are facing when increasing drought and heat stress threaten their survival in healthy populations. We coupled intensive observations of mistletoe population dynamics with measurements of host tree stem growth, canopy turnover and stand structure in a severely infected temperate eucalypt woodland to monitor how mistletoe infection alters aboveground biomass distribution and to assess ecosystem recovery from severe mistletoe infection during and after a three-year drought. We show that severe mistletoe infection reduces live standing biomass and canopy volume, with mistletoe leaves contributing up to 43% to total stand litter fall. We further identified that a mistletoe:host leaf area ratio above 60% significantly reduced basal area growth, which provides a threshold for productivity losses due to mistletoe infection in eucalypts. Yet, concurrent increases in basal area and the thickening of canopy volume indicate that host trees recover rapidly after the three-year drought combined with record summer heat nearly extinguished the mistletoe population. How common, or how widespread such dynamic changes in mistletoe population dynamics are within Australian or global ecosystems remains subject to further exploration.

Griebel, A, Peters, JMR, Metzen, D, Maier, C, Barton, CVM, Speckman, HN, Boer, MM, Nolan, RH, Choat, B & Pendall, E 2022, 'Tapping into the physiological responses to mistletoe infection during heat and drought stress', Tree Physiology, vol. 42, no. 3, pp. 523-536.
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Abstract Mistletoes are important co-contributors to tree mortality globally, particularly during droughts. In Australia, mistletoe distributions are expanding in temperate woodlands, while their hosts have experienced unprecedented heat and drought stress in recent years. We investigated whether the excessive water use of mistletoes increased the probability of xylem emboli in a mature woodland during the recent record drought that was compounded by multiple heatwaves. We continuously recorded transpiration ($T_{SLA}$) of infected and uninfected branches from two eucalypt species over two summers, monitored stem and leaf water potentials ($\Psi $) and used hydraulic vulnerability curves to estimate percent loss in conductivity (PLC) for each species. Variations in weather (vapor pressure deficit, photosynthetically active radiation, soil water content), host species and % mistletoe foliage explained 78% of hourly $T_{SLA}$. While mistletoe acted as an uncontrollable sink for water in the host even during typical summer days, daily $T_{SLA}$ increased up to 4-fold in infected branches on hot days, highlighting the previously overlooked importance of temperature stress in amplifying water loss in mistletoes. The increased water use of mistletoes resulted in significantly decreased host $\Psi _{\rm{leaf}}$ and $\Psi _{\rm{trunk}}$. It further translated to an estimated increase of up to 11% PLC for infected hosts, confirming greater hydraulic dysfunction of infected trees that place them at higher risk of hydraulic failure. However, uninfected branches of Eucalyptus fibrosa F.Muell. had much tighter controls on water loss than uninfected branches of Eucalyptus moluccana Roxb., which shifted the risk of hydraulic failure towards an increased risk of carbon starvation for E. fibrosa. The contrasting mechanistic responses to heat and drought stress between both co-occurring species demonstrates the complexity o...

Grima, AJ, Clases, D, Gonzalez de Vega, R, Nitschke, MR, Goyen, S, Suggett, DJ & Camp, EF 2022, 'Species-specific elementomes for scleractinian coral hosts and their associated Symbiodiniaceae', Coral Reefs, vol. 41, no. 4, pp. 1115-1130.
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AbstractIncreasing anthropogenic pressure on coral reefs is creating an urgent need to understand how and where corals can proliferate both now and under future scenarios. Resolving environmental limits of corals has progressed through the accurate identification of corals’ ‘realised ecological niche’. Here we expand the ecological niche concept to account for corals’ ‘biogeochemical niche’ (BN), defined as the chemical space in which a coral is adapted to survive, and which is identifiable by a unique quantity and proportion of elements (termed “elementome”). BN theory has been commonly applied to other taxa, successfully predicting species distributions and stress responses by their elementomes. Here, we apply the BN theory to corals for the first time, by using dry combustion and inductively coupled plasma–mass spectrometry (ICP-MS) to determine five key macronutrients and thirteen trace elements of four diverse scleractinian coral species from the Great Barrier Reef (GBR): Acropora hyacinthus; Echinopora lamellosa; Pocillopora cf. meandrina; and Pocillopora cf. verrucosa. The elementomes were investigated in both host and Symbiodiniaceae, and the latter had the highest elemental concentrations (except molybdenum). Each coral species associated with distinct members of the genus Cladocopium (determined by ITS2 analysis) with photo-physiological data suggesting specialisation of Cladocopium functional biology. Distinct endosymbiont community structure and functioning between corals with different elementomes confirms that BN theory holds as metabolic compatibility alters across host–symbiont associations. Additional work is needed to understand the plasticity of coral elementomes, and in turn BN, over space and time to aid predictions on coral distribution and survival with environmenta...

Gu, H, Lam, HC & Zinder, Y 2022, 'A hybrid genetic algorithm for scheduling jobs sharing multiple resources under uncertainty', EURO Journal on Computational Optimization, vol. 10, pp. 100050-100050.
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Gu, H, Lam, HC & Zinder, Y 2022, 'Planning rolling stock maintenance: Optimization of train arrival dates at a maintenance center', Journal of Industrial & Management Optimization, vol. 18, no. 2, pp. 747-747.
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<p style='text-indent:20px;'>A railway network is an indispensable part of the public transportation system in many major cities around the world. In order to provide a safe and reliable service, a fleet of passenger trains must undergo regular maintenance. These maintenance operations are lengthy procedures, which are planned for one year or a longer period. The planning specifies the dates of trains' arrival at the maintenance center and should take into account the uncertain duration of maintenance operations, the periods of validity of the previous maintenance, the desired number of trains in service, and the capacity of the maintenance center. The paper presents a nonlinear programming formulation of the considered problem and several optimization procedures which were compared by computational experiments using real world data. The results of these experiments indicate that the presented approach is capable to be used in real world planning process.</p>

Gu, H, Zhang, Y & Zinder, Y 2022, 'An efficient optimisation procedure for the Workforce Scheduling and Routing Problem: Lagrangian relaxation and iterated local search', Computers & Operations Research, vol. 144, pp. 105829-105829.
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The paper is concerned with the Workforce Scheduling and Routing Problem where certain service providers complete tasks at different locations. The presented optimisation procedure is an amalgamation of the iterated local search and Lagrangian relaxation. This optimisation procedure has been tested on benchmark problems from the literature, and showed superior performance in comparison with a previously published implementation of the iterated local search.

Guan, M, Wang, M, Zhanghao, K, Zhang, X, Li, M, Liu, W, Niu, J, Yang, X, Chen, L, Jing, Z, Zhang, MQ, Jin, D, Xi, P & Gao, J 2022, 'Polarization modulation with optical lock-in detection reveals universal fluorescence anisotropy of subcellular structures in live cells', Light: Science & Applications, vol. 11, no. 1, p. 4.
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AbstractThe orientation of fluorophores can reveal crucial information about the structure and dynamics of their associated subcellular organelles. Despite significant progress in super-resolution, fluorescence polarization microscopy remains limited to unique samples with relatively strong polarization modulation and not applicable to the weak polarization signals in samples due to the excessive background noise. Here we apply optical lock-in detection to amplify the weak polarization modulation with super-resolution. This novel technique, termed optical lock-in detection super-resolution dipole orientation mapping (OLID-SDOM), could achieve a maximum of 100 frames per second and rapid extraction of 2D orientation, and distinguish distance up to 50 nm, making it suitable for monitoring structural dynamics concerning orientation changes in vivo. OLID-SDOM was employed to explore the universal anisotropy of a large variety of GFP-tagged subcellular organelles, including mitochondria, lysosome, Golgi, endosome, etc. We found that OUF (Orientation Uniformity Factor) of OLID-SDOM can be specific for different subcellular organelles, indicating that the anisotropy was related to the function of the organelles, and OUF can potentially be an indicator to distinguish normal and abnormal cells (even cancer cells). Furthermore, dual-color super-resolution OLID-SDOM imaging of lysosomes and actins demonstrates its potential in studying dynamic molecular interactions. The subtle anisotropy changes of expanding and shrinking dendritic spines in live neurons were observed with real-time OLID-SDOM. Revealing previously unobservable fluorescence anisotropy in various samples and indicating their underlying dynamic molecular structural changes, OLID-SDOM expands the toolkit for live cell research.

Guo, X, Gao, H, Wang, S, Yang, G, Zhang, X, Zhang, J, Liu, H & Wang, G 2022, 'MXene-Based Aerogel Anchored with Antimony Single Atoms and Quantum Dots for High-Performance Potassium-Ion Batteries', Nano Letters, vol. 22, no. 3, pp. 1225-1232.
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Rationally electronic structure engineering of nanocomposite electrodes shows great promise for enhancing the electrochemical performance of rechargeable batteries. Herein, we report antimony single atoms and quantum dots (∼5 nm) codecorated Ti3C2Tx MXene-based aerogels (Sb SQ@MA) for high-performance potassium-ion batteries (PIBs). We found that the atomically dispersed Sb could modify the electronic structure of the Sb/Ti3C2Tx composite, improve the charge transfer kinetics, and enhance the potassium storage capability at the heterointerfaces. Additionally, the MXene-based aerogel with rich surface functional groups and defects provides abundant anchoring sites and endows the composite reinforced structural stability and highly efficient electron transfer. The high loading of Sb (∼60.3 wt %) with short ionic transport pathways is desired potassium reservoirs. These features synergistically enhance the rate and cycling performance of the Sb SQ@MA electrodes in PIBs. This work has demonstrated an enlightening technique to tailor the interface activity of heterostructured electrodes for electrochemical applications.

Guo, Z, Wang, T, Liu, H, Qiu, S, Zhang, X, Xu, Y, Langford, SJ & Sun, C 2022, 'Theoretical investigation of novel p-block metal-based electrocatalysts for nitrogen reduction reaction', Applied Surface Science, vol. 572, pp. 151441-151441.
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Gupta, G, Oliver, BG, Dua, K, Singh, A & MacLoughlin, R 2022, 'Preface', Microbiome in Inflammatory Lung Diseases, pp. v-vi.

Haifer, C, Paramsothy, S, Kaakoush, NO, Saikal, A, Ghaly, S, Yang, T, Luu, LDW, Borody, TJ & Leong, RW 2022, 'Lyophilised oral faecal microbiota transplantation for ulcerative colitis (LOTUS): a randomised, double-blind, placebo-controlled trial', The Lancet Gastroenterology & Hepatology, vol. 7, no. 2, pp. 141-151.
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BACKGROUND: Faecal microbiota transplantation (FMT) delivered via colonoscopic infusion or enemas have been shown to induce remission in a proportion of patients with active ulcerative colitis. Whether orally administered FMT is effective in ulcerative colitis is unknown. We aimed to assess the efficacy of oral lyophilised FMT for the treatment of active ulcerative colitis. METHODS: A double-blind, randomised, placebo-controlled trial was conducted at two centres in Australia. Eligible patients were aged 18-75 years with active ulcerative colitis (defined as clinical and endoscopic active ulcerative colitis, with a total Mayo score of 4-10, and a Mayo endoscopic subscore ≥1). After 2 weeks of amoxicillin, metronidazole, and doxycycline, patients were randomly assigned in a 1:1 ratio to receive either oral lyophilised FMT or placebo capsules for 8 weeks, using a prespecified computer-generated randomisation list with a permuted block size of 8. The primary outcome was corticosteroid-free clinical remission with endoscopic remission or response (total Mayo score ≤2, all subscores ≤1, and ≥1 point reduction in endoscopic subscore) at week 8. At week 8, FMT responders were randomly assigned (in a 1:1 ratio, permuted block size of 8) to either continue or withdraw FMT for a further 48 weeks. Analyses were done by modified intention-to-treat, including all patients who received at least one study dose. This trial is registered with Australian New Zealand Trial Registry, number ACTRN 12619000611123; this is the final report of the trial. FINDINGS: Between May 20, 2019, and March 24, 2020, 35 patients were randomly assigned: 15 to receive FMT and 20 to receive placebo. Recruitment was terminated early due to the COVID-19 pandemic. At week 8, eight (53%) of 15 patients in the FMT group were in corticosteroid-free clinical remission with endoscopic remission or response, as were three (15%) of 20 patients in the placebo group (difference 38·3%, 95% CI 8·6-68·0; p=0·027; od...

Hallstrøm, S, Raina, J-B, Ostrowski, M, Parks, DH, Tyson, GW, Hugenholtz, P, Stocker, R, Seymour, JR & Riemann, L 2022, 'Chemotaxis may assist marine heterotrophic bacterial diazotrophs to find microzones suitable for N2 fixation in the pelagic ocean', The ISME Journal, vol. 16, no. 11, pp. 2525-2534.
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Abstract Heterotrophic bacterial diazotrophs (HBDs) are ubiquitous in the pelagic ocean, where they have been predicted to carry out the anaerobic process of nitrogen fixation within low-oxygen microenvironments associated with marine pelagic particles. However, the mechanisms enabling particle colonization by HBDs are unknown. We hypothesized that HBDs use chemotaxis to locate and colonize suitable microenvironments, and showed that a cultivated marine HBD is chemotactic toward amino acids and phytoplankton-derived DOM. Using an in situ chemotaxis assay, we also discovered that diverse HBDs at a coastal site are motile and chemotactic toward DOM from various phytoplankton taxa and, indeed, that the proportion of diazotrophs was up to seven times higher among the motile fraction of the bacterial community compared to the bulk seawater community. Finally, three of four HBD isolates and 16 of 17 HBD metagenome assembled genomes, recovered from major ocean basins and locations along the Australian coast, each encoded &gt;85% of proteins affiliated with the bacterial chemotaxis pathway. These results document the widespread capacity for chemotaxis in diverse and globally relevant marine HBDs. We suggest that HBDs could use chemotaxis to seek out and colonize low-oxygen microenvironments suitable for nitrogen fixation, such as those formed on marine particles. Chemotaxis in HBDs could therefore affect marine nitrogen and carbon biogeochemistry by facilitating nitrogen fixation within otherwise oxic waters, while also altering particle degradation and the efficiency of the biological pump.

Hamidian, M 2022, 'Tn6553, a Tn7-family transposon encoding putative iron uptake functions found in Acinetobacter', Archives of Microbiology, vol. 204, no. 11, p. 678.
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AbstractAcinetobacter baumannii is an opportunistic pathogen that has become difficult to eradicate mainly because of its high level of antibiotic resistance. Other features that contribute to this organism's success are the ability to compete for nutrients and iron. Recently, several novel Tn7-family transposons that encode synthesis and transport of siderophore and iron uptake systems were characterised. Here, another Tn7-type transposon (named Tn6553) is described. Tn6553 contains a set of iron utilisation genes with a transposition module related to Tn7. Tn7-family transposons that carry iron uptake systems facilitate the spread of these functions in Acinetobacter strains. Given that Tn7 is known to transpose efficiently into its preferred target site, finding siderophore functions on Tn7 family transposons is important in the context of dissemination of virulence genes amongst Acinetobacter strains.

Hamidian, M, Maharjan, RP, Farrugia, DN, Delgado, NN, Dinh, H, Short, FL, Kostoulias, X, Peleg, AY, Paulsen, IT & Cain, AK 2022, 'Genomic and phenotypic analyses of diverse non-clinical Acinetobacter baumannii strains reveals strain-specific virulence and resistance capacity', Microbial Genomics, vol. 8, no. 2.
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Acinetobacter baumannii is a critically important pathogen known for its widespread antibiotic resistance and ability to persist in hospital-associated environments. Whilst the majority of A. baumannii infections are hospital-acquired, infections from outside the hospital have been reported with high mortality. Despite this, little is known about the natural environmental reservoir(s) of A. baumannii and the virulence potential underlying non-clinical strains. Here, we report the complete genome sequences of six diverse strains isolated from environments such as river, soil, and industrial sites around the world. Phylogenetic analyses showed that four of these strains were unrelated to representative nosocomial strains and do not share a monophyletic origin, whereas two had sequence types belonging to the global clone lineages GC1 and GC2. Further, the majority of these strains harboured genes linked to virulence and stress protection ...

Hanh Duong, NM, Saerens, G, Timpu, F, Buscaglia, MT, Buscaglia, V, Morandi, A, Müller, JS, Maeder, A, Kaufmann, F, Solntsev, AS & Grange, R 2022, 'Spontaneous parametric down-conversion in bottom-up grown lithium niobate microcubes', Optical Materials Express, vol. 12, no. 9, pp. 3696-3696.
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Nonclassical light sources are highly sought-after as they are an integral part of quantum communication and quantum computation devices. Typical sources use bulk nonlinear crystals that rely on stringent phase-matching conditions, limiting the operating wavelength and bandwidth. In this work, we demonstrate the generation of photon pairs from a free-standing lithium niobate microcube at the telecommunication wavelength of 1.56 µm through the spontaneous parametric down-conversion process. The maximum photon pair generation rate obtained from a single microcube with the size of 3.6 µm is 490 Hz, resulting in an efficiency of 20.6 GHz/Wm, which is three orders of magnitude larger than the efficiency of biphoton generation in bulk nonlinear crystals. The microcubes are synthesized through a solvothermal method, offering the possibility for scalable devices via bottom-up assembly on any substrates. Our work constitutes an important step forward in the realization of compact nonclassical light sources with a wide bandwidth for various quantum applications.

Harasti, D, Brennan, M & Booth, DJ 2022, 'Assessing the Effectiveness of Conservation Stocking for the Endangered White’s Seahorse Hippocampus whitei', Frontiers in Marine Science, vol. 9, pp. 1-11.
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The White’s seahorse Hippocampus whitei was listed as an Endangered species in 2020 on Australian state and federal legislation, as a result of population declines across its range attributed to habitat loss over the past decade. A captive-bred reintroduction program has been implemented as a possible management tool for species recovery, however, the viability of such a reintroduction program for seahorses has not been assessed to date. This study implemented a pilot captive-breeding program using adult H. whitei from Sydney Harbour, Australia, as brood stock. A total of 90 captive-bred seahorses were released into the wild on two different artificial habitat types (“seahorse hotels” and protective swimming net). Following release, a monthly post-release monitoring program was implemented for 12 months that involved underwater visual census surveys of the tagged seahorses. Sightings of captive-bred seahorse numbers were found to gradually decline over the 12-month period, with fewer seahorses found on the swimming net compared to the seahorse hotels and higher resighting probability of captive-bred animals on the seahorse hotels. After 12 months, 20% of the captive-bred seahorses were detected on the seahorse hotels, whilst two individuals were still observed 18 months after release on the hotels. Only 2% of captive-bred seahorses were observed on the swimming net after 12 months, with two individuals still detected on the net after two years. Nine of the captive-bred seahorses were found to reproduce in the wild, with two individuals observed mating with the wild population. This pilot study indicates that captive-bred seahorses can survive for up to two years in the wild, as well as contribute to local population recovery through reproductive success. However, while conservation stocking shows promise as a potential management tool to assist with threatened seahorse species recovery, there...

Hardy, S, Patrick, R, Liesinger, L, Pöttler, M, Rech, L, Gindlhuber, J, Mabotuwana, N, Ashour, D, Stangl, V, Bigland, M, Murtha, L, Starkey, M, Scherr, D, Hansbro, P, Höfler, G, Ramos, G, Cochain, C, Harvey, R, Birner-Gruenberger, R, Boyle, A & Rainer, P 2022, 'Extracellular Matrix Protein 1 as a Mediator of Inflammation-Induced Fibrosis After Myocardial Infarction', Heart, Lung and Circulation, vol. 31, no. S3, pp. S311-S311.
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BackgroundFibrosis is a hallmark of heart disease, particularly following myocardial infarction (MI) and in heart failure. We previously identified a key role for extracellular matrix protein (ECM1) in wound healing post-MI but the cellular origin and mechanism of ECM1 remained elusive. Here, we investigate the spatiotemporal cellular origin of ECM1 in healthy and diseased human and mouse hearts, and ECM1 dependent human cardiac fibroblast (HuCFb) signalling mechanisms.MethodsECM1 specific analysis of existing single-cell/-nuclei RNA sequencing data was conducted. ECM1 expression was assessed in non-failing (NF), ischaemic (ICM) and dilated (DCM) failing human heart tissue via immunoblotting (n=8), immunohistochemistry (ICM; n=8, NF; n=4) and mRNA in-situ hybridisation (n=3). HuCFbs were treated with recombinant ECM1 and assessed via phosphoproteomics (n=6), wound healing assay (n=4), MTT assay (n=8), qPCR (n=6).ResultsECM1 originates from fibroblasts, macrophages/monocytes (MΦ/Mo), and pericytes/vascular cells in uninjured human and mouse hearts. In mouse hearts post-MI, ECM1 originates predominantly from M1MΦ/Mo at day-3, and myofibroblasts and M2MΦ’s at day-7, and expression correlated with cell-cell communication, collagen organisation, inflammation, adhesion, and migration. Fittingly, ECM1 expression was upregulated in human ICM (p=0.048) and DCM (p=0.027), localised interstitially to fibrotic, inflammatory, and peri-vascular areas. In vitro, ECM1 inhibited HuCFb migration (p=0.044) and CCL2 mRNA expression, and stimulated inflammatory (IL-6, IL-1β), fibrotic (TGF-β1, Col1a2), and non-canonical Wnt5a mRNA expression (p<0.05). Phosphoproteomics showed ECM1 stimulates HuCFb Rho protein, cell-cell adhesion, and chemotactic signalling pathways.ConclusionsECM1 may represent a novel mechanism in facilitating inflammation-fibrosis crosstalk post-MI, and a potential therapeutic target.

Hartmann, LM, Garcia, A, Deplazes, E & Cranfield, CG 2022, 'Determining the Pore Size of Multimeric Peptide Ion Channels Using Cation Conductance Measures of Tethered Bilayer Lipid Membranes', pp. 81-92.
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Hasan, S, Kouzani, AZ, Adams, S, Long, J & Mahmud, MAP 2022, 'Comparative study on the contact-separation mode triboelectric nanogenerator', Journal of Electrostatics, vol. 116, pp. 103685-103685.
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Hasan, S, Kouzani, AZ, Adams, S, Long, J & Mahmud, MAP 2022, 'Recent progress in hydrogel-based sensors and energy harvesters', Sensors and Actuators A: Physical, vol. 335, pp. 113382-113382.
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Hasebe, K, Kendig, MD, Kaakoush, NO, Tajaddini, A, Westbrook, RF & Morris, MJ 2022, 'The influence of maternal unhealthy diet on maturation of offspring gut microbiota in rat', Animal Microbiome, vol. 4, no. 1.
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Abstract Background Despite well-known effects of diet on gut microbiota diversity, relatively little is known about how maternal diet quality shapes the longitudinal maturation of gut microbiota in offspring. To investigate, we fed female rats standard chow (Chow) or a western-style, high-choice cafeteria diet (Caf) prior to and during mating, gestation and lactation. At weaning (3 weeks), male and female offspring were either maintained on their mother’s diet (ChowChow, CafCaf groups) or switched to the other diet (ChowCaf, CafChow). Fecal microbial composition was assessed in dams and longitudinally in offspring at 3, 7 and 14 weeks of age. Results The effect of maternal diet on maturation of offspring gut microbiota was assessed by α- and β-diversities, Deseq2/LEfSe, and SourceTracker analyses. Weanling gut microbiota composition was characterised by reduced α- and β-diversity profiles that clustered away from dams and older siblings. After weaning, offspring gut microbiota came to resemble an adult-like gut microbiota, with increased α-diversity and reduced dissimilarity of β-diversity. Similarly, Deseq2/LEfSe analyses found fewer numbers of altered operational taxonomic units (OTUs) between groups from weaning to adulthood. SourceTracker analyses indicated a greater overall contribution of Caf mothers’ microbial community (up to 20%) to that of their offspring than the contribution of Chow mothers (up to 8%). Groups maintained on the maternal diet (ChowChow, CafCaf), versus those switched to the other diet (ChowCaf, CafChow) post-weaning significantly differed from each other at 14 weeks (Permutational Multivariate Analysis of Variance), indicating interactive effects of maternal and post-weaning diet on offspring gut microbiota maturation. ...

Haydon, TD, Suggett, DJ, Siboni, N, Kahlke, T, Camp, EF & Seymour, JR 2022, 'Temporal Variation in the Microbiome of Tropical and Temperate Octocorals', Microbial Ecology, vol. 83, no. 4, pp. 1073-1087.
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Bacterial members of the coral holobiont play an important role in determining coral fitness. However, most knowledge of the coral microbiome has come from reef-building scleractinian corals, with far less known about the nature and importance of the microbiome of octocorals (subclass Octocorallia), which contribute significantly to reef biodiversity and functional complexity. We examined the diversity and structure of the bacterial component of octocoral microbiomes over summer and winter, with a focus on two temperate (Erythropodium hicksoni, Capnella gaboensis; Sydney Harbour) and two tropical (Sinularia sp., Sarcophyton sp.; Heron Island) species common to reefs in eastern Australia. Bacterial communities associated with these octocorals were also compared to common temperate (Plesiastrea versipora) and tropical (Acropora aspera) hard corals from the same reefs. Using 16S rRNA amplicon sequencing, bacterial diversity was found to be heterogeneous among octocorals, but we observed changes in composition between summer and winter for some species (C. gaboensis and Sinularia sp.), but not for others (E. hicksoni and Sarcophyton sp.). Bacterial community structure differed significantly between all octocoral species within both the temperate and tropical environments. However, on a seasonal basis, those differences were less pronounced. The microbiomes of C. gaboensis and Sinularia sp. were dominated by bacteria belonging to the genus Endozoicomonas, which were a key conserved feature of their core microbiomes. In contrast to previous studies, our analysis revealed that Endozoicomonas phylotypes are shared across different octocoral species, inhabiting different environments. Together, our data demonstrates that octocorals harbour a broad diversity of bacterial partners, some of which comprise 'core microbiomes' that potentially impart important functional roles to their hosts.

He, F, Mahmud, MAP, Kouzani, AZ, Anwar, A, Jiang, F & Ling, SH 2022, 'An Improved SLIC Algorithm for Segmentation of Microscopic Cell Images.', Biomed. Signal Process. Control., vol. 73, pp. 103464-103464.
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He, J, Feng, P, Wang, B, Zhuang, W, Zhang, Y, Liu, DL, Cleverly, J, Huete, A & Yu, Q 2022, 'Centennial Annual Rainfall Pattern Changes Show an Increasing Trend with Higher Variation over Northern Australia', Journal of Hydrometeorology, vol. 23, no. 8, pp. 1333-1349.
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AbstractGlobal warming and anthropogenic activities have imposed noticeable impacts on rainfall pattern changes at both spatial and temporal scales in recent decades. Systematic diagnosis of rainfall pattern changes is urgently needed at spatiotemporal scales for a deeper understanding of how climate change produces variations in rainfall patterns. The objective of this study was to identify rainfall pattern changes systematically under climate change at a subcontinental scale along a rainfall gradient ranging from 1800 to 200 mm yr−1 by analyzing centennial rainfall data covering 230 sites from 1910 to 2017 in the Northern Territory of Australia. Rainfall pattern changes were characterized by considering aspects of trends and periodicity of annual rainfall, abrupt changes, rainfall distribution, and extreme rainfall events. Our results illustrated that rainfall patterns in northern Australia have changed significantly compared with the early period of the twentieth century. Specifically, 1) a significant increasing trend in annual precipitation associated with greater variation in recent decades was observed over the entire study area, 2) temporal variations represented a mean rainfall periodicity of 27 years over wet to dry regions, 3) an abrupt change of annual rainfall amount occurred consistently in both humid and arid regions during the 1966–75 period, and 4) partitioned long-term time series of rainfall demonstrated a wetter rainfall distribution trend across coastal to inland areas that was associated with more frequent extreme rainfall events in recent decades. The findings of this study could facilitate further studies on the mechanisms of climate change that influence rainfall pattern changes.Significance StatementCharacterizing long-term rainfall pattern changes under different rainfall conditions is important to understand the impac...

Hegarty, A, Stewart, J & Gladstone, W 2022, 'Geographical variation in age and growth of the endemic Australian sciaenid Atractoscion atelodus', Journal of Fish Biology, vol. 100, no. 2, pp. 474-485.
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AbstractGrowth rates and other age‐related population characteristics are essential parameters underpinning management of a stock. This is the first study to estimate length‐at‐age of Atractoscion atelodus (family Sciaenidae) in New South Wales (NSW), despite the species being exploited since the 1940s. The aim of the current study was to quantify the age‐based biological characteristics of A. atelodus and in particular: (a) validate the use of sagittal otoliths to quantify age; (b) estimate the growth rates and longevity of males and females; (c) examine geographical variation in age and growth; (d) document the age composition in commercial landings and (e) estimate mortality rates. A. atelodus is relatively fast growing, reaching 40 cm fork length (LF) in the first year of life and living to at least 14 years. Growth was significantly different between sexes, with modelled asymptotic lengths of females (L∞ = 84.6 cm LF) greater than males (L∞ = 69.0 cm LF). Growth rates were also significantly different between northern and southern populations. Fish sampled from the southern region were younger and faster growing than those sampled in the northern region, supporting the counter‐gradient growth theory and the influence of upwelling providing greater nutrient and food availability. The commercial fishery was predominantly based on young fish <3 years. with few (c. 5%) greater than 5 years. Fishing mortality estimates (F = 0.42) were similar to natural mortality estimates (M =

Hem, S, Jarocki, VM, Baker, DJ, Charles, IG, Drigo, B, Aucote, S, Donner, E, Burnard, D, Bauer, MJ, Harris, PNA, Wyrsch, ER & Djordjevic, SP 2022, 'Genomic analysis of Elizabethkingia species from aquatic environments: Evidence for potential clinical transmission', Current Research in Microbial Sciences, vol. 3, pp. 100083-100083.
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Hem, S, Wyrsch, ER, Drigo, B, Baker, DJ, Charles, IG, Donner, E, Jarocki, VM & Djordjevic, SP 2022, 'Genomic Analysis of Carbapenem-Resistant Comamonas in Water Matrices: Implications for Public Health and Wastewater Treatments', Applied and Environmental Microbiology, vol. 88, no. 13, p. e0064622.
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Antimicrobial resistance (AMR) poses a global public health threat, and the increase in resistance to “last-resort drugs,” such as carbapenems, is alarming. Wastewater has been flagged as a hot spot for AMR evolution. Comamonas spp. are among the most common bacteria in wastewater and play a role in its bioaugmentation.

Herdean, A, Sutherland, DL & Ralph, PJ 2022, 'Phenoplate: An innovative method for assessing interacting effects of temperature and light on non-photochemical quenching in microalgae under chemical stress', New Biotechnology, vol. 66, pp. 89-96.
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Hitchcock, JN 2022, 'Microplastics can alter phytoplankton community composition', Science of The Total Environment, vol. 819, pp. 153074-153074.
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Microplastic pollution is a growing concern globally due to the risks they may pose to ecological communities. Phytoplankton are key ecological community in aquatic ecosystems providing both energy to food webs and have critical roles in ecosystem functions such as carbon cycling. To date studies on how microplastics effect phytoplankton have largely been limited to laboratory exposure studies using monocultures of algae. It remains unknown how the structure of phytoplankton communities will be influenced by growing microplastic pollution. The aim of this study was to determine how different concentrations microplastic fibers influence phytoplankton community structure. Two six-day microcosm studies were conducted testing the response of the phytoplankton community to low, medium, and high microplastics concentrations on the Georges River, Australia. The results showed the highest concentrations of microplastics significantly altered the structure phytoplankton community. These differences were largely driven by increased abundances of cyanobacteria taxa Aphanocapsa and Pseudanabaena, and to a lesser extent reduced abundances of taxa including Crucigenia and Chlamydmonas. There were no significant differences between controls and the low and medium treatments in either experiment. The high concentrations used in this experiment whilst likely rare in the environment are environmentally relevant and equivalent to some of more polluted ecosystems. The results highlight the potential risk to food webs and ecosystem functioning through altering the dynamics of primary production and provide evidence for further study examining the response of ecological communities to microplastics in the environment.

Holt, SA, Oliver, TE & Nelson, ARJ 2022, 'Using refnx to Model Neutron Reflectometry Data from Phospholipid Bilayers', Methods Mol Biol, vol. 2402, pp. 179-197.
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Neutron reflectometry has emerged as a powerful method for studying the structure of thin films in contact with solution at sub-molecular spatial resolution (Penfold and Thomas, J Phys Condens Matter 2:1369-1412, 1990). This type of experiment is undertaken at large international central facilities and experience in data analysis and interpretation is not always available 'locally'. Here, we describe the application of the refnx software suite (Nelson and Prescott, J Appl Crystallogr 52:193-200, 2019) to the analysis of a single phospholipid bilayer deposited at a silicon/buffer interface. The data is modeled such that the fitted parameters are readily interpretable by researchers working with lipid bilayers.

Honsell, G, Gaiani, G, Hirama, M, Pelin, M, Tubaro, A, Tsumuraya, T & Campàs, M 2022, 'Cell immunolocalization of ciguatoxin-like compounds in the benthic dinoflagellate Gambierdiscus australes M. Chinain & M.A. Faust by confocal microscopy', Harmful Algae, vol. 120, pp. 102353-102353.
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Dinoflagellates of the genera Gambierdiscus and Fukuyoa are able to produce potent neurotoxins like ciguatoxins (CTXs), which, after biooxidation in fish, are responsible for ciguatera intoxication. An isolate of G. australes from the Canary Islands, that revealed the presence of CTX-like compounds by immunosensing tools, was studied by immunocytochemistry to localize intracellular CTX-like compounds, using 8H4 monoclonal antibody that specifically recognizes the right wing of CTX1B and CTX3C analogues. Confocal microscopy observations of immunostained whole cells revealed a strong positive reaction on cell surface and all along the cell outline, while no reaction was detected inside the cells, probably because the antibody was not able to pass through thecal plates. Cell sections showed a positive antibody staining not only on thecal plates, but also inside cytoplasm, with numerous small dots and larger tubule-like reticulate structures. Small fluorescent dots were detected also on the nuclear surface. These observations indicate that CTX-like compounds are present in G. australes cytoplasm, and then are, at least in part, released to cover the cell surface.

Hoque, MM, Noorian, P, Espinoza-Vergara, G, Manuneedhi Cholan, P, Kim, M, Rahman, MH, Labbate, M, Rice, SA, Pernice, M, Oehlers, SH & McDougald, D 2022, 'Adaptation to an amoeba host drives selection of virulence-associated traits in Vibrio cholerae', The ISME Journal, vol. 16, no. 3, pp. 856-867.
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Abstract Predation by heterotrophic protists drives the emergence of adaptive traits in bacteria, and often these traits lead to altered interactions with hosts and persistence in the environment. Here we studied adaptation of the cholera pathogen, Vibrio cholerae during long-term co-incubation with the protist host, Acanthamoeba castellanii. We determined phenotypic and genotypic changes associated with long-term intra-amoebal host adaptation and how this impacts pathogen survival and fitness. We showed that adaptation to the amoeba host leads to temporal changes in multiple phenotypic traits in V. cholerae that facilitate increased survival and competitive fitness in amoeba. Genome sequencing and mutational analysis revealed that these altered lifestyles were linked to non-synonymous mutations in conserved regions of the flagellar transcriptional regulator, flrA. Additionally, the mutations resulted in enhanced colonisation in zebrafish, establishing a link between adaptation of V. cholerae to amoeba predation and enhanced environmental persistence. Our results show that pressure imposed by amoeba on V. cholerae selects for flrA mutations that serves as a key driver for adaptation. Importantly, this study provides evidence that adaptive traits that evolve in pathogens in response to environmental predatory pressure impact the colonisation of eukaryotic organisms by these pathogens.

Horder, J, White, SJU, Gale, A, Li, C, Watanabe, K, Taniguchi, T, Kianinia, M, Aharonovich, I & Toth, M 2022, 'Coherence Properties of Electron-Beam-Activated Emitters in Hexagonal Boron Nitride Under Resonant Excitation', Physical Review Applied, vol. 18, no. 6.
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Two-dimensional (2D) materials are becoming increasingly popular as a platform for studies of quantum phenomena and for the production of prototype quantum technologies. Quantum emitters in 2D materials can host two-level systems that can act as qubits for quantum information processing. Here, we characterize the behavior of position-controlled quantum emitters in hexagonal boron nitride at cryogenic temperatures. Over two dozen sites, we observe an ultranarrow distribution of the zero phonon line at approximately 436 nm, together with strong linearly polarized emission. We employ resonant excitation to characterize the emission lineshape and find spectral diffusion and phonon broadening contribute to linewidths in the range 1-2 GHz. Rabi oscillations are observed at a range of resonant excitation powers, and under 1-μW excitation a coherent superposition is maintained up to 0.90 ns. Our results are promising for future employment of quantum emitters in h-BN for scalable quantum technologies.

Hortle, E, Tran, VLT, Wright, K, Fontaine, ARM, Pinello, N, O’Rourke, MB, Wong, JJ-L, Hansbro, PM, Britton, WJ & Oehlers, SH 2022, 'OXSR1 inhibits inflammasome activation by limiting potassium efflux during mycobacterial infection', Life Science Alliance, vol. 5, no. 9, pp. e202201476-e202201476.
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Pathogenic mycobacteria inhibit inflammasome activation to establish infection. Although it is known that potassium efflux is a trigger for inflammasome activation, the interaction between mycobacterial infection, potassium efflux, and inflammasome activation has not been investigated. Here, we use Mycobacterium marinum infection of zebrafish embryos and Mycobacterium tuberculosis infection of THP-1 cells to demonstrate that pathogenic mycobacteria up-regulate the host WNK signalling pathway kinases SPAK and OXSR1 which control intracellular potassium balance. We show that genetic depletion or inhibition of OXSR1 decreases bacterial burden and intracellular potassium levels. The protective effects of OXSR1 depletion are at least partially mediated by NLRP3 inflammasome activation, caspase-mediated release of IL-1β, and downstream activation of protective TNF-α. The elucidation of this druggable pathway to potentiate inflammasome activation provides a new avenue for the development of host-directed therapies against intracellular infections.

Hossain, KR, Escobar Bermeo, JD, Warton, K & Valenzuela, SM 2022, 'New Approaches and Biomarker Candidates for the Early Detection of Ovarian Cancer', Frontiers in Bioengineering and Biotechnology, vol. 10, p. 819183.
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Hossain, MJ, Kendig, MD, Letton, ME, Morris, MJ & Arnold, R 2022, 'Peripheral Neuropathy Phenotyping in Rat Models of Type 2 Diabetes Mellitus: Evaluating Uptake of the Neurodiab Guidelines and Identifying Future Directions', Diabetes & Metabolism Journal, vol. 46, no. 2, pp. 198-221.
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Diabetic peripheral neuropathy (DPN) affects over half of type 2 diabetes mellitus (T2DM) patients, with an urgent need for effective pharmacotherapies. While many rat and mouse models of T2DM exist, the phenotyping of DPN has been challenging with inconsistencies across laboratories. To better characterize DPN in rodents, a consensus guideline was published in 2014 to accelerate the translation of preclinical findings. Here we review DPN phenotyping in rat models of T2DM against the ‘Neurodiab’ criteria to identify uptake of the guidelines and discuss how DPN phenotypes differ between models and according to diabetes duration and sex. A search of PubMed, Scopus and Web of Science databases identified 125 studies, categorised as either diet and/or chemically induced models or transgenic/spontaneous models of T2DM. The use of diet and chemically induced T2DM models has exceeded that of transgenic models in recent years, and the introduction of the Neurodiab guidelines has not appreciably increased the number of studies assessing all key DPN endpoints. Combined high-fat diet and low dose streptozotocin rat models are the most frequently used and well characterised. Overall, we recommend adherence to Neurodiab guidelines for creating better animal models of DPN to accelerate translation and drug development.

Hossain, MR, Tasmin, N, Golder, S & Mahmud, MAP 2022, 'Environment and object design for 3D simulation in context of commercial vehicles', International Journal on Interactive Design and Manufacturing (IJIDeM), vol. 16, no. 3, pp. 969-985.
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Hossain, SI, Seppelt, M, Nguyen, N, Stokes, C & Deplazes, E 2022, 'The role of ion-lipid interactions and lipid packing in transient defects caused by phenolic compounds', Biophysical Journal, vol. 121, no. 18, pp. 3520-3532.
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Hosseinkhani, N, McCauley, JI & Ralph, PJ 2022, 'Key challenges for the commercial expansion of ingredients from algae into human food products', Algal Research, vol. 64, pp. 102696-102696.
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Hou, J, Yang, M, Sun, B & Wang, G 2022, 'Improvement Strategies toward Stable Lithium‐Metal Anodes for High‐Energy Batteries', Batteries & Supercaps, vol. 5, no. 12.
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AbstractLithium‐metal (Li‐metal) batteries are one of the most potential energy storage devices available these days. However, uncontrollable lithium dendritic growth and parasitic reactions lead to poor cycling efficiency and severe safety concerns, which restricts the use of Li‐metal batteries in practical applications. This article reviews the current development status of Li‐metal anodes, including investigations of reaction mechanisms and performance improvement strategies. In addition, future opportunities for developing safe and high‐performance Li‐metal batteries are also outlined.

Hou, W, Feng, P, Guo, X, Wang, Z, Bai, Z, Bai, Y, Wang, G & Sun, K 2022, 'Catalytic Mechanism of Oxygen Vacancies in Perovskite Oxides for Lithium–Sulfur Batteries', Advanced Materials, vol. 34, no. 26, pp. e2202222-2202222.
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AbstractDefective materials have been demonstrated to possess adsorptive and catalytic properties in lithium–sulfur (Li–S) batteries, which can effectively solve the problems of lithium polysulfides (LiPSs) shuttle and sluggish conversion kinetics during charging and discharging of Li–S batteries. However, there is still a lack of research on the quantitative relationship between the defect concentration and the adsorptive‐catalytic performance of the electrode. In this work, perovskites Sr0.9Ti1−xMnxO3−δ (STMnx) (x = 0.1–0.3) with different oxygen‐vacancy concentrations are quantitatively regulated as research models. Through a series of tests of the adsorptive property and electrochemical performance, a quantitative relationship between oxygen‐vacancy concentration and adsorptive‐catalytic properties is established. Furthermore, the catalytic mechanism of oxygen vacancies in Li–S batteries is investigated using density functional theory calculations and in situ experiments. The increased oxygen vacancies can effectively increase the binding energy between perovskite and LiPSs, reduce the energy barrier of LiPSs decomposition reaction, and promote LiPSs conversion reaction kinetics. Therefore, the perovskite STMn0.3 with high oxygen‐vacancy concentrations exhibits excellent LiPSs adsorptive and catalytic properties, realizing high‐efficiency Li–S batteries. This work is helpful to realize the application of the quantitative regulation strategy of defect engineering in Li–S batteries.

Howe, ENW, Chang, V-VT, Wu, X, Fares, M, Lewis, W, Macreadie, LK & Gale, PA 2022, 'Halide-selective, proton-coupled anion transport by phenylthiosemicarbazones', Biochimica et Biophysica Acta (BBA) - Biomembranes, vol. 1864, no. 2, pp. 183828-183828.
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Phenylthiosemicarbazones (PTSCs) are proton-coupled anion transporters with pH-switchable behaviour known to be regulated by an imine protonation equilibrium. Previously, chloride/nitrate exchange by PTSCs was found to be inactive at pH 7.2 due to locking of the thiourea anion binding site by an intramolecular hydrogen bond, and switched ON upon imine protonation at pH 4.5. The rate-determining process of the pH switch, however, was not examined. We here develop a new series of PTSCs and demonstrate their conformational behaviour by X-ray crystallographic analysis and pH-switchable anion transport properties by liposomal assays. We report the surprising finding that the protonated PTSCs are extremely selective for halides over oxyanions in membrane transport. Owing to the high chloride over nitrate selectivity, the pH-dependent chloride/nitrate exchange of PTSCs originates from the rate-limiting nitrate transport process being inhibited at neutral pH.

Howlett, L, Camp, EF, Edmondson, J, Edmondson, J, Agius, T, Hosp, R, Coulthard, P, Edmondson, S & Suggett, DJ 2022, 'Adoption of coral propagation and out-planting via the tourism industry to advance site stewardship on the northern Great Barrier Reef', Ocean & Coastal Management, vol. 225, pp. 106199-106199.
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Htet, CS, Manjón-Sanz, AM, Liu, J, Kong, J, Marlton, FP, Nayak, S, Jørgensen, MRV & Pramanick, A 2022, 'Effect of Local Structural Distortions on Antiferroelectric–Ferroelectric Phase Transition in Dilute Solid Solutions of K_xNa_1–xNbO₃', Inorganic Chemistry, vol. 61, no. 50, pp. 20277-20287.
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Htet, CS, Nayak, S, Manjón-Sanz, A, Liu, J, Kong, J, Sørensen, DR, Marlton, F, Jørgensen, MRV & Pramanick, A 2022, 'Atomic structural mechanism for ferroelectric-antiferroelectric transformation in perovskite NaNbO3', Physical Review B, vol. 105, no. 17, p. 174113.
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Sodium niobate (NaNbO3 or NN) is described as 'the most complex perovskite system,'which exhibits transitions between, as well as coexistence of, several ferroelectrics (FE) and antiferroelectric (AFE) phases at different temperatures. Recently, solid solutions of NN with stabilized AFE phases(s) have gained attention for energy-related applications, such as high-density energy storage and electrocaloric cooling. A better understanding of the atomic mechanisms responsible for AFE/FE phase transitions in NaNbO3 can enable a more rational design of its solid-solution systems with tunable functional properties. Here, we have investigated changes in the average and local atomic structure of NN using a combination of x-ray/neutron diffraction and neutron pair-distribution function (PDF) analyses. The Rietveld refinement of the x-ray/neutron-diffraction patterns indicates a coexistence of the FE Q (P21ma) and AFE P (Pbma) phases in the temperature range of 300K≤T≤615K, while PDF analysis indicated that the local structure (r<8Å) is better described by a P21ma symmetry. Above 615 K, the average structure transitions to an AFE R phase (Pmmn or Pnma), while PDF analysis shows an increased disordering of the octahedral distortions and Na displacements at the local scale. These results indicate that the average P/Q/R phase transitions in NN can be described as a result of complex ordering of distorted octahedral tilts at the nanoscale and off-centered displacements of the Na atoms.

Hu, B, Bao, G, Xu, X & Yang, K 2022, 'Topical hemostatic materials for coagulopathy', Journal of Materials Chemistry B, vol. 10, no. 12, pp. 1946-1959.
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We present a thorough analysis on the hemostatic mechanisms and the design principles of hemostatic materials for coagulopathy, survey their remarkable success, and briefly discuss the challenges and perspectives for their clinical translation.

Huang, G, Zhu, Y, Wen, S, Mei, H, Liu, Y, Wang, D, Maddahfar, M, Su, QP, Lin, G, Chen, Y & Jin, D 2022, 'Single Small Extracellular Vesicle (sEV) Quantification by Upconversion Nanoparticles', Nano Letters, vol. 22, no. 9, pp. 3761-3769.
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Cancer-derived small extracellular vesicles (sEVs) are potential circulating biomarkers in liquid biopsies. However, their small sizes, low abundance, and heterogeneity in molecular makeups pose major technical challenges for detecting and characterizing them quantitatively. Here, we demonstrate a single-sEV enumeration platform using lanthanide-doped upconversion nanoparticles (UCNPs). Taking advantage of the unique optical properties of UCNPs and the background-eliminating property of total internal reflection fluorescence (TIRF) imaging technique, a single-sEV assay recorded a limit of detection 1.8 × 106 EVs/mL, which was nearly 3 orders of magnitude lower than the standard enzyme-linked immunosorbent assay (ELISA). Its specificity was validated by the difference between EpCAM-positive and EpCAM-negative sEVs. The accuracy of the UCNP-based single-sEV assay was benchmarked with immunomagnetic-beads flow cytometry, showing a high correlation (R2> 0.99). The platform is suitable for evaluating the heterogeneous antigen expression of sEV and can be easily adapted for biomarker discoveries and disease diagnosis.

Huang, J, Cui, L, Natarajan, M, Barone, PW, Wolfrum, JM, Lee, YH, Rice, SA & Springs, SL 2022, 'The ratio of nicotinic acid to nicotinamide as a microbial biomarker for assessing cell therapy product sterility', Molecular Therapy - Methods & Clinical Development, vol. 25, pp. 410-424.
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Controlling microbial risks in cell therapy products (CTPs) is important for product safety. Here, we identified the nicotinic acid (NA) to nicotinamide (NAM) ratio as a biomarker that detects a broad spectrum of microbial contaminants in cell cultures. We separately added six different bacterial species into mesenchymal stromal cell and T cell culture and found that NA was uniquely present in these bacteria-contaminated CTPs due to the conversion from NAM by microbial nicotinamidases, which mammals lack. In cells inoculated with 1 × 104 CFUs/mL of different microorganisms, including USP <71> defined organisms, the increase in NA to NAM ratio ranged from 72 to 15,000 times higher than the uncontaminated controls after 24 h. Importantly, only live microorganisms caused increases in this ratio. In cells inoculated with 18 CFUs/mL of Escherichia coli, 20 CFUs/mL of Bacillus subtilis, and 10 CFUs/mL of Candida albicans, significant increase of NA to NAM ratio was detected using LC-MS after 18.5, 12.5, and 24.5 h, respectively. In contrast, compendial sterility test required >24 h to detect the same amount of these three organisms. In conclusion, the NA to NAM ratio is a useful biomarker for detection of early-stage microbial contaminations in CTPs.

Huang, T, Huang, X, Li, H, Qi, J, Wang, N, Xu, Y, Zeng, Y, Xiao, X, Liu, R, Chan, YL, Oliver, BG, Yi, C, Li, D & Chen, H 2022, 'Maternal Cigarette Smoke Exposure Exaggerates the Behavioral Defects and Neuronal Loss Caused by Hypoxic-Ischemic Brain Injury in Female Offspring', Frontiers in Cellular Neuroscience, vol. 16, p. 818536.
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ObjectiveHypoxic-ischemic encephalopathy affects ∼6 in 1,000 preterm neonates, leading to significant neurological sequela (e.g., cognitive deficits and cerebral palsy). Maternal smoke exposure (SE) is one of the common causes of neurological disorders; however, female offspring seems to be less affected than males in our previous study. We also showed that maternal SE exaggerated neurological disorders caused by neonatal hypoxic-ischemic brain injury in adolescent male offspring. Here, we aimed to examine whether female littermates of these males are protected from such insult.MethodsBALB/c dams were exposed to cigarette smoke generated from 2 cigarettes twice daily for 6 weeks before mating, during gestation and lactation. To induce hypoxic-ischemic brain injury, half of the pups from each litter underwent left carotid artery occlusion, followed by exposure to 8% oxygen (92% nitrogen) at postnatal day (P) 10. Behavioral tests were performed at P40–44, and brain tissues were collected at P45.ResultsMaternal SE worsened the defects in short-term memory and motor function in females with hypoxic-ischemic injury; however, reduced anxiety due to injury was observed in the control offspring, but not the SE offspring. Both hypoxic-ischemic injury and maternal SE caused significant loss of neuronal cells and synaptic proteins, along with increased oxidative stress and inflammatory responses.ConclusionOxidative stress and inflammatory response due to maternal SE may be the mechanism of worsened neurological outcomes by hypoxic-ischemic brain injury in females, which was similar to their male littermates shown in our previous study.

Huang, X, Luu, LDW, Jia, N, Zhu, J, Fu, J, Xiao, F, Liu, C, Li, S, Shu, G, Hou, J, Kang, M, Zhang, D, Xu, Y, Wang, Y, Cui, X, Lai, J, Li, J & Tai, J 2022, 'Multi-Platform Omics Analysis Reveals Molecular Signatures for Pathogenesis and Activity of Systemic Lupus Erythematosus', Frontiers in Immunology, vol. 13, pp. 1-15.
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Systemic lupus erythematosus (SLE) is a complex autoimmune disease with heterogeneous clinical manifestations and the pathogenesis of SLE is still unclear. Various omics results have been reported for SLE, but the molecular hallmarks of SLE, especially in patients with different disease activity, using an integrated multi-omics approach have not been fully investigated. Here, we collected blood samples from 10 healthy controls (HCs) and 40 SLE patients with different clinical activity including inactive (IA), low activity (LA), and high activity (HA). Using an integrative analysis of proteomic, metabolomic and lipidomic profiles, we report the multi-omics landscape for SLE. The molecular changes suggest that both the complement system and the inflammatory response were activated in SLEs and were associated with disease activity. Additionally, activation of the immunoglobulin mediated immune response were observed in the LA stage of the disease, however this immune response was suppressed slightly in the HA stage. Finally, an imbalance in lipid metabolism, especially in sphingolipid metabolism, accompanied with dysregulated apolipoproteins were observed to contribute to the disease activity of SLE. The multi-omics data presented in this study and the characterization of peripheral blood from SLE patients may thus help provide important clues regarding the pathogenesis of SLE.

Huber, E, Davila, YC & Thomson, ACG 2022, 'Designing intensive mode science subjects: improving the student and teacher experience', Journal of University Teaching and Learning Practice, vol. 19, no. 5.
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Intensive mode delivery (IMD) of subjects and courses offer a flexible option for today’s diverse student body, many of whom juggle work and carer responsibilities alongside study. However, little focus has been placed on the detailed design of IMD for different teaching roles. Responding to a call for science specific data, we investigated students’ and staff perceptions of learning and teaching in IMD undergraduate science subjects. Using data collected via student surveys and teacher interviews, we present our findings through the transition pedagogy framework which will help learning designers and teachers make quality design decisions. We found students and staff identified positive aspects of IMD, such as accelerating progression, high engagement, and smaller class size. The challenges with IMD include the intensity associated with workload. In most subjects, student attainment was higher in IMD compared to standard delivery over a semester. By comparing the perceptions to achievements, we examine the implications for designing positive and effective student learning experiences for IMD in science subjects. Practitioner Notes 1. Institutions need to invest time and resources into supporting staff to redesign their units for intensive mode delivery (IMD) – you cannot simply transpose from a standard mode to IMD. 2. Undergraduate science students’ grade distributions display complex relationships but are significantly different for IMD compared to standard mode. 3. Intensive mode assessment design needs to acknowledge that students often choose to study in this mode to accelerate their degree program. 4. Smaller class sizes are associated with IMD and staff can leverage this to create more personal engagement opportunities with students. 5. We provide a set of practical guidelines for both the lecturer and the tutor specifically for the design and delivery of IMD subjects in the sciences.

Hughes, DJ, Alexander, J, Cobbs, G, Kühl, M, Cooney, C, Pernice, M, Varkey, D, Voolstra, CR & Suggett, DJ 2022, 'Widespread oxyregulation in tropical corals under hypoxia', Marine Pollution Bulletin, vol. 179, pp. 113722-113722.
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Hughes, DJ, Raina, J-B, Nielsen, DA, Suggett, DJ & Kühl, M 2022, 'Disentangling compartment functions in sessile marine invertebrates', Trends in Ecology & Evolution, vol. 37, no. 9, pp. 740-748.
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Sessile invertebrates are frequently sampled and processed whole for downstream analyses. However, their apparent structural simplicity is deceptive as these organisms often harbour discrete compartments. These compartments have physicochemical conditions that differ markedly from neighbouring tissues, and that have likely evolved to support specific functions. Here, we argue that such compartments should be specifically targeted when characterising sessile invertebrate biology and we use the coral gastrovascular cavity to support our argument. This complex compartment displays steep and dynamic chemical gradients, harbours distinct microorganisms, and presumably plays a key role in coral biology. Disentangling the functions played by (and amongst) compartments will likely provide transformative insight into the biology of sessile invertebrates and their future under environmental change.

Hughes, DM, García-Fiñana, M & Wand, MP 2022, 'Fast approximate inference for multivariate longitudinal data', Biostatistics, vol. 24, no. 1, pp. 177-192.
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Summary Collecting information on multiple longitudinal outcomes is increasingly common in many clinical settings. In many cases, it is desirable to model these outcomes jointly. However, in large data sets, with many outcomes, computational burden often prevents the simultaneous modeling of multiple outcomes within a single model. We develop a mean field variational Bayes algorithm, to jointly model multiple Gaussian, Poisson, or binary longitudinal markers within a multivariate generalized linear mixed model. Through simulation studies and clinical applications (in the fields of sight threatening diabetic retinopathy and primary biliary cirrhosis), we demonstrate substantial computational savings of our approximate approach when compared to a standard Markov Chain Monte Carlo, while maintaining good levels of accuracy of model parameters.

Hughes, JM, Meadows, NM, Stewart, J, Booth, DJ & Fowler, AM 2022, 'Movement patterns of an iconic recreational fish species, mulloway (Argyrosomus japonicus), revealed by cooperative citizen-science tagging programs in coastal eastern Australia', Fisheries Research, vol. 247, pp. 106179-106179.
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Huo, J, Shen, Z, Cao, X, Li, L, Zhao, Y, Liu, H & Wang, G 2022, 'Macro/Micro‐Environment Regulating Carbon‐Supported Single‐Atom Catalysts for Hydrogen/Oxygen Conversion Reactions', Small, vol. 18, no. 32, pp. e2202394-2202394.
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AbstractSingle‐atom catalysts (SACs) have attracted tremendous research interest due to their unique atomic structure, maximized atom utilization, and remarkable catalytic performance. Among the SACs, the carbon‐supported SACs have been widely investigated due to their easily controlled properties of the carbon substrates, such as the tunable morphologies, ordered porosity, and abundant anchoring sites. The electrochemical performance of carbon‐supported SACs is highly related to the morphological structure of carbon substrates (macro‐environment) and the local coordination environments of center metals (micro‐environment). This review aims to provide a comprehensive summary on the macro/micro‐environment regulating carbon‐supported SACs for highly efficient hydrogen/oxygen conversion reactions. The authors first summarize the macro‐environment engineering strategies of carbon‐supported SACs with altered specific surface areas and porous properties of the carbon substrates, facilitating the mass diffusion kinetics and structural stability. Then the micro‐environment engineering strategies of carbon‐supported SACs are discussed with the regulated atomic structure and electronic structure of metal centers, boosting the catalytic performance. Insights into the correlation between the co‐boosted effect from the macro/micro‐environments and catalytic activity for hydrogen/oxygen conversion reactions are summarized and discussed. Finally, the challenges and perspectives are addressed in building highly efficient carbon‐supported SACs for practical applications.

Hurtado-McCormick, V, Commault, A, Herdean, A, Price, S, Pernice, M & Ralph, P 2022, 'Generation of Synechocystis sp. PCC 6803 mutant with enhanced laccase-like activity', Bioresource Technology Reports, vol. 20, pp. 101266-101266.
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Cyanobacteria offer a good alternative to fungi for laccase production at industrial scales. Random mutagenesis approaches with ethyl methanesulfonate were used in combination with enzymatic assays screenings to select a mutant of Synechocystis sp., A2, with enhanced extracellular laccase-like activity. Anthraquinone dye decolourisation assay revealed 7 % enhanced decolourisation in A2 relative to wild type after 24 h. Comparison of the microbiome composition, structure and richness of the wild type and A2 strains confirmed that the improved traits were due to the mutation(s) and not the associated bacteria. The newly isolated Synechocystis mutant is the first example of successful random mutagenesis of cyanobacteria for laccase production. Attempts to characterise the biochemical reaction and putative laccase in A2 strain were unsuccessful but will be the subject of further research. This study suggests that random mutagenesis as a powerful approach for generating cyanobacterial strains with enhanced laccase-like activity for prospective commercial applications.

Huston, WM, Lawrence, A, Wee, BA, Thomas, M, Timms, P, Vodstrcil, LA, McNulty, A, McIvor, R, Worthington, K, Donovan, B, Phillips, S, Chen, MY, Fairley, CK & Hocking, JS 2022, 'Repeat infections with chlamydia in women may be more transcriptionally active with lower responses from some immune genes', Frontiers in Public Health, vol. 10, p. 1012835.
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Chlamydia trachomatis, the most common bacterial sexually transmitted infection worldwide, is responsible for considerable health burden due to its significant sequelae. There are growing concerns about chlamydial treatment and management due to widely documented increasing burden of repeat infections. In the current study, a cohort study design of 305 women with urogenital chlamydial infections demonstrated that 11.8% of women experienced repeat infections after treatment with azithromycin. The chlamydial DNA load measured by quantitative PCR was higher in women who experienced a repeat infection (p = 0.0097) and repeat infection was associated with sexual contact. There was no genomic or phenotypic evidence of azithromycin resistance within the chlamydial isolates. During repeat infection, or repeat positive tests during follow up, vaginal chlamydial gene expression (ompA, euo, omcB, htrA, trpAB) was markedly higher compared to baseline, and two of the selected immune genes analyzed had significantly lower expression at the time of repeat infection. Overall, there are two implications of these results. The results could be generalized to all recent infections, or repeat positive events, and indicate that chlamydial infections are have higher transcriptional activity of select genes early in the infection in women. Alternatively, after azithromycin treatment, repeat infections of Chlamydia may be more transcriptionally active at certain genes, and there may be post-treatment immunological alterations that interplay into repeat exposures establishing an active infection. The potential that recent infections may involve a higher level of activity from the organism may have implications for management by more regular testing of the most at risk women to reduce the risk of sequelae.

Hwang, J, Strange, N, Mazraani, R, Phillips, MJ, Gamble, AB, Huston, WM & Tyndall, JDA 2022, 'Design, synthesis and biological evaluation of P2-modified proline analogues targeting the HtrA serine protease in Chlamydia', European Journal of Medicinal Chemistry, vol. 230, pp. 114064-114064.
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High temperature requirement A (HtrA) serine proteases have emerged as a novel class of antibacterial target, which are crucial in protein quality control and are involved in the pathogenesis of a wide array of bacterial infections. Previously, we demonstrated that HtrA in Chlamydia is essential for bacterial survival, replication and virulence. Here, we report a new series of proline (P2)-modified inhibitors of Chlamydia trachomatis HtrA (CtHtrA) developed by proline ring expansion and Cγ-substitutions. The structure-based drug optimization process was guided by molecular modelling and in vitro pharmacological evaluation of inhibitory potency, selectivity and cytotoxicity. Compound 25 from the first-generation 4-substituted proline analogues increased antiCtHtrA potency and selectivity over human neutrophil elastase (HNE) by approximately 6- and 12-fold, respectively, relative to the peptidic lead compound 1. Based on this compound, second-generation substituted proline residues containing 1,2,3-triazole moieties were synthesized by regioselective azide-alkyne click chemistry. Compound 49 demonstrated significantly improved antichlamydial activity in whole cell assays, diminishing the bacterial infectious progeny below the detection limit at the lowest dose tested. Compound 49 resulted in approximately 9- and 22-fold improvement in the inhibitory potency and selectivity relative to 1, respectively. To date, compound 49 is the most potent HtrA inhibitor developed against Chlamydia spp.

Ibrahim, I, Hossain, SM, Seo, DH, McDonagh, A, Foster, T, Shon, HK & Tijing, L 2022, 'Insight into the role of polydopamine nanostructures on nickel foam-based photothermal materials for solar water evaporation', Separation and Purification Technology, vol. 293, pp. 121054-121054.
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Ibrahim, I, Seo, DH, Park, MJ, Angeloski, A, McDonagh, A, Bendavid, A, Shon, HK & Tijing, L 2022, 'Highly stable gold nanolayer membrane for efficient solar water evaporation under a harsh environment', Chemosphere, vol. 299, pp. 134394-134394.
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Imran, M, Jha, LA, Hasan, N, Shrestha, J, Pangeni, R, Parvez, N, Mohammed, Y, Jha, SK & Paudel, KR 2022, '“Nanodecoys” - Future of drug delivery by encapsulating nanoparticles in natural cell membranes', International Journal of Pharmaceutics, vol. 621, pp. 121790-121790.
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Imran, M, Paudel, KR, Jha, SK, Hansbro, PM, Dua, K & Mohammed, Y 2022, 'Dressing multifunctional nanoparticles with natural cell-derived membranes for superior chemotherapy', Nanomedicine, vol. 17, no. 10, pp. 665-670.
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Inomura, K, Masuda, T, Eichner, M, Rabouille, S, Zavřel, T, Červený, J, Vancová, M, Bernát, G, Armin, G, Claquin, P, Kotabová, E, Stephan, S, Suggett, DJ, Deutsch, C & Prášil, O 2022, 'Erratum to “Quantifying Cyanothece growth under DIC limitation” [Comput. Struct. Biotechnol. J. 19 (2021) 6456–6464]', Computational and Structural Biotechnology Journal, vol. 20, pp. 385-385.
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[This corrects the article DOI: 10.1016/j.csbj.2021.11.036.].

Iqbal, S, Flux, C, Briggs, DA, Deplazes, E, Long, J, Skrzypek, R, Rothnie, A, Kerr, ID & Callaghan, R 2022, 'Vinca alkaloid binding to P-glycoprotein occurs in a processive manner', Biochimica et Biophysica Acta (BBA) - Biomembranes, vol. 1864, no. 10, pp. 184005-184005.
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Irvine, CP, Stopic, A, Westerhausen, MT, Phillips, MR & Ton-That, C 2022, 'Enhancement of excitonic and defect-related luminescence in neutron transmutation doped β−Ga2O3', Physical Review Materials, vol. 6, no. 11, p. 114603.
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Neutron irradiation analysis, inductively coupled plasma mass spectrometry (ICPMS), and cathodoluminescence (CL) spectroscopy are used to investigate the influence of transmuted Ge incorporation on the luminescence properties of β-Ga2O3 single crystals. Calculations based on Ga2O3-neutron interaction reveal temporal variations of both Ge and Zn concentrations as a function of time during and after neutron irradiation. To produce a concentration of 5×1018Gedonors/cm3 from the neutron transmutation of Ga, the β-Ga2O3 crystal was irradiated for 27 h, which was accompanied by the incorporation of 1016Znacceptors/cm3. These calculated dopant concentrations are confirmed by ICPMS. The β-Ga2O3 crystals exhibit a UV band at 3.40 eV due to self-trapped holes (STHs) and two blue donor-acceptor pair (DAP) peaks at 3.14 eV (BL1) and 2.92 eV (BL2). In addition to the neutron-induced incorporation of substitutional Ge donors and Zn acceptors on Ga sites, Ga vacancies (VGa) were created by high-energy neutrons in the flux, which strongly enhanced the BL1 peak. The VGa acceptors compensate the neutron-induced Ge donors, making the Ga2O3 crystal highly resistive. Concurrent temperature-resolved CL measurements of the β-Ga2O3 before and after neutron irradiation reveal a twofold increase in both the STH and BL1 peaks. This result suggests that STHs are preferentially localized at an O site adjacent to VGa, as theoretically predicted by Kananen et al. [Appl. Phys. Lett. 110, 202104 (2017)10.1063/1.4983814.]. Analysis of the Ga2O3 CL temperature dependence reveals that the UV and BL1 bands after the neutron irradiation exhibit an equivalent activation energy of 100±10meV due to the presence of a neutron-induced defect that acts as an efficient competitive nonradiative recombination channel. The results also provide evidence that the BL1 and BL2 bands arise from different DAP pairs.

Islam, MZ, Hossain, SI, Deplazes, E & Saha, SC 2022, 'Concentration-dependent cortisone adsorption and interaction with model lung surfactant monolayer', Molecular Simulation, vol. 48, no. 18, pp. 1627-1638.
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Corticosteroids are drugs used to treat inflammatory conditions. In the case of lung diseases, corticosteroids can be administered by inhalation. The main barrier for inhaled particles is the lung surfactant monolayer (LSM) that lines the alveolar air–water interface and reduces surface tension during breathing. In this study, we use coarse-grained molecular dynamics simulations to study the concentration-dependent interaction of cortisone with an LSM composed of neutral and negatively charged phospholipids, cholesterol, and surfactant proteins. Simulations were carried out at surface tensions mimicking inhalation and exhalation conditions and different compressibilities. In-depth analysis shows that cortisone causes a concentration-dependent expansion of the monolayer that at high surface tension and high drug concentrations results in the monolayer collapsing. This instability is associated with the accumulation of drugs and surfactant proteins that prevent adsorption into the monolayer. Our findings help to improve the understanding of how corticosteroids alter lung surfactants structure and assist efforts to improve drug adsorption.

Islam, MZ, Hossain, SI, Deplazes, E & Saha, SC 2022, 'The steroid mometasone alters protein containing lung surfactant monolayers in a concentration-dependent manner', Journal of Molecular Graphics and Modelling, vol. 111, pp. 108084-108084.
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Mometasone is an investigational anti-inflammatory steroidal drug to treat inflammation via pulmonary administration. For steroid drugs to be effective they need to be adsorbed by lung surfactants, a thin monolayer at the air-water interface in alveoli that reduces surface tension. Information on the molecular-level interactions of the drug with lung surfactants is useful to understand the mechanism of adsorption. In this study, we use coarse-grained molecular dynamics simulation to understand the concentration-dependent effect of mometasone on a lung surfactant monolayer (LSM) composed of lipids and surfactant proteins, under two different breathing conditions (exhalation, at surface tension 0 mNm-1 and inhalation, surface tension 20-25 mNm-1). A series of fixed-APL and fixed-surface tension simulations were used to demonstrate that in the absence of drugs, the model LSM reproduces the surface tensions for the compressed and expanded states, as well as compressibility at different surface tensions. In-depth analysis of simulations of a LSM in the presence of five different drug concentrations shows that mometasone alters the structure and dynamics of the LSM in a concentration-dependent manner. Mometasone induces a collapse in the monolayer that is affected by the surfactant protein and surface tension. Overall, these findings suggest that the surfactant proteins, surface tension and drug concentration are all critical components affecting monolayer stability and drug adsorption. The outcomes of this study may be beneficial for a more in-depth understanding of how mometasone is adsorbed by lung surfactants.

Islam, MZ, Hossain, SI, Deplazes, E, Luo, Z & Saha, SC 2022, 'The concentration-dependent effect of hydrocortisone on the structure of model lung surfactant monolayer by using an in silico approach', RSC Advances, vol. 12, no. 51, pp. 33313-33328.
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Adsorption mechanism of corticosteroid drug hydrocortisone in the lung surfactant monolayer.

Islam, MZ, Krajewska, M, Hossain, SI, Prochaska, K, Anwar, A, Deplazes, E & Saha, SC 2022, 'Concentration-Dependent Effect of the Steroid Drug Prednisolone on a Lung Surfactant Monolayer', Langmuir, vol. 38, no. 14, pp. 4188-4199.
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The lung surfactant monolayer (LSM) is the main barrier for particles entering the lung, including steroid drugs used to treat lung diseases. The present study combines Langmuir experiments and coarse-grained (CG) molecular dynamics simulations to investigate the concentration-dependent effect of steroid drug prednisolone on the structure and morphology of a model LSM. The surface pressure-area isotherms for the Langmuir monolayers reveal a concentration-dependent decrease in area per lipid (APL). Results from simulations at a fixed surface tension, representing inhalation and exhalation conditions, suggest that at high drug concentrations, prednisolone induces a collapse of the LSM, which is likely caused by the inability of the drug to diffuse into the bilayer. Overall, the monolayer is most susceptible to drug-induced collapse at surface tensions representing exhalation conditions. The presence of cholesterol also exacerbates the instability. The findings of this investigation might be helpful for better understanding the interaction between steroid drug prednisolone and lung surfactants in relation to off-target effects.

Iwasaki, K, Szabó, M, Tamburic, B, Evenhuis, C, Zavafer, A, Kuzhiumparambil, U & Ralph, P 2022, 'Investigating the impact of light quality on macromolecular of', Functional Plant Biology, vol. 49, no. 6, pp. 554-564.
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Diatoms (Bacillariophyceae) are important to primary productivity of aquatic ecosystems. This algal group is also a valuable source of high value compounds that are utilised as aquaculture feed. The productivity of diatoms is strongly driven by light and CO2 availability, and macro- and micronutrient concentrations. The light dependency of biomass productivity and metabolite composition is well researched in diatoms, but information on the impact of light quality, particularly the productivity return on energy invested when using different monochromatic light sources, remains scarce. In this work, the productivity return on energy invested of improving growth rate, photosynthetic activity, and metabolite productivity of the diatom Chaetoceros muelleri under defined wavelengths (blue, red, and green) as well as while light is analysed. By adjusting the different light qualities to equal photosynthetically utilisable radiation, it was found that the growth rate and photosynthetic oxygen evolution was unchanged under white, blue, and green light, but it was lower under red light. Blue light improved the productivity return on energy invested for biomass, total protein, total lipid, total carbohydrate, and in fatty acids production, which would suggest that blue light should be used for aquaculture feed production.

Jain, A, Wadhwa, R, Kundu, K, Nebhinani, N & Gupta, R 2022, 'Assessment of Knowledge About RLS Among Medical Teachers and Undergraduate Students Using Newly Developed Questionnaire: K-RLS', Sleep and Vigilance, vol. 6, no. 1, pp. 131-137.
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Jansen, MI, Broome, ST & Castorina, A 2022, 'Targeting the neurological comorbidities of multiple sclerosis: the beneficial effects of VIP and PACAP neuropeptides', Journal of Integrative Neuroscience, vol. 21, no. 1, pp. 033-033.
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Vasoactive intestinal peptide (VIP) and pituitary adenylate cyclase-activating polypeptide (PACAP) are two widely expressed neuropeptides with important immunomodulatory and neuroprotective properties in the central nervous system (CNS). Both VIP and PACAP have been implicated in several neurological diseases and have shown favourable effects in different animal models of multiple sclerosis (MS). MS is a chronic inflammatory and neurodegenerative disease of the CNS affecting over 2.5 million people worldwide. The disease is characterised by extensive neuroinflammation, demyelination and axonal loss. Currently, there is no cure for MS, with treatment options only displaying partial efficacy. Importantly, epidemiological studies in the MS population have demonstrated that there is a high incidence of neurological and psychological comorbidities such as depression, anxiety, epilepsy and stroke among afflicted people. Hence, given the widespread protective effects of the VIP/PACAP system in the CNS, this review will aim at exploring the beneficial roles of VIP and PACAP in ameliorating some of the most common neurological comorbidities associated with MS. The final scope of the review is to put more emphasis on how targeting the VIP/PACAP system may be an effective therapeutic strategy to modify MS disease course and its associated comorbidities.

Javanshir, A, Nguyen, TT, Mahmud, MAP & Kouzani, AZ 2022, 'Advancements in Algorithms and Neuromorphic Hardware for Spiking Neural Networks', Neural Computation, vol. 34, no. 6, pp. 1289-1328.
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Abstract Artificial neural networks (ANNs) have experienced a rapid advancement for their success in various application domains, including autonomous driving and drone vision. Researchers have been improving the performance efficiency and computational requirement of ANNs inspired by the mechanisms of the biological brain. Spiking neural networks (SNNs) provide a power-efficient and brain-inspired computing paradigm for machine learning applications. However, evaluating large-scale SNNs on classical von Neumann architectures (central processing units/graphics processing units) demands a high amount of power and time. Therefore, hardware designers have developed neuromorphic platforms to execute SNNs in and approach that combines fast processing and low power consumption. Recently, field-programmable gate arrays (FPGAs) have been considered promising candidates for implementing neuromorphic solutions due to their varied advantages, such as higher flexibility, shorter design, and excellent stability. This review aims to describe recent advances in SNNs and the neuromorphic hardware platforms (digital, analog, hybrid, and FPGA based) suitable for their implementation. We present that biological background of SNN learning, such as neuron models and information encoding techniques, followed by a categorization of SNN training. In addition, we describe state-of-the-art SNN simulators. Furthermore, we review and present FPGA-based hardware implementation of SNNs. Finally, we discuss some future directions for research in this field.

Jena, R, Vishwas, S, Kumar, R, Kaur, J, Khursheed, R, Gulati, M, Singh, TG, Vanathi, BM, Alam, A, Kumar, B, Chaitanya, MVNL, Gupta, S, Negi, P, Pandey, NK, Bhatt, S, Gupta, G, Chellappan, DK, Oliver, BG, Dua, K & Singh, SK 2022, 'Treatment strategies for HIV infection with emphasis on role of CRISPR/Cas9 gene: Success so far and road ahead', European Journal of Pharmacology, vol. 931, pp. 175173-175173.
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Advances in biotechnology have led to improving human health with number of novel approaches to mitigate life-threatening diseases such as human immunodeficiency virus (HIV) infection, cancer, and neurodegenerative diseases. In the case of HIV, the damage caused by the retrovirus to the immune system leads to opportunistic infection as well as an elevated risk of autoimmune disease and cancer. Furthermore, clinical symptoms associated with the virus itself may arise. Antiretroviral drug therapy using reverse transcriptase inhibitors, protease inhibitors, fusion inhibitor, chemokine receptor 5 antagonist and integrase strand transfer inhibitors have shown promising results in treating HIV infection and available in market in the form of various dosage forms. However, they are unable to completely cure the disease because of complexity in pathogenesis of HIV. In addition, these drugs have some limitations of poor solubility, permeability or, poor receptor binding capacity. To overcome these drawbacks, many novel drug delivery systems for the drugs belonging to above mentioned categories have been developed. The possibility of treating HIV infection using CRISPR-Cas9 gene editing has been found in 2015. This provided a new area of research to the scientists who are working towards alternative treatment strategies for HIV infections. The present article describes about various treatment strategies used to treat HIV infections with special emphasis on the role of CRISPR/Cas9 gene-based technology. The potential benefits of specific epigenetic modification in the c-c chemokine receptor 5 gene (CCR5) via various delivery methods are also highlighted.

Jenkins, C, Micallef, ML, Padula, MP & Bogema, DR 2022, 'Characterisation of the Theileria orientalis Piroplasm Proteome across Three Common Genotypes', Pathogens, vol. 11, no. 10, pp. 1135-1135.
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Theileria orientalis is an emerging apicomplexan pathogen of cattle occurring in areas populated by the principal vector tick, Haemaphysalis longicornis. Unlike transforming Theileria spp. that induce cancer-like proliferation of lymphocytes via their schizont stage, T. orientalis destroys host erythrocytes during its piroplasm phase resulting in anaemia. The underlying pathogenic processes of T. orientalis infection are poorly understood; consequently, there are no vaccines for prevention of T. orientalis infection and chemotherapeutic options are limited. To identify antigens expressed during the piroplasm phase of T. orientalis, including those which may be useful targets for future therapeutic development, we examined the proteome across three common genotypes of the parasite (Ikeda, Chitose and Buffeli) using preparations of piroplasms purified from bovine blood. A combination of Triton X-114 extraction, one-dimensional electrophoresis and LC-MS/MS identified a total of 1113 proteins across all genotypes, with less than 3% of these representing host-derived proteins. Just over three quarters of T. orientalis proteins (78%) identified were from the aqueous phase of the TX-114 extraction representing cytosolic proteins, with the remaining 22% from the detergent phase, representing membrane-associated proteins. All enzymes involved in glycolysis were expressed, suggesting that this is the major metabolic pathway used during the T. orientalis piroplasm phase. Proteins involved in binding and breakdown of haemoglobin were also identified, suggesting that T. orientalis uses haemoglobin as a source of amino acids. A number of proteins involved in host cell interaction were also identified which may be suitable targets for the development of chemotherapeutics or vaccines.

Jha, SK, Imran, M, Paudel, KR, Mohammed, Y, Hansbro, P & Dua, K 2022, 'Treating primary lymphoma of the brain in AIDS patients via multifunctional oral nanoparticulate systems', Nanomedicine, vol. 17, no. 7, pp. 425-429.
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Jiang, J, Huang, B, Daiyan, R, Subhash, B, Tsounis, C, Ma, Z, Han, C, Zhao, Y, Effendi, LH, Gallington, LC, Hart, JN, Scott, JA & Bedford, NM 2022, 'Defective Sn-Zn perovskites through bio-directed routes for modulating CO2RR', Nano Energy, vol. 101, pp. 107593-107593.
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Jiang, J, Wand, MP & Bhaskaran, A 2022, 'Usable and Precise Asymptotics for Generalized Linear Mixed Model Analysis and Design', Journal of the Royal Statistical Society Series B: Statistical Methodology, vol. 84, no. 1, pp. 55-82.
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AbstractWe derive precise asymptotic results that are directly usable for confidence intervals and Wald hypothesis tests for likelihood-based generalized linear mixed model analysis. The essence of our approach is to derive the exact leading term behaviour of the Fisher information matrix when both the number of groups and number of observations within each group diverge. This leads to asymptotic normality results with simple studentizable forms. Similar analyses result in tractable leading term forms for the determination of approximate locally D-optimal designs.

Jiang, S, Suo, H, Zheng, X, Zhang, T, Lei, Y, Wang, Y, Lai, W & Wang, G 2022, 'Lightest Metal Leads to Big Change: Lithium‐Mediated Metal Oxides for Oxygen Evolution Reaction', Advanced Energy Materials, vol. 12, no. 33, pp. 2201934-2201934.
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AbstractAs the lightest metal, the reversible insertion/extraction properties of lithium have been key findings in lithium metal oxide chemistry. Lithium has been widely used in the oxygen evolution reaction (OER), and the reaction mechanism of lithium‐mediated metal oxides has both similarities and uniqueness compared to typical dual metal oxides. Notably, the insertion/extraction of lithium during the OER is also crucial for the construction of novel surface reconstruction models. This review aims to provide the concepts of general OER pathways and key features of dual metal oxides for the OER. As a comparison then the development of lithium metal oxides for the OER is introduced and the chemistry underlying lithium metal oxide catalysts is unveiled. This review also examines the challenges remaining for the relevant catalysts, with prospects for further improving their OER activities.

Jiang, Z, Liu, S, Cui, L, He, J, Fang, Y, Premarathne, C, Li, L, Wu, Y, Huang, X & Kumar, M 2022, 'Sand supplementation favors tropical seagrass Thalassia hemprichii in eutrophic bay: implications for seagrass restoration and management', BMC Plant Biology, vol. 22, no. 1, p. 296.
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Abstract Background Sediment is crucial for the unique marine angiosperm seagrass growth and successful restoration. Sediment modification induced by eutrophication also exacerbates seagrass decline and reduces plantation and transplantation survival rates. However, we lack information regarding the influence of sediment on seagrass photosynthesis and the metabolics, especially regarding the key secondary metabolic flavone. Meanwhile, sulfation of flavonoids in seagrass may mitigate sulfide intrusion, but limited evidence is available. Results We cultured the seagrass Thalassia hemprichii under controlled laboratory conditions in three sediment types by combining different ratios of in-situ eutrophic sediment and coarse beach sand. We examined the effects of beach sand mixed with natural eutrophic sediments on seagrass using photobiology, metabolomics and isotope labelling approaches. Seagrasses grown in eutrophic sediments mixed with beach sand exhibited significantly higher photosynthetic activity, with a larger relative maximum electron transport rate and minimum saturating irradiance. Simultaneously, considerably greater belowground amino acid and flavonoid concentrations were observed to counteract anoxic stress in eutrophic sediments without mixed beach sand. This led to more positive belowground stable sulfur isotope ratios in eutrophic sediments with a lower Eh. Conclusions These results indicated that coarse beach sand indirectly enhanced photosynthesis in T. hemprichii by reducing sulfide intrusion with lower amino acid and flavonoid concentrations. This could explain why

Jiang, Z-K, Ren, R-J, Chang, Y-J, Zhou, W-H, Lu, Y-H, Wang, X-W, Wang, L, Wang, C-S, Solntsev, AS & Jin, X-M 2022, 'Direct Observation of Dynamically Localized Quantum Optical States', Physical Review Letters, vol. 129, no. 17, p. 173602.
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Quantum-correlated biphoton states play an important role in quantum communication and processing, especially considering the recent advances in integrated photonics. However, it remains a challenge to flexibly transport quantum states on a chip, when dealing with large-scale sophisticated photonic designs. The equivalence between certain aspects of quantum optics and solid-state physics makes it possible to utilize a range of powerful approaches in photonics, including topologically protected boundary states, graphene edge states, and dynamic localization. Optical dynamic localization allows efficient protection of classical signals in photonic systems by implementing an analogue of an external alternating electric field. Here, we report on the observation of dynamic localization for quantum-correlated biphotons, including both the generation and the propagation aspects. As a platform, we use sinusoidal waveguide arrays with cubic nonlinearity. We record biphoton coincidence count rates as evidence of robust generation of biphotons and demonstrate the dynamic localization features in both spatial and temporal space by analyzing the quantum correlation of biphotons at the output of the waveguide array. Experimental results demonstrate that various dynamic modulation parameters are effective in protecting quantum states without introducing complex topologies. Our Letter opens new avenues for studying complex physical processes using photonic chips and provides an alternative mechanism of protecting communication channels and nonclassical quantum sources in large-scale integrated quantum optics.

Johansen, MD, Mahbub, RM, Idrees, S, Nguyen, DH, Miemczyk, S, Pathinayake, P, Nichol, K, Hansbro, NG, Gearing, LJ, Hertzog, PJ, Gallego-Ortega, D, Britton, WJ, Saunders, BM, Wark, PA, Faiz, A & Hansbro, PM 2022, 'Increased SARS-CoV-2 Infection, Protease, and Inflammatory Responses in Chronic Obstructive Pulmonary Disease Primary Bronchial Epithelial Cells Defined with Single-Cell RNA Sequencing', American Journal of Respiratory and Critical Care Medicine, vol. 206, no. 6, pp. 712-729.
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Rationale: Patients with chronic obstructive pulmonary disease (COPD) develop more severe coronavirus disease (COVID-19); however, it is unclear whether they are more susceptible to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and what mechanisms are responsible for severe disease. Objectives: To determine whether SARS-CoV-2 inoculated primary bronchial epithelial cells (pBECs) from patients with COPD support greater infection and elucidate the effects and mechanisms involved. Methods: We performed single-cell RNA sequencing analysis on differentiated pBECs from healthy subjects and patients with COPD 7 days after SARS-CoV-2 inoculation. We correlated changes with viral titers, proinflammatory responses, and IFN production. Measurements and Main Results: Single-cell RNA sequencing revealed that COPD pBECs had 24-fold greater infection than healthy cells, which was supported by plaque assays. Club/goblet and basal cells were the predominant populations infected and expressed mRNAs involved in viral replication. Proteases involved in SARS-CoV-2 entry/infection (TMPRSS2 and CTSB) were increased, and protease inhibitors (serpins) were downregulated more so in COPD. Inflammatory cytokines linked to COPD exacerbations and severe COVID-19 were increased, whereas IFN responses were blunted. Coexpression analysis revealed a prominent population of club/goblet cells with high type 1/2 IFN responses that were important drivers of immune responses to infection in both healthy and COPD pBECs. Therapeutic inhibition of proteases and inflammatory imbalances reduced viral titers and cytokine responses, particularly in COPD pBECs. Conclusions: COPD pBECs are more susceptible to SARS-CoV-2 infection because of increases in coreceptor expression and protease imbalances and have greater inflammatory responses. A prominent cluster of IFN-responsive club/goblet cells emerges during infection, which may be important drivers of immunity. Therapeutic i...

John, AR, Singh, AK, Do, T-TN, Eidels, A, Nalivaiko, E, Gavgani, AM, Brown, S, Bennett, M, Lal, S, Simpson, AM, Gustin, SM, Double, K, Walker, FR, Kleitman, S, Morley, J & Lin, C-T 2022, 'Unraveling the Physiological Correlates of Mental Workload Variations in Tracking and Collision Prediction Tasks', IEEE Transactions on Neural Systems and Rehabilitation Engineering, vol. 30, no. 99, pp. 770-781.
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Modern work environments have extensive interactions with technology and greater cognitive complexity of the tasks, which results in human operators experiencing increased mental workload. Air traffic control operators routinely work in such complex environments, and we designed tracking and collision prediction tasks to emulate their elementary tasks. The physiological response to the workload variations in these tasks was elucidated to untangle the impact of workload variations experienced by operators. Electroencephalogram (EEG), eye activity, and heart rate variability (HRV) data were recorded from 24 participants performing tracking and collision prediction tasks with three levels of difficulty. Our findings indicate that variations in task load in both these tasks are sensitively reflected in EEG, eye activity and HRV data. Multiple regression results also show that operators' performance in both tasks can be predicted using the corresponding EEG, eye activity and HRV data. The results also demonstrate that the brain dynamics during each of these tasks can be estimated from the corresponding eye activity, HRV and performance data. Furthermore, the markedly distinct neurometrics of workload variations in the tracking and collision prediction tasks indicate that neurometrics can provide insights on the type of mental workload. These findings have applicability to the design of future mental workload adaptive systems that integrate neurometrics in deciding not just 'when' but also 'what' to adapt. Our study provides compelling evidence in the viability of developing intelligent closed-loop mental workload adaptive systems that ensure efficiency and safety in complex work environments.

Johnson, B & Havas, A 2022, 'Western Bias, Canonicity, and Cultural Globalization: Introduction to “Jazz Diasporas”', Popular Music and Society, vol. 45, no. 4, pp. 371-376.
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Johnson, B, Zhuang, L, Rath, EM, Yuen, ML, Cheng, NC, Shi, H, Kao, S, Reid, G & Cheng, YY 2022, 'Exploring MicroRNA and Exosome Involvement in Malignant Pleural Mesothelioma Drug Response', Cancers, vol. 14, no. 19, pp. 4784-4784.
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Malignant pleural mesothelioma (MPM) is a deadly thoracic malignancy and existing treatment options are limited. Chemotherapy remains the most widely used first-line treatment regimen for patients with unresectable MPM, but is hampered by drug resistance issues. The current study demonstrated a modest enhancement of MPM cell sensitivity to chemotherapy drug treatment following microRNA (miRNA) transfection in MPM cell lines, albeit not for all tested miRNAs. This effect was more pronounced for FAK (PND-1186) small molecule inhibitor treatment; consistent with previously published data. We previously established that MPM response to survivin (YM155) small molecule inhibitor treatment is unrelated to basal survivin expression. Here, we showed that MPM response to YM155 treatment is enhanced following miRNA transfection of YM155-resistant MPM cells. We determined that YM155-resistant MPM cells secrete a higher level of exosomes in comparison to YM155-sensitive MPM cells. Despite this, an exosome inhibitor (GW4896) did not enhance MPM cell sensitivity to YM155. Additionally, our study showed no evidence of a correlation between the mRNA expression of inhibitor of apoptosis (IAP) gene family members and MPM cell sensitivity to YM155. However, two drug transporter genes, ABCA6 and ABCA10, were upregulated in the MPM cell lines and correlated with poor sensitivity to YM155.

Johnson, D, Clases, D, Fernández-Sánchez, ML, Eiro, N, González, LO, Vizoso, FJ, Doble, PA & Gonzalez de Vega, R 2022, 'Quantitative multiplexed analysis of MMP-11 and CD45 in metastatic breast cancer tissues by immunohistochemistry-assisted LA–ICP–MS', Metallomics, vol. 14, no. 8, p. mfac052.
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Abstract Breast cancer is the leading cause of cancer death in woman and tremendous efforts are undertaken to limit its dissemination and to provide effective treatment. Various histopathological parameters are routinely assessed in breast cancer biopsies to provide valuable diagnostic and prognostic information. MMP-11 and CD45 are tumor-associated antigens and potentially valuable biomarkers for grading aggressiveness and metastatic probability. This paper presents methods for quantitative and multiplexed imaging of MMP-11 and CD45 in breast cancer tissues and investigates their potential for improved cancer characterization and patient stratification. An immunohistochemistry-assisted laser ablation–inductively coupled plasma–mass spectrometry (LA–ICP–MS) method was successfully developed and optimized using lanthanide-tagged monoclonal antibodies as proxies to determine spatial distributions and concentrations of the two breast cancer biomarkers. The labeling degree of antibodies was determined via size exclusion–ICP–tandem mass spectrometry (SEC–ICP–MS/MS) employing online calibration via post-column isotope dilution analysis (IDA). The calibration of spatial distributions of labeled lanthanides in tissues was performed by ablating mold-prepared gelatin standards spiked with element standards. Knowledge of labeling degrees enabled the translation of lanthanide concentrations into biomarkers concentrations. The k-means clustering was used to select tissue areas for statistical analysis and mean concentrations were compared for sets of metastatic, non-metastatic and healthy samples. MMP-11 was expressed in stroma surrounding tumor areas, while CD45 was predominantly found inside tumor areas with high cell density. There was no significant correlation between CD45 and metastasis (P = 0.70); however, MMP-11 was significantly up-regulated (202%) in metastatic samples compared to non-metastatic (P = 0.0077) ...

Johnson, M, Burns, B, Herdean, A, Angeloski, A, Ralph, P, Morris, T, Kindler, G, Wong, H, Kuzhiumparambil, U, Sedger, L & Larkum, A 2022, 'A Cyanobacteria Enriched Layer of Shark Bay Stromatolites Reveals a New Acaryochloris Strain Living in Near Infrared Light', Microorganisms, vol. 10, no. 5, pp. 1035-1035.
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The genus Acaryochloris is unique among phototrophic organisms due to the dominance of chlorophyll d in its photosynthetic reaction centres and light-harvesting proteins. This allows Acaryochloris to capture light energy for photosynthesis over an extended spectrum of up to ~760 nm in the near infra-red (NIR) spectrum. Acaryochloris sp. has been reported in a variety of ecological niches, ranging from polar to tropical shallow aquatic sites. Here, we report a new Acarychloris strain isolated from an NIR-enriched stratified microbial layer 4–6 mm under the surface of stromatolite mats located in the Hamelin Pool of Shark Bay, Western Australia. Pigment analysis by spectrometry/fluorometry, flow cytometry and spectral confocal microscopy identifies unique patterns in pigment content that likely reflect niche adaption. For example, unlike the original A. marina species (type strain MBIC11017), this new strain, Acarychloris LARK001, shows little change in the chlorophyll d/a ratio in response to changes in light wavelength, displays a different Fv/Fm response and lacks detectable levels of phycocyanin. Indeed, 16S rRNA analysis supports the identity of the A. marina LARK001 strain as close to but distinct from from the A. marina HICR111A strain first isolated from Heron Island and previously found on the Great Barrier Reef under coral rubble on the reef flat. Taken together, A. marina LARK001 is a new cyanobacterial strain adapted to the stromatolite mats in Shark Bay.

Jolliffe, KKA & Gale, PA 2022, 'The supramolecular chemistry of anions', Organic & Biomolecular Chemistry, vol. 20, no. 4, pp. 713-714.
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Guest editors Katrina Jolliffe and Philip Gale introduce the Organic & Biomolecular Chemistry themed collection on the supramolecular chemistry of anions.

Jones, NI, Harmer, CJ, Hamidian, M & Hall, RM 2022, 'Evolution of Acinetobacter baumannii plasmids carrying the oxa58 carbapenemase resistance gene via plasmid fusion, IS26-mediated events and dif module shuffling', Plasmid, vol. 121, pp. 102628-102628.
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Acinetobacter baumannii RepAci1-RepAci10 plasmids pA388 from a global clone 1 (GC1) isolate from Greece, and pACICU1 and variant pACICU1b from an Italian GC2 isolate were found to share a common ancestor. The ancestor formed via recombination between pdif sites in the widely-distributed RepAci1 plasmid pA1-1 and in a RepAci10 plasmid carrying the oxa58 carbapenem-resistance gene in a dif module. Each plasmid includes copies of IS26 and multiple dif modules surrounded by 28 bp pdif sites resembling the chromosomal dif site, including one carrying the oxa58 gene. Plasmid sequences were compared to identify factors driving their evolution and divergence. IS26-mediated events, recombination between pdif sites and homologous recombination have all contributed. A translocatable unit that includes oxa58, generated by an IS26-mediated adjacent deletion, had been re-inserted by IS26 adjacent to an IS26 in pACICU1b to create the oxa58 gene duplication previously found in pACICU1. The oxa58 duplication has been lost from pACICU1b and the Tn6020 variant carrying the aphA1 (kanamycin, neomycin resistance) gene in pA388 has been lost from pACICU1/1b via recombination between directly-oriented IS26 copies. Two dif modules located between directly-oriented pdif sites in pA388 have been lost from pACICU1/1b and the product of this and other deletion events as well as inversion of dif modules located between inversely-oriented pdif sites were detected experimentally in pA388 DNA by PCR. Also, the new junctions were detected in a minority of reads in pA388 long-read sequence data. Inversion and deletion were only detected when the spacers in the pdif sites were identical and equivalent events involving mismatched spacers were not detected.

Ju, Z, Zhao, Q, Chao, D, Hou, Y, Pan, H, Sun, W, Yuan, Z, Li, H, Ma, T, Su, D & Jia, B 2022, 'Energetic Aqueous Batteries', Advanced Energy Materials, vol. 12, no. 27, pp. 2201074-2201074.
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AbstractRechargeable aqueous batteries are considered to be one of the most effective energy storage technologies to balance the cost‐efficiency, safety, and energy/power demands. The further progress of aqueous batteries with high energy density is needed to meet the ever‐increasing energy‐storage demands. This review highlights the strategies proposed so far to pursue the high energy density aqueous batteries, including the aspects of the electrolytes (from concentrated to dilute), the electrode chemistry (from inserted to converted), the cathode materials (from inorganic to organic), the anode materials (from compound to metallic), and the battery configurations (from integrated to decoupled). Critical appraisals of the emerging electrochemistry are presented for addressing the key issues in boosting the energy densities. Finally, the authors render insights into the future development of high‐energy aqueous batteries.

Kam, JY, Hortle, E, Krogman, E, Warner, SE, Wright, K, Luo, K, Cheng, T, Manuneedhi Cholan, P, Kikuchi, K, Triccas, JA, Britton, WJ, Johansen, MD, Kremer, L & Oehlers, SH 2022, 'Rough and smooth variants of Mycobacterium abscessus are differentially controlled by host immunity during chronic infection of adult zebrafish', Nature Communications, vol. 13, no. 1, pp. 1-11.
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AbstractPrevalence of Mycobacterium abscessus infections is increasing in patients with respiratory comorbidities. After initial colonisation, M. abscessus smooth colony (S) variants can undergo an irreversible genetic switch into highly inflammatory, rough colony (R) variants, often associated with a decline in pulmonary function. Here, we use an adult zebrafish model of chronic infection with R and S variants to study M. abscessus pathogenesis in the context of fully functioning host immunity. We show that infection with an R variant causes an inflammatory immune response that drives necrotic granuloma formation through host TNF signalling, mediated by the tnfa, tnfr1 and tnfr2 gene products. T cell-dependent immunity is stronger against the R variant early in infection, and regulatory T cells associate with R variant granulomas and limit bacterial growth. In comparison, an S variant proliferates to high burdens but appears to be controlled by TNF-dependent innate immunity early during infection, resulting in delayed granuloma formation. Thus, our work demonstrates the applicability of adult zebrafish to model persistent M. abscessus infection, and illustrates differences in the immunopathogenesis induced by R and S variants during granulomatous infection.

Karacan, I, Ben‐Nissan, B, Santos, J, Yiu, S, Bradbury, P, Valenzuela, SM & Chou, J 2022, 'In vitro testing and efficacy of poly‐lactic acid coating incorporating antibiotic loaded coralline bioceramic on Ti6Al4V implant against Staphylococcus aureus', Journal of Tissue Engineering and Regenerative Medicine, vol. 16, no. 12, pp. 1149-1162.
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Biofilm formation on an implant surface is most commonly caused by the human pathogenic bacteria Staphylococcus aureus, which can lead to implant related infections and failure. It is a major problem for both implantable orthopedic and maxillofacial devices. The current antibiotic treatments are typically delivered orally or in an injectable form. They are not highly effective in preventing or removing biofilms, and they increase the risk of antibiotic resistance of bacteria and have a dose-dependent negative biological effect on human cells. Our aim was to improve current treatments via a localized and controlled antibiotic delivery-based implant coating system to deliver the antibiotic, gentamicin (Gm). The coating contains coral skeleton derived hydroxyapatite powders (HAp) that act as antibiotic carrier particles and have a biodegradable poly-lactic acid (PLA) thin film matrix. The system is designed to prevent implant related infections while avoiding the deleterious effects of high concentration antibiotics in implants on local cells including primary human adipose derived stem cells (ADSCs). Testing undertaken in this study measured the rate of S. aureus biofilm formation and determined the growth rate and proliferation of ADSCs. After 24 h, S. aureus biofilm formation and the percentage of live cells found on the surfaces of all 5%-30% (w/w) PLA-Gm-(HAp-Gm) coated Ti6Al4V implants was lower than the control samples. Furthermore, Ti6Al4V implants coated with up to 10% (w/w) PLA-Gm-(HAp-Gm) did not have noticeable Gm related adverse effect on ADSCs, as assessed by morphological and surface attachment analyses. These results support the use and application of the antibacterial PLA-Gm-(HAp-Gm) thin film coating design for implants, as an antibiotic release control mechanism to prevent implant-related infections.

Kaur, J, Gulati, M, Corrie, L, Awasthi, A, Jha, NK, Chellappan, DK, Gupta, G, MacLoughlin, R, Oliver, BG, Dua, K & Singh, SK 2022, 'Role of nucleic acid-based polymeric micelles in treating lung diseases', Nanomedicine, vol. 17, no. 25, pp. 1951-1960.
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The prevalence of lung diseases is increasing year by year and existing drug therapies only provide symptomatic relief rather than targeting the actual cause. Nucleic acids can be used as an alternative therapeutic approach owing to their potential to reform a homeostatic balance by upregulating protective genes or downregulating damaging genes. However, their inherent properties, such as poor stability, ineffective cellular uptake, negative charge and so on, hinder their clinical utility. Such limitations can be overcome by exploiting the functional chemistry of polymeric micelles (PMs) for site-specific delivery, transfection efficiency and improved stability. With this objective, the present work describes the advancements made in designing nucleic acid-based PMs for treating lung diseases followed by approaches requiring consideration for clinical applications.

Kaur, J, Gulati, M, Famta, P, Corrie, L, Awasthi, A, Saini, S, Khatik, GL, Bettada, VG, Madhunapantula, SV, Paudel, KR, Gupta, G, Chellappan, DK, Arshad, MF, Adams, J, Gowthamarajan, K, Dua, K, Hansbro, PM & Singh, SK 2022, 'Polymeric micelles loaded with glyburide and vanillic acid: I. Formulation development, in-vitro characterization and bioavailability studies', International Journal of Pharmaceutics, vol. 624, pp. 121987-121987.
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Kc, BB, Khanal, P, Oli, LK, Dhital, SR, Pradhan, B, Pahari, DP & Paudel, KR 2022, 'Prevalence and Factors Associated with Tobacco Use among High School Students.', J Nepal Health Res Counc, vol. 20, no. 2, pp. 310-315.
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BACKGROUND: Tobacco use is the leading cause of morbidity and mortality worldwide. Tobacco use among school-level students is a growing a public health problem in Nepal. A number of factors may be associated with tobacco use, but there is lack of literature showcasing an in-depth understanding of the growing prevalence of tobacco use in the Nepalese context. Therefore, our study aims to determine the prevalence of tobacco use and examine the factors associated with tobacco use among high school students at public schools in Budhanilkantha municipality, Kathmandu, Nepal. METHODS: A cross-sectional survey was conducted, and 378 students were selected for this study. The schools were selected randomly. Data collection was carried out using the self-administered questionnaires adapted from the World Health Organization used Global Youth Tobacco Survey and the Center for Disease Control and Prevention used Youth Tobacco Survey. RESULTS: Overall, 31.7% of the students ever consumed any tobacco products, and 20.1% were current tobacco users. One in five students started smoking when they were less than ten years of age. The proportion of students seeing at least one family member smoking and using smokeless tobacco was 52.1% and 47.1% respectively. Male and older students were significantly more likely to consume tobacco products than female and young students. CONCLUSIONS: This study showed that a significant proportion of school students had experienced tobacco use. Age and sex of the students were significantly associated with the status of current smoking and the use of smokeless tobacco.

Keen, B, Cawley, A, Reedy, B & Fu, S 2022, 'Metabolomics in clinical and forensic toxicology, sports anti‐doping and veterinary residues', Drug Testing and Analysis, vol. 14, no. 5, pp. 794-807.
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AbstractMetabolomics is a multidisciplinary field providing workflows for complementary approaches to conventional analytical determinations. It allows for the study of metabolically related groups of compounds or even the study of novel pathways within the biological system. The procedural stages of metabolomics; experimental design, sample preparation, analytical determinations, data processing and statistical analysis, compound identification and validation strategies are explored in this review. The selected approach will depend on the type of study being conducted. Experimental design influences the whole metabolomics workflow and thus needs to be properly assessed to ensure sufficient sample size, minimal introduced and biological variation and appropriate statistical power. Sample preparation needs to be simple, yet potentially global in order to detect as many compounds as possible. Analytical determinations need to be optimised either for the list of targeted compounds or a universal approach. Data processing and statistical analysis approaches vary widely and need to be better harmonised for review and interpretation. This includes validation strategies that are currently deficient in many presented workflows. Common compound identification approaches have been explored in this review. Metabolomics applications are discussed for clinical and forensic toxicology, human and equine sports anti‐doping and veterinary residues.

Keen, B, Cawley, A, Reedy, B, Noble, G & Fu, S 2022, 'A statistical focus on doping using a metabolomics approach', Toxicologie Analytique et Clinique, vol. 34, no. 3, pp. S58-S58.
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Kendig, MD & Bradfield, LA 2022, 'Association learning: Dopamine and the formation of backward associations', Current Biology, vol. 32, no. 14, pp. R769-R771.
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The activity of dopamine neurons is critical for the ability to learn and update cue-reward associations. New work in rats shows that dopamine transients are also critical for the formation of backward associations in which the reward precedes the neutral stimulus.

Kendig, MD, Hasebe, K, McCague, R, Lee, F, Leigh, S-J, Arnold, R & Morris, MJ 2022, 'Adolescent exposure to a solid high-fat, high-sugar ‘cafeteria’ diet leads to more pronounced changes in metabolic measures and gut microbiome composition than liquid sugar in female rats', Appetite, vol. 172, pp. 105973-105973.
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Khan, JU, Sayyar, S, Jin, D, Paull, B & Innis, PC 2022, 'Surface functionalization of low-cost textile-based microfluidics for manipulation of electrophoretic selectivity of charged analytes', Microfluidics and Nanofluidics, vol. 26, no. 12.
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AbstractTextile-based microfluidics offer new opportunities for developing low-cost, open surface-assessable analytical systems for the electrophoretic analysis of complex chemical and biological matrixes. In contrast to electrophoretic fluidic transport in typical chip-based enclosed capillaries where direct access to the sample zone during analysis is a real challenge. Herein, we demonstrate that electrophoretic selectivity could be easily manipulated on these inverted low-cost bespoke textile substrates via a simple surface-functionalization to manipulate, redirect, extract, and characterize charged analytes. This simple approach enables significant improvement in the electrophoretic separation and isotachophoretic (ITP) preconcentration of charged solutes at the surface of open surface-accessible 3D textile constructs. In this work, polyester 3D braided structures have been developed using the conventional braiding technique and used as the electrophoretic substrates, which were modified by dip-coating with polycationic polymers such as chitosan and polyethyleneimine (PEIn). The surface functionalization resulted in the modulation of the electroosmotic flow (EOF) and electrophoretic mobilities of the charged solutes with respect to the unmodified substrates. Chitosan outperformed PEIn in terms of efficient electrophoretic separation and isotachophoretic stacking of an anionic solute. However, PEIn modification resulted in significant suppression of the EOF over a broad range of pH values from 3 to 9 and exhibited fast EOF at acidic pH compared to controlled polyester, which could be promising for the analysis of basic proteins. These findings suggest a great potential for the development of affordable surface-accessible textile-based analytical devices for controlling the specific migration, direction, analysis time, and separation and preconcentration of charged analytes. ...

Khan, K, Tareen, AK, Iqbal, M, Zhang, Y, Mahmood, A, Mahmood, N, Yin, J, Khatoon, R & Zhang, H 2022, 'Recent advance in MXenes: New horizons in electrocatalysis and environmental remediation technologies', Progress in Solid State Chemistry, vol. 68, pp. 100370-100370.
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Khursheed, R, Dua, K, Vishwas, S, Gulati, M, Jha, NK, Aldhafeeri, GM, Alanazi, FG, Goh, BH, Gupta, G, Paudel, KR, Hansbro, PM, Chellappan, DK & Singh, SK 2022, 'Biomedical applications of metallic nanoparticles in cancer: Current status and future perspectives', Biomedicine & Pharmacotherapy, vol. 150, pp. 112951-112951.
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Khursheed, R, Paudel, KR, Gulati, M, Vishwas, S, Jha, NK, Hansbro, PM, Oliver, BG, Dua, K & Singh, SK 2022, 'Expanding the arsenal against pulmonary diseases using surface-functionalized polymeric micelles: breakthroughs and bottlenecks', Nanomedicine, vol. 17, no. 12, pp. 881-911.
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Pulmonary diseases such as lung cancer, asthma and tuberculosis have remained one of the common challenges globally. Polymeric micelles (PMs) have emerged as an effective technique for achieving targeted drug delivery for a local as well as a systemic effect. These PMs encapsulate and protect hydrophobic drugs, increase pulmonary targeting, decrease side effects and enhance drug efficacy through the inhalation route. In the current review, emphasis has been placed on the different barriers encountered by the drugs given via the pulmonary route and the mechanism of PMs in achieving drug targeting. The applications of PMs in different pulmonary diseases have also been discussed in detail.

Kianinia, M, Xu, Z-Q, Toth, M & Aharonovich, I 2022, 'Quantum emitters in 2D materials: Emitter engineering, photophysics, and integration in photonic nanostructures', Applied Physics Reviews, vol. 9, no. 1, pp. 1-18.
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Quantum emitters have become a vital tool for both fundamental science and emerging technologies. In recent years, the focus in the field has shifted to exploration and identification of new quantum systems enabled by the emerging library of atomically thin, two dimensional materials. In this review, we highlight the current state of the art in engineering of quantum emitters in 2D systems, with an emphasis on transition metal di-chalcogenides (TMDCs) and hexagonal boron nitride. We start by reviewing progress in TMDCs, with focus on emitter engineering, ability to tune their spectral properties, and observation of interlayer excitons. We then discuss emitters in hBN and focus on emitters' origin, engineering, and emerging phenomena—spanning super-resolution imaging and optical spin readout. We summarize by discussing practical advances of integration of emitters in 2D hosts with plasmonic and dielectric photonic cavities, underpinned by quantum light–matter interactions. We conclude by outlining pathways for practical on-chip quantum photonics applications and highlight challenges and opportunities within this field of research.

Kim, E, Kim, Y-J, Ji, Z, Kang, JM, Wirianto, M, Paudel, KR, Smith, JA, Ono, K, Kim, J-A, Eckel-Mahan, K, Zhou, X, Lee, HK, Yoo, JY, Yoo, S-H & Chen, Z 2022, 'ROR activation by Nobiletin enhances antitumor efficacy via suppression of IκB/NF-κB signaling in triple-negative breast cancer', Cell Death & Disease, vol. 13, no. 4.
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AbstractTriple-negative breast cancer (TNBC) is a heterogeneous disease characterized by poor response to standard therapies and therefore unfavorable clinical outcomes. Better understanding of TNBC and new therapeutic strategies are urgently needed. ROR nuclear receptors are multifunctional transcription factors with important roles in circadian pathways and other processes including immunity and tumorigenesis. Nobiletin (NOB) is a natural compound known to display anticancer effects, and our previous studies showed that NOB activates RORs to enhance circadian rhythms and promote physiological fitness in mice. Here, we identified several TNBC cell lines being sensitive to NOB, by itself or in combination. Cell and xenograft experiments showed that NOB significantly inhibited TNBC cell proliferation and motility in vitro and in vivo. ROR loss- and gain-of-function studies showed concordant effects of the NOB–ROR axis on MDA-MB-231 cell growth. Mechanistically, we found that NOB activates ROR binding to the ROR response elements (RRE) of the IκBα promoter, and NOB strongly inhibited p65 nuclear translocation. Consistent with transcriptomic analysis indicating cancer and NF-κB signaling as major pathways altered by NOB, p65-inducible expression abolished NOB effects, illustrating a requisite role of NF-κB suppression mediating the anti-TNBC effect of NOB. Finally, in vivo mouse xenograft studies showed that NOB enhanced the antitumor efficacy in mammary fat pad implanted TNBC, as a single agent or in combination with the chemotherapy agent Docetaxel. Together, our study highlights an anti-TNBC mechanism of ROR-NOB via suppression of NF-κB signaling, suggesting novel preventive and chemotherapeutic strategies against this devastating disease.

Kim, T-H, Alraek, T, Bian, Z-X, Birch, S, Bovey, M, Lee, J, Lee, MS, Robinson, N & Zaslawski, C 2022, 'Corrigendum to “Clinical reasoning in traditional medicine exemplified by the clinical encounter of Korean medicine” [Integr Med Res 2021: 10; 100641]', Integrative Medicine Research, vol. 11, no. 1, pp. 100817-100817.
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Kindler, GS, Wong, HL, Larkum, AWD, Johnson, M, MacLeod, FI & Burns, BP 2022, 'Genome-resolved metagenomics provides insights into the functional complexity of microbial mats in Blue Holes, Shark Bay', FEMS Microbiology Ecology, vol. 98, no. 1, p. fiab158.
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ABSTRACTThe present study describes for the first time the community composition and functional potential of the microbial mats found in the supratidal, gypsum-rich and hypersaline region of Blue Holes, Shark Bay. This was achieved via high-throughput metagenomic sequencing of total mat community DNA and complementary analyses using hyperspectral confocal microscopy. Mat communities were dominated by Proteobacteria (29%), followed by Bacteroidetes/Chlorobi group (11%) and Planctomycetes (10%). These mats were found to also harbour a diverse community of potentially novel microorganisms, including members from the DPANN, Asgard archaea and candidate phyla radiation, with highest diversity found in the lower regions (∼14–20 mm depth) of the mat. In addition to pathways for major metabolic cycles, a range of putative rhodopsins with previously uncharacterized motifs and functions were identified along with heliorhodopsins and putative schizorhodopsins. Critical microbial interactions were also inferred, and from 117 medium- to high-quality metagenome-assembled genomes, viral defence mechanisms (CRISPR, BREX and DISARM), elemental transport, osmoprotection, heavy metal resistance and UV resistance were also detected. These analyses have provided a greater understanding of these distinct mat systems in Shark Bay, including key insights into adaptive responses and proposing that photoheterotrophy may be an important lifestyle in Blue Holes.

King, K, Bramucci, AR, Labbate, M, Raina, J-B & Seymour, JR 2022, 'Heterogeneous Growth Enhancement of Vibrio cholerae in the Presence of Different Phytoplankton Species', Applied and Environmental Microbiology, vol. 88, no. 17, p. e0115822.
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Many environmental strains of V. cholerae do not cause cholera epidemics but remain a public health concern due to their roles in milder gastrointestinal illnesses. With emerging evidence that these infections are increasing due to climate change, determining the ecological drivers that enable outbreaks of V. cholerae in coastal environments is becoming critical.

Kirkby, K, Webster, J, Landa, BB, Olivares, C, Roser, S, Falconer, L, Gopurenko, D & Chapman, TA 2022, 'First report of the presence of Verticillium dahliae VCG6 in Australia', Australasian Plant Disease Notes, vol. 17, no. 1, p. 9.
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Klein, SG, Geraldi, NR, Anton, A, Schmidt‐Roach, S, Ziegler, M, Cziesielski, MJ, Martin, C, Rädecker, N, Frölicher, TL, Mumby, PJ, Pandolfi, JM, Suggett, DJ, Voolstra, CR, Aranda, M & Duarte, CM 2022, 'Projecting coral responses to intensifying marine heatwaves under ocean acidification', Global Change Biology, vol. 28, no. 5, pp. 1753-1765.
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AbstractOver this century, coral reefs will run the gauntlet of climate change, as marine heatwaves (MHWs) become more intense and frequent, and ocean acidification (OA) progresses. However, we still lack a quantitative assessment of how, and to what degree, OA will moderate the responses of corals to MHWs as they intensify throughout this century. Here, we first projected future MHW intensities for tropical regions under three future greenhouse gas emissions scenario (representative concentration pathways, RCP2.6, RCP4.5 and RCP8.5) for the near‐term (2021–2040), mid‐century (2041–2060) and late‐century (2081–2100). We then combined these MHW intensity projections with a global data set of 1,788 experiments to assess coral attribute performance and survival under the three emissions scenarios for the near‐term, mid‐century and late‐century in the presence and absence of OA. Although warming and OA had predominately additive impacts on the coral responses, the contribution of OA in affecting most coral attributes was minor relative to the dominant role of intensifying MHWs. However, the addition of OA led to greater decreases in photosynthesis and survival under intermediate and unrestricted emissions scenario for the mid‐ and late‐century than if intensifying MHWs were considered as the only driver. These results show that role of OA in modulating coral responses to intensifying MHWs depended on the focal coral attribute and extremity of the scenario examined. Specifically, intensifying MHWs and OA will cause increasing instances of coral bleaching and substantial declines in coral productivity, calcification and survival within the next two decades under the low and intermediate emissions scenario. These projections suggest that corals must rapidly adapt or acclimatize to projected ocean conditions to persist, which is far more likely under a low emissions scenario and with increasing efforts to manage reefs to enhance...

Kliment, CR & Gosens, R 2022, 'Chymase-1: a “MAST”-er switch in COPD?', European Respiratory Journal, vol. 60, no. 6, pp. 2201356-2201356.
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Klingberg, J, Keen, B, Cawley, A, Pasin, D & Fu, S 2022, 'Developments in high-resolution mass spectrometric analyses of new psychoactive substances', Archives of Toxicology, vol. 96, no. 4, pp. 949-967.
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AbstractThe proliferation of new psychoactive substances (NPS) has necessitated the development and improvement of current practices for the detection and identification of known NPS and newly emerging derivatives. High-resolution mass spectrometry (HRMS) is quickly becoming the industry standard for these analyses due to its ability to be operated in data-independent acquisition (DIA) modes, allowing for the collection of large amounts of data and enabling retrospective data interrogation as new information becomes available. The increasing popularity of HRMS has also prompted the exploration of new ways to screen for NPS, including broad-spectrum wastewater analysis to identify usage trends in the community and metabolomic-based approaches to examine the effects of drugs of abuse on endogenous compounds. In this paper, the novel applications of HRMS techniques to the analysis of NPS is reviewed. In particular, the development of innovative data analysis and interpretation approaches is discussed, including the application of machine learning and molecular networking to toxicological analyses.

Knott, GJ, Chong, YS, Passon, DM, Liang, X-H, Deplazes, E, Conte, MR, Marshall, AC, Lee, M, Fox, AH & Bond, CS 2022, 'Structural basis of dimerization and nucleic acid binding of human DBHS proteins NONO and PSPC1', Nucleic Acids Research, vol. 50, no. 1, pp. 522-535.
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Abstract The Drosophila behaviour/human splicing (DBHS) proteins are a family of RNA/DNA binding cofactors liable for a range of cellular processes. DBHS proteins include the non-POU domain-containing octamer-binding protein (NONO) and paraspeckle protein component 1 (PSPC1), proteins capable of forming combinatorial dimers. Here, we describe the crystal structures of the human NONO and PSPC1 homodimers, representing uncharacterized DBHS dimerization states. The structures reveal a set of conserved contacts and structural plasticity within the dimerization interface that provide a rationale for dimer selectivity between DBHS paralogues. In addition, solution X-ray scattering and accompanying biochemical experiments describe a mechanism of cooperative RNA recognition by the NONO homodimer. Nucleic acid binding is reliant on RRM1, and appears to be affected by the orientation of RRM1, influenced by a newly identified ‘β-clasp’ structure. Our structures shed light on the molecular determinants for DBHS homo- and heterodimerization and provide a basis for understanding how DBHS proteins cooperatively recognize a broad spectrum of RNA targets.

Kondaveeti, S, Petri, DFS & Jeong, HE 2022, 'Efficiency of air-dried and freeze-dried alginate/xanthan beads in batch, recirculating and column adsorption processes', International Journal of Biological Macromolecules, vol. 204, pp. 345-355.
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Kong, J, Li, L, Liu, J, Marlton, FP, Jørgensen, MRV & Pramanick, A 2022, 'A Local Atomic Mechanism for Monoclinic-Tetragonal Phase Boundary Creation in Li-Doped Na_0.5K_0.5NbO₃ Ferroelectric Solid Solution', Inorganic Chemistry, vol. 61, no. 10, pp. 4335-4349.
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Kononov, A, Memar, J & Zinder, Y 2022, 'On a borderline between the NP-hard and polynomial-time solvable cases of the flow shop with job-dependent storage requirements', Journal of Global Optimization, vol. 83, no. 3, pp. 445-456.
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Kordzakhia, NE & Novikov, AA 2022, 'On Maximal Inequalities for Ornstein--Uhlenbeck Processes with Jumps', Theory of Probability & Its Applications, vol. 66, no. 4, pp. 713-728.
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Kottek, M & Yuen, ML 2022, 'Public health risks from asbestos cement roofing', American Journal of Industrial Medicine, vol. 65, no. 3, pp. 157-161.
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AbstractThere is no identified risk‐free threshold exposure to asbestos. Based on epidemiology and toxicology, asbestos fiber dimensions have been implicated in causing asbestos‐related diseases. Phase‐contrast microscopy provides only a limited index of exposure to fiber dimensions implicated in mesothelioma induction. Installed asbestos‐containing materials (ACMs) create an ongoing risk of intense exposure during natural disasters and remodeling, along with low‐level exposure arising from the continual emission of airborne asbestos into the environment arising from weathering of installed ACM. Epidemiological studies have demonstrated a risk of disease associated with proximity to asbestos cement roofing (ACR), while ongoing environmental emissions of asbestos from installed ACR have also been demonstrated. Owing to the limitations of the available data, a precautionary approach is warranted; asbestos‐free roofing materials should be used in new construction and existing ACR should be removed at the earliest opportunity.

Krich, C, Mahecha, MD, Migliavacca, M, De Kauwe, MG, Griebel, A, Runge, J & Miralles, DG 2022, 'Decoupling between ecosystem photosynthesis and transpiration: a last resort against overheating', Environmental Research Letters, vol. 17, no. 4, pp. 044013-044013.
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Abstract Ecosystems are projected to face extreme high temperatures more frequently in the near future. Various biotic coping strategies exist to prevent heat stress. Controlled experiments have recently provided evidence for continued transpiration in woody plants during high air temperatures, even when photosynthesis is inhibited. Such a decoupling of photosynthesis and transpiration would represent an effective strategy (‘known as leaf or canopy cooling’) to prevent lethal leaf temperatures. At the ecosystem scale, continued transpiration might dampen the development and propagation of heat extremes despite further desiccating soils. However, at the ecosystem scale, evidence for the occurrence of this decoupling is still limited. Here, we aim to investigate this mechanism using eddy-covariance data of thirteen woody ecosystems located in Australia and a causal graph discovery algorithm. Working at half-hourly time resolution, we find evidence for a decoupling of photosynthesis and transpiration in four ecosystems which can be classified as Mediterranean woodlands. The decoupling occurred at air temperatures above 35 ∘C. At the nine other investigated woody sites, we found that vegetation CO2 exchange remained coupled to transpiration at the observed high air temperatures. Ecosystem characteristics suggest that the canopy energy balance plays a crucial role in determining the occurrence of a decoupling. Our results highlight the value of causal-inference approaches for the analysis of complex physiological processes. With regard to projected increasing temperatures and especially extreme events in future climates, further vegetation types might be pushed to threatening canopy temperatures. Our findings suggest that the coupling of leaf-level photosynthesis and stomatal conductance, common in land surface schemes, may need be re-examined when applied to high-tempe...

Kumar, R, Kumar, R, Sharma, N, Khurana, N, Singh, SK, Satija, S, Mehta, M & Vyas, M 2022, 'Pharmacological evaluation of bromelain in mouse model of Alzheimer’s disease', NeuroToxicology, vol. 90, pp. 19-34.
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Kumar, V, Horvat, J, Wark, P, Whiteman, M & Hansbro, P 2022, 'Hydrogen sulfide attenuates cigarette smoke-induced oxidative stress and inflammation in human primary bronchial epithelial cells and experimental COPD', 03.03 - Mechanisms of lung injury and repair.
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Kumari, N, Srivastava, A & Dumka, UC 2022, 'Correction: Kumari et al. A Long-Term Spatiotemporal Analysis of Vegetation Greenness over the Himalayan Region Using Google Earth Engine. Climate 2021, 9, 109', Climate, vol. 10, no. 8, pp. 116-116.
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There was an error in the original publication [...]

Kumari, N, Srivastava, A & Kumar, S 2022, 'Hydrological Analysis Using Observed and Satellite-Based Estimates: Case Study of a Lake Catchment in Raipur, India', Journal of the Indian Society of Remote Sensing, vol. 50, no. 1, pp. 115-128.
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Rainfall plays an essential role in different water management sectors ranging from industries, farming, livestock, and domestic utilization both in rural and urban areas. The surface water bodies like rivers, lakes, ponds, and reservoirs hold a huge proportion of the rainfall. However, due to spatio-temporal variability of rainfall and limited availability of meteorological stations, accurate estimation of the hydrological components such as surface runoff, evaporation, and baseflow is a challenging task. In this study, we have used hydrological information, Soil Conservation Service Curve Number method to develop an empirical relationship between rainfall and runoff in the Telibandha Lake Catchment (TLC), situated in Raipur district of Chhattisgarh, central India. Further, we have used Landsat derived remote sensing product, Normalized Difference Water Index (NDWI) to understand its temporal variation of water spread in the TLC over the fifteen years (2001–2015). The water spread areas are assessed by using the mean monthly NDWI data set and analyzing its seasonal and annual patterns. It is found that Telibandha Lake has a maximum depth of 2.9 m and its surface area is 0.12 km2. Apart from that, the annual runoff is around 232.28 mm, which accounts for almost 22% of the estimated rainfall. The monthly runoff coefficient varies from 0 to 0.25 in TLC. Both the temporal and spatial NDWI plots show that July–September months have high NDWI values in the TLC. The seasonal NDWI showed a good relationship with mean monthly rainfall data and depicts r2 = 0.78. The findings from this study helps in determining the temporal changes of water spread within the TLC and supports in understanding the lake characteristics.

Kuzhiumparambil, U, Labeeuw, L, Commault, A, Vu, HP, Nguyen, LN, Ralph, PJ & Nghiem, LD 2022, 'Effects of harvesting on morphological and biochemical characteristics of microalgal biomass harvested by polyacrylamide addition, pH-induced flocculation, and centrifugation', Bioresource Technology, vol. 359, pp. 127433-127433.
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The effects of microalgae harvesting methods on microalgal biomass quality were evaluated using three species namely the freshwater green alga Chlorella vulgaris, marine red alga Porphyridium purpureum and marine diatom Phaeodactylum tricornutum. Harvesting efficiencies of polyacrylamide addition, alkaline addition, and centrifugation ranged from 85 to 95, 59-92 and 100%, respectively, across these species. Morphology of the harvested cells (i.e. compromised cell walls) was significantly impacted by alkaline pH-induced flocculation for all three species. Over 50% of C. vulgaris cells were compromised with alkaline pH compared to < 10% with polyacrylamide and centrifugation. The metabolic profiles varied depending on harvesting methods. Species-specific decrease of certain metabolites was observed. These results suggest that the method of harvest can alter the metabolic profile of the biomass amongst the three harvesting methods, polyacrylamide addition showed higher harvesting efficiency with less compromised cells and higher retention of industry important biochemicals.

Kyu, HH, Vongpradith, A, Sirota, SB, Novotney, A, Troeger, CE, Doxey, MC, Bender, RG, Ledesma, JR, Biehl, MH, Albertson, SB, Frostad, JJ, Burkart, K, Bennitt, FB, Zhao, JT, Gardner, WM, Hagins, H, Bryazka, D, Dominguez, R-MV, Abate, SM, Abdelmasseh, M, Abdoli, A, Abdoli, G, Abedi, A, Abedi, V, Abegaz, TM, Abidi, H, Aboagye, RG, Abolhassani, H, Abtew, YD, Abubaker Ali, H, Abu-Gharbieh, E, Abu-Zaid, A, Adamu, K, Addo, IY, Adegboye, OA, Adnan, M, Adnani, QES, Afzal, MS, Afzal, S, Ahinkorah, BO, Ahmad, A, Ahmad, AR, Ahmad, S, Ahmadi, A, Ahmadi, S, Ahmed, H, Ahmed, JQ, Ahmed Rashid, T, Akbarzadeh-Khiavi, M, Al Hamad, H, Albano, L, Aldeyab, MA, Alemu, BM, Alene, KA, Algammal, AM, Alhalaiqa, FAN, Alhassan, RK, Ali, BA, Ali, L, Ali, MM, Ali, SS, Alimohamadi, Y, Alipour, V, Al-Jumaily, A, Aljunid, SM, Almustanyir, S, Al-Raddadi, RM, Al-Rifai, RHH, AlRyalat, SAS, Alvis-Guzman, N, Alvis-Zakzuk, NJ, Ameyaw, EK, Aminian Dehkordi, JJ, Amuasi, JH, Amugsi, DA, Anbesu, EW, Ansar, A, Anyasodor, AE, Arabloo, J, Areda, D, Argaw, AM, Argaw, ZG, Arulappan, J, Aruleba, RT, Asemahagn, MA, Athari, SS, Atlaw, D, Attia, EF, Attia, S, Aujayeb, A, Awoke, T, Ayana, TM, Ayanore, MA, Azadnajafabad, S, Azangou-Khyavy, M, Azari, S, Azari Jafari, A, Badar, M, Badiye, AD, Baghcheghi, N, Bagherieh, S, Baig, AA, Banach, M, Banerjee, I, Bardhan, M, Barone-Adesi, F, Barqawi, HJ, Barrow, A, Bashiri, A, Bassat, Q, Batiha, A-MM, Belachew, AB, Belete, MA, Belgaumi, UI, Bhagavathula, AS, Bhardwaj, N, Bhardwaj, P, Bhatt, P, Bhojaraja, VS, Bhutta, ZA, Bhuyan, SS, Bijani, A, Bitaraf, S, Bodicha, BBA, Briko, NI, Buonsenso, D, Butt, MH, Cai, J, Camargos, P, Cámera, LA, Chakraborty, PA, Chanie, MG, Charan, J, Chattu, VK, Ching, PR, Choi, S, Chong, YY, Choudhari, SG, Chowdhury, EK, Christopher, DJ, Chu, D-T, Cobb, NL, Cohen, AJ, Cruz-Martins, N, Dadras, O, Dagnaw, FT, Dai, X, Dandona, L, Dandona, R, Dao, ATM, Debela, SA, Demisse, B, Demisse, FW, Demissie, S, Dereje, D, Desai, HD, Desta, AA, Desye, B, Dhingra, S, Diao, N, Diaz, D, Digesa, LE, Doan, LP, Dodangeh, M, Dongarwar, D, Dorostkar, F, dos Santos, WM, Dsouza, HL, Dubljanin, E, Durojaiye, OC, Edinur, HA, Ehsani-Chimeh, E, Eini, E, Ekholuenetale, M, Ekundayo, TC, El Desouky, ED, El Sayed, I, El Sayed Zaki, M, Elhadi, M, Elkhapery, AMR, Emami, A, Engelbert Bain, L, Erkhembayar, R, Etaee, F, Ezati Asar, M & et al. 2022, 'Age–sex differences in the global burden of lower respiratory infections and risk factors, 1990–2019: results from the Global Burden of Disease Study 2019', The Lancet Infectious Diseases, vol. 22, no. 11, pp. 1626-1647.
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BACKGROUND: The global burden of lower respiratory infections (LRIs) and corresponding risk factors in children older than 5 years and adults has not been studied as comprehensively as it has been in children younger than 5 years. We assessed the burden and trends of LRIs and risk factors across all age groups by sex, for 204 countries and territories. METHODS: In this analysis of data for the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2019, we used clinician-diagnosed pneumonia or bronchiolitis as our case definition for LRIs. We included International Classification of Diseases 9th edition codes 079.6, 466-469, 470.0, 480-482.8, 483.0-483.9, 484.1-484.2, 484.6-484.7, and 487-489 and International Classification of Diseases 10th edition codes A48.1, A70, B97.4-B97.6, J09-J15.8, J16-J16.9, J20-J21.9, J91.0, P23.0-P23.4, and U04-U04.9. We used the Cause of Death Ensemble modelling strategy to analyse 23 109 site-years of vital registration data, 825 site-years of sample vital registration data, 1766 site-years of verbal autopsy data, and 681 site-years of mortality surveillance data. We used DisMod-MR 2.1, a Bayesian meta-regression tool, to analyse age-sex-specific incidence and prevalence data identified via systematic reviews of the literature, population-based survey data, and claims and inpatient data. Additionally, we estimated age-sex-specific LRI mortality that is attributable to the independent effects of 14 risk factors. FINDINGS: Globally, in 2019, we estimated that there were 257 million (95% uncertainty interval [UI] 240-275) LRI incident episodes in males and 232 million (217-248) in females. In the same year, LRIs accounted for 1·30 million (95% UI 1·18-1·42) male deaths and 1·20 million (1·07-1·33) female deaths. Age-standardised incidence and mortality rates were 1·17 times (95% UI 1·16-1·18) and 1·31 times (95% UI 1·23-1·41) greater in males than in females in 2019. Between 1990 and 2019, LRI incidence and mortali...

Lagune, M, Le Moigne, V, Johansen, MD, Vásquez Sotomayor, F, Daher, W, Petit, C, Cosentino, G, Paulowski, L, Gutsmann, T, Wilmanns, M, Maurer, FP, Herrmann, J-L, Girard-Misguich, F & Kremer, L 2022, 'The ESX-4 substrates, EsxU and EsxT, modulate Mycobacterium abscessus fitness', PLOS Pathogens, vol. 18, no. 8, pp. e1010771-e1010771.
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ESX type VII secretion systems are complex secretion machineries spanning across the mycobacterial membrane and play an important role in pathogenicity, nutrient uptake and conjugation. We previously reported the role of ESX-4 in modulating Mycobacterium abscessus intracellular survival. The loss of EccB4 was associated with limited secretion of two effector proteins belonging to the WXG-100 family, EsxU and EsxT, and encoded by the esx-4 locus. This prompted us to investigate the function of M. abscessus EsxU and EsxT in vitro and in vivo. Herein, we show that EsxU and EsxT are substrates of ESX-4 and form a stable 1:1 heterodimer that permeabilizes artificial membranes. While expression of esxU and esxT was up-regulated in M. abscessus-infected macrophages, their absence in an esxUT deletion mutant prevented phagosomal membrane disruption while maintaining M. abscessus in an unacidified phagosome. Unexpectedly, the esxUT deletion was associated with a hyper-virulent phenotype, characterised by increased bacterial loads and mortality in mouse and zebrafish infection models. Collectively, these results demonstrate that the presence of EsxU and EsxT dampens survival and persistence of M. abscessus during infection.

LaJeunesse, TC, Wiedenmann, J, Casado-Amezúa, P, D’Ambra, I, Turnham, KE, Nitschke, MR, Oakley, CA, Goffredo, S, Spano, CA, Cubillos, VM, Davy, SK & Suggett, DJ 2022, 'Revival of Philozoon Geddes for host-specialized dinoflagellates, ‘zooxanthellae’, in animals from coastal temperate zones of northern and southern hemispheres', European Journal of Phycology, vol. 57, no. 2, pp. 166-180.
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Lam, T, Barratt, MJ, Bartlett, M, Latimer, J, Jauncey, M, Hiley, S, Clark, N, Gerostamoulos, D, Glowacki, L, Roux, C, Morelato, M & Nielsen, S 2022, 'Infrequent detection of unintentional fentanyl use via urinalysis among people who regularly inject opioids in Sydney and Melbourne, Australia', Addiction, vol. 117, no. 8, pp. 2331-2337.
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AbstractBackground and aimThe current phase of the North American ‘opioid crisis’ is characterised by illicit fentanyl use; however, the presence of illicit fentanyl in Australia is unknown. This study aimed to monitor unintentional fentanyl consumption in Australia.DesignRapid urine drug screens (UDS) paired with surveys conducted within supervised injecting facilities (SIFs) and confirmatory laboratory testing.SettingSydney and Melbourne, Australia.ParticipantsClients who used heroin within the past 2 days (n = 911 tests, 2017–2021). Participants were demographically similar to the overall client base (median age 43, 72% male).MeasurementsUDS were conducted using BTNX Rapid Response fentanyl urine strip tests with cross‐reactivity to numerous fentanyl analogues. Positive urine samples were analysed using liquid chromatography coupled with tandem mass spectrometry. Surveys covered past 3 day drug use and lifetime report of fentanyl in heroin.FindingsTwo percent of participants reported intentional use of fentanyl, mostly through fentanyl patches. Of the 911 rapid UDS conducted, 17 (1.9%) yielded positive results. Eight of these (all from Melbourne) were not explained by survey‐reported fentanyl use in the past 3 days. Of these 8 unexplained positives, confirmatory laboratory analysis was conducted on 6, with 4 deemed to be false positives, and 2 confirmed for the presence of fentanyl. This represents the first confirmation of unintended use of fentanyl type substances in this population.Conclusion

Lao, JC, Bui, CB, Pang, MA, Cho, SX, Rudloff, I, Elgass, K, Schröder, J, Maksimenko, A, Mangan, NE, Starkey, MR, Skuza, EM, Sun, YBY, Beker, F, Collins, CL, Kamlin, OF, König, K, Malhotra, A, Tan, K, Theda, C, Young, MJ, McLean, CA, Wilson, NJ, Sehgal, A, Hansbro, PM, Pearson, JT, Polo, JM, Veldman, A, Berger, PJ, Nold-Petry, CA & Nold, MF 2022, 'Type 2 immune polarization is associated with cardiopulmonary disease in preterm infants', Science Translational Medicine, vol. 14, no. 639, p. eaaz8454.
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Postnatal maturation of the immune system is poorly understood, as is its impact on illnesses afflicting term or preterm infants, such as bronchopulmonary dysplasia (BPD) and BPD-associated pulmonary hypertension. These are both cardiopulmonary inflammatory diseases that cause substantial mortality and morbidity with high treatment costs. Here, we characterized blood samples collected from 51 preterm infants longitudinally at five time points, 20 healthy term infants at birth and age 3 to 16 weeks, and 5 healthy adults. We observed strong associations between type 2 immune polarization in circulating CD3 + CD4 + T cells and cardiopulmonary illness, with odds ratios up to 24. Maternal magnesium sulfate therapy, delayed hepatitis B vaccination, and increasing fetal, but not maternal, chorioamnionitis severity were associated with attenuated type 2 polarization. Blocking type 2 mediators such as interleukin-4 (IL-4), IL-5, IL-13, or signal transducer and activator of transcription 6 (STAT6) in murine neonatal cardiopulmonary disease in vivo prevented changes in cell type composition, increases in IL-1β and IL-13, and losses of pulmonary capillaries, but not gains in larger vessels. Thereby, type 2 blockade ameliorated lung inflammation, protected alveolar and vascular integrity, and confirmed the pathological impact of type 2 cytokines and STAT6. In-depth flow cytometry and single-cell transcriptomics of mouse lungs further revealed complex associations between immune polarization and cardiopulmonary disease. Thus, this work advances knowledge on developmental immunology and its impact on early life disease and identifies multiple therapeutic approaches that may relieve inflammation-driven suffering in the youngest patients.

Larkin, BP, Nguyen, LT, Hou, M, Glastras, SJ, Chen, H, Faiz, A, Chen, J, Wang, R, Pollock, CA & Saad, S 2022, 'Low‐dose hydralazine reduces albuminuria and glomerulosclerosis in a mouse model of obesity‐related chronic kidney disease', Diabetes, Obesity and Metabolism, vol. 24, no. 10, pp. 1939-1949.
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AbstractAimTo determine, using a mouse model of obesity, whether low‐dose hydralazine prevents obesity‐related chronic kidney disease (CKD).MethodsFrom 8 weeks of age, male C57BL/6 mice received a high‐fat diet (HFD) or chow, with or without low‐dose hydralazine (25 mg/L) in drinking water, for 24 weeks. Biometric and metabolic variables, renal function and structural changes, renal global DNA methylation, DNA methylation profile and markers of renal fibrosis, injury, inflammation and oxidative stress were assessed.ResultsThe HFD‐fed mice developed obesity, with glucose intolerance, hyperinsulinaemia and dyslipidaemia. Obesity increased albuminuria and glomerulosclerosis, which were significantly ameliorated by low‐dose hydralazine in the absence of a blood pressure‐lowering effect. Obesity increased renal global DNA methylation and this was attenuated by low‐dose hydralazine. HFD‐induced changes in methylation of individual loci were also significantly reversed by low‐dose hydralazine. Obese mice demonstrated increased markers of kidney fibrosis, inflammation and oxidative stress, but these markers were not significantly improved by hydralazine.ConclusionLow‐dose hydralazine ameliorated HFD‐induced albuminuria and glomerulosclerosis, independent of alterations in biometric and metabolic variables or blood pressure regulation. Although the precise mechanism of renoprotection in obesity is unclear, an epigenetic basis may be implicated. These data support repurposing hydralazine as a novel therapy to prevent CKD progression in obese patients.

Larsson, ME, Bramucci, AR, Collins, S, Hallegraeff, G, Kahlke, T, Raina, J-B, Seymour, JR & Doblin, MA 2022, 'Mucospheres produced by a mixotrophic protist impact ocean carbon cycling', Nature Communications, vol. 13, no. 1, p. 1301.
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AbstractMixotrophic protists (unicellular eukaryotes) that engage in both phototrophy (photosynthesis) and phago-heterotrophy (engulfment of particles)—are predicted to contribute substantially to energy fluxes and marine biogeochemical cycles. However, their impact remains largely unquantified. Here we describe the sophisticated foraging strategy of a widespread mixotrophic dinoflagellate, involving the production of carbon-rich ‘mucospheres’ that attract, capture, and immobilise microbial prey facilitating their consumption. We provide a detailed characterisation of this previously undescribed behaviour and reveal that it represents an overlooked, yet quantitatively significant mechanism for oceanic carbon fluxes. Following feeding, the mucospheres laden with surplus prey are discarded and sink, contributing an estimated 0.17–1.24 mg m−2 d−1 of particulate organic carbon, or 0.02–0.15 Gt to the biological pump annually, which represents 0.1–0.7% of the estimated total export from the euphotic zone. These findings demonstrate how the complex foraging behaviour of a single species of mixotrophic protist can disproportionally contribute to the vertical flux of carbon in the ocean.

Law, AMK, Chen, J, Colino‐Sanguino, Y, Fuente, LRDL, Fang, G, Grimes, SM, Lu, H, Huang, RJ, Boyle, ST, Venhuizen, J, Castillo, L, Tavakoli, J, Skhinas, JN, Millar, EKA, Beretov, J, Rossello, FJ, Tipper, JL, Ormandy, CJ, Samuel, MS, Cox, TR, Martelotto, L, Jin, D, Valdes‐Mora, F, Ji, HP & Gallego‐Ortega, D 2022, 'ALTEN: A High‐Fidelity Primary Tissue‐Engineering Platform to Assess Cellular Responses Ex Vivo', Advanced Science, vol. 9, no. 21, pp. e2103332-2103332.
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AbstractTo fully investigate cellular responses to stimuli and perturbations within tissues, it is essential to replicate the complex molecular interactions within the local microenvironment of cellular niches. Here, the authors introduce Alginate‐based tissue engineering (ALTEN), a biomimetic tissue platform that allows ex vivo analysis of explanted tissue biopsies. This method preserves the original characteristics of the source tissue's cellular milieu, allowing multiple and diverse cell types to be maintained over an extended period of time. As a result, ALTEN enables rapid and faithful characterization of perturbations across specific cell types within a tissue. Importantly, using single‐cell genomics, this approach provides integrated cellular responses at the resolution of individual cells. ALTEN is a powerful tool for the analysis of cellular responses upon exposure to cytotoxic agents and immunomodulators. Additionally, ALTEN's scalability using automated microfluidic devices for tissue encapsulation and subsequent transport, to enable centralized high‐throughput analysis of samples gathered by large‐scale multicenter studies, is shown.

Lazenby, JJ, Li, ES & Whitchurch, CB 2022, 'Cell wall deficiency – an alternate bacterial lifestyle?', Microbiology, vol. 168, no. 8.
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Historically, many species of bacteria have been reported to produce viable, cell wall deficient (CWD) variants. A variety of terms have been used to refer to CWD bacteria and a plethora of methods described in which to induce, cultivate and propagate them. In this review, we will examine the long history of scientific research on CWD bacteria examining the methods by which CWD bacteria are generated; the requirements for survival in a CWD state; the replicative processes within a CWD state; and the reversion of CWD bacteria into a walled state, or lack thereof. In doing so, we will present evidence that not all CWD variants are alike and that, at least in some cases, CWD variants arise through an adaptive lifestyle switch that enables them to live and thrive without a cell wall, often to avoid antimicrobial activity. Finally, the implications of CWD bacteria in recurring infections, tolerance to antibiotic therapy and antimicrobial resistance will be examined to illustrate the importance of greater understanding of the CWD bacteria in human health and disease.

Le Reun, N, Bramucci, A, O’Brien, J, Ostrowski, M, Brown, MV, Van de Kamp, J, Bodrossy, L, Raina, J-B, Ajani, P & Seymour, J 2022, 'Diatom Biogeography, Temporal Dynamics, and Links to Bacterioplankton across Seven Oceanographic Time-Series Sites Spanning the Australian Continent', Microorganisms, vol. 10, no. 2, pp. 338-338.
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Diatom communities significantly influence ocean primary productivity and carbon cycling, but their spatial and temporal dynamics are highly heterogeneous and are governed by a complex diverse suite of abiotic and biotic factors. We examined the seasonal and biogeographical dynamics of diatom communities in Australian coastal waters using amplicon sequencing data (18S-16S rRNA gene) derived from a network of oceanographic time-series spanning the Australian continent. We demonstrate that diatom community composition in this region displays significant biogeography, with each site harbouring distinct community structures. Temperature and nutrients were identified as the key environmental contributors to differences in diatom communities at all sites, collectively explaining 21% of the variability observed in diatoms assemblages. However, specific groups of bacteria previously implicated in mutualistic ecological interactions with diatoms (Rhodobacteraceae, Flavobacteriaceae and Alteromonadaceae) also explained a further 4% of the spatial dynamics observed in diatom community structure. We also demonstrate that the two most temperate sites (Port Hacking and Maria Island) exhibited strong seasonality in diatom community and that at these sites, winter diatom communities co-occurred with higher proportion of Alteromonadaceae. In addition, we identified significant co-occurrence between specific diatom and bacterial amplicon sequence variants (ASVs), with members of the Roseobacter and Flavobacteria clades strongly correlated with some of the most abundant diatom genera (Skeletonema, Thalassiosira, and Cylindrotheca). We propose that some of these co-occurrences might be indicative of ecologically important interactions between diatoms and bacteria. Our analyses reveal that in addition to physico-chemical conditions (i.e., temperature, nutrients), the relative abundance of specific groups of bacteria appear to play an important role in shaping the sp...

Lee, HW, Lee, MS, Kim, T-H, Alraek, T, Zaslawski, C, Kim, JW & Moon, DG 2022, 'Ginseng for Erectile Dysfunction: A Cochrane Systematic Review', The World Journal of Men's Health, vol. 40, no. 2, pp. 264-264.
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Lee, PLT, Kanodarwala, FK, Lennard, C, Spindler, X, Spikmans, V, Roux, C & Moret, S 2022, 'Latent fingermark detection using functionalised silicon oxide nanoparticles: Investigation into novel application procedures', Forensic Science International, vol. 335, pp. 111275-111275.
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Investigations into the application of carboxyl-functionalised silicon oxide nanoparticles doped with a ruthenium complex (RuBpy-doped CES-SiO2 NPs) for latent fingermark development on non-porous surfaces were reported in previous studies. These studies suggested that an optimised NP-based method demonstrated advantages in fingermark selectivity and sensitivity. To continue the series of research into using RuBpy-doped CES-SiO2 NPs for fingermark detection, the versatility and overall practicality of the optimised SiO2 NP-based reagent for latent fingermark detection and enhancement was evaluated. When the optimised NP-based method was used in a repeated fashion (application of multiple NP treatment cycles), it was found that the overall fingermark detection quality increased across the evaluated fingermarks without a high risk of overdevelopment. The possibility of incorporating the optimised NP-based reagent for potential operational use (e.g., at crime scenes) was successfully demonstrated via spray application on three test surfaces (aluminium foil, transparent polypropylene film and green polyethylene film). It was also shown that further enhancement of 'spray-detected' fingermarks was achievable via subsequent treatment using the NP-based reagent in a colloidal dispersion bath. Additionally, the compatibility of the optimised NP-based method with two-step cyanoacrylate fuming for latent fingermark detection was evaluated. It was concluded that the two techniques are not compatible for application in a fingermark detection sequence. While encouraging results were demonstrated in this study, further optimisation and comparison will be required before the multiple-treatment and spray-treatment approaches can be considered for operational implementation.

Lee, S-H, Kang, M, Jang, H, Kondaveeti, S, Sun, K, Kim, S, Park, H-H & Jeong, HE 2022, 'Bifunctional Amphiphilic Nanospikes with Antifogging and Antibiofouling Properties', ACS Applied Materials & Interfaces, vol. 14, no. 34, pp. 39478-39488.
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Leggat, W, Heron, SF, Fordyce, A, Suggett, DJ & Ainsworth, TD 2022, 'Experiment Degree Heating Week (eDHW) as a novel metric to reconcile and validate past and future global coral bleaching studies', Journal of Environmental Management, vol. 301, pp. 113919-113919.
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Coral bleaching has increasingly impacted reefs worldwide over the past four decades. Despite almost 40 years of research into the mechanistic, physiological, ecological, biophysical and climatic drivers of coral bleaching, metrics to allow comparison between ecological observations and experimental simulations still do not exist. Here we describe a novel metric - experimental Degree Heating Week (eDHW) - with which to standardise the persistently variable thermal conditions employed across experimental studies of coral bleaching by modify the widely used Degree Heating Week (DHW) metric used in ecological studies to standardise cumulative heat loading.

Leigh, A 2022, 'Using leaf shape to determine leaf size could be a game-changer. A commentary on: ‘Leaf size estimation based on leaf length, width and shape’', Annals of Botany, vol. 129, no. 2, pp. i-ii.
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This article comments on: Julian Schrader, Peijian Shi, Dana L Royer, Daniel J Peppe, Rachael V Gallagher, Yirong Li, Rong Wang, Ian J Wright, Leaf size estimation based on leaf length, width and shape, Annals of Botany, Volume 128, Issue 4, 17 September 2021, Pages 395–406 https://doi.org/10.1093/aob/mcab078

Leng, S, Huete, A, Cleverly, J, Gao, S, Yu, Q, Meng, X, Qi, J, Zhang, R & Wang, Q 2022, 'Assessing the Impact of Extreme Droughts on Dryland Vegetation by Multi-Satellite Solar-Induced Chlorophyll Fluorescence', Remote Sensing, vol. 14, no. 7, pp. 1581-1581.
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Satellite-estimated solar-induced chlorophyll fluorescence (SIF) is proven to be an effective indicator for dynamic drought monitoring, while the capability of SIF to assess the variability of dryland vegetation under water and heat stress remains challenging. This study presents an analysis of the responses of dryland vegetation to the worst extreme drought over the past two decades in Australia, using multi-source spaceborne SIF derived from the Global Ozone Monitoring Experiment-2 (GOME-2) and TROPOspheric Monitoring Instrument (TROPOMI). Vegetation functioning was substantially constrained by this extreme event, especially in the interior of Australia, in which there was hardly seasonal growth detected by neither satellite-based observations nor tower-based flux measurements. At a 16-day interval, both SIF and enhanced vegetation index (EVI) can timely capture the reduction at the onset of drought over dryland ecosystems. The results demonstrate that satellite-observed SIF has the potential for characterizing and monitoring the spatiotemporal dynamics of drought over water-limited ecosystems, despite coarse spatial resolution coupled with high-retrieval noise as compared with EVI. Furthermore, our study highlights that SIF retrieved from TROPOMI featuring substantially enhanced spatiotemporal resolution has the promising capability for accurately tracking the drought-induced variation of heterogeneous dryland vegetation.

Leng, S, Huete, A, Cleverly, J, Lu, X, Ma, X, Gao, S & Yu, Q 2022, 'Response of dryland vegetation under extreme wet events with satellite measures of greenness and fluorescence', Science of The Total Environment, vol. 842, pp. 156860-156860.
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Extreme wet events in central Australia triggered large vegetation responses that contributed greatly to large global land carbon sink anomalies. There remain significant uncertainties on the extent to which these events over dryland vegetation can be monitored and assessed with satellite data. In this study, we investigated the vegetation responses of the major Australian semiarid biomes to two extreme wet events utilizing multi-satellite observations of (1) solar-induced chlorophyll fluorescence (SIF), as a proxy for photosynthetic activity and (2) the enhanced vegetation index (EVI), as a measure of canopy chlorophyll or greenness. We related these satellite observations with gross primary productivity (GPP) estimated from eddy covariance tower sites, as a performance benchmark. The C3-dominated Mulga woodland was the most responsive biome to both wet pulses and exhibited the highest sensitivity to soil moisture. The C4-dominated Hummock grassland was more responsive to the 2011 'big wet' event, relative to the later 2016-2017 wet pulse. EVI swiftly responded to the extreme wet events and showed markedly amplified seasonal amplitude, however, there was a time lag as compared with SIF during the post-wet period, presumably due to the relatively slower chlorophyll degradation in contrast with declines in photosynthetic activity. Despite a robust linear SIF-GPP relationship (r2 ranging from 0.59 to 0.85), the spatially coarse SIF derived from the Global Ozone Monitoring Experiment-2 (GOME-2) yielded high retrieval noise over the xeric biomes, hindering its capacity to capture thoroughly the dryland vegetation dynamics in central Australia. Our study highlights that synchronous satellite observations of greenness and fluorescence can potentially offer an improved understanding of dryland vegetation dynamics and can advance our ability to detect ecosystem alterations under future changing climates.

Leng, S, Huete, A, Cleverly, J, Yu, Q, Zhang, R & Wang, Q 2022, 'Spatiotemporal Variations of Dryland Vegetation Phenology Revealed by Satellite-Observed Fluorescence and Greenness across the North Australian Tropical Transect', Remote Sensing, vol. 14, no. 13, pp. 2985-2985.
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Accurate characterization of spatial patterns and temporal variations in dryland vegetation is of great importance for improving our understanding of terrestrial ecosystem functioning under changing climates. Here, we explored the spatiotemporal variability of dryland vegetation phenology using satellite-observed Solar-Induced chlorophyll Fluorescence (SIF) and the Enhanced Vegetation Index (EVI) along the North Australian Tropical Transect (NATT). Substantial impacts of extreme drought and intense wetness on the phenology and productivity of dryland vegetation are observed by both SIF and EVI, especially in the arid/semiarid interior of Australia without detectable seasonality in the dry year of 2018–2019. The greenness-based vegetation index (EVI) can more accurately capture the seasonal and interannual variation in vegetation production than SIF (EVI r2: 0.47~0.86, SIF r2: 0.47~0.78). However, during the brown-down periods, the rate of decline in EVI is evidently slower than that in SIF and in situ measurement of gross primary productivity (GPP), due partially to the advanced seasonality of absorbed photosynthetically active radiation. Over 70% of the variability of EVI (except for Hummock grasslands) and 40% of the variability of SIF (except for shrublands) can be explained by the water-related drivers (rainfall and soil moisture). By contrast, air temperature contributed to 25~40% of the variability of the effective fluorescence yield (SIFyield) across all biomes. In spite of high retrieval noises and variable accuracy in phenological metrics (MAE: 8~60 days), spaceborne SIF observations, offsetting the drawbacks of greenness-based phenology products with a potentially lagged end of the season, have the promising capability of mapping and characterizing the spatiotemporal dynamics of dryland vegetation phenology.

Leong, W, Poh, WH, Williams, J, Lutz, C, Hoque, MM, Poh, YH, Yee, BYK, Chua, C, Givskov, M, Sanderson-Smith, M, Rice, SA & McDougald, D 2022, 'Adaptation to an Amoeba Host Leads to Pseudomonas aeruginosa Isolates with Attenuated Virulence', Applied and Environmental Microbiology, vol. 88, no. 5, p. aem0232221.
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Pseudomonas aeruginosa is an opportunistic pathogen that causes both acute infections in plants and animals, including humans, and chronic infections in immunocompromised and cystic fibrosis patients. This bacterium is commonly found in soils and water, where bacteria are constantly under threat of being consumed by bacterial predators, e.g., protozoa.

Lewis, BM, Suggett, DS, Prentis, PJ & Nothdurft, LD 2022, 'Cellular adaptations leading to coral fragment attachment on artificial substrates in Acropora millepora (Am-CAM)', Scientific Reports, vol. 12, no. 1, p. 18431.
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AbstractReproductive propagation by asexual fragmentation in the reef-building coral Acropora millepora depends on (1) successful attachment to the reef substrate through modification of soft tissues and (2) a permanent bond with skeletal encrustation. Despite decades of research examining asexual propagation in corals, the initial response, cellular reorganisation, and development leading to fragment substrate attachment via a newly formed skeleton has not been documented in its entirety. Here, we establish the first 'coral attachment model' for this species ('Am-CAM') by developing novel methods that allow correlation of fluorescence and electron microscopy image data with in vivo microscopic time-lapse imagery. This multi-scale imaging approach identified three distinct phases involved in asexual propagation: (1) the contact response of the coral fragment when contact with the substrate, followed by (2) fragment stabilisation through anchoring by the soft tissue, and (3) formation of a 'lappet-like appendage' structure leading to substrate bonding of the tissue for encrustation through the onset of skeletal calcification. In developing Am-CAM, we provide new biological insights that can enable reef researchers, managers and coral restoration practitioners to begin evaluating attachment effectiveness, which is needed to optimise species-substrate compatibility and achieve effective outplanting.

Lewis, RE, Davy, SK, Gardner, SG, Rongo, T, Suggett, DJ & Nitschke, MR 2022, 'Colony self-shading facilitates Symbiodiniaceae cohabitation in a South Pacific coral community', Coral Reefs, vol. 41, no. 5, pp. 1433-1447.
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AbstractThe ecological success of tropical corals is regulated by symbiotic dinoflagellate algae (Symbiodiniaceae). Corals can associate with multiple Symbiodiniaceae species simultaneously, yet the conditions that permit Symbiodiniaceae cohabitation are not understood. We examined how corals self-shade their own tissues causing within-colony light gradients that drive Symbiodiniaceae photoacclimatory processes and positional genetic disparity. Paired light ‘exposed’ and ‘shaded’ samples from 20 coral species were collected from a shallow coral reef (Rarotonga, Cook Islands). Through active chlorophyll fluorometry, rapid light curves revealed that exposed Symbiodiniaceae exhibited 50% higher values in minimum saturating irradiances and demonstrated a shift towards preferential nonphotochemical quenching [1 – Q], consistent with higher overall light exposure. High-throughput or targeted DNA sequencing of ITS2 and psbAncr markers demonstrated that corals harboured distinct and/or differentially abundant Symbiodiniaceae ITS2 sequences (typically rare in relative abundance) or multiple ITS2 intragenomic variant profiles across shaded vs exposed regions. In Hydnophora cf. microconos, within-colony symbiont genetic disparity was positively correlated with the magnitude of difference in [1 – Q] utilisation. Together, these results suggest that within-colony light gradients produce distinct optical niches that enable symbiont cohabitation via photoadaptation, a phenomenon that is expected to increase the adaptive capacity of corals under future climates.

Li, J, Ahmed, W, Metcalfe, S, Smith, WJM, Tscharke, B, Lynch, P, Sherman, P, Vo, PHN, Kaserzon, SL, Simpson, SL, McCarthy, DT, Thomas, KV, Mueller, JF & Thai, P 2022, 'Monitoring of SARS-CoV-2 in sewersheds with low COVID-19 cases using a passive sampling technique', Water Research, vol. 218, pp. 118481-118481.
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Monitoring SARS-CoV-2 RNA in sewer systems, upstream of a wastewater treatment plant, is an effective approach for understanding potential COVID-19 transmission in communities with higher spatial resolutions. Passive sampling devices provide a practical solution for frequent sampling within sewer networks where the use of autosamplers is not feasible. Currently, the design of upstream sampling is impeded by limited understanding of the fate of SARS-CoV-2 RNA in sewers and the sensitivity of passive samplers for the number of infected individuals in a catchment. In this study, passive samplers containing electronegative membranes were applied for at least 24-h continuous sampling in sewer systems. When monitoring SARS-CoV-2 along a trunk sewer pipe, we found RNA signals decreased proportionally to increasing dilutions, with non-detects occurring at the end of pipe. The passive sampling membranes were able to detect SARS-CoV-2 shed by >2 COVID-19 infection cases in 10,000 people. Moreover, upstream monitoring in multiple sewersheds using passive samplers identified the emergence of SARS-CoV-2 in wastewater one week ahead of clinical reporting and reflected the spatiotemporal spread of a COVID-19 cluster within a city. This study provides important information to guide the development of wastewater surveillance strategies at catchment and subcatchment levels using different sampling techniques.

Li, J, Luu, LDW, Wang, X, Cui, X, Huang, X, Fu, J, Zhu, X, Li, Z, Wang, Y & Tai, J 2022, 'Metabolomic analysis reveals potential biomarkers and the underlying pathogenesis involved in Mycoplasma pneumoniae pneumonia', Emerging Microbes & Infections, vol. 11, no. 1, pp. 593-605.
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Although previous studies have reported the use of metabolomics for infectious diseases, little is known about the potential function of plasma metabolites in children infected with Mycoplasma pneumoniae (MP). Here, a combination of liquid chromatography-quadrupole time-of-flight mass spectrometry and random forest-based classification model was used to provide a broader range of applications in MP diagnosis. In the training cohort, plasma from 63 MP pneumonia children (MPPs), 37 healthy controls (HC) and 29 infectious disease controls (IDC) was collected. After multivariate analyses, 357 metabolites were identified to be differentially expressed among MPP, HC and IDC groups, and 3 metabolites (568.5661, 459.3493 and 411.3208) had high diagnostic values. In an independent cohort with 57 blinded subjects, samples were successfully classified into different groups, demonstrating the reliability of these biomarkers for distinguishing MPPs from controls. A metabolomic signature analysis identified major classes of glycerophospholipids, sphingolipids and fatty acyls were increased in MPPs. These markedly altered metabolites are mainly involved in glycerophospholipid and sphingolipid metabolism. As the ubiquitous building blocks of eukaryotic cell membranes, dysregulated lipid metabolism indicates damage of the cellular membrane and the activation of immunity in MPPs. Moreover, lipid metabolites, differentially expressed between severe and mild MPPs, were correlated with the markers of extrapulmonary complications, suggesting that they may be involved in MPP disease severity. These findings may offer new insights into biomarker selection and the pathogenesis of MPP in children.

Li, L, Mac Aogáin, M, Xu, T, Jaggi, TK, Chan, LLY, Qu, J, Wei, L, Liao, S, Cheng, HS, Keir, HR, Dicker, AJ, Tan, KS, De Yun, W, Koh, MS, Ong, TH, Lim, AYH, Abisheganaden, JA, Low, TB, Hassan, TM, Long, X, Wark, PAB, Oliver, B, Drautz-Moses, DI, Schuster, SC, Tan, NS, Fang, M, Chalmers, JD & Chotirmall, SH 2022, 'Neisseria species as pathobionts in bronchiectasis', Cell Host & Microbe, vol. 30, no. 9, pp. 1311-1327.e8.
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Neisseria species are frequently identified in the bronchiectasis microbiome, but they are regarded as respiratory commensals. Using a combination of human cohorts, next-generation sequencing, systems biology, and animal models, we show that bronchiectasis bacteriomes defined by the presence of Neisseria spp. associate with poor clinical outcomes, including exacerbations. Neisseria subflava cultivated from bronchiectasis patients promotes the loss of epithelial integrity and inflammation in primary epithelial cells. In vivo animal models of Neisseria subflava infection and metabolipidome analysis highlight immunoinflammatory functional gene clusters and provide evidence for pulmonary inflammation. The murine metabolipidomic data were validated with human Neisseria-dominant bronchiectasis samples and compared with disease in which Pseudomonas-, an established bronchiectasis pathogen, is dominant. Metagenomic surveillance of Neisseria across various respiratory disorders reveals broader importance, and the assessment of the home environment in bronchiectasis implies potential environmental sources of exposure. Thus, we identify Neisseria species as pathobionts in bronchiectasis, allowing for improved risk stratification in this high-risk group.

Li, M, Kobayashi, R, Amos, RD, Ford, MJ & Reimers, JR 2022, 'Density functionals with asymptotic-potential corrections are required for the simulation of spectroscopic properties of materials', Chemical Science, vol. 13, no. 5, pp. 1492-1503.
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Spectroscopic transitions in materials that involve charge transfer require asymptotically corrected density functionals. As most transitions do have some charge transfer character, use of such methods are generally warranted.

Li, M, Wen Ma, Z, Jun Deng, S, Oliver, BG, Wang, T, Ping Zhang, H, Wang, L, McDonald, VM, Wang, J, Liu, D, Gibson, PG, Ming Luo, F, Min Li, W, Jing Wan, H & Wang, G 2022, 'Development and validation of a noninvasive prediction model for identifying eosinophilic asthma', Respiratory Medicine, vol. 201, pp. 106935-106935.
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BACKGROUND: Identification of eosinophilic asthma (EA) using sputum analysis is important for disease monitoring and individualized treatment. But it is laborious and technically demanding. We aimed to develop and validate an effective model to predict EA with multidimensional assessment (MDA). METHODS: The asthma patients who underwent a successful sputum induction cytological analysis were consecutively recruited from March 2014 to January 2021. The variables assessed by MDA were screened by least absolute shrinkage and selection operator (LASSO) and logistic regression to develop a nomogram and an online web calculator. Validation was performed internally by a bootstrap sampling method and externally in the validation cohort. Diagnostic accuracy of the model in different asthma subgroups were also investigated. RESULTS: In total of 304 patients in the training cohort and 95 patients in the validation cohort were enrolled. Five variables were identified in the EA prediction model: gender, nasal polyp, blood eosinophils, blood basophils and FeNO. The C-index of the model was 0.86 (95% CI: 0.81-0.90) in the training cohort and 0.84 (95% CI: 0.72-0.89) in the validation cohort. The calibration curve showed good agreement between the prediction and actual observation. The decision curve analysis (DCA) also demonstrated that the EA prediction model was clinically beneficial. An online publicly available web calculator was constructed (https://asthmaresearcherlimin.shinyapps.io/DynNomapp/). CONCLUSION: We developed and validated a multivariable model based on MDA to help the diagnosis of EA, which has good diagnostic performance and clinical practicability. This practical tool may be a useful alternative for predicting EA in the clinic.

Li, M-Y, Qin, Y-Q, Tian, Y-G, Li, K-C, Oliver, BG, Liu, X-F, Zhao, P & Li, J-S 2022, 'Effective-component compatibility of Bufei Yishen formula III ameliorated COPD by improving airway epithelial cell senescence by promoting mitophagy via the NRF2/PINK1 pathway', BMC Pulmonary Medicine, vol. 22, no. 1, p. 434.
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Abstract Background Effective-component compatibility of Bufei Yishen formula III (ECC-BYF III) demonstrates positive effects on stable chronic obstructive pulmonary disease (COPD). Purpose To investigate the mechanisms of ECC-BYF III on COPD rats from the aspect of airway epithelial cell senescence. Methods COPD model rats (Sprague-Dawley rat) were treated with ECC-BYF III for 8 weeks, and the efficacy was evaluated. Cigarette smoke extract (CSE)-induced senescence model of airway epithelial cells was treated with ECC-BYF III, and related enzymes and proteins involved in oxidative stress and mitophagy were detected. Results ECC-BYF III markedly rescued pulmonary function and histopathological changes, which might be associated with the amelioration of lung senescence, including the reduction of malondialdehyde (MDA) and tumor necrosis factor-α (TNF-α), interleukin (IL)-6 and matrix metalloproteinase (MMP)-9 levels, increase of the level in total superoxide dismutase (T-SOD), and decease in the p21 level in the airways. Furthermore, ECC-BYF III suppressed p16 and p21 expressions and senescence-associated β-galactosidase (SA-β-Gal) in CSE-induced airway epithelial cells. Moreover, ECC-BYF III upregulated mitophagy-related proteins, including the co-localizations of TOM20 and LC3B, PINK1 and PARK2, and improved mitochondrial function by upregulating mitochondrial mitofusin (MFN)2 and reducing dynamin-related protein 1 (DRP1) expression. ECC-BYF III enhanced the activities of T-SOD and GSH-PX by up-regulating NRF2, thus inhibiting oxi...

Li, T, Geier, M, Ingham, J & D Scammell, H 2022, 'Higher-order topological superconductivity from repulsive interactions in kagome and honeycomb systems', 2D Materials, vol. 9, no. 1, pp. 015031-015031.
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AbstractWe discuss a pairing mechanism in interacting two-dimensional multipartite lattices that intrinsically leads to a second order topological superconducting state with a spatially modulated gap. When the chemical potential is close to Dirac points, oppositely moving electrons on the Fermi surface undergo an interference phenomenon in which the Berry phase converts a repulsive electron–electron interaction into an effective attraction. The topology of the superconducting phase manifests as gapped edge modes in the quasiparticle spectrum and Majorana Kramers pairs at the corners. We present symmetry arguments which constrain the possible form of the electron–electron interactions in these systems and classify the possible superconducting phases which result. Exact diagonalization of the Bogoliubov-de Gennes Hamiltonian confirms the existence of gapped edge states and Majorana corner states, which strongly depend on the spatial structure of the gap. Possible applications to vanadium-based superconducting kagome metals AV3Sb5(A = K, Rb, Cs) are discussed.

Li, T, Ingham, J & Scammell, HD 2022, 'Nested Fermi surfaces and correlated electronic phases in hole-doped semiconductor quantum wells', Physical Review B, vol. 105, no. 11, p. 115302.
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We demonstrate the existence of novel interaction effects in hole-doped semiconductor quantum wells which are connected to dramatic changes in the Fermi surface geometry occurring upon variation of the doping. We present band structure calculations showing that quantum wells formed in p-type cubic semiconductors develop perfectly nested Fermi surfaces at a critical hole density p~1/d2 set by the width d of the quantum well. Nesting gives rise to competing superconducting and charge or spin density wave order, which we analyze using the perturbative renormalization group method. The correlated phases may be created or destroyed by tuning the hole density towards or away from the critical density. Our results establish p-type semiconductor quantum wells as a platform for novel correlated phases, which may be precisely controlled using electrostatic gating and external magnetic fields.

Li, Y, Ji, X, Chang, L, Tang, J, Hua, M, Liu, J, O'Neill, C, Huang, X & Jin, X 2022, 'Click-iT&#174; Plus OPP Alexa Fluor&#174; Protein Synthesis Assay in Embryonic Cells', BIO-PROTOCOL, vol. 12, no. 11.
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Liao, J, Yang, L, Wu, S, Yang, Z, Zhou, J, Jin, D & Guan, M 2022, 'NIR-II emissive properties of 808 nm-excited lanthanide-doped nanoparticles for multiplexed in vivo imaging', Journal of Luminescence, vol. 242, pp. 118597-118597.
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The second near-infrared window (1000–1700 nm, NIR-II) emissive lanthanide-doped nanoparticles excited by 808 nm laser are ideal for in vivo bioimaging due to their non-heating excitation. The study of 808 nm excited lanthanide-doped nanoparticles not only provides high-quality NIR-II imaging but also can promote in vivo multiplexed bioimaging under single excitation. Herein, we prepared three sets of typical 808 nm excited lanthanide-doped nanoparticles (NaYF4: Nd3+@NaYF4, NaErF4@NaYF4, and NaYbF4: Er3+/Ce3+@NaYbF4@NaYF4: Yb3+/Nd3+) and then systematically compared their optical properties in the NIR-II window. Furthermore, we prepared water-soluble and biocompatible nanoprobes and achieved multiplexed NIR-II in vivo imaging in mice under single 808 nm excitation. These results highlight the potential of 808 nm excited lanthanide probes for physiological studies and biomedical applications.

Liepa, R, Mann, R, Osman, M, Hamze, M, Gunawan, C & Hamidian, M 2022, 'Cl415, a carbapenem-resistant Acinetobacter baumannii isolate containing four AbaR4 and a new variant of AbGRI2, represents a novel global clone 2 strain', Journal of Antimicrobial Chemotherapy, vol. 77, no. 2, pp. 345-350.
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Abstract Objectives To determine the genetic context of genes conferring antibiotic resistance on the carbapenem-resistant Acinetobacter baumannii Cl415, recovered in 2017 at El Youssef Hospital Centre in Akkar Governorate, North Lebanon. Methods Antibiotic resistance phenotype for 22 antibiotics was determined using disc diffusion or MIC determination. The whole-genome sequence of Cl415 was determined using a combination of the Illumina MiSeq and Oxford Nanopore (MinION) platforms. Complete genome was assembled using Unicycler and antibiotic resistance determinants and ISs were identified using ResFinder and ISFinder, respectively. Results Cl415 is a global clone 2 (GC2) strain and belongs to the most common STs of this clone, ST2IP and ST218OX. Cl415 is resistant to several antibiotics, including aminoglycosides and carbapenems to a high level. Genomic analysis of Cl415 revealed that it carries four chromosomal AbaR4 copies. One copy was found in the comM gene replacing the AbGRI1 island. Cl415 also contains a novel variant of AbGRI2, herein called AbGRI2-15, carrying only the blaTEM and aphA1 resistance genes. Cl415 belongs to a subclade of GC2 strains that appear to have diverged recently with a wide geographical distribution. Conclusions The resistance gene complement of Cl415 was found in the chromosome with four oxa23 located in AbaR4 copies and the remaining genes in a novel variant of the AbGRI2 resistance island. Cl415 was isolated in Leban...

Lin, J-X, Siriviboon, P, Scammell, HD, Liu, S, Rhodes, D, Watanabe, K, Taniguchi, T, Hone, J, Scheurer, MS & Li, JIA 2022, 'Zero-field superconducting diode effect in small-twist-angle trilayer graphene', Nature Physics, vol. 18, no. 10, pp. 1221-1227.
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The critical current of a superconductor can be different for opposite directions of current flow when both time-reversal and inversion symmetry are broken. Such non-reciprocal behaviour creates a superconducting diode and has recently been experimentally demonstrated by breaking these symmetries with an applied magnetic field or by the construction of a magnetic tunnel junction. Here we report an intrinsic superconducting diode effect that is present at zero external magnetic field in mirror-symmetric twisted trilayer graphene. Such non-reciprocal behaviour, with sign that can be reversed through training with an out-of-plane magnetic field, provides direct evidence of the microscopic coexistence between superconductivity and time-reversal symmetry breaking. In addition to the magnetic-field trainability, we show that the zero-field diode effect can be controlled by varying the carrier density or twist angle. A natural interpretation for the origin of the intrinsic diode effect is an imbalance in the valley occupation of the underlying Fermi surface, which probably leads to finite-momentum Cooper pairing and nematicity in the superconducting phase.

Liu, B, Liao, J, Song, Y, Chen, C, Ding, L, Lu, J, Zhou, J & Wang, F 2022, 'Multiplexed structured illumination super-resolution imaging with lifetime-engineered upconversion nanoparticles', Nanoscale Advances, vol. 4, no. 1, pp. 30-38.
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We report a tailor-made multiplexed super-resolution imaging method using the lifetime fingerprints from luminescent nanoparticles, which can resolve the particles within the diffraction-limited spots and enable higher multiplexing capacity in space.

Liu, G, Jarnicki, AG, Paudel, KR, Lu, W, Wadhwa, R, Philp, AM, Van Eeckhoutte, H, Marshall, JE, Malyla, V, Katsifis, A, Fricker, M, Hansbro, NG, Dua, K, Kermani, NZ, Eapen, MS, Tiotiu, A, Chung, KF, Caramori, G, Bracke, K, Adcock, IM, Sohal, SS, Wark, PA, Oliver, BG & Hansbro, PM 2022, 'Adverse roles of mast cell chymase-1 in COPD', European Respiratory Journal, vol. 60, no. 6, pp. 2101431-2101431.
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BackgroundCOPD is the third leading cause of death worldwide. Cigarette smoke (CS)-induced chronic inflammation inducing airway remodelling, emphysema and impaired lung function is the primary cause. Effective therapies are urgently needed. Human chymase (hCMA)1 and its orthologue mCMA1/mouse mast cell protease (mMCP)5 are exocytosed from activated mast cells and have adverse roles in numerous disorders, but their role in COPD is unknown.MethodsWe evaluated hCMA1 levels in lung tissues of COPD patients. We usedmmcp5-deficient (−/−) mice to evaluate this protease's role and potential for therapeutic targeting in CS-induced experimental COPD. In addition, we usedex vivo/in vitrostudies to define mechanisms.ResultsThe levels of hCMA1 mRNA and CMA1+mast cells were increased in lung tissues from severe compared to early/mild COPD patients, non-COPD smokers and healthy controls. Degranulated mast cell numbers and mMCP5 protein were increased in lung tissues of wild-type mice with experimental COPD.mmcp5−/−mice were protected against CS-induced inflammation and macrophage accumulation, airway remodelling, emphysema and impaired lung function in experimental COPD. CS extract challenge of co-cultures of mast cells from wild-type, but notmmcp5−/−mice with wild-type lung macrophages increased in tumour necrosis factor (TNF)-α release. It also caused the release of CMA1 from human mast cells, and recombinant hCMA-1 induced TNF-α release from human macrophages. Treatment with CMA1 inhibitor potently suppressed these hallmark features of experimental COPD.Conclusion

Liu, H, Mendelson, N, Abidi, IH, Li, S, Liu, Z, Cai, Y, Zhang, K, You, J, Tamtaji, M, Wong, H, Ding, Y, Chen, G, Aharonovich, I & Luo, Z 2022, 'Rational Control on Quantum Emitter Formation in Carbon-Doped Monolayer Hexagonal Boron Nitride', ACS Applied Materials & Interfaces, vol. 14, no. 2, pp. 3189-3198.
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Liu, J, Bo, F, Chang, L, Dong, C-H, Ou, X, Regan, B, Shen, X, Song, Q, Yao, B, Zhang, W, Zou, C-L & Xiao, Y-F 2022, 'Emerging material platforms for integrated microcavity photonics', Science China Physics, Mechanics & Astronomy, vol. 65, no. 10.
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Liu, T, Zhang, W, Li, J, Ueland, M, Forbes, SL, Zheng, WX & Su, SW 2022, 'A Multiscale Wavelet Kernel Regularization-Based Feature Extraction Method for Electronic Nose', IEEE Transactions on Systems, Man, and Cybernetics: Systems, vol. 52, no. 11, pp. 7078-7089.
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Liu, Y, Li, Y, Carroll, RJ & Wang, N 2022, 'Predictive functional linear models with diverging number of semiparametric single-index interactions', Journal of Econometrics, vol. 230, no. 2, pp. 221-239.
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Liu, Y, Zhang, X, Zhang, L, Oliver, BG, Wang, HG, Liu, ZP, Chen, ZH, Wood, L, Hsu, AC-Y, Xie, M, McDonald, V, Wan, HJ, Luo, FM, Liu, D, Li, WM & Wang, G 2022, 'Sputum Metabolomic Profiling Reveals Metabolic Pathways and Signatures Associated With Inflammatory Phenotypes in Patients With Asthma', Allergy, Asthma & Immunology Research, vol. 14, no. 4, pp. 393-393.
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PURPOSE: The molecular links between metabolism and inflammation that drive different inflammatory phenotypes in asthma are poorly understood. We aimed to identify the metabolic signatures and underlying molecular pathways of different inflammatory asthma phenotypes. METHODS: In the discovery set (n = 119), untargeted ultra-high-performance liquid chromatography-mass spectrometry (UHPLC-MS) was applied to characterize the induced sputum metabolic profiles of asthmatic patients with different inflammatory phenotypes using orthogonal partial least-squares discriminant analysis (OPLS-DA), and pathway topology enrichment analysis. In the validation set (n = 114), differential metabolites were selected to perform targeted quantification. Correlations between targeted metabolites and clinical indices in asthmatic patients were analyzed. Logistic and negative binomial regression models were established to assess the association between metabolites and severe asthma exacerbations. RESULTS: Seventy-seven differential metabolites were identified in the discovery set. Pathway topology analysis uncovered that histidine metabolism, glycerophospholipid metabolism, nicotinate and nicotinamide metabolism, linoleic acid metabolism as well as phenylalanine, tyrosine and tryptophan biosynthesis were involved in the pathogenesis of different asthma phenotypes. In the validation set, 24 targeted quantification metabolites were significantly expressed between asthma inflammatory phenotypes. Finally, adenosine 5'-monophosphate (adjusted relative risk [adj RR] = 1.000; 95% confidence interval [CI] = 1.000-1.000; P = 0.050), allantoin (adj RR = 1.000; 95% CI = 1.000-1.000; P = 0.043) and nicotinamide (adj RR = 1.001; 95% CI = 1.000-1.002; P = 0.021) were demonstrated to predict severe asthma exacerbation rates. CONCLUSIONS: Different inflammatory asthma phenotypes have specific metabolic profiles in induced sputum. The potential metabolic signatures may identify therapeutic tar...

Long, MQ, Tang, KK, Xiao, J, Li, JY, Chen, J, Gao, H, Chen, WH, Liu, CT & Liu, H 2022, 'Recent advances on MXene based materials for energy storage applications', Materials Today Sustainability, vol. 19, pp. 100163-100163.
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Lundgren, EJ, Ramp, D, Middleton, OS, Wooster, EIF, Kusch, E, Balisi, M, Ripple, WJ, Hasselerharm, CD, Sanchez, JN, Mills, M & Wallach, AD 2022, 'A novel trophic cascade between cougars and feral donkeys shapes desert wetlands', Journal of Animal Ecology, vol. 91, no. 12, pp. 2348-2357.
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AbstractIntroduced large herbivores have partly filled ecological gaps formed in the late Pleistocene, when many of the Earth's megafauna were driven extinct. However, extant predators are generally considered incapable of exerting top‐down influences on introduced megafauna, leading to unusually strong disturbance and herbivory relative to native herbivores.We report on the first documented predation of juvenile feral donkeys Equus africanus asinus by cougars Puma concolor in the Mojave and Sonoran Deserts of North America. We then investigated how cougar predation corresponds with differences in feral donkey behaviour and associated effects on desert wetlands.Focusing on a feral donkey population in the Death Valley National Park, we used camera traps and vegetation surveys to compare donkey activity patterns and impacts between wetlands with and without cougar predation.Donkeys were primarily diurnal at wetlands with cougar predation, thereby avoiding cougars. However, donkeys were active throughout the day and night at sites without predation. Donkeys were ~87% less active (measured as hours of activity a day) at wetlands with predation (p < 0.0001). Sites with predation had reduced donkey disturbance and herbivory, including ~46% fewer access trails, 43% less trampled bare ground and 192% more canopy cover (PERMANOVA, R2 = 0.22, p = 0.0003).Our study is the first to reveal a trophic cascade involving cougars, feral equids and vegetation. Cougar predation appears to rewire an ancient food web, with diverse implications ...

Luo, Y, Chen, Z, Wen, S, Han, Q, Fu, L, Yan, L, Jin, D, Bünzli, J-CG & Bao, G 2022, 'Magnetic regulation of the luminescence of hybrid lanthanide-doped nanoparticles', Coordination Chemistry Reviews, vol. 469, pp. 214653-214653.
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The unique optical properties of lanthanide-doped nanomaterials have made them broadly attractive to a wide range of applications in chemical, physical, and biomedical fields. As an external and real-time regulation tool, the magnetic field is highly useful for modulating the luminescence of lanthanide ions by spectral splitting, wavelength shifting, and intensity variation. The dynamic regulation of the luminescence further endows the nanosystems with many valuable optical features, extending their versatility. Here, we analyze the magnetic regulation mechanisms of luminescence, survey the structure design of magnetooptic nanosystems, highlight their advances in imaging agents, responsive probes, nanomagnets and nanogenerators, microrobots, and miniature reactors; we also identify the challenges and future opportunities for hybrid magnetooptic nanosystems.

Luu, LD, Singh, H, Castaño-Rodríguez, N, Leach, ST, Stephen, R, Tedla, N, Krishnan, U & Kaakoush, NO 2022, 'Mo1603: ENRICHMENT OF PREVOTELLA IS A CONSISTENT SIGNATURE IN THE METAPLASTIC ESOPHAGUS IN CHILDREN AND ADULTS', Gastroenterology, vol. 162, no. 7, pp. S-833.
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Luu, LDW & Lan, R 2022, 'Rapid Surface Shaving for Proteomic Identification of Novel Surface Antigens for Vaccine Development', Methods Mol Biol, vol. 2414, pp. 47-62.
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The bacterial cell surface (surfaceome) is the first site encountered by immune cells and is thus an important site for immune recognition. As such, the characterization of bacterial surface proteins can lead to the discovery of novel antigens for potential vaccine development. In this chapter, we describe a rapid 5-min surface shaving proteomics protocol where live bacterial cells are incubated with trypsin and surface peptides are 'shaved' off. The shaved peptides are subsequently identified with liquid chromatography-tandem mass spectrometry (LC-MS/MS). Several checkpoints, including colony forming unit (CFU) counts, flow cytometry, and a false positive unshaved control, are introduced to ensure cell viability/membrane integrity are maintained and that proteins identified are true surface proteins. The protein topology of shaved peptides can be bioinformatically confirmed for surface location. Surface shaving facilitates identification of surface proteins expressed under different conditions, by different strains as well as highly abundant essential and immunogenic bacterial surface antigens for potential vaccine development.

Luu, LDW, Popple, G, Tsang, SPW, Vinasco, K, Hilmi, I, Ng, RT, Chew, KS, Wong, SY, Riordan, S, Lee, WS, Mitchell, HM, Kaakoush, NO & Castaño‐Rodríguez, N 2022, 'Genetic variants involved in innate immunity modulate the risk of inflammatory bowel diseases in an understudied Malaysian population', Journal of Gastroenterology and Hepatology, vol. 37, no. 2, pp. 342-351.
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AbstractBackground and AimInflammatory bowel diseases (IBD) are chronic gastrointestinal inflammatory conditions comprising two major subtypes: Crohn's disease (CD) and ulcerative colitis (UC). The incidence of IBD is increasing in Asian countries including Malaysia. The aim of this study was to determine whether 32 single nucleotide polymorphisms (SNPs) strongly associated with IBD from genome‐wide association studies, performed mainly in Caucasian populations, are associated with IBD in a Malaysian population, correlating these findings with local and systemic inflammation.MethodsSelected SNPs were investigated in a Malaysian cohort comprising 36 IBD patients and 75 controls using customized matrix‐assisted laser desorption ionization time‐of‐flight genotyping. Local mRNA and/or systemic protein levels of IL‐10, IL‐12, IL‐22, IL‐23, and TNF‐α were measured in these same subjects.ResultsATG16L2 rs11235667 and LINC00824 rs6651252 was significantly associated with increased CD risk while IL12B rs56167332 was a significant protective factor. Three SNPs (SBNO2 rs2024092, CARD9 rs10781499, and rs17085007 between GPR12‐USP12) were significantly associated with increased UC risk while NKX2‐3 rs4409764 was a significant protective factor. After adjusting for age, gender, and ethnicity, SBNO2 rs2024092, ATG16L2 rs11235667, CARD9 rs10781499, and LINC00824 rs6651252 remained associated with IBD. Interestingly, the risk alleles of IL10

Luu, LDW, Singh, H, Castaño-Rodríguez, N, Leach, ST, Riordan, SM, Tedla, N, Krishnan, U & Kaakoush, NO 2022, 'Changes to the upper gastrointestinal microbiotas of children with reflux oesophagitis and oesophageal metaplasia', Microbial Genomics, vol. 8, no. 9, pp. 1-12.
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Little is known of the relationships among paediatric upper gastrointestinal microbiotas, and the impact of medication use and disease on their diversity. Here, we investigated the diversity of three microbiotas in the upper gastrointestinal tract of paediatric patients in relation to each other and to host factors. Oral, oesophageal and gastric microbiotas from a prospective paediatric cohort (n=54) were profiled using the 16S rRNA gene and ITS2 amplicon sequencing. 16S rRNA gene amplicon sequencing of oesophageal biopsies from a retrospective paediatric cohort (n=96) and shotgun metagenomics data from oesophageal brushings (n=88) were employed for genomic signature validation. Bacterial diversity and composition showed substantial differences across oral, oesophageal and gastric fluid samples that were not replicated for fungi, and the presence of reflux led to increased homogeneity in the bacterial component of these three microbiotas. The oral and oesophageal microbiotas were associated with age, sex, history of oesophageal atresia and presence of oesophageal metaplasia, with the latter characterized by Prevotella enrichment. Proton pump inhibitor use was associated with increased oral bacterial richness in the gastric fluid, and this correlated with increased levels of gastric pro-inflammatory cytokines. Profiling of oesophageal biopsies from a retrospective paediatric cohort confirmed an increased Sensors and Actuators B: Chemical, vol. 360, pp. 131681-131681.
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Macreadie, LK, Gilchrist, AM, McNaughton, DA, Ryder, WG, Fares, M & Gale, PA 2022, 'Progress in anion receptor chemistry', Chem, vol. 8, no. 1, pp. 46-118.
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This review covers advances made in anion complexation in the years 2019 and 2020. Included here are developments in self-assembly, sensing, anion separation, transport, catalysis, and fundamental advances in anion recognition systems.

Mahmud, MA, Zheng, J, Tang, S, Wang, G, Bing, J, Bui, AD, Qu, J, Yang, L, Liao, C, Chen, H, Bremner, SP, Nguyen, HT, Cairney, J & Ho‐Baillie, AWY 2022, 'Cation‐Diffusion‐Based Simultaneous Bulk and Surface Passivations for High Bandgap Inverted Perovskite Solar Cell Producing Record Fill Factor and Efficiency', Advanced Energy Materials, vol. 12, no. 36, pp. 2201672-2201672.
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AbstractHigh bandgap perovskite solar cells are integral to perovskite‐based multi‐junction tandem solar cells with efficiency potentials over 40%. However, at present, high bandgap perovskite devices underperform compared to their mid bandgap counterparts in terms of voltage outputs and fill factors resulting in lower than ideal efficiencies. Here, the low fill factor aspect of high bandgap perovskite is addressed by developing a cation‐diffusion‐based double‐sided interface passivation scheme that simultaneously provides bulk passivation for a 1.75 eV perovskite cell that is also compatible with a p‐i‐n cell architecture. The champion cell achieves a record fill factor of 86.5% and a power conversion efficiency of 20.2%. Results of ionic distribution profiling, Fourier transform infrared spectroscopy, and X‐ray diffraction crystallography reveal evidence of cation diffusion from the surface perovskite passivation layer into bulk. The diffused cations reduce Shockley–Read–Hall recombination in the perovskite bulk and at the surfaces with the latter being more dominant as confirmed by light‐intensity dependent and temperature‐dependent open‐circuit voltage measurements as well as thermal admittance spectroscopy. This concurrent bulk and surface passivation scheme renders record fill factor and efficiency in the double‐side passivated cells. This provides new insights for future passivation strategies based on ionic diffusion of functionalized materials.

Mahmud, MAP & Farjana, SH 2022, 'Comparative life cycle environmental impact assessment of renewable electricity generation systems: A practical approach towards Europe, North America and Oceania', Renewable Energy, vol. 193, pp. 1106-1120.
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Mahmud, MAP, Adhikary, P, Zolfagharian, A, Adams, S, Kaynak, A & Kouzani, AZ 2022, 'Advanced Design, Fabrication, and Applications of 3D-Printable Piezoelectric Nanogenerators', Electronic Materials Letters, vol. 18, no. 2, pp. 129-144.
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Mahmud, MAP, Bazaz, SR, Dabiri, S, Mehrizi, AA, Asadnia, M, Warkiani, ME & Wang, ZL 2022, 'Advances in MEMS and Microfluidics‐Based Energy Harvesting Technologies', Advanced Materials Technologies, vol. 7, no. 7, pp. 2101347-2101347.
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AbstractEnergy harvesting from mechanical vibrations, thermal gradients, electromagnetic radiations, and solar radiations has experienced rapid progress in recent times not only to develop an alternative power source that can replace conventional batteries to energize portable and personal electronics smartly but also to achieve sustainable self‐sufficient micro/nanosystems. Utilizing micro‐electromechanical system (MEMS) and microfluidics technologies through selective designs and fabrications effectively, those energy harvesters can be considerably downsized while ensuring a stable, portable, and consistent power supply. Although ambient energy sources such as solar radiation are harvested for decades, recent developments have enabled ambient vibrations, electromagnetic radiation, and heat to be harvested wirelessly, independently, and sustainably. Developments in the field of microfluidics have also led to the design and fabrication of novel energy harvesting devices. This paper reviews the recent advancements in energy harvesting technologies such as piezoelectric, electromagnetic, electrostatic, thermoelectric, radio frequency, and solar to drive self‐powered portable electronics. Moreover, the potential application of MEMS and microfluidics as well as MEMS‐based structures and fabrication techniques for energy harvesting are summarized and presented. Finally, a few crucial challenges affecting the performance of energy harvesters are addressed.

Maitre, M, Horder, M, Kirkbride, KP, Gassner, A-L, Weyermann, C, Gupta, A, Beavis, A & Roux, C 2022, 'An application example of the likelihood ratio approach to the evaluation of organic gunshot residues using a fictional scenario and recently published data', Forensic Science International, vol. 335, pp. 111267-111267.
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Mallen‐Cooper, M, Atkinson, J, Xirocostas, ZA, Wijas, B, Chiarenza, GM, Dadzie, FA & Eldridge, DJ 2022, 'Global synthesis reveals strong multifaceted effects of eucalypts on soils', Global Ecology and Biogeography, vol. 31, no. 8, pp. 1667-1678.
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AbstractAimEucalypts have a widespread global distribution owing to their popularity for agroforestry and as environmental plantings. Despite an abundance of site‐specific evidence that eucalypts modify soils and soil processes, we lack a quantitative synthesis of their overall effects at the global scale. This limits our capacity to assess the likely impacts of future introductions in any given region of the world.LocationGlobal.Time period1986–2021.Major taxa studiedEucalyptus, Angophora and Corymbia.MethodsWe used a systematic search to derive a database of empirical data from 227 studies across 33 countries (neffect size = 2,806) and tested three predictions about the effects of eucalypts on soil properties and whether these effects varied with plantation age and soil depth.ResultsCompared with (non‐eucalypt) native vegetation, eucalypts significantly reduced soil moisture, microbial abundance, nitrogen, cations and anions. Relative reductions in soil microbes and ions were stronger in older eucalypt plantations. A comparison of eucalypts with (non‐eucalypt) silvicultural and agropastoral systems revealed similar effects on most soil properties, although eucalypts tended to reduce potassium and enhance carbon to a greater extent than other managed systems. We found no consistent effects of eucalypts on soil pH.Main conclusionsOur study provides the first extensive global meta‐analysis ...

Manandhar, B, Paudel, KR, Panth, N, Hansbro, P, Oliver, BG & Dua, K 2022, 'Applications of extracellular vesicles as a drug-delivery system for chronic respiratory diseases', Nanomedicine, vol. 17, no. 12, pp. 817-820.
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Mann, R, Rafei, R, Gunawan, C, Harmer, CJ & Hamidian, M 2022, 'Variants of Tn 6924 , a Novel Tn 7 Family Transposon Carrying the bla _NDM Metallo-β-Lactamase and 14 Copies of the aphA6 Amikacin Resistance Genes Found in Acinetobacter baumannii', Microbiology Spectrum, vol. 10, no. 1.
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To date, efforts to study the resistance mechanisms of carbapenem-resistant Acinetobacter baumannii have been largely focused on the two major globally distributed clones (GC1 and GC2). ST85 is an emerging sequence type, and unlike other clones, it is associated with the carriage of the bla NDM gene.

Marlton, FP, Mullens, BG, Chater, PA & Kennedy, BJ 2022, 'Tetrahedral Displacive Disorder in the Scheelite-Type Oxide RbReO₄', Inorganic Chemistry, vol. 61, no. 38, pp. 15130-15137.
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Martinez-Maldonado, R, Echeverria, V, Mangaroska, K, Shibani, A, Fernandez-Nieto, G, Schulte, J & Buckingham Shum, S 2022, 'Moodoo the Tracker: Spatial Classroom Analytics for Characterising Teachers’ Pedagogical Approaches', International Journal of Artificial Intelligence in Education, vol. 32, no. 4, pp. 1025-1051.
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Maslin, LA, Weeks, BR, Carroll, RJ, Byrne, DH & Turner, ND 2022, 'Chlorogenic Acid and Quercetin in a Diet with Fermentable Fiber Influence Multiple Processes Involved in DSS-Induced Ulcerative Colitis but Do Not Reduce Injury', Nutrients, vol. 14, no. 18, pp. 3706-3706.
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Ulcerative colitis (UC) patients often avoid foods containing fermentable fibers as some can promote symptoms during active disease. Pectin has been identified as a more protective fermentable fiber, but little has been done to determine the interaction between pectin and bioactive compounds present in foods containing that fiber type. Quercetin and chlorogenic acid, two bioactives in stone fruits, may have anti-cancer, anti-oxidant, and anti-inflammatory properties. We hypothesized that quercetin and chlorogenic acid, in the presence of the fermentable fiber pectin, may suppress the expression of pro-inflammatory molecules, alter the luminal environment, and alter colonocyte proliferation, thereby protecting against recurring bouts of UC. Rats (n = 63) received one of three purified diets (control, 0.45% quercetin, 0.05% chlorogenic acid) containing 6% pectin for 3 weeks before exposure to dextran sodium sulfate (DSS, 3% for 48 h, 3x, 2 wk separation, n = 11/diet) in drinking water to initiate UC, or control (no DSS, n = 10/diet) treatments prior to termination at 9 weeks. DSS increased the fecal moisture content (p < 0.05) and SCFA concentrations (acetate, p < 0.05; butyrate, p < 0.05). Quercetin and chlorogenic acid diets maintained SLC5A8 (SCFA transporter) mRNA levels in DSS-treated rats at levels similar to those not exposed to DSS. DSS increased injury (p < 0.0001) and inflammation (p < 0.01) scores, with no differences noted due to diet. Compared to the control diet, chlorogenic acid decreased NF-κB activity in DSS-treated rats (p < 0.05). Quercetin and chlorogenic acid may contribute to the healthy regulation of NF-κB activation (via mRNA expression of IκΒα, Tollip, and IL-1). Quercetin enhanced injury-repair molecule FGF-2 expression (p < 0.01), but neither diet nor DSS treatment altered proliferation. Although quercetin and chlorogenic acid did not protect against overt indicators of injury and inflammation, or fe...

Mathew, M, Rad, MA, Mata, JP, Mahmodi, H, Kabakova, IV, Raston, CL, Tang, Y, Tipper, JL & Tavakoli, J 2022, 'Hyperbranched polymers tune the physicochemical, mechanical, and biomedical properties of alginate hydrogels', Materials Today Chemistry, vol. 23, pp. 100656-100656.
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The current research aimed to fabricate an alginate-hyperbranched polymer (HBP) complex, using a vortex fluidic device (VFD), to control the physicochemical, structural, and mechanical properties of alginate hydrogel; thus, providing a dominant biomaterial system for different biomedical applications. Samples were prepared by mixing alginate (6%w/w) with HBP (0.85 μM) before cross-linking with Ca2+ (100 mM). Magnet stirrer (600 rpm) and VFD (6000 rpm) were used to prepare experimental samples, and alginate was used as control. Comprehensive evaluations of bulk and surface morphology, microstructural analysis, swelling kinetics, mechanical characteristics, cytotoxicity, and formation of hydrogen bonds were conducted. The findings from this study revealed that the addition of HBP to alginate structure led to a higher swelling capability (86%), increased diffusion coefficient (66-fold), and enhanced failure mechanical properties (160% and 20% increases for failure stress and elongation at break, respectively) than control. Traditional mixing affected the surface morphology, while the bulk structure remained unchanged. Moreover, the rate of degradation was not significantly different between alginate and alginate-HBP samples. When VFD was incorporated, a higher swelling ratio (30%) was observed than the control sample and the coefficient of diffusion increased (34-fold). The associated degradation rate increased 30-fold, and the failure stress and elongation at break were increased 310% and 83%, respectively, compared to the control sample. The micromixing of alginate with HBP under high shear stress using a VFD created a micro-hybrid composite formed by alginate microparticles embedded in an alginate sheet.

Maunders, EA, Ngu, DHY, Ganio, K, Hossain, SI, Lim, BYJ, Leeming, MG, Luo, Z, Tan, A, Deplazes, E, Kobe, B & McDevitt, CA 2022, 'The Impact of Chromate on Pseudomonas aeruginosa Molybdenum Homeostasis', Frontiers in Microbiology, vol. 13, p. 903146.
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Acquisition of the trace-element molybdenum via the high-affinity ATP-binding cassette permease ModABC is essential for Pseudomonas aeruginosa respiration in anaerobic and microaerophilic environments. This study determined the X-ray crystal structures of the molybdenum-recruiting solute-binding protein ModA from P. aeruginosa PAO1 in the metal-free state and bound to the group 6 metal oxyanions molybdate, tungstate, and chromate. Pseudomonas aeruginosa PAO1 ModA has a non-contiguous dual-hinged bilobal structure with a single metal-binding site positioned between the two domains. Metal binding results in a 22° relative rotation of the two lobes with the oxyanions coordinated by four residues, that contribute six hydrogen bonds, distinct from ModA orthologues that feature an additional oxyanion-binding residue. Analysis of 485 Pseudomonas ModA sequences revealed conservation of the metal-binding residues and β-sheet structural elements, highlighting their contribution to protein structure and function. Despite the capacity of ModA to bind chromate, deletion of modA did not affect P. aeruginosa PAO1 sensitivity to chromate toxicity nor impact cellular accumulation of chromate. Exposure to sub-inhibitory concentrations of chromate broadly perturbed P. aeruginosa metal homeostasis and, unexpectedly, was associated with an increase in ModA-mediated molybdenum uptake. Elemental analyses of the proteome from anaerobically grown P. aeruginosa revealed that, despite the increase in cellular molybdenum upon chromate exposure, distribution of the metal within the proteome was substantially perturbed. This suggested that molybdoprotein cofactor acquisition may be disrupted, consistent with the potent toxicity of chrom...

McBride, I, Fransen, J, Woodcock, S, De Andrade, G, Novak, A, Barela, JA & Rodrigues, ST 2022, 'Modelling implicit pre-cues and collision avoidance in a driving simulator', ANZIAM Journal, vol. 63, pp. C56-C68.
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It is well-established that pre-cues, including those observed in an implicit manner, can affect motor skills and reaction times. However, little research currently exists on how pre-cues influence complex motor skills such as driving a car at high speed. This pilot study investigates the effect of implicit pre-cues on collision avoidance under a repeat trial experiment design using a car driving simulator. Seventeen par- ticipants (aged 23.8 ± 4.2 years) were included in this investigation, which consisted of four different one-kilometre driving scenarios. This investigation considers two of the four scenarios. Two scenarios had the stimulus of a child crossing the road, however only one of these scenarios had an implicit pre-cue appear before the stimulus. The remaining two scenarios had no stimulus or pre-cue and were included to reduce any learning effect by participants. The proportion of participants who had a collision differed significantly between scenarios with and without a pre-cue. The primary effect size of the pre-cue is modelled using a logis- tic regression and distributions for point estimators are obtained from bootstrapping results. A power analysis exploring different primary effect sizes is performed to inform sample size considerations for repeat studies. Implications for motor control, such as experiment design and statistical modelling methods, are discussed to inform future large scale trials. ReferencesJ. A. Barela, A. A. Rocha, A. R. Novak, J. Fransen, and G. A. Figueiredo. Age differences in the use of implicit visual cues in a response time task. Braz. J. Motor Behav. 13.2 (2019), pp. 86–93. doi: 10.20338/bjmb.v13i2.139J. Cohen. Statistical power analysis for the behavioral sciences. Routledge, 1988. doi: 10.4324/9780203771587U. Eversheim and O. Bock. The role of precues in the preparation of motor responses in humans. J. Mot. Behav. 34.3 (2002), pp. 271–276. doi: 10.1080/00222890209601945D. G. Jenkins an...

McClements, L, Richards, C, Patel, N, Chen, H, Sesperez, K, Bubb, KJ, Karlstaedt, A & Aksentijevic, D 2022, 'Impact of reduced uterine perfusion pressure model of preeclampsia on metabolism of placenta, maternal and fetal hearts', Scientific Reports, vol. 12, no. 1, p. 1111.
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AbstractPreeclampsia is a cardiovascular pregnancy complication characterised by new onset hypertension and organ damage or intrauterine growth restriction. It is one of the leading causes of maternal and fetal mortality in pregnancy globally. Short of pre-term delivery of the fetus and placenta, treatment options are limited. Consequently, preeclampsia leads to increased cardiovascular disease risk in both mothers and offspring later in life. Here we aim to examine the impact of the reduced uterine perfusion pressure (RUPP) rat model of preeclampsia on the maternal cardiovascular system, placental and fetal heart metabolism. The surgical RUPP model was induced in pregnant rats by applying silver clips around the aorta and uterine arteries on gestational day 14, resulting in ~ 40% uterine blood flow reduction. The experiment was terminated on gestational day 19 and metabolomic profile of placentae, maternal and fetal hearts analysed using high-resolution 1H NMR spectroscopy. Impairment of uterine perfusion in RUPP rats caused placental and cardiac hypoxia and a series of metabolic adaptations: altered energetics, carbohydrate, lipid and amino acid metabolism of placentae and maternal hearts. Comparatively, the fetal metabolic phenotype was mildly affected. Nevertheless, long-term effects of these changes in both mothers and the offspring should be investigated further in the future.

McLean, D, Speed, CW, Birt, MJ, Colquhoun, J, Case, M, Stowar, M, Bond, T, Ierodiaconou, D, Whitmarsh, SK, Taylor, MD, Wines, S, Booth, DJ, Fowler, AM & Vaughan, BI 2022, 'Habitat value of subsea wells and pipelines for fishery target species in Australia', Frontiers in Marine Science, vol. 9, pp. 1-23.
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Subsea pipelines and wells installed to support the oil and gas industry represent some of the most extensive and numerous anthropogenic structures throughout global marine ecosystems. There remains a paucity of information on the habitat value of these structures for fishery target species and, as a result, little understanding of how decommissioning should be conducted to minimise impacts to populations of these economically and socially important species. We assess the diversity and abundance of species that are targets of recreational and commercial fisheries on 33 subsea wells and 17 pipelines across the tropical northwest and temperate southeast marine regions of Australia. We examine relationships between fish identity and abundance and a range of environmental (e.g., depth, location), infrastructure-specific (e.g., pipeline position, diameter, age, length of pipeline, height of well, position on well), and biological (% cover of epibiota) variables using video filmed by remotely operated vehicles during their routine offshore inspection and maintenance campaigns. A total of 100 fishery target species were observed across subsea well and pipeline infrastructure, 56 species uniquely observed on pipelines and nine unique to wells. The families Lutjanidae (snapper), Serranidae (rock cods, groupers, perch), and Carangidae (trevallies) were most common and abundant on both wells and pipelines. In the northwest, lutjanids were most abundant around the base of wells, in shallow depths, on shorter wells, and where pipelines spanned the seafloor. A greater number of fishery target species and abundance of ocean perch (Helicolenus spp.) were also associated with pipelines that spanned the seafloor in temperate southeast Australia. The combined biomass of three species of snapper on wells in the northwest was 1,270 kg, with production levels for these species on each well estimated to be 105.2 g m2 yea...

McLean, DL, Ferreira, LC, Benthuysen, JA, Miller, KJ, Schläppy, M, Ajemian, MJ, Berry, O, Birchenough, SNR, Bond, T, Boschetti, F, Bull, AS, Claisse, JT, Condie, SA, Consoli, P, Coolen, JWP, Elliott, M, Fortune, IS, Fowler, AM, Gillanders, BM, Harrison, HB, Hart, KM, Henry, L, Hewitt, CL, Hicks, N, Hock, K, Hyder, K, Love, M, Macreadie, PI, Miller, RJ, Montevecchi, WA, Nishimoto, MM, Page, HM, Paterson, DM, Pattiaratchi, CB, Pecl, GT, Porter, JS, Reeves, DB, Riginos, C, Rouse, S, Russell, DJF, Sherman, CDH, Teilmann, J, Todd, VLG, Treml, EA, Williamson, DH & Thums, M 2022, 'Influence of offshore oil and gas structures on seascape ecological connectivity', Global Change Biology, vol. 28, no. 11, pp. 3515-3536.
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AbstractOffshore platforms, subsea pipelines, wells and related fixed structures supporting the oil and gas (O&G) industry are prevalent in oceans across the globe, with many approaching the end of their operational life and requiring decommissioning. Although structures can possess high ecological diversity and productivity, information on how they interact with broader ecological processes remains unclear. Here, we review the current state of knowledge on the role of O&G infrastructure in maintaining, altering or enhancing ecological connectivity with natural marine habitats. There is a paucity of studies on the subject with only 33 papers specifically targeting connectivity and O&G structures, although other studies provide important related information. Evidence for O&G structures facilitating vertical and horizontal seascape connectivity exists for larvae and mobile adult invertebrates, fish and megafauna; including threatened and commercially important species. The degree to which these structures represent a beneficial or detrimental net impact remains unclear, is complex and ultimately needs more research to determine the extent to which natural connectivity networks are conserved, enhanced or disrupted. We discuss the potential impacts of different decommissioning approaches on seascape connectivity and identify, through expert elicitation, critical knowledge gaps that, if addressed, may further inform decision making for the life cycle of O&G infrastructure, with relevance for other industries (e.g. renewables). The most highly ranked critical knowledge gap was a need to understand how O&G structures modify and influence the movement patterns of mobile species and dispersal stages of sessile marine species. Understanding how different decommissioning options affect species survival and movement was also highly ranked, as was understanding the extent to which O&G structures contribute...

McLeod, IM, Hein, MY, Babcock, R, Bay, L, Bourne, DG, Cook, N, Doropoulos, C, Gibbs, M, Harrison, P, Lockie, S, van Oppen, MJH, Mattocks, N, Page, CA, Randall, CJ, Smith, A, Smith, HA, Suggett, DJ, Taylor, B, Vella, KJ, Wachenfeld, D & Boström-Einarsson, L 2022, 'Coral restoration and adaptation in Australia: The first five years', PLOS ONE, vol. 17, no. 11, pp. e0273325-e0273325.
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While coral reefs in Australia have historically been a showcase of conventional management informed by research, recent declines in coral cover have triggered efforts to innovate and integrate intervention and restoration actions into management frameworks. Here we outline the multi-faceted intervention approaches that have developed in Australia since 2017, from newly implemented in-water programs, research to enhance coral resilience and investigations into socio-economic perspectives on restoration goals. We describe in-water projects using coral gardening, substrate stabilisation, coral repositioning, macro-algae removal, and larval-based restoration techniques. Three areas of research focus are also presented to illustrate the breadth of Australian research on coral restoration, (1) the transdisciplinary Reef Restoration and Adaptation Program (RRAP), one of the world’s largest research and development programs focused on coral reefs, (2) interventions to enhance coral performance under climate change, and (3) research into socio-cultural perspectives. Together, these projects and the recent research focus reflect an increasing urgency for action to confront the coral reef crisis, develop new and additional tools to manage coral reefs, and the consequent increase in funding opportunities and management appetite for implementation. The rapid progress in trialling and deploying coral restoration in Australia builds on decades of overseas experience, and advances in research and development are showing positive signs that coral restoration can be a valuable tool to improve resilience at local scales (i.e., high early survival rates across a variety of methods and coral species, strong community engagement with local stakeholders). RRAP is focused on creating interventions to help coral reefs at multiple scales, from micro scales (i.e., interventions targeting small areas within a specific reef site) to large scales (i.e., interventions target...

McPherson, DJ, Dowd, A, Arnold, MD, Gentle, A & Cortie, MB 2022, 'Electrochemical energy storage on nanoporous copper sponge', Journal of Materials Research, vol. 37, no. 13, pp. 2195-2203.
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AbstractA proof-of-principle double-layer symmetrical supercapacitor with nanoporous copper/copper oxide electrodes and an aqueous electrolyte is investigated. The electrodes are manufactured by selective dissolution of Al from a eutectic composition of Cu17.5Al82.5using 5 M NaOH. The ostensible (i.e., net external) capacitance of a symmetrical two-electrode cell with 0.1 M KNO3electrolyte is assessed over a series of charge/discharge cycles and is about 2 F per gram of Cu in this simple prototype. Capacitance varies during a discharge cycle due evidently to the deeply buried surfaces and pseudocapacitive reactions contributing charge toward the end of a discharge cycle. In principle such a device should have very low ohmic losses due to its highly conductive backbone and would be suitable for applications requiring maximum energy efficiency over repeated cycling. The aqueous electrolyte ensures fire safety but this comes at the cost of lower energy content.Graphical abstract

Medvecky, M, Papagiannitsis, CC, Wyrsch, ER, Bitar, I, Cummins, ML, Djordjevic, SP & Dolejska, M 2022, 'Interspecies Transmission of CMY-2-Producing Escherichia coli Sequence Type 963 Isolates between Humans and Gulls in Australia', mSphere, vol. 7, no. 4, p. e0023822.
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We have provided the first comprehensive genomic study of E. coli ST963 by analyzing various genomic and phenotypic data sets of isolates from Australian silver gulls and comparison with genomes from geographically dispersed regions of human and animal origin. Our study suggests the emergence of a specific bla CMY-2 -carrying E. coli ST963 clone in Australia that is widely spread across the continent by humans and birds.

Mendelson, N, Ritika, R, Kianinia, M, Scott, J, Kim, S, Fröch, JE, Gazzana, C, Westerhausen, M, Xiao, L, Mohajerani, SS, Strauf, S, Toth, M, Aharonovich, I & Xu, Z 2022, 'Coupling Spin Defects in a Layered Material to Nanoscale Plasmonic Cavities', Advanced Materials, vol. 34, no. 1, pp. 1-7.
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AbstractSpin defects in hexagonal boron nitride, and specifically the negatively charged boron vacancy (VB‐) centers, are emerging candidates for quantum sensing. However, the VB‐ defects suffer from low quantum efficiency and, as a result, exhibit weak photoluminescence. In this work, a scalable approach is demonstrated to dramatically enhance the VB‐ emission by coupling to a plasmonic gap cavity. The plasmonic cavity is composed of a flat gold surface and a silver cube, with few‐layer hBN flakes positioned in between. Employing these plasmonic cavities, two orders of magnitude are extracted in photoluminescence enhancement associated with a corresponding twofold enhancement in optically detected magnetic resonance contrast. The work will be pivotal to progress in quantum sensing employing 2D materials, and in realization of nanophotonic devices with spin defects in hexagonal boron nitride.

Merklein, M, Kabakova, IV, Zarifi, A & Eggleton, BJ 2022, '100 years of Brillouin scattering: Historical and future perspectives', Applied Physics Reviews, vol. 9, no. 4, pp. 041306-041306.
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The Year 2022 marks 100 years since Leon Brillouin predicted and theoretically described the interaction of optical waves with acoustic waves in a medium. Accordingly, this resonant multi-wave interaction is referred to as Brillouin scattering. Today, Brillouin scattering has found a multitude of applications, ranging from microscopy of biological tissue, remote sensing over many kilometers, and signal processing in compact photonic integrated circuits smaller than the size of a thumbnail. What allows Brillouin scattering to be harnessed over such different length scales and research domains are its unique underlying properties, namely, its narrow linewidth in the MHz range, a frequency shift in the GHz range, large frequency selective gain or loss, frequency tunability, and optical reconfigurability. Brillouin scattering is also a ubiquitous effect that can be observed in many different media, such as freely propagating in gases and liquids, as well as over long lengths of low-loss optical glass fibers or short semiconductor waveguides. A recent trend of Brillouin research focuses on micro-structured waveguides and integrated photonic platforms. The reduction in the size of waveguides allows tailoring the overlap between the optical and acoustic waves and promises many novel applications in a compact footprint. In this review article, we give an overview of the evolution and development of the field of Brillouin scattering over the last one hundred years toward current lines of active research. We provide the reader with a perspective of recent trends and challenges that demand further research efforts and give an outlook toward the future of this exciting and diverse research field.

Meyer, F, Fritz, A, Deng, Z-L, Koslicki, D, Lesker, TR, Gurevich, A, Robertson, G, Alser, M, Antipov, D, Beghini, F, Bertrand, D, Brito, JJ, Brown, CT, Buchmann, J, Buluç, A, Chen, B, Chikhi, R, Clausen, PTLC, Cristian, A, Dabrowski, PW, Darling, AE, Egan, R, Eskin, E, Georganas, E, Goltsman, E, Gray, MA, Hansen, LH, Hofmeyr, S, Huang, P, Irber, L, Jia, H, Jørgensen, TS, Kieser, SD, Klemetsen, T, Kola, A, Kolmogorov, M, Korobeynikov, A, Kwan, J, LaPierre, N, Lemaitre, C, Li, C, Limasset, A, Malcher-Miranda, F, Mangul, S, Marcelino, VR, Marchet, C, Marijon, P, Meleshko, D, Mende, DR, Milanese, A, Nagarajan, N, Nissen, J, Nurk, S, Oliker, L, Paoli, L, Peterlongo, P, Piro, VC, Porter, JS, Rasmussen, S, Rees, ER, Reinert, K, Renard, B, Robertsen, EM, Rosen, GL, Ruscheweyh, H-J, Sarwal, V, Segata, N, Seiler, E, Shi, L, Sun, F, Sunagawa, S, Sørensen, SJ, Thomas, A, Tong, C, Trajkovski, M, Tremblay, J, Uritskiy, G, Vicedomini, R, Wang, Z, Wang, Z, Wang, Z, Warren, A, Willassen, NP, Yelick, K, You, R, Zeller, G, Zhao, Z, Zhu, S, Zhu, J, Garrido-Oter, R, Gastmeier, P, Hacquard, S, Häußler, S, Khaledi, A, Maechler, F, Mesny, F, Radutoiu, S, Schulze-Lefert, P, Smit, N, Strowig, T, Bremges, A, Sczyrba, A & McHardy, AC 2022, 'Critical Assessment of Metagenome Interpretation: the second round of challenges', Nature Methods, vol. 19, no. 4, pp. 429-440.
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AbstractEvaluating metagenomic software is key for optimizing metagenome interpretation and focus of the Initiative for the Critical Assessment of Metagenome Interpretation (CAMI). The CAMI II challenge engaged the community to assess methods on realistic and complex datasets with long- and short-read sequences, created computationally from around 1,700 new and known genomes, as well as 600 new plasmids and viruses. Here we analyze 5,002 results by 76 program versions. Substantial improvements were seen in assembly, some due to long-read data. Related strains still were challenging for assembly and genome recovery through binning, as was assembly quality for the latter. Profilers markedly matured, with taxon profilers and binners excelling at higher bacterial ranks, but underperforming for viruses and Archaea. Clinical pathogen detection results revealed a need to improve reproducibility. Runtime and memory usage analyses identified efficient programs, including top performers with other metrics. The results identify challenges and guide researchers in selecting methods for analyses.

Meyer, S, Clases, D, Gonzalez de Vega, R, Padula, MP & Doble, PA 2022, 'Separation of intact proteins by capillary electrophoresis', The Analyst, vol. 147, no. 13, pp. 2988-2996.
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This work presents novel methods of intact protein analysis using surfactant coated neutral dimethyl polysiloxane capillaries for rapid and targeted selection of appropriate background electrolytesviaconsideration of protein isoelectric points.

Mi, C, Guan, M, Zhang, X, Yang, L, Wu, S, Yang, Z, Guo, Z, Liao, J, Zhou, J, Lin, F, Ma, E, Jin, D & Yuan, X 2022, 'High Spatial and Temporal Resolution NIR-IIb Gastrointestinal Imaging in Mice', Nano Letters, vol. 22, no. 7, pp. 2793-2800.
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Conventional biomedical imaging modalities, including endoscopy, X-rays, and magnetic resonance, are invasive and insufficient in spatial and temporal resolutions for gastrointestinal (GI) tract imaging to guide prognosis and therapy. Here we report a noninvasive method based on lanthanide-doped nanocrystals with ∼1530 nm fluorescence in the near-infrared-IIb window (NIR-IIb, 1500-1700 nm). The rational design of nanocrystals have led to an absolute quantum yield (QY) up to 48.6%. Further benefiting from the minimized scattering through the NIR-IIb window, we enhanced the spatial resolution to ∼1 mm in GI tract imaging, which is ∼3 times higher compared with the near-infrared-IIa (NIR-IIa, 1000-1500 nm) method. The approach also realized a high temporal resolution of 8 frames per second; thus the moment of mice intestinal peristalsis can be captured. Furthermore, with a light-sheet imaging system, we demonstrated a three-dimensional (3D) imaging on the GI tract. Moreover, we successfully translated these advances to diagnose inflammatory bowel disease.

Mitchell, A, Booth, DJ & Nagelkerken, I 2022, 'Ocean warming and acidification degrade shoaling performance and lateralization of novel tropical–temperate fish shoals', Global Change Biology, vol. 28, no. 4, pp. 1388-1401.
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AbstractGregarious behaviours are common in animals and provide various benefits such as food acquisition and protection against predators. Many gregarious tropical species are shifting poleward under current ocean warming, creating novel species and social interactions with local temperate taxa. However, how the dynamics of these novel shoals might be altered by future ocean warming and acidification remains untested. Here we evaluate how novel species interactions, ocean acidification and warming affect shoaling dynamics, motor lateralization and boldness of range‐extending tropical and co‐shoaling temperate fishes under controlled laboratory conditions. Fishes were exposed to 1 of 12 treatments (combinations of three temperature levels, two pCO2 levels and two shoal type levels: mixed species or temperate only) for 38 days. Lateralization (a measure of asymmetric expression of cognitive function in group coordination and predator escape) of tropical and temperate species was right‐side biased under present‐day conditions, but side bias significantly diminished in tropical and temperate fishes under ocean acidification. Ocean acidification also decreased shoal cohesion irrespective of shoaling type, with mixed‐species shoals showing significantly lower cohesion than temperate‐only shoals irrespective of climate stressors. Tropical fish became bolder under ocean acidification (after 4 weeks), and temperate fish became bolder with increasing temperature, while ocean acidification dampened temperate fish boldness. Our findings highlight the direct effect of climate stressors on fish behaviour and the interplay with the indirect effects of novel species interactions. Because strong shoal cohesion and lateralization are key determinants of species fitness, their degradation under ocean warming and acidification could adversely affect species performance in novel assemblages in...

Mohanty, M, Jena, R & Singh, P 2022, 'Can Zoom video conferencing tool be misused for real‐time cybercrime?', WIREs Forensic Science, vol. 4, no. 1.
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AbstractVideo conferencing tool Zoom has boomed during this COVID pandemic situation. Although Zoom has been very useful for facilitating work‐from‐home and study‐from‐home arrangements, its misuse can result in cybercrime cases. The world has already seen the adverse effect of a Zoom‐related cybercrime, Zoombombing. In this article, we discuss how Zoom can also be misused for launching real‐time cybercrime, such as piracy and real‐time pornography. The end‐to‐end encryption proposed to be used by Zoom can further complicate these cybercrime issues. The existing mechanisms may not be sufficient in dealing with these real‐time issues. New mechanisms need to be found.This article is categorized under:Digital and Multimedia Science > Multimedia Forensics

Mohd Yusop, AY, Xiao, L & Fu, S 2022, 'Isolation and identification of an isomeric sildenafil analogue as an adulterant in an instant coffee premix', Forensic Sciences Research, vol. 7, no. 2, pp. 290-298.
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Moheimani, F, Shahdab, N, Cummings, S, Hansbro, PM & Ward, C 2022, 'Key role of dysregulated airway epithelium in response to respiratory viral infections in asthma', ERJ Open Research, vol. 8, no. 3, pp. 00314-2022.
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A differentiated air-liquid interface model shows that the airway epithelium plays a key role in response to respiratory viral infections in people with asthma https://bit.ly/3yDgiX1.

Mohid, SA, Sharma, P, Alghalayini, A, Saini, T, Datta, D, Willcox, MDP, Ali, H, Raha, S, Singha, A, Lee, D, Sahoo, N, Cranfield, CG, Roy, S & Bhunia, A 2022, 'A rationally designed synthetic antimicrobial peptide against Pseudomonas-associated corneal keratitis: Structure-function correlation', Biophysical Chemistry, vol. 286, pp. 106802-106802.
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Moiteiro, C, Marques, I, Ryder, WG, Cachatra, V, Carvalho, S, Chen, L, Goodfellow, BJ, Gale, PA & Félix, V 2022, 'Binding and Transport Properties of a Benzo[b]thiophene‐Based Mono‐(thio)urea Library', European Journal of Organic Chemistry, vol. 2022, no. 3.
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AbstractUsing the chemical versatility of the benzo[b]thiophene motif, an extensive library of 24 (thio)urea receptors, with different binding properties and lipophilicities, was prepared and included α,α‐, α,β‐, β,β‐, β,γ‐, α,γ‐, and γ,γ‐benzo[b]thiophene positional isomers, as well as β‐ or γ‐benzo[b]thiophene‐based molecules decorated with aliphatic chains or aryl moieties with different fluorination degrees. 1H NMR titrations, X‐ray crystallographic studies, and DFT calculations were used to study the chloride binding affinities between receptors and substrates. Experimental efflux studies suggested that the anion transmembrane transport activity is dependent on the receptors′ lipophilicity and hydrogen bonding ability. Moreover, LUV based assays indicated that anion efflux occurs mainly through an uniport mechanism. Further MD simulations showed that anion transport is highly dependent on the orientation and interactions of the receptors at the water/lipid interface.

Montgomery, E, Newton, PJ, Chang, S, Peng, W, Jha, SR, Wilhelm, K, Macdonald, PS & Malouf, M 2022, 'Frailty Measures in Patients Listed for Lung Transplantation', Transplantation, vol. 106, no. 5, pp. 1084-1092.
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Background. The study aimed to determine whether the addition of cognitive impairment, depression, or both, to the assessment of physical frailty (PF) is associated with the risk of lung transplant (LTX) waitlist mortality. Methods. Since March 2013, all patients referred for LTX evaluation underwent PF assessment. Cognition was assessed using the Montreal Cognitive Assessment and depression assessed using the Depression in Medical Illness questionnaire. We assessed the association of 4 composite frailty measures: PF ≥3 of 5 = frail, cognitive frailty (CogF ≥3 of 6 = frail), depressive frailty (DepF ≥3 of 6 = frail), and combined frailty (ComF ≥3 of 7 = frail) with waitlist mortality. Results. The prevalence of PF was 78 (22%), CogF 100 (28%), DepF 105 (29%), and ComF 124 (34%). Waitlist survival in the non-PF group was 94% ± 2% versus 71% ± 7% in the PF group (P < 0.001). Cox proportional hazards regression analysis demonstrated that PF (adjusted hazard ratio [HR], 4.88; 95% confidence interval [CI], 2.06-11.56), mild cognitive impairment (adjusted HR, 3.03; 95% CI, 1.05-8.78), and hypoalbuminemia (adjusted HR, 0.89; 95% CI, 0.82-0.97) were independent predictors of waitlist mortality. There was no significant difference in the area under the curve of the 4 frailty measures. Conclusions. The addition of cognitive function and depression variables to the PF assessment increased the number of patients classified as frail. However, the addition of these variables does not strengthen the association with LTX waitlist mortality...

Moody, G, Sorger, VJ, Blumenthal, DJ, Juodawlkis, PW, Loh, W, Sorace-Agaskar, C, Jones, AE, Balram, KC, Matthews, JCF, Laing, A, Davanco, M, Chang, L, Bowers, JE, Quack, N, Galland, C, Aharonovich, I, Wolff, MA, Schuck, C, Sinclair, N, Lončar, M, Komljenovic, T, Weld, D, Mookherjea, S, Buckley, S, Radulaski, M, Reitzenstein, S, Pingault, B, Machielse, B, Mukhopadhyay, D, Akimov, A, Zheltikov, A, Agarwal, GS, Srinivasan, K, Lu, J, Tang, HX, Jiang, W, McKenna, TP, Safavi-Naeini, AH, Steinhauer, S, Elshaari, AW, Zwiller, V, Davids, PS, Martinez, N, Gehl, M, Chiaverini, J, Mehta, KK, Romero, J, Lingaraju, NB, Weiner, AM, Peace, D, Cernansky, R, Lobino, M, Diamanti, E, Vidarte, LT & Camacho, RM 2022, '2022 Roadmap on integrated quantum photonics', Journal of Physics: Photonics, vol. 4, no. 1, pp. 012501-012501.
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Abstract Integrated photonics will play a key role in quantum systems as they grow from few-qubit prototypes to tens of thousands of qubits. The underlying optical quantum technologies can only be realized through the integration of these components onto quantum photonic integrated circuits (QPICs) with accompanying electronics. In the last decade, remarkable advances in quantum photonic integration have enabled table-top experiments to be scaled down to prototype chips with improvements in efficiency, robustness, and key performance metrics. These advances have enabled integrated quantum photonic technologies combining up to 650 optical and electrical components onto a single chip that are capable of programmable quantum information processing, chip-to-chip networking, hybrid quantum system integration, and high-speed communications. In this roadmap article, we highlight the status, current and future challenges, and emerging technologies in several key research areas in integrated quantum photonics, including photonic platforms, quantum and classical light sources, quantum frequency conversion, integrated detectors, and applications in computing, communications, and sensing. With advances in materials, photonic design architectures, fabrication and integration processes, packaging, and testing and benchmarking, in the next decade we can expect a transition from single- and few-function prototypes to large-scale integration of multi-functional and reconfigurable devices that will have a transformative impact on quantum information science and engineering.

Morgan, AL, Torpy, FR, Irga, PJ, Fleck, R, Gill, RL & Pettit, T 2022, 'The botanical biofiltration of volatile organic compounds and particulate matter derived from cigarette smoke', Chemosphere, vol. 295, pp. 133942-133942.
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Morshedi Rad, D, Rezaei, M, Radfar, P & Ebrahimi Warkiani, M 2022, 'Microengineered filters for efficient delivery of nanomaterials into mammalian cells', Scientific Reports, vol. 12, no. 1, p. 4383.
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AbstractIntracellular delivery of nanomaterials into the cells of interest has enabled cell manipulation for numerous applications ranging from cell-based therapies to biomedical research. To date, different carriers or membrane poration-based techniques have been developed to load nanomaterials to the cell interior. These biotools have shown promise to surpass the membrane barrier and provide access to the intracellular space followed by passive diffusion of exogenous cargoes. However, most of them suffer from inconsistent delivery, cytotoxicity, and expensive protocols, somewhat limiting their utility in a variety of delivery applications. Here, by leveraging the benefits of microengineered porous membranes with a suitable porosity, we demonstrated an efficient intracellular loading of diverse nanomaterials to different cell types based on inducing mechanical disruption to the cell membrane. In this work, for the first time, we used ultra-thin silicon nitride (SiN) filter membranes with uniform micropores smaller than the cell diameter to load impermeable nanomaterials into adherent and non-adherent cell types. The delivery performance using SiN microsieves has been validated through the loading of functional nanomaterials from a few nanometers to hundreds of nanometers into mammalian cells with minimal undesired impacts. Besides the high delivery efficiency and improved cell viability, this simple and low-cost approach offers less clogging and higher throughput (107 cell min−1). Therefore, it yields to the efficient introduction of exogenous nanomaterials into the large population of cells, illustrating the potential of these microengineered filters to be widely used in the microfiltroporation (MFP) setup.

Munawar, HS, Mojtahedi, M, Hammad, AWA, Kouzani, A & Mahmud, MAP 2022, 'Disruptive technologies as a solution for disaster risk management: A review', Science of The Total Environment, vol. 806, pp. 151351-151351.
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Muthiah, K, Wilhelm, K, Robson, D, Raju, H, Aili, SR, Jha, SR, Pierce, R, Fritis-Lamora, R, Montgomery, E, Gorrie, N, Deveza, R, Brennan, X, Schnegg, B, Jabbour, A, Kotlyar, E, Keogh, AM, Bart, N, Conellan, M, Iyer, A, Watson, A, Granger, E, Jansz, PC, Hayward, C & Macdonald, PS 2022, 'Impact of frailty on mortality and morbidity in bridge to transplant recipients of contemporary durable mechanical circulatory support', The Journal of Heart and Lung Transplantation, vol. 41, no. 6, pp. 829-839.
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Nazrul‐Islam, SMK, Rahman, MR, Ahmed, AJ, Yun, FF, Cortie, DL, Wang, X & Cortie, MB 2022, 'Beneficial Effect of Na₂CO₃ Additions on the Thermoelectric Performance of Melt‐Route Cu₂Se', Advanced Electronic Materials, vol. 8, no. 3, pp. 2100802-2100802.
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AbstractHigh‐performance thermoelectric materials require simultaneous reduction of thermal conductivity and electrical resistivity, among other criteria. Here it is shown that the introduction of Na2CO3 into the melt‐route fabrication process for the well‐known thermoelectric Cu2Se has a beneficial and surprisingly strong effect. There is a significant enhancement in electrical conductivity which density functional theory calculations suggest may be due to the effect of Na and O doping in the Cu2Se matrix. There is also a 34% reduction in thermal conductivity which is likely due to a high density of defects causing scattering of phonons. Overall, however, there is only relatively a small change in Seebeck coefficient. A higher power factor of 12.6 µW cm−1 K−2 is achieved versus 8.8 µW cm−1 K−2 for standard Cu2Se. A very high value of zT of 2.3 is obtained at 804 K versus 1.1 for standard Cu2Se.

Neville, SL, Cunningham, BA, Maunders, EA, Tan, A, Watts, JA, Ganio, K, Eijkelkamp, BA, Pederick, VG, Gonzalez de Vega, R, Clases, D, Doble, PA & McDevitt, CA 2022, 'Host-Mediated Copper Stress Is Not Protective against Streptococcus pneumoniae D39 Infection', Microbiology Spectrum, vol. 10, no. 6, p. e0249522.
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Streptococcus pneumoniae (the pneumococcus) is one of the world’s foremost bacterial pathogens. Treatment of both localized and systemic pneumococcal infection is becoming complicated by increasing rates of multidrug resistance globally.

Newing, TP, Brewster, JL, Fitschen, LJ, Bouwer, JC, Johnston, NP, Yu, H & Tolun, G 2022, 'Redβ177 annealase structure reveals details of oligomerization and λ Red-mediated homologous DNA recombination', Nature Communications, vol. 13, no. 1, p. 5649.
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AbstractThe Redβ protein of the bacteriophage λ red recombination system is a model annealase which catalyzes single-strand annealing homologous DNA recombination. Here we present the structure of a helical oligomeric annealing intermediate of Redβ, consisting of N-terminal residues 1-177 bound to two complementary 27mer oligonucleotides, determined via cryogenic electron microscopy (cryo-EM) to a final resolution of 3.3 Å. The structure reveals a continuous binding groove which positions and stabilizes complementary DNA strands in a planar orientation to facilitate base pairing via a network of hydrogen bonding. Definition of the inter-subunit interface provides a structural basis for the propensity of Redβ to oligomerize into functionally significant long helical filaments, a trait shared by most annealases. Our cryo-EM structure and molecular dynamics simulations suggest that residues 133-138 form a flexible loop which modulates access to the binding groove. More than half a century after its discovery, this combination of structural and computational observations has allowed us to propose molecular mechanisms for the actions of the model annealase Redβ, a defining member of the Redβ/RecT protein family.

Nguyen, LN, Aditya, L, Vu, HP, Johir, AH, Bennar, L, Ralph, P, Hoang, NB, Zdarta, J & Nghiem, LD 2022, 'Nutrient Removal by Algae-Based Wastewater Treatment', Current Pollution Reports, vol. 8, no. 4, pp. 369-383.
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AbstractAlgae cultivation complements wastewater treatment (WWT) principles as the process uptakes nutrients while assimilates CO2 into biomass. Thus, the application of algae-based WWT is on the upward trajectory as more attention for recovery nutrients and CO2 capture while reducing its economic challenge in the circular economy concept. However, the complexity of wastewater and algal ecological characteristics induces techno-economic challenges for industry implementation. Algae-based WWT relies totally on the ability of algae to uptake and store nutrients in the biomass. Therefore, the removal efficiency is proportional to biomass productivity. This removal mechanism limits algae applications to low nutrient concentration wastewater. The hydraulic retention time (HRT) of algae-based WWT is significantly long (i.e. > 10 days), compared to a few hours in bacteria-based process. Phototrophic algae are the most used process in algae-based WWT studies as well as in pilot-scale trials. Application of phototrophic algae in wastewater faces challenges to supply CO2 and illumination. Collectively, significant landscape is required for illumination. Algae-based WWT has limited organic removals, which require pretreatment of wastewaters before flowing into the algal process. Algae-based WWT can be used in connection with the bacteria-based WWT to remove partial nutrients while capturing CO2. Future research should strive to achieve fast and high growth rate, strong environmental tolerance species, and simple downstream processing and high-value biomass. There is also a clear and urgent need for more systematic analysis of biomass for both carbon credit assessment and economic values to facilitate identification and prioritisation of barriers to lower the cost algae-based WWT. Graphical abstract

Nguyen, LN, Vu, HP, Fu, Q, Abu Hasan Johir, M, Ibrahim, I, Mofijur, M, Labeeuw, L, Pernice, M, Ralph, PJ & Nghiem, LD 2022, 'Synthesis and evaluation of cationic polyacrylamide and polyacrylate flocculants for harvesting freshwater and marine microalgae', Chemical Engineering Journal, vol. 433, pp. 133623-133623.
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This study addresses the challenge of microalgae harvesting through the development of flocculants. Two positively charged cationic polymers including poly[2 (acryloyloxy)ethyl]trimethylammonium chloride (PAETAC) and poly(3 acrylamidopropyl)trimethylammonium chloride (PAmPTAC) were synthesized using the UV-induced radical polymerization, for harvesting both freshwater and marine microalgae. The results show that the synthesized polymers have excellent flocculation performance for both freshwater green microalgae (Chlorella vulgaris) and marine red microalgae (Porphyridium purpureum). PAETAC outperformed PAmPTAC for both Chlorella vulgaris and Porphyridium purpureum microalgae. The optimal PAETAC doses for Chlorella vulgaris and Porphyridium purpureum microalgae were 50 and 4.8 mg/g of dry biomass while the optimal PAmPTAC doses were 252 and 35 mg/g of dry biomass respectively. Additionally, the floc formation with the PAETAC was more stable than PAmPTAC, which supported the dewatering step via sieving. The superior performance can be attributed to the higher molecular weight of the PAETAC polymer when compared to the PAmPTAC polymer. In comparison to commercially available polydiallyldimethylammonium chloride (PolyDADMAC), the newly synthesised PAETAC and PAmPTAC polymers demonstrated superior flocculation efficiency at a lower dose. The findings of this study established a platform technology for designing and synthesising cationic flocculants for use in microalgae harvesting.

Nguyen, TMH, Bräunig, J, Kookana, RS, Kaserzon, SL, Knight, ER, Vo, HNP, Kabiri, S, Navarro, DA, Grimison, C, Riddell, N, Higgins, CP, McLaughlin, MJ & Mueller, JF 2022, 'Assessment of Mobilization Potential of Per- and Polyfluoroalkyl Substances for Soil Remediation', Environmental Science & Technology, vol. 56, no. 14, pp. 10030-10041.
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This study investigated the mobilization of a wide range of per- and polyfluoroalkyl substances (PFASs) present in aqueous film-forming foams (AFFFs) in water-saturated soils through one-dimensional (1-D) column experiments with a view to assessing the feasibility of their remediation by soil desorption and washing. Results indicated that sorption/desorption of most of the shorter-carbon-chain PFASs (C ≤ 6) in soil reached greater than 99% rapidly─after approximately two pore volumes (PVs) and were well predicted by an equilibrium transport model, indicating that they will be readily removed by soil washing technologies. In contrast, the equilibrium model failed to predict the mobilization of longer-chain PFASs (C ≥ 7), indicating the presence of nonequilibrium sorption/desorption (confirmed by a flow interruption experiment). The actual time taken to attain 99% sorption/desorption was up to 5 times longer than predicted by the equilibrium model (e.g., ∼62 PVs versus ∼12 PVs predicted for perfluorooctane sulfonate (PFOS) in loamy sand). The increasing contribution of hydrophobic interactions over the electrostatic interactions is suggested as the main driving factor of the nonequilibrium processes. The inverse linear relationship (R2 = 0.6, p < 0.0001) between the nonequilibrium mass transfer rate coefficient and the Freundlich sorption coefficient could potentially be a useful means for preliminary evaluation of potential nonequilibrium sorption/desorption of PFASs in soils.

Nicolle, P, Hughes, J, Fowler, A & Schilling, HT 2022, 'Long-term increase in growth of an estuarine predator, mulloway Argyrosomus japonicus, predicted to continue under future warming scenarios', Marine Ecology Progress Series, vol. 688, pp. 1-17.
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Understanding the effects of climate change on fish biology and ecology is crucial for effective management of fisheries resources. Estuaries are warming at a faster rate than nearby oceans in south-eastern Australia, yet there is little understanding of how this may impact the growth of estuarine fish. We examined long-term changes and drivers of growth in an ecologically and economically important estuarine fish in this region, the mulloway Argyrosomus japonicus, using a growth chronology spanning 39 yr (1980-2018). The chronology was developed using 3112 otoliths collected over 12° of latitude. Mixed effects models identified a long-term increase in the growth rate of A. japonicus spanning nearly 3 decades in south-eastern Australia and a positive growth response to temperature. Temperature during the months of November-February best explained this growth response, likely representing a specific growing season for the species. However, there also remained some variation in growth not explained by increasing temperature over the period. We also found evidence of faster growth in individuals sampled at both younger and older ages, potentially caused by selectivity mechanisms. Regional climate forecasts predict that, based upon the observed response to temperature, the mean annual growth rate of A. japonicus in south-eastern Australia may increase by up to 8.9% by 2099. These results add to the growing body of literature demonstrating positive growth responses by marine species in warming environments and highlight the value of understanding the drivers of long-term growth variation in exploited fish stocks in order to predict future productivity under a range of environmental and fisheries management scenarios.

Nielsen, JJV, Matthews, G, Frith, KR, Harrison, HB, Marzonie, MR, Slaughter, KL, Suggett, DJ & Bay, LK 2022, 'Experimental considerations of acute heat stress assays to quantify coral thermal tolerance', Scientific Reports, vol. 12, no. 1, pp. 1-13.
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AbstractUnderstanding the distribution and abundance of heat tolerant corals across seascapes is imperative for predicting responses to climate change and to support novel management actions. Thermal tolerance is variable in corals and intrinsic and extrinsic drivers of tolerance are not well understood. Traditional experimental evaluations of coral heat and bleaching tolerance typically involve ramp-and-hold experiments run across days to weeks within aquarium facilities with limits to colony replication. Field-based acute heat stress assays have emerged as an alternative experimental approach to rapidly quantify heat tolerance in many samples yet the role of key methodological considerations on the stress response measured remains unresolved. Here, we quantify the effects of coral fragment size, sampling time point, and physiological measures on the acute heat stress response in adult corals. The effect of fragment size differed between species (Acropora tenuis and Pocillopora damicornis). Most physiological parameters measured here declined over time (tissue colour, chlorophyll-a and protein content) from the onset of heating, with the exception of maximum photosynthetic efficiency (Fv/Fm) which was surprisingly stable over this time scale. Based on our experiments, we identified photosynthetic efficiency, tissue colour change, and host-specific assays such as catalase activity as key physiological measures for rapid quantification of thermal tolerance. We recommend that future applications of acute heat stress assays include larger fragments (> 9 cm2) where possible and sample between 10 and 24 h after the end of heat stress. A validated high-throughput experimental ...

Nitschke, MR, Rosset, SL, Oakley, CA, Gardner, SG, Camp, EF, Suggett, DJ & Davy, SK 2022, 'The diversity and ecology of Symbiodiniaceae: A traits-based review', Advances in Marine Biology, vol. 92, pp. 55-127.
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Among the most successful microeukaryotes to form mutualisms with animals are dinoflagellates in the family Symbiodiniaceae. These photosynthetic symbioses drive significant primary production and are responsible for the formation of coral reef ecosystems but are particularly sensitive when environmental conditions become extreme. Annual episodes of widespread coral bleaching (disassociation of the mutualistic partnership) and mortality are forecasted from the year 2060 under current trends of ocean warming. However, host cnidarians and dinoflagellate symbionts display exceptional genetic and functional diversity, and meaningful predictions of the future that embrace this biological complexity are difficult to make. A recent move to trait-based biology (and an understanding of how traits are shaped by the environment) has been adopted to move past this problem. The aim of this review is to: (1) provide an overview of the major cnidarian lineages that are symbiotic with Symbiodiniaceae; (2) summarise the symbiodiniacean genera associated with cnidarians with reference to recent changes in taxonomy and systematics; (3) examine the knowledge gaps in Symbiodiniaceae life history from a trait-based perspective; (4) review Symbiodiniaceae trait variation along three abiotic gradients (light, nutrients, and temperature); and (5) provide recommendations for future research of Symbiodiniaceae traits. We anticipate that a detailed understanding of traits will further reveal basic knowledge of the evolution and functional diversity of these mutualisms, as well as enhance future efforts to model stability and change in ecosystems dependent on cnidarian-dinoflagellate organisms.

Nolan, RH, Collins, L, Gibson, RK, Samson, SA, Rolls, KT, Milner, K, Medlyn, BE, Price, OF, Griebel, A, Choat, B, Jiang, M & Boer, MM 2022, 'The carbon cost of the 2019–20 Australian fires varies with fire severity and forest type', Global Ecology and Biogeography, vol. 31, no. 10, pp. 2131-2146.
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AbstractAimTo estimate loss of above‐ground carbon (AGC) and conversion of live carbon to dead carbon following understorey and canopy fire.LocationSouth‐eastern Australia.Time period2019–2020.Major taxa studiedFour widespread resprouting eucalypt forests.MethodsAbove‐ground carbon was measured in 15 plots in each of four forest types one‐year post‐fire. We also assessed topkill, that is, trees subject to canopy loss that failed to resprout epicormically.ResultsWhile canopy fire was associated with greater declines in AGC than understorey fire, this was only statistically significant for only one forest type, where AGC declined from 154 to 85 Mg C ha−1 following canopy fire. Significant post‐fire increases in dead AGC were observed in one forest type, where dead carbon increased from 22 to 60% after canopy fire. Topkill of trees following canopy fire (48–78% of stems) was higher than topkill after understorey fire (36–53% of stems) and in unburnt forest (12–55%). Topkill occurred primarily in small‐diameter stems. Consequently, there was no effect of fire on the proportion of dead AGC in trees, with the exception of the forest with lowest productivity (i.e., lowest biomass) and lowest annual rainfall, where dead tree carbon increased from 8% in unburnt forest to 13 and 53% after understorey and canopy fire, respectively. AGC in understorey vegetation and coarse woody debris was similar or lower in burnt compared with unburnt forest. Litter carbon was significantly lower and pyrogenic carbon significantly higher in burnt forest, with no difference between un...

Nolan, RH, Foster, B, Griebel, A, Choat, B, Medlyn, BE, Yebra, M, Younes, N & Boer, MM 2022, 'Drought-related leaf functional traits control spatial and temporal dynamics of live fuel moisture content', Agricultural and Forest Meteorology, vol. 319, pp. 108941-108941.
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Large forest fires generally occur when the moisture content of fuels is low. For live fuels, our understanding of the physiological basis of variation in moisture content has recently advanced. However, process-based models of live fuel moisture content (LFMC) remain elusive. Here, we aim to further our understanding of the role of physiological mechanisms and plant functional traits in driving spatiotemporal variations in LFMC. We examined whether temporal variation in LFMC could be predicted from pressure-volume curve data, which measures leaf water potential and water content on cut shoots dehydrating on a bench. We also examined whether leaf dry mass traits could predict spatial variation in maximum LFMC. We undertook our study in eucalypt forests and woodlands spanning a large climatic gradient in eastern Australia. We found that LFMC models developed from pressure-volume curves reliably predicted seasonal variation in LFMC across four co-occurring species. A two-phase LFMC model, which fit models above and below the turgor loss point (mean absolute error = 3.7-33.2%), performed similarly well to a simple linear model (mean absolute error = 3.4-35.3%). Across a large climatic gradient, the maximum LFMC of 16 species was correlated with specific leaf area (R2 = 0.54), with the exception of one species with terete terminal stems. Maximum LFMC was highly correlated with aridity (R2 = 0.82), with lower LFMC observed in more arid sites. Our study demonstrates that spatiotemporal dynamics of LFMC are governed by both leaf dry mass traits and the relationship between leaf water potential and water content, which in turn is determined by traits such as cell wall elasticity. Thus, incorporating these traits into models of LFMC, whether these models are based on drought indices, soil moisture, or remotely sensed imagery, is likely to improve overall model performance, and subsequently improve forecasts of wildfire danger.

Nonahal, M, Li, C, Tjiptoharsono, F, Ding, L, Stewart, C, Scott, J, Toth, M, Ha, ST, Kianinia, M & Aharonovich, I 2022, 'Coupling spin defects in hexagonal boron nitride to titanium dioxide ring resonators', Nanoscale, vol. 14, no. 40, pp. 14950-14955.
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Spin defects in hexagonal boron nitride are coupled to microring cavity resonator.

Nouman, M, Khoo, SY, Mahmud, MAP & Kouzani, AZ 2022, 'Recent Advances in Contactless Sensing Technologies for Mental Health Monitoring', IEEE Internet of Things Journal, vol. 9, no. 1, pp. 274-297.
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The process of monitoring mental health has relied on methods, such as invasive sensing and self-reporting. The use of these methods has been limited because of the invasiveness of sensing devices or the subjective nature of patients' responses. Recent research focuses on the contactless sensing methods used to objectively monitor mental health issues. These methods allow continuous collection of real-time data in a nondisruptive manner. Machine learning methods are then applied to the sensed data to predict information, such as physical activity, gestures, and heart rate. This information can be then used to assess mental health issues, such as depression, stress, and anxiety, among others. This article presents a comprehensive review of contactless sensing methods for mental health monitoring. It investigates the published research that focuses on contactless sensing methods to predict mental health condition. Moreover, this review categorizes the applications of contactless sensing methods into detection, recognition, and monitoring of vital signs. Furthermore, a comparison of recent studies on contactless sensing methods is presented, which shows the effectiveness and reliability of these methods. This study also highlights the existing challenges in contactless sensing methods and provides future research directions to mitigate these challenges.

NUCERA, F, MUMBY, S, PAUDEL, KR, DHARWAL, V, DI STEFANO, A, CASOLARO, V, HANSBRO, PM, ADCOCK, IM & CARAMORI, G 2022, 'Role of oxidative stress in the pathogenesis of COPD', Minerva Medica, vol. 113, no. 3.
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Nunes, MH, Camargo, JLC, Vincent, G, Calders, K, Oliveira, RS, Huete, A, Mendes de Moura, Y, Nelson, B, Smith, MN, Stark, SC & Maeda, EE 2022, 'Forest fragmentation impacts the seasonality of Amazonian evergreen canopies', Nature Communications, vol. 13, no. 1, p. 917.
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AbstractPredictions of the magnitude and timing of leaf phenology in Amazonian forests remain highly controversial. Here, we use terrestrial LiDAR surveys every two weeks spanning wet and dry seasons in Central Amazonia to show that plant phenology varies strongly across vertical strata in old-growth forests, but is sensitive to disturbances arising from forest fragmentation. In combination with continuous microclimate measurements, we find that when maximum daily temperatures reached 35 °C in the latter part of the dry season, the upper canopy of large trees in undisturbed forests lost plant material. In contrast, the understory greened up with increased light availability driven by the upper canopy loss, alongside increases in solar radiation, even during periods of drier soil and atmospheric conditions. However, persistently high temperatures in forest edges exacerbated the upper canopy losses of large trees throughout the dry season, whereas the understory in these light-rich environments was less dependent on the altered upper canopy structure. Our findings reveal a strong influence of edge effects on phenological controls in wet forests of Central Amazonia.

O’Brien, J, McParland, EL, Bramucci, AR, Ostrowski, M, Siboni, N, Ingleton, T, Brown, MV, Levine, NM, Laverock, B, Petrou, K & Seymour, J 2022, 'The Microbiological Drivers of Temporally Dynamic Dimethylsulfoniopropionate Cycling Processes in Australian Coastal Shelf Waters', Frontiers in Microbiology, vol. 13, pp. 1-19.
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The organic sulfur compounds dimethylsulfoniopropionate (DMSP) and dimethyl sulfoxide (DMSO) play major roles in the marine microbial food web and have substantial climatic importance as sources and sinks of dimethyl sulfide (DMS). Seasonal shifts in the abundance and diversity of the phytoplankton and bacteria that cycle DMSP are likely to impact marine DMS (O) (P) concentrations, but the dynamic nature of these microbial interactions is still poorly resolved. Here, we examined the relationships between microbial community dynamics with DMS (O) (P) concentrations during a 2-year oceanographic time series conducted on the east Australian coast. Heterogenous temporal patterns were apparent in chlorophyll a (chl a) and DMSP concentrations, but the relationship between these parameters varied over time, suggesting the phytoplankton and bacterial community composition were affecting the net DMSP concentrations through differential DMSP production and degradation. Significant increases in DMSP were regularly measured in spring blooms dominated by predicted high DMSP-producing lineages of phytoplankton (Heterocapsa, Prorocentrum, Alexandrium, and Micromonas), while spring blooms that were dominated by predicted low DMSP-producing phytoplankton (Thalassiosira) demonstrated negligible increases in DMSP concentrations. During elevated DMSP concentrations, a significant increase in the relative abundance of the key copiotrophic bacterial lineage Rhodobacterales was accompanied by a three-fold increase in the gene, encoding the first step of DMSP demethylation (dmdA). Significant temporal shifts in DMS concentrations were measured and were significantly correlated with both fractions (0.2–2 μm and &gt;2 μm) of microbial DMSP lyase activity....

O’Brien, J, McParland, EL, Bramucci, AR, Siboni, N, Ostrowski, M, Kahlke, T, Levine, NM, Brown, MV, van de Kamp, J, Bodrossy, L, Messer, LF, Petrou, K & Seymour, JR 2022, 'Biogeographical and seasonal dynamics of the marine Roseobacter community and ecological links to DMSP-producing phytoplankton', ISME Communications, vol. 2, no. 1, p. 16.
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Abstract Ecological interactions between marine bacteria and phytoplankton play a pivotal role in governing the ocean’s major biogeochemical cycles. Among these, members of the marine Roseobacter Group (MRG) can establish mutualistic relationships with phytoplankton that are, in part, maintained by exchanges of the organosulfur compound, dimethylsulfoniopropionate (DMSP). Yet most of what is known about these interactions has been derived from culture-based laboratory studies. To investigate temporal and spatial co-occurrence patterns between members of the MRG and DMSP-producing phytoplankton we analysed 16S and 18S rRNA gene amplicon sequence variants (ASVs) derived from 5 years of monthly samples from seven environmentally distinct Australian oceanographic time-series. The MRG and DMSP-producer communities often displayed contemporaneous seasonality, which was greater in subtropical and temperate environments compared to tropical environments. The relative abundance of both groups varied latitudinally, displaying a poleward increase, peaking (MRG at 33% of total bacteria, DMSP producers at 42% of eukaryotic phototrophs) during recurrent spring-summer phytoplankton blooms in the most temperate site (Maria Island, Tasmania). Network analysis identified 20,140 significant positive correlations between MRG ASVs and DMSP producers and revealed that MRGs exhibit significantly stronger correlations to high DMSP producers relative to other DMSP-degrading bacteria (Pelagibacter, SAR86 and Actinobacteria). By utilising the power of a continental network of oceanographic time-series, this study provides in situ confirmation of interactions found in laboratory studies and demonstrates that the ecological dynamics of an important group of marine bacteria are shaped by the production of an abundant and biogeochemically significant organosulfur compound.

O’Donnell, AW, Redmond, G, Arciuli, J, Robinson, S, Skattebol, J, Raghavendra, P, Thomson, C, Wang, JJJ & Emerson, E 2022, 'The Association between Parental Educational Expectations and School Functioning among Young People with Disabilities: A Longitudinal Investigation', Exceptional Children, vol. 89, no. 1, pp. 60-78.
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Past research has established clear educational inequities between young people with disabilities and their peers. In part, some of these inequities may be attributed to expectations. In this study, we examined whether parental expectations were related to school functioning at high school, with school functioning broadly defined as ease and frequency of engagement in school-based activities. Using the Longitudinal Study of Australian Children ( N = 3,956; 48.9% female; 5.01% with disability), we examined parental expectations and school functioning measured at three time-points, biennially from the ages of 12 and 13 through to 16 and 17. A multigroup, parallel latent growth curve analysis revealed that high parental expectations at the first timepoint predicted steeper increases in the trajectory of school functioning over time, but only among young people with disability. Parental expectations did not significantly predict school functioning trajectories for the remainder of the sample. Subsequent multigroup analyses that compared disability characteristics revealed that learning difficulties and speech problems, in particular, were associated with lower parental expectations. These results suggest that the perceptions of parents in the lives of young people with disability are important and efforts to shape them may have long-term benefits.

O’Rourke, MB, Roediger, BR, Jolly, CJ, Crossett, B, Padula, MP & Hansbro, PM 2022, 'Viral Biomarker Detection and Validation Using MALDI Mass Spectrometry Imaging (MSI)', Proteomes, vol. 10, no. 3, pp. 33-33.
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(1) Background: MALDI imaging is a technique that still largely depends on time of flight (TOF)-based instrument such as the Bruker UltrafleXtreme. While capable of performing targeted MS/MS, these instruments are unable to perform fragmentation while imaging a tissue section necessitating the reliance of MS1 values for peptide level identifications. With this premise in mind, we have developed a hybrid bioinformatic/image-based method for the identification and validation of viral biomarkers. (2) Methods: Formalin-Fixed Paraffin-Embedded (FFPE) mouse samples were sectioned, mounted and prepared for mass spectrometry imaging using our well-established methods. Peptide identification was achieved by first extracting confident images corresponding to theoretical viral peptides. Next, those masses were used to perform a Peptide Mmass Fingerprint (PMF) searched against known viral FASTA sequences against a background mouse FASTA database. Finally, a correlational analysis was performed with imaging data to confirm pixel-by-pixel colocalization and intensity of viral peptides. (3) Results: 14 viral peptides were successfully identified with significant PMF Scores and a correlational result of >0.79 confirming the presence of the virus and distinguishing it from the background mouse proteins. (4) Conclusions: this novel approach leverages the power of mass spectrometry imaging and provides confident identifications for viral proteins without requiring MS/MS using simple MALDI Time Of Flight/Time Of Flight (TOF/TOF) instrumentation.

O'Brien, J, Focardi, A, Deschaseaux, ESM, Petrou, K, Ostrowski, M, Beckley, LE & Seymour, JR 2022, 'Microbial dimethylsulfoniopropionate (DMSP) cycling in the ultraoligotrophic eastern Indian Ocean', Deep Sea Research Part II: Topical Studies in Oceanography, vol. 206, pp. 105195-105195.
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Dimethylsulfoniopropionate (DMSP) is an important source of dissolved organic matter for the marine food web and its cycling is a key step in ocean-atmosphere fluxes involved in the global sulfur cycle. To date, the abundance and biogeography of the genes encoding bacterial DMSP cycling in the eastern Indian Ocean (EIO) is virtually unknown. Moreover, DMSP measurements from the IO are sparse compared to other major oceans. In May–June 2019, we characterized dissolved DMSP (DMSPd) concentrations and the abundance of representative bacterial DMSP cycling genes along the 110 °E transect line as part of a voyage that contributed to Australia's involvement in the second International Indian Ocean Expedition. During the multidisciplinary voyage, surface water samples were collected from 19 stations spanning temperate to tropical waters of the EIO (39.5 °S to 11.5 °S, 110 °E). Somewhat surprisingly, a trend of greater DMSPd was measured in ultraoligotrophic (<0.02 μmol L−1 of nitrate/nitrite), low latitude waters compared to relatively nutrient-rich high latitudes, which contradicts global DMSPd patterns of high concentrations at high latitudes. Additionally, the average DMSPd concentration in EIO samples (17.2 ± 18.64 nM) was an order of magnitude greater than concentrations previously reported at similar latitudes in the Pacific and Atlantic Oceans, which suggests DMSPd is a readily available food source for microbes in a region that is often considered an ocean desert. The abundances of the bacterial DMSP production gene (dsyB), the DMSP lyase gene (dddP) and phylogenetically diverse DMSP demethylation genes (dmdA subclade A/1, D/all and E/2) were reported for the first time in the EIO region, demonstrating significant shifts in all genes with latitude. The SAR11 dmdA (D/all) gene was the dominant DMSP degradation gene across the transect (3.4 ± 0.94% of bacteria) and was notably positively correlated to DMSPd, demonstrating a tight coupling between the var...

O'Connell, MJ, Fowler, AM, Allan, SJ, Beretta, GA & Booth, DJ 2022, 'Recruiting a long way from home: Domino damselfish Dascyllus trimaculatus can detect new temperate coral habitat and conspecifics', Journal of Fish Biology, vol. 100, no. 6, pp. 1548-1552.
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AbstractClimate change is driving tropicalisation of temperate reefs, yet it is unclear how range‐shifting tropical fishes locate suitable habitat. The authors tested whether juvenile tropical damsels Dascyllus trimaculatus could detect rare coral habitat (Pocillopora aliciae) and conspecifics on temperate rocky reefs using olfactory and visual preference experiments. For all cues, individuals selected and spent more time than expected in aquarium areas with the cue present, which included coral odour and conspecific odour and visual cues. This indicates that vagrant coral‐reef fish can detect rare suitable habitat outside of their natal range.

O'Donnell, AW, Redmond, G, Thomson, C, Wang, JJJ & Turkmani, S 2022, 'Reducing educational disparities between Australian adolescents in regional and metropolitan communities: The compensatory effects of extracurricular activities.', Developmental Psychology, vol. 58, no. 12, pp. 2358-2371.
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Australian adolescents living in regional communities are significantly more likely to perform worse at school, relative to those in metropolitan communities. These disparities are partially due to the development of lower educational expectations among regional adolescents. In the current study, we tested whether the differences in educational expectations across communities were reduced when adolescents engage in extracurricular activities, and any subsequent downstream effects on academic outcomes. The current study used a subsample of 1,477 adolescents recruited as part of the Longitudinal Study of Australian Children who have graduated from high school. Using a random-intercept cross-lagged panel model, we found that residing in a regional community at the start of secondary education predicted worse academic performance when graduating 6 years later. This association was partially mediated by lower educational expectations and school functioning, measured biennially. However, the significant difference between adolescents in metropolitan and regional communities dissipated when participants engaged in three or more types of extracurricular activities. These results highlight that increasing access and support to participate in extracurricular activities in regional communities may contribute to reducing inequities in educational outcomes. (PsycInfo Database Record (c) 2022 APA, all rights reserved).

Oglobline, AN, Padula, MP & Doble, PA 2022, 'Quality control of A1-free dairy', Food Control, vol. 135, pp. 108685-108685.
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Oo, CZ, Chew, AW, Wong, ALH, Gladding, J & Stenstrom, C 2022, 'Delineating the successful features of research data management training: a systematic review', International Journal for Academic Development, vol. 27, no. 3, pp. 249-264.
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Pai, TY, Meyer, W, Torpy, FR, Donahoe, SL, Ellis, J, Malik, R & Lee, R 2022, 'Host transmission dynamics of first- and third-stage Angiostrongylus cantonensis larvae in Bullastra lessoni', Parasitology, vol. 149, no. 8, pp. 1034-1044.
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AbstractGiven the importance of angiostrongyliasis as an emerging infectious disease of humans, companion animals, and wildlife, the current study focused on the transmission dynamics of first- and third-stage larvae of the parasitic nematode, Angiostrongylus cantonensis. The migration of infective larvae and their subsequent distribution within the Lymnaeidae snail, Bullastra lessoni, were investigated over time using microscopic examination of histological sections and fresh tissue. Snails were divided into four anatomical regions: (i) anterior and (ii) posterior cephalopedal masses, (iii) mantle skirt and (iv) visceral mass. The viability of free-swimming third-stage larvae, after their release from snail tissues, was evaluated in vitro by propidium iodide staining and infectivity by in vivo infection of Wistar rats. Snails were sequentially dissected over time to assess the number and anatomical distribution of larvae within each snail and hence infer their migration pathway. Herein, ongoing larval migratory activity was detected over 28 days post-infection. A comparison of infection rates and the larval distribution within the four designated snail regions demonstrated a significant relationship between anatomical region and density of infective larvae, with larvae mostly distributed in the anterior cephalopedal mass (43.6 ± 10.8%) and the mantle skirt (33.0 ± 8.8%). Propidium iodide staining showed that free-swimming third-stage larvae retained viability for between 4 and 8 weeks when stored under laboratory conditions. In contrast to viability, larval infectivity in rats remained for up to 2 weeks only. Knowledge gained from the current work could provide information on the development of new approaches to controlling the transmission of this parasite.

Paijmans, KC, Booth, DJ & Wong, MYL 2022, 'Single-species subgroups form within mixed-species shoals of tropical and temperate fishes', Environmental Biology of Fishes, vol. 105, no. 12, pp. 1975-1988.
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Shoaling behaviour is commonly displayed by fishes and is thought to reduce predation and increase foraging efficiency. Shoaling relies on coordination between individuals, with higher cohesion and alignment among individuals within a shoal providing greater net benefits of this behaviour. Whilst single species often shoal together in conspecific groups, mixed-species shoaling is frequently observed and has been identified as an important determinant of individual fitness for the multiple species involved. Despite their prevalence, the structure of mixed-species shoals and the mechanisms by which individuals gain protection from predators and enhance their foraging efficiency are not as well understood as for single-species shoals. In fact, mixed-species shoals may be less coordinated than single-species shoals, raising the intriguing question of why fishes form mixed-species shoals when this behaviour could be less beneficial than single-species shoaling. Here we used in situ stereo-video techniques to compare within and between shoal differences in cohesion and alignment, for mixed- and single-species shoals containing the tropical vagrant Indo pacific sergeant major damselfish, Abudefduf vaigiensis, in temperate waters. As expected, mixed-species shoals were less aligned than single-species shoals. However, within mixed-species shoals conspecifics were more cohesive and aligned than were heterospecifics, suggesting coordinated single-species subgroups formed within larger mixed-species shoals. The formation of subgroups may mitigate costs associated with differences between species, therefore enhancing benefits of mixed-species shoaling. As such, multiple levels of social structure may exist within mixed-species shoals that could facilitate growth and survival for vagrant A. vaigiensis in temperate regions. More broadly, this research highlights the importance of considering detailed internal structures of mixed-species shoals when trying to understa...

Palinski, RM, Brito, B, Jaya, FR, Sangula, A, Gakuya, F, Bertram, MR, Pauszek, SJ, Hartwig, EJ, Smoliga, GR, Obanda, V, Omondi, GP, VanderWaal, K & Arzt, J 2022, 'Viral Population Diversity during Co-Infection of Foot-And-Mouth Disease Virus Serotypes SAT1 and SAT2 in African Buffalo in Kenya', Viruses, vol. 14, no. 5, pp. 897-897.
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African buffalo are the natural reservoirs of the SAT serotypes of foot-and-mouth disease virus (FMDV) in sub-Saharan Africa. Most buffalo are exposed to multiple FMDV serotypes early in life, and a proportion of them become persistently infected carriers. Understanding the genetic diversity and evolution of FMDV in carrier animals is critical to elucidate how FMDV persists in buffalo populations. In this study, we obtained oropharyngeal (OPF) fluid from naturally infected African buffalo, and characterized the genetic diversity of FMDV. Out of 54 FMDV-positive OPF, 5 were co-infected with SAT1 and SAT2 serotypes. From the five co-infected buffalo, we obtained eighty-nine plaque-purified isolates. Isolates obtained directly from OPF and plaque purification were sequenced using next-generation sequencing (NGS). Phylogenetic analyses of the sequences obtained from recombination-free protein-coding regions revealed a discrepancy in the topology of capsid proteins and non-structural proteins. Despite the high divergence in the capsid phylogeny between SAT1 and SAT2 serotypes, viruses from different serotypes that were collected from the same host had a high genetic similarity in non-structural protein-coding regions P2 and P3, suggesting interserotypic recombination. In two of the SAT1 and SAT2 co-infected buffalo identified at the first passage of viral isolation, the plaque-derived SAT2 genomes were distinctly grouped in two different genotypes. These genotypes were not initially detected with the NGS from the first passage (non-purified) virus isolation sample. In one animal with two SAT2 haplotypes, one plaque-derived chimeric sequence was found. These findings demonstrate within-host evolution through recombination and point mutation contributing to broad viral diversity in the wildlife reservoir. These mechanisms may be critical to FMDV persistence at the individual animal and population levels, and may contribute to the emergence of new virus...

Pamphlett, R & Bishop, DP 2022, 'Mercury is present in neurons and oligodendrocytes in regions of the brain affected by Parkinson’s disease and co-localises with Lewy bodies', PLOS ONE, vol. 17, no. 1, pp. e0262464-e0262464.
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ObjectiveEnvironmental toxicants are suspected to play a part in the pathogenesis of idiopathic Parkinson’s disease (PD) and may underlie its increasing incidence. Mercury exposure in humans is common and is increasing due to accelerating levels of atmospheric mercury, and mercury damages cells via oxidative stress, cell membrane damage, and autoimmunity, mechanisms suspected in the pathogenesis of PD. We therefore compared the cellular distribution of mercury in the tissues of people with and without PD who had evidence of previous mercury exposure by mercury being present in their locus ceruleus neurons.Materials and methodsParaffin sections from the brain and general organs of two people with PD, two people without PD with a history of mercury exposure, and ten people without PD or known mercury exposure, were stained for inorganic mercury using autometallography, combined with immunostaining for a-synuclein and glial cells. All had mercury-containing neurons in locus ceruleus neurons. Laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) was used to confirm the presence of mercury and to look for other potentially toxic elements. Autometallography-stained locus ceruleus paraffin sections were examined to compare the frequency of previous mercury exposure between 20 PD and 40 non-PD individuals.ResultsIn PD brains, autometallography-detected mercury was seen in neurons affected by the disease, such as those in the substantia nigra, motor cortex, striatum, thalamus, and cerebellum. Mercury was seen in oligodendrocytes in white and grey matter. Mercury often co-localised with Lewy bodies and neurites. A more restricted distribution of brain mercury was seen in people without PD (both with or without known mercury exposure),...

Pan, Y, Wang, Y, Zheng, S, Huete, AR, Shen, M, Zhang, X, Huang, J, He, G, Yu, L, Xu, X, Xie, Q & Peng, D 2022, 'Characteristics of Greening along Altitudinal Gradients on the Qinghai–Tibet Plateau Based on Time-Series Landsat Images', Remote Sensing, vol. 14, no. 10, pp. 2408-2408.
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The Qinghai–Tibet Plateau (QTP) is ecologically fragile and is especially sensitive to climate change. Previous studies have shown that the vegetation on the QTP is undergoing overall greening with variations along altitudinal gradients. However, the mechanisms that cause the differences in the spatiotemporal patterns of vegetation greening among different types of terrain and vegetation have not received sufficient attention. Therefore, in this study, we used a Landsat NDVI time-series for the period 1992–2020 and climate data to observe the effects of terrain and vegetation types on the spatiotemporal patterns in vegetation greening on the QTP and to analyze the factors driving this greening using the geographical detector and the velocity of the vertical movement of vegetation greenness isolines. The results showed the following: (1) The vertical movement of the vegetation greenness isolines was affected by the temperature and precipitation at all elevations. The precipitation had a more substantial effect than the temperature below 3000 m. In contrast, above 3000 m, the temperature had a greater effect than the precipitation. (2) The velocity of the vertical movement of the vegetation greenness isolines of woody plants was higher than that of herbaceous plants. (3) The influence of slope on the vertical movement of vegetation greenness isolines was more significant than that of the aspect. The results of this study provided details of the spatiotemporal differences in vegetation greening between different types of terrain and vegetation at a 30-m scale as well as of the underlying factors driving this greening. These results will help to support ecological protection policies on the QTP.

Panthi, VK, Jha, SK, Pangeni, R & Paudel, KR 2022, 'Formulation and Development of Adapalene Topical Nanohydrogel Using Different Surfactants and Cosurfactants for Antiacne Activity: In Vitro and Ex Vivo Evaluation', Journal of Nanomaterials, vol. 2022, pp. 1-19.
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A formulation of an adapalene nanohydrogel (ADP-NH) using different surfactants and cosurfactants for topical application was developed and characterized. The best formulation was obtained with nanohydrogel (NH) containing Tween-80- (NH-Tween-80-) incorporated carbopol-940 and ethanol, 0.67% and 3.00% $w/w$ , respectively. The optimized formulations of NH-Tween-80, nanohydrogel containing sodium lauryl sulphate (NH-SLS), and nanohydrogel containing glycerol (NH-glycerol) were separately evaluated to examine their in vitro and ex vivo permeability characteristics and compared with 0.3% dimethyl sulfoxide (control) solution. The polydispersity index of NH-Tween-80, NH-SLS, and NH-glycerol were found to be $0.264\pm 0.312$ , $0.382\pm 0.0045$ , and $0.310\pm 0.412$ , respectively. All NH formulations showed pH within human skin pH ranges throughout the stability period. The NH-Tween-80 revealed 191.22 ...

Papanicolaou, M, Parker, AL, Yam, M, Filipe, EC, Wu, SZ, Chitty, JL, Wyllie, K, Tran, E, Mok, E, Nadalini, A, Skhinas, JN, Lucas, MC, Herrmann, D, Nobis, M, Pereira, BA, Law, AMK, Castillo, L, Murphy, KJ, Zaratzian, A, Hastings, JF, Croucher, DR, Lim, E, Oliver, BG, Mora, FV, Parker, BL, Gallego-Ortega, D, Swarbrick, A, O’Toole, S, Timpson, P & Cox, TR 2022, 'Temporal profiling of the breast tumour microenvironment reveals collagen XII as a driver of metastasis', Nature Communications, vol. 13, no. 1, p. 4587.
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AbstractThe tumour stroma, and in particular the extracellular matrix (ECM), is a salient feature of solid tumours that plays a crucial role in shaping their progression. Many desmoplastic tumours including breast cancer involve the significant accumulation of type I collagen. However, recently it has become clear that the precise distribution and organisation of matrix molecules such as collagen I is equally as important in the tumour as their abundance. Cancer-associated fibroblasts (CAFs) coexist within breast cancer tissues and play both pro- and anti-tumourigenic roles through remodelling the ECM. Here, using temporal proteomic profiling of decellularized tumours, we interrogate the evolving matrisome during breast cancer progression. We identify 4 key matrisomal clusters, and pinpoint collagen type XII as a critical component that regulates collagen type I organisation. Through combining our proteomics with single-cell transcriptomics, and genetic manipulation models, we show how CAF-secreted collagen XII alters collagen I organisation to create a pro-invasive microenvironment supporting metastatic dissemination. Finally, we show in patient cohorts that collagen XII may represent an indicator of breast cancer patients at high risk of metastatic relapse.

Parast, L, Garcia, TP, Prentice, RL & Carroll, RJ 2022, 'Robust methods to correct for measurement error when evaluating a surrogate marker', Biometrics, vol. 78, no. 1, pp. 9-23.
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AbstractThe identification of valid surrogate markers of disease or disease progression has the potential to decrease the length and costs of future studies. Most available methods that assess the value of a surrogate marker ignore the fact that surrogates are often measured with error. Failing to adjust for measurement error can erroneously identify a useful surrogate marker as not useful or vice versa. We investigate and propose robust methods to correct for the effect of measurement error when evaluating a surrogate marker using multiple estimators developed for parametric and nonparametric estimates of the proportion of treatment effect explained by the surrogate marker. In addition, we quantify the attenuation bias induced by measurement error and develop inference procedures to allow for variance and confidence interval estimation. Through a simulation study, we show that our proposed estimators correct for measurement error in the surrogate marker and that our inference procedures perform well in finite samples. We illustrate these methods by examining a potential surrogate marker that is measured with error, hemoglobin A1c, using data from the Diabetes Prevention Program clinical trial.

Pasin, D, Nedahl, M, Mollerup, CB, Tortzen, C, Reitzel, LA & Dalsgaard, PW 2022, 'Identification of the synthetic cannabinoid‐type new psychoactive substance, CH‐PIACA, in seized material', Drug Testing and Analysis, vol. 14, no. 9, pp. 1645-1651.
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AbstractSynthetic cannabinoids (SCs) remain the largest class of new psychoactive substances (NPS), and while the number of NPS that are reported to the European Monitoring Centre for Drugs and Drug Addiction (EMCDDA) for the first time each year declines, the number of newly reported SCs still exceeds other NPS classes. This decline can be seen as a result of legislative changes by different jurisdictions which have sometimes transitioned to a more generalized approach when controlling substances by defining common structural scaffolds rather than explicit structures. While the consequences of such legislative changes have been expected over the years, the introduction of so‐called “class‐wide” bans puts further pressure on clandestine laboratories to synthesize compounds which are out of the scope of the legislation, and thus, these compounds are initially harder to detect and/or identify in the absence of analytical data. Recently, a SC with an indole‐3‐acetamide core‐linker scaffold, AD‐18 (i.e., ADB‐FUBIATA or ADB‐FUBIACA), was reported for the first time in China in 2021. Here, an additional cannabinoid with the indole‐3‐acetamide scaffold, N‐cyclohexyl‐2‐(1‐pentyl‐1H‐indol‐3‐yl)acetamide (CH‐PIACA), is reported which was identified for the first time in a seized material in Denmark. Structural characterization was performed using gas chromatography–mass spectrometry (GC–MS), liquid chromatography‐high‐resolution mass spectrometry (LC‐HRMS), and nuclear magnetic resonance (NMR) spectroscopy.

Pasin, D, Pan, M, Rasmussen, BS, Linnet, K, Dalsgaard, PW & Mollerup, CB 2022, 'Metabolomics‐driven determination of targets for salicylic acid and ibuprofen in positive electrospray ionization using LC‐HRMS', Drug Testing and Analysis, vol. 14, no. 4, pp. 747-756.
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AbstractDue to the large number of basic therapeutic and illicit drugs, systematic toxicological analysis has widely been performed with liquid chromatography coupled to mass spectrometry using positive electrospray ionization. However, there exist a smaller number of drugs, typically acidic drugs, which require the use of negative electrospray ionization either via a separate analysis or polarity switching. Here, targets relating to salicylic acid and ibuprofen in positive electrospray ionization were determined through a metabolomics‐driven retrospective investigation of forensic casework. Samples were previously screened using liquid chromatography coupled with high‐resolution mass spectrometry with quantification of target analytes performed using liquid chromatography with tandem mass spectrometry. Of the 1,717 whole‐blood samples submitted between 2014 and 2019, 48 were positive for salicylic acid (1.1–1,400 mg/kg) and 78 for ibuprofen (1–46 mg/kg). Based on the retrospective analysis, 19 and 90 targets were identified for salicylic acid and ibuprofen, respectively. For targets of salicylic acid, the protonated adduct of salicyluric acid ([M + H]+, m/z 196.0605) was present in 89.6% (n = 32) of the salicylic acid positive cases, while the [M + HCOOH + CH3CN + Ca ‐ H]+ adduct (m/z 264.0179) of salicylic acid was present in all positive samples with concentrations above 66 mg/kg salicylic acid. Similarly, the [M + 2Na ‐ H]+ adduct (m/z 251.1018) of ibuprofen was present in 98.7% (n = 77) of positive cases and was present in all samples with concentrations above 3 mg/kg ibuprofen.

Patel, VK, Paudel, KR, Shukla, SD, Liu, G, Oliver, BG, Hansbro, PM & Dua, K 2022, 'Toll-like receptors, innate immune system, and lung diseases: a vital trilateral association.', EXCLI J, vol. 21, pp. 519-523.
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Pathinayake, PS, Waters, DW, Nichol, KS, Brown, AC, Reid, AT, Hsu, AC-Y, Horvat, JC, Wood, LG, Baines, KJ, Simpson, JL, Gibson, PG, Hansbro, PM & Wark, PAB 2022, 'Endoplasmic reticulum-unfolded protein response signalling is altered in severe eosinophilic and neutrophilic asthma', Thorax, vol. 77, no. 5, pp. 443-451.
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IntroductionThe significance of endoplasmic reticulum (ER) stress in asthma is unclear. Here, we demonstrate that ER stress and the unfolded protein response (UPR) are related to disease severity and inflammatory phenotype.MethodsInduced sputum (n=47), bronchial lavage (n=23) and endobronchial biopsies (n=40) were collected from participants with asthma with varying disease severity, inflammatory phenotypes and from healthy controls. Markers for ER stress and UPR were assessed. These markers were also assessed in established eosinophilic and neutrophilic murine models of asthma.ResultsOur results demonstrate increased ER stress and UPR pathways in asthma and these are related to clinical severity and inflammatory phenotypes. Genes associated with ER protein chaperone (BiP, CANX, CALR), ER-associated protein degradation (EDEM1, DERL1)and ER stress-induced apoptosis (DDIT3, PPP1R15A) were dysregulated in participants with asthma and are associated with impaired lung function (forced expiratory volume in 1 s) and active eosinophilic and neutrophilic inflammation. ER stress genes also displayed a significant correlation with classic Th2 (interleukin-4, IL-4/13) genes, Th17 (IL-17F/CXCL1) genes, proinflammatory (IL-1b, tumour necrosis factor α, IL-8) genes and inflammasome activation (NLRP3) in sputum from asthmatic participants. Mice with allergic airway disease (AAD) and severe steroid insensitive AAD also showed increased ER stress signalling in their lungs.ConclusionHeightened ER stress is associated with severe eosinophilic and neutrophilic inflammation in asthma and may play a crucial role in the pathogenesis of asthma.

Paudel, KR, De Rubis, G, Panth, N, Singh, SK, Chellappan, DK, Hansbro, PM & Dua, K 2022, 'Nanomedicine and medicinal plants: Emerging symbiosis in managing lung diseases and associated infections.', EXCLI J, vol. 21, pp. 1299-1303.
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Paudel, KR, Dua, K, Panth, N, Hansbro, PM & Chellappan, DK 2022, 'Advances in research with rutin-loaded nanoformulations in mitigating lung diseases', Future Medicinal Chemistry, vol. 14, no. 18, pp. 1293-1295.
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Paudel, KR, Mehta, M, Shukla, SD, Panth, N, Chellappan, DK, Dua, K & Hansbro, P 2022, 'Advancements in nanotherapeutics targeting senescence in chronic obstructive pulmonary disease', Nanomedicine, vol. 17, no. 23, pp. 1757-1760.
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Paudel, KR, Mehta, M, Yin, GHS, Yen, LL, Malyla, V, Patel, VK, Panneerselvam, J, Madheswaran, T, MacLoughlin, R, Jha, NK, Gupta, PK, Singh, SK, Gupta, G, Kumar, P, Oliver, BG, Hansbro, PM, Chellappan, DK & Dua, K 2022, 'Berberine-loaded liquid crystalline nanoparticles inhibit non-small cell lung cancer proliferation and migration in vitro', Environmental Science and Pollution Research, vol. 29, no. 31, pp. 46830-46847.
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AbstractNon-small cell lung cancer (NSCLC) is reported to have a high incidence rate and is one of the most prevalent types of cancer contributing towards 85% of all incidences of lung cancer. Berberine is an isoquinoline alkaloid which offers a broad range of therapeutical and pharmacological actions against cancer. However, extremely low water solubility and poor oral bioavailability have largely restricted its therapeutic applications. To overcome these limitations, we formulated berberine-loaded liquid crystalline nanoparticles (LCNs) and investigated their in vitro antiproliferative and antimigratory activity in human lung epithelial cancer cell line (A549). 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT), trypan blue staining, and colony forming assays were used to evaluate the anti-proliferative activity, while scratch wound healing assay and a modified Boyden chamber assay were carried out to determine the anti-migratory activity. We also investigated major proteins associated with lung cancer progression. The developed nanoparticles were found to have an average particle size of 181.3 nm with spherical shape, high entrapment efficiency (75.35%) and have shown sustained release behaviour. The most remarkable findings reported with berberine-loaded LCNs were significant suppression of proliferation, inhibition of colony formation, inhibition of invasion or migration via epithelial mesenchymal transition, and proliferation related proteins associated with cancer progression. Our findings suggest that anti-cancer compounds with the problem of poor solubility and bioavailability can be overcome by formulating them into nanotechnology-based delivery systems for better efficacy. Further in-depth investigations into anti-cancer mechanistic research will expand and strengthen the current findings of berberine-LCNs as a potential NSCLC treatment option.

Paudel, KR, Patel, V, Vishwas, S, Gupta, S, Sharma, S, Chan, Y, Jha, NK, Shrestha, J, Imran, M, Panth, N, Shukla, SD, Jha, SK, Devkota, HP, Warkiani, ME, Singh, SK, Ali, MK, Gupta, G, Chellappan, DK, Hansbro, PM & Dua, K 2022, 'Nutraceuticals and COVID‐19: A mechanistic approach toward attenuating the disease complications', Journal of Food Biochemistry, vol. 46, no. 12, p. e14445.
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Nutraceuticals have emerged as potential compounds to attenuate the COVID-19 complications. Precisely, these food additives strengthen the overall COVID treatment and enhance the immunity of a person. Such compounds have been used at a large scale, in almost every household due to their better affordability and easy access. Therefore, current research is focused on developing newer advanced formulations from potential drug candidates including nutraceuticals with desirable properties viz, affordability, ease of availability, ease of administration, stability under room temperature, and potentially longer shelf-lives. As such, various nutraceutical-based products such as compounds could be promising agents for effectively managing COVID-19 symptoms and complications. Most importantly, regular consumption of such nutraceuticals has been shown to boost the immune system and prevent viral infections. Nutraceuticals such as vitamins, amino acids, flavonoids like curcumin, and probiotics have been studied for their role in the prevention of COVID-19 symptoms such as fever, pain, malaise, and dry cough. In this review, we have critically reviewed the potential of various nutraceutical-based therapeutics for the management of COVID-19. We searched the information relevant to our topic from search engines such as PubMed and Scopus using COVID-19, nutraceuticals, probiotics, and vitamins as a keyword. Any scientific literature published in a language other than English was excluded. PRACTICAL APPLICATIONS: Nutraceuticals possess both nutritional values and medicinal properties. They can aid in the prevention and treatment of diseases, as well as promote physical health and the immune system, normalizing body functions, and improving longevity. Recently, nutraceuticals such as probiotics, vitamins, polyunsaturated fatty acids, trace minerals, and medicinal plants have attracted considerable attention and are widely regarded as potential alternatives to current the...

Paulowski, L, Beckham, KSH, Johansen, MD, Berneking, L, Van, N, Degefu, Y, Staack, S, Sotomayor, FV, Asar, L, Rohde, H, Aldridge, BB, Aepfelbacher, M, Parret, A, Wilmanns, M, Kremer, L, Combrink, K & Maurer, FP 2022, 'C25-modified rifamycin derivatives with improved activity against Mycobacterium abscessus', PNAS Nexus, vol. 1, no. 4, p. pgac130.
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Abstract Infections caused by Mycobacterium abscessus are difficult to treat due to its intrinsic resistance to most antibiotics. Formation of biofilms and the capacity of M. abscessus to survive inside host phagocytes further complicate eradication. Herein, we explored whether addition of a carbamate-linked group at the C25 position of rifamycin SV blocks enzymatic inactivation by ArrMab, an ADP-ribosyltransferase conferring resistance to rifampicin (RMP). Unlike RMP, 5j, a benzyl piperidine rifamycin derivative with a morpholino substituted C3 position and a naphthoquinone core, is not modified by purified ArrMab. Additionally, we show that the ArrMab D82 residue is essential for catalytic activity. Thermal profiling of ArrMab in the presence of 5j, RMP, or rifabutin shows that 5j does not bind to ArrMab. We found that the activity of 5j is comparable to amikacin against M. abscessus planktonic cultures and pellicles. Critically, 5j also exerts potent antimicrobial activity against M. abscessus in human macrophages and shows synergistic activity with amikacin and azithromycin.

Payne, M, Bottomley, AL, Och, A, Hiscocks, HG, Asmara, AP, Harry, EJ & Ung, AT 2022, 'Synthesis and biological evaluation of tetrahydroisoquinoline-derived antibacterial compounds', Bioorganic & Medicinal Chemistry, vol. 57, pp. 116648-116648.
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Antibiotic resistance is one of the greatest threats to modern medicine. Drugs that were once routinely used to treat infections are being rendered ineffective, increasing the demand for novel antibiotics with low potential for resistance. Here we report the synthesis of 18 novel cationic tetrahydroisoquinoline-triazole compounds. Five of the developed molecules were active against S. aureus at a low MIC of 2-4 μg/mL. Hit compound 4b was also found to eliminate M. tuberculosis H37Rv at MIC of 6 μg/mL. This potent molecule was found to eliminate S. aureus effectively, with no resistance observed after thirty days of sequential passaging. These results identified compound 4b and its analogues as potential candidates for further drug development that could help tackle the threat of antibiotic resistance.

Peacock, L, Waszczuk, J, Raymond, J & Chadwick, S 2022, 'Investigating the Effectiveness of Chemical Etchanton Medium Carbon (0.40% C) Steel', AFTE Journal, vol. 54, no. 1, pp. 17-27.
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Serial number restoration allows forensic investigators to recover a potentially lost chain of ownership relating to a piece of evidence in an investigation. The ability to restore an obliterated serial number relies on the permanent residual stress left in the metal substrate from a cold working application of the stamped serial number. The application of chemical etching reagents is one method which is used to exploit this stress, and there are a number of different formulations available for this purpose. This research aimed to review and compile historically successful and other proposed etching reagents, to further understand how each formulation can be used more efficiently in the field of serial number restoration. The importance of the composition of the metal substrate being etched is well established, although from the current literature there is a lack of consistent knowledge surrounding which reagent should be used with specific metal compositions. This research intended to aid forensic investigators in determining the most suitable etching reagent for medium carbon (0.40%) steel. The efficacy of reagents at varying depths of obliteration on a consistently stamped steel substrate was tested. The standard Fry’s Reagent, consisting of 90 g copper (II) chloride, 120 mL hydrochloric acid and 100 mL deionized water with 15% nitric acid, was determined to provide the best quality of restored marks and the highest percentage of correctly interpreted restored marks per plate out of the six reagents tested in this study.

Pearce, BJ, Dallo, I, Choi, V, Freihardt, J & Middel, CNH 2022, 'Forks in the road: Critical design moments for identifying key processes in stakeholder interaction', GAIA - Ecological Perspectives for Science and Society, vol. 31, no. 4, pp. 222-230.
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Much of the knowledge regarding “what works” in creating stakeholder events remains tacit. This article describes the concept of critical design moments (CDMs) as a guide for designing context-sensitive and inclusive stakeholder interactions. The approach makes often implicit processes explicit. It is rooted in the experiences of coordinating and participating in a transdisciplinary winter school in a village in Switzerland.While the importance of transdisciplinary (Td) processes as a means to address societal problems is well-established, guidance for the intentional design of stakeholder interactions to meet specific goals, under different conditions and contexts, remains less explored. We propose the concept of critical design moments (CDMs) as a lens through which to identify key processes in the design of stakeholder interactions that affect the relevance and impact of its outcomes. We demonstrate how an approach using CDMs can help to make explicit not only the goals of stakeholder interactions, but also how these goals might be met through the process design of specific activities orienting these interactions. The CDMs were identified as part of the implementation of a Td winter school for early career researchers to provide them with real-world experiences of interacting with stakeholders and local residents of a community. This work provides an approach for how Td stakeholder interactions can be designed in other Td contexts.

Pelucchi, E, Fagas, G, Aharonovich, I, Englund, D, Figueroa, E, Gong, Q, Hannes, H, Liu, J, Lu, C-Y, Matsuda, N, Pan, J-W, Schreck, F, Sciarrino, F, Silberhorn, C, Wang, J & Jöns, KD 2022, 'The potential and global outlook of integrated photonics for quantum technologies', Nature Reviews Physics, vol. 4, no. 3, pp. 194-208.
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Integrated quantum photonics uses classical integrated photonic technologies and devices for quantum applications. As in classical photonics, chip-scale integration has become critical for scaling up and translating laboratory demonstrators to real-life technologies. Integrated quantum photonics efforts are centred around the development of quantum photonic integrated circuits, which can be monolithically, hybrid or heterogeneously integrated. In this Roadmap, we argue, through specific examples, for the value that integrated photonics brings to quantum technologies and discuss what applications may become possible in the future by overcoming the current roadblocks. We provide an overview of the research landscape and discuss the innovation and market potential. Our aim is to stimulate further research by outlining not only the scientific challenges of materials, devices and components associated with integrated photonics for quantum technologies but also those related to the development of the necessary manufacturing infrastructure and supply chains for delivering these technologies to the market.

Pendall, E, Hewitt, A, Boer, MM, Carrillo, Y, Glenn, NF, Griebel, A, Middleton, JH, Mumford, PJ, Ridgeway, P, Rymer, PD & Steenbeeke, GL 2022, 'Remarkable Resilience of Forest Structure and Biodiversity Following Fire in the Peri-Urban Bushland of Sydney, Australia', Climate, vol. 10, no. 6, pp. 86-86.
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In rapidly urbanizing areas, natural vegetation becomes fragmented, making conservation planning challenging, particularly as climate change accelerates fire risk. We studied urban forest fragments in two threatened eucalypt-dominated (scribbly gum woodland, SGW, and ironbark forest, IF) communities across ~2000 ha near Sydney, Australia, to evaluate effects of fire frequency (0–4 in last 25 years) and time since fire (0.5 to >25 years) on canopy structure, habitat quality and biodiversity (e.g., species richness). Airborne lidar was used to assess canopy height and density, and ground-based surveys of 148 (400 m2) plots measured leaf area index (LAI), plant species composition and habitat metrics such as litter cover and hollow-bearing trees. LAI, canopy density, litter, and microbiotic soil crust increased with time since fire in both communities, while tree and mistletoe cover increased in IF. Unexpectedly, plant species richness increased with fire frequency, owing to increased shrub richness which offset decreased tree richness in both communities. These findings indicate biodiversity and canopy structure are generally resilient to a range of times since fire and fire frequencies across this study area. Nevertheless, reduced arboreal habitat quality and subtle shifts in community composition of resprouters and obligate seeders signal early concern for a scenario of increasing fire frequency under climate change. Ongoing assessment of fire responses is needed to ensure that biodiversity, canopy structure and ecosystem function are maintained in the remaining fragments of urban forests under future climate change which will likely drive hotter and more frequent fires.

Pettersen, AK, Coleman, MA, Latombe, G, Gonzalez, SV, Williams, NLR, Seymour, JR, Campbell, AH, Thomas, T, Ferrari, R, Stuart‐Smith, RD, Edgar, GJ, Steinberg, PD & Marzinelli, EM 2022, 'Spatial compositional turnover varies with trophic level and body size in marine assemblages of micro‐ and macroorganisms', Global Ecology and Biogeography, vol. 31, no. 8, pp. 1556-1570.
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AbstractAimSpatial compositional turnover varies considerably among co‐occurring assemblages of organisms, presumably shaped by common processes related to species traits. We investigated patterns of spatial turnover in a diverse set of marine assemblages using zeta diversity, which extends traditional pairwise measures of turnover to capture the roles of both rare and common species in shaping assemblage turnover. We tested the generality of hypothesized patterns related to ecological traits and provide insights into mechanisms of biodiversity change.LocationTemperate pelagic and benthic marine assemblages of micro‐ and macroorganisms along south‐eastern Australia (30–36° S latitude).Time period2008–2021.Major taxa studiedBacteria, phytoplankton, zooplankton, fish, and macrobenthic groups.MethodsSix marine datasets spanning bacteria to fishes were collated for measures of “species” occurrence, with a 1° latitude grain. For each assemblage, ecological traits of body size, habitat and trophic level were analysed for the form and rate of decline in zeta diversity and for the species retention rate.ResultsSpecies at higher trophic levels showed two to three times the rate of zeta diversity decline compared with lower trophic levels, indicating an increase in turnover from phytoplankton to carnivorous fishes. Body size showed the hypothesized unimodal relationship with rates of turnover for macroorganisms. Patterns of bacterial turnover contrasted with those found for macroorganisms, with the highest levels of turnover in pelagic habitats compared with benthic (kelp‐associated) hab...

Pinkerton, JW, Kim, RY, Brown, AC, Rae, BE, Donovan, C, Mayall, JR, Carroll, OR, Khadem Ali, M, Scott, HA, Berthon, BS, Baines, KJ, Starkey, MR, Kermani, NZ, Guo, Y-K, Robertson, AAB, O’Neill, LAJ, Adcock, IM, Cooper, MA, Gibson, PG, Wood, LG, Hansbro, PM & Horvat, JC 2022, 'Relationship between type 2 cytokine and inflammasome responses in obesity-associated asthma', Journal of Allergy and Clinical Immunology, vol. 149, no. 4, pp. 1270-1280.
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BACKGROUND: Obesity is a risk factor for asthma, and obese asthmatic individuals are more likely to have severe, steroid-insensitive disease. How obesity affects the pathogenesis and severity of asthma is poorly understood. Roles for increased inflammasome-mediated neutrophilic responses, type 2 immunity, and eosinophilic inflammation have been described. OBJECTIVE: We investigated how obesity affects the pathogenesis and severity of asthma and identified effective therapies for obesity-associated disease. METHODS: We assessed associations between body mass index and inflammasome responses with type 2 (T2) immune responses in the sputum of 25 subjects with asthma. Functional roles for NLR family, pyrin domain-containing (NLRP) 3 inflammasome and T2 cytokine responses in driving key features of disease were examined in experimental high-fat diet-induced obesity and asthma. RESULTS: Body mass index and inflammasome responses positively correlated with increased IL-5 and IL-13 expression as well as C-C chemokine receptor type 3 expression in the sputum of subjects with asthma. High-fat diet-induced obesity resulted in steroid-insensitive airway hyperresponsiveness in both the presence and absence of experimental asthma. High-fat diet-induced obesity was also associated with increased NLRP3 inflammasome responses and eosinophilic inflammation in airway tissue, but not lumen, in experimental asthma. Inhibition of NLRP3 inflammasome responses reduced steroid-insensitive airway hyperresponsiveness but had no effect on IL-5 or IL-13 responses in experimental asthma. Depletion of IL-5 and IL-13 reduced obesity-induced NLRP3 inflammasome responses and steroid-insensitive airway hyperresponsiveness in experimental asthma. CONCLUSION: We found a relationship between T2 cytokine and NLRP3 inflammasome responses in obesity-associated asthma, highlighting the potential utility of T2 cytokine-targeted biologics and inflammasome inhibitors.

Plumanns-Pouton, E, Bennett, LT, Najera-Umaña, JC, Griebel, A & Hinko-Najera, N 2022, 'Species and Competition Interact to Influence Seasonal Stem Growth in Temperate Eucalypts', Forests, vol. 13, no. 2, pp. 224-224.
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Insights on tree species and competition effects on seasonal stem growth are critical to understanding the impacts of changing climates on tree productivity, particularly for eucalypts species that occur in narrow climatic niches and have unreliable tree rings. To improve our understanding of climate effects on forest productivity, we examined the relative importance of species, competition and climate to the seasonal stem growth of co-occurring temperate eucalypts. We measured monthly stem growth of three eucalypts (Eucalyptus obliqua, E. radiata, and E. rubida) over four years in a natural mixed-species forest in south-eastern Australia, examining the relative influences of species, competition index (CI) and climate variables on the seasonal basal area increment (BAI). Seasonal BAI varied with species and CI, and was greatest in spring and/or autumn, and lowest in summer. Our study highlights the interactive effects of species and competition on the seasonal stem growth of temperate eucalypts, clearly indicating that competitive effects are strongest when conditions are favourable to growth (spring and autumn), and least pronounced in summer, when reduced BAI was associated with less rainfall. Thus, our study indicates that management to reduce inter-tree competition would have minimal influence on stem growth during less favourable (i.e., drier) periods.

Poddar, N, Scofield, J, Shi, S, Prime, EL, Kentish, SE, Qiao, GG & Martin, GJO 2022, 'Evaporation reduction and salinity control in microalgae production ponds using chemical monolayers', Algal Research, vol. 66, pp. 102783-102783.
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Poh, WH & Rice, SA 2022, 'Recent Developments in Nitric Oxide Donors and Delivery for Antimicrobial and Anti-Biofilm Applications', Molecules, vol. 27, no. 3, pp. 674-674.
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The use of nitric oxide (NO) is emerging as a promising, novel approach for the treatment of antibiotic resistant bacteria and biofilm infections. Depending on the concentration, NO can induce biofilm dispersal, increase bacteria susceptibility to antibiotic treatment, and induce cell damage or cell death via the formation of reactive oxygen or reactive nitrogen species. The use of NO is, however, limited by its reactivity, which can affect NO delivery to its target site and result in off-target effects. To overcome these issues, and enable spatial or temporal control over NO release, various strategies for the design of NO-releasing materials, including the incorporation of photo-activable, charge-switchable, or bacteria-targeting groups, have been developed. Other strategies have focused on increased NO storage and delivery by encapsulation or conjugation of NO donors within a single polymeric framework. This review compiles recent developments in NO drugs and NO-releasing materials designed for applications in antimicrobial or anti-biofilm treatment and discusses limitations and variability in biological responses in response to the use of NO for bacterial eradiation.

Polidori, C, Piwczynski, M, Ronchetti, F, Johnston, NP & Szpila, K 2022, 'Host-trailing satellite flight behaviour is associated with greater investment in peripheral visual sensory system in miltogrammine flies', Scientific Reports, vol. 12, no. 1, pp. 1-17.
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AbstractInsect sensory systems are the subjects of different selective pressures that shape their morphology. In many species of the flesh fly subfamily Miltogramminae (Diptera: Sarcophagidae) that are kleptoparasitic on bees and wasps, females perch on objects close to the host nests and, once a returning host is detected, they follow it in flight at a fixed distance behind until reaching the nest. We hypothesized that such satellite (SAT) flight behaviour, which implies a finely coordinated trailing flight, is associated with an improved visual system, compared to species adopting other, non-satellite (NON-SAT) strategies. After looking at body size and common ancestry, we found that SAT species have a greater number of ommatidia and a greater eye surface area when compared to NON-SAT species. Ommatidium area is only affected by body size, suggesting that selection changes disproportionately (relative to body size variation) the number of ommatidia and as a consequence the eye area, instead of ommatidium size. SAT species also tend to have larger ocelli, but their role in host-finding was less clear. This suggests that SAT species may have a higher visual acuity by increasing ommatidia number, as well as better stability during flight and motion perception through larger ocelli. Interestingly, antennal length was significantly reduced in SAT species, and ommatidia number negatively correlated with antennal length. While this finding does not imply a selection pressure of improved antennal sensory system in species adopting NON-SAT strategies, it suggests an inverse resource (i.e. a single imaginal disc) allocation between eyes and antennae in this fly subfamily.

Popovic, A, Morelato, M, Baechler, S, De Grazia, A, Tahtouh, M, Roux, C & Beavis, A 2022, 'Understanding Australian methylamphetamine drug markets through relational, temporal and spatial analyses', Drug Testing and Analysis, vol. 14, no. 3, pp. 481-495.
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AbstractIn the area of illicit drugs, forensic case data have proven effective at detecting links between seizures and providing greater insights into illicit drug markets. This research explored the application of mathematical and statistical techniques to several chemical profiles of Australian methylamphetamine seizures. The main aim was to create and deliver a method that would expand the use of illicit drug profiling for strategic intelligence purposes, contributing to the fight against illicit drug trafficking. The use of comparison metrics and clustering analysis to determine links between existing illicit drug specimens and subsequent new specimens was evaluated and automated. Relational, temporal and spatial analyses were subsequently used to gain an insight into illicit drug markets. Relational analysis identified clusters of seizures central to the network. Temporal analysis then provided insights into the behaviour of distribution markets, specifically the emergence and extinction of certain clusters of seizures over time. Spatial analysis aided the understanding of the inter‐jurisdictional nature of illicit drug markets. These analyses allowed for the generation of strategic intelligence relating to when and where the Australian methylamphetamine illicit drug market was the most active. Additionally, the strategic level trends identified clusters of seizures that were worth investigating further. These clusters were explored through a case study, which exploited additional chemical profiling data to provide drug market knowledge at an operational level. In turn, the intelligence produced at various levels could allow relevant law enforcement agencies to take necessary measures in disrupting markets.

Pradhan, B, Jena, R, Talukdar, D, Mohanty, M, Sahu, BK, Raul, AK & Abdul Maulud, KN 2022, 'A New Method to Evaluate Gold Mineralisation-Potential Mapping Using Deep Learning and an Explainable Artificial Intelligence (XAI) Model', Remote Sensing, vol. 14, no. 18, pp. 4486-4486.
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Geoscientists have extensively used machine learning for geological mapping and exploring the mineral prospect of a province. However, the interpretation of results becomes challenging due to the complexity of machine learning models. This study uses a convolutional neural network (CNN) and Shapley additive explanation (SHAP) to estimate potential locations for gold mineralisation in Rengali Province, a tectonised mosaic of volcano-sedimentary sequences juxtaposed at the interface of the Archaean cratonic segment in the north and the Proterozoic granulite provinces of the Eastern Ghats Belt in Eastern India. The objective is to integrate multi-thematic data involving geological, geophysical, mineralogical and geochemical surveys on a 1:50 K scale with the aim of prognosticating gold mineralisation. The available data utilised during the integration include aero-geophysical (aeromagnetic and aerospectrometric), geochemical (national geochemical mapping), ground geophysical (gravity), satellite gravity, remote sensing (multispectral) and National Geomorphology and Lineament Project structural lineament maps obtained from the Geological Survey of India Database. The CNN model has an overall accuracy of 90%. The SHAP values demonstrate that the major contributing factors are, in sequential order, antimony, clay, lead, arsenic content and a magnetic anomaly in CNN modelling. Geochemical pathfinders, including geophysical factors, have high importance, followed by the shear zones in mineralisation mapping. According to the results, the central parts of the study area, including the river valley, have higher gold prospects than the surrounding areas. Gold mineralisation is possibly associated with intermediate metavolcanics along the shear zone, which is later intruded by quartz veins in the northern part of the Rengali Province. This work intends to model known occurrences with respect to multiple themes so that the results can be replicated in surrou...

Prasad, E, Hitchcock, C, Raymond, J, Cole, A, Barash, M, McNevin, D & van Oorschot, RAH 2022, 'Touch DNA recovery from unfired and fired cartridges: Comparison of swabbing, tape lifting and soaking', Forensic Science International, vol. 330, pp. 111101-111101.
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Over the recent few years, several DNA collection techniques and methodologies have been published for the recovery of DNA from fired cartridge cases. In this study, swabbing, the DNA collection technique currently used in our jurisdiction (NSW, Australia), was compared with tape lifting and soaking to assess DNA recovery rates, DNA quality and profile quality. Brass.22LR and 9mmP cartridges were used as they are the most commonly encountered in our jurisdiction. The cartridges (n = 107) were loaded into cleaned firearm magazines by three volunteers of unknown shedder status, to mimic routine casework sample types. Half of the handled cartridges were fired whilst the other half were kept unfired. STR genotypes were produced at both 29 and 30 PCR cycles to evaluate which improved handler allele detection. DNA recovery rates showed that swabbing recovered significantly less DNA than tape lifting and soaking. Whilst there were no significant differences between tape lifting and soaking, tape lifting, on average, yielded more DNA than soaking. The calibre of ammunition had no influence on DNA recovery and in line with expectations, firing was found to decrease DNA recovery for all three sampling techniques. Assessment of DNA quality showed no evidence of PCR inhibition in any of the samples for this study. However, degradation indices showed that most samples were slightly to moderately degraded. Fewer handler alleles were detected from both fired tape lifted and soaked cartridges than unfired cartridges. Whilst 30 amplification cycles allowed for the detection of slightly more handler alleles, no statistically significant differences were found between 29 and 30 PCR cycles. Nonetheless, 50% of the profiles from unfired soaked cartridges that were non-uploadable after 29 cycles were uploadable after 30 cycles. Furthermore, 83% of profiles from unfired cartridges that were tape lifted were uploadable onto our jurisdiction's database at both 29 and 30 PCR cycles. All m...

Prasher, P, Sharma, M, Kumar Singh, S, Gulati, M, Kumar, D, Gupta, G, Kumar Chellappan, D, Gregory George Oliver, B, Wich, PR & Dua, K 2022, 'Versatility of acetalated dextran in nanocarriers targeting respiratory diseases', Materials Letters, vol. 323, pp. 132600-132600.
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Prasher, P, Sharma, M, Singh, SK, Gulati, M, Jha, NK, Gupta, PK, Gupta, G, Chellappan, DK, Zacconi, F, de Jesus Andreoli Pinto, T, Chan, Y, Liu, G, Paudel, KR, Hansbro, PM, George Oliver, BG & Dua, K 2022, 'Targeting mucus barrier in respiratory diseases by chemically modified advanced delivery systems', Chemico-Biological Interactions, vol. 365, pp. 110048-110048.
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Prasher, P, Sharma, M, Singh, SK, Gulati, M, Patravale, V, Oliver, BG & Dua, K 2022, 'Mucoadhesive particles: an emerging toolkit for advanced respiratory drug delivery', Nanomedicine, vol. 17, no. 12, pp. 821-826.
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Prasher, P, Sharma, M, Singh, SK, Haghi, M, MacLoughlin, R, Chellappan, DK, Gupta, G, Paudel, KR, Hansbro, PM, George Oliver, BG, Wich, PR & Dua, K 2022, 'Advances and applications of dextran-based nanomaterials targeting inflammatory respiratory diseases', Journal of Drug Delivery Science and Technology, vol. 74, pp. 103598-103598.
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Price, S, Kuzhiumparambil, U, Pernice, M & Ralph, P 2022, 'Techno-economic analysis of cyanobacterial PHB bioplastic production', Journal of Environmental Chemical Engineering, vol. 10, no. 3, pp. 107502-107502.
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Qadir, Z, Zafar, MH, Moosavi, SKR, Le, KN & Mahmud, MAP 2022, 'Autonomous UAV Path-Planning Optimization Using Metaheuristic Approach for Predisaster Assessment', IEEE Internet of Things Journal, vol. 9, no. 14, pp. 12505-12514.
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Qays, MO, Ahmed, MM, Parvez Mahmud, MA, Abu‐Siada, A, Muyeen, SM, Hossain, ML, Yasmin, F & Rahman, MM 2022, 'Monitoring of renewable energy systems by IoT‐aided SCADA system', Energy Science & Engineering, vol. 10, no. 6, pp. 1874-1885.
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AbstractWith the rapid increase of renewable energy generation worldwide, real‐time information has become essential to manage such assets, especially for systems installed offshore and in remote areas. To date, there is no cost‐effective condition monitoring technique that can assess the state of renewable energy sources in real‐time and provide suitable asset management decisions to optimize the utilization of such valuable assets and avoid any full or partial blackout due to unexpected faults. Based on the Internet of Things scheme, this paper represents a new application for the Supervisory Control and Data Acquisition (SCADA) system to monitor a hybrid system comprising photovoltaic, wind, and battery energy storage systems. Electrical parameters such as voltage, current, and power are monitored in real‐time via the ThingSpeak website. Network operators can control components of the hybrid power system remotely by the proposed SCADA system. The SCADA system is interfaced with the Matlab/Simulink software tool through KEPServerEX client. For cost‐effective design, low‐cost electronic components and Arduino Integrated Development Environment ATMega2560 remote terminal unit are employed to develop a hardware prototype for experimental analysis. Simulation and experimental results attest to the feasibility of the proposed system. Compared with other existing techniques, the developed system features advantages in terms of reliability and cost‐effectiveness.

Qiao, L, Li, H, Zhong, S, Xu, X, Su, F, Peng, X, Jin, D & Zhanghao, K 2022, 'Laterally swept light-sheet microscopy enhanced by pixel reassignment for photon-efficient volumetric imaging', Advanced Photonics Nexus, vol. 2, no. 01.
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Quan, DH, Kwong, AJ, Hansbro, PM & Britton, WJ 2022, 'No smoke without fire: the impact of cigarette smoking on the immune control of tuberculosis', European Respiratory Review, vol. 31, no. 164, pp. 210252-210252.
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Cigarette smoke (CS) exposure is a key risk factor for both active and latent tuberculosis (TB). It is associated with delayed diagnosis, more severe disease progression, unfavourable treatment outcomes and relapse after treatment. Critically, CS exposure is common in heavily populated areas with a high burden of TB, such as China, India and the Russian Federation. It is therefore prudent to evaluate interventions for TB while taking into account the immunological impacts of CS exposure. This review is a mechanistic examination of how CS exposure impairs innate barrier defences, as well as alveolar macrophage, neutrophil, dendritic cell and T-cell functions, in the context of TB infection and disease.

Quetglas-Llabrés, MM, Quispe, C, Herrera-Bravo, J, Catarino, MD, Pereira, OR, Cardoso, SM, Dua, K, Chellappan, DK, Pabreja, K, Satija, S, Mehta, M, Sureda, A, Martorell, M, Satmbekova, D, Yeskaliyeva, B, Sharifi-Rad, J, Rasool, N, Butnariu, M, Bagiu, IC, Bagiu, RV, Calina, D & Cho, WC 2022, 'Pharmacological Properties of Bergapten: Mechanistic and Therapeutic Aspects', Oxidative Medicine and Cellular Longevity, vol. 2022, pp. 1-10.
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Bergapten (BP) or 5-methoxypsoralen (5-MOP) is a furocoumarin compound mainly found in bergamot essential oil but also in other citrus essential oils and grapefruit juice. This compound presents antibacterial, anti-inflammatory, hypolipemic, and anticancer effects and is successfully used as a photosensitizing agent. The present review focuses on the research evidence related to the therapeutic properties of bergapten collected in recent years. Many preclinical and in vitro studies have been evidenced the therapeutic action of BP; however, few clinical trials have been carried out to evaluate its efficacy. These clinical trials with BP are mainly focused on patients suffering from skin disorders such as psoriasis or vitiligo. In these trials, the administration of BP (oral or topical) combined with UV irradiation induces relevant lesion clearance rates. In addition, beneficial effects of bergamot extract were also observed in patients with altered serum lipid profiles and in people with nonalcoholic fatty liver. On the contrary, there are no clinical trials that investigate the possible effects on cancer. Although the bioavailability of BP is lower than that of its 8-methoxypsoralen (8-MOP) isomer, it has fewer side effects allowing higher concentrations to be administered. In conclusion, although the use of BP has therapeutic applications on skin disorders as a sensitizing agent and as components of bergamot extract as hypolipemic therapy, more trials are necessary to define the doses and treatment guidelines and its usefulness against other pathologies such as cancer or bacterial infections.

Quigley, KM, Hein, M & Suggett, DJ 2022, 'Translating the 10 golden rules of reforestation for coral reef restoration', Conservation Biology, vol. 36, no. 4, pp. 1-8.
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AbstractEfforts are accelerating to protect and restore ecosystems globally. With trillions of dollars in ecosystem services at stake, no clear framework exists for developing or prioritizing approaches to restore coral reefs even as efforts and investment opportunities to do so grow worldwide. Restoration may buy time for climate change mitigation, but it lacks rigorous guidance to meet objectives of scalability and effectiveness. Lessons from restoration of terrestrial ecosystems can and should be rapidly adopted for coral reef restoration. We propose how the 10 golden rules of effective forest restoration can be translated to accelerate efforts to restore coral reefs based on established principles of resilience, management, and local stewardship. We summarize steps to undertake reef restoration as a management strategy in the context of the diverse ecosystem service values that coral reefs provide. Outlining a clear blueprint is timely as more stakeholders seek to undertake restoration as the UN Decade on Ecosystem Restoration begins.

Quinteros, SL, O'Brien, B & Donnelly, S 2022, 'Exploring the role of macrophages in determining the pathogenesis of liver fluke infection', Parasitology, vol. 149, no. 10, pp. 1364-1373.
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AbstractThe food-borne trematodes, Opisthorchis viverrini and Clonorchis sinensis, are classified as group 1 biological carcinogens: definitive causes of cancer. By contrast, infections with Fasciola hepatica, also a food-borne trematode of the phylum Platyhelminthes, are not carcinogenic. This review explores the premise that the differential activation of macrophages during infection with these food-borne trematodes is a major determinant of the pathological outcome of infection. Like most helminths, the latter stages of infection with all 3 flukes induce M2 macrophages, a phenotype that mediates the functional repair of tissue damaged by the feeding and migratory activities of the parasites. However, there is a critical difference in how the development of pro-inflammatory M1 macrophages is regulated during infection with these parasites. While the activation of the M1 macrophage phenotype is largely suppressed during the early stages of infection with F. hepatica, M1 macrophages predominate in the bile ducts following infection with O. viverrini and C. sinensis. The anti-microbial factors released by M1 macrophages create an environment conducive to mutagenesis, and hence the initiation of tumour formation. Subsequently, the tissue remodelling processes induced by the M2 macrophages promote the proliferation of mutated cells, and the expansion of cancerous tissue. This review will also explore the interactions between macrophages and parasite-derived signals, and their contributions to the stark differences in the innate immune responses to infection with these parasites.

Quinton, AR, Kelty, SF & Scudder, N 2022, 'Attitudes towards police use of consumer/private DNA databases in investigations', Science & Justice, vol. 62, no. 3, pp. 263-271.
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Rad, MA, Mahmodi, H, Filipe, EC, Cox, TR, Kabakova, I & Tipper, JL 2022, 'Micromechanical characterisation of 3D bioprinted neural cell models using Brillouin microspectroscopy', Bioprinting, vol. 25, pp. e00179-e00179.
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Biofabrication of three-dimensional (3D) in vitro neural cell models that closely mimic the central nervous system (CNS) is an emerging field of research with applications from fundamental biology to regenerative medicine, and far reaching benefits for the economy, healthcare and the ethical use of animals. The micromechanical properties of such models are an important factor dictating the success of modelling outcomes in relation to accurate reproduction of the processes in native tissues. Characterising the micromechanical properties of such models non-destructively and over a prolonged span of time, however, are key challenges. Brillouin microspectroscopy (BM) could provide a solution to this problem since this technology is non-invasive, label-free and is capable of micro-scale 3D imaging. In this work, the micromechanical properties of 3D bioprinted neural cell models consisting of NG 108-15 neuronal cells and Gelatin methacryloyl (GelMA) hydrogels of various concentrations were investigated using BM. We demonstrate changes in the volume-averaged (VA) and local micro-scale mechanical properties of these models over a 7 day period, in which the hydrogel component of the model are found to soften as the cells grow, multiply and form stiffer spheroid-type structures. These findings signify the necessity to resolve in microscopic detail the mechanics of in vitro 3D tissue models and suggest Brillouin microspectroscopy to be a suitable technology to bridge this gap.

Rädecker, N, Pogoreutz, C, Gegner, HM, Cárdenas, A, Perna, G, Geißler, L, Roth, F, Bougoure, J, Guagliardo, P, Struck, U, Wild, C, Pernice, M, Raina, J-B, Meibom, A & Voolstra, CR 2022, 'Heat stress reduces the contribution of diazotrophs to coral holobiont nitrogen cycling', The ISME Journal, vol. 16, no. 4, pp. 1110-1118.
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Abstract Efficient nutrient cycling in the coral-algal symbiosis requires constant but limited nitrogen availability. Coral-associated diazotrophs, i.e., prokaryotes capable of fixing dinitrogen, may thus support productivity in a stable coral-algal symbiosis but could contribute to its breakdown when overstimulated. However, the effects of environmental conditions on diazotroph communities and their interaction with other members of the coral holobiont remain poorly understood. Here we assessed the effects of heat stress on diazotroph diversity and their contribution to holobiont nutrient cycling in the reef-building coral Stylophora pistillata from the central Red Sea. In a stable symbiotic state, we found that nitrogen fixation by coral-associated diazotrophs constitutes a source of nitrogen to the algal symbionts. Heat stress caused an increase in nitrogen fixation concomitant with a change in diazotroph communities. Yet, this additional fixed nitrogen was not assimilated by the coral tissue or the algal symbionts. We conclude that although diazotrophs may support coral holobiont functioning under low nitrogen availability, altered nutrient cycling during heat stress abates the dependence of the coral host and its algal symbionts on diazotroph-derived nitrogen. Consequently, the role of nitrogen fixation in the coral holobiont is strongly dependent on its nutritional status and varies dynamically with environmental conditions.

Raes, EJ, Hörstmann, C, Landry, MR, Beckley, LE, Marin, M, Thompson, P, Antoine, D, Focardi, A, O'Brien, J, Ostrowski, M & Waite, AM 2022, 'Dynamic change in an ocean desert: Microbial diversity and trophic transfer along the 110 °E meridional in the Indian Ocean', Deep Sea Research Part II: Topical Studies in Oceanography, vol. 201, pp. 105097-105097.
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The eastern Indian Ocean is among the most oligotrophic regions in the world and has been described as an ocean desert. Limited information exists on microbial community profiles from marker gene data, and an open question in this system is how energy is transported from the base of the food web to higher trophic levels. Here we show that, along a 3300 km long transect in the ultra-oligotrophic eastern Indian Ocean, both alpha and beta diversity metrics for prokaryotic and eukaryotic trophic groups revealed remarkably strong latitudinal trends. The latitudinal Shannon diversity pattern for autotrophic eukaryotes furthermore aligned with the isotopic δ13C ratios of particulate organic carbon, fractionated zooplankton and hand-picked fish larvae, suggesting a close trophic linkage between autotrophic eukaryotes and higher trophic levels. Our data also showed an increasing contribution of eukaryotic mixotrophs and a high contribution of heterotrophic eukaryotes towards warmer waters. These findings highlight that not only the recycling of organic matter via bacterial regeneration is important in this system but that mixo- and heterotrophic eukaryotes play a major role in redistributing energy within the marine food web of these oligotrophic waters. Our data provide a baseline to understand how environmental changes such as warming surface waters might impact the open-ocean food web in this oligotrophic basin.

Rafei, R, Koong, J, Osman, M, Al Atrouni, A, Hamze, M & Hamidian, M 2022, 'Analysis of pCl107 a large plasmid carried by an ST25Acinetobacter baumanniistrain reveals a complex evolutionary history and links to multiple antibiotic resistance and metabolic pathways', FEMS Microbes, vol. 3, p. xtac027.
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AbstractAcinetobacter baumannii has successfully spread during the last decades as one of the main critically important pathogens. However, many aspects including plasmids, are still under-investigated. Here, we report the complete sequence of an Acinetobacter baumannii strain, belonging to the ST25IP (Institut Pasteur) sequence type recovered in 2012 in Lebanon, using a combination of Illumina MiSeq and Oxford Nanopore sequencing and a hybrid assembly approach. This strain (Cl107) carries a 198 kb plasmid called pCl107 that encodes the MPFI conjugative transfer system. The plasmid carries the aacA1, aacC2, sul2, strAB, and tetA(B) antibiotic resistance genes. pCl107 region encompassing the sul2, strAB, tetA(B) is closely related to AbGRI1 chromosomal resistance islands, which are widespread in A. baumannii strains belonging to Global Clone 2. The resistance region found in pCl107 is one of the missing links in the evolutionary history of the AbGRI1 islands. pCl107 also contains a BREX Type 1 region and represents one of the two main evolution patterns observed in BREX clusters found in plasmids related to pCl107. pCl107 also harbours a ptx phosphonate metabolism module, which plays an ancestral structure compared to other large plasmids in ST25 strains. While the uric acid metabolic module found in pCl107 is incomplete, we identified possible ancestors from plasmids and chromosomes of Acinetobacter spp. Our analyses indicate a complex evolutionary history of plasmids related to pCl107 with many links to multiple antibiotic resistance and metabolic pathways.

Rahman, FH, Newaz, SHS, Au, T-W, Suhaili, WS, Mahmud, MAP & Lee, GM 2022, 'EnTruVe: ENergy and TRUst-aware Virtual Machine allocation in VEhicle fog computing for catering applications in 5G', Future Generation Computer Systems, vol. 126, pp. 196-210.
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It is undoubted that fog computing contributes in catering the latency-stringent applications of 5G, and one of the enabling technologies that fundamentally ensures the success of fog computing is virtualization as it offers isolation and platform independence. Although the emergence of vehicle-based fog (referred to as v-fog) facilities can certainly benefit from these desirable features of virtualization, there are several challenges that need to be addressed in order to realize the full potential that v-fogs can offer. One of the challenges of virtualization in v-fog is Virtual Machine (VM) migration. There are several factors that trigger a VM migration in a v-fog such as vehicle resource depletion. VM migrations would not only lead to nonessential usage of valuable resources (e.g. energy, bandwidth, memory) in the v-fogs, but also incur various overheads and performance degradation throughout the whole network. Thus, minimizing VM migrations is necessary. Furthermore, to ensure the seamless VM migrations between v-fogs, trust of v-fogs is required. While there exists studies of trust in the virtualization of cloud, they are irrelevant to v-fogs as v-fogs are different in nature (i.e. heterogeneous, mobile) from the cloud. Additionally, trust is not included in the decision making mechanisms of VM allocation for vehicular environments in the existing works. Moreover, as vehicle resources are constrained, their energy has to be utilized efficiently. In this paper, we propose EnTruVe, an ENergy and TRUst-aware VM allocation in VEhicle fog computing solution that aims to minimize the number of VM migrations while reducing VM processing associated energy consumption as much as possible. The VM allocation algorithm in EnTruVe provides a larger selection pool of v-fogs that meets the VMs requirements (e.g. trust, latency), thereby ensuring higher chances of success of VM allocation. Using Analytic Hierarchy Process (AHP), the proposed EnTruVe solution evaluates the...

Rahman, MA, Ali, S, Phillips, MR & Ton-That, C 2022, 'Multi-wavelength emission through self-induced defects in GaZnO microrods', Journal of Alloys and Compounds, vol. 895, pp. 162693-162693.
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Multi-wavelength emission in wide bandgap semiconductors is commonly achieved through ternary alloying or quantum size effects. However, multi-wavelength emission within a single microstructure is highly challenging using these approaches. Here, we demonstrate that the luminescence wavelength within individual GaZnO microrods can be tailored via defect engineering. Fast chemical vapor growth of oxygen-rich ZnO microrods with Ga2O3 as an additive in the ZnO vapour leads to formation of a tapered morphology with graded distribution of Ga dopants, while the Ga incorporation does not significantly alter their crystal structure. With increasing Ga content from 1 to 6 at% from tip to base, the GaZnO microrods increase in diameter towards the substrate in accordance with the birth-and-spread mechanism. The local near-band-edge emission within single ZnO microrods, analyzed by nanoscale cathodoluminescence spectroscopy, exhibits a red shift of ~0.6 eV with increasing Ga content and exhibits signature characteristics of an excitonic emission. Density Functional Theory calculations reveal that the variation in the emission wavelength arises from bandgap narrowing due to the merging of the electronic states of Ga defect complexes with ZnO energy bands. The experimental and theoretical results demonstrate (i) the utility of using the self-regulation of defect compensation effects for band gap engineering and (ii) the possibility of multi-wavelength light sources within individual microrods.

Rahman, MA, Islam, MJ, Islam, MR & Mahmud, MAP 2022, 'Correction to: Strain Dependent Performance Analysis of InGaN Multi‑junction Solar Cell', Transactions on Electrical and Electronic Materials, vol. 23, no. 1, pp. 105-105.
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Unfortunately, the original publication of the article was published without keywords. The keywords are given in this correction. The original article has been corrected.

Rahman, MH, Mahbub, KR, Espinoza-Vergara, G, Ritchie, A, Hoque, MM, Noorian, P, Cole, L, McDougald, D & Labbate, M 2022, 'Protozoal food vacuoles enhance transformation in Vibrio cholerae through SOS-regulated DNA integration', The ISME Journal, vol. 16, no. 8, pp. 1993-2001.
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Abstract Vibrio cholerae, the bacterial pathogen responsible for the diarrheal disease cholera, resides in the aquatic environment between outbreaks. For bacteria, genetic variation by lateral gene transfer (LGT) is important for survival and adaptation. In the aquatic environment, V. cholerae is predominantly found in biofilms associated with chitinous organisms or with chitin “rain”. Chitin induces competency in V. cholerae, which can lead to LGT. In the environment, V. cholerae is also subjected to predation pressure by protist. Here we investigated whether protozoal predation affected LGT using the integron as a model. Integrons facilitate the integration of mobile DNA (gene cassettes) into the bacterial chromosome. We report that protozoal predation enhances transformation of a gene cassette by as much as 405-fold. We show that oxidative radicals produced in the protozoal phagosome induces the universal SOS response, which in turn upregulates the integron-integrase, the recombinase that facilitates cassette integration. Additionally, we show that during predation, V. cholerae requires the type VI secretion system to acquire the gene cassette from Escherichia coli. These results show that protozoal predation enhances LGT thus producing genetic variants that may have increased capacity to survive grazing. Additionally, the conditions in the food vacuole may make it a “hot spot” for LGT by accumulating diverse bacteria and inducing the SOS response helping drive genetic diversification and evolution.

Raina, J-B, Lambert, BS, Parks, DH, Rinke, C, Siboni, N, Bramucci, A, Ostrowski, M, Signal, B, Lutz, A, Mendis, H, Rubino, F, Fernandez, VI, Stocker, R, Hugenholtz, P, Tyson, GW & Seymour, JR 2022, 'Chemotaxis shapes the microscale organization of the ocean’s microbiome', Nature, vol. 605, no. 7908, pp. 132-138.
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The capacity of planktonic marine microorganisms to actively seek out and exploit microscale chemical hotspots has been widely theorized to affect ocean-basin scale biogeochemistry1-3, but has never been examined comprehensively in situ among natural microbial communities. Here, using a field-based microfluidic platform to quantify the behavioural responses of marine bacteria and archaea, we observed significant levels of chemotaxis towards microscale hotspots of phytoplankton-derived dissolved organic matter (DOM) at a coastal field site across multiple deployments, spanning several months. Microscale metagenomics revealed that a wide diversity of marine prokaryotes, spanning 27 bacterial and 2 archaeal phyla, displayed chemotaxis towards microscale patches of DOM derived from ten globally distributed phytoplankton species. The distinct DOM composition of each phytoplankton species attracted phylogenetically and functionally discrete populations of bacteria and archaea, with 54% of chemotactic prokaryotes displaying highly specific responses to the DOM derived from only one or two phytoplankton species. Prokaryotes exhibiting chemotaxis towards phytoplankton-derived compounds were significantly enriched in the capacity to transport and metabolize specific phytoplankton-derived chemicals, and displayed enrichment in functions conducive to symbiotic relationships, including genes involved in the production of siderophores, B vitamins and growth-promoting hormones. Our findings demonstrate that the swimming behaviour of natural prokaryotic assemblages is governed by specific chemical cues, which dictate important biogeochemical transformation processes and the establishment of ecological interactions that structure the base of the marine food web.

Rajala, P, Cheng, D-Q, Rice, SA & Lauro, FM 2022, 'Sulfate-dependant microbially induced corrosion of mild steel in the deep sea: a 10-year microbiome study', Microbiome, vol. 10, no. 1.
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AbstractBackgroundMetal corrosion in seawater has been extensively studied in surface and shallow waters. However, infrastructure is increasingly being installed in deep-sea environments, where extremes of temperature, salinity, and high hydrostatic pressure increase the costs and logistical challenges associated with monitoring corrosion. Moreover, there is currently only a rudimentary understanding of the role of microbially induced corrosion, which has rarely been studied in the deep-sea. We report here an integrative study of the biofilms growing on the surface of corroding mooring chain links that had been deployed for 10 years at ~2 km depth and developed a model of microbially induced corrosion based on flux-balance analysis.MethodsWe used optical emission spectrometry to analyze the chemical composition of the mooring chain and energy-dispersive X-ray spectrometry coupled with scanning electron microscopy to identify corrosion products and ultrastructural features. The taxonomic structure of the microbiome was determined using shotgun metagenomics and was confirmed by 16S amplicon analysis and quantitative PCR of thedsrBgene. The functional capacity was further analyzed by generating binned, genomic assemblies and performing flux-balance analysis on the metabolism of the dominant taxa.ResultsThe surface of the chain links showed intensive and localized corrosion with structural features typical of microbially induced corrosion. The microbiome on the links differed considerably from that of the surrounding sediment, suggesting selection for specific metal-corroding biofilms dominated by sulfur-cycling bacteria. The core metabolism of the microbiome was reconstructed to generate a mechanistic model that combines biotic and abiotic...

Ramanunny, AK, Wadhwa, S, Gulati, M, Vishwas, S, Khursheed, R, Paudel, KR, Gupta, S, Porwal, O, Alshahrani, SM, Jha, NK, Chellappan, DK, Prasher, P, Gupta, G, Adams, J, Dua, K, Tewari, D & Singh, SK 2022, 'Journey of Alpinia galanga from kitchen spice to nutraceutical to folk medicine to nanomedicine', Journal of Ethnopharmacology, vol. 291, pp. 115144-115144.
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Ramanunny, AK, Wadhwa, S, Kumar Singh, S, Kumar, B, Gulati, M, Kumar, A, Almawash, S, Al Saqr, A, Gowthamarajan, K, Dua, K, Singh, H, Vishwas, S, Khursheed, R, Rahana Parveen, S, Venkatesan, A, Paudel, KR, Hansbro, PM & Kumar Chellappan, D 2022, 'Topical non-aqueous nanoemulsion of Alpinia galanga extract for effective treatment in psoriasis: In vitro and in vivo evaluation', International Journal of Pharmaceutics, vol. 624, pp. 121882-121882.
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Rasheedkhan Regina, V, Noorian, P, Sim, CBW, Constancias, F, Kaliyamoorthy, E, Booth, SC, Espinoza-Vergara, G, Rice, SA & McDougald, D 2022, 'Loss of the Acetate Switch in Vibrio vulnificus Enhances Predation Defense against Tetrahymena pyriformis', Applied and Environmental Microbiology, vol. 88, no. 2, p. AEM0166521.
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Bacteria in the environment, including Vibrio spp., interact with protozoan predators. To defend against predation, bacteria evolve antipredator mechanisms ranging from changing morphology, biofilm formation, and secretion of toxins or virulence factors.

Ravalli, S, Roggio, F, Magrì, B, Lauretta, G, Broggi, G, Caltabiano, R, Vecchio, GM, Magro, G, Loreto, C, Castorina, A & Musumeci, G 2022, 'Immunohistochemical evaluation of autotaxin and lubricin in mild osteoarthritic rat model performing moderate physical activity', Acta Histochemica, vol. 124, no. 6, pp. 151936-151936.
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Raza, A, Hassan, JZ, Mahmood, A, Nabgan, W & Ikram, M 2022, 'Recent advances in membrane-enabled water desalination by 2D frameworks: Graphene and beyond', Desalination, vol. 531, pp. 115684-115684.
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The growing population rate and expansion of industrial sector are associated with climate variation, which steered towards global water complications. The current review summarizes the next-generation hybrid graphene-based membrane materials for water cleansing to come across global freshwater supplies. In this regard, graphene-based membrane materials are assumed as innovative materials headed for desalination route owing to their tunable functionalities as well as atomic thickness. The discussion of operating conditions and production procedures of membrane on membrane fouling and separation mechanisms are described. Furthermore, its development merits, and limitations compared to traditional polymeric membranes are also discussed. This review discusses the use of 2D materials as building blocks for membrane structures, current developments in 2D-enabled membranes, and their prospects. More devotion is required for membrane selectivity and water permeability for long-term setup at environments alike with the field for performance examination; this helps to prolong applications of graphene-based membranes materials. In this regard, we summarized the research growth on 2D materials for membrane-based water desalination for more attention. Moreover, the design strategies containing layer-layer spacing and pore size optimization to sustain the constancy of the membranes are predominantly explained. Finally, present tasks and future research directions are also offered.

Razavi Bazaz, S, Mihandust, A, Salomon, R, Joushani, HAN, Li, W, A. Amiri, H, Mirakhorli, F, Zhand, S, Shrestha, J, Miansari, M, Thierry, B, Jin, D & Ebrahimi Warkiani, M 2022, 'Zigzag microchannel for rigid inertial separation and enrichment (Z-RISE) of cells and particles', Lab on a Chip, vol. 22, no. 21, pp. 4093-4109.
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Overview of the zigzag microchannel for rigid inertial separation and enrichment (Z-RISE). The proposed device has superior performance for particle focusing and separation.

Rehn, S, Raymond, JS, Boakes, RA & Bowen, MT 2022, 'Sucrose intake by rats affected by both intraperitoneal oxytocin administration and time of day', Psychopharmacology, vol. 239, no. 2, pp. 429-442.
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RATIONALE: Daily limited access to palatable food or drink at a fixed time is commonly used in rodent models of bingeing. Under these conditions, entrainment may modulate intake patterns. Oxytocin is involved in circadian patterns of intake and, when administered peripherally, reduces sucrose intake. However, oxytocin's effects on intake under limited-access conditions and its potential interaction with entrainment have not been explored. OBJECTIVES: This study examined the role of entrainment on intake patterns, oxytocin's effects on sucrose intakes and locomotor activity and whether oxytocin's effects were mediated by its actions at the oxytocin receptor. METHODS: Sated rats received daily 1-h access to 10% sucrose solution either at a fixed or varied time of day. Rats received intraperitoneal oxytocin (0 mg/kg, 0.3 mg/kg, 1 mg/kg, 3 mg/kg) prior to sucrose access, and spontaneous locomotor activity was assessed in an open-field test. Rats were then pre-treated with an oxytocin receptor antagonist, L368,899, prior to oxytocin before sucrose access. RESULTS: Intake patterns did not differ between fixed- or varied-time presentations; rats consumed more sucrose solution in the middle as opposed to the early-dark phase. Oxytocin dose-dependently reduced sucrose intakes, but also reduced locomotor activity. There was some evidence of partial blockade of oxytocin-induced sucrose intake reductions by L368,899, but the results were unclear. CONCLUSIONS: Time of day and oxytocin impact sucrose solution intake under daily limited access in rats and the sedative-like effects of oxytocin should be considered in future studies on oxytocin and food intake.

Rehn, S, Raymond, JS, Boakes, RA & Leenaars, CHC 2022, 'A systematic review and meta-analysis of animal models of binge eating - Part 1: Definitions and food/drink intake outcomes', Neuroscience & Biobehavioral Reviews, vol. 132, pp. 1137-1156.
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Binge eating involves consuming excessive amounts of food within a discrete period of time and is associated with significant impairments in binge-eating disorder and bulimia nervosa. While research on clinical binge eating has provided valuable aetiological insights, animal models allow for closer examination of environmental, biological, and developmental risk factors. Numerous animal models of binge eating exist and differ widely in operational definitions of bingeing, animal characteristics and methodological parameters. The current review aimed to synthesise the available published evidence on these models. A systematic review of binge definitions in 170 articles found most studies displayed good face validity. Meta-analyses on 150 articles confirmed that the amount of food or drink consumed by animals under binge conditions was larger than that of non-binge conditions across many protocols. The meta-regression revealed species, strain, and sex moderated binge effect size, with the largest effect observed in studies with female animals and mice. Risk of bias assessment identified that improved reporting of allocation, baseline characteristics and outcome assessment is required in future studies.

Reid, CJ, Cummins, ML, Börjesson, S, Brouwer, MSM, Hasman, H, Hammerum, AM, Roer, L, Hess, S, Berendonk, T, Nešporová, K, Haenni, M, Madec, J-Y, Bethe, A, Michael, GB, Schink, A-K, Schwarz, S, Dolejska, M & Djordjevic, SP 2022, 'A role for ColV plasmids in the evolution of pathogenic Escherichia coli ST58', Nature Communications, vol. 13, no. 1, p. 683.
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AbstractEscherichia coli ST58 has recently emerged as a globally disseminated uropathogen that often progresses to sepsis. Unlike most pandemic extra-intestinal pathogenic E. coli (ExPEC), which belong to pathogenic phylogroup B2, ST58 belongs to the environmental/commensal phylogroup B1. Here, we present a pan-genomic analysis of a global collection of 752 ST58 isolates from diverse sources. We identify a large ST58 sub-lineage characterized by near ubiquitous carriage of ColV plasmids, which carry genes encoding virulence factors, and by a distinct accessory genome including genes typical of the Yersiniabactin High Pathogenicity Island. This sub-lineage includes three-quarters of all ExPEC sequences in our study and has a broad host range, although poultry and porcine sources predominate. By contrast, strains isolated from cattle often lack ColV plasmids. Our data indicate that ColV plasmid acquisition contributed to the divergence of the major ST58 sub-lineage, and different sub-lineages inhabit poultry, swine and cattle.

Reimers, JR, Rätsep, M, Linnanto, JM & Freiberg, A 2022, 'Chlorophyll spectroscopy: conceptual basis, modern high-resolution approaches, and current challenges', Proceedings of the Estonian Academy of Sciences, vol. 71, no. 2, pp. 127-127.
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The conceptual formalism to understand the properties and function of chlorophylls in the gas and solution phases as well as in protein matrices is reviewed. This formalism is then applied to interpret modern high-resolution spectroscopic data, resulting from methods such as differential fluorescence line-narrowing spectroscopy and selective fluorescence excitation spectroscopy, which resolve individual vibrational transitions within the inhomogeneously broadened emission and absorption spectra of chlorophyll-a, bacteriochlorophyll-a, and pheophytin-a. Density functional theory and ab initio quantum chemical calculations are applied to interpret this data and fill in missing information needed to understand photosynthetic processes. The focus is placed on recognizing environmental and thermal effects, as well as the roles of Duschinsky rotation and non-adiabatic coupling in controlling the spectra. A critical feature of chlorophyll spectroscopy is determined to be absorption-emission asymmetry. Its ramifications for chlorophyll’s function in photosystems are expected to be significant, as most current models for understanding their function assume that absorption and emission are symmetric, i.e. in the absence of relaxation processes, molecules coherently re-emit the light that they absorbed to enact exciton transport. The effect of the Duschinsky rotation is that after vibrational excitation during the electronic transition chlorophylls mostly emit light at different energies to what they absorb, while the effect of non-adiabatic coupling is that the polarization of the light is changed.

Ren, D, Leslie, LM, Huang, Y & Hu, A 2022, 'Correction of GRACE measurements of the Earth’s moment of inertia (MOI)', Climate Dynamics, vol. 58, no. 9-10, pp. 2525-2538.
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AbstractThe widely used 15-year Gravity Recovery and Climate Experiment (GRACE) data sets do not conserve global total mass. They have a spurious decreasing trend of ~ 280 Gt/year. Various regions contribute differently to the global total mass loss error, with the Greenland Ice Sheet (GrIS) generating ~ 10% of the error alone. Atmospheric parameters from reanalysis datasets drive a well-tested ice model to generate mass variation time series over the GrIS for 2002–2015. Because shorter timescale spikes of ~ 10–30 Gt in GRACE measurements are physically based, only the overall trend of ~ 30 Gt/year requires correcting. A more accurate mass loss rate estimate for 2002–2015 is ~ 120 Gt/year, considerably below previous estimates. With the water redistribution to lower latitudes and other effects from a warming climate, the nontidal Earth moment of inertia (MOI) also increases. After rectification, the GRACE measured mass redistribution shows a steady, statistically robust (passed a two-tailed t-test at p = 0.04 for dof = 15) rate of MOI increase reaching ~ 10.1 × 1027 kg m2/year, equivalent to a 10.91 μs/year increase in the length of a day, during 2002–2017.

Ren, D, Leslie, LM, Huang, Y & Hu, A 2022, 'Correction to: Correction of GRACE measurements of the Earth’s moment of inertia (MOI)', Climate Dynamics, vol. 58, no. 9-10, pp. 2539-2539.
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Ren, R-J, Lu, Y-H, Jiang, Z-K, Gao, J, Zhou, W-H, Wang, Y, Jiao, Z-Q, Wang, X-W, Solntsev, AS & Jin, X-M 2022, 'Topologically protecting squeezed light on a photonic chip', Photonics Research, vol. 10, no. 2, pp. 456-456.
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Squeezed light is a critical resource in quantum sensing and information processing. Due to the inherently weak optical nonlinearity and limited interaction volume, considerable pump power is typically needed to obtain efficient interactions to generate squeezed light in bulk crystals. Integrated photonics offers an elegant way to increase the nonlinearity by confining light strictly inside the waveguide. For the construction of large-scale quantum systems performing many-photon operations, it is essential to integrate various functional modules on a chip. However, fabrication imperfections and transmission cross talk may add unwanted diffraction and coupling to other photonic elements, reducing the quality of squeezing. Here, by introducing the topological phase, we experimentally demonstrate the topologically protected nonlinear process of four-wave mixing, enabling the generation of squeezed light on a silica chip. We measure the cross-correlations at different evolution distances for various topological sites and verify the nonclassical features with high fidelity. The squeezing parameters are measured to certify the protection of cavity-free, strongly squeezed states. The demonstration of topological protection for squeezed light on a chip brings new opportunities for quantum integrated photonics, opening novel approaches for the design of advanced multi-photon circuits.

Ren, S, Hansbro, PM, Srikusalanukul, W, Horvat, JC, Hunter, T, Brown, AC, Peel, R, Faulkner, J, Evans, T-J, Li, SC, Newby, D, Hure, A, Abhayaratna, WP, Tsimikas, S, Gonen, A, Witztum, JL, Attia, J, Ren, S, Hansbro, PM, Peel, R, Srikusalanukul, W, Abhayaratna, W, Newby, D, Hure, A, D'Este, C, Tonkin, A, Hopper, I, Thrift, A, Levi, C, Sturm, J, Durrheim, D, Hung, J, Briffa, T, Chew, D, Anderson, P, Moon, L, McEvoy, M & Attia, J 2022, 'Generation of cardio-protective antibodies after pneumococcal polysaccharide vaccine: Early results from a randomised controlled trial', Atherosclerosis, vol. 346, pp. 68-74.
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BACKGROUND AND AIMS: Observational studies have demonstrated that the pneumococcal polysaccharide vaccine (PPV) is associated with reduced risk of cardiovascular events. This may be mediated through IgM antibodies to OxLDL, which have previously been associated with cardioprotective effects. The Australian Study for the Prevention through Immunisation of Cardiovascular Events (AUSPICE) is a double-blind, randomised controlled trial (RCT) of PPV in preventing ischaemic events. Participants received PPV or placebo once at baseline and are being followed-up for incident fatal and non-fatal myocardial infarction or stroke over 6 years. METHODS: A subgroup of participants at one centre (Canberra; n = 1,001) were evaluated at 1 month and 2 years post immunisation for changes in surrogate markers of atherosclerosis, as pre-specified secondary outcomes: high-sensitive C-reactive protein (CRP), pulse wave velocity (PWV), and carotid intima-media thickness (CIMT). In addition, 100 participants were randomly selected in each of the intervention and control groups for measurement of anti-pneumococcal antibodies (IgG, IgG2, IgM) as well as anti-OxLDL antibodies (IgG and IgM to CuOxLDL, MDA-LDL, and PC-KLH). RESULTS: Concentrations of anti-pneumococcal IgG and IgG2 increased and remained high at 2 years in the PPV group compared to the placebo group, while IgM increased and then declined, but remained detectable, at 2 years. There were statistically significant increases in all anti-OxLDL IgM antibodies at 1 month, which were no longer detectable at 2 years; there was no increase in anti-OxLDL IgG antibodies. There were no significant changes in CRP, PWV or CIMT between the treatment groups at the 2-year follow-up. CONCLUSIONS: PPV engenders a long-lasting increase in anti-pneumococcal IgG, and to a lesser extent, IgM titres, as well as a transient increase in anti-OxLDL IgM antibodies. However, there were no detectable changes in surrogate markers of atherosclerosis...

Ricafrente, A, Cwiklinski, K, Nguyen, H, Dalton, JP, Tran, N & Donnelly, S 2022, 'Stage-specific miRNAs regulate gene expression associated with growth, development and parasite-host interaction during the intra-mammalian migration of the zoonotic helminth parasite Fasciola hepatica', BMC Genomics, vol. 23, no. 1, p. 419.
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Abstract Background MiRNAs are small non-coding RNAs that post-transcriptionally regulate gene expression in organisms ranging from viruses to mammals. There is great relevance in understanding how miRNAs regulate genes involved in the growth, development, and maturation of the many parasitic worms (helminths) that together afflict more than 2 billion people. Results Here, we describe the miRNAs expressed by each of the predominant intra-mammalian development stages of Fasciola hepatica, a foodborne flatworm that infects a wide range of mammals worldwide, most importantly humans and their livestock. A total of 124 miRNAs were profiled, 72 of which had been previously reported and three of which were conserved miRNA sequences described here for the first time. The remaining 49 miRNAs were novel sequences of which, 31 were conserved with F. gigantica and the remaining 18 were specific to F. hepatica. The newly excysted juveniles express 22 unique miRNAs while the immature liver and mature bile duct stages each express 16 unique miRNAs. We discovered several sequence variant miRNAs (IsomiRs) as well as miRNA clusters that exhibit strict temporal expression paralleling parasite development. Target analysis revealed the close association between miRNA expression and stage-specific changes in the transcriptome; for example, we identified specific miRNAs that target parasite proteases known to be essential for intestinal wall penetration (cathepsin L3). Moreover, we demonstrate that miRNAs fine-tune the expression of genes involved in the metabolic pathways that allow the parasites to move from an aerobic external environment to the anerobic environment of the host....

Ridlen, R, McGrath, K & Gorrie, CA 2022, 'Animal models of compression spinal cord injury', Journal of Neuroscience Research, vol. 100, no. 12, pp. 2201-2212.
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AbstractCompression spinal cord injuries are a common cause of morbidity in people who experience a spinal cord injury (SCI). Either as a by‐product of a traumatic injury or due to nontraumatic conditions such as cervical myelitis, compression injuries are growing in prevalence clinically and many attempts of animal replication have been described within the literature. These models, however, often focus on the traumatic side of injury or mimic short‐term injuries that are not representative of the majority of compression SCI. Of this, nontraumatic spinal cord injuries are severely understudied and have an increased prevalence in elderly populations, adults, and children. Therefore, there is a need to critically evaluate the current animal models of compression SCI and their suitability as a method for clinically relevant data that can help reduce morbidity and mortality of SCI. In this review, we reviewed the established and emerging methods of animal models of compression SCI. These models are the clip, balloon, solid spacer, expanding polymer, remote, weight drop, calibrated forceps, screw, and strap methods. These methods showed that there is a large reliance on the use of laminectomy to induce injury. Furthermore, the age range of many studies does not reflect the elderly and young populations that commonly suffer from compression injuries. It is therefore important to have techniques and methods that are able to minimize secondary effects of the surgeries, and are representative of the clinical cases seen so that treatments and interventions can be developed that are specific.

Rodrigo, N, Chen, H, Pollock, CA & Glastras, SJ 2022, 'Preconception weight loss improves fertility and maternal outcomes in obese mice', Journal of Endocrinology, vol. 253, no. 1, pp. 27-38.
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Women with obesity have higher incidences of infertility, with longer time to conception and increased risk of pregnancy complications compared to women with normal body weight. There is a lack of evidence demonstrating the benefit of preconception maternal weight loss on fertility and pregnancy outcomes. We aimed to determine if preconception weight loss, either with diet modification or glucose-like peptide 1 receptor agonist liraglutide, improves maternal weight, fertility, and pregnancy outcomes. C57BL/6 female mice were fed either a high-fat diet (HFD) or chow for 8 weeks. HFD-fed dams were administered liraglutide (0.3 mg/kg, s.c., for 4 weeks) or switched to chow to induce weight loss. Prior to mating, liraglutide was ceased and mice continued on HFD. Mice in the ‘diet switch’ group continued on chow. Pregnancy rates were recorded. Maternal anthropometry and glucose tolerance were measured before and after the intervention and at late gestation. Offspring outcomes were assessed. Liraglutide or diet switch led to weight reduction, improved insulin resistance (P< 0.001), and enhanced fertility, particularly in the liraglutide group (P< 0.005). Liraglutide-treated mice had significantly higher gestational weight gain (GWG) compared to the diet switch group (P< 0.05), with similar weight and glucose tolerance in late gestation to HFD mice. In contrast, diet switch maintained similar weight and glucose tolerance in late gestation to control mice. Pre-pregnancy weight intervention with liraglutide was effective at restoring fertility. Diet modification also improved fertility and avoided catch up weight gain in pregnancy. Liraglutide may be a therapeutic strategy for weight loss to prepare for pregnancy. However, our study provides caution about the potential for excessive GWG without diet intervention in pregnancy.

Rodriguez-Dominguez, A, Connell, SD, Coni, EOC, Sasaki, M, Booth, DJ & Nagelkerken, I 2022, 'Phenotypic responses in fish behaviour narrow as climate ramps up', Climatic Change, vol. 171, no. 1-2, pp. 1-18.
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AbstractNatural selection alters the distribution of phenotypes as animals adjust their behaviour and physiology to environmental change. We have little understanding of the magnitude and direction of environmental filtering of phenotypes, and therefore how species might adapt to future climate, as trait selection under future conditions is challenging to study. Here, we test whether climate stressors drive shifts in the frequency distribution of behavioural and physiological phenotypic traits (17 fish species) at natural analogues of climate change (CO2 vents and warming hotspots) and controlled laboratory analogues (mesocosms and aquaria). We discovered that fish from natural populations (4 out of 6 species) narrowed their phenotypic distribution towards behaviourally bolder individuals as oceans acidify, representing loss of shyer phenotypes. In contrast, ocean warming drove both a loss (2/11 species) and gain (2/11 species) of bolder phenotypes in natural and laboratory conditions. The phenotypic variance within populations was reduced at CO2 vents and warming hotspots compared to control conditions, but this pattern was absent from laboratory systems. Fishes that experienced bolder behaviour generally showed increased densities in the wild. Yet, phenotypic alterations did not affect body condition, as all 17 species generally maintained their physiological homeostasis (measured across 5 different traits). Boldness is a highly heritable trait that is related to both loss (increased mortality risk) and gain (increased growth, reproduction) of fitness. Hence, climate conditions that mediate the relative occurrence of shy and bold phenotypes may reshape the strength of species interactions and consequently alter fish population and community dynamics in a future ocean.

Roffel, MP, Boudewijn, IM, van Nijnatten, JLL, Faiz, A, Vermeulen, CJ, van Oosterhout, AJ, Affleck, K, Timens, W, Bracke, KR, Maes, T, Heijink, IH, Brandsma, C-A & van den Berge, M 2022, 'Identification of asthma-associated microRNAs in bronchial biopsies', European Respiratory Journal, vol. 59, no. 3, pp. 2101294-2101294.
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BackgroundChanges in microRNA (miRNA) expression can contribute to the pathogenesis of many diseases, including asthma. We aimed to identify miRNAs that are differentially expressed between asthma patients and healthy controls, and explore their association with clinical and inflammatory parameters of asthma.MethodsDifferentially expressed miRNAs were determined by small RNA sequencing on bronchial biopsies of 79 asthma patients and 82 healthy controls using linear regression models. Differentially expressed miRNAs were associated with clinical and inflammatory asthma features. Potential miRNA–mRNA interactions were analysed using mRNA data available from the same bronchial biopsies, and enrichment of pathways was identified with Enrichr and g:Profiler.ResultsIn total, 78 differentially expressed miRNAs were identified in bronchial biopsies of asthma patients compared with controls, of which 60 remained differentially expressed after controlling for smoking and inhaled corticosteroid treatment. We identified several asthma-associated miRNAs, including miR-125b-5p and miR-223-3p, based on a significant association with multiple clinical and inflammatory asthma features and their negative correlation with genes associated with the presence of asthma. The most enriched biological pathway(s) affected by miR-125b-5p and miR-223-3p were inflammatory response and cilium assembly/organisation. Of interest, we identified that lower expression of miR-26a-5p was linked to more severe eosinophilic inflammation as measured in blood, sputum as well as bronchial biopsies.ConclusionCollectively, we identified miR-125b-5p, miR-223-3p and miR-26a-5p as potential regulators that could contribute to the pathogenesis of asthma.

Roffey, P & Scudder, N 2022, 'Privacy implications of the new “omic” technologies in law enforcement', WIREs Forensic Science, vol. 4, no. 3.
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Abstract“Omic” technologies have opened a new revolution in law enforcement and are now solving decades‐old cold cases as well as current investigations. The Golden State Killer case is probably the most notable of the cold case investigations that has been solved by one of the new “omic” technologies, namely forensic genetic genealogy. The resolution of this case epitomizes the power of the “omic” technologies to solve crime while simultaneously unearthing serious legal and ethical concerns around the individuals' privacy in the use of their genetic information. The legislation that is currently used by the state, territory, and Commonwealth jurisdictions in Australia to regulate the use of DNA for criminal investigation is now two decades old and does not address the application of “omic” technologies to criminal investigation. The Australian government is reviewing current privacy laws, and this review could include the use of “omic” technologies. In the absence of specific legislation, law enforcement must continue to develop processes to consider privacy, law, and ethics around the use of “omic” technologies for criminal investigation and the identification of human remains.This article is categorized under:Forensic Biology > Ethical and Social ImplicationsJurisprudence and Regulatory Oversight > Communication Across Science and LawForensic Biology > Forensic DNA Technologies

Rohilla, S, Awasthi, R, Mehta, M, Chellappan, DK, Gupta, G, Gulati, M, Singh, SK, Anand, K, Oliver, BG, Dua, K & Dureja, H 2022, 'Preparation and Evaluation of Gefitinib Containing Nanoliposomal Formulation for Lung Cancer Therapy', BioNanoScience, vol. 12, no. 1, pp. 241-255.
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Roper, CD, Camp, EF, Edmondson, J & Suggett, DJ 2022, 'Combined impacts of natural recruitment and active propagation for coral population recovery on the Great Barrier Reef', Marine Ecology Progress Series, vol. 700, pp. 95-109.
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Coral populations on the Great Barrier Reef (GBR) are experiencing long-term shifts in size structure, including steep declines in small colonies, driving major concerns for recovery through the supply of new recruits. Whilst coral restoration began on the GBR in 2018, the combined influence of natural recruitment and outplanting for coral population recovery has not been evaluated. Here, we assessed 2 sites (Rayban and Mojo) at Opal Reef that were subject to intensive outplant efforts over a 3 yr period (2018-2021). Coral cover did not change significantly, with a baseline of 15% in 2018 and a cover of 28 and 25% in Rayban outplant and control areas, respectively, in 2021, while Mojo exhibited a coral cover of 38% in 2018 and 52% (outplant area) and 29% (control area) in 2021. Natural recruitment in 2021 did not vary by site and was characterised by a settlement rate of 5.5 and 3.7 recruits tile-1 at Rayban and Mojo, respectively. Juvenile coral abundance and diversity were similar for control and outplant areas at each site. Over the 3 yr period, coral cover as a metric did not identify differences between control and outplant areas; however, size-frequency distributions of key coral taxa revealed a higher frequency of small to mid-sized colonies in outplant communities compared to controls. Given that no differences were observed in recruitment rates or juvenile abundances, variations in population structure appear to be driven by planting efforts rather than natural recovery. Our results demonstrate the need for combined monitoring of natural versus intervention-based rehabilitation to understand the impact of coral propagation efforts for local site recovery.

Rose, ML, Nickels, L, Copland, D, Togher, L, Godecke, E, Meinzer, M, Rai, T, Cadilhac, DA, Kim, J, Hurley, M, Foster, A, Carragher, M, Wilcox, C, Pierce, JE & Steel, G 2022, 'Results of the COMPARE trial of Constraint-induced or Multimodality Aphasia Therapy compared with usual care in chronic post-stroke aphasia', Journal of Neurology, Neurosurgery & Psychiatry, vol. 93, no. 6, pp. 573-581.
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BackgroundWhile meta-analyses confirm treatment for chronic post-stroke aphasia is effective, a lack of comparative evidence for different interventions limits prescription accuracy. We investigated whether Constraint-Induced Aphasia Therapy Plus (CIAT-plus) and/or Multimodality Aphasia Therapy (M-MAT) provided greater therapeutic benefit compared with usual community care and were differentially effective according to baseline aphasia severity.MethodsWe conducted a three-arm, multicentre, parallel group, open-label, blinded endpoint, phase III, randomised-controlled trial. We stratified eligible participants by baseline aphasia on the Western Aphasia Battery-Revised Aphasia Quotient (WAB-R-AQ). Groups of three participants were randomly assigned (1:1:1) to 30 hours of CIAT-Plus or M-MAT or to usual care (UC). Primary outcome was change in aphasia severity (WAB-R-AQ) from baseline to therapy completion analysed in the intention-to-treat population. Secondary outcomes included word retrieval, connected speech, functional communication, multimodal communication, quality of life and costs.ResultsWe analysed 201 participants (70 in CIAT-Plus, 70 in M-MAT and 61 in UC). Aphasia severity was not significantly different between groups at postintervention: 1.05 points (95% CI −0.78 to 2.88; p=0.36) UC group vs CIAT-Plus; 1.06 points (95% CI −0.78 to 2.89; p=0.36) UC group vs M-MAT; 0.004 points (95% CI −1.76 to 1.77; p=1.00) CIAT-Plus vs M-MAT. Word retrieval, functional communication and communication-related quality of life were significantly improved following CIAT-Plus and M-MAT. Word retrieval benefits were maintained at 12-week follow-up.ConclusionsCIAT-Plus and M-MAT were effective for word retrieval, functional communication,...

Ross, PM, Scanes, E, Poronnik, P, Coates, H & Locke, W 2022, 'Understanding STEM academics’ responses and resilience to educational reform of academic roles in higher education', International Journal of STEM Education, vol. 9, no. 1.
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AbstractBackgroundAcross the globe, there have been significant reforms to improve STEM education at all levels. A significant part of this has been teacher reform. While the responses and resilience of STEM teachers to educational reforms in secondary education have received significant attention, the responses and resilience of STEM teachers in higher education remains understudied. In higher education, educational reforms of academic roles have seen increasing numbers of STEM academics focussed on education. Responses of STEM academics to education reform of the academic role have some parallels with teacher resilience, but there are also potential misalignments within a culture which values and prioritises science disciplinary research. This study examined the responses of STEM academics in higher education to educational reform of the academic role using the theoretical construct of resilience and Bronfenbrenner’s socio-ecological model. This was a 2-year case study of 32 academics and senior educational leaders in higher education in STEM. Data collection included semi-structured interviews which were theme coded and inductively analysed.ResultsThe responses and resilience of STEM academics focussed on education appeared to be dependent on interactions between individual disposition in the microsystem and influences of the exosystem and the external macrosystem. Five major themes emerged about the value and quality, scholarship and expertise, progress and mobility, status and identity and community and culture of STEM academics focussed on education. The exosystem was a significant unidirectional influence on STEM academics where judgements were made concerning academic performance, awards, and promotion. Responses of senior leaders in the exosystem were influenced by the macrosystem and culture of science. Academics f...

Rourke, ML, Fowler, AM, Hughes, JM, Broadhurst, MK, DiBattista, JD, Fielder, S, Wilkes Walburn, J & Furlan, EM 2022, 'Environmental DNA (eDNA) as a tool for assessing fish biomass: A review of approaches and future considerations for resource surveys', Environmental DNA, vol. 4, no. 1, pp. 9-33.
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AbstractEnvironmental DNA (eDNA) has revolutionized our ability to identify the presence and distributions of terrestrial and aquatic organisms. Recent evidence suggests the concentration of eDNA could also provide a rapid, cost‐effective indicator of abundance and/or biomass for fisheries stock assessments. Globally, fisheries resources are under immense pressure, and their sustainable harvest requires accurate information on the sizes of fished stocks. However, in many cases the required information remains elusive because of a reliance on imprecise or costly fishery‐dependent and independent data. Here, we review the literature describing relationships between eDNA concentrations and fish abundance and/or biomass, as well as key influencing factors, as a precursor to determining the broader utility of eDNA for monitoring fish populations. We reviewed 63 studies published between 2012 and 2020 and found 90% identified positive relationships between eDNA concentrations and the abundance and/or biomass of focal species. Key influencing biotic factors included the taxon examined as well as their body size, distribution, reproduction, and migration. Key abiotic factors mostly comprised hydrological processes affecting the dispersal and persistence of eDNA, especially water flow and temperature, although eDNA collection methods were also influential. The cumulative influence of these different factors likely explains the substantial variability observed in eDNA concentrations, both within and among studies. Nevertheless, there is considerable evidence to support using eDNA as an ancillary tool for assessing fish population abundance and/or biomass across discrete spatio‐temporal scales, following preliminary investigations to determine species‐ and context‐specific factors influencing the eDNA abundance/biomass relationship. Advantages of eDNA monitoring relative to other approaches include reduced costs, increased efficien...

Roux, C, Bucht, R, Crispino, F, De Forest, P, Lennard, C, Margot, P, Miranda, MD, NicDaeid, N, Ribaux, O, Ross, A & Willis, S 2022, 'The Sydney declaration – Revisiting the essence of forensic science through its fundamental principles', Forensic Science International, vol. 332, pp. 111182-111182.
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Roy Chowdhury, P, Alhamami, T, Venter, H, Veltman, T, Carr, M, Mollinger, J, Trott, DJ & Djordjevic, SP 2022, 'Complete Genome Sequence of Pasteurella multocida Sequence Type 394, Isolated from a Case of Bovine Respiratory Disease in Australia', Microbiology Resource Announcements, vol. 11, no. 3.
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Here, we present the completely closed genome sequence of Pasteurella multocida 17BRD-035, a bovine respiratory disease (BRD) pathogen from Queensland, Australia, with genes that confer resistance to β-lactams, tilmicosin, and tetracycline. It consists of a single 2,624,884-bp chromosome and an average GC content of 40.23% and belongs to the newly described Rural Industries Research and Development Corporation (RIRDC) sequence type 394.

Royce, SG, Licciardi, PV, Beh, RC, Bourke, JE, Donovan, C, Hung, A, Khurana, I, Liang, JJ, Maxwell, S, Mazarakis, N, Pitsillou, E, Siow, YY, Snibson, KJ, Tobin, MJ, Ververis, K, Vongsvivut, J, Ziemann, M, Samuel, CS, Tang, MLK, El-Osta, A & Karagiannis, TC 2022, 'Sulforaphane prevents and reverses allergic airways disease in mice via anti-inflammatory, antioxidant, and epigenetic mechanisms', Cellular and Molecular Life Sciences, vol. 79, no. 11, p. 579.
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Sulforaphane has been investigated in human pathologies and preclinical models of airway diseases. To provide further mechanistic insights, we explored L-sulforaphane (LSF) in the ovalbumin (OVA)-induced chronic allergic airways murine model, with key hallmarks of asthma. Histological analysis indicated that LSF prevented or reversed OVA-induced epithelial thickening, collagen deposition, goblet cell metaplasia, and inflammation. Well-known antioxidant and anti-inflammatory mechanisms contribute to the beneficial effects of LSF. Fourier transform infrared microspectroscopy revealed altered composition of macromolecules, following OVA sensitization, which were restored by LSF. RNA sequencing in human peripheral blood mononuclear cells highlighted the anti-inflammatory signature of LSF. Findings indicated that LSF may alter gene expression via an epigenetic mechanism which involves regulation of protein acetylation status. LSF resulted in histone and α-tubulin hyperacetylation in vivo, and cellular and enzymatic assays indicated decreased expression and modest histone deacetylase (HDAC) inhibition activity, in comparison with the well-known pan-HDAC inhibitor suberoylanilide hydroxamic acid (SAHA). Molecular modeling confirmed interaction of LSF and LSF metabolites with the catalytic domain of metal-dependent HDAC enzymes. More generally, this study confirmed known mechanisms and identified potential epigenetic pathways accounting for the protective effects and provide support for the potential clinical utility of LSF in allergic airways disease.

Runtsch, MC, Angiari, S, Hooftman, A, Wadhwa, R, Zhang, Y, Zheng, Y, Spina, JS, Ruzek, MC, Argiriadi, MA, McGettrick, AF, Mendez, RS, Zotta, A, Peace, CG, Walsh, A, Chirillo, R, Hams, E, Fallon, PG, Jayaraman, R, Dua, K, Brown, AC, Kim, RY, Horvat, JC, Hansbro, PM, Wang, C & O’Neill, LAJ 2022, 'Itaconate and itaconate derivatives target JAK1 to suppress alternative activation of macrophages', Cell Metabolism, vol. 34, no. 3, pp. 487-501.e8.
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Ruprecht, JE, King, IP, Dafforn, KA, Mitrovic, SM, Harrison, AJ, Birrer, SC, Crane, SL & Glamore, WC 2022, 'Implications of bacterial mineralisation in aquatic ecosystem response models', Water Research, vol. 209, pp. 117888-117888.
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Ruprecht, JE, King, IP, Mitrovic, SM, Dafforn, KA, Miller, BM, Deiber, M, Westhorpe, DP, Hitchcock, JN, Harrison, AJ & Glamore, WC 2022, 'Assessing the validity and sensitivity of microbial processes within a hydrodynamic model', Water Research, vol. 218, pp. 118445-118445.
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Ryan, L, Henstridge, J & Kasza, J 2022, 'The SSA is 60!', Significance, vol. 19, no. 6, pp. 34-40.
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Abstract To celebrate the 60th anniversary of the Statistical Society of Australia, we put the spotlight on four members past and present. Interviews and profiles by Louise Ryan, John Henstridge and Jessica Kasza

Sadraeian, M, Junior, FFP, Miranda, M, Galinskas, J, Fernandes, RS, da Cruz, EF, Fu, L, Zhang, L, Diaz, RS, Cabral-Miranda, G & Guimarães, FEG 2022, 'Study of Viral Photoinactivation by UV-C Light and Photosensitizer Using a Pseudotyped Model', Pharmaceutics, vol. 14, no. 3, pp. 683-683.
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Different light-based strategies have been investigated to inactivate viruses. Herein, we developed an HIV-based pseudotyped model of SARS-CoV-2 (SC2) to study the mechanisms of virus inactivation by using two different strategies; photoinactivation (PI) by UV-C light and photodynamic inactivation (PDI) by Photodithazine photosensitizer (PDZ). We used two pseudoviral particles harboring the Luciferase-IRES-ZsGreen reporter gene with either a SC2 spike on the membrane or without a spike as a naked control pseudovirus. The mechanism of viral inactivation by UV-C and PDZ-based PDI were studied via biochemical characterizations and quantitative PCR on four levels; free-cell viral damage; viral cell entry; DNA integration; and expression of reporter genes. Both UV-C and PDZ treatments could destroy single stranded RNA (ssRNA) and the spike protein of the virus, with different ratios. However, the virus was still capable of binding and entering into the HEK 293T cells expressing angiotensin-converting enzyme 2 (ACE-2). A dose-dependent manner of UV-C irradiation mostly damages the ssRNA, while PDZ-based PDI mostly destroys the spike and viral membrane in concentration and dose-dependent manners. We observed that the cells infected by the virus and treated with either UV-C or PDZ-based PDI could not express the luciferase reporter gene, signifying the viral inactivation, despite the presence of RNA and DNA intact genes.

Sadraeian, M, Zhang, L, Aavani, F, Biazar, E & Jin, D 2022, 'Photodynamic viral inactivation assisted by photosensitizers', Materials Today Physics, vol. 28, pp. 100882-100882.
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The deadly viruses, which are spreading worldwide at an alarming rate, are a major challenge for the life sciences. More efficient and cost-effective methods with fewer side effects can provide a good alternative to traditional drug-based methods. Currently, physical phenomena such as light in the form of photodynamic action are increasingly being used to inactivate viruses. Photodynamic inactivation (PDI) uses a photosensitizer (PS), light, and oxygen to generate reactive oxygen species (ROS) to inactivate microorganisms. This article reviews the use of existing PSs, as one of the essential anti-viral agents, and introduces new materials and strategies combined with PDI. Physiochemical properties of PSs and their role in interaction with virus components are discussed. Furthermore, the effectiveness of optical sensitizers with radiation methods to inactivate viruses is highlighted.

Sadraeian, M, Zhang, L, Aavani, F, Biazar, E & Jin, D 2022, 'Viral inactivation by light', eLight, vol. 2, no. 1, p. 18.
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AbstractNowadays, viral infections are one of the greatest challenges for medical sciences and human society. While antiviral compounds and chemical inactivation remain inadequate, physical approaches based on irradiation provide new potentials for prevention and treatment of viral infections, without the risk of drug resistance and other unwanted side effects. Light across the electromagnetic spectrum can inactivate the virions using ionizing and non-ionizing radiations. This review highlights the anti-viral utility of radiant methods from the aspects of ionizing radiation, including high energy ultraviolet, gamma ray, X-ray, and neutron, and non-ionizing photo-inactivation, including lasers and blue light.

Saerens, G, Duong, NMH, Solntsev, AS, Karvounis, A, Dursap, T, Regreny, P, Morandi, A, Chapman, RJ, Maeder, A, Danescu, A, Penuelas, J, Chauvin, N & Grange, R 2022, 'Spontaneous Parametric Down-Conversion from GaAs Nanowires at Telecom Wavelength', EPJ Web of Conferences, vol. 266, pp. 08010-08010.
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We report on the generation of photon pairs at 1550 nm from free-standing epitaxially grown self-assisted micrometre long GaAs nanowires. The efficiency of the spontaneous parametric down-conversion process has a rate of 320 GHz/Wm normalized to the transmission of the setup, the pump intensity, and the volume of the nanostructure. GaAs is a high index dielectric that can support electromagnetic Mie modes, therefore we model how shorter nanowires could improve the second-harmonic signal and we found that sub-micro long nanowires (600 nm length and 250 nm diameter) can support quality factors up to 15 at the pump wavelength (780 nm). We anticipate that the near field enhancement compared to micrometre long nanowires will boost the second-harmonic generation and, correspondingly, the biphoton rate efficiency.

Samadi, A, Sartipi, Z, Ahmad Nasrollahi, S, Sheikholeslami, B, Nassiri Kashani, M, Rouini, MR, Dinarvand, R & Firooz, A 2022, 'Efficacy assessments of tretinoin-loaded nano lipid carriers in acne vulgaris: a double blind, split-face randomized clinical study', Archives of Dermatological Research, vol. 314, no. 6, pp. 553-561.
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Santangelo, JS, Ness, RW, Cohan, B, Fitzpatrick, CR, Innes, SG, Koch, S, Miles, LS, Munim, S, Peres-Neto, PR, Prashad, C, Tong, AT, Aguirre, WE, Akinwole, PO, Alberti, M, Álvarez, J, Anderson, JT, Anderson, JJ, Ando, Y, Andrew, NR, Angeoletto, F, Anstett, DN, Anstett, J, Aoki-Gonçalves, F, Arietta, AZA, Arroyo, MTK, Austen, EJ, Baena-Díaz, F, Barker, CA, Baylis, HA, Beliz, JM, Benitez-Mora, A, Bickford, D, Biedebach, G, Blackburn, GS, Boehm, MMA, Bonser, SP, Bonte, D, Bragger, JR, Branquinho, C, Brans, KI, Bresciano, JC, Brom, PD, Bucharova, A, Burt, B, Cahill, JF, Campbell, KD, Carlen, EJ, Carmona, D, Castellanos, MC, Centenaro, G, Chalen, I, Chaves, JA, Chávez-Pesqueira, M, Chen, X-Y, Chilton, AM, Chomiak, KM, Cisneros-Heredia, DF, Cisse, IK, Classen, AT, Comerford, MS, Fradinger, CC, Corney, H, Crawford, AJ, Crawford, KM, Dahirel, M, David, S, De Haan, R, Deacon, NJ, Dean, C, del-Val, E, Deligiannis, EK, Denney, D, Dettlaff, MA, DiLeo, MF, Ding, Y-Y, Domínguez-López, ME, Dominoni, DM, Draud, SL, Dyson, K, Ellers, J, Espinosa, CI, Essi, L, Falahati-Anbaran, M, Falcão, JCF, Fargo, HT, Fellowes, MDE, Fitzpatrick, RM, Flaherty, LE, Flood, PJ, Flores, MF, Fornoni, J, Foster, AG, Frost, CJ, Fuentes, TL, Fulkerson, JR, Gagnon, E, Garbsch, F, Garroway, CJ, Gerstein, AC, Giasson, MM, Girdler, EB, Gkelis, S, Godsoe, W, Golemiec, AM, Golemiec, M, González-Lagos, C, Gorton, AJ, Gotanda, KM, Granath, G, Greiner, S, Griffiths, JS, Grilo, F, Gundel, PE, Hamilton, B, Hardin, JM, He, T, Heard, SB, Henriques, AF, Hernández-Poveda, M, Hetherington-Rauth, MC, Hill, SJ, Hochuli, DF, Hodgins, KA, Hood, GR, Hopkins, GR, Hovanes, KA, Howard, AR, Hubbard, SC, Ibarra-Cerdeña, CN, Iñiguez-Armijos, C, Jara-Arancio, P, Jarrett, BJM, Jeannot, M, Jiménez-Lobato, V, Johnson, M, Johnson, O, Johnson, PP, Johnson, R, Josephson, MP, Jung, MC, Just, MG, Kahilainen, A, Kailing, OS, Kariñho-Betancourt, E, Karousou, R, Kirn, LA, Kirschbaum, A, Laine, A-L, LaMontagne, JM, Lampei, C, Lara, C, Larson, EL, Lázaro-Lobo, A, Le, JH, Leandro, DS, Lee, C, Lei, Y, León, CA, Lequerica Tamara, ME, Levesque, DC, Liao, W-J, Ljubotina, M, Locke, H, Lockett, MT, Longo, TC, Lundholm, JT, MacGillavry, T, Mackin, CR, Mahmoud, AR, Manju, IA, Mariën, J, Martínez, DN, Martínez-Bartolomé, M, Meineke, EK, Mendoza-Arroyo, W, Merritt, TJS, Merritt, LEL, Migiani, G & et al. 2022, 'Global urban environmental change drives adaptation in white clover', Science, vol. 375, no. 6586, pp. 1275-1281.
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Urbanization transforms environments in ways that alter biological evolution. We examined whether urban environmental change drives parallel evolution by sampling 110,019 white clover plants from 6169 populations in 160 cities globally. Plants were assayed for a Mendelian antiherbivore defense that also affects tolerance to abiotic stressors. Urban-rural gradients were associated with the evolution of clines in defense in 47% of cities throughout the world. Variation in the strength of clines was explained by environmental changes in drought stress and vegetation cover that varied among cities. Sequencing 2074 genomes from 26 cities revealed that the evolution of urban-rural clines was best explained by adaptive evolution, but the degree of parallel adaptation varied among cities. Our results demonstrate that urbanization leads to adaptation at a global scale.

Saura-Múzquiz, M, Marlton, FP, Mullens, BG, Manjón-Sanz, AM, Neuefeind, JC, Everett, M, Brand, HEA, Mondal, S, Vaitheeswaran, G & Kennedy, BJ 2022, 'Understanding the Re-entrant Phase Transition in a Non-magnetic Scheelite', Journal of the American Chemical Society, vol. 144, no. 34, pp. 15612-15621.
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Scammell, HD, Ingham, J, Geier, M & Li, T 2022, 'Intrinsic first- and higher-order topological superconductivity in a doped topological insulator', Physical Review B, vol. 105, no. 19, p. 195149.
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We explore higher-order topological superconductivity in an artificial Dirac material with intrinsic spin-orbit coupling, which is a doped Z2 topological insulator in the normal state. A mechanism for superconductivity due to repulsive interactions, pseudospin pairing, has recently been shown to naturally result in higher-order topology in Dirac systems past a minimum chemical potential [T. Li et al., 2D Mater. 9, 015031 (2022)2053-158310.1088/2053-1583/ac4060]. Here we apply this theory through microscopic modeling of a superlattice potential imposed on an inversion-symmetric hole-doped semiconductor heterostructure, known as hole-based semiconductor artificial graphene, and extend previous work to include the effects of spin-orbit coupling. We find that spin-orbit coupling enhances interaction effects, providing an experimental handle to increase the efficiency of the superconducting mechanism. We show that the phase diagram of these systems, as a function of chemical potential and interaction strength, contains three superconducting states: a first-order topological p+ip state, a second-order topological spatially modulated p+iτp state, and a second-order topological extended s-wave state sτ. We calculate the symmetry-based indicators for the p+iτp and sτ states, which prove these states possess second-order topology. Exact diagonalization results are presented which illustrate the interplay between the boundary physics and spin-orbit interaction. We argue that this class of systems offers an experimental platform to engineer and explore first- and higher-order topological superconducting states.

Scammell, HD, Li, JIA & Scheurer, MS 2022, 'Theory of zero-field superconducting diode effect in twisted trilayer graphene', 2D Materials, vol. 9, no. 2, pp. 025027-025027.
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Abstract In a recent experiment (Lin et al 2021 arXiv:2112.07841 [cond-mat.str-el]), the superconducting phase hosted by a heterostructure of mirror-symmetric twisted trilayer graphene and WSe2 was shown to exhibit significantly different critical currents in opposite directions in the absence of external magnetic fields. We here develop a microscopic theory and analyze necessary conditions for this zero-field superconducting diode effect. Taking into account the spin–orbit coupling induced in trilayer graphene via the proximity effect, we classify the pairing instabilities and normal-state orders and derive which combinations are consistent with the observed diode effect, in particular, its field trainability. We perform explicit calculations of the diode effect in several different models, including the full continuum model for the system, and illuminate the relation between the diode effect and finite-momentum pairing. Our theory also provides a natural explanation of the observed sign change of the current asymmetry with doping, which can be related to an approximate chiral symmetry of the system, and of the enhanced transverse resistance above the superconducting transition. Our findings not only elucidate the rich physics of trilayer graphene on WSe2, but also establish a means to distinguish between various candidate interaction-induced orders in spin-orbit-coupled graphene moiré systems, and could therefore serve as a guide for future experiments as well.

Schaeper, O, Yang, Z, Kianinia, M, Fröch, JE, Komar, A, Mu, Z, Gao, W, Neshev, DN & Aharonovich, I 2022, 'Monolithic Silicon Carbide Metalenses', ACS Photonics, vol. 9, no. 4, pp. 1409-1414.
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Schell, KR, Fernandes, KE, Shanahan, E, Wilson, I, Blair, SE, Carter, DA & Cokcetin, NN 2022, 'The Potential of Honey as a Prebiotic Food to Re-engineer the Gut Microbiome Toward a Healthy State', Frontiers in Nutrition, vol. 9, pp. 1-10.
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Honey has a long history of use for the treatment of digestive ailments. Certain honey types have well-established bioactive properties including antibacterial and anti-inflammatory activities. In addition, honey contains non-digestible carbohydrates in the form of oligosaccharides, and there is increasing evidence from in vitro, animal, and pilot human studies that some kinds of honey have prebiotic activity. Prebiotics are foods or compounds, such as non-digestible carbohydrates, that are used to promote specific, favorable changes in the composition and function of the gut microbiota. The gut microbiota plays a critical role in human health and well-being, with disturbances to the balance of these organisms linked to gut inflammation and the development and progression of numerous conditions, such as colon cancer, irritable bowel syndrome, obesity, and mental health issues. Consequently, there is increasing interest in manipulating the gut microbiota to a more favorable balance as a way of improving health by dietary means. Current research suggests that certain kinds of honey can reduce the presence of infection-causing bacteria in the gut including Salmonella, Escherichia coli, and Clostridiodes difficile, while simultaneously stimulating the growth of potentially beneficial species, such as Lactobacillus and Bifidobacteria. In this paper, we review the current and growing evidence that shows the prebiotic potential of honey to promote healthy gut function, regulate the microbial communities in the gut, and reduce infection and inflammation. We outline gaps in knowledge and explore the potential of honey as a viable option to promote or re-engineer a healthy gut microbiome.

Scott, JA, Bishop, J & Toth, M 2022, 'Suppression of Surface Roughening during Ion Bombardment of Semiconductors', Chemistry of Materials, vol. 34, no. 19, pp. 8968-8974.
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Ion beams are used routinely for processing of semiconductors, particularly sputtering, ion implantation, and direct-write fabrication of nanostructures. However, the utility of ion beam techniques is limited by crystal damage and surface roughening. Damage can be reduced or eliminated by performing irradiation at elevated temperatures. However, under these conditions, surface roughening is highly problematic due to thermal mobility of adatoms and surface vacancies. Here, we solve this problem using hydrogen gas, which we use to stabilize surface mass flow and suppress roughening during ion bombardment of elemental and compound semiconductors. We achieve smooth surfaces during ion beam processing and show that the method can be enhanced by radicalizing H2gas using a remote plasma source. Our approach is broadly applicable and expands the utility of ion beam techniques for the processing and fabrication of functional materials and nanostructures.

Senanayake, S, Pradhan, B, Huete, A & Brennan, J 2022, 'Spatial modeling of soil erosion hazards and crop diversity change with rainfall variation in the Central Highlands of Sri Lanka', Science of The Total Environment, vol. 806, no. Pt 2, pp. 150405-150405.
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The spatial variation of soil erosion is essential for farming system management and resilience development, specifically in the high climate hazard vulnerable tropical countries like Sri Lanka. This study aimed to investigate climate and human-induced soil erosion through spatial modeling. Remote sensing was used for spatial modeling to detect soil erosion, crop diversity, and rainfall variation. The study employed a time-series analysis of several variables such as rainfall, land-use land-cover (LULC) and crop diversity to detect the spatial variability of soil erosion in farming systems. Rain-use efficiency (RUE) and residual trend analysis (RESTREND) combined with a regression approach were applied to partition the soil erosion due to human and climate-induced land degradation. Results showed that soil erosion has increased from 9.08 Mg/ha/yr to 11.08 Mg/ha/yr from 2000 to 2019 in the Central Highlands of Sri Lanka. The average annual rainfall has increased in the western part of the Central Highlands, and soil erosion hazards such as landslides incidence also increased during this period. However, crop diversity has been decreasing in farming systems, namely wet zone low country (WL1a) and wet zone mid-country (WM1a), in the western part of the Central Highlands. The RUE and RESTREND analyses reveal climate-induced soil erosion is responsible for land degradation in these farming systems and is a threat to sustainable food production in the farming systems of the Central Highlands.

Seymour, JR 2022, 'Forecasting ocean microbiome shifts', Nature Microbiology, vol. 7, no. 6, pp. 747-748.
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Shabbir, B, Liu, J, Krishnamurthi, V, Ayyubi, RAW, Tran, K, Tawfik, SA, Hossain, MM, Khan, H, Wu, Y, Shivananju, BN, Sagar, RUR, Mahmood, A, Younis, A, Uddin, MH, Bukhari, SA, Walia, S, Li, Y, Spencer, MJS, Mahmood, N & Jasieniak, JJ 2022, 'Soft X‐ray Detectors Based on SnS Nanosheets for the Water Window Region', Advanced Functional Materials, vol. 32, no. 3, pp. 2105038-2105038.
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AbstractThe structural characteristics of biological specimens, such as wet proteins and fixed living cells, can be conveniently probed in their host aqueous media using soft X‐rays in the water window region (200–600 eV). Conventional X‐ray detectors in this area exhibit low spatial resolution, have limited sensitivity, and require complex fabrication procedures. Here, many of these limitations are overcome by introducing a direct soft X‐ray detector based on ultrathin tin mono‐sulfide (SnS) nanosheets. The distinguishing characteristic of SnS is its high photon absorption efficiency in the soft X‐ray region. This factor enables the fabricated soft X‐ray detectors to exhibit excellent sensitivity values on the order of at peak energies of ≈600 eV. The peak signal is found to be sensitive to the number of stacked SnS layers, with thicker SnS nanosheet assemblies yielding a peak response at higher energies and with peak sensitives of over 2.5 at 1 V. Detailed current–voltage and temporal characteristics of these detectors are also presented. These results showcase the excellent performance of SnS nanosheet‐based soft X‐ray detectors compared to existing direct soft X‐ray detectors, including that of the emerging organic–inorganic perovskite class of materials.

Shad, KF, Soubra, W & Cordato, DJ 2022, 'The Auditory Afferent Pathway as a Clinical Marker of Alzheimer’s Disease', Journal of Alzheimer's Disease, vol. 85, no. 1, pp. 47-53.
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Brain stem neural tracts and nuclei may be disturbed prior to observable neuronal atrophy in AD. In this perspective, we discuss the notion of functional deficits presenting prior to structural abnormalities in Alzheimer’s disease (AD). Imaging of inferior colliculi using magnetic resonance spectroscopy (MRS) shows significant decrease in the neuronal markers, N acetyl aspartate/creatine ratio and increase in the glial marker myo-Inositol, in subjects with Mini-Mental State Examination scores greater than 24 and with no signs of atrophy in their MRI of the medial temporal lobe. Abnormalities in components of the auditory event-related potentials (ERPs) are described in cognitive impairment including AD. We observed a significant decrease in amplitude and increase in latency during the first 10 ms of auditory evoked potentials measured on electroencephalography (EEG) indicating slow auditory response of the brainstem. EEG spectral power recorded at the cortex is also associated with neural activity at the level of the inferior colliculi. We postulate that a functional examination of auditory afferent pathways, using non-invasive techniques, such as MRS, brain stem auditory evoked potentials (BAEPs) and ERPs may improve diagnostic accuracy of AD. Functional changes precede structural changes and it is important to further understand the relationship between biochemical and electrophysiological measures such as MRS, BAEPs and EEG.

Shahrokhi, S, Dubajic, M, Dai, Z, Bhattacharyya, S, Mole, RA, Rule, KC, Bhadbhade, M, Tian, R, Mussakhanuly, N, Guan, X, Yin, Y, Nielsen, MP, Hu, L, Lin, C, Chang, SLY, Wang, D, Kabakova, IV, Conibeer, G, Bremner, S, Li, X, Cazorla, C & Wu, T 2022, 'Anomalous Structural Evolution and Glassy Lattice in Mixed‐Halide Hybrid Perovskites', Small, vol. 18, no. 21, pp. e2200847-2200847.
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AbstractHybrid halide perovskites have emerged as highly promising photovoltaic materials because of their exceptional optoelectronic properties, which are often optimized via compositional engineering like mixing halides. It is well established that hybrid perovskites undergo a series of structural phase transitions as temperature varies. In this work, the authors find that phase transitions are substantially suppressed in mixed‐halide hybrid perovskite single crystals of MAPbI3‐xBrx (MA = CH3NH3+ and x = 1 or 2) using a complementary suite of diffraction and spectroscopic techniques. Furthermore, as a general behavior, multiple crystallographic phases coexist in mixed‐halide perovskites over a wide temperature range, and a slightly distorted monoclinic phase, hitherto unreported for hybrid perovskites, is dominant at temperatures above 100 K. The anomalous structural evolution is correlated with the glassy behavior of organic cations and optical phonons in mixed‐halide perovskites. This work demonstrates the complex interplay between composition engineering and lattice dynamics in hybrid perovskites, shedding new light on their unique properties.

Sharif, HMA, Ali, M, Mahmood, A, Asif, MB, Din, MAU, Sillanpää, M, Mahmood, A & Yang, B 2022, 'Separation of Fe from wastewater and its use for NOx reduction; a sustainable approach for environmental remediation', Chemosphere, vol. 303, no. Pt 2, pp. 135103-135103.
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The nitrogen and sulphur oxide (NOx and SO2) emissions are causing a serious threat to the existence of life on earth, requiring their effective removal for a sustainable future. Among various approaches, catalytic or electrochemical reduction of air pollutants (NOx) has gained much attention due to its high efficiency and the possibility of converting these gases into valuable products. However, the required catalysts are generally synthesized from lab-grade chemicals, which may not be a sustainable approach. Herein, a sustainable approach is presented to synthesize an efficient iron-based catalyst directly from industrial/lake wastewater (WW) for NOx-reduction. According to the theoretical calculations and experimental results, Fe-ions could be readily recovered from wastewater because it has the best adsorption efficiency among all other co-existing metals (Ni2+, Cd2+, Co2+, Cu2+, and Cr6+). The subsequent experimental investigations confirmed the preferential Fe adsorption from different WW streams to develop Fe3O4@EDTA-Fe composite, whereby Fe3O4 could be used due to its high recycling ability, and ethylenediaminetetraacetic acid (EDTA) acted as a chelating agent to adsorb Fe-metal from effluents. The Fe3O4@EDTA-Fe exhibited high efficiency (≥87%) for NOx reduction even in the presence of high-degree oxygen contents (10-12%). Moreover, Fe3O4-EDTA-Fe showed excellent long-term stability for 24 h and maintained more than 80% NOx reduction. The fabricated catalyst has a great potential for executing a dual role simultaneously for Fe-recovery and NOx removal, promoting the circular economy concept and providing a potentially sustainable remediation approach for large-scale applications.

Sharma, B, Kumar, S, Preeti, Johansen, MD, Kremer, L & Kumar, V 2022, '1H‐1,2,3‐triazole embedded Isatin‐Benzaldehyde‐bis(heteronuclearhydrazones): design, synthesis, antimycobacterial, and cytotoxic evaluation', Chemical Biology & Drug Design, vol. 99, no. 2, pp. 301-307.
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AbstractRapid growth of global drug‐resistant tuberculosis and urgent requirement for short treatment regimens is stimulating the need for discovery of new TB drugs. In this work, we report the design, synthesis and in vitro antimycobacterial evaluation of a library of isatin‐derived bis(heteronuclear hydrazones). Evaluation results revealed that the inclusion of isoniazid core into 1H‐1,2,3‐triazole tethered isatin‐benzaldehydes improved the antimycobacterial activity on tuberculosis mc26230 strain and significantly reduced the cytotoxicity against Vero cells. However, the introduction of semicarbazones/thiosemicarbazones or pyrazine‐2‐carbohydrazide produced the opposite effects. The compounds with isoniazid and polar‐donating groups at the C‐5 position of isatin emerged as the most promising conjugates with MIC99 = 0.36 µg/ml. The most active compounds were non‐cytotoxic to Vero cells (IC50>100 µg/ml) with selectivity indices >277.

Sharma, N, Kulkarni, GT, Bhatt, AN, Satija, S, Singh, L, Sharma, A, Dua, K, Karwasra, R, Khan, AA, Ahmad, N & Raza, K 2022, 'Therapeutic Options for the SARS-CoV-2 Virus: Is There a Key in Herbal Medicine?', Natural Product Communications, vol. 17, no. 9, pp. 1934578X2211263-1934578X2211263.
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SARS-CoV-2 has been responsible for over 500 million cumulative cases all over the world since December 2019 and has marked the third introduction of a highly pathogenic virus after SARS-CoV and MERS-CoV. This virus is in a winning situation because scientists are still racing to explore effective therapeutics, vaccines, and event treatment regimens. In view of progress in current disease management, until now none of the preventive/treatment measures can be considered entirely effective to treat SARS-CoV-2 infection. Therefore, it is required to look up substitute ways for the management of this disease. In this context, herbal medicines could be a good choice. This article emphasizes the antiviral potential of some herbal constituents which further can be a drug of choice in SARS-CoV-2 treatment. This article may be a ready reference for discovering natural lead compounds and targets in SARS-CoV-2 associated works.

Sharma, P, Dhanjal, DS, Chopra, C, Tambuwala, MM, Sohal, SS, van der Spek, PJ, Sharma, HS & Satija, S 2022, 'Targeting eosinophils in chronic respiratory diseases using nanotechnology-based drug delivery', Chemico-Biological Interactions, vol. 365, pp. 110050-110050.
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Shi, H, Rath, EM, Lin, RCY, Sarun, KH, Clarke, CJ, McCaughan, BC, Ke, H, Linton, A, Lee, K, Klebe, S, Maitz, J, Song, K, Wang, Y, Kao, S & Cheng, YY 2022, '3-Dimensional mesothelioma spheroids provide closer to natural pathophysiological tumor microenvironment for drug response studies', Frontiers in Oncology, vol. 12, pp. 1-12.
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Traditional studies using cancer cell lines are often performed on a two-dimensional (2D) cell culture model with a low success rate of translating to Phase I or Phase II clinical studies. In comparison, with the advent of developments three-dimensional (3D) cell culture has been championed as the latest cellular model system that better mimics in vivo conditions and pathological conditions such as cancer. In comparison to biospecimens taken from in vivo tissue, the details of gene expression of 3D culture models are largely undefined, especially in mesothelioma – an aggressive cancer with very limited effective treatment options. In this study, we examined the veracity of the 3D mesothelioma cell culture model to study cell-to-cell interaction, gene expression and drug response from 3D cell culture, and compared them to 2D cell and tumor samples. We confirmed via SEM analysis that 3D cells grown using the spheroid methods expressed highly interconnected cell-to-cell junctions. The 3D spheroids were revealed to be an improved mini-tumor model as indicated by the TEM visualization of cell junctions and microvilli, features not seen in the 2D models. Growing 3D cell models using decellularized lung scaffold provided a platform for cell growth and infiltration for all cell types including primary cell lines. The most time-effective method was growing cells in spheroids using low-adhesive U-bottom plates. However, not every cell type grew into a 3D model using the the other methods of hanging drop or poly-HEMA. Cells grown in 3D showed more resistance to chemotherapeutic drugs, exhibiting reduced apoptosis. 3D cells stained with H&amp;E showed cell-to-cell interactions and internal architecture that better represent that of in vivo patient tumors when compared to 2D cells. IHC staining revealed increased protein expression in 3D spheroids ...

Shi, H, Tsai, KH, Ma, D, Wang, X, Desai, R, Parungao, RJ, Hunt, NJ, Cheng, YY, Zhang, H, Xu, Y, Simanainen, U, Tan, Q, Cooper, MS, Handelsman, DJ, Maitz, PK & Wang, Y 2022, 'Controlled dual release of dihydrotestosterone and flutamide from polycaprolactone electrospun scaffolds accelerate burn wound healing', The FASEB Journal, vol. 36, no. 5, p. e22310.
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Wound healing is a complex process involving multiple independent and overlapping sequential physiological mechanisms. In addition to cutaneous injury, a severe burn stimulates physiological derangements that induce a systemic hypermetabolic response resulting in impaired wound healing. Topical application of the anti-androgen drug, flutamide accelerates cutaneous wound healing, whereas paradoxically systemic dihydrotestosterone (DHT) improves burn wound healing. We developed and characterized a PCL scaffold that is capable of controlled release of androgen (DHT) and anti-androgen (F) individually or together. This study aims to investigate whether local modification of androgen actions has an impact on burn injury wound healing. In a full-thickness burn wound healing, mouse model, DHT/F-scaffold showed a significantly faster wound healing compared with F-scaffold or DHT-scaffold. Histology analysis confirmed that DHT/F-scaffold exhibited higher re-epithelization, cell proliferation, angiogenesis, and collagen deposition. Dual release of DHT and F from PCL scaffolds promoted cell proliferation of human keratinocytes and alters the keratinocyte cell cycle. Lastly, no adverse effects on androgen-dependent organs, spleen and liver were observed. In conclusion, we demonstrated DHT plus F load PCL scaffolds accelerated burn wound healing when loading alone did not. These findings point to a complex role of androgens in burn wound healing and open novel therapeutic avenues for treating severe burn patients.

Shi, Y, Wu, Y, Chin, LK, Li, Z, Liu, J, Chen, MK, Wang, S, Zhang, Y, Liu, PY, Zhou, X, Cai, H, Jin, W, Yu, Y, Yu, R, Huang, W, Yap, PH, Xiao, L, Ser, W, Nguyen, TTB, Lin, Y, Wu, PC, Liao, J, Wang, F, Chan, CT, Kivshar, Y, Tsai, DP & Liu, AQ 2022, 'Multifunctional Virus Manipulation with Large‐Scale Arrays of All‐Dielectric Resonant Nanocavities', Laser & Photonics Reviews, vol. 16, no. 5, pp. 2100197-2100197.
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AbstractSpatial manipulation of a precise number of viruses for host cell infection is essential for the extensive studies of virus pathogenesis and evolution. Albeit optical tweezers have been advanced to the atomic level via optical cooling, it is still challenging to efficiently trap and manipulate arbitrary number of viruses in an aqueous environment, being restricted by insufficient strength of optical forces and a lack of multifunctional spatial manipulation techniques. Here, by employing the virus hopping and flexibility of moving the laser position, multifunctional virus manipulation with a large trapping area is demonstrated, enabling single or massive (a large quantity of) virus transporting, positioning, patterning, sorting, and concentrating. The enhanced optical forces are produced by the confinement of light in engineered arrays of nanocavities by fine tuning of the interference resonances, and this approach allows trapping and moving viruses down to 40 nm in size. The work paves the way to efficient and precise manipulation of either single or massive groups of viruses, opening a wide range of novel opportunities for virus pathogenesis and inhibitor development at the single‐virus level.

Shi, Y-L, Huang, D, Ling, FC-C, Tian, Q-S, Liao, L-S, Phillips, MR & Ton-That, C 2022, 'Correlation between small polaron tunneling relaxation and donor ionization in Ga2O3', Applied Physics Letters, vol. 120, no. 17, pp. 172105-172105.
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Pulsed laser deposition is employed to fabricate as-grown amorphous and post-growth annealed crystalline β-Ga2O3 films. The films annealed at temperatures above 600 °C are found to exhibit a pure monolithic phase with a bandgap of 4.7 eV. The thermally activated donor ionization and dielectric relaxation of these films are systematically investigated by temperature-dependent DC and AC conductivity measurements, and complex electric modulus analysis. A donor level at ∼180 meV below the conduction band edge and a small polaron tunneling (SPT) relaxation with an activation energy of ∼180 meV are observed in the as-grown amorphous Ga2O3 film but not in the monolithic β-Ga2O3 film. The SPT occurs between donor sites with its thermal relaxation of polarization being associated with the thermal ionization of the donor state. Thermal annealing of the amorphous films removes the 180 meV donors as well the corresponding SPT relaxation.

Shilling, PJ, Khananisho, D, Cumming, AJ, Söderström, B & Daley, DO 2022, 'Signal amplification of araC pBAD using a standardized translation initiation region', Synthetic Biology, vol. 7, no. 1, p. ysac009.
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Abstract araC pBAD is a genetic fragment that regulates the expression of the araBAD operon in bacteria, which is required for the metabolism of L-arabinose. It is widely used in bioengineering applications because it can drive regulatable and titratable expression of genes and genetic pathways in microbial cell factories. A notable limitation of araC pBAD is that it generates a low signal when induced with high concentrations of L-arabinose (the maximum ON state). Herein we have amplified the maximum ON state of araC pBAD by coupling it to a synthetically evolved translation initiation region (TIREVOL). The coupling maintains regulatable and titratable expression from araC pBAD and yet increases the maximal ON state by &gt;5-fold. The general principle demonstrated in the study can be applied to amplify the signal from similar genetic modules. Graphical Abstract

Shirazi, RS, Vyssotski, M, Lagutin, K, Thompson, D, MacDonald, C, Luscombe, V, Glass, M, Parker, K, Gowing, EK, Williams, DBG & Clarkson, AN 2022, 'Neuroprotective activity of new Δ3‐N‐acylethanolamines in a focal ischemia stroke model', Lipids, vol. 57, no. 1, pp. 17-31.
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AbstractN‐acylethanolamines (NAE, also called ethanolamides) are significant lipid signaling molecules with anti‐inflammatory, pain‐relieving, cell‐protective, and anticancer properties. Here, we present the use of a hitherto unreported group of Δ3‐NAE and also some Δ4‐ and Δ5‐NAE, in in vitro and in vivo assays to gain a better understanding of their structure–bioactivity relationships. We have developed an efficient synthetic method to rapidly produce novel unlabeled and 13C‐labeled Δ3‐NAE (NAE‐18:5n‐3, NAE‐18:4n‐6) and Δ4‐NAE (NAE‐22:5n‐6). The new NAE with shorter carbon backbone structures confers greater neuroprotection than their longer carbon backbone counterparts, including anandamide (Δ5‐NAE‐20:4n‐6) in a focal ischemia mouse model of stroke. This study highlights structure‐dependent protective effects of new NAE following focal ischemia, in which some of the new NAE, administered intranasally, lead to significantly reduced infarct volume and improved recovery of limb use. The relative affinity of the new NAE toward cannabinoid receptors was assessed against anandamide, NAE‐22:6n‐3 and NAE‐20:5n‐3, which are known cannabinoid receptor ligands with high‐binding constants. Among the newly synthesized NAE, Δ4‐NAE‐22:5n‐6 shows the greatest relative affinity to cannabinoid receptors hCB1 and hCB2, and inhibition of cyclic adenosine monophosphate activity through hCB2 compared to anandamide.

Shrestha, J, Razavi Bazaz, S, Ding, L, Vasilescu, S, Idrees, S, Söderström, B, Hansbro, PM, Ghadiri, M & Ebrahimi Warkiani, M 2022, 'Rapid separation of bacteria from primary nasal samples using inertial microfluidics', Lab on a Chip, vol. 23, no. 1, pp. 146-156.
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Development of an inertial microfluidic device based on a zigzag configuration for rapid separation of bacteria from primary nasal samples.

Shukla, MK, Dubey, A, Pandey, S, Singh, SK, Gupta, G, Prasher, P, Chellappan, DK, Oliver, BG, Kumar, D & Dua, K 2022, 'Managing Apoptosis in Lung Diseases using Nano-assisted Drug Delivery System', Current Pharmaceutical Design, vol. 28, no. 39, pp. 3202-3211.
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Abstract:Several factors exist that limit the efficacy of lung cancer treatment. These may be tumor-specificdelivery of therapeutics, airway geometry, humidity, clearance mechanisms, presence of lung diseases, andtherapy against tumor cell resistance. Advancements in drug delivery using nanotechnology based multifunctionalnanocarriers, have emerged as a viable method for treating lung cancer with more efficacy and fewer adverseeffects. This review does a thorough and critical examination of effective nano-enabled approaches forlung cancer treatment, such as nano-assisted drug delivery systems. In addition, to therapeutic effectiveness,researchers have been working to determine several strategies to produce nanotherapeutics by adjusting thesize, drug loading, transport, and retention. Personalized lung tumor therapies using sophisticated nano modalitieshave the potential to provide great therapeutic advantages based on individual unique genetic markers anddisease profiles. Overall, this review provides comprehensive information on newer nanotechnological prospectsfor improving the management of apoptosis in lung cancer.

Shukla, SD, Shastri, MD, Vanka, SK, Jha, NK, Dureja, H, Gupta, G, Chellappan, DK, Oliver, BG, Dua, K & Walters, EH 2022, 'Correction to: Targeting intercellular adhesion molecule-1 (ICAM-1) to reduce rhinovirus-induced acute exacerbations in chronic respiratory diseases', Inflammopharmacology, vol. 30, no. 4, pp. 1477-1477.
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Shukla, SD, Shastri, MD, Vanka, SK, Jha, NK, Dureja, H, Gupta, G, Chellappan, DK, Oliver, BG, Dua, K & Walters, EH 2022, 'Targeting intercellular adhesion molecule-1 (ICAM-1) to reduce rhinovirus-induced acute exacerbations in chronic respiratory diseases', Inflammopharmacology, vol. 30, no. 3, pp. 725-735.
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AbstractThe chronic respiratory non-communicable diseases, asthma and chronic obstructive pulmonary disease (COPD) are among the leading causes of global mortality and morbidity. Individuals suffering from these diseases are particularly susceptible to respiratory infections caused by bacterial and/or viral pathogens, which frequently result in exacerbation of symptoms, lung function decline, frequent hospital emergency visits and increased socioeconomic burden. Human rhinoviruses (HRV) remain the major viral pathogen group implicated in exacerbations of both asthma and COPD. The rhinoviral entry into the host lung epithelium is facilitated primarily by the adhesion site (“receptor”) intercellular adhesion molecule-1 (ICAM-1), coincidentally expressed on the respiratory epithelium in these conditions. Multiple observations of increased airway ICAM-1 protein in asthmatics, smokers and smoking-related COPD have been recorded in the literature. However, the lack of robust therapies for COPD in particular has triggered a renewed interest in assessing receptor antagonism-based anti-viral strategies for treatment of intercurrent viral infections in those with pre-existing chronic lung diseases. Given the crucial role ICAM-1 plays in facilitating HRV adhesion and, thus, transmissibility to the host respiratory system, as well as the up-regulation of ICAM-1 by smoking, we summarize the role of HRV in smoking-induced COPD and especially highlight the role of ICAM-1 in epithelial viral adhesion and chronic lung disease progression. Further, the review also sheds light specifically on evolving precision therapeutic strategies in blocking ICAM-1 for preventing viral adhesion and exacerbations of COPD.

Shute, RH, Didaskalou, E & Dedousis-Wallace, A 2022, 'Does emotional intelligence play a role in teachers' likelihood of intervening in students' indirect bullying? A preliminary study', Teaching and Teacher Education, vol. 119, pp. 103851-103851.
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Sillapachaiyaporn, C, Chuchawankul, S, Nilkhet, S, Moungkote, N, Sarachana, T, Ung, AT, Baek, SJ & Tencomnao, T 2022, 'Ergosterol isolated from cloud ear mushroom (Auricularia polytricha) attenuates bisphenol A-induced BV2 microglial cell inflammation', Food Research International, vol. 157, pp. 111433-111433.
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Sim, JXF, Doolette, CL, Vasileiadis, S, Drigo, B, Wyrsch, ER, Djordjevic, SP, Donner, E, Karpouzas, DG & Lombi, E 2022, 'Pesticide effects on nitrogen cycle related microbial functions and community composition', Science of The Total Environment, vol. 807, pp. 150734-150734.
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Slob, EMA, Faiz, A, van Nijnatten, J, Vijverberg, SJH, Longo, C, Kutlu, M, Chew, FT, Sio, YY, Herrera‐Luis, E, Espuela‐Ortiz, A, Perez‐Garcia, J, Pino‐Yanes, M, Burchard, EG, Potočnik, U, Gorenjak, M, Palmer, C, Maroteau, C, Turner, S, Verhamme, K, Karimi, L, Mukhopadhyay, S, Timens, W, Hiemstra, PS, Pijnenburg, MW, Neighbors, M, Grimbaldeston, MA, Tew, GW, Brandsma, CA, Berce, V, Aliee, H, Theis, F, Sin, DD, Li, X, van den Berge, M, Maitland‐van der Zee, AH & Koppelman, GH 2022, 'Association of bronchial steroid inducible methylation quantitative trait loci with asthma and chronic obstructive pulmonary disease treatment response', Clinical and Translational Allergy, vol. 12, no. 8, pp. 1-5.
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Slobozhanyuk, AP, Shchelokova, AV, Dobrykh, DA, Seregin, PS, Powell, DA, Shadrivov, IV, Webb, AG, Belov, PA & Lapine, M 2022, 'Detunable Wire Metasurface for Applications in Magnetic Resonance Imaging', Bulletin of the Russian Academy of Sciences: Physics, vol. 86, no. S1, pp. S216-S221.
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Smit, R, Awadallah, M, Bagheri, S & Surawski, NC 2022, 'Real-world emission factors for SUVs using on-board emission testing and geo-computation', Transportation Research Part D: Transport and Environment, vol. 107, pp. 103286-103286.
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A Portable Emissions Measurement System (PEMS) was used to measure emissions of five sports utility vehicles (SUVs) in a wide range of real-world driving conditions. The program included testing of fuel quality, coast-down and emissions in start, hot running and extended idling conditions. Geo-computation methods were used to add critical information (road gradient) to the PEMS data. Results from this study are generally in good agreement with international PEMS data. Hot running NOx emission factors are on average seven times higher than the type-approval limit for diesel SUVs, and they reach about 2100 and 400 mg/km in urban conditions for NOx and NO2, respectively. They are 7 (NOx) and 4 (NO2) times higher than current emission factors in COPERT Australia. COPERT Australia emission algorithms for CO2 are well behaved and the PEMS data suggest an update is not required. COPERT Australia emission algorithms should be revised for diesel SUVs (NOx, NO2) and petrol SUVs (CO, THC, NO2) to ensure accurate estimation of vehicle emissions at fleet level. Inclusion of logistic regression is proposed for future COPERT updates.

Smith, GB, Gentle, AR & Arnold, MD 2022, 'Partial coherence and amplified internal energy when thermal radiation is sourced within matter', Journal of Physics Communications, vol. 6, no. 6, pp. 065004-065004.
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Abstract Photons excited into ground state modes at finite temperature display partitioning among photon phases, lifetimes and distances travelled since creation. These distributions set the distance from an interface a created photon has some chance of emission. Excited photons have phase velocity set by their mode’s propagation index n which sets mode density then internal energy contribution. All photons that strike an interface obliquely if emitted are refracted, and their exit intensities are irreversible except when weak internal attenuation occurs. Attenuation index k near zero degrees is small, so reversibility is approximate. As temperature rises refraction of exiting photons varies. Total emission remains reversible after transitioning through a nonequilibrium state with no other heat inputs. In equilibrium the densities of excitations that create and annihilate photons are in balance with photon densities, and emissivity dependent on n, k, temperature, and internal incident direction. Exit intensities from pure water and crystalline silica are modelled. They contain strong resonant intensities, and match data accurately. Intrinsic resonances formed within liquids and compounds are due to photon modes hybridising with localized excitations, including molecular oscillations and the anharmonic component of lattice distortions. They explain the many resonant spectral intensities seen in remote sensing. Each hybrid oscillator is a photonic virtual bound state whose energy fluctuates between levels separated by hf. Other features addressed are radiance when solid angle changes at exit, anomalous refraction, thermal recycling of internally reflected photons, fluxes within multilayers, and enhanced internal heat flux from phonon drag by photon density gradients under an external temperature gradient.

Smith, P, Beaumont, L, Bernacchi, CJ, Byrne, M, Cheung, W, Conant, RT, Cotrufo, F, Feng, X, Janssens, I, Jones, H, Kirschbaum, MUF, Kobayashi, K, LaRoche, J, Luo, Y, McKechnie, A, Penuelas, J, Piao, S, Robinson, S, Sage, RF, Sugget, DJ, Thackeray, SJ, Way, D & Long, SP 2022, 'Essential outcomes for COP26', Global Change Biology, vol. 28, no. 1, pp. 1-3.
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Söderström, B, Pittorino, MJ, Daley, DO & Duggin, IG 2022, 'Assembly dynamics of FtsZ and DamX during infection-related filamentation and division in uropathogenic E. coli', Nature Communications, vol. 13, no. 1, p. 3648.
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AbstractDuring infection of bladder epithelial cells, uropathogenic Escherichia coli (UPEC) can stop dividing and grow into highly filamentous forms. Here, we find that some filaments of E. coli UTI89 released from infected cells grow very rapidly and by more than 100 μm before initiating division, whereas others do not survive, suggesting that infection-related filamentation (IRF) is a stress response that promotes bacterial dispersal. IRF is accompanied by unstable, dynamic repositioning of FtsZ division rings. In contrast, DamX, which is associated with normal cell division and is also essential for IRF, is distributed uniformly around the cell envelope during filamentation. When filaments initiate division to regenerate rod cells, DamX condenses into stable rings prior to division. The DamX rings maintain consistent thickness during constriction and remain at the septum until after membrane fusion. Deletion of damX affects vegetative cell division in UTI89 (but not in the model E. coli K-12), and, during infection, blocks filamentation and reduces bacterial cell integrity. IRF therefore involves DamX distribution throughout the membrane and prevention of FtsZ ring stabilization, leading to cell division arrest. DamX then reassembles into stable division rings for filament division, promoting dispersal and survival during infection.

Solntsev, AS, Batalov, SV, Langford, NK & Sukhorukov, AA 2022, 'Complete conversion between one and two photons in nonlinear waveguides: theory of dispersion engineering', New Journal of Physics, vol. 24, no. 6, pp. 065002-065002.
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Abstract High-efficiency photon-pair production is a long-sought-after goal for many optical quantum technologies, and coherent photon conversion (CPC) processes are promising candidates for achieving this. We show theoretically how to control coherent conversion between a narrow-band pump photon and broadband photon pairs in nonlinear optical waveguides by tailoring frequency dispersion for broadband quantum frequency mixing. We reveal that complete deterministic conversion as well as pump-photon revival can be achieved at a finite propagation distance. We also find that high conversion efficiencies can be realised robustly over long propagation distances. These results demonstrate that dispersion engineering is a promising way to tune and optimise the CPC process.

Song, A, Tian, H, Yang, W, Yang, W, Xie, Y, Liu, H, Wang, G & Shao, G 2022, 'Enhanced confinement synthesis of atomically dispersed Fe-N-C catalyst from resin polymer for oxygen reduction', Journal of Energy Chemistry, vol. 65, pp. 630-636.
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Due to larger atom utilization, unique electronic properties and unsaturated coordination, atomically dispersed non-precious metal catalysts with outstanding performances have received great attention in electrocatalysis. Considering the challenge of serious aggregation, rational synthesis of an atomic catalyst with good dispersion of atoms is paramount to the development of these catalysts. Herein, we report an enhanced confinement strategy to synthesize a catalyst comprised of atomically dispersed Fe supported on porous nitrogen-doped graphitic carbon from the novel and more cross-linkable Melamine-Glyoxal Resin. Densified isolated grid trapping, excessive melamine restricting, and nitrogen anchoring are strongly combined to ensure the final atomic-level dispersion of metal atoms. Experimental studies revealed enhanced kinetics of the obtained catalyst towards oxygen reduction reaction (ORR). This catalytic activity originates from the highly active surface with atomically dispersed iron sites as well as the multi-level three-dimensional structure with fast mass and electron transfer. The enhanced confinement strategy endows the resin-derived atomic catalyst with a great prospect to develop for commercialization in future.

Sow, SLS, Brown, MV, Clarke, LJ, Bissett, A, van de Kamp, J, Trull, TW, Raes, EJ, Seymour, JR, Bramucci, AR, Ostrowski, M, Boyd, PW, Deagle, BE, Pardo, PC, Sloyan, BM & Bodrossy, L 2022, 'Biogeography of Southern Ocean prokaryotes: a comparison of the Indian and Pacific sectors', Environmental Microbiology, vol. 24, no. 5, pp. 2449-2466.
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SummaryWe investigated the Southern Ocean (SO) prokaryote community structure via zero‐radius operational taxonomic unit (zOTU) libraries generated from 16S rRNA gene sequencing of 223 full water column profiles. Samples reveal the prokaryote diversity trend between discrete water masses across multiple depths and latitudes in Indian (71–99°E, summer) and Pacific (170–174°W, autumn‐winter) sectors of the SO. At higher taxonomic levels (phylum‐family) we observed water masses to harbour distinct communities across both sectors, but observed sectorial variations at lower taxonomic levels (genus‐zOTU) and relative abundance shifts for key taxa such as Flavobacteria, SAR324/Marinimicrobia, Nitrosopumilus and Nitrosopelagicus at both epi‐ and bathy‐abyssopelagic water masses. Common surface bacteria were abundant in several deep‐water masses and vice‐versa suggesting connectivity between surface and deep‐water microbial assemblages. Bacteria from same‐sector Antarctic Bottom Water samples showed patchy, high beta‐diversity which did not correlate well with measured environmental parameters or geographical distance. Unconventional depth distribution patterns were observed for key archaeal groups: Crenarchaeota was found across all depths in the water column and persistent high relative abundances of common epipelagic archaeon Nitrosopelagicus was observed in deep‐water masses. Our findings reveal substantial regional variability of SO prokaryote assemblages that we argue should be considered in wide‐scale SO ecosystem microbial modelling.

Speer, M, Hartigan, J & Leslie, L 2022, 'Machine Learning Assessment of the Impact of Global Warming on the Climate Drivers of Water Supply to Australia’s Northern Murray-Darling Basin', Water, vol. 14, no. 19, pp. 3073-3073.
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Droughts and long dry spells, interspersed with intense rainfall events, have been characteristic of the northern Murray-Darling Basin (NMDB), a major Australian agricultural region. The NMDB precipitation results from weather systems ranging from thunderstorms to larger scale events. The larger scale events exhibit high seasonal and annual rainfall variability. To detect attributes shaping the NMDB precipitation patterns, and hence net water inflows to the vast Darling River catchment area, numerous (45) possible attributes were assessed for their influence on rainfall trends. Four periods were assessed: annual, April–May (early cool-season), June–September (remaining cool-season), and October–March (warm-season). Linear and non-linear regression machine learning (ML) methods were used to identify the dominant attributes. We show the impact of climate drivers on the increasingly dry April–May months on annual precipitation and warmer temperatures since the early 1990s. The NMDB water supply was further reduced during 1992–2018 by the lack of compensating rainfall trends for the April–May decline. The identified attributes include ENSO, the Southern Annular Mode, the Indian Ocean Dipole, and both local and global sea surface temperatures. A key finding is the prominence of global warming as an attribute, both individually and in combination with other climate drivers.

Speer, MS, Leslie, LM & Hartigan, J 2022, 'Jet Stream Changes over Southeast Australia during the Early Cool Season in Response to Accelerated Global Warming', Climate, vol. 10, no. 6, pp. 84-84.
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In recent decades, southeast Australia has experienced both extreme drought and record-breaking rainfall, with devastating societal impacts. Variations in the Australian polar-front jet (PFJ) and the subtropical jet (STJ) determine, for example, the location and frequency of the cool season (April–September) weather systems influencing rainfall events and, consequently, water availability for the southern half of Australia. Changes in jet stream wind speeds also are important for aviation fuel and safety requirements. A split jet occurs when the single jet separates into the STJ and PFJ in the early cool season (April–May). This study focusses on split jet characteristics over Australian/New Zealand longitudes in recent decades. During the accelerated global warming from the mid-1990s, higher mean wind speeds were found in the PJF across the Australian region during June–September, compared to the STJ. In contrast, significant wind speed increases occur in the early cool season (April–May) at STJ latitudes, which straddle the East Coast of Australia and the adjacent Tasman Sea. These changes are linked to major changes in the mean atmospheric circulation, and they include relative vorticity and humidity, both being vital for the development of rain-bearing weather systems that affect the region.

Spennati, E, Casazza, AA, Converti, A, Padula, MP, Dehghani, F, Perego, P & Valtchev, P 2022, 'Winery waste valorisation as microalgae culture medium: A step forward for food circular economy', Separation and Purification Technology, vol. 293, pp. 121088-121088.
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Wastewater is one of the critical environmental problems worldwide. In this study, the circular economy concept was applied to winery wastewater that has been considered as a rich source of nutrients for growing edible microalgae to produce a high value protein product. To this end, Chlorella vulgaris and Arthrospira platensis were co-cultured. The effects of processing parameters on the microalgae yield and protein recovery were examined. Different microalgae growth systems: open pond, column and tubular photobioreactor were used for obtaining more than two grams of dry weight biomass per liter. The protein fraction was extracted and recovered by ultrasound-assisted extraction. The image analysis shows that wastewater strongly affected the intracellular components concentration, cell morphology, and resistivity to cell rupture. The results of our study demonstrate that it is viable to use microalgae to substantially reduce the pollutant impact of the wastewater and produce high value products such as proteins.

Srivastava, A, Yetemen, O, Saco, PM, Rodriguez, JF, Kumari, N & Chun, KP 2022, 'Influence of orographic precipitation on coevolving landforms and vegetation in semi‐arid ecosystems', Earth Surface Processes and Landforms, vol. 47, no. 12, pp. 2846-2862.
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AbstractTopography affects the intensity and spatial distribution of precipitation due to orographic lifting mechanisms and, in turn, influences the prevailing climate and vegetation distribution. Previous modelling studies on the impact of orographic precipitation on landform evolution have considered bare soil conditions. However, research on the effect of changes in precipitation regimes induced by elevation gradients (particularly in aspect‐controlled semi‐arid ecosystems) on landform patterns, trying to understand feedbacks and consequences for coevolving vegetation, has been limited. In this study, the Channel–Hillslope Integrated Landscape Development (CHILD) landscape evolution model coupled with the vegetation dynamics Bucket Grassland Model (BGM) is used to analyse the coevolution of semi‐arid landform–vegetation ecosystems. The CHILD+BGM model is run under different combinations of precipitation and solar radiation settings. Three precipitation settings, including uniform, elevation control, and orographic control on precipitation, are considered in combination with spatially uniform and spatially varied radiation settings. Based on the results, elevation control, aspect, and drainage network are identified as the major drivers of the distribution of vegetation cover on the landscapes. Further, the combination of orographic precipitation and spatially varied solar radiation created the highest asymmetry in the landscape and divide migration due to the emergence of gentler slopes on the windward than the leeward sides of the domain. The modelling outcomes from this study indicate that aspect control of solar radiation in combination with orographic precipitation plays a key role in the generation of topographic asymmetry in semi‐arid ecosystems.

Steele, JR, Italiano, CJ, Phillips, CR, Violi, JP, Pu, L, Rodgers, KJ & Padula, MP 2022, 'Correction: Steele et al. Misincorporation Proteomics Technologies: A Review. Proteomes 2021, 9, 2', Proteomes, vol. 10, no. 2, pp. 22-22.
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In the original publication, there was a mistake in Table 2 as published [...]

Steiner, R, Roux, C & Moret, S 2022, 'Production of artificial fingermarks. Part I – Synthetic secretions formulation', Forensic Science International, vol. 331, pp. 111166-111166.
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Fingermark variability is a critical parameter. To mitigate the effects of this variability, synthetic secretions in the form of simple mixtures of target compounds found in eccrine sweat have been described in the literature, but they are usually reactive towards only a minimal range of detection techniques. If this approach is acceptable for the production of single-technique test strips, such artificial secretions cannot be considered as reliable fingermark simulants because they do not reproduce the complex matrix that makes up real secretions. Research has shown that sebaceous and eccrine compounds are probably present simultaneously in fingermark residue in the form of an emulsion. This paper is the first part of a research project that aims at producing realistic artificial fingermarks containing an extensive range of eccrine and sebaceous compounds. This first study aimed to reproduce and compare two synthetic fingermark residues formulations and assess their potential to be used as fingermark simulants. Spot tests of the artificial secretions were deposited on paper substrates, and their reactivity with four common detection techniques was tested: 1,2-indanedione-zinc, ninhydrin, oil red O, and physical developer. Both formulations showed very good results when processed with the two amino acid reagents, as well as oil red O, and no obvious differences were observed between the two versions. The results obtained with the physical developer were inconsistent and demonstrated that the fundamental working principle of physical developer needs to be further understood. The results were extremely promising as they showed the potential of such reproducible artificial secretions to be used to assess an extensive range of detection techniques, which would be highly beneficial to guarantee better research and quality control in fingermark detection. The use of spot tests to deposit the simulant was shown to be unreliable and a more controllable and repr...

Stern, HL, Gu, Q, Jarman, J, Eizagirre Barker, S, Mendelson, N, Chugh, D, Schott, S, Tan, HH, Sirringhaus, H, Aharonovich, I & Atatüre, M 2022, 'Room-temperature optically detected magnetic resonance of single defects in hexagonal boron nitride', Nature Communications, vol. 13, no. 1, pp. 1-9.
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AbstractOptically addressable solid-state spins are important platforms for quantum technologies, such as repeaters and sensors. Spins in two-dimensional materials offer an advantage, as the reduced dimensionality enables feasible on-chip integration into devices. Here, we report room-temperature optically detected magnetic resonance (ODMR) from single carbon-related defects in hexagonal boron nitride with up to 100 times stronger contrast than the ensemble average. We identify two distinct bunching timescales in the second-order intensity-correlation measurements for ODMR-active defects, but only one for those without an ODMR response. We also observe either positive or negative ODMR signal for each defect. Based on kinematic models, we relate this bipolarity to highly tuneable internal optical rates. Finally, we resolve an ODMR fine structure in the form of an angle-dependent doublet resonance, indicative of weak but finite zero-field splitting. Our results offer a promising route towards realising a room-temperature spin-photon quantum interface in hexagonal boron nitride.

Stewart, EL, Counoupas, C, Johansen, MD, Nguyen, DH, Miemczyk, S, Hansbro, NG, Ferrell, KC, Ashhurst, A, Alca, S, Ashley, C, Steain, M, Britton, WJ, Hansbro, PM, Petrovsky, N & Triccas, JA 2022, 'Mucosal immunization with a delta-inulin adjuvanted recombinant spike vaccine elicits lung-resident immune memory and protects mice against SARS-CoV-2', Mucosal Immunology, vol. 15, no. 6, pp. 1405-1415.
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Multiple SARS-CoV-2 vaccine candidates have been approved for use and have had a major impact on the COVID-19 pandemic. There remains, however, a significant need for vaccines that are safe, easily transportable and protective against infection, as well as disease. Mucosal vaccination is favored for its ability to induce immune memory at the site of infection, making it appealing for SARS-CoV-2 vaccine strategies. In this study we performed in-depth analysis of the immune responses in mice to a subunit recombinant spike protein vaccine formulated with the delta-inulin adjuvant Advax when administered intratracheally (IT), versus intramuscular delivery (IM). Both routes produced robust neutralizing antibody titers (NAb) and generated sterilizing immunity against SARS-CoV-2. IT delivery, however, produced significantly higher systemic and lung-local NAb that resisted waning up to six months post vaccination, and only IT delivery generated inducible bronchus-associated lymphoid tissue (iBALT), a site of lymphocyte antigen presentation and proliferation. This was coupled with robust and long-lasting lung tissue-resident memory CD4+ and CD8+ T cells that were not observed in IM-vaccinated mice. This study provides a detailed view of the lung-resident cellular response to IT vaccination against SARS-CoV-2 and demonstrates the importance of delivery site selection in the development of vaccine candidates.

Stewart, J, Fowler, AM, Meadows, NM & Johnson, DD 2022, 'Life-history traits and commercial catch composition of Chelidonichthys kumu in south-eastern Australia', Regional Studies in Marine Science, vol. 56, pp. 102720-102720.
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Stothard, JR & Ellis, JT 2022, 'Updates on Parasitology and adopting a Gold Open Access model of production', Parasitology, vol. 149, no. 12, pp. 1523-1525.
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Strudwick, P, Seymour, J, Camp, EF, Edmondson, J, Haydon, T, Howlett, L, Le Reun, N, Siboni, N & Suggett, DJ 2022, 'Correction to: Impacts of nursery-based propagation and out-planting on coral-associated bacterial communities', Coral Reefs, vol. 41, no. 2, pp. 473-473.
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Strudwick, P, Seymour, J, Camp, EF, Edmondson, J, Haydon, T, Howlett, L, Le Reun, N, Siboni, N & Suggett, DJ 2022, 'Impacts of nursery-based propagation and out-planting on coral-associated bacterial communities', Coral Reefs, vol. 41, no. 1, pp. 95-112.
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Efforts to manage coral reef declines are increasingly turning towards in situ propagation of corals to aid reef recovery. Understanding the factors that influence ‘success’ throughout the propagation process is therefore critical to ensure efforts are viable and cost-effective, yet the extent to which propagation practices potentially impact the underlying coral biology remains unknown. Given growing evidence for the importance of the coral microbiome, we examined the influence of nursery-based propagation and out-planting on the bacterial communities of two coral species–Acropora millepora and Pocillopora verrucosa–increasingly propagated on the northern Great Barrier Reef (Opal Reef). Bacterial communities of coral fragments were characterised over four months of nursery propagation (sampling points: zero, seven and 125 days) and one month of subsequent out-planting (sampling points: zero, one and 30 days). Bacterial community structure differed between A. millepora and P. verrucosa throughout the experiment and species-specific temporal dynamics were observed during the transplantation of corals into nurseries and subsequent out-planting back to the reef. P. verrucosa bacterial community structure remained stable over time in the natural reef environment and within the nursery. In contrast, A. millepora bacterial communities within the nursery significantly changed over time, whereas those associated with source colonies within the natural reef environment remained unchanged. However, after one month of out-planting, the composition, richness and diversity of A. millepora bacterial communities were not statistically different to those associated with the source colonies. We interpret the transient shift of A. millepora bacterial communities within the nursery as an impact of distinctive environmental conditions in nurseries compared to natural reef settings, and the greater responsiveness of A. millepora bacterial communities to environmental change...

Stuart, J, Smith, KF, Rhodes, L, Murray, JS, Viallon, J, Henry, K, Darius, HT, Murray, SA, De Azevedo, CD, Argyle, P & Chinain, M 2022, 'Geographical distribution, molecular and toxin diversity of the dinoflagellate species Gambierdiscus honu in the Pacific region', Harmful Algae, vol. 118, pp. 102308-102308.
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An increase in cases of ciguatera poisoning (CP) and expansion of the causative species in the South Pacific region highlight the need for baseline data on toxic microalgal species to help identify new areas of risk and manage known hot spots. Gambierdiscus honu is a toxin producing and potential CP causing dinoflagellate species, first described in 2017. Currently no high-resolution geographical distribution, intraspecific genetic variation or toxin production diversity data is available for G. honu. This research aimed to further characterize G. honu by investigating its distribution using species-specific real-time polymerase chain reaction assays at 25 sites in an area spanning ∼8000 km of the Coral Sea/Pacific Ocean, and assessing intraspecific genetic variation, toxicity and toxin production of isolated strains. Assessment of genetic variation of the partial rRNA operon of isolates demonstrated no significant intraspecific population structure, in addition to a lack of adherence to isolation by distance (IBD) model of evolution. The detected distribution of G. honu in the Pacific region was within the expected tropical to temperate latitudinal ranges of 10° to -30° and extended from Australia to French Polynesia. In the lipophilic fractions, the neuroblastoma cell-based assay (CBA-N2a) showed no ciguatoxin (CTX)-like activity for nine of the 10 isolates, and an atypical pattern for CAWD233 isolate which showed cytotoxic activity in OV- and OV+ conditions. In the same way, liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis confirmed no Pacific-CTXs (CTX-3B, CTX-3C, CTX-4A, CTX-4B) were produced by the ten strains. The CBA-N2a assessment of the hydrophilic fractions showed moderate to high cytotoxicity in both OV- and OV+ condition for all the strains showing a cytotoxic profile similar to that of gambierone. Indeed, this study is the first to show the cytotoxic activity of gambierone on mouse neuroblastoma cells while no cytotoxicit...

Su, D 2022, 'Powerful qua-functional electrolyte additive for lithium metal batteries', Green Energy & Environment, vol. 7, no. 3, pp. 361-364.
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Lithium metal batteries (LMBs) have attracted tremendous research attention because of the high theoretical capacity (3860 mAh g−1) and the lowest electrochemical potential (−3.04 V vs standard hydrogen electrode). However, the Lithium dendrites, forming from plating/stripping processes, cause the excessive consumption of electrolyte and active Li and the puncture on the separator. This limits the commercialization of LMBs. Recently, Ma's group proposed heptafluorobutyric anhydride (HFA) as qua-functional electrolyte additive and verified the protection mechanism from the structure and electrochemical properties. Such results creatively put forward qua-functional electrolyte additive for the improvement of LMBs and provides good experience for the exploration of multi-functional additive, inspiring researchers to explore new multi-functional electrolyte additives in future.

Su, F, Luo, X, Du, Z, Chen, Z, Liu, Y, Jin, X, Guo, Z, Lu, J & Jin, D 2022, 'High-Contrast Luminescent Immunohistochemistry Using PEGylated Lanthanide Complexes', Analytical Chemistry, vol. 94, no. 50, pp. 17587-17594.
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Immunohistochemistry (IHC) using fluorescent probes provides high resolution with multiplexing capability, but the imaging contrast is limited by the brightness of the fluorescent probe and the intrinsic autofluorescence background from tissues. Herein, we improved the contrast by high-density labeling of long-lifetime lanthanide complexes and time-gated imaging. As the large (∼280 nm) Stokes shift of lanthanide complexes effectively prevents the issue of concentration quenching, we succeeded in conjugating seven europium complexes to an eight-arm hydrophilic poly(ethylene glycol) (PEG) linker for signal amplification with improved water solubility to the level of up to 10 mg/mL. Moreover, we demonstrated that both human epidermal growth factor receptor 2 (HER2) in a formalin-fixed paraffin-embedded (FFPE) tissue section and cytokeratin 18 (CK18) in a frozen section can be resolved with the enhanced contrast by 2-fold and 3-fold, respectively. Furthermore, we show that the PEGylation of multiple lanthanide complexes is compatible with tyramide signal amplification (TSA). This work suggests new opportunities for sensitive imaging of low-abundance biomarkers in a tissue matrix.

Suggett, DJ & van Oppen, MJH 2022, 'Horizon scan of rapidly advancing coral restoration approaches for 21st century reef management', Emerging Topics in Life Sciences, vol. 6, no. 1, pp. 125-136.
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Coral reef restoration activity is accelerating worldwide in efforts to offset the rate of reef health declines. Many advances have already been made in restoration practices centred on coral biology (coral restoration), and particularly those that look to employ the high adaptive state and capacity of corals in order to ensure that efforts rebuilding coral biomass also equip reefs with enhanced resilience to future stress. We horizon scan the state-of-play for the many coral restoration innovations already underway across the complex life cycle for corals that spans both asexual and sexual reproduction — assisted evolution (manipulations targeted to the coral host and host-associated microbes), biobanking, as well as scalable coral propagation and planting — and how these innovations are in different stages of maturity to support new 21st century reef management frameworks. Realising the potential for coral restoration tools as management aids undoubtedly rests on validating different approaches as their application continues to scale. Whilst the ecosystem service responses to increased scaling still largely remain to be seen, coral restoration has already delivered immense new understanding of coral and coral-associated microbial biology that has long lagged behind advances in other reef sciences.

Suggett, DJ, Nitschke, MR, Hughes, DJ, Bartels, N, Camp, EF, Dilernia, N, Edmondson, J, Fitzgerald, S, Grima, A, Sage, A & Warner, ME 2022, 'Toward bio‐optical phenotyping of reef‐forming corals using Light‐Induced FluorescenceTransient‐FastRepetition Rate fluorometry', Limnology and Oceanography: Methods, vol. 20, no. 3, pp. 172-191.
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AbstractActive chlorophyllafluorometry is a well‐established tool for noninvasively diagnosing coral functional state, but has not yet been developed as a rapid phenotyping (functional screening) platform as for agriculture and forestry. Here, we present a proof‐of‐concept using Light‐Induced Fluorescence Transient‐Fast Repetition Rate fluorometry (LIFT‐FRRf) to identify coral photobiological‐based phenotypes in the context of rapidly scaling coral propagation practices on the northern Great Barrier Reef. For example, resolving light niche plasticity to inform transplantation, and identifying functionally diverse colonies to maximize stock selection. We first used optically diverse laboratory‐reared corals and coral endosymbiont (Symbiodiniaceae) isolates to develop a phenotyping approach integrating FRRf instantaneous kinetic parameters (light harvesting, electron turnover rates) and light‐dependent parameters (dynamic “quenching” terms, saturating light intensity [EK]). Subsequent field‐based LIFT‐FRRf phenotyping of coral from a selective (2‐4 m depth) reef habitat revealed that widely topographically dispersed platingAcroporataxa exhibited broad light niche plasticity (EKvariance) underpinned by multiple phenotypes that were predominantly differentiated by minimum electron turnover capacity; fluorometer configurations that cannot resolve kinetic parameters will thus likely have more limited capacity to resolve phenotypes. As such, platingAcroporahave broad propagation potential in terms of multiple functional variants for stock and across diverse light environments (growth, transplantation). In contrast, coral taxa (Pocillopora verrucosa,Echinopora lamellosa) with relatively restricted topo...

Sukjamnong, S, Chen, H, Saad, S & Santiyanont, R 2022, 'Fimbristylis ovata and Artemisia vulgaris extracts inhibited AGE-mediated RAGE expression, ROS generation, and inflammation in THP-1 cells', Toxicological Research, vol. 38, no. 3, pp. 331-343.
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Suzzi, AL, Stat, M, MacFarlane, GR, Seymour, JR, Williams, NLR, Gaston, TF, Alam, MR & Huggett, MJ 2022, 'Legacy metal contamination is reflected in the fish gut microbiome in an urbanised estuary', Environmental Pollution, vol. 314, pp. 120222-120222.
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Szpila, K, Johnston, NP, Akbarzadeh, K, Richet, R & Tofilski, A 2022, 'Wing measurements are a possible tool for the identification of European forensically important Sarcophagidae', Forensic Science International, vol. 340, pp. 111451-111451.
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The flesh flies are a group of insects well known for their forensic importance. Reliable identification of these flies relies on the use of either molecular markers or the morphology of the male genital apparatus. Identification of female flesh flies is more time consuming and less reliable than their male counterparts. This is particularly problematic for forensic entomology practitioners, because female flesh flies are more abundant than males in carrion arthropod assemblages. As such, it is critical that alternative methods for flesh fly identification are established that are equally effective for both sexes. One promising technique is the use of wing measurements, which have been shown to be reliable for the identification of some groups of necrophagous Diptera from several geographical regions. We applied this method to the European Sarcophagidae for the first time, using a dataset of 881 specimens representing 29 species and 5 genera. Species identifications were based on 15 landmarks located at wing vein junctions. We also combined our results with data from previous studies of Calliphoridae and Muscidae which utilised the same methodology, enabling the testing of family level identification using wing morphometrics. Species identifications using wing measurements had varied success. While some species were successfully identified without error, others, particularly from the genus Sarcophaga, were often misclassified. Notably, in several species wing measurements successfully identified both males and females. The results presented here suggest that wing measurements are a promising complementary method to other methods for the identification of necrophagous Sarcophagidae especially in material unsorted at the family level. It can also be used to double check identification performed by a taxonomist using traditional methods.

Tai, MC, Arnold, MD, Estherby, C, de Silva, KSB, Gentle, AR, Cortie, DL, Mitchell, DRG, Westerhausen, MT & Cortie, MB 2022, 'Spontaneous Emergence of Optically Polarizing Nanoscale Structures by Co-Deposition of Aluminum with Refractory Metals: Implications for High-Temperature Polarizers', ACS Applied Nano Materials, vol. 5, no. 3, pp. 4316-4324.
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The unexpected growth of highly aligned and optically polarizing metallic fins during physical vapor deposition under modestly oblique conditions is investigated. The fins exhibit nanoscale dimensions and are formed when Al is co-sputtered with any of V, Cr, Nb, Mo, Ta, W, Ru, Fe, Ni, Pt, Zr, Mg, and Ti. It is proposed that the phenomenon is caused by anomalously low atomic mobility in the alloys and intermetallic compounds formed by co-depositing with Al. In contrast, when Cu, Ag, and Au (which diffuse more rapidly in Al) are deposited, no fins form. There is a sharp visible transition in optical properties as the ratio of Al to other element is decreased: the color of the sample changes from black to silver-white for compositions containing less than about 55 atom % Al. The region over which the color change occurs is associated with a very strongly polarized reflectance. Cross-sectional elemental mapping and Monte Carlo simulations suggest that growth of the fins may be nucleated by Al hillocks and enhanced by shadowing effects. The diversity of suitable metals makes this a versatile technique for producing nanoscale polarizing surfaces suitable for high-flux and high-temperature applications.

Tajaddini, A, Kendig, MD, Prates, KV, Westbrook, RF & Morris, MJ 2022, 'Male Rat Offspring Are More Impacted by Maternal Obesity Induced by Cafeteria Diet than Females—Additive Effect of Postweaning Diet', International Journal of Molecular Sciences, vol. 23, no. 3, pp. 1442-1442.
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Maternal obesity increases the risk of health complications in offspring, but whether these effects are exacerbated by offspring exposure to unhealthy diets warrants further investigation. Female Sprague-Dawley rats were fed either standard chow (n = 15) or ‘cafeteria’ (Caf, n = 21) diets across pre-pregnancy, gestation, and lactation. Male and female offspring were weaned onto chow or Caf diet (2–3/sex/litter), forming four groups; behavioural and metabolic parameters were assessed. At weaning, offspring from Caf dams were smaller and lighter, but had more retroperitoneal (RP) fat, with a larger effect in males. Maternal Caf diet significantly increased relative expression of ACACA and Fasn in male and female weanling liver, but not CPT-1, SREBP and PGC1; PPARα was increased in males from Caf dams. Maternal obesity enhanced the impact of postweaning Caf exposure on adult body weight, RP fat, liver mass, and plasma leptin in males but not females. Offspring from Caf dams appeared to exhibit reduced anxiety-like behaviour on the elevated plus maze. Hepatic CPT-1 expression was reduced only in adult males from Caf fed dams. Post weaning Caf diet consumption did not alter liver gene expression in the adult offspring. Maternal obesity exacerbated the obesogenic phenotype produced by postweaning Caf diet in male, but not female offspring. Thus, the impact of maternal obesity on adiposity and liver gene expression appeared more marked in males. Our data underline the sex-specific detrimental effects of maternal obesity on offspring.

Talley, NJ, Zuccala, E, Geronimo, F, Janusic, T & Villanueva, EV 2022, 'Strengthening the presence of Aboriginal and Torres Strait Islander voices in the Medical Journal of Australia', Medical Journal of Australia, vol. 217, no. 1, pp. 24-25.
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Tan, CL, Chan, Y, Candasamy, M, Chellian, J, Madheswaran, T, Sakthivel, LP, Patel, VK, Chakraborty, A, MacLoughlin, R, Kumar, D, Verma, N, Malyla, V, Gupta, PK, Jha, NK, Thangavelu, L, Devkota, HP, Bhatt, S, Prasher, P, Gupta, G, Gulati, M, Singh, SK, Paudel, KR, Hansbro, PM, Oliver, BG, Dua, K & Chellappan, DK 2022, 'Unravelling the molecular mechanisms underlying chronic respiratory diseases for the development of novel therapeutics via in vitro experimental models', European Journal of Pharmacology, vol. 919, pp. 174821-174821.
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Tan, J, Walford, S-A, Dennis, ES & Llewellyn, DJ 2022, 'Erratum To: Trichomes at the Base of the Petal are Regulated by the Same Transcription Factors as Cotton Seed Fibers', Plant and Cell Physiology, vol. 63, no. 3, pp. 441-441.
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Tan, J, Wu, L, Peacock, J & Dennis, ES 2022, 'Capturing hybrid vigor for lentil breeding', Crop Science, vol. 62, no. 5, pp. 1787-1796.
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AbstractConventional breeding has produced low levels of yield increase in lentils (Lens culinaris ssp. culinaris Medik.) in recent decades. As hybrids have led to large increases in yield in other crops, we examined the possibility of using hybrids in lentils. In 52 hybrids between Australian commercial cultivars and lines from a global collection of cultivated and wild accessions, we found 15 of the hybrids had seed yield hybrid vigor, with better parent heterosis (BPH) gains ranging from 10.4 to 125%. Flowering time, seed size, cotyledon color, and branch number were important but not critical for the level of hybrid vigor in seed yield. Plant height at 28 days post sowing (dps) could be an indicator of seed yield vigor of hybrids grown in glasshouse conditions. In the absence of male sterile lines in lentils, we used high‐yielding hybrid combinations in a program of repeated selfing and selection to produce stable, high‐yielding lines (Hybrid Mimics) with grain yields similar to the F1 hybrids, avoiding the limitation of the hybrid advantage to the F1 generation. Seed yield increased in successive generations (F3–F5); yields of the F4 plants were close to that of the F1 hybrid. Our results indicate that there is potential for hybrid seed yield vigor in lentil to be accessed through hybrid mimic selection. This is a breeding method not dependent on male sterility that can be initiated with a low number of hand‐pollinated hybrids. Hybrid mimic breeding may be applicable to a wide range of crops.

Tan, Q, Lai, J-M, Liu, X-L, Guo, D, Xue, Y, Dou, X, Sun, B-Q, Deng, H-X, Tan, P-H, Aharonovich, I, Gao, W & Zhang, J 2022, 'Donor–Acceptor Pair Quantum Emitters in Hexagonal Boron Nitride', Nano Letters, vol. 22, no. 3, pp. 1331-1337.
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Quantum emitters are needed for a myriad of applications ranging from quantum sensing to quantum computing. Hexagonal boron nitride (hBN) quantum emitters are one of the most promising solid-state platforms to date due to their high brightness and stability and the possibility of a spin-photon interface. However, the understanding of the physical origins of the single-photon emitters (SPEs) is still limited. Here we report dense SPEs in hBN across the entire visible spectrum and present evidence that most of these SPEs can be well explained by donor-acceptor pairs (DAPs). On the basis of the DAP transition generation mechanism, we calculated their wavelength fingerprint, matching well with the experimentally observed photoluminescence spectrum. Our work serves as a step forward for the physical understanding of SPEs in hBN and their applications in quantum technologies.

Tareen, AK, Khan, K, Iqbal, M, Golovynskyi, S, Zhang, Y, Mahmood, A, Mahmood, N, Long, J, Al-Ghamdi, A, Li, C & Zhang, H 2022, 'Recent advances in MXenes: new horizons in biomedical technologies', Materials Today Chemistry, vol. 26, pp. 101205-101205.
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Tareen, AK, Khan, K, Iqbal, M, Zhang, Y, Long, J, Mahmood, A, Mahmood, N, Xie, Z, Li, C & Zhang, H 2022, 'Recent advance in two-dimensional MXenes: New horizons in flexible batteries and supercapacitors technologies', Energy Storage Materials, vol. 53, pp. 783-826.
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MXenes (two dimensional (2D) transition metal (TM) carbides (TMCs), TM nitrides (TMNs), and TM carbonitrides (TMCNs) are emerged as future biggest 2D materials (2DMs) family with novel applications in different nanotechnological research in academic as well as industrial level. MXenes NMs have the potential to be classified as a “wonder material” in the category of 2D nanomaterials (NMs). MXenes were studied and synthesized for over a decade since their first discovery in 2011, and till now more than 50 members are experimentally studied and more than 100 are theoretically investigated. Synthesis techniques are not restricted to the first introduced top-down HF based etching method but new innovative synthesis methods, such as, water (H2O)-free etching, molten salts etching and bottom-up method, like Chemical vapor deposition (CVD) method etc were also studied, providing multifunctional surface chemistry based MXenes NMs with novel configuration, and desirable characteristics. MXenes are used as important components in a number of flexible energy storage devices (FESDs), for instance secondary batteries, supercapacitors (SCs), Micro-SCs (MSCs) and Micro-batteries (MBs), etc due to their distinctive layered structures, high electrochemical performance and fascinating functional capabilities. In this review, we first will discuss in detail the MXenes NMs synthesis methods, secondly selected properties, and third their applications in various FESDs. After that, we will summarize and discuss the most present problems associated with MXenes NMs synthesis and their applications in FESDs, and possible solutions to those problems. Finally we will discuss the presents interesting vision for the future progress of the MXenes-based NMs in wearable and FESDs, their limitations, and suggestions.

Tareen, AK, Khan, K, Iqbal, M, Zhang, Y, Long, J, Nazeer, F, Mahmood, A, Mahmood, N, Shi, Z, Ma, C, Huan, W, Khan, MF, Yin, J, Li, C & Zhang, H 2022, 'Recent advances in novel graphene: new horizons in renewable energy storage technologies', Journal of Materials Chemistry C, vol. 10, no. 32, pp. 11472-11531.
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Graphene based supercapacitors and batteries are a highly competitive choice for electrochemical energy storage devices, thanks to their ultrahigh power density, improved rate capability, long-term cyclability, and remarkable safety.

Tareen, AK, Khan, K, Iqbal, M, Zhang, Y, Xie, Z, Mahmood, A, Mahmood, N, Long, J, Li, C & Zhang, H 2022, 'Recent major advances and challenges in the emerging graphene-based nanomaterials in electrocatalytic fuel cell technology', Journal of Materials Chemistry C, vol. 10, no. 47, pp. 17812-17873.
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Graphene and its derivatives with unique chemical and physical features have motivated great efforts and achieved substantial advances in fuel cell applications for renewable energy production.

Tashima, T, Takashima, H, Schell, AW, Tran, TT, Aharonovich, I & Takeuchi, S 2022, 'Hybrid device of hexagonal boron nitride nanoflakes with defect centres and a nano-fibre Bragg cavity', Scientific Reports, vol. 12, no. 1, pp. 1-7.
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AbstractSolid-state quantum emitters coupled with a single mode fibre are of interest for photonic and quantum applications. In this context, nanofibre Bragg cavities (NFBCs), which are microcavities fabricated in an optical nanofibre, are promising devices because they can efficiently couple photons emitted from the quantum emitters to the single mode fibre. Recently, we have realized a hybrid device of an NFBC and a single colloidal CdSe/ZnS quantum dot. However, colloidal quantum dots exhibit inherent photo-bleaching. Thus, it is desired to couple an NFBC with hexagonal boron nitride (hBN) as stable quantum emitters. In this work, we realize a hybrid system of an NFBC and ensemble defect centres in hBN nanoflakes. In this experiment, we fabricate NFBCs with a quality factor of 807 and a resonant wavelength at around 573 nm, which matches well with the fluorescent wavelength of the hBN, using helium-focused ion beam (FIB) system. We also develop a manipulation system to place hBN nanoflakes on a cavity region of the NFBCs and realize a hybrid device with an NFBC. By exciting the nanoflakes via an objective lens and collecting the fluorescence through the NFBC, we observe a sharp emission peak at the resonant wavelength of the NFBC.

Tekwe, CD, Zhang, M, Carroll, RJ, Luan, Y, Xue, L, Zoh, RS, Carter, SJ, Allison, DB & Geraci, M 2022, 'Estimation of sparse functional quantile regression with measurement error: a SIMEX approach', Biostatistics, vol. 23, no. 4, pp. 1218-1241.
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Summary Quantile regression is a semiparametric method for modeling associations between variables. It is most helpful when the covariates have complex relationships with the location, scale, and shape of the outcome distribution. Despite the method’s robustness to distributional assumptions and outliers in the outcome, regression quantiles may be biased in the presence of measurement error in the covariates. The impact of function-valued covariates contaminated with heteroscedastic error has not yet been examined previously; although, studies have investigated the case of scalar-valued covariates. We present a two-stage strategy to consistently fit linear quantile regression models with a function-valued covariate that may be measured with error. In the first stage, an instrumental variable is used to estimate the covariance matrix associated with the measurement error. In the second stage, simulation extrapolation (SIMEX) is used to correct for measurement error in the function-valued covariate. Point-wise standard errors are estimated by means of nonparametric bootstrap. We present simulation studies to assess the robustness of the measurement error corrected for functional quantile regression. Our methods are applied to National Health and Examination Survey data to assess the relationship between physical activity and body mass index among adults in the United States.

Thomson, S, Chan, YL, Yi, C, Wang, B, Machaalani, R, Oliver, BG, Gorrie, CA & Chen, H 2022, 'Impact of High Fat Consumption on Neurological Functions after Traumatic Brain Injury in Rats', Journal of Neurotrauma, vol. 39, no. 21-22, pp. 1547-1560.
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Tiotiu, A, Badi, Y, Kermani, NZ, Sanak, M, Kolmert, J, Wheelock, CE, Hansbro, PM, Dahlén, S-E, Sterk, PJ, Djukanovic, R, Guo, Y, Mumby, S, Adcock, IM, Chung, KF, Hoda, U, Rossios, C, Bel, E, Rao, N, Myles, D, Compton, C, Van Geest, M, Howarth, P, Roberts, G, Lefaudeux, D, De Meulder, B, Bansal, AT, Knowles, R, Erzen, D, Wagers, S, Krug, N, Higenbottam, T, Matthews, J, Erpenbeek, V, Carayannopoulos, L, Roberts, A, Supple, D, deBoer, P, Caruso, M, Chanez, P, Horváth, I, Musial, J & Sandström, T 2022, 'Association of Differential Mast Cell Activation with Granulocytic Inflammation in Severe Asthma', American Journal of Respiratory and Critical Care Medicine, vol. 205, no. 4, pp. 397-411.
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BACKGROUND: Mast cells (MC) play a role in inflammation and both innate and adaptive immunity but their involvement in severe asthma (SA) remains undefined. OBJECTIVE: We investigated the phenotypic characteristics of the U-BIOPRED asthma cohort by applying published MC activation signatures to the sputum cell transcriptome. METHODS: 84 SA, 20 mild/moderate (MMA) asthma, and 16 non-asthmatic healthy participants were studied. We calculated enrichment scores (ES) for nine MC activation signatures by asthma severity, sputum granulocyte status and three previously-defined sputum molecular phenotypes or transcriptome-associated clusters (TAC1, 2, 3) using gene-set variation analysis. RESULTS: MC signatures except unstimulated, repeated FcεR1-stimulated and IFNγ-stimulated were enriched in SA. A FcεR1-IgE-stimulated and a single cell signature from asthmatic bronchial biopsies were highly enriched in eosinophilic asthma and in the TAC1 molecular phenotype. Subjects with a high ES for these signatures had elevated sputum levels of similar genes and pathways. IL-33- and LPS-stimulated MC signatures had greater ES in neutrophilic and mixed granulocytic asthma and in the TAC2 molecular phenotype. These subjects exhibited neutrophil, NF-κB, and IL-1β/TNFα pathway activation. The IFNγ-stimulated signature had the greatest ES in TAC2 and TAC3 that was associated with responses to viral infection. Similar results were obtained in an independent ADEPT asthma cohort. CONCLUSIONS: Gene signatures of MC activation allow the detection of SA phenotypes and indicate that MC can be induced to take on distinct transcriptional phenotypes associated with specific clinical phenotypes. IL-33-stimulated MCs signature was associated with severe neutrophilic asthma while IgE-activated MC with an eosinophilic phenotype.

Tou, K, Cawley, A, Bishop, D, Bowen, C, Noble, G & Fu, S 2022, 'Complementary biomarker detection for bisphosphonate use in racehorses', Toxicologie Analytique et Clinique, vol. 34, no. 3, pp. S23-S24.
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Aim Determining the use of off-label bisphosphonates (BPs) in young horses (  4 years old) is of interest due to the threat to racing integrity and welfare associated with this class of drugs that have the potential to manipulate bone structure. The analysis of BPs in biological matrices is challenging by liquid chromatography coupled to mass spectrometry (LC-MS/MS) and alternative sample preparation approaches are needed to detect their misuse in racehorses. There are currently two classes of BPs: non-nitrogen and nitrogen-containing with each having a distinct mode of action. Currently two non-nitrogenous based BPs are available for use in horses, tiludronic acid (or tiludronate) and chlodronate for the treatment of navicular syndrome (Mitchell et al. BMC Veterinary Research 2019;15(1):211) in horses over the age of 4. There is, however, evidence that BPs can persist in the bone for several years after administration since they can form hydroxyapatite crystals prior to being fully absorbed by active osteoclasts where full inhibitory action is performed (Riggs et al. Equine veterinary journal 2021;53(6):1287–1295). Therefore, with this prolonged detection time for the BPs, it is necessary to investigate whether the use of metabolomic biomarkers can provide a complementary method for the detection of their misuse. The aim of this research was to develop a biomarker approach for complementary direct detection of bisphosphonate drugs in equine plasma. Method BPs are hydrophilic therefore the targeted detection of tiludronic acid in equine plasma required an orthogonal solid phase extraction (SPE) method using both a polymeric reversed-phase sorbent and a weak anion exchange cartridge prior to derivatisation using trimethyl orthoacetate and reverse LC-MS/MS. Endogenous lipids and corticosteroids in equine plasma were detected after protein precipitation and SPE with a polymeric reverse phase cartridge prior to liquid chromatography high-resolution mass spectrometry. Da

Tou, K, Cawley, A, Bowen, C, Sornalingam, K & Fu, S 2022, 'Measurements of hydrocortisone and cortisone for longitudinal profiling of equine plasma by liquid chromatography–tandem mass spectrometry', Drug Testing and Analysis, vol. 14, no. 5, pp. 943-952.
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AbstractThe conventional detection of exogenous drugs in equine doping samples has been used for confirmation and subsequent prosecution of participants responsible. In recent years, alternative methods using indirect detection have been investigated due to the expanding number of pharmaceutical agents available with the potential of misuse. The monitoring of endogenous biomarkers such as hydrocortisone (HC) has been studied in equine urine with an international threshold of 1 μg/ml established; however, there is no current threshold for equine plasma. The aim of this research was to investigate plasma concentrations of HC and cortisone (C) in race day samples compared to an administration of Triamcinolone Acetonide (TACA). The reference population (n = 1150) provided HC (6 to 145 ng/ml) and C (0.7 to 13 ng/ml) levels to derive the HC to C ratio (HC/C). Population reference limits (PRLs) were proposed for HC/C values at 0.2 (lower) and 61 (upper). Administration of TACA resulted in down‐regulation of HC/C values below the estimated PRLs for up to 96 h post‐administration. This indirect detection period was longer than the detection of TACA for 72 h. The use of individual reference limits (IRLs) for HC/C values was investigated to support the Equine Biological Passport (EBP), an intelligence model developed by Racing NSW for longitudinal monitoring of biomarkers.

Tran, KB, Lang, JJ, Compton, K, Xu, R, Acheson, AR, Henrikson, HJ, Kocarnik, JM, Penberthy, L, Aali, A, Abbas, Q, Abbasi, B, Abbasi-Kangevari, M, Abbasi-Kangevari, Z, Abbastabar, H, Abdelmasseh, M, Abd-Elsalam, S, Abdelwahab, AA, Abdoli, G, Abdulkadir, HA, Abedi, A, Abegaz, KH, Abidi, H, Aboagye, RG, Abolhassani, H, Absalan, A, Abtew, YD, Abubaker Ali, H, Abu-Gharbieh, E, Achappa, B, Acuna, JM, Addison, D, Addo, IY, Adegboye, OA, Adesina, MA, Adnan, M, Adnani, QES, Advani, SM, Afrin, S, Afzal, MS, Aggarwal, M, Ahinkorah, BO, Ahmad, AR, Ahmad, R, Ahmad, S, Ahmad, S, Ahmadi, S, Ahmed, H, Ahmed, LA, Ahmed, MB, Ahmed Rashid, T, Aiman, W, Ajami, M, Akalu, GT, Akbarzadeh-Khiavi, M, Aklilu, A, Akonde, M, Akunna, CJ, Al Hamad, H, Alahdab, F, Alanezi, FM, Alanzi, TM, Alessy, SA, Algammal, AM, Al-Hanawi, MK, Alhassan, RK, Ali, BA, Ali, L, Ali, SS, Alimohamadi, Y, Alipour, V, Aljunid, SM, Alkhayyat, M, Al-Maweri, SAA, Almustanyir, S, Alonso, N, Alqalyoobi, S, Al-Raddadi, RM, Al-Rifai, RHH, Al-Sabah, SK, Al-Tammemi, AB, Altawalah, H, Alvis-Guzman, N, Amare, F, Ameyaw, EK, Aminian Dehkordi, JJ, Amirzade-Iranaq, MH, Amu, H, Amusa, GA, Ancuceanu, R, Anderson, JA, Animut, YA, Anoushiravani, A, Anoushirvani, AA, Ansari-Moghaddam, A, Ansha, MG, Antony, B, Antwi, MH, Anwar, SL, Anwer, R, Anyasodor, AE, Arabloo, J, Arab-Zozani, M, Aremu, O, Argaw, AM, Ariffin, H, Aripov, T, Arshad, M, Artaman, A, Arulappan, J, Aruleba, RT, Aryannejad, A, Asaad, M, Asemahagn, MA, Asemi, Z, Asghari-Jafarabadi, M, Ashraf, T, Assadi, R, Athar, M, Athari, SS, Atout, MMW, Attia, S, Aujayeb, A, Ausloos, M, Avila-Burgos, L, Awedew, AF, Awoke, MA, Awoke, T, Ayala Quintanilla, BP, Ayana, TM, Ayen, SS, Azadi, D, Azadnajafabad, S, Azami-Aghdash, S, Azanaw, MM, Azangou-Khyavy, M, Azari Jafari, A, Azizi, H, Azzam, AYY, Babajani, A, Badar, M, Badiye, AD, Baghcheghi, N, Bagheri, N, Bagherieh, S, Bahadory, S, Baig, AA, Baker, JL, Bakhtiari, A, Bakshi, RK, Banach, M, Banerjee, I, Bardhan, M, Barone-Adesi, F, Barra, F, Barrow, A, Bashir, NZ, Bashiri, A, Basu, S, Batiha, A-MM, Begum, A, Bekele, AB, Belay, AS, Belete, MA, Belgaumi, UI, Bell, AW, Belo, L, Benzian, H, Berhie, AY, Bermudez, ANC, Bernabe, E, Bhagavathula, AS, Bhala, N, Bhandari, BB, Bhardwaj, N, Bhardwaj, P, Bhattacharyya, K, Bhojaraja, VS, Bhuyan, SS, Bibi, S, Bilchut, AH, Bintoro, BS, Biondi, A & et al. 2022, 'The global burden of cancer attributable to risk factors, 2010–19: a systematic analysis for the Global Burden of Disease Study 2019', The Lancet, vol. 400, no. 10352, pp. 563-591.
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BACKGROUND: Understanding the magnitude of cancer burden attributable to potentially modifiable risk factors is crucial for development of effective prevention and mitigation strategies. We analysed results from the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2019 to inform cancer control planning efforts globally. METHODS: The GBD 2019 comparative risk assessment framework was used to estimate cancer burden attributable to behavioural, environmental and occupational, and metabolic risk factors. A total of 82 risk-outcome pairs were included on the basis of the World Cancer Research Fund criteria. Estimated cancer deaths and disability-adjusted life-years (DALYs) in 2019 and change in these measures between 2010 and 2019 are presented. FINDINGS: Globally, in 2019, the risk factors included in this analysis accounted for 4·45 million (95% uncertainty interval 4·01-4·94) deaths and 105 million (95·0-116) DALYs for both sexes combined, representing 44·4% (41·3-48·4) of all cancer deaths and 42·0% (39·1-45·6) of all DALYs. There were 2·88 million (2·60-3·18) risk-attributable cancer deaths in males (50·6% [47·8-54·1] of all male cancer deaths) and 1·58 million (1·36-1·84) risk-attributable cancer deaths in females (36·3% [32·5-41·3] of all female cancer deaths). The leading risk factors at the most detailed level globally for risk-attributable cancer deaths and DALYs in 2019 for both sexes combined were smoking, followed by alcohol use and high BMI. Risk-attributable cancer burden varied by world region and Socio-demographic Index (SDI), with smoking, unsafe sex, and alcohol use being the three leading risk factors for risk-attributable cancer DALYs in low SDI locations in 2019, whereas DALYs in high SDI locations mirrored the top three global risk factor rankings. From 2010 to 2019, global risk-attributable cancer deaths increased by 20·4% (12·6-28·4) and DALYs by 16·8% (8·8-25·0), with the greatest percentage increase in metabolic ri...

Tran, VLT, Hortle, E, Britton, WJ & Oehlers, SH 2022, 'Common anti-haemostatic medications increase the severity of systemic infection by uropathogenic Escherichia coli', Microbiological Research, vol. 254, pp. 126918-126918.
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Trist, BG, Genoud, S, Roudeau, S, Rookyard, A, Abdeen, A, Cottam, V, Hare, DJ, White, M, Altvater, J, Fifita, JA, Hogan, A, Grima, N, Blair, IP, Kysenius, K, Crouch, PJ, Carmona, A, Rufin, Y, Claverol, S, Van Malderen, S, Falkenberg, G, Paterson, DJ, Smith, B, Troakes, C, Vance, C, Shaw, CE, Al-Sarraj, S, Cordwell, S, Halliday, G, Ortega, R & Double, KL 2022, 'Altered SOD1 maturation and post-translational modification in amyotrophic lateral sclerosis spinal cord', Brain, vol. 145, no. 9, pp. 3108-3130.
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Abstract Aberrant self-assembly and toxicity of wild-type and mutant superoxide dismutase 1 (SOD1) has been widely examined in silico, in vitro and in transgenic animal models of amyotrophic lateral sclerosis. Detailed examination of the protein in disease-affected tissues from amyotrophic lateral sclerosis patients, however, remains scarce. We used histological, biochemical and analytical techniques to profile alterations to SOD1 protein deposition, subcellular localization, maturation and post-translational modification in post-mortem spinal cord tissues from amyotrophic lateral sclerosis cases and controls. Tissues were dissected into ventral and dorsal spinal cord grey matter to assess the specificity of alterations within regions of motor neuron degeneration. We provide evidence of the mislocalization and accumulation of structurally disordered, immature SOD1 protein conformers in spinal cord motor neurons of SOD1-linked and non-SOD1-linked familial amyotrophic lateral sclerosis cases, and sporadic amyotrophic lateral sclerosis cases, compared with control motor neurons. These changes were collectively associated with instability and mismetallation of enzymatically active SOD1 dimers, as well as alterations to SOD1 post-translational modifications and molecular chaperones governing SOD1 maturation. Atypical changes to SOD1 protein were largely restricted to regions of neurodegeneration in amyotrophic lateral sclerosis cases, and clearly differentiated all forms of amyotrophic lateral sclerosis from controls. Substantial heterogeneity in the presence of these changes was also observed between amyotrophic lateral sclerosis cases. Our data demonstrate that varying forms of SOD1 proteinopathy are a common feature of all forms of amyotrophic lateral sclerosis, and support the presence of one or more convergent b...

Tsounis, C, Subhash, B, Kumar, PV, Bedford, NM, Zhao, Y, Shenoy, J, Ma, Z, Zhang, D, Toe, CY, Cheong, S, Tilley, RD, Lu, X, Dai, L, Han, Z & Amal, R 2022, 'Pt Single Atom Electrocatalysts at Graphene Edges for Efficient Alkaline Hydrogen Evolution', Advanced Functional Materials, vol. 32, no. 38.
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AbstractGraphene edges exhibit a highly localized density of states that result in increased reactivity compared to its basal plane. However, exploiting this increased reactivity to anchor and tune the electronic states of single atom catalysts (SACs) remains elusive. To investigate this, a method to anchor Pt SACs with ultra‐low mass loadings at the edges of edge‐rich vertically aligned graphene (as low as 0.71 µg Pt cm–2) is developed. Angle‐dependent X‐ray absorption spectroscopy and density‐functional theory calculations reveal that edge‐anchored Pt SACs has a robust coupling with the π‐electrons of graphene. This interaction results in a higher occupancy of the Pt 5d orbital, shifting the d‐band center toward the Fermi level, improving the adsorption of *H for the hydrogen evolution reaction (HER). Pt primarily coordinated to the graphene edge shows improved alkaline HER performance compared to Pt coordinated in mixed environments (turnover frequencies of 22.6 and 10.9 s–1 at an overpotential of 150 mV, respectively). This work demonstrates an effective route to engineering the coordination environment of Pt SACs by using the graphene edge for enhanced energy conversion reactions.

Tu, X, Kim, RY, Brown, AC, de Jong, E, Jones-Freeman, B, Ali, MK, Gomez, HM, Budden, KF, Starkey, MR, Cameron, GJM, Loering, S, Nguyen, DH, Nair, PM, Haw, TJ, Alemao, CA, Faiz, A, Tay, HL, Wark, PAB, Knight, DA, Foster, PS, Bosco, A, Horvat, JC, Hansbro, PM & Donovan, C 2022, 'Airway and parenchymal transcriptomics in a novel model of asthma and COPD overlap', Journal of Allergy and Clinical Immunology, vol. 150, no. 4, pp. 817-829.e6.
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BACKGROUND: Asthma and chronic obstructive pulmonary disease (COPD) are common chronic respiratory diseases, and some patients have overlapping disease features, termed asthma-COPD overlap (ACO). Patients characterized with ACO have increased disease severity; however, the mechanisms driving this have not been widely studied. OBJECTIVES: This study sought to characterize the phenotypic and transcriptomic features of experimental ACO in mice induced by chronic house dust mite antigen and cigarette smoke exposure. METHODS: Female BALB/c mice were chronically exposed to house dust mite antigen for 11 weeks to induce experimental asthma, cigarette smoke for 8 weeks to induce experimental COPD, or both concurrently to induce experimental ACO. Lung inflammation, structural changes, and lung function were assessed. RNA-sequencing was performed on separated airway and parenchyma lung tissues to assess transcriptional changes. Validation of a novel upstream driver SPI1 in experimental ACO was assessed using the pharmacological SPI1 inhibitor, DB2313. RESULTS: Experimental ACO recapitulated features of both asthma and COPD, with mixed pulmonary eosinophilic/neutrophilic inflammation, small airway collagen deposition, and increased airway hyperresponsiveness. Transcriptomic analysis identified common and distinct dysregulated gene clusters in airway and parenchyma samples in experimental asthma, COPD, and ACO. Upstream driver analysis revealed increased expression of the transcription factor Spi1. Pharmacological inhibition of SPI1 using DB2313, reduced airway remodeling and airway hyperresponsiveness in experimental ACO. CONCLUSIONS: A new experimental model of ACO featuring chronic dual exposures to house dust mite and cigarette smoke mimics key disease features observed in patients with ACO and revealed novel disease mechanisms, including upregulation of SPI1, that are amenable to therapy.

Turan, Y, Kalkandelen, C, Palaci, Y, Sahin, A, Gokce, H, Gunduz, O & Ben-Nissan, B 2022, 'Synthesis and cytotoxicity analysis of porous β-TCP/starch bioceramics', Journal of the Australian Ceramic Society, vol. 58, no. 2, pp. 487-494.
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Turpin, GA, Nelson, A, Holt, SA, Giles, LW, Milogrodzka, I, Teo, BM, Raghuwanshi, VS, Horn, RG, van 't Hag, L & Tabor, RF 2022, 'Investigating Adsorption of Cellulose Nanocrystals at Air–Liquid and Solid–Liquid Interfaces in the Presence of Hydrotropes', Advanced Materials Interfaces, vol. 9, no. 31.
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AbstractCoating a substrate with anisotropic nanoparticles such as cellulose nanocrystals (CNCs) confers some of their desirable physicochemical properties, such as strength, wettability, and barrier properties. The formation of monolayer coatings of CNCs via dip coating is affected by the enrichment of CNCs at both air–liquid and substrate–liquid interfaces. In this work, a surfactant‐free method for dip coating CNCs is presented through use of the hydrotrope tetraethylammonium chloride. Hydrotropes demonstrate a different mechanism for facilitating interfacial enrichment, adsorbing to CNCs and rendering them weakly hydrophobic, causing them to adsorb to both solid–liquid and air–liquid interfaces without affecting the surface tension of the system. This new coating mechanism may be more robust as adsorption onto the substrate from the bulk dispersion is less sensitive to the air–liquid interface. Adsorption at the solid–liquid interface showed two distinct CNC layers, with a tightly bound, close‐packed CNC layer at the interface, and a loosely associated outer layer. Adsorption of both layers is shown to be fully reversible after washing with ultra pure water, highlighting the potential of hydrotropes for facilitating new coating mechanisms.

Unzueta-Martínez, A, Scanes, E, Parker, LM, Ross, PM, O’Connor, W & Bowen, JL 2022, 'Microbiomes of the Sydney Rock Oyster are acquired through both vertical and horizontal transmission', Animal Microbiome, vol. 4, no. 1.
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AbstractBackgroundThe term holobiont is widely accepted to describe animal hosts and their associated microorganisms. The genomes of all that the holobiont encompasses, are termed the hologenome and it has been proposed as a unit of selection in evolution. To demonstrate that natural selection acts on the hologenome, a significant portion of the associated microbial genomes should be transferred between generations. Using the Sydney Rock Oyster (Saccostrea glomerata) as a model, we tested if the microbes of this broadcast spawning species could be passed down to the next generation by conducting single parent crosses and tracking the microbiome from parent to offspring and throughout early larval stages using 16S rRNA gene amplicon sequencing. From each cross, we sampled adult tissues (mantle, gill, stomach, gonad, eggs or sperm), larvae (D-veliger, umbo, eyed pediveliger, and spat), and the surrounding environment (water and algae feed) for microbial community analysis.ResultsWe found that each larval stage has a distinct microbiome that is partially influenced by their parental microbiome, particularly the maternal egg microbiome. We also demonstrate the presence of core microbes that are consistent across all families, persist throughout early life stages (from eggs to spat), and are not detected in the microbiomes of the surrounding environment. In addition to the core microbiomes that span all life cycle stages, there is also evidence of environmentally acquired microbial communities, with earlier larval stages (D-veliger and umbo), more influenced by seawater microbiomes, and later larval stages (eyed pediveliger and spat) dominated by microbial members that are specific to oysters and not detected in the surrounding environment.Conclusion

Usman, M, Ahsan, MT, Javed, S, Ali, Z, Zhan, Y, Ahmed, I, Butt, S, Islam, M, Mahmood, A & Akram, MA 2022, 'Facile synthesis of iron nickel cobalt ternary oxide (FNCO) mesoporous nanowires as electrode material for supercapacitor application', Journal of Materiomics, vol. 8, no. 1, pp. 221-228.
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van den Berge, M & Faiz, A 2022, 'Transcriptome-based Signatures: The Future Biomarkers in Obstructive Pulmonary Diseases Such as Asthma and Chronic Obstructive Pulmonary Disease?', American Journal of Respiratory and Critical Care Medicine, vol. 205, no. 2, pp. 139-140.
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van der Mierden, S, Hooijmans, CR, Tillema, AHJ, Rehn, S, Bleich, A & Leenaars, CHC 2022, 'Laboratory animals search filter for different literature databases: PubMed, Embase, Web of Science and PsycINFO', Laboratory Animals, vol. 56, no. 3, pp. 279-286.
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Systematic reviews are important tools in animal research, but the ever-increasing number of studies makes retrieval of all relevant publications challenging. Search filters aid in retrieving as many animal studies as possible. In this paper we provide updated and expanded versions of the SYRCLE animal filters for PubMed and Embase. We provide the Embase filter for both Embase.com and via Ovid. Furthermore, we provide new animal search filters for Web of Science (WoS) and APA PsycINFO via psycnet.apa.org and via Ovid. Compared with previous versions, the new filters retrieved 0.5–47.1% (19 references for PubMed, 837 for WoS) more references in a real-life example. All filters retrieved additional references, comprising multiple relevant reviews. A random sample from WoS found at least one potentially relevant primary study. These animal search filters facilitate identifying as many animal studies as possible while minimising the number of non-animal studies.

van Nijnatten, J, Brandsma, C-A, Steiling, K, Hiemstra, PS, Timens, W, van den Berge, M & Faiz, A 2022, 'High miR203a-3p and miR-375 expression in the airways of smokers with and without COPD', Scientific Reports, vol. 12, no. 1.
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AbstractSmoking is a leading cause of chronic obstructive pulmonary disease (COPD). It is known to have a significant impact on gene expression and (inflammatory) cell populations in the airways involved in COPD pathogenesis. In this study, we investigated the impact of smoking on the expression of miRNAs in healthy and COPD individuals. We aimed to elucidate the overall smoking-induced miRNA changes and those specific to COPD. In addition, we investigated the downstream effects on regulatory gene expression and the correlation to cellular composition. We performed a genome-wide miRNA expression analysis on a dataset of 40 current- and 22 ex-smoking COPD patients and a dataset of 35 current- and 38 non-smoking respiratory healthy controls and validated the results in an independent dataset. miRNA expression was then correlated with mRNA expression in the same patients to assess potential regulatory effects of the miRNAs. Finally, cellular deconvolution analysis was used to relate miRNAs changes to specific cell populations. Current smoking was associated with increased expression of three miRNAs in the COPD patients and 18 miRNAs in the asymptomatic smokers compared to respiratory healthy controls. In comparison, four miRNAs were lower expressed with current smoking in asymptomatic controls. Two of the three smoking-related miRNAs in COPD, miR-203a-3p and miR-375, were also higher expressed with current smoking in COPD patients and the asymptomatic controls. The other smoking-related miRNA in COPD patients, i.e. miR-31-3p, was not present in the respiratory healthy control dataset. miRNA-mRNA correlations demonstrated that miR-203a-3p, miR-375 and also miR-31-3p expression were negatively associated with genes involved in pro-inflammatory pathways and positively associated with genes involved in the xenobiotic pathway. Cellular deconvolution showed that higher levels of miR-203a-3p were associated with higher proportions...

van Zandwijk, N, Rasko, JEJ, George, AM, Frank, AL & Reid, G 2022, 'The silent malignant mesothelioma epidemic: a call to action', The Lancet Oncology, vol. 23, no. 10, pp. 1245-1248.
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Vanka, KS, Shukla, S, Gomez, HM, James, C, Palanisami, T, Williams, K, Chambers, DC, Britton, WJ, Ilic, D, Hansbro, PM & Horvat, JC 2022, 'Understanding the pathogenesis of occupational coal and silica dust-associated lung disease', European Respiratory Review, vol. 31, no. 165, pp. 210250-210250.
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Workers in the mining and construction industries are at increased risk of respiratory and other diseases as a result of being exposed to harmful levels of airborne particulate matter (PM) for extended periods of time. While clear links have been established between PM exposure and the development of occupational lung disease, the mechanisms are still poorly understood. A greater understanding of how exposures to different levels and types of PM encountered in mining and construction workplaces affect pathophysiological processes in the airways and lungs and result in different forms of occupational lung disease is urgently required. Such information is needed to inform safe exposure limits and monitoring guidelines for different types of PM and development of biomarkers for earlier disease diagnosis. Suspended particles with a 50% cut-off aerodynamic diameter of 10 µm and 2.5 µm are considered biologically active owing to their ability to bypass the upper respiratory tract's defences and penetrate deep into the lung parenchyma, where they induce potentially irreversible damage, impair lung function and reduce the quality of life. Here we review the current understanding of occupational respiratory diseases, including coal worker pneumoconiosis and silicosis, and how PM exposure may affect pathophysiological responses in the airways and lungs. We also highlight the use of experimental models for better understanding these mechanisms of pathogenesis. We outline the urgency for revised dust control strategies, and the need for evidence-based identification of safe level exposures using clinical and experimental studies to better protect workers’ health.

Verma, N, Arora, V, Awasthi, R, Chan, Y, Jha, NK, Thapa, K, Jawaid, T, Kamal, M, Gupta, G, Liu, G, Paudel, KR, Hansbro, PM, George Oliver, BG, Singh, SK, Chellappan, DK, Dureja, H & Dua, K 2022, 'Recent developments, challenges and future prospects in advanced drug delivery systems in the management of tuberculosis', Journal of Drug Delivery Science and Technology, vol. 75, pp. 103690-103690.
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Verma, NK, Tan, SJ, Chen, J, Chen, H, Ismail, MH, Rice, SA, Bifani, P, Hariharan, S, Paul, VD, Sriram, B, Dam, LC, Chan, CC, Ho, P, Goh, BC, Chung, SJ, Goh, KCM, Thong, SH, Kwa, AL-H, Ostrowski, A, Aung, TT, Razali, H, Low, SWY, Bhattacharyya, MS, Gautam, HK, Lakshminarayanan, R, Sicheritz-Pontén, T, Clokie, MRJ, Moreira, W & van Steensel, MAM 2022, 'inPhocus: Current State and Challenges of Phage Research in Singapore', PHAGE, vol. 3, no. 1, pp. 6-11.
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Villani, M, Quiroz, M, Kohn, R & Salomone, R 2022, 'Spectral Subsampling MCMC for Stationary Multivariate Time Series with Applications to Vector ARTFIMA Processes', Econometrics and Statistics.
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Vindin, HJ, Oliver, BGG & Weiss, AS 2022, 'Elastin in healthy and diseased lung', Current Opinion in Biotechnology, vol. 74, pp. 15-20.
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Elastic fibers are an essential part of the pulmonary extracellular matrix (ECM). Intact elastin is required for normal function and its damage contributes profoundly to the etiology and pathology of lung disease. This highlights the need for novel lung-specific imaging methodology that enables high-resolution 3D visualization of the ECM. We consider elastin's involvement in chronic respiratory disease and examine recent methods for imaging and modeling of the lung in the context of advances in lung tissue engineering for research and clinical application.

Vo, HNP, Nguyen, TMH, Ngo, HH, Guo, W & Shukla, P 2022, 'Biochar sorption of perfluoroalkyl substances (PFASs) in aqueous film-forming foams-impacted groundwater: Effects of PFASs properties and groundwater chemistry', Chemosphere, vol. 286, no. Pt 1, pp. 131622-131622.
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The widespread use of per- and polyfluoroalkyl substances (PFASs)-related products such as aqueous film-forming foams (AFFF) has led to increasing contamination of groundwater systems. The concentration of PFASs in AFFF-impacted groundwater can be several orders of magnitude higher than the drinking water standard. There is a need for a sustainable and effective sorbent to remove PFASs from groundwater. This work aims to investigate the sorption of PFASs in groundwater by biochar column. The specific objectives are to understand the influences of PFASs properties and groundwater chemistry to PFASs sorption by biochar. The PFASs-spiked Milli-Q water (including 19 PFASs) and four aqueous film-forming foams (AFFF)-impacted groundwater were used. The partitioning coefficients (log Kd) of long chain PFASs ranged from 0.77 to 4.63 while for short chain PFASs they remained below 0.68. For long chain PFASs (C ≥ 7), log Kd increased by 0.5 and 0.8 for each CF2 moiety of PFCAs and PFSAs, respectively. Dissolved organic matter (DOM) was the most influential factor in PFASs sorption over pH, salinity, and specific ultraviolet absorbance (SUVA). DOM contained hydrophobic compounds and metal ions which can form DOM-PFASs complexes to provide more sorption sites for PFASs. The finding is useful for executing PFASs remediation by biochar filtration column, especially legacy long chain PFASs, for groundwater remediation.

Vuitika, L, Prates-Syed, WA, Silva, JDQ, Crema, KP, Côrtes, N, Lira, A, Lima, JBM, Camara, NOS, Schimke, LF, Cabral-Marques, O, Sadraeian, M, Chaves, LCS & Cabral-Miranda, G 2022, 'Vaccines against Emerging and Neglected Infectious Diseases: An Overview', Vaccines, vol. 10, no. 9, pp. 1385-1385.
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Neglected Tropical Diseases (NTDs) are a group of diseases that are highly prevalent in tropical and subtropical regions, and closely associated with poverty and marginalized populations. Infectious diseases affect over 1.6 billion people annually, and vaccines are the best prophylactic tool against them. Along with NTDs, emerging and reemerging infectious diseases also threaten global public health, as they can unpredictably result in pandemics. The recent advances in vaccinology allowed the development and licensing of new vaccine platforms that can target and prevent these diseases. In this work, we discuss the advances in vaccinology and some of the difficulties found in the vaccine development pipeline for selected NTDs and emerging and reemerging infectious diseases, including HIV, Dengue, Ebola, Chagas disease, malaria, leishmaniasis, zika, and chikungunya.

Wajahat, M, Kouzani, AZ, Khoo, SY & Mahmud, MAP 2022, 'A review on extrusion-based 3D-printed nanogenerators for energy harvesting', Journal of Materials Science, vol. 57, no. 1, pp. 140-169.
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Wand, MP & Yu, JCF 2022, 'Density estimation via Bayesian inference engines', AStA Advances in Statistical Analysis, vol. 106, no. 2, pp. 199-216.
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We explain how effective automatic probability density function estimates can be constructed using contemporary Bayesian inference engines such as those based on no-U-turn sampling and expectation propagation. Extensive simulation studies demonstrate that the proposed density estimates have excellent comparative performance and scale well to very large sample sizes due to a binning strategy. Moreover, the approach is fully Bayesian and all estimates are accompanied by point-wise credible intervals. An accompanying package in the R language facilitates easy use of the new density estimates.

Wang, C, Li, J, Liu, Q, Huete, A, Li, L, Dong, Y & Zhao, J 2022, 'Eastern‐Pacific and Central‐Pacific Types of ENSO Elicit Diverse Responses of Vegetation in the West Pacific Region', Geophysical Research Letters, vol. 49, no. 3.
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AbstractThe El Niño‐Southern Oscillation (ENSO) is one of the main factors causing extreme climate events and, thus, has a significant influence on global climate systems. However, the long‐term effects of ENSO on vegetation are not well understood due to the complexity of the ENSO phenomenon under global warming. Here, we examined the variations in the response of Leaf Area Index (LAI) to different types of ENSO from 1982 to 2017 in the west Pacific region and explored their relationship with climatic factors. Results show that about 34.5% of the vegetated area in the west Pacific region displayed LAI anomalies correlated with ENSO index from 1982 to 2017, which distributed differently across climatic types. Moreover, LAI anomalies elicited by the Central‐Pacific type and by the Eastern‐Pacific type of ENSO events were significantly different, which were contributed to the controls of the different types of ENSO on precipitation and temperature.

Wang, H, Mao, W, Lou, W, Jin, D, Wu, W, Wang, D, Kuang, T, Rong, Y, Xu, X & Zhang, L 2022, 'PYCR1: A Potential Prognostic Biomarker in Pancreatic Ductal Adenocarcinoma', Journal of Cancer, vol. 13, no. 5, pp. 1501-1511.
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Wang, JJ & Ooi, E 2022, 'The effect of parole supervision onrecidivism', Crime and Justice Bulletin.

Wang, JJ, Fung, T & Poynton, S 2022, 'Takeaway alcohol sales and violent crime: the implications of extended trading hours.', Crime and Justice Bulletin.

Wang, KYX, Pupo, GM, Tembe, V, Patrick, E, Strbenac, D, Schramm, S-J, Thompson, JF, Scolyer, RA, Muller, S, Tarr, G, Mann, GJ & Yang, JYH 2022, 'Cross-Platform Omics Prediction procedure: a statistical machine learning framework for wider implementation of precision medicine', npj Digital Medicine, vol. 5, no. 1, p. 85.
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AbstractIn this modern era of precision medicine, molecular signatures identified from advanced omics technologies hold great promise to better guide clinical decisions. However, current approaches are often location-specific due to the inherent differences between platforms and across multiple centres, thus limiting the transferability of molecular signatures. We present Cross-Platform Omics Prediction (CPOP), a penalised regression model that can use omics data to predict patient outcomes in a platform-independent manner and across time and experiments. CPOP improves on the traditional prediction framework of using gene-based features by selecting ratio-based features with similar estimated effect sizes. These components gave CPOP the ability to have a stable performance across datasets of similar biology, minimising the effect of technical noise often generated by omics platforms. We present a comprehensive evaluation using melanoma transcriptomics data to demonstrate its potential to be used as a critical part of a clinical screening framework for precision medicine. Additional assessment of generalisation was demonstrated with ovarian cancer and inflammatory bowel disease studies.

Wang, N, Yao, H, Tao, Q, Sun, J, Ma, H, Wang, Y, Zhou, C, Fan, H, Shao, H, Qin, A, Su, D, Wang, C & Chong, H 2022, 'TPE based aggregation induced emission fluorescent sensors for viscosity of liquid and mechanical properties of hydrogel', Chinese Chemical Letters, vol. 33, no. 1, pp. 252-256.
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Two amphiphilic TPE E/Z isomers with aggregation induced emission (AIE) property have been synthesized and characterized. The logarithmic fluorescent intensity of the two molecules was in positive relationship with logarithmic viscosity of liquid. To note, the Z-TPE isomer exhibited more sensitivity in the viscosity of liquid sensing in comparison with the corresponding E-TPE counterpart (around 1.80 folds). Furthermore, two molecules could be used as fluorescent sensors for mechanical properties (viscosity and storage modulus) of hydrogel as well. In addition, two sensors displayed low cytotoxicity in normal tissue cell line (L929) within the concentration range of 2–10 µmol/L. These results potentially promised their applications as fluorescent sensors for mechanical properties in the fields of biological and biomedical.

Wang, Q, Huang, X, Su, Y, Yin, G, Wang, S, Yu, B, Li, H, Qi, J, Chen, H, Zeng, W, Zhang, K, Verkhratsky, A, Niu, J & Yi, C 2022, 'Activation of Wnt/β-catenin pathway mitigates blood–brain barrier dysfunction in Alzheimer’s disease', Brain, vol. 145, no. 12, pp. 4474-4488.
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Abstract Alzheimer’s disease is a neurodegenerative disorder that causes age-dependent neurological and cognitive declines. The treatments for Alzheimer’s disease pose a significant challenge, because the mechanisms of disease are not being fully understood. Malfunction of the blood–brain barrier is increasingly recognized as a major contributor to the pathophysiology of Alzheimer’s disease, especially at the early stages of the disease. However, the underlying mechanisms remain poorly characterized, while few molecules can directly target and improve blood–brain barrier function in the context of Alzheimer’s disease. Here, we showed dysfunctional blood–brain barrier in patients with Alzheimer’s disease reflected by perivascular accumulation of blood-derived fibrinogen in the hippocampus and cortex, accompanied by decreased tight junction proteins Claudin-5 and glucose transporter Glut-1 in the brain endothelial cells. In the APPswe/PS1dE9 (APP/PS1) mouse model of Alzheimer’s disease, blood–brain barrier dysfunction started at 4 months of age and became severe at 9 months of age. In the cerebral microvessels of APP/PS1 mice and amyloid-β-treated brain endothelial cells, we found suppressed Wnt/β-catenin signalling triggered by an increase of GSK3β activation, but not an inhibition of the AKT pathway or switching to the Wnt/planar cell polarity pathway. Furthermore, using our newly developed optogenetic tool for controlled regulation of LRP6 (upstream regulator of the Wnt signalling) to activate Wnt/β-catenin pathway, blood–brain barrier malfunction was restored by preventing amyloid-β-induced brain endothelial cells impairments and promoting the barrier repair. In conclusion, targeting LRP6 in the Wnt/β-catenin pathway in the brain endothelium can alleviate blood–brain barrier malfunction induced by amyloid-β, which may be a potential treatment strategy for Alzheimer’s disease.

Wang, S, Zhao, S, Guo, X & Wang, G 2022, '2D Material‐Based Heterostructures for Rechargeable Batteries', Advanced Energy Materials, vol. 12, no. 4, pp. 2100864-2100864.
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Abstract2D materials are regarded as promising electrode materials for rechargeable batteries because of their advantages in providing ample active sites and improving electrochemical reaction kinetics. However, it remains a great challenge for 2D materials to fulfill all requirements for high‐performance energy storage devices in terms of electronic conductivity, the number of accessible active sites, structural stability, and mass production capability. Recent advances in constructing 2D material‐based heterostructures offer opportunities for utilizing synergistic effects between the individual blocks to achieve optimized properties and enhanced performance. In this perspective, the latest advances of 2D material‐based heterostructures are summarized, with particular emphasis on their multifunctional roles in high‐performance rechargeable batteries. Synthetic strategies, structural features in mixed dimensionalities, structure engineering strategies, and distinct functionalities of the 2D material‐based heterostructures in various electrochemical applications are systematically introduced. Finally, challenges and perspectives are presented to highlight future opportunities for developing 2D material‐based heterostructures for practical energy storage.

Wang, T, He, D, Yao, H, Guo, X, Sun, B & Wang, G 2022, 'Development of Proteins for High‐Performance Energy Storage Devices: Opportunities, Challenges, and Strategies', Advanced Energy Materials, vol. 12, no. 44, pp. 2202568-2202568.
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AbstractIn pursuit of reducing environmental impact during battery manufacture, the utilization of nontoxic and renewable materials is essential for building a sustainable future. As one of the most intensively investigated biomaterials, proteins have recently been applied in various high‐performance rechargeable batteries. In this review, the opportunities and challenges of using protein‐based materials for high‐performance energy storage devices are discussed. Recent developments of directly using proteins as active components (e.g., electrolytes, separators, catalysts or binders) in rechargeable batteries are summarized. The advantages and disadvantages of using proteins are compared with the traditional counterparts, and the working mechanisms when using proteins to improve the electrochemical performances of rechargeable batteries are elucidated. Finally, the future development of applying biomaterials to build better batteries is predicted.

Wang, Y, Cui, X, Zhang, J, Qiao, J, Huang, H, Shi, J & Wang, G 2022, 'Advances of atomically dispersed catalysts from single-atom to clusters in energy storage and conversion applications', Progress in Materials Science, vol. 128, pp. 100964-100964.
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Owing to the special structural characteristics and maximized efficiency, atomically dispersed catalysts (ADCs) with different atom sizes ranged from the single atom to clusters can bridge the gap between heterogeneous and homogeneous catalysis. Tremendous progress has been made in ADCs including developing advanced synthesis strategies, promoting electrochemical performance and unraveling the underlying fundamental mechanisms. Herein, the recent progress of ADCs ranged from single-atom to clusters has been systematically reviewed with emphasis on key issues of synthesis methods, stabilization strategies, performance evaluation, mechanistic understanding, integrated experimental and theoretical studies in typical applications of energy storage and conversion, including oxygen reduction reaction in fuel cell and metal-air battery, oxygen evolution and hydrogen evolution reactions in water splitting, hydrogen oxidation reactions, carbon dioxide reduction and nitrogen reduction reaction. Centering on the topics, the most up-to-date results are present, along with the perspectives and challenges for the future development of ADCs.

Wang, Y, Wang, X, Luu, LDW, Li, J, Cui, X, Yao, H, Chen, S, Fu, J, Wang, L, Wang, C, Yuan, R, Cai, Q, Huang, X, Huang, J, Li, Z, Li, S, Zhu, X & Tai, J 2022, 'Single‐cell transcriptomic atlas reveals distinct immunological responses between COVID‐19 vaccine and natural SARS‐CoV‐2 infection', Journal of Medical Virology, vol. 94, no. 11, pp. 5304-5324.
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AbstractTo control the ongoing coronavirus disease‐2019 (COVID‐19) pandemic, CoronaVac (Sinovac), an inactivated vaccine, has been granted emergency use authorization by many countries. However, the underlying mechanisms of the inactivated COVID‐19 vaccine‐induced immune response remain unclear, and little is known about its features compared to (Severe acute respiratory syndrome coronavirus 2) SARS‐CoV‐2 infection. Here, we implemented single‐cell RNA sequencing (scRNA‐seq) to profile longitudinally collected PBMCs (peripheral blood mononuclear cells) in six individuals immunized with CoronaVac and compared these to the profiles of COVID‐19 infected patients from a Single Cell Consortium. Both inactivated vaccines and SARS‐CoV‐2 infection altered the proportion of different immune cell types, caused B cell activation and differentiation, and induced the expression of genes associated with antibody production in the plasma. The inactivated vaccine and SARS‐COV‐2 infection also caused alterations in peripheral immune activity such as interferon response, inflammatory cytokine expression, innate immune cell apoptosis and migration, effector T cell exhaustion and cytotoxicity, however, the magnitude of change was greater in COVID‐19 patients, especially those with severe disease, than in immunized individuals. Further analyses revealed a distinct peripheral immune cell phenotype associated with CoronaVac immunization (HLA class II upregulation and IL21R upregulation in naïve B cells) versus SARS‐CoV‐2 infection (HLA class II downregulation and IL21R downregulation in naïve B cells from severe disease individuals). There were also differences in the expression of important genes associated with proinflammatory cytokines and thrombosis. In conclusion, this study provides a single‐cell atlas of the systemic immune response to CoronaVac immunization and revealed distinct imm...

Wang, Z, Kuang, T, Wu, W, Wang, D, Lou, W, Jin, D, Xu, X & Zhang, L 2022, 'GFAT1 is highly expressed in cancer stem cells of pancreatic cancer', Annals of Translational Medicine, vol. 10, no. 10, pp. 544-544.
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Wang, Z, Wang, Z, Rahman, MA, Ton-That, C & Ling, FCC 2022, 'Convertible Green Luminescence Determined by Surface Band Bending in ZnO', The Journal of Physical Chemistry C, vol. 126, no. 8, pp. 4082-4088.
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Green luminescence (GL) of ZnO is a typical defect emission and an important research topic for defect-controlling engineering. Two kinds of spectral characteristics, namely, Gaussian GL (GGL) and fine-structure GL (FSGL), are designated from a variety of spectra. It is found that GGL and FSGL can be reversibly converted through surface modification techniques where the location of the recombination center, the surface state, or the degree of band bending is modified. This convertible feature proves that the carrier recombination could be precisely controlled by surface modification. On the other hand, the effect of surface treatment on defects has achieved an unambiguous understanding, which is beneficial to effectively improve the performance of ZnO devices.

Ward, J 2022, 'A multifaceted, multijurisdictional, multiagency, and multidisciplinary approach to investigating unidentified and missing persons cases in Australia', Forensic Science International: Genetics Supplement Series, vol. 8, pp. 53-55.
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Watanabe, S, Iwai, T, Matsushita, R, Nakanishi, T, Kuzhiumparambil, U, Fu, S & Seto, Y 2022, 'Comparison between human liver microsomes and the fungus Cunninghamella elegans for biotransformation of the synthetic cannabinoid JWH-424 having a bromo-naphthyl moiety analysed by high-resolution mass spectrometry', Forensic Toxicology, vol. 40, no. 2, pp. 278-288.
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Watherston, J, Watson, J, Bruce, D, Ueland, M, McNevin, D & Ward, J 2022, 'An in-field evaluation of rapid DNA instruments for disaster victim identification', International Journal of Legal Medicine, vol. 136, no. 2, pp. 493-499.
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In 2019 and 2020, disaster victim identification (DVI) simulations were conducted at the Australian Facility for Taphonomic Experimental Research. Whole and fragmented cadavers were positioned to replicate a building collapse scenario and left to decompose for up to 4 weeks. This study evaluated the utility of the ANDE™ 6C Rapid DNA System and the RapidHITTM ID System for DVI in the field and mortuary. Applying post-mortem nail and tissue biopsy samples showed promise, with the added benefit of minimally invasive collection procedures and limited preparation requirements. The preferred platform will depend on a number of factors, including its intended use and operating environment.

Watson, P, O’Callaghan, C, Perkes, I, Bradfield, L & Turner, K 2022, 'Making habits measurable beyond what they are not: A focus on associative dual-process models', Neuroscience & Biobehavioral Reviews, vol. 142, pp. 104869-104869.
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Habits are the subject of intense international research. Under the associative dual-process model the outcome devaluation paradigm has been used extensively to classify behaviours as being either goal-directed (sensitive to shifts in the value of associated outcomes) or habitual (triggered by stimuli without anticipation of consequences). This has proven to be a useful framework for studying the neurobiology of habit and relevance of habits in clinical psychopathology. However, in recent years issues have been raised about this rather narrow definition of habits in comparison to habitual behaviour experienced in the real world. Specifically, defining habits as the absence of goal-directed control, the very specific set-ups required to demonstrate habit experimentally and the lack of direct evidence for habits as stimulus-response behaviours are viewed as problematic. In this review paper we address key critiques that have been raised about habit research within the framework of the associative dual-process model. We then highlight novel research approaches studying different features of habits with methods that expand beyond traditional paradigms.

Webster, J, Kehoe, MA, Nogarotto, E, Falconer, L, Donovan, NJ & Chapman, TA 2022, 'Using Genomics to Design a Pathovar-Specific Loop-Mediated Isothermal Amplification (LAMP) Assay, for the Improved Detection of Xanthomonas citri pv. citri', Microorganisms, vol. 10, no. 6, pp. 1153-1153.
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The ability to swiftly respond to pathogen incursions relies heavily on fast and accurate diagnostics. Current published assays for citrus bacterial canker do not target Xanthomonas citri pv. citri, the causative agent, with high specificity when testing Australian samples. While the current diagnostics are useful in countries where canker is endemic, the detection of canker in Australia requires an emergency response. Close relatives to X. citri pv. citri found in Australia may generate false positives with the current recommended diagnostic assays. Therefore, we developed a more specific detection tool for citrus bacterial canker to provide greater diagnostic confidence for surveillance and eradication efforts. We used genomic comparisons of 161 Xanthomonad genomes and identified and confirmed genomic regions specific for X. citri pv. citri by performing local alignments of unique regions to reference genomes. We then developed loop-mediated isothermal amplification primers and validated them against a panel of 190 isolates to confirm specificity. Our diagnostic assay showed 100% corroboration with the concurrently developed multiplex primers and represents an improved diagnostic method capable of effective citrus bacterial canker identification.

Wen, S, Li, D, Liu, Y, Chen, C, Wang, F, Zhou, J, Bao, G, Zhang, L & Jin, D 2022, 'Power-Dependent Optimal Concentrations of Tm³⁺ and Yb³⁺ in Upconversion Nanoparticles', The Journal of Physical Chemistry Letters, vol. 13, no. 23, pp. 5316-5323.
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Lanthanide-doped upconversion nanoparticles (UCNPs) have enabled a broad range of emerging nanophotonics and biophotonics applications. Here, we provide a quantitative guide to the optimum concentrations of Yb3+ sensitizer and Tm3+ emitter ions, highly dependent on the excitation power densities. To achieve this, we fabricate the inert-core@active-shell@inert-shell architecture to sandwich the same volume of the optically active section. Our results show that highly doped UCNPs enable an approximately 18-fold enhancement in brightness over that of conventional ones. Increasing the Tm3+ concentration improves the brightness by 6 times and increases the NIR/blue ratio by 11 times, while the increase of Yb3+ concentration enhances the brightness by 3 times and only slightly affects the NIR/blue ratio. Moreover, the optimal doping concentration of Tm3+ varies from 2% to 16%, which is highly dependent on the excitation power density ranging from 102 to 107 W/cm2. This work provides a guideline for designing bright UCNPs under different excitation conditions.

Werry, LP, Bundschuh, M, Mitrovic, SM, Lim, RP & Kefford, BJ 2022, 'Leaf litter breakdown along an elevational gradient in Australian alpine streams', Ecology and Evolution, vol. 12, no. 10.
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AbstractThe breakdown of allochthonous organic matter, is a central step in nutrient cycling in stream ecosystems. There is concern that increased temperatures from climate change will alter the breakdown rate of organic matter, with important consequences for the ecosystem functioning of alpine streams. This study investigated the rate of leaf litter breakdown and how temperature and other factors such as microbial and invertebrate activities influenced this over elevational and temporal gradients. Dried leaves of Snow Gum (Eucalyptus pauciflora) and cotton strips were deployed in coarse (6 mm), and fine (50 μm) mesh size bags along an 820 m elevation gradient. Loss of mass in leaf litter and cotton tensile strength per day (k per day), fungal biomass measured as ergosterol concentration, invertebrate colonization of leaf litter, and benthic organic matter (mass and composition) were determined. Both microbial and macroinvertebrate activities were equally important in leaf litter breakdown with the abundance of shredder invertebrate taxa. The overall leaf litter breakdown rate and loss of tensile strength in cotton strips (both k per day) were greater during warmer deployment periods and at lower elevations, with significant positive relationships between mean water temperature and leaf breakdown and loss of tensile strength rate, but no differences between sites, after accounting for the effects of temperature. Despite considerably lower amounts of benthic organic matter in streams above the tree line relative to those below, shredders were present in coarse mesh bags at all sites. Ergosterol concentration was greater on leaves in coarse mesh bags than in fine mesh bags, implying differences in the microbial communities. The importance of water temperatures on the rate of leaf litter breakdown suggests the potential effects of climate chan...

Wezenberg, SJ, Chen, L-J, Bos, JE, Feringa, BL, Howe, ENW, Wu, X, Siegler, MA & Gale, PA 2022, 'Photomodulation of Transmembrane Transport and Potential by Stiff-Stilbene Based Bis(thio)ureas', Journal of the American Chemical Society, vol. 144, no. 1, pp. 331-338.
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Membrane transport proteins fulfill important regulatory functions in biology with a common trait being their ability to respond to stimuli in the environment. Various small-molecule receptors, capable of mediating transmembrane transport, have been successfully developed. However, to confer stimuli-responsiveness on them poses a fundamental challenge. Here we demonstrate photocontrol of transmembrane transport and electric potential using bis(thio)ureas derived from stiff-stilbene. UV-vis and 1H NMR spectroscopy are used to monitor E-Z photoisomerization of these bis(thio)ureas and 1H NMR titrations reveal stronger binding of chloride to the (Z)-form than to the (E)-form. Additional insight into the binding properties is provided by single crystal X-ray crystallographic analysis and DFT geometry optimization. Importantly, the (Z)-isomers are much more active in transmembrane transport than the respective (E)-isomers as shown through various assays. As a result, both membrane transport and depolarization can be modulated upon irradiation, opening up new prospects toward light-based therapeutics as well as physiological and optopharmacological tools for studying anion transport-associated diseases and to stimulate neuronal activity, respectively.

White, SJU, Yang, T, Dontschuk, N, Li, C, Xu, Z-Q, Kianinia, M, Stacey, A, Toth, M & Aharonovich, I 2022, 'Author Correction: Electrical control of quantum emitters in a Van der Waals heterostructure', Light: Science & Applications, vol. 11, no. 1, p. 226.
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White, SJU, Yang, T, Dontschuk, N, Li, C, Xu, Z-Q, Kianinia, M, Stacey, A, Toth, M & Aharonovich, I 2022, 'Electrical control of quantum emitters in a Van der Waals heterostructure', Light: Science & Applications, vol. 11, no. 1, pp. 1-9.
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AbstractControlling and manipulating individual quantum systems in solids underpins the growing interest in the development of scalable quantum technologies. Recently, hexagonal boron nitride (hBN) has garnered significant attention in quantum photonic applications due to its ability to host optically stable quantum emitters. However, the large bandgap of hBN and the lack of efficient doping inhibits electrical triggering and limits opportunities to study the electrical control of emitters. Here, we show an approach to electrically modulate quantum emitters in an hBN-graphene van der Waals heterostructure. We show that quantum emitters in hBN can be reversibly activated and modulated by applying a bias across the device. Notably, a significant number of quantum emitters are intrinsically dark and become optically active at non-zero voltages. To explain the results, we provide a heuristic electrostatic model of this unique behavior. Finally, employing these devices we demonstrate a nearly-coherent source with linewidths of ~160 MHz. Our results enhance the potential of hBN for tunable solid-state quantum emitters for the growing field of quantum information science.

Wilder, BK, Vigdorovich, V, Carbonetti, S, Minkah, N, Hertoghs, N, Raappana, A, Cardamone, H, Oliver, BG, Trakhimets, O, Kumar, S, Dambrauskas, N, Arredondo, SA, Camargo, N, Seilie, AM, Murphy, SC, Kappe, SHI & Sather, DN 2022, 'Anti-TRAP/SSP2 monoclonal antibodies can inhibit sporozoite infection and may enhance protection of anti-CSP monoclonal antibodies', npj Vaccines, vol. 7, no. 1.
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AbstractVaccine-induced sterilizing protection from infection by Plasmodium parasites, the pathogens that cause malaria, will be essential in the fight against malaria as it would prevent both malaria-related disease and transmission. Stopping the relatively small number of parasites injected by the mosquito before they can migrate from the skin to the liver is an attractive means to this goal. Antibody-eliciting vaccines have been used to pursue this objective by targeting the major parasite surface protein present during this stage, the circumsporozoite protein (CSP). While CSP-based vaccines have recently had encouraging success in disease reduction, this was only achieved with extremely high antibody titers and appeared less effective for a complete block of infection (i.e., sterile protection). While such disease reduction is important, these and other results indicate that strategies focusing on CSP alone may not achieve the high levels of sterile protection needed for malaria eradication. Here, we show that monoclonal antibodies (mAbs) recognizing another sporozoite protein, TRAP/SSP2, exhibit a range of inhibitory activity and that these mAbs may augment CSP-based protection despite conferring no sterile protection on their own. Therefore, pursuing a multivalent subunit vaccine immunization is a promising strategy for improving infection-blocking malaria vaccines.

Wilkes Walburn, J, Rourke, ML, Furlan, E, DiBattista, JD, Broadhurst, MK, Fowler, AM, Hughes, JM & Fielder, S 2022, 'Robust environmental DNA assay development and validation: A case study with two vulnerable Australian fish', Aquatic Conservation: Marine and Freshwater Ecosystems, vol. 32, no. 7, pp. 1225-1231.
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AbstractAnalysis of environmental (e)DNA can facilitate an understanding of the presence and distribution of aquatic species. However, eDNA detection using quantitative PCR requires validated and standardized species‐specific assay designs.This study presents two eDNA assays to detect Murray cod, Maccullochella peelii, and mulloway, Argyrosomus japonicus (two ecologically vulnerable Australian species), based on small fragments of the mitochondrial 12S ribosomal RNA gene. A comprehensive description of species‐specific assay development, from assay design to testing in silico, in vitro and in situ, has been included to guide effective assay design and validation in future studies.The results indicate that the assay was species specific for M. peelii within its natural distribution. However, the assay also amplified genomic DNA from two allopatric and endangered congeners (Maccullochella ikei and Maccullochella mariensis), thus potentially facilitating their eDNA detection elsewhere. In contrast, the A. japonicus assay was highly species specific with no amplification among close relatives. Both target‐species assays are highly sensitive to as few as four and 10 copies per PCR reaction, respectively.This study has demon...

Wille, M, Grillo, V, Ban de Gouvea Pedroso, S, Burgess, GW, Crawley, A, Dickason, C, Hansbro, PM, Hoque, MA, Horwood, PF, Kirkland, PD, Kung, NY-H, Lynch, SE, Martin, S, McArthur, M, O’Riley, K, Read, AJ, Warner, S, Hoye, BJ, Lisovski, S, Leen, T, Hurt, AC, Butler, J, Broz, I, Davies, KR, Mileto, P, Neave, MJ, Stevens, V, Breed, AC, Lam, TTY, Holmes, EC, Klaassen, M & Wong, FYK 2022, 'Australia as a global sink for the genetic diversity of avian influenza A virus', PLOS Pathogens, vol. 18, no. 5, pp. e1010150-e1010150.
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Most of our understanding of the ecology and evolution of avian influenza A virus (AIV) in wild birds is derived from studies conducted in the northern hemisphere on waterfowl, with a substantial bias towards dabbling ducks. However, relevant environmental conditions and patterns of avian migration and reproduction are substantially different in the southern hemisphere. Through the sequencing and analysis of 333 unique AIV genomes collected from wild birds collected over 15 years we show that Australia is a global sink for AIV diversity and not integrally linked with the Eurasian gene pool. Rather, AIV are infrequently introduced to Australia, followed by decades of isolated circulation and eventual extinction. The number of co-circulating viral lineages varies per subtype. AIV haemagglutinin (HA) subtypes that are rarely identified at duck-centric study sites (H8-12) had more detected introductions and contemporary co-circulating lineages in Australia. Combined with a lack of duck migration beyond the Australian-Papuan region, these findings suggest introductions by long-distance migratory shorebirds. In addition, on the available data we found no evidence of directional or consistent patterns in virus movement across the Australian continent. This feature corresponds to patterns of bird movement, whereby waterfowl have nomadic and erratic rainfall-dependant distributions rather than consistent intra-continental migratory routes. Finally, we detected high levels of virus gene segment reassortment, with a high diversity of AIV genome constellations across years and locations. These data, in addition to those from other studies in Africa and South America, clearly show that patterns of AIV dynamics in the Southern Hemisphere are distinct from those in the temperate north.

Williams, NLR, Siboni, N, King, WL, Balaraju, V, Bramucci, A & Seymour, JR 2022, 'Latitudinal Dynamics of Vibrio along the Eastern Coastline of Australia', Water, vol. 14, no. 16, pp. 2510-2510.
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The marine genus of bacteria, Vibrio, includes several significant human and animal pathogens, highlighting the importance of defining the factors that govern their occurrence in the environment. To determine what controls large-scale spatial patterns among this genus, we examined the abundance and diversity of Vibrio communities along a 4000 km latitudinal gradient spanning the Australian coast. We used a Vibrio-specific amplicon sequencing assay to define Vibrio community diversity, as well as quantitative PCR and digital droplet PCR to identify patterns in the abundances of the human pathogens V. cholera, V. parahaemolyticus and V. vulnificus. The hsp60 amplicon sequencing analysis revealed significant differences in the composition of tropical and temperate Vibrio communities. Over 50% of Vibrio species detected, including the human pathogens V. parahaemolyticus and V. vulnificus, displayed significant correlations with either temperature, salinity, or both, as well as different species of phytoplankton. High levels of V. parahaemolyticus and V. vulnificus were detected in the tropical site at Darwin and the subtropical Gold Coast site, along with high levels of V. parahaemolyticus at the subtropical Sydney site. This study has revealed the key ecological determinants and latitudinal patterns in the abundance and diversity of coastal Vibrio communities, including insights into the distribution of human pathogens, within a region experiencing significant ecological shifts due to climate change.

Williams, NLR, Siboni, N, McLellan, SL, Potts, J, Scanes, P, Johnson, C, James, M, McCann, V & Seymour, JR 2022, 'Rainfall leads to elevated levels of antibiotic resistance genes within seawater at an Australian beach', Environmental Pollution, vol. 307, pp. 119456-119456.
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Anthropogenic waste streams can be major sources of antibiotic resistant microbes within the environment, creating a potential risk to public health. We examined patterns in the occurrence of a suite of antibiotic resistance genes (ARGs) and their links to enteric bacteria at a popular swimming beach in Australia that experiences intermittent contamination by sewage, with potential points of input including stormwater drains and a coastal lagoon. Samples were collected throughout a significant rainfall event (40.8 mm over 3 days) and analysed using both qPCR and 16S rRNA amplicon sequencing. Before the rainfall event, low levels of faecal indicator bacteria and a microbial source tracking human faeces (sewage) marker (Lachno3) were observed. These levels increased over 10x following rainfall. Within lagoon, drain and seawater samples, levels of the ARGs sulI, dfrA1 and qnrS increased by between 1 and 2 orders of magnitude after 20.4 mm of rain, while levels of tetA increased by an order of magnitude after a total of 40.8 mm. After 40.8 mm of rain sulI, tetA and qnrS could be detected 300 m offshore with levels remaining high five days after the rain event. Highest levels of sewage markers and ARGs were observed adjacent to the lagoon (when opened) and in-front of the stormwater drains, pinpointing these as the points of ARG input. Significant positive correlations were observed between all ARGs, and a suite of Amplicon Sequence Variants that were identified as stormwater drain indicator taxa using 16S rRNA amplicon sequencing data. Of note, some stormwater drain indicator taxa, which exhibited correlations to ARG abundance, included the human pathogens Arcobacter butzleri and Bacteroides fragilis. Given that previous research has linked high levels of ARGs in recreationally used environments to antimicrobial resistant pathogen infections, the observed patterns indicate a potentially elevated human health risk at a popular swimming beach following signif...

Williams, NLR, Siboni, N, Potts, J, Campey, M, Johnson, C, Rao, S, Bramucci, A, Scanes, P & Seymour, JR 2022, 'Molecular microbiological approaches reduce ambiguity about the sources of faecal pollution and identify microbial hazards within an urbanised coastal environment', Water Research, vol. 218, pp. 118534-118534.
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Urbanised beaches are regularly impacted by faecal pollution, but management actions to resolve the causes of contamination are often obfuscated by the inability of standard Faecal Indicator Bacteria (FIB) analyses to discriminate sources of faecal material or detect other microbial hazards, including antibiotic resistance genes (ARGs). We aimed to determine the causes, spatial extent, and point sources of faecal contamination within Rose Bay, a highly urbanised beach within Sydney, Australia's largest city, using molecular microbiological approaches. Sampling was performed across a network of transects originating at 9 stormwater drains located on Rose Bay beach over the course of a significant (67.5 mm) rainfall event, whereby samples were taken 6 days prior to any rain, on the day of initial rainfall (3.8 mm), three days later after 43 mm of rain and then four days after any rain. Quantitative PCR (qPCR) was used to target marker genes from bacteria (i.e., Lachnospiraceae and Bacteroides) that have been demonstrated to be specific to human faeces (sewage), along with gene sequences from Heliobacter and Bacteriodes that are specific to bird and dog faeces respectively, and ARGs (sulI, tetA, qnrS, dfrA1 and vanB). 16S rRNA gene amplicon sequencing was also used to discriminate microbial signatures of faecal contamination. Prior to the rain event, low FIB levels (mean: 2.4 CFU/100 ml) were accompanied by generally low levels of the human and animal faecal markers, with the exception of one transect, potentially indicative of a dry weather sewage leak. Following 43 mm of rain, levels of both human faecal markers increased significantly in stormwater drain and seawater samples, with highest levels of these markers pinpointing several stormwater drains as sources of sewage contamination. During this time, sewage contamination was observed up to 1000 m from shore and was significantly and positively correlated with often highly elevated levels of the ARGs d...

Windhagauer, M, Abbriano, RM, Pittrich, DA & Doblin, MA 2022, 'Phosphate-inducible poly-hydroxy butyrate production dynamics in CO2 supplemented upscaled cultivation of engineered Phaeodactylum tricornutum', Journal of Applied Phycology, vol. 34, no. 5, pp. 2259-2270.
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AbstractDiatoms such as Phaeodactylum tricornutum are emerging as sustainable alternatives to traditional eukaryotic microbial cell factories. In order to facilitate a viable process for production of heterologous metabolites, a rational genetic design specifically tailored to metabolic requirements as well as optimised culture conditions are required. In this study we investigated the effect of constitutive and inducible expression of the heterologous poly-3-hydroxybutyrate (PHB) pathway in P. tricornutum using non-integrative episomes in 3 different configurations. Constitutive expression led to downregulation of at least one individual gene out of three (phaA, phaB and phaC) and was outperformed by inducible expression. To further asses and optimise the dynamics of PHB accumulation driven by the inducible alkaline phosphatase 1 promoter, we upscaled the production to lab-scale bioreactors and tested the effect of supplemented CO2 on biomass and PHB accumulation. While ambient CO2 cultivation resulted in a maximum PHB yield of 2.3% cell dry weight (CDW) on day 11, under elevated CO2 concentrations PHB yield peaked at 1.7% CDW on day 8, coincident with PHB titres at 27.9 mg L−1 that were approximately threefold higher than ambient CO2. With other more valuable bio-products in mind, these results highlight the importance of the genetic design as well as substrate availability to supply additional reduction equivalents to boost biomass accumulation and relieve potential enzymatic bottlenecks for improved product accumulation.

Winskel‐Wood, B, Padula, MP, Marks, DC & Johnson, L 2022, 'Cold storage alters the immune characteristics of platelets and potentiates bacterial‐induced aggregation', Vox Sanguinis, vol. 117, no. 8, pp. 1006-1015.
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AbstractBackground and ObjectivesCold‐stored platelets are currently under clinical evaluation and have been approved for limited clinical use in the United States. Most studies have focused on the haemostatic functionality of cold‐stored platelets; however, limited information is available examining changes to their immune function.Materials and MethodsTwo buffy‐coat‐derived platelet components were combined and split into two treatment arms: room temperature (RT)‐stored (20–24°C) or refrigerated (cold‐stored, 2–6°C). The concentration of select soluble factors was measured in the supernatant using commercial ELISA kits. The abundance of surface receptors associated with immunological function was assessed by flow cytometry. Platelet aggregation was assessed in response to Escherichia coli and Staphylococcus aureus, in the presence and absence of RGDS (blocks active conformation of integrin α2β3).ResultsCold‐stored platelet components contained a lower supernatant concentration of C3a, RANTES and PF4. The abundance of surface‐bound P‐selectin and integrin α2β3 in the activated conformation increased during cold storage. In comparison, the abundance of CD86, CD44, ICAM‐2, CD40, TLR1, TLR2, TLR4, TLR3, TLR7 and TLR9 was lower on the surface membrane of cold‐stored platelets compared to RT‐stored components. Cold‐stored platelets exhibited an increased responsiveness to E. coli‐ and S. aureus‐induced aggregation compared to RT‐stored platelets. Inhibition of the active conformation of integrin α2β3 using RGDS reduced the potentiation o...

Wooster, EIF, Fleck, R, Torpy, F, Ramp, D & Irga, PJ 2022, 'Urban green roofs promote metropolitan biodiversity: A comparative case study', Building and Environment, vol. 207, pp. 108458-108458.
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Worden, PJ, Bogema, DR, Micallef, ML, Go, J, Deutscher, AT, Labbate, M, Green, TJ, King, WL, Liu, M, Seymour, JR & Jenkins, C 2022, 'Phylogenomic diversity of Vibrio species and other Gammaproteobacteria isolated from Pacific oysters (Crassostrea gigas) during a summer mortality outbreak', Microbial Genomics, vol. 8, no. 12.
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The Pacific oyster (PO), Crassostrea gigas, is an important commercial marine species but periodically experiences large stock losses due to disease events known as summer mortality. Summer mortality has been linked to environmental perturbations and numerous viral and bacterial agents, indicating this disease is multifactorial in nature. In 2013 and 2014, several summer mortality events occurred within the Port Stephens estuary (NSW, Australia). Extensive culture and molecular-based investigations were undertaken and several potentially pathogenic Vibrio species were identified. To improve species identification and genomically characterise isolates obtained from this outbreak, whole-genome sequencing (WGS) and subsequent genomic analyses were performed on 48 bacterial isolates, as well as a further nine isolates from other summer mortality studies using the same batch of juveniles. Average nucleotide identity (ANI) identified most isolates to the species level and included members of the Photobacterium , Pseudoalteromonas<...

Wright, AS, Doblin, MA & Scanes, PR 2022, 'Improper Maintenance Activities Alter Benefits of Urban Stormwater Treatment in a Temperate Constructed Wetland in NSW, Australia', Frontiers in Environmental Chemistry, vol. 3, pp. 1-14.
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Constructed wetlands (CWs) are an effective means to treat nutrient and sediment pollution in urban stormwater runoff to minimise impact on receiving waterways. Maintenance of devices is recognised as a major contributing factor to performance. There is a lack of evidence-based guidance on maintenance activities to optimise treatment, due to a paucity of data from long-term field studies into CW performance before and after maintenance. In this study, the nutrient and sediment removal efficiency (% RE) of a CW was evaluated by calculating removal efficiencies of nitrogen (N), phosphorus (P) and total suspended sediment (TSS) following a long-term sampling program under baseflow and event flow conditions. Sampling was carried out before, during and after maintenance. Maintenance involved removing all aquatic vegetation and 200–300 mm of sediments over a 3-week period, aiming to improve the wetland’s performance. Assessment of dissolved and particulate nutrient fractions allowed a comprehensive investigation into drivers of nutrient removal efficiency. Under baseflow conditions differences in inflow and outflow pollutant concentrations were used to calculate removal efficiency and pollutant loads were used during event flow conditions. Before maintenance, during baseflow conditions the wetland was removing total N (36% RE) but exporting total P (-52% RE) and total sediment (-94% RE). During event-flow conditions all target pollutants were being removed (total N 63% RE, total P 25% RE and TSS 69% RE). phosphorusDuring maintenance, the device continued to remove total N (18% RE) but the physical disturbance of the maintenance resulted in mass export of total P (-120% RE) and total sediment (−2,000% RE) over a short time period, effectively undoing previous treatment. After maintenance, during baseflow conditions, the wetlands’ ability to treat total N decreased (28% RE), improved for total P (1% RE), and became a chronic source of suspended sediment...

Wu, X, Gilchrist, AM & Gale, PA 2022, 'Janus metal-organic layer functioning as a biomimetic photosynthetic reaction center', Chem, vol. 8, no. 3, pp. 604-606.
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Wu, X, Wang, P, Lewis, W, Jiang, Y-B & Gale, PA 2022, 'Measuring anion binding at biomembrane interfaces', Nature Communications, vol. 13, no. 1, p. 4623.
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AbstractThe quantification of anion binding by molecular receptors within lipid bilayers remains challenging. Here we measure anion binding in lipid bilayers by creating a fluorescent macrocycle featuring a strong sulfate affinity. We find the determinants of anion binding in lipid bilayers to be different from those expected that govern anion binding in solution. Charge-dense anions H2PO4–and Cl–that prevail in dimethyl sulfoxide fail to bind to the macrocycle in lipids. In stark contrast, ClO4–and I–that hardly bind in dimethyl sulfoxide show surprisingly significant affinities for the macrocycle in lipids. We reveal a lipid bilayer anion binding principle that depends on anion polarisability and bilayer penetration depth of complexes leading to unexpected advantages of charge-diffuse anions. These insights enhance our understanding of how biological systems select anions and guide the design of functional molecular systems operating at biomembrane interfaces.

Wuerz, M, Lawson, CA, Ueland, M, Oakley, CA, Grossman, AR, Weis, VM, Suggett, DJ & Davy, SK 2022, 'Symbiosis induces unique volatile profiles in the model cnidarian Aiptasia', Journal of Experimental Biology, vol. 225, no. 19, p. jeb244600.
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ABSTRACT The establishment and maintenance of the symbiosis between a cnidarian host and its dinoflagellate symbionts is central to the success of coral reefs. To explore the metabolite production underlying this symbiosis, we focused on a group of low molecular weight secondary metabolites, biogenic volatile organic compounds (BVOCs). BVOCs are released from an organism or environment, and can be collected in the gas phase, allowing non-invasive analysis of an organism's metabolism (i.e. ‘volatilomics’). We characterised volatile profiles of the sea anemone Aiptasia (Exaiptasia diaphana), a model system for cnidarian–dinoflagellate symbiosis, using comprehensive two-dimensional gas chromatography coupled with time-of-flight mass spectrometry. We compared volatile profiles between: (1) symbiotic anemones containing their native symbiont, Breviolum minutum; (2) aposymbiotic anemones; and (3) cultured isolates of B. minutum. Overall, 152 BVOCs were detected, and classified into 14 groups based on their chemical structure, the most numerous groups being alkanes and aromatic compounds. A total of 53 BVOCs were differentially abundant between aposymbiotic anemones and B. minutum cultures; 13 between aposymbiotic and symbiotic anemones; and 60 between symbiotic anemones and cultures of B. minutum. More BVOCs were differentially abundant between cultured and symbiotic dinoflagellates than between aposymbiotic and symbiotic anemones, suggesting that symbiosis may modify symbiont physiology more than host physiology. This is the first volatilome analysis of the Aiptasia model system and provides a foundation from which to explore how BVOC production is perturbed under environmental stress, and ultimately the role they play in this important symbiosis.

Wyrsch, ER, Bushell, RN, Marenda, MS, Browning, GF & Djordjevic, SP 2022, 'Global Phylogeny and F Virulence Plasmid Carriage in Pandemic Escherichia coli ST1193', Microbiology Spectrum, vol. 10, no. 6, p. e0255422.
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We have generated an updated ST1193 phylogeny using publicly available sequences, reinforcing previous assertions that Escherichia coli ST1193 is a human-associated lineage, with many examples sourced from human extraintestinal infections. ST1193 from urban-adapted birds, wastewater, and companion animals are frequent, but isolates from animal agriculture are notably absent.

Wyrsch, ER, Nesporova, K, Tarabai, H, Jamborova, I, Bitar, I, Literak, I, Dolejska, M & Djordjevic, SP 2022, 'Urban Wildlife Crisis: Australian Silver Gull Is a Bystander Host to Widespread Clinical Antibiotic Resistance', mSystems, vol. 7, no. 3, p. e0015822.
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By compiling various genomic and phenotypic data sets, we have provided one of the most comprehensive genomic studies of Escherichia coli isolates from the Australian silver gull, on media containing clinically relevant antibiotics. The analysis of genetic structures capturing antimicrobial resistance genes across three gull breeding colonies in New South Wales, Australia, and comparisons to clinical data have revealed a range of trackable genetic signatures that highlight the broad distribution of clinical antimicrobial resistance in more than 170 different lineages of E. coli .

Xie, Q, Cleverly, J, Moore, CE, Ding, Y, Hall, CC, Ma, X, Brown, LA, Wang, C, Beringer, J, Prober, SM, Macfarlane, C, Meyer, WS, Yin, G & Huete, A 2022, 'Land surface phenology retrievals for arid and semi-arid ecosystems', ISPRS Journal of Photogrammetry and Remote Sensing, vol. 185, pp. 129-145.
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Land surface phenology (LSP) plays a critical role in the regulation of photosynthesis, evapotranspiration, and energy fluxes. Significant progress has been made in extracting LSP information over large areas using satellite data, yet LSP retrievals remain a challenge over vast arid and semi-arid ecosystems because of sparse greenness, high variability and the lack of distinct annual patterns; for example, the MODerate Imaging Spectrometer (MODIS) Land Cover Dynamics Product MCD12Q2 that provides LSP metrics globally often failed to provide LSP information in these ecosystems. In this study, we used a modified threshold algorithm to extract LSP timing metrics, including the start, peak, and end of growing seasons, using the 16-day composite Enhanced Vegetation Index (EVI) time series from MODIS data. We applied this regionally customized algorithm across all arid and semi-arid climate regions of Australia (75% of the continental land area) encompassing shrublands, grasslands, savannas, woodlands, and croplands, extracting LSP metrics annually from 2003 to 2018, with up to two (phenology) seasons accounted for in each year. Our algorithm yielded an average of 64.9% successful rate of retrieval (proportion of pixels with retrieved LSP metrics) across 16 years in Arid and Semi-arid AUStralia (AS-AUS), which was a significant increase compared to the 14.5% rate of retrieval yielded in our study area by the global product and the major cause of the different performances between these two approaches was the different EVI amplitude restrictions utilized to avoid spurious peaks (i.e. EVI amplitude ≥ 0.1 used by the global product and peak EVI ≥ time series average EVI used by our algorithm). Gross primary productivity (GPP) measurements at OzFlux eddy covariance (EC) tower sites were used to cross-compare with the presence/absence of growing seasons detected by our algorithm, and 97% of our retrieved seasons matched with those extracted using EC data. Prelimin...

Xie, Q, Huete, A, Hall, CC, Medlyn, BE, Power, SA, Davies, JM, Medek, DE & Beggs, PJ 2022, 'Satellite-observed shifts in C3/C4 abundance in Australian grasslands are associated with rainfall patterns', Remote Sensing of Environment, vol. 273, pp. 112983-112983.
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Species composition is a key determinant of grassland ecosystem function and resilience. Climate change is predicted to alter the distribution of cool season (C3) and warm season (C4) grasses, however, the lack of spatial distributions and temporal variations of grass functional type information severely limits our understanding of climate impacts on grasslands. This study classified C3 and C4 grasses per pixel according to the peak of growing season generated from Enhanced Vegetation Index time series. From 2003 to 2017, the C3-C4 composition of Australian rain-fed grasslands and pastures was mapped at 500 m resolution on an annual basis across a wide geographical range (10°S – 45°S), and revealed extreme inter-annual fluctuations. Over the 15-year period, the satellite-derived ratio of C4 to C3 grasses significantly increased (p < 0.05), indicating a long-term shift in community composition that was confirmed with 182,911 Atlas of Living Australia ground observations. The most pronounced changes occurred in mid-latitude transitional areas where C3 and C4 grasses co-dominate. Our climate analysis indicated the inter-annual fluctuations of C4/C3 grass ratios were significantly associated (p < 0.05) with warm/cool season rainfall ratios, and not with temperature or annual rainfall. This suggests that an increase in the warm/cool season rainfall ratio favors C4 grasses and a decrease in the warm/cool season rainfall ratio favors C3 grasses. Our findings reveal spatially-detailed dynamics of grasslands and demonstrate large-scale grassland compositional changes over 15 years. The grass composition maps should help improve ecological forecasting of grass distributions and enable researches on grassland ecosystem responses to climate change that are relevant to both adaptation of rangeland agricultural and fire management practices. Our study should also help predict grass distribution under future climate conditions, and assist in the accurate modelling of ...

Xie, T, Dickson, K-A, Yee, C, Ma, Y, Ford, CE, Bowden, NA & Marsh, DJ 2022, 'Targeting Homologous Recombination Deficiency in Ovarian Cancer with PARP Inhibitors: Synthetic Lethal Strategies That Impact Overall Survival', Cancers, vol. 14, no. 19, pp. 4621-4621.
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The advent of molecular targeted therapies has made a significant impact on survival of women with ovarian cancer who have defects in homologous recombination repair (HRR). High-grade serous ovarian cancer (HGSOC) is the most common histological subtype of ovarian cancer, with over 50% displaying defective HRR. Poly ADP ribose polymerases (PARPs) are a family of enzymes that catalyse the transfer of ADP-ribose to target proteins, functioning in fundamental cellular processes including transcription, chromatin remodelling and DNA repair. In cells with deficient HRR, PARP inhibitors (PARPis) cause synthetic lethality leading to cell death. Despite the major advances that PARPis have heralded for women with ovarian cancer, questions and challenges remain, including: can the benefits of PARPis be brought to a wider range of women with ovarian cancer; can other drugs in clinical use function in a similar way or with greater efficacy than currently clinically approved PARPis; what can we learn from long-term responders to PARPis; can PARPis sensitise ovarian cancer cells to immunotherapy; and can synthetic lethal strategies be employed more broadly to develop new therapies for women with ovarian cancer. We examine these, and other, questions with focus on improving outcomes for women with ovarian cancer.

Xirocostas, ZA, Debono, SA, Slavich, E & Moles, AT 2022, 'The ZAX Herbivory Trainer—Free software for training researchers to visually estimate leaf damage', Methods in Ecology and Evolution, vol. 13, no. 3, pp. 596-602.
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AbstractPlants lose a remarkable amount of energy to herbivorous animals, and this damage has substantial impacts on plant fitness and species' distributions. There are many ways ecologists can measure leaf damage, with some methods being more time‐consuming than others. Due to a high variance in herbivory, accurate quantification of damage at the population level requires sampling of many leaves. A simple yet effective solution to this problem is to estimate leaf damage visually.Visually estimating leaf damage may be less accurate than scanning methods, but visual estimates of leaf damage are much faster than digital measurements. Using simulations, we show that gathering larger quantities of data at a slightly higher level of inaccuracy gives a more accurate estimate of a population's overall leaf damage than fewer, exact measurements.We then introduce the ZAX Herbivory Trainer, a free online application that teaches researchers to accurately visually estimate leaf damage. On average, users took ~9 min and 48 images to complete our trainer which significantly decreased their estimate inaccuracy from 13.2% to 6%. This low level of inaccuracy can be retained up to 3 months post‐training so researchers can use the ZAX Herbivory Trainer once prior to short fieldwork or every 3 months for extensive fieldwork. We also recommend a cut‐off point, whereby if a person has not completed the app in 17.5 min or 85 images (90th percentile), they may not be suitable to estimate herbivory for research purposes.The ZAX Herbivory Trainer will allow researchers of any experience level to assess herbivory quickly and accurately in a globally standardised way. International collaborators, students and citizen scientists can all find use in this app,...

Xu, J, Fang, H, Su, Y, Kang, Y, Xu, D, Cheng, YY, Nie, Y, Wang, H, Liu, T & Song, K 2022, 'A 3D bioprinted decellularized extracellular matrix/gelatin/quaternized chitosan scaffold assembling with poly(ionic liquid)s for skin tissue engineering', International Journal of Biological Macromolecules, vol. 220, pp. 1253-1266.
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Currently, a suitable bioink for 3D bioprinting and capable of mimicking the microenvironment of native skin and preventing bacterial infection remains a major challenge in skin tissue engineering. In this study, we prepared a tissue-specific extracellular matrix-based bioink, and dECM/Gel/QCS (dGQ) 3D scaffold assembling with poly(ionic liquid)s (PILs) (dGQP) was obtained by an extrusion 3D bioprinting technology and dynamic hydrogen bonding method. The morphologies, mechanical properties, porosity, hydrophilicity, biodegradation, hemostatic effect, antibacterial ability, and biocompatibility of the hybrid scaffolds were characterized and evaluated. Results showed that the rapid release (2 h) of PILs on the dGQP scaffold can quickly kill gram-negative (E. coli) and gram-positive (S. aureus) bacteria with almost 100 % antibacterial activity and maintained a stable sterile environment for a long time (7 d), which was superior to the dGQ scaffold. The hemostasis and hemolysis test showed that the dGQP scaffold had a good hemostatic effect and excellent hemocompatibility. In vitro cytocompatibility studies showed that although the cell growth on dGQP scaffold was slow in the early stage, the cells proliferated rapidly since day 4 and had high ECM secretion at day 7. Overall, this advanced dGQP scaffold has a considerable potential to be applied in skin tissue engineering.

Xu, J, Jin, Y, Liu, K, Lyu, N, Zhang, Z, Sun, B, Jin, Q, Lu, H, Tian, H, Guo, X, Shanmukaraj, D, Wu, H, Li, M, Armand, M & Wang, G 2022, 'A green and sustainable strategy toward lithium resources recycling from spent batteries', Science Advances, vol. 8, no. 40, p. eabq7948.
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Recycling lithium from spent batteries is challenging because of problems with poor purity and contamination. Here, we propose a green and sustainable lithium recovery strategy for spent batteries containing LiFePO 4 , LiCoO 2 , and LiNi 0.5 Co 0.2 Mn 0.3 O 2 electrodes. Our proposed configuration of “lithium-rich electrode || LLZTO@LiTFSI+P3HT || LiOH” system achieves double-side and roll-to-roll recycling of lithium-containing electrode without destroying its integrity. The LiTFSI+P3HT-modified LLZTO membrane also solves the H + /Li + exchange problem and realizes a waterproof protection of bare LLZTO in the aqueous working environment. On the basis of these advantages, our system shows high Li selectivity (97%) and excellent Faradaic efficiency (≥97%), achieving high-purity (99%) LiOH along with the production of H 2 . The Li extraction processes for spent LiFePO 4 , LiNi 0.5 Co 0.2 Mn 0.3 O 2 , and LiCoO 2 batteries is shown to be economically feasible. Therefore, this study provides a previously unexplored technology with low energy consumption as well as high economic and environmental benefits to realize sustainable lithium recycling from spent batteries.

Xu, J, Lv, W, Yang, W, Jin, Y, Jin, Q, Sun, B, Zhang, Z, Wang, T, Zheng, L, Shi, X, Sun, B & Wang, G 2022, 'In Situ Construction of Protective Films on Zn Metal Anodes via Natural Protein Additives Enabling High-Performance Zinc Ion Batteries', ACS Nano, vol. 16, no. 7, pp. 11392-11404.
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The strong activity of water molecules causes a series of parasitic side reactions on Zn anodes in the aqueous electrolytes. Herein, we introduce silk fibroin (SF) as a multifunctional electrolyte additive for aqueous zinc-ion (Zn-ion) batteries. The secondary structure transformation of SF molecules from α-helices to random coils in the aqueous electrolytes allows them to break the hydrogen bond network among free water molecules and participate in Zn2+ ion solvation structure. The SF molecules released from the [Zn(H2O)4(SF)]2+ solvation sheath appear to be gradually adsorbed on the surface of Zn anodes and in situ form a hydrostable and self-healable protective film. This SF-based protective film not only shows strong Zn2+ ion affinity to promote homogeneous Zn deposition but also has good insulating behavior to suppress parasitic reactions. Benefiting from these multifunctional advantages, the cycle life of the Zn||Zn symmetric cells reaches over 1600 h in SF-containing ZnSO4 electrolytes. In addition, by adopting a potassium vanadate cathode, the full cell shows excellent cycling stability for 1000 cycles at 3 A g-1. The in situ construction of a protective film on the Zn anode from natural protein molecules provides an effective strategy to achieve high-performance Zn metal anodes for Zn-ion batteries.

Xu, Z, Hu, D, Luu, LDW, Octavia, S, Keil, AD, Sintchenko, V, Tanaka, MM, Mooi, FR, Robson, J & Lan, R 2022, 'Genomic dissection of the microevolution of Australian epidemic Bordetella pertussis', Emerging Microbes & Infections, vol. 11, no. 1, pp. 1460-1473.
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Yam, JKH, Aung, TT, Chua, SL, Cheng, Y, Kohli, GS, Zhou, J, Constancias, F, Liu, Y, Cai, Z, Salido, MMS, Drautz-Moses, DI, Rice, SA, Schuster, SC, Boo, ZZ, Wu, B, Kjelleberg, S, Tolker-Nielsen, T, Lakshminarayanan, R, Beuerman, RW, Yang, L & Givskov, M 2022, 'Elevated c-di-GMP Levels and Expression of the Type III Secretion System Promote Corneal Infection by Pseudomonas aeruginosa', Infection and Immunity, vol. 90, no. 8, pp. 1-17.
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Pseudomonas aeruginosa is generally believed to establish biofilm-associated infections under the regulation of the secondary messenger c-di-GMP. To evaluate P. aeruginosa biofilm physiology during ocular infections, comparative transcriptomic analysis was performed on wild-type P. aeruginosa PAO1, a Δ wspF mutant strain (high c-di-GMP levels), and a p lac - yhjH -containing strain (low c-di-GMP levels) from mouse corneal infection, as well as in vitro biofilm and planktonic cultures. The c-di-GMP content in P. aeruginosa during corneal infection was monitored using a fluorescent c-di-GMP reporter strain. Biofilm-related genes were induced in in vivo PAO1 compared to in vitro planktonic bacteria. Several diguanylate cyclases and phosphodiesterases were commonly regulated in in vivo PAO1 and in vitro biofilm compared to in vitro planktonic bacteria.

Yamamura, K, Zhu, L, Irvine, CP, Scott, JA, Singh, M, Jallandhra, A, Bansal, V, Phillips, MR & Ton-That, C 2022, 'Defect Compensation in Nitrogen-Doped β-Ga₂O₃ Nanowires: Implications for Bipolar Nanoscale Devices', ACS Applied Nano Materials, vol. 5, no. 9, pp. 12087-12094.
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Nitrogen (N) is a promising candidate currently being pursued for p-type doping in Ga2O3. In this work, the results of detailed investigations into N-doped β-Ga2O3nanowires using microstructural, chemical, and optical analyses are described. Monoclinic β-Ga2O3nanowires are grown by chemical vapor deposition using a metallic gallium (Ga) precursor and subsequently doped with N by remote plasma by exploiting their nanoscale cross sections and large surface-to-volume ratios. The N incorporation into β-Ga2O3is confirmed by X-ray absorption near-edge and Raman spectroscopies without changes in the nanowire morphology. N is found to exist mainly as molecular N2and N-O chemical states, but a significant portion of N substitutes on oxygen (O) sites. Concurrent temperature-resolved cathodoluminescence measurements of the undoped and N-doped β-Ga2O3are used to track the temperature dependences of their intrinsic ultraviolet (UV) luminescence and defect-related visible bands from 80 to 480 K. The blue and green bands increase in intensity relative to the UV after N doping; however, their intensity variations with temperature are found to be identical for the undoped and N-doped β-Ga2O3, indicating that these bands originate from existing recombination pathways in Ga2O3rather than from radiative N-related centers. The enhancement in defect-related luminescence in N-doped β-Ga2O3is explained by an increase in the concentration of O vacancies as a result of the compensation of NOacceptors.

Yang, T, Mendelson, N, Li, C, Gottscholl, A, Scott, J, Kianinia, M, Dyakonov, V, Toth, M & Aharonovich, I 2022, 'Spin defects in hexagonal boron nitride for strain sensing on nanopillar arrays', Nanoscale, vol. 14, no. 13, pp. 5239-5244.
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Successful integration of spin defects in hBN on SiO2 nanopillars, which leads to enhanced PL and better ODMR contrast. Also, the spin defects provide useful information about the strain fields associated with the hBN at the nanopillar sites.

Yang, X, Leys, J, Gray, J & Zhang, M 2022, 'Hillslope erosion improvement targets: Towards sustainable land management across New South Wales, Australia', CATENA, vol. 211, pp. 105956-105956.
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Hillslope erosion, including sheet and rill erosion, is the dominant form of erosion in Australia and many parts of the world. Hillslope erosion improvement (HEI) targets are necessary for the evaluation of natural resource condition and sustainable land use and land management practices. The tolerable soil loss concept has been widely applied to agricultural lands for setting soil erosion targets. It is a static target that is difficult to apply to diverse land uses and soil conditions. In this study, we developed a new approach for setting HEI resource condition targets by considering seasonal erosion levels over a large climate gradient and range of land management practices across New South Wales (NSW), Australia. A 20-year fractional vegetation cover and rainfall erosivity time-series have been used to estimate hillslope erosion rates and assign monthly and annual HEI targets across NSW. To assist with land management action target, monthly vegetation cover levels have been set to meet the HEI targets on a pixel-by-pixel (100 m) basis. We further assessed the HEI targets against land and soil capability classes and their spatial and temporal variation across local land service regions. The findings can help identify the locations and periods of time with hillslope erosion exceeding a desirable threshold level and indicate management actions that might be required to improve the soil condition over areas of concern. The processes are fully automated in a geographic information system (GIS) environment, thus providing a useful tool to determine HEI targets for sustainable soil and land management at any location and period. The methods are globally portable as the input datasets are widely available.

Yao, W, Hu, S, Jia, F, Reimers, JR, Wang, Y, Singh, DJ & Ren, W 2022, 'Lattice strain and band overlap of the thermoelectric composite Mg2Si1−xSnx', Physical Review B, vol. 106, no. 10.
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Mg2Si1-xSnx solid solutions show enhanced thermoelectric performance when the Sn mole fraction x is approximately x=0.7. This has been discussed in terms of complexity of the electronic structure arising from the crossover of two bottom conduction bands, but direct detailed understanding of the origins and the precise nature of this band convergence is limited. Here, we report first-principles calculations of the band edge changes analyzed by band unfolding and crystal orbital Hamilton population techniques. We find that strain is particularly important at this crossing. Mg2Si and Mg2Sn show opposite trends in the conduction band edge shifts leading to a band crossover at x∼0.625. However, there are also important effects due to disorder. Transport calculations show that enhancement of the figure of merit ZT value owes to the combined effects of lattice strain, band edge overlap, composition change, and disorder.

Yee, C, Dickson, K-A, Muntasir, MN, Ma, Y & Marsh, DJ 2022, 'Three-Dimensional Modelling of Ovarian Cancer: From Cell Lines to Organoids for Discovery and Personalized Medicine', Frontiers in Bioengineering and Biotechnology, vol. 10.
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Ovarian cancer has the highest mortality of all of the gynecological malignancies. There are several distinct histotypes of this malignancy characterized by specific molecular events and clinical behavior. These histotypes have differing responses to platinum-based drugs that have been the mainstay of therapy for ovarian cancer for decades. For histotypes that initially respond to a chemotherapeutic regime of carboplatin and paclitaxel such as high-grade serous ovarian cancer, the development of chemoresistance is common and underpins incurable disease. Recent discoveries have led to the clinical use of PARP (poly ADP ribose polymerase) inhibitors for ovarian cancers defective in homologous recombination repair, as well as the anti-angiogenic bevacizumab. While predictive molecular testing involving identification of a genomic scar and/or the presence of germline or somatic BRCA1 or BRCA2 mutation are in clinical use to inform the likely success of a PARP inhibitor, no similar tests are available to identify women likely to respond to bevacizumab. Functional tests to predict patient response to any drug are, in fact, essentially absent from clinical care. New drugs are needed to treat ovarian cancer. In this review, we discuss applications to address the currently unmet need of developing physiologically relevant in vitro and ex vivo models of ovarian cancer for fundamental discovery science, and personalized medicine approaches. Traditional two-dimensional (2D) in vitro cell culture of ovarian cancer lacks critical cell-to-cell interactions afforded by culture in three-dimensions. Additionally, modelling interactions with the tumor microenvironment, including the surface of organs in the peritoneal cavity that support metastatic growth of ovarian cancer, will improve the power of these models. Being able to reli...

Yi, C, Wang, Q, Qu, Y, Niu, J, Oliver, BG & Chen, H 2022, 'In-utero exposure to air pollution and early-life neural development and cognition', Ecotoxicology and Environmental Safety, vol. 238, pp. 113589-113589.
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Yi, GY, He, W & Carroll, RJ 2022, 'Feature screening with large‐scale and high‐dimensional survival data', Biometrics, vol. 78, no. 3, pp. 894-907.
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AbstractData with a huge size present great challenges in modeling, inferences, and computation. In handling big data, much attention has been directed to settings with “large p small n”, and relatively less work has been done to address problems with p and n being both large, though data with such a feature have now become more accessible than before, where p represents the number of variables and n stands for the sample size. The big volume of data does not automatically ensure good quality of inferences because a large number of unimportant variables may be collected in the process of gathering informative variables. To carry out valid statistical analysis, it is imperative to screen out noisy variables that have no predictive value for explaining the outcome variable. In this paper, we develop a screening method for handling large‐sized survival data, where the sample size n is large and the dimension p of covariates is of non‐polynomial order of the sample size n, or the so‐called NP‐dimension. We rigorously establish theoretical results for the proposed method and conduct numerical studies to assess its performance. Our research offers multiple extensions of existing work and enlarges the scope of high‐dimensional data analysis. The proposed method capitalizes on the connections among useful regression settings and offers a computationally efficient screening procedure. Our method can be applied to different situations with large‐scale data including genomic data.

Yonathan, K, Mann, R, Mahbub, KR & Gunawan, C 2022, 'The impact of silver nanoparticles on microbial communities and antibiotic resistance determinants in the environment', Environmental Pollution, vol. 293, pp. 118506-118506.
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Nanosilver (NAg) is currently one of the major alternative antimicrobials to control microorganisms. With its broad-spectrum efficacy and lucrative commercial values, NAg has been used in medical devices and increasingly, in consumer products and appliances. This widespread use has inevitably led to the release and accumulation of the nanoparticle in water and sediment, in soil and even, wastewater treatment plants (WWTPs). This Article describes the physical and chemical transformations of NAg as well as the impact of the nanoparticle on microbial communities in different environmental settings; how the nanoparticle shifts not only the diversity and abundance of microbes, including those that are important in nitrogen cycles and decomposition of organic matters, but also their associated genes and in turn, the key metabolic processes. Current findings on the microbiological activity of the leached soluble silver, solid silver particulates and their respective transformed products, which underpin the mechanism of the nanoparticle toxicity in environmental microbes, is critically discussed. The Article also addresses the emerging evidence of silver-driven co-selection of antibiotic resistance determinants. The mechanism has been linked to the increasing pools of many antibiotic resistance genes already detected in samples from different environmental settings, which could ultimately find their ways to animals and human. The realized ecological impact of NAg calls for more judicial use of the nanoparticle. The generated knowledge can inform strategies for a better 'risks versus benefits' assessment of NAg applications, including the disposal stage.

York, E, McNaughton, DA, Roseblade, A, Cranfield, CG, Gale, PA & Rawling, T 2022, 'Structure–Activity Relationship and Mechanistic Studies of Bisaryl Urea Anticancer Agents Indicate Mitochondrial Uncoupling by a Fatty Acid-Activated Mechanism', ACS Chemical Biology, vol. 17, no. 8, pp. 2065-2073.
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Targeting the cancer cell mitochondrion is a promising approach for developing novel anticancer agents. The experimental anticancer agent N,N'-bis(3,5-dichlorophenyl)urea (SR4) induces apoptotic cell death in several cancer cell lines by uncoupling mitochondrial oxidative phosphorylation (OxPhos) using a protein-free mechanism. However, the precise mechanism by which SR4 depolarizes mitochondria is unclear because SR4 lacks an acidic functional group typically found in protein-independent uncouplers. Recently, it was shown that structurally related thioureas can facilitate proton transport across lipid bilayers by a fatty acid-activated mechanism, in which the fatty acid acts as the site of protonation/deprotonation and the thiourea acts as an anion transporter that shuttles deprotonated fatty acids across the phospholipid bilayer to enable proton leak. In this paper, we show that SR4-mediated proton transport is enhanced by the presence of free fatty acids in the lipid bilayer, indicating that SR4 uncouples mitochondria through the fatty acid-activated mechanism. This mechanistic insight was used to develop a library of substituted bisaryl ureas for structure-activity relationship studies and subsequent cell testing. It was found that lipophilic electron-withdrawing groups on bisaryl ureas enhanced electrogenic proton transport via the fatty acid-activated mechanism and had the capacity to depolarize mitochondria and reduce the viability of MDA-MB-231 breast cancer cells. The most active compound in the series reduced cell viability with greater potency than SR4 and was more effective at inhibiting adenosine triphosphate production.

Yousaf, M, Naseer, U, Ali, I, Li, Y, Aftab, W, Mahmood, A, Mahmood, N, Gao, P, Jiang, Y & Guo, S 2022, 'Role of binary metal chalcogenides in extending the limits of energy storage systems: Challenges and possible solutions', Science China Materials, vol. 65, no. 3, pp. 559-592.
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Yousaf, M, Naseer, U, Imran, A, Li, Y, Aftab, W, Mahmood, A, Mahmood, N, Zhang, X, Gao, P, Lu, Y, Guo, S, Pan, H & Jiang, Y 2022, 'Visualization of battery materials and their interfaces/interphases using cryogenic electron microscopy', Materials Today, vol. 58, pp. 238-274.
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Yu, G, Su, Y, Guo, C, Yi, C, Yu, B, Chen, H, Cui, Y, Wang, X, Wang, Y, Chen, X, Wang, S, Wang, Q, Chen, X, Hu, X, Mei, F, Verkhratsky, A, Xiao, L & Niu, J 2022, 'Pathological oligodendrocyte precursor cells revealed in human schizophrenic brains and trigger schizophrenia-like behaviors and synaptic defects in genetic animal model', Molecular Psychiatry, vol. 27, no. 12, pp. 5154-5166.
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AbstractAlthough the link of white matter to pathophysiology of schizophrenia is documented, loss of myelin is not detected in patients at the early stages of the disease, suggesting that pathological evolution of schizophrenia may occur before significant myelin loss. Disrupted-in-schizophrenia-1 (DISC1) protein is highly expressed in oligodendrocyte precursor cells (OPCs) and regulates their maturation. Recently, DISC1-Δ3, a major DISC1 variant that lacks exon 3, has been identified in schizophrenia patients, although its pathological significance remains unknown. In this study, we detected in schizophrenia patients a previously unidentified pathological phenotype of OPCs exhibiting excessive branching. We replicated this phenotype by generating a mouse strain expressing DISC1-Δ3 gene in OPCs. We further demonstrated that pathological OPCs, rather than myelin defects, drive the onset of schizophrenic phenotype by hyperactivating OPCs’ Wnt/β-catenin pathway, which consequently upregulates Wnt Inhibitory Factor 1 (Wif1), leading to the aberrant synaptic formation and neuronal activity. Suppressing Wif1 in OPCs rescues synaptic loss and behavioral disorders in DISC1-Δ3 mice. Our findings reveal the pathogenetic role of OPC-specific DISC1-Δ3 variant in the onset of schizophrenia and highlight the therapeutic potential of Wif1 as an alternative target for the treatment of this disease.

Zaidan, I, Tavares, LP, Sugimoto, MA, Lima, KM, Negreiros-Lima, GL, Teixeira, LCR, Miranda, TC, Valiate, BVS, Cramer, A, Vago, JP, Campolina-Silva, GH, Souza, JAM, Grossi, LC, Pinho, V, Campagnole-Santos, MJ, Santos, RAS, Teixeira, MM, Galvão, I & Sousa, LP 2022, 'Angiotensin-(1-7)/MasR axis promotes migration of monocytes/macrophages with a regulatory phenotype to perform phagocytosis and efferocytosis', JCI Insight, vol. 7, no. 1.
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Zakria, M, Rogers, DJ, Scola, J, Zhu, L, Lockrey, M, Bove, P, Sandana, EV, Teherani, FH, Phillips, MR & Ton-That, C 2022, 'Two-dimensional confinement of excitons at the interface in nonpolar MgZnO/ZnO heterostructures', Physical Review Materials, vol. 6, no. 3.
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We report on the polarity-dependent excitonic emission at the interface in MgZnO/ZnO heterostructures grown on both polar and nonpolar ZnO single-crystal substrates. Structural and morphological analyses confirm that the heterostructures grow homoepitaxially on nonpolar m-plane and a-plane crystal substrates. The nonpolar heterostructures are investigated by depth-resolved cathodoluminescence spectroscopy revealing an excitonic interface emission centered at 3.12 eV, identified as the H-band signature of indirect excitons. These results reveal the formation of robust indirect excitons confined at the MgZnO/ZnO interface due to the presence of an epitaxially strained interfacial layer near the interface in the MgZnO, which is confirmed by high-order X-ray diffraction. It is also found that the H-band emission originates from the self-absorption of the ZnO free exciton emission in the proximity of the interface. Temperature-dependent studies of the H band yields a thermal activation energy of 47 meV for the indirect exciton in the nonpolar heterojunctions. This activation energy is the largest among all free and bound excitons in ZnO and is much higher than the values found in AlGaN/GaN and MgZnO/ZnO/sapphire hetrostructures. Our findings indicate that the optical properties of nonpolar heterostructures are strongly influenced by the piezoelectric effect.

Zeng, HZ, Ngyuen, MAP, Ai, X, Bennet, A, Solntsev, AS, Laucht, A, Al-Juboori, A, Toth, M, Mildren, RP, Malaney, R & Aharonovich, I 2022, 'Integrated room temperature single-photon source for quantum key distribution: publisher’s note', Optics Letters, vol. 47, no. 9, pp. 2161-2161.
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This publisher’s note contains a correction to Opt. Lett. 47, 1673 (2022)10.1364/OL.454450.

Zeng, HZJ, Ngyuen, MAP, Ai, X, Bennet, A, Solntsev, AS, Laucht, A, Al-Juboori, A, Toth, M, Mildren, RP, Malaney, R & Aharonovich, I 2022, 'Integrated room temperature single-photon source for quantum key distribution', Optics Letters, vol. 47, no. 7, pp. 1673-1673.
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High-purity single-photon sources (SPS) that can operate at room temperature are highly desirable for a myriad of applications, including quantum photonics and quantum key distribution. In this work, we realize an ultra-bright solid-state SPS based on an atomic defect in hexagonal boron nitride (hBN) integrated with a solid immersion lens (SIL). The SIL increases the source efficiency by a factor of six, and the integrated system is capable of producing over ten million single photons per second at room temperature. Our results are promising for practical applications of SPS in quantum communication protocols.

Zeng, Y, Hao, D, Huete, A, Dechant, B, Berry, J, Chen, JM, Joiner, J, Frankenberg, C, Bond-Lamberty, B, Ryu, Y, Xiao, J, Asrar, GR & Chen, M 2022, 'Optical vegetation indices for monitoring terrestrial ecosystems globally', Nature Reviews Earth & Environment, vol. 3, no. 7, pp. 477-493.
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Vegetation indices (VIs), which describe remotely sensed vegetation properties such as photosynthetic activity and canopy structure, are widely used to study vegetation dynamics across scales. However, VI-based results can vary between indices, sensors, quality control measures, compositing algorithms, and atmospheric and sun–target–sensor geometry corrections. These variations make it difficult to draw robust conclusions about ecosystem change and highlight the need for consistent VI application and verification. In this Technical Review, we summarize the history and ecological applications of VIs and the linkages and inconsistencies between them. VIs have been used since the early 1970s and have evolved rapidly with the emergence of new satellite sensors with more spectral channels, new scientific demands and advances in spectroscopy. When choosing VIs, the spectral sensitivity and features of VIs and their suitability for target application should be considered. During data analyses, steps must be taken to minimize the impact of artefacts, VI results should be verified with in situ data when possible and conclusions should be based on multiple sets of indicators. Next-generation VIs with higher signal-to-noise ratios and fewer artefacts will be possible with new satellite missions and integration with emerging vegetation metrics such as solar-induced chlorophyll fluorescence, providing opportunities for studying terrestrial ecosystems globally.

Zhang, H, Li, J, Liu, Q, Lin, S, Huete, A, Liu, L, Croft, H, Clevers, JGPW, Zeng, Y, Wang, X, Gu, C, Zhang, Z, Zhao, J, Dong, Y, Mumtaz, F & Yu, W 2022, 'A novel red‐edge spectral index for retrieving the leaf chlorophyll content', Methods in Ecology and Evolution, vol. 13, no. 12, pp. 2771-2787.
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AbstractThe leaf chlorophyll content (Chlleaf) is a crucial vegetation parameter in carbon cycle modelling and agricultural monitoring at local, regional and global scales. The red‐edge spectral region is sensitive to variations in Chlleaf. An increasing number of sensors are capable of sampling red‐edge bands, providing opportunities to estimate Chlleaf. However, the contributions of canopy/foliar/soil factors are always combined in the reflectance signal, which limits the generalizability of vegetation index (VI)‐based Chlleaf inversions. This study aims to propose a new red‐edge chlorophyll index to decouple the effects of the canopy and soil background from the Chlleaf estimation.The chlorophyll sensitive index (CSI) was proposed, and the regression equations between the CSI and Chlleaf were acquired using PROSAIL (PROSPECT + SAIL) and the 4‐Scale‐PROSPECT model.Sensitivity analyses showed that the CSI is resistant to variations in the canopy structure and soil background. Validation results obtained using 308 ground‐measured samples over nine sites world‐wide revealed that CSI improves the Chlleaf retrieval accuracy (root mean square error (RMSE = 9.39 μg cm−2) compared with the existing Medium Resolution Imaging Spectrometer (MERIS) terrestrial chlorophyll index (MTCI; RMSE = 13.00 μg cm−2). Moreover, the CSI method steadily achieves a highly accurate inversion under different LAI and Chlleaf conditions. Based on the CSI regression method, a Chlleaf product with a 30‐m/10‐day resolution across China was generated.

Zhang, J, Zhao, Y, Sun, B, Xie, Y, Tkacheva, A, Qiu, F, He, P, Zhou, H, Yan, K, Guo, X, Wang, S, McDonagh, AM, Peng, Z, Lu, J & Wang, G 2022, 'A long-life lithium-oxygen battery via a molecular quenching/mediating mechanism', Science Advances, vol. 8, no. 3, p. eabm1899.
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The advancement of lithium-oxygen (Li-O 2 ) batteries has been hindered by challenges including low discharge capacity, poor energy efficiency, severe parasitic reactions, etc. We report an Li-O 2 battery operated via a new quenching/mediating mechanism that relies on the direct chemical reactions between a versatile molecule and superoxide radical/Li 2 O 2 . The battery exhibits a 46-fold increase in discharge capacity, a low charge overpotential of 0.7 V, and an ultralong cycle life >1400 cycles. Featuring redox-active 2,2,6,6-tetramethyl-1-piperidinyloxy moieties bridged by a quenching-active perylene diimide backbone, the tailor-designed molecule acts as a redox mediator to catalyze discharge/charge reactions and serves as a reusable superoxide quencher to chemically react with superoxide species generated during battery operation. The all-in-one molecule can simultaneously tackle issues of parasitic reactions associated with superoxide radicals, singlet oxygen, high overpotentials, and lithium corrosion. The molecular design of multifunctional additives combining various capabilities opens a new avenue for developing high-performance Li-O 2 batteries.

Zhang, K, Liu, J, Liu, Y, Zhang, P & Carroll, RJ 2022, 'Bayesian adjustment for measurement error in an offset variable in a Poisson regression model', Statistical Modelling, vol. 22, no. 6, pp. 509-526.
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Fatal car crashes are the leading cause of death among teenagers in the USA. The Graduated Driver Licensing (GDL) programme is one effective policy for reducing the number of teen fatal car crashes. Our study focuses on the number of fatal car crashes in Michigan during 1990–2004 excluding 1997, when the GDL started. We use Poisson regression with spatially dependent random effects to model the county level teen car crash counts. We develop a measurement error model to account for the fact that the total teenage population in the county level is used as a proxy for the teenage driver population. To the best of our knowledge, there is no existing literature that considers adjustment for measurement error in an offset variable. Furthermore, limited work has addressed the measurement errors in the context of spatial data. In our modelling, a Berkson measurement error model with spatial random effects is applied to adjust for the error-prone offset variable in a Bayesian paradigm. The Bayesian Markov chain Monte Carlo (MCMC) sampling is implemented in rstan. To assess the consequence of adjusting for measurement error, we compared two models with and without adjustment for measurement error. We found the effect of a time indicator becomes less significant with the measurement-error adjustment. It leads to our conclusion that the reduced number of teen drivers can help explain, to some extent, the effectiveness of GDL.

Zhang, L, Cao, C, Kaushik, N, Lai, RY, Liao, J, Wang, G, Ariotti, N, Jin, D & Stenzel, MH 2022, 'Controlling the Biological Behaviors of Polymer-Coated Upconverting Nanoparticles by Adjusting the Linker Length of Estrone Ligands', Biomacromolecules, vol. 23, no. 6, pp. 2572-2585.
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The estrone ligand is used for modifying nanoparticle surfaces to improve their targeting effect on cancer cell lines. However, to date, there is no common agreement on the ideal linker length to be used for the optimum targeting performance. In this study, we aimed to investigate the impact of poly(poly ethylene glycol methyl ether methacrylate) (PPEGMEMA) linker length on the cellular uptake behavior of polymer-coated upconverting nanoparticles (UCNPs). Different triblock terpolymers, poly(poly (ethylene glycol) methyl ether methacrylate)-block-polymethacrylic acid-block-polyethylene glycol methacrylate phosphate (PPEGMEMAx-b-PMAAy-b-PEGMP3: x = 7, 15, 33, and 80; y = 16, 20, 18, and 18), were synthesized with different polymer linker chain lengths between the surface and the targeting ligand by reversible addition-fragmentation chain transfer polymerization. The estrone ligand was attached to the polymer via specific terminal conjugation. The cellular association of polymer-coated UCNPs with linker chain lengths was evaluated in MCF-7 cells by flow cytometry. Our results showed that the bioactivity of ligand modification is dependent on the length of the polymer linker. The shortest polymer PPEGMEMA7-b-PMAA16-b-PEGMP3 with estrone at the end of the polymer chain was found to have the best cellular association behavior in the estrogen receptor (ER)α-positive expression cell line MCF-7. Additionally, the anticancer drug doxorubicin•HCl was encapsulated in the nanocarrier to evaluate the 2D and 3D cytotoxicity. The results showed that estrone modification could efficiently improve the cellular uptake in ERα-positive expression cell lines and in 3D spheroid models.

Zhang, L, Rath, EM & Cheng, YY 2022, 'The Use of Epigenetic Biomarkers as Diagnostic and Therapeutic Options', Epigenomes, vol. 6, no. 4, pp. 30-30.
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The last few decades have brought tremendous advances in the mechanisms of epigenetic regulation, with DNA methylation, histone methylation and acetylation, microRNAs and other noncoding RNAs being among the most prominent [...]

Zhang, M, Viscarra Rossel, RA, Zhu, Q, Leys, J, Gray, JM, Yu, Q & Yang, X 2022, 'Dynamic Modelling of Water and Wind Erosion in Australia over the Past Two Decades', Remote Sensing, vol. 14, no. 21, pp. 5437-5437.
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Soil erosion caused by water and wind is a complicated natural process that has been accelerated by human activity. It results in increasing areas of land degradation, which further threaten the productive potential of landscapes. Consistent and continuous erosion monitoring will help identify the location, magnitude, and trends of soil erosion. This information can then be used to evaluate the impact of land management practices and inform programs that aim to improve soil conditions. In this study, we applied the Revised Universal Soil Loss Equation (RUSLE) and the Revised Wind Erosion Equation (RWEQ) to simulate water and wind erosion dynamics. With the emerging earth observation big data, we estimated the monthly and annual water erosion (with a resolution of 90 m) and wind erosion (at 1 km) from 2001 to 2020. We evaluated the performance of three gridded precipitation products (SILO, GPM, and TRMM) for monthly rainfall erosivity estimation using ground-based rainfall. For model validation, water erosion products were compared with existing products and wind erosion results were verified with observations. The datasets we developed are particularly useful for identifying finer-scale erosion dynamics, where more sustainable land management practices should be encouraged.

Zhang, M, Yang, X, Cleverly, J, Huete, A, Zhang, H & Yu, Q 2022, 'Heat wave tracker: A multi-method, multi-source heat wave measurement toolkit based on Google Earth Engine', Environmental Modelling & Software, vol. 147, pp. 105255-105255.
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Under ongoing global warming due to climate change, heat waves in Australia are expected to become more frequent and severe. Extreme heat waves have devastating impacts on both terrestrial and marine ecosystems. A multi-characteristic heat wave framework is used to estimate historical and future projected heat waves across Australia. A Google Earth Engine-based toolkit named heat wave tracker (HWT) is developed, which can be used for dynamic visualization, extraction, and processing of complex heat wave events. The toolkit exploits the public long-term high-resolution climate datasets to developed nine heat wave datasets across Australia for extreme heat wave value analysis. To examine climate change on heat waves and how they vary in time and space, we also explore the probability and return periods of extreme heat waves over a period of 100 years. The datasets, toolkit and findings we developed contribute to global studies on heat waves under accelerated global warming.

Zhang, Q, Liao, J, Huang, Q, Lai, N, Zhang, B, Wen, X, Yang, J, Yang, Y, Wang, J, Zhang, G, Wang, C & Wang, R 2022, 'Regulated broadband visible emission of Bi ions-doped borosilicate glass', Ceramics International, vol. 48, no. 22, pp. 34046-34052.
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Zhang, S, Zhang, X, Deng, K, Wang, C, Wood, LG, Wan, H, Liu, L, Wang, J, Zhang, L, Liu, Y, Cheng, G, Gibson, PG, Oliver, BG, Luo, F, McDonald, VM, Li, W & Wang, G 2022, 'Reduced Skeletal Muscle Mass Is Associated with an Increased Risk of Asthma Control and Exacerbation', Journal of Clinical Medicine, vol. 11, no. 23, pp. 7241-7241.
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Background: Skeletal muscle mass (SMM) has been suggested to be associated with multiple health-related outcomes. However, the potential influence of SMM on asthma has not been largely explored. Objective: To study the association between SMM and clinical features of asthma, including asthma control and exacerbation, and to construct a model based on SMM to predict the risk of asthma exacerbation (AEx). Methods: In this prospective cohort study, we consecutively recruited patients with asthma (n = 334), classified as the SMM Normal group (n = 223), SMM Low group (n = 88), and SMM High group (n = 23). We investigated the association between SMM and clinical asthma characteristics and explored the association between SMM and asthma control and AEx within a 12-month follow-up period. Based on SMM, an exacerbation prediction model was developed, and the overall performance was externally validated in an independent cohort (n = 157). Results: Compared with the SMM Normal group, SMM Low group exhibited more airway obstruction and worse asthma control, while SMM High group had a reduced eosinophil percentage in induced sputum. Furthermore, SMM Low group was at a significantly increased risk of moderate-to-severe exacerbation compared with the SMM Normal group (relative risk adjusted 2.02 [95% confidence interval (CI), 1.35–2.68]; p = 0.002). In addition, a model involving SMM was developed which predicted AEx (area under the curve: 0.750, 95% CI: 0.691–0.810). Conclusions: Low SMM was an independent risk factor for future AEx. Furthermore, a model involving SMM for predicting the risk of AEx in patients with asthma indicated that assessment of SMM has potential clinical implications for asthma management.

Zhang, W, Liu, T, Brown, A, Ueland, M, Forbes, SL & Su, SW 2022, 'The Use of Electronic Nose for the Classification of Blended and Single Malt Scotch Whisky', IEEE Sensors Journal, vol. 22, no. 7, pp. 7015-7021.
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As with any profitable industry, the whisky market is subject to fraudulent activity, including adulteration. An expert can identify the differences between whiskies, but it is difficult for the majority of consumers to differentiate fraudulent beverages. Complex chemical and analytical analyses have been able to detect the differences between whiskies; however, this type of analysis is time-consuming, complex, requires trained professionals, and can only be conducted in the laboratory. A rapid and real-time assessment of whisky quality could prove beneficial to wholesalers and consumers. The odour of whiskies can be used to identify their brands, regions and styles, as thus has the potential for quality assessment and fraudulent detection. One type of technology used for real-time odour analysis is an electronic nose (e-nose). This study investigates the capability of a new e-nose prototype (called NOS.E) developed by our team to identify the differences between six whiskies with respect to their brand names, regions, and styles. This study investigates the capability of a new e-nose prototype (called NOS.E) developed by our team in identifying the differences among whiskies. Ensemble of several classifiers is adopted to improve the classification accuracy of the system. The proposed e-nose solution was verified by a field testing displayed at the CEBIT Australia 2019 trade show, by reaching an accuracy of 96.15%, 100%, and 92.31% in brand name, region, and style classification, respectively. Confirmation of the NOS.E findings was further carried out using comprehensive two-dimensional gas chromatography coupled with time-of-flight mass spectrometry (GC $\times $ GC-TOFMS).

Zhang, Y, Almazi, JG, Ong, HX, Johansen, MD, Ledger, S, Traini, D, Hansbro, PM, Kelleher, AD & Ahlenstiel, CL 2022, 'Nanoparticle Delivery Platforms for RNAi Therapeutics Targeting COVID-19 Disease in the Respiratory Tract', International Journal of Molecular Sciences, vol. 23, no. 5, pp. 2408-2408.
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Since December 2019, a pandemic of COVID-19 disease, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has rapidly spread across the globe. At present, the Food and Drug Administration (FDA) has issued emergency approval for the use of some antiviral drugs. However, these drugs still have limitations in the specific treatment of COVID-19, and as such, new treatment strategies urgently need to be developed. RNA-interference-based gene therapy provides a tractable target for antiviral treatment. Ensuring cell-specific targeted delivery is important to the success of gene therapy. The use of nanoparticles (NPs) as carriers for the delivery of small interfering RNA (siRNAs) to specific tissues or organs of the human body could play a crucial role in the specific therapy of severe respiratory infections, such as COVID-19. In this review, we describe a variety of novel nanocarriers, such as lipid NPs, star polymer NPs, and glycogen NPs, and summarize the pre-clinical/clinical progress of these nanoparticle platforms in siRNA delivery. We also discuss the application of various NP-capsulated siRNA as therapeutics for SARS-CoV-2 infection, the challenges with targeting these therapeutics to local delivery in the lung, and various inhalation devices used for therapeutic administration. We also discuss currently available animal models that are used for preclinical assessment of RNA-interference-based gene therapy. Advances in this field have the potential for antiviral treatments of COVID-19 disease and could be adapted to treat a range of respiratory diseases.

Zhang, Y, Chen, P, Wang, T, Su, D & Wang, C 2022, 'Development of Small‐Scale Monitoring and Modeling Strategies for Safe Lithium‐Ion Batteries', Batteries & Supercaps, vol. 5, no. 2.
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AbstractLithium‐ion batteries (LIBs) have the advantages of high energy density, stable working voltage, long cycling life, and no memory effect. They have been widely used as power sources for electric vehicles (EVs) and hybrid electric vehicles (HEVs). However, during periods of usage or storage, some unfavorable factors such as thermal runaway, volumetric expansion, and growth of lithium dendrites can severely reduce the reliability and safety of LIBs. Therefore, an accurate health estimation system and a reliable life expectancy strategy toward LIBs have been proved significantly important. However, due to the large volume and high price, most characterization methods in the laboratory cannot be applied directly to commercial electric devices. Therefore, small portable monitor methods are more practical. In this review, we first systematically reviewed the recent progress of modeling methods towards LIBs. Some typical modeling strategies (e. g., thermal models, electrical models and aging models) and advanced sensors which can be imbedded in LIBs are emphatically introduced and compared. At last, some promising directions of development on portable in‐situ monitor strategies are also predicted and supposed.

Zhang, Z, Mahmud, MAP & Kouzani, AZ 2022, 'FitNN: A Low-Resource FPGA-Based CNN Accelerator for Drones', IEEE Internet of Things Journal, vol. 9, no. 21, pp. 21357-21369.
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Zhang, Z, Mahmud, MAP & Kouzani, AZ 2022, 'Resource-constrained FPGA implementation of YOLOv2', Neural Computing and Applications, vol. 34, no. 19, pp. 16989-17006.
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AbstractProgress is being made to deploy convolutional neural networks (CNNs) into the Internet of Things (IoT) edge devices for handling image analysis tasks locally. These tasks require low-latency and low-power computation on low-resource IoT edge devices. However, CNN-based algorithms, e.g. YOLOv2, typically contain millions of parameters. With the increase in the CNN’s depth, filters are increased by a power of two. A large number of filters and operations could lead to frequent off-chip memory access that affects the operation speed and power consumption of the device. Therefore, it is a challenge to map a deep CNN into a low-resource edge IoT platform. To address this challenge, we present a resource-constrained Field-Programmable Gate Array implementation of YOLOv2 with optimized data transfer and computing efficiency. Firstly, a scalable cross-layer dataflow strategy is proposed which allows on-chip data transfer between different types of layers, and offers flexible off-chip data transfer when the intermediate results are unaffordable on-chip. Next, a filter-level data-reuse dataflow strategy together with a filter-level parallel multiply-accumulate operation computing processing elements array is developed. Finally, multi-level sliding buffers are developed to optimize the convolutional computing loop and reuse the input feature maps and weights. Experiment results show that our implementation has achieved 4.8 W of low-power consumption for executing YOLOv2, an 8-bit deep CNN containing 50.6 MB weights, using low-resource of 8.3 Mbits on-chip memory. The throughput and power efficiency are 100.33 GOP/s and 20.90 GOP/s/W, respectively.

Zhang, Z, Yang, X, Li, P, Wang, Y, Zhao, X, Safaei, J, Tian, H, Zhou, D, Li, B, Kang, F & Wang, G 2022, 'Biomimetic Dendrite‐Free Multivalent Metal Batteries', Advanced Materials, vol. 34, no. 47, pp. e2206970-2206970.
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AbstractRechargeable multivalent metal (e.g., zinc (Zn) and aluminum (Al)) batteries are ideal choices for large‐scale energy storage owing to their intrinsic low cost and safety. However, the poor compatibility between metallic anodes and electrolytes strongly hampers their practical applications. Herein, it is demonstrated that confining multivalent metals in a biomimetic scaffold (Bio‐scaffold) can achieve highly efficient multivalent metal plating/stripping. This Bio‐scaffold is well‐tailored through the synergy of a parallel‐aligned array of fractal copper branches and a CaTiO3 (CTO)‐based coating layer. By virtue of this design strategy, the as‐developed Bio‐scaffold‐based Zn‐ and Al‐metal anodes exhibited dendrite‐free morphologies with high reversibility and long lifespan, as well as excellent performance for Zn and Al full batteries. Theoretical modeling and experimental investigations reveal that the fractal copper array not only facilitates multivalent ion diffusion and electrolyte wetting but also effectively reduces the local current densities during cycling; Meanwhile, the CTO‐based coating layer effectively blocks interfacial side reactions and enables a homogeneous ionic flux. This work opens a new avenue for developing multivalent metal batteries.

Zhao, F, Liang, C, John Zaslawski, C & Cao, Z 2022, 'Effects of Qigong Therapy on the Anaerobic Threshold in Patients with Stable Coronary Artery Disease: A Randomized Controlled Trial', Evidence-Based Complementary and Alternative Medicine, vol. 2022, pp. 1-8.
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Objective. This study aims to identify whether Qigong (QG) rehabilitation therapy can significantly improve the cardiac function of patients with stable coronary artery disease (SCAD) compared with routine therapy. Thus, a randomized controlled trial was conducted to evaluate the curative effects of a three-month QG rehabilitation therapy on cardiac rehabilitation. Patients and Methods. In this trial, a total of 68 patients with SCAD were randomly divided into the QG group (34 patients) and the control (CON) group (34 patients). Patients in the CON group received routine cardiologic medication without any special intervention. Based on the treatment in the CON group, patients in the QG group were provided additionally with a 12-week traditional Chinese medicine (TCM) cardiac rehabilitation QG exercise training program. The outcomes of these patients were assessed at baseline and after 12 weeks of intervention through the treadmill (anaerobic threshold (AT)) test. Results. After 12 weeks of intervention, the AT, volume of oxygen (VO2), oxygen uptake/kilogram (VO2/kg), metabolic equivalents (METS), and oxygen pulse (VO2/HR) of patients in the QG group were significantly higher than those of patients in the CON group ( $P<0.05$ ). Conclusion. QG therapy can achieve certain curative effects and safety for patients with SCAD. This trial is registered with Clinicaltrials.gov identifier (ChiCTR1800015823).

Zhao, H, Cun, Y, Bai, X, Xiao, D, Qiu, J, Song, Z, Liao, J & Yang, Z 2022, 'Entirely Reversible Photochromic Glass with High Coloration and Luminescence Contrast for 3D Optical Storage', ACS Energy Letters, vol. 7, no. 6, pp. 2060-2069.
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Zhao, K, Xu, X, Ren, W, Jin, D & Xi, P 2022, 'Two-photon MINFLUX with doubled localization precision', eLight, vol. 2, no. 1, p. 5.
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AbstractAchieving localization with molecular precision has been of great interest for extending fluorescence microscopy to nanoscopy. MINFLUX pioneers this transition through point spread function (PSF) engineering, yet its performance is primarily limited by the signal-to-background ratio. Here we demonstrate theoretically that two-photon MINFLUX (2p-MINFLUX) could double its localization precision through PSF engineering by nonlinear effect. Cramér-Rao Bound (CRB) is studied as the maximum localization precision, and CRB of two-photon MINFLUX is halved compared to single-photon MINFLUX (1p-MINFLUX) in all three dimensions. Meanwhile, in order to achieve same localization precision with 1p-MINFLUX, 2p-MINFLUX requires only 1/4 of fluorescence photons. Exploiting simultaneous two-photon excitation of multiple fluorophore species, 2p-MINFLUX may have the potential for registration-free nanoscopy and multicolor tracking.

Zhao, S, Liu, Z, Xie, G, Guo, Z, Wang, S, Zhou, J, Xie, X, Sun, B, Guo, S & Wang, G 2022, 'High-efficiency cathode potassium compensation and interfacial stability improvement enabled by dipotassium squarate for potassium-ion batteries', Energy & Environmental Science, vol. 15, no. 7, pp. 3015-3023.
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A low-cost and high-efficiency K2C4O4 is used as a potassium reservoir source to boost the electrochemical performance of potassium-ion batteries, and how this strategy is expected to promote their practical application.

Zhao, Z, Tang, B, Yan, X, Wu, X, Li, Z, Gale, PA & Jiang, Y-B 2022, 'Crown ether-thiourea conjugates as ion transporters', Frontiers of Chemical Science and Engineering, vol. 16, no. 1, pp. 81-91.
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Na+, Cl− and K+ are the most abundant electrolytes present in biological fluids that are essential to the regulation of pH homeostasis, membrane potential and cell volume in living organisms. Herein, we report synthetic crown ether-thiourea conjugates as a cation/anion symporter, which can transport both Na+ and Cl− across lipid bilayers with relatively high transport activity. Surprisingly, the ion transport activities were diminished when high concentrations of K+ ions were present outside the vesicles. This unusual behavior resulted from the strong affinity of the transporters for K+ ions, which led to predominant partitioning of the transporters as the K+ complexes in the aqueous phase preventing the transporter incorporation into the membrane. Synthetic membrane transporters with Na+, Cl− and K+ transport capabilities may have potential biological and medicinal applications. [Figure not available: see fulltext.]

Zhong, X, Zhang, L, van Wezel, GP, Vijgenboom, E & Claessen, D 2022, 'Role for a Lytic Polysaccharide Monooxygenase in Cell Wall Remodeling in Streptomyces coelicolor', mBio, vol. 13, no. 2, p. e0045622.
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Lytic polysaccharide monooxygenases are used in industry for the efficient degradation of recalcitrant polysaccharide substrates. Only recently, we have begun to appreciate some of their important biological roles.

Zhou, T, Li, X, Zhang, Q, Dong, S, Liu, H, Liu, Y, Chaves, AV, Ralph, PJ, Ruan, R & Wang, Q 2022, 'Ecotoxicological response of Spirulina platensis to coexisted copper and zinc in anaerobic digestion effluent', Science of The Total Environment, vol. 837, pp. 155874-155874.
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Copper ion (Cu2+) and zinc ion (Zn2+) are widely co-existent in anaerobic digestion effluent as typical contaminants. This work aims to explore how Cu2+-Zn2+ association affects physiological properties of S. platensis using Schlösser medium (SM) and sterilized anaerobic digestion effluent (SADE). Microalgae cells viability, biochemical properties, uptake of Cu2+ and Zn2+, and risk assessment associated with the biomass reuse as additives to pigs were comprehensively assessed. Biomass production ranged from 0.03 to 0.28 g/L in SM and 0.63 to 0.79 g/L in SADE due to the presence of Cu2+ and Zn2+. Peak value of chlorophyll-a and carotenoid content during the experiment decreased by 70-100% and 40-100% in SM, and by 70-77% and 30-55% in SADE. Crude protein level reduced by 4-41% in SM and by 65-75% in SADE. The reduction ratio of these compounds was positively related to the Cu2+ and Zn2+ concentrations. Maximum value of saturated and unsaturated fatty acids was both obtained at 0.3 Cu + 2.0 Zn (50.8% and 22.8%, respectively) and 25% SADE reactors (33.8% and 27.7%, respectively). Uptake of Cu in biomass was facilitated by Zn2+ concentration (> 4.0 mg/L). Risk of S. platensis biomass associated with Cu2+ was higher than Zn2+. S. platensis from SM (Cu2+ ≤ 0.3 mg/L and Zn2+ ≤ 4.0 mg/L) and diluted SADE (25% and 50% SADE) reactors could be used as feed additives without any risk (hazard index <1), which provides sufficient protein and fatty acids for pig consumption. These results revealed the promising application of using S. platensis for bioremediation of Cu2+ and Zn2+ in anaerobic digestion effluent and harvesting biomass for animal feed additives.

Zhou, W, Li, A, Gale, PA & He, Q 2022, 'A highly selective superphane for ReO4− recognition and extraction', Cell Reports Physical Science, vol. 3, no. 5, pp. 100875-100875.
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Highly selective anion recognition and extraction is challenging and yet critical for removal of pollutants from the environment and the effective recovery of valuable chemicals from low-content (at sub-ppm or ppb level) sources. In this paper, we detail the gram-scale synthesis of a superphane 2, an anion receptor that selectively binds ReO4−. Superphane 2 can extract perrhenate from solid mixtures containing traces of ReO4− anion (as low as 200 ppb) and aqueous media with near 100% selectivity over large excesses of competing anions. Meanwhile, up to 99.99% of ReO4− can be separated from complex simulated aqueous waste streams containing ppm-level perrhenate via either liquid-liquid extraction or simple column adsorption. Importantly, after extraction or adsorption, superphane 2 can be recycled and reused by simple treatment with aqueous NaHCO3.

Zhou, X, Wang, T, liu, H, Zhang, L, Zhang, C, Kong, N, Su, D & Wang, C 2022, 'Design of S-scheme heterojunction catalyst based on structural defects for photocatalytic oxidative desulfurization application', Journal of Photochemistry and Photobiology A: Chemistry, vol. 433, pp. 114162-114162.
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Carbon nitride (g-C3N4) is promising for many applications, but its photocatalytic activity is limited by weak visible light absorption and photogenerated carrier complexes. Herein, the thermally defective carbon nitride (d-C3N4) has a larger specific surface area and more reactive sites. d-C3N4 helped Ag3PO4 nanoparticles to be uniformly deposited on the surface of it and made it easier for particle dispersion. d-C3N4 and Ag3PO4 form an S-scheme heterojunction, facilitating the transfer and separation of photogenerated electrons and holes, and possessing high redox ability, which results in improved photocatalytic performance. The experimental results showed that the conversion of 10: 1 Ag3PO4/d-C3N4 for photocatalytic oxidative desulfurization (PODS) under visible light was as high as 92.5 % at 3 h, mainly due to the S-scheme heterojunction further promoting the transfer and separation of photogenerated carriers, suppressing the fast complexation and improving the efficiency of photocatalysis. In addition, the conversion mechanism of PODS was demonstrated using radical capture test, electron paramagnetic resonance spectrometer (EPR), and gas chromatography-mass spectrometry (GC–MS). This study helps researchers to understand the S-scheme heterojunctions constructed based on defects and provides new ideas for the design and application of photocatalysts.

Zhou, X, Wang, T, Zhang, L, Che, S, Liu, H, Liu, S, Wang, C, Su, D & Teng, Z 2022, 'Highly efficient Ag2O/Na-g-C3N4 heterojunction for photocatalytic desulfurization of thiophene in fuel under ambient air conditions', Applied Catalysis B: Environmental, vol. 316, pp. 121614-121614.
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A composite photocatalyst of Ag2O and Na doped g-C3N4 (Ag2O/Na-CN) with high efficiency was investigated for photocatalytic oxidative desulfurization (PODS). The concentration and lifetime of carriers are increased with Na-CN. Under light conditions, it produces more charge carriers for the generation of radical species, such as superoxide radicals and holes. In addition, Na-CN and Ag2O form a p-n heterojunction, facilitating the transfer and separation of photogenerated electrons and holes, and increasing the concentration of holes on the valence band of Ag2O. The significantly improved charge separation alone with the higher carrier concentration of Ag2O/Na-CN makes the activation and oxidation of thiophene easier. Free radical capture experiments, electron paramagnetic resonance, and gas chromatography-mass spectrometry tests showed that holes, electrons, and superoxide radicals are the most critical active species in the PODS process, supporting the proposed PODS mechanism.

Zinder, Y, Lazarev, A & Musatova, E 2022, 'Single Track Transportation in a Two-Machine Production System', IFAC-PapersOnLine, vol. 55, no. 10, pp. 2893-2897.
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Zou, Y, Sun, X, Yang, Q, Zheng, M, Shimoni, O, Ruan, W, Wang, Y, Zhang, D, Yin, J, Huang, X, Tao, W, Park, JB, Liang, X-J, Leong, KW & Shi, B 2022, 'Blood-brain barrier–penetrating single CRISPR-Cas9 nanocapsules for effective and safe glioblastoma gene therapy', Science Advances, vol. 8, no. 16, p. eabm8011.
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We designed a unique nanocapsule for efficient single CRISPR-Cas9 capsuling, noninvasive brain delivery and tumor cell targeting, demonstrating an effective and safe strategy for glioblastoma gene therapy. Our CRISPR-Cas9 nanocapsules can be simply fabricated by encapsulating the single Cas9/sgRNA complex within a glutathione-sensitive polymer shell incorporating a dual-action ligand that facilitates BBB penetration, tumor cell targeting, and Cas9/sgRNA selective release. Our encapsulating nanocapsules evidenced promising glioblastoma tissue targeting that led to high PLK1 gene editing efficiency in a brain tumor (up to 38.1%) with negligible (less than 0.5%) off-target gene editing in high-risk tissues. Treatment with nanocapsules extended median survival time (68 days versus 24 days in nonfunctional sgRNA-treated mice). Our new CRISPR-Cas9 delivery system thus addresses various delivery challenges to demonstrate safe and tumor-specific delivery of gene editing Cas9 ribonucleoprotein for improved glioblastoma treatment that may potentially be therapeutically useful in other brain diseases.

Zuo, Y, Li, R, Zhang, Y, Bao, G, Le, Y & Yan, L 2022, 'Design, synthesis and antitumor activity of 5-trifluoromethylpyrimidine derivatives as EGFR inhibitors', Journal of Enzyme Inhibition and Medicinal Chemistry, vol. 37, no. 1, pp. 2742-2754.
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A new series of 5-trifluoromethylpyrimidine derivatives were designed and synthesised as EGFR inhibitors. Three tumour cells A549, MCF-7, PC-3 and EGFR kinase were employed to evaluate their biological activities. The results were shown that most of the target compounds existed excellent antitumor activities. In particular, the IC50 values of compound 9u (E)-3-((2-((4-(3-(3-fluorophenyl)acrylamido)phenyl)amino)-5-(trifluoromethyl)pyrimidin-4-yl)amino)-N-methylthiophene-2-carboxamide against A549, MCF-7, PC-3 cells and EGFR kinase reached to 0.35 μM, 3.24 μM, 5.12 μM, and 0.091 μM, respectively. Additionally, further researches revealed that compound 9u could induce early apoptosis of A549 cells and arrest the cells in G2/M phase. Taken together, these findings indicated that compound 9u was potential for developing as antitumor reagent.