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.
Abraham, J, Ng, R, Morelato, M, Tahtouh, M & Roux, C 2021, 'Automatically classifying crime scene images using machine learning methodologies', Forensic Science International: Digital Investigation, vol. 39, pp. 301273-301273.
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Acharya, SK, Galli, E, Mallinson, JB, Bose, SK, Wagner, F, Heywood, ZE, Bones, PJ, Arnold, MD & Brown, SA 2021, 'Stochastic Spiking Behavior in Neuromorphic Networks Enables True Random Number Generation', ACS Applied Materials & Interfaces, vol. 13, no. 44, pp. 52861-52870.
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There is currently a great deal of interest in the use of nanoscale devices to emulate the behaviors of neurons and synapses and to facilitate brain-inspired computation. Here, it is shown that percolating networks of nanoparticles exhibit stochastic spiking behavior that is strikingly similar to that observed in biological neurons. The spiking rate can be controlled by the input stimulus, similar to "rate coding" in biology, and the distributions of times between events are log-normal, providing insights into the atomic-scale spiking mechanism. The stochasticity of the spiking behavior is then used for true random number generation, and the high quality of the generated random bit-streams is demonstrated, opening up promising routes toward integration of neuromorphic computing with secure information processing.
Adams, FG, Pokhrel, A, Brazel, EB, Semenec, L, Li, L, Trappetti, C, Paton, JC, Cain, AK, Paulsen, IT & Eijkelkamp, BA 2021, 'Acinetobacter baumanniiFatty Acid Desaturases Facilitate Survival in Distinct Environments', ACS Infectious Diseases, vol. 7, no. 8, pp. 2221-2228.
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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–xLaxTiO3with Nanostructured Rectangular Pores', Advanced Electronic Materials, vol. 7, no. 4, pp. 2001044-2001044.
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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, vol. 23, no. 1, pp. 207-223.
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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, pp. 102095-102095.
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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...
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, vol. 11.
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The genusBrassicaincludes oil crops, vegetables, condiments, fodder crops, and ornamental plants.Brassicaspecies underwent a whole genome triplication event after speciation between ancestral species ofBrassicaand closely related genera includingArabidopsis thaliana. Diploid species such asBrassica rapaandBrassica oleraceahave three copies of genes orthologous to eachA. thalianagene, although deletion in one or two of the three homologs has occurred in some genes. The floral transition is one of the crucial events in a plant’s life history, and time of flowering is an important agricultural trait. There is a variation in flowering time within species of the genusBrassica, and this variation is largely dependent on a difference in vernalization requirements. InBrassica, like inA. thaliana, the key gene of vernalization isFLOWERING LOCUS C(FLC). InBrassicaspecies, the vernalization response including the repression ofFLCexpression by cold treatment and the enrichment of the repressive histone modification tri-methylated histone H3 lysine 27 (H3K27me3) at theFLClocus is similar toA. thaliana.B. rapaandB. oleraceaeach have four paralogs ofFLC, and the allotetraploid species,Brassica napus, has nine paralogs. The increased number of paralogs makes the role ofFLCin vernalization more complicated; in a single plant, paralogs vary in the expression level ofFLCbefore and after vern...
AlAjmi, MF, Khan, S, Choudhury, A, Mohammad, T, Noor, S, Hussain, A, Lu, W, Eapen, MS, Chimankar, V, Hansbro, PM, Sohal, SS, Elasbali, AM & Hassan, MI 2021, 'Impact of Deleterious Mutations on Structure, Function and Stability of Serum/Glucocorticoid Regulated Kinase 1: A Gene to Diseases Correlation', Frontiers in Molecular Biosciences, vol. 8.
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Serum and glucocorticoid-regulated kinase 1 (SGK1) is a Ser/Thr protein kinase involved in regulating cell survival, growth, proliferation, and migration. Its elevated expression and dysfunction are reported in breast, prostate, hepatocellular, lung adenoma, and renal carcinomas. We have analyzed the SGK1 mutations to explore their impact at the sequence and structure level by utilizing state-of-the-art computational approaches. Several pathogenic and destabilizing mutations were identified based on their impact on SGK1 and analyzed in detail. Three amino acid substitutions, K127M, T256A, and Y298A, in the kinase domain of SGK1 were identified and incorporated structurally into original coordinates of SGK1 to explore their time evolution impact using all-atom molecular dynamic (MD) simulations for 200 ns. MD results indicate substantial conformational alterations in SGK1, thus its functional loss, particularly upon T256A mutation. This study provides meaningful insights into SGK1 dysfunction upon mutation, leading to disease progression, including cancer, and neurodegeneration.
Alder, R, Xiao, L & Fu, S 2021, 'Comparison of commercial surface‐enhanced Raman spectroscopy substrates for the analysis of cocaine', Drug Testing and Analysis, vol. 13, no. 5, pp. 944-952.
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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, Suggett, DJ, Cárdenas, A, Hughes, DJ, Kühl, M, Pernice, M & Voolstra, CR 2021, 'Divergent expression of hypoxia response systems under deoxygenation in reef‐forming corals aligns with bleaching susceptibility', Global Change Biology, vol. 27, no. 2, pp. 312-326.
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Alemao, CA, Budden, KF, Gomez, HM, Rehman, SF, Marshall, JE, Shukla, SD, Donovan, C, Forster, SC, Yang, IA, Keely, S, Mann, ER, El Omar, EM, Belz, GT & Hansbro, PM 2021, 'Impact of diet and the bacterial microbiome on the mucous barrier and immune disorders', Allergy, vol. 76, no. 3, pp. 714-734.
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Alhamami, T, Chowdhury, P, Gomes, N, Carr, M, Veltman, T, Khazandi, M, Mollinger, J, Deutscher, A, Turni, C, Mahdi, L, Venter, H, Abraham, S, Djordjevic, S & Trott, D 2021, 'First Emergence of Resistance to Macrolides and Tetracycline Identified in Mannheimia haemolytica and Pasteurella multocida Isolates from Beef Feedlots in Australia', Microorganisms, vol. 9, no. 6, pp. 1322-1322.
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Bovine respiratory disease (BRD) causes high morbidity and mortality in beef cattle worldwide. Antimicrobial resistance (AMR) monitoring of BRD pathogens is critical to promote appropriate antimicrobial stewardship in veterinary medicine for optimal treatment and control. Here, the susceptibility of Mannheimia haemolytica and Pasteurella multicoda isolates obtained from BRD clinical cases (deep lung swabs at post-mortem) among feedlots in four Australian states (2014–2019) was determined for 19 antimicrobial agents. The M. haemolytica isolates were pan-susceptible to all tested agents apart from a single macrolide-resistant isolate (1/88; 1.1%) from New South Wales (NSW). Much higher frequencies of P. multocida isolates were resistant to tetracycline (18/140; 12.9%), tilmicosin (19/140; 13.6%), tulathromycin/gamithromycin (17/140; 12.1%), and ampicillin/penicillin (6/140; 4.6%). Five P. multocida isolates (3.6%), all obtained from NSW in 2019, exhibited dual resistance to macrolides and tetracycline, and a further two Queensland isolates from 2019 (1.4%) exhibited a multidrug-resistant phenotype to ampicillin/penicillin, tetracycline, and tilmicosin. Random-amplified polymorphic DNA (RAPD) typing identified a high degree of genetic homogeneity among the M. haemolytica isolates, whereas P. multocida isolates were more heterogeneous. Illumina whole genome sequencing identified the genes msr(E) and mph(E)encoding macrolide resistance, tet(R)-tet(H) or tet(Y) encoding tetracycline resistance, and blaROB-1 encoding ampicillin/penicillin resistance in all isolates exhibiting a corresponding resistant phenotype. The exception was the tilmicosin-resistant, tulathromycin/gamithromycin-susceptible phenotype identified in two Queensland isolates, the genetic basis of which could not be determined. These results confirm the first emergence of AMR in M. haemolytica and P. multocida from BRD cases in Australia, which should be closely monitored.
Ali, S, Jameel, MA, Gupta, A, Langford, SJ & Shafiei, M 2021, 'Capacitive humidity sensing performance of naphthalene diimide derivatives at ambient temperature', Synthetic Metals, vol. 275, pp. 116739-116739.
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Allam, VSRR, Faiz, A, Lam, M, Rathnayake, SNH, Ditz, B, Pouwels, SD, Brandsma, C, 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, vol. 76, no. 4, pp. 1123-1135.
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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, vol. 12.
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Diabetes in pregnancy is associated with adverse pregnancy outcomes including preterm birth. Although the mechanisms leading to these pregnancy complications are still poorly understood, aberrant angiogenesis and endothelial dysfunction play a key role. FKBPL and SIRT-1 are critical regulators of angiogenesis, however, their roles in pregnancies affected by diabetes have not been examined before in detail. Hence, this study aimed to investigate the role of FKBPL and SIRT-1 in pre-gestational (type 1 diabetes mellitus, T1D) and gestational diabetes mellitus (GDM). Placental protein expression of important angiogenesis proteins, FKBPL, SIRT-1, PlGF and VEGF-R1, was determined from pregnant women with GDM or T1D, and in the first trimester trophoblast cells exposed to high glucose (25 mM) and varying oxygen concentrations [21%, 6.5%, 2.5% (ACH-3Ps)]. Endothelial cell function was assessed in high glucose conditions (30 mM) and following FKBPL overexpression. Placental FKBPL protein expression was downregulated in T1D (FKBPL; p<0.05) whereas PlGF/VEGF-R1 were upregulated (p<0.05); correlations adjusted for gestational age were also significant. In the presence of GDM, only SIRT-1 was significantly downregulated (p<0.05) even when adjusted for gestational age (r=-0.92, p=0.001). Both FKBPL and SIRT-1 protein expression was reduced in ACH-3P cells in high glucose conditions associated with 6.5%/2.5% oxygen concentrations compared to experimental normoxia (21%; p<0.05). FKBPL overexpression in endothelial cells (HUVECs) exacerbated reduction in tubule formation compared to empty vector control, in high glucose conditions (junctions; p<0.01, branches; p<0.05). In conclusion, FKBPL and/or SIRT-1 downregulation in response to diabetic pregnancies may have a key role in the development of vascular dysfunction and associated complications affected by impaired placental angiogenesis.
Alsahafi, S & Woodcock, S 2021, 'Local analysis for a mutual inhibition in presence of two viruses in a chemostat', Nonlinear Dynamics and Systems Theory, vol. 21, no. 4, pp. 337-359.
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A competition with mutual inhibition is a form of direct competition between the populations of two species where each actively inhibits the other. In this paper, we consider a mathematical system of ordinary differential equations describing two species, with mutual inhibition, competing for a limiting substrate in the presence of two viruses. A detailed local qualitative analysis of the restriction of the system to the attractor set is carried out. We prove that for general nonlinear response functions, the Competitive Exclusion Principle is still fulfilled so that at most one species can survive. Initial species concentrations are important in determining which is the winning species. The results obtained were validated by numerical simulations using Matlab software.
Alsahafi, S & Woodcock, S 2021, 'Mathematical Study for Chikungunya Virus with Nonlinear General Incidence Rate', Mathematics, vol. 9, no. 18, pp. 2186-2186.
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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, pp. 114726-114726.
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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.
Anburajan, P, Kim, Y, Rice, SA & Oh, H-S 2021, 'Bacterial signaling and signal responses as key factors in water and wastewater treatment', Journal of Water Process Engineering, vol. 44, pp. 102434-102434.
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Ansari, S, Walsh, JC, Bottomley, AL, Duggin, IG, Burke, C & Harry, EJ 2021, 'A Newly Identified Prophage Gene, ymfM , Causes SOS-Inducible Filamentation in Escherichia coli', Journal of Bacteriology, vol. 203, no. 11.
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Filamentation is an important biological mechanism that aids in the survival, pathogenesis, and antibiotic resistance of bacteria within different environments, including pathogenic bacteria such as uropathogenic
Escherichia coli
. Here, we have identified a bacteriophage-encoded cell division inhibitor which contributes to the filamentation that occurs during the SOS response.
Argyle, PA, Walworth, NG, Hinners, J, Collins, S, Levine, NM & Doblin, MA 2021, 'Multivariate trait analysis reveals diatom plasticity constrained to a reduced set of biological axes', ISME Communications, vol. 1, no. 1.
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AbstractTrait-based approaches to phytoplankton ecology have gained traction in recent decades as phenotypic traits are incorporated into ecological and biogeochemical models. Here, we use high-throughput phenotyping to explore both intra- and interspecific constraints on trait combinations that are expressed in the cosmopolitan marine diatom genus Thalassiosira. We demonstrate that within Thalassiosira, phenotypic diversity cannot be predicted from genotypic diversity, and moreover, plasticity can create highly divergent phenotypes that are incongruent with taxonomic grouping. Significantly, multivariate phenotypes can be represented in reduced dimensional space using principal component analysis with 77.7% of the variance captured by two orthogonal axes, here termed a ‘trait-scape’. Furthermore, this trait-scape can be recovered with a reduced set of traits. Plastic responses to the new environments expanded phenotypic trait values and the trait-scape, however, the overall pattern of response to the new environments was similar between strains and many trait correlations remained constant. These findings demonstrate that trait-scapes can be used to reveal common constraints on multi-trait plasticity in phytoplankton with divergent underlying phenotypes. Understanding how to integrate trait correlational constraints and trade-offs into theoretical frameworks like biogeochemical models will be critical to predict how microbial responses to environmental change will impact elemental cycling now and into the future.
Ashcroft, SP, Fletcher, G, Philp, AM, Jenkinson, C, Das, S, Hansbro, PM, Atherton, PJ & Philp, A 2021, 'Diet-induced vitamin D deficiency reduces skeletal muscle mitochondrial respiration', Journal of Endocrinology, vol. 249, no. 2, pp. 113-124.
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Vitamin D deficiency is associated with symptoms of skeletal muscle myopathy including muscle weakness and fatigue. Recently, vitamin D-related metabolites have been linked to the maintenance of mitochondrial function within skeletal muscle. However, current evidence is limited to in vitro models and the effects of diet-induced vitamin D deficiency upon skeletal muscle mitochondrial function in vivo have received little attention. In order to examine the role of vitamin D in the maintenance of mitochondrial function in vivo, we utilised an established model of diet-induced vitamin D deficiency in C57BL/6J mice. Mice were either fed a control diet (2200 IU/kg i.e. vitamin D replete) or a vitamin D-deplete (0 IU/kg) diet for periods of 1, 2 and 3 months. Gastrocnemius muscle mitochondrial function and ADP sensitivity were assessed via high-resolution respirometry and mitochondrial protein content via immunoblotting. As a result of 3 months of diet-induced vitamin D deficiency, respiration supported via complex I + II (CI + IIP) and the electron transport chain (ETC) were 35 and 37% lower when compared to vitamin D-replete mice (P < 0.05). Despite functional alterations, citrate synthase activity, AMPK phosphorylation, mitofilin, OPA1 and ETC subunit protein content remained unchanged in response to dietary intervention (P > 0.05). In conclusion, we report that 3 months of diet-induced vitamin D deficiency reduced skeletal muscle mitochondrial respiration in C57BL/6J mice. Our data, when combined with previous in vitro observations, suggest that vitamin D-mediated regulation of mitochondrial function may underlie the exacerbated muscle fatigue and performance deficits observed during vitamin D deficiency.
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, vol. 138, pp. 111425-111425.
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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, pp. 101015-101015.
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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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Abstract
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.
Bagheri, S, Huang, Y, Walker, PD, Zhou, JL & Surawski, NC 2021, 'Strategies for improving the emission performance of hybrid electric vehicles', Science of The Total Environment, vol. 771, pp. 144901-144901.
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Bake, A, Rezoanur Rahman, M, Evans, PJ, Cortie, M, Nancarrow, M, Abrudan, R, Radu, F, Khaydukov, Y, Causer, G, Callori, S, Livesey, KL, Mitchell, D, Pastuovic, Z, Wang, X & Cortie, D 2021, 'Structure and magnetism of ultra-small cobalt particles assembled at titania surfaces by ion beam synthesis', Applied Surface Science, vol. 570, pp. 151068-151068.
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Bannister, T, Ebert, EE, Williams, T, Douglas, P, Wain, A, Carroll, M, Silver, J, Newbigin, E, Lampugnani, ER, Hughes, N, Looker, C, Mulvenna, V, Csutoros, D, Jones, PJ, Davies, JM, Suphioglu, C, Beggs, PJ, Emmerson, KM, Huete, A & Nguyen, H 2021, 'A Pilot Forecasting System for Epidemic Thunderstorm Asthma in Southeastern Australia', Bulletin of the American Meteorological Society, vol. 102, no. 2, pp. E399-E420.
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AbstractIn November 2016, an unprecedented epidemic thunderstorm asthma event in Victoria, Australia, resulted in many thousands of people developing breathing difficulties in a very short period of time, including 10 deaths, and created extreme demand across the Victorian health services. To better prepare for future events, a pilot forecasting system for epidemic thunderstorm asthma (ETSA) risk has been developed for Victoria. The system uses a categorical risk-based approach, combining operational forecasting of gusty winds in severe thunderstorms with statistical forecasts of high ambient grass pollen concentrations, which together generate the risk of epidemic thunderstorm asthma. This pilot system provides the first routine daily epidemic thunderstorm asthma risk forecasting service in the world that covers a wide area, and integrates into the health, ambulance, and emergency management sector. Epidemic thunderstorm asthma events have historically occurred infrequently, and no event of similar magnitude has impacted the Victorian health system since. However, during the first three years of the pilot, 2017–19, two high asthma presentation events and four moderate asthma presentation events were identified from public hospital emergency department records. The ETSA risk forecasts showed skill in discriminating between days with and without health impacts. However, even with hindsight of the actual weather and airborne grass pollen conditions, some high asthma presentation events occurred in districts that were assessed as low risk for ETSA, reflecting the challenge of predicting this unusual phenomenon.
Bao, G, Wen, S, Lin, G, Yuan, J, Lin, J, Wong, K-L, Bünzli, J-CG & Jin, D 2021, 'Learning from lanthanide complexes: The development of dye-lanthanide nanoparticles and their biomedical applications', Coordination Chemistry Reviews, vol. 429, pp. 213642-213642.
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Bao, G, Wen, S, Wang, W, Zhou, J, Zha, S, Liu, Y, Wong, K-L & Jin, D 2021, 'Enhancing Hybrid Upconversion Nanosystems via Synergistic Effects of Moiety Engineered NIR Dyes', Nano Letters, vol. 21, no. 23, pp. 9862-9868.
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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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Abstract
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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Bashir, F, Rehman, AU, Szabó, M & Vass, I 2021, 'Singlet oxygen damages the function of Photosystem II in isolated thylakoids and in the green alga Chlorella sorokiniana', Photosynthesis Research, vol. 149, no. 1-2, pp. 93-105.
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AbstractSinglet oxygen (1O2) is an important damaging agent, which is produced during illumination by the interaction of the triplet excited state pigment molecules with molecular oxygen. In cells of photosynthetic organisms 1O2 is formed primarily in chlorophyll containing complexes, and damages pigments, lipids, proteins and other cellular constituents in their environment. A useful approach to study the physiological role of 1O2 is the utilization of external photosensitizers. In the present study, we employed a multiwell plate-based screening method in combination with chlorophyll fluorescence imaging to characterize the effect of externally produced 1O2 on the photosynthetic activity of isolated thylakoid membranes and intact Chlorella sorokiniana cells. The results show that the external 1O2 produced by the photosensitization reactions of Rose Bengal damages Photosystem II both in isolated thylakoid membranes and in intact cells in a concentration dependent manner indicating that 1O2 plays a significant role in photodamage of Photosystem II.
Behary, J, Amorim, N, Jiang, X-T, Raposo, A, Gong, L, McGovern, E, Ibrahim, R, Chu, F, Stephens, C, Jebeili, H, Fragomeli, V, Koay, YC, Jackson, M, O’Sullivan, J, Weltman, M, McCaughan, G, El-Omar, E & Zekry, A 2021, 'Gut microbiota impact on the peripheral immune response in non-alcoholic fatty liver disease related hepatocellular carcinoma', Nature Communications, vol. 12, no. 1.
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AbstractThe gut microbiota is reported to modulate the immune response in hepatocellular carcinoma (HCC). Here, we employ metagenomic and metabolomic studies to characterise gut microbiota in patients with non-alcoholic fatty liver disease (NAFLD) related cirrhosis, with or without HCC, and evaluate its effect on the peripheral immune response in an ex vivo model. We find that dysbiosis characterises the microbiota of patients with NAFLD-cirrhosis, with compositional and functional shifts occurring with HCC development. Gene function of the microbiota in NAFLD-HCC supports short chain fatty acid production, and this is confirmed by metabolomic studies. Ex vivo studies show that bacterial extracts from the NAFLD-HCC microbiota, but not from the control groups, elicit a T cell immunosuppressive phenotype, characterised by expansion of regulatory T cells and attenuation of CD8 + T cells. Our study suggest that the gut microbiota in NAFLD-HCC is characterised by a distinctive microbiome/metabolomic profile, and can modulate the peripheral immune response.
Behary, J, Raposo, AE, Amorim, NML, Zheng, H, Gong, L, McGovern, E, Chen, J, Liu, K, Beretov, J, Theocharous, C, Jackson, MT, Seet-Lee, J, McCaughan, GW, El-Omar, EM & Zekry, A 2021, 'Defining the temporal evolution of gut dysbiosis and inflammatory responses leading to hepatocellular carcinoma in Mdr2 −/− mouse model', BMC Microbiology, vol. 21, no. 1.
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Abstract
Background
Emerging evidence implicates the gut microbiome in liver inflammation and hepatocellular carcinoma (HCC) development. We aimed to characterize the temporal evolution of gut dysbiosis, in relation to the phenotype of systemic and hepatic inflammatory responses leading to HCC development. In the present study, Mdr2 −/− mice were used as a model of inflammation-based HCC. Gut microbiome composition and function, in addition to serum LPS, serum cytokines/chemokines and intrahepatic inflammatory genes were measured throughout the course of liver injury until HCC development.
Results
Early stages of liver injury, inflammation and cirrhosis, were characterized by dysbiosis. Microbiome functional pathways pertaining to gut barrier dysfunction were enriched during the initial phase of liver inflammation and cirrhosis, whilst those supporting lipopolysaccharide (LPS) biosynthesis increased as cirrhosis and HCC ensued. In parallel, serum LPS progressively increased during the course of liver injury, corresponding to a shift towards a systemic Th1/Th17 proinflammatory phenotype. Alongside, the intrahepatic inflammatory gene profile transitioned from a proinflammatory phenotype in the initial phases of liver injury to an immunosuppressed one in HCC. In established HCC, a switch in microbiome function from carbohydrate to amino acid metabolism occurred.
Conclusion
In Mdr2 −/− mice, dysbiosis precedes HCC development, with temporal evolution of microbiome function to support gut barrier dysfunction, LPS biosynthesis, and redirection of energy source utilization. A corresponding shift in systemic and intrahepatic inflammatory responses occurred ...
Belfiore, L, Aghaei, B, Law, AMK, Dobrowolski, JC, Raftery, LJ, Tjandra, AD, Yee, C, Piloni, A, Volkerling, A, Ferris, CJ & Engel, M 2021, 'Generation and analysis of 3D cell culture models for drug discovery', European Journal of Pharmaceutical Sciences, vol. 163, pp. 105876-105876.
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Beltrán, VH, Puill-Stephan, E, Howells, E, Flores-Moya, A, Doblin, M, Núñez-Lara, E, Escamilla, V, López, T & van Oppen, MJH 2021, 'Physiological diversity among sympatric, conspecific endosymbionts of coral (Cladocopium C1acro) from the Great Barrier Reef', Coral Reefs, vol. 40, no. 4, pp. 985-997.
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BERDINSKY, D, ELDER, M & TABACK, J 2021, 'BEING CAYLEY AUTOMATIC IS CLOSED UNDER TAKING WREATH PRODUCT WITH VIRTUALLY CYCLIC GROUPS', Bulletin of the Australian Mathematical Society, vol. 104, no. 3, pp. 464-474.
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AbstractWe extend work of Berdinsky and Khoussainov [‘Cayley automatic representations of wreath products’, International Journal of Foundations of Computer Science27(2) (2016), 147–159] to show that being Cayley automatic is closed under taking the restricted wreath product with a virtually infinite cyclic group. This adds to the list of known examples of Cayley automatic groups.
Berlińska, J, Kononov, A & Zinder, Y 2021, 'Two-machine flow shop with dynamic storage space', Optimization Letters, vol. 15, no. 7, pp. 2433-2454.
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AbstractThe 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, Fröch, 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. 564-564.
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Hexagonal boron nitride (hBN) is a layered dielectric material with a wide range of applications in optics and photonics. In this work, we demonstrate a fabrication method for few-layer hBN flakes with areas up to
5000
µ
m
2
. We show that hBN in this form can be integrated with photonic microstructures: as an example, we use a circular Bragg grating (CBG). The layer quality of the exfoliated hBN flake on and off a CBG is confirmed by Raman spectroscopy and second-harmonic generation (SHG) microscopy. We show that the SHG signal is uniform across the hBN sample outside the CBG and is amplified in the center of the CBG.
Berry, IJ, Widjaja, M, Jarocki, VM, Steele, JR, Padula, MP & Djordjevic, SP 2021, 'Protein cleavage influences surface protein presentation in Mycoplasma pneumoniae', Scientific Reports, vol. 11, no. 1.
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AbstractMycoplasma pneumoniae is a significant cause of pneumonia and post infection sequelae affecting organ sites distant to the respiratory tract are common. It is also a model organism where extensive ‘omics’ studies have been conducted to gain insight into how minimal genome self-replicating organisms function. An N-terminome study undertaken here identified 4898 unique N-terminal peptides that mapped to 391 (56%) predicted M. pneumoniae proteins. True N-terminal sequences beginning with the initiating methionine (iMet) residue from the predicted Open Reading Frame (ORF) were identified for 163 proteins. Notably, almost half (317; 46%) of the ORFS derived from M. pneumoniae strain M129 are post-translationally modified, presumably by proteolytic processing, because dimethyl labelled neo-N-termini were characterised that mapped beyond the predicted N-terminus. An analysis of the N-terminome describes endoproteolytic processing events predominately targeting tryptic-like sites, though cleavages at negatively charged residues in P1′ (D and E) with lysine or serine/alanine in P2′ and P3′ positions also occurred frequently. Surfaceome studies identified 160 proteins (23% of the proteome) to be exposed on the extracellular surface of M. pneumoniae. The two orthogonal methodologies used to characterise the surfaceome each identified the same 116 proteins, a 72% (116/160) overlap. Apart from lipoproteins, transporters, and adhesins, 93/160 (58%) of the surface proteins lack signal peptides and have well characterised, canonical functions in the cell. Of the 160 surface proteins identified, 134 were also targets of endo-proteolytic processing. These processing events are likely to have profound implications for how the host immune system recognises and responds to M. pneumoniae.
Bertram, MR, Brito, B, Palinski, RM, Fish, IH, Pauszek, SJ, Hartwig, EJ, Smoliga, GR, Vu, LT, Hoang, BH, Phuong, NT, Hung, VV, Vu, PP, Dung, NK, Tien, NN, Dong, PV, Dung, DH & Arzt, J 2021, 'Novel Recombinant Foot-and-Mouth Disease Virus Circulating in Vietnam', Microbiology Resource Announcements, vol. 10, no. 1.
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We report the genome sequences of 12 recombinant foot-and-mouth disease virus isolates from Vietnam. The recombinant strain has a capsid region from an A/Sea-97 strain and a nonstructural segment from an O/ME-SA/PanAsia strain. The isolates were obtained from two outbreak samples collected in June 2017 and 10 subclinical samples collected between 2017 and 2019.
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, vol. 11, no. 1.
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AbstractEmerging and promising therapeutic interventions for Duchenne muscular dystrophy (DMD) are confounded by the challenges of quantifying dystrophin. Current approaches have poor precision, require large amounts of tissue, and are difficult to standardize. This paper presents an immuno-mass spectrometry imaging method using gadolinium (Gd)-labeled anti-dystrophin antibodies and laser ablation-inductively coupled plasma-mass spectrometry to simultaneously quantify and localize dystrophin in muscle sections. Gd is quantified as a proxy for the relative expression of dystrophin and was validated in murine and human skeletal muscle sections following k-means clustering segmentation, before application to DMD patients with different gene mutations where dystrophin expression was measured up to 100 µg kg−1 Gd. These results demonstrate that immuno-mass spectrometry imaging is a viable approach for pre-clinical to clinical research in DMD. It rapidly quantified relative dystrophin in single tissue sections, efficiently used valuable patient resources, and may provide information on drug efficacy for clinical translation.
Blomme, EE, Provoost, S, De Smet, EG, De Grove, KC, Van Eeckhoutte, HP, De Volder, J, Hansbro, PM, Bonato, M, Saetta, M, Wijnant, SRA, Verhamme, F, Joos, GF, Bracke, KR, Brusselle, GG & Maes, T 2021, 'Quantification and role of innate lymphoid cell subsets in Chronic Obstructive Pulmonary Disease', Clinical & Translational Immunology, vol. 10, no. 6.
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Bogema, DR, Yam, J, Micallef, ML, Gholipourkanani, H, Go, J, Jenkins, C & Dang, C 2021, 'Draft genomes of Perkinsus olseni and Perkinsus chesapeaki reveal polyploidy and regional differences in heterozygosity', Genomics, vol. 113, no. 1, pp. 677-688.
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© 2020 Perkinsus spp. parasites have significant impact on aquaculture and wild mollusc populations. We sequenced the genomes of five monoclonal isolates of Perkinsus olseni and one Perkinsus chesapeaki from international sources. Sequence analysis revealed similar levels of repetitive sequence within species, a polyploid genome structure, and substantially higher heterozygosity in Oceanian-sourced isolates. We also identified tandem replication of the rRNA transcriptional unit, with high strain variation. Characterized gene content was broadly similar amongst all Perkinsus spp. but P. olseni Oceanian isolates contained an elevated number of genes compared to other P. olseni isolates and cox3 could not be identified in any Perkinsus spp. sequence. Phylogenetics and average nucleotide identity scans were consistent with all P. olseni isolates being within one species. These are the first genome sequences generated for both P. olseni and P. chesapeaki and will allow future advances in diagnostic design and population genomics of these important aquatic parasites.
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, pp. 111338-111338.
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Booth, DJ & Beretta, GA 2021, 'Long-term demographics of a coral-reef fish: growth, survival and abundance at several spatial scales', Coral Reefs, vol. 40, no. 4, pp. 1257-1266.
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Borchhardt, N, Chomérat, N, Bilien, G, Zentz, F, Rhodes, L, Murray, SA & Hoppenrath, M 2021, 'Morphology and molecular phylogeny of Bindiferia gen. nov. (Dinophyceae), a new marine, sand-dwelling dinoflagellate genus formerly classified within Amphidinium', Phycologia, vol. 60, no. 6, pp. 631-643.
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Bordin, DM, Bishop, D, de Campos, EG, Blanes, L, Doble, P, Roux, C & De Martinis, BS 2021, 'Analysis of Stimulants in Sweat and Urine Using Disposable Pipette Extraction and Gas Chromatography Coupled to Mass Spectrometry in the Context of Doping Control', Journal of Analytical Toxicology.
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Abstract
Urine is initially collected from athletes to screen for the presence of illicit drugs. Sweat is an alternative sample matrix that provides advantages over urine including reduced opportunity for sample adulteration, longer detection-time window and non-invasive collection. Sweat is suitable for analysis of the parent drug and metabolites. In this study, a method was developed and validated to determine the presence of 13 amphetamine- and cocaine-related substances and their metabolites in sweat and urine using disposable pipette extraction (DPX) by gas chromatography coupled to mass spectrometry. The DPX extraction was performed using 0.1 M HCl and dichloromethane:isopropanol:ammonium hydroxide (78:20:2, v/v/v) followed by derivatization with N-methyl-N-(trimethylsilyl) trifluoroacetamide at 90°C for 20 min. DPX extraction efficiencies ranged between 65.0% and 96.0% in urine and 68.0% and 101.0% in sweat. Method accuracy was from 90.0% to 104.0% in urine and from 89.0% to 105.0% in sweat. Intra-assay precision in urine and in sweat were <15.6% and <17.8%, respectively, and inter-assay precision ranged from 4.70% to 15.3% in urine and from 4.05% to 15.4% in sweat. Calibration curves presented a correlation coefficient –0.99 for all analytes in both matrices. The validated method was applied to urine and sweat samples collected from 40 professional athletes who knowingly took one or more of the target illicit drugs. Thirteen of 40 athletes were positive for at least one drug. All the drugs detected in the urine were also detected in sweat samples indicating that sweat is a viable matrix for screening or confirmatory drug testing.
Bousquet, J, Anto, JM, Czarlewski, W, Haahtela, T, Fonseca, SC, Iaccarino, G, Blain, H, Vidal, A, Sheikh, A, Akdis, CA, Zuberbier, T, Hamzah Abdul Latiff, A, Abdullah, B, Aberer, W, Abusada, N, Adcock, I, Afani, A, Agache, I, Aggelidis, X, Agustin, J, Akdis, M, Al‐Ahmad, M, Al‐Zahab Bassam, A, Alburdan, H, Aldrey‐Palacios, O, Alvarez Cuesta, E, Alwan Salman, H, Alzaabi, A, Amade, S, Ambrocio, G, Angles, R, Annesi‐Maesano, I, Ansotegui, IJ, Anto, J, Ara Bardajo, P, Arasi, S, Arshad, H, Cristina Artesani, M, Asayag, E, Avolio, F, Azhari, K, Bachert, C, Bagnasco, D, Baiardini, I, Bajrović, N, Bakakos, P, Bakeyala Mongono, S, Balotro‐Torres, C, Barba, S, Barbara, C, Barbosa, E, Barreto, B, Bartra, J, Bateman, ED, Battur, L, Bedbrook, A, Bedolla Barajas, M, Beghé, B, Bekere, A, Bel, E, Ben Kheder, A, Benson, M, Berghea, EC, Bergmann, K, Bernardini, R, Bernstein, D, Bewick, M, Bialek, S, Białoszewski, A, Bieber, T, Billo, NE, Bilo, MB, Bindslev‐Jensen, C, Bjermer, L, Bobolea, I, Bochenska Marciniak, M, Bond, C, Boner, A, Bonini, M, Bonini, S, Bosnic‐Anticevich, S, Bosse, I, Botskariova, S, Bouchard, J, Boulet, L, Bourret, R, Bousquet, P, Braido, F, Briggs, A, Brightling, CE, Brozek, J, Brussino, L, Buhl, R, Bumbacea, R, Buquicchio, R, Burguete Cabañas, M, Bush, A, Busse, WW, Buters, J, Caballero‐Fonseca, F, Calderon, MA, Calvo, M, Camargos, P, Camuzat, T, Canevari, FR, Cano, A, Canonica, GW, Capriles‐Hulett, A, Caraballo, L, Cardona, V, Carlsen, K, Carmon Pirez, J, Caro, J, Carr, W, Carreiro‐Martins, P, Carreon‐Asuncion, F, Carriazo, A, Casale, T, Castor, M, Castro, E, Caviglia, AG, Cecchi, L, Cepeda Sarabia, A, Chandrasekharan, R, Chang, Y, Chato‐Andeza, V, Chatzi, L, Chatzidaki, C, Chavannes, NH, Chaves Loureiro, C, Chelninska, M, Chen, Y, Cheng, L, Chinthrajah, S, Chivato, T, Chkhartishvili, E, Christoff, G, Chrystyn, H, Chu, DK, Chua, A, Chuchalin, A, Chung, KF, Cicerán, A, Cingi, C, Ciprandi, G, Cirule, I, Coelho, AC, Compalati, E, Constantinidis, J, Correia de Sousa, J, Costa, EM, Costa, D, Costa Domínguez, MDC, Coste, A, Cottini, M, Cox, L, Crisci, C, Crivellaro, MA, Cruz, AA, Cullen, J, Custovic, A, Cvetkovski, B, Czarlewski, W, D'Amato, G, Silva, J, Dahl, R, Dahlen, S, Daniilidis, V, DarjaziniNahhas, L, Darsow, U, Davies, J, Blay, F, De Feo, G, De Guia, E, los Santos, C, De Manuel Keenoy, E & et al. 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, M-Á, 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, pp. 2-15.
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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.
Bradac, C, Xu, Z-Q & Aharonovich, I 2021, 'Quantum Energy and Charge Transfer at Two-Dimensional Interfaces', Nano Letters, vol. 21, no. 3, pp. 1193-1204.
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Bradbury, P, Nader, CP, Cidem, A, Rutting, S, Sylvester, D, He, P, Rezcallah, MC, O’Neill, GM & Ammit, AJ 2021, 'Tropomyosin 2.1 collaborates with fibronectin to promote TGF-β1-induced contraction of human lung fibroblasts', Respiratory Research, vol. 22, no. 1.
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AbstractMany lung diseases are characterized by fibrosis, leading to impaired tissue patency and reduced lung function. Development of fibrotic tissue depends on two-way interaction between the cells and the extra-cellular matrix (ECM). Concentration-dependent increased stiffening of the ECM is sensed by the cells, which in turn increases intracellular contraction and pulling on the matrix causing matrix reorganization and further stiffening. It is generally accepted that the inflammatory cytokine growth factor β1 (TGF-β1) is a major driver of lung fibrosis through the stimulation of ECM production. However, TGF-β1 also regulates the expression of members of the tropomyosin (Tm) family of actin associating proteins that mediate ECM reorganization through intracellular-generated forces. Thus, TGF-β1 may mediate the bi-directional signaling between cells and the ECM that promotes tissue fibrosis. Using combinations of cytokine stimulation, mRNA, protein profiling and cellular contractility assays with human lung fibroblasts, we show that concomitant induction of key Tm isoforms and ECM by TGF-β1, significantly accelerates fibrotic phenotypes. Knocking down Tpm2.1 reduces fibroblast-mediated collagen gel contraction. Collectively, the data suggest combined ECM secretion and actin cytoskeleton contractility primes the tissue for enhanced fibrosis. Our study suggests that Tms are at the nexus of inflammation and tissue stiffening. Small molecules targeting specific Tm isoforms have recently been designed; thus targeting Tpm2.1 may represent a novel therapeutic target in lung fibrosis.
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, vol. 11, no. 18, pp. 12605-12616.
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Bramucci, AR, Focardi, A, Rinke, C, Hugenholtz, P, Tyson, GW, Seymour, JR & Raina, J-B 2021, 'Microvolume DNA extraction methods for microscale amplicon and metagenomic studies', ISME Communications, vol. 1, no. 1.
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AbstractInvestigating the composition and metabolic capacity of aquatic microbial assemblages usually requires the filtration of multi-litre samples, which are up to 1 million-fold larger than the microenvironments within which microbes are predicted to be spatially organised. To determine if community profiles can be reliably generated from microlitre volumes, we sampled seawater at a coastal and an oceanic site, filtered and homogenised them, and extracted DNA from bulk samples (2 L) and microvolumes (100, 10 and 1 μL) using two new approaches. These microvolume DNA extraction methods involve either physical or chemical lysis (through pH/thermal shock and lytic enzymes/surfactants, respectively), directly followed by the capture of DNA on magnetic beads. Downstream analysis of extracted DNA using both amplicon sequencing and metagenomics, revealed strong correlation with standard large volume approaches, demonstrating the fidelity of taxonomic and functional profiles of microbial communities in as little as 1 μL of seawater. This volume is six orders of magnitude smaller than most standard operating procedures for marine metagenomics, which will allow precise sampling of the heterogenous landscape that microbes inhabit.
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', Forensic Science International: Animals and Environments, vol. 1, pp. 100024-100024.
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Brunet, M, Bettignies, F, Le Duff, N, Tanguy, G, Davoult, D, Leblanc, C, Gobet, A & Thomas, F 2021, 'Accumulation of detached kelp biomass in a subtidal temperate coastal ecosystem induces succession of epiphytic and sediment bacterial communities', Environmental Microbiology, vol. 23, no. 3, pp. 1638-1655.
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Kelps are dominant primary producers in temperate coastal ecosystems. Large amounts of kelp biomass can be exported to the seafloor during the algal growth cycle or following storms, creating new ecological niches for the associated microbiota. Here, we investigated the bacterial community associated with the kelp Laminaria hyperborea during its accumulation and degradation on the seafloor. Kelp tissue, seawater and sediment were sampled during a 6-month in situ experiment simulating kelp detritus accumulation. Evaluation of the epiphytic bacterial community abundance, structure, taxonomic composition and predicted functional profiles evidenced a biphasic succession. Initially, dominant genera (Hellea, Litorimonas, Granulosicoccus) showed a rapid and drastic decrease in sequence abundance, probably outcompeted by algal polysaccharide-degraders such as Bacteroidia members which responded within 4 weeks. Acidimicrobiia, especially members of the Sva0996 marine group, colonized the degrading kelp biomass after 11 weeks. These secondary colonizers could act as opportunistic scavenger bacteria assimilating substrates exposed by early degraders. In parallel, kelp accumulation modified bacterial communities in the underlying sediment, notably favouring anaerobic taxa potentially involved in the sulfur and nitrogen cycles. Overall, this study provides insights into the bacterial degradation of algal biomass in situ, an important link in coastal trophic chains.
Brunet, M, Le Duff, N, Fuchs, BM, Amann, R, Barbeyron, T & Thomas, F 2021, 'Specific detection and quantification of the marine flavobacterial genus Zobellia on macroalgae using novel qPCR and CARD-FISH assays', Systematic and Applied Microbiology, vol. 44, no. 6, pp. 126269-126269.
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The flavobacterial genus Zobellia is considered as a model to study macroalgal polysaccharide degradation. The lack of data regarding its prevalence and abundance in coastal habitats constitutes a bottleneck to assess its ecological strategies. To overcome this issue, real-time quantitative PCR (qPCR) and fluorescence in situ hybridization (FISH) methods targeting the 16S rRNA gene were optimized to specifically detect and quantify Zobellia on the surface of diverse macroalgae. The newly designed qPCR primers and FISH probes targeted 98 and 100% of the Zobellia strains in silico and their specificity was confirmed using pure bacterial cultures. The dynamic range of the qPCR assay spanned 8 orders of magnitude from 10 to 108 16S rRNA gene copies and the detection limit was 0.01% relative abundance of Zobellia in environmental samples. Zobellia-16S rRNA gene copies were detected on all surveyed brown, green and red macroalgae, in proportion varying between 0.1 and 0.9% of the total bacterial copies. The absolute and relative abundance of Zobellia varied with tissue aging on the kelp Laminaria digitata. Zobellia cells were successfully visualized in Ulva lactuca and stranded Palmaria palmata surface biofilm using CARD-FISH, representing in the latter 105Zobellia cells·cm-2 and 0.43% of total bacterial cells. Overall, qPCR and CARD-FISH assays enabled robust detection, quantification and localization of Zobellia representatives in complex samples, underlining their ecological relevance as primary biomass degraders potentially cross-feeding other microorganisms.
Bryant, CJ, Burke, C & Huston, WM 2021, 'Cervicovaginal microbiota and women’s health outcomes', Microbiology Australia, vol. 42, no. 2, pp. 65-65.
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The human cervicovaginal microbiome has an important role in the health and homoeostasis of the female reproductive tract. A eubiotic microbiome is typically dominated with lactic acid producing bacteria and is categorised into five community state types. Issues arise when the microbiome becomes dysbiotic, with the microbial composition shifting to contain a greater relative abundance of strict and facultative anaerobes. This shift will lead to several adverse changes in the vaginal environment including compromised epithelial cells, cell death, inflammation, and greater susceptibility to infection. These changes are associated with various adverse outcomes including infections, preterm birth, and infertility. In this review, we discuss how the cervicovaginal microbiome influences these outcomes and possible future directions of treatment and research.
Burnett, DL, Jackson, KJL, Langley, DB, Aggarwal, A, Stella, AO, Johansen, MD, Balachandran, H, Lenthall, H, Rouet, R, Walker, G, Saunders, BM, Singh, M, Li, H, Henry, JY, Jackson, J, Stewart, AG, Witthauer, F, Spence, MA, Hansbro, NG, Jackson, C, Schofield, P, Milthorpe, C, Martinello, M, Schulz, SR, Roth, E, Kelleher, A, Emery, S, Britton, WJ, Rawlinson, WD, Karl, R, Schäfer, S, Winkler, TH, Brink, R, Bull, RA, Hansbro, PM, Jäck, H-M, Turville, S, Christ, D & Goodnow, CC 2021, 'Immunizations with diverse sarbecovirus receptor-binding domains elicit SARS-CoV-2 neutralizing antibodies against a conserved site of vulnerability', Immunity, vol. 54, no. 12, pp. 2908-2921.e6.
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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, vol. 34, no. 3, pp. 558-570.
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Cai, X, Li, JJ, Liu, T, Brian, O & Li, J 2021, 'Infectious disease mRNA vaccines and a review on epitope prediction for vaccine design', Briefings in Functional Genomics, vol. 20, no. 5, pp. 289-303.
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Abstract
Messenger RNA (mRNA) vaccines have recently emerged as a new type of vaccine technology, showing strong potential to combat the COVID-19 pandemic. In addition to SARS-CoV-2 which caused the pandemic, mRNA vaccines have been developed and tested to prevent infectious diseases caused by other viruses such as Zika virus, the dengue virus, the respiratory syncytial virus, influenza H7N9 and Flavivirus. Interestingly, mRNA vaccines may also be useful for preventing non-infectious diseases such as diabetes and cancer. This review summarises the current progresses of mRNA vaccines designed for a range of diseases including COVID-19. As epitope study is a primary component in the in silico design of mRNA vaccines, we also survey on advanced bioinformatics and machine learning algorithms which have been used for epitope prediction, and review on user-friendly software tools available for this purpose. Finally, we discuss some of the unanswered concerns about mRNA vaccines, such as unknown long-term side effects, and present with our perspectives on future developments in this exciting area.
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, pp. e1009365-e1009365.
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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.
Camaya, I, Mok, TY, Lund, M, To, J, Braidy, N, Robinson, MW, Santos, J, O’Brien, B & Donnelly, S 2021, 'The parasite-derived peptide FhHDM-1 activates the PI3K/Akt pathway to prevent cytokine-induced apoptosis of β-cells', Journal of Molecular Medicine, vol. 99, no. 11, pp. 1605-1621.
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Cant, J, Salguero‐Gómez, R, Kim, SW, Sims, CA, Sommer, B, Brooks, M, Malcolm, HA, Pandolfi, JM & Beger, M 2021, 'The projected degradation of subtropical coral assemblages by recurrent thermal stress', Journal of Animal Ecology, vol. 90, no. 1, pp. 233-247.
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Capriola-Hall, NN, McFayden, T, Ollendick, TH & White, SW 2021, 'Caution When Screening for Autism among Socially Anxious Youth', Journal of Autism and Developmental Disorders, vol. 51, no. 5, pp. 1540-1549.
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Social anxiety disorder (SAD) is commonly comorbid with autism spectrum disorder (ASD). Here, in a sample of 86 children and adolescents (MAGE = 12.62 years; 68.6% male), 28 of whom were diagnosed with ASD, 34 with SAD, and 24 with comorbid ASD and SAD, we compared parent-reported scores from the Social Responsiveness Scale-Second Edition (SRS-2; Constantino and Gruber in Social Responsiveness Scale (SRS; Constantino and Gruber 2012) to determine the sensitivity and specificity of the measure in cases of differential diagnosis between SAD and ASD. Results suggest that neither the subscales, nor the SRS-2 total score, consistently differed between ASD and SAD. Sensitivity and specificity analyses suggested that the SRS-2 total poorly discriminated ASD from SAD. When screening socially anxious youth for possible ASD, caution should be taken.
Cardoso, BR, Hare, DJ & Macpherson, H 2021, 'Correction to: Sex‑dependent association between selenium status and cognitive performance in older adults', European Journal of Nutrition, vol. 60, no. 2, pp. 1161-1161.
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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, vol. 10, no. 4, pp. 882-882.
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Alzheimer’s disease is a progressive, devastating, and irreversible brain disorder that, day by day, destroys memory skills and social behavior. Despite this, the number of known genes suitable for discriminating between AD patients is insufficient. Among the genes potentially involved in the development of AD, there are the chitinase-like proteins (CLPs) CHI3L1, CHI3L2, and CHID1. The genes of the first two have been extensively investigated while, on the contrary, little information is available on CHID1. In this manuscript, we conducted transcriptome meta-analysis on an extensive sample of brains of healthy control subjects (n = 1849) (NDHC) and brains of AD patients (n = 1170) in order to demonstrate CHID1 involvement. Our analysis revealed an inverse correlation between the brain CHID1 expression levels and the age of NDHC subjects. Significant differences were highlighted comparing CHID1 expression of NDHC subjects and AD patients. Exclusive in AD patients, the CHID1 expression levels were correlated positively to calcium-binding adapter molecule 1 (IBA1) levels. Furthermore, both in NDHC and in AD patient’s brains, the CHID1 expression levels were directly correlated with calbindin 1 (CALB1) and neurogranin (NRGN). According to brain regions, correlation differences were shown between the expression levels of CHID1 in prefrontal, frontal, occipital, cerebellum, temporal, and limbic system. Sex-related differences were only highlighted in NDHC. CHID1 represents a new chitinase potentially involved in the principal processes underlying Alzheimer’s disease.
Celis-Plá, PSM, Rearte, TA, Neori, A, Masojídek, J, Bonomi-Barufi, J, Álvarez-Gómez, F, Ranglová, K, Carmo da Silva, J, Abdala, R, Gómez, C, Caporgno, M, Torzillo, G, Silva Benavides, AM, Ralph, PJ, Fávero Massocato, T, Atzmüller, R, Vega, J, Chávez, P & Figueroa, FL 2021, 'A new approach for cultivating the cyanobacterium Nostoc calcicola (MACC-612) to produce biomass and bioactive compounds using a thin-layer raceway pond', Algal Research, vol. 59, pp. 102421-102421.
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Chadwick, S, Cvetanovski, M, Ross, M, Sharp, A & Moret, S 2021, 'Comparison of NIR powders to conventional fingerprint powders', Forensic Science International, vol. 328, pp. 111023-111023.
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Chai, H, Cheng, W, Jin, D & Miao, P 2021, 'Recent Progress in DNA Hybridization Chain Reaction Strategies for Amplified Biosensing', ACS Applied Materials & Interfaces, vol. 13, no. 33, pp. 38931-38946.
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With the continuous development of DNA nanotechnology, various spatial DNA structures and assembly techniques emerge. Hybridization chain reaction (HCR) is a typical example with exciting features and bright prospects in biosensing, which has been intensively investigated in the past decade. In this Spotlight on Applications, we summarize the assembly principles of conventional HCR and some novel forms of linear/nonlinear HCR. With advantages like great assembly kinetics, facile operation, and an enzyme-free and isothermal reaction, these strategies can be integrated with most mainstream reporters (e.g., fluorescence, electrochemistry, and colorimetry) for the ultrasensitive detection of abundant targets. Particularly, we select several representative studies to better illustrate the novel ideas and performances of HCR strategies. Theoretical and practical utilities are confirmed for a range of biosensing applications. In the end, a deep discussion is provided about the challenges and future tasks of this field.
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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Abstract
Background
Bacterial communities are responsible for biological nutrient removal and flocculation in engineered systems such as activated floccular sludge. Predators such as bacteriophage and protozoa exert significant predation pressure and cause bacterial mortality within these communities. However, the roles of bacteriophage and protozoan predation in impacting granulation process remain limited. Recent studies hypothesised that protozoa, particularly sessile ciliates, could have an important role in granulation as these ciliates were often observed in high abundance on surfaces of granules. Bacteriophages were hypothesized to contribute to granular stability through bacteriophage-mediated extracellular DNA release by lysing bacterial cells. This current study investigated the bacteriophage and protozoan communities throughout the granulation process. In addition, the importance of protozoan predation during granulation was also determined through chemical killing of protozoa in the floccular sludge.
Results
Four independent bioreactors seeded with activated floccular sludge were operated for aerobic granulation for 11 weeks. Changes in the phage, protozoa and bacterial communities were characterized throughout the granulation process. The filamentous phage, Inoviridae, increased in abundance at the initiation phase of granulation. However, the abundance shifted towards lytic phages during the maturation phase. In contrast, the abundance and diversity of protozoa decreased initially, possibly due to the reduction in settling time and subsequent washout. Upon the formation of granules, ciliated protozoa from the class Oligohymenophorea were the dominant group of protozoa based on metacommunity analysis. These protozoa h...
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, 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, vol. 70, no. 11, pp. 754-763.
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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, Ng, SW, Singh, SK, Gulati, M, Gupta, G, Chaudhary, SK, Hing, GB, Collet, T, MacLoughlin, R, Löbenberg, R, Oliver, BG, Chellappan, DK & Dua, K 2021, 'Revolutionizing polymer-based nanoparticle-linked vaccines for targeting respiratory viruses: A perspective', Life Sciences, vol. 280, pp. 119744-119744.
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Viral respiratory tract infections have significantly impacted global health as well as socio-economic growth. Respiratory viruses such as the influenza virus, respiratory syncytial virus (RSV), and the recent SARS-CoV-2 infection (COVID-19) typically infect the upper respiratory tract by entry through the respiratory mucosa before reaching the lower respiratory tract, resulting in respiratory disease. Generally, vaccination is the primary method in preventing virus pathogenicity and it has been shown to remarkably reduce the burden of various infectious diseases. Nevertheless, the efficacy of conventional vaccines may be hindered by certain limitations, prompting the need to develop novel vaccine delivery vehicles to immunize against various strains of respiratory viruses and to mitigate the risk of a pandemic. In this review, we provide an insight into how polymer-based nanoparticles can be integrated with the development of vaccines to effectively enhance immune responses for combating viral respiratory tract infections.
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, vol. 16, no. 10, pp. 783-786.
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Charon, J, Murray, S & Holmes, EC 2021, 'Revealing RNA virus diversity and evolution in unicellular algae transcriptomes', Virus Evolution, vol. 7, no. 2.
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Abstract
Remarkably little is known about the diversity and evolution of RNA viruses in unicellular eukaryotes. We screened a total of 570 transcriptomes from the Marine Microbial Eukaryote Transcriptome Sequencing Project that encompasses a wide diversity of microbial eukaryotes, including most major photosynthetic lineages (i.e. the microalgae). From this, we identified thirty new and divergent RNA virus species, occupying a range of phylogenetic positions within the overall diversity of RNA viruses. Approximately one-third of the newly described viruses comprised single-stranded positive-sense RNA viruses from the order Lenarviricota associated with fungi, plants, and protists, while another third were related to the order Ghabrivirales, including members of the protist and fungi-associated Totiviridae. Other viral species showed sequence similarity to positive-sense RNA viruses from the algae-associated Marnaviridae, the double-stranded RNA (ds-RNA) Partitiviridae, as well as tentative evidence for one negative-sense RNA virus related to the Qinviridae. Importantly, we were able to identify divergent RNA viruses from distant host taxa, revealing the ancestry of these viral families and greatly extending our knowledge of the RNA viromes of microalgal cultures. Both the limited number of viruses detected per sample and the low sequence identity to known RNA viruses imply that additional microalgal viruses exist that could not be detected at the current sequencing depth or were too divergent to be identified using sequence similarity. Together, these results highlight the need for further investigation of algal-associated RNA viruses as well as the development of new tools to identify RNA viruses that exhibit very high levels of sequence divergence.
Chayambuka, K, Cardinaels, R, Gering, KL, Raijmakers, L, Mulder, G, Danilov, DL & Notten, PHL 2021, 'An experimental and modeling study of sodium-ion battery electrolytes', Journal of Power Sources, vol. 516, pp. 230658-230658.
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Chayambuka, K, Mulder, G, Danilov, DL & Notten, PHL 2021, 'Determination of state-of-charge dependent diffusion coefficients and kinetic rate constants of phase changing electrode materials using physics-based models', Journal of Power Sources Advances, vol. 9, pp. 100056-100056.
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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, vol. 13, no. 15, pp. 1249-1251.
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Chen, C, Jiang, M, Zhou, T, Raijmakers, L, Vezhlev, E, Wu, B, Schülli, TU, Danilov, DL, Wei, Y, Eichel, R & Notten, PHL 2021, 'Interface Aspects in All‐Solid‐State Li‐Based Batteries Reviewed', Advanced Energy Materials, vol. 11, no. 13, pp. 2003939-2003939.
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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 & Interfaces, vol. 13, no. 21, pp. 24785-24794.
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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, vol. 33, no. 23, pp. 2008847-2008847.
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Chen, C-H, Chao, K-M, Hwang, F-J, Han, C & Pu, L 2021, 'Editorial', International Journal of Distributed Sensor Networks, vol. 17, no. 2, pp. 155014772199288-155014772199288.
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Chen, H, Chhor, M, Rayner, BS, McGrath, K & McClements, L 2021, 'Evaluation of the diagnostic accuracy of current biomarkers in heart failure with preserved ejection fraction: A systematic review and meta-analysis', Archives of Cardiovascular Diseases, vol. 114, no. 12, pp. 793-804.
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Background: A number of circulating biomarkers are currently utilized for the diagnosis of chronic heart failure with preserved ejection fraction (HFpEF). However, due to HFpEF heterogeneity, the accuracy of these biomarkers remains unclear. Aims: This study aimed to systematically determine the diagnostic accuracy of currently available biomarkers for chronic HFpEF. Methods: PubMed, Web of Science, MEDLINE and SCOPUS databases were searched systematically to identify studies assessing the diagnostic accuracy of biomarkers of chronic HFpEF with left ventricular ejection fraction (LVEF) ≥ 50%. All included studies were independently assessed for quality and relevant information was extracted. Random-effects models were used to estimate the pooled diagnostic accuracy of HFpEF biomarkers. Results: The search identified 6145 studies, of which 19 were included. Four biomarkers were available for meta-analysis. The pooled sensitivity of B-type natriuretic peptide (BNP) (0.787, 95% confidence interval [CI] 0.719–0.842) was higher than that of N-terminal pro-BNP (NT-proBNP) (0.696, 95% CI 0.599–0.779) in chronic HFpEF diagnosis. However, NT-proBNP showed improved specificity (0.882, 95% CI 0.778–0.941) compared to BNP (\0.796, 95% CI 0.672–0.882). Galectin-3 (Gal-3) exhibited a reliable diagnostic adequacy for HFpEF (sensitivity 0.760, 95% CI 0.631–0.855; specificity 0.803, 95% CI 0.667–0.893). However, suppression of tumorigenesis-2 (ST2) displayed limited diagnostic performance for chronic HFpEF diagnosis (sensitivity 0.636, 95% CI 0.465–0.779; specificity 0.595, 95% CI 0.427–0.743). Conclusion: NT-proBNP and BNP appear to be the most reliable biomarkers in chronic HFpEF with NT-proBNP showing higher specificity and BNP showing higher sensitivity. Although Gal-3 appears more reliable than ST2 in HFpEF diagnosis, the conclusions are limited as only three studies were included in this meta-analysis.
Chen, H, Lin, Y, Chen, Y, Chen, S, Nassif, N & McGowan, E 2021, 'P-86 The importance of sphingosine kinase 1 isoform expression in the gut-liver axis', Annals of Oncology, vol. 32, pp. S127-S127.
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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, P, Bornhorst, J, Patton, S, Bagai, K, Nitin, R, Miah, M, Hare, DJ, Kysenius, K, Crouch, PJ, Xiong, L, Rouleau, GA, Schwerdtle, T, Connor, J, Aschner, M, Bowman, AB & Walters, AS 2021, 'A potential role for zinc in restless legs syndrome', Sleep, vol. 44, no. 4.
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Abstract
Study Objectives
Evaluate serum and brain noniron metals in the pathology and genetics of restless legs syndrome (RLS).
Methods
In two independent studies (cohorts 1 and 2), in which subjects either remained on medications or tapered off medications, we analyzed serum levels of iron, calcium, magnesium, manganese, copper, and zinc both in RLS patients and controls, and assessed the prevalence of the MEIS1 and BTBD9 risk alleles previously established through genome-wide association studies. Human brain sections and a nematode genetic model were also quantified for metal levels using mass spectrometry.
Results
We found a significant enrichment for the BTBD9 risk genotype in the RLS affected group compared to control (p = 0.0252), consistent with previous literature. Serum (p = 0.0458 and p = 0.0139 for study cohorts 1 and 2, respectively) and brain (p = 0.0413) zinc levels were significantly elevated in the RLS patients versus control subjects.
Conclusion
We show for the first time that serum and brain levels of zinc are elevated in RLS. Further, we confirm the BTBD9 genetic risk factor in a new population, although the zinc changes were not significantly associated with risk genotypes. Zinc and iron homeostasis are interrelated, and zinc biology impacts neurotransmitter systems previously linked to RLS. Given the modest albeit statistically significant increase in serum zinc of ~20%, and the lack of association with two known genetic risk factors, zin...
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, vol. 117, pp. 154724-154724.
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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, vol. 64, no. 10, pp. 2593-2600.
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Chen, Y, Li, C, White, S, Nonahal, M, Xu, Z-Q, Watanabe, K, Taniguchi, T, Toth, M, Tran, TT & Aharonovich, I 2021, 'Generation of High-Density Quantum Emitters in High-Quality, Exfoliated Hexagonal Boron Nitride', ACS Applied Materials & Interfaces, vol. 13, no. 39, pp. 47283-47292.
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Chen, Y, Wang, T, Tian, H, Su, D, Zhang, Q & Wang, G 2021, 'Advances in Lithium–Sulfur Batteries: From Academic Research to Commercial Viability', Advanced Materials, vol. 33, no. 29, pp. 2003666-2003666.
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Chen, Y, Westerhausen, MT, Li, C, White, S, Bradac, C, Bendavid, A, Toth, M, Aharonovich, I & Tran, TT 2021, 'Solvent-Exfoliated Hexagonal Boron Nitride Nanoflakes for Quantum Emitters', ACS Applied Nano Materials, vol. 4, no. 10, pp. 10449-10457.
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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, vol. 17, no. 17, pp. 2008062-2008062.
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Chen, Z, Danilov, DL, Raijmakers, LHJ, Chayambuka, K, Jiang, M, Zhou, L, Zhou, J, Eichel, R-A & Notten, PHL 2021, 'Overpotential analysis of graphite-based Li-ion batteries seen from a porous electrode modeling perspective', Journal of Power Sources, vol. 509, pp. 230345-230345.
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Choi, JP, Yang, X, He, S, Song, R, Xu, Z-R, Foley, M, Wong, JJ-L, Xu, C-R & Zheng, X 2021, 'CCM2L (Cerebral Cavernous Malformation 2 Like) Deletion Aggravates Cerebral Cavernous Malformation Through Map3k3-KLF Signaling Pathway', Stroke, vol. 52, no. 4, pp. 1428-1436.
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Background and Purpose:
Cerebral cavernous malformation (CCM) is a common cerebrovascular disease. CCMs are major causes of stroke, cerebral hemorrhage, and neurological deficits in young individuals. Loss-of-function mutations in
CCM1
,
CCM2
, and
CCM3
have been identified to cause CCM in humans.
Ccm2-like
(
Ccm2l
) is a paralog of
Ccm2
and is predominantly expressed in endothelial cells (ECs). CCM2L (CCM2-like) competes with CCM2 for binding to CCM1 and has been shown to have an antagonistic function to that of CCM2 during vascular development. The role of CCM2L in CCM pathogenesis is unknown.
Methods:
We isolated brain ECs from the inducible-CCM mouse models for gene expression analysis. Micro-computed tomography imaging was used to analyze CCM lesion burden from the genetic cross of
Ccm2l
knockout mice (
Ccm2l
−/−
) with
Ccm1
or
Ccm2
-deficient mice to determine the role of
Ccm2l
in CCM pathogenesis. Genetic crosses with
Map3k3
fl/fl
mice were used to determine the role...
Chong, H, Xu, Y, Han, Y, Yan, C, Su, D & Wang, C 2021, 'Pillar[5]arene‐based “Three‐components” Supramolecular Assembly and the Performance of Nitrobenzene‐based Explosive Fluorescence Sensing', ChemistrySelect, vol. 6, no. 34, pp. 9363-9367.
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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, vol. 10, no. 2.
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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, pp. 209-209.
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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.
Chow, WS, Larkum, AWD, Pfündel, E, Ritchie, RJ, Scheer, H & Strid, Å 2021, 'A tribute to Robert John Porra (august 7, 1931–may 16, 2019)', Photosynthesis Research, vol. 147, no. 2, pp. 125-130.
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Christie, MJ, Irving, AT, Forster, SC, Marsland, BJ, Hansbro, PM, Hertzog, PJ, Nold-Petry, CA & Nold, MF 2021, 'Of bats and men: Immunomodulatory treatment options for COVID-19 guided by the immunopathology of SARS-CoV-2 infection', Science Immunology, vol. 6, no. 63.
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SARS-CoV-2 evades immune recognition in humans but not bats, pointing to potential strategies for therapeutic intervention.
Ciobanu, L & Elder, M 2021, 'The complexity of solution sets to equations in hyperbolic groups', Israel Journal of Mathematics, vol. 245, no. 2, pp. 869-920.
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Clancy, L, Philp, M, Shimmon, R & Fu, S 2021, 'Development and validation of a color spot test method for the presumptive detection of 25‐NBOMe compounds', Drug Testing and Analysis, vol. 13, no. 5, pp. 929-943.
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Clark, AS, Blanco-Redondo, A & Aharonovich, I 2021, 'Special Topic on Integrated Quantum Photonics', APL Photonics, vol. 6, no. 12, pp. 120401-120401.
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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 NaYF4nanosheets with upconversion luminescence', 2D Materials, vol. 8, no. 1, pp. 015005-015005.
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AbstractNaYF4is an efficient host material for lanthanide-based upconversion luminescence and has attracted immense interest for potential applications in photovoltaics, lasers and bioimaging. However, being a non-van der Waals (non-vdW) material, there have been thus far no reports on exfoliation of bulk NaYF4to nanosheets and their upconversion luminescence properties. Here, we demonstrate for the first time the fabrication of lanthanide-containing NaYF42D nanosheets using a soft liquid-phase exfoliation method and report on their optical, electronic and chemical characteristics. The nanosheets exfoliated from NaYF4:Yb,Er microcrystals consisting mainly ofβ-NaYF4become enriched inα-NaYF4post exfoliation and have a large micron-sized planar area with a preferential (100) surface orientation. X-ray absorption spectroscopy confirms that both Yb and Er doping ions are retained in the exfoliated nanosheets. Through centrifugation, NaYF42D nanosheets are successfully obtained with thicknesses ranging from a monolayer to tens of layers. Optical analysis of individual nanosheets shows that they exhibit both optical down-conversion and upconversion properties, albeit with reduced emission intensities compared with the parent microparticles. Further exploration of their electronic structure by density functional theory (DFT) calculations and photoelectron spectroscopy reveals the formation of surface F atom defects and a shrinkage of the electronic bandgap in ultrathin nanosheets. Our findings will trigger further interest in non-vdW 2D upconversion nanomaterials.
Clases, D, Ueland, M, Gonzalez de Vega, R, Doble, P & Pröfrock, D 2021, 'Quantitative speciation of volatile sulphur compounds from human cadavers by GC-ICP-MS', Talanta, vol. 221, pp. 121424-121424.
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Clifton, J, Osman, EO, Suggett, DJ & Smith, DJ 2021, 'Resolving conservation and development tensions in a small island state: A governance analysis of Curieuse Marine National Park, Seychelles', Marine Policy, vol. 127, pp. 103617-103617.
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© 2019 Elsevier Ltd The management and conservation of marine resources in Seychelles, a small island developing state (SIDS) in the western Indian Ocean, is fundamental to maintaining the flow of international visitors which forms the mainstay of the nation's economy. There is an increasing trend towards empowering non-governmental organisations and parastatal entities with protected area management responsibilities, which partly reflects the chronic underfunding of the state protected area management institution. This paper explores these and related issues through a governance analysis of Curieuse Marine National Park, which is the most popular state-owned marine national park in terms of recorded visitor numbers. This demonstrates that the inability to implement economic incentives through not fully capitalising on the use and non-use values of the park has deleterious consequences for managing the combined impacts of tourism and fisheries on the ecological assets of the park. Furthermore, the capacity of the state management institution is being eroded through a focus on the development of an extensive network of new marine protected areas under the direction of an international non-governmental organisation. Suggestions are made that could strengthen economic, participative and interpretative incentives to provide a more sustainable basis for marine national park management.
Coetzee, L-CC, Muller, AJ, Adeyinka, AS, Sonopo, MS & Williams, DBG 2021, 'Synthesis, characterisation and DFT studies of [3,5-bis(2-hydroxyphenyl)-1H-1,2,4-triazol-1-yl](phenyl)methanone derivatives', Results in Chemistry, vol. 3, pp. 100165-100165.
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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, A-M, 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, Y-J, 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, Feillel, V, Leroux, D, Dreyfus, H, Rebischung, C, Peysselon, M, Coron, F, Faivre, L, Baurand, A, Jacquot, C, Bertolone, G, Lizard, S, Prieur, F, Lebrun, M, Kientz, C, Ferrer, SF, Mari, V, Vénat-Bouvet, L, Delnatte, C, Bézieau, S, Mortemousque, I, Coulet, F, Colas, C, Soubrier, F, Warcoin, M, Sokolowska, J, Bronner, M, Collonge-Rame, M-A, Damette, A, Gesta, P, Lallaoui, H, Chiesa, J, Molina-Gomes, D, Ingster, O, Gregory, H, Miedzybrodzka, Z, Morrison, PJ, Ong, K-R, Donaldson, A, Rogers, MT, Kennedy, MJ, Porteous, ME, Brewer, C, Davidson, R, Izatt, L, Brady, A, Barwell, J, Adlard, J, Foo, C, Lalloo, F, Side, LE, Eason, J, Henderson, A, Walker, L, Eeles, RA, Cook, J, Snape, K, Eccles, D, Murray, A, McCann, E, Collée, JM, Conroy, DM, Czene, K, Daly, MB, Devilee, P, Diez, O, Ding, YC, Domchek, SM, Dörk, T, dos-Santos-Silva, I, Dunning, AM, Dwek, M, Eccles, DM, Eliassen, AH, Engel, C, Eriksson, M, Evans, DG, Fasching, PA, Flyger, H, Fostira, F, Friedman, E, Fritschi, L, Frost, D, Gago-Dominguez, M, Gapstur, SM, Garber, J, Garcia-Barberan, V, García-Closas, M, García-Sáenz, JA, Gaudet, MM & et al. 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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AbstractBreast 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.
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, A-M, 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, Y-J, 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, Feillel, V, Leroux, D, Dreyfus, H, Rebischung, C, Peysselon, M, Coron, F, Faivre, L, Baurand, A, Jacquot, C, Bertolone, G, Lizard, S, Prieur, F, Lebrun, M, Kientz, C, Ferrer, SF, Mari, V, Vénat-Bouvet, L, Delnatte, C, Bézieau, S, Mortemousque, I, Coulet, F, Colas, C, Soubrier, F, Warcoin, M, Sokolowska, J, Bronner, M, Collonge-Rame, M-A, Damette, A, Gesta, P, Lallaoui, H, Chiesa, J, Molina-Gomes, D, Ingster, O, Gregory, H, Miedzybrodzka, Z, Morrison, PJ, Ong, K-R, Donaldson, A, Rogers, MT, Kennedy, MJ, Porteous, ME, Brewer, C, Davidson, R, Izatt, L, Brady, A, Barwell, J, Adlard, J, Foo, C, Lalloo, F, Side, LE, Eason, J, Henderson, A, Walker, L, Eeles, RA, Cook, J, Snape, K, Eccles, D, Murray, A, McCann, E, Collée, JM, Conroy, DM, Czene, K, Daly, MB, Devilee, P, Diez, O, Ding, YC, Domchek, SM, Dörk, T, dos-Santos-Silva, I, Dunning, AM, Dwek, M, Eccles, DM, Eliassen, AH, Engel, C, Eriksson, M, Evans, DG, Fasching, PA, Flyger, H, Fostira, F, Friedman, E, Fritschi, L, Frost, D, Gago-Dominguez, M, Gapstur, SM, Garber, J, Garcia-Barberan, V, García-Closas, M, García-Sáenz, JA, Gaudet, MM & et al. 2021, 'Author Correction: 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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A Correction to this paper has been published: https://doi.org/10.1038/s41467-021-23162-4
Cole, AJ, Dickson, K-A, Liddle, C, Stirzaker, C, Shah, JS, Clifton-Bligh, R & Marsh, DJ 2021, 'Ubiquitin chromatin remodelling after DNA damage is associated with the expression of key cancer genes and pathways', Cellular and Molecular Life Sciences, vol. 78, no. 3, pp. 1011-1027.
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Cole, VJ, Parker, LM, Scanes, E, Wright, J, Barnett, L & Ross, PM 2021, 'Climate change alters shellfish reef communities: A temperate mesocosm experiment', Marine Pollution Bulletin, vol. 173, pp. 113113-113113.
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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. 125-125.
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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, Booth, DJ & Nagelkerken, I 2021, 'Novel species interactions and environmental conditions reduce foraging competency at the temperate range edge of a range-extending coral reef fish', Coral Reefs, vol. 40, no. 5, pp. 1525-1536.
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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, vol. 11, no. 3, pp. 249-256.
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Cook, AM, Berry, N, Milner, KV & Leigh, A 2021, 'Water availability influences thermal safety margins for leaves', Functional Ecology, vol. 35, no. 10, pp. 2179-2189.
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Counoupas, C, Johansen, MD, Stella, AO, Nguyen, DH, Ferguson, AL, Aggarwal, A, Bhattacharyya, ND, Grey, A, Hutchings, O, Patel, K, Siddiquee, R, Stewart, EL, Feng, CG, Hansbro, NG, Palendira, U, Steain, MC, Saunders, BM, Low, JKK, Mackay, JP, Kelleher, AD, Britton, WJ, Turville, SG, Hansbro, PM & Triccas, JA 2021, 'A single dose, BCG-adjuvanted COVID-19 vaccine provides sterilising immunity against SARS-CoV-2 infection', npj Vaccines, vol. 6, no. 1, p. 143.
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AbstractGlobal control of COVID-19 requires broadly accessible vaccines that are effective against SARS-CoV-2 variants. In this report, we exploit the immunostimulatory properties of bacille Calmette-Guérin (BCG), the existing tuberculosis vaccine, to deliver a vaccination regimen with potent SARS-CoV-2-specific protective immunity. Combination of BCG with a stabilised, trimeric form of SARS-CoV-2 spike antigen promoted rapid development of virus-specific IgG antibodies in the blood of vaccinated mice, that was further augmented by the addition of alum. This vaccine formulation, BCG:CoVac, induced high-titre SARS-CoV-2 neutralising antibodies (NAbs) and Th1-biased cytokine release by vaccine-specific T cells, which correlated with the early emergence of T follicular helper cells in local lymph nodes and heightened levels of antigen-specific plasma B cells after vaccination. Vaccination of K18-hACE2 mice with a single dose of BCG:CoVac almost completely abrogated disease after SARS-CoV-2 challenge, with minimal inflammation and no detectable virus in the lungs of infected animals. Boosting BCG:CoVac-primed mice with a heterologous vaccine further increased SARS-CoV-2-specific antibody responses, which effectively neutralised B.1.1.7 and B.1.351 SARS-CoV-2 variants of concern. These findings demonstrate the potential for BCG-based vaccination to protect against major SARS-CoV-2 variants circulating globally.
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, vol. 13, no. 4, pp. 485-486.
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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.
Cranwell Schaeper, O, Fröch, JE, Kim, S, Mu, Z, Toth, M, Gao, W & Aharonovich, I 2021, 'Fabrication of Photonic Resonators in Bulk 4H‐SiC', Advanced Materials Technologies, vol. 6, no. 11, pp. 2100589-2100589.
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Cuartas-Villa, S & Webb, JK 2021, 'Nest site selection in a southern and northern population of the velvet gecko (Amalosia lesueurii)', Journal of Thermal Biology, vol. 102, pp. 103121-103121.
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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, vol. 22, no. 1.
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AbstractBackgroundThe major pathogenesis associated withFasciola hepaticainfection results from the extensive tissue damage caused by the tunnelling and feeding activity of immature flukes during their migration, growth and development in the liver. This is compounded by the pathology caused by host innate and adaptive immune responses that struggle to simultaneously counter infection and repair tissue damage.ResultsComplementary transcriptomic and proteomic approaches defined theF. hepaticafactors associated with their migration in the liver, and the resulting immune-pathogenesis. Immature liver-stage flukes express ~ 8000 transcripts that are enriched for transcription and translation processes reflective of intensive protein production and signal transduction pathways. Key pathways that regulate neoblast/pluripotent cells, including the PI3K-Akt signalling pathway, are particularly dominant and emphasise the importance of neoblast-like cells for the parasite’s rapid development. The liver-stage parasites display different secretome profiles, reflecting their distinct niche within the host, and supports the view that cathepsin peptidases, cathepsin peptidase inhibitors, saposins and leucine aminopeptidases play a central role in the parasite’s destructive migration, and digestion of host tissue and blood. Immature flukes are also primed for countering immune attack by secreting immunomodulating fatty acid binding proteins (FABP) and helminth defence molecules (FhHDM). Combined with published host microarray data, our results suggest that considerable immune cell infiltration and subsequent fibrosis of the liver tissue exacerbates oxidative stress within parenchyma that compels the expression of a range of antioxidant molecules within both host and parasite.
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, vol. 7.
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For millennia, coastal and marine ecosystems have adapted and flourished in the Red Sea’s unique environment. Surrounded by deserts on all sides, the Red Sea is subjected to high dust inputs and receives very little freshwater input, and so harbors a high salinity. Coral reefs, seagrass meadows, and mangroves flourish in this environment and provide socio-economic and environmental benefits to the bordering coastlines and countries. Interestingly, while coral reef ecosystems are currently experiencing rapid decline on a global scale, those in the Red Sea appear to be in relatively better shape. That said, they are certainly not immune to the stressors that cause degradation, such as increasing ocean temperature, acidification and pollution. In many regions, ecosystems are already severely deteriorating and are further threatened by increasing population pressure and large coastal development projects. Degradation of these marine habitats will lead to environmental costs, as well as significant economic losses. Therefore, it will result in a missed opportunity for the bordering countries to develop a sustainable blue economy and integrate innovative nature-based solutions. Recognizing that securing the Red Sea ecosystems’ future must occur in synergy with continued social and economic growth, we developed an action plan for the conservation, restoration, and growth of marine environments of the Red Sea. We then investigated the level of resources for financial and economic investment that may incentivize these activities. This study presents a set of commercially viable financial investment strategies, ecological innovations, and sustainable development opportunities, which can, if implemented strategically, help ensure long-term economic benefits while promoting environmental conservation. We make a case for investing in blue natural capital and propose a strategic development model that relies on maintaining the health of natural ecosystems to safeguard ...
D’Agostino, D, Burt, JA, Santinelli, V, Vaughan, GO, Fowler, AM, Reader, T, Taylor, BM, Hoey, AS, Cavalcante, GH, Bauman, AG & Feary, DA 2021, 'Growth impacts in a changing ocean: insights from two coral reef fishes in an extreme environment', Coral Reefs, vol. 40, no. 2, pp. 433-446.
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AbstractDetermining the life-history consequences for fishes living in extreme and variable environments will be vital in predicting the likely impacts of ongoing climate change on reef fish demography. Here, we compare size-at-age and maximum body size of two common reef fish species (Lutjanus ehrenbergii and Pomacanthus maculosus) between the environmentally extreme Arabian/Persian Gulf (‘Arabian Gulf’) and adjacent comparably benign Oman Sea. Additionally, we use otolith increment width profiles to investigate the influence of temperature, salinity and productivity on the individual growth rates. Individuals of both species showed smaller size-at-age and lower maximum size in the Arabian Gulf compared to conspecifics in the less extreme and less variable environment of the Oman Sea, suggesting a life-history trade-off between size and metabolic demands. Salinity was the best environmental predictor of interannual growth across species and regions, with low growth corresponding to more saline conditions. However, salinity had a weaker negative effect on interannual growth of fishes in the Arabian Gulf than in the Oman Sea, indicating Arabian Gulf populations may be better able to acclimate to changing environmental conditions. Temperature had a weak positive effect on the interannual growth of fishes in the Arabian Gulf, suggesting that these populations may still be living within their thermal windows. Our results highlight the potential importance of osmoregulatory cost in impacting growth, and the need to consider the effect of multiple stressors when investigating the consequences of future climate change on fish demography.
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.
Dai, R, Sun, W, Lv, L, Wu, M, Liu, H, Wang, G & Wang, Y 2021, 'Bimetal‐Organic‐Framework Derivation of Ball‐Cactus‐Like Ni‐Sn‐P@C‐CNT as Long‐Cycle Anode for Lithium Ion Battery', Small, vol. 17, no. 49, pp. 2106491-2106491.
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Damaso, NJ, White, SJU & Kim, S 2021, 'Analysis of anapole resonators in low index materials', Journal of Optics, vol. 23, no. 3, pp. 034003-034003.
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Abstract
Photonic cavities are valued in current research owing to the multitude of linear and nonlinear effects arising from densely confined light. Cavity designs consisting of low loss dielectric materials can achieve significant light confinement. Until now, the basic concepts in all-dielectric photonics such as anapole resonances have been primarily studied in high index materials. Here, we use photonic simulation to propose fabricable designs for higher confinement in low index dielectric cavities by incorporating the extensively studied isolated dielectric nanodisk into broader host structures. We further discuss on hexagonal boron nitride nanodisks for their potential use in quantum and nanophotonics applications.
Das, A, Lee, DJ, Shandilya, PK, Kim, S, Kang, G, Lake, DP, Behera, B, Sukachev, D, Aharonovich, I, Lee, J-H, Park, J & Barclay, PE 2021, 'Demonstration of Hybrid High-Q Hexagonal Boron Nitride Microresonators', ACS Photonics, vol. 8, no. 10, pp. 3027-3033.
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Dawson, BM, Barton, PS & Wallman, JF 2021, 'Field succession studies and casework can help to identify forensically useful Diptera', Journal of Forensic Sciences, vol. 66, no. 6, pp. 2319-2328.
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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, vol. 58, no. 6, pp. 2228-2235.
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Abstract
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, 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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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 water and 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-phase...
Dean, S, Razavy, S, Walsh, S, Zaslawski, C, Levett-Jones, T & Cant, R 2021, 'Building empathy awareness in undergraduate traditional Chinese Medicine students via an undercover ‘mystery shopper’ experience', Advances in Integrative Medicine, vol. 8, no. 4, pp. 267-271.
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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, vol. 24, no. 1, pp. 92-119.
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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', The Journal of Allergy and Clinical Immunology: In Practice, vol. 9, no. 6, pp. 2344-2355.
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Deplazes, E, Tafalla, BD, Murphy, C, White, J, Cranfield, CG & Garcia, A 2021, 'Calcium Ion Binding at the Lipid–Water Interface Alters the Ion Permeability of Phospholipid Bilayers', Langmuir, vol. 37, no. 48, pp. 14026-14033.
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Devkota, HP, Gaire, BP, Hori, K, Subedi, L, Adhikari-Devkota, A, Belwal, T, Paudel, KR, Jha, NK, Singh, SK, Chellappan, DK, Hansbro, PM, Dua, K & Kurauchi, Y 2021, 'The science of matcha: Bioactive compounds, analytical techniques and biological properties', Trends in Food Science & Technology, vol. 118, pp. 735-743.
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Devkota, HP, Paudel, KR, Jha, NK, Gupta, PK, Singh, SK, Chellappan, DK, Hansbro, PM & Dua, K 2021, 'Applications of drug-delivery systems targeting inflammasomes in pulmonary diseases', Nanomedicine, vol. 16, no. 27, pp. 2407-2410.
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Dhouib, R, Nasreen, M, Othman, DSMP, Ellis, D, Lee, S, Essilfie, A-T, Hansbro, PM, McEwan, AG & Kappler, U 2021, 'The DmsABC Sulfoxide Reductase Supports Virulence in Non-typeable Haemophilus influenzae', Frontiers in Microbiology, vol. 12.
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Although molybdenum-containing enzymes are well-established as having a key role in bacterial respiration, it is increasingly recognized that some may also support bacterial virulence. Here, we show that DmsABC, a putative dimethylsulfoxide (DMSO) reductase, is required for fitness of the respiratory pathogen Haemophilus influenzae (Hi) in different models of infection. Expression of the dmsABC operon increased with decreasing oxygen availability, but despite this, a Hi2019ΔdmsA strain did not show any defects in anaerobic growth on chemically defined medium (CDM), and viability was also unaffected. Although Hi2019ΔdmsA exhibited increased biofilm formation in vitro and greater resistance to hypochlorite killing compared to the isogenic wild-type strain, its survival in contact with primary human neutrophils, in infections of cultured tissue cells, or in a mouse model of lung infection was reduced compared to Hi2019WT. The tissue cell infection model revealed a two-fold decrease in intracellular survival, while in the mouse model of lung infection Hi2019ΔdmsA was strongly attenuated and below detection levels at 48 h post-inoculation. While Hi2019WT was recovered in approximately equal numbers from bronchoalveolar lavage fluid (BALF) and lung tissue, survival of Hi2019ΔdmsA was reduced in lung tissue compared to BALF samples, indicating that Hi2019
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, vol. 21, no. 4, pp. 1651-1658.
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Diaz, D, Vidal, X, Sunna, A & Care, A 2021, 'Bioengineering a Light-Responsive Encapsulin Nanoreactor: A Potential Tool for In Vitro Photodynamic Therapy', ACS Applied Materials & Interfaces, vol. 13, no. 7, pp. 7977-7986.
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DiBattista, JD, West, KM, Hay, AC, Hughes, JM, Fowler, AM & McGrouther, MA 2021, 'Community‐based citizen science projects can support the distributional monitoring of fishes', Aquatic Conservation: Marine and Freshwater Ecosystems, vol. 31, no. 12, pp. 3580-3593.
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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, vol. 22, no. 16, pp. 8506-8506.
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Several poly (adenosine diphosphate-ribose) polymerase (PARP) inhibitors are now in clinical use for tumours with defects in BReast CAncer genes BRCA1 or BRCA2 that result in deficient homologous recombination repair (HRR). Use of olaparib, niraparib or rucaparib for the treatment of high-grade serous ovarian cancer, including in the maintenance setting, has extended both progression free and overall survival for women with this malignancy. While different PARP inhibitors (PARPis) are mechanistically similar, differences are apparent in their chemical structures, toxicity profiles, PARP trapping abilities and polypharmacological landscapes. We have treated ovarian cancer cell line models of known BRCA status, including the paired cell lines PEO1 and PEO4, and UWB1.289 and UWB1.289+BRCA1, with five PARPis (olaparib, niraparib, rucaparib, talazoparib and veliparib) and observed differences between PARPis in both cell viability and cell survival. A cell line model of acquired resistance to veliparib showed increased resistance to the other four PARPis tested, suggesting that acquired resistance to one PARPi may not be able to be rescued by another. Lastly, as a proof of principle, HRR proficient ovarian cancer cells were sensitised to PARPis by depletion of BRCA1. In the future, guidelines will need to emerge to assist clinicians in matching specific PARPis to specific patients and tumours.
Dickson-Deane, C 2021, 'Influencing the design outcome', Educational Technology Research and Development, vol. 69, no. 1, pp. 269-271.
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Dickson-Deane, C 2021, 'Moving practical learning online', Educational Technology Research and Development, vol. 69, no. 1, pp. 235-237.
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Dickson-Deane, C & Edwards, M 2021, 'Transcribing accounting lectures: Enhancing the pedagogical practice by acknowledging student behaviour', Journal of Accounting Education, vol. 54, pp. 100709-100709.
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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, pp. 111979-111979.
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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, vol. 121, no. 19, pp. 11769-11822.
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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, pp. 102961-102961.
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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, vol. 37, no. 12, pp. 1031-1033.
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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.
DOOLEY, AH & JARRETT, K 2021, 'Non-singular -actions: an ergodic theorem over rectangles with application to the critical dimensions', Ergodic Theory and Dynamical Systems, vol. 41, no. 12, pp. 3722-3739.
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AbstractWe adapt techniques developed by Hochman to prove a non-singular ergodic theorem for
$\mathbb {Z}^d$
-actions where the sums are over rectangles with side lengths increasing at arbitrary rates, and in particular are not necessarily balls of a norm. This result is applied to show that the critical dimensions with respect to sequences of such rectangles are invariants of metric isomorphism. These invariants are calculated for the natural action of
$\mathbb {Z}^d$
on a product of d measure spaces.
Douglas, ANJ, Morgan, AL, Rogers, EIE, Irga, PJ & Torpy, FR 2021, 'Evaluating and comparing the green wall retrofit suitability across major Australian cities', Journal of Environmental Management, vol. 298, pp. 113417-113417.
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Douna, V, Barraza, V, Grings, F, Huete, A, Restrepo-Coupe, N & Beringer, J 2021, 'Towards a remote sensing data based evapotranspiration estimation in Northern Australia using a simple random forest approach', Journal of Arid Environments, vol. 191, pp. 104513-104513.
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Douraghi, M, Aris, P, To, J, Myers, GSA & Hamidian, M 2021, 'Two carbapenem-resistant ST1:ST231:KL1:OCL1Acinetobacter baumanniistrains recovered in Tehran, Iran, carry AbaR31 in the chromosome and AbaR4 and TnaphA6in a RepAci6 plasmid', JAC-Antimicrobial Resistance, vol. 3, no. 3.
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AbstractObjectivesTo analyse the context of genes conferring antibiotic resistance in two carbapenem-resistant Acinetobacter baumannii isolates recovered in Tehran, Iran.MethodsThe antibiotic resistance phenotype for 28 antibiotics was determined using disc diffusion. The whole genome sequences of ABH008 and ABS200 were determined using the Illumina HiSeq X Ten platform. Resistance genes were identified using ResFinder and multilocus sequence types were determined using the Oxford and Institut Pasteur schemes.ResultsIsolates ABH008 and ABS200, recovered in 2012 and 2013, respectively, in two different Tehran hospitals, belong to the common global clone 1 lineage, ST1IP and ST231OX. They are resistant to sulfamethoxazole, tetracycline, gentamicin, amikacin, third-generation cephalosporins and carbapenems. Despite being isolated in different hospitals, phylogenetic analysis indicated they are closely related. Consistent with this, both isolates carry catA1, sul1, aacC1 and aadA1 in a novel variant of the AbaR3-type resistance island, named AbaR31. Both isolates are resistant to amikacin and carbapenems owing to aphA6 and oxa23, respectively. The oxa23 gene is located in the AbaR4 resistance island, and aphA6 in TnaphA6, and both mobile elements are in an ∼90 kbp plasmid encoding the putative RepAci6 replication initiation protein. Resistance to third-generation cephalosporins is due to the acquisition by homologous recombination of a 5 kb DNA segment that contains ISAba1-ampC from a ST623 strain.ConclusionsThe resistance gene complements of ABH008 and ABS200 were found in AbaR31 and a plasmid that encodes RepAci6. The close genetic relationship of ABH008 and ABS200, despite each being recovered from different hos...
Dowla, R, Murnion, B, Hung, C, Currell, K, Kendig, M, Freeston, J & Rooney, K 2021, 'Exercise Capacity and Acute Effect of Exercise on Affect in a Substance Use Disorder Population', Journal of Clinical Exercise Physiology, vol. 10, no. 4, pp. 142-149.
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ABSTRACT
Background
It is known that exercise is beneficial to people with substance use disorder, however little evidence exists regarding their exercise capacity. This pilot study investigates the exercise capacity of patients with substance use disorder and effects of an acute bout of exercise on affect.
Methods
Twenty-nine participants admitted to a withdrawal management facility were recruited to complete a health and exercise assessment (18 females, 11 males; 41 ± 11 years old). Mood was measured before and after exercise assessments using the subjective experience to exercise scale. Data was grouped by sex, and descriptive analyses were performed against age-matched normative data. Within group, before and after subjective experience to exercise scale measures were analyzed using 2-way ANOVA with sex as a between subject factor.
Results
Participants ranged from having 2 to 6 modifiable cardiovascular risk factors. Participants performed below average compared to age-matched and sex-matched normative data for the 6-minute walk test (females: 539 ± 54 m, males: 606 ± 89 m); and push-up test (females: 22% good, males: 36% good). Of the 29 participants, 29% failed to achieve the average range for sex-matched norms in the sit-to-stand test. However, all participants achieved above average for curl-ups, and 72% achieved an average or above score in the step-up test. Exercise significantly increased wellbeing (P < 0.001, effect size = 1.12) and decreased psychological distress (P = 0.045, effect size = 1.03) and fatigue (P < 0.001, effect size = 1.32).
...
Duncan, RJ, Andrew, ME & Forchhammer, MC 2021, 'Snow mediates climatic impacts on Arctic herbivore populations', Polar Biology, vol. 44, no. 7, pp. 1251-1271.
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AbstractArctic ecosystems are particularly vulnerable to impacts of climate change; however, the complex relationships between climate and ecosystems make incorporating effects of climate change into population management difficult. This study used structural equation modelling (SEM) and a 24-year multifaceted monitoring data series collected at Zackenberg, North-East Greenland, to untangle the network of climatic and local abiotic and biotic drivers, determining their direct and indirect effects on two herbivores: musk ox (Ovibos moschatus) and collared lemming (Dicrostonyx groenlandicus). Snow conditions were determined to be the central driver within the system, mediating the effects of climate on herbivore abundance. Under current climate change projections, snow is expected to decrease in the region. Snow had an indirect negative effect on musk ox, as decreased snow depth led to an earlier start to the Arctic willow growing season, shown to increase fecundity and decrease mortality. Musk ox are therefore expected to be more successful under future conditions, within a certain threshold. Snow had both positive and negative effects on lemming, with lemming expected to ultimately be less successful under climate change, as reduction in snow increases their vulnerability to predation. Through their capacity to determine effects of climatic and local drivers within a hierarchy, and the relative strength and direction of these effects, SEMs were demonstrated to have the potential to be valuable in guiding population management.
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, vol. 148, no. 10, pp. 1125-1136.
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Abstract
Ellis, J, Ellis, B, Tyler, K & Reichel, MP 2021, 'Recent trends in the use of social media in parasitology and the application of alternative metrics', Current Research in Parasitology & Vector-Borne Diseases, vol. 1, pp. 100013-100013.
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Estherby, CA, Arnold, MD, Tai, MC & Gentle, AR 2021, 'Dynamic control of polarized thermal emission from VO2 nanofins', Journal of Photonics for Energy, vol. 11, no. 04.
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Ewart, KM, Johnson, RN, Joseph, L, Ogden, R, Frankham, GJ & Lo, N 2021, 'Phylogeography of the iconic Australian pink cockatoo,Lophochroa leadbeateri', Biological Journal of the Linnean Society, vol. 132, no. 3, pp. 704-723.
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AbstractThe pink cockatoo (Lophochroa leadbeateri; or Major Mitchell’s cockatoo) is one of Australia’s most iconic bird species. Two subspecies based on morphology are separated by a biogeographical divide, the Eyrean Barrier. Testing the genetic basis for this subspecies delineation, clarifying barriers to gene flow and identifying any cryptic genetic diversity will likely have important implications for conservation and management. Here, we used genome-wide single nucleotide polymorphisms (SNPs) and mitochondrial DNA data to conduct the first range-wide genetic assessment of the species. The aims were to investigate the phylogeography of the pink cockatoo, to characterize conservation units and to reassess subspecies boundaries. We found consistent but weak genetic structure between the two subspecies based on nuclear SNPs. However, phylogenetic analysis of nuclear SNPs and mitochondrial DNA sequence data did not recover reciprocally monophyletic groups, indicating incomplete evolutionary separation between the subspecies. Consequently, we have proposed that the two currently recognized subspecies be treated as separate management units rather than evolutionarily significant units. Given that poaching is suspected to be a threat to this species, we assessed the utility of our data for wildlife forensic applications. We demonstrated that a subspecies identification test could be designed using as few as 20 SNPs.
Facey, JA, Rogers, TA, Apte, SC & Mitrovic, SM 2021, 'Micronutrients as growth limiting factors in cyanobacterial blooms; a survey of freshwaters in South East Australia', Aquatic Sciences, vol. 83, no. 2.
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Faisal, SN, Amjadipour, M, Izzo, K, Singer, JA, Bendavid, A, Lin, C-T & Iacopi, F 2021, 'Non-invasive on-skin sensors for brain machine interfaces with epitaxial graphene', Journal of Neural Engineering, vol. 18, no. 6, pp. 066035-066035.
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Abstract
Objective. Brain–machine interfaces are key components for the development of hands-free, brain-controlled devices. Electroencephalogram (EEG) electrodes are particularly attractive for harvesting the neural signals in a non-invasive fashion. Approach. Here, we explore the use of epitaxial graphene (EG) grown on silicon carbide on silicon for detecting the EEG signals with high sensitivity. Main results and significance. This dry and non-invasive approach exhibits a markedly improved skin contact impedance when benchmarked to commercial dry electrodes, as well as superior robustness, allowing prolonged and repeated use also in a highly saline environment. In addition, we report the newly observed phenomenon of surface conditioning of the EG electrodes. The prolonged contact of the EG with the skin electrolytes functionalize the grain boundaries of the graphene, leading to the formation of a thin surface film of water through physisorption and consequently reducing its contact impedance more than three-fold. This effect is primed in highly saline environments, and could be also further tailored as pre-conditioning to enhance the performance and reliability of the EG sensors.
Faiz, A, Rathnayake, SNH, ten Hacken, NHT, Guryev, V, van den Berge, M & Pouwels, SD 2021, 'Single-nucleotide polymorphism rs2070600 regulates AGER splicing and the sputum levels of the COPD biomarker soluble receptor for advanced glycation end-products', ERJ Open Research, vol. 7, no. 2, pp. 00947-2020.
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The COPD susceptibility SNP rs2070600 affects the levels of the COPD biomarker sRAGE in sputum as well as splicing of AGER. Moreover, @PouwelsScience et al. demonstrate large differences in sRAGE levels between serum and sputum. https://bit.ly/3t0pJtK.
Falkenberg, LJ, Scanes, E, Ducker, J & Ross, PM 2021, 'Biotic habitats as refugia under ocean acidification', Conservation Physiology, vol. 9, no. 1.
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Abstract
Habitat-forming organisms have an important role in ameliorating stressful conditions and may be of particular relevance under a changing climate. Increasing CO2 emissions are driving a range of environmental changes, and one of the key concerns is the rapid acceleration of ocean acidification and associated reduction in pH. Such changes in seawater chemistry are anticipated to have direct negative effects on calcifying organisms, which could, in turn, have negative ecological, economic and human health impacts. However, these calcifying organisms do not exist in isolation, but rather are part of complex ecosystems. Here, we use a qualitative narrative synthesis framework to explore (i) how habitat-forming organisms can act to restrict environmental stress, both now and in the future; (ii) the ways their capacity to do so is modified by local context; and (iii) their potential to buffer the effects of future change through physiological processes and how this can be influenced by management adopted. Specifically, we highlight examples that consider the ability of macroalgae and seagrasses to alter water carbonate chemistry, influence resident organisms under current conditions and their capacity to do so under future conditions, while also recognizing the potential role of other habitats such as adjacent mangroves and saltmarshes. Importantly, we note that the outcome of interactions between these functional groups will be context dependent, influenced by the local abiotic and biotic characteristics. This dependence provides local managers with opportunities to create conditions that enhance the likelihood of successful amelioration. Where individuals and populations are managed effectively, habitat formers could provide local refugia for resident organisms of ecological and economic importance under an acidifying ocean.
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 Li 2 S/Mo Interlayer', Advanced Energy and Sustainability Research, vol. 2, no. 11, pp. 2100051-2100051.
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Fan, L, Sun, B, Yan, K, Xiong, P, Guo, X, Guo, Z, Zhang, N, Feng, Y, Sun, K & Wang, G 2021, 'A Dual‐Protective Artificial Interface for Stable Lithium Metal Anodes', Advanced Energy Materials, vol. 11, no. 48, pp. 2102242-2102242.
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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, pp. 112833-112833.
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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, vol. 8, no. 21, pp. 2102418-2102418.
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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.
Fang, L, Ruan, M, Yang, S, Qu, X, Chen, H, Zhao, J & Cheng, J 2021, 'Prednisone combined with letrozole reduced risk of ovarian hyperstimulation syndrome (OHSS) in women undergoing long-term gonadotropin-releasing hormone analog treatment', Annals of Palliative Medicine, vol. 10, no. 8, pp. 8837-8847.
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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.
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, pp. 1891-1891.
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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.
Fernandez-Nieto, G, Martinez-Maldonado, R, Echeverria, V, Kitto, K, An, P & Buckingham Shum, S 2021, 'What Can Analytics for Teamwork Proxemics Reveal About Positioning Dynamics In Clinical Simulations?', Proceedings of the ACM on Human-Computer Interaction, vol. 5, no. CSCW1, pp. 1-24.
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Effective teamwork is critical to improve patient outcomes in healthcare. However, achieving this capabilityrequires that pre-service nurses develop the spatial abilities they will require in their clinical placements, suchas: learning when to remain close to the patient and to other team members; positioning themselves correctlyat the right time; and deciding on specific team formations (e.g. face-to-face or side-by-side) to enable effectiveinteraction or avoid disrupting clinical procedures. However, positioning dynamics are ephemeral and caneasily become occluded by the multiple tasks nurses have to accomplish. Digital traces automatically capturedby indoor positioning sensors can be used to address this problem for the purpose of improving nurses' reflection, learning and professional development. This paper presents; i) a qualitative study that illustrateshow to elicit spatial behaviours from educators' pedagogical expectations, and ii) a modelling approachthat transforms nurses' low-level position traces into higher-order proxemics constructs, informed by sucheducatos' expectations, in the context of simulation-based teamwork training. To illustrate our modellingapproach, we conducted an in-the-wild study with 55 undergraduate students and five educators from whompositioning traces were captured in eleven authentic nursing education classes. Low-levelx-ydata was usedto model three proxemic constructs: i) co-presence in interactional spaces, ii) socio-spatial formations (i.e.f-formations), and ii) presence in spaces of interest. Through a number of vignettes, we illustrate how indoorpositioning analytics can be used to address questions that educators and researchers have about teamwork inhealthcare simulation settings.
Fernandez-Nieto, GM, Echeverria, V, Shum, SB, Mangaroska, K, Kitto, K, Palominos, E, Axisa, C & Martinez-Maldonado, R 2021, 'Storytelling With Learner Data: Guiding Student Reflection on Multimodal Team Data', IEEE Transactions on Learning Technologies, vol. 14, no. 5, pp. 695-708.
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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 & Evolution, vol. 36, no. 12, pp. 1093-1101.
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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.
Finkelstein, DI, Billings, JL, Adlard, PA, Ayton, S, Sedjahtera, A, Masters, CL, Wilkins, S, Shackleford, DM, Charman, SA, Bal, W, Zawisza, IA, Kurowska, E, Gundlach, AL, Ma, S, Bush, AI, Hare, DJ, Doble, PA, Crawford, S, Gautier, ECL, Parsons, J, Huggins, P, Barnham, KJ & Cherny, RA 2021, 'Correction to: The novel compound PBT434 prevents iron mediated neurodegeneration and alpha-synuclein toxicity in multiple models of Parkinson’s disease', Acta Neuropathologica Communications, vol. 9, no. 1.
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Following publication of the original article [1], the author identified an error in Fig. 4E. The data and statistics were correct, but the synaptophysin blot was incorrect. The incorrect (Fig. 1) and correct figure (Fig. 2) are shown in this correction article. (Figure presented.).
Fitzpatrick, KJ, Rohlf, HJ, Sutherland, TD, Koo, KM, Beckett, S, Okelo, WO, Keyburn, AL, Morgan, BS, Drigo, B, Trau, M, Donner, E, Djordjevic, SP & De Barro, PJ 2021, 'Progressing Antimicrobial Resistance Sensing Technologies across Human, Animal, and Environmental Health Domains', ACS Sensors, vol. 6, no. 12, pp. 4283-4296.
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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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Abstract
Background
Targeted amplicon deep sequencing (TADS) has enabled characterization of diverse bacterial communities, yet the application of TADS to communities of parasites has been relatively slow to advance. The greatest obstacle to this has been the genetic diversity of parasitic agents, which include helminths, protozoa, arthropods, and some acanthocephalans. Meanwhile, universal amplification of conserved loci from all parasites without amplifying host DNA has proven challenging. Pan-eukaryotic PCRs preferentially amplify the more abundant host DNA, obscuring parasite-derived reads following TADS. Flaherty et al. (2018) described a pan-parasitic TADS method involving amplification of eukaryotic 18S rDNA regions possessing restriction sites only in vertebrates. Using this method, host DNA in total DNA extracts could be selectively digested prior to PCR using restriction enzymes, thereby increasing the number of parasite-derived reads obtained following NGS. This approach showed promise though was only as sensitive as conventional PCR.
Results
Here, we expand on this work by designing a second set of pan-eukaryotic primers flanking the priming sites already described, enabling nested PCR amplification of the established 18S rDNA target. This nested approach facilitated introduction of a second restriction digestion between the first and second PCR, reducing the proportional mass of amplifiable host-derived DNA while increasing the number of PCR amplification cycles. We applied this method to blood specimens containing Babesia, Plasmodium, various kinetoplastids, and filarial nematodes and confirmed its limit of detection (LOD) to be approximately 10-fold lower than previously described, falling...
Ford, BA, Sullivan, GJ, Moore, L, Varkey, D, Zhu, H, Ostrowski, M, Mabbutt, BC, Paulsen, IT & Shah, BS 2021, 'Functional characterisation of substrate-binding proteins to address nutrient uptake in marine picocyanobacteria', Biochemical Society Transactions, vol. 49, no. 6, pp. 2465-2481.
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Marine cyanobacteria are key primary producers, contributing significantly to the microbial food web and biogeochemical cycles by releasing and importing many essential nutrients cycled through the environment. A subgroup of these, the picocyanobacteria (Synechococcus and Prochlorococcus), have colonised almost all marine ecosystems, covering a range of distinct light and temperature conditions, and nutrient profiles. The intra-clade diversities displayed by this monophyletic branch of cyanobacteria is indicative of their success across a broad range of environments. Part of this diversity is due to nutrient acquisition mechanisms, such as the use of high-affinity ATP-binding cassette (ABC) transporters to competitively acquire nutrients, particularly in oligotrophic (nutrient scarce) marine environments. The specificity of nutrient uptake in ABC transporters is primarily determined by the peripheral substrate-binding protein (SBP), a receptor protein that mediates ligand recognition and initiates translocation into the cell. The recent availability of large numbers of sequenced picocyanobacterial genomes indicates both Synechococcus and Prochlorococcus apportion >50% of their transport capacity to ABC transport systems. However, the low degree of sequence homology among the SBP family limits the reliability of functional assignments using sequence annotation and prediction tools. This review highlights the use of known SBP structural representatives for the uptake of key nutrient classes by cyanobacteria to compare with predicted SBP functionalities within sequenced marine picocyanobacteria genomes. This review shows the broad range of conserved biochemical functions of picocyanobacteria and the range of novel and hypothetical ABC transport systems that require further functional characterisation.
Fowler, AM, Hall, KC, Liggins, GW & Chick, RC 2021, 'Prioritising fished stocks for monitoring and assessment: A decision analysis approach for diverse fisheries of limited commercial value', Ocean & Coastal Management, vol. 199, pp. 105404-105404.
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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'.
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Color centers in hexagonal boron nitride (hBN) are becoming an increasingly
important building block for quantum photonic applications. Herein, we
demonstrate the efficient coupling of recently discovered spin defects in hBN
to purposely designed bullseye cavities. We show that the all monolithic hBN
cavity system exhibits an order of magnitude enhancement in the emission of the
coupled boron vacancy spin defects. In addition, by comparative finite
difference time domain modelling, we shed light on the emission dipole
orientation, which has not been experimentally demonstrated at this point.
Beyond that, the coupled spin system exhibits an enhanced contrast in optically
detected magnetic resonance readout and improved signal to noise ratio. Thus,
our experimental results supported by simulations, constitute a first step
towards integration of hBN spin defects with photonic resonators for a scalable
spin photon interface.
Froehlich, CYM, Klanten, OS, Hing, ML, Dowton, M & Wong, MYL 2021, 'Uneven declines between corals and cryptobenthic fish symbionts from multiple disturbances', Scientific Reports, vol. 11, no. 1.
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AbstractWith the onset and increasing frequency of multiple disturbances, the recovery potential of critical ecosystem-building species and their mutual symbionts is threatened. Similar effects to both hosts and their symbionts following disturbances have been assumed. However, we report unequal declines between hosts and symbionts throughout multiple climate-driven disturbances in reef-building Acropora corals and cryptobenthic coral-dwelling Gobiodon gobies. Communities were surveyed before and after consecutive cyclones (2014, 2015) and heatwaves (2016, 2017). After cyclones, coral diameter and goby group size (i.e., the number of gobies within each coral) decreased similarly by 28–30%. After heatwave-induced bleaching, coral diameter decreased substantially (47%) and gobies mostly inhabited corals singly. Despite several coral species persisting after bleaching, all goby species declined, leaving 78% of corals uninhabited. These findings suggest that gobies, which are important mutual symbionts for corals, are unable to cope with consecutive disturbances. This disproportionate decline could lead to ecosystem-level disruptions through loss of key symbiont services to corals.
Fronzi, M, Isayev, O, Winkler, DA, Shapter, JG, Ellis, AV, Sherrell, PC, Shepelin, NA, Corletto, A & Ford, MJ 2021, 'Active Learning in Bayesian Neural Networks for Bandgap Predictions of Novel Van der Waals Heterostructures', Advanced Intelligent Systems, vol. 3, no. 11, pp. 2100080-2100080.
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Fu, X, Qiang, Y, Wang, J, Zhao, X, Hwang, F-J & 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.
Fujise, L, Suggett, DJ, Stat, M, Kahlke, T, Bunce, M, Gardner, SG, Goyen, S, Woodcock, S, Ralph, PJ, Seymour, JR, Siboni, N & Nitschke, MR 2021, 'Unlocking the phylogenetic diversity, primary habitats, and abundances of free‐living Symbiodiniaceae on a coral reef', Molecular Ecology, vol. 30, no. 1, pp. 343-360.
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Dinoflagellates of the family Symbiodiniaceae form mutualistic symbioses with marine invertebrates such as reef-building corals, but also inhabit reef environments as free-living cells. Most coral species acquire Symbiodiniaceae horizontally from the surrounding environment during the larval and/or recruitment phase, however the phylogenetic diversity and ecology of free-living Symbiodiniaceae on coral reefs is largely unknown. We coupled environmental DNA sequencing and genus-specific qPCR to resolve the community structure and cell abundances of free-living Symbiodiniaceae in the water column, sediment, and macroalgae and compared these to coral symbionts. Sampling was conducted at two time points, one of which coincided with the annual coral spawning event when recombination between hosts and free-living Symbiodiniaceae is assumed to be critical. Amplicons of the internal transcribed spacer (ITS2) region were assigned to 12 of the 15 Symbiodiniaceae genera or genera-equivalent lineages. Community compositions were separated by habitat, with water samples containing a high proportion of sequences corresponding to coral symbionts of the genus Cladocopium, potentially as a result of cell expulsion from in hospite populations. Sediment-associated Symbiodiniaceae communities were distinct, potentially due to the presence of exclusively free-living species. Intriguingly, macroalgal surfaces displayed the highest cell abundances of Symbiodiniaceae, suggesting a key role for macroalgae in ensuring the ecological success of corals through maintenance of a continuum between environmental and symbiotic populations of Symbiodiniaceae.
Gaio, D, DeMaere, MZ, Anantanawat, K, Chapman, TA, Djordjevic, SP & Darling, AE 2021, 'Post-weaning shifts in microbiome composition and metabolism revealed by over 25 000 pig gut metagenome-assembled genomes', Microbial Genomics, vol. 7, no. 8.
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Using a previously described metagenomics dataset of 27 billion reads, we reconstructed over 50 000 metagenome-assembled genomes (MAGs) of organisms resident in the porcine gut, 46.5 % of which were classified as >70 % complete with a <10 % contamination rate, and 24.4 % were nearly complete genomes. Here, we describe the generation and analysis of those MAGs using time-series samples. The gut microbial communities of piglets appear to follow a highly structured developmental programme in the weeks following weaning, and this development is robust to treatments including an intramuscular antibiotic treatment and two probiotic treatments. The high resolution we obtained allowed us to identify specific taxonomic ‘signatures’ that characterize the gut microbial development immediately after weaning. Additionally, we characterized the carbohydrate repertoire of the organisms resident in the porcine gut. We tracked the abundance shifts of 294 carbohydrate active enzymes, and identified the species and higher-level taxonomic groups carrying each of these enzymes in their MAGs. This knowledge can contribute to the design of probiotics and prebiotic interventions as a means to modify the piglet gut microbiome.
Gaio, D, DeMaere, MZ, Anantanawat, K, Eamens, GJ, Liu, M, Zingali, T, Falconer, L, Chapman, TA, Djordjevic, SP & Darling, AE 2021, 'A large-scale metagenomic survey dataset of the post-weaning piglet gut lumen', GigaScience, vol. 10, no. 6.
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Abstract
Background
Early weaning and intensive farming practices predispose piglets to the development of infectious and often lethal diseases, against which antibiotics are used. Besides contributing to the build-up of antimicrobial resistance, antibiotics are known to modulate the gut microbial composition. As an alternative to antibiotic treatment, studies have previously investigated the potential of probiotics for the prevention of postweaning diarrhea. In order to describe the post-weaning gut microbiota, and to study the effects of two probiotics formulations and of intramuscular antibiotic treatment on the gut microbiota, we sampled and processed over 800 faecal time-series samples from 126 piglets and 42 sows.
Results
Here we report on the largest shotgun metagenomic dataset of the pig gut lumen microbiome to date, consisting of >8 Tbp of shotgun metagenomic sequencing data. The animal trial, the workflow from sample collection to sample processing, and the preparation of libraries for sequencing, are described in detail. We provide a preliminary analysis of the dataset, centered on a taxonomic profiling of the samples, and a 16S-based beta diversity analysis of the mothers and the piglets in the first 5 weeks after weaning.
Conclusions
This study was conducted to generate a publicly available databank of the faecal metagenome of weaner piglets aged between 3 and 9 weeks old, treated with different probiotic formulations and intramuscular antibiotic treatment. Besides investigating the effects of the probiotic and intramuscular antibiotic treatment, the dataset can be exp...
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', The ISME Journal, vol. 15, no. 12, pp. 3668-3682.
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AbstractElevated seawater temperatures have contributed to the rise of coral disease mediated by bacterial pathogens, such as the globally distributed Vibrio coralliilyticus, which utilizes coral mucus as a chemical cue to locate stressed corals. However, the physiological events in the pathogens that follow their entry into the coral host environment remain unknown. Here, we present simultaneous measurements of the behavioral and transcriptional responses of V. coralliilyticus BAA-450 incubated in coral mucus. Video microscopy revealed a strong and rapid chemokinetic behavioral response by the pathogen, characterized by a two-fold increase in average swimming speed within 6 min of coral mucus exposure. RNA sequencing showed that this bacterial behavior was accompanied by an equally rapid differential expression of 53% of the genes in the V. coralliilyticus genome. Specifically, transcript abundance 10 min after mucus exposure showed upregulation of genes involved in quorum sensing, biofilm formation, and nutrient metabolism, and downregulation of flagella synthesis and chemotaxis genes. After 60 min, we observed upregulation of genes associated with virulence, including zinc metalloproteases responsible for causing coral tissue damage and algal symbiont photoinactivation, and secretion systems that may export toxins. Together, our results suggest that V. coralliilyticus employs a suite of behavioral and transcriptional responses to rapidly shift into a distinct infection mode within minutes of exposure to the coral microenvironment.
Gao, X, Pandey, S, Kianinia, M, Ahn, J, Ju, P, Aharonovich, I, Shivaram, N & Li, T 2021, 'Femtosecond Laser Writing of Spin Defects in Hexagonal Boron Nitride', ACS Photonics, vol. 8, no. 4, pp. 994-1000.
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Garczarek, L, Guyet, U, Doré, H, Farrant, GK, Hoebeke, M, Brillet-Guéguen, L, Bisch, A, Ferrieux, M, Siltanen, J, Corre, E, Le Corguillé, 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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Abstract
Cyanorak v2.1 (http://www.sb-roscoff.fr/cyanorak) is an information system dedicated to visualizing, comparing and curating the genomes of Prochlorococcus, Synechococcus and Cyanobium, the most abundant photosynthetic microorganisms on Earth. The database encompasses sequences from 97 genomes, covering most of the wide genetic diversity known so far within these groups, and which were split into 25,834 clusters of likely orthologous groups (CLOGs). The user interface gives access to genomic characteristics, accession numbers as well as an interactive map showing strain isolation sites. The main entry to the database is through search for a term (gene name, product, etc.), resulting in a list of CLOGs and individual genes. Each CLOG benefits from a rich functional annotation including EggNOG, EC/K numbers, GO terms, TIGR Roles, custom-designed Cyanorak Roles as well as several protein motif predictions. Cyanorak also displays a phyletic profile, indicating the genotype and pigment type for each CLOG, and a genome viewer (Jbrowse) to visualize additional data on each genome such as predicted operons, genomic islands or transcriptomic data, when available. This information system also includes a BLAST search tool, comparative genomic context as well as various data export options. Altogether, Cyanorak v2.1 constitutes an invaluable, scalable tool for comparative genomics of ecologically relevant marine microorganisms.
Geange, SR, Arnold, PA, Catling, AA, Coast, O, Cook, AM, Gowland, KM, Leigh, A, Notarnicola, RF, Posch, BC, Venn, SE, Zhu, L & Nicotra, AB 2021, 'The thermal tolerance of photosynthetic tissues: a global systematic review and agenda for future research', New Phytologist, vol. 229, no. 5, pp. 2497-2513.
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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, vol. 1637, pp. 461860-461860.
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Gibbs, MC, Parker, LM, Scanes, E, Byrne, M, O’Connor, WA & Ross, PM 2021, 'Adult exposure to ocean acidification and warming leads to limited beneficial responses for oyster larvae', ICES Journal of Marine Science, vol. 78, no. 6, pp. 2017-2030.
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Abstract
There is a need to understand the responses of marine molluscs in this era of rapid climate change. Transgenerational plasticity that results in resilient offspring provides a mechanism for rapid acclimation of marine organisms to climate change. This study tested the hypothesis that adult parental exposure to elevated pCO2 and warming will have transgenerational benefits for offspring in the oysters Saccostrea glomerata and Crassostrea gigas. Adult S. glomerata and C. gigas were exposed to orthogonal treatments of ambient and elevated pCO2, and ambient and elevated temperature for 8 weeks. Gametes were collected and fertilized, larvae were then reared for 9 days under ambient and elevated pCO2. Egg lipidome and larval morphology and lipidome were measured. Parental exposure to warming and elevated pCO2 led to limited beneficial transgenerational responses for eggs and larvae of S. glomerata and C. gigas. Overall, larvae of S. glomerata were more sensitive than C. gigas, and both species had some capacity for transgenerational plasticity. This study supports the idea that transgenerational plasticity acts as an acclimatory mechanism for marine organisms to cope with the stress of climate change, but there are limitations, and it may not be a panacea or act equally in different species.
Gibbs, MC, Parker, LM, Scanes, E, Byrne, M, O’Connor, WA & Ross, PM 2021, 'Adult exposure to ocean acidification and warming remains beneficial for oyster larvae following starvation', ICES Journal of Marine Science, vol. 78, no. 5, pp. 1587-1598.
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Abstract
Climate change is expected to warm and acidify oceans and alter the phenology of phytoplankton, creating a mismatch between larvae and their food. Transgenerational plasticity (TGP) may allow marine species to acclimate to climate change; however, it is expected that this may come with elevated energetic demands. This study used the oysters, Saccostrea glomerata and Crassostrea gigas, to test the effects of adult parental exposure to elevated pCO2 and temperature on larvae during starvation and recovery. It was anticipated that beneficial effects of TGP will be limited when larvae oyster are starved. Transgenerational responses and lipid reserves of larvae were measured for 2 weeks. Larvae of C. gigas and S. glomerata from parents exposed to elevated pCO2 had greater survival when exposed to elevated CO2, but this differed between species and temperature. For S. glomerata, survival of larvae was greatest when the conditions experienced by larvae matched the condition of their parents. For C. gigas, survival of larvae was greater when parents and larvae were exposed to elevated pCO2. Larvae of both species used lipids when starved. The total lipid content was dependent on parental exposure and temperature. Against expectations, the beneficial TGP responses of larvae remained, despite starvation.
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, pp. 112441-112441.
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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, D, Horvat, JC, Walker, MM & 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, vol. 320, no. 4, pp. G420-G438.
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HIF-1 plays an important role in epithelial restitution, selectively inducing integrins α6 and α2 to promote migration and proliferation, respectively. HIF-stabilizing prolyl-hydroxylase inhibitors accelerate intestinal mucosal healing by inducing epithelial integrin expression.
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, pp. 462423-462423.
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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.
Gonzalez de Vega, R, 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, pp. 338737-338737.
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Goodswen, SJ, Barratt, JLN, Kennedy, PJ, Kaufer, A, Calarco, L & Ellis, JT 2021, 'Machine learning and applications in microbiology', FEMS Microbiology Reviews, vol. 45, no. 5.
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ABSTRACT
To understand the intricacies of microorganisms at the molecular level requires making sense of copious volumes of data such that it may now be humanly impossible to detect insightful data patterns without an artificial intelligence application called machine learning. Applying machine learning to address biological problems is expected to grow at an unprecedented rate, yet it is perceived by the uninitiated as a mysterious and daunting entity entrusted to the domain of mathematicians and computer scientists. The aim of this review is to identify key points required to start the journey of becoming an effective machine learning practitioner. These key points are further reinforced with an evaluation of how machine learning has been applied so far in a broad scope of real-life microbiology examples. This includes predicting drug targets or vaccine candidates, diagnosing microorganisms causing infectious diseases, classifying drug resistance against antimicrobial medicines, predicting disease outbreaks and exploring microbial interactions. Our hope is to inspire microbiologists and other related researchers to join the emerging machine learning revolution.
Goodswen, SJ, Kennedy, PJ & Ellis, JT 2021, 'Applying Machine Learning to Predict the Exportome of Bovine and Canine Babesia Species That Cause Babesiosis', Pathogens, vol. 10, no. 6, pp. 660-660.
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Babesia infection of red blood cells can cause a severe disease called babesiosis in susceptible hosts. Bovine babesiosis causes global economic loss to the beef and dairy cattle industries, and canine babesiosis is considered a clinically significant disease. Potential therapeutic targets against bovine and canine babesiosis include members of the exportome, i.e., those proteins exported from the parasite into the host red blood cell. We developed three machine learning-derived methods (two novel and one adapted) to predict for every known Babesia bovis, Babesia bigemina, and Babesia canis protein the probability of being an exportome member. Two well-studied apicomplexan-related species, Plasmodium falciparum and Toxoplasma gondii, with extensive experimental evidence on their exportome or excreted/secreted proteins were used as important benchmarks for the three methods. Based on 10-fold cross validation and multiple train–validation–test splits of training data, we expect that over 90% of the predicted probabilities accurately provide a secretory or non-secretory indicator. Only laboratory testing can verify that predicted high exportome membership probabilities are creditable exportome indicators. However, the presented methods at least provide those proteins most worthy of laboratory validation and will ultimately save time and money.
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, vol. 12, no. 1.
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AbstractSpin defects in solid-state materials are strong candidate systems for quantum information technology and sensing applications. Here we explore in details the recently discovered negatively charged boron vacancies (VB−) in hexagonal boron nitride (hBN) and demonstrate their use as atomic scale sensors for temperature, magnetic fields and externally applied pressure. These applications are possible due to the high-spin triplet ground state and bright spin-dependent photoluminescence of the VB−. Specifically, we find that the frequency shift in optically detected magnetic resonance measurements is not only sensitive to static magnetic fields, but also to temperature and pressure changes which we relate to crystal lattice parameters. We show that spin-rich hBN films are potentially applicable as intrinsic sensors in heterostructures made of functionalized 2D materials.
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, vol. 7, no. 14.
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Atomic defects in 2D materials show excellent spin coherence time and become promising contenders for quantum applications.
Green, DW, Watson, JA, Ben-Nissan, B, Watson, GS & Stamboulis, A 2021, 'Synthetic tissue engineering with smart, cytomimetic protocells', Biomaterials, vol. 276, pp. 120941-120941.
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Greene, RW & Haynes, S 2021, 'An Alternative to Exclusionary Discipline', Childhood Education, vol. 97, no. 5, pp. 72-76.
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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, no. 1.
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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, Woesik, R, Vega Thurber, R, Warner, ME, McLachlan, RH, Price, JT, Bahr, KD, Baums, IB, Castillo, KD, Coffroth, MA, Cunning, R, Dobson, KL, Donahue, MJ, Hench, JL, Iglesias‐Prieto, R, Kemp, DW, Kenkel, CD, Kline, DI, Kuffner, IB, Matthews, JL, Mayfield, AB, Padilla‐Gamiño, JL, Palumbi, S, Voolstra, CR, Weis, VM & Wu, HC 2021, 'Increasing comparability among coral bleaching experiments', Ecological Applications, vol. 31, no. 4.
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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, 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, vol. 15, no. 9, pp. 712-712.
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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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Guo, Z, Qiu, S, Li, H, Xu, Y, Langford, SJ & Sun, C 2021, 'Electrocatalytic Nitrogen Reduction Performance of Si‐doped 2D Nanosheets of Boron Nitride Evaluated via Density Functional Theory', ChemCatChem, vol. 13, no. 4, pp. 1239-1245.
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Guo, Z, Qiu, S, Li, H, Xu, Y, Langford, SJ & Sun, C 2021, 'Evaluation of electrocatalytic dinitrogen reduction performance on diamond carbon via density functional theory', Diamond and Related Materials, vol. 111, pp. 108210-108210.
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Gupta, A, Corzo, R, Akmeemana, A, Lambert, K, Jimenez, K, Curran, JM & Almirall, JR 2021, 'Dimensionality reduction of multielement glass evidence to calculate likelihood ratios', Journal of Chemometrics, vol. 35, no. 1.
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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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Gupta, G, Chellappan, DK, Singh, SK, Gupta, PK, Kesari, KK, Jha, NK, Thangavelu, L, G Oliver, B & Dua, K 2021, 'Advanced drug delivery approaches in managing TGF-β-mediated remodeling in lung diseases', Nanomedicine, vol. 16, no. 25, pp. 2243-2247.
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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, vol. 10, no. 2, pp. 194-194.
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Superficial dermatophyte infections, commonly known as tineas, are the most prevalent fungal ailment and are increasing in incidence, leading to an interest in alternative treatments. Many floral honeys possess antimicrobial activity due to high sugar, low pH, and the production of hydrogen peroxide (H2O2) from the activity of the bee-derived enzyme glucose oxidase. Australian jarrah (Eucalyptus marginata) honey produces particularly high levels of H2O2 and has been found to be potently antifungal. This study characterized the activity of jarrah honey on fungal dermatophyte species. Jarrah honey inhibited dermatophytes with minimum inhibitory concentrations (MICs) of 1.5–3.5% (w/v), which increased to ≥25% (w/v) when catalase was added. Microscopic analysis found jarrah honey inhibited the germination of Trichophyton rubrum conidia and scanning electron microscopy of mature T. rubrum hyphae after honey treatment revealed bulging and collapsed regions. When treated hyphae were stained using REDOX fluorophores these did not detect any internal oxidative stress, suggesting jarrah honey acts largely on the hyphal surface. Although H2O2 appears critical for the antifungal activity of jarrah honey and its action on fungal cells, these effects persisted when H2O2 was eliminated and could not be replicated using synthetic honey spiked with H2O2, indicating jarrah honey contains agents that augment antifungal activity.
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, vol. 3, no. 3.
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Many Australian native honeys possess significant antimicrobial properties due to the production of hydrogen peroxide (H2O2) by glucose oxidase, an enzyme derived from the honeybee. The level of H2O2 produced in different honey samples is highly variable, and factors governing its production and stability are not well understood. In this study, highly active Australian honeys that had been stored for >10 years lost up to 54 % of their antibacterial activity, although almost all retained sufficient activity to be considered potentially therapeutically useful. We used a simple colourimetric assay to quantify H2O2 production. Although we found a significant correlation between H2O2 production and antibacterial activity across diverse honey samples, variation in H2O2 only explained 47 % of the variation observed in activity, limiting the assay as a screening tool and highlighting the complexity of the relationship between H2O2 and the killing power of honey. To further examine this, we tested whether H2O2 detection in honey was being inhibited by pigmented compounds and if H2O2 might be directly degraded in some honey samples. We found no correlation between H2O2 detection and honey colour. Some honey samples rapidly lost endogenous and spiked H2O2, suggesting that components in honey, such as catalase or antioxidant polyphenols, may degrade or quench H2O2. Despite this rapid loss of H2O2, these honeys had significant peroxide-based antibacterial activity, indic...
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, vol. 102, pp. 101848-101848.
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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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Acinetobacter baumanniiis a successful opportunistic pathogen that can compete for iron under iron-limiting conditions. Here, large novel transposons that carry genes for synthesis and transport of the fimsbactin siderophores present in someA. baumanniistrains were examined. Tn6171, originally found in theA. baumanniiglobal clone 1 (GC1) lineage 2 isolate D36, includestnsgenes encoding proteins related to the TnsA, TnsB, TnsC transposition proteins (50–59 % identity), TnsD targeting protein (43 % identity) and TnsE (31 % identity) of Tn7, and is found in the chromosome downstream of theglmSgene, the preferred location for Tn7, flanked by a 5 bp target site duplication. Tn6171is bounded by 29 bp inverted repeats and, like Tn7, includes additional TnsB binding sites at each end. Tn6171or minor variants were detected in the equivalent location in complete or draft genomes of several further
Hamidian, M, Ambrose, SJ, Blackwell, GA, Nigro, SJ & Hall, RM 2021, 'An outbreak of multiply antibiotic-resistant ST49:ST128:KL11:OCL8Acinetobacter baumanniiisolates at a Sydney hospital', Journal of Antimicrobial Chemotherapy, vol. 76, no. 4, pp. 893-900.
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AbstractObjectivesTo understand the acquisition of resistance genes by a non-GC1, non-GC2 Acinetobacter baumannii strain responsible for a 4 year outbreak at a Sydney hospital.MethodsRepresentative isolates were screened for resistance to antibiotics. Three were subjected to WGS using Illumina HiSeq. One genome was completed with MinION long reads. Resistance regions were compared with known sequences using bioinformatics.ResultsIsolates were resistant to third-generation cephalosporins, gentamicin and tobramycin, sulfamethoxazole and erythromycin. Sequenced isolates were ST49 (Institut Pasteur scheme) and ST128 (Oxford scheme) and carried KL11 at the capsule locus and OCL8 at the lipooligosaccharide outer core locus. The complete genome of isolate J9 revealed that the resistance genes were all in plasmids; pRAY* contained aadB, and a large plasmid, pJ9-3, contained sul2 and floR genes and a dif module containing the mph(E)-msr(E) macrolide resistance genes. Transposon Tn6168, consisting of a second copy of the chromosomal ampC gene region flanked by ISAba1s, confers resistance to third-generation cephalosporins. Tn6168 is located inside the mph(E)-msr(E) dif module. pJ9-3 includes a set of four dif modules and the orientation of the pdif sites, XerC-XerD or XerD-XerC, alternates. A large transposon, Tn6175, containing tniCABDE transposition genes and genes annotated as being involved in heavy metal metabolism, uptake or export was found in the comM gene. Other ST49:ST128:KL11:OCL8 genomes found in the GenBank WGS database carried Tn6175 but neither of the plasmids carrying the resistance genes.ConclusionsAn early carbapenem-susceptible A. baumannii outbreak recorded in Australia was caused by an unusual clone ...
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, vol. 9, no. 1, pp. 349-362.e18.
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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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Curcumin is a major curcuminoid present in turmeric. The compound is attributed to various therapeutic
properties, which include anti-oxidant, anti-inflammatory, anti-bacterial, anti-malarial, and neuroprotection.
Due to its therapeutic potential, curcumin has been employed for centuries in treating different ailments. Curcumin
has been investigated lately as a novel therapeutic agent in the treatment of cancer. However, the mechanisms
by which curcumin exerts its cytotoxic effects on malignant cells are still not fully understood. One of the
main limiting factors in the clinical use of curcumin is its poor bioavailability and rapid elimination. Advancements
in drug delivery systems such as nanoparticle-based vesicular drug delivery platforms have improved several
parameters, namely, drug bioavailability, solubility, stability, and controlled release properties. The use of
curcumin-encapsulated niosomes to improve the physical and pharmacokinetic properties of curcumin is one such
approach. This review provides an up-to-date summary of nanoparticle-based vesicular drug carriers and their
therapeutic applications. Specifically, we focus on niosomes as novel drug delivery formulations and their potential
in improving the delivery of challenging small molecules, including curcumin. Overall, the applications of
such carriers will provide a new direction for novel pharmaceutical drug delivery, as well as for biotechnology,
nutraceutical, and functional food industries.
Hasan, M, Altaf, M, Zafar, A, Hassan, SG, Ali, Z, Mustafa, G, Munawar, T, Saif, MS, Tariq, T, Iqbal, F, Khan, MW, Mahmood, A, Mahmood, N & Shu, X 2021, 'Bioinspired synthesis of zinc oxide nano-flowers: A surface enhanced antibacterial and harvesting efficiency', Materials Science and Engineering: C, vol. 119, pp. 111280-111280.
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Hasan, M, Gulzar, H, Zafar, A, ul Haq, A, Mustafa, G, Tariq, T, Khalid, A, Mahmmod, A, Shu, X & Mahmood, N 2021, 'Multiplexing surface anchored functionalized iron carbide nanoparticle: A low molecular weight proteome responsive nano-tracer', Colloids and Surfaces B: Biointerfaces, vol. 203, pp. 111746-111746.
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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, pp. 147602-147602.
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Häußler, S, Bayer, G, Waltrich, R, Mendelson, N, Li, C, Hunger, D, Aharonovich, I & Kubanek, A 2021, 'Tunable Fiber‐Cavity Enhanced Photon Emission from Defect Centers in hBN', Advanced Optical Materials, vol. 9, no. 17, pp. 2002218-2002218.
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Realization of quantum photonic devices requires coupling single quantum emitters to the mode of optical resonators. In this work, a hybrid system consisting of defect centers in few-layer hexagonal boron nitride (hBN) grown by chemical vapor deposition and a fiber-based Fabry–Pérot cavity is presented. The sub 10-nm thickness of hBN and its smooth surface enable efficient integration into the cavity mode. This hybrid platform is operated over a broad spectral range larger than 30 nm and its tuneability is used to explore different coupling regimes. Consequently, very large cavity-assisted signal enhancement up to 50-fold and strongly narrowed linewidths are achieved, which is owing to cavity funneling, a record for hBN-cavity systems. Additionally, an excitation and readout scheme is implemented for resonant excitation that allows to establish cavity-assisted photoluminescence excitation (PLE) spectroscopy. This work marks an important milestone for the deployment of 2D materials coupled to fiber-based cavities in practical quantum technologies.
Haydon, TD, Seymour, JR, Raina, J-B, Edmondson, J, Siboni, N, Matthews, JL, Camp, EF & Suggett, DJ 2021, 'Rapid Shifts in Bacterial Communities and Homogeneity of Symbiodiniaceae in Colonies of Pocillopora acuta Transplanted Between Reef and Mangrove Environments', Frontiers in Microbiology, vol. 12.
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It has been proposed that an effective approach for predicting whether and how reef-forming corals persist under future climate change is to examine populations thriving in present day extreme environments, such as mangrove lagoons, where water temperatures can exceed those of reef environments by more than 3°C, pH levels are more acidic (pH < 7.9, often below 7.6) and O2 concentrations are regularly considered hypoxic (<2 mg/L). Defining the physiological features of these “extreme” corals, as well as their relationships with the, often symbiotic, organisms within their microbiome, could increase our understanding of how corals will persist into the future. To better understand coral-microbe relationships that potentially underpin coral persistence within extreme mangrove environments, we therefore conducted a 9-month reciprocal transplant experiment, whereby specimens of the coral Pocillopora acuta were transplanted between adjacent mangrove and reef sites on the northern Great Barrier Reef. Bacterial communities associated with P. acuta specimens native to the reef environment were dominated by Endozoicomonas, while Symbiodiniaceae communities were dominated by members of the Cladocopium genus. In contrast, P. acuta colonies native to the mangrove site exhibited highly diverse bacterial communities with no dominating members, and Symbiodiniaceae communities dominated by Durusdinium. All corals survived for 9 months after being transplanted from reef-to-mangrove, mangrove-to-reef environments (as well as control within environment transplants), and during this time there were significant changes in the bacterial communities, but not in the Symbiodiniaceae communities or their photo-physiological functioning. In reef-to-mangrove transplanted corals, there were ...
Hayward, RJ, Humphrys, MS, Huston, WM & Myers, GSA 2021, 'Dual RNA-seq analysis of in vitro infection multiplicity and RNA depletion methods in Chlamydia-infected epithelial cells', Scientific Reports, vol. 11, no. 1.
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AbstractDual RNA-seq experiments examining viral and bacterial pathogens are increasing, but vary considerably in their experimental designs, such as infection rates and RNA depletion methods. Here, we have applied dual RNA-seq to Chlamydia trachomatis infected epithelial cells to examine transcriptomic responses from both organisms. We compared two time points post infection (1 and 24 h), three multiplicity of infection (MOI) ratios (0.1, 1 and 10) and two RNA depletion methods (rRNA and polyA). Capture of bacterial-specific RNA were greatest when combining rRNA and polyA depletion, and when using a higher MOI. However, under these conditions, host RNA capture was negatively impacted. Although it is tempting to use high infection rates, the implications on host cell survival, the potential reduced length of infection cycles and real world applicability should be considered. This data highlights the delicate nature of balancing host–pathogen RNA capture and will assist future transcriptomic-based studies to achieve more specific and relevant infection-related biological insights.
He, Y, Zhang, Y, Liao, Y, Dennis, ES, Peacock, WJ & Wu, X 2021, 'Rice hybrid mimics have stable yields equivalent to those of the F1 hybrid and suggest a basis for hybrid vigour', Planta, vol. 254, no. 3.
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Hegarty, A, Stewart, J & Gladstone, W 2021, 'Reproductive strategies of a temperate Australian sciaenid (teraglin, Atractoscion atelodus )', Journal of Applied Ichthyology, vol. 37, no. 5, pp. 735-747.
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Herdean, A, Hall, CC, Pham, LL, Macdonald Miller, S, 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 (BBA) - Bioenergetics, vol. 1862, no. 9, pp. 148461-148461.
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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, vol. 21, no. 10, pp. 3461-3461.
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Recently, there has been an increase in the production of devices to monitor mental health and stress as means for expediting detection, and subsequent management of these conditions. The objective of this review is to identify and critically appraise the most recent smart devices and wearable technologies used to identify depression, anxiety, and stress, and the physiological process(es) linked to their detection. The MEDLINE, CINAHL, Cochrane Central, and PsycINFO databases were used to identify studies which utilised smart devices and wearable technologies to detect or monitor anxiety, depression, or stress. The included articles that assessed stress and anxiety unanimously used heart rate variability (HRV) parameters for detection of anxiety and stress, with the latter better detected by HRV and electroencephalogram (EGG) together. Electrodermal activity was used in recent studies, with high accuracy for stress detection; however, with questionable reliability. Depression was found to be largely detected using specific EEG signatures; however, devices detecting depression using EEG are not currently available on the market. This systematic review highlights that average heart rate used by many commercially available smart devices is not as accurate in the detection of stress and anxiety compared with heart rate variability, electrodermal activity, and possibly respiratory rate.
Hiscocks, HG, Yit, DL, Pascali, G & Ung, AT 2021, 'Incorporation of the pentafluorosulfanyl group through common synthetic transformations', Monatshefte für Chemie - Chemical Monthly, vol. 152, no. 4, pp. 449-459.
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Holland, MM, Everett, JD, Cox, MJ, Doblin, MA & Suthers, IM 2021, 'Pelagic forage fish distribution in a dynamic shelf ecosystem – Thermal demands and zooplankton prey distribution', Estuarine, Coastal and Shelf Science, vol. 249, pp. 107074-107074.
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Honey, R, McLean, C, Murray, BR & Webb, JK 2021, 'Insulated nest boxes provide thermal refuges for wildlife in urban bushland during summer heatwaves', Journal of Urban Ecology, vol. 7, no. 1.
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Abstract
In urban bushland, the installation of nest boxes is widely used to compensate for the loss of natural tree hollows. However, current nest box designs may not provide thermal refuges for wildlife during summer heatwaves, particularly if internal temperatures exceed the upper critical temperatures of wildlife. We investigated whether the addition of roofing insulation to nest boxes deployed for sugar gliders (Petaurus breviceps) and squirrel gliders (Petaurus norfolcensis) in urban bushland would reduce internal nest box temperatures during summer heatwaves. We measured temperatures of 44 insulated and 47 uninsulated nest boxes during one of the hottest summers on record (2018–2019) in the Lake Macquarie region of NSW, Australia, a period during which several prolonged heatwaves occurred. Over the 90-day study, maximum temperatures were, on average, 3.1°C lower in insulated boxes than in uninsulated boxes. The addition of insulation significantly lowered nest box temperatures regardless of aspect (north or south facing) or day of measurement. Temperatures exceeded the upper critical temperature (35.1°C) of gliders more frequently in uninsulated nest boxes (28% of days) than in insulated nest boxes (8% days). Although the addition of insulation to nest boxes lowered their internal temperatures, during heatwaves spanning 23 days, nest box temperatures exceeded the upper critical temperatures of gliders on 58% and 23% of days in uninsulated and insulated nest boxes respectively. These findings underscore the importance of retaining natural hollows in urban bushland to provide thermally suitable refuges for wildlife during extreme heat events.
Honey, R, McLean, CM, Murray, BR, Callan, MN & Webb, JK 2021, 'Choice of monitoring method can influence estimates of usage of artificial hollows by vertebrate fauna', Australian Journal of Zoology, vol. 69, no. 1, pp. 18-18.
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The loss of hollow-bearing trees is a key threat for many hollow-dependent taxa. Nesting boxes have been widely used to offset tree hollow loss, but they have high rates of attrition, and, often, low rates of usage by target species. To counter these problems, chainsaw carved hollows (artificial cavities cut into trees) have become a popular alternative, yet little research has been published on their effectiveness. We examined the usage of 150 chainsaw carved hollows by cavity-dependent fauna in the central west of New South Wales using observations from traditional inspection methods and remote cameras. Between October 2017 and April 2019, we detected 21 species of vertebrates (two reptile, one amphibian, 10 bird, and eight mammal species) inside chainsaw carved hollows, but the number of species detected was dependent on the chosen monitoring method. We detected six species inside hollows during physical inspections, whereas remote cameras detected 21 species entering hollows. Cameras detected eight species using hollows as breeding sites, whereas physical inspections detected just four species. Cameras detected two threatened mammals (squirrel glider (Petaurus norfolcensis) and greater glider (Petauroides volans)) raising young inside hollows, yet we failed to detect these species during physical inspections. For birds, the two methods yielded equivalent results for detection of breeding events. Overall, our study showed that few cavity-dependent species used chainsaw carved hollows as breeding sites. This highlights how artificial hollows are not a substitute for retaining naturally occurring hollows in large trees and revegetation programs.
Horstmann, M, Gonzalez de Vega, R, 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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Speciation analysis of Gd-based MRI contrast agents in fresh and oceanic waters employing an automatised micro-solid phase extraction method and HILIC-ICP-MS detection operating an increased mass bandpass.
Hossain, MA, Brito-Rodriguez, B, Sedger, LM & Canning, J 2021, 'A Cross-Disciplinary View of Testing and Bioinformatic Analysis of SARS-CoV-2 and Other Human Respiratory Viruses in Pandemic Settings', IEEE Access, vol. 9, pp. 163716-163734.
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Hossain, MJ, Kendig, MD, Wild, BM, Morris, MJ & Arnold, R 2021, 'Effects of Diet Reversal on Metabolic and Peripheral Neuropathy Endpoints in a Rat Model of Cafeteria Diet-Induced Obesity', Metabolism, vol. 116, pp. 154638-154638.
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Hossain, R, Ahmed, AJ, Yun, FF, Sang, L, Islam, SMKN, Yang, G, Cortie, MB & Wang, X 2021, 'Significant enhancement of electrical conductivity by incorporating carbon fiber into CoSb3 thermoelectric skutterudite fabricated by spark plasma sintering method', Journal of Materials Science, vol. 56, no. 36, pp. 20138-20153.
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Hossain, SI, Luo, Z, Deplazes, E & Saha, SC 2021, 'Shape matters—the interaction of gold nanoparticles with model lung surfactant monolayers', Journal of The Royal Society Interface, vol. 18, no. 183.
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The lung surfactant monolayer (LSM) forms the main biological barrier for any inhaled particles to enter our bloodstream, including gold nanoparticles (AuNPs) present as air pollutants and under investigation for use in biomedical applications. Understanding the interaction of AuNPs with lung surfactant can assist in understanding how AuNPs enter our lungs. In this study, we use coarse-grained molecular dynamics simulations to investigate the effect of four different shape D AuNPs (spherical, box, icosahedron and rod) on the structure and dynamics of a model LSM, with a particular focus on differences resulting from the shape of the AuNP. Monolayer-AuNP systems were simulated in two different states: the compressed state and the expanded state, representing inhalation and exhalation conditions, respectively. Our results indicate that the compressed state is more affected by the presence of the AuNPs than the expanded state. Our results show that in the compressed state, the AuNPs prevent the monolayer from reaching the close to zero surface tension required for normal exhalation. In the compressed state, all four nanoparticles (NPs) reduce the lipid order parameters and cause a thinning of the monolayer where the particles drag surfactant molecules into the water phase. Comparing the different properties shows no trend concerning which shape has the biggest effect on the monolayer, as shape-dependent effects vary among the different properties. Insights from this study might assist future work of how AuNP shapes affect the LSM during inhalation or exhalation conditions.
Hosseini, F, Lotfalizadeh, H, Rakhshani, E, Norouzi, M, Butterworth, NJ & Dadpour, M 2021, 'Significance of wing interference patterns as taxonomic characters in Aphidiinae (Hymenoptera: Braconidae)', Journal of Zoological Systematics and Evolutionary Research, vol. 59, no. 7, pp. 1481-1490.
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Howlett, L, Camp, EF, Edmondson, J, Henderson, N & Suggett, DJ 2021, 'Coral growth, survivorship and return-on-effort within nurseries at high-value sites on the Great Barrier Reef', PLOS ONE, vol. 16, no. 1, pp. e0244961-e0244961.
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Coral reefs are deteriorating worldwide prompting reef managers and stakeholders to increasingly explore new management tools. Following back-to-back bleaching in 2016/2017, multi-taxa coral nurseries were established in 2018 for the first time on the Great Barrier Reef (GBR) to aid reef maintenance and restoration at a “high-value” location–Opal Reef–frequented by the tourism industry. Various coral species (n = 11) were propagated within shallow water (ca. 4-7m) platforms installed across two sites characterised by differing environmental exposure–one adjacent to a deep-water channel (Blue Lagoon) and one that was relatively sheltered (RayBan). Growth rates of coral fragments placed onto nurseries were highly variable across taxa but generally higher at Blue Lagoon (2.1–10.8 cm2 month-1 over 12 months) compared to RayBan (0.6–6.6 cm2 month-1 over 9 months). Growth at Blue Lagoon was largely independent of season, except for Acropora tenuis and Acropora hyacinthus, where growth rates were 15–20% higher for December 2018-July 2019 (“warm season”) compared to August-December 2018 (“cool season”). Survivorship across all 2,536 nursery fragments was ca. 80–100%, with some species exhibiting higher survivorship at Blue Lagoon (Acropora loripes, Porites cylindrica) and others at RayBan (A. hyacinthus, Montipora hispida). Parallel measurements of growth and survivorship were used to determine relative return-on-effort (RRE) scores as an integrated metric of “success” accounting for life history trade-offs, complementing the mutually exclusive assessment of growth or survivorship. RRE scores within sites (across species) were largely driven by growth, whereas RRE scores between sites were large...
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, pp. 559-559.
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Chronic inflammation of the gastrointestinal (GI) tract contributes to colorectal cancer (CRC) progression. While the role of adaptive T cells in CRC is now well established, the role of innate immune cells, specifically innate lymphoid cells (ILCs), is not well understood. To define the role of ILCs in CRC we employed complementary heterotopic and chemically-induced CRC mouse models. We discovered that ILCs were abundant in CRC tumours and contributed to anti-tumour immunity. We focused on ILC2 and showed that ILC2-deficient mice developed a higher tumour burden compared with littermate wild-type controls. We generated an ILC2 gene signature and using machine learning models revealed that CRC patients with a high intratumor ILC2 gene signature had a favourable clinical prognosis. Collectively, our results highlight a critical role for ILC2 in CRC, suggesting a potential new avenue to improve clinical outcomes through ILC2-agonist based therapeutic approaches.
Huang, T, Yang, M, Zeng, Y, Huang, X, Wang, N, Chen, Y, Li, P, Yuan, J, Chen, C, Oliver, BG & Yi, C 2021, 'Maternal High Fat Diet Consumption Exaggerates Metabolic Disorders in Mice With Cigarette-Smoking Induced Intrauterine Undernutrition', Frontiers in Nutrition, vol. 8.
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Objectives: Maternal smoking causes fetal underdevelopment and results in births which are small for gestation age due to intrauterine undernutrition, leading to various metabolic disorders in adulthood. Furthermore, postnatal high fat diet (HFD) consumption is also a potent obesogenic factor, which can interact with maternal smoking. In this study, we aimed to determine whether maternal HFD consumption during pregnancy can reverse the adverse impact of maternal smoking and change the response to postnatal HFD consumption.Methods: Female mice were exposed to cigarette smoke (SE, 2 cigarettes/day) or sham exposed for 5 weeks before mating, with half of the SE dams fed HFD (43% fat, SE+HFD). The same treatment continued throughout gestation and lactation. Male offspring from each maternal group were fed the same HFD or chow after weaning and sacrificed at 13 weeks.Results: Maternal SE alone increased body weight and fat mass in HFD-fed offspring, while SE+HFD offspring showed the highest energy intake and glucose metabolic disorder in adulthood. In addition, postnatal HFD increased the body weight and aggravated the metabolic disorder caused by maternal SE and SE+HFD.Conclusions: Maternal HFD consumption could not ameliorate the adverse effect of maternal SE but exaggerate metabolic disorders in adult offspring. Smoking cessation and a healthy diet are needed during pregnancy to optimize the health outcome in the offspring.
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 Biology, vol. 5, no. 5, pp. 2000134-2000134.
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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, vol. 14.
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Astrocytes play a crucial role in the maintenance of the normal functions of the Central Nervous System (CNS). During the pathogenesis of neurodegenerative diseases, astrocytes undergo morphological and functional remodeling, a process called reactive astrogliosis, in response to the insults to the CNS. One of the key aspects of the reactive astrocytes is the change in the expression and function of connexins. Connexins are channel proteins that highly expressed in astrocytes, forming gap junction channels and hemichannels, allowing diffusional trafficking of small molecules. Alterations of astrocytic connexin expression and function found in neurodegenerative diseases have been shown to affect the disease progression by changing neuronal function and survival. In this review, we will summarize the role of astroglial connexins in neurodegenerative diseases including Alzheimer’s disease, Huntington’s disease, Parkinson’s disease, and amyotrophic lateral sclerosis. Also, we will discuss why targeting connexins can be a plausible therapeutic strategy to manage these neurodegenerative diseases.
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.
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Abstract
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 micr...
Hughes, DJ, Giannini, FC, Ciotti, AM, Doblin, MA, Ralph, PJ, Varkey, D, Verma, A & Suggett, DJ 2021, 'Taxonomic Variability in the Electron Requirement for Carbon Fixation Across Marine Phytoplankton', Journal of Phycology, vol. 57, no. 1, pp. 111-127.
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Fast Repetition Rate fluorometry (FRRf) has been increasingly used to measure marine primary productivity by oceanographers to understand how carbon (C) uptake patterns vary over space and time in the global ocean. As FRRf measures electron transport rates through photosystem II (ETRPSII ), a critical, but difficult to predict conversion factor termed the "electron requirement for carbon fixation" (Φe,C ) is needed to scale ETRPSII to C-fixation rates. Recent studies have generally focused on understanding environmental regulation of Φe,C , while taxonomic control has been explored by only a handful of laboratory studies encompassing a limited diversity of phytoplankton species. We therefore assessed Φe,C for a wide range of marine phytoplankton (n = 17 strains) spanning multiple taxonomic and size classes. Data mined from previous studies were further considered to determine whether Φe,C variability could be explained by taxonomy versus other phenotypic traits influencing growth and physiological performance (e.g., cell size). We found that Φe,C exhibited considerable variability (~4-10 mol e- · [mol C]-1 ) and was negatively correlated with growth rate (R2 = 0.7, P < 0.01). Diatoms exhibited a lower Φe,C compared to chlorophytes during steady-state, nutrient-replete growth. Inclusion of meta-analysis data did not find significant relationships between Φe,C and class, or growth rate, although confounding factors inherent to methodological inconsistencies between studies likely contributed to this. Knowledge of empirical relationships between Φe,C and growth rate coupled with recent improvements in quantifying phytoplankton growth rates in situ, facilitate up-scaling of FRRf campaigns to routinely derive Φe,C needed to assess ocean C-cycling.
Hundal, AK, Ali, S, Agarwal, A, Jameel, MA, Jones, LA, Li, J-L, Evans, RA, Langford, SJ & Gupta, A 2021, 'Enhanced Photovoltaic Efficiency via Control of Self-Assembly in Cyanopyridone-Based Oligothiophene Donors', The Journal of Physical Chemistry Letters, vol. 12, no. 2, pp. 919-924.
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Huo, J, Lu, L, Shen, Z, Gao, H & Liu, H 2021, 'Rational design of CoNi alloy and atomic Co/Ni composite as an efficient electrocatalyst', Surface Innovations, vol. 9, no. 1, pp. 37-48.
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Highly efficient, non-precious and stable electrocatalysts for both oxygen (O2) reduction reaction (ORR) and oxygen evolution reaction (OER) have drawn attention as alternatives to noble-metal catalysts. The rational construction of dual-functional catalysts is meaningful because most nanomaterials can perform only a single electrocatalytic activity. Herein, nitrogen (N)-doped carbon (C) nanotubes encapsulating CoNi alloy (CoNi@NCNTs) nanoparticles coupled with a cobalt (Co) and nickel (Ni) dual atom hybrid are successfully designed and synthesized through a simple metal–organic-framework-assisted strategy, which are explored as a catalyst for ORR and OER. The optimized catalyst exhibits highly efficient bifunctional catalytic activity with a low voltage spacing of 0.78 V between an overpotential of 370 mV (at 10 mA/cm2) toward OER and a half-wave potential of 0.822 V toward ORR, as well as high durability. The excellent electrocatalytic performance should be attributed to the advantages of uniformly dispersed CoNi alloy nanoparticles, highly conductive nitrogen-doped carbon nanotubes and the formation of metal–N x species. This work provides a novel strategy for rationally designing bifunctional catalysts for reversible energy conversion.
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. 1303-1303.
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Seagrass wasting disease (SWD), an infection believed to be caused by Labyrinthula zosterae, has been linked to seagrass declines in several places around the world. However, there is uncertainty about the mechanisms of disease and the potential involvement of opportunistic colonising microorganisms. Using 16S rRNA gene amplicon sequencing, we compared the microbiome of SWD lesions in leaves of Zostera muelleri with communities in adjacent asymptomatic tissues and healthy leaves. The microbiome of healthy leaf tissues was dominated by Pseudomonas and Burkholderia, whereas the most predominant taxa within adjacent tissues were Pseudomonas and Rubidimonas. Members of the Saprospiraceae, potential macroalgal pathogens, were over-represented within SWD lesions. These pronounced changes in microbiome structure were also apparent when we examined the core microbiome of different tissue types. Although the core microbiome associated with healthy leaves included three operational taxonomic units (OTUs) classified as Burkholderia, Cryomorphaceae and the SAR11 clade, a single core OTU from the Arenicella was found within adjacent tissues. Burkholderia are diazotrophic microorganisms and may play an important role in seagrass nitrogen acquisition. In contrast, some members of the Arenicella have been implicated in necrotic disease in other benthic animals. Moreover, microbiome structure was maintained across sites within healthy tissues, but not within SWD lesions or the tissues immediately adjacent to lesions. Predicted functional profiles revealed increased photoautotrophic functions in SWD tissues relative to healthy leaves, but no increase in pathogenicity or virulence. Notably, we demonstrated the presence of L. zosterae in SWD lesions by polymerase chain reaction, but only in one of the two sampled locations, which indicates that other microbiological factors may be involved in the initiation or development of SWD-like symptoms. This study suggests that the d...
Hussain, MS, Sharma, P, Dhanjal, DS, Khurana, N, Vyas, M, Sharma, N, Mehta, M, Tambuwala, MM, Satija, S, Sohal, SS, Oliver, BGG & Sharma, HS 2021, 'Nanotechnology based advanced therapeutic strategies for targeting interleukins in chronic respiratory diseases', Chemico-Biological Interactions, vol. 348, pp. 109637-109637.
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Both communicable and non-communicable chronic respiratory conditions have accorded for suffering of millions of people of all ages and stated to be leading cause of death, morbidity, economic and social pressures, and disability-adjusted life-years (DALYs) worldwide. These illnesses impair patient's health and negatively impacts families and society, particularly in low and middle-income countries. Chronic respiratory diseases (CRDs) affect different organs of respiratory system, involving airways, parenchyma, and pulmonary vasculature. As the number of respiratory diseases are exponentially escalating but still the stakeholders are not paying attention towards its serious complications. Currently, the treatment being used primarily focusses only on alleviating symptoms of these illness rather delivering the therapeutic agent at target site for optimal care and/or prevention. Lately, extensive research is being conducted on airways and systemic inflammation, oxidative stress, airway, or parenchymal rehabilitation. From which macrophages, neutrophils, and T cells, as well as structural cells as fibroblasts, epithelial, endothelial, and smooth muscle cells have been found to be active participants that are involved in these chronic respiratory diseases. The pathogenesis of all these chronic respiratory diseases gets caused differently via mediators and proteins, including cytokines, chemokines, growth factors and oxidants. Presently, the target of prescription therapies is to reduce the inflammation of airways and relieve the airway contraction. In all studies, cytokines have been found to play an imperative role in fostering chronic airway inflammation and remodelling. Owing to the limitations of conventional treatments, the current review aims to summarize the current knowledge about the chronic respiratory disease and discuss further about the various conventional methods that can be used for treating this ailment. Additionally, it also highlights and discusses...
Hwang, FJ & Huang, Y-H 2021, 'An effective logarithmic formulation for piecewise linearization requiring no inequality constraint', Computational Optimization and Applications, vol. 79, no. 3, pp. 601-631.
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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, pp. 113692-113692.
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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.
Hynen, AL, Lazenby, JJ, Savva, GM, McCaughey, LC, Turnbull, L, Nolan, LM & Whitchurch, CB 2021, 'Multiple holins contribute to extracellular DNA release in Pseudomonas aeruginosa biofilms', Microbiology, vol. 167, no. 2.
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Bacterial biofilms are composed of aggregates of cells encased within a matrix of extracellular polymeric substances (EPS). One key EPS component is extracellular DNA (eDNA), which acts as a ‘glue’, facilitating cell–cell and cell–substratum interactions. We have previously demonstrated that eDNA is produced in
Pseudomonas aeruginosa
biofilms via explosive cell lysis. This phenomenon involves a subset of the bacterial population explosively lysing, due to peptidoglycan degradation by the endolysin Lys. Here we demonstrate that in
P. aeruginosa
three holins, AlpB, CidA and Hol, are involved in Lys-mediated eDNA release within both submerged (hydrated) and interstitial (actively expanding) biofilms, albeit to different extents, depending upon the type of biofilm and the stage of biofilm development. We also demonstrate that eDNA release events determine the sites at which cells begin to cluster to initiate microcolony formation during the early stages of submerged biofilm development. Furthermore, our results show that sustained release of eDNA is required for cell cluster consolidation and subsequent microcolony development in submerged biofilms. Overall, this study adds to our understanding of how eDNA release is controlled temporally and spatially within
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, pp. 111377-111377.
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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, vol. 500, pp. 114853-114853.
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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, vol. 51, no. 3, pp. 581-592.
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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 with this, injury frameworks, ...
Indigo, NL, Jolly, CJ, Kelly, E, Smith, J, Webb, JK & Phillips, BL 2021, 'Effects of learning and adaptation on population viability', Conservation Biology, vol. 35, no. 4, pp. 1245-1255.
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Inomura, K, Masuda, T, Eichner, M, Rabouille, S, Zavřel, T, Červený, J, Vancová, M, Bernát, G, Armin, G, Claquin, P, Kotabová, E, Stephan, S, Suggett, DJ, Deutsch, C & Prášil, O 2021, 'Quantifying Cyanothece growth under DIC limitation', Computational and Structural Biotechnology Journal, vol. 19, pp. 6456-6464.
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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, vol. 13, no. 8, pp. 1614-1614.
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It has been shown that the filamentous phage, Pf4, plays an important role in biofilm development, stress tolerance, genetic variant formation and virulence in Pseudomonas aeruginosa PAO1. These behaviours are linked to the appearance of superinfective phage variants. Here, we have investigated the molecular mechanism of superinfection as well as how the Pf4 phage can control host gene expression to modulate host behaviours. Pf4 exists as a prophage in PAO1 and encodes a homologue of the P2 phage repressor C and was recently named Pf4r. Through a combination of molecular techniques, ChIPseq and transcriptomic analyses, we show a critical site in repressor C (Pf4r) where a mutation in the site, 788799A>G (Ser4Pro), causes Pf4r to lose its function as the immunity factor against reinfection by Pf4. X-ray crystal structure analysis shows that Pf4r forms symmetric homo-dimers homologous to the E.coli bacteriophage P2 RepC protein. A mutation, Pf4r*, associated with the superinfective Pf4r variant, found at the dimer interface, suggests dimer formation may be disrupted, which derepresses phage replication. This is supported by multi-angle light scattering (MALS) analysis, where the Pf4r* protein only forms monomers. The loss of dimerisation also explains the loss of Pf4r’s immunity function. Phenotypic assays showed that Pf4r increased LasB activity and was also associated with a slight increase in the percentage of morphotypic variants. ChIPseq and transcriptomic analyses suggest that Pf4r also likely functions as a transcriptional regulator for other host genes. Collectively, these data suggest the mechanism by which filamentous phages play such an important role in P. aeruginosa biofilm development.
Italiano, CJ, Pu, L, Violi, JP, Duggin, IG & Rodgers, KJ 2021, 'Cysteine biosynthesis contributes to β-methylamino-l-alanine tolerance in Escherichia coli', Research in Microbiology, vol. 172, no. 6, pp. 103852-103852.
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In contrast to mammalian cells, bacteria such as Escherichia coli have been shown to display tolerance towards the neurotoxin β-methylamino-L-alanine (BMAA) suggesting that these prokaryotes possess a way to metabolise BMAA or its products, resulting in their export, degradation, or detoxification. Single gene deletion mutants of E. coli K-12 with inactivated amino acid biosynthesis pathways were treated with 500 μg/ml BMAA and the resulting growth was monitored. Wild type E. coli and most of the gene deletion mutants displayed unaltered growth in the presence of BMAA over 12 h. Conversely, deletion of genes in the cysteine biosynthesis pathway, cysE, cysK or cysM resulted in a BMAA dose-dependent growth delay in minimal medium. Through further studies of the ΔcysE strain, we observed increased susceptibility to oxidative stress from H2O2 in minimal medium, and disruptions in glutathione levels and oxidation state. The cysteine biosynthesis pathway is therefore linked to the tolerance of BMAA and oxidative stress in E. coli, which potentially represents a mechanism of BMAA detoxification.
Iwasaki, K, Evenhuis, C, Tamburic, B, Kuzhiumparambil, U, O'Connor, W, Ralph, P & Szabó, M 2021, 'Improving light and CO2 availability to enhance the growth rate of the diatom, Chaetoceros muelleri', Algal Research, vol. 55, pp. 102234-102234.
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Iwasaki, K, Szabó, M, Tamburic, B, Evenhuis, C, Zavafer, A, Kuzhiumparambil, U & Ralph, P 2021, 'Investigating the impact of light quality on macromolecular of', Functional Plant Biology, vol. 49, no. 6, pp. 554-564.
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Diatoms (Bacillariophyceae) are important to primary productivity of aquatic ecosystems. This algal group is also a valuable source of high value compounds that are utilised as aquaculture feed. The productivity of diatoms is strongly driven by light and CO2 availability, and macro- and micronutrient concentrations. The light dependency of biomass productivity and metabolite composition is well researched in diatoms, but information on the impact of light quality, particularly the productivity return on energy invested when using different monochromatic light sources, remains scarce. In this work, the productivity return on energy invested of improving growth rate, photosynthetic activity, and metabolite productivity of the diatom Chaetoceros muelleri under defined wavelengths (blue, red, and green) as well as while light is analysed. By adjusting the different light qualities to equal photosynthetically utilisable radiation, it was found that the growth rate and photosynthetic oxygen evolution was unchanged under white, blue, and green light, but it was lower under red light. Blue light improved the productivity return on energy invested for biomass, total protein, total lipid, total carbohydrate, and in fatty acids production, which would suggest that blue light should be used for aquaculture feed production.
Jackman, JA, Yoon, BK, Mokrzecka, N, Kohli, GS, Valle‐González, ER, Zhu, X, Pumera, M, Rice, SA & Cho, N 2021, 'Graphene Oxide Mimics Biological Signaling Cue to Rescue Starving Bacteria', Advanced Functional Materials, vol. 31, no. 25, pp. 2102328-2102328.
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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. 851-864.
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Jain, SK, Low, MX, Vashishtha, P, Nirantar, S, Zhu, L, Ton‐That, C, Ahmed, T, Sriram, S, Walia, S, Gupta, G & Bhaskaran, M 2021, 'Influence of Temperature on Photodetection Properties of Honeycomb‐like GaN Nanostructures', Advanced Materials Interfaces, vol. 8, no. 14, pp. 2100593-2100593.
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Jamil, R, Ali, R, Loomba, S, Xian, J, Yousaf, M, Khan, K, Shabbir, B, McConville, CF, Mahmood, A & Mahmood, N 2021, 'The role of nitrogen in transition-metal nitrides in electrochemical water splitting', Chem Catalysis, vol. 1, no. 4, pp. 802-854.
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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, pp. 2008644-2008644.
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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.
Jerotić, Đ, Matić, M & McClements, L 2021, 'The importance of polymorphisms of regulatory and catalytic antioxidant proteins in chronic kidney disease', Medicinski podmladak, vol. 72, no. 1, pp. 25-33.
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Both excessive production of reactive oxygen species (ROS) and impaired antioxidant function are found in patients with chronic kidney disease (CKD). Therefore, individual susceptibility towards CKD can be induced by functional variations of genes encoding antioxidant regulatory (nuclear factor erythroid 2 - related factor 2 (Nrf2)) and catalytic (superoxide dismutase (SOD2) and glutathione peroxidase (GPX1)) proteins. Several types of single nucleotide polymorphisms (SNPs) have been found within the genes encoding these proteins, with Nrf2 (-617C/A), SOD2 (Ala16Val) and GPX1 (Pro198Leu) conferring impaired catalytic activity. The most unexplored gene polymorphism in CKD susceptibility, progression and survival, with only two original studies published, is the Nrf2 (-617C/A) polymorphism. The results of these studies showed that there was no individual impact of this polymorphism on the susceptibility towards end stage renal disease (ESRD) development, oxidative phenotype and mortality. However, Nrf2 had a significant role in ESRD risk and survival, when combined with other antioxidant genes. The results regarding the impact of SOD2 (Ala16Val) and GPX1 (Pro198Leu) polymorphisms on either CKD or ESRD are still inconclusive. Namely, some studies showed that patients having variant SOD2 (Val) or GPX1 (Leu) allele were at increased risk of CKD development and progression, while other studies reported only weak or no association between these polymorphisms and CKD. Surprisingly, the only study that reported an association of GPX1 polymorphism with overall/cardiovascular survival in ESRD patients showed a significant impact of low activity GPX1 (Leu/Leu) genotype on better survival. In this review, we comprehensively and critically appraise the literature on these polymorphisms related to oxidative stress in CKD patients, in order to identify gaps and provide recommendations for further clinical research and translation. New developments in the field of antioxi...
Jerotic, D, Suvakov, S, Alqudah, A, Savic-Radojevic, A, Pljesa-Ercegovac, M, Coric, V, McClements, L, Simic, T & Matic, M 2021, 'The influence of uremic serum and GSTM1 knockdown on redox homeostasis in HUVECs', Free Radical Biology and Medicine, vol. 177, pp. S82-S83.
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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, vol. 2021, pp. 1-12.
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Deletion polymorphism of glutathione S-transferase M1 (GSTM1), a phase II detoxification and antioxidant enzyme, increases susceptibility to end-stage renal disease (ESRD) as well as the development of cardiovascular diseases (CVD) among ESRD patients and leads to their shorter cardiovascular survival. The mechanisms by which GSTM1 downregulation contributes to oxidative stress and inflammation in endothelial cells in uremic conditions have not been investigated so far. Therefore, the aim of the present study was to elucidate the effects of GSTM1 knockdown on oxidative stress and expression of a panel of inflammatory markers in human umbilical vein endothelial cells (HUVECs) exposed to uremic serum. Additionally, we aimed to discern whether GSTM1-null genotype is associated with serum levels of adhesion molecules in ESRD patients. HUVECs treated with uremic serum exhibited impaired redox balance characterized by enhanced lipid peroxidation and decreased antioxidant enzyme activities, independently of the GSTM1 knockdown. In response to uremic injury, HUVECs exhibited alteration in the expression of a series of inflammatory cytokines including retinol-binding protein 4 (RBP4), regulated on activation, normal T cell expressed and secreted (RANTES), C-reactive protein (CRP), angiogenin, dickkopf-1 (Dkk-1), and platelet factor 4 (PF4). GSTM1 knockdown in HUVECs showed upregulation of monocyte chemoattractant protein-1 (MCP-1), a cytokine involved in the regulation of monocyte migration and adhesion. These cells also have shown upregulated intracellular and vascular cell adhesion molecules (ICAM-1 and VCAM-1). In accordance with these findings, the levels of serum ICAM-1 and VCAM-1 (sICAM-1 and sVCAM-1) were increased in ESRD patients lacking GSTM1, in comparison with patients with the GSTM1-active genotype. Based on these results, it may be concluded that incubation of endothelial cells in uremic serum induces redox imbalance accompanied with altered expressi...
Jiang, M, Danilov, DL, Eichel, R & Notten, PHL 2021, 'A Review of Degradation Mechanisms and Recent Achievements for Ni‐Rich Cathode‐Based Li‐Ion Batteries', Advanced Energy Materials, vol. 11, no. 48, pp. 2103005-2103005.
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Jiang, M, Wu, X, Zhang, Q, Danilov, DL, Eichel, R-A & Notten, PHL 2021, 'Fabrication and interfacial characterization of Ni-rich thin-film cathodes for stable Li-ion batteries', Electrochimica Acta, vol. 398, pp. 139316-139316.
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Jiang, M, Zhang, Q, Danilov, DL, Eichel, R-A & Notten, PHL 2021, 'Formation of a Stable Solid-Electrolyte Interphase at Metallic Lithium Anodes Induced by LiNbO3 Protective Layers', ACS Applied Energy Materials, vol. 4, no. 9, pp. 10333-10343.
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Jiang, Q, Zeng, H, Liu, X, Yan, J, Li, A & Zhou, J 2021, 'Superhydrophobic surface of glass powder derived from wet milling with aliphatic chemicals modification', Ceramics International, vol. 47, no. 20, pp. 29091-29098.
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Jiang, Z, Liu, S, Cui, L, He, J, Fang, Y, Premarathne, C, Li, L, Wu, Y, Huang, X & Kumar, M 2021, 'Sand Supplementation to Eutrophic Sediments Improves the Growth and Survival of Seagrass Thalassia Hemprichii: Implication for Seagrass Restoration and Management'.
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Abstract
Aims Sediment composition is highly crucial for seagrass growth and survival. Eutrophication has been suggested a major cause of seagrass decline globally. We investigated the effects of beach sand supplementation to natural sediments under eutrophic condition on the growth and survival of tropical dominant seagrass Thalassia hemprichii. Methods We cultured seagrass T. hemprichii under the controlled laboratory conditions in three sediment types by combining different ratio of in-situ eutrophic sediment and coarse beach sand. We examined the effect of beach sand mixing to natural eutrophic sediments on the growth of seagrass using photobiology, metabolomics and isotope labeling approaches. Results Seagrass grown in eutrophic sediments mixed with sand exhibited significantly higher photosynthetic activity with high relative maximum electron transport rate and minimum saturating irradiance. Simultaneously, considerably greater belowground amino acid and flavonoid concentrations were observed to counteract anoxic stress in eutrophic sediment without mixing sand. This led to more positive belowground stable sulfur isotope in the eutrophic sediment with lower Eh. Conclusions These results indicated coarse beach sand indirectly enhanced photosynthesis and growth for T. hemprichii by reducing sulfide intrusion with lower concentrations of amino acid and flavonoid. This could possibly explain why T. hemprichii often grow better in the coarse sand substrate. Therefore, it is imperative to consider adding sand soil in the sediments to improve the growth condition for seagrass and restoring the seagrass shoots during trans...
Johansen, MD, Alcaraz, M, Dedrick, RM, Roquet-Banères, F, Hamela, C, Hatfull, GF & Kremer, L 2021, 'Mycobacteriophage–antibiotic therapy promotes enhanced clearance of drug-resistant Mycobacterium abscessus', Disease Models & Mechanisms, vol. 14, no. 9.
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ABSTRACT
Infection by multidrug-resistant Mycobacterium abscessus is increasingly prevalent in cystic fibrosis (CF) patients, leaving clinicians with few therapeutic options. A compassionate study showed the clinical improvement of a CF patient with a disseminated M. abscessus (GD01) infection, following injection of a phage cocktail, including phage Muddy. Broadening the use of phage therapy in patients as a potential antibacterial alternative necessitates the development of biological models to improve the reliability and successful prediction of phage therapy in the clinic. Herein, we demonstrate that Muddy very efficiently lyses GD01 in vitro, an effect substantially increased with standard drugs. Remarkably, this cooperative activity was retained in an M. abscessus model of infection in CFTR-depleted zebrafish, associated with a striking increase in larval survival and reduction in pathological signs. The activity of Muddy was lost in macrophage-ablated larvae, suggesting that successful phage therapy relies on functional innate immunity. CFTR-depleted zebrafish represent a practical model to rapidly assess phage treatment efficacy against M. abscessus isolates, allowing the identification of drug combinations accompanying phage therapy and treatment prediction in patients.
This article has an associated First Person interview with the first author of the paper.
Johansen, MD, Shalini, Kumar, S, Raynaud, C, Quan, DH, Britton, WJ, Hansbro, PM, Kumar, V & Kremer, L 2021, 'Biological and Biochemical Evaluation of Isatin-Isoniazid Hybrids as Bactericidal Candidates against Mycobacterium tuberculosis', Antimicrobial Agents and Chemotherapy, vol. 65, no. 8.
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Tuberculosis remains a leading cause of mortality among infectious diseases worldwide, prompting the need to discover new drugs to fight this disease. We report here the design, synthesis, and antimycobacterial activity of isatin-mono/bis-isoniazid hybrids.
Johnson, L, Vekariya, S, Wood, B, Costa, M, Waters, L, Green, S & Marks, DC 2021, 'The in vitro quality of X‐irradiated platelet components in PAS‐E is equivalent to gamma‐irradiated components', Transfusion, vol. 61, no. 11, pp. 3075-3080.
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Background
Blood components are irradiated to inactivate lymphocytes in an effort to prevent transfusion-associated graft versus host disease. Although gamma irradiators are commonly used, they are subjected to rigorous health, safety, and compliance regulations, compared with X-irradiators which have the advantage of only emitting radiation while the machine is switched on. While the effects of gamma irradiation on platelet components are well known, there is little or no data comparing the effects of X- and gamma-irradiation on the quality of these components. Therefore, this study examined the in vitro quality of platelet components (pooled and apheresis) following X- or gamma-irradiation.Study design and methods
Whole-blood-derived (pooled) and apheresis platelet components in platelet additive solution (n = 20 pairs for each type) were irradiated (X vs. gamma). In vitro platelet quality was tested prior to irradiation (day 1) and subsequently on days 2, 5, and 7. Non-irradiated components were tested on day 5 in parallel as reference controls. Metabolic parameters, surface expression of glycoproteins and activation markers (CD62P and annexin-V binding), and agonist-induced aggregation were measured.Results
All components met Council of Europe specifications. There were no statistical differences in any in vitro quality measurements between X- and gamma-irradiated pooled or apheresis platelet components.Conclusion
X- and gamma-irradiation have similar effects on the in vitro quality of stored blood components, indicating that either technology represents a suitable option for irradiation of platelet components.
Johnson, L, Vekariya, S, Wood, B, Tan, S, Roan, C & Marks, DC 2021, 'Refrigeration of apheresis platelets in platelet additive solution ( PAS‐E ) supports in vitro platelet quality to maximize the shelf‐life', Transfusion, vol. 61, no. S1.
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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, 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, Guénel, P, Hahnen, E, Haiman, CA, Håkansson, N, Hall, P, Hamann, U, Harrington, PA, Hart, SN, Hooning, MJ, Hopper, JL, Howell, A, Hunter, DJ, Jager, A, Jakubowska, A, John, EM, Kaaks, R, Keeman, R, Khusnutdinova, E, Kitahara, CM, Kosma, V-M, Koutros, S, Kraft, P, Kristensen, VN, Kurian, AW, Lambrechts, D, Le Marchand, L, Linet, M, Lubiński, J, Mannermaa, A, Manoukian, S, Margolin, S, Martens, JWM, Mavroudis, D, Mayes, R, Meindl, A, Milne, RL, Neuhausen, SL, Nevanlinna, H, Newman, WG, Nielsen, SF, Nordestgaard, BG, Obi, N, Olshan, AF, Olson, JE, Olsson, H, Orban, E, Park-Simon, T-W, Peterlongo, P, Plaseska-Karanfilska, D, Pylkäs, K, Rennert, G, Rennert, HS, Ruddy, KJ, Saloustros, E, Sandler, DP, Sawyer, EJ, Schmutzler, RK, Scott, C, Shu, X-O, Simard, J, Smichkoska, S, Sohn, C, Southey, MC, Spinelli, JJ, Stone, J, Tamimi, RM, Taylor, JA, Tollenaar, RAEM, Tomlinson, I, Troester, MA, Truong, T, Vachon, CM, van Veen, EM, Wang, SS, Weinberg, CR, Wendt, C, Wildiers, H, Winqvist, R, Wolk, A, Zheng, W, Ziogas, A, Dunning, AM, Pharoah, PDP, Easton, DF, Howie, AF, Peto, J, dos-Santos-Silva, I, Swerdlow, AJ, Chang-Claude, J, Schmidt, MK, Orr, N & Fletcher, O 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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Abstract
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-positiv...
Johnston, NP & Wallman, JF 2021, 'A new species of carrion-breeding “golden blowfly” from south-eastern Australia (Diptera: Calliphoridae)', Transactions of the Royal Society of South Australia, vol. 145, no. 2, pp. 143-151.
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Jolly, CJ, Smart, AS, Moreen, J, Webb, JK, Gillespie, GR & Phillips, BL 2021, 'Trophic cascade driven by behavioral fine‐tuning as naïve prey rapidly adjust to a novel predator', Ecology, vol. 102, no. 7.
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Jolly, CJ, Von Takach, B & Webb, JK 2021, 'Slow life history leaves endangered snake vulnerable to illegal collecting', Scientific Reports, vol. 11, no. 1.
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AbstractGlobal wildlife trade is a multibillion-dollar industry and a significant driver of vertebrate extinction risk. Yet, few studies have quantified the impact of wild harvesting for the illicit pet trade on populations. Long-lived species, by virtue of their slow life history characteristics, may be unable to sustain even low levels of collecting. Here, we assessed the impact of illegal collecting on populations of endangered broad-headed snakes (Hoplocephalus bungaroides) at gated (protected) and ungated (unprotected) sites. Because broad-headed snakes are long-lived, grow slowly and reproduce infrequently, populations are likely vulnerable to increases in adult mortality. Long-term data revealed that annual survival rates of snakes were significantly lower in the ungated population than the gated population, consistent with the hypothesis of human removal of snakes for the pet trade. Population viability analysis showed that the ungated population has a strongly negative population growth rate and is only prevented from ultimate extinction by dispersal of small numbers of individuals from the gated population. Sensitivity analyses showed that the removal of a small number of adult females was sufficient to impose negative population growth and suggests that threatened species with slow life histories are likely to be especially vulnerable to illegal collecting.
Joshi, RV, Gunawan, C & Mann, R 2021, 'We Are One: Multispecies Metabolism of a Biofilm Consortium and Their Treatment Strategies', Frontiers in Microbiology, vol. 12.
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The ecological and medical significance of bacterial biofilms have been well recognized. Biofilms are harder to control than their planktonic free-living counterparts and quite recently, the focus of the study has shifted to the multispecies consortia, which represent the vast majority of real-case infection scenarios. Studies have begun to explore the complex interspecies interactions within these biofilms. However, only little attention is currently given to the role of cellular metabolites in the cell-to-cell communication. The concentration gradients of metabolic substrates and products affect the spatial growth of bacteria in multispecies biofilm. This, if looked into more deeply, can lead to identification of potential therapies targeting the specific metabolites and hence the coordinated protection in the bacterial community. Herein, we review the interspecies communications, including their metabolic cross-talking, in multispecies biofilm, to signify the importance of such interactions on the initial formation and subsequent growth of these biofilms. Multispecies biofilms with their species heterogeneity are more resilient to antimicrobial agents than their single species biofilm counterparts and this characteristic is of particular interest when dealing with pathogenic bacteria. In this Review, we also discuss the treatment options available, to include current and emerging avenues to combat pathogenic multispecies biofilms in the clinical, environmental, as well as industrial settings.
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, vol. 2021, pp. 1-13.
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Background. Eight-Constitution Medicine (ECM), an extension of Traditional Korean Medicine, divides the population into eight groups based on their physiological characteristics. ECM divides these eight groups into two larger groups based on autonomic reactivity: the Sympathicotonic group and the Vagotonic group (herein referred to as the Disympathetic Dimension). Heart Rate Variability (HRV) is a widely used biomedical tool to assess cardiac autonomic function. This raises the question of the utility of using HRV to correctly diagnose ECM constitutions. Methods. A systematic literature review was conducted to evaluate the correlation between HRV and constitutions in Korean Constitutional Medicine, including Eight-Constitution Medicine (ECM) and Sasang Constitution Medicine (SCM). The articles were obtained from both English (Scopus, PubMed, EMBASE, ProQuest, and Medline) and Korean databases (NDSL and RISS), in addition to Google Scholar, without date restriction. 20 studies met the inclusion criteria, and data were extracted against three aspects: (1) correlation between HRV and constitution, (2) HRV reporting and interpretation, and (3) extraneous factors that were controlled in the studies. Results. 386 articles were initially identified, which was reduced to n = 20 studies which met the inclusion criteria. Of these, 19 were SCM studies and 1 was an ECM study. Sample sizes varied from 10 to 8498 men and women, with an age range of 10–80 years. SCM studies explored HRV differences by constitution, measuring HRV at resting, with controlled breathing, before and after acupuncture stimulation, and by other interventions. SCM studies reported either no significant differences (HRV at resting or with controlled breathing studies) or conflicting data (HRV with acupuncture stimulation studies). The single ECM study measured HRV at resting and after acupuncture stimulation but reported no significant differences between the two groups of Sympathicotonia and Va...
Kanodarwala, FK, Leśniewski, A, Olszowska-Łoś, I, Spindler, X, Pieta, IS, Lennard, C, Niedziółka-Jönsson, J, Moret, S & Roux, C 2021, 'Fingermark detection using upconverting nanoparticles and comparison with cyanoacrylate fuming', Forensic Science International, vol. 326, pp. 110915-110915.
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Kanodarwala, FK, Moret, S, Spindler, X, Lennard, C & Roux, C 2021, 'Novel upconverting nanoparticles for fingermark detection', Optical Materials, vol. 111, pp. 110568-110568.
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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, vol. 4, no. 4.
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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, Thomas Broome, S, 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, pp. 10947-10947.
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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 small-sized, 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.
Keen, B, Cawley, A, Fouracre, C, Pyke, J & Fu, S 2021, 'Towards an untargeted mass spectrometric approach for improved screening in equine antidoping', Drug Testing and Analysis, vol. 13, no. 5, pp. 1001-1007.
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Kelly, E, Jolly, CJ, Indigo, N, Smart, A, Webb, J & Phillips, B 2021, 'No outbreeding depression in a trial of targeted gene flow in an endangered Australian marsupial', Conservation Genetics, vol. 22, no. 1, pp. 23-33.
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Kendig, MD, Leigh, S-J & Morris, MJ 2021, 'Unravelling the impacts of western-style diets on brain, gut microbiota and cognition', Neuroscience & Biobehavioral Reviews, vol. 128, pp. 233-243.
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Kendig, MD, Martire, SI, Boakes, RA & Rooney, KB 2021, 'Comparable metabolic effects of isocaloric sucrose and glucose solutions in rats', Physiology & Behavior, vol. 229, pp. 113239-113239.
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Kerkar, AU, Tripathy, SC, Hughes, DJ, Sabu, P, Pandi, SR, Sarkar, A & Tiwari, M 2021, 'Characterization of phytoplankton productivity and bio-optical variability in a polar marine ecosystem', Progress in Oceanography, vol. 195, pp. 102573-102573.
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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', Journal of Allergy and Clinical Immunology, vol. 147, no. 1, pp. 144-157.
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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, pp. 108504-108504.
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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, pp. e202000915-e202000915.
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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.
Kim, HJ, Wang, K, Chen, C, Lin, Y, Tam, PPL, Lin, DM, Yang, JYH & Yang, P 2021, 'Uncovering cell identity through differential stability with Cepo', Nature Computational Science, vol. 1, no. 12, pp. 784-790.
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Kim, RY, Oliver, BG, Wark, PAB, Hansbro, PM & Donovan, C 2021, 'COPD exacerbations: targeting IL-33 as a new therapy', The Lancet Respiratory Medicine, vol. 9, no. 11, pp. 1213-1214.
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Kim, RY, Sunkara, KP, Bracke, KR, Jarnicki, AG, Donovan, C, Hsu, AC, Ieni, A, Beckett, EL, Galvão, I, Wijnant, S, Ricciardolo, FLM, Di Stefano, A, Haw, TJ, Liu, G, Ferguson, AL, Palendira, U, Wark, PA, Conickx, G, Mestdagh, P, Brusselle, GG, Caramori, G, Foster, PS, Horvat, JC & Hansbro, PM 2021, 'A microRNA-21–mediated SATB1/S100A9/NF-κB axis promotes chronic obstructive pulmonary disease pathogenesis', Science Translational Medicine, vol. 13, no. 621, p. eaav7223.
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Inhibition of cigarette smoke–induced microRNA-21 suppresses chronic obstructive pulmonary disease through effects on a SATB1/S100A9/NF-κB axis.
Kim, T-H, Alraek, T, Bian, Z-X, Birch, S, Bovey, M, Lee, J, Lee, MS, Robinson, N & Zaslawski, C 2021, 'Clinical reasoning in traditional medicine exemplified by the clinical encounter of Korean medicine', Integrative Medicine Research, vol. 10, no. 2, pp. 100641-100641.
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King, WL, Kaestli, M, Siboni, N, Padovan, A, Christian, K, Mills, D, Seymour, J & Gibb, K 2021, 'Pearl Oyster Bacterial Community Structure Is Governed by Location and Tissue-Type, but Vibrio Species Are Shared Among Oyster Tissues', Frontiers in Microbiology, vol. 12.
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Diseases of bivalves of aquacultural importance, including the valuable Australian silver-lipped pearl oyster (Pinctada maxima), have been increasing in frequency and severity. The bivalve microbiome is linked to health and disease dynamics, particularly in oysters, with putative pathogens within the Vibrio genus commonly implicated in oyster diseases. Previous studies have been biased toward the Pacific oyster because of its global dominance in oyster aquaculture, while much less is known about the microbiome of P. maxima. We sought to address this knowledge gap by characterizing the P. maxima bacterial community, and we hypothesized that bacterial community composition, and specifically the occurrence of Vibrio, will vary according to the sampled microenvironment. We also predicted that the inside shell swab bacterial composition could represent a source of microbial spillover biofilm into the solid pearl oyster tissues, thus providing a useful predictive sampling environment. We found that there was significant heterogeneity in bacterial composition between different pearl oyster tissues, which is consistent with patterns reported in other bivalve species and supports the hypothesis that each tissue type represents a unique microenvironment for bacterial colonization. We suggest that, based on the strong effect of tissue-type on the pearl oyster bacterial community, future studies should apply caution when attempting to compare microbial patterns from different locations, and when searching for disease agents. The lack of association with water at each farm also supported the unique nature of the microbial communities in oyster tissues. In contrast to the whole bacterial community, there was no significant difference in the Vibrio community among tissue types nor location. These results sugges...
Klingberg, J, Cawley, A, Shimmon, R & Fu, S 2021, 'Towards compound identification of synthetic opioids in nontargeted screening using machine learning techniques', Drug Testing and Analysis, vol. 13, no. 5, pp. 990-1000.
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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, vol. 13, no. 5, pp. 977-989.
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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, vol. 20, no. 11, pp. 5218-5221.
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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.
Koong, J, Johnson, C, Rafei, R, Hamze, M, Myers, GSA, Kenyon, JJ, Lopatkin, AJ & Hamidian, M 2021, 'Phylogenomics of two ST1 antibiotic-susceptible non-clinical Acinetobacter baumannii strains reveals multiple lineages and complex evolutionary history in global clone 1', Microbial Genomics, vol. 7, no. 12.
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Acinetobacter baumannii
is an opportunistic pathogen that is difficult to treat due to its resistance to extreme conditions, including desiccation and antibiotics. Most strains causing outbreaks around the world belong to two main global lineages, namely global clones 1 and 2 (GC1 and GC2). Here, we used a combination of Illumina short read and MinION (Oxford Nanopore) long-read sequence data with a hybrid assembly approach to complete the genome sequence of two antibiotic-sensitive GC1 strains, Ex003 and Ax270, recovered in Lebanon from water and a rectal swab of a cat, respectively. Phylogenetic analysis of Ax270 and Ex003 with 186 publicly available GC1 genomes revealed two major clades, including five main lineages (L1–L5), and four single-isolate lineages outside of the two clades. Ax270 and Ex003, along with AB307-0294 and MRSN7213 (both predicted antibiotic-susceptible isolates) represent these individual lineages. Antibiotic resistance islands and transposons interrupting the comM gene remain important features in L1–L5, with L1 associated with the AbaR-type resistance islands, L2 with AbaR4, L3 strains containing either AbaR4 or its variants as well as Tn6022::ISAba42, and L4 and L5 associated with Tn6022 or its variants. Analysis of the capsule (KL) and outer core (OCL) polysaccharide loci further revealed a complex evolutionary history probably involving many recombination events. As more genomes become available, more GC1 lineages continue to emerge. However, genome sequence data from more diverse geographical regi...
Kumar, U, Srivastava, A, Kumari, N, Rashmi, Sahoo, B, Chatterjee, C & Raghuwanshi, NS 2021, 'Evaluation of Spatio-Temporal Evapotranspiration Using Satellite-Based Approach and Lysimeter in the Agriculture Dominated Catchment', Journal of the Indian Society of Remote Sensing, vol. 49, no. 8, pp. 1939-1950.
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Kumari, N, Srivastava, A, Sahoo, B, Raghuwanshi, NS & Bretreger, D 2021, 'Identification of Suitable Hydrological Models for Streamflow Assessment in the Kangsabati River Basin, India, by Using Different Model Selection Scores', Natural Resources Research, vol. 30, no. 6, pp. 4187-4205.
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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, pp. 141708-141708.
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Lachs, L, Sommer, B, Cant, J, Hodge, JM, Malcolm, HA, Pandolfi, JM & Beger, M 2021, 'Linking population size structure, heat stress and bleaching responses in a subtropical endemic coral', Coral Reefs, vol. 40, no. 3, pp. 777-790.
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AbstractAnthropocene coral reefs are faced with increasingly severe marine heatwaves and mass coral bleaching mortality events. The ensuing demographic changes to coral assemblages can have long-term impacts on reef community organisation. Thus, understanding the dynamics of subtropical scleractinian coral populations is essential to predict their recovery or extinction post-disturbance. Here we present a 10-yr demographic assessment of a subtropical endemic coral, Pocillopora aliciae (Schmidt-Roach et al. in Zootaxa 3626:576–582, 2013) from the Solitary Islands Marine Park, eastern Australia, paired with long-term temperature records. These coral populations are regularly affected by storms, undergo seasonal thermal variability, and are increasingly impacted by severe marine heatwaves. We examined the demographic processes governing the persistence of these populations using inference from size-frequency distributions based on log-transformed planar area measurements of 7196 coral colonies. Specifically, the size-frequency distribution mean, coefficient of variation, skewness, kurtosis, and coral density were applied to describe population dynamics. Generalised Linear Mixed Effects Models were used to determine temporal trends and test demographic responses to heat stress. Temporal variation in size-frequency distributions revealed various population processes, from recruitment pulses and cohort growth, to bleaching impacts and temperature dependencies. Sporadic recruitment pulses likely support population persistence, illustrated in 2010 by strong positively skewed size-frequency distributions and the highest density of juvenile corals measured during the study. Increasing mean colony size over the following 6 yr indicates further cohort growth of these recruits. Severe heat stress in 2016 resulted in mass bleaching mortality and a 51% decline in coral density. Moderate heat stress in the following yea...
Lagune, M, Petit, C, Sotomayor, FV, Johansen, MD, Beckham, KSH, Ritter, C, Girard-Misguich, F, Wilmanns, M, Kremer, L, Maurer, FP & Herrmann, J-L 2021, 'Conserved and specialized functions of Type VII secretion systems in non-tuberculous mycobacteria', Microbiology, vol. 167, no. 7.
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Non-tuberculous mycobacteria (NTM) are a large group of micro-organisms comprising more than 200 individual species. Most NTM are saprophytic organisms and are found mainly in terrestrial and aquatic environments. In recent years, NTM have been increasingly associated with infections in both immunocompetent and immunocompromised individuals, prompting significant efforts to understand the diverse pathogenic and signalling traits of these emerging pathogens. Since the discovery of Type VII secretion systems (T7SS), there have been significant developments regarding the role of these complex systems in mycobacteria. These specialised systems, also known as Early Antigenic Secretion (ESX) systems, are employed to secrete proteins across the inner membrane. They also play an essential role in virulence, nutrient uptake and conjugation. Our understanding of T7SS in mycobacteria has significantly benefited over the last few years, from the resolution of ESX-3 structure in
Mycobacterium smegmatis
, to ESX-5 structures in
Mycobacterium xenopi
and
Mycobacterium t...
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, pp. 103460-103460.
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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...
Lapwong, Y, Dejtaradol, A & Webb, JK 2021, 'Plasticity in thermal hardening of the invasive Asian house gecko', Evolutionary Ecology, vol. 35, no. 4, pp. 631-641.
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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, vol. 9.
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BackgroundMaternal obesity is a risk factor for chronic kidney disease (CKD) in offspring, underpinning the theory of the developmental origins of health and disease. DNA methylation has been implicated in the programming of adult chronic disease by maternal obesity, therefore, DNA demethylating agents may mitigate offspring risk of disease. In rodent models, low-dose hydralazine has previously been shown to reduce renal fibrosis via DNA demethylation. We used mouse models of maternal obesity and offspring obesity to determine whether administration of low-dose hydralazine during gestation can prevent fetal programming of CKD in offspring.MethodsFemale C57BL/6 mice received high fat diet (HFD) or chow prior to mating, during gestation and lactation. During gestation, dams received subcutaneous hydralazine (5 mg/kg) or saline thrice-weekly. Male offspring weaned to HFD or chow, which continued until endpoint at 32 weeks. Biometric and metabolic parameters, renal global DNA methylation, renal functional and structural changes, and renal markers of fibrosis, inflammation and oxidative stress were assessed at endpoint.ResultsOffspring exposed to maternal obesity or diet-induced obesity had significantly increased renal global DNA methylation, together with other adverse renal effects including albuminuria, glomerulosclerosis, renal fibrosis, and oxidative stress. Offspring exposed to gestational hydralazine had significantly reduced renal global DNA methylation. In obese offspring of obese mothers, gestational hydralazine significantly decreased albuminuria, glomerulosclerosis, and serum creatinine. Obese offspring of hydralazine-treated lean mothers displayed reduced markers of renal fibrosis and oxidative stress.ConclusionGestational hyd...
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, vol. 16, no. 3, pp. e0248854-e0248854.
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Background
Maternal high fat diet (HFD) promotes chronic kidney disease (CKD) in offspring. This is in accordance with the theory of fetal programming, which suggests adverse conditions occurring in utero predispose offspring to chronic conditions later in life. DNA methylation has been proposed as a key mechanism by which fetal programming occurs and is implicated in CKD progression. DNA demethylating drugs may interrupt the fetal programming of CKD by maternal obesity. Hydralazine, an antihypertensive agent, demethylates DNA at low doses which do not reduce blood pressure. We used a mouse model of maternal obesity to determine whether gestational administration of low-dose hydralazine to mothers can prevent CKD in offspring.
Methods
C57BL/6 dams received HFD or chow from 6 weeks prior to mating and were administered subcutaneous hydralazine (5mg/kg) or saline thrice weekly during gestation. Male offspring were weaned to chow and were sacrificed at either postnatal week 9 or week 32. Biometric and metabolic parameters, renal global DNA methylation, renal structural and functional changes and markers of fibrosis, oxidative stress and inflammation were measured in offspring at weeks 9 and 32.
Results
In week 9 offspring, maternal HFD consumption did not significantly alter anthropometric or metabolic parameters, or renal global DNA methylation. Week 32 offspring had increased renal global DNA methylation, together with albuminuria, glomerulosclerosis, renal fibrosis and oxidative stress. Administration of low-dose hydralazine to obese mothers during gestation reduced renal global DNA methylation and renal fibrotic markers in week 32 offspring.
Conclusion
G...
Lawson, CA, Raina, J, Deschaseaux, E, Hrebien, V, Possell, M, Seymour, JR & Suggett, DJ 2021, 'Heat stress decreases the diversity, abundance and functional potential of coral gas emissions', Global Change Biology, vol. 27, no. 4, pp. 879-891.
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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, pp. 736077-736077.
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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, L-Y, Hew, GSY, Mehta, M, 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, H-S 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.
Lee, U, Carroll, RJ, Marder, K, Wang, Y & Garcia, TP 2021, 'Estimating disease onset from change points of markers measured with error', Biostatistics, vol. 22, no. 4, pp. 819-835.
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Summary
Huntington disease is an autosomal dominant, neurodegenerative disease without clearly identified biomarkers for when motor-onset occurs. Current standards to determine motor-onset rely on a clinician’s subjective judgment that a patient’s extrapyramidal signs are unequivocally associated with Huntington disease. This subjectivity can lead to error which could be overcome using an objective, data-driven metric that determines motor-onset. Recent studies of motor-sign decline—the longitudinal degeneration of motor-ability in patients—have revealed that motor-onset is closely related to an inflection point in its longitudinal trajectory. We propose a nonlinear location-shift marker model that captures this motor-sign decline and assesses how its inflection point is linked to other markers of Huntington disease progression. We propose two estimating procedures to estimate this model and its inflection point: one is a parametric method using nonlinear mixed effects model and the other one is a multi-stage nonparametric approach, which we developed. In an empirical study, the parametric approach was sensitive to correct specification of the mean structure of the longitudinal data. In contrast, our multi-stage nonparametric procedure consistently produced unbiased estimates regardless of the true mean structure. Applying our multi-stage nonparametric estimator to Neurobiological Predictors of Huntington Disease, a large observational study of Huntington disease, leads to earlier prediction of motor-onset compared to the clinician’s subjective judgment.
Lenzen, M, Li, M & Murray, SA 2021, 'Impacts of harmful algal blooms on marine aquaculture in a low-carbon future', Harmful Algae, vol. 110, pp. 102143-102143.
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Leong, HS, Watanabe, S, Kuzhiumparambil, U, Fong, CY, Moy, HY, Yao, YJ, Witting, PK & Fu, S 2021, 'Monitoring metabolism of synthetic cannabinoid 4F-MDMB-BINACA via high-resolution mass spectrometry assessed in cultured hepatoma cell line, fungus, liver microsomes and confirmed using urine samples', Forensic Toxicology, vol. 39, no. 1, pp. 198-212.
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Abstract
Purpose
A tert-leucinate derivative synthetic cannabinoid, methyl (2S)-2-([1-(4-fluorobutyl)-1H-indazole-3-carbonyl]amino)-3,3-dimethylbutanoate (4F-MDMB-BINACA, 4F-MDMB-BUTINACA or 4F-ADB) is known to adversely impact health. This study aimed to evaluate the suitability of three different modes of monitoring metabolism: HepG2 liver cells, fungus Cunninghamella elegans (C. elegans) and pooled human liver microsomes (HLM) for comparison with human in-vivo metabolism in identifying suitable urinary marker(s) for 4F-MDMB-BINACA intake.
Methods
Tentative structure elucidation of in-vitro metabolites was performed on HepG2, C. elegans and HLM using liquid chromatography–tandem mass spectrometry and high-resolution mass spectrometry analysis. In-vivo metabolites obtained from twenty authentic human urine samples were analysed using liquid chromatography–Orbitrap mass spectrometry.
Results
Incubation with HepG2, C. elegans and HLM yielded nine, twenty-three and seventeen metabolites of 4F-MDMB-BINACA, respectively, formed via ester hydrolysis, hydroxylation, carboxylation, dehydrogenation, oxidative defluorination, carbonylation or reaction combinations. Phase II metabolites of glucosidation and sulfation were also exclusively identified using C. elegans model. Eight in-vivo metabolites tentatively identified were mainly products of ester hydrolysis with or without additional dehydrogenation, N
Li, C, Fröch, JE, Nonahal, M, Tran, TN, Toth, M, Kim, S & Aharonovich, I 2021, 'Integration of hBN Quantum Emitters in Monolithically Fabricated Waveguides', ACS Photonics, vol. 8, no. 10, pp. 2966-2972.
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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, 'Correction to Highly Doped Upconversion Nanoparticles for In Vivo Applications Under Mild Excitation Power', Analytical Chemistry, vol. 93, no. 32, pp. 11346-11346.
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Li, D, Wyrsch, ER, Elankumaran, P, Dolejska, M, Marenda, MS, Browning, GF, Bushell, RN, McKinnon, J, Chowdhury, PR, Hitchick, N, Miller, N, Donner, E, Drigo, B, Baker, D, Charles, IG, Kudinha, T, Jarocki, VM & Djordjevic, SP 2021, 'Genomic comparisons of Escherichia coli ST131 from Australia', Microbial Genomics, vol. 7, no. 12.
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Escherichia coli
ST131 is a globally dispersed extraintestinal pathogenic
E. coli
lineage contributing significantly to hospital and community acquired urinary tract and bloodstream infections. Here we describe a detailed phylogenetic analysis of the whole genome sequences of 284 Australian ST131
E. coli
isolates from diverse sources, including clinical, food and companion animals, wildlife and the environment. Our phylogeny and the results of single nucleotide polymorphism (SNP) analysis show the typical ST131 clade distribution with clades A, B and C clearly displayed, but no niche associations were observed. Indeed, interspecies relatedness was a feature of this study. Thirty-five isolates (29 of human and six of wild bird origin) from clade A (32 fimH41, 2 fimH89, 1 fimH141) were observed to differ by an average of 76 SNPs. Forty-five isolates from clade C1 from...
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, pp. 101433-101433.
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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, vol. 118, no. 22, pp. 223701-223701.
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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, vol. 83, pp. 153475-153475.
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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, vol. 8, no. 16, pp. 2101090-2101090.
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Li, M, Reimers, JR, Ford, MJ, Kobayashi, R & Amos, RD 2021, 'Accurate prediction of the properties of materials using the CAM‐B3LYP density functional', Journal of Computational Chemistry, vol. 42, no. 21, pp. 1486-1497.
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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, pp. 129501-129501.
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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, S, Huang, J, Ren, L, Jiang, W, Wang, M, Zhuang, L, Zheng, Q, Yang, R, Zeng, Y, Luu, LDW, Wang, Y & Tai, J 2021, 'A one-step, one-pot CRISPR nucleic acid detection platform (CRISPR-top): Application for the diagnosis of COVID-19', Talanta, vol. 233, pp. 122591-122591.
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The existing CRISPR-mediated diagnostic tests require a two-step procedure (DNA or RNA amplification followed by CRISPR-mediated sequence-specific detection) for nucleic acid detection, which increases complexity and the risk of sample cross-contamination. Here, we report a new CRISPR-mediated test, called CRISPR-top (CRISPR-mediated testing in one-pot), which integrates simultaneous target pre-amplification with CRISPR/cas12b-mediated detection into a one-pot reaction mixture, performed at a constant temperature. The novel CRISPR-top assay was applied to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent for COVID-19 (coronavirus disease 2019). COVID-19 CRISPR-top targets the ORF1ab (opening reading frame 1a/b) and NP (nucleoprotein) genes of SARS-CoV-2, and operates at 59 °C for 40 min with minimal instrument. The COVID-19 CRISPR-top assay can return results within 60-min and is easily interpreted by visual fluorescence or lateral flow readouts. The analytical limit of detection (LoD) for COVID-19 CRISPR-top is 10 copies (for each detection target) per reaction with no cross-reactivity observed from non-SARS-CoV-2 templates. Among clinically collected non-COVID-19 samples, the assay's specificity was 100% (80/80 oropharynx swab samples). Among 52 COVID-19 positive clinical samples collected, the COVID-19 CRISPR-top assay yielded 38 (73.1%) positive results using fluorescence readout and 35 (67.3%) positive results with lateral-flow readout. These diagnostic results were similar to those obtained using RT-PCR (34 positive (65.4%)). These data indicate that COVID-19 CRISPR-top is a simple, rapid, accurate and highly sensitive method for SARS-CoV-2 detection which can be used in the clinic, field laboratories and primary care facilities in resource-challenged settings.
Li, Y, Faiz, A, Moshage, H, Schubert, R, Schilling, L & Kamps, JA 2021, 'Comparative transcriptome analysis of inner blood-retinal barrier and blood–brain barrier in rats', Scientific Reports, vol. 11, no. 1.
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AbstractAlthough retinal microvessels (RMVs) and brain microvessels (BMVs) are closely related in their developmental and share similar blood-neural barriers, studies have reported markedly different responses to stressors such as diabetes. Therefore, we hypothesized that RMVs and BMVs will display substantial differences in gene expression levels even though they are of the same embryological origin. In this study, both RMVs and BMVs were mechanically isolated from rats. Full retinal and brain tissue samples (RT, BT) were collected for comparisons. Total RNA extracted from these four groups were processed on Affymetrix rat 2.0 microarray Chips. The transcriptional profiles of these tissues were then analyzed. In the present paper we looked at differentially expressed genes (DEGs) in RMVs (against RT) and BMVs (against BT) using a rather conservative threshold value of ≥ ± twofold change and a false discovery rate corrected for multiple comparisons (p < 0.05). In RMVs a total of 1559 DEGs were found, of which 1004 genes were higher expressed in RMVs than in RT. Moreover, 4244 DEGs between BMVs and BT were identified, of which 1956 genes were ≥ twofold enriched in BMVs. Using these DEGs, we comprehensively analyzed the actual expression levels and highlighted their involvement in critical functional structures in RMVs and BMVs, such as junctional complex, transporters and signaling pathways. Our work provides for the first time the transcriptional profiles of rat RMVs and BMVs. These results may help to understand why retina and brain microvasculature show different susceptibilities to stressors, and they might even provide new insight for pharmacological interventions.
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, pp. 159780-159780.
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Liao, J, Zhou, J, Song, Y, Liu, B, Chen, Y, Wang, F, Chen, C, Lin, J, Chen, X, Lu, J & Jin, D 2021, 'Preselectable Optical Fingerprints of Heterogeneous Upconversion Nanoparticles', Nano Letters, vol. 21, no. 18, pp. 7659-7668.
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Liao, J, Zhou, J, Song, Y, Liu, B, Lu, J & Jin, D 2021, 'Optical Fingerprint Classification of Single Upconversion Nanoparticles by Deep Learning', The Journal of Physical Chemistry Letters, vol. 12, no. 41, pp. 10242-10248.
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Liao, Y, Ithurbide, S, Evenhuis, C, Löwe, 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. 594-605.
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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', mBio, vol. 12, no. 4.
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Cell division is a central mechanism of life and is essential for growth and development. Members of the
Bacteria
and
Eukarya
have different mechanisms for cell division, which have been studied in detail.
Lin, C, Wang, K & Mueller, S 2021, 'MCVIS: A New Framework for Collinearity Discovery, Diagnostic, and Visualization', Journal of Computational and Graphical Statistics, vol. 30, no. 1, pp. 125-132.
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Lin, G & Jin, D 2021, 'Responsive Sensors of Upconversion Nanoparticles', ACS Sensors, vol. 6, no. 12, pp. 4272-4282.
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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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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. 2000205-2000205.
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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.
Ling, L, Yelland, N, Hatzigianni, M & Dickson-Deane, C 2021, 'Toward a conceptualization of the internet of toys', Australasian Journal of Early Childhood, vol. 46, no. 3, pp. 249-262.
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The Internet of Things is reshaping many households’ digital landscape and influencing children’s play and learning, especially in the form of toys that are named the Internet of Toys (IoToys). IoToys may generate a significant influence on children’s growth. While increasing attention is drawn to the IoToys, confusion around their conceptualization and use is evident. Without a thorough understanding of what the IoToys are, the progress of meaningful research on this topic will be greatly hindered. We, thus, conducted a systematic review to determine existing definitions of the IoToys using seven major databases over the past 20 years. After analyzing the definitions identified, we found that the previous definitions neglected the significance of defining “toys” in their work. The review led to a discussion around how to understand “toys” and then a more precise conceptualization of the IoToys, based on which implications for future research are offered.
Liu, B, Zhang, F & Hwang, F-J 2021, 'Comfort Value of Water: Natural-artificial Dual-structured Analytical Framework for Comfort Assessment of Regional Water Environment and Landscape System', Water Resources Management, vol. 35, no. 14, pp. 4747-4768.
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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, vol. 11, no. 3, pp. 654-654.
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Highly controllable anisotropic shell growth is essential for further engineering the function and properties of lanthanide-doped luminescence nanocrystals, especially in some of the advanced applications such as multi-mode bioimaging, security coding and three-dimensional (3D) display. However, the understanding of the transversal shell growth mechanism is still limited today, because the shell growth direction is impacted by multiple complex factors, such as the anisotropy of surface ligand-binding energy, anisotropic core–shell lattice mismatch, the size of cores and varied shell crystalline stability. Herein, we report a highly controlled transversal shell growth method for hexagonal sodium rare-earth tetrafluoride (β-NaLnF4) nanocrystals. Exploiting the relationship between reaction temperature and shell growth direction, we found that the shell growth direction could be tuned from longitudinal to transversal by decreasing the reaction temperature from 310 °C to 280 °C. In addition to the reaction temperature, we also discussed the roles of other factors in the transversal shell growth of nanocrystals. A suitable core size and a relative lower shell precursor concentration could promote transversal shell growth, although different shell hosts played a minor role in changing the shell growth direction.
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 & Therapeutics, vol. 225, pp. 107839-107839.
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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, vol. 7, no. 8, pp. 1993-2021.
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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, Lin, G & Jin, D 2021, 'Off-axis gyration induces large-area circular motion of anisotropic microparticles in a dynamic magnetic trap', Applied Physics Letters, vol. 119, no. 3, pp. 034102-034102.
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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, vol. 15, no. 12, pp. 19924-19937.
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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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<b><i>Background:</i></b> Emerging evidence has indicated that small airway dysfunction (SAD) contributes to the clinical expression of asthma. <b><i>Objectives:</i></b> The aim of the study was to explore the relationships of SAD assessed by forced expiratory flow between 25 and 75% (FEF<sub>25–75</sub>%), with clinical and inflammatory profile and treatment responsiveness in asthma. <b><i>Method:</i></b> 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. <b><i>Results:</i></b> SAD subjects had more elevated ΔVAS for dyspnea (<i>p</i> = 0.027) and chest tightness (<i>p</i> = 0.032) after MCT. Asthma patients with SAD had significantly elevated interferon (IFN)-γ in sputum (<i>p</i> < 0.05), and Spearman partial correlation found FEF<sub>25–75</sub>% significantly related to IFN-γ and interleukin-8 (both having <i>p</i> < 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) (<i>p</i> = 0.022 and <i>p</i> = 0.032). <b><i>Conclusions:</i></b> This study indicates that SAD in asthma predisposes patients to greater dyspnea intensity and chest tightness during bronchocons...
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, vol. 12, no. 1.
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AbstractSub-diffraction limited localization of fluorescent emitters is a key goal of microscopy imaging. Here, we report that single upconversion nanoparticles, containing multiple emission centres with random orientations, can generate a series of unique, bright and position-sensitive patterns in the spatial domain when placed on top of a mirror. Supported by our numerical simulation, we attribute this effect to the sum of each single emitter’s interference with its own mirror image. As a result, this configuration generates a series of sophisticated far-field point spread functions (PSFs), e.g. in Gaussian, doughnut and archery target shapes, strongly dependent on the phase difference between the emitter and its image. In this way, the axial locations of nanoparticles are transferred into far-field patterns. We demonstrate a real-time distance sensing technology with a localization accuracy of 2.8 nm, according to the atomic force microscope (AFM) characterization values, smaller than 1/350 of the excitation wavelength.
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', Gaodeng Xuexiao Huaxue Xuebao/Chemical Journal of Chinese Universities, vol. 42, no. 2, pp. 633-642.
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Sodium-ion batteries(SIBs) based on Sn-based anodes have attracted increasing attention due to their high theoretical capacity(847 mA•h/g), high electrical conductivity and suitable operation potential. Unfortunately, the huge structural change upon cycling often causes particle pulverization and rapid capacity decay. In this work, ultrafine Sn nanoparticles with dual protection from graphitic carbon nitride(g-C3N4) and polydopamine derived N-doped carbon(g-C3N4/Sn/NC) were successfully fabricated through a designed strategy. Generally, the introduction of g-C3N4 and NC can dramatically accelerate the transport of electrons/ions as well as the reaction dynamics, thus contributing to the alloying reaction between Sn and Na+. Importantly, the ultrafine Sn as well as the dual buffering matrices can efficiently maintain the integrity of electrode upon cycling, guaranteeing the superior electrochemical performance. Benefitting from the structural advantages inhe-rited from the ultrafine Sn nanoparticles and dual protection scaffolds, the as-obtained g-C3N4/Sn/NC displays excellent sodium storage performances, with high reversible capacity(450.7 mA•h/g at 0.5 A/g after 100 cycles), remarkable rate capability(388.3 mA•h/g at 1.0 A/g) and stable long-term cycling stability(363.3 mA•h/g after 400 cycles at 1.0 A/g).
Lockwood, TE, Westerhausen, MT & Doble, PA 2021, 'Pew2: 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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Lodge, CJ, Lowe, AJ, Milanzi, E, Bowatte, G, Abramson, MJ, Tsimiklis, H, Axelrad, C, Robertson, B, Darling, AE, Svanes, C, Wjst, M, Dharmage, SC & Bode, L 2021, 'Human milk oligosaccharide profiles and allergic disease up to 18 years', Journal of Allergy and Clinical Immunology, vol. 147, no. 3, pp. 1041-1048.
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BACKGROUND:Human milk oligosaccharides (HMO) are a diverse range of sugars secreted in breast milk that have direct and indirect effects on immunity. The profiles of HMOs produced differ between mothers. OBJECTIVE:We sought to determine the relationship between maternal HMO profiles and offspring allergic diseases up to age 18 years. METHODS:Colostrum and early lactation milk samples were collected from 285 mothers enrolled in a high-allergy-risk birth cohort, the Melbourne Atopy Cohort Study. Nineteen HMOs were measured. Profiles/patterns of maternal HMOs were determined using LCA. Details of allergic disease outcomes including sensitization, wheeze, asthma, and eczema were collected at multiple follow-ups up to age 18 years. Adjusted logistic regression analyses and generalized estimating equations were used to determine the relationship between HMO profiles and allergy. RESULTS:The levels of several HMOs were highly correlated with each other. LCA determined 7 distinct maternal milk profiles with memberships of 10% and 20%. Compared with offspring exposed to the neutral Lewis HMO profile, exposure to acidic Lewis HMOs was associated with a higher risk of allergic disease and asthma over childhood (odds ratio asthma at 18 years, 5.82; 95% CI, 1.59-21.23), whereas exposure to the acidic-predominant profile was associated with a reduced risk of food sensitization (OR at 12 years, 0.08; 95% CI, 0.01-0.67). CONCLUSIONS:In this high-allergy-risk birth cohort, some profiles of HMOs were associated with increased and some with decreased allergic disease risks over childhood. Further studies are needed to confirm these findings and realize the potential for intervention.
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 & Cell Biology, vol. 99, no. 5, pp. 542-551.
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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, Vanden Berghe, T, Brusselle, GG, Horvat, JC, Murphy, JM, Wark, PA, Bracke, KR, Fricker, M & Hansbro, PM 2021, 'Necroptosis Signaling Promotes Inflammation, Airway Remodeling, and Emphysema in Chronic Obstructive Pulmonary Disease', American Journal of Respiratory and Critical Care Medicine, vol. 204, no. 6, pp. 667-681.
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Rationale: Necroptosis, mediated by RIPK3 (receptor-interacting protein kinase 3) and MLKL (mixed lineage kinase domain-like), is a form of regulated necrosis that can drive tissue inflammation and destruction; however, its contribution to chronic obstructive pulmonary disease (COPD) pathogenesis is poorly understood. Objectives: To determine the role of necroptosis in COPD. Methods: Total and active (phosphorylated) RIPK3 and MLKL were measured in the lung tissue of patients with COPD and control subjects without COPD. Necroptosis-related mRNA and proteins as well as cell death were examined in lungs and pulmonary macrophages of mice with cigarette smoke (CS)-induced experimental COPD. The responses of Ripk32/2 and Mlkl2/2 mice to acute and chronic CS exposure were compared with those of wild-type mice. The combined inhibition of apoptosis (with the pan-caspase inhibitor quinoline-Val-Asp-difluorophenoxymethylketone [qVD-OPh]) and necroptosis (with deletion of Mlkl in mice) was assessed. Measurements and Main Results: The total MLKL protein in the epithelium and macrophages and the pRIPK3 and pMLKL in lung tissue were increased in patients with severe COPD compared with never-smokers or smoker control subjects without COPD. Necroptosis-related mRNA and protein levels were increased in the lungs and macrophages in CS-exposed mice and experimental COPD. Ripk3 or Mlkl deletion prevented airway inflammation upon acute CS exposure. Ripk3 deficiency reduced airway inflammation and remodeling as well as the development of emphysematous pathology after chronic CS exposure. Mlkl deletion and qVD-OPh treatment reduced chronic CS-induced airway inflammation, but only Mlkl deletion prevented airway remodeling and emphysema. Ripk3 or Mlkl deletion and qVD-OPh treatment reduced CS-induced lung-cell death. Conclusions: Necroptosis is induced by CS exposure and is increased in the lungs of patients with COPD and in experimental COPD. Inhibiting necroptosis attenuates CS-induced...
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, vol. 12, no. 1.
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Zinc is an essential nutrient for the virulence of bacterial pathogens such as
Streptococcus pneumoniae
. Many Gram-positive bacteria use a two-domain lipoprotein for zinc acquisition, but how this class of metal-recruiting proteins acquire zinc and interact with the uptake machinery has remained poorly defined.
Luu, LDW, Payne, M, Zhang, X, Luo, L & Lan, R 2021, 'Development and comparison of novel multiple cross displacement amplification (MCDA) assays with other nucleic acid amplification methods for SARS-CoV-2 detection', Scientific Reports, vol. 11, no. 1.
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AbstractThe development of alternative isothermal amplification assays including multiple cross displacement amplification (MCDA) may address speed and portability limitations of real-time PCR (rt-PCR) methods for SARS-CoV-2 detection. We developed a novel SARS-CoV-2 MCDA assay and compared its speed and sensitivity to loop-mediated isothermal amplification (LAMP) and rt-PCR. Two MCDA assays targeting SARS-CoV-2 N gene and ORF1ab were designed. The fastest time to detection and sensitivity of MCDA was compared to LAMP and rt-PCR using DNA standards and transcribed RNA. For the N gene, MCDA was faster than LAMP and rt-PCR by 10 and 20 min, respectively with fastest time to detection at 5.2 min. rt-PCR had the highest sensitivity with the limit of detection at 10 copies/µl compared with MCDA (100 copies/µl) and LAMP (500 copies/µl). For ORF1ab, MCDA and LAMP had similar speed with fastest time to detection at 9.7 and 8.4 min, respectively. LAMP was more sensitive for ORF1ab detection with 50 copies/µl compared to MCDA (500 copies/µl). In conclusion, different nucleic acid amplification methods provide different advantages. MCDA is the fastest nucleic acid amplification method for SARS-CoV-2 while rt-PCR is the most sensitive. These advantages should be considered when determining the most suitable nucleic acid amplification methods for different applications.
Ma, H, Li, J, Yang, J, Wang, N, Liu, Z, Wang, T, Su, D, Wang, C & Wang, G 2021, 'Bismuth Nanoparticles Anchored on Ti 3 C 2 T x MXene Nanosheets for High‐Performance Sodium‐Ion Batteries', Chemistry – An Asian Journal, vol. 16, no. 22, pp. 3774-3780.
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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, vol. 16, no. 16, pp. 2314-2320.
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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: Applied Physics, vol. 54, no. 18, pp. 183001-183001.
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Abstract
Sun, wind and tides have huge potential in providing us electricity in an environmental-friendly way. However, its intermittency and non-dispatchability are major reasons preventing full-scale adoption of renewable energy generation. Energy storage will enable this adoption by enabling a constant and high-quality electricity supply from these systems. But which storage technology should be considered is one of important issues. Nowadays, great effort has been focused on various kinds of batteries to store energy, lithium-related batteries, sodium-related batteries, zinc-related batteries, aluminum-related batteries and so on. Some cathodes can be used for these batteries, such as sulfur, oxygen, layered compounds. In addition, the construction of these batteries can be changed into flexible, flow or solid-state types. There are many challenges in electrode materials, electrolytes and construction of these batteries and research related to the battery systems for energy storage is extremely active. With the myriad of technologies and their associated technological challenges, we were motivated to assemble this 2020 battery technology roadmap.
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, vol. 27, no. 4, pp. 688-699.
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Macdonald, PS, Gorrie, N, Brennan, X, Aili, SR, De Silva, R, Jha, SR, Fritis-Lamora, R, Montgomery, E, Wilhelm, K, Pierce, R, Lam, F, Schnegg, B, Hayward, C, Jabbour, A, Kotlyar, E, Muthiah, K, Keogh, AM, Granger, E, Connellan, M, Watson, A, Iyer, A & Jansz, PC 2021, 'The impact of frailty on mortality after heart transplantation', The Journal of Heart and Lung Transplantation, vol. 40, no. 2, pp. 87-94.
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BACKGROUND
Frailty is prevalent in the patients with advanced heart failure; however, its impact on clinical outcomes after heart transplantation (HTx) is unclear. The aim of this study was to assess the impact of pre-transplant frailty on mortality and the duration of hospitalization after HTx.
METHODS
We retrospectively reviewed the post-transplant outcomes of 140 patients with advanced heart failure who had undergone frailty assessment within the 6-month interval before HTx: 43 of them were frail (F) and 97 were non-frail (NF).
RESULTS
Post-transplant survival rates for the NF cohort at 1 and 12 months were 97% (93–100) and 95% (91–99) (95% CI), respectively. In contrast, post-transplant survival rates for the F cohort at the same time points were 86% (76–96) and 74% (60–84) (p < 0.0008 vs NF cohort), respectively. The Cox proportional hazards regression analysis demonstrated that pre-transplant frailty was an independent predictor of post-transplant mortality with a hazard ratio of 3.8 (95% CI: 1.4–10.5). Intensive care unit and hospital length of stay were 2 and 7 days longer in the F cohort (both p < 0.05), respectively, than in the NF cohort.
CONCLUSIONS
Frailty within 6 months before HTx is independently associated with increased mortality and prolonged hospitalization after transplantation. Future research should focus on the development of strategies to mitigate the adverse effects of pre-transplant frailty.
Macnamara, J 2021, 'A ‘macro’ view of strategic communication management: Beyond ‘siloes’, dominant paradigms, and pandemics', Essachess : Journal for Communication Studies, vol. 14, no. 1, pp. 65-91.
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Communication in and by organizations is ostensibly managed under a plethora of titles and functions including public relations, communication management, corporate communication, marketing communication, organizational communication, and strategic communication. Theory in a number of these fields claims to include all internal and external communication in and by organizations. Building on previous literature, this analysis of the internal and external communication of three companies operating in three different countries explores the boundaries of contemporary communication management. In doing so, it challenges disciplinary ‘siloes’ and normative theories and suggests ways to reimagine the future. While three cases do not provide generalizable findings, this analysis adds weight to arguments for broadening understanding of strategic communication and contributes to discussion of paradigms and theories of public relations, as well as the future of corporate communication.
Macnamara, J 2021, 'Challenging post-communication: Beyond focus on a ‘few bad apples’ to multi-level public communication reform', Communication Research and Practice, vol. 7, no. 1, pp. 35-55.
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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, vol. 10, no. 2, pp. 237-262.
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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, Hosseinpour Mashkani, SM, Zhang, L, Shimoni, O, Stenzel, M, Zhou, J, Fazekas de St Groth, B & Jin, D 2021, 'Stable and Highly Efficient Antibody–Nanoparticles Conjugation', Bioconjugate Chemistry, vol. 32, no. 6, pp. 1146-1155.
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Maestrini, L & Wand, MP 2021, 'The Inverse G‐Wishart distribution and variational message passing', Australian & New Zealand Journal of Statistics, vol. 63, no. 3, pp. 517-541.
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Mahmodi, H, Piloni, A, Utama, RH & Kabakova, I 2021, 'Mechanical mapping of bioprinted hydrogel models by brillouin microscopy', Bioprinting, vol. 23, pp. e00151-e00151.
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Mahmood, A, Yuan, Z, Sui, X, Riaz, MA, Yu, Z, Liu, C, Chen, J, Wang, C, Zhao, S, Mahmood, N, Pei, Z, Wei, L & Chen, Y 2021, 'Foldable and scrollable graphene paper with tuned interlayer spacing as high areal capacity anodes for sodium-ion batteries', Energy Storage Materials, vol. 41, pp. 395-403.
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Mai-Prochnow, A, Zhou, R, Zhang, T, Ostrikov, K, 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, vol. 7, no. 1.
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AbstractBiofilms have several characteristics that ensure their survival in a range of adverse environmental conditions, including high cell numbers, close cell proximity to allow easy genetic exchange (e.g., for resistance genes), cell communication and protection through the production of an exopolysaccharide matrix. Together, these characteristics make it difficult to kill undesirable biofilms, despite the many studies aimed at improving the removal of biofilms. An elimination method that is safe, easy to deliver in physically complex environments and not prone to microbial resistance is highly desired. Cold atmospheric plasma, a lightning-like state generated from air or other gases with a high voltage can be used to make plasma-activated water (PAW) that contains many active species and radicals that have antimicrobial activity. Recent studies have shown the potential for PAW to be used for biofilm elimination without causing the bacteria to develop significant resistance. However, the precise mode of action is still the subject of debate. This review discusses the formation of PAW generated species and their impacts on biofilms. A focus is placed on the diffusion of reactive species into biofilms, the formation of gradients and the resulting interaction with the biofilm matrix and specific biofilm components. Such an understanding will provide significant benefits for tackling the ubiquitous problem of biofilm contamination in food, water and medical areas.
Maire, J, Girvan, SK, Barkla, SE, Perez-Gonzalez, A, Suggett, DJ, Blackall, LL & van Oppen, MJH 2021, 'Correction to: Intracellular bacteria are common and taxonomically diverse in cultured and in hospite algal endosymbionts of coral reefs', The ISME Journal, vol. 15, no. 7, pp. 2168-2170.
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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', The ISME Journal, vol. 15, no. 7, pp. 2028-2042.
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AbstractCorals 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.
Maitre, M, Chiaravalle, A, Horder, M, Chadwick, S & Beavis, A 2021, 'Evaluating the effect of barrel length on pellet distribution patterns of sawn-off shotguns', Forensic Science International, vol. 320, pp. 110685-110685.
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Mak, WCK & Walsh, S 2021, 'The Characterization of Steam Distillation as an Extraction Method to Extract Volatile Compounds from <i>Prunella vulgaris</i> and the Investigation of Their Anti-Tumorous Effect', Journal of Biosciences and Medicines, vol. 09, no. 08, pp. 120-142.
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Man, Z, Safaei, J, Zhang, Z, Wang, Y, Zhou, D, Li, P, Zhang, X, Jiang, L & Wang, G 2021, 'Serosa-Mimetic Nanoarchitecture Membranes for Highly Efficient Osmotic Energy Generation', Journal of the American Chemical Society, vol. 143, no. 39, pp. 16206-16216.
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Mandal, PK, Ballerin, G, Nolan, LM, Petty, NK & Whitchurch, CB 2021, 'Bacteriophage infection of Escherichia coli leads to the formation of membrane vesicles via both explosive cell lysis and membrane blebbing', Microbiology, vol. 167, no. 4.
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Membrane vesicles (MVs) are membrane-bound spherical nanostructures that prevail in all three domains of life. In Gram-negative bacteria, MVs are thought to be produced through blebbing of the outer membrane and are often referred to as outer membrane vesicles (OMVs). We have recently described another mechanism of MV formation in
Pseudomonas aeruginosa
that involves explosive cell-lysis events, which shatters cellular membranes into fragments that rapidly anneal into MVs. Interestingly, MVs are often observed within preparations of lytic bacteriophage, however the source of these MVs and their association with bacteriophage infection has not been explored. In this study we aimed to determine if MV formation is associated with lytic bacteriophage infection. Live super-resolution microscopy demonstrated that explosive cell lysis of
Escherichia coli
cells infected with either bacteriophage T4 or T7, resulted in the formation of MVs derived from shattered membrane fragments. Infection by either bacteriophage was also associated with the formation of membrane blebs on intact bacteria. TEM revealed multiple classes of MVs within phage lysates, consistent with multiple mechanisms of MV formation. These findings suggest that bacteriophage infection may be a major contributor to the abundance of bacter...
Mann, R, Holmes, A, McNeilly, O, Cavaliere, R, Sotiriou, GA, Rice, SA & Gunawan, C 2021, 'Evolution of biofilm-forming pathogenic bacteria in the presence of nanoparticles and antibiotic: adaptation phenomena and cross-resistance', Journal of Nanobiotechnology, vol. 19, no. 1.
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Abstract
Background
Treatment of bacterial biofilms are difficult and in many cases, expensive. Bacterial biofilms are naturally more resilient to antimicrobial agents than their free-living planktonic counterparts, rendering the community growth harder to control. The present work described the risks of long-term use of an important alternative antimicrobial, silver nanoparticles (NAg), for the first time, on the dominant mode of bacterial growth.
Results
NAg could inhibit the formation as well as eradicating an already grown biofilm of Pseudomonas aeruginosa, a pathogen notorious for its resilience to antibiotics. The biofilm-forming bacterium however, evolved a reduced sensitivity to the nanoparticle. Evidence suggests that survival is linked to the development of persister cells within the population. A similar adaptation was also seen upon prolonged exposures to ionic silver (Ag+). The persister population resumed normal growth after subsequent passage in the absence of silver, highlighting the potential risks of recurrent infections with long-term NAg (and Ag+) treatments of biofilm growth. The present study further observed a potential silver/antibiotic cross-resistance, whereby NAg (as well as Ag+) could not eradicate an already growing gentamicin-resistant P. aeruginosa biofilm. The phenomena is thought to result from the hindered biofilm penetration of the silver species. In contrast, both silver formulations inhibited biofilm formation of the resistant strain, presenting a promising avenue for the control of biofilm-forming antibiotic-resistant bacteria.
Concl...
Mann, R, Mitsidis, D, Xie, Z, McNeilly, O, Ng, YH, Amal, R & Gunawan, C 2021, 'Antibacterial Activity of Reduced Graphene Oxide', Journal of Nanomaterials, vol. 2021, pp. 1-10.
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The increasing biological use of graphene-based materials has prompted research inquiries on their effects on microorganisms. The work herein reported different types of microbiological activity of reduced graphene oxide (RGO). At relatively high concentrations (200 and 400 μg/mL), RGO exhibited antibacterial activity on the model bacterium Escherichia coli, while at lower concentrations (10 and 50 μg/mL), interestingly, no antibacterial effect was observed. Instead, an increase in the viable population after exposure at lower concentrations was observed, verified by colony counting and fluorescence microscopy. Further investigation ruled out the possibility of nutrient release from RGO being responsible for this growth-enhancing effect, whereby a comparable number of viable cells were found in the particle-free RGO leachate systems relative to the control. A before and after exposure X-ray photoelectron spectroscopy (XPS) analysis of the RGO detected less presence of C-C bond on the particle surface, suggesting the ability of the bacterium for the use of the carbon-based materials for growth. This potential RGO-cell interaction is further supported by the observed emergence of C-N bond on the particle surface, the nitrogen moieties most likely of bacterial (cell envelope) origins. Although still an early evidence, such RGO-cell interactions could explain the viable cell increase observed at the lower concentration RGO systems. The present study highlights the concentration-dependent microbiological effects of RGO, clarifying the contradicting reports on the growth enhancing versus antibacterial effect of graphene-based materials. The knowledge is important not only for the antibacterial formulation of carbon-based materials but also when assessing their environmental impact.
Manning, EE, Bradfield, LA & Iordanova, MD 2021, 'Adaptive behaviour under conflict: Deconstructing extinction, reversal, and active avoidance learning', Neuroscience & Biobehavioral Reviews, vol. 120, pp. 526-536.
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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, vol. 18, no. 14, pp. 7431-7431.
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Air pollution exposure during pregnancy may be a risk factor for altered immune maturation in the offspring. We investigated the association between ambient air pollutants during pregnancy and cell populations in cord blood from babies born to mothers with asthma enrolled in the Breathing for Life Trial. For each patient (n = 91), daily mean ambient air pollutant levels were extracted during their entire pregnancy for sulfur dioxide (SO2), nitric oxide, nitrogen dioxide, carbon monoxide, ozone, particulate matter <10 μm (PM10) or <2.5 μm (PM2.5), humidity, and temperature. Ninety-one cord blood samples were collected, stained, and assessed using fluorescence-activated cell sorting (FACS). Principal Component (PC) analyses of both air pollutants and cell types with linear regression were employed to define associations. Considering risk factors and correlations between PCs, only one PC from air pollutants and two from cell types were statistically significant. PCs from air pollutants were characterized by higher PM2.5 and lower SO2 levels. PCs from cell types were characterized by high numbers of CD8 T cells, low numbers of CD4 T cells, and by high numbers of plasmacytoid dendritic cells (pDC) and low numbers of myeloid DCs (mDCs). PM2.5 levels during pregnancy were significantly associated with high numbers of pDCs (p = 0.006), and SO2 with high numbers of CD8 T cells (p = 0.002) and low numbers of CD4 T cells (p = 0.011) and mDCs (p = 4.43 × 10−6) in cord blood. These data suggest that ambient SO2 and PM2.5 exposure are associated with shifts in cord blood cell types that are known to play significant roles in inflammatory respiratory disease in childhood.
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, vol. 10, no. 4, pp. 351-351.
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We recently described the genetic antimicrobial resistance and virulence profile of a collection of 279 commensal E. coli of food-producing animal (FPA), pet, wildlife and human origin. Phenotypic antimicrobial resistance (AMR) and the role of commensal E. coli as reservoir of extra-intestinal pathogenic Escherichia coli (ExPEC) virulence-associated genes (VAGs) or as potential ExPEC pathogens were evaluated. The most common phenotypic resistance was to tetracycline (76/279, 27.24%), sulfamethoxazole/trimethoprim (73/279, 26.16%), streptomycin and sulfisoxazole (71/279, 25.45% both) among the overall collection. Poultry and rabbit were the sources mostly associated to AMR, with a significant resistance rate (p > 0.01) to quinolones, streptomycin, sulphonamides, tetracycline and, only for poultry, to ampicillin and chloramphenicol. Finally, rabbit was the source mostly associated to colistin resistance. Different pandemic (ST69/69*, ST95, ST131) and emerging (ST10/ST10*, ST23, ST58, ST117, ST405, ST648) ExPEC sequence types (STs) were identified among the collection, especially in poultry source. Both ST groups carried high number of ExPEC VAGs (pandemic ExPEC STs, mean = 8.92; emerging ExPEC STs, mean = 6.43) and showed phenotypic resistance to different antimicrobials (pandemic ExPEC STs, mean = 2.23; emerging ExPEC STs, mean = 2.43), suggesting their role as potential ExPEC pathogens. Variable phenotypic resistance and ExPEC VAG distribution was also observed in uncommon ExPEC lineages, suggesting commensal flora as a potential reservoir of virulence (mean = 3.80) and antimicrobial resistance (mean = 1.69) determinants.
Mathieu, C, Gonzalez, A, Garcia, A, Johow, M, Badia, C, Jara, C, Nuñez, P, Neira, V, Montiel, NA, Killian, ML & Brito, BP 2021, 'H7N6 low pathogenic avian influenza outbreak in commercial turkey farms in Chile caused by a native South American Lineage', Transboundary and Emerging Diseases, vol. 68, no. 1, pp. 2-12.
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© 2019 Blackwell Verlag GmbH In December 2016, low pathogenic avian influenza (LPAI) caused by an H7N6 subtype was confirmed in a grow-out turkey farm located in Valparaiso Region, Chile. Depopulation of exposed animals, zoning, animal movement control and active surveillance were implemented to contain the outbreak. Two weeks later, a second grow-out turkey farm located 70 km north of the first site was also infected by H7N6 LPAI, which subsequently spilled over to one backyard poultry flock. The virus involved in the outbreak shared a close genetic relationship with Chilean aquatic birds’ viruses collected in previous years. The A/turkey/Chile/2017(H7N6) LPAI virus belonged to a native South American lineage. Based on the H7 and most of the internal genes’ phylogenies, these viruses were also closely related to the ones that caused a highly pathogenic avian influenza outbreak in Chile in 2002. Results from this study help to understand the regional dynamics of influenza outbreaks, highlighting the importance of local native viruses circulating in the natural reservoir hosts.
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, vol. 10, no. 6, pp. 1542-1542.
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The multifold benefits of regular physical exercise have been largely demonstrated in human and animal models. Several studies have reported the beneficial effects of physical activity, both in peripheral tissues and in the central nervous system (CNS). Regular exercise improves cognition, brain plasticity, neurogenesis and reduces the symptoms of neurodegenerative diseases, making timeless the principle of “mens sana in corpore sano” (i.e., a healthy mind in a healthy body). Physical exercise promotes morphological and functional changes in the brain, acting not only in neurons but also in astrocytes, which represent the most numerous glial cells in the brain. The multiple effects of exercise on astrocytes comprise the increased number of new astrocytes, the maintenance of basal levels of catecholamine, the increase in glutamate uptake, the major release of trophic factors and better astrocytic coverage of cerebral blood vessels. The purpose of this review is to highlight the effects of exercise on brain function, emphasize the role of astrocytes in the healthy CNS, and provide an update for a better understanding of the effects of physical exercise in the modulation of astrocyte function.
Maugeri, G, D'Agata, V, Trovato, B, Roggio, F, Castorina, A, Vecchio, M, Di Rosa, M & Musumeci, G 2021, 'The role of exercise on peripheral nerve regeneration: from animal model to clinical application', Heliyon, vol. 7, no. 11, pp. e08281-e08281.
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McCausland, JW, Yang, X, Squyres, GR, Lyu, Z, Bruce, KE, Lamanna, MM, Söderström, B, Garner, EC, Winkler, ME, Xiao, J & Liu, J 2021, 'Treadmilling FtsZ polymers drive the directional movement of sPG-synthesis enzymes via a Brownian ratchet mechanism', Nature Communications, vol. 12, no. 1.
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AbstractThe FtsZ protein is a central component of the bacterial cell division machinery. It polymerizes at mid-cell and recruits more than 30 proteins to assemble into a macromolecular complex to direct cell wall constriction. FtsZ polymers exhibit treadmilling dynamics, driving the processive movement of enzymes that synthesize septal peptidoglycan (sPG). Here, we combine theoretical modelling with single-molecule imaging of live bacterial cells to show that FtsZ’s treadmilling drives the directional movement of sPG enzymes via a Brownian ratchet mechanism. The processivity of the directional movement depends on the binding potential between FtsZ and the sPG enzyme, and on a balance between the enzyme’s diffusion and FtsZ’s treadmilling speed. We propose that this interplay may provide a mechanism to control the spatiotemporal distribution of active sPG enzymes, explaining the distinct roles of FtsZ treadmilling in modulating cell wall constriction rate observed in different bacteria.
McDonald, AG, Murray, BR, Krix, DW & Murray, ML 2021, 'Complex soil contamination severely impacts seed-sown crop viability in Australia', April 2021, vol. 15, no. 15(04):2021, pp. 531-537.
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Food security is a critical issue for many global communities. Heavy metal contamination in soils present a major and ongoing ecological risk associated with human activities which may impact the viability and safety of seed-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 vegetable crop species to copper, zinc, and lead contamination at levels likely to be found in contaminated regions in Australia. We compared the germination attributes of days to first germination, germination period, and total proportion of seeds germinated under concentration limits of heavy metals detected at degraded sites and current Australian National Environment Protection Measure thresholds for domestic soils (i.e., copper 6,000 mg kg-1, zinc 4,700 mg kg-1, lead 300 mg kg-1). The combined 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-contaminated conditions. Seed viability was significantly decreased in mulberry (M. alba var. tatarica, M. nigra, and M. rubra) and lettuce (L. sativa), with lowered seed germination in all metals compared to carrot (D. carota), radish (R. sativus), tomato (S. lycopersicum) and common bean (P. vulgaris). These results indicate heavy metal contamination is a notable risk to seed-sown crop species, with multi-metal contamination events likely to be severely damaging to 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 (Lond), vol. 16, no. 22, pp. 1999-2012.
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Background: Overexpression of sFlt-1 or modulation of FKBPL, key antiangiogenic proteins, are important in the pathogenesis of preeclampsia. Methods: A newly developed nonviral gene-delivery system, RALA, capable of overexpressing sFlt-1 (e15a isoform) was delivered in vivo in transgenic haploinsufficient (Fkbpl+/-) mice. RALA was also used in vitro to deliver human Flt1 (hFlt1) in trophoblast cells. Results: Serum stable and nontoxic RALA/DNA-based nanoparticles induced an increase in sFlt-1 protein levels in the blood and total protein in the urine; the effect was more pronounced in Fkbpl+/- mice. In vitro, RALA-hFlt nanoparticles significantly reduced secretion of sFlt-1 in trophoblast cells. Conclusion: The RALA-based genetic nanodelivery system can be safely and effectively applied to emulate preeclampsia-like features or reduce sFlt-1 levels in vitro.
McNeilly, O, Mann, R, Hamidian, M & Gunawan, C 2021, 'Emerging Concern for Silver Nanoparticle Resistance in Acinetobacter baumannii and Other Bacteria', Frontiers in Microbiology, vol. 12.
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The misuse of antibiotics combined with a lack of newly developed ones is the main contributors to the current antibiotic resistance crisis. There is a dire need for new and alternative antibacterial options and nanotechnology could be a solution. Metal-based nanoparticles, particularly silver nanoparticles (NAg), have garnered widespread popularity due to their unique physicochemical properties and broad-spectrum antibacterial activity. Consequently, NAg has seen extensive incorporation in many types of products across the healthcare and consumer market. Despite clear evidence of the strong antibacterial efficacy of NAg, studies have raised concerns over the development of silver-resistant bacteria. Resistance to cationic silver (Ag+) has been recognised for many years, but it has recently been found that bacterial resistance to NAg is also possible. It is also understood that exposure of bacteria to toxic heavy metals like silver can induce the emergence of antibiotic resistance through the process of co-selection. Acinetobacter baumannii is a Gram-negative coccobacillus and opportunistic nosocomial bacterial pathogen. It was recently listed as the “number one” critical level priority pathogen because of the significant rise of antibiotic resistance in this species. NAg has proven bactericidal activity towards A. baumannii, even against strains that display multi-drug resistance. However, despite ample evidence of heavy metal (including silver; Ag+) resistance in this bacterium, combined with reports of heavy metal-driven co-selection of antibiotic resistance, little research has been dedicated to assessing the potential for NAg resistance development in A. baumannii. This is worrisome, as the increasingly indiscriminate use of NAg could promote the development of silver resistance in this species, like what has occurred with antibi...
Meakin, GE, Kokshoorn, B, Oorschot, RAH & Szkuta, B 2021, 'Evaluating forensic DNA evidence: Connecting the dots', WIREs Forensic Science, vol. 3, no. 4.
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Mehraj, H, Takahashi, S, Miyaji, N, Akter, A, Suzuki, Y, Seki, M, Dennis, ES & Fujimoto, R 2021, 'Characterization of Histone H3 Lysine 4 and 36 Tri-methylation in Brassica rapa L.', Frontiers in Plant Science, vol. 12.
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Covalent modifications of histone proteins act as epigenetic regulators of gene expression. We report the distribution of two active histone marks (H3K4me3 and H3K36me3) in 14-day leaves in two lines of Brassica rapa L. by chromatin immunoprecipitation sequencing. Both lines were enriched with H3K4me3 and H3K36me3 marks at the transcription start site, and the transcription level of a gene was associated with the level of H3K4me3 and H3K36me3. H3K4me3- and H3K36me3-marked genes showed low tissue-specific gene expression, and genes with both H3K4me3 and H3K36me3 had a high level of expression and were constitutively expressed. Bivalent active and repressive histone modifications such as H3K4me3 and H3K27me3 marks or antagonistic coexistence of H3K36me3 and H3K27me3 marks were observed in some genes. Expression may be susceptible to changes by abiotic and biotic stresses in genes having both H3K4me3 and H3K27me3 marks. We showed that the presence of H3K36me3 marks was associated with different gene expression levels or tissue specificity between paralogous paired genes, suggesting that H3K36me3 might be involved in subfunctionalization of the subgenomes.
Mehta, M, Malyla, V, Paudel, KR, Chellappan, DK, Hansbro, PM, Oliver, BG & Dua, K 2021, 'Berberine loaded liquid crystalline nanostructure inhibits cancer progression in adenocarcinomic human alveolar basal epithelial cells in vitro', Journal of Food Biochemistry, vol. 45, no. 11, p. e13954.
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Metastasis represents the leading cause of death in lung cancer patients. C-X-C Motif Chemokine Ligand 8 (CXCL-8), Chemokine (C-C motif) ligand 20 (CCL-20) and heme oxygenase -1 (HO-1) play an important role in cancer cell proliferation and migration. Berberine is an isoquinoline alkaloid isolated from several herbs in the Papaveraceae family that exhibits anti-inflammatory, anticancer and antidiabetic properties. Therefore, the aim of present study is to investigate the inhibitory potential of berberine monoolein loaded liquid crystalline nanoparticles (berberine-LCNs) against cancer progression. Berberine-LCNs were prepared by mixing berberine, monoolein and poloxamer 407 (P407) using ultrasonication method. A549 cells were treated with or without 5 µM dose of berberine LCNs for 24 hr and total cellular protein was extracted and further analyzed for the protein expression of CCl-20, CXCL-8 and HO-1 using human oncology array kit. Our results showed that berberine-LCNs significantly reduced the expression of CCl-20, CXCL-8 and HO-1 at dose of 5µM. Collectively, our findings suggest that berberine-LCNs have inhibitory effect on inflammation/oxidative stress related cytokines i.e. CCL20, CXCL-8, and HO-1 which could be a novel therapeutic target for the management of lung cancer. PRACTICAL APPLICATIONS: Berberine is an isoquinoline alkaloid extracted from various plants of Papaveraceae family. CXCL-8, CCL-20 and HO-1 play an important role in cancer progression. Our study showed that Berberine LCNs significantly downregulate the expression of CXCL-8, CCL-20 and HO-1 which suggests that Berberine loaded nanoparticles could be a promising therapeutic alternative for the management of lung cancer.
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, MK, 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, vol. 337, pp. 629-644.
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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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Aim: In the present study, the inhibitory potential of rutin-loaded liquid crystalline nanoparticles (LCNs) on oxidative stress was determined in human bronchial epithelial cells (BEAS-2B) by analysing the expression levels of different antioxidant (NADPH quinine oxidoreductase-1 ( NQO1); γ-glutamyl cysteine synthetase catalytic subunit ( GCLC)) and pro-oxidant (NADPH oxidase (Nox)-4; Nox2B) genes. Results: Our findings revealed that the rutin-loaded LCNs inhibited the genes, namely Nox2B and Nox4, which caused oxidative stress. In addition, these nanoparticles demonstrated an upregulation in the expression of the antioxidant genes Gclc and Nqo-1 in a dose-dependent manner. Conclusion: The study indicates the promising potential of rutin-loaded LCNs as an effective treatment strategy in patients with high oxidant loads in various respiratory diseases.
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, pp. 102303-102303.
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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, vol. 8, no. 6, pp. 2003325-2003325.
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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, vol. 413, no. 21, pp. 5509-5516.
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Melo, EM, Oliveira, VLS, Boff, D & Galvão, I 2021, 'Pulmonary macrophages and their different roles in health and disease', The International Journal of Biochemistry & Cell Biology, vol. 141, pp. 106095-106095.
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Mena, J, Ariyama, N, Navarro, C, Quezada, M, Brevis, C, Rojas, D, Medina, RA, Brito, B, Ruiz, Á & Neira, V 2021, 'Ubiquitous influenza A virus in Chilean swine before the H1N1pdm09 introduction', Transboundary and Emerging Diseases, vol. 68, no. 6, pp. 3174-3179.
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Mendelson, N, Chugh, D, Reimers, JR, Cheng, TS, Gottscholl, A, Long, H, Mellor, CJ, Zettl, A, Dyakonov, V, Beton, PH, Novikov, SV, Jagadish, C, Tan, HH, Ford, MJ, Toth, M, Bradac, C & Aharonovich, I 2021, 'Identifying carbon as the source of visible single-photon emission from hexagonal boron nitride', Nature Materials, vol. 20, no. 3, pp. 321-328.
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Mendelson, N, Morales‐Inostroza, L, Li, C, Ritika, R, Nguyen, MAP, Loyola‐Echeverria, J, Kim, S, Götzinger, S, Toth, M & Aharonovich, I 2021, 'Grain Dependent Growth of Bright Quantum Emitters in Hexagonal Boron Nitride', Advanced Optical Materials, vol. 9, no. 1, pp. 2001271-2001271.
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Menounos, S, Hansbro, PM, Diwan, AD & Das, A 2021, 'Pathophysiological Correlation between Cigarette Smoking and Amyotrophic Lateral Sclerosis', NeuroSci, vol. 2, no. 2, pp. 120-134.
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Cigarette smoke (CS) has been consistently demonstrated to be an environmental risk factor for amyotrophic lateral sclerosis (ALS), although the molecular pathogenic mechanisms involved are yet to be elucidated. Here, we propose different mechanisms by which CS exposure can cause sporadic ALS pathogenesis. Oxidative stress and neuroinflammation are widely implicated in ALS pathogenesis, with blood–spinal cord barrier disruption also recognised to be involved in the disease process. In addition, immunometabolic, epigenetic and microbiome alterations have been implicated in ALS recently. Identification of the underlying pathophysiological mechanisms that underpin CS-associated ALS will drive future research to be conducted into new targets for treatment.
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, vol. 16, no. 4, pp. 1785-1801.
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Mitchell, AB, Li, C-X, Oliver, BGG, Holmes, EC & Glanville, AR 2021, 'High-resolution Metatranscriptomic Characterization of the Pulmonary RNA Virome After Lung Transplantation', Transplantation, vol. 105, no. 12, pp. 2546-2553.
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Miyaji, N, Akter, MA, Suzukamo, C, Mehraj, H, Shindo, T, Itabashi, T, Okazaki, K, Shimizu, M, Kaji, M, Katsumata, M, Dennis, ES & Fujimoto, R 2021, 'Development of a New DNA Marker for Fusarium Yellows Resistance in Brassica rapa Vegetables', Plants, vol. 10, no. 6, pp. 1082-1082.
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In vegetables of Brassica rapa L., Fusarium oxysporum f. sp. rapae (For) or F. oxysporum f. sp. conglutinans (Foc) cause Fusarium yellows. A resistance gene against Foc (FocBr1) has been identified, and deletion of this gene results in susceptibility (focbr1-1). In contrast, a resistance gene against For has not been identified. Inoculation tests showed that lines resistant to Foc were also resistant to For, and lines susceptible to Foc were susceptible to For. However, prediction of disease resistance by a dominant DNA marker on FocBr1 (Bra012688m) was not associated with disease resistance of For in some komatsuna lines using an inoculation test. QTL-seq using four F2 populations derived from For susceptible and resistant lines showed one causative locus on chromosome A03, which covers FocBr1. Comparison of the amino acid sequence of FocBr1 between susceptible and resistant alleles (FocBr1 and FocBo1) showed that six amino acid differences were specific to susceptible lines. The presence and absence of FocBr1 is consistent with For resistance in F2 populations. These results indicate that FocBr1 is essential for For resistance, and changed amino acid sequences result in susceptibility to For. This susceptible allele is termed focbr1-2, and a new DNA marker (focbr1-2m) for detection of the focbr1-2 allele was developed.
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, C-H, 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, vol. 147, no. 6, pp. 2134-2145.e20.
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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, AMT, 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.
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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.
Mohanty, M, Zhang, M, Asghar, MR & Russello, G 2021, 'e-PRNU: Encrypted Domain PRNU-Based Camera Attribution for Preserving Privacy', IEEE Transactions on Dependable and Secure Computing, vol. 18, no. 1, pp. 426-437.
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IEEE Photo Response Non-Uniformity (PRNU) noise-based source camera attribution is a popular digital forensic method. In this method, a camera fingerprint computed from a set of known images of the camera is matched against the extracted noise of an anonymous questionable image to find out if the camera had taken the anonymous image. The possibility of privacy leak, however, is one of the main concerns of the PRNU-based method. Using the camera fingerprint (or the extracted noise), an adversary can identify the owner of the camera by matching the fingerprint with the noise of an image (or with the fingerprint computed from a set of images) crawled from a social media account. In this article, we address this privacy concern by encrypting both the fingerprint and the noise using the Boneh-Goh-Nissim (BGN) encryption scheme, and performing the matching in encrypted domain. To overcome leakage of privacy from the content of an image that is used in the fingerprint calculation, we compute the fingerprint within a trusted environment, such as ARM TrustZone. We present e-PRNU that aims at minimizing privacy loss and allows authorized forensic experts to perform camera attribution. The security analysis shows that the proposed approach is semantically secure.
Mohd Yusop, AY, Xiao, L & Fu, S 2021, 'Fluorescence polarisation for high‐throughput screening of adulterated food products via phosphodiesterase 5 inhibition assay', Drug Testing and Analysis, vol. 13, no. 5, pp. 953-964.
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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, vol. 322, 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.
Mohd Yusop, AY, Xiao, L & Fu, S 2021, 'Suspected‐target and non‐targeted screenings of phosphodiesterase 5 inhibitors in herbal remedies using liquid chromatography–quadrupole time‐of‐flight–mass spectrometry', Drug Testing and Analysis, vol. 13, no. 5, pp. 965-976.
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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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Monaco, CJ, Nagelkerken, I, Booth, DJ, Figueira, WF, Gillanders, BM, Schoeman, DS & Bradshaw, CJA 2021, 'Opposing life stage‐specific effects of ocean warming at source and sink populations of range‐shifting coral‐reef fishes', Journal of Animal Ecology, vol. 90, no. 3, pp. 615-627.
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Climate change is altering the latitudinal distributions of species, with their capacity to keep pace with a shifting climate depending on the stochastic expression of population growth rates, and the influence of compensatory density feedback on age-specific survival rates. We use population-abundance time series at the leading edge of an expanding species' range to quantify the contribution of stochastic environmental drivers and density feedbacks to the dynamics of life stage-specific population growth. Using a tropical, range-shifting Indo-Pacific damselfish (Abudefduf vaigiensis) as a model organism, we applied variants of the phenomenological Gompertz-logistic model to a 14-year dataset to quantify the relative importance of density feedback and stochastic environmental drivers on the separate and aggregated population growth rates of settler and juvenile life stages. The top-ranked models indicated that density feedback negatively affected the growth of tropical settlers and juveniles. Rates of settlement were negatively linked to temperatures experienced by parents at potential source populations in the tropics, but their subsequent survival and that of juveniles increased with the temperatures experienced at the temperate sink. Including these stochastic effects doubled the deviance explained by the models, corroborating an important role of temperature. By incorporating sea-surface temperature projections for the remainder of this century into these models, we anticipate improved conditions for the population growth of juvenile coral-reef fishes, but not for settlers in temperate ecosystems. Previous research has highlighted the association between temperature and the redistribution of species. Our analyses reveal the contrasting roles of different life stages in the dynamics of range-shifting species responding to climate change, as they transition from vagrancy to residency in their novel ranges.
Morris, S, Wright, K, Malyla, V, Britton, WJ, Hansbro, PM, Manuneedhi Cholan, P & Oehlers, SH 2021, 'Exposure to the gut microbiota from cigarette smoke-exposed mice exacerbates cigarette smoke extract-induced inflammation in zebrafish larvae', Current Research in Immunology, vol. 2, pp. 229-236.
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Murashko, K, Li, D, Danilov, DL, Notten, PHL, Pyrhönen, J & Jokiniemi, J 2021, 'Applicability of Heat Generation Data in Determining the Degradation Mechanisms of Cylindrical Li-Ion Batteries', Journal of The Electrochemical Society, vol. 168, no. 1, pp. 010511-010511.
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The applicability of heat generation data obtained after cylindrical Li-ion cells discharging with a constant current was analyzed thoroughly to determine cell degradation mechanisms. Different commercial and noncommercial cylindrical Li-ion cells, wherein graphite was used for negative electrode creation, were considered in this study and the degradation mechanisms were analyzed during cycling and storage. The heat generation in the cylindrical cells was estimated using heat flux and temperature measurements of the cell surface. The results obtained using analysis of the heat generation data were compared with those obtained using differential voltage analysis. The use of the heat generation data was shown to improve the detection and separation of the degradation mechanisms in Li-ion batteries during cycling and storage. The differential curve, which is based on the heat generation data, was proposed to investigate the degradation mechanisms. Moreover, the effects of the C-rate current and temperature on the form of the proposed differential curve were evaluated.
Muus, C, Luecken, MD, Eraslan, G, Sikkema, L, Waghray, A, Heimberg, G, Kobayashi, Y, Vaishnav, ED, Subramanian, A, Smillie, C, Jagadeesh, KA, Duong, ET, Fiskin, E, Torlai Triglia, E, Ansari, M, Cai, P, Lin, B, Buchanan, J, Chen, S, Shu, J, Haber, AL, Chung, H, Montoro, DT, Adams, T, Aliee, H, Allon, SJ, Andrusivova, Z, Angelidis, I, Ashenberg, O, Bassler, K, Bécavin, C, Benhar, I, Bergenstråhle, J, Bergenstråhle, L, Bolt, L, Braun, E, Bui, LT, Callori, S, Chaffin, M, Chichelnitskiy, E, Chiou, J, Conlon, TM, Cuoco, MS, Cuomo, ASE, Deprez, M, Duclos, G, Fine, D, Fischer, DS, Ghazanfar, S, Gillich, A, Giotti, B, Gould, J, Guo, M, Gutierrez, AJ, Habermann, AC, Harvey, T, He, P, Hou, X, Hu, L, Hu, Y, Jaiswal, A, Ji, L, Jiang, P, Kapellos, TS, Kuo, CS, Larsson, L, Leney-Greene, MA, Lim, K, Litviňuková, M, Ludwig, LS, Lukassen, S, Luo, W, Maatz, H, Madissoon, E, Mamanova, L, Manakongtreecheep, K, Leroy, S, Mayr, CH, Mbano, IM, McAdams, AM, Nabhan, AN, Nyquist, SK, Penland, L, Poirion, OB, Poli, S, Qi, C, Queen, R, Reichart, D, Rosas, I, Schupp, JC, Shea, CV, Shi, X, Sinha, R, Sit, RV, Slowikowski, K, Slyper, M, Smith, NP, Sountoulidis, A, Strunz, M, Sullivan, TB, Sun, D, Talavera-López, C, Tan, P, Tantivit, J, Travaglini, KJ, Tucker, NR, Vernon, KA, Wadsworth, MH, Waldman, J, Wang, X, Xu, K, Yan, W, Zhao, W, Ziegler, CGK, Deutsch, GH, Dutra, J, Gaulton, KJ, Holden-Wiltse, J, Huyck, HL, Mariani, TJ, Misra, RS, Poole, C, Preissl, S, Pryhuber, GS, Rogers, L, Sun, X, Wang, A, Whitsett, JA, Xu, Y, Alladina, J, Banovich, NE, Barbry, P, Beane, JE, Bhattacharyya, RP, Black, KE, Brazma, A, Campbell, JD, Cho, JL, Collin, J, Conrad, C, de Jong, K, Desai, T, Ding, DZ, Eickelberg, O, Eils, R, Ellinor, PT, Faiz, A, Falk, CS, Farzan, M, Gellman, A, Getz, G, Glass, IA, Greka, A, Haniffa, M, Hariri, LP, Hennon, MW, Horvath, P, Hübner, N, Hung, DT, Huyck, HL, Janssen, WJ, Juric, D, Kaminski, N, Koenigshoff, M, Koppelman, GH, Krasnow, MA, Kropski, JA, Kuhnemund, M, Lafyatis, R, Lako, M, Lander, ES, Lee, H, Lenburg, ME, Marquette, C-H, Metzger, RJ, Linnarsson, S, Liu, G, Lo, YMD, Lundeberg, J, Marioni, JC, Mazzilli, SA, Medoff, BD, Meyer, KB, Miao, Z, Misharin, AV, Nawijn, MC, Nikolić, MZ, Noseda, M, Ordovas-Montanes, J, Oudit, GY, Pe’er, D, Powell, JE, Quake, SR, Rajagopal, J, Tata, PR, Rawlins, EL, Regev, A, Reid, ME, Reyfman, PA, Rieger-Christ, KM, Rojas, M & et al. 2021, 'Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics', Nature Medicine, vol. 27, no. 3, pp. 546-559.
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Mwampashi, MM, Sklibosios Nikitopoulos, C, Konstandatos, O & Rai, A 2021, 'Large Scale and Rooftop Solar Generation in the NEM: A Tale of Two Renewables Strategies'.
Mwampashi, MM, Sklibosios Nikitopoulos, C, Konstandatos, O & Rai, A 2021, 'Wind Generation and the Dynamics of Electricity Prices in Australia'.
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Australia's National Electricity Market (NEM) is experiencing one of the world's fastest and marked transitions toward variable renewable energy generation. This transformation poses challenges to system security and reliability and has triggered increased variability and uncertainty in electricity prices. By employing an exponential generalized autoregressive conditional heteroskedasticity (eGARCH) model, we gauge the effects of wind power generation on the dynamics of electricity prices in the NEM. We find that a 1 GWh increase in wind generation decreases daily prices up to 1.3 AUD/MWh and typically increases price volatility up to 2%. Beyond consumption and gas prices, hydro generation also contributes to an increase in electricity prices and their volatility. The cross-border interconnectors play a significant role in determining price levels and volatility dynamics. This underscores the important role of strategic provisions and investment in the connectivity within the NEM to ensure the reliable and effective delivery of renewable energy generation. Regulatory interventions, such as the carbon pricing mechanism and nationwide lockdown restrictions due to COVID-19 pandemic, also had a measurable impact on electricity price dynamics.
Naidu, V, Shah, B, Kamath, KS, Chien, A, Nagy, S, Pokhrel, A, Molloy, M, Hassan, KA & Paulsen, IT 2021, 'Identification of a Novel Ciprofloxacin Tolerance Gene, aciT , Which Contributes to Filamentation in Acinetobacter baumannii', Antimicrobial Agents and Chemotherapy, vol. 65, no. 6.
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Fluoroquinolones are one of the most prescribed broad-spectrum antibiotics. However, their effectiveness is being compromised by high rates of resistance in clinically important organisms, including
Acinetobacter baumannii
.
Nair, HAS, Subramoni, S, Poh, WH, Hasnuddin, NTB, Tay, M, Givskov, M, Tolker-Nielsen, T, Kjelleberg, S, McDougald, D & Rice, SA 2021, 'Carbon starvation of Pseudomonas aeruginosa biofilms selects for dispersal insensitive mutants', BMC Microbiology, vol. 21, no. 1.
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Abstract
Background
Biofilms disperse in response to specific environmental cues, such as reduced oxygen concentration, changes in nutrient concentration and exposure to nitric oxide. Interestingly, biofilms do not completely disperse under these conditions, which is generally attributed to physiological heterogeneity of the biofilm. However, our results suggest that genetic heterogeneity also plays an important role in the non-dispersing population of P. aeruginosa in biofilms after nutrient starvation.
Results
In this study, 12.2% of the biofilm failed to disperse after 4 d of continuous starvation-induced dispersal. Cells were recovered from the dispersal phase as well as the remaining biofilm. For 96 h starved biofilms, rugose small colony variants (RSCV) were found to be present in the biofilm, but were not observed in the dispersal effluent. In contrast, wild type and small colony variants (SCV) were found in high numbers in the dispersal phase. Genome sequencing of these variants showed that most had single nucleotide mutations in genes associated with biofilm formation, e.g. in wspF, pilT, fha1 and aguR. Complementation of those mutations restored starvation-induced dispersal from the biofilms. Because c-di-GMP is linked to biofilm formation and dispersal, we introduced a c-di-GMP reporter into the wild-type P. aeruginosa and monitored green fluorescent protein (GFP) expression before and after starvation-induced dispersal. Post dispersal, the microcolonies were smaller and significantly brighter in GFP intensity, suggesting the relative concentration of c-di-GMP per cell within the microcolonies was also increased. ...
Nair, PC, Gillani, TB, Rawling, T & Murray, M 2021, 'Differential inhibition of human CYP2C8 and molecular docking interactions elicited by sorafenib and its major N-oxide metabolite', Chemico-Biological Interactions, vol. 338, pp. 109401-109401.
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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, vol. 17, no. 9, pp. 1902085-1902085.
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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, vol. 215, pp. 117026-117026.
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Neira, V, Brito, B, Agüero, B, Berrios, F, Valdés, V, Gutierrez, A, Ariyama, N, Espinoza, P, Retamal, P, Holmes, EC, Gonzalez-Reiche, AS, Khan, Z, van de Guchte, A, Dutta, J, Miorin, L, Kehrer, T, Galarce, N, Almonacid, LI, Levican, J, van Bakel, H, García-Sastre, A & Medina, RA 2021, 'A household case evidences shorter shedding of SARS-CoV-2 in naturally infected cats compared to their human owners', Emerging Microbes & Infections, vol. 10, no. 1, pp. 376-383.
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Nemani, SSP, Vermeulen, CJ, Pech, M, Faiz, A, Oliver, BGG, van den Berge, M, Burgess, JK, Kopp, MV & Weckmann, M 2021, 'COL4A3 expression in asthmatic epithelium depends on intronic methylation and ZNF263 binding', ERJ Open Research, vol. 7, no. 2, pp. 00802-2020.
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BackgroundReduction of COL4A3, one of the six isoforms of collagen 4, in asthmatic airways results in increased inflammation and angiogenesis, implicating it as a central part of asthma pathogenesis. However, to date, the path underlying these diminished COL4A3 levels has been elusive. This study investigated a possible mechanism underlying the reduction of COL4A3 expression.MethodsBronchial biopsies of 76 patients with asthma and 83 controls were subjected to RNA-sequencing and DNA methylation bead arrays to identify expression and methylation changes. The binding of ZNF263 was analysed by chromatin-immunoprecipitation sequencing coupled with quantitative (q)PCR. Effects of ZNF263 silencing, using small interfering RNA, on the COL4A3 expression were studied using qPCR.ResultsCOL4A3 expression was significantly reduced in bronchial biopsies compared to healthy controls, whereas DNA methylation levels at cg11797365 were increased. COL4A3 expression levels were significantly low in asthmatics without inhaled corticosteroid (ICS) use, whereas the expression was not statistically different between asthmatics using ICS and controls. Methylation levels at cg11797365 in vitro were increased upon consecutive rhinovirus infections.ConclusionOur data indicate an epigenetic modification as a contributing factor for the loss of COL4A3 expression in asthmatic airway epithelium.
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, pp. 146964-146964.
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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, HM, Bulleri, F, Marín-Guirao, L, Pernice, M & Procaccini, G 2021, 'Photo-physiology and morphology reveal divergent warming responses in northern and southern hemisphere seagrasses', Marine Biology, vol. 168, no. 8.
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Nguyen, HM, Ralph, PJ, Marín‐Guirao, L, Pernice, M & Procaccini, G 2021, 'Seagrasses in an era of ocean warming: a review', Biological Reviews, vol. 96, no. 5, pp. 2009-2030.
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Nguyen, LN, Kumar, J, Vu, MT, Mohammed, JAH, Pathak, N, Commault, AS, Sutherland, D, Zdarta, J, Tyagi, VK & Nghiem, LD 2021, 'Biomethane production from anaerobic co-digestion at wastewater treatment plants: A critical review on development and innovations in biogas upgrading techniques', Science of The Total Environment, vol. 765, pp. 142753-142753.
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© 2020 Elsevier B.V. Anaerobic co-digestion (AcoD) can utilise spare digestion capacity at existing wastewater treatment plants (WWTP) to generate surplus biogas beyond the plant's internal energy requirement. Data from industry reports and the peer-reviewed literature show that through AcoD, numerous examples of WWTPs have become net energy producers, necessitating other high-value applications for surplus biogas. A globally emerging trend is to upgrade biogas to biomethane, which can then be used as town gas or transport fuel. Water, organic solvent and chemical scrubbing, pressure swing adsorption, membrane separation, and cryogenic technology are commercially available CO2 removal technologies for biogas upgrade. Although water scrubbing is currently the most widely applied technology due to low capital and operation cost, significant market growth in membrane separation has been seen over the 2015–2019 period. Further progress in materials engineering and sciences is expected and will further enhance the membrane separation competitiveness for biogas upgrading. Several emerging biotechnologies to i) improve biogas quality from AcoD; ii) accelerate the absorption rate, and iii) captures CO2 in microalgal culture have also been examined and discussed in this review. Through a combination of AcoD and biogas upgrade, more WWTPs are expected to become net energy producers.
Nguyen, LN, Vu, MT, Abu Hasan Johir, M, Pernice, M, Ngo, HH, Zdarta, J, Jesionowski, T & Nghiem, LD 2021, 'Promotion of direct interspecies electron transfer and potential impact of conductive materials in anaerobic digestion and its downstream processing - a critical review', Bioresource Technology, vol. 341, pp. 125847-125847.
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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, pp. 021103-021103.
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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, pp. 736821-736821.
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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, vol. 71, no. 3, pp. 565-582.
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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.
Nielsen, DA, Fierer, N, Geoghegan, JL, Gillings, MR, Gumerov, V, Madin, JS, Moore, L, Paulsen, IT, Reddy, TBK, Tetu, SG & Westoby, M 2021, 'Aerobic bacteria and archaea tend to have larger and more versatile genomes', Oikos, vol. 130, no. 4, pp. 501-511.
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Nieves, OA, Arnold, MD, Schmidt, MK, Steel, MJ & Poulton, CG 2021, 'Noise in Brillouin based information storage', Optics Express, vol. 29, no. 24, pp. 39486-39486.
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We theoretically and numerically study the efficiency of Brillouin-based opto-acoustic data storage in a photonic waveguide in the presence of thermal noise and laser phase noise. We compare the physics of the noise processes and how they affect different storage techniques, examining both amplitude and phase storage schemes. We investigate the effects of storage time and pulse properties on the quality of the retrieved signal and find that phase storage is less sensitive to thermal noise than amplitude storage.
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, vol. 38, no. 8, pp. 2343-2343.
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We present a numerical method for modeling noise in stimulated Brillouin scattering (SBS). The model applies to dynamic cases such as optical pulses and accounts for both thermal noise and phase noise from the input lasers. Using this model, we compute the statistical properties of the optical and acoustic power in the pulsed spontaneous and stimulated Brillouin cases, and investigate the effects of gain and pulse width on noise levels. We find that thermal noise plays an important role in the statistical properties of the fields and that laser phase noise impacts the SBS interaction when the laser coherence time is close to the time scale of the optical pulses. This algorithm is applicable to arbitrary waveguide geometries and material properties and, thus, presents a versatile way of performing noise-based SBS numerical simulations, which are important in signal processing, sensing, microwave photonics, and opto-acoustic memory storage.
Nikolaeva, A, Frizyuk, K, Olekhno, N, Solntsev, A & Petrov, M 2021, 'Directional emission of down-converted photons from a dielectric nanoresonator', Physical Review A, vol. 103, no. 4.
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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, vol. 4, no. 7, pp. 2100037-2100037.
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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, pp. 2577-2653.
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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.
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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O'Connor, C & Booth, DJ 2021, 'Response of estuarine fishes to elevated temperatures within temperate Australia: Implications of climate change on fish growth and foraging performance', Journal of Experimental Marine Biology and Ecology, vol. 544, pp. 151626-151626.
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O'Farrell, HE, Brown, R, Brown, Z, Miljevic, B, Ristovski, ZD, Bowman, RV, Fong, KM, Vaughan, A & Yang, IA 2021, 'E-cigarettes induce toxicity comparable to tobacco cigarettes in airway epithelium from patients with COPD', Toxicology in Vitro, vol. 75, pp. 105204-105204.
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Olander, A, Lawson, CA, Possell, M, Raina, J-B, 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.
Oliver, BG 2021, 'Food for thought: why is there more airway smooth muscle in asthma?', European Respiratory Journal, vol. 58, no. 5, pp. 2101565-2101565.
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Ollendick, T, Muskett, A, Radtke, SR & Smith, I 2021, 'Adaptation of One-Session Treatment for Specific Phobias for Children with Autism Spectrum Disorder Using a Non-concurrent Multiple Baseline Design: A Preliminary Investigation', Journal of Autism and Developmental Disorders, vol. 51, no. 4, pp. 1015-1027.
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Anxiety disorders are among the most common co-occurring disorders for individuals with ASD. Several adaptations to cognitive behavioral approaches have been proposed for this population (Moree & Davis, 2010). The current study examined feasibility and preliminary efficacy of an ASD-specific adaptation of one-session treatment (OST) for specific phobia (SP). Standard OST consists of one 3-h session followed by four weekly phone calls. Modifications for ASD included increased parental involvement, use of visual aids, and inclusion of four 1-h booster sessions in place of the four weekly phone calls. Visual inspection and Friedman tests revealed significant reductions in fear ratings and phobia severity from pre- to post-treatment and follow-up assessments. Modest changes were observed in behavioral avoidance. These findings provide initial evidence that this treatment merits further study.
O'Rourke, MB, Sahni, S, Samra, J, Mittal, A & Molloy, MP 2021, 'Data independent acquisition of plasma biomarkers of response to neoadjuvant chemotherapy in pancreatic ductal adenocarcinoma', Journal of Proteomics, vol. 231, pp. 103998-103998.
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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, vol. 35, no. 7, pp. 551-579.
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Padovan, A, Siboni, N, Kaestli, M, King, WL, Seymour, JR & Gibb, K 2021, 'Occurrence and dynamics of potentially pathogenic vibrios in the wet-dry tropics of northern Australia', Marine Environmental Research, vol. 169, pp. 105405-105405.
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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, vol. 127, no. 2, pp. 125-134.
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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, vol. 16, no. 2, pp. e0246748-e0246748.
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Objective
Mercury and other toxic metals have been suggested to be involved in thyroid disorders, but the distribution and prevalence of mercury in the human thyroid gland is not known. We therefore used two elemental bio-imaging techniques to look at the distribution of mercury and other toxic metals in the thyroid glands of people over a wide range of ages.
Materials and methods
Formalin-fixed paraffin-embedded thyroid tissue blocks were obtained from 115 people aged 1–104 years old, with varied clinicopathological conditions, who had thyroid samples removed during forensic/coronial autopsies. Seven-micron sections from these tissue blocks were used to detect intracellular inorganic mercury using autometallography. The presence of mercury was confirmed using laser ablation-inductively coupled plasma-mass spectrometry which can detect multiple elements.
Results
Mercury was found on autometallography in the thyroid follicular cells of 4% of people aged 1–29 years, 9% aged 30–59 years, and 38% aged 60–104 years. Laser ablation-inductively coupled plasma-mass spectrometry confirmed the presence of mercury in samples staining with autometallography, and detected cadmium, lead, iron, nickel and silver in selected samples.
Conclusions
The proportion of people with mercury in their thyroid follicular cells increases with age, until it is present in over one-third of people aged 60 years and over. Other toxic metals in thyroid cells could enhance mercury toxicity. Mercury can trigger genotoxicity, autoimmune reactions, and oxidative damage, which raises the possibility that mercury could play a role in the pathogenesis of thyroid cancers, autoimmune thyroiditis, and hypothyroidism.
Pamphlett, R, Doble, PA & Bishop, DP 2021, 'The Prevalence of Inorganic Mercury in Human Kidneys Suggests a Role for Toxic Metals in Essential Hypertension', Toxics, vol. 9, no. 3, pp. 67-67.
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The kidney plays a dominant role in the pathogenesis of essential hypertension, but the initial pathogenic events in the kidney leading to hypertension are not known. Exposure to mercury has been linked to many diseases including hypertension in epidemiological and experimental studies, so we studied the distribution and prevalence of mercury in the human kidney. Paraffin sections of kidneys were available from 129 people ranging in age from 1 to 104 years who had forensic/coronial autopsies. One individual had injected himself with metallic mercury, the other 128 were from varied clinicopathological backgrounds without known exposure to mercury. Sections were stained for inorganic mercury using autometallography. Laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) was used on six samples to confirm the presence of autometallography-detected mercury and to look for other toxic metals. In the 128 people without known mercury exposure, mercury was found in: (1) proximal tubules of the cortex and Henle thin loops of the medulla, in 25% of kidneys (and also in the man who injected himself with mercury), (2) proximal tubules only in 16% of kidneys, and (3) Henle thin loops only in 23% of kidneys. The age-related proportion of people who had any mercury in their kidney was 0% at 1–20 years, 66% at 21–40 years, 77% at 41–60 years, 84% at 61–80 years, and 64% at 81–104 years. LA-ICP-MS confirmed the presence of mercury in samples staining with autometallography and showed cadmium, lead, iron, nickel, and silver in some kidneys. In conclusion, mercury is found commonly in the adult human kidney, where it appears to accumulate in proximal tubules and Henle thin loops until an advanced age. Dysfunctions of both these cortical and medullary regions have been implicated in the pathogenesis of essential hypertension, so these findings suggest that further studies of the effects of mercury on blood pressure are warranted.
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, vol. 11, no. 1.
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AbstractPlasma noradrenaline levels increase with aging, and this could contribute to the sympathetic overactivity that is associated with essential hypertension and the metabolic syndrome. The underlying cause of this rise in noradrenaline is unknown, but a clue may be that mercury increases noradrenaline output from the adrenal medulla of experimental animals. We therefore determined the proportion of people from 2 to 104 years of age who had mercury in their adrenal medulla. Mercury was detected in paraffin sections of autopsied adrenal glands using two methods of elemental bioimaging, autometallography and laser ablation-inductively coupled plasma-mass spectrometry. Mercury first appeared in cells of the adrenal medulla in the 21–40 years group, where it was present in 52% of samples, and increased progressively in frequency in older age groups, until it was detected in 90% of samples from people aged over 80 years. In conclusion, the proportion of people having mercury in their adrenal medulla increases with aging. Mercury could alter the metabolism of catecholamines in the adrenal medulla that leads to the raised levels of plasma noradrenaline in aging. This retrospective autopsy study was not able to provide a definitive link between adrenal mercury, noradrenaline levels and hypertension, but future functional human and experimental studies could provide further evidence for these associations.
Parker, LM, Scanes, E, O'Connor, WA & Ross, PM 2021, 'Transgenerational plasticity responses of oysters to ocean acidification differ with habitat', Journal of Experimental Biology, vol. 224, no. 12.
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ABSTRACT
Transgenerational plasticity (TGP) has been identified as a critical mechanism of acclimation that may buffer marine organisms against climate change, yet whether the TGP response of marine organisms is altered depending on their habitat is unknown. Many marine organisms are found in intertidal zones where they experience episodes of emersion (air exposure) daily as the tide rises and recedes. During episodes of emersion, the accumulation of metabolic carbon dioxide (CO2) leads to hypercapnia for many species. How this metabolic hypercapnia impacts the TGP response of marine organisms to climate change is unknown as all previous transgenerational studies have been done under subtidal conditions, where parents are constantly immersed. Here, we assess the capacity of the ecologically and economically important oyster, Saccostrea glomerata, to acclimate to elevated CO2 dependent on habitat, across its vertical distribution, from the subtidal to intertidal zone. Tidal habitat altered both the existing tolerance and transgenerational response of S. glomerata to elevated CO2. Overall, larvae from parents conditioned in an intertidal habitat had a greater existing tolerance to elevated CO2 than larvae from parents conditioned in a subtidal habitat, but had a lower capacity for beneficial TGP following parental exposure to elevated CO2. Our results suggest that the TGP responses of marine species will not be uniform across their distribution and highlights the need to consider the habitat of a species when assessing TGP responses to climate change stressors.
Pasin, D, Mollerup, CB, Rasmussen, BS, Linnet, K & Dalsgaard, PW 2021, 'Development of a single retention time prediction model integrating multiple liquid chromatography systems: Application to new psychoactive substances', Analytica Chimica Acta, vol. 1184, pp. 339035-339035.
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Database-driven suspect screening has proven to be a useful tool to detect new psychoactive substances (NPS) outside the scope of targeted screening; however, the lack of retention times specific to a liquid chromatography (LC) system can result in a large number of false positives. A singular stream-lined, quantitative structure-retention relationship (QSRR)-based retention time prediction model integrating multiple LC systems with different elution conditions is presented using retention time data (n = 1281) from the online crowd-sourced database, HighResNPS. Modelling was performed using an artificial neural network (ANN), specifically a multi-layer perceptron (MLP), using four molecular descriptors and one-hot encoding of categorical labels. Evaluation of test set predictions (n = 193) yielded coefficient of determination (R2) and mean absolute error (MAE) values of 0.942 and 0.583 min, respectively. The model successfully differentiated between LC systems, predicting 54%, 81% and 97% of the test set within ±0.5, ±1 and ±2 min, respectively. Additionally, retention times for an analyte not previously observed by the model were predicted within ±1 min for each LC system. The developed model can be used to predict retention times for all analytes on HighResNPS for each participating laboratory's LC system to further support suspect screening.
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, vol. 8, no. 1.
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Pateetin, P, Hutvagner, G, Bajan, S, Padula, MP, McGowan, EM & Boonyaratanakornkit, V 2021, 'Triple SILAC identified progestin-independent and dependent PRA and PRB interacting partners in breast cancer', Scientific Data, vol. 8, no. 1.
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AbstractProgesterone receptor (PR) isoforms, PRA and PRB, act in a progesterone-independent and dependent manner to differentially modulate the biology of breast cancer cells. Here we show that the differences in PRA and PRB structure facilitate the binding of common and distinct protein interacting partners affecting the downstream signaling events of each PR-isoform. Tet-inducible HA-tagged PRA or HA-tagged PRB constructs were expressed in T47DC42 (PR/ER negative) breast cancer cells. Affinity purification coupled with stable isotope labeling of amino acids in cell culture (SILAC) mass spectrometry technique was performed to comprehensively study PRA and PRB interacting partners in both unliganded and liganded conditions. To validate our findings, we applied both forward and reverse SILAC conditions to effectively minimize experimental errors. These datasets will be useful in investigating PRA- and PRB-specific molecular mechanisms and as a database for subsequent experiments to identify novel PRA and PRB interacting proteins that differentially mediated different biological functions in breast cancer.
Patel, D, Taudte, RV, Nizio, K, Herok, G, Cranfield, C & Shimmon, R 2021, 'Headspace analysis of E-cigarette fluids using comprehensive two dimensional GC×GC-TOF-MS reveals the presence of volatile and toxic compounds', Journal of Pharmaceutical and Biomedical Analysis, vol. 196, pp. 113930-113930.
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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, pp. 119436-119436.
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Paul, B, Kysenius, K, Hilton, JB, Jones, MWM, Hutchinson, RW, Buchanan, DD, Rosty, C, Fryer, F, Bush, AI, Hergt, JM, Woodhead, JD, Bishop, DP, Doble, PA, Hill, MM, Crouch, PJ & Hare, DJ 2021, 'An integrated mass spectrometry imaging and digital pathology workflow for objective detection of colorectal tumours by unique atomic signatures', Chemical Science, vol. 12, no. 30, pp. 10321-10333.
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Digital pathology and laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) imaging reveals a unique elemental signature of colorectal cancer.
Paull, NJ, Krix, D, Irga, PJ & Torpy, FR 2021, 'Green wall plant tolerance to ambient urban air pollution', Urban Forestry & Urban Greening, vol. 63, pp. 127201-127201.
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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.
Payne, M, Bottomley, AL, Och, A, Asmara, AP, Harry, EJ & Ung, AT 2021, 'Synthesis and biological evaluation of 3,5-substituted pyrazoles as possible antibacterial agents', Bioorganic & Medicinal Chemistry, vol. 48, pp. 116401-116401.
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Pedersen, JL, Barry, SE, Bokil, NJ, Ellis, M, Yang, Y, Guan, G, Wang, X, Faiz, A, Britton, WJ & Saunders, BM 2021, 'High sensitivity and specificity of a 5‐analyte protein and microRNA biosignature for identification of active tuberculosis', Clinical & Translational Immunology, vol. 10, no. 6.
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Peneaux, C, Hansbro, PM & Griffin, AS 2021, 'The potential utility of carotenoid‐based coloration as a biomonitor of environmental change', Ibis, vol. 163, no. 1, pp. 20-37.
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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, pp. 112133-112133.
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Perez Gomez, AA, Karmakar, M, Carroll, RJ, Lawley, KS, Amstalden, K, Young, CR, Threadgill, DW, Welsh, CJ & Brinkmeyer-Langford, C 2021, 'Genetic and immunological contributors to virus-induced paralysis', Brain, Behavior, & Immunity - Health, vol. 18, pp. 100395-100395.
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Petrou, K, Nunn, BL, Padula, MP, Miller, DJ & Nielsen, DA 2021, 'Broad scale proteomic analysis of heat-destabilised symbiosis in the hard coral Acropora millepora', Scientific Reports, vol. 11, no. 1.
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AbstractCoral reefs across the globe are threatened by warming oceans. The last few years have seen the worst mass coral bleaching events recorded, with more than one quarter of all reefs irreversibly impacted. Considering the widespread devastation, we need to increase our efforts to understanding the physiological and metabolic shifts underlying the breakdown of this important symbiotic ecosystem. Here, we investigated the proteome (PRIDE accession # PXD011668) of both host and symbionts of the reef-building coral Acropora millepora exposed to ambient (~ 28 °C) and elevated temperature (~ 32 °C for 2 days, following a five-day incremental increase) and explored associated biomolecular changes in the symbiont, with the aim of gaining new insights into the mechanisms underpinning the collapse of the coral symbiosis. We identified 1,230 unique proteins (774 host and 456 symbiont) in the control and thermally stressed corals, of which 107 significantly increased and 125 decreased in abundance under elevated temperature relative to the control. Proteins involved in oxidative stress and proteolysis constituted 29% of the host proteins that increased in abundance, with evidence of impairment to endoplasmic reticulum and cytoskeletal regulation proteins. In the symbiont, we detected a decrease in proteins responsible for photosynthesis and energy production (33% of proteins decreased in abundance), yet minimal signs of oxidative stress or proteolysis. Lipid stores increased > twofold despite reduction in photosynthesis, suggesting reduced translocation of carbon to the host. There were significant changes in proteins related to symbiotic state, including proteins linked to nitrogen metabolism in the host and the V-ATPase (-0.6 fold change) known to control symbiosome acidity. These results highlight key differences in host and symbiont proteomic adjustments under elevated temperature and identify two key pr...
Pettit, T, Torpy, FR, Surawski, NC, Fleck, R & Irga, PJ 2021, 'Effective reduction of roadside air pollution with botanical biofiltration', Journal of Hazardous Materials, vol. 414, pp. 125566-125566.
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Pham, AK, Miller, M, Rosenthal, P, Das, S, Weng, N, Jang, S, Kurten, RC, Badrani, J, Doherty, TA, Oliver, B & Broide, DH 2021, 'ORMDL3 expression in ASM regulates hypertrophy, hyperplasia via TPM1 and TPM4, and contractility', JCI Insight, vol. 6, no. 7.
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Phung, D, Nguyen-Huy, T, Tran, NN, Tran, DN, Doan, VQ, Nghiem, S, Nguyen, NH, Nguyen, TH & Bennett, T 2021, 'Hydropower dams, river drought and health effects: A detection and attribution study in the lower Mekong Delta Region', Climate Risk Management, vol. 32, pp. 100280-100280.
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Pinkerton, JW, Kim, RY, Koeninger, L, Armbruster, NS, Hansbro, NG, Brown, AC, Jayaraman, R, Shen, S, Malek, N, Cooper, MA, Nordkild, P, Horvat, JC, Jensen, BAH, Wehkamp, J & Hansbro, PM 2021, 'Human β‐defensin‐2 suppresses key features of asthma in murine models of allergic airways disease', Clinical & Experimental Allergy, vol. 51, no. 1, pp. 120-131.
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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. 2972-2972.
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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.
Platen, E & Tappe, S 2021, 'No-arbitrage concepts in topological vector lattices', Positivity, vol. 25, no. 5, pp. 1853-1898.
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AbstractWe provide a general framework for no-arbitrage concepts in topological vector lattices, which covers many of the well-known no-arbitrage concepts as particular cases. The main structural condition we impose is that the outcomes of trading strategies with initial wealth zero and those with positive initial wealth have the structure of a convex cone. As one consequence of our approach, the concepts NUPBR, NAA$$_1$$1and NA$$_1$$1may fail to be equivalent in our general setting. Furthermore, we derive abstract versions of the fundamental theorem of asset pricing (FTAP), including an abstract FTAP on Banach function spaces, and investigate when the FTAP is warranted in its classical form with a separating measure. We also consider a financial market with semimartingales which does not need to have a numéraire, and derive results which show the links between the no-arbitrage concepts by only using the theory of topological vector lattices and well-known results from stochastic analysis in a sequence of short proofs.
Plucinski, MM & Barratt, JLN 2021, 'Nonparametric Binary Classification to Distinguish Closely Related versus Unrelated Plasmodium falciparum Parasites', The American Journal of Tropical Medicine and Hygiene, vol. 104, no. 5, pp. 1830-1835.
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ABSTRACTAssessing genetic relatedness of Plasmodium falciparum genotypes is a key component of antimalarial efficacy trials. Previous methods have focused on determining a priori definitions of the level of genetic similarity sufficient to classify two infections as sharing the same strain. However, factors such as mixed-strain infections, allelic suppression, imprecise typing methods, and heterozygosity complicate comparisons of apicomplexan genotypes. Here, we introduce a novel method for nonparametric statistical testing of relatedness for P. falciparum parasites. First, the background distribution of genetic distance between unrelated strains is computed. Second, a threshold genetic distance is computed from this empiric distribution of distances to demarcate genetic distances that are unlikely to have arisen by chance. Third, the genetic distance between paired samples is computed, and paired samples with genetic distances below the threshold are classified as related. The method is designed to work with any arbitrary genetic distance definition. We validated this procedure using two independent approaches to calculating genetic distance. We assessed the concordance of the novel nonparametric classification with a gold-standard Bayesian approach for 175 pairs of recurrent P. falciparum episodes from previously published malaria efficacy trials with microsatellite data from five studies in Guinea and Angola. The novel nonparametric approach was 98% sensitive and 84–89% specific in correctly identifying related genotypes compared with a gold-standard Bayesian algorithm. The approach provides a unified and systematic method to statistically assess relatedness of P. falciparum parasites using arbitrary genetic distance methodologies.
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, vol. 12.
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Unicellular nitrogen fixing cyanobacteria (UCYN) are abundant members of phytoplankton communities in a wide range of marine environments, including those with rapidly changing nitrogen (N) concentrations. We hypothesized that differences in N availability (N2 vs. combined N) would cause UCYN to shift strategies of intracellular N and C allocation. We used transmission electron microscopy and nanoscale secondary ion mass spectrometry imaging to track assimilation and intracellular allocation of 13C-labeled CO2 and 15N-labeled N2 or NO3 at different periods across a diel cycle in Cyanothece sp. ATCC 51142. We present new ideas on interpreting these imaging data, including the influences of pre-incubation cellular C and N contents and turnover rates of inclusion bodies. Within cultures growing diazotrophically, distinct subpopulations were detected that fixed N2 at night or in the morning. Additional significant within-population heterogeneity was likely caused by differences in the relative amounts of N assimilated into cyanophycin from sources external and internal to the cells. Whether growing on N2 or NO3, cells prioritized cyanophycin synthesis when N assimilation rates were highest. N assimilation in cells growing on NO3 switched from cyanophycin synthesis to protein synthesis, suggesting that once a cyanophycin quota is met, it is bypassed in favor of protein synthesis. Growth on NO3 also revealed that at night, there is a very low level of CO2 assimilation into polysaccharides simultaneous with their catabolism for protein synthesis. This study revealed multiple, detailed mechanisms underlying C and N management in Cyanothece that facilitate its suc...
Polonchuk, L, Surija, L, Lee, MH, Sharma, P, Liu Chung Ming, C, Richter, F, Ben-Sefer, E, Rad, MA, Mahmodi Sheikh Sarmast, H, Shamery, WA, 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, vol. 13, no. 4, pp. 045009-045009.
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Abstract
Current in vivo and in vitro models fail to accurately recapitulate the human heart microenvironment for biomedical applications. This study explores the use of cardiac spheroids (CSs) to biofabricate advanced in vitro models of the human heart. CSs were created from human cardiac myocytes, fibroblasts and endothelial cells (ECs), mixed within optimal alginate/gelatin hydrogels and then bioprinted on a microelectrode plate for drug testing. Bioprinted CSs maintained their structure and viability for at least 30 d after printing. Vascular endothelial growth factor (VEGF) promoted EC branching from CSs within hydrogels. Alginate/gelatin-based hydrogels enabled spheroids fusion, which was further facilitated by addition of VEGF. Bioprinted CSs contracted spontaneously and under stimulation, allowing to record contractile and electrical signals on the microelectrode plates for industrial applications. Taken together, our findings indicate that bioprinted CSs can be used to biofabricate human heart tissues for long term in vitro testing. This has the potential to be used to study biochemical, physiological and pharmacological features of human heart tissue.
Popkova, AA, Antropov, IM, Fröch, 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.
Pouwels, SD, Hesse, L, Wu, X, Allam, VSRR, van Oldeniel, D, Bhiekharie, LJ, Phipps, S, Oliver, BG, Gosens, R, Sukkar, MB & Heijink, IH 2021, 'LL-37 and HMGB1 induce alveolar damage and reduce lung tissue regeneration via RAGE', American Journal of Physiology-Lung Cellular and Molecular Physiology, vol. 321, no. 4, pp. L641-L652.
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The receptor for advanced glycation end-products (RAGE) has been implicated in the pathophysiology of chronic obstructive pulmonary disease (COPD). However, it is still unknown whether RAGE directly contributes to alveolar epithelial damage and abnormal repair responses. We hypothesize that RAGE activation not only induces lung tissue damage but also hampers alveolar epithelial repair responses. The effects of the RAGE ligands LL-37 and HMGB1 were examined on airway inflammation and alveolar tissue damage in wild-type and RAGE-deficient mice and on lung damage and repair responses using murine precision cut lung slices (PCLS) and organoids. In addition, their effects were studied on the repair response of human alveolar epithelial A549 cells, using siRNA knockdown of RAGE and treatment with the RAGE inhibitor FPS-ZM1. We observed that intranasal installation of LL-37 and HMGB1 induces RAGE-dependent inflammation and severe alveolar tissue damage in mice within 6 h, with stronger effects in a mouse strain susceptible for emphysema compared with a nonsusceptible strain. In PCLS, RAGE inhibition reduced the recovery from elastase-induced alveolar tissue damage. In organoids, RAGE ligands reduced the organoid-forming efficiency and epithelial differentiation into pneumocyte-organoids. Finally, in A549 cells, we confirmed the role of RAGE in impaired repair responses upon exposure to LL-37. Together, our data indicate that activation of RAGE by its ligands LL-37 and HMGB1 induces acute lung tissue damage and that this impedes alveolar epithelial repair, illustrating the therapeutic potential of RAGE inhibitors for lung tissue repair in emphysema.
Pouwels, SD, Wiersma, VR, Fokkema, IE, Berg, M, Hacken, NHT, Berge, M, Heijink, I & Faiz, A 2021, 'Acute cigarette smoke‐induced eQTL affects formyl peptide receptor expression and lung function', Respirology, vol. 26, no. 3, pp. 233-240.
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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, vol. 53, no. 5, pp. 512-522.
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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.
Prasher, P, Sharma, M, Mehta, M, Satija, S, Aljabali, AA, Tambuwala, MM, Anand, K, Sharma, N, Dureja, H, Jha, NK, Gupta, G, Gulati, M, Singh, SK, Chellappan, DK, Paudel, KR, Hansbro, PM & Dua, K 2021, 'Current-status and applications of polysaccharides in drug delivery systems', Colloid and Interface Science Communications, vol. 42, pp. 100418-100418.
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The polysaccharide-based advanced drug delivery system owing to their biocompatibility, ability to encapsulate the drug molecules in their interspaces, and ability to achieve a controlled release of the cargo drug molecules result in improved drug pharmacokinetics. The drug-loaded polysaccharides possess ability to evade the multidrug-resistant microbial efflux pumps by aggregation effect, whereas the drug loaded polysaccharide-fabricated metal nanoparticles present an exceptional candidature for effectively transporting the drug molecules across the membrane barriers while enabling the theranostic applications at the same time. The biodegradability of polysaccharide based drug delivery systems ensure a sustained release of the encapsulated drug molecules, which minimizes the side effects caused by a burst release of the cargo therapeutics. These drug delivery systems proved highly beneficial for the NSAIDs that otherwise manifest ulcerogenic effect in the gastrointestinal tract. The large surface area of polysaccharides further provide a higher drug-loading capacity, which maintains the optimal concentration of the cargo drug at the target sites. The emerging applications of biodegradable polysaccharides in the designing of multicompartmental microspheres revolutionized tissue engineering, multi drug delivery, and cell culturing technologies. The present review deals with the current-status of polysaccharides as advanced drug delivery systems.
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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Qashlan, A, Nanda, P, He, X & Mohanty, M 2021, 'Privacy-Preserving Mechanism in Smart Home Using Blockchain', IEEE Access, vol. 9, pp. 103651-103669.
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Quince, C, Nurk, S, Raguideau, S, James, R, Soyer, OS, Summers, JK, Limasset, A, Eren, AM, Chikhi, R & Darling, AE 2021, 'STRONG: metagenomics strain resolution on assembly graphs', Genome Biology, vol. 22, no. 1.
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AbstractWe introduce STrain Resolution ON assembly Graphs (STRONG), which identifies strains de novo, from multiple metagenome samples. STRONG performs coassembly, and binning into metagenome assembled genomes (MAGs), and stores the coassembly graph prior to variant simplification. This enables the subgraphs and their unitig per-sample coverages, for individual single-copy core genes (SCGs) in each MAG, to be extracted. A Bayesian algorithm, BayesPaths, determines the number of strains present, their haplotypes or sequences on the SCGs, and abundances. STRONG is validated using synthetic communities and for a real anaerobic digestor time series generates haplotypes that match those observed from long Nanopore reads.
Quinn, AW, Phillips, CR, Violi, JP, Steele, JR, Johnson, MS, Westerhausen, MT & Rodgers, KJ 2021, 'β-Methylamino-L-alanine-induced protein aggregation in vitro and protection by L-serine', Amino Acids, vol. 53, no. 9, pp. 1351-1359.
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Quiroz, M, Tran, M-N, Villani, M, Kohn, R & Dang, K-D 2021, 'The Block-Poisson Estimator for Optimally Tuned Exact Subsampling MCMC', Journal of Computational and Graphical Statistics, vol. 30, no. 4, pp. 877-888.
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R. Cardoso, B, Hare, DJ & Macpherson, H 2021, 'Sex-dependent association between selenium status and cognitive performance in older adults', European Journal of Nutrition, vol. 60, no. 2, pp. 1153-1159.
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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, vol. 118, no. 5, pp. e2022653118-e2022653118.
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Significance
Ocean warming is causing repeated mass coral bleaching, leading to catastrophic losses of coral reefs worldwide. Our ability to slow or revert this decline is hampered by an incomplete understanding of the processes underlying the breakdown of the coral–algal symbiosis. Here, we show that heat stress destabilizes the nutrient cycling between corals and their endosymbiotic algae long before bleaching becomes apparent. Notably, increased metabolic energy demands shift the coral–algal symbiosis from a nitrogen- to a carbon-limited state, reducing translocation and recycling of photosynthetic carbon. This effectively undermines the ecological advantage of harboring algal symbionts and directly contributes to the breakdown of the coral–algal symbiosis during heat stress.
Raes, EJ, Karsh, K, Sow, SLS, Ostrowski, M, Brown, MV, van de Kamp, J, Franco-Santos, RM, Bodrossy, L & Waite, AM 2021, 'Metabolic pathways inferred from a bacterial marker gene illuminate ecological changes across South Pacific frontal boundaries', Nature Communications, vol. 12, no. 1.
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AbstractGlobal oceanographic monitoring initiatives originally measured abiotic essential ocean variables but are currently incorporating biological and metagenomic sampling programs. There is, however, a large knowledge gap on how to infer bacterial functions, the information sought by biogeochemists, ecologists, and modelers, from the bacterial taxonomic information (produced by bacterial marker gene surveys). Here, we provide a correlative understanding of how a bacterial marker gene (16S rRNA) can be used to infer latitudinal trends for metabolic pathways in global monitoring campaigns. From a transect spanning 7000 km in the South Pacific Ocean we infer ten metabolic pathways from 16S rRNA gene sequences and 11 corresponding metagenome samples, which relate to metabolic processes of primary productivity, temperature-regulated thermodynamic effects, coping strategies for nutrient limitation, energy metabolism, and organic matter degradation. This study demonstrates that low-cost, high-throughput bacterial marker gene data, can be used to infer shifts in the metabolic strategies at the community scale.
Rafeek, AD, Choi, G & Evans, LA 2021, 'Controlled synthesis of dicalcium phosphate dihydrate (DCPD) from metastable solutions: insights into pathogenic calcification', Journal of Materials Science: Materials in Medicine, vol. 32, no. 12.
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AbstractCalcium phosphate (CaP) compounds may occur in the body as abnormal pathogenic phases in addition to their normal occurrence as bones and teeth. Dicalcium phosphate dihydrate (DCPD; CaPO4·2H2O), along with other significant CaP phases, have been observed in pathogenic calcifications such as dental calculi, kidney stones and urinary stones. While other studies have shown that polar amino acids can inhibit the growth of CaPs, these studies have mainly focused on hydroxyapatite (HAp; Ca10(PO4)6(OH)2) formation from highly supersaturated solutions, while their effects on DCPD nucleation and growth from metastable solutions have been less thoroughly explored. By further elucidating the mechanisms of DCPD formation and the influence of amino acids on those mechanisms, insights may be gained into ways that amino acids could be used in treatment and prevention of unwanted calcifications. The current study involved seeded growth of DCPD from metastable solutions at constant pH in the presence of neutral, acidic and phosphorylated amino acid side chains. As a comparison, solutions were also seeded with calcium pyrophosphate (CPP; Ca2P2O7), a known calcium phosphate inhibitor. The results show that polar amino acids inhibit DCPD growth; this likely occurs due to electrostatic interactions between amino acid side groups and charged DCPD surfaces. Phosphoserine had the greatest inhibitory ability of the amino acids tested, with an effect equal to that of CPP. Clustering of DCPD crystals giving rise to a “chrysanthemum-like” morphology was noted with glutamic acid. This study concludes that molecules containing an increased number of polar side groups will enhance the inhibition of DCPD seeded growth from metastable solutions.
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, vol. 11, no. 2, pp. 158-172.
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Rather, IA, Kim, B-C, Lew, L-C, Cha, S-K, Lee, JH, Nam, G-J, Majumder, R, Lim, J, Lim, S-K, Seo, Y-J & Park, Y-H 2021, 'Oral Administration of Live and Dead Cells of Lactobacillus sakei proBio65 Alleviated Atopic Dermatitis in Children and Adolescents: a Randomized, Double-Blind, and Placebo-Controlled Study', Probiotics and Antimicrobial Proteins, vol. 13, no. 2, pp. 315-326.
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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.
Reddy, KD, Lan, A, Boudewijn, IM, Rathnayake, SNH, Koppelman, GH, Aliee, H, Theis, F, Oliver, BG, van den Berge, M & Faiz, A 2021, 'Current Smoking Alters Gene Expression and DNA Methylation in the Nasal Epithelium of Patients with Asthma', American Journal of Respiratory Cell and Molecular Biology, vol. 65, no. 4, pp. 366-377.
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Current smoking contributes to worsened asthma prognosis and more severe symptoms and limits the beneficial effects of corticosteroids. As the nasal epithelium can reflect smoking-induced changes in the lower airways, it is a relevant source to investigate changes in gene expression and DNA methylation. This study explores gene expression and DNA methylation changes in current and ex-smokers with asthma. Matched gene expression and epigenome-wide DNA methylation samples collected from nasal brushings of 55 patients enrolled in a clinical trial investigation of current and ex-smoker patients with asthma were analyzed. Differential gene expression and DNA methylation analyses were conducted comparing current smokers with ex-smokers. Expression quantitative trait methylation (eQTM) analysis was completed to explore smoking-relevant genes by CpG sites that differ between current and ex-smokers. To investigate the relevance of the smoking-associated DNA methylation changes for the lower airways, significant CpG sites were explored in bronchial biopsies from patients who had stopped smoking. A total of 809 genes and 18,814 CpG sites were differentially associated with current smoking in the nose. The cis-eQTM analysis uncovered 171 CpG sites with a methylation status associated with smoking-related gene expression, including AHRR, ALDH3A1, CYP1A1, and CYP1B1. The methylation status of CpG sites altered by current smoking reversed with 1 year of smoking cessation. We confirm that current smoking alters epigenetic patterns and affects gene expression in the nasal epithelium of patients with asthma, which is partially reversible in bronchial biopsies after smoking cessation. We demonstrate the ability to discern molecular changes in the nasal epithelium, presenting this as a tool in future investigations into disease-relevant effects of tobacco smoke.
Regan, B, Trycz, A, Fröch, JE, Schaeper, OC, Kim, S & Aharonovich, I 2021, 'Nanofabrication of high Q, transferable diamond resonators', Nanoscale.
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Schematic illustration of a 1D diamond nanobeam cavity.
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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Reid, G, Klebe, S, van Zandwijk, N & George, AM 2021, 'Correction to Asbestos and Zeolites: from A to Z via a Common Ion', Chemical Research in Toxicology, vol. 34, no. 6, pp. 1694-1694.
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Ren, Y, Huang, W, Ye, H, Zhou, X, Ma, H, Dong, Y, Shi, Y, Geng, Y, Huang, Y, Jiao, Q & Xie, Q 2021, 'Quantitative identification of yellow rust in winter wheat with a new spectral index: Development and validation using simulated and experimental data', International Journal of Applied Earth Observation and Geoinformation, vol. 102, pp. 102384-102384.
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Rennie, C, Fernandez, R, Donnelly, S & McGrath, KCY 2021, 'The Impact of Helminth Infection on the Incidence of Metabolic Syndrome: A Systematic Review and Meta-Analysis', Frontiers in Endocrinology, vol. 12.
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BackgroundThere are a growing number of publications that report an absence of inflammatory based disease among populations that are endemic to parasitic worms (helminths) demonstrating the ability of these parasites to potentially regulate human immune responses. The aim of this systematic review and meta-analysis was to determine the impact of helminth infection on metabolic outcomes in human populations.MethodsUsing PRISMA guidelines, six databases were searched for studies published up to August 2020. Random effects meta-analysis was performed to estimate pooled proportions with 95% confidence intervals using the Review Manager Software version 5.4.1.ResultsFourteen studies were included in the review. Fasting blood glucose was significantly lower in persons with infection (MD -0.22, 95% CI -0.40- -0.04, P=0.02), HbA1c levels were lower, although not significantly, and prevalence of the metabolic syndrome (P=0.001) and type 2 diabetes was lower (OR 1.03, 95% CI 0.34-3.09, P<0.0001). Infection was negatively associated with type 2 diabetes when comparing person with diabetes to the group without diabetes (OR 0.44, 95% CI 0.29-0.67, P=0.0001).ConclusionsWhile infection with helminths was generally associated with improved metabolic function, there were notable differences in efficacy between parasite species. Based on the data assessed, live infection with S. mansoni resulted in the most significant positive changes to metabolic outcomes.Systematic Review RegistrationWebsite: PROSPERO Identified: CRD42021227619.
Reyna, J, Hanham, J, Vlachopoulos, P & Meier, P 2021, 'A Systematic Approach to Designing, Implementing, and Evaluating Learner-Generated Digital Media (LGDM) Assignments and Its Effect on Self-regulation in Tertiary Science Education', Research in Science Education, vol. 51, no. 6, pp. 1501-1527.
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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, 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, Morshedi Rad, D, Shimoni, O, Jin, D, Rawlinson, W & Ebrahimi Warkiani, M 2021, 'A Portable RT-LAMP/CRISPR Machine for Rapid COVID-19 Screening', Biosensors, vol. 11, no. 10, pp. 369-369.
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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.
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. 109868-109868.
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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, vol. 11.
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Understanding mechanisms by which parasitic worms (helminths) control their hosts’ immune responses is critical to the development of effective new disease interventions. Fasciola hepatica, a global scourge of humans and their livestock, suppresses host innate immune responses within hours of infection, ensuring that host protective responses are quickly incapacitated. This allows the parasite to freely migrate from the intestine, through the liver to ultimately reside in the bile duct, where the parasite establishes a chronic infection that is largely tolerated by the host. The recent identification of micro(mi)RNA, small RNAs that regulate gene expression, within the extracellular vesicles secreted by helminths suggest that these non-coding RNAs may have a role in the parasite-host interplay. To date, 77 miRNAs have been identified in F. hepatica comprising primarily of ancient conserved species of miRNAs. We hypothesized that many of these miRNAs are utilized by the parasite to regulate host immune signaling pathways. To test this theory, we first compiled all of the known published F. hepatica miRNAs and critically curated their sequences and annotations. Then with a focus on the miRNAs expressed by the juvenile worms, we predicted gene targets within human innate immune cells. This approach revealed the existence of targets within every immune cell, providing evidence for the universal management of host immunology by this parasite. Notably, there was a high degree of redundancy in the potential for the parasite to regulate the activation of dendritic cells, eosinophils and neutrophils, with multiple miRNAs predicted to act on singular gene targets within these cells. This original exploration of the Fasciola miRnome offers the first molecular insight into mechanisms by which F. hepatica can regulate the host protecti...
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, vol. 12, no. 1.
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Abstract
Background
Preeclampsia is a dangerous cardiovascular disorder of pregnancy that leads to an increased risk of future cardiovascular and metabolic disorders. Much of the pathogenesis and mechanisms involved in cardiac health in preeclampsia are unknown. A novel anti-angiogenic protein, FKBPL, is emerging as having a potential role in both preeclampsia and cardiovascular disease (CVD). Therefore, in this study we aimed to characterise cardiac health and FKBPL regulation in the rat reduced uterine perfusion pressure (RUPP) and a 3D cardiac spheroid model of preeclampsia.
Methods
The RUPP model was induced in pregnant rats and histological analysis performed on the heart, kidney, liver and placenta (n ≥ 6). Picrosirius red staining was performed to quantify collagen I and III deposition in rat hearts, placentae and livers as an indicator of fibrosis. RT-qPCR was used to determine changes in Fkbpl, Icam1, Vcam1, Flt1 and Vegfa mRNA in hearts and/or placentae and ELISA to evaluate cardiac brain natriuretic peptide (BNP45) and FKBPL secretion. Immunofluorescent staining was also conducted to analyse the expression of cardiac FKBPL. Cardiac spheroids were generated using human cardiac fibroblasts and human coronary artery endothelial cells and treated with patient plasma from normotensive controls, early-onset preeclampsia (EOPE) and late-onset preeclampsia (LOPE); n = 3. FKBPL and CD31 expression was quantified by immunofluorescent labelling.
Results
The RUPP procedure induced significan...
Rittweger, F, Modrzynski, C, Roscher, V, Danilov, DL, Notten, PHL & Riemschneider, K-R 2021, 'Investigation of charge carrier dynamics in positive lithium-ion battery electrodes via optical in situ observation', Journal of Power Sources, vol. 482, pp. 228943-228943.
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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, vol. 9.
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This paper provides a perspective on how art and cross-cultural conversations can facilitate understanding of important scientific processes, outcomes and conclusions, using the Marine Ecosystem Assessment for the Southern Ocean (MEASO) as a case study. First, we reflect on our rationale and approach, describing the importance of deeper communication, such as through the arts, to the policy process; more enduring decisions are possible by engaging and obtaining perspectives through more than just a utilitarian lens. Second, we draw on the LivingData Website [http://www.livingdata.net.au] where art in all its forms is made to bridge differences in knowledge systems and their values, provide examples of how Indigenous knowledge and Western science can be complementary, and how Indigenous knowledge can show the difference between historical natural environmental phenomena and current unnatural phenomena, including how the Anthropocene is disrupting cultural connections with the environment that ultimately impact everyone. Lastly, we document the non-linear process of our experience and draw lessons from it that can guide deeper communication between disciples and cultures, to potentially benefit decision-making. Our perspective is derived as a collective from diverse backgrounds, histories, knowledge systems and values.
Rodrigo, N, Chen, H, Pollock, C & Glastras, S 2021, 'Pre-Conception Weight Loss Improves Reproductive, Metabolic and Kidney Health in Obese Mice and Their Offspring', Journal of the Endocrine Society, vol. 5, no. Suppl 1, pp. A322-A323.
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Abstract Background and Aims: An alarming 40% of women of reproductive age have obesity and during pregnancy obesity adversely impacts metabolic health in mothers and offspring. Maternal complications include diabetes, preeclampsia and chronic kidney disease (CKD). Our previous work showed that offspring have increased risks of obesity, diabetes, and CKD. While pre-pregnancy weight optimisation is advocated, evidence of benefits for mother and offspring are lacking. We aimed to determine if weight loss prior to pregnancy, either with diet modification or liraglutide, improves maternal and offspring metabolic outcomes, and reduces kidney complications in obese mothers and the offspring. Methods: C57BL/6 female mice were fed a high-fat-diet (HFD) for 8 weeks and compared to lean chow-fed controls. HFD-fed dams were administered liraglutide (0.3mg/kg, s.c., for 4weeks) or switched to chow, to induce pre-conception weight loss. Pregnancy rates were observed after mating. Maternal anthropometry and glucose tolerance were measured before and after intervention, and at late gestation. Pregnant dams were either culled at gestational day 18–20 with blood and kidney harvested, or allowed to deliver their offspring. Offspring anthropometry, and glucose tolerance were assessed at postnatal week 12 after either HFD or chow feeding. Immunohistochemistry (IHC), western blotting and RT-PCR were used to measure kidney metabolic (FAS, SREBP) and inflammatory markers (CD-68,TGF-b). Results: HFD-fed dams had reduced glucose tolerance compared to chow-fed dams (p<0.0001), and higher expression of renal metabolic and inflammatory markers in late gestation (eg FAS <0.05, TGFb <0.05). Intervention with liraglutide or diet lowered body weight, improving glucose tolerance (both p<0.001), and fecundity. Markers of kidney damage, namely albuminuria and fibronectin (by RT-PCR and IHC) were reduced (both p<0.05). Liraglutide treated mice exhibited greater gestational weight gain than mice swi...
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, vol. 40, no. 2, pp. 595-607.
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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 & Weyermann, C 2021, 'From Research Integrity to Research Relevance to Advance Forensic Science', Forensic Sciences Research, vol. 6, no. 4, pp. 292-294.
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Roux, C, Willis, S & Weyermann, C 2021, 'Shifting forensic science focus from means to purpose: A path forward for the discipline?', Science & 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.
Rouzé, H, Galand, PE, Medina, M, Bongaerts, P, Pichon, M, Pérez-Rosales, G, Torda, G, Moya, A, Raina, J-B & Hédouin, L 2021, 'Symbiotic associations of the deepest recorded photosynthetic scleractinian coral (172 m depth)', The ISME Journal, vol. 15, no. 5, pp. 1564-1568.
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Ruan, M, Fang, L, Yang, S, Chen, Z, Wu, Y, Qu, X, Zhao, J & Cheng, J 2021, 'Prolonged pituitary downregulation with gonadotropin-releasing hormone agonist improves the live-birth rate: a retrospective cohort study comparing 3 different protocols', Annals of Palliative Medicine, vol. 10, no. 9, pp. 9984-9992.
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Rudd, R, McWalter, T, Kienitz, J & Platen, E 2021, 'Robust Product Markovian Quantization', Journal of Computational Finance, vol. 25.
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, pp. 117206-117206.
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Rutting, S, Xenaki, D, Reddy, KD, Baraket, M, Chapman, DG, King, GG, Oliver, BG & Tonga, KO 2021, 'Airway smooth muscle cells from severe asthma patients with fixed airflow obstruction are responsive to steroid and bronchodilator treatment in vitro', ERJ Open Research, vol. 7, no. 2, pp. 00117-2021.
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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, vol. 22, no. 6, pp. 3023-3023.
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Over the past two decades, mesenchymal stromal cells (MSCs) have demonstrated great potential in the treatment of inflammation-related conditions. Numerous early stage clinical trials have suggested that this treatment strategy has potential to lead to significant improvements in clinical outcomes. While promising, there remain substantial regulatory hurdles, safety concerns, and logistical issues that need to be addressed before cell-based treatments can have widespread clinical impact. These drawbacks, along with research aimed at elucidating the mechanisms by which MSCs exert their therapeutic effects, have inspired the development of extracellular vesicles (EVs) as anti-inflammatory therapeutic agents. The use of MSC-derived EVs for treating inflammation-related conditions has shown therapeutic potential in both in vitro and small animal studies. This review will explore the current research landscape pertaining to the use of MSC-derived EVs as anti-inflammatory and pro-regenerative agents in a range of inflammation-related conditions: osteoarthritis, rheumatoid arthritis, Alzheimer’s disease, cardiovascular disease, and preeclampsia. Along with this, the mechanisms by which MSC-derived EVs exert their beneficial effects on the damaged or degenerative tissues will be reviewed, giving insight into their therapeutic potential. Challenges and future perspectives on the use of MSC-derived EVs for the treatment of inflammation-related conditions will be discussed.
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, pp. 115967-115967.
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Sadraeian, M, da Cruz, EF, Boyle, RW, Bahou, C, Chudasama, V, Janini, LMR, Diaz, RS & Guimarães, FEG 2021, 'Photoinduced Photosensitizer–Antibody Conjugates Kill HIV Env-Expressing Cells, Also Inactivating HIV', ACS Omega, vol. 6, no. 25, pp. 16524-16534.
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Safaei, J, Mashkani, SMH, Tian, H, Ye, C, Xiong, P & Wang, G 2021, 'Self-Assembled NbOPO4 Nanosheet/Reduced Graphene Oxide Heterostructure for Capacitive Desalination', ACS Applied Nano Materials, vol. 4, no. 11, pp. 12629-12639.
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Saini, V, Joglekar, MV, Wong, WKM, Jiang, G, Nassif, NT, Simpson, AM, Ma, RCW, Dalgaard, LT & Hardikar, AA 2021, 'Manipulating cellular microRNAs and analyzing high-dimensional gene expression data using machine learning workflows', STAR Protocols, vol. 2, no. 4, pp. 100910-100910.
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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, pp. 160-160.
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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, vol. 116, no. 535, pp. 1075-1087.
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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.
Sarkar, TR, McNeal, CJ, Meininger, CJ, Niu, Y, Mallick, BK, Carroll, RJ & Wu, G 2021, 'Dietary Intakes of Amino Acids and Other Nutrients by Adult Humans', pp. 211-227.
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Scanes, E, Parker, LM, Seymour, JR, Siboni, N, Dove, MC, O’Connor, WA & Ross, PM 2021, 'Microbiomes of an oyster are shaped by metabolism and environment', Scientific Reports, vol. 11, no. 1.
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AbstractMicrobiomes can both influence and be influenced by metabolism, but this relationship remains unexplored for invertebrates. We examined the relationship between microbiome and metabolism in response to climate change using oysters as a model marine invertebrate. Oysters form economies and ecosystems across the globe, yet are vulnerable to climate change. Nine genetic lineages of the oyster Saccostrea glomerata were exposed to ambient and elevated temperature and PCO2 treatments. The metabolic rate (MR) and metabolic by-products of extracellular pH and CO2 were measured. The oyster-associated bacterial community in haemolymph was characterised using 16 s rRNA gene sequencing. We found a significant negative relationship between MR and bacterial richness. Bacterial community composition was also significantly influenced by MR, extracellular CO2 and extracellular pH. The effects of extracellular CO2 depended on genotype, and the effects of extracellular pH depended on CO2 and temperature treatments. Changes in MR aligned with a shift in the relative abundance of 152 Amplicon Sequencing Variants (ASVs), with 113 negatively correlated with MR. Some spirochaete ASVs showed positive relationships with MR. We have identified a clear relationship between host metabolism and the microbiome in oysters. Altering this relationship will likely have consequences for the 12 billion USD oyster economy.
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, pp. 111991-111991.
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Scanes, E, Parker, LM, Seymour, JR, Siboni, N, King, WL, Wegner, KM, Dove, MC, O'Connor, WA & Ross, PM 2021, 'Microbiome response differs among selected lines of Sydney rock oysters to ocean warming and acidification', FEMS Microbiology Ecology, vol. 97, no. 8.
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ABSTRACT
Oyster microbiomes are integral to healthy function and can be altered by climate change conditions. Genetic variation among oysters is known to influence the response of oysters to climate change and may ameliorate any adverse effects on oyster microbiome; however, this remains unstudied. Nine full-sibling selected breeding lines of the Sydney rock oyster (Saccostrea glomerata) were exposed to predicted warming (ambient = 24°C, elevated = 28°C) and ocean acidification (ambient pCO2 = 400, elevated pCO2 = 1000 µatm) for 4 weeks. The haemolymph bacterial microbiome was characterized using 16S rRNA (V3–V4) gene sequencing and varied among oyster lines in the control (ambient pCO2, 24°C) treatment. Microbiomes were also altered by climate change dependent on oyster lines. Bacterial α-diversity increased in response to elevated pCO2 in two selected lines, while bacterial β-diversity was significantly altered by combinations of elevated pCO2 and temperature in four selected lines. Climate change treatments caused shifts in the abundance of multiple amplicon sequence variants driving change in the microbiome of some selected lines. We show that oyster genetic background may influence the Sydney rock oyster haemolymph microbiome under climate change and that future assisted evolution breeding programs to enhance resilience should consider the oyster microbiome.
Schanin, J, Gebremeskel, S, Korver, W, Falahati, R, Butuci, M, Haw, TJ, Nair, PM, Liu, G, Hansbro, NG, Hansbro, PM, Evensen, E, Brock, EC, Xu, A, Wong, A, Leung, J, Bebbington, C, Tomasevic, N & Youngblood, BA 2021, 'A monoclonal antibody to Siglec-8 suppresses non-allergic airway inflammation and inhibits IgE-independent mast cell activation', Mucosal Immunology, vol. 14, no. 2, pp. 366-376.
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AbstractIn addition to their well characterized role in mediating IgE-dependent allergic diseases, aberrant accumulation and activation of mast cells (MCs) is associated with many non-allergic inflammatory diseases, whereby their activation is likely triggered by non-IgE stimuli (e.g., IL-33). Siglec-8 is an inhibitory receptor expressed on MCs and eosinophils that has been shown to inhibit IgE-mediated MC responses and reduce allergic inflammation upon ligation with a monoclonal antibody (mAb). Herein, we evaluated the effects of an anti-Siglec-8 mAb (anti-S8) in non-allergic disease models of experimental cigarette-smoke-induced chronic obstructive pulmonary disease and bleomycin-induced lung injury in Siglec-8 transgenic mice. Therapeutic treatment with anti-S8 inhibited MC activation and reduced recruitment of immune cells, airway inflammation, and lung fibrosis. Similarly, using a model of MC-dependent, IL-33-induced inflammation, anti-S8 treatment suppressed neutrophil influx, and cytokine production through MC inhibition. Transcriptomic profiling of MCs further demonstrated anti-S8-mediated downregulation of MC signaling pathways induced by IL-33, including TNF signaling via NF-κB. Collectively, these findings demonstrate that ligating Siglec-8 with an antibody reduces non-allergic inflammation and inhibits IgE-independent MC activation, supporting the evaluation of an anti-Siglec-8 mAb as a therapeutic approach in both allergic and non-allergic inflammatory diseases in which MCs play a role.
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, vol. 8.
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Phytoplankton photosynthetic physiology can be investigated through single-turnover variable chlorophyll fluorescence (ST-ChlF) approaches, which carry unique potential to autonomously collect data at high spatial and temporal resolution. Over the past decades, significant progress has been made in the development and application of ST-ChlF methods in aquatic ecosystems, and in the interpretation of the resulting observations. At the same time, however, an increasing number of sensor types, sampling protocols, and data processing algorithms have created confusion and uncertainty among potential users, with a growing divergence of practice among different research groups. In this review, we assist the existing and upcoming user community by providing an overview of current approaches and consensus recommendations for the use of ST-ChlF measurements to examine in-situ phytoplankton productivity and photo-physiology. We argue that a consistency of practice and adherence to basic operational and quality control standards is critical to ensuring data inter-comparability. Large datasets of inter-comparable and globally coherent ST-ChlF observations hold the potential to reveal large-scale patterns and trends in phytoplankton photo-physiology, photosynthetic rates and bottom-up controls on primary productivity. As such, they hold great potential to provide invaluable physiological observations on the scales relevant for the development and validation of ecosystem models and remote sensing algorithms.
Semisch-Dieter, OK, Choi, AH, Ben-Nissan, B & Stewart, MP 2021, 'Modifying an Implant: A Mini-review of Dental Implant Biomaterials', BIO Integration, vol. 2, no. 1, pp. 12-21.
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Dental implants have been used as far back as 2000BC, and since then have developed into highly sophisticated solutions for tooth replacement. It is becoming increasingly important for the materials used in dental implants to exhibit and maintain favorable long-term mechanical, biological
and more recently, aesthetic properties. This review aims to assess the biomaterials used in modern dental implants, introducing their properties, and concentrating on modifications to improve these biomaterials. Focus is drawn to the prominent biomaterials, titanium (Ti) and zirconia due
to their prevalence in implant dentistry. Additionally, novel coatings and materials with potential use as viable improvements or alternatives are reviewed. An effective dental biomaterial should osseointegrate, maintain structural integrity, resist corrosion and infection, and not cause systemic
toxicity or cytotoxicity. Current materials such as bioactive glass offer protection against biofilm formation, and when combined with a titanium‐zirconium (TiZr) alloy, provide a reliable combination of properties to represent a competitive alternative. Further long-term clinical studies
are needed to inform the development of next-generation materials.Significance StatementBiomaterials have become essential for modern implants. A suitable implant biomaterial integrates into the body to perform a key function, whilst minimizing negative immune response. Focusing
on dentistry, the use of dental implants for tooth replacement requires a balance between bodily response, mechanical structure and performance, and aesthetics. This mini-review addresses the use of biomaterials in dental implants with significant comparisons drawn between Ti and zirconia.
Attention is drawn to optimizing surface modification processes and the additional use of coatings. Alternatives and novel developments are addressed, providing potential implications of combining biomaterials to form nov...
Senanayake, S, Pradhan, B, Huete, A & Brennan, J 2021, 'Proposing an ecologically viable and economically sound farming system using a matrix-based geo-informatics approach', Science of The Total Environment, vol. 794, pp. 148788-148788.
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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 and Microbiomes, vol. 7, no. 1, p. 27.
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AbstractExtracellular 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, PAN, M, ZHAO, D, WANG, D, HWANG, F-J & CHEN, C-H 2021, 'Maritime Target Detection Based on Electronic Image Stabilization Technology of Shipborne Camera', IEICE Transactions on Information and Systems, vol. E104.D, no. 7, pp. 948-960.
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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, pp. 531-537.
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Shariev, A, Menounos, S, Laos, AJ, Laxman, P, Lai, D, Hua, S, Zinger, A, McRae, CR, Casbolt, LS, Combes, V, Smith, G, Hung, T-T, Dixon, KM, Thordarson, P, Mason, RS & Das, A 2021, 'Skin protective and regenerative effects of RM191A, a novel superoxide dismutase mimetic', Redox Biology, vol. 38, pp. 101790-101790.
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Superoxide dismutase (SOD) is known to be protective against oxidative stress-mediated skin dysfunction. Here we explore the potential therapeutic activities of RM191A, a novel SOD mimetic, on skin. RM191A is a water-soluble dimeric copper (Cu2+-Cu3+)-centred polyglycine coordination complex. It displays 10-fold higher superoxide quenching activity compared to SOD as well as significant antioxidant, anti-inflammatory and immunomodulatory activities through beneficial modulation of several significant inflammatory cytokines in vitro and in vivo. We tested the therapeutic potential of RM191A in a topical gel using a human skin explant model and observed that it significantly inhibits UV-induced DNA damage in the epidermis and dermis, including cyclobutane pyrimidine dimers (CPD), 8-oxo-guanine (8-oxoG) and 8-nitroguanine (8NGO). RM191A topical gel is found to be non-toxic, non-teratogenic and readily distributed in the body of mice. Moreover, it significantly accelerates excisional wound healing, reduces 12-O-tetradecanoylphorbol-13-acetate (TPA)-induced inflammation and attenuates age-associated oxidative stress in skin, demonstrating both skin regenerative and geroprotective properties of RM191A.
Sharif, HMA, Li, T, Mahmood, N, Ahmad, M, Xu, J, Mahmood, A, Djellabi, R & Yang, B 2021, 'Thermally activated epoxy-functionalized carbon as an electrocatalyst for efficient NOx reduction', Carbon, vol. 182, pp. 516-524.
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Sharif, HMA, Mahmood, A, Djellabi, R, Cheng, H-Y, Dong, H, Ajibade, FO, Ali, I, Yang, B & Wang, A-J 2021, 'Utilization of electrochemical treatment and surface reconstruction to achieve long lasting catalyst for NOx removal', Journal of Hazardous Materials, vol. 401, pp. 123440-123440.
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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, vol. 283, pp. 119871-119871.
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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, 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, vol. 591, no. 7849, pp. 240-245.
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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, pp. 035028-035028.
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Abstract
Obstructive sleep apnea (OSA) is a chronic disorder that involves a decrease or complete cessation of airflow during sleep. It occurs when the muscles supporting the soft tissues in the throat relax during sleep, causing narrowing or closure of the upper airway. Sleep apnea is a serious medical condition with an increased risk of cardiovascular complications and impaired quality of life. Continuous positive airway pressure (CPAP) is the most effective treatment for moderate to severe cases of OSA and is effective in mild sleep apnea. However, CPAP therapy is associated with the development of several nasal side effects and is inconvenient for the user, leading to low compliance rates. The effects of CPAP treatment on the upper respiratory system, as well as the pathogenesis of side effects, are incompletely understood and not adequately researched. To better understand the effects of CPAP treatment on the upper respiratory system, we developed an in vitro 3D-printed microfluidic platform. A nasal epithelial cell line, RPMI 2650, was then exposed to certain conditions to mimic the in vivo environment. To create these conditions, the microfluidic device was utilized to expose nasal epithelial cells grown and differentiated at the air–liquid interface. The airflow was similar to what is experienced with CPAP, with pressure ranging between 0 and 20 cm of H2O. Cells exposed to pressure showed decreased barrier integrity, change in cellular shape, and increased cell death (lactate dehydrogenase release into media) compared to unstressed cells. Stressed cells also showed increased secretions of inflammatory markers IL-6 and IL-8 and had increased production of ATP. Our results suggest that stress induced by airflow leads to structural, metabolic, and inflammatory changes in the nasal epithelium, which may be responsible for developing nasal...
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, pp. 1001-1001.
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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.
Sim, DZH, Mowe, MAD, Song, Y, Lu, J, Tan, HTW, Mitrovic, SM, Roelke, DL & Yeo, DCJ 2021, 'Tropical macrophytes promote phytoplankton community shifts in lake mesocosms: relevance for lake restoration in warm climates', Hydrobiologia, vol. 848, no. 20, pp. 4861-4884.
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Skerrett‐Byrne, DA, Bromfield, EG, Murray, HC, Jamaluddin, MFB, Jarnicki, AG, Fricker, M, Essilfie, AT, Jones, B, Haw, TJ, Hampsey, D, Anderson, AL, Nixon, B, Scott, RJ, Wark, PAB, Dun, MD & Hansbro, PM 2021, 'Time‐resolved proteomic profiling of cigarette smoke‐induced experimental chronic obstructive pulmonary disease', Respirology, vol. 26, no. 10, pp. 960-973.
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Skinnider, MA, Wang, F, Pasin, D, Greiner, R, Foster, LJ, Dalsgaard, PW & Wishart, DS 2021, 'A deep generative model enables automated structure elucidation of novel psychoactive substances', Nature Machine Intelligence, vol. 3, no. 11, pp. 973-984.
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Smith, C, Cokcetin, N, Truong, T, Harry, E, Hutvagner, G & Bajan, S 2021, 'Cataloguing the small RNA content of honey using next generation sequencing', Food Chemistry: Molecular Sciences, vol. 2, pp. 100014-100014.
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Solntsev, AS, Agarwal, GS & Kivshar, YS 2021, 'Metasurfaces for quantum photonics', Nature Photonics, vol. 15, no. 5, pp. 327-336.
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Sommer, B, Butler, IR & Pandolfi, JM 2021, 'Trait-based approach reveals how marginal reefs respond to acute and chronic disturbance', Coral Reefs, vol. 40, no. 3, pp. 735-749.
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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, vol. 11, no. 1.
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AbstractThe Murray-Darling Basin (MDB) is Australia’s major agricultural region. The southern MDB receives most of its annual catchment runoff during the cool season (April–September). Focusing on the Murrumbidgee River measurements at Wagga Wagga and further downstream at Hay, cool season river heights are available year to year. The 27-year period April–September Hay and Wagga Wagga river heights exhibit decreases between 1965 and 1991 and 1992–2018 not matched by declining April-September catchment rainfall. However, permutation tests of means and variances of late autumn (April–May) dam catchment precipitation and net inflows, produced p-values indicating a highly significant decline since the early 1990s. Consequently, dry catchments in late autumn, even with average cool season rainfall, have reduced dam inflows and decreased river heights downstream from Wagga Wagga, before water extraction for irrigation. It is concluded that lower April–September mean river heights at Wagga Wagga and decreased river height variability at Hay, since the mid-1990s, are due to combined lower April–May catchment precipitation and increased mean temperatures. Machine learning attribute detection revealed the southern MDB drivers as the southern annular mode (SAM), inter-decadal Pacific oscillation (IPO), Indian Ocean dipole (IOD) and global sea-surface temperature (GlobalSST). Continued catchment drying and warming will drastically reduce future water availability.
Srivastava, A, Saco, PM, Rodriguez, JF, Kumari, N, Chun, KP & Yetemen, O 2021, 'The role of landscape morphology on soil moisture variability in semi‐arid ecosystems', Hydrological Processes, vol. 35, no. 1.
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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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Biopolymer-capped silver nanoparticle synthesis. Compositional and stability analysis of synthesised particles. Proteomic analysis of particles following serum exposure. In vitro hemolytic assays. Organ distribution following administration in mice.
Steele, JR, Italiano, CJ, Phillips, CR, Violi, JP, Pu, L, Rodgers, KJ & Padula, MP 2021, 'Misincorporation Proteomics Technologies: A Review', Proteomes, vol. 9, no. 1, pp. 2-2.
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Proteinopathies are diseases caused by factors that affect proteoform conformation. As such, a prevalent hypothesis is that the misincorporation of noncanonical amino acids into a proteoform results in detrimental structures. However, this hypothesis is missing proteomic evidence, specifically the detection of a noncanonical amino acid in a peptide sequence. This review aims to outline the current state of technology that can be used to investigate mistranslations and misincorporations whilst framing the pursuit as Misincorporation Proteomics (MiP). The current availability of technologies explored herein is mass spectrometry, sample enrichment/preparation, data analysis techniques, and the hyphenation of approaches. While many of these technologies show potential, our review reveals a need for further development and refinement of approaches is still required.
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, pp. 24-24.
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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, 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 & Cell Biology, vol. 99, no. 10, pp. 1085-1092.
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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. This study 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 the growth of Mycobacterium bovis BCG and Mycobacterium tuberculosis, although the 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 in 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 inducible nitric oxide synthase activity than IC-21 cells, indicative of a more polarized M1 response. The expression of multiple surface markers was 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. The results support the notion that the origin of tissue-resident macrophages influences their phenotype and antimicrobial response and demonstrate hereto unrecognized potential for these cell lines in in vitro studies.
Stewart, J, Hegarty, A-M & 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, pp. 105456-105456.
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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, pp. 105981-105981.
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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, vol. 12, no. 1.
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AbstractPhoton upconversion of near-infrared (NIR) irradiation into ultraviolet-C (UVC) emission offers many exciting opportunities for drug release in deep tissues, photodynamic therapy, solid-state lasing, energy storage, and photocatalysis. However, NIR-to-UVC upconversion remains a daunting challenge due to low quantum efficiency. Here, we report an unusual six-photon upconversion process in Gd3+/Tm3+-codoped nanoparticles following a heterogeneous core-multishell architecture. This design efficiently suppresses energy consumption induced by interior energy traps, maximizes cascade sensitizations of the NIR excitation, and promotes upconverted UVC emission from high-lying excited states. We realized the intense six-photon-upconverted UV emissions at 253 nm under 808 nm excitation. This work provides insight into mechanistic understanding of the upconversion process within the heterogeneous architecture, while offering exciting opportunities for developing nanoscale UVC emitters that can be remotely controlled through deep tissues upon NIR illumination.
Sun, J, Zhu, D & Platen, E 2021, 'DYNAMIC ASSET ALLOCATION FOR TARGET DATE FUNDS UNDER THE BENCHMARK APPROACH', ASTIN Bulletin, vol. 51, no. 2, pp. 449-474.
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ABSTRACTTarget date funds (TDFs) are becoming increasingly popular investment choices among investors with long-term prospects. Examples include members of superannuation funds seeking to save for retirement at a given age. TDFs provide efficient risk exposures to a diversified range of asset classes that dynamically match the risk profile of the investment payoff as the investors age. This is often achieved by making increasingly conservative asset allocations over time as the retirement date approaches. Such dynamically evolving allocation strategies for TDFs are often referred to as glide paths. We propose a systematic approach to the design of optimal TDF glide paths implied by retirement dates and risk preferences and construct the corresponding dynamic asset allocation strategy that delivers the optimal payoffs at minimal costs. The TDF strategies we propose are dynamic portfolios consisting of units of the growth-optimal portfolio (GP) and the risk-free asset. Here, the GP is often approximated by a well-diversified index of multiple risky assets. We backtest the TDF strategies with the historical returns of the S&P500 total return index serving as the GP approximation.
Sun, X, Yang, J, Su, D, Wang, C & Wang, G 2021, 'Highly Efficient Adsorption of Bilirubin by Ti 3 C 2 T x MXene', Chemistry – An Asian Journal, vol. 16, no. 14, pp. 1949-1955.
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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, vol. 9, no. 6, pp. 983-983.
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The integrity of coral reef ecosystems worldwide rests on a fine-tuned symbiotic interaction between an invertebrate and a dinoflagellate microalga from the family Symbiodiniaceae. Recent advances in bottom-up shotgun proteomic approaches and the availability of vast amounts of genetic information about Symbiodiniaceae have provided a unique opportunity to better understand the molecular mechanisms underpinning the interactions of coral-Symbiodiniaceae. However, the resilience of this dinoflagellate cell wall, as well as the presence of polyanionic and phenolics cell wall components, requires the optimization of sample preparation techniques for successful implementation of bottom-up proteomics. Therefore, in this study we compare three different workflows—filter-aided sample preparation (FASP), single-pot solid-phase-enhanced sample preparation (SP3), and stop-and-go-extraction tips (STAGETips, ST)—to develop a high-throughput proteotyping protocol for Symbiodiniaceae algal research. We used the model isolate Symbiodinium tridacnidorum. We show that SP3 outperformed ST and FASP with regard to robustness, digestion efficiency, and contaminant removal, which led to the highest number of total (3799) and unique proteins detected from 23,593 peptides. Most of these proteins were detected with ≥2 unique peptides (73%), zero missed tryptic peptide cleavages (91%), and hydrophilic peptides (>70%). To demonstrate the functionality of this optimized SP3 sample preparation workflow, we examined the proteome of S. tridacnidorum to better understand the molecular mechanism of peridinin-chlorophyll-protein complex (PCP, light harvesting protein) accumulation under low light (LL, 30 μmol photon m−2 s−1). Cells exposed to LL for 7 days upregulated various light harvesting complex (LHCs) proteins through the mevalonate-independent pathway; proteins of this pathway were at 2- to 6-fold higher levels than the control of 120 μmol photon m−2 s−1. Potentially, LHCs which ...
Sutherland, DL & Ralph, PJ 2021, 'Differing growth responses in four related microalgal genera grown under autotrophic, mixotrophic and heterotrophic conditions', Journal of Applied Phycology, vol. 33, no. 6, pp. 3539-3553.
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Sutherland, DL & Ralph, PJ 2021, 'Productivity and community response along an ammonia gradient in cultured wild marine microalgae, using wastewater-derived nutrients for cost-effective feedstock production', Journal of Applied Phycology, vol. 33, no. 5, pp. 2933-2945.
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Sutherland, DL & Ralph, PJ 2021, 'Shortening hydraulic retention time through effluent recycling: impacts on wastewater treatment and biomass production in microalgal treatment systems', Journal of Applied Phycology, vol. 33, no. 6, pp. 3873-3884.
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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, vol. 3, pp. 100050-100050.
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Sutherland, DL, Park, J, Ralph, PJ & Craggs, R 2021, 'Ammonia, pH and dissolved inorganic carbon supply drive whole pond metabolism in full-scale wastewater high rate algal ponds', Algal Research, vol. 58, pp. 102405-102405.
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Sutherland, TC, Ricafrente, A, Gomola, K, O’Brien, BA & Gorrie, CA 2021, 'Neonatal Rats Exhibit a Predominantly Anti-Inflammatory Response following Spinal Cord Injury', Developmental Neuroscience, vol. 43, no. 1, pp. 18-26.
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It has been reported that children may respond better than adults to a spinal cord injury (SCI) of similar severity. There are known biomechanical differences in the developing spinal cord that may contribute to this “infant lesion effect,” but the underlying mechanisms are unknown. Using immunohistochemistry, we have previously demonstrated a different injury progression and immune cell response after a mild thoracic contusion SCI in infant rats, as compared to adult rats. Here, we investigated the acute inflammatory responses using flow cytometry and ELISA at 1 h, 24 h, and 1 week after SCI in neonatal (P7) and adult (9 weeks) rats, and locomotor recovery was examined for 6 weeks after injury. Adult rats exhibited a pronounced pro-inflammatory response characterized by neutrophils and M1-like macrophage infiltration and Th1 cytokine secretion. Neonatal rats exhibited a decreased pro-inflammatory response characterized by a higher proportion of M2-like macrophages and reduced Th1 cytokine responses, as compared to adults. These results suggest that the initial inflammatory response to SCI is predominantly anti-inflammatory in very young animals.
Szabó, M & Zavafer, A 2021, 'Photoinhibition, photo-ecophysiology, and biophysics, a special issue in honor of Wah Soon Chow', Photosynthesis Research, vol. 149, no. 1-2, pp. 1-3.
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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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AbstractThe first instar larva of a species of the Australian endemic genus Aenigmetopia Malloch is described for the first time, along with the first instar larvae of three other Australian species representing the genera Amobia Robineau-Desvoidy and Protomiltogramma Townsend. Larval morphology was analysed using a combination of light microscopy, confocal laser scanning microscopy and scanning electron microscopy. The following morphological structures are documented: pseudocephalon, antennal complex, maxillary palpus, facial mask, modifications of thoracic and abdominal segments, anal region, spiracular field, posterior spiracles and details of the cephaloskeleton. Substantial morphological differences are observed between the three genera, most notably in the labrum and mouthhooks of the cephaloskeleton, sensory organs of the pseudocephalon, spinulation, sculpture of the integument and form of the spiracular field. The first instar larval morphology of Aenigmetopia amissa Johnston, Wallman, Szpila & Pape corroborates the close phylogenetic affinity of Aenigmetopia Malloch with Metopia Meigen, inferred from recent molecular analysis. The larval morphology of Amobia auriceps (Baranov), Protomiltogramma cincta Townsend and Protomiltogramma plebeia Malloch is mostly congruent with the morphology of Palaearctic representatives of both genera.
Tan, CH, Yeo, YP, Hafiz, M, Ng, NKJ, Subramoni, S, Taj, S, Tay, M, Chao, X, Kjelleberg, S & Rice, SA 2021, 'Functional metagenomic analysis of quorum sensing signaling in a nitrifying community', npj Biofilms and Microbiomes, vol. 7, no. 1.
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AbstractQuorum sensing (QS) can function to shape the microbial community interactions, composition, and function. In wastewater treatment systems, acylated homoserine lactone (AHL)-based QS has been correlated with the conversion of floccular biomass into microbial granules, as well as EPS production and the nitrogen removal process. However, the role of QS in such complex communities is still not fully understood, including the QS-proficient taxa and the functional QS genes involved. To address these questions, we performed a metagenomic screen for AHL genes in an activated sludge microbial community from the Ulu Pandan wastewater treatment plant (WWTP) in Singapore followed by functional validation of luxI activity using AHL biosensors and LC–MSMS profiling. We identified 13 luxI and 30 luxR homologs from the activated sludge metagenome. Of those genes, two represented a cognate pair of luxIR genes belonging to a Nitrospira spp. and those genes were demonstrated to be functionally active. The LuxI homolog synthesized AHLs that were consistent with the dominant AHLs in the activated sludge system. Furthermore, the LuxR homolog was shown to bind to and induce expression of the luxI promoter, suggesting this represents an autoinduction feedback system, characteristic of QS circuits. Additionally, a second, active promoter was upstream of a gene encoding a protein with a GGDEF/EAL domain, commonly associated with modulating the intracellular concentration of the secondary messenger, c-di-GMP. Thus, the metagenomic approach used here was demonstrated to effectively identify functional QS genes and suggests that Nitrospira spp. maybe QS is active in the activated sludge community.
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, vol. 12, no. 1.
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AbstractRechargeable multivalent metal (e.g., Ca, Mg or, Al) batteries are ideal candidates for large–scale electrochemical energy storage due to their intrinsic low cost. However, their practical application is hampered by the low electrochemical reversibility, dendrite growth at the metal anodes, sluggish multivalent–ion kinetics in metal oxide cathodes and, poor electrode compatibility with non–aqueous organic–based electrolytes. To circumvent these issues, here we report various aqueous multivalent–ion batteries comprising of concentrated aqueous gel electrolytes, sulfur–containing anodes and, high-voltage metal oxide cathodes as alternative systems to the non–aqueous multivalent metal batteries. This rationally designed aqueous battery chemistry enables satisfactory specific energy, favorable reversibility and improved safety. As a demonstration model, we report a room–temperature calcium-ion/sulfur| |metal oxide full cell with a specific energy of 110 Wh kg–1 and remarkable cycling stability. Molecular dynamics modeling and experimental investigations reveal that the side reactions could be significantly restrained through the suppressed water activity and formation of a protective inorganic solid electrolyte interphase. The unique redox chemistry of the multivalent–ion system is also demonstrated for aqueous magnesium–ion/sulfur||metal oxide and aluminum–ion/sulfur||metal oxide full cells.
Tangella, LP, Arooj, M, Deplazes, E, Gray, ES & Mancera, RL 2021, 'Identification and characterisation of putative drug binding sites in human ATP-binding cassette B5 (ABCB5) transporter', Computational and Structural Biotechnology Journal, vol. 19, pp. 691-704.
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Taras, AK, Tuniz, A, Bajwa, MA, Ng, V, Dawes, JM, Poulton, CG & De Sterke, CM 2021, 'Shortcuts to adiabaticity in waveguide couplers–theory and implementation', Advances in Physics: X, vol. 6, no. 1.
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Taudte, RV, Roux, C, Bishop, DP, Fouracre, C & Beavis, A 2021, 'High-throughput screening for target compounds in smokeless powders using online-SPE tandem mass spectrometry', Australian Journal of Forensic Sciences, vol. 53, no. 1, pp. 16-26.
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Thi, DD, Miranda, A, Trestrail, C, De Souza, H, Dinh, KV & Nugegoda, D 2021, 'Antagonistic effects of copper and microplastics in single and binary mixtures on development and reproduction in the freshwater cladoceran Daphnia carinata', Environmental Technology & Innovation, vol. 24, pp. 102045-102045.
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The combined effect of microplastics (MPs) and other contaminants such as trace metals is largely unknown although MPs can act as a vector for other contaminants. The present study investigated the impact of a single and mixture of MPs and a common trace contaminant, copper (Cu) on the Australian freshwater cladoceran Daphnia carina. No acute value was recorded when D. carinata was exposed to clear polyethylene size of 1–10 μm with the concentration ranging from 5, 25, 50, 100, 200 and 300 mg/L during 48 h of exposure. D. carinata showed a tendency to utilize MPs from the surrounding environment to prolong their life when the food was scarce. When D. carinata were exposed to environmentally relevant concentrations of Cu: 1 and 3 μg/L or MPs concentration of 0.25 and 1 mg/L for 21 days, no effects on reproduction was recorded. The impacts of Cu and MPs on molting frequency in the mixture treatments were less than in the single contaminant treatments. D. carinata juveniles were more sensitive to Cu than the adults regardless of the presence or absence of MPs. The findings highlight the importance of clarifying the interaction between traditional and contaminants of emerging concern for effective risk assessment.
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, vol. 10, no. 6, pp. 1312-1312.
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Buspirone is an anxiolytic drug with robust serotonin receptor 1A (Htr1a) agonist activities. However, evidence has demonstrated that this drug also targets the dopamine D3 receptor (Drd3), where it acts as a potent antagonist. In vivo, Drd3 blockade is neuroprotective and reduces inflammation in models of Parkinson’s disease. To test if buspirone also elicited anti-inflammatory activities in vitro, we generated stable Drd3−/− and Htr1a−/− BV2 microglial cell lines using CRISPR-Cas9 technology and then tested the effects of buspirone after lipopolysaccharide (LPS) challenge. We found that LPS exposure had no effect on cell viability, except in Htr1a−/− cells, where viability was reduced (p < 0.001). Drug treatment reduced viability in Drd3−/− cells, but not in WT or Htr1a−/− cells. Buspirone counteracted LPS-induced NO release, NOS2, IL-1β and TNF-α gene expression in WT cells, whereas it exerted limited effects in Drd3−/− or Htr1a−/− microglia. In summary, our findings indicate that buspirone attenuates microglial polarization after LPS challenge. These results also highlight some major effects of Drd3 or Htr1a genetic ablation on microglial biology, raising important questions on the complex role of neurotransmitters in regulating microglia functions.
Thomas, M, Lawrence, A, Kroon, S, Vodstrcil, LA, Phillips, S, Hocking, JS, Timms, P & Huston, WM 2021, 'Chlamydial clinical isolates show subtle differences in persistence phenotypes and growth in vitro', Access Microbiology, vol. 3, no. 3.
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Urogenital
Chlamydia trachomatis
infection is the most common sexually transmitted bacterial infection throughout the world. While progress has been made to better understand how type strains develop and respond to environmental stress in vitro, very few studies have examined how clinical isolates behave under similar conditions. Here, we examined the development and persistence phenotypes of several clinical isolates, to determine how similar they are to each other, and the type strain
C. trachomatis
D/UW-3/Cx. The type strain was shown to produce infectious progeny at a higher magnitude than each of the clinical isolates, in each of the six tested cell lines. All chlamydial strains produced the highest number of infectious progeny at 44 h post-infection in the McCoy B murine fibroblast cell line, yet showed higher levels of infectivity in the MCF-7 human epithelial cell line. The clinical isolates were shown to be more susceptible than the type strain to the effects of penicillin and iron deprivation persistence models in the MCF-7 cell line. While subtle differences between clinical isolates were observed throughout the experiments conducted, no significant differences were identified. This study reinforces the importance of examining clinical isolates when trying ...
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, vol. 12, no. 22, pp. 7656-7676.
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Single-atom catalysts are reviewed, aiming to achieve optimized properties to boost electrochemical performances of high-energy batteries.
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, pp. 2101796-2101796.
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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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Tiotiu, A, Zounemat Kermani, N, Badi, Y, Pavlidis, S, Hansbro, PM, Guo, Y, Chung, KF & Adcock, IM 2021, 'Sputum macrophage diversity and activation in asthma: Role of severity and inflammatory phenotype', Allergy, vol. 76, no. 3, pp. 775-788.
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Tkacheva, A, Sun, B, Zhang, J, Wang, G & McDonagh, AM 2021, 'Nitronyl Nitroxide-Based Redox Mediators for Li-O2 Batteries', The 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', The Journal of Clinical Endocrinology & Metabolism, vol. 106, no. 1, pp. 26-41.
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Abstract
Context
Preeclampsia is a leading cardiovascular complication in pregnancy lacking effective diagnostic and treatment strategies.
Objective
To investigate the diagnostic and therapeutic target potential of the angiogenesis proteins, FK506-binding protein like (FKBPL) and CD44.
Design and Intervention
FKBPL and CD44 plasma concentration or placental expression were determined in women pre- or postdiagnosis of preeclampsia. Trophoblast and endothelial cell function was assessed following mesenchymal stem cell (MSC) treatment and in the context of FKBPL signaling.
Settings and Participants
Human samples prediagnosis (15 and 20 weeks of gestation; n ≥ 57), or postdiagnosis (n = 18 for plasma; n = 4 for placenta) of preeclampsia were used to determine FKBPL and CD44 levels, compared to healthy controls. Trophoblast or endothelial cells were exposed to low/high oxygen, and treated with MSC-conditioned media (MSC-CM) or a FKBPL overexpression plasmid.
Main Outcome Measures
Preeclampsia risk stratification and diagnostic potential of FKBPL and CD44 were investigated. MSC treatment effects and FKBPL-CD44 signaling in trophoblast and endothelial cells were assessed.
Results
The CD44/FKBPL ratio was reduc...
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, vol. 11, no. 1.
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AbstractFasciola hepatica, a global worm parasite of humans and their livestock, regulates host innate immune responses within hours of infection. Host macrophages, essential to the first-line defence mechanisms, are quickly restricted in their ability to initiate a classic protective pro-inflammatory immune response. We found that macrophages from infected animals are enriched with parasite-derived micro(mi)RNAs. The most abundant of these miRNAs, fhe-miR-125b, is released by the parasite via exosomes and is homologous to a mammalian miRNA, hsa-miR-125b, that is known to regulate the activation of pro-inflammatory M1 macrophages. We show that the parasite fhe-miR-125b loads onto the mammalian Argonaut protein (Ago-2) within macrophages during infection and, therefore, propose that it mimics host miR-125b to negatively regulate the production of inflammatory cytokines. The hijacking of the miRNA machinery controlling innate cell function could be a fundamental mechanism by which worm parasites disarm the early immune responses of their host to ensure successful infection.
Tran, TN, Kim, S, White, SJU, Nguyen, MAP, Xiao, L, Strauf, S, Yang, T, Aharonovich, I & Xu, Z 2021, 'Enhanced Emission from Interlayer Excitons Coupled to Plasmonic Gap Cavities', Small, vol. 17, no. 45, pp. 2103994-2103994.
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The emergence of interlayer excitons (IEs) from atomic layered transition metal dichalcogenides (TMDCs) heterostructures has drawn tremendous attention due to their unique and exotic optoelectronic properties. Coupling the IEs into optical cavities provides distinctive electromagnetic environments which plays an important role in controlling multiple optical processes such as optical nonlinear generation or photoluminescence enhancement. Here, the integration of IEs in TMDCs into plasmonic nanocavities based on a nanocube on a metallic mirror is reported. Spectroscopic studies reveal an order of magnitude enhancement of the IE at room temperature and a 5-time enhancement in fluorescence at cryogenic temperatures. Cavity modeling reveals that the enhancement of the emission is attributed to both increased excitation efficiency and Purcell effect from the cavity. The results show a novel method to control the excitonic processes in TMDC heterostructures to build high performance photonics and optoelectronics devices.
Tran, W, Kusay, AS, Hawkins, PME, Cheung, C-Y, Nagalingam, G, Pujari, V, Ford, DJ, Stoye, A, Ochoa, JL, Audette, RE, Hortle, E, Oehlers, SH, Charman, SA, Linington, RG, Rubin, EJ, Dowson, CG, Roper, DI, Crick, DC, Balle, T, Cook, GM, Britton, WJ & Payne, RJ 2021, 'Synthetic Sansanmycin Analogues as Potent Mycobacterium tuberculosis Translocase I Inhibitors', Journal of Medicinal Chemistry, vol. 64, no. 23, pp. 17326-17345.
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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.
Trestrail, C, Walpitagama, M, Miranda, A, Nugegoda, D & Shimeta, J 2021, 'Microplastics alter digestive enzyme activities in the marine bivalve, Mytilus galloprovincialis', Science of The Total Environment, vol. 779, pp. 146418-146418.
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Microplastics are eaten by many invertebrates, particularly filter-feeding organisms like mussels. Since microplastics can be retained in the digestive system for extended periods, there is ample opportunity for them to interact with the functions of digestive enzymes. This study determined how the polymer type, size and concentration of ingested spherical microplastics affects the activities of seven key digestive enzymes in the digestive gland of Mytilus galloprovincialis, a common marine mussel. Polymer type significantly affected the activities of carbohydrase enzymes: polystyrene reduced amylase and xylanase activities, and increased cellulase activity. High concentrations of microplastics (5 × 104 microplastics L-1) caused a 2.5-fold increase in total protease activity. The activities of laminarinase, lipases and lipolytic esterases were unaffected by the polymer type, size or concentration of microplastics. Microplastics-induced changes to digestive enzyme activities can affect mussels' ability to acquire energy from food and reduce their energy reserves.
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 Edition, vol. 60, no. 17, pp. 9215-9246.
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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.
Trouve, J, Zapun, A, Arthaud, C, Durmort, C, Di Guilmi, AM, Söderström, B, Pelletier, A, Grangeasse, C, Bourgeois, D, Wong, Y-S & Morlot, C 2021, 'Nanoscale dynamics of peptidoglycan assembly during the cell cycle of Streptococcus pneumoniae', Current Biology, vol. 31, no. 13, pp. 2844-2856.e6.
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Tschida, JE, Maddox, BB, Bertollo, JR, Kuschner, ES, Miller, JS, Ollendick, TH, Greene, RW & Yerys, BE 2021, 'Caregiver perspectives on interventions for behavior challenges in autistic children', Research in Autism Spectrum Disorders, vol. 81, pp. 101714-101714.
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Tseng, P-H, Zhou, A & Hwang, F-J 2021, 'Northeast passage in Asia-Europe liner shipping: an economic and environmental assessment', International Journal of Sustainable Transportation, vol. 15, no. 4, pp. 273-284.
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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, Horvat, JC & Hansbro, PM 2021, 'Asthma-COPD overlap: current understanding and the utility of experimental models', European Respiratory Review, vol. 30, no. 159, pp. 190185-190185.
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Pathological features of both asthma and COPD coexist in some patients and this is termed asthma-COPD overlap (ACO). ACO is heterogeneous and patients exhibit various combinations of asthma and COPD features, making it difficult to characterise the underlying pathogenic mechanisms. There are no controlled studies that define effective therapies for ACO, which arises from the lack of international consensus on the definition and diagnostic criteria for ACO, as well as scantin vitroandin vivodata. There remain unmet needs for experimental models of ACO that accurately recapitulate the hallmark features of ACO in patients. The development and interrogation of such models will identify underlying disease-causing mechanisms, as well as enabling the identification of novel therapeutic targets and providing a platform for assessing new ACO therapies. Here, we review the current understanding of the clinical features of ACO and highlight the approaches that are best suited for developing representative experimental models of ACO.
Turkewitz, DR, Moghaddasi, S, Alghalayini, A, D'Amario, C, Ali, HM, Wallach, M & Valenzuela, SM 2021, 'Comparative study of His- and Non-His-tagged CLIC proteins, reveals changes in their enzymatic activity', Biochemistry and Biophysics Reports, vol. 26, pp. 101015-101015.
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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, pp. 1809-1809.
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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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Ueland, M, Collins, S, Maestrini, L, Forbes, SL & Luong, S 2021, 'Fresh vs. frozen human decomposition – A preliminary investigation of lipid degradation products as biomarkers of post-mortem interval', Forensic Chemistry, vol. 24, pp. 100335-100335.
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Ueland, M, Harris, S & Forbes, SL 2021, 'Detecting volatile organic compounds to locate human remains in a simulated collapsed building', Forensic Science International, vol. 323, pp. 110781-110781.
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Valiate, BVS, Queiroz‐Junior, CM, Levi‐Schaffer, F, Galvão, I & Teixeira, MM 2021, 'CD300a contributes to the resolution of articular inflammation triggered by MSU crystals by controlling neutrophil apoptosis', Immunology, vol. 164, no. 2, pp. 305-317.
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van der Molen, MC, Hartman, JE, Vermeulen, CJ, van den Berge, M, Faiz, A, Kerstjens, HAM, Charbonnier, J-P, Vanfleteren, LEGW & Slebos, D-J 2021, 'Determinants of Lung Fissure Completeness', American Journal of Respiratory and Critical Care Medicine, vol. 204, no. 7, pp. 807-816.
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Vardi, T, Hoot, WC, Levy, J, Shaver, E, Winters, RS, Banaszak, AT, Baums, IB, Chamberland, VF, Cook, N, Gulko, D, Hein, MY, Kaufman, L, Loewe, M, Lundgren, P, Lustic, C, MacGowan, P, Matz, MV, McGonigle, M, McLeod, I, Moore, J, Moore, T, Pivard, S, Pollock, FJ, Rinkevich, B, Suggett, DJ, Suleiman, S, Viehman, TS, Villalobos, T, Weis, VM, Wolke, C & Montoya‐Maya, PH 2021, 'Six priorities to advance the science and practice of coral reef restoration worldwide', Restoration Ecology, vol. 29, no. 8.
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Coral reef restoration is a rapidly growing movement galvanized by the accelerating degradation of the world's tropical coral reefs. The need for concerted and collaborative action focused on the recovery of coral reef ecosystems coalesced in the creation of the Coral Restoration Consortium (CRC) in 2017. In March 2020, the CRC leadership team met for a biennial review of international coral reef restoration efforts and a discussion of perceived knowledge and implementation bottlenecks that may impair scalability and efficacy. Herein we present six priorities wherein the CRC will foster scientific advancement and collaboration to: (1) increase restoration efficiency, focusing on scale and cost-effectiveness of deployment; (2) scale up larval-based coral restoration efforts, emphasizing recruit health, growth, and survival; (3) ensure restoration of threatened coral species proceeds within a population-genetics management context; (4) support a holistic approach to coral reef ecosystem restoration; (5) develop and promote the use of standardized terms and metrics for coral reef restoration; and (6) support coral reef restoration practitioners working in diverse geographic locations. These priorities are not exhaustive nor do we imply that accomplishing these tasks alone will be sufficient to restore coral reefs globally; rather these are topics where we feel the CRC community of practice can make timely and significant contributions to facilitate the growth of coral reef restoration as a practical conservation strategy. The goal for these collective actions is to provide tangible, local-scale advancements in reef condition that offset declines resulting from local and global stressors including climate change.
Vicedomini, R, Quince, C, Darling, AE & Chikhi, R 2021, 'Strainberry: automated strain separation in low-complexity metagenomes using long reads', Nature Communications, vol. 12, no. 1.
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AbstractHigh-throughput short-read metagenomics has enabled large-scale species-level analysis and functional characterization of microbial communities. Microbiomes often contain multiple strains of the same species, and different strains have been shown to have important differences in their functional roles. Recent advances on long-read based methods enabled accurate assembly of bacterial genomes from complex microbiomes and an as-yet-unrealized opportunity to resolve strains. Here we present Strainberry, a metagenome assembly pipeline that performs strain separation in single-sample low-complexity metagenomes and that relies uniquely on long-read data. We benchmarked Strainberry on mock communities for which it produces strain-resolved assemblies with near-complete reference coverage and 99.9% base accuracy. We also applied Strainberry on real datasets for which it improved assemblies generating 20-118% additional genomic material than conventional metagenome assemblies on individual strain genomes. We show that Strainberry is also able to refine microbial diversity in a complex microbiome, with complete separation of strain genomes. We anticipate this work to be a starting point for further methodological improvements on strain-resolved metagenome assembly in environments of higher complexities.
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, pp. 462530-462530.
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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...
Voolstra, CR, Suggett, DJ, Peixoto, RS, Parkinson, JE, Quigley, KM, Silveira, CB, Sweet, M, Muller, EM, Barshis, DJ, Bourne, DG & Aranda, M 2021, 'Extending the natural adaptive capacity of coral holobionts', Nature Reviews Earth & Environment, vol. 2, no. 11, pp. 747-762.
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Anthropogenic climate change and environmental degradation destroy coral reefs, the ecosystem services they provide, and the livelihoods of close to a billion people who depend on these services. Restoration approaches to increase the resilience of corals are therefore necessary to counter environmental pressures relevant to climate change projections. In this Review, we examine the natural processes that can increase the adaptive capacity of coral holobionts, with the aim of preserving ecosystem functioning under future ocean conditions. Current approaches that centre around restoring reef cover can be integrated with emerging approaches to enhance coral stress resilience and, thereby, allow reefs to regrow under a new set of environmental conditions. Emerging approaches such as standardized acute thermal stress assays, selective sexual propagation, coral probiotics, and environmental hardening could be feasible and scalable in the real world. However, they must follow decision-making criteria that consider the different reef, environmental, and ecological conditions. The implementation of adaptive interventions tailored around nature-based solutions will require standardized frameworks, appropriate ecological risk–benefit assessments, and analytical routines for consistent and effective utilization and global coordination.
Vu, HP, Nguyen, LN, Emmerton, B, Wang, Q, Ralph, PJ & Nghiem, LD 2021, 'Factors governing microalgae harvesting efficiency by flocculation using cationic polymers', Bioresource Technology, vol. 340, pp. 125669-125669.
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Vu, HP, Nguyen, LN, Vu, MT, Labeeuw, L, Emmerton, B, Commault, AS, Ralph, PJ, Mahlia, TMI & 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, pp. 142412-142412.
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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...
Walker, GJ, Naing, Z, Ospina Stella, A, Yeang, M, Caguicla, J, Ramachandran, V, Isaacs, SR, Agapiou, D, Bull, RA, Stelzer-Braid, S, Daly, J, Gosbell, IB, Hoad, VC, Irving, DO, Pink, JM, Turville, S, Kelleher, AD & Rawlinson, WD 2021, 'SARS Coronavirus-2 Microneutralisation and Commercial Serological Assays Correlated Closely for Some but Not All Enzyme Immunoassays', Viruses, vol. 13, no. 2, pp. 247-247.
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Serological testing for SARS-CoV-2-specific antibodies provides important research and diagnostic information relating to COVID-19 prevalence, incidence and host immune response. A greater understanding of the relationship between functionally neutralising antibodies detected using microneutralisation assays and binding antibodies detected using scalable enzyme immunoassays (EIA) is needed in order to address protective immunity post-infection or vaccination, and assess EIA suitability as a surrogate test for screening of convalescent plasma donors. We assessed whether neutralising antibody titres correlated with signal cut-off ratios in five commercially available EIAs, and one in-house assay based on expressed spike protein targets. Sera from recovered patients or convalescent plasma donors who reported laboratory-confirmed SARS-CoV-2 infection (n = 200), and negative control sera collected prior to the COVID-19 pandemic (n = 100), were assessed in parallel. Performance was assessed by calculating EIA sensitivity and specificity with reference to microneutralisation. Neutralising antibodies were detected in 166 (83%) samples. Compared with this, the most sensitive EIAs were the Cobas Elecsys Anti-SARS-CoV-2 (98%) and Vitros Immunodiagnostic Anti-SARS-CoV-2 (100%), which detect total antibody targeting the N and S1 antigens, respectively. The assay with the best quantitative relationship with microneutralisation was the Euroimmun IgG. These results suggest the marker used (total Ab vs. IgG vs. IgA) and the target antigen are important determinants of assay performance. The strong correlation between microneutralisation and some commercially available assays demonstrates their potential for clinical and research use in assessing protection following infection or vaccination, and use as a surrogate test to assess donor suitability for convalescent plasma donation.
Walworth, NG, Hinners, J, Argyle, PA, Leles, SG, Doblin, MA, Collins, S & Levine, NM 2021, 'The evolution of trait correlations constrains phenotypic adaptation to high CO 2 in a eukaryotic alga', Proceedings of the Royal Society B: Biological Sciences, vol. 288, no. 1953, pp. 20210940-20210940.
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Microbes form the base of food webs and drive biogeochemical cycling. Predicting the effects of microbial evolution on global elemental cycles remains a significant challenge due to the sheer number of interacting environmental and trait combinations. Here, we present an approach for integrating multivariate trait data into a predictive model of trait evolution. We investigated the outcome of thousands of possible adaptive walks parameterized using empirical evolution data from the alga
Chlamydomonas
exposed to high CO
2
. We found that the direction of historical bias (existing trait correlations) influenced both the rate of adaptation and the evolved phenotypes (trait combinations). Critically, we use fitness landscapes derived directly from empirical trait values to capture known evolutionary phenomena. This work demonstrates that ecological models need to represent both changes in traits and changes in the correlation between traits in order to accurately capture phytoplankton evolution and predict future shifts in elemental cycling.
Wang, B, Chan, Y-L, 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, pp. 1029-1029.
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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 removed 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 hypersecretion, 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 inflammation. 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, pp. 129616-129616.
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Wang, D, Tang, K, Xiao, J, Li, X, Long, M, Chen, J, Gao, H, Chen, W, Liu, C & Liu, H 2021, 'Advances of electrospun Mo-based nanocomposite fibers as anode materials for supercapacitors', Sustainable Materials and Technologies, vol. 29, pp. e00302-e00302.
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Wang, F, Langford, S & Nakai, H 2021, 'Robust design of D-π-A model compounds using digital structures for organic DSSC applications', Journal of Molecular Graphics and Modelling, vol. 102, pp. 107798-107798.
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Wang, JJJ & Weatherburn, D 2021, 'The effect of police searches and move-on directions on property and violent crime in New South Wales', Journal of Criminology, vol. 54, no. 3, pp. 383-401.
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The New South Wales (NSW) Law Enforcement (Powers and Responsibilities) Act 2002 gave the NSW Police the power in certain circumstances the power to stop, search and detain a person without warrant. The same legislation gave the police the power to direct a person to move on from a place if they believe on reasonable grounds that the person in question is obstructing traffic or another person; engaging in behaviour that is considered harassment or intimidation to another person (or people); behaving in a way that is causing or likely to cause fear to a reasonable person or present in the place in order to unlawfully supply or cause another person to unlawfully supply drugs. The exercise of these powers has attracted considerable controversy, but little is known about their effectiveness in controlling crime. We investigate the relationship between police activity and crime using panel data of 17 Local Area Command for the period 2001 to 2013. We find a significant and strongly negative long-run relationship between both indices of police activity and each of break and enter, motor vehicle theft and robbery. No significant long-run relationship is found between assault and move-on directions. The person search activity is negatively related to assault, but the effect is weak; with a 10% increase in person search only resulting in a 0.5% fall in assaults. The implications for the exercise of police move-on and search powers are discussed.
Wang, JJJ, Fung, T & Weatherburn, D 2021, 'The impact of the COVID-19, social distancing, and movement restrictions on crime in NSW, Australia', Crime Science, vol. 10, no. 1.
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AbstractThe spread of COVID-19 has prompted Governments around the world to impose draconian restrictions on business activity, public transport, and public freedom of movement. The effect of these restrictions appears to vary from country to country and, in some cases, from one area to another within a country. This paper examines the impact of the COVID-19 restrictions imposed in New South Wales (NSW) by the State Government. We examine week-to-week changes in 13 categories of crime (and four aggregated categories) from 2 January 2017 to 28 June 2020. Rather than using the pre-intervention data to make a forecast and then comparing that with what is actually observed, we use a Box–Jenkins (ARIMA) approach to model the entire time series. Our results are broadly in accord with those of other studies, but we find no effect of the lockdown (upward or downward) on domestic assault.
Wang, R, Wu, S-T, Yang, X, Qian, Y, Choi, JP, Gao, R, Song, S, Wang, Y, Zhuang, T, Wong, JJL, Zhang, Y, Han, Z, Lu, HA, Alexander, SI, Liu, R, Xia, Y & Zheng, X 2021, 'Pdcd10-Stk24/25 complex controls kidney water reabsorption by regulating Aqp2 membrane targeting', JCI Insight, vol. 6, no. 12.
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Wang, S, Huang, S, Liu, C, Tang, Z, Shi, Q & Schulte, J 2021, 'A Simple Method to Measure the Local Geomagnetic Field Accurately in a First-Year Physics Laboratory', The Physics Teacher, vol. 59, no. 1, pp. 44-47.
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The directional feature of Earth’s geomagnetic field has been contributing to the technological development and prosperity of humankind since the invention of the magnetic compass navigation centuries ago. Today, for instance, magnetoresistance sensors are commonly used in nanosatellites and unmanned aerial vehicles for high accuracy geomagnetic field-based navigation and mineral survey exploration.
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 Ti3 C2 Tx MXene.', Small Methods, vol. 5, no. 5, p. e2001108.
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During the global outbreak of COVID-19 pandemic, 'cytokine storm' conditions are regarded as the fatal step resulting in most mortality. Hemoperfusion is widely used to remove cytokines from the blood of severely ill patients to prevent uncontrolled inflammation induced by a cytokine storm. This article discoveres, for the first time, that 2D Ti3 C2 Tx MXene sheet demonstrates an ultrahigh removal capability for typical cytokine interleukin-6. In particular, MXene shows a 13.4 times higher removal efficiency over traditional activated carbon absorbents. Molecular-level investigations reveal that MXene exhibits a strong chemisorption mechanism for immobilizing cytokine interleukin-6 molecules, which is different from activated carbon absorbents. MXene sheet also demonstrates excellent blood compatibility without any deleterious side influence on the composition of human blood. This work can open a new avenue to use MXene sheets as an ultraefficient hemoperfusion absorbent to eliminate the cytokine storm syndrome in treatment of severe COVID-19 patients.
Wang, Y, Zhang, T, Duan, R, Zhao, Y, Su, D, Liu, Z & Li, C 2021, 'A novel conjugated heterotriangulene polymer for high performance organic lithium-ion battery', Dyes and Pigments, vol. 191, pp. 109352-109352.
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Wark, PAB, MacIntyre, CR, Bell, S, Oliver, B & Marks, GB 2021, 'We are not doing enough to prevent the spread of COVID‐19 and other respiratory viruses in Australian hospitals', Medical Journal of Australia, vol. 215, no. 4, pp. 152-152.
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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, 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, vol. 26, no. 5, pp. 442-451.
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Watson, CJ, Ueland, M, Schotsmans, EMJ, Sterenberg, J, Forbes, SL & Blau, S 2021, 'Detecting grave sites from surface anomalies: A longitudinal study in an Australian woodland', Journal of Forensic Sciences, vol. 66, no. 2, pp. 479-490.
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Waziri, I, Isa, MA, Sonopo, M, Williams, DBG & Muller, A 2021, 'Synthesis, anti-microbial, toxicity and molecular docking studies of N-nitroso-N-phenylhydroxylamine (cupferron) and its derivatives', Bioorganic & Medicinal Chemistry Letters, vol. 52, pp. 128381-128381.
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Weckmann, M, Bahmer, T, Sand, JM, Rank Rønnow, S, Pech, M, Vermeulen, C, Faiz, A, Leeming, DJ, Karsdal, MA, Lunding, L, Oliver, BGG, Wegmann, M, Ulrich-Merzenich, G, Juergens, UR, Duhn, J, Laumonnier, Y, Danov, O, Sewald, K, Zissler, U, Jonker, M, König, I, Hansen, G, von Mutius, E, Fuchs, O, Dittrich, A-M, Schaub, B, Happle, C, Rabe, KF, van de Berge, M, Burgess, JK & Kopp, MV 2021, 'COL4A3 is degraded in allergic asthma and degradation predicts response to anti-IgE therapy', European Respiratory Journal, vol. 58, no. 6, pp. 2003969-2003969.
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BackgroundAsthma is a heterogeneous syndrome substantiating the urgent requirement for endotype-specific biomarkers. Dysbalance of fibrosis and fibrolysis in asthmatic lung tissue leads to reduced levels of the inflammation-protective collagen 4 (COL4A3).ObjectiveTo delineate the degradation of COL4A3 in allergic airway inflammation and evaluate the resultant product as a biomarker for anti-IgE therapy response.MethodsThe serological COL4A3 degradation marker C4Ma3 (Nordic Bioscience, Denmark) and serum cytokines were measured in the ALLIANCE cohort (paediatric cases/controls: n=134/n=35; adult cases/controls: n=149/n=31). Exacerbation of allergic airway disease in mice was induced by sensitising to ovalbumin (OVA), challenge with OVA aerosol and instillation of poly(cytidylic-inosinic). Fulacimstat (chymase inhibitor; Bayer) was used to determine the role of mast cell chymase in COL4A3 degradation. Patients with cystic fibrosis (n=14) and cystic fibrosis with allergic bronchopulmonary aspergillosis (ABPA; n=9) as well as patients with severe allergic uncontrolled asthma (n=19) were tested for COL4A3 degradation. Omalizumab (anti-IgE) treatment was assessed using the Asthma Control Test.ResultsSerum levels of C4Ma3 were increased in asthma in adults and children alike and linked to a more severe, exacerbating allergic asthma phenotype. In an experimental asthma mouse model, C4Ma3 was dependent on mast cell chymase. Serum C4Ma3 was significantly elevated in cystic fibrosis plus ABPA and at baseline predicted the success of the anti-IgE therapy in allergic, uncontrolled asthmatics (diagnostic OR 31.5).ConclusionC4Ma3 levels depend on lung mast cell chymase and are increased i...
Wei, Z, Dong, Z, Jia, J, Liang, X, Wang, T, Hu, M, Fu, S & Yun, K 2021, 'Application of Q-TOF–MS based metabonomics techniques to analyze the plasma metabolic profile changes on rats following death due to acute intoxication of phorate', International Journal of Legal Medicine, vol. 135, no. 4, pp. 1437-1447.
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Wei, Z, lan, Y, Zhang, C, Jia, J, Niu, W, Wei, Y, Fu, S & Yun, K 2021, 'A label-free Exonuclease I-assisted fluorescence aptasensor for highly selective and sensitive detection of silver ions', Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, vol. 260, pp. 119927-119927.
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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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Despite previous detection of Chlamydia pecorum in sporadic ovine abortions, published descriptions of naturally occurring infections with fetoplacental lesions are lacking. This report provides the first descriptions of severe necrosuppurative chorionitis with vasculitis, and fetal pyelonephritis and enteritis in late-term abortions of maiden ewes. Chlamydial infection was detected using a Chlamydia genus-specific qPCR (quantitative polymerase chain reaction) on tissue extracts from 3 fetuses. C. pecorum was identified using a targeted qPCR assay, which also determined infectious load within fetal tissues. The presence of viable C. pecorum in fetal samples was confirmed by cell culture. Multilocus sequence typing (MLST) data indicated that the C. pecorum strains from each fetus were identical and of sequence type (ST) 23. Chlamydia sp. immunohistochemistry showed strong positive immunolabeling of fetoplacental lesions. Other infectious abortigenic agents were excluded with specific testing. This report confirms C. pecorum as a likely cause of ovine abortion and provides the first descriptions of associated fetoplacental lesions in naturally infected sheep.
Westoby, M, Gillings, MR, Madin, JS, Nielsen, DA, Paulsen, IT & Tetu, SG 2021, 'Trait dimensions in bacteria and archaea compared to vascular plants', Ecology Letters, vol. 24, no. 7, pp. 1487-1504.
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Westoby, M, Nielsen, DA, Gillings, MR, Gumerov, VM, Madin, JS, Paulsen, IT & Tetu, SG 2021, 'Strategic traits of bacteria and archaea vary widely within substrate-use groups', FEMS Microbiology Ecology, vol. 97, no. 11.
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ABSTRACT
Quantitative traits such as maximum growth rate and cell radial diameter are one facet of ecological strategy variation across bacteria and archaea. Another facet is substrate-use pathways, such as iron reduction or methylotrophy. Here, we ask how these two facets intersect, using a large compilation of data for culturable species and examining seven quantitative traits (genome size, signal transduction protein count, histidine kinase count, growth temperature, temperature-adjusted maximum growth rate, cell radial diameter and 16S rRNA operon copy number). Overall, quantitative trait variation within groups of organisms possessing a particular substrate-use pathway was very broad, outweighing differences between substrate-use groups. Although some substrate-use groups had significantly different means for some quantitative traits, standard deviation of quantitative trait values within each substrate-use pathway mostly averaged between 1.6 and 1.8 times larger than standard deviation across group means. Most likely, this wide variation reflects ecological strategy: for example, fast maximum growth rate is likely to express an early successional or copiotrophic strategy, and maximum growth varies widely within most substrate-use pathways. In general, it appears that these quantitative traits express different and complementary information about ecological strategy, compared with substrate use.
Westoby, M, Nielsen, DA, Gillings, MR, Litchman, E, Madin, JS, Paulsen, IT & Tetu, SG 2021, 'Cell size, genome size, and maximum growth rate are near‐independent dimensions of ecological variation across bacteria and archaea', Ecology and Evolution, vol. 11, no. 9, pp. 3956-3976.
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Weyermann, C & Roux, C 2021, 'A different perspective on the forensic science crisis', Forensic Science International, vol. 323, pp. 110779-110779.
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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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Quantum emitters in hexagonal boron nitride (hBN) are emerging as bright and robust sources of single photons for applications in quantum optics. In this work we present detailed studies on the limiting factors to achieve Fourier transform limited spectral lines. Specifically, we study phonon dephasing and spectral diffusion of quantum emitters in hBN via resonant excitation spectroscopy at cryogenic temperatures. We show that the linewidths of hBN quantum emitters are phonon broadened, even at 5 K, with typical values of the order of
∼
1
G
H
z
. While spectral diffusion dominates at increasing pump powers, it can be minimized by working well below saturation excitation power. Our results are important for future utilization of quantum emitters in hBN for quantum interference experiments.
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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Abstract
Quantum random number generation (QRNG) harnesses the intrinsic randomness of quantum mechanical phenomena. On-chip photonic circuitry provides a robust and versatile platform that can address and explore fundamental questions in quantum as well as classical physics. Likewise, integrated waveguide-based architectures hold the potential for intrinsically scalable, efficient and compact implementations of photonic QRNG. Here, we harness the quantum emission from the two-dimensional material hexagonal boron nitride an emerging atomically thin medium that can generate single photons on demand while operating at room temperature. By means of a customized splitter arrangement, we achieve true random number generation through the measurement of single photons exiting one of four designated output ports, and subsequently verify the randomness of the sequences in accordance with the National Institute of Standards and Technology benchmark suite. Our results clearly demonstrate the viability and efficiency of this approach to on-chip deterministic random number generators.
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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ATR–FTIR with a machine learning model predicts ESBL genotype of unknown E. coli strains with 86.5% AUC.
Williams, A-J, Paramsothy, R, Wu, N, Ghaly, S, Leach, S, Paramsothy, S, Corte, C, O'Brien, C, Burke, C, Wark, G, Samocha-Bonet, D, Lambert, K, Ahlenstiel, G, Wasinger, V, Dutt, S, Pavli, P, Grimm, M, Lemberg, D, Connor, S, Leong, R & Hold, G 2021, 'Australia IBD Microbiome (AIM) Study: protocol for a multicentre longitudinal prospective cohort study', BMJ Open, vol. 11, no. 2, pp. e042493-e042493.
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IntroductionCrohn’s disease and ulcerative colitis are common chronic idiopathic inflammatory bowel diseases (IBD), which cause considerable morbidity. Although the precise mechanisms of disease remain unclear, evidence implicates a strong multidirectional interplay between diet, environmental factors, genetic determinants/immune perturbations and the gut microbiota. IBD can be brought into remission using a number of medications, which act by suppressing the immune response. However, none of the available medications address any of the underlying potential mechanisms. As we understand more about how the microbiota drives inflammation, much interest has focused on identifying microbial signals/triggers in the search for effective therapeutic targets. We describe the establishment of the Australian IBD Microbiota (AIM) Study, Australia’s first longitudinal IBD bioresource, which will identify and correlate longitudinal microbial and metagenomics signals to disease activity as evaluated by validated clinical instruments, patient-reported surveys, as well as biomarkers. The AIM Study will also gather extensive demographic, clinical, lifestyle and dietary data known to influence microbial composition in order to generate a more complete understanding of the interplay between patients with IBD and their microbiota.MethodsThe AIM Study is an Australian multicentre longitudinal prospective cohort study, which will enrol 1000 participants; 500 patients with IBD and 500 healthy controls over a 5-year period. Assessment occurs at 3 monthly intervals over a 24-month period. At each assessment oral and faecal samples are self-collected along with patient-reported outcome measures, with clinical data also collected at baseline, 12 and 24 months. Intestinal tissue will be sampled whenever a colonoscopy is performed. Dietary intake, general health and psychological state wi...
Williams, DBG & Bodachivskyi, I 2021, 'Comment on ‘Chitosan dissolution with sulfopropyl imidazolium Brønsted acidic ionic liquids’', Journal of Molecular Liquids, vol. 328, pp. 115403-115403.
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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, vol. 296, pp. 100282-100282.
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Win, AK, Dowty, JG, Reece, JC, Lee, G, Templeton, AS, Plazzer, J-P, Buchanan, DD, Akagi, K, Aksoy, S, Alonso, A, Alvarez, K, Amor, DJ, Ankathil, R, Aretz, S, Arnold, JL, Aronson, M, Austin, R, Backman, A-S, Bajwa-ten Broeke, SW, Barca-Tierno, V, Barwell, J, Bernstein, I, Berthet, P, Betz, B, Bignon, Y-J, Boisjoli, T, Bonadona, V, Briollais, L, Brunet, J, Bucksch, K, Buecher, B, Buettner, R, Burn, J, Caldés, T, Capella, G, Caron, O, Casey, G, Chew, MH, Choi, Y-H, Church, J, Clendenning, M, Colas, C, Cops, EJ, Coupier, I, Cruz-Correa, M, de la Chapelle, A, de Wind, N, Dębniak, T, Della Valle, A, Delnatte, C, Dhooge, M, Dominguez-Valentin, M, Drouet, Y, Duijkers, FA, Engel, C, Esperon, P, Evans, DG, Falcón de Vargas, A, Figueiredo, JC, Foulkes, W, Fourme, E, Frebourg, T, Gallinger, S, Garre, P, Genuardi, M, Gerdes, A-M, Gima, LM, Giraud, S, Goodwin, A, Görgens, H, Green, K, Guillem, J, Guillén-Ponce, C, Guimbaud, R, Guindalini, RSC, Half, EE, Hall, MJ, Hampel, H, Hansen, TVO, Heinimann, K, Hes, FJ, Hill, J, Ho, JWC, Holinski-Feder, E, Hoogerbrugge, N, Hüneburg, R, Huntley, V, James, PA, Jensen, UB, John, T, Juhari, WKW, Kalady, M, Kastrinos, F, Kloor, M, Kohonen-Corish, MRJ, Krogh, LN, Kupfer, SS, Ladabaum, U, Lagerstedt-Robinson, K, Lalloo, F, Lasset, C, Latchford, A, Laurent-Puig, P, Lautrup, CK, Leggett, BA, Lejeune, S, LeMarchand, L, Ligtenberg, M, Lindor, N, Loeffler, M, Longy, M, Lopez, F, Lowery, J, Lubiński, J, Lucassen, AM, Lynch, PM, Malińska, K, Matsubara, N, Mecklin, J-P, Møller, P, Monahan, K, Morrison, PJ, Nattermann, J, Navarro, M, Neffa, F, Neklason, D, Newcomb, PA, Ngeow, J, Nichols, C, Nielsen, M, Nixon, DM, Nogues, C, Okkels, H, Olschwang, S, Pachter, N, Pai, RK, Palmero, EI, Pande, M, Parry, S, Patel, SG, Pearlman, R, Perne, C, Pineda, M, Poplawski, NK, Pylvänäinen, K, Qiu, J, Rahner, N, Ramesar, R, Rasmussen, LJ, Redler, S, Reis, RM, Ricciardiello, L, Rogoża-Janiszewska, E, Rosty, C, Samadder, NJ, Sampson, JR, Schackert, HK, Schmiegel, W, Schulmann, K, Schuster, H, Scott, R, Senter, L, Seppälä, TT, Shtoyerman, R, Sijmons, RH, Snyder, C, Solomon, IB, Soto, JL, Southey, MC, Spigelman, A, Spirandelli, F, Spurdle, AB, Steinke-Lange, V, Stoffel, EM, Strassburg, CP, Sunde, L, Susman, R, Syngal, S, Tanakaya, K, Tezcan, G, Therkildsen, C, Thibodeau, S, Tomita, N, Tucker, KM, Tunca, B, Turchetti, D & et al. 2021, 'Variation in the risk of colorectal cancer in families with Lynch syndrome: a retrospective cohort study', The Lancet Oncology, vol. 22, no. 7, pp. 1014-1022.
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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, vol. 53, pp. 102159-102159.
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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, vol. 76, no. 5, pp. 508-511.
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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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Brillouin scattering is an important and interesting nonlinear effect involving the interaction between optical and acoustic fields in optical waveguides. It is increasingly useful in the field of photonics, where it supplies a tunable ultra-narrow linewidth response that can be used for applications including sensing, filtering, and lasing, as well as the acoustic storage of optical pulses. This tutorial gives an overview of the fundamentals of Brillouin scattering aimed at newcomers to the field, and covers the physics underlying the interaction, the mathematical theory, and setup details of foundational Brillouin experiments.
Wong, WKM, Joglekar, MV, Saini, V, Jiang, G, Dong, CX, Chaitarvornkit, A, Maciag, GJ, Gerace, D, Farr, RJ, Satoor, SN, Sahu, S, Sharangdhar, T, Ahmed, AS, Chew, YV, Liuwantara, D, Heng, B, Lim, CK, Hunter, J, Januszewski, AS, Sørensen, AE, Akil, ASA, Gamble, JR, Loudovaris, T, Kay, TW, Thomas, HE, O'Connell, PJ, Guillemin, GJ, Martin, D, Simpson, AM, Hawthorne, WJ, Dalgaard, LT, Ma, RCW & Hardikar, AA 2021, 'Machine learning workflows identify a microRNA signature of insulin transcription in human tissues', iScience, vol. 24, no. 4, pp. 102379-102379.
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Wood, B, Padula, MP, Marks, DC & Johnson, L 2021, 'Cryopreservation alters the immune characteristics of platelets', Transfusion, vol. 61, no. 12, pp. 3432-3442.
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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, vol. 116, no. 5, pp. 477-488.
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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, MP, Jones, CI, Lippy, A, Oliver, BG, Walund, B, Fancher, KA, Fisher, BS, Wright, PJ, Fuller, JT, Murapa, P, Habib, J, Mavigner, M, Chahroudi, A, Sather, DN, Fuller, DH & Sodora, DL 2021, 'Rapid progression is associated with lymphoid follicle dysfunction in SIV-infected infant rhesus macaques', PLOS Pathogens, vol. 17, no. 5, pp. e1009575-e1009575.
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HIV-infected infants are at an increased risk of progressing rapidly to AIDS in the first weeks of life. Here, we evaluated immunological and virological parameters in 25 SIV-infected infant rhesus macaques to understand the factors influencing a rapid disease outcome. Infant macaques were infected with SIVmac251 and monitored for 10 to 17 weeks post-infection. SIV-infected infants were divided into either typical (TypP) or rapid (RP) progressor groups based on levels of plasma anti-SIV antibody and viral load, with RP infants having low SIV-specific antibodies and high viral loads. Following SIV infection, 11 out of 25 infant macaques exhibited an RP phenotype. Interestingly, TypP had lower levels of total CD4 T cells, similar reductions in CD4/CD8 ratios and elevated activation of CD8 T cells, as measured by the levels of HLA-DR, compared to RP. Differences between the two groups were identified in other immune cell populations, including a failure to expand activated memory (CD21-CD27+) B cells in peripheral blood in RP infant macaques, as well as reduced levels of germinal center (GC) B cells and T follicular helper (Tfh) cells in spleens (4- and 10-weeks post-SIV). Reduced B cell proliferation in splenic germinal GCs was associated with increased SIV+ cell density and follicular type 1 interferon (IFN)-induced immune activation. Further analyses determined that at 2-weeks post SIV infection TypP infants exhibited elevated levels of the GC-inducing chemokine CXCL13 in plasma, as well as significantly lower levels of viral envelope diversity compared to RP infants. Our findings provide evidence that early viral and immunologic events following SIV infection contributes to impairment of B cells, Tfh cells and germinal center formation, ultimately impeding the development of SIV-specific antibody responses in rapidly progressing infant macaques.
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, vol. 17, no. 4, pp. e1009186-e1009186.
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Pathogenic mycobacteria actively dysregulate protective host immune signalling pathways during infection to drive the formation of permissive granuloma microenvironments. Dynamic regulation of host microRNA (miRNA) expression is a conserved feature of mycobacterial infections across host-pathogen pairings. Here we examine the role of miR-206 in the zebrafish model ofMycobacterium marinuminfection, which allows investigation of the early stages of granuloma formation. We find miR-206 is upregulated following infection by pathogenicM.marinumand that antagomir-mediated knockdown of miR-206 is protective against infection. We observed striking upregulation ofcxcl12aandcxcr4bin infected miR-206 knockdown zebrafish embryos and live imaging revealed enhanced recruitment of neutrophils to sites of infection. We used CRISPR/Cas9-mediated knockdown ofcxcl12aandcxcr4bexpression and AMD3100 inhibition of Cxcr4 to show that the enhanced neutrophil response and reduced bacterial burden caused by miR-206 knockdown was dependent on the Cxcl12/Cxcr4 signalling axis. Together, our data illustrate a pathway through which pathogenic mycobacteria induce host miR-206 expression to suppress Cxcl12/Cxcr4 signalling and prevent protective neutrophil recruitment to granulomas.
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, vol. 9, no. 7, pp. 2770-2782.
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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.
Wurdack, M, Yun, T, Estrecho, E, Syed, N, Bhattacharyya, S, Pieczarka, M, Zavabeti, A, Chen, S, Haas, B, Müller, J, Lockrey, MN, Bao, Q, Schneider, C, Lu, Y, Fuhrer, MS, Truscott, AG, Daeneke, T & Ostrovskaya, EA 2021, 'Ultrathin Ga 2 O 3 Glass: A Large‐Scale Passivation and Protection Material for Monolayer WS 2', Advanced Materials, vol. 33, no. 3, pp. 2005732-2005732.
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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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We summarized the recent progress of cathode materials used for SIBs and modified strategies, expecting to give an inspiration for the development of high-performance cathode materials.
Xiong, L, Sheng, G, Fan, Z-M, Yang, H, Hwang, F-J & Zhu, B-W 2021, 'Environmental Design Strategies to Decrease the Risk of Nosocomial Infection in Medical Buildings Using a Hybrid MCDM Model', Journal of Healthcare Engineering, vol. 2021, pp. 1-17.
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The prevention and control of nosocomial infection (NI) are becoming increasingly difficult, and its mechanism is becoming increasingly complex. A globally aging population means that an increasing proportion of patients have a susceptible constitution, and the frequent occurrence of severe infectious diseases has also led to an increase in the cost of prevention and control of NI. Medical buildings’ spatial environment design for the prevention of NI has been a hot subject of considerable research, but few previous studies have summarized the design criteria for a medical building environment to control the risk of NI. Thus, there is no suitable evaluation framework to determine whether the spatial environment of a medical building is capable of inhibiting the spread of NI. In the context of the global spread of COVID-19, it is necessary to evaluate the performance of the existing medical building environment in terms of inhibiting the spread of NI and to verify current environmental improvement strategies for the efficient and rational use of resources. This study determines the key design elements for the spatial environment of medical buildings, constructs an evaluation framework using exploratory factor analysis, verifies the complex dominant influence relationship, and prioritizes criteria in the evaluation framework using the decision-making trial and evaluation laboratory- (DEMATEL-) based analytical network process (ANP) (DANP). Using representative real cases, this study uses the technique for order preference by similarity to ideal solution (TOPSIS) to evaluate and analyze the performance with the aspiration level of reducing the NI risk. A continuous and systematic transformation design strategy for these real cases is proposed. The main contributions of this study include the following: (1) it creates a systematic framework that allows hospital decision-makers to evaluate the spatial environment of medical buildings; (2) it provides a referen...
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, vol. 12, no. 1.
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AbstractThe regulation of anions and cations at the atomic scale is of great significance in membrane-based separation technologies. Ionic transport regulation techniques could also play a crucial role in developing high-performance alkali metal batteries such as alkali metal-sulfur and alkali metal-selenium batteries, which suffer from the non-uniform transport of alkali metal ions (e.g., Li+ or Na+) and detrimental shuttling effect of polysulfide/polyselenide anions. These drawbacks could cause unfavourable growth of alkali metal depositions at the metal electrode and irreversible consumption of cathode active materials, leading to capacity decay and short cycling life. Herein, we propose the use of a polypropylene separator coated with negatively charged Ti0.87O2 nanosheets with Ti atomic vacancies to tackle these issues. In particular, we demonstrate that the electrostatic interactions between the negatively charged Ti0.87O2 nanosheets and polysulfide/polyselenide anions reduce the shuttling effect. Moreover, the Ti0.87O2-coated separator regulates the migration of alkali ions ensuring a homogeneous ion flux and the Ti vacancies, acting as sub-nanometric pores, promote fast alkali-ion diffusion.
Xu, X, Xu, Y, Ma, J, Yin, Y, Fronzi, M, Wang, X & Bi, L 2021, 'Tailoring electronic structure of perovskite cathode for proton-conducting solid oxide fuel cells with high performance', Journal of Power Sources, vol. 489, pp. 229486-229486.
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Tailoring the electronic structure of the perovskite oxide could potentially allow dramatic improvements in the properties of cathode materials in proton-conducting solid oxide fuel cells (SOFCs). This has been demonstrated in the case of Mo-doped La0.5Sr0.5FeO3-δ, where the electronic structure of the La0.5Sr0.5FeO3-δ oxide has been changed with the Mo-doping, leading to a less strong metal-oxygen bond as well as a more active surface towards oxygen reduction. As a result, the more active oxygen atoms make the formation of oxygen vacancy and hydration that are critical for protonation more feasible. Furthermore, the electric field induced by Mo-doping provides an additional driving force for the movement of protons, accelerating the proton migrations in the oxide and thus improving the cathode performance. With the Mo-doped La0.5Sr0.5FeO3-δ as the cathode, a proton-conducting SOFC exhibits an impressive fuel cell output of 1174 mW cm−2 at 700 °C that surpasses most of the cells using similar types of cathodes. This study not only provides a proper cathode material without involving cobalt and barium elements but also gives an understanding of the design of the cathode by tailoring the electronic structures.
Xu, Y, Xu, X, Cao, N, Wang, X, Liu, X, Fronzi, M & Bi, L 2021, 'Perovskite ceramic oxide as an efficient electrocatalyst for nitrogen fixation', International Journal of Hydrogen Energy, vol. 46, no. 17, pp. 10293-10302.
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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 & Child Neurology, vol. 63, no. 5, pp. 552-559.
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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.
Yan, J, Kuzhiumparambil, U, Bandodkar, S, Dale, RC & Fu, S 2021, 'Cerebrospinal fluid metabolomics: detection of neuroinflammation in human central nervous system disease', Clinical & Translational Immunology, vol. 10, no. 8.
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YANG, J, KOSOV, DS & REIMERS, JR 2021, 'Electron transport properties of molecular devices based on silicon-1, 6-hexanedithiol-silicon', Journal of Shenzhen University Science and Engineering, vol. 38, no. 06, pp. 636-642.
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To reveal how the electronic transport properties of the silicon-sulfur molecular junction depend on its microscopic structure, we studied the configuration and electronic transport properties of a silicon-1, 6-hexanedithiol-silicon molecular device, based on density functional theory (DFT) combined with the non-equilibrium Green's function (NEGF) method. Eight groups of molecular junctions were modeled, each consisting of a 1, 6-hexanedithiol molecule spanning two silicon tips. Following optimisation of the molecular structure, first of the 1, 6-hexanedithiol by itself and then of the junction as a whole, the zero-bias conductance and electronic transmission spectrum were calculated. The results show that silicon-sulfur molecular junctions have characteristics that differ significantly from those of gold-sulfur molecular junctions. The structural details of the silicon-sulfur molecular junction are shown to have a crucial influence on its electronic transport properties such as zero-bias piezoelectric conductance and transmission spectra.
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, pp. 127169-127169.
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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.
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, vol. 94, pp. 102238-102238.
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Yuan, YL, Zhang, X, Liu, L, Wang, G, Chen-Yu Hsu, A, Huang, D, Wang, G & Oliver, BG 2021, 'Total IgE Variability Is Associated with Future Asthma Exacerbations: A 1-Year Prospective Cohort Study', The Journal of Allergy and Clinical Immunology: In Practice, vol. 9, no. 7, pp. 2812-2824.
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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, vol. 12, no. 1.
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AbstractDNA methylation plays a fundamental role in the control of gene expression and genome integrity. Although there are multiple tools that enable its detection from Nanopore sequencing, their accuracy remains largely unknown. Here, we present a systematic benchmarking of tools for the detection of CpG methylation from Nanopore sequencing using individual reads, control mixtures of methylated and unmethylated reads, and bisulfite sequencing. We found that tools have a tradeoff between false positives and false negatives and present a high dispersion with respect to the expected methylation frequency values. We described various strategies to improve the accuracy of these tools, including a consensus approach, METEORE (https://github.com/comprna/METEORE), based on the combination of the predictions from two or more tools that shows improved accuracy over individual tools. Snakemake pipelines are also provided for reproducibility and to enable the systematic application of our analyses to other datasets.
Zajaczkowski, P, Lee, R, Fletcher-Lartey, SM, Alexander, K, Mahimbo, A, Stark, D & Ellis, JT 2021, 'The controversies surrounding Giardia intestinalis assemblages A and B', Current Research in Parasitology & Vector-Borne Diseases, vol. 1, pp. 100055-100055.
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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, vol. 76, no. 7, pp. 647-655.
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RationaleIn 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.ObjectivesDetermine if COPD ASM cells have a unique epigenetic response to profibrotic cytokine transforming growth factor β1 (TGF-β1).MethodsPrimary 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
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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 resultsCOPD 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. C...
Zavafer, A, Bates, H, Labeeuw, L, Kofler, JR & Ralph, PJ 2021, 'Normalized chlorophyll fluorescence imaging: A method to determine irradiance and photosynthetically active radiation in phytoplankton cultures', Algal Research, vol. 56, pp. 102309-102309.
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Zavafer, A, Losciale, P, Öquist, G, He, J, Evans, JR, Fitzpatrick, D, Oguchi, R, Fan, D, Osmond, CB, Zhang, M, Huang, W, McCaffery, S & Szabó, M 2021, 'Wah Soon Chow, a teacher, a friend and a colleague', Photosynthesis Research, vol. 149, no. 1-2, pp. 253-258.
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Zavřel, T, Schoffman, H, Lukeš, M, Fedorko, J, Keren, N & Červený, J 2021, 'Monitoring fitness and productivity in cyanobacteria batch cultures', Algal Research, vol. 56, pp. 102328-102328.
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Zeng, Y, Huang, T, Wang, N, Xu, Y, Sun, C, Huang, M, Chen, C, Oliver, BG, Yi, C & Chen, H 2021, 'L-Leucine Improves Metabolic Disorders in Mice With in-utero Cigarette Smoke Exposure', Frontiers in Physiology, vol. 12.
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Objectives: Maternal cigarette smoke exposure (SE) causes intrauterine undernutrition, resulting in increased risk for metabolic disorders and type 2 diabetes in the offspring without sex differences. L-leucine supplementation has been shown to reduce body weight and improve glucose metabolism in both obese animals and humans. In this study, we aimed to determine whether postnatal L-leucine supplementation in female offspring can ameliorate the detrimental impact of maternal SE.Methods: Female Balb/c mice (6-week) were exposed to cigarette smoke (SE, 2 cigarettes/day) prior to mating for 5 weeks until the pups weaned. Sham dams were exposed to air during the same period. Half of the female offspring from the SE and SHAM dams were supplied with L-leucine via drinking water (1.5% w/w) after weaning (21-day) for 10 weeks and sacrificed at 13 weeks (adulthood).Results: Maternal SE during pregnancy resulted in smaller body weight and glucose intolerance in the offspring. L-leucine supplement in Sham offspring reduced body weight, fat mass, and fasting blood glucose levels compared with their untreated littermates; however somatic growth was not changed. L-leucine supplement in SE offspring improved glucose tolerance and reduced fat mass compared with untreated littermates.Conclusions: Postnatal L-leucine supplement could reduce fat accumulation and ameliorate glucose metabolic disorder caused by maternal SE. The application of leucine may provide a potential strategy for reducing metabolic disorders in offspring from mothers who continued to smoke during pregnancy.
Zhand, S, Xiao, K, Razavi Bazaz, S, 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, pp. 100994-100994.
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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, 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, vol. 133, no. 21, pp. 11831-11835.
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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, vol. 33, no. 17, pp. 2100472-2100472.
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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, J, Luo, L, Zhao, J, He, J, Zhao, X, Liu, H, Qin, Y, Wang, F & Song, J 2021, 'Hierarchically porous MXene decorated carbon coated LiFePO4 as cathode material for high-performance lithium-ion batteries', Journal of Alloys and Compounds, vol. 876, pp. 160210-160210.
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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, vol. 22, no. 8, pp. 3168-3201.
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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, Y, Wang, Q, Li, L, Le, Y, Liu, L, Yang, J, Li, Y, Bao, G & Yan, L 2021, 'Synthesis and preliminary structure-activity relationship study of 3-methylquinazolinone derivatives as EGFR inhibitors with enhanced antiproliferative activities against tumour cells', Journal of Enzyme Inhibition and Medicinal Chemistry, vol. 36, no. 1, pp. 1205-1216.
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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, vol. 17, no. 48, pp. 2007431-2007431.
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Zhao, S, Liu, Z, Xie, G, Guo, X, Guo, Z, Song, F, Li, G, Chen, C, Xie, X, Zhang, N, Sun, B, Guo, S & Wang, G 2021, 'Achieving High‐Performance 3D K + ‐Pre‐intercalated Ti 3 C 2 T x MXene for Potassium‐Ion Hybrid Capacitors via Regulating Electrolyte Solvation Structure', Angewandte Chemie, vol. 133, no. 50, pp. 26450-26457.
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Zhao, S, Liu, Z, Xie, G, Guo, X, Guo, Z, Song, F, Li, G, Chen, C, Xie, X, Zhang, N, Sun, B, Guo, S & Wang, G 2021, 'Achieving High‐Performance 3D K + ‐Pre‐intercalated Ti 3 C 2 T x MXene for Potassium‐Ion Hybrid Capacitors via Regulating Electrolyte Solvation Structure', Angewandte Chemie International Edition, vol. 60, no. 50, pp. 26246-26253.
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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, vol. 31, no. 31, pp. 2102060-2102060.
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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 Edition, vol. 60, no. 5, pp. 2208-2220.
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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, Jiang, W, Zhang, J, Lovell, EC, Amal, R, Han, Z & Lu, X 2021, 'Anchoring Sites Engineering in Single‐Atom Catalysts for Highly Efficient Electrochemical Energy Conversion Reactions', Advanced Materials, vol. 33, no. 41, pp. 2102801-2102801.
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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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Zheng, S, Zhang, B, Peng, D, Yu, L, Lin, B, Pan, Y & Xie, Q 2021, 'The trend towards a warmer and wetter climate observed in arid and semi-arid areas of northwest China from 1959 to 2019', Environmental Research Communications, vol. 3, no. 11, pp. 115011-115011.
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Abstract
The observed trend towards a warmer and wetter climate in northwest China is a controversial issue lacking sufficient scientific research. Based on monthly meteorological data from 201 weather stations in northwest China and surrounding regions from 1959 to 2019, we calculated potential evapotranspiration using Penman-Monteith (PM) equation. By analyzing the spatial–temporal variations in temperature and precipitation and by studying changing drought trends, we systematically explored the climate trends in northwest China over the past 60 years. Our findings include: (1) From 1959 to 2019, during the growing season, there was a significant upward trend in temperature across northwest China. The most obvious trend, ranged between 0.4 °C–0.6 °C per decade, was observed in northern Qinghai and northeastern Xinjiang. On a per-month basis, the average temperature increased in all months, with April showing a maximum rate of 0.41 °C per decade. (2) The amount of precipitation in the growing season increased in most regions, especially in western Xinjiang and Qinghai. The areas of reduced precipitation were mainly concentrated in the south of Gansu and Ningxia, the west of Shaanxi and the northeast of Xinjiang. The average precipitation also increased in all months, with June showing a maximum change rate of 1.8 mm per decade. (3) There were obvious spatial differences in the climate trends in northwest China with the warming shifting from areas of bare land to grassland and the trend towards increased rainfall shifting from grassland to bare land. These effects were most obvious in Xinjiang’s Tarim Basin. (4) From 1959 to 2019, the degree of drought in northwest China significantly decreased in most areas. The areas where drought decreased and precipitation increased were fairly consistent, which produced a strong spatial correlation between them.
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, pp. 214178-214178.
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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, Danilov, DL, Eichel, R & Notten, PHL 2021, 'Host Materials Anchoring Polysulfides in Li–S Batteries Reviewed', Advanced Energy Materials, vol. 11, no. 15, pp. 2001304-2001304.
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Lithium–sulfur batteries (Li–S) have become a viable alternative to future energy storage devices. The electrochemical reaction based on lithium and sulfur promises an extraordinary theoretical energy density, which is far higher than current commercialized Li-ion batteries. However, the principal disadvantage impeding the success of Li–S batteries lies in the severe leakage and migration of soluble lithium polysulfide intermediates out of cathodes upon cycling. The loss of active sulfur species incurs significant capacity decay and poor battery lifespans. Considerable efforts have been devoted to developing various sulfur host materials that can effectively anchor lithium polysulfides. Herein, a comprehensive review is presented of recent advances in sulfur host materials. On the basis of the electrochemistry of Li–S batteries, the strategies for anchoring polysulfides are systematically categorized into physical confinement and chemical bonding. The structural merits of various sulfur host materials are highlighted, and the interaction mechanisms with sulfur species are discussed in detail, which provides valuable insights into the rational design and engineering of advanced sulfur host materials facilitating the commercialization of Li–S batteries. Future challenges and promising research prospects for sulfur host materials are proposed at the end of the review.
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, vol. 26, pp. 102133-102133.
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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, vol. 26, no. 4, pp. 360-369.
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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.
Zhou, X, Wang, T, Liu, H, Gao, X, Wang, C & Wang, G 2021, 'Desulfurization through Photocatalytic Oxidation: A Critical Review', ChemSusChem, vol. 14, no. 2, pp. 492-511.
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Zhu, WJ, Liu, Y, Wang, G, Deng, K, Liu, L, Wang, J, Oliver, BG, Wang, T, Kang, DY, Wang, L, Li, WM & Wang, G 2021, 'Interaction effects of asthma and rhinitis control on work productivity and activity impairment: A cross-sectional study', Allergy and Asthma Proceedings, vol. 42, no. 5, pp. 409-416.
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Background: Symptomatic asthma and rhinitis negatively impact patients' work productivity and activity. However, little is known about the potential interaction effect of both asthma and rhinitis control on work productivity and activity impairment. Objective:
This study aimed to explore whether there are interaction effects of asthma and rhinitis control on work productivity and activity impairment in patients with asthma and with rhinitis. Methods: A total of 206 adult patients were prospectively recruited and were divided
into four groups: both poorly controlled (BPC) n = 53), poorly controlled asthma (PCA) with controlled rhinitis (CR) (n = 38), well controlled asthma with uncontrolled rhinitis (n = 43), and both well controlled (BWC) (n = 72) based on the symptom control status of asthma and rhinitis. Work
productivity loss and activity impairment, asthma control, and rhinitis control were assessed by using work productivity and activity impairment questionnaire: general health, the asthma control test, and the rhinitis control assessment test, respectively. General linear regression models
were used to study the contribution of asthma control, rhinitis control, and the interaction effect on work productivity and activity impairment. Results: Work productivity loss was most frequently reported in patients in the BPC group. Compared with the patients in the
BWC group, the patients in the PCA-CR group had significantly higher activity impairment and worse asthma-related quality of life (both p < 0.001). There were significant interaction effects of asthma and rhinitis control, which accounted for the increase in presenteeism, work productivity
loss, and activity impairment (all p < 0.001). Although differences in absenteeism were not significant among the groups, there was a significant interaction effect of control levels accounted for absenteeis...
Ziegler, M, Anton, A, Klein, SG, Rädecker, N, Geraldi, NR, Schmidt‐Roach, S, Saderne, V, Mumby, PJ, Cziesielski, MJ, Martin, C, Frölicher, TL, Pandolfi, JM, Suggett, DJ, Aranda, M, Duarte, CM & Voolstra, CR 2021, 'Integrating environmental variability to broaden the research on coral responses to future ocean conditions', Global Change Biology, vol. 27, no. 21, pp. 5532-5546.
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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, vol. 42, no. 2, pp. 276-309.
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Кордзахия, НЕ, Kordzahiya, NE, Новиков, АА & Novikov, AA 2021, 'On maximal inequalities for Ornstein-Uhlenbeck processes with jumps', Teoriya Veroyatnostei i ee Primeneniya, vol. 66, no. 4, pp. 895-913.
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Получены моментные и экспоненциальные неравенства для максимума обобщенного процесса Орнштейна-Уленбека при некоторых предположениях на хвосты распределения скачкообразной компоненты.