Publications

Sahoo, JP, Tripathy, AK, Mohanty, M, Li, KC & Nayak, AK 2022, Preface.

Alghalayini, A, Cranfield, CG, Cornell, BA & Valenzuela, SM 2022, 'Preparing Ion Channel Switch Membrane-Based Biosensors' in Methods in Molecular Biology, Springer US, 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.

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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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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Cranfield, CG, Le Brun, AP, Garcia, A, Cornell, BA & Holt, SA 2022, 'Langmuir-Schaefer Deposition to Create an Asymmetrical Lipopolysaccharide Sparsely Tethered Lipid Bilayer' in Methods in Molecular Biology, Springer US, pp. 21-30.
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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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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' in Methods in Molecular Biology, Springer US, pp. 81-92.
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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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Luu, LDW & Lan, R 2022, 'Rapid Surface Shaving for Proteomic Identification of Novel Surface Antigens for Vaccine Development' in Methods in Molecular Biology, Springer US, 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.

Nucera, F, Hansbro, PM, 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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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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Wadhwa, R, Paudel, KR, Shukla, S, Shastri, M, Gupta, G, Devkota, HP, Chellappan, DK, Hansbro, PM & Dua, K 2022, 'Epigenetic Therapy as a Potential Approach for Targeting Oxidative Stress–Induced Non-Small-Cell Lung Cancer' in Handbook of Oxidative Stress in Cancer: Mechanistic Aspects, Springer Singapore, pp. 1-16.
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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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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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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.

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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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, Nijnatten, J, Kersten, ETG, Kermani, NZ, Khuder, B, Vonk, JM, Vermeulen, RCH, Neighbors, M, Tew, GW, Grimbaldeston, MA, 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, 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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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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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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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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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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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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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...

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 & 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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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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Butt, N, Halpern, BS, O'Hara, CC, Allcock, AL, Polidoro, B, Sherman, S, Byrne, M, Birkeland, C, Dwyer, RG, Frazier, M, Woodworth, BK, Arango, CP, Kingsford, MJ, Udyawer, V, Hutchings, P, Scanes, E, McClaren, EJ, Maxwell, SM, Diaz‐Pulido, G, Dugan, E, Simmons, BA, Wenger, AS, Linardich, C & Klein, CJ 2022, 'A trait‐based framework for assessing the vulnerability of marine species to human impacts', Ecosphere, vol. 13, no. 2.
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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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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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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

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.

Chalmers, T & Lal, S 2022, 'Assessing cardiovascular links to depression and anxiety in Australian professional drivers', Journal of Integrative Neuroscience, vol. 21, no. 1, pp. 043-043.
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Chalmers, T, Eaves, S, Lees, T, Lin, C, Newton, PJ, Clifton‐Bligh, R, McLachlan, CS, Gustin, SM & Lal, S 2022, 'The relationship between neurocognitive performance and HRV parameters in nurses and non‐healthcare participants', Brain and Behavior, vol. 12, no. 3.
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Chan, H, Mohamed, AMT, Grainge, I & Rodrigues, CDA 2022, 'FtsK and SpoIIIE, coordinators of chromosome segregation and envelope remodeling in bacteria', Trends in Microbiology, vol. 30, no. 5, pp. 480-494.
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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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Che, S, Zhang, L, Wang, T, Su, D & Wang, C 2022, 'Graphitic Carbon Nitride‐Based Photocatalysts for Biological Applications', Advanced Sustainable Systems, vol. 6, no. 1, pp. 2100294-2100294.
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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, 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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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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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.

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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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...

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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Crispino, F, Weyermann, C, Delémont, O, Roux, C & Ribaux, O 2022, 'Towards another paradigm for forensic science?', WIREs Forensic Science, vol. 4, no. 3.
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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.

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.
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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.

Ditz, B, Boekhoudt, J, Couto, N, Brandsma, CA, Hiemstra, PS, Tew, GW, Neighbors, M, Grimbaldeston, MA, Timens, W, Kerstjens, HAM, Rossen, JWA, Guryev, V, van den Berge, M & Faiz, A 2022, 'The Microbiome in Bronchial Biopsies from Smokers and Ex-Smokers with Stable COPD - A Metatranscriptomic Approach', COPD: Journal of Chronic Obstructive Pulmonary Disease, vol. 19, no. 1, pp. 81-87.
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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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dos Remedios, C, Cranfield, C, Whelan, D, Cox, C, Shearwin, K, Ho, J, Allen, T, Shibuya, R, Hibino, E, Hayashi, K & Li, A 2022, 'A special issue of the Australian society for Biophysics', Biophysical Reviews, vol. 14, no. 1, pp. 1-2.
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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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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).

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

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.
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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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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.

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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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...

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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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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Giacomucci, S, Alvarez, L, Rodrigues, CDA, Cava, F & Paradis-Bleau, C 2022, 'Hydroxyl Radical Overproduction in the Envelope: an Achilles’ Heel in Peptidoglycan Synthesis', Microbiology Spectrum, vol. 10, no. 1.
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Oxidative stress is caused by the production and excessive accumulation of oxygen reactive species. In bacterial cells, oxidative stress mediated by hydroxyl radicals is typically associated with DNA damage in the cytoplasm.

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.

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, 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...

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...

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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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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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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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.

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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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.
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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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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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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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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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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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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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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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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.

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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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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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.

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.

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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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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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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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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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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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.

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.

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

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.

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.

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...

Liu, B, Chan, H, Bauda, E, Contreras-Martel, C, Bellard, L, Villard, A-M, Mas, C, Neumann, E, Fenel, D, Favier, A, Serrano, M, Henriques, AO, Rodrigues, CDA & Morlot, C 2022, 'Structural insights into ring-building motif domains involved in bacterial sporulation', Journal of Structural Biology, vol. 214, no. 1, pp. 107813-107813.
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Components of specialized secretion systems, which span the inner and outer membranes in Gram-negative bacteria, include ring-forming proteins whose oligomerization was proposed to be promoted by domains called RBM for "Ring-Building Motifs". During spore formation in Gram-positive bacteria, a transport system called the SpoIIIA-SpoIIQ complex also assembles in the double membrane that surrounds the forespore following its endocytosis by the mother cell. The presence of RBM domains in some of the SpoIIIA proteins led to the hypothesis that they would assemble into rings connecting the two membranes and form a conduit between the mother cell and forespore. Among them, SpoIIIAG forms homo-oligomeric rings in vitro but the oligomerization of other RBM-containing SpoIIIA proteins, including SpoIIIAH, remains to be demonstrated. In this work, we identified RBM domains in the YhcN/YlaJ family of proteins that are not related to the SpoIIIA-SpoIIQ complex. We solved the crystal structure of YhcN from Bacillus subtilis, which confirmed the presence of a RBM fold, flanked by additional secondary structures. As the protein did not show any oligomerization ability in vitro, we investigated the structural determinants of ring formation in SpoIIIAG, SpoIIIAH and YhcN. We showed that in vitro, the conserved core of RBM domains alone is not sufficient for oligomerization while the β-barrel forming region in SpoIIIAG forms rings on its own. This work suggests that some RBMs might indeed participate in the assembly of homomeric rings but others might have evolved toward other functions.

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, pp. 1-12.
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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.

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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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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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.

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, ...

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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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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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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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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Montgomerie, C, Raneri, D & Maynard, P 2022, 'Validation study of three-dimensional scanning of footwear impressions', Australian Journal of Forensic Sciences, vol. 54, no. 1, pp. 119-132.
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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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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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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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Ni, Z, Gale, A, Johnson, MS & Sedger, LM 2022, 'Analysis insights for three FRET pairs of chemically unlinked two‐molecule FRET cytometry', Cytometry Part A, vol. 101, no. 5, pp. 387-399.
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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.

Oglobline, AN, Padula, MP & Doble, PA 2022, 'Quality control of A1-free dairy', Food Control, vol. 135, pp. 108685-108685.
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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, pp. 1-11.
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Abstract Given 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.

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.

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 Journal, 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.

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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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. 178-178.
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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 (250–6000kgha–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 250kgha–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 1.5–30mgL–1 in the different treatments, whereas total phosphorus (TP) increased from 0.01 to 0.05–5.0mgL–1. Chlorophyll-a levels increased from &lt;5µgL–1 to levels between 100 and 1000µgL–1 in the different treatments. Mean nutrient levels (TN and TP), chlorophyll-a and phytoplankton biovolume all showed a significant (P&lt;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 (250kgha–1).

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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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...

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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Qian, B, Ye, H, Huang, W, Xie, Q, Pan, Y, Xing, N, Ren, Y, Guo, A, Jiao, Q & Lan, Y 2022, 'A sentinel-2-based triangular vegetation index for chlorophyll content estimation', Agricultural and Forest Meteorology, vol. 322, pp. 109000-109000.
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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, pp. 105097-105097.
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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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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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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.

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.

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

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.

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

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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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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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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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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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. 147-147.
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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.

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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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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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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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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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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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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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.

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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Su, D 2022, 'Powerful qua-functional electrolyte additive for lithium metal batteries', Green Energy & Environment, vol. 7, no. 3, pp. 361-364.
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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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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, 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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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.

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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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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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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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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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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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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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, N, Yao, H, Tao, Q, Sun, J, Ma, H, Wang, Y, Zhou, C, Fan, H, Shao, H, Qin, A, Su, D, Wang, C & Chong, H 2022, 'TPE based aggregation induced emission fluorescent sensors for viscosity of liquid and mechanical properties of hydrogel', Chinese Chemical Letters, vol. 33, no. 1, pp. 252-256.
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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, 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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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.

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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Williams, NLR, Siboni, N, McLellan, S, 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, 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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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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Wu, C, Lei, Y, Simonelli, L, Tonti, D, Black, A, Lu, X, Lai, W, Cai, X, Wang, Y, Gu, Q, Chou, S, Liu, H, Wang, G & Dou, S 2022, 'Continuous Carbon Channels Enable Full Na‐Ion Accessibility for Superior Room‐Temperature Na–S Batteries', Advanced Materials, vol. 34, no. 8, pp. 2108363-2108363.
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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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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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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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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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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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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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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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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, 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, Y, Chen, P, Wang, T, Su, D & Wang, C 2022, 'Development of Small‐Scale Monitoring and Modeling Strategies for Safe Lithium‐Ion Batteries', Batteries & Supercaps, vol. 5, no. 2.
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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.

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.

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.

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.

Crump, V & Davila, Y 1970, 'Understanding Students' Experiences After Incorporating Indigenous Perspectives in a Postgraduate Science Communication Subject.', Education and New Developments, 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 beliefs.

Elder, M, Dietrich, H, Piggott, A, Qiao, Y & Weiss, A 1970, 'The Isomorphism Problem for Plain Groups Is in ∑₃P', 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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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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Kononov, A, Memar, J & Zinder, Y 1970, 'Algorithms for Flow Shop with Job-Dependent Buffer Requirements'.
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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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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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Cranfield, CG 2022, 'Preface', p. v.

Fernandez, TT, Johnston, B, Gross, S, Cozic, S, Poulain, M, Mahmodi, H, Kabakova, I, Withford, M & Fuerbach, A 2022, 'Ultrafast laser inscribed waveguides in tailored fluoride glasses: An enabling technology for mid-infrared integrated photonics devices'.

He, VX & Wand, MP 2022, 'Bayesian Generalized Additive Model Selection Including a Fast Variational Option'.

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

Schaeper, OC, Yang, Z, Kianinia, M, Fröch, JE, Komar, A, Mu, Z, Gao, W, Neshev, D & Aharonovich, I 2022, 'Monolithic Silicon Carbide Metalenses'.

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'.

Woodcock, S 2022, 'Have the NRL’s rule changes made boring blowouts the norm? The stats say no', The Conversation.