Publications

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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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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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, pp. 103-121.
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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 that outdoor 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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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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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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Matthews, JL, Cunning, R, Witson-Williams, R, Oakley, CA, Lutz, A, Roessner, U, Grossman, AR, Weis, VM, Gates, RD & Davy, SK 2022, 'The metabolic significance of symbiont community composition in the coral-algal symbiosis' in Applied Environmental Metabolomics, Elsevier, pp. 211-229.
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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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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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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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Reimers, JR & Mckemmish, LK 2022, 'Unified Understanding of Structure, Reactivity and Spectroscopy Within General Valence Bond Scenarios, Obtained by Transferring Techniques Developed Within Electron-Transfer Theory' in Shaik, S & Hibberty, PC (eds), Reference Module in Chemistry, Molecular Sciences and Chemical Engineering, Elsevier.
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Valence bond theory and electron transfer theory are both widely applied throughout Chemical Science, usually to different applications. Nevertheless, electron transfer theory is just an extensive development of one type of valence bond model. In this article, we demonstrate how electron-transfer theory can be more broadly applied to other valence-bond scenarios. This involves (1) rederivation for Morse oscillators of many key analytical expressions from electron-transfer transfer theory pertinent to harmonic oscillators, (2) renormalization of the key parameters from electron transfer theory to facilitate broad applications, and (3) development of 3 Morse-oscillator applications.

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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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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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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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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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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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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Abu Bakar, NA, Ali, S, Hisamuddin, SN, Supangat, A, Langford, SJ & Roslan, NA 2022, 'Effect of different deposition techniques of PCDTBT:PC71BM composite on the performance of capacitive-type humidity sensors', Synthetic Metals, vol. 285, pp. 117020-117020.
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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.
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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 identified IMA, UA,...

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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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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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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Akkaya Hocagil, T, Ryan, LM, Cook, RJ, Jacobson, SW, Richardson, GA, Day, NL, Coles, CD, Carmichael Olson, H & Jacobson, JL 2022, 'A hierarchical meta‐analysis for settings involving multiple outcomes across multiple cohorts', Stat, vol. 11, no. 1.
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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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Ocean 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', 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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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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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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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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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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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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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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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 host range I...

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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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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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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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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Assadi, MHN, Fronzi, M & Hanaor, DAH 2022, 'Unusual ferrimagnetic ground state in rhenium ferrite', The European Physical Journal Plus, vol. 137, no. 1.
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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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Azimi, Z, Gopakumar, A, Li, L, Kremer, F, Lockrey, M, Wibowo, AA, Nguyen, HT, Tan, HH, Jagadish, C & Wong‐Leung, J 2022, 'Effective Passivation of InGaAs Nanowires for Telecommunication Wavelength Optoelectronics', Advanced Optical Materials, vol. 10, no. 18, pp. 2200739-2200739.
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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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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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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 • Extracell...

Barratt, J, Ahart, L, Rice, M, Houghton, K, Richins, T, Cama, V, Arrowood, M, Qvarnstrom, Y & Straily, A 2022, 'Genotyping Cyclospora cayetanensis From Multiple Outbreak Clusters With An Emphasis on a Cluster Linked to Bagged Salad Mix—United States, 2020', The Journal of Infectious Diseases, vol. 225, no. 12, pp. 2176-2180.
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Abstract Cyclosporiasis is a diarrheal illness caused by the foodborne parasite Cyclospora cayetanensis. Annually reported cases have been increasing in the United States prompting development of genotyping tools to aid cluster detection. A recently developed Cyclospora genotyping system based on 8 genetic markers was applied to clinical samples collected during the cyclosporiasis peak period of 2020, facilitating assessment of its epidemiologic utility. While the system performed well and helped inform epidemiologic investigations, inclusion of additional markers to improve cluster detection was supported. Consequently, investigations have commenced to identify additional markers to enhance performance.

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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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, identify a p...

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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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 [CO ₂ ] are reduced under drought‐like conditions in temperate eucalypts', Functional Ecology, vol. 36, no. 7, pp. 1542-1558.
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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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Berdinsky, D, Elder, M & Kruengthomya, P 2022, 'Cayley polynomial–time computable groups', Information and Computation, vol. 288, pp. 104768-104768.
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Berdinsky, D, Elder, M & Taback, J 2022, 'On the geometry of Cayley automatic groups', International Journal of Algebra and Computation, vol. 32, no. 03, pp. 383-409.
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In contrast to being automatic, being Cayley automatic a priori has no geometric consequences. Specifically, Cayley graphs of automatic groups enjoy a fellow traveler property. Here, we study a distance function introduced by the first author and Trakuldit which aims to measure how far a Cayley automatic group is from being automatic, in terms of how badly the Cayley graph fails the fellow traveler property. The first author and Trakuldit showed that if it fails by at most a constant amount, then the group is in fact automatic. In this paper, we show that for a large class of non-automatic Cayley automatic groups this function is bounded below by a linear function in a precise sense defined herein. In fact, for all Cayley automatic groups which have super-quadratic Dehn function, or which are not finitely presented, we can construct a non-decreasing function which (1) depends only on the group and (2) bounds from below the distance function for any Cayley automatic structure on the group.

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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Bishop, A & Elder, M 2022, 'A virtually 2-step nilpotent group with polynomial geodesic growth', Algebra and Discrete Mathematics, vol. 33, no. 2, pp. 21-28.
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A direct consequence of Gromov's theorem is that if a group has polynomial geodesic growth with respect to some finite generating set then it is virtually nilpotent. However, until now the only examples known were virtually abelian. In this note we furnish an example of a virtually 2-step nilpotent group having polynomial geodesic growth with respect to a certain finite generating set.

Bordes, A, Danilov, DL, Desprez, P, Lecocq, A, Marlair, G, Truchot, B, Dahmani, M, Siret, C, Laurent, S, Herreyre, S, Dominget, A, Hamelin, L, Rigobert, G, Benjamin, S, Legrand, N, Belerrajoul, M, Maurer, W, Chen, Z, Raijmakers, LHJ, Li, D, Zhou, J, Notten, PHL, Perlo, P, Biasiotto, M, Introzzi, R, Petit, M, Martin, J, Bernard, J, Koffel, S, Lorentz, V, Durling, E, Kolari, S, Wang, Z, Massazza, M & Lamontarana, S 2022, 'A holistic contribution to fast innovation in electric vehicles: An overview of the DEMOBASE research project', eTransportation, vol. 11, pp. 100144-100144.
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Boyton, I, Goodchild, SC, Diaz, D, Elbourne, A, Collins-Praino, LE & Care, A 2022, 'Characterizing the Dynamic Disassembly/Reassembly Mechanisms of Encapsulin Protein Nanocages', ACS Omega, vol. 7, no. 1, pp. 823-836.
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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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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.
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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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AbstractMacroalgae 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.

Budnik, G, Scott, JA, Jiao, C, Maazouz, M, Gledhill, G, Fu, L, Tan, HH & Toth, M 2022, 'Nanoscale 3D Tomography by In-Flight Fluorescence Spectroscopy of Atoms Sputtered by a Focused Ion Beam', Nano Letters, vol. 22, no. 20, pp. 8287-8293.
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Burmuzoska, I, Hogg, K, Raymond, J, Hitchcock, C & Meakin, GE 2022, 'Comparison of operational DNA recovery methods: Swabs versus tapelifts', Forensic Science International: Genetics Supplement Series, vol. 8, pp. 50-52.
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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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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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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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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 2022, 'Contingency planning for coral reefs in the Anthropocene; The potential of reef safe havens', Emerging Topics in Life Sciences, vol. 6, no. 1, pp. 107-124.
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Reducing the global reliance on fossil fuels is essential to ensure the long-term survival of coral reefs, but until this happens, alternative tools are required to safeguard their future. One emerging tool is to locate areas where corals are surviving well despite the changing climate. Such locations include refuges, refugia, hotspots of resilience, bright spots, contemporary near-pristine reefs, and hope spots that are collectively named reef ‘safe havens' in this mini-review. Safe havens have intrinsic value for reefs through services such as environmental buffering, maintaining near-pristine reef conditions, or housing corals naturally adapted to future environmental conditions. Spatial and temporal variance in physicochemical conditions and exposure to stress however preclude certainty over the ubiquitous long-term capacity of reef safe havens to maintain protective service provision. To effectively integrate reef safe havens into proactive reef management and contingency planning for climate change scenarios, thus requires an understanding of their differences, potential values, and predispositions to stress. To this purpose, I provide a high-level review on the defining characteristics of different coral reef safe havens, how they are being utilised in proactive reef management and what risk and susceptibilities they inherently have. The mini-review concludes with an outline of the potential for reef safe haven habitats to support contingency planning of coral reefs under an uncertain future from intensifying climate change.

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.
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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.
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Abstract Background Elements 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 genera Breviolum, 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. Results Symbiodiniaceae 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 (C19.8N2.6 P

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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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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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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AbstractThe 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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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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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.
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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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Chayambuka, K, Jiang, M, Mulder, G, Danilov, DL & Notten, PHL 2022, 'Physics-based modeling of sodium-ion batteries part I: Experimental parameter determination', Electrochimica Acta, vol. 404, pp. 139726-139726.
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Chayambuka, K, Mulder, G, Danilov, DL & Notten, PHL 2022, 'Physics-based modeling of sodium-ion batteries part II. Model and validation', Electrochimica Acta, vol. 404, pp. 139764-139764.
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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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Chen, C & Jin, D 2022, 'Giant nonlinearity in upconversion nanoparticles', Nature Photonics, vol. 16, no. 8, pp. 553-554.
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Chen, D, Fröch, JE, Ru, S, Cai, H, Wang, N, Adamo, G, Scott, J, Li, F, Zheludev, N, Aharonovich, I & Gao, W 2022, 'Quantum Interference of Resonance Fluorescence from Germanium-Vacancy Color Centers in Diamond', Nano Letters, vol. 22, no. 15, pp. 6306-6312.
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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, 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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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, 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, 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.
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Chen, L, Wu, X, Gilchrist, AM & Gale, PA 2022, 'Organoplatinum Compounds as Anion‐Tuneable Uphill Hydroxide Transporters', Angewandte Chemie, vol. 134, no. 19.
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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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Chen, Z, Danilov, DL, Eichel, R & Notten, PHL 2022, 'Porous Electrode Modeling and its Applications to Li‐Ion Batteries', Advanced Energy Materials, vol. 12, no. 32, pp. 2201506-2201506.
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Battery modeling has become increasingly important with the intensive development of Li-ion batteries (LIBs). The porous electrode model, relating battery performances to the internal physical and (electro)chemical processes, is one of the most adopted models in scientific research and engineering fields. Since Newman and coworkers’ first implementation in the 1990s, the porous electrode model has kept its general form. Soon after that, many publications have focused on the applications to LIBs. In this review, the applications of the porous electrode model to LIBs are systematically summarized and discussed. With this model, various internal battery properties have been studied, such as Li+ concentration and electric potential in the electrolyte and electrodes, reaction rate distribution, overpotential, and impedance. When coupled with thermal, mechanical, and aging models, the porous electrode model can simulate the temperature and stress distribution inside batteries and predict degradation during battery operation. With the help of state observers, the porous electrode model can monitor various battery states in real-time for battery management systems. Even though the porous electrode models have multiple advantages, some challenges and limitations still have to be addressed. The present review also gives suggestions to overcome these limitations in future research.

Chen, Z, Danilov, DL, Eichel, R-A & Notten, PHL 2022, 'Li+ concentration waves in a liquid electrolyte of Li-ion batteries with porous graphite-based electrodes', Energy Storage Materials, vol. 48, pp. 475-486.
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Chen, Z, Danilov, DL, Zhang, Q, Jiang, M, Zhou, J, Eichel, R-A & Notten, PHL 2022, 'Modeling NCA/C6-Si battery ageing', Electrochimica Acta, vol. 430, pp. 141077-141077.
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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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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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Clemons, B, Barratt, J, Lane, M, Qvarnstrom, Y, Teal, AE, Zayas, G & Madison-Antenucci, S 2022, 'Assessing an Adaptation of the Universal Parasite Diagnostic Assay for Bloodborne Parasites in a US State Public Health Laboratory', The American Journal of Tropical Medicine and Hygiene, vol. 106, no. 2, pp. 671-677.
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ABSTRACT. For complex clinical cases where a parasitic infection is suspected, it can be difficult for clinicians to recommend an appropriate laboratory test. These tests are usually pathogen-specific and require a certain degree of suspicion for the precise etiology. A recently described assay, the universal parasite diagnostic (UPDx) can potentially provide a diagnosis of any parasite present in a specimen. Using primers that amplify DNA from all eukaryotes, UPDx differentiates several parasitic infections in blood by amplicon-based next-generation sequencing (NGS) of the 18S rDNA locus. As the state’s public health reference laboratory, the Parasitology Laboratory at the Wadsworth Center (Albany, NY) receives specimens from patients who have potentially encountered a wide variety of parasites. As such, the ability to differentiate several blood parasites using a single assay is of interest. We assessed UPDx for its ability to confirm parasitic infections for 20 specimens that were previously identified by real-time PCR (RT-PCR). This included specimens positive for Babesia microti, Trypanosoma cruzi, Leishmania tropica, various Plasmodium species, and specimens comprising mixed Plasmodium sp. infections. Results obtained using UPDx were largely concordant with the RT-PCR assays. A T. cruzi positive specimen was negative by UPDx and for two mixed Plasmodium sp. infections only one species was detected. The results obtained for other specimens were concordant. We conclude that UPDx shows promise for the detection of blood parasites in diagnostic laboratories. As NGS becomes cheaper, assays like UPDx will become increasingly amenable to use in clinical settings.

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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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.
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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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Corletto, A, Ellis, AV, Shepelin, NA, Fronzi, M, Winkler, DA, Shapter, JG & Sherrell, PC 2022, 'Energy Interplay in Materials: Unlocking Next‐Generation Synchronous Multisource Energy Conversion with Layered 2D Crystals', Advanced Materials, vol. 34, no. 36, pp. 2203849-2203849.
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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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ABSTRACT 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. Objectives We examined the construct and criterion validity of the Total Nutrient Index (TNI) among US adults (≥19 years; nonpregnant or lactating). Methods The TNI includes 8 underconsumed 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 RDA 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 (≥19 years; n = 8861) and 2011–2014 NHANES (≥19 years; n = 9954) were employed. Exemplary menus were used to determine whether the TNI yielded high scores from dietary sources (women, 31–50 years; men ≥ 70 years). 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 correlat...

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', pp. 21-30.
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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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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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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.

Dadd-Daigle, P, Collins, D, Kirkby, K, Roser, S, Lonergan, P, Chowdhury, PR, Labbate, M & Chapman, TA 2022, 'Characterisation of Verticillium dahliae by inter-simple sequence repeats identified a virulent subpopulation affecting Australian cotton', Australasian Plant Pathology, vol. 51, no. 4, pp. 409-418.
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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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Dai, G, Ma, Y, Hasler, J, Chen, J & Carroll, RJ 2022, 'A robust approach for electronic health record–based case‐control studies with contaminated case pools', Biometrics.
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We consider analyses of case-control studies assembled from electronic health records (EHRs) where the pool of cases is contaminated by patients who are ineligible for the study. These ineligible patients, referred to as 'false cases,' should be excluded from the analyses if known. However, the true outcome status of a patient in the case pool is unknown except in a subset whose size may be arbitrarily small compared to the entire pool. To effectively remove the influence of the false cases on estimating odds ratio parameters defined by a working association model of the logistic form, we propose a general strategy to adaptively impute the unknown case status without requiring a correct phenotyping model to help discern the true and false case statuses. Our method estimates the target parameters as the solution to a set of unbiased estimating equations constructed using all available data. It outperforms existing methods by achieving robustness to mismodeling the relationship between the outcome status and covariates of interest, as well as improved estimation efficiency. We further show that our estimator is root-n-consistent and asymptotically normal. Through extensive simulation studies and analysis of real EHR data, we demonstrate that our method has desirable robustness to possible misspecification of both the association and phenotyping models, along with statistical efficiency superior to the competitors.

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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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, pp. 113762-113762.
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Dawson, BM, Wallman, JF, Evans, MJ, Butterworth, NJ & Barton, PS 2022, 'Priority effects and density promote coexistence between the facultative predator Chrysomya rufifacies and its competitor Calliphora stygia', Oecologia, vol. 199, no. 1, pp. 181-191.
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AbstractHighly competitive ephemeral resources like carrion tend to support much greater diversity relative to longer-lived resources. The coexistence of diverse communities on short-lived carrion is a delicate balance, maintained by several processes including competition. Despite this balance, few studies have investigated the effect of competition on carrion, limiting our understanding of how competition drives coexistence. We investigated how priority effects and larval density influence coexistence between two blowfly species, the facultative predator Chrysomya rufifacies and its competitor Calliphora stygia, which occupy broadly similar niches but differ in their ecological strategies for exploiting carrion. We examined how adult oviposition, larval survival, developmental duration, and adult fitness were affected by the presence of differently aged heterospecific larval masses, and how these measures varied under three larval densities. We found C. rufifacies larval survival was lowest in conspecific masses with low larval densities. In heterospecific masses, survival increased, particularly at high larval density, with priority effects having minimal effect, suggesting a dependency on collective exodigestion. For C. stygia, we found survival to be constant across larval densities in a conspecific mass. In heterospecific masses, survival decreased drastically when C. rufifacies arrived first, regardless of larval density, suggesting C. stygia is temporally constrained to avoid competition with C. rufifacies. Neither species appeared to completely outcompete the other, as they were either constrained by density requirements (C. rufifacies) or priority effects (C. stygia). Our results pr...

Day, DM, Butterworth, NJ, Tagat, A, Markowsky, G & Wallman, JF 2022, 'Development of larvae of the Australian blowfly, Calliphora augur (Diptera: Calliphoridae), at constant temperatures', Australian Journal of Forensic Sciences, vol. 54, no. 5, pp. 710-721.
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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 associated...

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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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.
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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.
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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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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, 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. 2203354-2203354.
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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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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 the searc...

Dukic, E, Gollan, PJ, Grebe, S, Paakkarinen, V, Herdean, A, Aro, E-M & Spetea, C 2022, 'The Arabidopsis thylakoid chloride channel ClCe regulates ATP availability for light-harvesting complex II protein phosphorylation', Frontiers in Plant Science, vol. 13, no. Women in Plant Physiology: 2022.
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Coping with changes in light intensity is challenging for plants, but well-designed mechanisms allow them to acclimate to most unpredicted situations. The thylakoid K+/H+ antiporter KEA3 and the voltage-dependent Cl− channel VCCN1 play important roles in light acclimation by fine-tuning electron transport and photoprotection. Good evidence exists that the thylakoid Cl− channel ClCe is involved in the regulation of photosynthesis and state transitions in conditions of low light. However, a detailed mechanistic understanding of this effect is lacking. Here we report that the ClCe loss-of-function in Arabidopsis thaliana results in lower levels of phosphorylated light-harvesting complex II (LHCII) proteins as well as lower levels of the photosystem I-LHCII complexes relative to wild type (WT) in low light conditions. The phosphorylation of the photosystem II core D1/D2 proteins was less affected either in low or high light conditions. In low light conditions, the steady-state levels of ATP synthase conductivity and of the total proton flux available for ATP synthesis were lower in ClCe loss-of-function mutants, but comparable to WT at standard and high light intensity. As a long-term acclimation strategy, expression of the ClCe gene was upregulated in WT plants grown in light-limiting conditions, but not in WT plants grown in standard light even when exposed for up to 8 h to low light. Taken together, these results suggest a role of ClCe in the regulation of the ATP synthase activity which under low light conditions impacts LHCII protein phosphorylation and state transitions.

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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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, 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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Elder, M & Piggott, A 2022, 'Rewriting systems, plain groups, and geodetic graphs', Theoretical Computer Science, vol. 903, pp. 134-144.
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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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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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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.

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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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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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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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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Abstract We 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.

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 <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.

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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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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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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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.
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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.
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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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Abstract Recreational 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.

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. 2104805-2104805.
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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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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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Fu, X, Xu, C, Liu, Y, Chen, C-H, Hwang, FJ & Wang, J 2022, 'Spatial heterogeneity and migration characteristics of traffic congestion—A quantitative identification method based on taxi trajectory data', Physica A: Statistical Mechanics and its Applications, vol. 588, pp. 126482-126482.
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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-selected libr...

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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Gao, H, Tang, K, Xiao, J, Guo, X, Chen, W, Liu, H & Wang, G 2022, 'Recent advances in “water in salt” electrolytes for aqueous rechargeable monovalent-ion (Li+, Na+, K+) batteries', Journal of Energy Chemistry, vol. 69, pp. 84-99.
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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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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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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).

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.
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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, older age, and...

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 of

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

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 environmental change.<...

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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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.
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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, C, Chen, C-H, Hwang, F-J, Chang, C-C & Chang, C-C 2022, 'Fast Spatiotemporal Learning Framework for Traffic Flow Forecasting', IEEE Transactions on Intelligent Transportation Systems, pp. 1-11.
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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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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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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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Hamidian, M 2022, 'Tn6553, a Tn7-family transposon encoding putative iron uptake functions found in Acinetobacter', Archives of Microbiology, vol. 204, no. 11.
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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 in nosocom...

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.

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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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. Neverthele...

Hatt, A, Brown, E, Berlowitz, DJ, O’Donoghue, F, Meaklim, H, Connelly, A, Jackson, G, Sutherland, K, Cistulli, PA, Lee, BSB & Bilston, LE 2022, 'Tetraplegic obstructive sleep apnoea patients dilate the airway similarly to able-bodied obstructive sleep apnoea patients', The Journal of Spinal Cord Medicine, vol. 45, no. 4, pp. 536-546.
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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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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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Abstract Global 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 Statement Characterizing long-term rainfall pattern changes under different rainfall conditions is important to understand the impacts of clim...

Hegarty, A, Stewart, J & Gladstone, W 2022, 'Geographical variation in age and growth of the endemic A ustralian sciaenid Atractoscion atelodus', Journal of Fish Biology, vol. 100, no. 2, pp. 474-485.
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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.
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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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Heywood, Z, Mallinson, J, Galli, E, Acharya, S, Bose, S, Arnold, M, Bones, P & Brown, S 2022, 'Self-organized nanoscale networks: are neuromorphic properties conserved in realistic device geometries?', Neuromorphic Computing and Engineering, vol. 2, no. 2, pp. 024009-024009.
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Abstract Self-organised nanoscale networks are currently under investigation because of their potential to be used as novel neuromorphic computing systems. In these systems, electrical input and output signals will necessarily couple to the recurrent electrical signals within the network that provide brain-like functionality. This raises important questions as to whether practical electrode configurations and network geometries might influence the brain-like dynamics. We use the concept of criticality (which is itself a key charactistic of brain-like processing) to quantify the neuromorphic potential of the devices, and find that in most cases criticality, and therefore optimal information processing capability, is maintained. In particular we find that devices with multiple electrodes remain critical despite the concentration of current near the electrodes. We find that broad network activity is maintained because current still flows through the entire network. We also develop a formalism to allow a detailed analysis of the number of dominant paths through the network. For rectangular systems we show that the number of pathways decreases as the system size increases, which consequently causes a reduction in network activity.

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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AbstractPredation 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.

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, 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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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. 2202222-2202222.
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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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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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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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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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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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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. 2202394-2202394.
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Single-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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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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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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Irga, PJ, Fleck, R, Arsenteva, E & Torpy, FR 2022, 'Biosolar green roofs and ambient air pollution in city centres: Mixed results', Building and Environment, vol. 226, pp. 109712-109712.
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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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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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Jacobson, D, Zheng, Y, Plucinski, MM, Qvarnstrom, Y & Barratt, JLN 2022, 'Evaluation of various distance computation methods for construction of haplotype-based phylogenies from large MLST datasets', Molecular Phylogenetics and Evolution, vol. 177, pp. 107608-107608.
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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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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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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, 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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Abstract We 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.

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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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, pp. 770-781.
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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.
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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) and health...

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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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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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.
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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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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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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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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. Graphical ...

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. 011306-011306.
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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.
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ABSTRACT The 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.
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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.
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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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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.

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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Krix, DW, Murray, ML & Murray, BR 2022, 'Increasing radiant heat flux affects leaf flammability patterns in plant species of eastern Australian fire‐prone woodlands', Plant Biology, vol. 24, no. 2, pp. 302-312.
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Kumar, D, Dua, K, Shukla, MK, Dubey, A, Pandey, S, Singh, SK, Gupta, G, Prasher, P, Chellappan, DK & Oliver, BG 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-specific delivery of therapeutics, airway geometry, humidity, clearance mechanisms, presence of lung diseases, and therapy against tumor cell resistance. Advancements in drug delivery using nanotechnology based multifunctional nanocarriers, have emerged as a viable method for treating lung cancer with more efficacy and fewer adverse effects. This review does a thorough and critical examination of effective nano-enabled approaches for lung 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 the size, drug loading, transport, and retention. Personalized lung tumor therapies using sophisticated nano modalities have the potential to provide great therapeutic advantages based on individual unique genetic markers and disease profiles. Overall, this review provides comprehensive information on newer nanotechnological prospects for improving the management of apoptosis in lung cancer.

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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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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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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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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Lachs, L, Chong, F, Beger, M, East, HK, Guest, JR & Sommer, B 2022, 'SizeExtractR: A workflow for rapid reproducible extraction of object size metrics from scaled images', Ecology and Evolution, vol. 12, no. 3.
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Laila, AZ, Fronzi, M, Kumegai, S, Sugiyama, K, Furui, R & Yamamoto, A 2022, 'High-Pressure Synthesis of High-Entropy Metal Disulfides with Pyrite-Type Structure', Journal of the Physical Society of Japan, vol. 91, no. 8.
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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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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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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.
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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. 2103332-2103332.
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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.

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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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.

Lei, Y, Wu, C, Lu, X, Hua, W, Li, S, Liang, Y, Liu, H, Lai, W, Gu, Q, Cai, X, Wang, N, Wang, Y, Chou, S, Liu, H, Wang, G & Dou, S 2022, 'Streamline Sulfur Redox Reactions to Achieve Efficient Room‐Temperature Sodium–Sulfur Batteries', Angewandte Chemie International Edition, vol. 61, no. 16.
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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, 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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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.
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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, 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, 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, J, Song, J, Luo, L, Zhang, H, Feng, J, Zhao, X, Guo, X, Dong, H, Chen, S, Liu, H, Shao, G, Anthopoulos, TD, Su, Y, Wang, F & Wang, G 2022, 'Synergy of MXene with Se Infiltrated Porous N‐Doped Carbon Nanofibers as Janus Electrodes for High‐Performance Sodium/Lithium–Selenium Batteries', Advanced Energy Materials, vol. 12, no. 32, pp. 2200894-2200894.
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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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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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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.

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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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 Lebanon, but ph...

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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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, 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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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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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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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', 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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BACKGROUND AND AIM: Inflammatory 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. METHODS: Selected 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. RESULTS: ATG16L2 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 rs3024505, CARD9 rs1078149, and IL12 rs6556412 were associated with higher levels of IL-10, IL-22, and IL-23 in these same subjects, respectively. CONCLUSIONS: This study identified eight SNPs associated with IBD and/or its subtypes in the Malaysia population, significantly advancing our understanding of the genetic contribution to IBD in this understudied population. Three of these SNPs modulated relevant cytokine levels and thus, may directly contribute to IBD pathogenesis.

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.
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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 Global Change Biology, vol. 28, no. 24, pp. 7186-7204.
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Machungo, C, Berna, AZ, McNevin, D, Wang, R & Trowell, S 2022, 'Comparison of the performance of metal oxide and conducting polymer electronic noses for detection of aflatoxin using artificially contaminated maize', 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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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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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.

Marsh, JW & Ley, RE 2022, 'Microbiome engineering: Taming the untractable', Cell, vol. 185, no. 3, pp. 416-418.
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In this issue of Cell, Jin et al. describe several innovative tools for microbiome engineering to enable in situ editing of complex communities. However, challenges remain to overcome the widespread genetic intractability of microbiome constituents.

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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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.
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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.

McFayden, T, Jarrett, MA, White, SW, Scarpa, A, Dahiya, A & Ollendick, TH 2022, 'Sluggish Cognitive Tempo in Autism Spectrum Disorder, ADHD, and Their Comorbidity: Implications for Impairment', Journal of Clinical Child & Adolescent Psychology, vol. 51, no. 2, pp. 195-202.
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© 2020, © 2020 Society of Clinical Child & Adolescent Psychology. Objective: Sluggish Cognitive Tempo (SCT), characterized by lethargy and daydreaming, has most commonly been studied in community samples and in youth with Attention-Deficit/Hyperactivity Disorder (ADHD). Despite shared neurodevelopmental symptoms with ADHD, few studies have investigated SCT in Autism Spectrum Disorders (ASD). The current study investigated SCT symptoms in youth with ASD, ADHD, and comorbid ASD+ADHD to explore the relations between SCT and global and social impairment. Method: Caregivers of children and adolescents (n = 98; ages 6–17) diagnosed with ADHD (n = 46), ASD (n = 28), or ASD+ADHD (n = 24) completed measures of social impairment, SCT, and demographic variables. Results: All three clinical groups demonstrated comparable levels of SCT. Diagnosis and SCT independently contributed to parent-rated social impairment, while SCT and IQ, but not diagnosis, contributed to clinician-rated global functioning. Specifically, having comorbid ASD+ADHD, but not an ASD or ADHD diagnosis alone, significantly predicted greater social impairment. Conclusion: These results extend previous literature investigating SCT in ASD and provide evidence to suggest that SCT is associated with social and global impairment above and beyond the impairment associated with ADHD and/or ASD. These results may have implications for clinical assessment and treatment of ASD and ADHD.

McLean, AEB, Kao, SC, Barnes, DJ, Wong, KKH, Scolyer, RA, Cooper, WA & Kohonen-Corish, MRJ 2022, 'Corrigendum to “The emerging role of the lung microbiome and its importance in non-small cell lung cancer diagnosis and treatment” [Lung Cancer 165C (2022) 124–132]', Lung Cancer, vol. 166, pp. 252-252.
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McLean, AEB, Kao, SC, Barnes, DJ, Wong, KKH, Scolyer, RA, Cooper, WA & Kohonen-Corish, MRJ 2022, 'The emerging role of the lung microbiome and its importance in non-small cell lung cancer diagnosis and treatment', Lung Cancer, vol. 165, pp. 124-132.
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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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Offshore 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 to extending species distributions by providing rest stops, foraging habitat, ...

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 Cu17.5Al82.5 using 5 M NaOH. The ostensible (i.e., net external) capacitance of a symmetrical two-electrode cell with 0.1 M KNO3 electrolyte 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.
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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. 2106046-2106046.
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Meng, Y, Gong, D, Li, W, Wen, Y, Fan, Z, Zhang, C, Wang, T, Fu, S, Wei, Z & Yun, K 2022, 'Liquid Chromatography-triple Quadrupole Mass Spectrometry Simultaneously Detecting Paraquat and Metabolites in Biological Samples', Forensic Science and Technology, vol. 47, no. 1, pp. 49-57.
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Objective To establish an LC-MS/MS method for determination of paraquat (PQ) and its main metabolites [monoquat, paraquat-monopyridone (MP), paraquat-dipyridone (DP) and 4-carboxy-1-methylpyridinium ion (MINA)] in biological samples. Methods The biological samples (blood and tissues for this assay) were added with Paraquat-d8 Dichloride (PQ-D8), the internal standard substance, successively having them adjusted of pH values and precipitated of proteins with acetonitrile so that their supernatants were cleansed with cyclohexane and consecutively centrifuged to receive the lower layer of acetonitrile. The received fluid was undergone with drying, re-dissolved into methanol, centrifuged and filtrated through membrane, thereafter having been brought to elution with different chromatographic columns of LC-MS/MS apparatus. For the analysis of mass spectrometry into the eluate from column separation, LC-MS/MS apparatus was set under multiple reaction monitoring (MRM) mode plus positive ionization. Results Linear ranges were present with PQ, monoquat, MP, DP and MINA at each individual’s 5-800ng/mL, 0.5-80ng/mL, 5-800ng/mL, 2.5-400ng/mL and 2-320ng/mL (all rendering an r higher than 0.993), with their intraand inter-day precision (RSDs) being 5%~14%, 3%~13%, 3%~15%, 5%~13% and 2%~15% plus the accuracy (RE) being 91%~116%, 80%~100%, 80%~111%, 85%~114% and 91%~114%, respectively. Besides, if the processed samples were placed with the autosampler at room temperature for 72 hours, each analyte (in the order of PQ, monoquat, MP, DP and MINA) demonstrated its own accuracy of 90~119%, 56%~125%, 60%~110%, 78%~98%, 83%~117%, respectively. Conclusions This approach set up here is of simple pretreatment, good separation effect and high extraction efficiency, capable of detecting PQ and metabolites from suspected paraquat poisoning samples. As the optimized update from our team’s earlier attempt to detect paraquat, monoquat and MP in biological samples, this approach could also have...

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.

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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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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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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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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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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Molloy, MP, Hill, C, O’Rourke, MB, Chandra, J, Steffen, P, McKay, MJ, Pascovici, D & Herbert, BR 2022, 'Proteomic Analysis of Whole Blood Using Volumetric Absorptive Microsampling for Precision Medicine Biomarker Studies', Journal of Proteome Research, vol. 21, no. 4, pp. 1196-1203.
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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 HR, 4.88; 95% 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 compared to the PF measure.

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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Morrell, S, Kohonen-Corish, MRJ, Ward, RL, Sorrell, TC, Roder, D & Currow, DC 2022, 'Antibiotic exposure within six months before systemic therapy was associated with lower cancer survival', Journal of Clinical Epidemiology, vol. 147, pp. 122-131.
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Murzakhanov, FF, Mamin, GV, Orlinskii, SB, Gerstmann, U, Schmidt, WG, Biktagirov, T, Aharonovich, I, Gottscholl, A, Sperlich, A, Dyakonov, V & Soltamov, VA 2022, 'Electron–Nuclear Coherent Coupling and Nuclear Spin Readout through Optically Polarized V_B^– Spin States in hBN', Nano Letters, vol. 22, no. 7, pp. 2718-2724.
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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 Na ₂ CO ₃ Additions on the Thermoelectric Performance of Melt‐Route Cu ₂ Se', Advanced Electronic Materials, vol. 8, no. 3, pp. 2100802-2100802.
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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.
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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.

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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Nguyen, VT, Doan, Q-V, Tran, NN, Luong, LTM, Chinh, PM, Thai, PK, Phung, D, Le, HHTC & Dang, TN 2022, 'The protective effect of green space on heat-related respiratory hospitalization among children under 5 years of age in Hanoi, Vietnam', Environmental Science and Pollution Research, vol. 29, no. 49, pp. 74197-74207.
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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.

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', pp. 55-127.
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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.
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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, 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.
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AbstractEcological 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'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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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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Oglobline, AN, Padula, MP & Doble, PA 2022, 'Quality control of A1-free dairy', Food Control, vol. 135, pp. 108685-108685.
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Ortega, JS, Corrales-Orovio, R, Ralph, P, Egaña, JT & Gentile, C 2022, 'Photosynthetic microorganisms for the oxygenation of advanced 3D bioprinted tissues', Acta Biomaterialia.
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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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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 μg/mL of A...

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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The 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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Synthetic 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 exceed 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 synthetic cannabinoid 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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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.

Patil, PP, Mohammad Aslam, S, Vass, I & Szabó, M 2022, 'Characterization of the wave phenomenon of flash-induced chlorophyll fluorescence in Chlamydomonas reinhardtii', Photosynthesis Research, vol. 152, no. 2, pp. 235-244.
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AbstractFlash-induced chlorophyll fluorescence relaxation is a powerful tool to monitor the reoxidation reactions of the reduced primary quinone acceptor, QA− by QB and the plastoquinone (PQ) pool, as well as the charge recombination reactions between the donor and acceptor side components of Photosystem II (PSII). Under certain conditions, when the PQ pool is highly reduced (e.g. in microaerobic conditions), a wave phenomenon appears in the fluorescence relaxation kinetics, which reflects the transient reoxidation and re-reduction of QA− by various electron transfer processes, which in cyanobacteria is mediated by NAD(P)H dehydrogenase (NDH-1). The wave phenomenon was also observed and assigned to the operation of type 2 NAD(P)H dehydrogenase (NDH-2) in the green alga Chlamydomonas reinhardtii under hydrogen-producing conditions, which required a long incubation of algae under sulphur deprivation (Krishna et al. J Exp Bot 70 (21):6321–6336, 2019). However, the conditions that induce the wave remained largely uncharacterized so far in microalgae. In this work, we investigated the wave phenomenon in Chlamydomonas reinhardtii under conditions that lead to a decrease of PSII activity by applying hydroxylamine treatment, which impacts the donor side of PSII in combination with a strongly reducing environment of the PQ pool (microaerobic conditions). A similar wave phenomenon could be induced by photoinhibitory conditions (illumination with strong light in the presence of the protein synthesis inhibitor lincomycin). These results indicate that the fluorescence wave phenomenon is activated in green algae when the PSII activity decreases relative to Photosystem I (PS I) activity and the PQ pool is strongly reduced. Therefore, the fluorescence wave could be used as a sensitive indic...

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.
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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.
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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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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.

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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Pera, JB, Davie, AW, Rohlfs, A-M & Mitrovic, SM 2022, 'Simulating the potential effects of a carp virus fish kill on water quality and phytoplankton in lentic environments', Marine and Freshwater Research, vol. 73, no. 2, pp. 178-192.
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Decaying fish play an important role in delivering nutrients into rivers and lakes but can create water quality issues. The release of cyprinid herpesvirus-3 (CyHV-3) in Australia with an associated mass common carp mortality may have serious effects on water quality in lakes. To evaluate the effect of a virus-induced fish kill, different biomasses of dead common carp (250–6000 kg ha–1) were placed into 2000-L mesocosms within Prospect Reservoir, Australia, for up to 40 days. Decaying carp created anoxic conditions within all treatments except the 250 kg ha–1 treatment, in which oxygen saturation dropped to 30%. A higher biomass of carp led to longer periods of anoxia. Total nitrogen (TN) increased from a baseline of 0.25 to 1.5–30 mg L–1 in the different treatments, whereas total phosphorus (TP) increased from 0.01 to 0.05–5.0 mg L–1. Chlorophyll-a levels increased from <5 µg L–1 to levels between 100 and 1000 µg L–1 in the different treatments. Mean nutrient levels (TN and TP), chlorophyll-a and phytoplankton biovolume all showed a significant (P < 0.05) linear relationship with carp biomass. This relationship can be used to support the quantification of water quality risk from a known biomass of carp. Our experiment suggests that carp mortality may significantly reduce water quality in shallow lakes where the biomass of dead carp is above moderate levels (250 kg ha–1).

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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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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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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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.
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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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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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Qi, X-R, Liu, Y, Ma, L-L, Hou, B-X, Zhang, H-W, Li, X-H, Wang, Y-S, Hui, Y-Q, Wang, R-X, Bai, C-Y, Liu, H, Song, J-J & Zhao, X-X 2022, 'Delicate synthesis of quasi-inverse opal structural Na3V2(PO4)3/N-C and Na4MnV(PO4)3/N-C as cathode for high-rate sodium-ion batteries', Rare Metals, vol. 41, no. 5, pp. 1637-1646.
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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.
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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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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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AbstractEfficient 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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Rafei, R, Koong, J, Osman, M, Al Atrouni, A, Hamze, M & Hamidian, M 2022, 'Analysis of pCl107 a large plasmid carried by an ST25 Acinetobacter baumannii strain reveals a complex evolutionary history and links to multiple antibiotic resistance and metabolic pathways', FEMS Microbes, vol. 3.
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Abstract Acinetobacter 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, 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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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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AbstractVibrio 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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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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Abstract Background Metal 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. Methods We 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 the dsrB gene. The functional capacity was further analyzed by generating binned, genomic assemblies and performing flux-balance analysis on the metabolism of the dominant taxa. Results The 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 bacter...

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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Rangel Pinagé, E, M. Bell, D, Longo, M, Gao, S, Keller, M, Silva, CA, Ometto, JP, Köhler, P, Frankenberg, C & Huete, A 2022, 'Forest structure and solar-induced fluorescence across intact and degraded forests in the Amazon', Remote Sensing of Environment, vol. 274, pp. 112998-112998.
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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.
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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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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.
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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, J, Wang, X, Parry, SN, Yee, C, Gorrell, MD, McLennan, SV & Twigg, SM 2022, 'Targeting CCN2 protects against progressive non-alcoholic steatohepatitis in a preclinical model induced by high-fat feeding and type 2 diabetes', Journal of Cell Communication and Signaling, vol. 16, no. 3, pp. 447-460.
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AbstractType 2 diabetes is an independent risk factor for non-alcoholic steatohepatitis (NASH) progression and its mediators have not been resolved. In this study, a pathogenic role of cellular communication network factor 2 (CCN2) protein in NASH pathology, was investigated in an established preclinical NASH model. Male wild type C57BL/6 mice received either Chow or high fat diet (HFD) for 26 weeks, with some mice in each group randomly selected to receive low dose streptozotocin (STZ: 3 i.p. injections, 65 mg/kg) at 15 weeks to induce type 2 diabetes. In the final 10 of the 26 weeks mice from each group were administered i.p. either rabbit anti-CCN2 neutralizing antibody (CCN2Ab) or as control normal rabbit IgG, at a dose of 150 µg per mouse twice/week. NASH developed in the HFD plus diabetes (HFD+DM) group. Administration of CCN2Ab significantly downregulated collagen I and collagen III mRNA induction and prevented pro-inflammatory MCP-1 mRNA induction in HFD+DM mice. At the protein level, CCN2Ab significantly attenuated collagen accumulation by PSR stain and collagen I protein induction in HFD+DM. Phosphorylation of the pro-fibrotic ERK signalling pathway in liver in HFD+DM was attenuated by CCN2Ab treatment. Intrahepatic CCN1 mRNA was induced, whereas CCN3 was downregulated at both the mRNA and protein levels in HFD+DM. CCN3 down-regulation was prevented by CCN2Ab treatment. This in vivo study indicates that CCN2 is a molecular target in NASH with high fat diet and diabetes, and that regulation of ERK signalling is implicated in this process.

Ren, J, Wang, X, Yee, C, Gorrell, MD, McLennan, SV & Twigg, SM 2022, 'Sitagliptin Is More Effective Than Gliclazide in Preventing  Pro-Fibrotic and Pro-Inflammatory Changes in a Rodent Model of Diet-Induced Non-Alcoholic Fatty Liver Disease', Molecules, vol. 27, no. 3, pp. 727-727.
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A diet-induced non-alcoholic fatty liver disease (NAFLD) model causing obesity in rodents was used to examine whether sitagliptin and gliclazide therapies have similar protective effects on pathological liver change. Methods: Male mice were fed a high-fat diet (HFD) or standard chow (Chow) ad libitum for 25 weeks and randomly allocated to oral sitagliptin or gliclazide treatment for the final 10 weeks. Fasting blood glucose and circulating insulin were measured. Inflammatory and fibrotic liver markers were assessed by qPCR. The second messenger ERK and autophagy markers were examined by Western immunoblot. F4/80, collagens and CCN2 were assessed by immunohistochemistry (IHC). Results: At termination, HFD mice were obese, hyperinsulinemic and insulin-resistant but non-diabetic. The DPP4 inhibitor sitagliptin prevented intrahepatic induction of pro-fibrotic markers collagen-IV, collagen-VI, CCN2 and TGF-β1 and pro-inflammatory markers TNF-α and IL-1β more effectively than sulfonylurea gliclazide. By IHC, liver collagen-VI and CCN2 induction by HFD were inhibited only by sitagliptin. Sitagliptin had a greater ability than gliclazide to normalise ERK-protein liver dysregulation. Conclusion: These data indicate that sitagliptin, compared with gliclazide, exhibits greater inhibition of pro-fibrotic and pro-inflammatory changes in an HFD-induced NAFLD model. Sitagliptin therapy, even in the absence of diabetes, may have specific benefits in diet-induced NAFLD.

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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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.
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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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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.
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Abstract Natural 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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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, and quali...

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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Environmental 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 efficiencies, and nonlethal sampling.

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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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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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.

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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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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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, pp. 150405-150405.
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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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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. 2200847-2200847.
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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, pp. 135103-135103.
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Sharma, B, Kumar, S, Preeti, Johansen, MD, Kremer, L & Kumar, V 2022, '1 H ‐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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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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Sheikholeslami, B, Lam, NW, Dua, K & Haghi, M 2022, 'Exploring the impact of physicochemical properties of liposomal formulations on their in vivo fate', Life Sciences, vol. 300, pp. 120574-120574.
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Sheldon, F, Barma, D, Baumgartner, LJ, Bond, N, Mitrovic, SM & Vertessy, R 2022, 'Assessment of the causes and solutions to the significant 2018–19 fish deaths in the Lower Darling River, New South Wales, Australia', Marine and Freshwater Research, vol. 73, no. 2, pp. 147-158.
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In late 2018 to early 2019, three significant fish death events occurred in the Lower Darling River, Australia, with mortality estimates of millions of fish. We examined the proximate and ultimate causes of these events. We determined that not only were the conditions existing at the time a significant contributing factor, but that antecedent conditions, particularly during the period 2010–17, also contributed. The extreme hot and dry climate during 2018, extending into 2019, shaped the conditions that saw a large fish biomass, which had flourished in the Darling River and Menindee Lakes since favourable spawning conditions in 2016, isolated in weir pools, with no means of escaping upstream or downstream. Strong and persistent weir pool stratification created hypoxic conditions in the hypolimnion. A series of sudden cool changes subsequently initiated rapid and sudden mixing of the stratified waters, causing depletion of oxygen throughout the water column and resulting in the fish deaths. The events were also shaped by broader climatic, hydrological and basin management contexts that placed the Lower Darling River at risk of such fish deaths. Our observations have implications for future river management, and we make several suggestions how policy makers and river operators can minimise fish death risks into the future.

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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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.
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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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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.
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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.
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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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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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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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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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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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Stella, CJ, Meakin, GE & van Oorschot, RAH 2022, 'DNA transfer in packaging: Attention required', Forensic Science International: Genetics Supplement Series, vol. 8, pp. 303-305.
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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.
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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, 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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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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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 Fluorescence Transient‐Fast Repetition Rate fluorometry', Limnology and Oceanography: Methods, vol. 20, no. 3, pp. 172-191.
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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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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, 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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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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Tang, K, Gao, H, Xiao, J, Long, M, Chen, J, Liu, H & Wang, G 2022, 'Hierarchical Oα-rich Co3O4 nanoarray anchored on Ni foam with superior lithiophilicity enabling ultrastable lithium metal batteries', Chemical Engineering Journal, vol. 436, pp. 134698-134698.
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Tang, K, Xiao, J, Long, M, Chen, J, Gao, H & Liu, H 2022, 'Superlithiophilic N, S-codoped carbon on Ni foam as a stable 3D host for dendrite-free Li metal anodes', Sustainable Materials and Technologies, vol. 32, pp. e00408-e00408.
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Tang, K, Xiao, J, Long, M, Chen, J, Gao, H & Liu, H 2022, 'Yolk–shell structured sulfur composite cathode for high performance lithium–sulfur battery', Surface Innovations, vol. 10, no. 3, pp. 209-216.
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Lithium–sulfur batteries (LSBs) suffer from the unavoidable ‘shuttle effects’ of lithium polysulfides (LPSs) and the infinite volume change of the sulfur. Herein, the authors prepared a yolk–shell structured N-doped carbon nanotubes/sulfur/poly(3,4-ethylenedioxythiophene) nanotube (N-CNTs/S@PEDOT) composite as a cathode for LSBs. The yolk–shell structure with void spaces can effectively buffer the volume expansion of sulfur, while the outer ‘shell’ can act as a physical barrier to minimise the ‘shuttle effects’ of LPSs. Moreover, the N-CNTs with high conductivity and superior structural stability are able to improve the electron transfer efficiency and cycling performance. Therefore, the specially designed yolk–shell structured N-CNTs/S@PEDOT composite cathode exhibits an extraordinary rate performance and enhanced cycling stability (602 mAh g−1 after 200 cycles at 0.1 C).

Tang, K, Xiao, J, Long, M, Chen, J, Gao, H, Liu, H & Wang, G 2022, 'Engineering a heteroatom-doped multidimensional carbon network for dendrite-free lithium metal anode', Materials Today Energy, vol. 24, pp. 100949-100949.
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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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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.
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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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Todorova, B, Godon, O, Conde, E, Gillis, CM, Iannascoli, B, Richard-Le Goff, O, Fiole, D, Roumenina, LT, Leusen, JHW, Murphy, AJ, Macdonald, LE, Reber, LL, Jönsson, F & Bruhns, P 2022, 'IgG Subclass-Dependent Pulmonary Antigen Retention during Acute IgG-Dependent Systemic Anaphylaxis in Mice', The Journal of Immunology, vol. 209, no. 7, pp. 1243-1251.
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Abstract Mouse models of active systemic anaphylaxis rely predominantly on IgG Abs forming IgG–allergen immune complexes that induce IgG receptor–expressing neutrophils and monocytes/macrophages to release potent mediators, leading to systemic effects. Whether anaphylaxis initiates locally or systemically remains unknown. In this study, we aimed at identifying the anatomical location of IgG–allergen immune complexes during anaphylaxis. Active systemic anaphylaxis was induced following immunization with BSA and i.v. challenge with fluorescently labeled BSA. Ag retention across different organs was examined using whole-body fluorescence imaging, comparing immunized and naive animals. Various mouse models and in vivo deletion strategies were employed to determine the contribution of IgG receptors, complement component C1q, myeloid cell types, and anaphylaxis mediators. We found that following challenge, Ag diffused systemically, but specifically accumulated in the lungs of mice sensitized to that Ag, where it formed large Ab-dependent aggregates in the vasculature. Ag retention in the lungs did not rely on IgG receptors, C1q, neutrophils, or macrophages. IgG2a-mediated, but neither IgG1- nor IgG2b-mediated, passive systemic anaphylaxis led to Ag retention in the lung. Neutrophils and monocytes significantly accumulated in the lungs after challenge and captured high amounts of Ag, which led to downmodulation of surface IgG receptors and triggered their activation. Thus, within minutes of systemic injection in sensitized mice, Ag formed aggregates in the lung and liver vasculature, but accumulated specifically and dose-dependently in the lung. Neutrophils and monocytes recruited to the lung captured Ag and became activated. However, Ag aggregation in the lung vasculature was not necessary for anaphylaxis induction.

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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TOWNSEND, KD 2022, 'SYLOW CLASSES OF REFLECTION SUBGROUPS AND PSEUDO-LEVI SUBGROUPS', Bulletin of the Australian Mathematical Society, vol. 106, no. 3, pp. 508-510.
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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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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 biochemical...

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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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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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 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 of prolif...

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.

Vega Thurber, R, Schmeltzer, ER, Grottoli, AG, van Woesik, R, Toonen, RJ, Warner, M, Dobson, KL, McLachlan, RH, Barott, K, Barshis, DJ, Baumann, J, Chapron, L, Combosch, DJ, Correa, AMS, DeCarlo, TM, Hagedorn, M, Hédouin, L, Hoadley, K, Felis, T, Ferrier-Pagès, C, Kenkel, C, Kuffner, IB, Matthews, J, Medina, M, Meyer, C, Oster, C, Price, J, Putnam, HM & Sawall, Y 2022, 'Unified methods in collecting, preserving, and archiving coral bleaching and restoration specimens to increase sample utility and interdisciplinary collaboration', PeerJ, vol. 10, pp. e14176-e14176.
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Coral reefs are declining worldwide primarily because of bleaching and subsequent mortality resulting from thermal stress. Currently, extensive efforts to engage in more holistic research and restoration endeavors have considerably expanded the techniques applied to examine coral samples. Despite such advances, coral bleaching and restoration studies are often conducted within a specific disciplinary focus, where specimens are collected, preserved, and archived in ways that are not always conducive to further downstream analyses by specialists in other disciplines. This approach may prevent the full utilization of unexpended specimens, leading to siloed research, duplicative efforts, unnecessary loss of additional corals to research endeavors, and overall increased costs. A recent US National Science Foundation-sponsored workshop set out to consolidate our collective knowledge across the disciplines of Omics, Physiology, and Microscopy and Imaging regarding the methods used for coral sample collection, preservation, and archiving. Here, we highlight knowledge gaps and propose some simple steps for collecting, preserving, and archiving coral-bleaching specimens that can increase the impact of individual coral bleaching and restoration studies, as well as foster additional analyses and future discoveries through collaboration. Rapid freezing of samples in liquid nitrogen or placing at −80 °C to −20 °C is optimal for most Omics and Physiology studies with a few exceptions; however, freezing samples removes the potential for many Microscopy and Imaging-based analyses due to the alteration of tissue integrity during freezing. For Microscopy and Imaging, samples are best stored in aldehydes. The use of sterile gloves and receptacles during collection supports the downstream analysis of host-associated bacterial and viral communities which are particularly germane to disease and restoration efforts. Across all disciplines, the use of aseptic techniques during co...

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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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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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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Wang, CY, Wang, J, Zhang, L, Zhang, SW, Wang, L, Zhao, SZ, Chen, ZH, Zhang, X, Xie, M, Wang, T, Chen-Yu Hsu, A, Qin, L, Oliver, BG, Liu, L, Wan, HJ, Liu, D, Luo, FM, Li, WM & Wang, G 2022, 'Self-Reported Insufficient Sleep Is Associated With Clinical and Inflammatory Features of Asthma: A Prospective Cohort Study', The Journal of Allergy and Clinical Immunology: In Practice.
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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, 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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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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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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Wang, Y, Yang, X, Zhang, Z, Hu, X, Meng, Y, Wang, X, Zhou, D, Liu, H, Li, B & Wang, G 2022, 'Electrolyte design for rechargeable anion shuttle batteries', eScience, vol. 2, no. 6, pp. 573-590.
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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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Wangpraseurt, D, Sun, Y, You, S, Chua, S, Noel, SK, Willard, HF, Berry, DB, Clifford, AM, Plummer, S, Xiang, Y, Hwang, HH, Kaandorp, J, Diaz, JM, La Jeunesse, TC, Pernice, M, Vignolini, S, Tresguerres, M & Chen, S 2022, 'Bioprinted Living Coral Microenvironments Mimicking Coral‐Algal Symbiosis', Advanced Functional Materials, vol. 32, no. 35, pp. 2202273-2202273.
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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 RapidHIT^TM 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.

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, 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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West, KM, Adam, AAS, White, N, Robbins, WD, Barrow, D, Lane, A & Richards, Z 2022, 'The applicability of eDNA metabarcoding approaches for sessile benthic surveying in the Kimberley region, north‐western Australia', Environmental DNA, vol. 4, no. 1, pp. 34-49.
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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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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.
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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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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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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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Wilson, BS, Peiser-Oliver, J, Gillis, A, Evans, S, Alamein, C, Mostyn, SN, Shimmon, S, Rawling, T, Christie, MJ, Vandenberg, RJ & Mohammadi, SA 2022, 'Peripheral Administration of Selective Glycine Transporter-2 Inhibitor, Oleoyl-_D-Lysine, Reverses Chronic Neuropathic Pain but Not Acute or Inflammatory Pain in Male Mice', Journal of Pharmacology and Experimental Therapeutics, vol. 382, no. 3, pp. 246-255.
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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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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

Wu, B, Chen, C, Danilov, DL, Jiang, M, Raijmakers, LHJ, Eichel, R-A & Notten, PHL 2022, 'Influence of the SEI Formation on the Stability and Lithium Diffusion in Si Electrodes', ACS Omega, vol. 7, no. 36, pp. 32740-32748.
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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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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.
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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.
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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.
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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 .

Xiao, J, Gao, H, Tang, K, Long, M, Chen, J, Liu, H & Wang, G 2022, 'Manipulating Stable Layered P2‐Type Cathode via a Co‐Substitution Strategy for High Performance Sodium Ion Batteries', Small Methods, vol. 6, no. 3, pp. 2101292-2101292.
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Xiao, J, Li, X, Tang, K, Long, M, Chen, J, Wang, D, Gao, H & Liu, H 2022, 'Enhanced electrochemical performance of Li-rich cathode material for lithium-ion batteries', Surface Innovations, vol. 10, no. 2, pp. 119-127.
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Lithium (Li)-rich cathodes have attracted great attention due to their high specific capacity and energy density. However, their dramatic capacity fading limits their practical application for lithium-ion batteries. Surface coating is recognized as a universal technology for improving the capacity retention of electrodes for many energy-storage applications. In this work, an aluminum fluoride (AlF3)-coated lithium-rich cathode with a rod-shaped structure is synthesized through a hydrothermal method, followed by a chemical coprecipitation process. The aluminum fluoride protective layer provides ideal elastic buffer interspace to ameliorate the structure stability and expedite the lithium-ion (Li+) diffusion dynamics, ensuring excellent electrochemical performance. Thereby the as-prepared aluminum fluoride-coated electrode has a high reversible discharge capacity of 195.6 mAh/g after 130 cycles at 0.1 C, corresponding to 89.9% of its initial specific capacity. A discharge capacity of 133.4 mAh/g can be achieved even at 2 C, much higher than that of the bare lithium-rich electrode (101.5 mAh/g). These results indicate that aluminum fluoride coating is an effective strategy to improve the electrochemical performance of lithium-rich cathodes.

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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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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Xing, N, Huang, W, Ye, H, Dong, Y, Kong, W, Ren, Y & Xie, Q 2022, 'Remote sensing retrieval of winter wheat leaf area index and canopy chlorophyll density at different growth stages', Big Earth Data, vol. 6, no. 4, pp. 580-602.
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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.
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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, J, Xu, L, Zhang, Z, Sun, B, Jin, Y, Jin, Q, Liu, H & Wang, G 2022, 'Heterostructure ZnSe-CoSe2 embedded with yolk-shell conductive dodecahedral as Two-in-one hosts for cathode and anode protection of Lithium–Sulfur full batteries', Energy Storage Materials, vol. 47, pp. 223-234.
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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 epidemicBordetella 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.
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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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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.

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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Yin, G, Qu, Y, Verger, A, Li, J, Jia, K, Xie, Q & Liu, G 2022, 'Smartphone Digital Photography for Fractional Vegetation Cover Estimation', Photogrammetric Engineering & Remote Sensing, vol. 88, no. 5, pp. 303-310.
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Accurate ground measurements of fractional vegetation cover (FVC) are key for characterizing ecosystem functions and evaluating remote sensing products. The increasing performance of cameras equipped in smartphones opens new opportunities for extensive FVC measurement through citizen science initiatives. However, the wide field of view (FOV) of smartphone cameras constitutes a key source of uncertainty in the estimation of vegetation parameters, which has been largely ignored. We designed a practical method to characterize the FOV of smartphones and improve the FVC estimation. The method was assessed in a mountainous forest based on the comparison with in situ fisheye photographs. After the FOV correction, the agreement of smart-phone and fisheye FVC estimates highly improved: root-mean-square error (RMSE) of 0.103 compared to 0.242 of the original smartphone FVC estimates without considering the FOV effect, mean difference of 0.074 versus 0.213, and coefficient of determination R2 of 0.719 versus 0.353. Smartphone cameras outperform traditional fisheye cameras: the overexposure and low vertical resolution of fisheye photographs introduced uncertainties in FVCestimation while the insensitivity to exposure and high spatial resolution of smartphone cameras make photograph acquisition and analysis more automatic and accurate. The smartphone FVCestimates highly agree with the GF-1 satellite product: RMSE = 0.066, bias = 0.007, and R2 = 0.745. This study opens new perspectives for the validation of satellite products.

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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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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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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Zavos, I, Danilov, DL & Notten, PHL 2022, 'Modeling and Implementation of a Highly Efficient Solar-Powered Storage Installation through Self-Reconfigurable Batteries', Open Journal of Energy Efficiency, vol. 11, no. 02, pp. 37-53.
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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.

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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Zhang, H, Song, J, Li, J, Feng, J, Ma, Y, Ma, L, Liu, H, Qin, Y, Zhao, X & Wang, F 2022, 'Interlayer-Expanded MoS₂ Nanoflowers Vertically Aligned on MXene@Dual-Phased TiO₂ as High-Performance Anode for Sodium-Ion Batteries', ACS Applied Materials & Interfaces, vol. 14, no. 14, pp. 16300-16309.
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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.
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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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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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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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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. 2206970-2206970.
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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.
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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, Y, Wang, M, Zhao, T, Luo, Y, Li, Y, Yan, K, Lu, L, Tran, NN, Wu, X & Ma, X 2022, 'Evaluating the potential of H8/AHI geostationary observations for monitoring vegetation phenology over different ecosystem types in northern China', International Journal of Applied Earth Observation and Geoinformation, vol. 112, pp. 102933-102933.
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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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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.
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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, L, Danilov, DL, Qiao, F, Eichel, R-A & Notten, PHL 2022, 'ZnFe2O4 hollow rods enabling accelerated polysulfide conversion for advanced lithium-sulfur batteries', Electrochimica Acta, vol. 414, pp. 140231-140231.
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Zhou, L, Danilov, DL, Qiao, F, Wang, J, Li, H, Eichel, R & Notten, PHL 2022, 'Sulfur Reduction Reaction in Lithium–Sulfur Batteries: Mechanisms, Catalysts, and Characterization', Advanced Energy Materials, vol. 12, no. 44, pp. 2202094-2202094.
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Lithium–sulfur batteries are one of the most promising alternatives for advanced battery systems due to the merits of extraordinary theoretical specific energy density, abundant resources, environmental friendliness, and high safety. However, the sluggish sulfur reduction reaction (SRR) kinetics results in poor sulfur utilization, which seriously hampers the electrochemical performance of Li–S batteries. It is critical to reveal the underlying reaction mechanisms and accelerate the SRR kinetics. Herein, the critical issues of SRR in Li–S batteries are reviewed. The conversion mechanisms and reaction pathways of sulfur reduction are initially introduced to give an overview of the SRR. Subsequently, recent advances in catalyst materials that can accelerate the SRR kinetics are summarized in detail, including carbon, metal compounds, metals, and single atoms. Besides, various characterization approaches for SRR are discussed, which can be divided into three categories: electrochemical measurements, spectroscopic techniques, and theoretical calculations. Finally, the conclusion and outlook part gives a summary and proposes several key points for future investigations on the mechanisms of the SRR and catalyst activities. This review can provide cutting-edge insights into the SRR in Li–S batteries.

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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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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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.

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.
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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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Zwerver, AMJ, Krähenmann, T, Watson, TF, Lampert, L, George, HC, Pillarisetty, R, Bojarski, SA, Amin, P, Amitonov, SV, Boter, JM, Caudillo, R, Correas-Serrano, D, Dehollain, JP, Droulers, G, Henry, EM, Kotlyar, R, Lodari, M, Lüthi, F, Michalak, DJ, Mueller, BK, Neyens, S, Roberts, J, Samkharadze, N, Zheng, G, Zietz, OK, Scappucci, G, Veldhorst, M, Vandersypen, LMK & Clarke, JS 2022, 'Author Correction: Qubits made by advanced semiconductor manufacturing', Nature Electronics, vol. 5, no. 5, pp. 319-319.
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Zwerver, AMJ, Krähenmann, T, Watson, TF, Lampert, L, George, HC, Pillarisetty, R, Bojarski, SA, Amin, P, Amitonov, SV, Boter, JM, Caudillo, R, Correas-Serrano, D, Dehollain, JP, Droulers, G, Henry, EM, Kotlyar, R, Lodari, M, Lüthi, F, Michalak, DJ, Mueller, BK, Neyens, S, Roberts, J, Samkharadze, N, Zheng, G, Zietz, OK, Scappucci, G, Veldhorst, M, Vandersypen, LMK & Clarke, JS 2022, 'Qubits made by advanced semiconductor manufacturing', Nature Electronics, vol. 5, no. 3, pp. 184-190.
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AbstractFull-scale quantum computers require the integration of millions of qubits, and the potential of using industrial semiconductor manufacturing to meet this need has driven the development of quantum computing in silicon quantum dots. However, fabrication has so far relied on electron-beam lithography and, with a few exceptions, conventional lift-off processes that suffer from low yield and poor uniformity. Here we report quantum dots that are hosted at a 28Si/28SiO2 interface and fabricated in a 300 mm semiconductor manufacturing facility using all-optical lithography and fully industrial processing. With this approach, we achieve nanoscale gate patterns with excellent yield. In the multi-electron regime, the quantum dots allow good tunnel barrier control—a crucial feature for fault-tolerant two-qubit gates. Single-spin qubit operation using magnetic resonance in the few-electron regime reveals relaxation times of over 1 s at 1 T and coherence times of over 3 ms.

Budden, K, Rehman, SF, Shukla, S, Bowerman, K, Donovan, C, Gomez, H, Alemao, C, Wood, L, Dennis, P, Hugenholtz, P, Wark, P & Hansbro, P 1970, 'Association between dietary fibre, microbial metabolites and airway obstruction in COPD patients and murine models', 05.01 - Airway pharmacology and treatment, ERS International Congress 2022 abstracts, European Respiratory Society.
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Carroll, O, Brown, A, Mayall, J, Zounemat-Kermani, N, Gomez, H, Kim, R, Donovan, C, Williams, E, Berthon, B, Pinkerton, J, Wynne, K, Scott, H, Guo, Y, Hansbro, P, Foster, P, Dahlen, S, Adcock, I, Wood, L & Horvat, J 1970, 'Female sex hormones affect asthma severity by altering cellular metabolism in the airways', 05.03 - Allergy and immunology, ERS International Congress 2022 abstracts, European Respiratory Society.
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Chen, H, Galvao, I, Donovan, C, Kim, R, Ortega, D, Idrees, S, Schulte-Schrepping, J, Schaar, A, Faiz, A, Schultze, J & Hansbro, P 1970, 'Spatial transcriptomics (ST) of cigarette smoke (CS)-induced experimental COPD', 03.01 - Molecular pathology and functional genomics, ERS International Congress 2022 abstracts, European Respiratory Society.
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Crump, V & Davila, YC 1970, 'UNDERSTANDING STUDENTS’ EXPERIENCES AFTER INCORPORATING INDIGENOUS PERSPECTIVES IN A POSTGRADUATE SCIENCE COMMUNICATION', Education and New Developments 2022 – Volume 2, International Conference on Education and New Developments, inScience Press, Madeira, Portugal.
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'Many Australian universities have recently incorporated Indigenous graduate attributes into their programs, and the University of Technology Sydney (UTS) is no exception. This project aimed to investigate students’ perceptions and experiences of learning about Indigenous Knowledge systems and culture while developing science communication skills. Advanced Communication Skills in Science is a core subject in the Master of Science program at UTS. An existing assessment task, a three-minute thesis style oral presentation, was reworked to include the Indigenous Graduate Attribute (IGA) developed for the Faculty of Science. Students researched an aspect of Indigenous Science, an area of emerging interest for cultural and scientific understanding, and a mechanism for empowering Australia’s diverse first nations peoples. They then presented their key message in three minutes using a single PowerPoint slide. This task allowed students to demonstrate an awareness and appreciation of multiple ways of developing understandings of nature while enhancing their ability to understand the role of science communication in the modern world. Students were surveyed at the beginning and end of the semester to establish their Indigenous Science conceptions and reflect on their experiences. Students demonstrated an outstanding ability to integrate appropriate Aboriginal and Torres Strait Islander knowledges, experience, and analysis into a key message. Most students reported greater familiarity with concepts such as Indigenous Science and provided richer definitions of what this means. When asked if understanding Aboriginal and Torres Strait Islander knowledges and cultural practices might impact their practice as a scientist, many felt their perspective had changed and that reflecting on their cultural values and beliefs had improved their cultural capability. Most students responded that this subject challenged (at least to a degree) some firmly held assumptions, ideas, and ...

Daly, K, Hsu, A, Nichol, K, Horvat, J, Mayall, J, Hansbro, P & Wark, P 1970, 'Histone deacetylase-6 (HDAC6) promotes protective responses during murine influenza A virus (IAV) infection', 10.01 - Respiratory infections and bronchiectasis, ERS International Congress 2022 abstracts, European Respiratory Society.
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Dietrich, H, Elder, M, Piggott, A, Qiao, Y & Weiß, A 1970, 'The Isomorphism Problem for Plain Groups Is in Σ^P3', Leibniz International Proceedings in Informatics, LIPIcs, 39th International Symposium on Theoretical Aspects of Computer Science, Schloss Dagstuhl -- Leibniz-Zentrum f{\u}r Informatik", Marsielle, France, pp. 26:1-26:14.
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Testing isomorphism of infinite groups is a classical topic, but from the complexity theory viewpoint, few results are known. Sénizergues and the fifth author (ICALP2018) proved that the isomorphism problem for virtually free groups is decidable in PSPACE when the input is given in terms of so-called virtually free presentations. Here we consider the isomorphism problem for the class of plain groups, that is, groups that are isomorphic to a free product of finitely many finite groups and finitely many copies of the infinite cyclic group. Every plain group is naturally and efficiently presented via an inverse-closed finite convergent length-reducing rewriting system. We prove that the isomorphism problem for plain groups given in this form lies in the polynomial time hierarchy, more precisely, in ΣP3. This result is achieved by combining new geometric and algebraic characterisations of groups presented by inverse-closed finite convergent length-reducing rewriting systems developed in recent work of the second and third authors (2021) with classical finite group isomorphism results of Babai and Szemerédi (1984).

Do, TH, Nonahal, M, Li, C, Valuckas, V, Kuznetsov, A, Nguyen, HS, Aharonovich, I & Ha, ST 1970, 'Room-temperature strong coupling of a single-photon emitter and a bound-state-in-the-continuum cavity (Conference Presentation)', Quantum Nanophotonic Materials, Devices, and Systems 2022, Quantum Nanophotonic Materials, Devices, and Systems 2022, SPIE.
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Duong, NMH, Saerens, G, Timpu, F, Buscaglia, MT, Buscaglia, V, Morandi, A, Muller, JS, Maeder, A, Kaufmann, F, Solntsev, AS & Grange, R 1970, 'Spontaneous parametric down-conversion in bottom-up grown lithium niobate microcubes', Conference on Lasers and Electro-Optics, CLEO: QELS_Fundamental Science, Optica Publishing Group.
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We demonstrate the generation of biphotons from a free-standing, bottom-up grown lithium niobate microcube at telecommunication wavelength through the spontaneous parametric down-conversion. The maximum biphoton rate obtained fromã4 µm microcube is ~80 Hz.

Etminaniesfahani, A, Gu, H & Salehipour, A 1970, 'An Efficient Relax-and-Solve Algorithm for the Resource-Constrained Project Scheduling Problem', Proceedings of the 11th International Conference on Operations Research and Enterprise Systems, 11th International Conference on Operations Research and Enterprise Systems, SCITEPRESS - Science and Technology Publications.
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Fröch, JE, Spencer, L, Kianinia, M, Totonjian, D, Nguyen, M, Dyakonov, V, Toth, M, Kim, S & Aharonovich, I 1970, 'Coupling Spin Defects in Hexagonal Boron Nitride to Monolithic Bullseye Cavities', Optica Advanced Photonics Congress 2022, Bragg Gratings, Photosensitivity and Poling in Glass Waveguides and Materials, Optica Publishing Group.
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This work couples spin defects in hexagonal boron nitride (hBN) to monolithic bullseye cavities. Demonstrating enhanced emission, optically detected magnetic resonance and improved signal to noise ratio. Constituting an initial step towards scalable spin-photon interfaces.

he, P, Papanicolaou, M, Rutting, S, Reddy, D, Ammit, A, Xenaki, D, Van Reyk, D, Oliver, B & Reddy, K 1970, 'Oxidative stress is a key driving mechanism in the pathogenesis of inflammatory lung diseases', 03.03 - Mechanisms of lung injury and repair, ERS International Congress 2022 abstracts, European Respiratory Society.
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Irga, P, Torpy, F, Fleck, R, Duani, G, Matheson, S, Douglas, A & Lyu, L 1970, 'The Benefits of Plants at Work', Workplace Wellness Festival, International Conference Centre, Sydney Australia.
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The human environment is the indoor environment. 86% of your time every day is spent indoors. As we spend more time indoors, we have an extended exposure time to the pollutants encountered in indoor environments. As far as workplace environments are concerned, more and more people are staying back doing overtime (paid or not), which puts the onus on the employer to provide an indoor environment that does not pose an ongoing risk for the occupants. In Australia, ambient air pollution standards are set by The National Environment Protection (Ambient Air quality) Measure (Air-NEPM). The standards used are similar to those from most western countries. The Air-NEPM standards cover most of the common air pollutants, including particulates less than 10 mm in size (PM10), particulates less than 2.5 mm (PM2.5), SO2, NO2, and CO. Australian threshold limits for indoor workspace CO2 and volatile organic compounds (VOC) are set by Work Safe Australia. Regarding the procedure of air purification by potted plants, many researchers and decades of work have confirmed that the plants remove CO2 through photosynthesis, degrade VOCs through the metabolic action of rhizospheric microbes, and can sequester particulate matter through a range of physical mechanisms. Apart from the occasional report documenting trivial VOC removal capacity by plant tissues , or bacteria on the leaf surface or phyllosphere, the quantitative bioremediation of VOCs is now generally accepted to primarily occur through microbial activity, where the VOCs are used directly as carbon sources by microorganisms. Most research suggests that all potted plant / substrate combinations can remove VOCs at similar rates, with slightly reduced rates for plants grown in hydroculture, probably due to the lower microbial density in the substrate. Two recent experiments have challenged this observation, finding significant variation between plant species, although in common with earlier research, found no patterns betwee...

Kapellos, T, Bassler, K, Fujii, W, Pecht, T, Bonaguro, L, Galvao, I, Saglam, A, Dudkin, E, Frishberg, A, De Domenico, E, Horne, A, Donovan, C, Kim, RY, Gallego-Ortega, D, Becker, M, Händler, K, Ulas, T, Hasenauer, J, Pizarro, C, Hansbro, PM, Skowasch, D & Schultze, JL 1970, 'Inflammatory blood neutrophils in COPD stem from activated bone marrow progenitors', Airway cell biology and immunopathology, ERS Lung Science Conference 2022 abstracts, European Respiratory Society.
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Kapellos, T, Bassler, K, Fujii, W, Pecht, T, Bonaguro, L, Galvao, I, Saglam, A, Dudkin, E, Frishberg, A, De Domenico, E, Horne, A, Donovan, C, Kim, RY, Gallego-Ortega, D, Becker, M, Händler, K, Ulas, T, Hasenauer, J, Pizarro, C, Hansbro, PM, Skowasch, D & Schultze, JL 1970, 'Inflammatory blood neutrophils in COPD stem from activated bone marrow progenitors', 03.02 - Airway cell biology and immunopathology, ERS International Congress 2022 abstracts, European Respiratory Society.
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Kole, T, Pouwels, SD, Bults, R, Ketelaar, ME, Guryev, V, Koll, L, Kerstjens, HAM, Van Den Berge, M & Faiz, A 1970, 'Airway Wall Splice-QTL Analysis Reveals Novel Downstream Mechanisms for Well-Known GWAS Asthma-SNPs', B101. VARIED OMICS TECHNIQUES APPLIED TO ALLERGIC AND RESPIRATORY TRAITS, American Thoracic Society 2022 International Conference, May 13-18, 2022 - San Francisco, CA, American Thoracic Society.
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Kononov, A, Memar, J & Zinder, Y 1970, 'Algorithms for Flow Shop with Job-Dependent Buffer Requirements'.
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Mahbub, R, Reddy, KD, Boudewijn, I, Koppelman, GH, Van Den Berge, M & Faiz, A 1970, 'Inhaled corticosteroids induce DNA methylation changes in nasal cells of asthma patients', 03.01 - Molecular pathology and functional genomics, ERS International Congress 2022 abstracts, European Respiratory Society.
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Mayall, J, Pillar, A, Daly, K, Brown, A, Essilfie, A, Gomez, H, Kim, R, Nichol, K, Donovan, C, Anderson, G, Frazer, D, Milward, E, Hansbro, P, Reid, D, Hsu, A, Wark, P & Horvat, J 1970, 'Crucial role of iron metabolism in determining outcomes of influenza A virus infection and disease', 10.01 - Respiratory infections and bronchiectasis, ERS International Congress 2022 abstracts, European Respiratory Society.
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Migulina, N, Tjin, G, Faiz, A, Borghuis, T, Metzlar, M, Dijk, EM, Timens, W, Gosens, R, Brandsma, C-AA & Burgess, JK 1970, 'Differential Roles for Lysyl Oxidase (Like) Family Members in Chronic Obstructive Pulmonary Disease; from Gene and Protein Expression to Function', B108. ORIGINS AND OUTCOMES OF COPD, American Thoracic Society 2022 International Conference, May 13-18, 2022 - San Francisco, CA, American Thoracic Society.
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Nunez Lendo, CI, Camp, E, Edmondson, J, Kuzhiumparambil, U, Gonzalez de Vega, R, David, H & David, S 1970, 'Beyond growth and survival measurements: integrating multiple traits to inform ecosystem service value of corals propagated for restoration on the Great Barrier Reef', Australian Marine Sciences Association, Cairns.

Pillar, A, Brown, A, Mayall, J, Weaver, J, Essilfie, A, Hoefel, G, Ali, MK, Kim, R, Donovan, C, Gomez, H, Vanka, KS, Tay, H, Kermani, N, Guo, Y, Mumby, S, Adcock, I, Anderson, G, Frazer, D, Johnstone, D, Milward, E, Hansbro, P, Wark, P, Reid, D, Foster, P & Horvat, J 1970, 'Relationship between interleukin-13 and transferrin receptor-1 responses in the pathogenesis of asthma', 05.03 - Allergy and immunology, ERS International Congress 2022 abstracts, European Respiratory Society.
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Pinkerton, J, Kim, R, Brown, A, Rae, B, Donovan, C, Mayall, J, Ali, MK, Scott, H, Berthon, B, Baines, K, Starkey, M, Kermani, N, Guo, Y, Robertson, A, O'Neill, L, Adcock, I, Cooper, M, Gibson, P, Wood, L, Hansbro, P & Horvat, J 1970, 'Interaction between type 2 cytokine and inflammasome responses in the pathogenesis of obesity-associated asthma', 03.02 - Airway cell biology and immunopathology, ERS International Congress 2022 abstracts, European Respiratory Society.
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Rathnayake, S, Ditz, B, Van Nijnatten, J, Brandsma, C, Timens, W, Hiemstra, P, Ten Hacken, N, Oliver, B, Kerstjens, H, Van Den Berge, M & Faiz, A 1970, 'Influence of smoking on bronchial epithelial cell composition by cellular deconvolution and IHC', 03.01 - Molecular pathology and functional genomics, ERS International Congress 2022 abstracts, European Respiratory Society.
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Rathnayake, S, Ditz, B, van Nijnatten, J, Hansbro, P, Brandsma, C, Timens, W, Hiemstra, P, ten-Hacken, N, Oliver, B, Kerstjens, H, van den Berge, M & Faiz, A 1970, 'Impact of smoking on bronchial-mucus barrier cellular composition and transcriptome', RESPIROLOGY, WILEY, pp. 116-117.

Reddy, K, Rathnayake, S, Xenaki, D, Faiz, A & Oliver, B 1970, 'The Y-chromosome regulates hallmark features of asthma and COPD', 03.01 - Molecular pathology and functional genomics, ERS International Congress 2022 abstracts, European Respiratory Society.
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Rehman, SF, Budden, KF, Quaranta, A, Fuchs, D, Shukla, SD, Brown, A, Alemao, C, Balachandra, L, Gomez, H, Kumar, V, Idrees, S, Horvat, J, Wood, LG, Wheelock, C & Hansbro, PM 1970, 'Soluble epoxide hydrolase inhibition alleviates inflammation in cigarette smoke-induced experimental COPD irrespective of dietary fat content', 05.03 - Allergy and immunology, ERS International Congress 2022 abstracts, European Respiratory Society.
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Stern, HL, Jarman, J, Gu, Q, Eizagirre Barker, S, Mendelson, N, Chugh, D, Schott, S, Tan, HH, Sirringhaus, H, Aharonovich, I & Atature, M 1970, 'Optically-addressable spins in hexagonal boron nitride at room temperature', 2D Photonic Materials and Devices V, 2D Photonic Materials and Devices V, SPIE.
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Torpy, F, Irga, P, Fleck, R, Matheson, S & Douglas, A 1970, 'Indoor plants, our environment and happiness', Happiness & Its Causes, Pyrmont Theatre, ICC Sydney.

Torpy, F, Irga, P, Fleck, R, Matheson, S, Smith, H, Duani, G, Surawski, N, Douglas, A & Lyu, L 1970, 'Phytoremediation of air pollution', 26th International Clean Air and Environment Conference, Adelaide, SA.

Van Eeckhoutte, HP, Donovan, C, Kim, R, Khan, H, Jayaraman, R, Dondelinger, Y, Delanghe, T, Beal, A, Geddes, B, Bertin, J, Vanden Berghe, T, Vandenabeele, P, Vanaudenaerde, B, Deforce, D, Skevin, S, Van Nieuwerburgh, F, Verhamme, F, Joos, G, Brusselle, GG, Bertrand, M, Hansbro, P & Bracke, K 1970, 'Inhibiting RIPK1 Kinase Activity Is Protective in Experimental Models of COPD', B21. BASIC, CLINICAL, AND TRANSLATIONAL COPD STUDIES: THE ONGOING HUNT FOR UNDERLYING MECHANISMS AND THERAPEUTIC TARGETS, American Thoracic Society 2022 International Conference, May 13-18, 2022 - San Francisco, CA, American Thoracic Society.
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Wang, Y, Thaler, M, Salgado-Benvindo, C, Ly, N, Leijs, AA, Ninaber, DK, Van Hemert, MJ, Hiemstra, PS, Van Der Does, AM & Faiz, A 1970, 'RNA sequencing unravels unique host transcriptional responses to infection with SARS-CoV-2 in well differentiated primary human bronchial epithelial cells compared to other coronaviruses', 03.02 - Airway cell biology and immunopathology, ERS International Congress 2022 abstracts, European Respiratory Society.
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Weiner, M, Kim, KW, Hu, TC, Solntsev, A & Blanco-Redondo, A 1970, 'Photon-Pair Generation in Defect-Free Surface Modes', 2022 Conference on Lasers and Electro-Optics, CLEO 2022 - Proceedings.
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We experimentally demonstrate simultaneous generation and propagation of photon pairs in defect-free surface modes in an array of coupled sinusoidal waveguides. The measured biphoton correlations remain robust to tuning the curvature.

Weiner, M, Kim, KW, Hu, TC, Solntsev, A & Blanco-Redondo, A 1970, 'Photon-Pair Generation in Defect-Free Surface Modes', Optics InfoBase Conference Papers.
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We experimentally demonstrate simultaneous generation and propagation of photon pairs in defect-free surface modes in an array of coupled sinusoidal waveguides. The measured biphoton correlations remain robust to tuning the curvature.

Yamamura, K, Zhu, L, Irvine, C, Singh, M, Bansal, V, Scott, J, Phillips, MR, Ton-That, C & Jallandhra, A 1970, 'Luminescence signatures of nitrogen in β-Ga2O3 nanowires', Oxide-based Materials and Devices XIII, Oxide-based Materials and Devices XIII, SPIE.
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Yaqub, W, Mohanty, M & Suleiman, B 1970, 'Privacy-Preserving Online Proctoring using Image-Hashing Anomaly Detection', 2022 International Wireless Communications and Mobile Computing (IWCMC), 2022 International Wireless Communications and Mobile Computing (IWCMC), IEEE.
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Zinder, Y, Lazarev, A & Musatova, E 1970, 'Single Track Transportation in a Two-Machine Production System', IFAC-PapersOnLine, Elsevier BV, pp. 2893-2897.
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Ajani, P, Dove, M, Farrell, H, O'Connor, W, Tesoriero, M, Verma, A, Hughes, B & Murray, S University of Sydney Australia 2022, Transforming Australian Shellfish Production: Lower Honeymoon Bay Harvest Area, Wagonga Inlet. Report on Stage 1, December 2017-March 2021., Sydney, Australia.

Ajani, P, Dove, M, Farrell, H, O'Connor, W, Tesoriero, M, Verma, A, Zammit, A, Hughes, B & Murray, S University of Technology Sydney 2022, Transforming Australian Shellfish Production. Pambula Lake Harvest Area, Pambula River. Report on Satge 1, Sept 2016-March 2021., Sydney Australia.

Ajani, P, Dove, M, Farrell, H, O'Connor, W, Tesoriero, M, Verma, A, Zammit, A, Hughes, B & Murray, S University of Technology Sydney 2022, Transforming Australian Shellfish Production: Goodnight Island Harvest Area, Shoalhaven and Crookhaven Rivers. Report on Stage 1, December 2017-March 2021, Sydney Australia.

Ajani, P, Dove, M, Farrell, H, O'Connor, W, Tesoriero, M, Verma, A, Zammit, A, Hughes, B & Murray, S University of Sydney Techology 2022, Transforming Australian Shellfish Production: Pelican Point Harvest Area - Manning River. Report on Stage 1, December 2017-March 2021., Sydney Australia.

Ajani, P, Dove, M, Farrell, H, O'Connor, W, Tesoriero, M, Verma, A, Zammit, A, Hughes, B & Murray, SA University of Technology Sydney 2022, Transforming Australian Shellfish Production: Long Island Harvest Area, Wallis Lake. Report on Stage 1, December 2017-March 2021., Sydney Australia.

Trestrail, C, Tondl, E, Fischer, A, Potts, J, Scanes, P, Seymour, J & Doblin, M University of Technology Sydney 2022, Research needs for the assessment and monitoring of nutrients, chemicals & antimicrobials in the marine environment: scoping study., no. Report 1.16, Sydney.

Ashhurst, A, Johansen, M, Maxwell, J, Ashley, C, Aggarwal, A, Siddiquee, R, Miemczyk, S, Nguyen, D, Mackay, J, Counoupas, C, Byrne, S, Turville, S, Steain, M, Triccas, J, Hansbro, P, Payne, R & Britton, W 2022, 'Mucosal TLR2-activating protein-based vaccination induces potent pulmonary immunity and protection against SARS-CoV-2 in mice', Research Square Platform LLC.
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Butterworth, NJ, Wallman, JF, Johnston, NP, Dawson, BM & McGaughran, A 2022, 'The blowfly Chrysomya latifrons inhabits fragmented rainforests, but lacks genetic diversity and population structure', Cold Spring Harbor Laboratory.
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Camara, M, Dubern, J, Romero, M, Mai-Prochnow, A, Messina, M, Trampari, E, Gijzel, HN-V, Chan, K-G, Carabelli, A, Barraud, N, Lazenby, J, Chen, Y, Robertson, S, Malone, J, Williams, P & Heeb, S 2022, 'ToxR is a c-di-GMP binding protein that modulates surface-associated behaviour in Pseudomonas aeruginosa', Research Square Platform LLC.
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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', Cold Spring Harbor Laboratory.
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Chen, H, Aneman, I, Nikolic, V, Orlic, NK, Mikovic, Z, Stefanovic, M, Cakic, Z, Jovanovic, H, Town, S, Padula, M & McClements, L 2022, 'Maternal plasma proteome profiling of biomarkers and pathogenic mechanisms of early-onset and late-onset preeclampsia', Research Square Platform LLC.
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Chen, L, Hoefel, GA, Pathinayake, PS, Reid, A, Kelly, C, HuiYing, T, Kim, RY, Hansbro, PM, Brody, SL, Foster, PS, Horvat, JC, Riveros, C, Wark, PAB & Kaiko, GE 2022, 'Single cell RNA-seq identifies inflammation-induced loss of CFTR-expressing airway ionocytes in non-eosinophilic asthma', Cold Spring Harbor Laboratory.
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Chhor, M, Tulpar, E, Nguyen, T, Cranfield, C, Gorrie, CA, Chan, YL, Chen, H, Oliver, BG, McClements, L & McGrath, KC 2022, 'E-cigarette Aerosol Condensate leads to Impaired Coronary Endothelial Cell Health and Restricted Angiogenesis', Research Square Platform LLC.
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Cui, G, Konciute, MK, Ling, L, Esau, L, Raina, J-B, Han, B, Salazar, OR, Presnell, JS, Rädecker, N, Zhong, H, Menzies, J, Cleves, PA, Liew, YJ, Krediet, CJ, Sawiccy, V, Cziesielski, MJ, Guagliardo, P, Bougoure, J, Pernice, M, Hirt, H, Voolstra, CR, Weis, VM, Pringle, JR & Aranda, M 2022, 'Molecular insights into the Darwin paradox of coral reefs from the sea anemone Aiptasia', Cold Spring Harbor Laboratory.
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Daniels, RK, Mallinson, JB, Heywood, ZE, Bones, PJ, Arnold, MD & Brown, SA 2022, 'Reservoir Computing with 3D Nanowire Networks'.

Dhungana, A, Becchi, S, Leake, J, Morris, G, Avgan, N, Balleine, BW, Vissel, B & Bradfield, LA 2022, 'Goal-directed action is transiently impaired in an hAPP-J20 mouse model of Alzheimer’s disease, and in aging male mice regardless of genotype', Cold Spring Harbor Laboratory.
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Di, X, Su, QP, Wang, D, Liu, Y, Maddahfar, M, Zhou, J & Jin, D 2022, 'Spatiotemporally Mapping Thermodynamics of Lysosomes and Mitochondria using Cascade Organelle-Targeting Upconversion Nanoparticles', Cold Spring Harbor Laboratory.
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Doane, MP, Ostrowski, M, Brown, M, Bramucci, A, Bodrossy, L, van de Kamp, J, Bissett, A, Steinberg, P, Doblin, MA & Seymour, J 2022, 'Defining marine bacterioplankton community assembly rules by contrasting the importance of environmental determinants and biotic interactions', Cold Spring Harbor Laboratory.
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Doré, H, Guyet, U, Leconte, J, Farrant, GK, Alric, B, Ratin, M, Ostrowski, M, Ferrieux, M, Brillet-Guéguen, L, Hoebeke, M, Siltanen, J, Corguillé, GL, Corre, E, Wincker, P, Scanlan, DJ, Eveillard, D, Partensky, F & Garczarek, L 2022, 'Differential global distribution of marine picocyanobacteria gene clusters reveals distinct niche-related adaptive strategies', Cold Spring Harbor Laboratory.
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Dougan, KE, Bellantuono, AJ, Kahlke, T, Abbriano, RM, Chen, Y, Shah, S, Granados-Cifuentes, C, van Oppen, MJH, Bhattacharya, D, Suggett, DJ, Chan, CX & Rodriguez-Lanetty, M 2022, 'Whole-genome duplication in an algal symbiont serendipitously confers thermal tolerance to corals', Cold Spring Harbor Laboratory.
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Eakin, CM, Devotta, D, Heron, S, Connolly, S, Liu, G, Geiger, E, Cour, JDL, Gomez, A, Skirving, W, Baird, A, Cantin, N, Couch, C, Donner, S, Gilmour, J, Gonzalez-Rivero, M, Gudka, M, Harrison, H, Hodgson, G, Hoegh-Guldberg, O, Hoey, A, Hoogenboom, M, Hughes, T, Johnson, M, Kerry, J, Mihaly, J, Muñiz-Castillo, A, Obura, D, Pratchett, M, Rivera-Sosa, A, Ross, C, Stein, J, Thompson, A, Torda, G, Viehman, TS, Walter, C, Wilson, S, Marsh, B, Spady, B, Dyer, N, Adam, T, Alidoostsalimi, M, Alidoostsalimi, P, Alvarez-Filip, L, Álvarez-Noriega, M, Bahr, K, Barnes, P, Sandoval, JB, Baum, J, Bauman, A, Beger, M, Berry, K, Bessell-Browne, P, Bigot, L, Bonito, V, Brodnicke, O, Burdick, D, Burkepile, D, Burt, A, Burt, J, Butler, I, Caldwell, J, Chancerelle, Y, Chen, CA, Cherh, K-L, Childress, M, Coken, D, Coward, G, Crabbe, MJ, Dallison, T, Dalton, S, DeCarlo, T, Drury, C, Drysdale, I, Edwards, C, Eggertsen, L, Elma, E, Ennis, R, Evans, R, Eyal, G, Fenner, D, Figueroa-Zavala, B, Fisch, J, Fox, M, Gadoutsis, E, Gilbert, A, Halford, A, Heintz, T, Hewlett, J, Hobbs, J-PA, Hoot, W, Houk, P, Johnston, L, Johnston, M, Kayanne, H, Kennedy, E, Kikuchi, R, Kloiber, U, Koike, H, Kramer, L, Kuo, C-Y, Lang, J, Leadbeater, A, Leão, Z, Lee, J, Lewis, C, Lirman, D, Longo, G, MacDonald, C, Mangubhai, S, Silva, ID, Mason-Parker, C, McDonough, V, McField, M, Mello, T, Agathe, CM, Moldzio, S, Monroe, A, Montefalcone, M, Moses, K, Mostafavi, PG, Moura, R, Munasinghe, C, Nakamura, T, Nicet, J-B, Nuttall, M, Oliveira, M, Oxenford, H, Pandolfi, J, Patankar, V, Perez, D, Perera, N, Prabuning, D, Precht, W, Raj, KD, Reimer, J, Richardson, L, Rotjan, R, Ryan, N, Salm, R, Sandin, S, Schopmeyer, S, Shokri, M, Smith, J, Smith, K, Smith, SR, Smith, T, Sommer, B, Soto, M, Sykes, H, Tagarino, K, Teoh, M, Thai, M, Toh, T, Tredinnick, A, Tso, A, Tyley, H, Ussi, A, Vaterlaus, C, Vermeij, M, Vo, ST, Voolstra, C, Wee, HB, Weiler, B, Yahya, S, Yeemin, T, Ziegler, M, Kimura, T & Manzello, D 2022, 'The 2014-17 Global Coral Bleaching Event: The Most Severe and Widespread Coral Reef Destruction', Research Square Platform LLC.
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Elder, M, Piggott, A & Townsend, K 2022, 'On $k$-geodetic groups and graphs'.

Fiedler, S, Ton-That, C & Phillips, MR 2022, 'Hydrothermally grown defect-free ZnO nanorods with high angular distribution for enhanced excitonic emission', Research Square Platform LLC.
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Fourment, M, Swanepoel, CJ, Galloway, JG, Ji, X, Gangavarapu, K, Suchard, MA & IV, FAM 2022, 'Automatic differentiation is no panacea for phylogenetic gradient computation'.

Fu, S, Shi, W, Luo, T, He, Y, Zhou, L, Yang, J, Yang, Z, Liu, J, Liu, X, Guo, Z, Yang, C, Liu, C, Huang, Z-L, Ries, J, Zhang, M, Xi, P, Jin, D & Li, Y 2022, 'Field dependent deep learning enables high-throughput whole-cell 3D super-resolution imaging', Cold Spring Harbor Laboratory.
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Gantier, M, Ullah, T, Johansen, M, Balka, K, Ambrose, R, Gearing, L, Wenholz, D, Zeng, J, Miemczyk, S, Nguyen, D, Venkatraman, R, Dennis, M, Alharbi, A, Ellyard, J, Wong, W, Kile, B, Vinuesa, C, Kelly, G, Hansbro, P, Laczka, O, De Nardo, D, Hansbro, N & Kumar, N 2022, 'Pharmacological inhibition of TBK1/IKKε blunts COVID-19 immunopathology', Research Square Platform LLC.
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Garces, LP, Kolar, J, Sherris, M & Ungolo, F 2022, 'Affine Mortality Models with Jumps: Parameter Estimation and Forecasting'.

Ghorbanpour, M, Richards, C, Pienaar, D, Sesperez, K, Es.c, HA, Nikolic, V, Orlic, NK, Mikovic, Z, Stefanovic, M, Cakic, Z, Alqudah, A, Cole, L, Gorrie, C, McGrath, K, Kavurma, MM, Warkianib, ME & McClements, L 2022, 'A placenta-on-a-chip model to determine the regulation of FKBPL and galectin-3 in preeclampsia', Research Square Platform LLC.
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He, VX & Wand, MP 2022, 'Bayesian Generalized Additive Model Selection Including a Fast Variational Option'.

Herdean, A 2022, 'PSI FluorCAM protocol for Rapid Light Curve with far red pre-ilumination. v1', ZappyLab, Inc..
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Hinners, J, Argyle, PA, Walworth, NG, Doblin, MA, Levine, NM & Collins, S 2022, 'Multitrait diversification in marine diatoms in constant and warmed environments', Cold Spring Harbor Laboratory.
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Horder, J, White, S, 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'.

Johnson, MS, Burns, BP, Herdean, A, Angeloski, A, Ralph, P, Morris, T, Kindler, G, Wong, HL, Kuzhiumparambil, U, Sedger, L & Larkum, AWD 2022, 'A Cyanobacteria Enriched Layer of Shark Bay Stromatolites Reveals a New <em>Acaryochloris</em> strain Living in near Infrared Light', MDPI AG.
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Krishnan, S, DeMaere, MZ, Beck, D, Ostrowski, M, Seymour, JR & Darling, AE 2022, 'Rhometa: Population recombination rate estimation from metagenomic read datasets', Cold Spring Harbor Laboratory.
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Kruk, D, Yeung, A, Faiz, A, Hacken, NHTT, Timens, W, Kuppevelt, TH, Daamen, W, Hof, D, Harmsen, MC, Rojas, M & Heijink, IH 2022, 'Gene expression profiles in mesenchymal stromal cells from bone marrow, adipose tissue and lung tissue of COPD patients and controls', Research Square Platform LLC.
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Lam, MMC, Koong, J, Holt, KE, Hall, RM & Hamidian, M 2022, 'Detection and typing of plasmids in Acinetobacter baumannii using rep genes encoding replication initiation proteins', Cold Spring Harbor Laboratory.
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Li, M-Y, Qin, Y-Q, Li, J-S, Zhao, P, Tian, Y-G, Li, K-C, Oliver, BG & Liu, X-F 2022, 'Effective-Component Compatibility of Bufei Yishen Formula Ⅲ Ameliorated COPD By Improving Airway Epithelial Cell Senescence Via Promoting Mitophagy By Nrf2/PINK1 Pathway', Research Square Platform LLC.
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Liddell, JR, Hilton, JBW, Kysenius, K, Nikseresht, S, McInnes, LE, Hare, DJ, Paul, B, Trist, BG, Double, KL, Mercer, SW, Ayton, S, Roberts, BR, Beckman, JS, McLean, CA, White, AR, Donnelly, PS, Bush, AI & Crouch, PJ 2022, 'Microglial ferroptotic stress causes non-cell autonomous neuronal death', Cold Spring Harbor Laboratory.
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Macaulay, M & Rognon, P 2022, 'Inertial Force Transmission in Dense Granular Flows'.

Macaulay, M, Darling, AE & Fourment, M 2022, 'Fidelity of Hyperbolic Space for Bayesian Phylogenetic Inference'.

Newing, T, Brewster, JL, Yu, H, Johnston, NP, Fitschen, LJ & Tolun, G 2022, 'Structure of phage λ Redβ₁₇₇ annealase shows how it anneals DNA strands during single-strand annealing homologous DNA recombination', Cold Spring Harbor Laboratory.
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Nielsen, JJV, Matthews, G, Frith, KR, Harrison, HB, Marzonie, Slaughter, KL, Suggett, DJ & Bay, LK 2022, 'Experimental considerations of acute heat stress assays to quantify coral thermal tolerance', Research Square Platform LLC.
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Niu, J-Q, 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 2022, 'Pathological oligodendrocyte precursor cells revealed in human schizophrenic brains and trigger schizophrenia-like behaviors and synaptic defects in genetic animal model', Research Square Platform LLC.
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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 Oxide Ring Resonators'.

Paudel, KR 2022, 'Defining and treating the physiological effects of bushfire smoke'.
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Bushfire Mini Symposium-2022

Peterson, E, Söderström, B, Prins, N, Le, GHB, Hartley-Tassell, LE, Evenhuis, C, Birkholm Grønnemose, R, Andersen, TE, Møller-Jensen, J, Iosifidis, G, Duggin, IG, Saunders, B, Harry, EJ & Bottomley, AL 2022, 'The role of bacterial size, shape and surface in macrophage engulfment of uropathogenicE. colicells', Cold Spring Harbor Laboratory.
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Pham, NHT, Joglekar, MV, Wong, WKM, Nassif, NT, Simpson, AM & Hardikar, AA 2022, 'The role of short-chain fatty acids on insulin sensitivity: a systematic review and meta-analysis', Cold Spring Harbor Laboratory.
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Rouet, R, Henry, JY, Johansen, MD, Sobti, M, Balachandran, H, Langley, DB, Walker, G, Lenthall, H, Jackson, J, Ubiparipovic, S, Mazigi, O, Schofield, P, Burnett, DL, Brown, SHJ, Martinello, M, Hudson, B, Gilroy, N, Post, JJ, Kelleher, A, Jäck, H-M, Goodnow, CC, Turville, SG, Rawlinson, WD, Bull, RA, Stewart, AG, Hansbro, PM & Christ, D 2022, 'Broadly neutralizing SARS-CoV-2 antibodies through epitope-based selection from convalescent patients', Cold Spring Harbor Laboratory.
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Scammell, H, Siriviboon, P, Lin, J-X, Liu, X, Liu, S, Rhodes, D, Watanabe, K, Taniguchi, T, Hone, J, Scheurer, M & Li, JIA 2022, 'A new flavor of correlation and superconductivity in small twist-angle trilayer graphene'.
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Schaeper, OC, Yang, Z, Kianinia, M, Fröch, JE, Komar, A, Mu, Z, Gao, W, Neshev, D & Aharonovich, I 2022, 'Monolithic Silicon Carbide Metalenses'.

Shan, X, Ding, L, Wen, S, Chen, C, Wang, D, Zhu, H, Nie, P, Lu, X, Wang, S, Zhong, X, Su, Q, Liu, B, Lu, J, Reece, P, Chang, L, Jin, D & Wang, F 2022, 'Single charge regime electrodynamic force measuring in solution by upconversion photonic force microscope', Research Square Platform LLC.
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Smith, GB, Gentle, AR & Arnold, MD 2022, 'Non-reciprocal emissivity, partial coherence, and amplification of internal energy from photon recycling when thermal radiation is sourced within matter'.

Strutt, JPB, Natarajan, M, Sin, WX, Lee, E, Barone, PW, Wolfrum, JM, Williams, RBH, Rice, SA & Springs, SL 2022, 'Machine-learning based detection of adventitious microbes in T-cell therapy cultures using long read sequencing', Cold Spring Harbor Laboratory.
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Suyama, H, Luu, LDW, Zhong, L, Raftery, MJ & Lan, R 2022, 'Integrating proteomic data with metabolic modelling provides insight into key pathways ofBordetella pertussisbiofilms', Cold Spring Harbor Laboratory.
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Swanepoel, C, Fourment, M, Ji, X, Nasif, H, Suchard, MA, IV, FAM & Drummond, A 2022, 'TreeFlow: probabilistic programming and automatic differentiation for phylogenetics'.

Thomson, J 2022, 'How Can We Predict a Nuclear War?', Newsweek.

Walworth, NG, Espinoza, JL, Argyle, PA, Hinners, J, Levine, NM, Doblin, MA, Dupont, CL & Collins, S 2022, 'Rapid reductions in population size drive evolutionary divergence in diatoms', Cold Spring Harbor Laboratory.
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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', Center for Open Science.
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Woodcock, S 2022, '433 people win a lottery jackpot – impossible? Probability and psychology suggest it’s more likely than you’d think', The Conversation.

Woodcock, S 2022, '433 people win a lottery jackpot – impossible? Probability and psychology suggest it’s more likely than you’d think', The Conversation.

Woodcock, S 2022, 'Did 433 people win the same jackpot lottery in the Philippines without cheating?', Australian Broadcasting Corporation.

Woodcock, S 2022, 'Morocco are the first-ever African semifinalists of the World Cup. Here’s what geographical data tell us about this result', The Conversation.

Wu, X, Wang, P, Lewis, W, Jiang, Y-B & Gale, PA 2022, 'Measuring anion binding at biomembrane interfaces', American Chemical Society (ACS).
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Xu, Z, Hu, D, Wai Luu, LD, 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', Cold Spring Harbor Laboratory.
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Yang, Y, Quiroz, M, Kohn, R & Sisson, SA 2022, 'A correlated pseudo-marginal approach to doubly intractable problems'.

Zamborain-Mason, J, Cinner, JE, MacNeil, MA, Graham, NAJ, Hoey, AS, Beger, M, Brooks, AJ, Booth, DJ, Edgar, GJ, Feary, DA, Ferse, SCA, Friedlander, AM, Gough, CLA, Green, AL, Mouillot, D, Polunin, NVC, Stuart-Smith, RD, Wantiez, L, Williams, ID, Wilson, SK & Connolly, SR 2022, 'Sustainable reference points for multispecies coral reef fisheries', Cold Spring Harbor Laboratory.
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Zeng, HZJ, Ngyuen, MAP, Ai, X, Bennet, A, Solnstev, A, Laucht, A, Al-Juboori, A, Toth, M, Mildren, R, Malaney, R & Aharonovich, I 2022, 'Integrated Room Temperature Single Photon Source for Quantum Key Distribution'.

Zhang, L, Guan, Y, Su, QP, Liao, Y, Duggin, I & Jin, D 2022, 'Induction of Bacteriophage PinR Facilitates the Evolution of Antibiotic Resistance', Cold Spring Harbor Laboratory.
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Zhang, L, Su, QP, Guan, Y, Cheng, YY, Cokcetin, N, Bottomley, A, Robinson, A, Harry, E, van Oijen, A & Jin, D 2022, 'Bacterial SOS-independent Superfast Evolution of Multi-Drug Resistance', Cold Spring Harbor Laboratory.
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Zhanghao, K, Li, M, Chen, X, Liu, W, Li, T, Wang, Y, Su, F, Wu, Z, Shan, C, Wu, J, Zhang, Y, Fu, J, Xi, P & Jin, D 2022, 'Fast imaging of 15 intracellular compartments and interactions by deep learning segmentation of super-resolution data', Research Square Platform LLC.
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Zhigulin, I, Horder, J, Ivady, V, White, SJU, Gale, A, Li, C, Lobo, CJ, Toth, M, Aharonovich, I & Kianinia, M 2022, 'Stark effect of quantum blue emitters in hBN'.