Publications

Nebel, CE, Aharonovich, I, Mizuochi, N & Hatano, M 2021, Preface.
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Phillips, C, Amigo, J, McNevin, D, de la Puente, M, Cheung, EYY & Victoria Lareu, M 2021, 'Online Population Data Resources for Forensic SNP Analysis with Massively Parallel Sequencing: An Overview of Online Population Data for Forensic Purposes' in Forensic DNA Analysis, Apple Academic Press, USA, pp. 241-287.
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Recently, extensive catalogs of human variation derived from whole-genome sequencing have been released as openly accessible archives of sequence variants—a resource that is highly suitable for selecting markers for new forensic tests using massively parallel sequencing. In particular, the comparison of population patterns in these databases of variants can help identify markers suitable for the inference of ancestry that can then form informative 242forensic assays for this purpose. This chapter outlines in detail the ancestry or co-ancestry composition, genotype data access details, and geographic distributions of the samples in the most extensive variant catalogs of: 1000 Genomes; the HGDP–CEPH panel; Simons Foundation Human Genome Diversity Project; and Estonian Biocentre Genome Diversity Panel. While 1000 Genomes systematically characterizes a large number of samples from a limted number of carefully selected populations and restricts itself to five to six populations per continent, both SGDP and EGDP have analyzed only 2–4 samples per geographic location and these are much more widely dispersed geographically. The pros and cons of each approach are discussed, and details are provided of more recently published variant compilation projects with much larger sample sizes, notably the genome aggregation database gnomAD.

Rahman, MA, Phillips, M & Ton-That, C 2021, 'Dopants and Impurity-Induced Defects in ZnO' in Defects in Functional Materials, World Scientific, Singapore, pp. 177-199.
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In recent years, there has been resurgent interest in ZnO due to its efficient UV emission and potential application in opto-electronic devices. The problem of self-compensating defects, especially those related to acceptor-like dopants, remains a major challenge to date. In this chapter, we provide an overview of the fundamental properties of point defects and dopants as well as their complexes in bulk crystals and nanostructures. Nominally undoped ZnO is typically n-type, which has been widely ascribed to O vacancies or Zn interstitials; however, these defect assignments are controversial as O vacancies are deep donors while Zn interstitials are highly mobile at room temperature and considered to be unstable. Accordingly, H and group III impurities have also been suggested to be responsible for the observed n-type conductivity. Although there are still many unanswered questions concerning defect-related luminescence bands in ZnO, great progress has been made in recent years to identify and characterize them using spatially resolved luminescence spectroscopies and first-principles calculations. The ubiquitous green emission has several possible origins, including O and Zn vacancies as well as Cu impurities. The properties of group I (Li, Na, and Cu), group III (Ga, Al, and In), and group V (N, P, and Sb) impurities as well as their complexes with native point defects and H are discussed, along with a concluding outlook for future research into the optical properties of ZnO.

Romero-Hall, E, Correia, AP, Branch, RM, Cevik, YD, Dickson-Deane, C, Chen, B, Liu, JC, Tang, H, Vasconcelos, L, Pallitt, N & Thankachan, B 2021, 'Futurama: Learning design and technology research methods' in Research Methods in Learning Design and Technology, Taylor and FRancis, pp. 206-226.

Stuart, B 2021, 'Infrared Spectroscopy' in Wolstenholme, R, Jickells, S & Forbes, S (eds), Analytical Techniques in Forensic Science, Wiley, pp. 145-160.

Tripathi, A, Kruk, S, Shang, Y, Zhou, J, Kravchenko, I, Jin, D & Kivshar, Y 2021, 'Topological nanophotonics for photoluminescence control' in Frontiers in Optics and Photonics, De Gruyter, pp. 447-454.
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Abiero, AR & Bradfield, LA 2021, 'The contextual regulation of goal-directed actions', Current Opinion in Behavioral Sciences, vol. 41, pp. 57-62.
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Goal-directed actions typically transfer readily between contexts, but this is not always the case. Goal-directed actions do not transfer across contexts just after they are initially learned, or when multiple, competing response-outcome contingencies exist, or when the context is highly emotionally salient. Goal-directed actions are, thus, context-dependent under each of these conditions. Here we review the studies that have led to these findings, and discuss the potentially unique psychological mechanisms that could underlie the context-dependency of goal-directed actions in each instance.

Ahmed, AJ, Cortie, DL, Yun, FF, Rahman, Y, Nazrul Islam, SMK, Bake, A, Konstantinov, K, Hossain, MSA, Alowasheeir, A, Yamauchi, Y & Wang, X 2021, 'Significant Reduction in Thermal Conductivity and Improved Thermopower of Electron-Doped Ba1-xLaxTiO3 with Nanostructured Rectangular Pores', ADVANCED ELECTRONIC MATERIALS, vol. 7, no. 4.
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Ahrens, CW, Challis, A, Byrne, M, Leigh, A, Nicotra, AB, Tissue, D & Rymer, P 2021, 'Repeated extreme heatwaves result in higher leaf thermal tolerances and greater safety margins.', The New phytologist.
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The frequency and severity of heatwave events are increasing, exposing species to conditions beyond their physiological limits. Species respond to heatwaves in different ways, however it remains unclear if plants have the adaptive capacity to successfully respond to hotter and more frequent heatwaves. We exposed eight tree populations from two climate regions grown under cool and warm temperatures to repeated heatwave events of moderate (40°C) and extreme (46°C) severity to assess adaptive capacity to heatwaves. Leaf damage and maximum quantum efficiency of photosystem II (F_v /F_m ) were significantly impacted by heatwave severity and growth temperatures, respectively; populations from a warm-origin avoided damage under moderate heatwaves compared to those from a cool-origin, indicating a degree of local adaptation. We found that plasticity to heatwave severity and repeated heatwaves contributed to enhanced thermal tolerance and lower leaf temperatures_, leading to greater thermal safety margins (thermal tolerance minus leaf temperature) in a second heatwave. Notably, while we show that adaptation and physiological plasticity are important factors affecting plant adaptive capacity to thermal stress, plasticity of thermal tolerances and thermal safety margins provides the opportunity for trees to persist among fluctuating heatwave exposures.

Ajani, PA, Petrou, K, Larsson, ME, Nielsen, DA, Burke, J & Murray, SA 2021, 'Phenotypic trait variability as an indication of adaptive capacity in a cosmopolitan marine diatom.', Environmental microbiology.
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Determining the adaptive capacity of marine phytoplankton is important in predicting changes in phytoplankton responses to ocean warming. Phytoplankton may consist of high levels of standing phenotypic and genetic variability, the basis of rapid evolution; however, few studies have quantified trait variability within and amongst closely related diatom species. Using 35 clonal cultures of the ubiquitous marine diatom Leptocylindrus isolated from six locations, spanning 2000 km of the south-eastern Australian coastline, we found evidence of significant intraspecific morphological and metabolic trait variability, which for 8 of 9 traits (growth rate, biovolume, C:N, silica deposition, silica incorporation rate, chl-a, and photosynthetic efficiency under dark adapted, growth irradiance, and high-light adaptation) were greater within a species than between species. Moreover, only two traits revealed a latitudinal trend with strains isolated from lower latitudes showing significantly higher silicification rates and protein:lipid content compared to their higher latitude counterparts. These data mirror recent studies on diatom intraspecific genetic diversity, which has found comparable levels of genetic diversity at a single site to those thousands of kilometres apart, and provide evidence of a functional role of diatom diversity that will allow for rapid adaptation via ecological selection on standing variation in response to changing conditions.

Ajani, PA, Verma, A, Kim, JH, Woodcock, S, Nishimura, T, Farrell, H, Zammit, A, Brett, S & Murray, SA 2021, 'Using qPCR and high-resolution sensor data to model a multi-species Pseudo-nitzschia (Bacillariophyceae) bloom in southeastern Australia', Harmful Algae, vol. 108.
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Harmful algal blooms, including those caused by the toxic diatom Pseudo-nitzschia, can have significant impacts on human health, ecosystem functioning and ultimately food security. In the current study we characterized a bloom of species of Pseudo-nitzschia that occurred in a south-eastern Australian oyster-growing estuary in 2019. Using light microscopy, combined with molecular (ITS/5.8S and LSU D1-D3 rDNA regions) and toxicological evidence, we observed the bloom to consist of multiple species of Pseudo-nitzschia including P. cf. cuspidata, P. hasleana, P. fraudulenta and P. multiseries, with P. cf. cuspidata being the only species that produced domoic acid (3.1 pg DA per cell). As several species of Pseudo-nitzschia co-occurred, only one of which produced DA, we developed a rapid, sensitive and efficient quantitative real-time polymerase chain reaction (qPCR) assay to detect only species belonging to the P. pseudodelicatissima complex Clade I, to which P. cf. cuspidata belongs, and this indicated that P. cuspidata or closely related strains may have dominated the Pseudo-nitzschia community at this time. Finally, using high resolution water temperature and salinity sensor data, we modeled the relationship between light microscopy determined abundance of P. delicatissima group and environmental variables (temperature, salinity, rainfall) at two sites within the estuary. A total of eight General Linear Models (GLMs) explaining between 9 and 54% of the deviance suggested that the temperature (increasing) and/or salinity (decreasing) data were generally more predictive of high cell concentrations than the rainfall data at both sites, and that overall, cell concentrations were more predictive at the more oceanic site than the more upstream site, using this method. We conclude that the combination of rapid molecular methods such as qPCR and real-time sensor data modeling, can provide a more rapid and effective early warning of harmful algal blooms of species of Pseud...

Akella, A, Singh, AK, Leong, D, Lal, S, Newton, P, Clifton-Bligh, R, McLachlan, CS, Gustin, SM, Maharaj, S, Lees, T, Cao, Z & Lin, C-T 2021, 'Classifying multi-level stress responses from brain cortical EEG in Nurses and Non-health professionals using Machine Learning Auto Encoder', IEEE Journal of Translational Engineering in Health and Medicine.
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Akter, A, Itabashi, E, Kakizaki, T, Okazaki, K, Dennis, ES & Fujimoto, R 2021, 'Genome Triplication Leads to Transcriptional Divergence of FLOWERING LOCUS C Genes During Vernalization in the Genus Brassica', Frontiers in Plant Science.
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Alder, R, Xiao, L & Fu, S 2021, 'Comparison of commercial surface-enhanced Raman spectroscopy substrates for the analysis of cocaine.', Drug Testing and Analysis.
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The use of illicit drugs across the world causes issues for users, healthcare workers and the public. Therefore, rapid and reliable onsite testing methods to detect these drugs are required. In this study, seven commercial surface-enhanced Raman spectroscopy (SERS) substrates A-G were compared for the analysis of cocaine. These substrates were compared using scanning electron microscopy to study the surface structure and Raman spectroscopy and to determine if there was any enhancement of the cocaine bands. Substrate B provided the best enhancement of known cocaine vibrational bands, allowing the detection down to concentrations of 1 ng/mL in standards and 10 ng/mL extracted from the oral fluid. The results showed that SERS is an ideal method for future rapid onsite analysis of illicit drugs in oral fluid. Commercial SERS substrates were compared for the analysis of cocaine. Substrate B provided the best result and was further tested with lower concentrations and extracts from the oral fluid. The application to oral fluid testing could prove useful for future onsite analysis.

Alderdice, R, Pernice, M, Cárdenas, A, Hughes, DJ, Harrison, PL, Boulotte, N, Chartrand, K, Kühl, M, Suggett, DJ & Voolstra, CR 2021, 'Hypoxia as a physiological cue and a pathological stress for coral larvae.', Mol Ecol.
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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 driven into a similar metabolic crisis 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 hours of deoxygenation stress (~2 mg O2 L-1 ), coral planulae demonstrated a low expression of HIF-targeted hypoxia response genes along with a significantly high expression of PHD2 (a promoter of HIFα proteasomal degradation), similar to corresponding adult samples. 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 HIF-targeted and conserved developmental regulators, e.g., Homeobox HOX, corroborating how changes in external oxygen levels can affect animal growth. 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 success.

Alhamami, T, Chowdhury, PR, Gomes, N, Carr, M, Veltman, T, Khazandi, M, Mollinger, J, Deutscher, AT, Turni, C, Mahdi, L, Venter, H, Abraham, S, Djordjevic, SP & Trott, DJ 2021, 'First Emergence of Resistance to Macrolides and Tetracycline Identified in Mannheimia haemolytica and Pasteurella multocida Isolates from Beef Feedlots in Australia', Microorganisms.
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Aliee, H, Massip, F, Qi, C, Stella de Biase, M, van Nijnatten, J, Kersten, ETG, Kermani, NZ, Khuder, B, Vonk, JM, Vermeulen, RCH, U-BIOPRED study group, Cambridge Lung Cancer Early Detection Programme, INER-Ciencias Mexican Lung Program, Neighbors, M, Tew, GW, Grimbaldeston, MA, Ten Hacken, NHT, Hu, S, Guo, Y, Zhang, X, Sun, K, Hiemstra, PS, Ponder, BA, Mäkelä, MJ, Malmström, K, Rintoul, RC, Reyfman, PA, Theis, FJ, Brandsma, C-A, Adcock, IM, Timens, W, Xu, C-J, van den Berge, M, Schwarz, RF, Koppelman, GH, Nawijn, MC & Faiz, A 2021, 'Determinants of expression of SARS-CoV-2 entry-related genes in upper and lower airways.', Allergy.
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Allam, VSRR, Faiz, A, Lam, M, Rathnayake, SNH, Ditz, B, Pouwels, SD, Brandsma, C-A, Timens, W, Hiemstra, PS, Tew, GW, Neighbors, M, Grimbaldeston, M, van den Berge, M, Donnelly, S, Phipps, S, Bourke, JE & Sukkar, MB 2021, 'RAGE and TLR4 differentially regulate airway hyperresponsiveness: implications for COPD.', Allergy.
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BACKGROUND:The receptor for advanced glycation end products (RAGE) and toll-like receptor 4 (TLR4) are implicated in COPD. Although these receptors share common ligands and signaling pathways, it is not known whether they act in concert to drive pathological processes in COPD. We examined the impact of RAGE and/or TLR4 gene deficiency in a mouse model of COPD and also determined whether expression of these receptors correlates with airway neutrophilia and airway hyperreactivity (AHR) in COPD patients. METHODS:We measured airway inflammation and AHR in wild-type, RAGE-/- , TLR4-/- and TLR4-/- RAGE-/- mice following acute exposure to cigarette smoke (CS). We also examined the impact of smoking status on AGER (encodes RAGE) and TLR4 bronchial gene expression in patients with and without COPD. Finally, we determined whether expression of these receptors correlates with airway neutrophilia and AHR in COPD patients. RESULTS:RAGE-/- mice were protected against CS-induced neutrophilia and AHR. In contrast, TLR4-/- mice were not protected against CS-induced neutrophilia and had more severe CS-induced AHR. TLR4-/- RAGE-/- mice were not protected against CS-induced neutrophilia but were partially protected against CS-induced mediator release and AHR. Current smoking was associated with significantly lower AGER and TLR4 expression irrespective of COPD status, possibly reflecting negative feedback regulation. However, consistent with preclinical findings, AGER expression correlated with higher sputum neutrophil counts and more severe AHR in COPD patients. TLR4 expression did not correlate with neutrophilic inflammation or AHR. CONCLUSIONS:Inhibition of RAGE but not TLR4 signalling may protect against airway neutrophilia and AHR in COPD.

Alqudah, A, Eastwood, K-A, Jerotic, D, Todd, N, Hoch, D, McNally, R, Obradovic, D, Dugalic, S, Hunter, AJ, Holmes, VA, McCance, DR, Young, IS, Watson, CJ, Robson, T, Desoye, G, Grieve, DJ & McClements, L 2021, 'FKBPL and SIRT-1 Are Downregulated by Diabetes in Pregnancy Impacting on Angiogenesis and Endothelial Function', Frontiers in Endocrinology.
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ALSAHAFI, S & Woodcock, S 2021, 'Local Analysis for a Mutual Inhibition in Presence of TwoViruses in a Chemostat', Nonlinear Dynamics and Systems Theory, vol. 21, no. 4, pp. 337-359.

Alsahafi, S & Woodcock, S 2021, 'Mathematical study for chikungunya virus with nonlinear general incidence rate', Mathematics, vol. 9, no. 18.
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In this article, we examine the dynamics of a Chikungunya virus (CHIKV) infection model with two routes of infection. The model uses four categories, namely, uninfected cells, infected cells, the CHIKV virus, and antibodies. The equilibrium points of the model, which consist of the free point for the CHIKV and CHIKV endemic point, are first analytically determined. Next, the local stability of the equilibrium points is studied, based on the basic reproduction number (R0 ) obtained by the next-generation matrix. From the analysis, it is found that the disease-free point is locally asymptotically stable if R0 ≤ 1, and the CHIKV endemic point is locally asymptotically stable if R0 > 1. Using the Lyapunov method, the global stability analysis of the steady-states confirms the local stability results. We then describe our design of an optimal recruitment strategy to minimize the number of infected cells, as well as a nonlinear optimal control problem. Some numerical simulations are provided to visualize the analytical results obtained.

ALSAHAFI, S & Woodcock, S 2021, 'Mutual inhibition in presence of a virus in continuous culture', Mathematical Biosciences and Engineering, vol. 18, no. 4, pp. 3258-3273.
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al-Zubaidi, Y, Chen, Y, Khalilur Rahman, M, Umashankar, B, Choucair, H, Bourget, K, Chung, L, Qi, Y, Witting, PK, Anderson, RL, O'Neill, GM, Dunstan, CR, Rawling, T & Murray, M 2021, 'PTU, a novel ureido-fatty acid, inhibits MDA-MB-231 cell invasion and dissemination by modulating Wnt5a secretion and cytoskeletal signaling', Biochemical Pharmacology, vol. 192.
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Migration and invasion promote tumor cell metastasis, which is the leading cause of cancer death. At present there are no effective treatments. Epidemiological studies have suggested that ω-3 polyunsaturated fatty acids (PUFA) may decrease cancer aggressiveness. In recent studies epoxide metabolites of ω-3 PUFA exhibited anti-cancer activity, although increased in vivo stability is required to develop useful drugs. Here we synthesized novel stabilized ureido-fatty acid ω-3 epoxide isosteres and found that one analogue - p-tolyl-ureidopalmitic acid (PTU) - inhibited migration and invasion by MDA-MB-231 breast cancer cells in vitro and in vivo in xenografted nu/nu mice. From proteomics analysis of PTU-treated cells major regulated pathways were linked to the actin cytoskeleton and actin-based motility. The principal finding was that PTU impaired the formation of actin protrusions by decreasing the secretion of Wnt5a, which dysregulated the Wnt/planar cell polarity (PCP) pathway and actin cytoskeletal dynamics. Exogenous Wnt5a restored invasion and Wnt/PCP signalling in PTU-treated cells. PTU is the prototype of a novel class of agents that selectively dysregulate the Wnt/PCP pathway by inhibiting Wnt5a secretion and actin dynamics to impair MDA-MB-231 cell migration and invasion.

Augustine, R, Dan, P, Hasan, A, Khalaf, IM, Prasad, P, Ghosal, K, Gentile, C, McClements, L & Maureira, P 2021, 'Stem cell-based approaches in cardiac tissue engineering: controlling the microenvironment for autologous cells', Biomedicine & Pharmacotherapy.
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Augustine, R, Kalva, SN, Ahmad, R, Zahid, AA, Hasan, S, Nayeem, A, McClements, L & Hasan, A 2021, '3D Bioprinted cancer models: Revolutionizing personalized cancer therapy', Translational Oncology, vol. 14, no. 4.
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After cardiovascular disease, cancer is the leading cause of death worldwide with devastating health and economic consequences, particularly in developing countries. Inter-patient variations in anti-cancer drug responses further limit the success of therapeutic interventions. Therefore, personalized medicines approach is key for this patient group involving molecular and genetic screening and appropriate stratification of patients to treatment regimen that they will respond to. However, the knowledge related to adequate risk stratification methods identifying patients who will respond to specific anti-cancer agents is still lacking in many cancer types. Recent advancements in three-dimensional (3D) bioprinting technology, have been extensively used to generate representative bioengineered tumor in vitro models, which recapitulate the human tumor tissues and microenvironment for high-throughput drug screening. Bioprinting process involves the precise deposition of multiple layers of different cell types in combination with biomaterials capable of generating 3D bioengineered tissues based on a computer-aided design. Bioprinted cancer models containing patient-derived cancer and stromal cells together with genetic material, extracellular matrix proteins and growth factors, represent a promising approach for personalized cancer therapy screening. Both natural and synthetic biopolymers have been utilized to support the proliferation of cells and biological material within the personalized tumor models/implants. These models can provide a physiologically pertinent cell–cell and cell–matrix interactions by mimicking the 3D heterogeneity of real tumors. Here, we reviewed the potential applications of 3D bioprinted tumor constructs as personalized in vitro models in anticancer drug screening and in the establishment of precision treatment regimens.

Baffour, B, Brown, JJ & Smith, PWF 2021, 'Latent Class Analysis for Estimating an Unknown Population Size - With Application to Censuses', Journal of Official Statistics, vol. 37, no. 3, pp. 673-697.
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Estimation of the unknown population size using capture-recapture techniques relies on the key assumption that the capture probabilities are homogeneous across individuals in the population. This is usually accomplished via post-stratification by some key covariates believed to influence individual catchability. Another issue that arises in population estimation from data collected from multiple sources is list dependence, where an individual's catchability on one list is related to that of another list. The earlier models for population estimation heavily relied upon list independence. However, there are methods available that can adjust the population estimates to account for dependence among lists. In this article, we propose the use of latent class analysis through log-linear modelling to estimate the population size in the presence of both heterogeneity and list dependence. The proposed approach is illustrated using data from the 1988 US census dress rehearsal.

Bao, G, Wen, S, Lin, G, Yuan, J, Lin, J, Wong, K-L, Bunzli, J-CG & Jin, D 2021, 'Learning from lanthanide complexes: The development of dye-lanthanide nanoparticles and their biomedical applications', COORDINATION CHEMISTRY REVIEWS, vol. 429.
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Barnes, JL, Plank, MW, Asquith, K, Maltby, S, Sabino, LR, Kaiko, GE, Lochrin, A, Horvat, JC, Mayall, JR, Kim, RY, Hansbro, PM, Keely, S, Belz, GT, Tay, HL & Foster, PS 2021, 'T-helper 22 cells develop as a distinct lineage from Th17 cells during bacterial infection and phenotypic stability is regulated by T-bet', MUCOSAL IMMUNOLOGY, vol. 14, no. 5, pp. 1077-1087.
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Barratt, J, Houghton, K, Richins, T, Straily, A, Threlkel, R, Bera, B, Kenneally, J, Clemons, B, Madison-Antenucci, S, Cebelinski, E, Whitney, BM, Kreil, KR, Cama, V, Arrowood, MJ & Qvarnstrom, Y 2021, 'Investigation of US Cyclospora cayetanensis outbreaks in 2019 and evaluation of an improved Cyclospora genotyping system against 2019 cyclosporiasis outbreak clusters.', Epidemiology and infection, vol. 149, p. e214.
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Cyclosporiasis is an illness characterised by watery diarrhoea caused by the food-borne parasite Cyclospora cayetanensis. The increase in annual US cyclosporiasis cases led public health agencies to develop genotyping tools that aid outbreak investigations. A team at the Centers for Disease Control and Prevention (CDC) developed a system based on deep amplicon sequencing and machine learning, for detecting genetically-related clusters of cyclosporiasis to aid epidemiologic investigations. An evaluation of this system during 2018 supported its robustness, indicating that it possessed sufficient utility to warrant further evaluation. However, the earliest version of CDC's system had some limitations from a bioinformatics standpoint. Namely, reliance on proprietary software, the inability to detect novel haplotypes and absence of a strategy to select an appropriate number of discrete genetic clusters would limit the system's future deployment potential. We recently introduced several improvements that address these limitations and the aim of this study was to reassess the system's performance to ensure that the changes introduced had no observable negative impacts. Comparison of epidemiologically-defined cyclosporiasis clusters from 2019 to analogous genetic clusters detected using CDC's improved system reaffirmed its excellent sensitivity (90%) and specificity (99%), and confirmed its high discriminatory power. This C. cayetanensis genotyping system is robust and with ongoing improvement will form the basis of a US-wide C. cayetanensis genotyping network for clinical specimens.

Barton, PS, Dawson, BM, Barton, AF, Joshua, S & Wallman, JF 2021, 'Temperature dynamics in different body regions of decomposing vertebrate remains', Forensic Science International, vol. 325, pp. 110900-110900.
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Batavia, C, Nelson, MP, Bruskotter, JT, Jones, MS, Yanco, E, Ramp, D, Bekoff, M & Wallach, AD 2021, 'Emotion as a source of moral understanding in conservation', CONSERVATION BIOLOGY.
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Batistic, F-K, Rhumorbarbe, D, Lefrancois, E, Tettey, J, Raithelhuber, M, Rossy, Q & Morelato, M 2021, 'Analysis of Google Trends to monitor New Psychoactive Substance. Is there an added value?', Forensic Science International.
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Berdinsky, D, Elder, M & Kruengthomya, P 2021, 'Cayley polynomial–time computable groups', Information and Computation, pp. 104768-104768.
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Berlińska, J, Kononov, A & Zinder, Y 2021, 'Two-machine flow shop with dynamic storage space', Optimization Letters.
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The publications on two-machine flow shop scheduling problems with job dependent storage requirements, where a job seizes a portion of the storage space for the entire duration of its processing, were motivated by various applications ranging from supply chains of mineral resources to multimedia systems. In contrast to the previous publications that assumed that the availability of the storage space remains unchanged, this paper is concerned with a more general case when the availability is a function of time. It strengthens the previously published result concerning the existence of an optimal permutation schedule, shows that the variable storage space availability leads to the NP-hardness in the strong sense even for unit processing times, and presents a polynomial-time approximation scheme together with several heuristic algorithms. The heuristics are evaluated by means of computational experiments.

Bernhardt, N, Kim, S, Froch, JE, White, SJU, Duong, NMH, He, Z, Chen, B, Liu, J, Aharonovich, I & Solntsev, AS 2021, 'Large few-layer hexagonal boron nitride flakes for nonlinear optics', OPTICS LETTERS, vol. 46, no. 3, pp. 564-567.
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Berry, IJ, Widjaja, M, Jarocki, VM, Steele, JR, Padula, MP & Djordjevic, SP 2021, 'Protein cleavage influences surface protein presentation in Mycoplasma pneumoniae', Scientific Reports.
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Bishop, A 2021, 'Geodesic growth in virtually abelian groups', Journal of Algebra.
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Bishop, DP, Westerhausen, MT, Barthelemy, F, Lockwood, T, Cole, N, Gibbs, EM, Crosbie, RH, Nelson, SF, Miceli, MC, Doble, PA & Wanagat, J 2021, 'Quantitative immuno-mass spectrometry imaging of skeletal muscle dystrophin', Scientific Reports.
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Bohaud, C, Johansen, MD, Jorgensen, C, Kremer, L, Ipseiz, N & Djouad, F 2021, 'The Role of Macrophages During Mammalian Tissue Remodeling and Regeneration Under Infectious and Non-Infectious Conditions', Frontiers in Immunology, vol. 12.
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Several infectious pathologies in humans, such as tuberculosis or SARS-CoV-2, are responsible for tissue or lung damage, requiring regeneration. The regenerative capacity of adult mammals is limited to few organs. Critical injuries of non-regenerative organs trigger a repair process that leads to a definitive architectural and functional disruption, while superficial wounds result in scar formation. Tissue lesions in mammals, commonly studied under non-infectious conditions, trigger cell death at the site of the injury, as well as the production of danger signals favouring the massive recruitment of immune cells, particularly macrophages. Macrophages are also of paramount importance in infected injuries, characterized by the presence of pathogenic microorganisms, where they must respond to both infection and tissue damage. In this review, we compare the processes implicated in the tissue repair of non-infected versus infected injuries of two organs, the skeletal muscles and the lungs, focusing on the primary role of macrophages. We discuss also the negative impact of infection on the macrophage responses and the possible routes of investigation for new regenerative therapies to improve the recovery state as seen with COVID-19 patients.

Bolitho, C, Moscova, M, Baxter, RC & Marsh, DJ 2021, 'Amphiregulin increases migration and proliferation of epithelial ovarian cancer cells by inducing its own expression via PI3-kinase signaling', MOLECULAR AND CELLULAR ENDOCRINOLOGY, vol. 533.
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Bousquet, J, Anto, JM, Czarlewski, W, Haahtela, T, Fonseca, SC, Iaccarino, G, Blain, H, Vidal, A, Sheikh, A, Akdis, CA, Zuberbier, T & ARIA group 2021, 'Cabbage and fermented vegetables: From death rate heterogeneity in countries to candidates for mitigation strategies of severe COVID-19.', Allergy, vol. 76, no. 3, pp. 735-750.
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Large differences in COVID-19 death rates exist between countries and between regions of the same country. Some very low death rate countries such as Eastern Asia, Central Europe, or the Balkans have a common feature of eating large quantities of fermented foods. Although biases exist when examining ecological studies, fermented vegetables or cabbage have been associated with low death rates in European countries. SARS-CoV-2 binds to its receptor, the angiotensin-converting enzyme 2 (ACE2). As a result of SARS-CoV-2 binding, ACE2 downregulation enhances the angiotensin II receptor type 1 (AT₁ R) axis associated with oxidative stress. This leads to insulin resistance as well as lung and endothelial damage, two severe outcomes of COVID-19. The nuclear factor (erythroid-derived 2)-like 2 (Nrf2) is the most potent antioxidant in humans and can block in particular the AT₁ R axis. Cabbage contains precursors of sulforaphane, the most active natural activator of Nrf2. Fermented vegetables contain many lactobacilli, which are also potent Nrf2 activators. Three examples are: kimchi in Korea, westernized foods, and the slum paradox. It is proposed that fermented cabbage is a proof-of-concept of dietary manipulations that may enhance Nrf2-associated antioxidant effects, helpful in mitigating COVID-19 severity.

Bowman, S, Casares-de-Cal, MÁ, Alvarez-Dios, J, Gomez Tato, A, Roffey, P, Richardson, A, McNevin, D & Gahan, ME 2021, 'Identification of Bacillus and Yersinia species and hoax agents by protein profiling using microfluidic capillary electrophoresis with peak detection algorithms', Australian Journal of Forensic Sciences, vol. 53, no. 1.
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© 2019, © 2019 Australian Academy of Forensic Sciences. Bacillus anthracis and Yersinia pestis are biological agents that pose an increasing concern to national security if deliberately disseminated. Hoax agents, including suspicious white powders and environmental bacterial species, can also cause disruption. In either scenario it is of high importance to rapidly and accurately identify any suspicious powder as hazardous or hoax. Protein profiling, using microfluidic capillary electrophoresis, provides a rapid (less than 40 minutes), reliable and field-based screening method. Two commonly encountered hoax agents, three Bacillus species (including B. anthracis Sterne strain), two Yersinia species and E. coli were profiled on the Experion™ System (Bio-Rad). Peak detection algorithms were developed for the identification of protein peaks in electropherograms. Boolean logic paths were then employed to predict the electrophoretic pattern of samples. Parameters assessed included variation within and between Experion™ Pro260 chips and the ability to discriminate between samples over time intervals, between operators and between field and laboratory analyses. Classification with optimal Boolean logic paths reported no misclassification with an accuracy of 100% for B. anthracis Sterne strain, B. thuringiensis (powder and culture-based), B. cereus and plain wheat flour. Overall there was 75% correct identification for the eight sample types tested.

Bradfield, LA & Iordanova, MD 2021, 'Threat perception: Fear and the retrorubal field', Current Biology, vol. 31, no. 10, pp. R469-R471.
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A new study has found that neurons within a structure of the rat midbrain known as the retrorubral field show diverse responses to stimuli that signal different levels of threat, as well as a separate pattern of diverse responses to differentially predicted aversive outcomes.

Bradley, DJ, Boada, J, Gladstone, W, Glasby, TM & Gribben, PE 2021, 'Sublethal effects of a rapidly spreading native alga on a key herbivore', Ecology and Evolution.
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Brandis, KJ, Mazumder, D, Gadd, P, Ji, B, Kingsford, RT & Ramp, D 2021, 'Using feathers to map continental‐scale movements of waterbirds and wetland importance', Conservation Letters.
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Brown, AO, Frankham, GJ, Bond, L, Stuart, BH, Johnson, RN & Ueland, M 2021, 'An overview of risk investment in the transnational illegal wildlife trade from stakeholder perspectives', WIREs Forensic Science, vol. 3, no. 2.
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Brown, AO, Frankham, GJ, Stuart, BH & Ueland, M 2021, 'Reptile volatilome profiling optimisation: A pathway towards forensic applications'.
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Burrage, K, Burrage, P & MacNamara, S 2021, 'The reflectionless properties of Toeplitz waves and Hankel waves: An analysis via Bessel functions', Applied Mathematics and Computation, vol. 389.
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© 2020 We study reflectionless properties at the boundary for the wave equation in one space dimension and time, in terms of a well-known matrix that arises from a simple discretisation of space. It is known that all matrix functions of the familiar second difference matrix representing the Laplacian in this setting are the sum of a Toeplitz matrix and a Hankel matrix. The solution to the wave equation is one such matrix function. Here, we study the behaviour of the corresponding waves that we call Toeplitz waves and Hankel waves. We show that these waves can be written as certain linear combinations of even Bessel functions of the first kind. We find exact and explicit formulae for these waves. We also show that the Toeplitz and Hankel waves are reflectionless on even, respectively odd, traversals of the domain. Our analysis naturally suggests a new method of computer simulation that allows control, so that it is possible to choose — in advance — the number of reflections. An attractive result that comes out of our analysis is the appearance of the well-known shift matrix, and also other matrices that might be thought of as Hankel versions of the shift matrix. By revealing the algebraic structure of the solution in terms of shift matrices, we make it clear how the Toeplitz and Hankel waves are indeed reflectionless at the boundary on even or odd traversals. Although the subject of the reflectionless boundary condition has a long history, we believe the point of view that we adopt here in terms of matrix functions is new.

Butterworth, NJ, White, TE, Byrne, PG & Wallman, JF 2021, 'Love at first flight: wing interference patterns are species‐specific and sexually dimorphic in blowflies (Diptera: Calliphoridae)', Journal of Evolutionary Biology.
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Callan, T, Woodcock, S & Huston, WM 2021, 'Ascension of Chlamydia is moderated by uterine peristalsis and the neutrophil response to infection', PLoS Computational Biology, vol. 17, no. 9.
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Chlamydia trachomatis is a common sexually transmitted infection that is associated with a range of serious reproductive tract sequelae including in women Pelvic Inflammatory Disease (PID), tubal factor infertility, and ectopic pregnancy. Ascension of the pathogen beyond the cervix and into the upper reproductive tract is thought to be necessary for these pathologies. However, Chlamydia trachomatis does not encode a mechanism for movement on its genome, and so the processes that facilitate ascension have not been elucidated. Here, we evaluate the factors that may influence chlamydial ascension in women. We constructed a mathematical model based on a set of stochastic dynamics to elucidate the moderating factors that might influence ascension of infections in the first month of an infection. In the simulations conducted from the stochastic model, 36% of infections ascended, but only 9% had more than 1000 bacteria ascend. The results of the simulations indicated that infectious load and the peristaltic contractions moderate ascension and are inter-related in impact. Smaller initial loads were much more likely to ascend. Ascension was found to be dependent on the neutrophil response. Overall, our results indicate that infectious load, menstrual cycle timing, and the neutrophil response are critical factors in chlamydial ascension in women.

Camirand Lemyre, F, Carroll, RJ & Delaigle, A 2021, 'Semiparametric Estimation of the Distribution of Episodically Consumed Foods Measured With Error', Journal of the American Statistical Association.
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© 2020 American Statistical Association. Dietary data collected from 24-hour dietary recalls are observed with significant measurement errors. In the nonparametric curve estimation literature, much of the effort has been devoted to designing methods that are consistent under contamination by noise, and which have been traditionally applied for analyzing those data. However, some foods such as alcohol or fruits are consumed only episodically, and may not be consumed during the day when the 24-hour recall is administered. These so-called excess zeros make existing nonparametric estimators break down, and new techniques need to be developed for such data. We develop two new consistent semiparametric estimators of the distribution of such episodically consumed food data, making parametric assumptions only on some less important parts of the model. We establish its theoretical properties and illustrate the good performance of our fully data-driven method in simulated and real data. Supplementary materials for this article are available online.

Castrogiovanni, P, Sanfilippo, C, Imbesi, R, Maugeri, G, Lo Furno, D, Tibullo, D, Castorina, A, Musumeci, G & Di Rosa, M 2021, 'Brain CHID1 Expression Correlates with NRGN and CALB1 in Healthy Subjects and AD Patients', Cells.
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Chan, SH, Ismail, MH, Tan, CH, Rice, SA & McDougald, D 2021, 'Microbial predation accelerates granulation and modulates microbial community composition', BMC Microbiology, vol. 21, no. 1, pp. 91-91.
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Chan, Y, Mehta, M, Paudel, KR, Madheswaran, T, Panneerselvam, J, Gupta, G, Su, QP, Hansbro, PM, MacLoughlin, R, Dua, K & Chellappan, DK 2021, 'Versatility of liquid crystalline nanoparticles in inflammatory lung diseases.', Nanomedicine (London, England), vol. 16, no. 18, pp. 1545-1548.
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Chan, Y, Ng, SW, Chellappan, DK, Madheswaran, T, Zeeshan, F, Kumar, P, Pillay, V, Gupta, G, Wadhwa, R, Mehta, M, Wark, P, Hsu, A, Hansbro, NG, Hansbro, PM, Dua, K & Panneerselvam, J 2021, 'Celastrol-loaded liquid crystalline nanoparticles as an anti-inflammatory intervention for the treatment of asthma', International Journal of Polymeric Materials and Polymeric Biomaterials.
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The present study aimed to formulate celastrol into liquid crystalline nanoparticles (LCNPs) through ultrasonication to enhance its therapeutic efficacy in the treatment of asthma. The physiochemical characteristics, in-vitro release studies were determined along with molecular simulations. Celastrol-loaded LCNPs showed the mean particle size of 194.1 ± 9.78 nm and high entrapment efficiency of 99.1 ± 0.02%. TEM revealed cubical-like structure of the nanoparticles and in-vitro release study demonstrated sustained drug release. They also demonstrated significant activity in reducing IL-1β production, when evaluated using immortalized human bronchial epithelial cell lines (BCi-NS1.1), that may help alleviate the symptoms of asthma.

Chan, Y, Prasher, P, Löbenberg, R, Gupta, G, Singh, SK, Oliver, BG, Chellappan, DK & Dua, K 2021, 'Applications and practice of advanced drug delivery systems for targeting Toll-like receptors in pulmonary diseases.', Nanomedicine (London, England), vol. 16, no. 10, pp. 783-786.
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Chellappan, DK, Dharwal, V, Paudel, KR, Jha, NK, MacLoughlin, R, Oliver, BG, M Hansbro, P & Dua, K 2021, 'Mitochondrial dysfunctions associated with chronic respiratory diseases and their targeted therapies: an update.', Future medicinal chemistry.
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Chen, C, Li, S, Notten, PHL, Zhang, Y, Hao, Q, Zhang, X & Lei, W 2021, '3D Printed Lithium-Metal Full Batteries Based on a High-Performance Three-Dimensional Anode Current Collector', ACS Applied Materials and Interfaces.
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A three-dimensional (3D) printing method has been developed for preparing a lithium anode base on 3D-structured copper mesh current collectors. Through in situ observations and computer simulations, the deposition behavior and mechanism of lithium ions in the 3D copper mesh current collector are clarified. Benefiting from the characteristics that the large pores can transport electrolyte and provide space for dendrite growth, and the small holes guide the deposition of dendrites, the 3D Cu mesh anode exhibits excellent deposition and stripping capability (50 mAh cm-2), high-rate capability (50 mA cm-2), and a long-term stable cycle (1000 h). A full lithium battery with a LiFePO4 cathode based on this anode exhibits a good cycle life. Moreover, a 3D fully printed lithium-sulfur battery with a 3D printed high-load sulfur cathode can easily charge mobile phones and light up 51 LED indicators, which indicates the great potential for the practicability of lithium-metal batteries with the characteristic of high energy densities. Most importantly, this unique and simple strategy is also able to solve the dendrite problem of other secondary metal batteries. Furthermore, this method has great potential in the continuous mass production of electrodes.

Chen, C, Liu, B, Liu, Y, Liao, J, Shan, X, Wang, F & Jin, D 2021, 'Heterochromatic Nonlinear Optical Responses in Upconversion Nanoparticles for Super‐Resolution Nanoscopy', Advanced Materials.
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Chen, C, Liu, B, Liu, Y, Liao, J, Shan, X, Wang, F & Jin, D 2021, 'Upconversion Nanoparticles: Heterochromatic Nonlinear Optical Responses in Upconversion Nanoparticles for Super‐Resolution Nanoscopy (Adv. Mater. 23/2021)', Advanced Materials.
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Chen, C-H, Chao, K-M, Hwang, FJ, Han, C & Pu, L 2021, 'Editorial: Machine Learning Methods for Distributed Sensor Network Applications', International Journal of Distributed Sensor Networks, vol. 17, no. 2, pp. 155014772199288-155014772199288.
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Chen, H, Wang, B, Li, G, Steele, JR, Stayte, S, Vissel, B, Chan, YL, Yi, C, Saad, S, Machaalani, R & Oliver, BG 2021, 'Brain health is independently impaired by E-vaping and high-fat diet', BRAIN BEHAVIOR AND IMMUNITY, vol. 92, pp. 57-66.
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Chen, S-Y, Beretta, M, Alexopoulos, SJ, Shah, DP, Olzomer, EM, Hargett, SR, Childress, ES, Salamoun, JM, Aleksovska, I, Roseblade, A, Cranfield, C, Rawling, T, Quinlan, KGR, Morris, MJ, Tucker, SP, Santos, WL & Hoehn, KL 2021, 'Mitochondrial uncoupler SHC517 reverses obesity in mice without affecting food intake', METABOLISM-CLINICAL AND EXPERIMENTAL, vol. 117.
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Chen, X, Yang, L, Liang, S, Dang, P, Jin, D, Cheng, Z & Lin, J 2021, 'Entropy-driven strand displacement reaction for ultrasensitive detection of circulating tumor DNA based on upconversion and Fe3O4 nanocrystals', Science China Materials.
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Chen, Y, Xu, X, Li, C, Bendavid, A, Westerhausen, MT, Bradac, C, Toth, M, Aharonovich, I & Tran, TT 2021, 'Bottom‐Up Synthesis of Hexagonal Boron Nitride Nanoparticles with Intensity‐Stabilized Quantum Emitters', Small.
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Cheng, Y, Zheng, R, Wu, X, Xu, K, Song, P, Wang, Y, Yan, J, Chen, R, Li, X & Zhang, H 2021, 'Thylakoid Membranes with Unique Photosystems Used to Simultaneously Produce Self-Supplying Oxygen and Singlet Oxygen for Hypoxic Tumor Therapy', ADVANCED HEALTHCARE MATERIALS, vol. 10, no. 6.
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Chong, H, Tan, C, Fang, S, Chen, X, Tao, Q, Yuan, X, Li, J, Zhai, C, Fei, C, Yang, D, Fan, H, Shao, H, Qin, A, Wang, G, Shi, Z, Z'hang, T, Yao, H, Li, H & Wang, C 2021, 'BODIPY-Appended Pt(II) Complexes with High Toxicities and Anti-chemoresistance Performances in a Cisplatin Resistant In Vivo Model', INORGANIC CHEMISTRY, vol. 60, no. 13, pp. 10047-10055.
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Chong, H, Zhang, G, Wu, Y, Xu, B, Wang, G & Wang, C 2021, 'Enantioselective recognition of amino acid based on electrochemical deposition and X-ray diffraction technology', JOURNAL OF INORGANIC BIOCHEMISTRY, vol. 218.
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Chong, WC, Shastri, MD, Peterson, GM, Patel, RP, Pathinayake, PS, Dua, K, Hansbro, NG, Hsu, AC, Wark, PA, Shukla, SD, Johansen, MD, Schroder, K & Hansbro, PM 2021, 'The complex interplay between endoplasmic reticulum stress and the NLRP3 inflammasome: a potential therapeutic target for inflammatory disorders', Clinical & Translational Immunology.
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Chotithammakul, S, Cortie, MB & Pissuwan, D 2021, 'Comparison of Single- and Mixed-Sized Gold Nanoparticles on Lateral Flow Assay for Albumin Detection.', Biosensors, vol. 11, no. 7.
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The sensitivity and reproducibility of the lateral flow assay can be influenced by multiple factors, such as the size of gold nanoparticles (GNPs) employed. Here, we evaluated the analytical performance of single-sized and mixed-sized GNPs using a simple lateral flow assay (LFA) platform. This platform was used as a model assay to diagnose albumin levels and demonstrate the analytical performance of single-sized and mixed-sized GNPs in LFA tests. Two sizes of GNPs@anti-bovine serum albumin (BSA) conjugate proteins were mixed at different ratios. The unique optical properties of the GNPs induced a distinguishing color-shedding effect on the single- and mixed-sized GNPs@anti-BSA conjugates interacting with the target analyte BSA spotted on the test line. The use of mixed-sized GNPs@anti-BSA conjugates enhanced signal relative to the 20 nm GNPs, and provided superior stability compared with solely employing the large GNPs (50 nm). The proposed platform in this study could provide an efficient BSA detection mechanism that can be utilized as a model biomarker for confronting chronic kidney disease.

Chu, Z, Gao, X, Wang, C, Wang, T & Wang, G 2021, 'Metal-organic frameworks as separators and electrolytes for lithium-sulfur batteries', JOURNAL OF MATERIALS CHEMISTRY A, vol. 9, no. 12, pp. 7301-7316.
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Clarke, C, Singh, M, Tawfik, SA, Xu, X, Spencer, MJS, Ramanathan, R, Reineck, P, Bansal, V & Ton-That, C 2021, 'Mono- to few-layer non-van der Waals 2D lanthanide-doped NaYF(4)nanosheets with upconversion luminescence', 2D MATERIALS, vol. 8, no. 1.
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Clases, D, Ueland, M, de Vega, RG, Doble, P & Proefrock, D 2021, 'Quantitative speciation of volatile sulphur compounds from human cadavers by GC-ICP-MS', TALANTA, vol. 221.
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Coignard, J, Lush, M, Beesley, J, O’Mara, TA, Dennis, J, Tyrer, JP, Barnes, DR, McGuffog, L, Leslie, G, Bolla, MK, Adank, MA, Agata, S, Ahearn, T, Aittomäki, K, Andrulis, IL, Anton-Culver, H, Arndt, V, Arnold, N, Aronson, KJ, Arun, BK, Augustinsson, A, Azzollini, J, Barrowdale, D, Baynes, C, Becher, H, Bermisheva, M, Bernstein, L, Białkowska, K, Blomqvist, C, Bojesen, SE, Bonanni, B, Borg, A, Brauch, H, Brenner, H, Burwinkel, B, Buys, SS, Caldés, T, Caligo, MA, Campa, D, Carter, BD, Castelao, JE, Chang-Claude, J, Chanock, SJ, Chung, WK, Claes, KBM, Clarke, CL, Bertrand, O, Caputo, S, Dupré, A, Le Mentec, M, Belotti, M, Birot, AM, Buecher, B, Fourme, E, Gauthier-Villars, M, Golmard, L, Houdayer, C, Moncoutier, V, de Pauw, A, Saule, C, Sinilnikova, O, Mazoyer, S, Damiola, F, Barjhoux, L, Verny-Pierre, C, Léone, M, Boutry-Kryza, N, Calender, A, Giraud, S, Caron, O, Guillaud-Bataille, M, Bressac-de-Paillerets, B, Bignon, YJ, Uhrhammer, N, Lasset, C, Bonadona, V, Berthet, P, Vaur, D, Castera, L, Noguchi, T, Popovici, C, Sobol, H, Bourdon, V, Noguchi, T, Remenieras, A, Noguès, C, Coupier, I, Pujol, P, Dumont, A, Révillion, F, Adenis, C, Muller, D, Barouk-Simonet, E, Bonnet, F, Bubien, V, Sevenet, N, Longy, M, Toulas, C, Guimbaud, R & Gladieff, L 2021, 'A case-only study to identify genetic modifiers of breast cancer risk for BRCA1/BRCA2 mutation carriers', Nature Communications, vol. 12, no. 1.
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Breast cancer (BC) risk for BRCA1 and BRCA2 mutation carriers varies by genetic and familial factors. About 50 common variants have been shown to modify BC risk for mutation carriers. All but three, were identified in general population studies. Other mutation carrier-specific susceptibility variants may exist but studies of mutation carriers have so far been underpowered. We conduct a novel case-only genome-wide association study comparing genotype frequencies between 60,212 general population BC cases and 13,007 cases with BRCA1 or BRCA2 mutations. We identify robust novel associations for 2 variants with BC for BRCA1 and 3 for BRCA2 mutation carriers, P < 10−8, at 5 loci, which are not associated with risk in the general population. They include rs60882887 at 11p11.2 where MADD, SP11 and EIF1, genes previously implicated in BC biology, are predicted as potential targets. These findings will contribute towards customising BC polygenic risk scores for BRCA1 and BRCA2 mutation carriers.

Commault, AS, Kuzhiumparambil, U, Herdean, A, Fabris, M, Jaramillo-Madrid, AC, Abbriano, RM, Ralph, PJ & Pernice, M 2021, 'Methyl jasmonate and methyl-β-cyclodextrin individually boost triterpenoid biosynthesis in chlamydomonas reinhardtii uvm4', Pharmaceuticals, vol. 14, no. 2, pp. 1-12.
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© 2021 by the authors. Licensee MDPI, Basel, Switzerland. The commercialisation of valuable plant triterpenoids faces major challenges, including low abundance in natural hosts and costly downstream purification procedures. Endeavours to produce these compounds at industrial scale using microbial systems are gaining attention. Here, we report on a strategy to enrich the biomass of the biotechnologically-relevant Chlamydomonas reinhardtii strain UVM4 with valuable triterpenes, such as squalene and (S)-2,3-epoxysqualene. C. reinhardtii UVM4 was subjected to the elicitor compounds methyl jasmonate (MeJA) and methyl-β-cyclodextrine (MβCD) to increase triterpene yields. MeJA treatment triggered oxidative stress, arrested growth, and altered the photosynthetic activity of the cells, while increasing squalene, (S)-2,3-epoxysqualene, and cycloartenol contents. Applying MβCD to cultures of C. reinhardtii lead to the sequestration of the two main sterols (ergosterol and 7-dehydroporiferasterol) into the growth medium and the intracellular accumulation of the intermediate cycloartenol, without compromising cell growth. When MβCD was applied in combination with MeJA, it counteracted the negative effects of MeJA on cell growth and physiology, but no synergistic effect on triterpene yield was observed. Together, our findings provide strategies for the triterpene enrichment of microalgal biomass and medium.

Coni, EOC, Nagelkerken, I, Ferreira, CM, Connell, SD & Booth, DJ 2021, 'Ocean acidification may slow the pace of tropicalization of temperate fish communities', Nature Climate Change.
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Cowan, AE, Jun, S, Tooze, JA, Dodd, KW, Gahche, JJ, Eicher-Miller, HA, Guenther, PM, Dwyer, JT, Potischman, N, Bhadra, A, Carroll, RJ & Bailey, RL 2021, 'A narrative review of nutrient based indexes to assess diet quality and the proposed total nutrient index that reflects total dietary exposures.', Critical reviews in food science and nutrition, pp. 1-11.
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A priori dietary indices provide a standardized, reproducible way to evaluate adherence to dietary recommendations across different populations. Existing nutrient-based indices were developed to reflect food/beverage intake; however, given the high prevalence of dietary supplement (DS) use and its potentially large contribution to nutrient intakes for those that use them, exposure classification without accounting for DS is incomplete. The purpose of this article is to review existing nutrient-based indices and describe the development of the Total Nutrient Index (TNI), an index developed to capture usual intakes from all sources of under-consumed micronutrients among the U.S. population. The TNI assesses U.S. adults' total nutrient intakes relative to recommended nutrient standards for eight under-consumed micronutrients identified by the Dietary Guidelines for Americans: calcium, magnesium, potassium, choline, and vitamins A, C, D, E. The TNI is scored from 0 to 100 (truncated at 100). The mean TNI score of U.S. adults (≥19 y; n = 9,954) based on dietary data from NHANES 2011-2014, was 75.4; the mean score for the index ignoring DS contributions was only 69.0 (t-test; p < 0.001). The TNI extends existing measures of diet quality by including nutrient intakes from all sources and was developed for research, monitoring, and policy purposes.

Cranfield, C, Whelan, D, Cox, C, Shearwin, K, Ho, J, Allen, T, Shibuya, R, Hibino, E, Hayashi, K, Dos Remedios, C & Li, A 2021, 'Announcing the call for the Special Issue on "The Australian Society for Biophysics (ASB) - 2021 Meeting".', Biophysical reviews, pp. 1-2.
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This Commentary describes a call for submissions for the upcoming Special Issue focused on the research topics presented at the Australian Society of Biophysics (ASB) in 2020 and 2021. Submissions from past and present ASB members who could not attend these meetings are also welcome as contributions to this special issue.

Cwiklinski, K, Robinson, MW, Donnelly, S & Dalton, JP 2021, 'Complementary transcriptomic and proteomic analyses reveal the cellular and molecular processes that drive growth and development of Fasciola hepatica in the host liver', BMC Genomics.
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Cziesielski, MJ, Duarte, CM, Aalismail, N, Al-Hafedh, Y, Anton, A, Baalkhuyur, F, Baker, AC, Balke, T, Baums, IB, Berumen, M, Chalastani, VI, Cornwell, B, Daffonchio, D, Diele, K, Farooq, E, Gattuso, J-P, He, S, Lovelock, CE, Mcleod, E, Macreadie, PI, Marba, N, Martin, C, Muniz-Barreto, M, Kadinijappali, KP, Prihartato, P, Rabaoui, L, Saderne, V, Schmidt-Roach, S, Suggett, DJ, Sweet, M, Statton, J, Teicher, S, Trevathan-Tackett, SM, Joydas, TV, Yahya, R & Aranda, M 2021, 'Investing in Blue Natural Capital to Secure a Future for the Red Sea Ecosystems', Frontiers in Marine Science.
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Dadd-Daigle, P, Kirkby, K, Chowdhury, PR, Labbate, M & Chapman, TA 2021, 'The Verticillium wilt problem in Australian cotton', Australasian Plant Pathology, vol. 50, no. 2, pp. 129-135.
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© 2021, Australasian Plant Pathology Society Inc. Verticillium dahliae is a soil-borne phytopathogen and the causal agent of Verticillium wilt. It affects many agriculturally important crops around the world, including cotton. In Australia, the billion-dollar cotton industry is increasingly impacted by Verticillium wilt. Internationally it has been reported that the defoliating V. dahliae Vegetative Compatibility Group (VCG) 1A causes severe damage to cotton. In Australia however, the non-defoliating VCG2A is causing more severe damage to crops in fields than the defoliating VCG1A. This review examines the current research to understand the Australian V. dahliae situation, including current classification systems, genetic analyses and management strategies. It appears that virulence cannot be defined solely by VCG in Australian Verticillium dahliae isolates causing disease in cotton, and that the industry must continually adapt their practices in order to keep the disease under control.

Dawson, BM, Wallman, JF, Evans, MJ & Barton, PS 2021, 'Is Resource Change a Useful Predictor of Carrion Insect Succession on Pigs and Humans?', Journal of medical entomology.
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Carrion is a dynamic and nutrient-rich resource that attracts numerous insect species that undergo succession due to the rapid change in the carrion resource. Despite this process being well-understood, few studies have examined resource change as a driver of carrion insect succession, and instead have focused on the effects of time per se, or on coarse, qualitative measures such as decay stage. Here we report on three field succession experiments using pig carcasses and human cadavers encompassing two winters and one summer. We quantified the effects of resource change (measured as total body score, TBS), carrion type, initial carrion mass, ambient temperature, and season on insect species richness and community composition. We found that all variables had an effect on different taxonomic or trophic components of the insect community composition, with the exception of initial carrion mass which had no effect. We found significant positive effects of TBS on beetle species richness and composition, while fly species richness was not significantly affected by TBS, but was by ambient temperature. TBS had a significant positive effect on all trophic groups, while ambient temperature also had a significant positive effect on the necrophages and predator/parasitoids. Our study indicates that resource change, as indicated by TBS, is an important driver of carrion insect species turnover and succession on carrion, and that TBS can provide information about insect ecological patterns on carrion that other temporal measures of change cannot.

de Silva, R, Abdul-Halim, M, Pittrich, D, Brown, H, Pohlschroder, M & Duggin, IG 2021, 'Improved growth and morphological plasticity of Haloferax volcanii', Microbiology, vol. 167, no. 2.
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Abstract Some microbes display pleomorphism, showing variable cell shapes in a single culture, whereas others differentiate to adapt to changed environmental conditions. The pleomorphic archaeon Haloferax volcanii commonly forms discoid-shaped (‘plate’) cells in culture, but may also be present as rods, and can develop into motile rods in soft agar, or longer filaments in certain biofilms. Here we report improvement of H. volcanii growth in both semi-defined and complex media by supplementing with eight trace-element micronutrients. With these supplemented media, transient development of plate cells into uniformly-shaped rods was clearly observed during the early log phase of growth; cells then reverted to plates for the late log and stationary phases. In media prepared with high-purity reagents, without supplemental trace elements, rods and other complex elongated morphologies (‘pleomorphic rods’) were observed at all growth stages of the culture; the highly-elongated cells sometimes displayed a substantial tubule at one or less frequently both poles, as well as unusual tapered and highly-curved forms. Polar tubules were observed forming by initial mid-cell narrowing or tubulation, causing a dumbbell-like shape, followed by cell division towards one end. Formation of the uniform early-log rods, as well as the pleomorphic rods and tubules were dependent on the function of the tubulin-like cytoskeletal protein, CetZ1. Our results have revealed the remarkable morphological plasticity of H. volcanii , and shown that its changes in cell shape occur in response to multiple signals. Importance Microbes can show morphological responses to changed environmental conditions, which are important for their survival in a wide variety of environments. These conditions and the specific role of such morphological changes are poorly defined. Here we describe improved growth media for the model archaeon Haloferax volcanii , and the identification and characterization of environmen...

de Silva, RT, Abdul-Halim, MF, Pittrich, DA, Brown, HJ, Pohlschroder, M & Duggin, IG 2021, 'Improved growth and morphological plasticity of Haloferax volcanii.', Microbiology, vol. 167, no. 2.
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de Vega, RG, Goyen, S, Lockwood, TE, Doble, PA, Camp, EF & Clases, D 2021, 'Characterisation of microplastics and unicellular algae in seawater by targeting carbon via single particle and single cell ICP-MS', ANALYTICA CHIMICA ACTA, vol. 1174.
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Dedousis-Wallace, A, Drysdale, SA, McAloon, J & Ollendick, TH 2021, 'Parental and Familial Predictors and Moderators of Parent Management Treatment Programs for Conduct Problems in Youth.', Clinical child and family psychology review.
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Despite the established efficacy of Parent Management Training (PMT) for conduct problems in youth, evidence suggests that up to half of all treated youth still display clinical levels of disruptive behavior post-treatment. The reasons for these unsatisfactory outcomes are poorly understood. The aim of the present review was to provide an updated analysis of studies from the past 15 years that examined parental and familial predictors and moderators of improvement in PMT for conduct problems. A systematic literature review of indicated prevention (children with conduct problem symptoms) and intervention (children with clinical diagnoses) studies published between 2004 and 2019 was conducted. This 15-year time period was examined since the last systematic reviews were reported in 2006 and summarized studies completed through mid-2004 (see Lundahl et al. in Clin Psychol Rev 26(1):86-104, 2006; Reyno and McGrath in J Child Psychol Psychiatry 47(1):99-111, 2006). Risk of bias indices was also computed (see Higgins et al. in Revised Cochrane risk of bias tool for randomized trials (RoB 2.0), University of Bristol, Bristol, 2016) in our review. A total of 21 studies met inclusion criteria. Results indicated that a positive parent-child relationship was most strongly associated with better outcomes; however, little additional consistency in findings was evident. Future PMT research should routinely examine predictors and moderators that are both conceptually and empirically associated with treatment outcomes. This would further our understanding of factors that are associated with poorer treatment outcome and inform the development of treatment components or modes of delivery that might likely enhance evidence-based treatments and our clinical science. Protocol Registration Number: PROSPERO CRD42017058996.

Deng, K, Zhang, X, Liu, Y, Zhang, L, Wang, G, Feng, M, Oliver, BG, Wang, L, Hansbro, PM, Qin, L, Xie, M, Chen, ZH, Simpson, J, Zhang, J, Li, WM, Wang, G & Gibson, PG 2021, 'Heterogeneity of Paucigranulocytic Asthma: A Prospective Cohort Study with Hierarchical Cluster Analysis', JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY-IN PRACTICE, vol. 9, no. 6, pp. 2344-2355.
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Deng, ZX, Tao, JW, Zhang, W, Mu, HJ, Wu, HJ, Wang, YB, Xu, XX & Zheng, W 2021, 'Effect of protein adsorption on electrospun hemoglobin/gelatin-MWCNTs microbelts modified electrode: Toward electrochemical measurement of hydrogen peroxide', MATERIALS CHEMISTRY AND PHYSICS, vol. 257.
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Desbiens, AA, Roff, G, Robbins, WD, Taylor, BM, Castro‐Sanguino, C, Dempsey, A & Mumby, PJ 2021, 'Revisiting the paradigm of shark‐driven trophic cascades in coral reef ecosystems', Ecology.
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Dey, A, Ni, Z, Johnson, MS & Sedger, LM 2021, 'A multi-colour confocal microscopy method for identifying and enumerating macrophage subtypes and adherent cells in the stromal vascular fraction of human adipose', Journal of Immunological Methods, vol. 491.
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© 2021 This study examines leukocytes present in lymphoedema (LE) adipose tissue (AT) by multi-colour confocal microscopy. LE AT, collected by liposuction surgery, was digested with collagenase to separate adipocytes from other tissue cells, comprising blood and lymphatic endothelial cells, fibroblasts, and all vessel- and tissue-resident leukocytes - the stromal vascular fraction (SVF). SVF cells were activated with phorbol 12-myristate 13-acetate (PMA) and ionomycin, adding Brefeldin-A to prevent cytokine secretion during the final 4 hours. Cells were incubated with CD11b-FITC and CD40-APC (M1 MØ)‚ or CD206-APC (M2 MØ) specific antibodies, fixed, permeabilised, then incubated with either (1) anti-TNF-PE, (2) anti- IL-1β-PE, (3) anti-IL-6-PE, (4) anti-IL-4-PE, (5) anti-TGFβ-PE or (6) isotype-IgG-PE (control), and stained with Hoechst 33342, preserved in permanent mounting media and examined by confocal microscopy. The FITC, PE and APC fluorescence channels were set to achieve minimal cross-channel emission using single-colour controls and voltages set for optimal detection by thresholding on isotype-IgG stained activated cells. Finally, transmission and z-stack images were captured. Cells were analysed as regions of interest (ROI) based on Hoechst-33342 then enumerated as FITC+, FITC+APC+ or FITC+APC+PE+ using an ImageJ script and exported into Excel. This permitted the examination of >9000 SVF cells individually, per LE sample. This method allows for the analysis of a high number of heterogeneous cells defined into any subtype or combination by the investigators' choice of surface and intracellular expression profiles. Fibroblasts, or other cytokine producing cells, can also be analysed by using other antibodies, and the cell count data can be correlated with any clinical or laboratory data.

Di, X, Wang, D, Zhou, J, Zhang, L, Stenzel, MH, Su, QP & Jin, D 2021, 'Quantitatively Monitoring In Situ Mitochondrial Thermal Dynamics by Upconversion Nanoparticles.', Nano Letters.
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Dickson, K-A, Xie, T, Evenhuis, C, Ma, Y & Marsh, DJ 2021, 'PARP Inhibitors Display Differential Efficacy in Models of BRCA Mutant High-Grade Serous Ovarian Cancer', International Journal of Molecular Sciences.
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Dikshit, A, Pradhan, B & Huete, A 2021, 'An improved SPEI drought forecasting approach using the long short-term memory neural network', JOURNAL OF ENVIRONMENTAL MANAGEMENT, vol. 283.
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Ding, L, Zhou, J, Fu, Q, Bao, G, Liu, Y & Jin, D 2021, 'Triplet Fusion Upconversion with Oxygen Resistance in Aqueous Media', ANALYTICAL CHEMISTRY, vol. 93, no. 10, pp. 4641-4646.
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Dirar, AI, Adhikari-Devkota, A, Kunwar, RM, Paudel, KR, Belwal, T, Gupta, G, Chellappan, DK, Hansbro, PM, Dua, K & Devkota, HP 2021, 'Genus Blepharis (Acanthaceae): A review of ethnomedicinally used species, and their phytochemistry and pharmacological activities.', Journal of ethnopharmacology, vol. 265, pp. 113255-113255.
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Ethnopharmacological relevance

Blepharis is an Afro-Asiatic genus belonging to the family Acanthaceae. It comprises about 126 species that occur in arid and semi-arid habitats. Some species of Blepharis are used in traditional medicines in different countries mainly for their anti-inflammatory, wound healing activities along with treatment of gastrointestinal disorders and bone fractures.

Aim of the review

The present review aims to collate and analyze the available data and information on distribution, traditional uses, chemical constituents and pharmacological activities of Blepharis.

Methods

Scientific information of genus Blepharis was retrieved from the online bibliographic databases such as MEDLINE/PubMed, SciFinder, Web of Science and Google Scholar and secondary resources including books and proceedings.

Results

Seven species of Blepharis were found to be reported frequently as useful in folklore in African and Asian countries. B. maderaspatensis was found to be widely used in Indian traditional medicines whereas the B. ciliaris and B. edulis were common in folklore of Egypt, Jordan, and Arabia. Active phytochemicals of Blepharis are flavonoids from B. ciliaris, alkaloids from B. sindica, phenolic acid derivatives, and phytosterols, and derivatives of hydroxamic acids from B. edulis resulted in possessing diverse biological properties such as anti-microbial, anti-inflammatory, and anti-cancer.

Conclusions

Various species of Blepharis were found to be used in traditional medicine systems in African and Asian countries. Few of these species were studied for their bioactive chemical constituents however the activity guided isolation studies are not performed. Similarly, detailed pharmacological studies in animal models to explore their mechanism of action are also not reported. Future studies should focus on these aspects related to the medicinally used species of Blepharis. The detailed and comprehensive comparative analy...

Doble, PA, De Vega, RG, Bishop, DP, Hare, DJ & Clases, D 2021, 'Laser Ablation-Inductively Coupled Plasma-Mass Spectrometry Imaging in Biology', Chemical Reviews.
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Elemental imaging gives insight into the fundamental chemical makeup of living organisms. Every cell on Earth is comprised of a complex and dynamic mixture of the chemical elements that define structure and function. Many disease states feature a disturbance in elemental homeostasis, and understanding how, and most importantly where, has driven the development of laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) as the principal elemental imaging technique for biologists. This review provides an outline of ICP-MS technology, laser ablation cell designs, imaging workflows, and methods of quantification. Detailed examples of imaging applications including analyses of cancers, elemental uptake and accumulation, plant bioimaging, nanomaterials in the environment, and exposure science and neuroscience are presented and discussed. Recent incorporation of immunohistochemical workflows for imaging biomolecules, complementary and multimodal imaging techniques, and image processing methods is also reviewed.

Dominici, L, Fleck, R, Gill, RL, Pettit, TJ, Irga, PJ, Comino, E & Torpy, FR 2021, 'Analysis of lighting conditions of indoor living walls: Effects on CO2 removal', Journal of Building Engineering, vol. 44.
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Vertical greening systems, or living walls, are becoming increasingly used indoors for improving the sustainability of buildings, including for the mitigation of excess CO2 levels, derived from human respiration. However, light provision within indoor environments is often insufficient for the efficient functioning of many plant species, leading to low photosynthetic CO2 removal rates, and the need for supplementary light sources. In this study, we investigated the performance of supplementary lighting employed for indoor living wall systems, and whether optimised lighting conditions could lead to improved CO2 removal. In situ trials with several medium-large indoor living walls were performed to sample the lighting scenarios currently employed. We concluded that the majority of plants in existing systems were exposed to suboptimal lighting and will have a net-zero CO2 removal efficiency. Sealed chamber experiments using two common living wall plant species were conducted to explore the effect of varying lighting conditions on CO2 removal efficiency. Comparisons on optimal and “best case” in situ conditions were carried out, showing that CO2 removal efficiency was significantly correlated with both leaf and stem angles, which suggest phototropism may influence in situ CO2 removal. After a ten-day experimental period, the highest CO2 removal efficiency for both test plant species was observed at 200 μmol m−2 s−1 light flux density (~10500 lux) at 15° from the vertical growing surface. Our results indicate that most current lighting systems are inadequate for healthy plant photosynthesis and CO2 removal, and that modified lighting systems could improve this performance. The estimation of the CO2 removal ability of a 5 m2 passive living wall decreases from an ACH of 0.21 h−1, achieved in an optimal light exposure condition, to only 0.03 h−1 when plants are exposed to sub-optimal conditions. To reduce maintenance costs, technical guidelines for indoor living wall lig...

Donnelly, S & Tran, N 2021, 'Commandeering the mammalian Ago2 miRNA network: a newly discovered mechanism of helminth immunomodulation', Trends in Parasitology.
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MicroRNAs (miRNAs) are a class of noncoding RNAs that contribute to a broad range of biological processes through post-transcriptional regulation of gene expression. Helminths exploit this system to target mammalian gene expression, to modulate the host immune response. Recent discoveries have shed new light on the mechanisms involved.

Douraghi, M, Aris, P, To, J, Myers, GSA & Hamidian, M 2021, 'Two carbapenem-resistant ST1:ST231:KL1:OCL1 Acinetobacter baumannii strains recovered in Tehran, Iran, carry AbaR31 in the chromosome and AbaR4 and TnaphA6 in a RepAci6 plasmid', JAC-Antimicrobial Resistance.
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Ellis, J, Barratt, J, Kaufer, A, Pearn, L, Armstrong, B, Johnson, M, Park, Y, Downey, L, Cao, M, Neill, L, Lee, R, Ellis, B, Tyler, K, Lun, Z-R & Stark, D 2021, 'A new subspecies of Trypanosoma cyclops found in the Australian terrestrial leech Chtonobdella bilineata.', Parasitology.
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Falbo, P, Hinz, J, Leelasilapasart, P & Pelizzari, C 2021, 'A Computational Approach to Sequential Decision Optimization in Energy Storage and Trading', Journal of Risk and Financial Management, vol. 14, no. 6, pp. 1-22.
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Due to recent technical progress, battery energy storages are becoming a viable option in the power sector. Their optimal operational management focuses on load shift and shaving of price spikes. However, this requires optimally responding to electricity demand, intermittent generation, and volatile electricity prices. More importantly, such optimization must take into account the so-called deep discharge costs, which have a significant impact on battery lifespan. We present a solution to a class of stochastic optimal control problems associated with these applications. Our numerical techniques are based on efficient algorithms which deliver a guaranteed accuracy

Fan, L, Guo, Z, Zhao, D, Zhao, C, Lu, X, Chen, A, Yin, X, Zhang, Y, Sun, B & Zhang, N 2021, 'Stable and Dendrite‐Free Lithium Metal Anodes Enabled by Ionic/Electronic Li2S/Mo Interlayer', Advanced Energy and Sustainability Research.
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Fang, G, Lu, H, Aboulkheyr Es, H, Wang, D, Liu, Y, Warkiani, ME, Lin, G & Jin, D 2021, 'Unidirectional intercellular communication on a microfluidic chip', Biosensors and Bioelectronics, vol. 175.

Fang, G, Lu, H, Rodriguez de la Fuente, L, Law, AMK, Lin, G, Jin, D & Gallego-Ortega, D 2021, 'Mammary Tumor Organoid Culture in Non-Adhesive Alginate for Luminal Mechanics and High-Throughput Drug Screening', Advanced Science.
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Mammary tumor organoids have become a promising in vitro model for drug screening and personalized medicine. However, the dependency on the basement membrane extract (BME) as the growth matrices limits their comprehensive application. In this work, mouse mammary tumor organoids are established by encapsulating tumor pieces in non-adhesive alginate. High-throughput generation of organoids in alginate microbeads is achieved utilizing microfluidic droplet technology. Tumor pieces within the alginate microbeads developed both luminal- and solid-like structures and displayed a high similarity to the original fresh tumor in cellular phenotypes and lineages. The mechanical forces of the luminal organoids in the alginate capsules are analyzed with the theory of the thick-wall pressure vessel (TWPV) model. The luminal pressure of the organoids increase with the lumen growth and can reach 2 kPa after two weeks’ culture. Finally, the mammary tumor organoids are treated with doxorubicin and latrunculin A to evaluate their application as a drug screening platform. It is found that the drug response is related to the luminal size and pressures of organoids. This high-throughput culture for mammary tumor organoids may present a promising tool for preclinical drug target validation and personalized medicine.

Farrell, LJ, Miyamoto, T, Donovan, CL, Waters, AM, Krisch, KA & Ollendick, TH 2021, 'Virtual Reality One-Session Treatment of Child-Specific Phobia of Dogs: A Controlled, Multiple Baseline Case Series.', Behavior therapy, vol. 52, no. 2, pp. 478-491.
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Specific phobia (SP) typically onsets in childhood and frequently predicts other mental health disorders later in life. Fortunately, childhood SP can be effectively treated with cognitive behavior therapy (CBT), including the exposure-based one-session treatment (OST) approach. Despite empirical support for CBT and OST, clinicians, for various reasons, frequently fail to implement exposure-based therapy in routine clinical practice, including perceived difficulties in implementing exposure. Virtual reality (VR) exposure therapy may overcome some of these challenges and provides an alternative modality of therapy. This preliminary study examined the efficacy of VR OST for 8 children with a SP of dogs (aged 8-12 years) (M = age 10.25; SD = 2.11) using a multiple-baseline controlled case series. Following a stable baseline period of either 2, 3, or 4 weeks, it was expected that specific phobia severity would significantly decline after VR OST and remain improved over the 3-week maintenance phase. Assessments were conducted posttreatment and at 1-month follow up (study end-point). It was found that phobia symptoms remained relatively stable across the baselines, with significant reductions from pretreatment to posttreatment and to follow-up on clinician severity ratings (pre- to post- g = 1.12; pre- to follow-up g = 2.40), target symptom ratings (g = 1.14; 1.29), and behavioral avoidance (g = -1.27; -1.96). The treatment was also associated with clinically significant outcomes, whereby at one-month follow up, 75% of children were considered "recovered" and 88% completed the BAT (interacted with their feared stimuli). This study provides support for the effectiveness of VR OST.

Feng, M, Zhang, X, Wu, WW, Chen, ZH, Oliver, BG, McDonald, VM, Zhang, HP, Xie, M, Qin, L, Zhang, J, Wang, L, Li, WM, Wang, G & Gibson, PG 2021, 'Clinical and Inflammatory Features of Exacerbation-Prone Asthma: A Cross-Sectional Study Using Multidimensional Assessment.', Respiration; international review of thoracic diseases, pp. 1-13.
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Background

Reducing asthma exacerbations is a major target of current clinical guidelines, but identifying features of exacerbation-prone asthma (EPA) using multidimensional assessment (MDA) is lacking.

Objective

To systemically explore the clinical and inflammatory features of adults with EPA in a Chinese population.

Methods

We designed a cross-sectional study using the Severe Asthma Web-based Database from the Australasian Severe Asthma Network (ASAN). Eligible Chinese adults with asthma (n = 546) were assessed using MDA. We stratified patients based on exacerbation frequency: none, few (1 or 2), and exacerbation prone (≥3). Univariate and multivariable negative binomial regression analyses were performed to investigate features associated with the frequency of exacerbations.

Results

Of 546 participants, 61.9% had no exacerbations (n = 338), 29.6% had few exacerbations (n = 162), and 8.4% were exacerbation prone (n = 46) within the preceding year. EPA patients were characterized by elevated blood and sputum eosinophils but less atopy, with more controller therapies but worse asthma control and quality of life (all p < 0.05). In multivariable models, blood and sputum eosinophils (adjusted rate ratio = 2.23, 95% confidence interval = [1.26, 3.84] and 1.67 [1.27, 2.21], respectively), FEV1 (0.90 [0.84, 0.96]), bronchodilator responsiveness (1.16 [1.05, 1.27]), COPD (2.22 [1.41, 3.51]), bronchiectasis (2.87 [1.69, 4.89]), anxiety (2.56 [1.10, 5.95]), and depression (1.94 [1.20, 3.13]) were found. Further, upper respiratory tract infection (1.83 [1.32, 2.54]) and food allergy (1.67 [1.23, 2.25]) were at high risk of asthma symptom triggers.

Conclusion

EPA is a clinically recognizable phenotype associated with several recognizable traits that could be addressed by targeted treatment.

Feng, Y, Rudd, R, Baker, C, Mashalaba, Q, Mavuso, M & Schlögl, E 2021, 'Quantifying the Model Risk Inherent in the Calibration and Recalibration of Option Pricing Models', Risks, vol. 9, no. 1, pp. 13-13.
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We focus on two particular aspects of model risk: the inability of a chosen model to fit observed market prices at a given point in time (calibration error) and the model risk due to the recalibration of model parameters (in contradiction to the model assumptions). In this context, we use relative entropy as a pre-metric in order to quantify these two sources of model risk in a common framework, and consider the trade-offs between them when choosing a model and the frequency with which to recalibrate to the market. We illustrate this approach by applying it to the seminal Black/Scholes model and its extension to stochastic volatility, while using option data for Apple (AAPL) and Google (GOOG). We find that recalibrating a model more frequently simply shifts model risk from one type to another, without any substantial reduction of aggregate model risk. Furthermore, moving to a more complicated stochastic model is seen to be counterproductive if one requires a high degree of robustness, for example, as quantified by a 99% quantile of aggregate model risk.

Fernandez, E, Ostrowski, M, Siboni, N, Seymour, JR & Petrou, K 2021, 'Uptake of dimethylsulfoniopropionate (Dmsp) by natural microbial communities of the great barrier reef (gbr), Australia', Microorganisms, vol. 9, no. 9.
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Dimethylsulfoniopropionate (DMSP) is a key organic sulfur compound that is produced by many phytoplankton and macrophytes and is ubiquitous in marine environments. Following its release into the water column, DMSP is primarily metabolised by heterotrophic bacterioplankton, but recent evidence indicates that non-DMSP producing phytoplankton can also assimilate DMSP from the surrounding environment. In this study, we examined the uptake of DMSP by communities of bacteria and phytoplankton within the waters of the Great Barrier Reef (GBR), Australia. We incubated natural GBR seawater with DMSP and quantified the uptake of DMSP by different fractions of the microbial community (>8 µm, 3–8 µm, <3 µm). We also evaluated how microbial community composition and the abundances of DMSP degrading genes are influenced by elevated dissolved DMSP levels. Our results showed uptake and accumulation of DMSP in all size fractions of the microbial community, with the largest fraction (>8 µm) forming the dominant sink, increasing in particulate DMSP by 44–115% upon DMSP enrichment. Longer-term incubations showed however, that DMSP retention was short lived (<24 h) and microbial responses to DMSP enrichment differed depending on the community carbon and sulfur demand. The response of the microbial communities from inside the reef indicated a preference towards cleaving DMSP into the climatically active aerosol dimethyl sulfide (DMS), whereas communities from the outer reef were sulfur and carbon limited, resulting in more DMSP being utilised by the cells. Our results show that DMSP uptake is shared across members of the microbial community, highlighting larger phytoplankton taxa as potentially relevant DMSP reservoirs and provide new information on sulfur cycling as a function of community metabolism in deeper, oligotrophic GBR waters.

Ferrari, R, Lachs, L, Pygas, DR, Humanes, A, Sommer, B, Figueira, WF, Edwards, AJ, Bythell, JC & Guest, JR 2021, 'Photogrammetry as a tool to improve ecosystem restoration', Trends in Ecology and Evolution.
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Ecosystem restoration has been practiced for over a century and is increasingly supported by the emergent applied science of restoration ecology. A prerequisite for successful ecosystem restoration is determining meaningful and measurable goals. This requires tools to monitor success in a standardized way. Photogrammetry uses images to reconstruct landscapes and organisms in three dimensions, enabling non-invasive measurement of key success indicators with unprecedented accuracy. We propose photogrammetry can improve restoration success by: (i) facilitating measurable goals; (ii) innovating and standardizing indicators of success; and (iii) standardizing monitoring. While the case we present is specific to coral reefs, photogrammetry has enormous potential to improve restoration practice in a wide range of ecosystems.

Flaherty, BR, Barratt, J, Lane, M, Talundzic, E & Bradbury, RS 2021, 'Sensitive universal detection of blood parasites by selective pathogen-DNA enrichment and deep amplicon sequencing', MICROBIOME, vol. 9, no. 1.
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Fröch, JE, Spencer, LP, Kianinia, M, Totonjian, DD, Nguyen, M, Gottscholl, A, Dyakonov, V, Toth, M, Kim, S & Aharonovich, I 2021, 'Coupling Spin Defects in Hexagonal Boron Nitride to Monolithic Bullseye Cavities', Nano Letters.
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Fu, X, Qiang, Y, Wang, J, Zhao, X, Hwang, FJ & Chen, C-H 2021, 'Urban Public Transport Accessibility to Medical Services From the Perspective of Residents’ Travel: A Hybrid Assessment Based on the Whole Process', IEEE Access, vol. 9, pp. 8977-8989.
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Equitable access to efficient medical services via public transport has always been one of the most important issues of healthcare in urban development. To accurately measure the urban public transport accessibility to medical services (PTAMS), this research proposes a hybrid assessment method based on multiple public-transport related indicators, including time, cost, and walking rate, which considers the whole process of residents’ public transport travel. The presented assessment technique is then applied in a case of Xi’an, China. Through the classification of medical facilities and PTAMS levels, the results show that: (a) PTAMS value of 3,080 residential areas in Xi’an are highly consistent with the standard normal distribution; (b) More than 80% of residential areas can obtain high PTAMS when considering the use of Class 1 (large-scale) hospitals, while the high PTAMS of Class 2 (small-scale) ones can only cover less than 40% residential areas; (c) There is obvious spatial heterogeneity in the distribution of PTAMS in Class 2 hospitals and a serious lack of medical equity; (d) Among large hospitals, the private ones retain higher PTAMS and equitability, making themselves best choice for residents, which is opposed to the government’s purpose of establishing public hospitals; (e) PTAMS of most residents substantially dropped about 4% during the morning peak-hour. However, subway protects PTAMS of nearby residents. This research provides references and suggestions on how to improve residents’ PTAMS under the existing public transport network and medical facilities layout.

Gao, C, Garren, M, Penn, K, Fernandez, VI, Seymour, JR, Thompson, JR, Raina, J-B & Stocker, R 2021, 'Coral mucus rapidly induces chemokinesis and genome-wide transcriptional shifts toward early pathogenesis in a bacterial coral pathogen', ISME JOURNAL.
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Garczarek, L, Guyet, U, Dore, H, Farrant, GK, Hoebeke, M, Brillet-Gueguen, L, Bisch, A, Ferrieux, M, Siltanen, J, Corre, E, Le Corguille, G, Ratin, M, Pitt, FD, Ostrowski, M, Conan, M, Siegel, A, Labadie, K, Aury, J-M, Wincker, P, Scanlan, DJ & Partensky, F 2021, 'Cyanorak v2.1: a scalable information system dedicated to the visualization and expert curation of marine and brackish picocyanobacteria genomes', NUCLEIC ACIDS RESEARCH, vol. 49, no. D1, pp. D667-D676.
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Gertner, DS, Bishop, DP, Oglobline, A & Padula, MP 2021, 'Enhancing Coverage of Phosphatidylinositol Species in Canola Through Specialised Liquid Chromatography-Mass Spectrometry Buffer Conditions', Journal of Chromatography A, pp. 461860-461860.
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Gibbs, MC, Parker, LM, Scanes, E, Byrne, M, O'Connor, WA & Ross, PM 2021, 'Energetic lipid responses of larval oysters to ocean acidification', MARINE POLLUTION BULLETIN, vol. 168.
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Glushkov, E, Mendelson, N, Chernev, A, Ritika, R, Lihter, M, Zamani, RR, Comtet, J, Navikas, V, Aharonovich, I & Radenovic, A 2021, 'Direct Growth of Hexagonal Boron Nitride on Photonic Chips for High-Throughput Characterization', ACS PHOTONICS, vol. 8, no. 7, pp. 2033-2040.
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Goggins, BJ, Minahan, K, Sherwin, S, Soh, WS, Pryor, J, Bruce, J, Liu, G, Mathe, A, Knight, DA, Horvat, JC, Walker, M & Keely, S 2021, 'Pharmacological HIF-1 stabilization promotes intestinal epithelial healing through regulation of α-integrin expression and function.', American journal of physiology. Gastrointestinal and liver physiology.
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Intestinal epithelia are critical for maintaining gastrointestinal homeostasis. Epithelial barrier injury, causing inflammation and vascular damage, results in inflammatory hypoxia and thus healing occurs in an oxygen-restricted environment. The transcription factor hypoxia inducible factor (HIF)-1 regulates genes important for cell survival and repair, including the cell adhesion protein β₁-integrin. Integrins function as αβ-dimers and α-integrin-matrix binding is critical for cell migration. We hypothesized that HIF-1 stabilization accelerates epithelial migration through integrin-dependent pathways. We aimed to examine functional and post-translational activity of α-integrins during HIF-1-mediated intestinal epithelial healing. Wound healing was assessed in T84 monolayers over 24 hours with/without prolyl-hydroxylase inhibitor (PHDi) (GB-004), which stabilizes HIF-1. Gene and protein expression were measured by RT-PCR and immunoblot, α-integrin localization was assessed by immunofluorescence. α-integrin function was assessed by antibody-mediated blockade and integrin-α6 regulation was determined by HIF-1α chromatin immunoprecipitation. Models of mucosal wounding and TNBS-induced colitis were used to examine integrin expression and localization in vivo. PHDi-treatment accelerated wound closure and migration within 12 hours, associated with increased integrin-α2 and α6 protein,but not α3. Functional blockade of integrins-α2 and α6 inhibited PHDi-mediated accelerated wound closure. HIF-1 bound directly to the integrin-α6 promoter. PHDi treatment accelerated mucosal healing, which was associated with increased α6 immunohistochemical staining in wound-associated epithelium and wound-adjacent tissue. PHDi-treatment increased α6 protein levels in colonocytes of TNBS mice and induced α6 staining in regenerating crypts and re-epithelialized inflammatory lesions. Together these data demonstrate a role for HIF-1 in regulating both integrin-α2 and α6 responses ...

Gong, Y, Xu, Z-Q, Li, D, Zhang, J, Aharonovich, I & Zhang, Y 2021, 'Two-Dimensional Hexagonal Boron Nitride for Building Next-Generation Energy-Efficient Devices', ACS ENERGY LETTERS, vol. 6, no. 3, pp. 985-996.
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Gonzalez de Vega, R, Cameron, A, Clases, D, Dodgen, TM, Doble, PA & Bishop, DP 2021, '"Simultaneous targeted and non-targeted analysis of per- and polyfluoroalkyl substances in environmental samples by liquid chromatography-ion mobility-quadrupole time of flight-mass spectrometry and mass defect analysis".', Journal of Chromatography A, vol. 1653.
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Per- and polyfluoroalkyl substances (PFAS) represent a large group of synthetic organic compounds which exhibit unique properties and have been extensively used for consumer and industrial products, resulting in a widespread presence in the environment. Regulation requiring PFAS monitoring has been implemented worldwide due to their potential health and eco-toxicological effects. Targeted methods are commonly used to monitor between twenty to forty PFAS compounds, representing only a small fraction of the number of compounds that may be present. Consequently, there is an increasing interest in complementary non-targeted methods to screen and identify unknown PFAS compounds with the aim to improve knowledge and to generate more accurate models regarding their environmental mobility and persistence. This work details the development of a method that simultaneously provided targeted and non-targeted PFAS analysis. Ultra-high performance liquid chromatography (UHPLC) was coupled to ion mobility-quadrupole time of flight-mass spectrometry (IMS-QTOF-MS) and used to quantify known and screen unknown PFAS in environmental samples collected within the greater Sydney basin (Australia). The method was validated for the quantification of 14 sulfonate-based PFAS, and a non-targeted data analysis workflow was developed using a combination of mass defect analysis with common fragment and neutral loss filtering to identify fluorine-containing species. The optimised method was applied to the environmental samples and enabled the determination of 3-7 compounds from the targeted list and the detection of a further 56-107 untargeted PFAS. This simultaneous analysis reduces the complexity of multiple analyses, and allows for greater interrogation of the full PFAS load in environmental samples.

Goodswen, SJ, Kennedy, PJ & Ellis, JT 2021, 'Applying Machine Learning to Predict the Exportome of Bovine and Canine Babesia Species That Cause Babesiosis', Pathogens.
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Goodswen, SJ, Kennedy, PJ & Ellis, JT 2021, 'Computational antigen discovery for eukaryotic pathogens using vacceed', vol. 2183, pp. 29-42.
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© Springer Science+Business Media, LLC, part of Springer Nature 2021. Bioinformatics programs have been developed that exploit informative signals encoded within protein sequences to predict protein characteristics. Unfortunately, there is no program as yet that can predict whether a protein will induce a protective immune response to a pathogen. Nonetheless, predicting those pathogen proteins most likely from those least likely to induce an immune response is feasible when collectively using predicted protein characteristics. Vacceed is a computational pipeline that manages different standalone bioinformatics programs to predict various protein characteristics, which offer supporting evidence on whether a protein is secreted or membrane -associated. A set of machine learning algorithms predicts the most likely pathogen proteins to induce an immune response given the supporting evidence. This chapter provides step by step descriptions of how to configure and operate Vacceed for a eukaryotic pathogen of the user’s choice.

Gottscholl, A, Diez, M, Soltamov, V, Kasper, C, Krauße, D, Sperlich, A, Kianinia, M, Bradac, C, Aharonovich, I & Dyakonov, V 2021, 'Spin defects in hBN as promising temperature, pressure and magnetic field quantum sensors', Nature Communications.
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Gottscholl, A, Diez, M, Soltamov, V, Kasper, C, Sperlich, A, Kianinia, M, Bradac, C, Aharonovich, I & Dyakonov, V 2021, 'Room temperature coherent control of spin defects in hexagonal boron nitride', Science Advances.
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Greenville, AC, Newsome, TM, Wardle, GM, Dickman, CR, Ripple, WJ & Murray, BR 2021, 'Simultaneously operating threats cannot predict extinction risk', Conservation Letters, vol. 14.
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© 2020 The Authors. Conservation Letters published by Wiley Periodicals, Inc. Species afflicted by multiple threats are thought to face greater extinction risk. However, it is not known whether multiple threats operate antagonistically, additively, or synergistically, or whether they vary across different taxonomic and spatial scales. We addressed these questions by analyzing threats to 10,378 species in six vertebrate classes at global and regional spatial scales using network analysis. The total number of threats was a poor predictor of extinction risk, and particular combinations of threats did not predict extinction risk in the same way at different spatial scales. The exception was cartilaginous fishes, which faced increased extinction risk with increasing numbers of threats. Except for cartilaginous fishes, our findings indicate that species facing more threats than others do not face a higher risk of extinction and suggest that effective conservation will require more investment in identifying how threats and different ecosystem stressors operate together at local scales.

Grottoli, AG, Toonen, RJ, van Woesik, R, Vega Thurber, R, Warner, ME, McLachlan, RH, Price, JT, Bahr, KD, Baums, IB, Castillo, K, Coffroth, MA, Cunning, R, Dobson, K, Donahue, M, Hench, JL, Iglesias-Prieto, R, Kemp, DW, Kenkel, CD, Kline, DI, Kuffner, IB, Matthews, JL, Mayfield, A, Padilla-Gamino, J, Palumbi, S, Voolstra, CR, Weis, VM & Wu, HC 2021, 'Increasing comparability among coral bleaching experiments.', Ecological Applications.
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Coral bleaching is the single largest global threat to coral reefs worldwide. Integrating the diverse body of work on coral bleaching is critical to understanding and combating this global problem. Yet investigating the drivers, patterns, and processes of coral bleaching poses a major challenge. A recent review of published experiments revealed a wide range of experimental variables used across studies. Such a wide range of approaches enhances discovery, but without full transparency in the experimental and analytical methods used, can also make comparisons among studies challenging. To increase comparability but not stifle innovation, we propose a common framework for coral bleaching experiments that includes consideration of coral provenance, experimental conditions, and husbandry. For example, reporting the number of genets used, collection site conditions, the experimental temperature offset(s) from the maximum monthly mean (MMM) of the collection site, experimental light conditions, flow, and the feeding regime will greatly facilitate comparability across studies. Similarly, quantifying common response variables of endosymbiont (Symbiodiniaceae) and holobiont phenotypes (i.e., color, chlorophyll, endosymbiont cell density, mortality, and skeletal growth) could further facilitate cross-study comparisons. While no single bleaching experiment can provide the data necessary to determine global coral responses of all corals to current and future ocean warming, linking studies through a common framework as outlined here, would help increase comparability among experiments, facilitate synthetic insights into the causes and underlying mechanisms of coral bleaching, and reveal unique bleaching responses among genets, species, and regions. Such a collaborative framework that fosters transparency in methods used would strengthen comparisons among studies that can help inform coral reef management and facilitate conservation strategies to mitigate coral bleaching worldw...

Gu, H, Lam, HC & Zinder, Y 2021, 'Planning rolling stock maintenance: Optimization of train arrival dates at a maintenance center', Journal of Industrial & Management Optimization, vol. 13, no. 5, pp. 0-0.
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Gu, Y, Guo, Z, Yuan, W, Kong, M, Liu, Y, Liu, Y, Gao, Y, Feng, W, Wang, F, Zhou, J, Jin, D & Li, F 2021, 'Author Correction: High-sensitivity imaging of time-domain near-infrared light transducer', Nature Photonics.
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Guan, M & Jin, D 2021, 'Dark bridge at the interface of hybrid nanosystem: Lanthanide-triplet NIR photosensitization', Chem, vol. 7, no. 6, pp. 1412-1414.
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Gupta, A, Ghosh, S, Thakur, MK, Zhou, J, (Ken) Ostrikov, K, Jin, D & Chattopadhyay, S 2021, 'Up-conversion hybrid nanomaterials for light- and heat-driven applications', Progress in Materials Science, vol. 121, pp. 100838-100838.
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Guttentag, A, Krishnakumar, K, Cokcetin, N, Hainsworth, S, Harry, E & Carter, D 2021, 'Inhibition of Dermatophyte Fungi by Australian Jarrah Honey', Pathogens.
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Guttentag, A, Krishnakumar, K, Cokcetin, N, Harry, E & Carter, D 2021, 'Factors affecting the production and measurement of hydrogen peroxide in honey samples', Access Microbiology.
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Hallegraeff, GM, Schweibold, L, Jaffrezic, E, Rhodes, L, MacKenzie, L, Hay, B & Farrell, H 2021, 'Overview of Australian and New Zealand harmful algal species occurrences and their societal impacts in the period 1985 to 2018, including a compilation of historic records', Harmful Algae.
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© 2020 Elsevier B.V. Similarities and differences between Australia and New Zealand in Harmful Algal species occurrences and Harmful Algal Events impacting on human society (HAEDAT) are reported and factors that explain their differences explored. Weekly monitoring of harmful phytoplankton and biotoxins commenced in Australia in 1986 and in New Zealand in 1993. Anecdotal historic HAB records in both countries are also catalogued. In Australia, unprecedented highly toxic Paralytic Shellfish Toxin (PST)-producing blooms of Alexandrium catenella have impacted the seafood industry along the 200 km east coast of Tasmania from 2012 to present. Toxic blooms in 1986-1993 by Gymnodinium catenatum in Tasmania were effectively mitigated by closing the affected area for shellfish farming, while a bloom by this same species in 2000 in New Zealand caused significant economic damage from restrictions on the movement of greenshell mussel spat. The biggest biotoxin event in New Zealand was an unexpected outbreak of Neurotoxic Shellfish Poisoning (NSP) in 1993 in Hauraki Gulf (putatively due to Karenia cf. mikimotoi) with 180 reported cases of human poisonings as well as reports of respiratory irritation north of Auckland. Strikingly, NSP never recurred in New Zealand since and no NSP events have ever been reported in Australia. In New Zealand, Paralytic Shellfish Poisoning (PSP) was the predominant seafood toxin syndrome, while in Australia Ciguatera Fish Poisoning (CFP) was the major reported seafood toxin syndrome, while no CFP has been recorded from consumption of New Zealand fish. In Australia, Diarrhetic Shellfish Poisoning (DSP) illnesses were recorded from two related outbreaks in 1997/98 following consumption of beach harvested clams (pipis) from a previously non-monitored area, whereas in New Zealand limited DSP illnesses are known. No human illnesses from Amnesic Shellfish Poisoning (ASP) have been reported in either Australia or New Zealand. Selected examples of HABs a...

Hamidian, M & Hall, RM 2021, 'Dissemination of novel Tn7 family transposons carrying genes for synthesis and uptake of fimsbactin siderophores among Acinetobacter baumannii isolates.', Microbial Genomics, vol. 7, no. 3.
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Han, YY, Zhang, X, Wang, J, Wang, G, Oliver, BG, Zhang, HP, Kang, DY, Wang, L, Qiu, ZX, Li, WM & Wang, G 2021, 'Multidimensional Assessment of Asthma Identifies Clinically Relevant Phenotype Overlap: A Cross-Sectional Study.', The journal of allergy and clinical immunology. In practice.
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BACKGROUND:Asthma is a heterogeneous disease with multiple phenotypes; however, the relevance of phenotype overlap remains largely unexplored. OBJECTIVE:To examine the relationship between phenotype overlap and clinical and inflammatory profiles of asthma. METHODS:In this cross-sectional study, adult participants with stable asthma (n = 522) underwent multidimensional assessments. The 10 most common phenotypes of asthma were defined and then classified into those commonly associated with Type (T) 2 or non-T2 inflammation. Furthermore, phenotype overlap scores (POS), representing the cumulative concomitant phenotypes, were used to analyze its association with clinical and inflammatory asthmatic profiles. RESULTS:Among the 522 participants, 73.4% (n = 383) had phenotype overlap, and mixed T2 and non-T2 inflammation coexisted in 47.5% (n = 248). T2 POS was positively associated with eosinophils, IgE, and fractional exhaled nitric oxide (FeNO), and negatively with Asthma Quality of Life Questionnaire (AQLQ), sputum neutrophils, IL-17A, IL-8, and TNF-α. Non-T2 POS was positively associated with Asthma Control Questionnaire, neutrophils and sputum IL-8, and negatively with AQLQ, forced expiratory volume in 1 s, blood eosinophils, IgE, and FeNO (all P < .05). Patients with phenotypes that are associated with mixed T2 and non-T2 inflammation had elevated T2 inflammation biomarkers but worse asthma control. Both T2 (adjusted β = -0.191, P = .035) and non-T2 (adjusted β = 0.310, P < .001) POS were significantly associated with severe exacerbations. CONCLUSIONS:Phenotype overlap is extremely common in asthmatic patients and significantly associated with clinical and inflammatory profiles. Patients with phenotypes associated with mixed T2 and non-T2 inflammation might be unresponsive to medications owing to increased non-T2 inflammation. Multidimensional asthma assessment identifies clinically relevant phenotype overlap.

Hardwick, J, Taylor, J, Mehta, M, Satija, S, Paudel, KR, Hansbro, PM, Chellappan, DK, Bebawy, M & Dua, K 2021, 'Targeting Cancer using Curcumin Encapsulated Vesicular Drug Delivery Systems', CURRENT PHARMACEUTICAL DESIGN, vol. 27, no. 1, pp. 2-14.
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Harvey, AM, Morton, JM, Mellor, DJ, Russell, V, Chapple, RS & Ramp, D 2021, 'Use of Remote Camera Traps to Evaluate Animal-Based Welfare Indicators in Individual Free-Roaming Wild Horses', Animals.
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Hasselerharm, CD, Yanco, E, McManus, JS, Smuts, BH & Ramp, D 2021, 'Wildlife-friendly farming recouples grazing regimes to stimulate recovery in semi-arid rangelands', SCIENCE OF THE TOTAL ENVIRONMENT, vol. 788.
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Haydon, TD, Suggett, DJ, Siboni, N, Kahlke, T, Camp, EF & Seymour, JR 2021, 'Temporal Variation in the Microbiome of Tropical and Temperate Octocorals.', Microbial ecology.
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Bacterial members of the coral holobiont play an important role in determining coral fitness. However, most knowledge of the coral microbiome has come from reef-building scleractinian corals, with far less known about the nature and importance of the microbiome of octocorals (subclass Octocorallia), which contribute significantly to reef biodiversity and functional complexity. We examined the diversity and structure of the bacterial component of octocoral microbiomes over summer and winter, with a focus on two temperate (Erythropodium hicksoni, Capnella gaboensis; Sydney Harbour) and two tropical (Sinularia sp., Sarcophyton sp.; Heron Island) species common to reefs in eastern Australia. Bacterial communities associated with these octocorals were also compared to common temperate (Plesiastrea versipora) and tropical (Acropora aspera) hard corals from the same reefs. Using 16S rRNA amplicon sequencing, bacterial diversity was found to be heterogeneous among octocorals, but we observed changes in composition between summer and winter for some species (C. gaboensis and Sinularia sp.), but not for others (E. hicksoni and Sarcophyton sp.). Bacterial community structure differed significantly between all octocoral species within both the temperate and tropical environments. However, on a seasonal basis, those differences were less pronounced. The microbiomes of C. gaboensis and Sinularia sp. were dominated by bacteria belonging to the genus Endozoicomonas, which were a key conserved feature of their core microbiomes. In contrast to previous studies, our analysis revealed that Endozoicomonas phylotypes are shared across different octocoral species, inhabiting different environments. Together, our data demonstrates that octocorals harbour a broad diversity of bacterial partners, some of which comprise 'core microbiomes' that potentially impart important functional roles to their hosts.

Herdean, A, Hall, CC, Le, LP, Miller, SM, Pernice, M & Ralph, PJ 2021, 'Action Spectra and Excitation Emission Matrices reveal the broad range of usable photosynthetic active radiation for Phaeodactylum tricornutum', BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, vol. 1862, no. 9.
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Hickey, BA, Chalmers, T, Newton, P, Lin, C-T, Sibbritt, D, McLachlan, CS, Clifton-Bligh, R, Morley, J & Lal, S 2021, 'Smart Devices and Wearable Technologies to Detect and Monitor Mental Health Conditions and Stress: A Systematic Review', Sensors.
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Hiscocks, HG, Yit, DL, Pascali, G & Ung, AT 2021, 'Incorporation of the pentafluorosulfanyl group through common synthetic transformations', MONATSHEFTE FUR CHEMIE, vol. 152, no. 4, pp. 449-459.
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Horstmann, M, de Vega, RG, Bishop, DP, Karst, U, Doble, PA & Clases, D 2021, 'Determination of gadolinium MRI contrast agents in fresh and oceanic waters of Australia employing micro-solid phase extraction, HILIC-ICP-MS and bandpass mass filtering', JOURNAL OF ANALYTICAL ATOMIC SPECTROMETRY, vol. 36, no. 4, pp. 767-775.
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Huang, M, Wang, J, Wang, B, Liu, DL, Feng, P, Yu, Q, Pan, X & Waters, C 2021, 'Assessing maize potential to mitigate the adverse effects of future rising temperature and heat stress in China', Agricultural and Forest Meteorology, vol. 311.
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Rising temperatures and frequent extreme high temperature events under future climate scenarios have posed pressing challenges with respect to global food security. Previous climate-crop modelling studies have investigated the impacts of rising temperature and heat stress on grain yield. However, the potential and priority of dealing with rising mean temperature or heat stress using genetically different cultivars have not been identified. We investigated the impacts of climate change on maize yield across China's Maize Belt (23°–48°N) using the CERES-Maize model driven by future climate scenarios under contrasting maize growing season temperatures of 18–24°C during the 2050s (2040–2069) and the 2080s (2070–2099). We also assessed the potential of different cultivars to adapt to rising temperatures and heat stress with an extreme hot global climate model from CMIP6 under a high emission scenario (SSP585). Our simulated results indicated that the shortened growth period resulting from rising temperatures, decreased photosynthesis caused by heat stress, and decreased grain-filling rate due to heat stress were the main reasons causing future maize (Zea mays L.) yield decreases in all subregions of China's Maize Belt. The priority applied to using a cultivar with a longer growth period or higher heat-tolerance to cope with climate warming depends on the particulars of the local climate and cropping system. Specifically, the potential for adapting to rising temperature is generally higher than the potential for adapting to heat stress in all subregions except the North China Plain (NCP) where the potential for adapting to heat stress is higher than the potential for adapting to rising temperature. Our study demonstrated the necessity of using cultivars with appropriate traits to alleviate the adverse effects of climate warming. Also, our findings provide important information for the direction and priority of future breeding in different climate regions with various c...

Huang, Q, Jacquelot, N, Preaudet, A, Hediyeh-zadeh, S, Souza-Fonseca-Guimaraes, F, McKenzie, ANJ, Hansbro, PM, Davis, MJ, Mielke, LA, Putoczki, TL & Belz, GT 2021, 'Type 2 Innate Lymphoid Cells Protect against Colorectal Cancer Progression and Predict Improved Patient Survival', CANCERS, vol. 13, no. 3.
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Huang, T, Zhang, Y, Wang, Z, Zeng, Y, Wang, N, Fan, H, Huang, Z, Su, Y, Huang, X, Chen, H, Zhang, K & Yi, C 2021, 'Optogenetically Controlled TrkA Activity Improves the Regenerative Capacity of Hair-Follicle-Derived Stem Cells to Differentiate into Neurons and Glia.', Advanced biosystems, pp. e2000134-e2000134.
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Hair-follicle-derived stem cells (HSCs) originating from the bulge region of the mouse vibrissa hair follicle are able to differentiate into neuronal and glial lineage cells. The tropomyosin receptor kinase A (TrkA) receptor that is expressed on these cells plays key roles in mediating the survival and differentiation of neural progenitors as well as in the regulation of the growth and regeneration of different neural systems. In this study, the OptoTrkA system is introduced, which is able to stimulate TrkA activity via blue-light illumination in HSCs. This allows to determine whether TrkA signaling is capable of influencing the proliferation, migration, and neural differentiation of these somatic stem cells. It is found that OptoTrkA is able to activate downstream molecules such as ERK and AKT with blue-light illumination, and subsequently able to terminate this kinase activity in the dark. HSCs with OptoTrkA activity show an increased ability for proliferation and migration and also exhibited accelerated neuronal and glial cell differentiation. These findings suggest that the precise control of TrkA activity using optogenetic tools is a viable strategy for the regeneration of neurons from HSCs, and also provides a novel insight into the clinical application of optogenetic tools in cell-transplantation therapy.

Huang, X, Cai, H, Li, H, Su, Y, Li, H, Li, W, Yi, C, Oliver, BG & Chen, H 2021, 'Cinnamon as Dietary Supplement Caused Hyperlipidemia in Healthy Rats', Evidence-Based Complementary and Alternative Medicine, vol. 2021, pp. 1-7.
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Objective. Cinnamon is a cooking spice and a medicinal herb. It is increasingly used as a health supplement due to its perceived benefit to prevent and or manage type 2 diabetes and metabolic disorders. However, it is unclear if regular consumption of this medicinal plant will interfere with normal physiological functions. Therefore, this study investigated the impact of daily cinnamon supplements on glucose and lipid metabolic profiles in healthy rats. Methods. Male rats (Sprague Dawley, 8 weeks) were supplied with cinnamon in their diet (equivalent to ∼1 g/day in humans) for two weeks. Blood glucose and lipid levels, as well as metabolic markers in both liver and abdominal white adipose tissue, were measured. Results. Cinnamon significantly increased fat mass and blood cholesterol and low-density lipoprotein (LDL) levels, but reduced fasting blood glucose level by 12%. Liver functional enzymes were normal in rats consuming cinnamon. However, several lipid metabolic markers were impaired which may contribute to dyslipidemia, including two main switches for energy metabolism (sirtuin 1 and peroxisome proliferator-activated receptor-gamma coactivator-1α) and the LDL receptor. However, de novo lipid synthesis enzymes and inflammatory markers were also reduced in the liver by cinnamon treatment, which may potentially prevent the development of steatosis. Markers for lipid oxidation were downregulated in fat tissue in cinnamon-treated rats, contributing to increased fat accumulation. Conclusion. Daily low-dose cinnamon supplementation seems to promote abdominal adipose tissue accumulation and disturb lipid homeostasis in healthy rats, raising the concerns regarding daily use in healthy people.

Huang, X, Su, Y, Wang, N, Li, H, Li, Z, Yin, G, Chen, H, Niu, J & Yi, C 2021, 'Astroglial Connexins in Neurodegenerative Diseases', Frontiers in Molecular Neuroscience.
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Hudspith, M, Rix, L, Achlatis, M, Bougoure, J, Guagliardo, P, Clode, PL, Webster, NS, Muyzer, G, Pernice, M & de Goeij, JM 2021, 'Subcellular view of host-microbiome nutrient exchange in sponges: insights into the ecological success of an early metazoan-microbe symbiosis.', Microbiome, vol. 9, no. 1, p. 44.
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Background

Sponges are increasingly recognised as key ecosystem engineers in many aquatic habitats. They play an important role in nutrient cycling due to their unrivalled capacity for processing both dissolved and particulate organic matter (DOM and POM) and the exceptional metabolic repertoire of their diverse and abundant microbial communities. Functional studies determining the role of host and microbiome in organic nutrient uptake and exchange, however, are limited. Therefore, we coupled pulse-chase isotopic tracer techniques with nanoscale secondary ion mass spectrometry (NanoSIMS) to visualise the uptake and translocation of ¹³C- and ¹⁵N-labelled dissolved and particulate organic food at subcellular level in the high microbial abundance sponge Plakortis angulospiculatus and the low microbial abundance sponge Halisarca caerulea.

Results

The two sponge species showed significant enrichment of DOM- and POM-derived ¹³C and ¹⁵N into their tissue over time. Microbial symbionts were actively involved in the assimilation of DOM, but host filtering cells (choanocytes) appeared to be the primary site of DOM and POM uptake in both sponge species overall, via pinocytosis and phagocytosis, respectively. Translocation of carbon and nitrogen from choanocytes to microbial symbionts occurred over time, irrespective of microbial abundance, reflecting recycling of host waste products by the microbiome.

Conclusions

Here, we provide empirical evidence indicating that the prokaryotic communities of a high and a low microbial abundance sponge obtain nutritional benefits from their host-associated lifestyle. The metabolic interaction between the highly efficient filter-feeding host and its microbial symbionts likely provides a competitive advantage to the sponge holobiont in the oligotrophic environments in which they thrive, by retaining and recycling limiting nutrients. Sponges present a unique model to link nutr...

Hung, MN, Ralph, PJ, Marin-Guirao, L, Pernice, M & Procaccini, G 2021, 'Seagrasses in an era of ocean warming: a review', BIOLOGICAL REVIEWS.
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Hurtado-McCormick, V, Krix, D, Tschitschko, B, Siboni, N, Ralph, PJ & Seymour, JR 2021, 'Shifts in the seagrass leaf microbiome associated with wasting disease in Zostera muelleri', MARINE AND FRESHWATER RESEARCH, vol. 72, no. 9, pp. 1303-1320.
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Hwang, J, Strange, N, Phillips, MJA, Krause, AL, Heywood, A, Gamble, AB, Huston, WM & Tyndall, JDA 2021, 'Optimization of peptide-based inhibitors targeting the HtrA serine protease in Chlamydia: Design, synthesis and biological evaluation of pyridone-based and N-Capping group-modified analogues', European Journal of Medicinal Chemistry, vol. 224.
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The obligate intracellular bacterium Chlamydia trachomatis (C. trachomatis) is responsible for the most common bacterial sexually transmitted infection and is the leading cause of preventable blindness, representing a major global health burden. While C. trachomatis infection is currently treatable with broad-spectrum antibiotics, there would be many benefits of a chlamydia-specific therapy. Previously, we have identified a small-molecule lead compound JO146 [Boc-Val-Pro-ValP(OPh)2] targeting the bacterial serine protease HtrA, which is essential in bacterial replication, virulence and survival, particularly under stress conditions. JO146 is highly efficacious in attenuating infectivity of both human (C. trachomatis) as well as koala (C. pecorum) species in vitro and in vivo, without host cell toxicity. Herein, we present our continuing efforts on optimizing JO146 by modifying the N-capping group as well as replacing the parent peptide structure with the 2-pyridone scaffold at P3/P2. The drug optimization process was guided by molecular modelling, enzyme and cell-based assays. Compound 18b from the pyridone series showed improved inhibitory activity against CtHtrA by 5-fold and selectivity over human neutrophil elastase (HNE) by 109-fold compared to JO146, indicating that 2-pyridone is a suitable bioisostere of the P3/P2 amide/proline for developing CtHtrA inhibitors. Most pyridone-based inhibitors showed superior anti-chlamydial potency to JO146 especially at lower doses (25 and 50 μM) in C. trachomatis and C. pecorum cell culture assays. Modifications of the N-capping group of the peptidyl inhibitors did not have much influence on the anti-chlamydial activities, providing opportunities for more versatile alterations and future optimization. In summary, we present 2-pyridone based analogues as a new generation of non-peptidic CtHtrA inhibitors, which hold better promise as anti-chlamydial drug candidates.

Ibrahim, I, Seo, DH, Angeloski, A, McDonagh, A, Shon, HK & Tijing, LD 2021, '3D microflowers CuS/Sn2S3 heterostructure for highly efficient solar steam generation and water purification', Solar Energy Materials and Solar Cells, vol. 232.
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Solar-driven interfacial steam generation is a promising method to produce potable water using renewable energy and help solve global clean water scarcity problems. However, the design of photothermal materials (PTMs) with excellent light absorption that can localize heat at the air/water interface, and facilitate water vapor generation remains a key challenge for its practical implementation. In this work, we demonstrate the synthesis of heterostructure microflowers composed of vertically aligned CuS/Sn2S3 nanosheets (3D CSS-NS MF) using a single-step solvothermal method for solar steam generation application. The microflower structures and the abundant nanocavities between the vertically aligned nanosheets resulted in significant sunlight harvesting over the solar spectrum, excellent heat localization through trapping and re-absorbing the heat, and fast escape of water vapor. Under 1 sun (1 kW m-2) illumination, a high water evaporation rate of 1.42 kg m-2 h-1, corresponding to an efficiency of 82.93% was obtained. The 3D CSS-NS MF based solar evaporator exhibited remarkable salt ions rejection efficiency and good reusability over 10 cycles. Furthermore, efficient removal of organic dyes was observed in application geared towards wastewater treatment with a rejection ∼99.9%. Our work demonstrates the potential of using novel semiconductor-based nanocomposites as effective photothermal materials for high-performance solar steam generation in water desalination and wastewater treatment applications.

Ibrahim, I, Seo, DH, McDonagh, AM, Shon, HK & Tijing, L 2021, 'Semiconductor photothermal materials enabling efficient solar steam generation toward desalination and wastewater treatment', Desalination.
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© 2020 Elsevier B.V. Water scarcity issues around the world have renewed interest in the use of solar water evaporation as a means of providing fresh water. Advances in photothermal materials and thermal management, together with new interfacial system designs, have considerably improved the overall efficiency of solar steam generation (SSG) for desalination and wastewater treatment. Several classes of rationally-designed photothermal materials (PTMs) and nanostructures have enabled effective absorption of broad solar spectrum resulting in improved solar evaporation efficiency. Among several classes of PTMs, semiconductor-based PTMs have demonstrated great potential for SSG. In this review, we highlight the progress and prospects in SSG with emphasis on the use and evolution of advanced semiconductor materials for PTMs and their various designs and engineered architectures. Applications and future prospects for desalination and wastewater treatment are also discussed.

Impellizzeri, FM, Woodcock, S, Coutts, AJ, Fanchini, M, McCall, A & Vigotsky, AD 2021, 'What Role Do Chronic Workloads Play in the Acute to Chronic Workload Ratio? Time to Dismiss ACWR and Its Underlying Theory.', Sports medicine (Auckland, N.Z.).
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Aim

The aim of this study was to examine the associations between the injury risk and the acute (AL) to chronic (CL) workload ratio (ACWR) by substituting the original CL with contrived values to assess the role of CL (i.e., the presence and implications of statistical artefacts).

Methods

Using previously published data, we generated a contrived ACWR by dividing the AL by fixed and randomly generated CLs, and we compared these results to real data. We also reproduced previously reported subgroup analyses, including dichotomising players' data above and below the median CL. Our analyses follow the same, previously published modelling approach.

Results

The analyses with original data showed effects compatible with higher injury risk for ACWR only (odd ratios, OR: 2.45, 95% CI 1.28-4.71). However, we observed similar effects by dividing AL by the "contrived" fixed and randomly generated CLs: OR 1.95 (1.18-3.52) dividing by 1510 (average CL); and OR ranging from 1.16 to 2.07, using random CL 1.53 (mean). Random ACWRs reduced the variance relative to the original AL and further inflated the ORs (mean OR 1.89, from 1.42 to 2.70). ACWR causes artificial reclassification of players compared to AL alone. Finally, neither ACWR nor AL alone confer a meaningful predictive advantage to an intercept-only model, even within the training sample (c-statistic 0.574/0.544 vs. 0.5 in both ACWR/AL and intercept-only models, respectively).

Discussion

ACWR is a rescaling of the explanatory variable (AL, numerator), in turn magnifying its effect estimates and decreasing its variance despite conferring no predictive advantage. Other ratio-related transformations (e.g., reducing the variance of the explanatory variable and unjustified reclassifications) further inflate the OR of AL alone with injury risk. These results also disprove the etiological theory behind this ratio and its components. We suggest ACWR be dismissed as a framework and model, and in line w...

Ismail, MH, Michie, KA, Goh, YF, Noorian, P, Kjelleberg, S, Duggin, IG, McDougald, D & Rice, SA 2021, 'The Repressor C Protein, Pf4r, Controls Superinfection of Pseudomonas aeruginosa PAO1 by the Pf4 Filamentous Phage and Regulates Host Gene Expression', Viruses.
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Iwasaki, K, Evenhuis, C, Tamburic, B, Kuzhiumparambil, U, O'Connor, W, Ralph, P & Szabo, M 2021, 'Improving light and CO2 availability to enhance the growth rate of the diatom, Chaetoceros muelleri', ALGAL RESEARCH-BIOMASS BIOFUELS AND BIOPRODUCTS, vol. 55.
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Jacquelot, N, Seillet, C, Wang, M, Pizzolla, A, Liao, Y, Hediyeh-zadeh, S, Grisaru-Tal, S, Louis, C, Huang, Q, Schreuder, J, Souza-Fonseca-Guimaraes, F, de Graaf, CA, Thia, K, Macdonald, S, Camilleri, M, Luong, K, Zhang, S, Chopin, M, Molden-Hauer, T, Nutt, SL, Umansky, V, Ciric, B, Groom, JR, Foster, PS, Hansbro, PM, McKenzie, ANJ, Gray, DHD, Behren, A, Cebon, J, Vivier, E, Wicks, IP, Trapani, JA, Munitz, A, Davis, MJ, Shi, W, Neeson, PJ & Belz, GT 2021, 'Blockade of the co-inhibitory molecule PD-1 unleashes ILC2-dependent antitumor immunity in melanoma', NATURE IMMUNOLOGY, vol. 22, no. 7, pp. 851-+.
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Jarman, LR, Elliott, JL, Lees, T, Clifton-Bligh, R, Simpson, AM, Nassif, N & Lal, S 2021, 'Heart Rate Variability as a Potential Non-invasive Marker of Blood Glucose Level', Human Physiology, vol. 47, no. 2, pp. 209-218.
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Abstract: Currently, monitoring of blood glucose level (BGL) is constrained by the invasive nature of BGL measures. We investigated heart rate variability (HRV) parameters as potential non-invasive markers of BGL. Healthy volunteers (n = 25; aged 27 ± 9 years) uninhibited by regular medications or chronic illness were recruited for this study. BGL and HRV were assessed during fasting (9:00 am), postprandial (12:00 pm), and postabsorptive (3:00 pm) periods using self-monitoring of blood glucose techniques and ten-minute electrocardiogram, respectively. Frequency-domain HRV measures, which estimate contributions of sympathetic and parasympathetic systems to autonomic modulation of the heart, were correlated against BGL data with the following significant (p < 0.05) findings. The change in BGL from fasting to postprandial levels was negatively correlated with fasting low frequency (LF) power and total power (TP). Postprandial BGL was negatively associated with fasting LF and TP, as well as with postprandial LF, high frequency (HF), and TP. The change in BGL from postprandial to postabsorptive levels was positively correlated with fasting LF power, as well as with postprandial LF, HF, and TP. Frequency-domain HRV parameters may be useful in predicting the magnitude and direction of acute fluctuations in BGL, and further research could develop them as non-invasive markers of BGL.

Jaumaux, P, Wu, J, Shanmukaraj, D, Wang, Y, Zhou, D, Sun, B, Kang, F, Li, B, Armand, M & Wang, G 2021, 'Non-Flammable Liquid and Quasi-Solid Electrolytes toward Highly-Safe Alkali Metal-Based Batteries', Advanced Functional Materials, vol. 31, no. 10.
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© 2020 Wiley-VCH GmbH Rechargeable alkali metal (i.e., lithium, sodium, potassium)-based batteries are considered as vital energy storage technologies in modern society. However, the traditional liquid electrolytes applied in alkali metal-based batteries mainly consist of thermally unstable salts and highly flammable organic solvents, which trigger numerous accidents related to fire, explosion, and leakage of toxic chemicals. Therefore, exploring non-flammable electrolytes is of paramount importance for achieving safe batteries. Although replacing traditional liquid electrolytes with all-solid-state electrolytes is the ultimate way to solve the above safety issues, developing non-flammable liquid electrolytes can more directly fulfill the current needs considering the low ionic conductivities and inferior interfacial properties of existing all-solid-state electrolytes. Moreover, the electrolyte leakage concern can be further resolved by gelling non-flammable liquid electrolytes to obtain quasi-solid electrolytes. Herein, a comprehensive review of the latest progress in emerging non-flammable liquid electrolytes, including non-flammable organic liquid electrolytes, aqueous electrolytes, and deep eutectic solvent-based electrolytes is provided, and systematically introduce their flame-retardant mechanisms and electrochemical behaviors in alkali metal-based batteries. Then, the gelation techniques for preparing quasi-solid electrolytes are also summarized. Finally, the remaining challenges and future perspectives are presented. It is anticipated that this review will promote a safety improvement of alkali metal-based batteries.

Jerotic, D, Suvakov, S, Matic, M, Alqudah, A, Grieve, DJ, Pljesa-Ercegovac, M, Savic-Radojevic, A, Damjanovic, T, Dimkovic, N, McClements, L & Simic, T 2021, 'GSTM1 Modulates Expression of Endothelial Adhesion Molecules in Uremic Milieu', Oxidative Medicine and Cellular Longevity.
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Jin, D, Wen, S, Liu, Y, Wang, F, Lin, G, zhou, J, Shi, B & Suh, YD 2021, 'Nanobarcodes with multidimensional optical information beyond diffraction limit'.
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Abstract Precise design and fabrication of heterogeneous nanostructures will enable nanoscale devices to integrate multiple desirable functionalities. But due to the diffraction limit (~200 nm), the optical uniformity and diversity within the heterogeneous functional nanostructures are hardly controlled and characterized. Here we report a set of nanobarcodes, each optically active section has its unique nonlinear responses to donut illumination patterns, so that one can discern each unit with super resolution. To achieve this, we first realized an approach of highly controlled epitaxial growth and produced a range of one-dimensional heterogeneous structures. Each section along the nanorod structure display tunable upconversion emissions, in four optically orthogonal dimensions, including colour, lifetime, excitation wavelength, and power dependency. Moreover, we demonstrated a 210 nm single nanorod as the smallest polychromatic light source for the on-demand generation of RGB photonic emissions. Remarkably, within a space of 50 nm, only 1/20th of the excitation wavelength, multiple codes can be successfully coded and decoded in 4 optical dimensions. This precision control enables the fabrication of super capacity geometrical barcodes with theoretical coding capacity up to (24-1)4. This work benchmarks our new ability towards the full control of sub-diffraction-limit optical diversities of single heterogeneous nanoparticles.

Johnson, N, Maguire, S, Morra, A, Kapoor, PM, Tomczyk, K, Jones, ME, Schoemaker, MJ, Gilham, C, Bolla, MK, Wang, Q, Dennis, J, Ahearn, TU, Andrulis, IL, Anton-Culver, H, Antonenkova, NN, Arndt, V, Aronson, KJ, Augustinsson, A, Baynes, C, Freeman, LEB, Beckmann, MW, Benitez, J, Bermisheva, M, Blomqvist, C, Boeckx, B, Bogdanova, NV, Bojesen, SE, Brauch, H, Brenner, H, Burwinkel, B, Campa, D, Canzian, F, Castelao, JE, Chanock, SJ, Chenevix-Trench, G, Clarke, CL, Børresen-Dale, AL, Alnæs, GIG, Sahlberg, KK, Ottestad, L, Kåresen, R, Schlichting, E, Holmen, MM, Sauer, T, Haakensen, V, Engebråten, O, Naume, B, Fosså, A, Kiserud, CE, Reinertsen, KV, Helland, Å, Riis, M, Geisler, J, Conroy, DM, Couch, FJ, Cox, A, Cross, SS, Czene, K, Dörk, T, Eliassen, AH, Engel, C, Evans, DG, Fasching, PA, Figueroa, J, Floris, G, Flyger, H, Gago-Dominguez, M, Gapstur, SM, García-Closas, M, Gaudet, MM, Giles, GG, Goldberg, MS, González-Neira, A, Bowtell, DDL, deFazio, A, Webb, PM, Guénel, P, Hahnen, E, Haiman, CA, Håkansson, N, Hall, P, Hamann, U, Harrington, PA, Hart, SN, Hooning, MJ, Hopper, JL, Howell, A, Hunter, DJ, Clarke, C, Marsh, D, Scott, R, Baxter, R, Yip, D, Carpenter, J, Davis, A, Pathmanathan, N, Simpson, P, Graham, D, Sachchithananthan, M & Amor, D 2021, 'CYP3A7*1C allele: linking premenopausal oestrone and progesterone levels with risk of hormone receptor-positive breast cancers', British Journal of Cancer, vol. 124, no. 4, pp. 842-854.
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Background: Epidemiological studies provide strong evidence for a role of endogenous sex hormones in the aetiology of breast cancer. The aim of this analysis was to identify genetic variants that are associated with urinary sex-hormone levels and breast cancer risk. Methods: We carried out a genome-wide association study of urinary oestrone-3-glucuronide and pregnanediol-3-glucuronide levels in 560 premenopausal women, with additional analysis of progesterone levels in 298 premenopausal women. To test for the association with breast cancer risk, we carried out follow-up genotyping in 90,916 cases and 89,893 controls from the Breast Cancer Association Consortium. All women were of European ancestry. Results: For pregnanediol-3-glucuronide, there were no genome-wide significant associations; for oestrone-3-glucuronide, we identified a single peak mapping to the CYP3A locus, annotated by rs45446698. The minor rs45446698-C allele was associated with lower oestrone-3-glucuronide (−49.2%, 95% CI −56.1% to −41.1%, P = 3.1 × 10–18); in follow-up analyses, rs45446698-C was also associated with lower progesterone (−26.7%, 95% CI −39.4% to −11.6%, P = 0.001) and reduced risk of oestrogen and progesterone receptor-positive breast cancer (OR = 0.86, 95% CI 0.82–0.91, P = 6.9 × 10–8). Conclusions: The CYP3A7*1C allele is associated with reduced risk of hormone receptor-positive breast cancer possibly mediated via an effect on the metabolism of endogenous sex hormones in premenopausal women.

Jolly, CJ, Von Takach, B & Webb, JK 2021, 'Slow life history leaves endangered snake vulnerable to illegal collecting', Scientific Reports.
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Kang, H, Walsh, S, Oliver, B, Royce, T & Cho, BJ 2021, 'Exploring Heart Rate Variability as a Biomedical Diagnostic Tool for the Disympathetic Dimension of Eight-Constitution Medicine', Evidence-based Complementary and Alternative Medicine.
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Kanodarwala, FK, Lesniewski, A, Olszowska-Los, I, Spindler, X, Pieta, IS, Lennard, C, Niedziolka-Jonsson, J, Moret, S & Roux, C 2021, 'Fingermark detection using upconverting nanoparticles and comparison with cyanoacrylate fuming', FORENSIC SCIENCE INTERNATIONAL, vol. 326.
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Kanodarwala, FK, Moret, S, Spindler, X, Lennard, C & Roux, C 2021, 'Novel upconverting nanoparticles for fingermark detection', Optical Materials.
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© 2020 This paper reports the synthesis of high-quality upconverter nanoparticles (UCNPs) – sodium yttrium tetrafluoride doped with ytterbium and erbium (NaYF4:Yb,Er) with a silica shell and capped with carboxyl functional groups. The effect of different synthesis methods on the silica capping has been studied in detail. The main goal of this research was to design tailor-made UCNPs for fingermark detection and to validate a NP-based detection technique that is user-friendly, cost-effective and can be implemented in routine practice by law enforcement agencies. UCNP powders and solutions were used as a proof-of-concept to detect latent fingermarks on an aluminium foil substrate. This study not only highlights the potential use of UCNPs as a fingermark detection method but also identifies a number of shortfalls in its application that need to be addressed before such an approach could be implemented as a valid detection technique.

Kar, R, Jha, SK, Ojha, S, Sharma, A, Dholpuria, S, Raju, VSR, Prasher, P, Chellappan, DK, Gupta, G, Singh, S, Paudel, KR, Hansbro, PM, Singh, S, Ruokolainen, J, Kesari, KK, Dua, K & Jha, NK 2021, 'The FBXW7‐NOTCH interactome: A ubiquitin proteasomal system‐induced crosstalk modulating oncogenic transformation in human tissues', Cancer Reports.
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Karacan, I, Cox, N, Dowd, A, Vago, R, Milthorpe, B, Cazalbou, S & Ben-Nissan, B 2021, 'The synthesis of hydroxyapatite from artificially grown Red Sea hydrozoan coral for antimicrobacterial drug delivery system applications', JOURNAL OF THE AUSTRALIAN CERAMIC SOCIETY, vol. 57, no. 2, pp. 399-407.
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Karunia, J, Niaz, A, Mandwie, M, Broome, ST, Keay, KA, Waschek, JA, Al-Badri, G & Castorina, A 2021, 'Pacap and vip modulate lps-induced microglial activation and trigger distinct phenotypic changes in murine bv2 microglial cells', International Journal of Molecular Sciences, vol. 22, no. 20.
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Pituitary adenylate cyclase-activating polypeptide (PACAP) and vasoactive intestinal peptide (VIP) are two structurally related immunosuppressive peptides. However, the underlying mechanisms through which these peptides regulate microglial activity are not fully understood. Using lipopolysaccharide (LPS) to induce an inflammatory challenge, we tested whether PACAP or VIP differentially affected microglial activation, morphology and cell migration. We found that both peptides attenuated LPS-induced expression of the microglial activation markers Iba1 and iNOS (### p < 0.001), as well as the pro-inflammatory mediators IL-1β, IL-6, Itgam and CD68 (### p < 0.001). In contrast, treatment with PACAP or VIP exerted distinct effects on microglial morphology and migration. PACAP reversed LPS-induced soma enlargement and increased the percentage of smallsized, rounded cells (54.09% vs. 12.05% in LPS-treated cells), whereas VIP promoted a phenotypic shift towards cell subpopulations with mid-sized, spindle-shaped somata (48.41% vs. 31.36% in LPS-treated cells). Additionally, PACAP was more efficient than VIP in restoring LPS-induced impairment of cell migration and the expression of urokinase plasminogen activator (uPA) in BV2 cells compared with VIP. These results suggest that whilst both PACAP and VIP exert similar immunosuppressive effects in activated BV2 microglia, each peptide triggers distinctive shifts towards phenotypes of differing morphologies and with differing migration capacities.

Ketelaar, ME, Portelli, MA, Dijk, FN, Shrine, N, Faiz, A, Vermeulen, CJ, Xu, CJ, Hankinson, J, Bhaker, S, Henry, AP, Billington, CK, Shaw, DE, Johnson, SR, Benest, AV, Pang, V, Bates, DO, Pogson, ZEK, Fogarty, A, McKeever, TM, Singapuri, A, Heaney, LG, Mansur, AH, Chaudhuri, R, Thomson, NC, Holloway, JW, Lockett, GA, Howarth, PH, Niven, R, Simpson, A, Tobin, MD, Hall, IP, Wain, LV, Blakey, JD, Brightling, CE, Obeidat, M, Sin, DD, Nickle, DC, Bossé, Y, Vonk, JM, van den Berge, M, Koppelman, GH, Sayers, I & Nawijn, MC 2021, 'Phenotypic and functional translation of IL33 genetics in asthma.', The Journal of allergy and clinical immunology.
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BACKGROUND:Asthma is a complex disease with multiple phenotypes that may differ in disease pathobiology and treatment response. IL33 single nucleotide polymorphisms (SNPs) have been reproducibly associated with asthma. IL33 levels are elevated in sputum and bronchial biopsies of patients with asthma. The functional consequences of IL33 asthma SNPs remain unknown. OBJECTIVE:This study sought to determine whether IL33 SNPs associate with asthma-related phenotypes and with IL33 expression in lung or bronchial epithelium. This study investigated the effect of increased IL33 expression on human bronchial epithelial cell (HBEC) function. METHODS:Association between IL33 SNPs (Chr9: 5,815,786-6,657,983) and asthma phenotypes (Lifelines/DAG [Dutch Asthma GWAS]/GASP [Genetics of Asthma Severity & Phenotypes] cohorts) and between SNPs and expression (lung tissue, bronchial brushes, HBECs) was done using regression modeling. Lentiviral overexpression was used to study IL33 effects on HBECs. RESULTS:We found that 161 SNPs spanning the IL33 region associated with 1 or more asthma phenotypes after correction for multiple testing. We report a main independent signal tagged by rs992969 associating with blood eosinophil levels, asthma, and eosinophilic asthma. A second, independent signal tagged by rs4008366 presented modest association with eosinophilic asthma. Neither signal associated with FEV1, FEV1/forced vital capacity, atopy, and age of asthma onset. The 2 IL33 signals are expression quantitative loci in bronchial brushes and cultured HBECs, but not in lung tissue. IL33 overexpression in vitro resulted in reduced viability and reactive oxygen species-capturing of HBECs, without influencing epithelial cell count, metabolic activity, or barrier function. CONCLUSIONS:We identify IL33 as an epithelial susceptibility gene for eosinophilia and asthma, provide mechanistic insight, and implicate targeting of the IL33 pathway specifically in eosinophilic asthma.

Khan, M, Willcox, MDP, Rice, SA, Sharma, S & Stapleton, F 2021, 'Development of antibiotic resistance in the ocular Pseudomonas aeruginosa clone ST308 over twenty years', Experimental Eye Research, vol. 205.
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Corneal infection caused by a bacteria Pseudomonas aeruginosa is common cause of ocular morbidity. Increasing antibiotic resistance by ocular P. aeruginosa is an emerging concern. In this study the resistome of ocular isolates of Pseudomonas aeruginosa clone ST308 isolated in India in 1997 (PA31, PA32, PA33, PA35 and PA37) and 2018 (PA198 and PA219) were investigated. All the isolates of ST308 had >95% nucleotide similarity. The isolates from 2018 had larger genomes, coding sequences, accessory and pan genes compared to the older isolates from 1997. The 2018 isolate PA219 was resistant to all antibiotics except polymyxin B, while the 2018 isolate PA198 was resistant to ciprofloxacin, levofloxacin, gentamicin and tobramycin. Among the isolates from 1997, five were resistant to gentamicin, tobramycin and ciprofloxacin, four were resistant to levofloxacin while two were resistant to polymyxin B. Twenty-four acquired resistance genes were present in the 2018 isolates compared to 11 in the historical isolates. All isolates contained genes encoding for aminoglycoside (aph(6)-Id, aph(3′)-lIb, aph(3″)-Ib), beta-lactam (blaPAO), tetracycline (tet(G)), fosfomycin (fosA), chloramphenicol (catB7), sulphonamide (sul1), quaternary ammonium (qacEdelta1) and fluoroquinolone (crpP) resistance. Isolate PA198 possessed aph(3′)-VI, rmtD2, qnrVC1, blaOXA-488, blaPME-1, while PA219 possessed aadA1, rmtB, qnrVC1, aac(6′)-Ib-cr, blaTEM-1B, blaVIM-2, blaPAO-1, mph(E), mph(A), msr(E). In both recent isolates qnrVC1 was present in Tn3 transposon. In 219 blaTEM-1 was carried on a transposon and blaOXA-10 on a class 1 integron. There were no notable differences in the number of single nucleotide polymorphisms, but recent isolates carried more insertions and deletions in their genes. These findings suggest that genomes of P. aeruginosa ocular clonal strains with >95% nucleotide identity isolated twenty years apart had changed over time with the acquisition of resistance genes. The pattern of ...

Khantisitthiporn, O, Shue, B, Eyre, NS, Nash, CW, Turnbull, L, Whitchurch, CB, Van der Hoek, KH, Helbig, KJ & Beard, MR 2021, 'Viperin interacts with PEX19 to mediate peroxisomal augmentation of the innate antiviral response.', Life science alliance, vol. 4, no. 7.
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Peroxisomes are recognized as significant platforms for the activation of antiviral innate immunity where stimulation of the key adapter molecule mitochondrial antiviral signaling protein (MAVS) within the RIG-I like receptor (RLR) pathway culminates in the up-regulation of hundreds of ISGs, some of which drive augmentation of multiple innate sensing pathways. However, whether ISGs can augment peroxisome-driven RLR signaling is currently unknown. Using a proteomics-based screening approach, we identified Pex19 as a binding partner of the ISG viperin. Viperin colocalized with numerous peroxisomal proteins and its interaction with Pex19 was in close association with lipid droplets, another emerging innate signaling platform. Augmentation of the RLR pathway by viperin was lost when Pex19 expression was reduced. Expression of organelle-specific MAVS demonstrated that viperin requires both mitochondria and peroxisome MAVS for optimal induction of IFN-β. These results suggest that viperin is required to enhance the antiviral cellular response with a possible role to position the peroxisome at the mitochondrial/MAM MAVS signaling synapse, furthering our understanding of the importance of multiple organelles driving the innate immune response against viral infection.

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 2021, 'Projecting coral responses to intensifying marine heatwaves under ocean acidification.', Global change biology.
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Over this century, coral reefs will run the gauntlet of climate change as marine heatwaves (MHWs) become more intense and frequent, and ocean acidification (OA) progresses. However, we still lack a quantitative assessment of how, and to what degree, OA will moderate the responses of corals to MHWs as they intensify throughout this century. Here, we first projected future MHW intensities for tropical regions under three future greenhouse gas emissions scenarios (RCP2.6, RCP4.5, and RCP8.5) for the near-term (2021-2040), mid-century (2041-2060), and late-century (2081-2100). We then combined these MHW intensity projections with a global dataset of 1,788 experiments to assess coral attribute performance and survival under the three emissions scenarios for the near term, mid-century, and late century in the presence and absence of OA. Although warming and OA had predominately additive impacts on the coral responses, the contribution of OA in affecting most coral attribute responses was minor relative to the dominant role of intensifying MHWs. However, the addition of OA led to greater decreases in photosynthesis and survival under intermediate and unrestricted emissions scenarios for the mid and late century than if intensifying MHWs were considered as the only driver. These results indicate that the role OA in affecting coral responses to intensifying MHWs temperatures is specific to the coral attribute examined and the extremity of temperatures tested. Specifically, intensifying MHWs and OA will cause increasing instances of coral bleaching and substantial declines in coral productivity, calcification, and survival within the next two decades under the low and intermediate emissions scenarios. These projections suggest that corals must rapidly adapt or acclimatize to projected ocean conditions to persist, which is far more likely under a low emissions scenario and with increasing efforts to manage reefs to enhance resilience.

Klingberg, J, Cawley, A, Shimmon, R, Fouracre, C, Pasin, D & Fu, S 2021, 'Finding the proverbial needle: Non-targeted screening of synthetic opioids in equine plasma.', Drug Testing and Analysis.
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Synthetic opioids are a class of compounds that are of particular concern due to their high potency and potential health impacts. With the relentless emergence of new synthetic opioid derivatives, non-targeted screening strategies are required that do not rely on the use of library spectra or reference materials. In this study, product ion searching, and Kendrick mass defect analysis were investigated for non-targeted screening of synthetic opioids. The estimated screening cut-offs for these techniques ranged between 0.05 and 0.1 ng/mL. These techniques were designed to not be reliant on a particular vendor's software, meaning that they can be applied to existing drug screening protocols, without requiring the development and validation of new analytical procedures. The efficacy of the developed techniques was tested through blind trials, with spiked samples inserted amongst authentic plasma samples, which demonstrated the usefulness of these methods for high-throughput screening. The use of a non-targeted screening workflow that contains complementary techniques can increase the likelihood of detecting compounds of interest within a sample, as well as the confidence in detections that are made.

Klont, F, Kwiatkowski, M, Faiz, A, van den Bosch, T, Pouwels, SD, Dekker, FJ, Ten Hacken, NHT, Horvatovich, P & Bischoff, R 2021, 'Adsorptive Microtiter Plates As Solid Supports in Affinity Purification Workflows.', Journal of proteome research.
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Affinity ligands such as antibodies are widely used in (bio)medical research for purifying proteins from complex biological samples. These ligands are generally immobilized onto solid supports which facilitate the separation of a captured protein from the sample matrix. Adsorptive microtiter plates are commonly used as solid supports prior to immunochemical detection (e.g., immunoassays) but hardly ever prior to liquid chromatography-mass spectrometry (LC-MS-)-based detection. Here, we describe the use of adsorptive microtiter plates for protein enrichment prior to LC-MS detection, and we discuss opportunities and challenges of corresponding workflows, based on examples of targeted (i.e., soluble receptor for advanced glycation end-products (sRAGE) in human serum) and discovery-based workflows (i.e., transcription factor p65 (NF-κB) in lysed murine RAW 264.7 macrophages and peptidyl-prolyl cis-trans isomerase FKBP5 (FKBP5) in lysed human A549 alveolar basal epithelial cells). Thereby, we aim to highlight the potential usefulness of adsorptive microtiter plates in affinity purification workflows prior to LC-MS detection, which could increase their usage in mass spectrometry-based protein research.

Labeeuw, L, Commault, AS, Kuzhiumparambil, U, Emmerton, B, Nguyen, LN, Nghiem, LD & Ralph, PJ 2021, 'A comprehensive analysis of an effective flocculation method for high quality microalgal biomass harvesting', SCIENCE OF THE TOTAL ENVIRONMENT, vol. 752.
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Laiolo, L, Matear, R, Soja-Woźniak, M, Suggett, DJ, Hughes, DJ, Baird, ME & Doblin, MA 2021, 'Modelling the impact of phytoplankton cell size and abundance on inherent optical properties (IOPs) and a remotely sensed chlorophyll-a product', Journal of Marine Systems, vol. 213.
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© 2020 Elsevier B.V. Ocean colour data are commonly used to quantify primary production, study phytoplankton dynamics and calibrate marine models, thus understanding the origin of errors in the retrieved chlorophyll-a (Chl-a) product is critical. One source of uncertainty in retrieved Chl-a products can be related to large photosynthetic cells, characterised by lower mass-specific absorption coefficients due to increased packaging effect. Here, we explore the relationship between phytoplankton size structure and an ocean colour product using optical simulations and in situ observations. Specifically, we use an optical model to explore how phytoplankton cell size and abundance influence phytoplankton absorption and backscattering coefficients and the implication this has for water leaving radiance and the estimated Chl-a derived from satellite ocean colour. The optical model simulations show phytoplankton cell size has a significant impact on the remote-sensing reflectance, with Chl-a packaged in 5 to 10 μm cells resulting in about 54 to 76% the simulated ocean colour Chl-a compared to 1 μm cells, as determined by an algorithm that converts reflectances to Chl-a. To support optical simulations, size-fractionated Chl-a samples were collected from several water masses to investigate the phytoplankton size contribution (i.e., < 2 μm, 2–10 μm and > 10 μm) to the total Chl-a. We focused on the offshore eastern Australian ocean region, largely characterised by oligotrophic waters in which phytoplankton dominate the optical properties of the water column. Of the 22 stations sampled, a total of ten in situ size fractionated Chl-a measurements were matched-up with the corresponding clear-sky satellite Chl-a product. The matched-up points revealed a systematic underestimation of in situ Chl-a. With the low amount of data, it was not possible to statistically relate the satellite underestimation to a specific phytoplankton size class, but the observations showed that the lar...

Landajuela, A, Braun, M, Rodrigues, CDA, Martínez-Calvo, A, Doan, T, Horenkamp, F, Andronicos, A, Shteyn, V, Williams, ND, Lin, C, Wingreen, NS, Rudner, DZ & Karatekin, E 2021, 'FisB relies on homo-oligomerization and lipid binding to catalyze membrane fission in bacteria', PLOS Biology.
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Lapwong, Y, Dejtaradol, A & Webb, JK 2021, 'Shifts in thermal tolerance of the invasive Asian house gecko (Hemidactylus frenatus) across native and introduced ranges', BIOLOGICAL INVASIONS, vol. 23, no. 4, pp. 989-996.
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Larkin, BP, Nguyen, LT, Hou, M, Glastras, SJ, Chen, H, Wang, R, Pollock, CA & Saad, S 2021, 'Novel Role of Gestational Hydralazine in Limiting Maternal and Dietary Obesity-Related Chronic Kidney Disease', Frontiers in Cell and Developmental Biology.
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Larkin, BP, Saad, S, Glastras, SJ, Nguyen, LT, Hou, M, Chen, H, Wang, R & Pollock, CA 2021, 'Low-dose hydralazine during gestation reduces renal fibrosis in rodent offspring exposed to maternal high fat diet', PLOS ONE.
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Leal, E, de Beyer, L, O'Connor, W, Dove, M, Ralph, PJ & Pernice, M 2021, 'Production optimisation of Tisochrysis lutea as a live feed for juvenile Sydney rock oysters, Saccostrea glomerata, using large-scale photobioreactors', Aquaculture, vol. 533.
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© 2020 Elsevier B.V. The aquaculture industry uses microalgae as a live feed for juvenile oysters in hatcheries to meet their nutritional requirements, including their need for several essential Poly Unsaturated Fatty Acids (PUFAs) such as eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA). The mass culture of microalgae is not only a major bottleneck for the production of juvenile oysters, but also a significant cost, accounting for 20–50% of hatchery operating costs. Currently, low biomass concentrations, high production costs and poor cultivation systems limit the quantity and quality of microalgae feed. This study focused on Tisochrysis lutea, a microalgae species commonly used in aquaculture, and we assessed the potential of photobioreactors with an improved light source and CO2 input to increase biomass production and improve biochemical composition of algal feed. Two photobioreactor systems were compared: the current industry set up (DPI) comprising fluorescent lighting and minimal CO2 input versus an optimized system utilising LEDs and increased CO2. Cultures of T. lutea were monitored over a 12-day growth period and harvested on day 14 for biochemical analysis. Final cell density was significantly higher in the optimized system relative to the conventional culture systems (6.2 × 106 cells / mL versus 3.7 × 106 cells / mL, respectively). The biochemical profile of T. lutea was not significantly different between the two photobioreactors systems. The algal biomass produced during this comparative experiment was used in a feeding trial on oyster spat, Saccostrea glomerata. Spat fed with algae produced in optimized vs conventional photobioreactors showed no significant difference in growth, but oyster spat fed with T. lutea grown in optimized photobioreactors did show a significant increase in their EPA content. Overall, our results contribute to our understanding of how altered culture conditions affect microalgal production and biochemical composit...

Lee, HW, Lee, MS, Kim, TH, Alraek, T, Zaslawski, C, Kim, JW & Moon, DG 2021, 'Ginseng for Erectile Dysfunction: A Cochrane Systematic Review', The World Journal of Men's Health.
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Lee, L-Y, Hew, GSY, Meenu, Shukla, SD, Satija, S, Khurana, N, Anand, K, Dureja, H, Singh, SK, Mishra, V, Singh, PK, Gulati, M, Prasher, P, Aljabali, AAA, Tambuwala, MM, Thangavelu, L, Panneerselvam, J, Gupta, G, Zacconi, FC, Shastri, M, Jha, NK, Xenaki, D, MacLoughlin, R, Oliver, BG, Chellappan, DK & Dua, K 2021, 'Targeting eosinophils in respiratory diseases: Biological axis, emerging therapeutics and treatment modalities.', Life sciences, vol. 267, pp. 118973-118973.
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Eosinophils are bi-lobed, multi-functional innate immune cells with diverse cell surface receptors that regulate local immune and inflammatory responses. Several inflammatory and infectious diseases are triggered with their build up in the blood and tissues. The mobilization of eosinophils into the lungs is regulated by a cascade of processes guided by Th2 cytokine generating T-cells. Recruitment of eosinophils essentially leads to a characteristic immune response followed by airway hyperresponsiveness and remodeling, which are hallmarks of chronic respiratory diseases. By analysing the dynamic interactions of eosinophils with their extracellular environment, which also involve signaling molecules and tissues, various therapies have been invented and developed to target respiratory diseases. Having entered clinical testing, several eosinophil targeting therapeutic agents have shown much promise and have further bridged the gap between theory and practice. Moreover, researchers now have a clearer understanding of the roles and mechanisms of eosinophils. These factors have successfully assisted molecular biologists to block specific pathways in the growth, migration and activation of eosinophils. The primary purpose of this review is to provide an overview of the eosinophil biology with a special emphasis on potential pharmacotherapeutic targets. The review also summarizes promising eosinophil-targeting agents, along with their mechanisms and rationale for use, including those in developmental pipeline, in clinical trials, or approved for other respiratory disorders.

Lee, S, Xu, H, Rice, SA, Chong, TH & Oh, HS 2021, 'Development of a quorum quenching-column to control biofouling in reverse osmosis water treatment processes', Journal of Industrial and Engineering Chemistry, vol. 94, pp. 188-194.
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© 2020 The Korean Society of Industrial and Engineering Chemistry Biofouling is recognized as one of the most problematic fouling types in reverse osmosis (RO) processes and lead to high energy requirements and operating costs. Over the past decade, many studies on membrane bioreactor (MBR) systems for wastewater applications demonstrated that disrupting cell-cell communications among bacteria, called quorum quenching (QQ), is a promising approach to inhibit biofouling of membranes. Here, we developed the QQ-column as a novel strategy to control biofouling in RO systems. The QQ-column was prepared by incorporating a recombinant bacterial QQ strain into hydrogel beads and embedding these beads inside a column. The QQ-column was installed upstream of the RO module to degrade N-acyl homoserine lactone, a quorum sensing (QS) signal, from the feed in a laboratory-scale RO system operating in total recycle mode. The QQ-column reduced the concentrations of signal molecules by ∼29% in an RO system and mitigated biofilm formation (38.6% reduction of cell number) on the membrane, consequently reducing the transmembrane pressure by 50.1%. These results demonstrate that integrating QQ bacteria into columns is a practical method to control biofouling in RO systems.

Li, C, Mendelson, N, Ritika, R, Chen, Y, Xu, Z-Q, Toth, M & Aharonovich, I 2021, 'Scalable and Deterministic Fabrication of Quantum Emitter Arrays from Hexagonal Boron Nitride', NANO LETTERS, vol. 21, no. 8, pp. 3626-3632.
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Li, D, Wen, S, Kong, M, Liu, Y, Hu, W, Shi, B, Shi, X & Jin, D 2021, 'Highly Doped Upconversion Nanoparticles for In Vivo Applications Under Mild Excitation Power (vol 92, pg 10913, 2020)', ANALYTICAL CHEMISTRY, vol. 93, no. 32, pp. 11346-11346.
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Li, H, Chen, H, Morgan, L, Li, W & Oliver, BG 2021, 'A narrative review of clinical studies of herbal treatment of difficult to manage asthma', Complementary Therapies in Clinical Practice, vol. 44.
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Asthma can be complex and difficult to manage. Patients often seek alternative treatment options, including Traditional Chinese Medicine (TCM). The paradigms that inform TCM treatments include a philosophy focusing on modifying the whole body status (‘bian zheng’) to treat the lungs. TCM practitioners use personalized treatment plans based on clusters of clinical patterns (eg. cold-related wheezing, kidney insufficiency/energy-deficiency-related wheezing). TCM includes herbal remedies and non-oral therapies such as cupping, acupuncture, and massage. The efficacy of TCM treatments of asthma is not well described as the majority of studies are published only in Chinese literature. We reviewed all available clinical trials in CNKI, Chaoxin, Wanfang, CQVIP, Springer-link, Science Direct, and Pubmed. Papers in Chinese were translated by dual lingual TCM and Western medicine doctors. Based on the identified studies, TCM is a safe additive treatment to Western medicine that can improve both symptoms and quality of life for patients with asthma.

Li, H, Wu, Z, Yang, Z, Zhanghao, K, Xi, P & Jin, D 2021, 'Axially overlapped multi-focus light sheet with enlarged field of view', Applied Physics Letters.
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Li, J, Ding, Z, Li, J, Wang, C, Pan, L & Wang, G 2021, 'Synergistic coupling of NiS1.03 nanoparticle with S-doped reduced graphene oxide for enhanced lithium and sodium storage', CHEMICAL ENGINEERING JOURNAL, vol. 407.
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Li, J, Ding, Z, Pan, L, Li, J, Wang, C & Wang, G 2021, 'Facile self-templating synthesis of layered carbon with N, S dual doping for highly efficient sodium storage', CARBON, vol. 173, pp. 31-40.
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Li, J, Xie, Y, Zhao, P, Qin, Y, Oliver, BG, Tian, Y, Li, S, Wang, M & Liu, X 2021, 'A chinese herbal formula ameliorates COPD by inhibiting the inflammatory response via downregulation of p65, JNK, and p38', Phytomedicine.
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Li, J, Zheng, M, Shimoni, O, Banks, WA, Bush, AI, Gamble, JR & Shi, B 2021, 'Development of Novel Therapeutics Targeting the Blood–Brain Barrier: From Barrier to Carrier', Advanced Science.
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Li, P, Guo, X, Zang, R, Wang, S, Zuo, Y, Man, Z, Li, P, Liu, S & Wang, G 2021, 'Nanoconfined SnO2/SnSe2 heterostructures in N-doped carbon nanotubes for high-performance sodium-ion batteries', Chemical Engineering Journal, vol. 418.
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Tin-based compounds are promising anode materials for sodium-ion batteries (SIBs), owing to their high theoretical capacities and relatively low sodiation potential. However, their high-rate performance and cycle life-span are severely impeded by the inherent sluggish reaction kinetics and large structural change during charging and discharging. Herein, we report a composite anode consisting of SnO2/SnSe2 heterostructure nanoparticles uniformly encapsulated in N-doped carbon nanotubes (SnO2/SnSe2@C) for high-performance SIBs. The hollow tube nano-architecture not only accommodates the volume expansion of SnO2/SnSe2, but also facilitates the electrolyte penetration and shortens Na+ pathways. Meanwhile, the N-doped carbon shells provide highways for electron transport and contribute to the total capacity. More importantly, the construction of heterostructures boosts the charge transfer kinetics and further stabilizes the electrode structure by the additional confining effects of the increased crystalline boundaries. Benefiting from the synergistic effects between the elaborately-designed electrode architecture and the incorporation of heterostructures, the SnO2/SnSe2@C composite delivered a superior rate capability (322 mAh g−1 at 4 A g−1) and remarkable cycling stability with a capacity retention of 87.7% after 1000 cycles at 2 A g−1.

Li, Y, Li, J, Yuan, J, Zhao, Y, Zhang, J, Liu, H, Wang, F, Tang, J & Song, J 2021, '3D CoS2/rGO aerogel as trapping-catalyst sulfur host to promote polysulfide conversion for stable Li-S batteries', JOURNAL OF ALLOYS AND COMPOUNDS, vol. 873.
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Li, Y, Yang, W, Yang, W, Huang, Y, Wang, G, Xu, C, Kang, F & Dong, L 2021, 'High-performance zinc-ion batteries enabled by electrochemically induced transformation of vanadium oxide cathodes', Journal of Energy Chemistry.
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Li, Y, Yang, W, Yang, W, Huang, Y, Wang, G, Xu, C, Kang, F & Dong, L 2021, 'High-performance zinc-ion batteries enabled by electrochemically induced transformation of vanadium oxide cathodes', JOURNAL OF ENERGY CHEMISTRY, vol. 60, pp. 233-240.
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Li, Y, Yang, W, Yang, W, Wang, Z, Rong, J, Wang, G, Xu, C, Kang, F & Dong, L 2021, 'Towards High-Energy and Anti-Self-Discharge Zn-Ion Hybrid Supercapacitors with New Understanding of the Electrochemistry', Nano-Micro Letters.
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Liao, Y, Ithurbide, S, Evenhuis, C, Lowe, J & Duggin, IG 2021, 'Cell division in the archaeon Haloferax volcanii relies on two FtsZ proteins with distinct functions in division ring assembly and constriction', NATURE MICROBIOLOGY, vol. 6, no. 5, pp. 594-+.
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Liao, Y, Ithurbide, S, Löwe, J & Duggin, IG 2021, 'Two FtsZ proteins orchestrate archaeal cell division through distinct functions in ring assembly and constriction', BioRxiv.
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AbstractThe tubulin homolog FtsZ assembles a ring in bacteria and plays a key role in the machinery that constricts to divide the cells. Many archaea encode two FtsZs from distinct families, FtsZ1 and FtsZ2, of previously unclear functions. We show that Haloferax volcanii cannot divide properly without either or both but proliferates in alternative ways via remarkable envelope plasticity. The FtsZs co-localize as a dynamic midcell division ring. FtsZ1 independently assembles and stabilizes FtsZ2 in the ring, and influences cell shape, whereas FtsZ2 functions in the constriction mechanism; their GTPase active sites are crucial for these activities. The two FtsZs are widespread in archaea with a single S-layer envelope, but those with a pseudomurein wall only have FtsZ1. FtsZ2 appears to be essential for constriction of the flexible membrane-S-layer, where an internal constriction force might dominate the division mechanism in contrast to bacteria and archaea that divide by wall ingrowth.

Lin, G, Liu, Y, Huang, G, Chen, Y, Makarov, D, Lin, J, Quan, Z & Jin, D 2021, '3D Rotation-Trackable and Differentiable Micromachines with Dimer-Type Structures for Dynamic Bioanalysis', Advanced Intelligent Systems, vol. 3, no. 2.
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Utilizing the magnetic interactions between microparticle building blocks allows creating long‐range ordered structures and constructing smart multifunctional systems at different scales. The elaborate control over the inter‐particle magnetic coupling interaction is entailed to unlock new magnetoactuation functionalities. Herein, dimer‐type microstructures consisting of a pair of magnetic emulsions with tailorable dimension and magnetic coupling strength are fabricated using a microfluidic emulsion‐templated assembly approach. The magnetite nanoparticles dispersed in vinylbenzene monomers are partitioned into a pair of emulsions with conserved volume, which are wrapped by an aqueous hydrogel shell and finally polymerized to form discrete structures. Tunable synchronous–asynchronous rotation over 60 dB is unlocked in magnetic dimers, which is shown to be dependent on the magnetic moments induced. This leads to a new class of magnetic actuators for the parallelized assay of distinctive virus DNAs and the dynamic optical evaluation of 3D cell cultures. The work suggests a new perspective to design smart multifunctional microstructures and devices by exploring their natural variance in magnetic coupling.

Lin, G, Liu, Y, Huang, G, Chen, Y, Makarov, D, Lin, J, Quan, Z & Jin, D 2021, '3D Rotation‐Trackable and Differentiable Micromachines with Dimer‐Type Structures for Dynamic Bioanalysis', Advanced Intelligent Systems, vol. 3, no. 2, pp. 2170020-2170020.
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Liu, D, Jin, Y, Dong, X, Liu, L, Jin, D, Capobianco, JA & Shen, D 2021, 'Low-Temperature-Induced Controllable Transversal Shell Growth of NaLnF4 Nanocrystals', Nanomaterials.
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Liu, D, Xu, X, Du, Y, Liao, J, Wen, S, Dong, X, Jin, Y, Liu, L, Jin, D, Capobianco, JA & Shen, D 2021, 'Reconstructing the Surface Structure of NaREF4 Upconversion Nanocrystals with a Novel K+ Treatment', CHEMISTRY OF MATERIALS, vol. 33, no. 7, pp. 2548-2556.
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Liu, G, Philp, AM, Corte, T, Travis, MA, Schilter, H, Hansbro, NG, Burns, CJ, Eapen, MS, Sohal, SS, Burgess, JK & Hansbro, PM 2021, 'Therapeutic targets in lung tissue remodelling and fibrosis', Pharmacology and Therapeutics, vol. 225.
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Structural changes involving tissue remodelling and fibrosis are major features of many pulmonary diseases, including asthma, chronic obstructive pulmonary disease (COPD) and idiopathic pulmonary fibrosis (IPF). Abnormal deposition of extracellular matrix (ECM) proteins is a key factor in the development of tissue remodelling that results in symptoms and impaired lung function in these diseases. Tissue remodelling in the lungs is complex and differs between compartments. Some pathways are common but tissue remodelling around the airways and in the parenchyma have different morphologies. Hence it is critical to evaluate both common fibrotic pathways and those that are specific to different compartments; thereby expanding the understanding of the pathogenesis of fibrosis and remodelling in the airways and parenchyma in asthma, COPD and IPF with a view to developing therapeutic strategies for each. Here we review the current understanding of remodelling features and underlying mechanisms in these major respiratory diseases. The differences and similarities of remodelling are used to highlight potential common therapeutic targets and strategies. One central pathway in remodelling processes involves transforming growth factor (TGF)-β induced fibroblast activation and myofibroblast differentiation that increases ECM production. The current treatments and clinical trials targeting remodelling are described, as well as potential future directions. These endeavours are indicative of the renewed effort and optimism for drug discovery targeting tissue remodelling and fibrosis.

Liu, Q, Wang, Y, Yang, X, Zhou, D, Wang, X, Jaumaux, P, Kang, F, Li, B, Ji, X & Wang, G 2021, 'Rechargeable anion-shuttle batteries for low-cost energy storage', Chem.
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As promising alternatives to lithium-ion batteries, rechargeable anion-shuttle batteries (ASBs) with anions as charge carriers stand out because of their low cost, long cyclic lifetime, and/or high energy density. In this review, we provide for the first time, comprehensive insights into the anion shuttling mechanisms of ASBs, including anion-based rocking-chair batteries (ARBs), dual-ion batteries (DIBs), including insertion-type, conversion-type, and conversion-insertion-type, and reverse dual-ion batteries (RDIBs). Thereafter, we review the latest progresses and challenges regarding electrode materials and electrolytes for ASBs. In addition, we summarize the existing dilemmas of ASBs and outline the perspective of ASB technology for future grid storage.

Liu, Y, Jiang, Y, Hu, Z, Peng, J, Lai, W, Wu, D, Zuo, S, Zhang, J, Chen, B, Dai, Z, Yang, Y, Huang, Y, Zhang, W, Zhao, W, Zhang, W, Wang, L & Chou, S 2021, 'In-Situ Electrochemically Activated Surface Vanadium Valence in V2C MXene to Achieve High Capacity and Superior Rate Performance for Zn-Ion Batteries', Advanced Functional Materials, vol. 31, no. 8.
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© 2020 Wiley-VCH GmbH Vanadium-based materials are fascinating potential cathodes for high energy density Zn-ion batteries (ZIBs), due to their high capacity arising from multi-electron redox chemistry. Most vanadium-based materials suffer from poor rate capability, however, owing to their low conductivity and large dimension. Here, we propose the application of V2C MXene (V2CTx), a conductive 2D nanomaterial, for achieving high energy density ZIBs with superior rate capability. Through an initial charging activation, the valence of surface vanadium in V2CTx cathode is raised significantly from V2+/V3+ to V4+/V5+, forming a nanoscale vanadium oxide (VOx) coating that effectively undergoes multi-electron reactions, whereas the inner V-C-V 2D multi-layers of V2CTx are intentionally preserved, providing abundant nanochannels with intrinsic high conductivity. Owing to the synergistic effects between the outer high-valence VOx and inner conductive V-C-V, the activated V2CTx presents an ultrahigh rate performance, reaching 358 mAh g−1 at 30 A g−1, together with remarkable energy and power density (318 Wh kg−1/22.5 kW kg−1). The structural advantages of activated V2CTx are maintained after 2000 cycles, offering excellent stability with nearly 100% Coulombic efficiency. This work provides key insights into the design of high-performance cathode materials for advanced ZIBs.

Liu, Y, Lin, D, Li, L, Chen, Y, Wen, J, Lin, Y & He, X 2021, 'Using machine-learning algorithms to identify patients at high risk of upper gastrointestinal lesions for endoscopy', JOURNAL OF GASTROENTEROLOGY AND HEPATOLOGY.
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Liu, Y, Lin, G & Jin, D 2021, 'Off-axis gyration induces large-area circular motion of anisotropic microparticles in a dynamic magnetic trap', Applied Physics Letters.
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Liu, Y, Lin, G, Bao, G, Guan, M, Yang, L, Liu, Y, Wang, D, Zhang, X, Liao, J, Fang, G, Di, X, Huang, G, Zhou, J, Cheng, YY & Jin, D 2021, 'Stratified Disk Microrobots with Dynamic Maneuverability and Proton-Activatable Luminescence for in Vivo Imaging.', ACS Nano.
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Microrobots can expand our abilities to access remote, confined, and enclosed spaces. Their potential applications inside our body are obvious, e.g., to diagnose diseases, deliver medicine, and monitor treatment efficacy. However, critical requirements exist in relation to their operations in gastrointestinal environments, including resistance to strong gastric acid, responsivity to a narrow proton variation window, and locomotion in confined cavities with hierarchical terrains. Here, we report a proton-activatable microrobot to enable real-time, repeated, and site-selective pH sensing and monitoring in physiological relevant environments. This is achieved by stratifying a hydrogel disk to combine a range of functional nanomaterials, including proton-responsive molecular switches, upconversion nanoparticles, and near-infrared (NIR) emitters. By leveraging the 3D magnetic gradient fields and the anisotropic composition, the microrobot can be steered to locomote as a gyrating "Euler's disk", i.e., aslant relative to the surface and along its low-friction outer circumference, exhibiting a high motility of up to 60 body lengths/s. The enhanced magnetomotility can boost the pH-sensing kinetics by 2-fold. The fluorescence of the molecular switch can respond to pH variations with over 600-fold enhancement when the pH decreases from 8 to 1, and the integration of upconversion nanoparticles further allows both the efficient sensitization of NIR light through deep tissue and energy transfer to activate the pH probes. Moreover, the embedded down-shifting NIR emitters provide sufficient contrast for imaging of a single microrobot inside a live mouse. This work suggests great potential in developing multifunctional microrobots to perform generic site-selective tasks in vivo.

Liu, Y, Zhang, L, Li, HL, Liang, BM, Wang, J, Zhang, X, Chen, ZH, Zhang, HP, Xie, M, Wang, L, Wang, G & Oliver, BG 2021, 'Small Airway Dysfunction in Asthma Is Associated with Perceived Respiratory Symptoms, Non-Type 2 Airway Inflammation, and Poor Responses to Therapy', Respiration, vol. 100, no. 8, pp. 767-779.
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Background: Emerging evidence has indicated that small airway dysfunction (SAD) contributes to the clinical expression of asthma. Objectives: The aim of the study was to explore the relationships of SAD assessed by forced expiratory flow between 25 and 75% (FEF_25-75%), with clinical and inflammatory profile and treatment responsiveness in asthma. Method: In study I, dyspnea intensity (Borg scale), chest tightness, wheezing and cough (visual analog scales, VASs), and pre- and post-methacholine challenge testing (MCT) were analyzed in asthma patients with SAD and non-SAD. In study II, asthma subjects with SAD and non-SAD underwent sputum induction, and inflammatory mediators in sputum were detected. Asthma patients with SAD and non-SAD receiving fixed treatments were prospectively followed up for 4 weeks in study III. Spirometry, Asthma Control Questionnaire (ACQ), and Asthma Control Test (ACT) were carried out to define treatment responsiveness. Results: SAD subjects had more elevated ΔVAS for dyspnea (p = 0.027) and chest tightness (p = 0.032) after MCT. Asthma patients with SAD had significantly elevated interferon (IFN)-γin sputum (p < 0.05), and Spearman partial correlation found FEF_25-75% significantly related to IFN-γand interleukin-8 (both having p < 0.05). Furthermore, multivariable regression analysis indicated SAD was significantly associated with worse treatment responses (decrease in ACQ ≥0.5 and increase in ACT ≥3) (p = 0.022 and p = 0.032). Conclusions: This study indicates that SAD in asthma predisposes patients to greater dyspnea intensity and chest tightness during bronchoconstriction. SAD patients with asthma are characterized by non-type 2 inflammation that may account for poor responsiveness to therapy.

Liu, Y, Zhou, Z, Wang, F, Kewes, G, Wen, S, Burger, S, Ebrahimi Wakiani, M, Xi, P, Yang, J, Yang, X, Benson, O & Jin, D 2021, 'Axial localization and tracking of self-interference nanoparticles by lateral point spread functions', Nature Communications.
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Liu, Z, Li, J, Yang, J, Ma, H, Wang, C, Guo, X & Wang, G 2021, 'Preparation of a Novel g-C3N4/Sn/N-doped Carbon Composite for Sodium Storage', CHEMICAL JOURNAL OF CHINESE UNIVERSITIES-CHINESE, vol. 42, no. 2, pp. 633-642.
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Lockwood, TE, Westerhausen, MT & Doble, PA 2021, 'Pew(2): Open-Source Imaging Software for Laser Ablation-Inductively Coupled Plasma-Mass Spectrometry', ANALYTICAL CHEMISTRY, vol. 93, no. 30, pp. 10418-10423.
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Loering, S, Cameron, GJM, Bhatt, NP, Belz, GT, Foster, PS, Hansbro, PM & Starkey, MR 2021, 'Differences in pulmonary group 2 innate lymphoid cells are dependent on mouse age, sex and strain', IMMUNOLOGY AND CELL BIOLOGY.
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Lu, Z, Van Eeckhoutte, HP, Liu, G, Nair, PM, Jones, B, Gillis, CM, Nalkurthi, BC, Verhamme, F, Buyle-Huybrecht, T, Vandenabeele, P, Berghe, TV, Brusselle, GG, Horvat, JC, Murphy, JM, Wark, PA, Bracke, KR, Fricker, M & Hansbro, PM 2021, 'Necroptosis Signalling Promotes Inflammation, Airway Remodelling and Emphysema in COPD.', American journal of respiratory and critical care medicine.
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Rationale

Necroptosis, mediated by RIPK3 and MLKL, is a form of regulated necrosis that can drive tissue inflammation and destruction, however its contribution to COPD pathogenesis is poorly understood.

Objectives

To determine the role of necroptosis in COPD.

Methods

Levels of RIPK3, MLKL and activated phospho-MLKL were measured in lung tissues of COPD patients and non-COPD controls. Necroptosis-related mRNA and proteins and cell death were examined in the lungs and pulmonary macrophages of mice with cigarette smoke (CS)-induced experimental COPD. The responses of Ripk3- and Mlkl-deficient (-/-) mice to CS exposure were compared to wild-type mice. Combined inhibition of apoptosis (pan-caspase inhibitor qVD-OPh) and necroptosis (Mlkl-/- mice) was assessed.

Measurements and main results

Protein levels of MLKL and pMLKL but not RIPK3 were increased in lung tissues of COPD patients compared to never smokers or smoker non-COPD controls. Necroptosis-related mRNA and protein levels were increased in lung tissue and macrophages in CS-exposed mice/experimental COPD. Ripk3 or Mlkl deletion prevented airway inflammation in response to acute CS-exposure. Ripk3 deficiency reduced airway inflammation and remodelling and development of emphysematous pathology following chronic CS-exposure. Mlkl deletion and qVD-OPh treatment reduced chronic CS-induced airway inflammation, but only Mlkl deletion prevented airway remodelling and emphysema. Ripk3 or Mlkl deletion and qVD-OPh treatment reduced CS-induced lung cell death.

Conclusions

Necroptosis is induced by CS exposure and increased in COPD patient lungs and experimental COPD. Inhibiting necroptosis attenuates CS-induced airway inflammation, airway remodelling and emphysema. Targeted inhibition of necroptosis is a potential therapeutic strategy in COPD.

Lundgren, EJ, Ramp, D, Stromberg, JC, Wu, J, Nieto, NC, Sluk, M, Moeller, KT & Wallach, AD 2021, 'Equids engineer desert water availability', Science.
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Lundgren, EJ, Ramp, D, Wu, J, Sluk, M, Moeller, KT, Stromberg, JC & Wallach, AD 2021, 'Response', Science, vol. 373, no. 6558, pp. 973-974.
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Lundgren, EJ, Schowanek, SD, Rowan, J, Middleton, O, Pedersen, RØ, Wallach, AD, Ramp, D, Davis, M, Sandom, CJ & Svenning, J-C 2021, 'Functional traits of the world’s late Quaternary large-bodied avian and mammalian herbivores', Scientific Data.
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Luo, Z, Morey, JR, Deplazes, E, Motygullina, A, Tan, A, Ganio, K, Neville, SL, Eleftheriadis, N, Isselstein, M, Pederick, VG, Paton, JC, Cordes, T, Harmer, JR, Kobe, B & McDevitt, CA 2021, 'A Trap-Door Mechanism for Zinc Acquisition by Streptococcus pneumoniae AdcA.', mBio.
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Ma, H, Wang, T, Li, J, Yang, J, Liu, Z, Wang, N, Su, D & Wang, C 2021, 'Nitrogen Doped Carbon Coated Bi Microspheres as High-performance Anode for Half and Full Sodium Ion Batteries', CHEMISTRY-AN ASIAN JOURNAL.
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Ma, J, Li, Y, Grundish, NS, Goodenough, JB, Chen, Y, Guo, L, Peng, Z, Qi, X, Yang, F, Qie, L, Wang, C-A, Huang, B, Huang, Z, Chen, L, Su, D, Wang, G, Peng, X, Chen, Z, Yang, J, He, S, Zhang, X, Yu, H, Fu, C, Jiang, M, Deng, W, Sun, C-F, Pan, Q, Tang, Y, Li, X, Ji, X, Wan, F, Niu, Z, Lian, F, Wang, C, Wallace, GG, Fan, M, Meng, Q, Xin, S, Guo, Y-G & Wan, L-J 2021, 'The 2021 battery technology roadmap', Journal of Physics D.
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Mac Aogáin, M, Narayana, JK, Tiew, PY, Ali, NABM, Yong, VFL, Jaggi, TK, Lim, AYH, Keir, HR, Dicker, AJ, Thng, KX, Tsang, A, Ivan, FX, Poh, ME, Oriano, M, Aliberti, S, Blasi, F, Low, TB, Ong, TH, Oliver, B, Giam, YH, Tee, A, Koh, MS, Abisheganaden, JA, Tsaneva-Atanasova, K, Chalmers, JD & Chotirmall, SH 2021, 'Integrative microbiomics in bronchiectasis exacerbations', Nature Medicine.
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Macaulay, M & Rognon, P 2021, 'Viscosity of cohesive granular flows', SOFT MATTER, vol. 17, no. 1, pp. 165-173.
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Macnamara, J 2021, 'Challenging post-communication: Beyond focus on a ‘few bad apples’ to multi-level public communication reform', Communication Research and Practice.
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Since declaration of post-truth as Oxford Dictionaries’ word of the year in 2016, studies show that ‘fake news’, ‘alternative facts’, and disinformation have continued unabated—and even increased. Fingers have pointed at individuals such as Donald Trump and the activities of Russian ‘troll farms’. Also, global outrage has risen in relation to the deceptive and manipulative practices of organisations such as Cambridge Analytica and social media oligopolies, notably Facebook. However, transdisciplinary research challenges the ‘few bad apples’ argument and proposes that a wide range of culprits are responsible for what this study calls post-communication. Based on review of reports and commentary related to public communication practices, and key informant interviews, this discussion proposes that reforms are required at three levels: top-down, such as updated regulation and legislation; bottom-up, including new approaches to media literacy; and increased attention to ethics and standards by those in the middle of the post-truth phenomenon—professionals in advertising, marketing, public relations, government and political communication, and journalism.

Macnamara, J 2021, 'New insights into crisis communication from an ‘inside’ emic perspective during COVID-19', Public Relations Inquiry.
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As the COVID-19 pandemic spread across the world, requiring emergency management by health authorities and providers, it created flow-on crises and ‘crisis contagion’ for organizations ranging from international airlines and tourism operators to local businesses, schools, and universities. In addition to the risks directly associated with the health emergency, many organizations were plunged into crisis because of severe restrictions to their operations and income losses. This analysis examines crisis communication in an organization faced with major financial losses, staff redundancies, and disruption. It analyses how these and necessary crisis responses were communicated to stakeholders, using situational crisis communication theory (SCCT), as its analytical framework. While noting alternative perspectives such as crisis and emergency risk communication (CERC) theory, SCCT is identified as the most widely applied theory of crisis communication, and thus warrants ongoing review in an era of media fragmentation, disinformation, and low public trust. Furthermore, this analysis provides a relatively rare ‘inside’ (emic) perspective through ethnography and autoethnography conducted by a senior decision-maker in the organization studied, which expands traditional outside (etic) perspectives and offers new insights into crisis communication.

Maddahfar, M, Wen, S, Mashkani, SMH, Zhang, L, Shimoni, O, Stenzel, M, Zhou, J, Groth, BFDS & Jin, D 2021, 'Stable and Highly Efficient Antibody-Nanoparticles Conjugation', BIOCONJUGATE CHEMISTRY, vol. 32, no. 6, pp. 1146-1155.
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Mai-Prochnow, A, Zhou, R, Zhang, T, Ostrikov, KK, Mugunthan, S, Rice, SA & Cullen, PJ 2021, 'Interactions of plasma-activated water with biofilms: inactivation, dispersal effects and mechanisms of action', npj Biofilms and Microbiomes.
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Maire, J, Girvan, SK, Barkla, SE, Perez-Gonzalez, A, Suggett, DJ, Blackall, LL & van Oppen, MJH 2021, 'Intracellular bacteria are common and taxonomically diverse in cultured and in hospite algal endosymbionts of coral reefs', ISME Journal.
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© 2021, The Author(s). Corals house a variety of microorganisms which they depend on for their survival, including endosymbiotic dinoflagellates (Symbiodiniaceae) and bacteria. While cnidarian–microorganism interactions are widely studied, Symbiodiniaceae–bacteria interactions are only just beginning to receive attention. Here, we describe the localization and composition of the bacterial communities associated with cultures of 11 Symbiodiniaceae strains from nine species and six genera. Three-dimensional confocal laser scanning and electron microscopy revealed bacteria are present inside the Symbiodiniaceae cells as well as closely associated with their external cell surface. Bacterial pure cultures and 16S rRNA gene metabarcoding from Symbiodiniaceae cultures highlighted distinct and highly diverse bacterial communities occur intracellularly, closely associated with the Symbiodiniaceae outer cell surface and loosely associated (i.e., in the surrounding culture media). The intracellular bacteria are highly conserved across Symbiodiniaceae species, suggesting they may be involved in Symbiodiniaceae physiology. Our findings provide unique new insights into the biology of Symbiodiniaceae.

Maisonhaute, JÉ & Forbes, SL 2021, 'Decomposition process and arthropod succession on pig carcasses in Quebec (Canada)', Journal of the Canadian Society of Forensic Science.
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© 2020 Canadian Society of Forensic Science. Necrophagous arthropods are essential ecosystem decomposers and are important indicator species in the discipline of forensic entomology. Studies around the world have evaluated the succession of arthropods on animal carcasses, but no published data are available for the province of Quebec (Canada). The objective of this study was to evaluate the diversity of arthropods associated with pig carcasses in Quebec, and to determine the colonization sequence of the different families/species throughout the decomposition process. Three pig carcasses were deposited in a small woodland area in Trois-Rivières, in mid-June 2019. The decomposition process and the arthropod community were studied until the beginning of November (first snowfall) by visual observation, and sample collection on the carcasses, using an entomological net and pitfall traps. Five species of blow fly (Diptera: Calliphoridae) were found to lay eggs on the carcasses: Calliphora livida, C. vomitoria, Lucilia illustris, Phormia regina, and Protophormia terraenovae. Eggs/larvae of the first three species were recorded during the first week only (fresh stage-beginning of active decay), while the other two species were recorded throughout the decomposition process until the dry remains stage. Coleoptera were observed from day 0 to day 141 (end of experiment). Some families/species were associated with early stages of decomposition (e.g. Necrophila americana, Silphidae), while others were only found during the dry remains stage (e.g. Carnicops pumilio, Histeridae).

Maisonhaute, J-É & Forbes, SL 2021, 'Overwintering behaviour of the skipper fly (Diptera: Piophilidae) of forensic importance in Québec, Canada', The Canadian Entomologist, vol. 153, no. 2, pp. 172-180.
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AbstractLaboratory experiments and field observations from August 2019 to April 2020 demonstrated that skipper flies (Diptera: Piophilidae) overwinter as larvae and likely present an obligatory winter diapause in Québec, Canada. Diapause was confirmed by the very few emergences of adults in the laboratory following collection from carrion at the end of summer and in fall, the migration of larvae deep in the soil, and the persistence of larvae inside carrion during the winter until the following spring when they became active again and initiated pupation (i.e., intra-puparial period). To our knowledge, our observations represent the first report of the overwintering of skipper fly larvae inside an animal carcass in North America. In addition, this winter diapause should be considered in forensic entomology when using the presence of skipper fly larvae on a body to estimate the time elapsed since death.

Mandwie, M, Piper, J, Gorrie, C, Keay, K, Musumeci, G, Al-Badri, G & Castorina, A 2021, 'Rapid GFAP and Iba1 Expression Changes in the Female Rat Brain following Spinal Cord Injury', Neural Regeneration Research.
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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.

Manning, EE, Bradfield, LA & Iordanova, MD 2021, 'Adaptive behaviour under conflict: Deconstructing extinction, reversal, and active avoidance learning.', Neuroscience and biobehavioral reviews.
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In complex environments, organisms must respond adaptively to situations despite conflicting information. Under natural (i.e. non-laboratory) circumstances, it is rare that cues or responses are consistently paired with a single outcome. Inconsistent pairings are more common, as are situations where cues and responses are associated with multiple outcomes. Such inconsistency creates conflict, and a response that is adaptive in one scenario may not be adaptive in another. Learning to adjust responses accordingly is important for species to survive and prosper. Here we review the behavioural and brain mechanisms of responding under conflict by focusing on three popular behavioural procedures: extinction, reversal learning, and active avoidance. Extinction involves adapting from reinforcement to non-reinforcement, reversal learning involves swapping the reinforcement of cues or responses, and active avoidance involves performing a response to avoid an aversive outcome, which may conflict with other defensive strategies. We note that each of these phenomena relies on somewhat overlapping neural circuits, suggesting that such circuits may be critical for the general ability to respond appropriately under conflict.

Martins Costa Gomes, G, de Gouveia Belinelo, P, Starkey, MR, Murphy, VE, Hansbro, PM, Sly, PD, Robinson, PD, Karmaus, W, Gibson, PG, Mattes, J & Collison, AM 2021, 'Cord blood group 2 innate lymphoid cells are associated with lung function at 6 weeks of age.', Clinical & translational immunology, vol. 10, no. 7, p. e1296.
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Objective

Offspring born to mothers with asthma in pregnancy are known to have lower lung function which tracks with age. Human group 2 innate lymphoid cells (ILC2) accumulate in foetal lungs, at 10-fold higher levels compared to adult lungs. However, there are no data on foetal ILC2 numbers and the association with respiratory health outcomes such as lung function in early life. We aimed to investigate cord blood immune cell populations from babies born to mothers with asthma in pregnancy.

Methods

Cord blood from babies born to asthmatic mothers was collected, and cells were stained in whole cord blood. Analyses were done using traditional gating approaches and computational methodologies (t-distributed stochastic neighbour embedding and PhenoGraph algorithms). At 6 weeks of age, the time to peak tidal expiratory flow as a percentage of total expiratory flow time (tPTEF/tE%) was determined as well as Lung Clearance Index (LCI), during quiet natural sleep.

Results

Of 110 eligible infants (March 2017 to November 2019), 91 were successfully immunophenotyped (82.7%). Lung function was attempted in 61 infants (67.0%), and 43 of those infants (70.5% of attempted) had technically acceptable tPTEF/tE% measurements. Thirty-four infants (55.7% of attempted) had acceptable LCI measurements. Foetal ILC2 numbers with increased expression of chemoattractant receptor-homologous molecule (CRTh2), characterised by two distinct analysis methodologies, were associated with poorer infant lung function at 6 weeks of age."

Conclusion

Foetal immune responses may be a surrogate variable for or directly influence lung function outcomes in early life.

Martins Costa Gomes, G, Karmaus, W, Murphy, VE, Gibson, PG, Percival, E, Hansbro, PM, Starkey, MR, Mattes, J & Collison, AM 2021, 'Environmental Air Pollutants Inhaled during Pregnancy Are Associated with Altered Cord Blood Immune Cell Profiles', International Journal of Environmental Research and Public Health.
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Massella, E, Giacometti, F, Bonilauri, P, Reid, CJ, Djordjevic, SP, Merialdi, G, Bacci, C, Fiorentini, L, Massi, P, Bardasi, L, Rubini, S, Savini, F, Serraino, A & Piva, S 2021, 'Antimicrobial Resistance Profile and ExPEC Virulence Potential in Commensal Escherichia coli of Multiple Sources.', Antibiotics.
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Maugeri, G, D’Agata, V, Magrì, B, Roggio, F, Castorina, A, Ravalli, S, Di Rosa, M & Musumeci, G 2021, 'Neuroprotective Effects of Physical Activity via the Adaptation of Astrocytes', Cells.
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McDonald, A, Murray, BR, Krix, D & Murray, M 2021, 'Complex soil contamination severely impacts seed-sown crop viability in Australia', Australian Journal of Crop Science, vol. 15, no. 4, pp. 531-537.
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Food security is a critical issue for many global communities. Heavy metal contaminationin soilspresenta majorand ongoingecologicalriskassociated with human activitieswhich may impactthe viability and safety ofseed-sown crops. To better understand the impacts of soil contamination by heavy metals on seed-sown crop viability, we examined germination responses of eight commercially-important fruit and vegetablecropspecies to copper, zinc, andleadcontaminationat levels likely to be foundin contaminated regions inAustralia. We compared the germination attributes of days to first germination, germination period, and total proportion of seeds germinated underconcentrationlimitsof heavy metals detectedat degraded sites andcurrentAustralianNational Environment Protection Measure thresholds for domestic soils (i.e., copper 6,000 mgkg-1, zinc 4,700 mgkg-1, lead 300 mgkg-1). Thecombined heavy metal treatment (i.e. all three metals) significantly inhibited germination for all edible crop species with only carrots able to germinate under complex, multi-metal-contaminatedconditions. Seed viability was significantly decreasedin mulberry (M.alba var.tatarica, M. nigra, and M. rubra) andlettuce(L. sativa),with loweredseed germination in all metalscomparedtocarrot(D. carota),radish(R. sativus), tomato(S. lycopersicum) andcommon bean(P. vulgaris). These results indicate heavy metal contamination is a notable risk to seed-sown crop species, with multi-metal contaminationeventslikely to be severely damagingto lettuce, tomato, radish, common bean, and mulberry crops.

McNally, R, Alqudah, A, McErlean, EM, Rennie, C, Morshed, N, Short, A, McGrath, K, Shimoni, O, Robson, T, McCarthy, HO & McClements, L 2021, 'Non-viral gene delivery utilizing RALA modulates sFlt-1 secretion, important for preeclampsia', NANOMEDICINE, vol. 16, no. 22, pp. 1999-2012.
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McNeilly, O, Mann, R, Hamidian, M & Gunawan, C 2021, 'Emerging Concern for Silver Nanoparticle Resistance in Acinetobacter baumannii and Other Bacteria', Frontiers in Microbiology.
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Meakin, GE, Kokshoorn, B, van Oorschot, RAH & Szkuta, B 2021, 'Evaluating forensic DNA evidence: Connecting the dots', WIREs Forensic Science.
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Mehta, M, Paudel, KR, Panth, N, Xenaki, D, Macloughlin, R, Oliver, BG, Lobenberg, R, Hansbro, PM, Chellappan, DK & Dua, K 2021, 'Drug delivery advances in mitigating inflammation via matrix metalloproteinases in respiratory diseases', NANOMEDICINE, vol. 16, no. 6, pp. 437-439.
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Mehta, M, Paudel, KR, Shukla, SD, Allam, VSRR, Kannaujiya, VK, Panth, N, Das, A, Parihar, VK, Chakraborty, A, Ali, K, Jha, NK, Xenaki, D, Su, QP, Wich, PR, Adams, J, Hansbro, PM, Chellappan, DK, Oliver, BGG & Dua, K 2021, 'Recent trends of NFκB decoy oligodeoxynucleotide-based nanotherapeutics in lung diseases', Journal of Controlled Release.
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Mehta, M, Paudel, KR, Shukla, SD, Shastri, MD, Satija, S, Singh, SK, Gulati, M, Dureja, H, Zacconi, FC, Hansbro, PM, Chellappan, DK & Dua, K 2021, 'Rutin-loaded liquid crystalline nanoparticles attenuate oxidative stress in bronchial epithelial cells: a PCR validation', FUTURE MEDICINAL CHEMISTRY, vol. 13, no. 6, pp. 543-549.
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Mehta, M, Satija, S, Paudel, KR, Malyla, V, Kannaujiya, VK, Chellappan, DK, Bebawy, M, Hansbro, PM, Wich, PR & Dua, K 2021, 'Targeting respiratory diseases using miRNA inhibitor based nanotherapeutics: Current status and future perspectives.', Nanomedicine: Nanotechnology, Biology and Medicine, vol. 31.
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MicroRNAs (miRNAs) play a fundamental role in the developmental and physiological processes that occur in both animals and plants. AntagomiRs are synthetic antagonists of miRNA, prevent the target mRNA from suppression. Therapeutic approaches that modulate miRNAs have immense potential in the treatment of chronic respiratory disorders. However, the successful delivery of miRNAs/antagomiRs to the lungs remains a major challenge in clinical applications. A range of materials, namely, polymer nanoparticles, lipid nanocapsules and inorganic nanoparticles have shown promising results for intracellular delivery of miRNA in chronic respiratory disorders. This review discusses the current understanding of miRNA biology, the biological roles of antagomiRs in chronic respiratory disease and the recent advances in the therapeutic utilization of antagomiRs as disease biomarkers. Furthermore our review provides a common platform to debate on the nature of antagomiRs and also address the viewpoint on the new generation of delivery systems that target antagomiRs in respiratory diseases.

Mei, S, Zhou, J, Sun, H, Cai, Y, Sun, L, Jin, D & Yan, C 2021, 'Networking State of Ytterbium Ions Probing the Origin of Luminescence Quenching and Activation in Nanocrystals', Advanced Science.
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Mello, MG, Westerhausen, MT, Singh, P, Doble, PA, Wanagat, J & Bishop, DP 2021, 'Assessing the reproducibility of labelled antibody binding in quantitative multiplexed immuno-mass spectrometry imaging', Analytical and Bioanalytical Chemistry.
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Immuno-mass spectrometry imaging (iMSI) uses laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) to determine the spatial expression of biomolecules in tissue sections following immunolabelling with antibodies conjugated to a metal reporter. As with all immunolabelling techniques, the binding efficiency of multiplexed staining can be affected by a number of factors including epitope blocking and other forms of steric hindrance. To date, the effects on the binding of metal-conjugated antibodies to their epitopes in a multiplexed analysis have yet to be quantitatively explored by iMSI. Here we describe a protocol to investigate the effects of multiplexing on reproducible binding using the muscle proteins, dystrophin, sarcospan, and myosin as a model, with antibodies conjugated with Maxpar® reagents before histological application to murine quadriceps sections using standard immunolabelling protocols and imaging with LA-ICP-MS. The antibodies were each individually applied to eight sections, and multiplexed to another eight sections. The average concentrations of the lanthanide analytes were determined, before statistical analyses found there was no significant difference between the individual and multiplexed application of the antibodies. These analyses provide a framework for ensuring reproducibility of antibody binding during multiplexed iMSI, which will allow quantitative exploration of protein-protein interactions and provide a greater understanding of fundamental biological processes during healthy and diseased states. Graphical abstract: [Figure not available: see fulltext.]

Menictas, M, Nolan, TH, Simpson, DG & Wand, MP 2021, 'Streamlined variational inference for higher level group-specific curve models', Statistical Modelling: An International Journal.
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© 2020 Statistical Modeling Society. A two-level group-specific curve model is such that the mean response of each member of a group is a separate smooth function of a predictor of interest. The three-level extension is such that one grouping variable is nested within another one, and higher level extensions are analogous. Streamlined variational inference for higher level group-specific curve models is a challenging problem. We confront it by systematically working through two-level and then three-level cases and making use of the higher level sparse matrix infrastructure laid down in (Nolan and Wand (2020), ANZIAM Journal, doi: 10.1017/S1446181120000061). A motivation is analysis of data from ultrasound technology for which three-level group-specific curve models are appropriate. Whilst extension to the number of levels exceeding three is not covered explicitly, the pattern established by our systematic approach sheds light on what is required for even higher level group-specific curve models.

Menounos, S, Hansbro, PM, Diwan, AD & Das, A 2021, 'Pathophysiological Correlation between Cigarette Smoking and Amyotrophic Lateral Sclerosis', NeuroSci.
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Messer, LF, Brown, MV, Van Ruth, PD, Doubell, M & Seymour, JR 2021, 'Temperate southern Australian coastal waters are characterised by surprisingly high rates of nitrogen fixation and diversity of diazotrophs', PeerJ.
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Meyer, F, Lesker, T-R, Koslicki, D, Fritz, A, Gurevich, A, Darling, AE, Sczyrba, A, Bremges, A & McHardy, AC 2021, 'Tutorial: assessing metagenomics software with the CAMI benchmarking toolkit', NATURE PROTOCOLS.
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Miyaji, N, Shimizu, M, Takasaki-Yasuda, T, Dennis, ES & Fujimoto, R 2021, 'The transcriptional response to salicylic acid plays a role in Fusarium yellows resistance in Brassica rapa L.', PLANT CELL REPORTS, vol. 40, no. 4, pp. 605-619.
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Mizerek, TL, Madin, JS, Benzoni, F, Huang, D, Luiz, OJ, Mera, H, Schmidt-Roach, S, Smith, SDA, Sommer, B & Baird, AH 2021, 'No evidence for tropicalization of coral assemblages in a subtropical climate change hot spot', Coral Reefs, vol. 40, no. 5, pp. 1451-1461.
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Climate change is causing the distribution and abundance of many organisms to change. In particular, organisms typical of the tropics are increasing in abundance in many subtropical regions, a process known as tropicalization. Here, we examine changes in coral abundance and assemblage structure in the Solitary Islands Marine Park (SIMP), over a 23-year period between 1990 and 2013–14. Total coral cover decreased at all six islands sampled with a concomitant decline in total coral cover at the regional scale (i.e. between sampling occasions). When coral taxa were classified as either cosmopolitan or subtropical, cosmopolitan corals decreased in cover at the regional scale. In contrast, subtropical coral cover did not change at the regional scale because large increases in cover at some islands, such as North Solitary Island, were matched by decreases at other islands. Of 16 common coral taxa examined at the regional level, one declined and two increased in cover with no change in the remaining 13 taxa. In particular, there was no increase in the abundance of coral taxa typically associated with tropical reefs. Similarly, multivariate analyses of coral assemblage structure using these 16 common taxa indicated changes in two of the six island assemblages but, again, provided no evidence for tropicalization. Modelling suggested very low probabilities of larval dispersal from the southern Great Barrier Reef to the SIMP suggesting that limited connectivity with tropical coral populations is one possible cause of the lack of tropicalization in the coral assemblages. We therefore conclude that, despite significant increases in mean sea surface temperature over the last few decades, there has been no tropicalization of the coral fauna in the SIMP. Furthermore, the small proportional reduction in total coral cover, despite the occasional incidence of coral bleaching, coral disease outbreaks and a number of large storms, suggest that the reefs of the SIMP were in reasonably...

Moecking, J, Laohamonthonkul, P, Chalker, K, White, MJ, Harapas, CR, Yu, CH, Davidson, S, Hrovat-Schaale, K, Hu, D, Eng, C, Huntsman, S, Calleja, DJ, Horvat, JC, Hansbro, PM, O'Donoghue, RJJ, Ting, JP, Burchard, EG, Geyer, M, Gerlic, M & Masters, SL 2021, 'NLRP1 variant M1184V decreases inflammasome activation in the context of DPP9 inhibition and asthma severity', Journal of Allergy and Clinical Immunology.
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© 2020 The Authors Background: NLRP1 is an innate immune sensor that can form cytoplasmic inflammasome complexes. Polymorphisms in NLRP1 are linked to asthma; however, there is currently no functional or mechanistic explanation for this. Objective: We sought to clarify the role of NLRP1 in asthma pathogenesis. Methods: Results from the GALA II cohort study were used to identify a link between NLRP1 and asthma in Mexican Americans. In vitro and in vivo models for NLRP1 activation were applied to investigate the role of this inflammasome in asthma at the molecular level. Results: We document the association of an NLRP1 haplotype with asthma for which the single nucleotide polymorphism rs11651270 (M1184V) individually is the most significant. Surprisingly, M1184V increases NLRP1 activation in the context of N-terminal destabilization, but decreases NLRP1 activation on dipeptidyl peptidase 9 inhibition. In vitro studies demonstrate that M1184V increases binding to dipeptidyl peptidase 9, which can account for its inhibitory role in this context. In addition, in vivo data from a mouse model of airway inflammation reveal a protective role for NLRP1 inflammasome activation reducing eosinophilia in this setting. Conclusions: Linking our in vitro and in vivo results, we found that the NLRP1 variant M1184V reduces inflammasome activation in the context of dipeptidyl peptidase 9 inhibition and could thereby increase asthma severity. Our studies may have implications for the treatment of asthma in patients carrying this variant of NLRP1.

Mohamed, A, Chan, H, Luhur, J, Bauda, E, Gallet, B, Morlot, C, Cole, L, Awad, M, Crawford, S, Lyras, D, Rudner, DZ & Rodrigues, CDA 2021, 'Chromosome Segregation and Peptidoglycan Remodeling Are Coordinated at a Highly Stabilized Septal Pore to Maintain Bacterial Spore Development.', Developmental Cell, vol. 56, no. 1, pp. 36-51.e5-36-51.e5.
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Asymmetric division, a hallmark of endospore development, generates two cells, a larger mother cell and a smaller forespore. Approximately 75% of the forespore chromosome must be translocated across the division septum into the forespore by the DNA translocase SpoIIIE. Asymmetric division also triggers cell-specific transcription, which initiates septal peptidoglycan remodeling involving synthetic and hydrolytic enzymes. How these processes are coordinated has remained a mystery. Using Bacillus subtilis, we identified factors that revealed the link between chromosome translocation and peptidoglycan remodeling. In cells lacking these factors, the asymmetric septum retracts, resulting in forespore cytoplasmic leakage and loss of DNA translocation. Importantly, these phenotypes depend on septal peptidoglycan hydrolysis. Our data support a model in which SpoIIIE is anchored at the edge of a septal pore, stabilized by newly synthesized peptidoglycan and protein-protein interactions across the septum. Together, these factors ensure coordination between chromosome translocation and septal peptidoglycan remodeling to maintain spore development.

Mohd Yusop, AY, Xiao, L & Fu, S 2021, 'Liquid chromatography-high-resolution mass spectrometry analysis of erectile dysfunction drugs and their analogues in food products', Forensic Science International, pp. 110748-110748.
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The presence of erectile dysfunction (ED) drugs in adulterated dietary supplements, mainly in pharmaceutical dosage forms, is frequently addressed in the literature. Little attention is given to food products despite their increasing adulteration trend. To address this knowledge gap targeted, suspected-target, and non-targeted strategies were utilised to analyse ED drugs and their analogues in powdered drink mix (PDM), honey, jelly, hard candy, and sugar-coated chewing gum using liquid chromatography-high-resolution mass spectrometry (LC-HRMS). The method was optimised and validated using 23 target analytes, representing different ED drugs with structural similarities. The modified quick, easy, cheap, effective, rugged, and safe (QuEChERS) extraction exhibited insignificant matrix effect (ME) within -9.2%–8.8% and provided complete coverage of target analytes with acceptable extraction recovery (RE) within 75.5%–123.9%, except for carbodenafil in the PDM matrix. Based on the ME and RE performance, the analytical method was validated to analyse 25 food samples that claimed to enhance male sexual performance. The method exhibited good specificity and linearity with a limit of detection within 10–70 ng/mL and limit of quantification of 80 ng/mL. Similarly, the accuracy and precision were satisfactory within 77.4%–122.0% and <16.7%RSD, respectively. The LC-HRMS targeted analysis, together with suspected-target and non-targeted screenings, identified and detected ten ED drugs from 24 food samples. The modified QuEChERS extraction with LC-HRMS-based method was demonstrated to be universally applicable to various food products, covering an extensive range of known and potentially novel ED drugs, which is valuable for routine casework.

Monaco, CJ, Booth, DJ, Figueira, WF, Gillanders, BM, Schoeman, DS, Bradshaw, CJA & Nagelkerken, I 2021, 'Natural and anthropogenic climate variability shape assemblages of range-extending coral-reef fishes', JOURNAL OF BIOGEOGRAPHY, vol. 48, no. 5, pp. 1063-1075.
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Morshedi Rad, D, Alsadat Rad, M, Razavi Bazaz, S, Kashaninejad, N, Jin, D & Ebrahimi Warkiani, M 2021, 'Intracellular Delivery: A Comprehensive Review on Intracellular Delivery (Adv. Mater. 13/2021)', Advanced Materials, vol. 33, no. 13, pp. 2170103-2170103.
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Nan, J, Guo, X, Xiao, J, Li, X, Chen, W, Wu, W, Liu, H, Wang, Y, Wu, M & Wang, G 2021, 'Nanoengineering of 2D MXene-Based Materials for Energy Storage Applications.', Small (Weinheim an der Bergstrasse, Germany).
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2D MXene-based nanomaterials have attracted tremendous attention because of their unique physical/chemical properties and wide range of applications in energy storage, catalysis, electronics, optoelectronics, and photonics. However, MXenes and their derivatives have many inherent limitations in terms of energy storage applications. In order to further improve their performance for practical application, the nanoengineering of these 2D materials is extensively investigated. In this Review, the latest research and progress on 2D MXene-based nanostructures is introduced and discussed, focusing on their preparation methods, properties, and applications for energy storage such as lithium-ion batteries, sodium-ion batteries, lithium-sulfur batteries, and supercapacitors. Finally, the critical challenges and perspectives required to be addressed for the future development of these 2D MXene-based materials for energy storage applications are presented.

Nazrul Islam, SMK, Mayank, P, Ouyang, Y, Chen, J, Sagotra, AK, Li, M, Cortie, MB, Mole, R, Cazorla, C, Yu, D, Wang, X, Robinson, RA & Cortie, DL 2021, 'Copper Diffusion Rates and Hopping Pathways in Superionic Cu2Se', Acta Materialia, pp. 117026-117026.
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Nelson, MP, Batavia, C, Brandis, KJ, Carroll, SP, Celermajer, D, Linklater, W, Lundgren, E, Ramp, D, Steer, J, Yanco, E & Wallach, AD 2021, 'Challenges at the intersection of conservation and ethics: Reply to Meyer et al. 2021.', Conservation Biology, vol. 35, no. 1, pp. 373-377.
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Nguyen, AQ, Vu, HP, Nguyen, LN, Wang, Q, Djordjevic, SP, Donner, E, Yin, H & Nghiem, LD 2021, 'Monitoring antibiotic resistance genes in wastewater treatment: Current strategies and future challenges', Science of the Total Environment, vol. 783.
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Antimicrobial resistance (AMR) is a growing threat to human and animal health. Progress in molecular biology has revealed new and significant challenges for AMR mitigation given the immense diversity of antibiotic resistance genes (ARGs), the complexity of ARG transfer, and the broad range of omnipresent factors contributing to AMR. Municipal, hospital and abattoir wastewater are collected and treated in wastewater treatment plants (WWTPs), where the presence of diverse selection pressures together with a highly concentrated consortium of pathogenic/commensal microbes create favourable conditions for the transfer of ARGs and proliferation of antibiotic resistant bacteria (ARB). The rapid emergence of antibiotic resistant pathogens of clinical and veterinary significance over the past 80 years has re-defined the role of WWTPs as a focal point in the fight against AMR. By reviewing the occurrence of ARGs in wastewater and sludge and the current technologies used to quantify ARGs and identify ARB, this paper provides a research roadmap to address existing challenges in AMR control via wastewater treatment. Wastewater treatment is a double-edged sword that can act as either a pathway for AMR spread or as a barrier to reduce the environmental release of anthropogenic AMR. State of the art ARB identification technologies, such as metagenomic sequencing and fluorescence-activated cell sorting, have enriched ARG/ARB databases, unveiled keystone species in AMR networks, and improved the resolution of AMR dissemination models. Data and information provided in this review highlight significant knowledge gaps. These include inconsistencies in ARG reporting units, lack of ARG/ARB monitoring surrogates, lack of a standardised protocol for determining ARG removal via wastewater treatments, and the inability to support appropriate risk assessment. This is due to a lack of standard monitoring targets and agreed threshold values, and paucity of information on the ARG-pathogen host...

Nguyen, MAP, Hite, J, Mastro, MA, Kianinia, M, Toth, M & Aharonovich, I 2021, 'Site control of quantum emitters in gallium nitride by polarity', APPLIED PHYSICS LETTERS, vol. 118, no. 2.
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Nguyen, VK, King, WL, Siboni, N, Mahbub, KR, Rahman, MH, Jenkins, C, Dove, M, O'Connor, W, Seymour, JR & Labbate, M 2021, 'Dynamics of the Sydney rock oyster microbiota before and during a QX disease event', AQUACULTURE, vol. 541.
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Niaz, A, Karunia, J, Mandwie, M, Keay, KA, Musumeci, G, Al-Badri, G & Castorina, A 2021, 'Robust Dopaminergic Differentiation and Enhanced LPS-Induced Neuroinflammatory Response in Serum-Deprived Human SH-SY5Y Cells: Implication for Parkinson's Disease.', Journal of molecular neuroscience : MN.
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Parkinson's disease (PD) is a chronic neurodegenerative condition characterized by motor symptoms such as bradykinesia, resting tremor, and rigidity. PD diagnosis is based on medical history, review of signs, symptoms, neurological and physical examinations. Unfortunately, by the time the disease is diagnosed, dopamine (DA) neuronal loss is often extended, thereby resulting in ineffective therapies. Recent evidence suggests that neuroinflammation may be pivotal during PD onset and progression. However, suitable cellular models and biomarkers to detect early signs of neuroinflammation are still missing. In this study, we developed a well-differentiated DAergic neuronal cell line where we triggered a neuroinflammatory response to assess the temporal expression of the tissue- and urokinase plasminogen activators (tPA and uPA) and their endogenous inhibitor (PAI-1) along with that of pro-inflammatory mediators and the neuronal marker nNOS. Human neuroblastoma cells SH-SY5Y were differentiated into DAergic neuronal-like cells using a combination of 12-O-tetradecanoylphorbol-13-acetate (TPA) and serum depletion. Terminally-differentiated neurons were then exposed to lipopolysaccharide (LPS) for short (up to 24 h) or long term (up to 10 days) to mimic acute or chronic inflammation. Results demonstrated that uPA protein expression was stably upregulated during chronic inflammation, whereas the expression of nNOS protein better reflected the cellular response to acute inflammation. Additional studies revealed that the temporal induction of uPA was associated with increased AKT phosphorylation, but did not seem to involve cAMP-responsive element-binding protein (CREB) activation, nor the mitogen-activated protein kinase (MAPK) pathway. In conclusion, our in vitro data suggests that nNOS and uPA may serve as viable candidate biomarkers of acute and chronic neuroinflammation.

Nieves, OA, Arnold, MD, Steel, MJ, Schmidt, MK & Poulton, CG 2021, 'Noise and pulse dynamics in backward stimulated Brillouin scattering', OPTICS EXPRESS, vol. 29, no. 3, pp. 3132-3146.
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Nieves, OA, Arnold, MD, Steel, MJ, Schmidt, MK & Poulton, CG 2021, 'Numerical simulation of noise in pulsed Brillouin scattering', JOURNAL OF THE OPTICAL SOCIETY OF AMERICA B-OPTICAL PHYSICS, vol. 38, no. 8, pp. 2343-2352.
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Nikolaeva, A, Frizyuk, K, Olekhno, N, Solntsev, A & Petrov, M 2021, 'Directional emission of down-converted photons from a dielectric nanoresonator', Physical Review A.
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Nolan, L, Turnbull, L, Katrib, M, Osvath, S, Losa, D & Whitchurch, C 2021, 'Pseudomonas aeruginosa is capable of natural transformation in biofilms'.
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Abstract Natural transformation is a mechanism that enables competent bacteria to acquire naked, exogenous DNA from the environment. It is a key process that facilitates the dissemination of antibiotic resistance and virulence determinants throughout bacterial populations. Pseudomonas aeruginosa is an opportunistic Gram-negative pathogen that produces large quantities of extracellular DNA (eDNA) that is required for biofilm formation. P. aeruginosa has a remarkable level of genome plasticity and diversity that suggests a high degree of horizontal gene transfer and recombination but is thought to be incapable of natural transformation. Here we show that P. aeruginosa possesses homologs of all proteins known to be involved in natural transformation in other bacterial species. We found that P. aeruginosa in biofilms is competent for natural transformation of both genomic and plasmid DNA. Furthermore, we demonstrate that type IV pili (T4P) facilitate but are not absolutely essential for natural transformation in P. aeruginosa .

Nonahal, M, White, SJU, Regan, B, Li, C, Trycz, A, Kim, S, Aharonovich, I & Kianinia, M 2021, 'Bottom-Up Synthesis of Single Crystal Diamond Pyramids Containing Germanium Vacancy Centers', Advanced Quantum Technologies.
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Diamond resonators containing color-centers are highly sought after for application in quantum technologies. Bottom-up approaches are promising for the generation of single-crystal diamond structures with purposely introduced color centers. Here the possibility of using a polycrystalline diamond to grow single-crystal diamond structures by employing a pattern growth method is demonstrated. For, the possible mechanism of growing a single-crystal structure with predefined shape and size from a polycrystalline substrate by controlling the growth condition is clarified. Then, by introducing germanium impurities during the growth, localized and enhanced emission from fabricated pyramid shaped single-crystal diamonds containing germanium vacancy (GeV) color centers is demonstrated. Finally, linewidth of ∼500 MHz at 4 K from a single GeV center in the pyramid shaped diamonds is measured. The method is an important step toward fabrication of 3D structures for integrated diamond photonics.

Nucera, F, Lo Bello, F, Shen, SS, Ruggeri, P, Coppolino, I, Di Stefano, A, Stellato, C, Casolaro, V, Hansbro, PM, Adcock, IM & Caramori, G 2021, 'Role of Atypical Chemokines and Chemokine Receptors Pathways In the Pathogenesis of COPD', Current Medicinal Chemistry, vol. 28, no. 13.
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Chronic obstructive pulmonary disease (COPD) represents a heightened inflammatory response in the lung generally resulting from tobacco smoking-induced recruitment and activation of inflammatory cells and/or activation of lower airway structural cells. Several mediators can modulate activation and recruitment of these cells, particularly those belonging to the chemokines (conventional and atypical) family. There is emerging evidence for complex roles of atypical chemokines and their receptors [such as high mobility group box 1 (HMGB1), antimicrobial peptides, receptor for advanced glycosylation end products (RAGE) or toll-like receptors (TLRs)] in the pathogenesis of COPD, both in the stable disease and during exacerbations. Modulators of these pathways represent potential novel therapies for COPD and many are now in preclinical development. Inhibition of only a single atypical chemokine or receptor may not block inflammatory processes because there is redundancy in this network. However, there are many animal studies that encourage studies for modulating the atypical chemokine network in COPD. Thus, few pharmaceutical companies maintain a significant interest in developing agents that target these molecules as potential antiinflammatory drugs. Antibody-based (biological) and small molecule drug (SMD)-based therapies targeting atypical chemokines and/or their receptors are mostly at the preclinical stage and their progression to clinical trials is eagerly awaited. These agents will most likely enhance our knowledge about the role of atypical chemokines in COPD pathophysiology and thereby improve COPD management.

Olander, A, Lawson, CA, Possell, M, Raina, JB, Ueland, M & Suggett, DJ 2021, 'Comparative volatilomics of coral endosymbionts from one- and comprehensive two-dimensional gas chromatography approaches', Marine Biology, vol. 168, no. 5.
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Volatilomics, the examination of all biogenic volatile organic compounds (BVOCs) emitted by an organism or system, holds potential as a novel screening tool for taxonomy, fitness, and ecological functioning. Volatilomics has been largely applied to terrestrial environments, but highly productive coastal marine systems, which are major sources of specific BVOCs, such as dimethyl sulfide, have been largely neglected. Volatilomic measurements are highly method-dependent, with different instrumentation impacting the diversity of identified BVOCs—therefore, understanding these biases is critical to reconcile studies. Here, we investigated BVOCs emitted by two species of coral endosymbiotic microalgae (Symbiodinium tridacnidorum and Durusdinium trenchii) using gas chromatography–mass spectrometry (GC–MS) and comprehensive two-dimensional gas chromatography–time-of-flight mass spectrometry (GC × GC–TOFMS). Seven chemical classes were detected by both instruments, the most common being aromatic hydrocarbons. However, GC × GC resolved seven times more BVOCs than GC–MS (290 vs. 40), with a higher proportion of compounds tentatively identified (173 vs. 14). Notably, nine chemical classes were exclusively identified by GC × GC, including alkane, alkene, aldehyde, ester, and nitrile BVOCs—each potentially fulfilling undescribed functions in marine organisms. The microalgal species investigated shared a large proportion of BVOCs, and this result was consistent across instruments (97 and 98% shared compounds via GC × GC and GC–MS, respectively), suggesting consistent retrieval of general patterns between instruments. This method comparison is the first of its kind in marine systems and confirms the greater analytical power of GC × GC, required to help resolve complex BVOC emissions and the identification of their roles in marine systems.

O'Rourke, MB, Viengkhou, B, Smith, CC, Sonderegger, L, Padula, MP, Sutherland, GT, Hofer, MJ & Crossett, B 2021, 'Matrix phase fractionation: Investigating the compromise between dynamic range of analyte extraction and spatial resolution in mass spectrometry imaging', RAPID COMMUNICATIONS IN MASS SPECTROMETRY, vol. 35, no. 13.
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Pacitti, D, Scotton, CJ, Kumar, V, Khan, H, Wark, PAB, Torregrossa, R, Hansbro, PM & Whiteman, M 2021, 'Gasping for Sulfide: A Critical Appraisal of Hydrogen Sulfide in Lung Disease and Accelerated Aging', ANTIOXIDANTS & REDOX SIGNALING.
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Paijmans, KC, Booth, DJ & Wong, MYL 2021, 'Odd one in: Oddity within mixed-species shoals does not affect shoal preference by vagrant tropical damselfish in the presence or absence of a predator', Ethology.
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© 2020 Wiley-VCH GmbH Grouping behaviour displayed by animals is usually attributed to predation and foraging-related benefits. The mechanisms of predator protection and foraging efficiency are diverse and often produce conflicting drivers of grouping behaviour. One key conflict is that between group size and phenotypic oddity. Theoretically, individuals should choose the largest available group due to multiple mechanisms associated with “safety in numbers”. However, individuals should also choose the most phenotypically similar group members due to the “predator confusion effect”. This conflict is particularly important within the context of mixed-species groups because, while their formation may facilitate large group size, phenotypic differences between species may be costly due to oddity. To investigate the interacting effects of shoal size, composition and predator presence on grouping decisions, choice experiments were conducted using displaced tropical damselfish, Abudefduf vaigiensis, settling in temperate south-eastern Australia (termed vagrants) as a model species. Contrary to predictions, A. vaigiensis displayed no preference for single- over mixed-species shoals, with or without a predator present. These results suggest that shoal composition may not be an important driver of shoal choice in this system. Further, A. vaigiensis showed no preference for larger mixed-species shoals over smaller single-species shoals. These outcomes are discussed within the context of climate change-driven redistribution of A. vaigiensis in temperate south-eastern Australia.

Pamphlett, R, Doble, PA & Bishop, DP 2021, 'Mercury in the human thyroid gland: Potential implications for thyroid cancer, autoimmune thyroiditis, and hypothyroidism', PLOS ONE.
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Pamphlett, R, Kum Jew, S, Doble, PA & Bishop, DP 2021, 'Mercury in the human adrenal medulla could contribute to increased plasma noradrenaline in aging', Scientific Reports.
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Parast, L, Garcia, TP, Prentice, RL & Carroll, RJ 2021, 'Robust methods to correct for measurement error when evaluating a surrogate marker.', Biometrics.
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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.

Pateetin, P, Hutvagner, G, Bajan, S, Padula, MP, McGowan, EM & Boonyaratanakornkit, V 2021, 'Author Correction: Triple SILAC identified progestin-independent and dependent PRA and PRB interacting partners in breast cancer', Scientific Data.
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Patel, D, Taudte, RV, Nizio, K, Herok, G, Cranfield, C & Shimmon, R 2021, 'Headspace analysis of E-cigarette fluids using comprehensive two dimensional GCxGC-TOF-MS reveals the presence of volatile and toxic compounds', JOURNAL OF PHARMACEUTICAL AND BIOMEDICAL ANALYSIS, vol. 196.
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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 2021, 'Endoplasmic reticulum-unfolded protein response signalling is altered in severe eosinophilic and neutrophilic asthma.', Thorax.
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Introduction

The 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.

Methods

Induced 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.

Results

Our 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.

Conclusion

Heightened ER stress is associated with severe eosinophilic and neutrophilic inflammation in asthma and may play a crucial role in the pathogenesis of asthma.

Paudel, KR, Wadhwa, R, Tew, XN, Lau, NJX, Madheswaran, T, Panneerselvam, J, Zeeshan, F, Kumar, P, Gupta, G, Anand, K, Singh, SK, Jha, NK, MacLoughlin, R, Hansbro, NG, Liu, G, Shukla, SD, Mehta, M, Hansbro, PM, Chellappan, DK & Dua, K 2021, 'Rutin loaded liquid crystalline nanoparticles inhibit non-small cell lung cancer proliferation and migration in vitro', LIFE SCIENCES, vol. 276.
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Paull, NJ, Krix, D, Irga, PJ & Torpy, FR 2021, 'Green wall plant tolerance to ambient urban air pollution', Urban Forestry and Urban Greening, vol. 63.
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Air pollution exposure can impact plant physiology, morphology and biochemistry, leading to dramatic alterations to plant systems, function and growth. The use of plants for air pollution mitigation is increasing in popularity, particularly in the form of green wall systems, making the identification and classification of pollution sensitive and tolerant species essential. This study aimed to examine the health of common green wall species exposed to ambient air pollution in situ, and thus to identify tolerant species for use in high pollution environments. To do this, 11 plant species were sampled across 15 outdoor green walls, over a 6 month period, and tested for leaf chlorophyll, pH, relative water content and carbon content. Control glasshouse samples were collected simultaneously. Linear mixed models were used to examine patterns in plant health traits across species. Significant differences in plant health between control and in situ samples were observed, however, plant species were not consistent in their responses across health variables. As such, there no clear distinction of the most tolerant species could be made. As most species showed no significant health differences from pollution exposure, it is reasonable to conclude that all test species were able to withstand pollution exposure at the trial sites without any adverse effects.

Peng, D, Wang, Y, Xian, G, Huete, AR, Huang, W, Shen, M, Wang, F, Yu, L, Liu, L, Xie, Q, Liu, L & Zhang, X 2021, 'Investigation of land surface phenology detections in shrublands using multiple scale satellite data', REMOTE SENSING OF ENVIRONMENT, vol. 252.
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Pettit, T, Torpy, FR, Surawski, NC, Fleck, R & Irga, PJ 2021, 'Effective reduction of roadside air pollution with botanical biofiltration', Journal of Hazardous Materials.
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Piotrowski, J, Schmidt, MK, Stiller, B, Poulton, CG & Steel, MJ 2021, 'Picosecond acoustic dynamics in stimulated Brillouin scattering', Optics Letters, vol. 46, no. 12, pp. 2972-2975.
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Recent experiments demonstrating storage of optical pulses in acoustic phonons via stimulated Brillouin scattering raise questions about the spectral and temporal capacities of such protocols and the limitations of the theoretical frameworks routinely used to describe them. We consider the dynamics of photon-phonon scattering induced by optical pulses with temporal widths comparable to the period of acoustic oscillations. We revisit the widely adopted classical formalism of coupled modes and demonstrate its breakdown. We use a simple extension to the formulation and find potentially measurable consequences in the dynamics of Brillouin experiments involving ultrashort pulses.

Polerecky, L, Masuda, T, Eichner, M, Rabouille, S, Vancová, M, Kienhuis, MVM, Bernát, G, Bonomi-Barufi, J, Campbell, DA, Claquin, P, Červený, J, Giordano, M, Kotabová, E, Kromkamp, J, Lombardi, AT, Lukeš, M, Prášil, O, Stephan, S, Suggett, D, Zavřel, T & Halsey, KH 2021, 'Temporal Patterns and Intra- and Inter-Cellular Variability in Carbon and Nitrogen Assimilation by the Unicellular Cyanobacterium Cyanothece sp. ATCC 51142', Frontiers in Microbiology.
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Polonchuk, L, Surija, L, Lee, MH, Sharma, P, Liu Chung Ming, C, Richter, F, Ben-Sefer, E, Alsadat Rad, M, Mahmodi Sheikh Sarmast, H, Al Shamery, W, Tran, HA, Vettori, L, Haeusermann, F, Filipe, EC, Rnjak-Kovacina, J, Cox, T, Tipper, J, Kabakova, I & Gentile, C 2021, 'Towards engineering heart tissues from bioprinted cardiac spheroids.', Biofabrication.
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Popkova, AA, Antropov, IM, Froch, JE, Kim, S, Aharonovich, I, Bessonov, VO, Solntsev, AS & Fedyanin, AA 2021, 'Optical Third-Harmonic Generation in Hexagonal Boron Nitride Thin Films', ACS PHOTONICS, vol. 8, no. 3, pp. 824-831.
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Popovic, A, Morelato, M, Roux, C & Beavis, A 2021, 'Interpreting the link value of similarity scores between illicit drug specimens through a dual approach, featuring deterministic and Bayesian frameworks.', Forensic science international, vol. 319, pp. 110651-110651.
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Illicit drug trafficking and in particular amphetamine-type stimulants continue to be a major problem in Australia. With the constant evolution of illicit drugs markets, it is necessary to gain as much knowledge about them to disrupt or reduce their impact. Illicit drug specimens can be analysed to generate forensic intelligence and understand criminal activities. Part of this analysis involves the evaluation of similarity scores between illicit drug profiles to interpret the link value. Most studies utilise one of two prominent score evaluation approaches, i.e. deterministic or Bayesian. In previous work, the notion of a dual approach was suggested, which emphasised the complementary nature of the two mentioned approaches. The aim of this study was to assess the operational capability of a dual approach in evaluating similarity scores between illicit drug profiles. Utilising a practical example, link values were generated individually from both approaches, then compared in parallel. As a result, it was possible to generate more informed hypotheses, relating to specimen linkage, due to the greater wealth of information available from the two approaches working concurrently. Additionally, it was shown that applying only one approach led to less information being generated during analysis as well as potentially important links between illicit drug specimens being missed.

Prasad, E, Barash, M, Hitchcock, C, van Oorschot, RAH, Raymond, J, McNevin, D & Gunn, P 2021, 'Evaluation of soaking to recover trace DNA from fired cartridge cases', Australian Journal of Forensic Sciences.
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© 2020, © 2020 Australian Academy of Forensic Sciences. The recovery of trace DNA from cartridge cases is of common interest across many jurisdictions. Soaking offers improved profiling success rates over traditional methods. We evaluated the effects of firing, calibre, and metal composition on controlled and handled DNA samples utilizing a soaking method. Our results show that firing decreases the quantities of DNA recoverable from cartridge cases and higher quantities of DNA are recoverable from nickel ammunition compared to brass. In spiked samples, calibre of ammunition had no significant effect on DNA recovery. Despite slight to moderate DNA degradation and variable profiling success rates, spiked unfired and fired nickel cartridges resulted in more usable profiles than brass cartridges. These findings can aid in triaging the types of ammunition subjected to DNA testing.

Prosser, C, Gresty, K, Ellis, J, Meyer, W, Anderson, K, Lee, R & Cheng, Q 2021, 'Plasmodium falciparum Histidine-Rich Protein 2 and 3 Gene Deletions in Strains from Nigeria, Sudan, and South Sudan', EMERGING INFECTIOUS DISEASES, vol. 27, no. 2, pp. 471-479.
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Rad, DM, Rad, MA, Bazaz, SR, Kashaninejad, N, Jin, D & Warkiani, ME 2021, 'A Comprehensive Review on Intracellular Delivery', ADVANCED MATERIALS, vol. 33, no. 13.
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Rädecker, N, Pogoreutz, C, Gegner, HM, Cárdenas, A, Roth, F, Bougoure, J, Guagliardo, P, Wild, C, Pernice, M, Raina, J-B, Meibom, A & Voolstra, CR 2021, 'Heat stress destabilizes symbiotic nutrient cycling in corals', Proceedings of the National Academy of Sciences of the United States of America.
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Rajendran, E, Clark, M, Goulart, C, Steinhöfel, B, Tjhin, ET, Gross, S, Smith, NC, Kirk, K & van Dooren, GG 2021, 'Substrate-mediated regulation of the arginine transporter of Toxoplasma gondii', PLOS Pathogens.
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Ramakrishnan, C & Smith, NC 2021, 'Recent achievements and doors opened for coccidian parasite research and development through transcriptomics of enteric sexual stages', Molecular and Biochemical Parasitology, vol. 243.
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The Coccidia is the largest group of parasites within the Apicomplexa, a phylum of unicellular, obligate parasites characterized by the possession of an apical complex of organelles and structures in the asexual stages of their life cycles, as well as by a sexual reproductive phase that occurs enterically in host animals. Coccidian sexual reproduction involves morphologically distinct microgametes and macrogametes that combine to form a diploid zygote and, ultimately, following meiosis and mitosis, haploid, infectious sporozoites, inside sporocysts within an oocyst. Recent transcriptomic analyses have identified genes involved in coccidian sexual stage development and reproduction, including genes encoding for microgamete- and macrogamete-specific proteins with roles in gamete motility, fusion and fertilization, and in the formation of the resilient oocyst wall that allows coccidians to persist for long periods in the environment. Transcriptomics has also provided important clues about the regulation of gene expression in the transformation of parasites from one developmental stage to the next, a complex sequence of events that may involve transcription factors such as the apicomplexan Apetala2 (ApiAP2) family, alternative splicing, regulatory RNAs and MORC (a microrchida homologue and regulator of sexual stage development in Toxoplasma gondii). The molecular dissection of coccidian sexual development and reproduction by transcriptomic analyses may lead to the development of novel transmission-blocking strategies.

Rangsinth, P, Sillapachaiyaporn, C, Nilkhet, S, Tencomnao, T, Ung, AT & Chuchawankul, S 2021, 'Mushroom-derived bioactive compounds potentially serve as the inhibitors of SARS-CoV-2 main protease: An in silico approach', Journal of Traditional and Complementary Medicine.
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Reddy, KD & Oliver, BGG 2021, 'Sex-specific effects of in utero and adult tobacco smoke exposure.', American journal of physiology. Lung cellular and molecular physiology, vol. 320, no. 1, pp. L63-L72.
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Tobacco smoke has harmful effects on a multiorgan level. Exposure to smoke, whether in utero or environmental, significantly increases susceptibility. This susceptibility has been identified to be divergent between males and females. However, there remains a distinct lack of thorough research into the relationship between sex and exposure to tobacco. Females tend to generate a more significant response than males during adulthood exposure. The intrauterine environment is meticulously controlled, and exposure to tobacco presents a significant factor that contributes to poor health outcomes and susceptibility later in life. Analysis of these effects in relation to the sex of the offspring is yet to be holistically reviewed and summarized. In this review, we will delineate the time-dependent relationship between tobacco smoke exposure and sex-specific disease susceptibility. We further outline possible biological mechanisms that may contribute to the identified pattern.

Regan, BEP, Trycz, A, Fröch, J, Schaeper, O, Kim, S & Aharonovich, I 2021, 'Nanofabrication of high Q, transferable, diamond resonators', Nanoscale.
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Reid, G, Klebe, S, van Zandwijk, N & George, AM 2021, 'Asbestos and Zeolites: from A to Z via a Common Ion', CHEMICAL RESEARCH IN TOXICOLOGY, vol. 34, no. 4, pp. 936-951.
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Rennie, C, Fernandez, R, Donnelly, S & McGrath, KC 2021, 'The Impact of Helminth Infection on the Incidence of Metabolic Syndrome: A Systematic Review and Meta-Analysis', Frontiers in Endocrinology.
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Reyna Zeballos, J, Hanham, J, Vlachopoulos, P & Meier, P 2021, 'A Systematic Approach to Designing, Implementing, and Evaluating Learner-Generated Digital Media (LGDM) Assignments and their Effect on Self-Regulation in Tertiary Science Education', Research in Science Education, pp. 1-27.
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This study explored the self-regulation strategies and learning experiences of undergraduate science students who were completing LDGM assignments that had been implemented using a theory-driven, systematic approach. The rationale for using LGDM in science education is to facilitate student learning of complex scientific concepts through the multimodal representation of content using digital media. The study was conducted in seven science subjects from first to third year in Autumn 2017, using a sample of 348 undergraduate science students attending a university located in Sydney, Australia. All the participants were enrolled in subjects that required them to communicate complex scientific concepts using digital media. Training on LGDM was conducted online (n=199) and in blended mode (n=149). The study used a mixed-methods approach with a validated self-regulation questionnaire, LMS logs, assessment scores, group contribution data, open-ended questions, and interviews. Online students were more likely than blended students to report using self-regulation strategies for goal setting, time management, task strategies, and help-seeking. Data triangulation revealed that participation in LDGM assignments was perceived by students to contribute to their science content knowledge, provide them with digital media skills, and nurture their capacity for working in groups. The findings of this study have implications for how LDGM is deployed in science education.

Rezaei, M, Bazaz, SR, Rad, DM, Shimoni, O, Jin, D, Rawlinson, W & Warkiani, ME 2021, 'A portable rt-lamp/crispr machine for rapid covid-19 screening', Biosensors, vol. 11, no. 10.
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The COVID-19 pandemic has changed people’s lives and has brought society to a sudden standstill, with lockdowns and social distancing as the preferred preventative measures. To lift these measurements and reduce society’s burden, developing an easy-to-use, rapid, and portable system to detect SARS-CoV-2 is mandatory. To this end, we developed a portable and semi-automated device for SARS-CoV-2 detection based on reverse transcription loop-mediated isothermal amplification followed by a CRISPR/Cas12a reaction. The device contains a heater element mounted on a printed circuit board, a cooler fan, a proportional integral derivative controller to control the temperature, and designated areas for 0.2 mL Eppendorf® PCR tubes. Our system has a limit of detection of 35 copies of the virus per microliter, which is significant and has the capability of being used in crisis centers, mobile laboratories, remote locations, or airports to diagnose individuals infected with SARS-CoV-2. We believe the current methodology that we have implemented in this article is beneficial for the early screening of infectious diseases, in which fast screening with high accuracy is necessary.

Rezaei, M, Radfar, P, Winter, M, McClements, L, Thierry, B & Warkiani, ME 2021, 'Simple-to-Operate Approach for Single Cell Analysis Using a Hydrophobic Surface and Nanosized Droplets', ANALYTICAL CHEMISTRY, vol. 93, no. 10, pp. 4584-4592.
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Rezaei, M, Razavi Bazaz, S, Zhand, S, Sayyadi, N, Jin, D, Stewart, MP & Ebrahimi Warkiani, M 2021, 'Point of Care Diagnostics in the Age of COVID-19.', Diagnostics (Basel, Switzerland), vol. 11, no. 1.
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The recent outbreak of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its associated serious respiratory disease, coronavirus disease 2019 (COVID-19), poses a major threat to global public health. Owing to the lack of vaccine and effective treatments, many countries have been overwhelmed with an exponential spread of the virus and surge in the number of confirmed COVID-19 cases. Current standard diagnostic methods are inadequate for widespread testing as they suffer from prolonged turn-around times (>12 h) and mostly rely on high-biosafety-level laboratories and well-trained technicians. Point-of-care (POC) tests have the potential to vastly improve healthcare in several ways, ranging from enabling earlier detection and easier monitoring of disease to reaching remote populations. In recent years, the field of POC diagnostics has improved markedly with the advent of micro- and nanotechnologies. Due to the COVID-19 pandemic, POC technologies have been rapidly innovated to address key limitations faced in existing standard diagnostic methods. This review summarizes and compares the latest available POC immunoassay, nucleic acid-based and clustered regularly interspaced short palindromic repeats- (CRISPR)-mediated tests for SARS-CoV-2 detection that we anticipate aiding healthcare facilities to control virus infection and prevent subsequent spread.

Rezcallah, MC, Al-Mazi, T & Ammit, AJ 2021, 'Cataloguing the phosphorylation sites of tristetraprolin (TTP): Functional implications for inflammatory diseases.', Cellular Signalling, vol. 78, pp. 1-12.
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Tristetraprolin (TTP) is a destabilizing mRNA binding protein known to regulate gene expression of a wide variety of targets, including those that control inflammation. TTP expression, regulation and function is controlled by phosphorylation. While the importance of key serine (S) sites (S⁵² and S¹⁷⁸ in mice and S¹⁸⁶ in humans) has been recognized, other sites on the hyperphosphorylated TTP protein have more recently emerged as playing an important role in regulating cellular signalling and downstream functions of TTP. In order to propel investigation of TTP and fully exploit its potential as a drug target in inflammatory disease, this review will catalogue TTP phosphorylation sites in both the murine and human TTP protein, the known and unknown roles and functions of these sites, the kinases and phosphatases that act upon TTP and overview methodological approaches to increase our knowledge of this important protein regulated by phosphorylation.

Ricafrente, A, Nguyen, H, Tran, N & Donnelly, S 2021, 'An Evaluation of the Fasciola hepatica miRnome Predicts a Targeted Regulation of Mammalian Innate Immune Responses', Frontiers in Immunology.
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Richards, C, Sesperez, K, Chhor, M, Ghorbanpour, S, Rennie, C, Ming, CLC, Evenhuis, C, Nikolic, V, Orlic, NK, Mikovic, Z, Stefanovic, M, Cakic, Z, McGrath, K, Gentile, C, Bubb, K & McClements, L 2021, 'Characterisation of cardiac health in the reduced uterine perfusion pressure model and a 3D cardiac spheroid model, of preeclampsia', Biology of Sex Differences.
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Roberts, L, Kutay, C, Melbourne-Thomas, J, Petrou, K, Benson, TM, Fiore, D, Fletcher, P, Johnson, E, Silk, M, Taberner, S, Filgueira, VV & Constable, AJ 2021, 'Enabling Enduring Evidence-Based Policy for the Southern Ocean Through Cultural Arts Practices', Frontiers in Ecology and Evolution.
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Ros, M, Suggett, DJ, Edmondson, J, Haydon, T, Hughes, DJ, Kim, M, Guagliardo, P, Bougoure, J, Pernice, M, Raina, J-B & Camp, EF 2021, 'Symbiont shuffling across environmental gradients aligns with changes in carbon uptake and translocation in the reef-building coral Pocillopora acuta', Coral Reefs.
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Rosset, SL, Oakley, CA, Ferrier-Pagès, C, Suggett, DJ, Weis, VM & Davy, SK 2021, 'The Molecular Language of the Cnidarian-Dinoflagellate Symbiosis.', Trends in microbiology, vol. 29, no. 4, pp. 320-333.
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The cnidarian-dinoflagellate symbiosis is of huge importance as it underpins the success of coral reefs, yet we know very little about how the host cnidarian and its dinoflagellate endosymbionts communicate with each other to form a functionally integrated unit. Here, we review the current knowledge of interpartner molecular signaling in this symbiosis, with an emphasis on lipids, glycans, reactive species, biogenic volatiles, and noncoding RNA. We draw upon evidence of these compounds from recent omics-based studies of cnidarian-dinoflagellate symbiosis and discuss the signaling roles that they play in other, better-studied symbioses. We then consider how improved knowledge of interpartner signaling might be used to develop solutions to the coral reef crisis by, for example, engineering more thermally resistant corals.

Roux, C, Willis, S & Weyermann, C 2021, 'Shifting forensic science focus from means to purpose: A path forward for the discipline?', Science and Justice, vol. 61, no. 6, pp. 678-686.
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Forensic science is facing a persistent crisis that is often addressed by organizational responses, with a strong focus on the improvement and standardisation of means and processes. However, organisations and processes are highly dependent on the political, economical and legal structures in which they operate. This may explain why most proposed solutions had difficulties in addressing the crisis up to now, as they could hardly be applied transversally to all forensic science models. Moreover, new tools and technologies are continuously developed by a quasi-infinite number of different scientific disciplines, thus leading to further diversity and fragmentation of forensic science. In this paper, it is proposed to shift the focus from means to purpose and consider forensic science current challenges in terms of discipline, before addressing organisations’ specific issues. As a distinct discipline, forensic science can refocus research and development on shared principles and purposes, such as reconstructing, monitoring, and preventing crime and security issues. This focus change will facilitate a better understanding of the trace as the object of study of forensic science and eventually lead to a more impactful and long-lasting effect. This approach will also foster the development of a forensic science culture (instead of a primarily technological culture) unified by purpose rather than means through more relevant education and research.

Rouze, H, Galand, PE, Medina, M, Bongaerts, P, Pichon, M, Perez-Rosales, G, Torda, G, Moya, A, Raina, J-B & Hedouin, L 2021, 'Symbiotic associations of the deepest recorded photosynthetic scleractinian coral (172 m depth)', ISME JOURNAL, vol. 15, no. 5, pp. 1564-1568.
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Ruprecht, JE, Birrer, SC, Dafforn, KA, Mitrovic, SM, Crane, SL, Johnston, EL, Wemheuer, F, Navarro, A, Harrison, AJ, Turner, IL & Glamore, WC 2021, 'Wastewater effluents cause microbial community shifts and change trophic status', WATER RESEARCH, vol. 200.
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Ryan, ST, Hosseini-Beheshti, E, Afrose, D, Ding, X, Xia, B, Grau, GE, Little, CB, McClements, L & Li, JJ 2021, 'Extracellular Vesicles from Mesenchymal Stromal Cells for the Treatment of Inflammation-Related Conditions', International Journal of Molecular Sciences.
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Sabir, S, Suresh, D, Subramoni, S, Das, T, Bhadbhade, M, Black, DS, Rice, SA & Kumar, N 2021, 'Thioether-linked dihydropyrrol-2-one analogues as PqsR antagonists against antibiotic resistant Pseudomonas aeruginosa', BIOORGANIC & MEDICINAL CHEMISTRY, vol. 31.
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Samardzic, K, Steele, JR, Violi, JP, Colville, A, Mitrovic, SM & Rodgers, KJ 2021, 'Toxicity and bioaccumulation of two non-protein amino acids synthesised by cyanobacteria, β-N-Methylamino-L-alanine (BMAA) and 2,4-diaminobutyric acid (DAB), on a crop plant.', Ecotoxicology and environmental safety, vol. 208, pp. 111515-111515.
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In order to study the toxicity of the cyanobacterial non-protein amino acids (NPAAs) L-β-N-methylamino-L-alanine (BMAA) and its structural isomer L-2,4-diaminobutyric acid (DAB) in the forage crop plant alfalfa (Medicago sativa), seedlings were exposed to NPAA-containing media for four days. Root growth was significantly inhibited by both treatments. The content of derivatised free and protein-bound BMAA and DAB in seedlings was then analysed by LC-MS/MS. Both NPAAs were detected in free and protein-bound fractions with higher levels detected in free fractions. Compared to shoots, there was approximately tenfold more BMAA and DAB in alfalfa roots. These results suggest that NPAAs might be taken up into crop plants from contaminated irrigation water and enter the food chain. This may present an exposure pathway for NPAAs in humans.

Santos, J, Dolai, S, O'Rourke, MB, Liu, F, Padula, MP, Molloy, MP & Milthorpe, BK 2021, 'Quantitative Proteomic Profiling of Small Molecule Treated Mesenchymal Stem Cells Using Chemical Probes.', International journal of molecular sciences, vol. 22, no. 1.
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The differentiation of human adipose derived stem cells toward a neural phenotype by small molecules has been a vogue topic in the last decade. The characterization of the produced cells has been explored on a broad scale, examining morphological and specific surface protein markers; however, the lack of insight into the expression of functional proteins and their interactive partners is required to further understand the extent of the process. The phenotypic characterization by proteomic profiling allows for a substantial in-depth analysis of the molecular machinery induced and directing the cellular changes through the process. Herein we describe the temporal analysis and quantitative profiling of neural differentiating human adipose-derived stem cells after sub-proteome enrichment using a bisindolylmaleimide chemical probe. The results show that proteins enriched by the Bis-probe were identified reproducibly with 133, 118, 126 and 89 proteins identified at timepoints 0, 1, 6 and 12, respectively. Each temporal timepoint presented several shared and unique proteins relative to neural differentiation and their interactivity. The major protein classes enriched and quantified were enzymes, structural and ribosomal proteins that are integral to differentiation pathways. There were 42 uniquely identified enzymes identified in the cells, many acting as hubs in the networks with several interactions across the network modulating key biological pathways. From the cohort, it was found by gene ontology analysis that 18 enzymes had direct involvement with neurogenic differentiation.

Sarkar, A, Pati, D, Mallick, BK & Carroll, RJ 2021, 'Bayesian Copula Density Deconvolution for Zero-Inflated Data in Nutritional Epidemiology', Journal of the American Statistical Association.
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© 2020, © 2020 American Statistical Association. Estimating the marginal and joint densities of the long-term average intakes of different dietary components is an important problem in nutritional epidemiology. Since these variables cannot be directly measured, data are usually collected in the form of 24-hr recalls of the intakes, which show marked patterns of conditional heteroscedasticity. Significantly compounding the challenges, the recalls for episodically consumed dietary components also include exact zeros. The problem of estimating the density of the latent long-time intakes from their observed measurement error contaminated proxies is then a problem of deconvolution of densities with zero-inflated data. We propose a Bayesian semiparametric solution to the problem, building on a novel hierarchical latent variable framework that translates the problem to one involving continuous surrogates only. Crucial to accommodating important aspects of the problem, we then design a copula based approach to model the involved joint distributions, adopting different modeling strategies for the marginals of the different dietary components. We design efficient Markov chain Monte Carlo algorithms for posterior inference and illustrate the efficacy of the proposed method through simulation experiments. Applied to our motivating nutritional epidemiology problems, compared to other approaches, our method provides more realistic estimates of the consumption patterns of episodically consumed dietary components. Supplementary materials for this article, including a standardized description of the materials available for reproducing the work, are available as an online supplement.

Scanes, E, Parker, LM, Seymour, JR, Siboni, N, King, WL, Danckert, NP, Wegner, KM, Dove, MC, O'Connor, WA & Ross, PM 2021, 'Climate change alters the haemolymph microbiome of oysters', MARINE POLLUTION BULLETIN, vol. 164.
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Schowanek, SD, Davis, M, Lundgren, EJ, Middleton, O, Rowan, J, Pedersen, RO, Ramp, D, Sandom, CJ & Svenning, J-C 2021, 'Reintroducing extirpated herbivores could partially reverse the late Quaternary decline of large and grazing species', GLOBAL ECOLOGY AND BIOGEOGRAPHY, vol. 30, no. 4, pp. 896-908.
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Schuback, N, Tortell, PD, Berman-Frank, I, Campbell, DA, Ciotti, A, Courtecuisse, E, Erickson, ZK, Fujiki, T, Halsey, K, Hickman, AE, Huot, Y, Gorbunov, MY, Hughes, DJ, Kolber, ZS, Moore, CM, Oxborough, K, Prášil, O, Robinson, CM, Ryan-Keogh, TJ, Silsbe, G, Simis, S, Suggett, DJ, Thomalla, S & Varkey, DR 2021, 'Single-Turnover Variable Chlorophyll Fluorescence as a Tool for Assessing Phytoplankton Photosynthesis and Primary Productivity: Opportunities, Caveats and Recommendations', Frontiers in Marine Science.
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Seviour, T, Winnerdy, FR, Wong, LL, Shi, X, Mugunthan, S, Foo, YH, Castaing, R, Adav, SS, Subramoni, S, Kohli, GS, Shewan, HM, Stokes, JR, Rice, SA, Phan, AT & Kjelleberg, S 2021, 'The biofilm matrix scaffold of Pseudomonas aeruginosa contains G-quadruplex extracellular DNA structures.', NPJ Biofilms Microbiomes, vol. 7, no. 1, p. 27.
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Extracellular DNA, or eDNA, is recognised as a critical biofilm component; however, it is not understood how it forms networked matrix structures. Here, we isolate eDNA from static-culture Pseudomonas aeruginosa biofilms using ionic liquids to preserve its biophysical signatures of fluid viscoelasticity and the temperature dependency of DNA transitions. We describe a loss of eDNA network structure as resulting from a change in nucleic acid conformation, and propose that its ability to form viscoelastic structures is key to its role in building biofilm matrices. Solid-state analysis of isolated eDNA, as a proxy for eDNA structure in biofilms, reveals non-canonical Hoogsteen base pairs, triads or tetrads involving thymine or uracil, and guanine, suggesting that the eDNA forms G-quadruplex structures. These are less abundant in chromosomal DNA and disappear when eDNA undergoes conformation transition. We verify the occurrence of G-quadruplex structures in the extracellular matrix of intact static and flow-cell biofilms of P. aeruginosa, as displayed by the matrix to G-quadruplex-specific antibody binding, and validate the loss of G-quadruplex structures in vivo to occur coincident with the disappearance of eDNA fibres. Given their stability, understanding how extracellular G-quadruplex structures form will elucidate how P. aeruginosa eDNA builds viscoelastic networks, which are a foundational biofilm property.

Shan, X, Pang, M, Zhao, D, Wang, D, Hwang, FJ & CHEN, C-H 2021, 'Maritime target detection based on electronic image stabilization technology of shipborne camera', IEICE Transactions on Information and Systems.
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Shan, X, Wang, F, Wang, D, Wen, S, Chen, C, Di, X, Nie, P, Liao, J, Liu, Y, Ding, L, Reece, PJ & Jin, D 2021, 'Optical tweezers beyond refractive index mismatch using highly doped upconversion nanoparticles', NATURE NANOTECHNOLOGY, vol. 16, no. 5.
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Shastri, MD, Allam, VSRR, Shukla, SD, Jha, NK, Paudel, KR, Peterson, GM, Patel, RP, Hansbro, PM, Chellappan, DK & Dua, K 2021, 'Interleukin-13: A pivotal target against influenza-induced exacerbation of chronic lung diseases.', Life sciences, p. 119871.
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Non-communicable, chronic respiratory diseases (CRDs) affect millions of individuals worldwide. The course of these CRDs (asthma, chronic obstructive pulmonary disease, and cystic fibrosis) are often punctuated by microbial infections that may result in hospitalization and are associated with increased risk of morbidity and mortality, as well as reduced quality of life. Interleukin-13 (IL-13) is a key protein that regulates airway inflammation and mucus hypersecretion. There has been much interest in IL-13 from the last two decades. This cytokine is believed to play a decisive role in the exacerbation of inflammation during the course of viral infections, especially, in those with pre-existing CRDs. Here, we discuss the common viral infections in CRDs, as well as the potential role that IL-13 plays in the virus-induced disease pathogenesis of CRDs. We also discuss, in detail, the immune-modulation potential of IL-13 that could be translated to in-depth studies to develop IL-13-based therapeutic entities.

Shastri, MD, Chong, WC, Dua, K, Peterson, GM, Patel, RP, Mahmood, MQ, Tambuwala, M, Chellappan, DK, Hansbro, NG, Shukla, SD & Hansbro, PM 2021, 'Emerging concepts and directed therapeutics for the management of asthma: regulating the regulators.', Inflammopharmacology: experimental and clinical studies, vol. 29, no. 1, pp. 15-33.
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Asthma is a common, heterogeneous and serious disease, its prevalence has steadily risen in most parts of the world, and the condition is often inadequately controlled in many patients. Hence, there is a major need for new therapeutic approaches. Mild-to-moderate asthma is considered a T-helper cell type-2-mediated inflammatory disorder that develops due to abnormal immune responses to otherwise innocuous allergens. Prolonged exposure to allergens and persistent inflammation results in myofibroblast infiltration and airway remodelling with mucus hypersecretion, airway smooth muscle hypertrophy, and excess collagen deposition. The airways become hyper-responsive to provocation resulting in the characteristic wheezing and obstructed airflow experienced by patients. Extensive research has progressed the understanding of the underlying mechanisms and the development of new treatments for the management of asthma. Here, we review the basis of the disease, covering new areas such as the role of vascularisation and microRNAs, as well as associated potential therapeutic interventions utilising reports from animal and human studies. We also cover novel drug delivery strategies that are being developed to enhance therapeutic efficacy and patient compliance. Potential avenues to explore to improve the future of asthma management are highlighted.

Shi, X, Zuo, Y, Zhai, P, Shen, J, Yang, Y, Gao, Z, Liao, M, Wu, J, Wang, J, Xu, X, Tong, Q, Zhang, B, Wang, B, Sun, X, Zhang, L, Pei, Q, Jin, D, Chen, P & Peng, H 2021, 'Large-area display textiles integrated with functional systems', Nature.
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Shrestha, J, Ryan, ST, Mills, O, Zhand, S, Razavi Bazaz, S, Hansbro, PM, Ghadiri, M & Ebrahimi Warkiani, M 2021, 'A 3D-printed microfluidic platform for simulating the effects of CPAP on the nasal epithelium', BIOFABRICATION, vol. 13, no. 3.
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Sillapachaiyaporn, C, Rangsinth, P, Nilkhet, S, Ung, AT, Chuchawankul, S & Tencomnao, T 2021, 'Neuroprotective effects against glutamate-induced ht-22 hippocampal cell damage and caenorhabditis elegans lifespan/healthspan enhancing activity of auricularia polytricha mushroom extracts', Pharmaceuticals, vol. 14, no. 10.
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Oxidative stress is associated with several diseases, particularly neurodegenerative diseases, commonly found in the elderly. The attenuation of oxidative status is one of the alternatives for neuroprotection and anti-aging. Auricularia polytricha (AP), an edible mushroom, contains many therapeutic properties, including antioxidant properties. Herein, we report the effects of AP extracts on antioxidant, neuroprotective, and anti-aging activities. The neuroprotective effect of AP extracts against glutamate-induced HT-22 neuronal damage was determined by evaluating the cytotoxicity, intracellular reactive oxygen species (ROS) accumulation, and expression of antioxidant enzyme genes. Lifespan and healthspan assays were performed to examine the effects of AP extracts from Caenorhabditis elegans. We found that ethanolic extract (APE) attenuated glutamate-induced HT-22 cytotoxicity and increased the expression of antioxidant enzyme genes. Moreover, APE promoted in the longevity and health of the C. elegans. Chemical analysis of the extracts revealed that APE contains the highest quantity of flavonoids and a reasonable percentage of phenols. The lipophilic compounds in APE were identified by gas chromatography/mass spectrometry (GC/MS), revealing that APE mainly contains linoleic acid. Interestingly, linoleic acid suppressed neuronal toxicity and ROS accumulation from glutamate induction. These results indicate that AP could be an exciting natural source that may potentially serves as neuroprotective and anti-aging agents.

Solntsev, AS, Agarwal, GS & Kivshar, YS 2021, 'Publisher Correction: Metasurfaces for quantum photonics', Nature Photonics.
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Solntsev, AS, Agarwal, GS & Kivshar, YY 2021, 'Metasurfaces for quantum photonics', Nature Photonics.
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Speer, MS, Leslie, LM, MacNamara, S & Hartigan, J 2021, 'From the 1990s climate change has decreased cool season catchment precipitation reducing river heights in Australia’s southern Murray-Darling Basin', Scientific Reports.
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Srivastava, P, Gunawan, C, Soeriyadi, A, Amal, R, Hoehn, K & Marquis, C 2021, 'In vitro coronal protein signatures and biological impact of silver nanoparticles synthesized with different natural polymers as capping agents', NANOSCALE ADVANCES, vol. 3, no. 15, pp. 4424-4439.
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Steele, JR, Italiano, CJ, Phillips, CR, Violi, JP, Pu, L, Rodgers, KJ & Padula, MP 2021, 'Misincorporation Proteomics Technologies: A Review', Proteomes.
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Steele, JR, Strange, N, Rodgers, KJ & Padula, MP 2021, 'A Novel Method for Creating a Synthetic L-DOPA Proteome and In Vitro Evidence of Incorporation.', Proteomes, vol. 9, no. 2.
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Proteinopathies are protein misfolding diseases that have an underlying factor that affects the conformation of proteoforms. A factor hypothesised to play a role in these diseases is the incorporation of non-protein amino acids into proteins, with a key example being the therapeutic drug levodopa. The presence of levodopa as a protein constituent has been explored in several studies, but it has not been examined in a global proteomic manner. This paper provides a proof-of-concept method for enzymatically creating levodopa-containing proteins using the enzyme tyrosinase and provides spectral evidence of in vitro incorporation in addition to the induction of the unfolded protein response due to levodopa.

Stevens, MT & Saunders, BM 2021, 'Targets and regulation of microRNA-652-3p in homoeostasis and disease', JOURNAL OF MOLECULAR MEDICINE-JMM, vol. 99, no. 6, pp. 755-769.
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Stevens, MT, Nagaria, BD, Britton, WJ & Saunders, BM 2021, 'Macrophages of different tissue origin exhibit distinct inflammatory responses to mycobacterial infection.', Immunology and cell biology.
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Macrophages display marked plasticity with functions in both inflammation and tissue repair. Evidence demonstrates that this spectrum of macrophage phenotypes is influenced by their local microenvironment and tissue origin. However, in vitro macrophage experiments often do not or cannot readily use macrophages from the most relevant tissue of origin. In this study we investigated if the origin of two C57BL/6 mouse macrophage cell lines of alveolar (AMJ2-C11) and peritoneal (IC-21) origin may influence their response to mycobacterial infection. Both cell lines equally controlled growth of Mycobacterium bovis BCG and Mycobacterium tuberculosis, although expression of all proinflammatory cytokines and chemokines measured (TNF, IL-6, MCP-1, MIP-1α, MIP-1β, and RANTES) was significantly higher in AMJ2-C11 cells than IC-21 cells. During M. tuberculosis infection, IL-6, MCP-1, and RANTES expression increased 5-fold, and MIP-1β expression increased 30-fold. Additionally, AMJ2-C11 cells exhibited significantly higher iNOS activity than IC-21 cells, indicative of a more polarised M1 response. Expression of multiple surface markers were also assessed by flow cytometry. CD80 and CD86 were significantly upregulated in AMJ2-C11 cells and downregulated in IC-21 cells during M. tuberculosis infection. Our results support the notion that the origin of tissue-resident macrophages influences their phenotype and antimicrobial response and demonstrate hereto unrecognised potential for these cell lines in in vitro studies.

Stewart, J, Hegarty, AM & Gladstone, W 2021, 'The influence of climatic and lunar drivers on landings cycles of the temperate Australian sciaenid (Atractoscion atelodus) at two temporal scales: A working hypothesis for future management of this resource', Marine Environmental Research, vol. 171.
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Commercial line-fishing catch rates of the endemic sciaenid Atractoscion atelodus in eastern-Australia were significantly affected by lunar phase. Periodic regression analysis indicated that catch rates were greatest during the full moon period and lowest during the new moon period. It is hypothesized that this observation is the result of the visual nocturnal feeding nature of A. atelodus, with schools of fish using the increased ambient light in the water column during the brighter part of the lunar phase to feed intensively. Increased feeding intensity during the brighter phase of the lunar month may also be related to spawning activity during the new moon phase; however this hypothesis remains to be tested. Annual commercial landings through a 71 year dataset (1950–2020) showed an approximately exponential decline, overlaid with periodic years of higher and lower landings. Such periods of higher landings were significantly positively correlated with coastal rainfall two and three years earlier, but not with rainfall in the same year or one, four or five years earlier. We hypothesize that increased coastal rainfall, likely in combination with unknown co-occurring factors, promotes increased recruitment success of A. atelodus, potentially through increased primary productivity in the nearshore marine environment. This translates into an increase in the fishable stock mainly two and three years later. If our hypothesis is correct, climate predictions of reduced rainfall in eastern Australia suggest a pessimistic outlook for this fishery.

Su, L, Zhang, J, Chen, Y, Yang, W, Wang, J, Ma, Z, Shao, G & Wang, G 2021, 'Cobalt-embedded hierarchically-porous hollow carbon microspheres as multifunctional confined reactors for high-loading Li-S batteries', NANO ENERGY, vol. 85.
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Su, Q, Wei, H-L, Liu, Y, Chen, C, Guan, M, Wang, S, Su, Y, Wang, H, Chen, Z & Jin, D 2021, 'Six-photon upconverted excitation energy lock-in for ultraviolet-C enhancement', Nature Communications.
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Su, Q, Wei, H-L, Wang, S, Chen, C, Ming, G, Su, Y, Wang, H, Chen, Z & Jin, D 2021, 'Upconverted excitation energy lock-in for deep-ultraviolet enhancement'.
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Abstract Photon upconversion of near-infrared (NIR) irradiation into deep-ultraviolet (UV) emission offers many exciting opportunities for drug release in deep tissues, photodynamic therapy, solid-state lasing, energy storage, and photocatalysis. However, NIR-to-deep-UV upconversion remains a daunting challenge due to low quantum efficiency. Here, we report an unusual six-photon upconversion process in Gd3+/Tm3+-codoped nanoparticles comprising a heterogeneous, core-multishell nanostructure. This multishell design efficiently suppresses energy consumption induced by interior energy traps, maximizes cascade sensitizations of the NIR excitation, and promotes upconverted deep-UV emission from high-lying excited states. We released the intense six-photon-upconverted UV emissions at 253 nm under 808-nm excitation. This work provides new insight into mechanistic understanding of the upconversion process within the heterogeneous architecture, while offering exciting opportunities for developing nanoscale deep-UV emitters that can be remotely controlled in deep tissues upon NIR illumination.

Supasri, KM, Kumar, M, Mathew, MJ, Signal, B, Padula, MP, Suggett, DJ & Ralph, PJ 2021, 'Evaluation of Filter, Paramagnetic, and STAGETips Aided Workflows for Proteome Profiling of Symbiodiniaceae Dinoflagellate', Processes.
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Sutherland, DL, Burke, J & Ralph, PJ 2021, 'High-throughput screening for heterotrophic growth in microalgae using the Biolog Plate assay', NEW BIOTECHNOLOGY, vol. 65, pp. 61-68.
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Sutherland, DL, Burke, J & Ralph, PJ 2021, 'Trade-offs between effluent quality and ammonia volatilisation with CO2 augmented microalgal treatment of anaerobically digested food-waste centrate.', Journal of environmental management, vol. 277, pp. 111398-111398.
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Diversion of food waste from landfill disposal to waste-to-energy facilities has become both an environmentally and economically viable option to support the circular bioeconomy. However, the liquid centrate produced during anaerobic digestion is high in total ammonia, with concentrations ~2000 g m-3, and can release gaseous emissions, including ammonia, methane, CO2 and nitrous oxide, to the atmosphere. Further treatment is required before discharge to sewer, or to the environment. Microalgal wastewater treatment systems augmented with CO2 offer a promising and cost-effective treatment solution for reducing both total ammonia concentrations and ammonia volatilisation. In this study, we investigate the effects of augmenting CO2 on nutrient removal and specifically nitrogen losses, as well as biomass productivity under two difference hydraulic retention times (HRT). Both CO2 addition and HRT affect nitrogen losses, with the percentage removal of total ammonia significantly lower (p < 0.01) when CO2 was added to the treatments, while increased HRT significantly increased (p < 0.05) total ammonia percentage removal. Total nitrogen budgets showed significantly lower (p < 0.01) abiotic nitrogen losses from the system when CO2 was added to the culture but at the expense of effluent quality. Both total suspended solids and volatile suspended solids significantly increased (p < 0.01) under longer HRT (8 days), with CO2 addition, while chlorophyll-a biomass significantly increased (p < 0.01) on longer HRT, regardless of CO2 addition. These results demonstrate that, while CO2 augmentation helped to mitigate ammonia losses to atmosphere, the trade-off was poorer effluent quality. Coupling CO2 augmentation with longer HRT increased biomass production and nutrient removal efficiency. This study provides an insight into how simple operational changes can alleviate some of the trade-offs between atmospheric losses and effluent quality. However, in order to manage the trade-off ...

Sutherland, DL, McCauley, J, Labeeuw, L, Ray, P, Kuzhiumparambil, U, Hall, C, Doblin, M, Nguyen, LN & Ralph, PJ 2021, 'How microalgal biotechnology can assist with the UN Sustainable Development Goals for natural resource management', Current Research in Environmental Sustainability.
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Szpila, K, Walczak, K, Johnston, NP, Pape, T & Wallman, JF 2021, 'First instar larvae of endemic Australian Miltogramminae (Diptera: Sarcophagidae)', SCIENTIFIC REPORTS, vol. 11, no. 1.
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Tang, X, Zhou, D, Zhang, B, Wang, S, Li, P, Liu, H, Guo, X, Jaumaux, P, Gao, X, Fu, Y, Wang, C, Wang, C & Wang, G 2021, 'A universal strategy towards high–energy aqueous multivalent–ion batteries', Nature Communications.
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Tao, S, Wang, T, Wu, Y, Wang, C & Wang, G 2021, 'Removal of extremely low concentration cobalt by intercalation composite material of carbon nitride/titanium dioxide', JOURNAL OF HAZARDOUS MATERIALS, vol. 415.
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Taylor, J, Patio, K, De Rubis, G, Morris, MB, Evenhuis, C, Johnson, M & Bebawy, M 2021, 'Membrane to cytosol redistribution of alpha II-spectrin drives extracellular vesicle biogenesis in malignant breast cells', PROTEOMICS, vol. 21, no. 13-14.
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Thomas Broome, S, Fisher, T, Faiz, A, Keay, KA, Musumeci, G, Al-Badri, G & Castorina, A 2021, 'Assessing the Anti-Inflammatory Activity of the Anxiolytic Drug Buspirone Using CRISPR-Cas9 Gene Editing in LPS-Stimulated BV-2 Microglial Cells', Cells.
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Tian, H, Song, A, Tian, H, Liu, J, Shao, G, Liu, H & Wang, G 2021, 'Single-atom catalysts for high-energy rechargeable batteries', Chemical Science.
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Tian, H, Tian, H, Yang, W, Zhang, F, Yang, W, Zhang, Q, Wang, Y, Liu, J, Silva, SRP, Liu, H & Wang, G 2021, 'Stable Hollow-Structured Silicon Suboxide-Based Anodes toward High-Performance Lithium-Ion Batteries', ADVANCED FUNCTIONAL MATERIALS, vol. 31, no. 25.
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Tiotiu, A, Badi, Y, Kermani, N, Hansbro, P, Wheelock, C, Dahlen, SE, Guo, YK, Sterk, P, Djukanovic, R, Adcock, I & Chung, KF 2021, 'Rôle des mastocytes dans l’asthme sévère : analyse de données transcriptomiques dans la cohorte U-BIOPRED', Revue des Maladies Respiratoires Actualités, vol. 13, no. 1, pp. 68-68.
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Tkacheva, A, Sun, B, Zhang, J, Wang, G & McDonagh, AM 2021, 'Nitronyl Nitroxide-Based Redox Mediators for Li-O-2 Batteries', JOURNAL OF PHYSICAL CHEMISTRY C, vol. 125, no. 5, pp. 2824-2830.
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Todd, N, McNally, R, Alqudah, A, Jerotic, D, Suvakov, S, Obradovic, D, Hoch, D, Hombrebueno, JR, Campos, GL, Watson, CJ, Gojnic-Dugalic, M, Simic, TP, Krasnodembskaya, A, Desoye, G, Eastwood, K-A, Hunter, AJ, Holmes, VA, McCance, DR, Young, IS, Grieve, DJ, Kenny, LC, Garovic, VD, Robson, T & McClements, L 2021, 'Role of A Novel Angiogenesis FKBPL-CD44 Pathway in Preeclampsia Risk Stratification and Mesenchymal Stem Cell Treatment', JOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM, vol. 106, no. 1, pp. 26-41.
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Tran, N, Ricafrente, A, To, J, Lund, M, Marques, TM, Gama-Carvalho, M, Cwiklinski, K, Dalton, JP & Donnelly, S 2021, 'Fasciola hepatica hijacks host macrophage miRNA machinery to modulate early innate immune responses', Scientific Reports.
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Travis, G, Haddadi, N, Simpson, AM, Marsh, DJ, McGowan, EM & Nassif, NT 2021, 'Studying the Oncosuppressive Functions of PTENP1 as a ceRNA', vol. 2324, pp. 165-185.
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PTENP1 is a processed pseudogene of the tumour suppressor phosphatase and tensin homolog deleted on chromosome 10 (PTEN). It functions posttranscriptionally to regulate PTEN by acting as a sponge for microRNAs that target PTEN. PTENP1 therefore functions as a competitive endogenous RNA (ceRNA), competing with PTEN for binding of microRNAs (miRNA) and thereby modulating PTEN cellular abundance. Studies of the overexpression of PTENP1 all confirm its oncosuppressive function to be mediated through the suppression of cell proliferation, induction of apoptosis, and inhibition of cell migration and invasion of cancer cells of differing types. These oncosuppressive functions are a direct consequence of miRNA binding by PTENP1 and the subsequent liberation of PTEN from miRNA induced suppression. In this chapter, we will focus initially on the description of a high efficiency transient transfection method to introduce and overexpress PTENP1 in the cell type of interest, followed by accurate methodologies to measure transfection efficiency by flow cytometry. We will then continue to describe two methods to analyze cell proliferation, namely the CCK-8 assay and Click-iT® EdU assay. Due to commonalities in the manifestation of the oncosuppressive effects of PTENP1, mediated through its role as a ceRNA, the methods presented in this chapter will have wide applicability to a variety of different cell types.

Tripathi, A, Kruk, S, Shang, Y, Zhou, J, Kravchenko, I, Jin, D & Kivshar, Y 2021, 'Topological nanophotonics for photoluminescence control', NANOPHOTONICS, vol. 10, no. 1, pp. 435-441.
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Trist, BG, Hilton, JB, Hare, DJ, Crouch, PJ & Double, KL 2021, 'Superoxide Dismutase 1 in Health and Disease: How a Frontline Antioxidant Becomes Neurotoxic.', Angewandte Chemie (International ed. in English).
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Cu/Zn superoxide dismutase (SOD1) is a frontline antioxidant enzyme catalysing superoxide breakdown and is important for most forms of eukaryotic life. The evolution of aerobic respiration by mitochondria increased cellular production of superoxide, resulting in an increased reliance upon SOD1. Consistent with the importance of SOD1 for cellular health, many human diseases of the central nervous system involve perturbations in SOD1 biology. But far from providing a simple demonstration of how disease arises from SOD1 loss-of-function, attempts to elucidate pathways by which atypical SOD1 biology leads to neurodegeneration have revealed unexpectedly complex molecular characteristics delineating healthy, functional SOD1 protein from that which likely contributes to central nervous system disease. This review summarises current understanding of SOD1 biology from SOD1 genetics through to protein function and stability.

Tseng, P-H, Zhou, A & Hwang, FJ 2021, 'Northeast passage in Asia-Europe liner shipping: an economic and environmental assessment', International Journal of Sustainable Transportation, pp. 1-12.
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In recent years, the Northeast Passage (NEP) has been widely discussed in the shipping industries since it can potentially bring economic benefit thanks to its relatively short sailing distance vis-a-vis the conventional Asia-Europe route via the Suez Canal. Concomitantly, due to the recent advocacy of green shipping, how to deploy effectively a shipping fleet so as to reduce the environmental cost has become an increasingly crucial issue in the shipping industries. However, it has not been investigated how the optimal shipping allocation between the conventional Asia-Europe route and NEP, based on both economic and environmental considerations, will be influenced by different aspects of shipping costs respectively, which will further affect the ocean carriers’ decision and adoption attitude toward the NEP. In this paper, a quantitative assessment model considering the shipment operating cost as well as the external cost of various pollutant emissions is presented to analyze the multi-port multi-trip liner service in an Asia-Europe container shipping network. Based on the shipping network with cargo demand of an Asian shipping company and empirical data from the existing literature, our study demonstrates how the optimal shipping allocation varies between scenarios by performing sensitivity analyses. Our findings indicate that the icebreaker fee, as well as Suez Canal toll, plays a more decisive role than the fuel price in affecting the adoption of the NEP. The relevant policy and managerial implications are discussed.

Tu, X, Donovan, C, Kim, RY, Wark, PAB, Horyat, JC & Hansbro, PM 2021, 'Asthma-COPD overlap: current understanding and the utility of experimental models', EUROPEAN RESPIRATORY REVIEW, vol. 30, no. 159.
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Turnbull, L, Leigh, R, Cavaliere, R, Osvath, SR, Nolan, LM, Smyth, D, Verhoeven, K, Chole, RA & Whitchurch, CB 2021, 'Device design modifications informed by in vitro testing of bacterial attachment reduce infection rates of cochlear implants in clinical practice', Microorganisms, vol. 9, no. 9.
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Recalcitrant chronic infections of implanted medical devices are often linked to the presence of biofilms. The prevention and treatment of medical device-associated infections is a major source of antibiotic use and driver of antimicrobial resistance globally. Lowering the incidence of infection in patients that receive implanted medical devices could therefore significantly improve antibiotic stewardship and reduce patient morbidity. Here we determined if modifying the design of an implantable medical device to reduce bacterial attachment, impacted the incidence of device-associated infections in clinical practice. Since the 1980s cochlear implants have provided long-term treatment of sensorineural hearing deficiency in hundreds of thousands of patients world-wide. Nonetheless, a relatively small number of devices are surgically explanted each year due to unresolvable infections. Features associated with the accumulation of bacteria on the Cochlear™ Nucleus® CI24RE™ model of cochlear implant devices were identified using both in vitro bacterial attachment assays and examination of explanted devices. Macro-scale design modifications that reduced bacterial attachment in vitro were incorporated into the design of the CI500™ and Profile™ series of Nucleus implant. Analyses of mandatory post-market vigilance data of 198,757 CI24RE and 123,084 CI500/Profile series implantation surgeries revealed that these design modifications correlated with significantly reduced infection rates. This study demonstrates that a design-centric approach aimed at mitigating bacterial attachment was a simple, and effective means of reducing infections associated with Cochlear Nucleus devices. This approach is likely to be applicable to improving the designs of other implantable medical devices to reduce device-associated infections.

Turner, KM, Balleine, BW & Bradfield, LA 2021, 'Does Disrupting the Orbitofrontal Cortex Alter Sensitivity to Punishment? A Potential Mechanism of Compulsivity', BEHAVIORAL NEUROSCIENCE, vol. 135, no. 2, pp. 174-181.
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Violi, JP, Bishop, DP, Padula, MP, Westerhausen, MT & Rodgers, KJ 2021, 'Acetonitrile adduct analysis of underivatised amino acids offers improved sensitivity for hydrophilic interaction liquid chromatography tandem mass-spectrometry', Journal of Chromatography A, vol. 1655.
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LC-MS/MS method development for native amino acid detection can be problematic due to low ionisation efficiencies, in source fragmentation, potential for cluster ion formation and incorrect application of chromatography techniques. This has led to the majority of the scientific community derivatising amino acids for more sensitive analysis. Derivatisation has several benefits including reduced signal-to-noise ratios, more efficient ionisation, and a change in polarity, allowing the use of reverse phase chromatography. However, derivatisation of amino acids can be expensive, requires additional sample preparation steps, is more time consuming and increases sample instability, due to the most derivatised amino acids only be stable for finite amount of time. While showing initial promise, development of reliable hydrophilic interaction liquid chromatography (HILIC) separation methods has presented difficulties for the analyst including irreproducible separation and poor sensitivity. This study aimed to find a means to improve the detection sensitivity of the 20 protein amino acids by HILIC-MS/MS. We describe the use of previously undescribed amino acid-acetonitrile (ACN) adducts to improve detection of 16 out of the 20 amino acids. While all amino acids examined did form an ACN adduct, 4 had low intensity adduct formation compared to their protonated state, 3 of which are classified as basic amino acids. For 15 of the 20 amino acids tested, we used the ACN adduct for both quantification and qualification ions and demonstrated a significant enhancement in signal-to-noise ratio, ranging from 23 to 1762% improvement. Lower LODs, LOQs and lower ranges of linearity were also achieved for these amino acids. The optimised method was applied to a human neuroblastoma cell line (SH-SY5Y) with the potential to be applied to other complex sample types. The improved sensitivity this method offers simplifies sample preparation and reduces the costs of amino acid analysis compared...

Vu, HP, Nguyen, LN, Vu, MT, Labeeuw, L, Emmerton, B, Commault, AS, Ralph, PJ, Mahlia, TM & Nghiem, LD 2021, 'Harvesting Porphyridium purpureum using polyacrylamide polymers and alkaline bases and their impact on biomass quality', SCIENCE OF THE TOTAL ENVIRONMENT, vol. 755.
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Wadhwa, R, Paudel, KR, Chin, LH, Hon, CM, Madheswaran, T, Gupta, G, Panneerselvam, J, Lakshmi, T, Singh, SK, Gulati, M, Dureja, H, Hsu, A, Mehta, M, Anand, K, Devkota, HP, Chellian, J, Chellappan, DK, Hansbro, PM & Dua, K 2021, 'Anti-inflammatory and anticancer activities of Naringenin-loaded liquid crystalline nanoparticles in vitro.', Journal of food biochemistry, vol. 45, no. 1.
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In this study, we had developed Naringenin-loaded liquid crystalline nanoparticles (LCNs) and investigated the anti-inflammatory and anticancer activities of Naringenin-LCNs against human airway epithelium-derived basal cells (BCi-NS1.1) and human lung epithelial carcinoma (A549) cell lines, respectively. The anti-inflammatory potential of Naringenin-LCNs evaluated by qPCR revealed a decreased expression of IL-6, IL-8, IL-1β, and TNF-α in lipopolysaccharide-induced BCi-NS1.1 cells. The activity of LCNs was comparable to the positive control drug Fluticasone propionate (10 nM). The anticancer activity was studied by evaluating the antiproliferative (MTT and trypan blue assays), antimigratory (scratch wound healing assay, modified Boyden chamber assay, and immunoblot), and anticolony formation activity in A549 cells. Naringenin LCNs showed promising antiproliferative, antimigratory, and anticolony formation activities in A549 cells, in vitro. Therefore, based on our observations and results, we conclude that Naringenin-LCNs may be employed as a potential therapy-based intervention to ameliorate airway inflammation and to inhibit the progression of lung cancer. PRACTICAL APPLICATIONS: Naringenin was encapsulated into liquid crystalline nanoparticles, thus, attributing to their sustained-release nature. In addition, Naringenin-loaded LCNs efficiently reduced the levels of pro-inflammatory markers, namely, IL-1β, IL-6, TNF-α, and IL-8. In addition, the Naringenin-loaded LCNs also possess potent anticancer activity, when tested in the A549 cell line, as revealed by the inhibition of proliferation and migration of cells. They also attenuated colony formation and induced apoptosis in the A549 cells. The findings from our study could form the basis for future research that may be translated into an in vivo model to validate the possible therapeutic alternative for lung cancer using Naringenin-loaded LCNs. In addition, the applications of Naringenin-loaded LCNs as an inter...

Wang, B, Chan, YL, Li, G, Ho, KF, Anwer, AG, Smith, BJ, Guo, H, Jalaludin, B, Herbert, C, Thomas, PS, Liao, J, Chapman, DG, Foster, PS, Saad, S, Chen, H & Oliver, BG 2021, 'Maternal particulate matter exposure impairs lung health and is associated with mitochondrial damage', Antioxidants, vol. 10, no. 7.
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Relatively little is known about the transgenerational effects of chronic maternal exposure to low-level traffic-related air pollution (TRAP) on the offspring lung health, nor are the effects of removing such exposure before pregnancy. Female BALB/c mice were exposed to PM2.5 (PM2.5, 5 µg/day) for 6 weeks before mating and during gestation and lactation; in a subgroup, PM was re-moved when mating started to model mothers moving to cleaner areas during pregnancy to protect their unborn child (Pre-exposure). Lung pathology was characterised in both dams and offspring. A subcohort of female offspring was also exposed to ovalbumin to model allergic airways disease. PM2.5 and Pre-exposure dams exhibited airways hyper-responsiveness (AHR) with mucus hyperse-cretion, increased mitochondrial reactive oxygen species (ROS) and mitochondrial dysfunction in the lungs. Female offspring from PM2.5 and Pre-exposure dams displayed AHR with increased lung inflammation and mitochondrial ROS production, while males only displayed increased lung in-flammation. After the ovalbumin challenge, AHR was increased in female offspring from PM2.5 dams compared with those from control dams. Using an in vitro model, the mitochondria-targeted antioxidant MitoQ reversed mitochondrial dysfunction by PM stimulation, suggesting that the lung pathology in offspring is driven by dysfunctional mitochondria. In conclusion, chronic exposure to low doses of PM2.5 exerted transgenerational impairment on lung health.

Wang, B, Chen, H, Xenaki, D, Liao, J, Cowie, C & Oliver, BG 2021, 'Differential inflammatory and toxic effects in-vitro of wood smoke and traffic-related particulate matter from Sydney, Australia', CHEMOSPHERE, vol. 272.
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Wang, S, Zhao, S, Guo, X & Wang, G 2021, '2D Material-Based Heterostructures for Rechargeable Batteries', ADVANCED ENERGY MATERIALS.
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Wang, T, Sun, X, Guo, X, Zhang, J, Yang, J, Tao, S, Guan, J, Zhou, L, Han, J, Wang, C, Yao, H & Wang, G 2021, 'Ultraefficiently Calming Cytokine Storm Using Ti3C2Tx MXene', Small Methods.
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Wark, PAB, Pathinayake, PS, Kaiko, G, Nichol, K, Ali, A, Chen, L, Sutanto, EN, Garratt, LW, Sohal, SS, Lu, W, Eapen, MS, Oldmeadow, C, Bartlett, N, Reid, A, Veerati, P, Hsu, AC-Y, Looi, K, Iosifidis, T, Stick, SM, Hansbro, PM & Kicic, A 2021, 'ACE2 expression is elevated in airway epithelial cells from older and male healthy individuals but reduced in asthma', RESPIROLOGY.
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Westermann, T, Jenkins, C, Onizawa, E, Gestier, S, McNally, J, Kirkland, P, Zhang, J, Bogema, D, Manning, LK, Walker, K & Pinczowski, P 2021, 'Chlamydia pecorum-Associated Sporadic Ovine Abortion', VETERINARY PATHOLOGY, vol. 58, no. 1, pp. 114-122.
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White, S, Stewart, C, Solntsev, AS, Li, C, Toth, M, Kianinia, M & Aharonovich, I 2021, 'Phonon dephasing and spectral diffusion of quantum emitters in hexagonal boron nitride', Optica, vol. 8, no. 9, pp. 1153-1153.
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White, SJU, Klauck, F, Trong Tran, T, Schmitt, N, Kianinia, M, Steinfurth, A, Heinrich, M, Toth, M, Szameit, A, Aharonovich, I & Solntsev, AS 2021, 'Quantum random number generation using a hexagonal boron nitride single photon emitter', Journal of Optics, vol. 23, no. 1, pp. 01LT01-01LT01.
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Wijesinghe, HGS, Hare, DJ, Mohamed, A, Shah, AK, Harris, PNA & Hill, MM 2021, 'Detecting antimicrobial resistance in Escherichia coli using benchtop attenuated total reflectance-Fourier transform infrared spectroscopy and machine learning.', The Analyst, vol. 146, no. 20, pp. 6211-6219.
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The widespread dissemination of resistance to third-generation cephalosporins in the Enterobacterales through the production of extended-spectrum β-lactamase (ESBL) is considered a critical global crisis requiring urgent attention of clinicians and scientists alike. Rapid diagnostic methods that can identify microbial resistance profiles closer to the point of care are crucial to minimize the overuse of antimicrobial agents and improve patient outcomes. Although Fourier transform infrared (FTIR) microscopy has shown promise in distinguishing between bacterial species, the high cost and technical requirements of the IR microscope may limit broad clinical use. To address the practical needs of a clinical microbiology laboratory, here, we examine the ability of a lower cost portable benchtop attenuated total reflectance (ATR)-FTIR spectrometer to achieve antimicrobial resistance detection, using a simple, clinically aligned sampling protocol. The technical reproducibility was confirmed through multi-day analysis of an Escherichia coli type strain, which serves as quality control. We generated a dataset of 100 E. coli clinical bloodstream isolates with 63 ceftriaxone resistant bla_CTX-M ESBL gene variant strains and developed a classifier for bla_CTX-M genotype detection. After assessing 35 machine learning methods using the training set (n = 71), four methods were further optimised, and the best performing method was evaluated using the held-out testing set (n = 29). A tuned support vector machine model with a polynomial kernel, using the 700-1500 cm^-1 range achieved a sensitivity of 89.2%, and specificity of 66.7% for detecting bla_CTX-M in independent testing, approaching the reported performance of FTIR microscopy. With further algorithm improvement, these data suggest the potential deployment of a portable FTIR spectrometer as a rapid antimicrobial susceptibility pre...

Wilson, KA, Mostyn, SN, Frangos, ZJ, Shimmon, S, Rawling, T, Vandenberg, RJ & O'Mara, ML 2021, 'The allosteric inhibition of glycine transporter 2 by bioactive lipid analgesics is controlled by penetration into a deep lipid cavity', Journal of Biological Chemistry.
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Windhagauer, M, Abbriano, RM, Ashworth, J, Barolo, L, Jaramillo-Madrid, AC, Pernice, M & Doblin, MA 2021, 'Characterisation of novel regulatory sequences compatible with modular assembly in the diatom Phaeodactylum tricornutum', ALGAL RESEARCH-BIOMASS BIOFUELS AND BIOPRODUCTS, vol. 53.
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Woldhuis, RR, Heijink, IH, van den Berge, M, Timens, W, Oliver, BGG, de Vries, M & Brandsma, C-A 2021, 'COPD-derived fibroblasts secrete higher levels of senescence-associated secretory phenotype proteins.', Thorax.
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COPD-derived fibroblasts have increased cellular senescence. Senescent cell accumulation can induce tissue dysfunction by their senescence-associated secretory phenotype (SASP). We aimed to determine the SASP of senescent fibroblasts and COPD-derived lung fibroblasts, including severe, early-onset (SEO)-COPD. SASP protein secretion was measured after paraquat-induced senescence in lung fibroblasts using Olink Proteomics and compared between (SEO-)COPD-derived and control-derived fibroblasts. We identified 124 SASP proteins of senescent lung fibroblasts, of which 42 were secreted at higher levels by COPD-derived fibroblasts and 35 by SEO-COPD-derived fibroblasts compared with controls. Interestingly, the (SEO-)COPD-associated SASP included proteins involved in chronic inflammation, which may contribute to (SEO-)COPD pathogenesis.

Wolff, C, Smith, MJA, Stiller, B & Poulton, CG 2021, 'Brillouin scattering—theory and experiment: tutorial', Journal of the Optical Society of America B, vol. 38, no. 4, pp. 1243-1243.
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Wood, B, Padula, MP, Marks, DC & Johnson, L 2021, 'The immune potential of ex vivo stored platelets: a review.', Vox sanguinis.
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Platelets are now acknowledged as key regulators of the immune system, as they are capable of mediating inflammation, leucocyte recruitment and activation. This activity is facilitated through platelet activation, which induces significant changes in the surface receptor profile and triggers the release of a range of soluble biological response modifiers (BRMs). In the field of transfusion medicine, the immune function of platelets has gained considerable attention as this may be linked to the development of adverse transfusion reactions. Further, component manufacturing and storage methodologies may impact the immunoregulatory role of platelets, and an understanding of this impact is crucial and should be considered alongside their haemostatic characteristics. This review highlights the key interactions between platelets and traditional immune modulators. Further, the potential impact of current and novel component storage methodologies, such as refrigeration and cryopreservation, on this functional capacity is examined, highlighting why further knowledge in this area would be of benefit.

Wood, SN, Wit, EC, Fasiolo, M & Green, PJ 2021, 'COVID-19 and the difficulty of inferring epidemiological parameters from clinical data', The Lancet Infectious Diseases, vol. 21, no. 1, pp. 27-28.
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Woodle, ES, Gill, JS, Clark, S, Stewart, D, Alloway, R & First, R 2021, 'Early Corticosteroid Cessation vs Long-term Corticosteroid Therapy in Kidney Transplant Recipients Long-term Outcomes of a Randomized Clinical Trial', JAMA SURGERY.
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Wright, K, de Silva, K, Plain, KM, Purdie, AC, Blair, TA, Duggin, IG, Britton, WJ & Oehlers, SH 2021, 'Mycobacterial infection-induced miR-206 inhibits protective neutrophil recruitment via the CXCL12/CXCR4 signalling axis', PLOS Pathogens.
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Wu, WW, Zhang, X, Li, M, Liu, Y, Chen, ZH, Xie, M, Zhao, SZ, Wang, G, Zhang, HP, Wang, T, Qin, L, Wang, L, Oliver, BG, Wan, HJ, Zhang, J, McDonald, VM, Marks, GB, Li, WM, Birring, SS, Wang, G & Gibson, PG 2021, 'Treatable Traits in Elderly Asthmatics from the Australasian Severe Asthma Network: A Prospective Cohort Study.', The journal of allergy and clinical immunology. In practice.
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Background

Data on treatable traits (TTs) in different populations are limited.

Objective

To assess TTs in elderly patients with asthma and compare them to younger patients, to evaluate the association of TTs with future exacerbations, and to develop an exacerbation prediction model.

Methods

We consecutively recruited 521 participants at West China Hospital, Sichuan University based on the Australasian Severe Asthma Network, classified as elderly (n = 62) and nonelderly (n = 459). Participants underwent a multidimensional assessment to characterize the TTs and were then followed up for 12 months. TTs and their relationship with future exacerbations were described. Based on the TTs and asthma control levels, an exacerbation prediction model was developed, and the overall performance was externally validated in an independent cohort.

Results

A total of 38 TTs were assessed. Elderly patients with asthma had more chronic metabolic diseases, fixed airflow limitation, emphysema, and neutrophilic inflammation, whereas nonelderly patients with asthma exhibited more allergic characteristics and psychiatric diseases. Nine traits were associated with increased future exacerbations, of which exacerbation prone, upper respiratory infection-induced asthma attack, cardiovascular disease, diabetes, and depression were the strongest. A model including exacerbation prone, psychiatric disease, cardiovascular disease, upper respiratory infection-induced asthma attack, noneosinophilic inflammation, cachexia, food allergy, and asthma control was developed to predict exacerbation risk and showed good performance.

Conclusions

TTs can be systematically assessed in elderly patients with asthma, some of which are associated with future exacerbations, proving their clinical utility of evaluating them. A model based on TTs can be used to predict exacerbation risk in people with asthma.

Wu, Z, Zhou, J, Li, D, Ao, Z, An, T & Wang, G 2021, 'Density functional theory study on the enhanced adsorption mechanism of gaseous pollutants on Al-doped Ti2CO2 monolayer', Sustainable Materials and Technologies, vol. 29, pp. e00294-e00294.
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Xiao, J, Li, X, Tang, K, Wang, D, Long, M, Gao, H, Chen, W, Liu, C, Liu, H & Wang, G 2021, 'Recent progress of emerging cathode materials for sodium ion batteries', MATERIALS CHEMISTRY FRONTIERS, vol. 5, no. 10, pp. 3735-3764.
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Xiong, P, Zhang, F, Zhang, X, Liu, Y, Wu, Y, Wang, S, Safaei, J, Sun, B, Ma, R, Liu, Z, Bando, Y, Sasaki, T, Wang, X, Zhu, J & Wang, G 2021, 'Atomic-scale regulation of anionic and cationic migration in alkali metal batteries', Nature Communications.
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Yan, J, Kuzhiumparambil, U, Bandodkar, A, Bandodkar, S, Dale, RC & Fu, S 2021, 'Cerebrospinal fluid metabolites in tryptophan-kynurenine and nitric oxide pathways: biomarkers for acute neuroinflammation.', Developmental Medicine and Child Neurology.
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Aim

To explore the cerebrospinal fluid (CSF) metabolite features in acute neuroinflammatory diseases and identify potential biomarkers to diagnose and monitor neuroinflammation.

Method

A cohort of 14 patients (five females, nine males; mean [median] age 7y 9mo [9y], range 6mo-13y) with acute encephalitis (acute disseminated encephalomyelitis n=6, unknown suspected viral encephalitis n=3, enteroviral encephalitis n=2, seronegative autoimmune encephalitis n=2, herpes simplex encephalitis n=1) and age-matched non-inflammatory neurological disease controls (n=14) were investigated using an untargeted metabolomics approach. CSF metabolites were analyzed with liquid chromatography coupled to high resolution mass spectrometry, followed by subsequent multivariate and univariate statistical methods.

Results

A total of 35 metabolites could be discriminated statistically between the groups using supervised orthogonal partial least squares discriminant analysis and analysis of variance. The tryptophan-kynurenine pathway contributed nine key metabolites. There was a statistical increase of kynurenine, quinolinic acid, and anthranilic acid in patients with encephalitis, whereas tryptophan, 3-hydroxyanthrnailic acid, and kynurenic acid were decreased. The nitric oxide pathway contributed four metabolites, with elevated asymmetric dimethylarginine and argininosuccinic acid, and decreased arginine and citrulline in patients with encephalitis. An increase in the CSF kynurenine/tryptophan ratio (p<0.001), anthranilic acid/3-hydroxyanthranilic acid ratio (p<0.001), asymmetric dimethylarginine/arginine ratio (p<0.001), and neopterin (p<0.001) strongly predicted neuroinflammation.

Interpretation

The combination of alterations in the tryptophan-kynurenine pathway, nitric oxide pathway, and neopterin represent a useful potential panel for neuroinflammation and holds potential for clinical translation practice.

Yang, J, Krix, ZE, Kim, S, Tang, J, Mayyas, M, Wang, Y, Watanabe, K, Taniguchi, T, Li, LH, Hamilton, AR, Aharonovich, I, Sushkov, OP & Kalantar-Zadeh, K 2021, 'Near-Field Excited Archimedean-like Tiling Patterns in Phonon-Polaritonic Crystals', ACS NANO, vol. 15, no. 5, pp. 9134-9142.
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Yang, J, Li, J, Wang, T, Notten, PHL, Ma, H, Liu, Z, Wang, C & Wang, G 2021, 'Novel hybrid of amorphous Sb/N-doped layered carbon for high-performance sodium-ion batteries', Chemical Engineering Journal, vol. 407.
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© 2020 Elsevier B.V. Antimony (Sb) based materials, which have been proved to be promising anodes to fabricate high-performance sodium-ion batteries (SIBs), have attracted considerable interest owing to its large theoretical capacity (660 mAh g−1), appropriate inserting potential of sodium (0.5–0.8 V vs Na+/Na), and moderate electrode polarization (~0.35 V). Unfortunately, fast capacity decay and serious structure pulverization resulting from large volume variation upon cycling are often observed for Sb-based anodes, and further structure design is needed. In this work, a novel hybrid of amorphous Sb/N-doped layered carbon (a-Sb/NC) was fabricated through a facile bottom-up method, where ultrafine amorphous Sb nanoparticles are uniformly anchored on layered N-doped carbon (NC). When applied as anode material for SIBs, this hybrid exhibits a large reversible capacity (479.6 mAh g−1 at 0.1 A g−1 up to 100 cycles), robust rate capability (298.7 mAh g−1 at current density of 2 A g−1), and remarkable stability upon long-term cycling (280.5 mAh g−1 at 1.0 A g−1 up to 500 cycles), outperforming most of the reported amorphous anodes for SIBs. In principle, such impressive sodium storage properties of a-Sb/NC should be mainly ascribed to the amorphous feature of Sb nanoparticles as well as the synergistic effect between amorphous Sb and layered NC, thereby endowing the composite with improved electron/ion dynamics and efficient self-buffering ability.

Yang, W, Yang, W, Dong, L, Shao, G, Wang, G & Peng, X 2021, 'Hierarchical ZnO nanorod arrays grown on copper foam as an advanced three-dimensional skeleton for dendrite-free sodium metal anodes', NANO ENERGY, vol. 80.
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Ye, W, van Dijk, AIJM, Huete, A & Yebra, M 2021, 'Global trends in vegetation seasonality in the GIMMS NDVI3g and their robustness', International Journal of Applied Earth Observation and Geoinformation.
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Yi, GY, He, W & Carroll, RJ 2021, 'Feature screening with large-scale and high-dimensional survival data', BIOMETRICS.
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Yuen, ZW-S, Srivastava, A, Daniel, R, McNevin, D, Jack, C & Eyras, E 2021, 'Systematic benchmarking of tools for CpG methylation detection from nanopore sequencing', Nature Communications.
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Zakarya, R, Chan, YL, Rutting, S, Reddy, K, Bozier, J, Woldhuis, RR, Xenaki, D, Van Ly, D, Chen, H, Brandsma, C-A, Adcock, IM & Oliver, BG 2021, 'BET proteins are associated with the induction of small airway fibrosis in COPD.', Thorax.
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Rationale

In COPD, small airway fibrosis occurs due to increased extracellular matrix (ECM) deposition in and around the airway smooth muscle (ASM) layer. Studies of immune cells and peripheral lung tissue have shown that epigenetic changes occur in COPD but it is unknown whether airway mesenchymal cells are reprogrammed.

Objectives

Determine if COPD ASM cells have a unique epigenetic response to profibrotic cytokine transforming growth factor β1 (TGF-β1).

Methods

Primary human ASM cells from COPD and non-COPD smoking patients were stimulated with TGF-β1. Gene array analysis performed to identify differences in ECM expression. Airway accumulation of collagen 15α1 and tenascin-C proteins was assessed. Aforementioned ASM cells were stimulated with TGF-β1 ± epigenetic inhibitors with qPCR quantification of COL15A1 and TNC. Global histone acetyltransferase (HAT) and histone deacetylase (HDAC) activity were assessed. chromatin immunoprecipitation (ChIP)-qPCR for histone H3 and H4 acetylation at COL15A1 and TNC promoters was carried out. Effects of bromoterminal and extraterminal domain (BET) inhibitor JQ1(+) on expression and acetylation of ECM target genes were assessed.

Measurements and main results

COPD ASM show significantly higher COL15A1 and TNC expression in vitro and the same trend for higher levels of collagen 15α1 and tenascin-c deposited in COPD airways in vivo. Epigenetic screening indicated differential response to HDAC inhibition. ChIP-qPCR revealed histone H4 acetylation at COL15A1 and TNC promoters in COPD ASM only. ChIP-qPCR found JQ1(+) pretreatment significantly abrogated TGF-β1 induced histone H4 acetylation at COL15A1 and TNC.

Conclusions

BET protein binding to acetylated histones is important in TGF-β1 induced expression of COL15A1 and TNC and maintenance of TGF-β1 induced histone H4 acetylation in cell progeny.

Zhand, S, Xiao, K, Bazaz, SR, Zhu, Y, Bordhan, P, Jin, D & Warkiani, ME 2021, 'Improving capture efficiency of human cancer cell derived exosomes with nanostructured metal organic framework functionalized beads', APPLIED MATERIALS TODAY, vol. 23.
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Zhang, G, Morrison, D, Bao, G, Yu, H, Yoon, CW, Song, T, Lee, J, Ung, AT & Huang, Z 2021, 'An Amine-Borane System Featuring Room-Temperature Dehydrogenation and Regeneration', ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, vol. 60, no. 21, pp. 11725-11729.
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Zhang, H, Li, J, Chen, Y, Wu, J, Wang, K, Chen, L, Wang, Y, Jiang, X, Liu, Y, Wu, Y, Jin, D & Bu, W 2021, 'Magneto-Electrically Enhanced Intracellular Catalysis of FePt-FeC Heterostructures for Chemodynamic Therapy', Advanced Materials.
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Intracellular catalytic reactions can tailor tumor cell plasticity toward high-efficiency treatments, but the application is hindered by the low efficiency of intracellular catalysis. Here, a magneto-electronic approach is developed for efficient intracellular catalysis by inducing eddy currents of FePt-FeC heterostructures in mild alternating magnetic fields (frequency of f = 96 kHz and amplitude of B ≤ 70 mT). Finite element simulation shows a high density of induced charges gathering at the interface of FePt-FeC heterostructure in the alternating magnetic field. As a result, the concentration of an essential coenzyme—β-nicotinamide adenine dinucleotide—in cancer cells is significantly reduced by the enhanced catalytic hydrogenation reaction of FePt-FeC heterostructures under alternating magnetic stimulation, leading to over 80% of senescent cancer cells—a vulnerable phenotype that facilitates further treatment. It is further demonstrated that senescent cancer cells can be efficiently killed by the chemodynamic therapy based on the enhanced Fenton-like reaction. By promoting intracellular catalytic reactions in tumors, this approach may enable precise catalytic tumor treatment.

Zhang, H, Li, Y, Zhang, P, Ren, C, Xu, X, Sun, B & Yang, Z 2021, 'A Flexible Implantable Polyimide Catheter Device for Targeted Treatment of Cardiovascular Diseases by Aggregating Magnetic Nanoparticles', IEEE TRANSACTIONS ON COMPONENTS PACKAGING AND MANUFACTURING TECHNOLOGY, vol. 11, no. 6, pp. 911-917.
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Zhang, L, Chen, C, Tay, SS, Wen, S, Cao, C, Biro, M, Jin, D & Stenzel, MH 2021, 'Optimizing the Polymer Cloak for Upconverting Nanoparticles: An Evaluation of Bioactivity and Optical Performance', ACS APPLIED MATERIALS & INTERFACES, vol. 13, no. 14, pp. 16142-16154.
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Zhang, L, Jin, D & Stenzel, MH 2021, 'Polymer-Functionalized Upconversion Nanoparticles for Light/Imaging-Guided Drug Delivery.', Biomacromolecules.
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The strong upconversion luminescence (UCL) of upconversion nanoparticles (UCNPs) endows the nanoparticles with attractive features for combined imaging and drug delivery. UCNPs convert near-infrared (NIR) light into light of shorter wavelengths such as light in the ultraviolet (UV) and visible regions, which can be used for light-guided drug delivery. Although light-responsive drug delivery systems as such have been known for many years, their application in medicine is limited, as strong UV-light can be damaging to tissue; moreover, UV light will not penetrate deeply into the skin, an issue that UCNPs can now address. However, UCNPs, as obtained after synthesis, are usually hydrophobic and require further surface functionalization to be stable in plasma. Polymers can serve as versatile surface coatings, as they can provide good colloidal stability, prevent the formation of a protein corona, provide a matrix for drugs, and be stimuli-responsive. In this Review, we provide a brief overview of the most recent progress in the synthesis of UCNPs with different shapes/sizes. We will then discuss the purpose of polymer coating for drug delivery before summarizing the strategies to coat UCNPs with various polymers. We will introduce the different polymers that have so far been used to coat UCNPs with the purpose to create a drug delivery system, focusing in detail on light-responsive polymers. To expand the application of UCNPs to allow photothermal therapy or magnetic resonance imaging (MRI) or to simply enhance the loading capacity of drugs, UCNPs were often combined with other materials to generate multifunctional nanoparticles such as carbon-based NPs and nanoMOFs. We then conclude with a discussion on drug loading and release and summarize the current knowledge on the toxicity of these polymer-coated UCNPs.

Zhang, T, Li, H, Liu, M, Zhou, H, Zhang, Z, Yu, C, Wang, C & Wang, G 2021, 'Improved the specificity of peroxidase-like carbonized polydopamine nanotubes with high nitrogen doping for glutathione detection', Sensors and Actuators, B: Chemical, vol. 341.
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The introduction of nitrogen heteroatoms into enzyme-like carbon materials is an effective strategy to enhance both catalytic activity and specificity. Herein, we described the preparation of the carbonized polydopamine nanotubes (C-DPANTs) using sacrificial halloysite nanotubes (HNTs) templates. The resulting nitrogen doped C-PDANTs (N-doped C-PDANTs) exhibit solely the peroxidase-like activity owing to the high N doping. N-doped C-PDANTs could catalyze the reduction of H O to produce OH radicals, which contributed to the oxidation of 3,3’, 5,5’-tetramethylbenzidine (TMB) substrates. Moreover, the catalytic mechanism of N-doped C-PDANTs was further revealed by electrochemical measurements. N-doped C-PDANTs with pyridinic N and graphitic N compositions possess the capability to accelerate the electron transfer, thus facilitating the reduction of H O . The application of N-doped C-PDANTs were demonstrated in the sensitive detection of glutathione (GSH) in serum samples. Therefore, the present study provides a facile way to prepared peroxidase-like nanomaterials with high specificity. 2 2 2 2 ●

Zhao, CS, Pan, X, Yang, ST, Xiang, H, Zhao, J, Gan, XJ, Ding, SY & Yu, Q 2021, 'Effects and prediction of nonpoint source pollution on the structure of aquatic food webs', Ecohydrology, vol. 14, no. 1.
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© 2020 John Wiley & Sons, Ltd. Nonpoint source pollution entering rivers will pollute water quality, degrading the health of aquatic ecosystems. However, owing to the lack of quantitative research on the effects of nonpoint source pollution on the structure of aquatic food webs, there is a lack of quantitative basis for river management. Nonpoint source pollution is not only difficult to control effectively, but also the success rate of water ecological restoration projects is low. With the increasing proportion of nonpoint source pollution in water environmental problems, it is urgent to quantitatively assess and predict the impact of nonpoint source pollution on the structure of food webs. Therefore, this thesis presents a method for quantitatively assessing and predicting the impact of nonpoint source pollution on the structure of food webs through using fuzzy clustering to screen the typical points of the impact of nonpoint source pollution, then using canonical correspondence analysis (CCA) and partial least squares regression analysis to comprehensively filtrate the driving factors affect food web that results in nonpoint source pollution, and then determining the impact of each driving factor on the structure of food webs. Finally, the change trend of food web structure is predicted. The results show that (1) the driving factors that the nonpoint source pollution that affects the food web structure is NH3-N and chemical oxygen demand (COD). The increase in NH3-N and COD promotes the growth of phytoplankton, causing the change of the primary productivity of the ecosystem, and ultimately changes the entire food web structure; (2) NH3-N and COD affect the stability, maturity, connectivity and complexity of the aquatic food web structure. The increase of NH3-N increases the connectivity and maturity of the food web structure but reduces complexity and stability; the increase of COD increases the connection of the food web structure, while reducing the other ...

Zhao, CS, Pan, X, Yang, ST, Xiang, H, Zhao, J, Gan, XJ, Ding, SY, Yu, Q & Yang, Y 2021, 'Standards for environmental flow verification', Ecohydrology, vol. 14, no. 1.
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© 2020 John Wiley & Sons, Ltd. Healthy river ecosystems are conducive to the sustainable use of water resources. As the climate change and human activities become more intense, the integrity of such ecosystems is seriously threatened. The maintenance of enough environmental flow (e-flow) for river ecosystems is the most effective way of protecting river health. Accurately and reasonably estimating e-flow is essential for river health maintenance. So far, few methods can quantitatively verify the e-flow results calculated by various e-flow methods, which reduces the success rate of ecological restoration projects on a global scale. Therefore, the Tennant method, wetted perimeter (WP) method, and adapted ecological hydraulic radius (AEHRA) method have been recognized by many scholars. The article used the combination of these three methods to calculate the e-flow and its meeting rate (actual flow/e-flow) and formed a new framework to verify e-flow results. First, the Shannon diversity index, index of biological integrity (IBI), and river health index are used to evaluate river health status. Then, we studied the relationship between e-flow meeting rates and three indices using field monitoring data on hydrology, water quality, and biological communities. Finally, we investigated the effects of different e-flow calculation methods on river health. Results show that the e-flow in the centre of the study area calculated by the Tennant and WP methods are relatively high (48.33–317 m3/s), whereas lower e-flow (0.03–21 m3/s) are observed in its southern and northern parts. The e-flow in the southern mountain area calculated by the AEHRA method (1.42 m3/s) is higher than those in the other regions determined by the same method. Furthermore, the highest values of river health—the Shannon diversity index (3.19), IBI (67.47), and river health index (0.65)—appear in mountainous areas that are less affected by human activities. The lowest values appear in the urban areas wit...

Zhao, S, Guo, Z, Yan, K, Guo, X, Wan, S, He, F, Sun, B & Wang, G 2021, 'The Rise of Prussian Blue Analogs: Challenges and Opportunities for High‐Performance Cathode Materials in Potassium‐Ion Batteries', Small Structures, vol. 2, no. 1, pp. 2000054-2000054.
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Zhao, S, Guo, Z, Yan, K, Wan, S, He, F, Sun, B & Wang, G 2021, 'Towards high-energy-density lithium-ion batteries: Strategies for developing high-capacity lithium-rich cathode materials', ENERGY STORAGE MATERIALS, vol. 34, pp. 716-734.
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Zhao, S, Guo, Z, Yang, J, Wang, C, Sun, B & Wang, G 2021, 'Nanoengineering of Advanced Carbon Materials for Sodium-Ion Batteries', SMALL.
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Zhao, S, Yan, K, Liang, J, Yuan, Q, Zhang, J, Sun, B, Munroe, P & Wang, G 2021, 'Phosphorus and Oxygen Dual-Doped Porous Carbon Spheres with Enhanced Reaction Kinetics as Anode Materials for High-Performance Potassium-Ion Hybrid Capacitors', ADVANCED FUNCTIONAL MATERIALS.
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Zhao, S, Yan, K, Zhang, J, Sun, B & Wang, G 2021, 'Reaction Mechanisms of Layered Lithium-Rich Cathode Materials for High-Energy Lithium-Ion Batteries.', Angewandte Chemie (International ed. in English).
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Layered lithium-rich cathode materials have attracted extensive interest owing to their high theoretical specific capacity (320-350 mA h g-1 ). However, poor cycling stability and sluggish reaction kinetics inhibit their practical applications. After many years of quiescence, interest in layered lithium-rich cathode materials is expected to revive in answer to our increasing dependence on high-energy-density lithium-ion batteries. Herein, we review recent research progress and in-depth descriptions of the structure characterization and reaction mechanisms of layered lithium-rich manganese-based cathode materials. In particular, we comprehensively summarize the proposed reaction mechanisms of both the cationic redox reaction of transition-metal ions and the anionic redox reaction of oxygen species. Finally, we discuss opportunities and challenges facing the future development of lithium-rich cathode materials for next-generation lithium-ion batteries.

Zhao, Y, Zhang, J, Xie, Y, Sun, B, Jiang, J, Jiang, W-J, Xi, S, Yang, HY, Yan, K, Wang, S, Guo, X, Li, P, Han, Z, Lu, X, Liu, H & Wang, G 2021, 'Constructing Atomic Heterometallic Sites in Ultrathin Nickel-Incorporated Cobalt Phosphide Nanosheets via a Boron-Assisted Strategy for Highly Efficient Water Splitting', NANO LETTERS, vol. 21, no. 1, pp. 823-832.
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Zhou, D, Tang, X, Zhang, X, Zhang, F, Wu, J, Kang, F, Li, B & Wang, G 2021, 'Multi-ion Strategy toward Highly Durable Calcium/Sodium-Sulfur Hybrid Battery', NANO LETTERS, vol. 21, no. 8, pp. 3548-3556.
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Zhou, J, Zheng, G, Liu, X, Dong, G & Qiu, J 2021, 'Defect engineering in lanthanide doped luminescent materials', Coordination Chemistry Reviews, vol. 448.
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Lanthanides doped luminescent materials (LLMs) have recently gained considerable attention in the areas of bioimaging, sensing, display, and lasers, benefitting from the intriguing optical characters of lanthanides. In LLMs, defect creates intermediate energy levels within the bandgap, which tailors the excited-state dynamics of lanthanides in photophysics and manipulates the spectroscopic characteristics of the lanthanides with much enhanced precision, and thus defect engineering could be a powerful tool in designing LLMs. In this review, we first discuss the creation and characterization of defects in LLMs, which are especially facilitated by the rapid development in nanofabrication, the state-of-the-art instrumental techniques and computation methods. This advances have pushed the manipulation, understanding and utilization of defects in LLMs to a whole new-level and the tailoring of LLMs with desinged performance to meet the requirements of specific application has been dramatically improved in recent years. We then review the emerging applications of the defect-involved LLMs ranging from colour displays, energy utilization, radiation detection to biological applications. Finally, we envision future potential directions in the research of defect engineerin of LLMs and highlight the unsolved problems in this rapidly growing field.

Zhou, L, Li, H, Zhang, Y, Jiang, M, Danilov, DL, Eichel, R-A & Notten, PHL 2021, 'Enhanced sulfur utilization in lithium-sulfur batteries by hybrid modified separators', Materials Today Communications.
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Zhou, M, Zhang, H, Li, F, Yu, Z, Yuan, C, Oliver, B & Li, J 2021, 'Pulmonary Daoyin as a traditional Chinese medicine rehabilitation programme for patients with IPF: A randomized controlled trial.', Respirology (Carlton, Vic.).
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BACKGROUND AND OBJECTIVE:IPF is a chronic progressive lung disease in which PR provides benefit for patients. PD, a TCM PR programme, has known effectiveness in COPD, but its utility in IPF is unknown. We investigated its effectiveness and safety in patients with IPF. METHODS:A 6-month randomized controlled trial (RCT) was conducted in three Chinese clinics. Ninety-six participants diagnosed with IPF were randomly assigned to one of the three groups: the PD group received a PD programme two times a day, 5 days/week for 2 months, and the exercise group exercised via a stationary cycle ergometer, 30 min/day, 5 days/week for 2 months. Volunteers in the control group were advised to maintain their usual activities. Primary outcomes were changes from baseline in the 6MWD and HRQoL score on the SGRQ-I at 1 and 2 months (at the end of the intervention) and at 6 months (4 months after the intervention). Secondary outcomes measures included FVC, DLCO (% predicted) and the changes in mMRC. RESULTS:The 6MWD was increased in the PD group compared to exercise and control groups. 6MWD increased by 60.44 m in the PD group, 32.16 m in the exercise group and 12.42 m in controls after the 2 months of rehabilitation programme. The between-group differences in the change from baseline were 28.78 m (95% CI: 0.54 to 56.01; P = 0.044) and 48.02 m (95% CI: 23.04 to 73.00; P < 0.001) at 2 months, and 25.61 m (95% CI: -0.67 to 51.89; P = 0.058) and 50.93 m (95% CI: 25.47 to 76.40; P < 0.001) at 6 months, respectively, including a difference exceeding the MCID. There was no significant change in the SGRQ-I score, the mMRC dyspnoea score, FVC and DLCO (% predicted) in either the PD or exercise groups. CONCLUSION:Two months after the intervention, a clinically meaningful difference in 6MWD was observed favouring the PD programme. The PD programme is safe and effective as a rehabilitation intervention designed to increase exercise tolerance and is an appropriate substitute for PR.

Zinder, Y, Kononov, A & Fung, J 2021, 'A 5-parameter complexity classification of the two-stage flow shop scheduling problem with job dependent storage requirements', Journal of Combinatorial Optimization.
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Alqudah, A, Suvakov, S, Richards, C, Todd, N, Eastwood, K-A, Hunter, AJ, Holmes, VA, McCance, DR, Young, IS, Furlong, F, Ali, A, Krasnodembskaya, A, Lopez-Campos, G, Garovic, VD & McClements, L 2021, 'NOVEL MIRNAS AS TARGETS OF MESENCHYMAL STEM CELL-BASED THERAPY AS A TREATMENT FOR PREECLAMPSIA', Journal of Hypertension, ESH-ISH, Lippincott, Williams & Wilkins, ON-AIR, pp. 26-27.
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Chen, B, He, Z, Liu, ZJ, Wang, YK, Gao, YN, Aharonovich, I, Xu, ZQ & Liu, J 2020, 'Enhanced emission and second harmonic generation from WS2 by using dielectric circular Bragg resonators', Optics InfoBase Conference Papers, Asia Communications and Photonics Conference (ACP) and International Conference on Information Photonics and Optical Communications, IEEE, Beijing, China.
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We demonstrate a two-dimensional monolayer WS efficiently coupled to a dielectric circular Bragg resonator (CBR). The coupling of the WS and CBR leads to the pronounced enhancements in both photoluminescence and second harmonic generation. 2 2

Chen, H, Wu, Y, Chen, Y, Li, Y, McGowan, E & Lin, Y 2021, 'Seaweed Laminaria japonica peptides possess strong anti-liver cancer effects', Annals of Oncology, The 22nd World Congress on Gastrointestinal Cancer, Elsevier, Virtual.
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Background: Seaweed Laminaria japonica is widely consumed worldwide. This seaweed has also been used in traditional Chinese medicine for hundreds of years. Recent studies have shown that Laminaria japonica has multiple beneficial effects for human health, however, little is known about its anti-tumour effects. In the current study, we extracted Laminaria japonica peptides (LJPs) using an activity tracking method and explored the anti-tumour (liver cancer) activity of the peptides both in vivo and in vitro. Methods: The LJP’s were isolated with fresh Laminaria japonica and purified by Reversed Phase-High Performance Liquid Chromatography and HPLC-ESI-MS. Liver cancer cell lines HuH7, HepG2 cells and the human liver cell line HL-7702 cells were used throughout the experiment. The HepG2 cells were treated with LJP-1 (0, 0.36 mM and 1.80 mM) for 24 h, and cell apoptosis and cell cycle were evaluated. MTT assay was used to examine the cytotoxicity activity of the LJPs. Pro-apoptotic factors (including. Bax, Bid) and anti-apoptotic factors (including, Bcl-2, Bcl-xL) were investigated in cells treated with LJP. Caspase activation was examined by detecting the protein expressions of Caspase 3, Caspase 9, Cleaved caspase 3, Cleaved caspase 9 and Cleaved PARP using western blot. The phosphatidylinositol-3-kinase (PI3K)/AKT pathway and the phosphorylation states of the MAPKs (p38 and JNK) were also examined. The in vivo anti-liver cancer effect of LJP was investigated using a mouse model. Results: Results showed that LJP-1 [EGFHL] performed the most anti-proliferative activity in H22 cells in vitro. LJP-1 blocked the H22 cells in G0/G1 phase accompanied by inhibition of cyclins expression. Further experiments revealed that LJP-1 induced H22 cell apoptosis via Caspase activation and ASK1/MAPKs pathway regulation. At the same time, LJP-1 significantly inhibited the tumour growth and induced tumour cell apoptosis and necrosis in vivo. Conclusions: Our results support that ...

Deplazes, E, Hartmann, LM, Cranfield, CG & Garcia, A 2021, 'Cation-Selectivity of a Self-Assembled Peptide Pore in Planar Phospho-lipid Bilayers using Electrical Impedance Spectroscopy', BIOPHYSICAL JOURNAL, CELL PRESS, pp. 141A-141A.

Deplazes, E, Tafalla, BD, Murphy, C, White, J, Cranfield, CG & Garcia, A 2021, 'The Role of Ion-Phospholipid Interactions in the Permeation of Cations Across Zwitterionic Phospholipid Bilayers', BIOPHYSICAL JOURNAL, CELL PRESS, pp. 42A-43A.

Gu, H 2020, 'Optimal Lagrangian Multipliers for the Multidimensional Knapsack Problem: a Bayesian Optimisation Approach', 2020 IEEE Symposium Series on Computational Intelligence (SSCI), 2020 IEEE Symposium Series on Computational Intelligence (SSCI), IEEE, Canberra.
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This paper considers the Lagrangian relaxation approach for the well-known multidimensional knapsack problem which maximises the total profits of selected items within the capacities of multiple resources. By relaxing “hard” constraints using Lagrangian multipliers, the Lagrangian relaxation approach provides a systematic framework for obtaining both the upper bound and the lower bound for hard combinatorial optimisation problems. Although tremendous efforts, both theoretical and computational, have been put into the study of the upper bound (assuming maximisation for the objective) for the Lagrangian relaxation approach, little attention has been drawn to the study of the impact of Lagrangian multipliers on the quality of the lower bound, or feasible solutions of the studied problem. In this paper, the lower bound problem is framed as an optimisation problem which chooses the best Lagrangian multipliers to obtain strong lower bound, i.e., good feasible solutions. A Bayesian optimisation approach is employed to solve this unconventional nonlinear optimisation problem. Computational experiments are carried out on the widely used benchmark instances with up to 250 items and 30 knapsack constraints. The preliminary results demonstrate the effectiveness of the proposed solution approach

Kianinia, M, White, S, Fröch, JE, Bradac, C & Aharonovich, I 1970, 'Engineering of Room Temperature Spin Defects in Hexagonal Boron Nitride', Conference on Lasers and Electro-Optics, CLEO: QELS_Fundamental Science, OSA.
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Lin, Y, Liu, Y, Chen, H, Lin, D & He, X 2021, 'Prediction of patients at high risk of upper gastrointestinal cancer for endoscopy using artificial intelligent technology', Annals of Oncology, The 22nd World Congress on Gastrointestinal Cancer, Elsevier, Virtual.
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Background: Endoscopic screening for early detection of upper gastrointestinal (UGI) cancer (oesophageal and stomach cancer) is important. However, population-based endoscopic screening is difficult to implement in populous countries. By identifying high-risk individuals from the general population, the screening targets can be narrowed to individuals who are in most need of an endoscopy. This study was designed to develop an artificial intelligence-based model to predict patient risk of UGI lesions to identify high-risk individuals for endoscopy. Methods: A total of 620 patients (from 5300 participants), 187 in normal group and 433 in lesion group, were equally allocated into 10 parts for 10-fold cross validation experiments. The machine-learning predictive models for UGI lesion risk were constructed using random forest, logistic regression, decision tree, and support vector machine (SVM) algorithms. A total of 48 variables covering lifestyles, social-economic status, clinical symptoms, serological results, and pathological data were used in the model construction. Results: The accuracies of the four models were between 79.3% and 93.4% in the training set and between 77.2% and 91.2% in the testing dataset (logistics regression:77.2%; decision tree:87.3%; random forest:88.2%; SVM:91.2%;). The AUCs of four models showed impressive predictive ability. Comparing the 4 models with the different algorithms, the SVM model featured the best sensitivity and specificity in all datasets tested. Conclusions: Machine-learning algorithms can accurately and reliably predict the risk of upper gastrointestinal cancer based on readily available parameters. The predictive models have the potential to be used clinically for identifying patients with high risk of UGI cancers and stratifying patients for necessary endoscopic screening.

Liu, D, Kaufmann, GF, Breitmeyer, JB, Dickson, K-A, Marsh, DJ & Ford, CE 2021, 'Abstract 1062: Inhibition of ovarian and endometrial cancer cell proliferation by an anti-ROR1 monoclonal antibody', Experimental and Molecular Therapeutics, Proceedings: AACR Annual Meeting 2021; April 10-15, 2021 and May 17-21, 2021; Philadelphia, PA, American Association for Cancer Research.
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Ma, S, Chen, S, Zou, C, An, H, Yin, H & Lin, Y 2021, 'Establishment of adoptive cell therapy with tumor infiltrating lymphocytes for liver and oesophageal cancer', Annals of Oncology, The 22nd World Congress on Gastrointestinal Cancer, Elsevier, Virtual.
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Background: Since the finding in 1986 that tumor infiltrating lymphocytes (TILs) were 50-100 times more effective than lymphokine-activated killer cells in killing cancer cells, TILs have attracted great attention in cancer research. Recently (2019) FDA approved LN-145 as a cancer therapy based on autologous tumor-infiltrating lymphocytes, thus reaffirming that TILs have a great potential as an effective cancer treatment. Hepatocellular carcinoma (HCC) is one of the most common malignant tumors in the world and effective adaptive cell therapy is lacking. In the present study, we aimed to establish a method for extracting and purifying TILs for effective adoptive therapy for liver cancer and oesophageal cancer. Methods: TILs were isolated by the traditional method of enzyme digestion combined with mechanical treatment for whole HCC tissues. Tissues were surgically removed and soaked in PBS, to remove the surrounding blood clots, fat and necrotic tissue, and further washed with PBS. Purity and Immunophenotype of TIL cultures were examined by flow cytometry. In the expansion stage of liver cancer TILs, anti-CD3 monoclonal antibody and inactivated PBMC from healthy donor as feeder cells (treated with 10μg/ml mitomycin) were added to the culture medium for stimulation. Results: TIL cells can be isolated from all tumor tissue specimens. TILs from liver cancer were obtained through enzyme digestion and direct induction of tissue mass methods. Phenotype analysis of TILs from liver cancer showed that the proportion of CD3+ and CD3+CD8+ cells in TILs separated by enzymatic digestion was 86.7% and 39.4% on day 7 respectively. On day 19 the proportions of CD3+ and CD3+CD8+ cells were 98.5% and 34.0%, respectively. After 19 days of culture, TIL cells (1.0×107) increased to 2.8×109 meaning that there was 280 times expansion in 19 days. Conclusions: Using an enzyme digestion method, we obtained TILs with higher purity from fresh tissues from patients with HCC. These TILs c...

Ma, X, Tran, NN, Leng, S, Xie, Q & Huete, A 2021, 'Monitoring Savanna Vegetation Phenology Using Advanced Himawari Imager', 2021 IEEE International Geoscience and Remote Sensing Symposium IGARSS, IGARSS 2021 - 2021 IEEE International Geoscience and Remote Sensing Symposium, IEEE.
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Mashkani, M, Gu, H, Thiruvady, D & Ernst, AT 2020, 'Minimizing Total Clinical Deterioration in Operating Theatres', 2020 IEEE Symposium Series on Computational Intelligence (SSCI), IEEE Symposium Series on Computational Intelligence, IEEE, Canberra, Australia.
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Efficient operating theatre (OT) planning and scheduling contributes substantially to better utilization of a hospitalgh2019;s expensive resources and superior management of its complex operations. This study investigates the OT planning and scheduling problem at both tactical and operational decision levels to meet the hospital administration’s expectations and patients’ satisfaction simultaneously. The main goal is to concurrently allocate surgical specialties to operating rooms by developing a master surgery schedule (MSS), and solve the surgical case assignment problem (SCAP), which assigns a particular surgery day and time block to each elective patient. To minimize the total patients’ clinical condition deterioration, we propose two dynamic programming based heuristic algorithms, a mixed integer programming model (MIP), and an iterated local search (ILS) approach. We perform extensive computational experiments with 1500 instances. The results demonstrate the efficacy of our heuristic algorithms as well as the proposed ILS, which generates high quality solutions across all problem instances with an average optimality gap of 1.51%

Rathnayake, S, Vermeulen, C, Ten Hacken, N, Timens, W, Kooistra, W, Heijink, H, Brandsma, C, Oliver, B, Van den Berge, M & Faiz, A 2021, 'LONGITUDINAL EFFECTS OF 12 MONTHS SMOKING CESSATION ON DNA METHYLATION AND GENE EXPRESSION IN BRONCHIAL BIOPSIES', RESPIROLOGY, WILEY, pp. 118-118.

Reddy, D, Boudewijn, I, Lan, A, Rathnayake, S, Koppelman, G, Oliver, B, Van den Berge, M & Faiz, A 2021, 'SMOKING CHANGES GENE EXPRESSION AND METHYLATION IN ASTHMATIC NASAL EPITHELIUM', RESPIROLOGY, WILEY, pp. 140-140.

Ton-That, C, Huynh, TT, Chikoidze, E, Irvine, C, Zakria, M, Dumont, Y, Teherani, F, Sandana, E, Bove, P, Rogers, D & Phillips, M 2021, 'Luminescence properties of beta-Ga2O3', Oxide-based Materials and Devices XII, Oxide-based Materials and Devices XII, SPIE.
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Torpy, F, Irga, P, Wilkinson, S, Fleck, R, Pettit, T & Douglas, A 2021, 'Challenges for the incorporation of food production into functional urban greening systems', https://www.beyondurbanagriculture.org/panelists/dr.-fraser-r-torpy, UN Food Systems Summit, Beyond Urban Agriculture section, Yale Center for Ecosystems + Agriculture.

White, SJU, Duong, NMH, Solntsev, AS, Kim, J-H, Kianinia, M & Aharonovich, I 1970, 'Coherent Excitation of Hexagonal Boron Nitride Single Photon Emitters via Optical Repumping', Conference on Lasers and Electro-Optics, CLEO: QELS_Fundamental Science, OSA.
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Zhang, Y, Liu, Y, Chung, C-L, Chen, C-H & Hwang, FJ 2020, 'Multiple Linear Regression Based on Stream Homomorphic Encryption Computing', Proceedings of 2020 IEEE International Symposium on Computer, Consumer and Control, 2020 IEEE International Symposium on Computer, Consumer and Control, IEEE, Taichung, Taiwan.

Zinder, Y, Berlińska, J & Peter, C 2021, 'Maximising the Total Weight of On-Time Jobs on Parallel Machines Subject to a Conflict Graph', Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), pp. 280-295.
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The paper considers scheduling on parallel machines under the constraint that some pairs of jobs cannot be processed concurrently. Each job has an associated weight, and all jobs have the same deadline. The objective is to maximise the total weight of on-time jobs. The problem is known to be strongly NP-hard in general. A polynomial-time algorithm for scheduling unit execution time jobs on two machines is proposed. The performance of a broad family of approximation algorithms for scheduling unit execution time jobs on more than two machines is analysed. For the case of arbitrary job processing times, two integer linear programming formulations are proposed and compared with two formulations known from the earlier literature. An iterated variable neighborhood search algorithm is also proposed and evaluated by means of computational experiments.

Irga, P, Fleck, R, Wooster, E, Torpy, F, Pettit, T, Gill, R & Ball, J City of Sydney Council 2021, Green Roof & Solar Array – Comparative Research Project. Final Report to City of Sydney 2021, City of Sydney, Council.

Alqudah, A, Mohammed, W, Qnais, E, Jawarneh, H & McClements, L 2021, 'Plasma Amino Acids Metabolomics’ Profile Important for Glucose Management in Jordanian people with Type 2 Diabetes'.
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Falster, D, Gallagher, R, Wenk, E, Wright, I, Indiarto, D, Baxter, C, Andrew, SC, Lawson, J, Allen, S, Fuchs, A, Adams, MA, Ahrens, CW, Alfonzetti, M, Angevin, T, Atkin, OK, Auld, T, Baker, A, Bean, A, Blackman, CJ, Bloomfield, K, Bowman, D, Bragg, J, Brodribb, TJ, Buckton, G, Burrows, G, Caldwell, E, Camac, J, Carpenter, R, Catford, JA, Cawthray, GR, Cernusak, LA, Chandler, G, Chapman, AR, Cheal, D, Cheesman, AW, Chen, S-C, Choat, B, Clinton, B, Clode, P, Coleman, H, Cornwell, WK, Cosgrove, M, Crisp, M, Cross, E, Crous, KY, Cunningham, S, Curtis, E, Daws, MI, DeGabriel, JL, Denton, MD, Dong, N, Duan, H, Duncan, DH, Duncan, RP, Duretto, M, Dwyer, JM, Edwards, C, Esperon-Rodriguez, M, Evans, JR, Everingham, SE, Firn, J, Fonseca, CR, French, BJ, Frood, D, Funk, JL, Geange, SR, Ghannoum, O, Gleason, SM, Gosper, CR, Gray, E, Groom, PK, Gross, C, Guerin, G, Guja, L, Hahs, AK, Harrison, MT, Hayes, PE, Henery, M, Hochuli, D, Howell, J, Huang, G, Hughes, L, Huisman, J, Ilic, J, Jagdish, A, Jin, D, Jordan, G, Jurado, E, Kasel, S, Kellermann, J, Kohout, M, Kooyman, RM, Kotowska, MM, Lai, HR, Laliberté, E, Lambers, H, Lamont, BB, Lanfear, R, van Langevelde, F, Laughlin, DC, Laugier-Kitchener, B-A, Lehmann, CER, Leigh, A, Leishman, MR, Lenz, T, Lepschi, B, Lewis, JD, Lim, F, Liu, U, Lord, J, Lusk, CH, Macinnis-Ng, C, McPherson, H, Manea, A, Mayfield, M, McCarthy, JK, Meers, T, van der Merwe, M, Metcalfe, D, Milberg, P, Mokany, K, Moles, AT, Moore, BD, Moore, N, Morgan, JW, Morris, W, Muir, A, Munroe, S, Nicholson, Á, Nicolle, D, Nicotra, AB, Niinemets, Ü, North, T, O’Reilly-Nugent, A, O’Sullivan, OS, Oberle, B, Onoda, Y, Ooi, MKJ, Osborne, CP, Paczkowska, G, Pekin, B, Pereira, CG, Pickering, C, Pickup, M, Pollock, LJ, Poot, P, Powell, JR, Power, SA, Prentice, IC, Prior, L, Prober, SM, Read, J, Reynolds, V, Richards, AE, Richardson, B, Roderick, ML, Rosell, JA, Rossetto, M, Rye, B, Rymer, PD, Sams, MA, Sanson, G, Schmidt, S, Schulze, E-D, Sendall, K, Sinclair, S, Smith, B, Smith, R, Soper, F, Sparrow, B, Standish, R, Staples, TL, Taseski, G, Thomas, F, Tissue, DT, Tjoelker, MG, Tng, DYP, Tomlinson, K, Turner, NC, Veneklaas, E, Venn, S, Vesk, P, Vlasveld, C, Vorontsova, MS, Warren, C, Weerasinghe, LK, Westoby, M, White, M, Williams, N, Wills, J, Wilson, PG, Yates, C, Zanne, AE & Ziemińska, K 2021, 'AusTraits – a curated plant trait database for the Australian flora'.
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Fröch, JE, Li, C, Chen, Y, Toth, M, Kianinia, M, Kim, S & Aharonovich, I 2021, 'Purcell enhancement of a cavity-coupled emitter in hexagonal boron nitride'.

Fröch, JE, Spencer, L, Kianinia, M, Totonjian, D, Nguyen, M, Dyakonov, V, Toth, M, Kim, S & Aharonovich, I 2021, 'Coupling spin defects in hexagonal boron nitride to monolithic bullseye cavities'.

Gottscholl, A, Diez, M, Soltamov, V, Kasper, C, Sperlich, A, Kianinia, M, Bradac, C, Aharonovich, I & Dyakonov, V 2021, 'Sub-nanoscale Temperature, Magnetic Field and Pressure sensing with Spin Centers in 2D hexagonal Boron Nitride'.

Liao, Y, Vogel, V, Hauber, S, Bartel, J, Alkhnbashi, OS, Maaß, S, Schwarz, TS, Backofen, R, Becher, D, Duggin, IG & Marchfelder, A 2021, 'CdrS is a global transcriptional regulator influencing cell division in Haloferax volcanii', 10.1101/2021.05.11.443588.
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Lundgren, EJ, Ramp, D, Middleton, OM, Balisi, M, Ripple, WJ, Hasselerharm, CD, Sanchez, JN, Wooster, EIF, Mills, M & Wallach, AD 2021, 'Echoes of the late Pleistocene in a novel trophic cascade between cougars and feral donkeys'.
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McClements, L 2021, 'FKBPL and SIRT-1, key angiogenesis proteins, are downregulated by diabetes in pregnancy'.
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Richards, C, Sesperez, K, Chhor, M, Ghorbanpour, S, Rennie, C, Ming, CLC, Evenhuis, C, Nikolic, VN, Orlic, NK, Mikovic, Z, Stefanovic, M, Cakic, Z, McGrath, K, Gentile, C, Bubb, K & McClements, L 2021, 'Characterisation of Cardiac Health in the Reduced Uterine Perfusion Pressure Model and a 3D Cardiac Spheroid Model, of Preeclampsia'.
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Torpy, FR, Irga, P, Wilkinson, S, Pettit, T, Fleck, R & Douglas, A 2021, 'Plants and urban air pollution in the COVID-19 age'.
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Insights into healthy buildings: Presentation to the Green Building Council of Australia webinar

Wang, H, Lian, D, Zhang, Y, Qin, L, He, X, Lin, Y & Lin, X 2021, 'Binarized graph neural network'.