Abayarathna, T, Murray, BR & Webb, JK 2019, 'Higher incubation temperatures produce long-lasting upward shifts in cold tolerance, but not heat tolerance, of hatchling geckos', Biology Open, vol. 8, no. 4.
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ABSTRACT
Heatwaves are a regular occurrence in Australia, and are predicted to increase in intensity and duration in the future. These changes may elevate temperatures inside lizard nests, shortening the incubation period, so that hatchlings are more likely to emerge during heatwaves. Potentially, developmental plasticity or heat hardening could buffer hatchings from future warming. For example, higher incubation temperatures could shift critical thermal maxima upwards, enabling lizards to withstand higher temperatures. To investigate whether developmental plasticity affects hatchling thermal tolerance, we incubated eggs of the velvet gecko Amalosia lesueurii under two fluctuating incubation treatments to mimic current (mean=24.3°C, range 18.4–31.1°C) and future ‘hot’ (mean=28.9°C, range 19.1–38.1°C) nest temperatures. We maintained the hatchlings under identical conditions, and measured their thermal tolerance (CTmax) aged 14 days and 42 days. We then released hatchlings at field sites, and recaptured individually marked lizards aged 6 months, to determine whether incubation induced shifts in thermal tolerance were transitory or long-lasting. We found that at age 14 days, hatchlings from hot-temperature incubation had higher CTmax [mean=39.96±0.25°C (s.d.)] than hatchlings from current-temperature incubation [mean=39.70±0.36°C (s.d.)]. Hatchlings from the current-incubation treatment also had significantly higher heat hardening capacity [mean=0.79±0.37°C (s.d.)] than hatchlings from hot-temperature incubation treatment [mean=0.47±0.17°C (s.d. )]. However, both of these incubation-induced effects did not persist into later life. By contrast, incubation treatment had significant and long-lasting effects on the cold tolerance of hatchlings. At age 14 days, current-incubated hatchlings tolerated colder temperatures [CTmin=11.24±0.41°C (s.d.)] better than hot-incubated hatchlings [CTmin=14.11±0.25°C (s.d.)]. This signif...
Abidi, IH, Mendelson, N, Tran, TT, Tyagi, A, Zhuang, M, Weng, L, Özyilmaz, B, Aharonovich, I, Toth, M & Luo, Z 2019, 'Selective Defect Formation in Hexagonal Boron Nitride', Advanced Optical Materials, vol. 7, no. 13, pp. 1900397-1900397.
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AbstractLuminescent defects in hexagonal boron nitride (hBN) have emerged as promising single photon emitters (SPEs) due to their high brightness and robust operation at room temperature. The ability to create such emitters with well‐defined optical properties is a cornerstone toward their integration into on‐chip photonic architectures. Here, an effective approach is reported to fabricate hBN SPEs with desired emission properties in distinct spectral regions via the manipulation of boron diffusion through copper during atmospheric pressure chemical vapor deposition (CVD)—a process termed gettering. Using the gettering technique the resulting zero‐phonon line is deterministically placed between the regions 550 and 600 nm or from 600 to 650 nm, paving the way for hBN SPEs with tailored emission properties. Additionally, rational control over the observed SPE density in the resulting films is demonstrated. The ability to control defect formation during hBN growth provides a cost effective means to improve the crystallinity of CVD hBN films, and lower defect density making it applicable to hBN growth for a wide‐range of applications. The results are important to understand defect formation of quantum emitters in hBN and deploy them for scalable photonic technologies.
Acherar, O, Truong, MQ, Robert, S, Crispino, F, Moret, S & Bécue, A 2019, 'Paper characteristics and their influence on the ability of single metal deposition to detect fingermarks', Forensic Chemistry, vol. 12, pp. 8-24.
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Achlatis, M, Pernice, M, Green, K, de Goeij, JM, Guagliardo, P, Kilburn, MR, Hoegh-Guldberg, O & Dove, S 2019, 'Single-cell visualization indicates direct role of sponge host in uptake of dissolved organic matter', Proceedings of the Royal Society B: Biological Sciences, vol. 286, no. 1916, pp. 20192153-20192153.
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Marine sponges are set to become more abundant in many near-future oligotrophic environments, where they play crucial roles in nutrient cycling. Of high importance is their mass turnover of dissolved organic matter (DOM), a heterogeneous mixture that constitutes the largest fraction of organic matter in the ocean and is recycled primarily by bacterial mediation. Little is known, however, about the mechanism that enables sponges to incorporate large quantities of DOM in their nutrition, unlike most other invertebrates. Here, we examine the cellular capacity for direct processing of DOM, and the fate of the processed matter, inside a dinoflagellate-hosting bioeroding sponge that is prominent on Indo-Pacific coral reefs. Integrating transmission electron microscopy with nanoscale secondary ion mass spectrometry, we track
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C-enriched DOM over time at the individual cell level of an intact sponge holobiont. We show initial high enrichment in the filter-feeding cells of the sponge, providing visual evidence of their capacity to process DOM through pinocytosis without mediation of resident bacteria. Subsequent enrichment of the endosymbiotic dinoflagellates also suggests sharing of host nitrogenous wastes. Our results shed light on the physiological mechanism behind the ecologically important ability of sponges to cycle DOM via the recently described sponge loop.
Aftab, W, Mahmood, A, Guo, W, Yousaf, M, Tabassum, H, Huang, X, Liang, Z, Cao, A & Zou, R 2019, 'Polyurethane-based flexible and conductive phase change composites for energy conversion and storage', Energy Storage Materials, vol. 20, pp. 401-409.
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Agbowuro, AA, Hwang, J, Peel, E, Mazraani, R, Springwald, A, Marsh, JW, McCaughey, L, Gamble, AB, Huston, WM & Tyndall, JDA 2019, 'Structure-activity analysis of peptidic Chlamydia HtrA inhibitors', Bioorganic & Medicinal Chemistry, vol. 27, no. 18, pp. 4185-4199.
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Chlamydia trachomatis high temperature requirement A (CtHtrA) is a serine protease that performs proteolytic and chaperone functions in pathogenic Chlamydiae; and is seen as a prospective drug target. This study details the strategies employed in optimizing the irreversible CtHtrA inhibitor JO146 [Boc-Val-Pro-ValP(OPh)2] for potency and selectivity. A series of adaptations both at the warhead and specificity residues P1 and P3 yielded 23 analogues, which were tested in human neutrophil elastase (HNE) and CtHtrA enzyme assays as well as Chlamydia cell culture assays. Trypsin and chymotrypsin inhibition assays were also conducted to measure off-target selectivity. Replacing the phosphonate moiety with α-ketobenzothiazole produced a reversible analogue with considerable CtHtrA inhibition and cell culture activity. Tertiary leucine at P3 (8a) yielded approximately 33-fold increase in CtHtrA inhibitory activity, with an IC50 = 0.68 ± 0.02 µM against HNE, while valine at P1 retained the best anti-chlamydial activity. This study provides a pathway for obtaining clinically relevant inhibitors.
Aguilar, C, Raina, J-B, Fôret, S, Hayward, DC, Lapeyre, B, Bourne, DG & Miller, DJ 2019, 'Transcriptomic analysis reveals protein homeostasis breakdown in the coral Acropora millepora during hypo-saline stress', BMC Genomics, vol. 20, no. 1.
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Aharonovich, I 2019, 'Clearly identical photons', Nature Nanotechnology, vol. 14, no. 6, pp. 502-503.
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Ahmad, M, Yousaf, M, Nasir, A, Bhatti, IA, Mahmood, A, Fang, X, Jian, X, Kalantar-Zadeh, K & Mahmood, N 2019, 'Porous Eleocharis@MnPE Layered Hybrid for Synergistic Adsorption and Catalytic Biodegradation of Toxic Azo Dyes from Industrial Wastewater', Environmental Science & Technology, vol. 53, no. 4, pp. 2161-2170.
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Akter, A, Takahashi, S, Deng, W, Shea, DJ, Itabashi, E, Shimizu, M, Miyaji, N, Osabe, K, Nishida, N, Suzuki, Y, Helliwell, CA, Seki, M, Peacock, WJ, Dennis, ES & Fujimoto, R 2019, 'The histone modification H3 lysine 27 tri-methylation has conserved gene regulatory roles in the triplicated genome of Brassica rapa L.', DNA Research, vol. 26, no. 5, pp. 433-443.
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Abstract
Brassica rapa L. is an important vegetable and oilseed crop. We investigated the distribution of the histone mark tri-methylation of H3K27 (H3K27me3) in B. rapa and its role in the control of gene expression at two stages of development (2-day cotyledons and 14-day leaves) and among paralogs in the triplicated genome. H3K27me3 has a similar distribution in two inbred lines, while there was variation of H3K27me3 sites between tissues. Sites that are specific to 2-day cotyledons have increased transcriptional activity, and low levels of H3K27me3 in the gene body region. In 14-day leaves, levels of H3K27me3 were associated with decreased gene expression. In the triplicated genome, H3K27me3 is associated with paralogs that have tissue-specific expression. Even though B. rapa and Arabidopsis thaliana are not closely related within the Brassicaceae, there is conservation of H3K27me3-marked sites in the two species. Both B. rapa and A. thaliana require vernalization for floral initiation with FLC being the major controlling locus. In all four BrFLC paralogs, low-temperature treatment increases H3K27me3 at the proximal nucleation site reducing BrFLC expression. Following return to normal temperature growth conditions, H3K27me3 spreads along all four BrFLC paralogs providing stable repression of the gene.
Akyol, S, Ben Nissan, B, Karacan, I, Yetmez, M, Gokce, H, Suggett, DJ & Oktar, FN 2019, 'Morphology, characterization, and conversion of the corals Goniopora spp. and Porites cylindrica to hydroxyapatite', Journal of the Australian Ceramic Society, vol. 55, no. 3, pp. 893-901.
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© 2019, Australian Ceramic Society. The aim of this study is to obtain pure natural hydroxyapatite (HAp) and tricalcium phosphate (TCP) from a Goniopora spp. and from hump coral (Porites cylindrica), both sourced from Australia. Due to the nature of the conversion process, commercial coralline HAp has retained coral or CaCO3, and the structure possesses both nano- and mesopores within the interpore trabeculae resulting in high dissolution rates. To overcome these limitations, a newly patented coral double-conversion technique has been developed. The current technique involves a two-stage application route where in the first-stage complete conversion of coral to pure HAp is achieved. In the second stage, a sol-gel-derived HAp nanocoating is directly applied to cover the meso- and nanopores within the intrapore material, while maintaining the large pores. Here, we specifically investigated the morphological changes and characterized these corals prior to and after conversion. For this purpose, four groups designated as C0, C1, C2, and C3 were used. C0 is Porites, Goniopora, and cylindrica; the original coral is calcium carbonate with aragonite structure that contains proteins and polysaccharides. C1 is coral cleaned under ultrasound in bleach diluted with water. C2 is coral converted to hydroxyapatite (HAp) by hydrothermal treatment method at 200 °C under pressure in the presence of ammonium biphosphate. C3 is obtained by coating C2 with sol-gel alkoxide-derived nanohydroxyapatite to obtain a more bioactive osteoconductive material and improve mechanical properties. All groups were characterized by XRD, EDAX, DTA/TGA, and SEM. The results showed that the biaxial strengths of the C2 and C3 were significantly higher than the original coral. The work also showed the advantages of the hydrothermal conversion method and the effect of the nanocoating which is expected to improve the final bioactivity through microstructural changes of the surfaces.
Al-Asadi, S, Malik, A, Bakiu, R, Santovito, G, Menz, I & Schuller, K 2019, 'Characterization of the peroxiredoxin 1 subfamily from Tetrahymena thermophila', Cellular and Molecular Life Sciences, vol. 76, no. 23, pp. 4745-4768.
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ALFEUS, M & SCHLÖGL, E 2019, 'ON SPREAD OPTION PRICING USING TWO-DIMENSIONAL FOURIER TRANSFORM', International Journal of Theoretical and Applied Finance, vol. 22, no. 05, pp. 1950023-1950023.
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Spread options are multi-asset options with payoffs dependent on the difference of two underlying financial variables. In most cases, analytically closed form solutions for pricing such payoffs are not available, and the application of numerical pricing methods turns out to be nontrivial. We consider several such nontrivial cases and explore the performance of the highly efficient numerical technique of Hurd & Zhou[(2010) A Fourier transform method for spread option pricing, SIAM J. Financial Math. 1(1), 142–157], comparing this with Monte Carlo simulation and the lower bound approximation formula of Caldana & Fusai[(2013) A general closed-form spread option pricing formula, Journal of Banking & Finance 37, 4893–4906]. We show that the former is in essence an application of the two-dimensional Parseval’s Identity. As application examples, we price spread options in a model where asset prices are driven by a multivariate normal inverse Gaussian (NIG) process, in a three-factor stochastic volatility model, as well as in examples of models driven by other popular multivariate Lévy processes such as the variance Gamma process, and discuss the price sensitivity with respect to volatility. We also consider examples in the fixed-income market, specifically, on cross-currency interest rate spreads and on LIBOR/OIS spreads.
Alfeus, M, Overbeck, L & Schlögl, E 2019, 'Regime switching rough Heston model', Journal of Futures Markets, vol. 39, no. 5, pp. 538-552.
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This model combines two important stylized features of volatility, the rough behavior consistent with a Hurst parameter less than urn:x-wiley:02707314:media:fut21993:fut21993-math-0001, and the regime switching property consistent with more long‐term economic considerations. It is nevertheless highly tractable in the sense of semianalytic formulae for European options, and permits a partial Monte Carlo method of similar computational speed as the semianalytic formula (at an appropriate number of Monte Carlo simulations). While option prices are relatively insensitive to the choice of Hurst parameter, introducing rough volatility allows for a better fit to the at‐the‐money skew.
Alghalayini, A, Garcia, A, Berry, T & Cranfield, C 2019, 'The Use of Tethered Bilayer Lipid Membranes to Identify the Mechanisms of Antimicrobial Peptide Interactions with Lipid Bilayers', Antibiotics, vol. 8, no. 1, pp. 12-12.
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This review identifies the ways in which tethered bilayer lipid membranes (tBLMs) can be used for the identification of the actions of antimicrobials against lipid bilayers. Much of the new research in this area has originated, or included researchers from, the southern hemisphere, Australia and New Zealand in particular. More and more, tBLMs are replacing liposome release assays, black lipid membranes and patch-clamp electrophysiological techniques because they use fewer reagents, are able to obtain results far more quickly and can provide a uniformity of responses with fewer artefacts. In this work, we describe how tBLM technology can and has been used to identify the actions of numerous antimicrobial agents.
Alinezhad, A, Gloag, L, Benedetti, TM, Cheong, S, Webster, RF, Roelsgaard, M, Iversen, BB, Schuhmann, W, Gooding, JJ & Tilley, RD 2019, 'Direct Growth of Highly Strained Pt Islands on Branched Ni Nanoparticles for Improved Hydrogen Evolution Reaction Activity', Journal of the American Chemical Society, vol. 141, no. 41, pp. 16202-16207.
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Almohaywi, B, Yu, TT, Iskander, G, Chan, DSH, Ho, KKK, Rice, S, Black, DS, Griffith, R & Kumar, N 2019, 'Dihydropyrrolones as bacterial quorum sensing inhibitors', Bioorganic & Medicinal Chemistry Letters, vol. 29, no. 9, pp. 1054-1059.
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Bacteria regulate their pathogenicity and biofilm formation through quorum sensing (QS), which is an intercellular communication system mediated by the binding of signaling molecules to QS receptors such as LasR. In this study, a range of dihydropyrrolone (DHP) analogues were synthesized via the lactone-lactam conversion of lactone intermediates. The synthesized compounds were tested for their ability to inhibit QS, biofilm formation and bacterial growth of Pseudomonas aeruginosa. The compounds were also docked into a LasR crystal structure to rationalize the observed structure-activity relationships. The most active compound identified in this study was compound 9i, which showed 63.1% QS inhibition of at 31.25 µM and 60% biofilm reduction at 250 µM with only moderate toxicity towards bacterial cell growth.
Alqudah, A, McMullan, P, Todd, A, O’Doherty, C, McVey, A, McConnell, M, O’Donoghue, J, Gallagher, J, Watson, CJ & McClements, L 2019, 'Service evaluation of diabetes management during pregnancy in a regional maternity hospital: potential scope for increased self-management and remote patient monitoring through mHealth solutions', BMC Health Services Research, vol. 19, no. 1.
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Abstract
Background
Pre-gestational and gestational diabetes mellitus are common complications in pregnancy affecting one in six pregnancies. The maternity services are under significant strain managing the increasing number of complex pregnancies. This has an impact on patients’ experience of antenatal care. Therefore, there is a clear need to address pregnancy care. One possible solution is to use home-based digital technology to reduce clinic visits and improve clinical monitoring.
Methods
The aim of this study was to evaluate the antenatal services provided to pregnant women with diabetes who were monitored at the joint metabolic and obstetric clinic at the Southern Health and Social Care Trust in Northern Ireland.
Results
The questionnaires were completed by sixty-three women, most of whom had gestational diabetes mellitus. Most of the participants were between 25 and 35 years of age (69.8%), had one or more children (65.1%) and spent over 2 h attending the clinics (63.9%); 78% of women indicated that their travel time to and from the clinic appointment was over 15 min. Over 70% of women used smartphones for health-related purposes. However, only 8.8% used smartphones to manage their health or diabetes. Less than 25% of the women surveyed expressed concerns about using digital technology from home to monitor various aspects of their health in pregnancy.
Conclusions
Overall, pregnant women who had or developed diabetes in pregnancy experience frequent hospital visits and long wa...
Al-Zubaidi, Y, Pazderka, C, Koolaji, N, Rahman, MK, Choucair, H, Umashankar, B, Bourget, K, Chen, Y, Rawling, T & Murray, M 2019, 'Aryl-urea fatty acids that activate the p38 MAP kinase and down-regulate multiple cyclins decrease the viability of MDA-MB-231 breast cancer cells', European Journal of Pharmaceutical Sciences, vol. 129, pp. 87-98.
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We recently developed a novel aryl-urea fatty acid (CTU; 16({[4-chloro-3-(trifluoromethyl)phenyl]carbamoyl}amino)hexadecanoic acid) that impaired the viability of MDA-MB-231 breast cancer cells in vitro and in mouse xenograft models in vivo. At present there is a deficiency of information on the structural requirements for the activity of CTU. Our initial study suggested that electron withdrawing groups were required on the aryl ring, and in this study we further evaluated the influence of the electronic properties of aromatic substitution on the capacity of CTU analogues to decrease MDA-MB-231 breast cancer cell viability. Analogues that contained strong electron-withdrawing groups in the meta- and para-positions of the aryl ring exhibited improved activity over CTU. Effective analogues down-regulated the cyclins D1, E1 and B1, and the cyclin-dependent kinases (CDKs) 4 and 6, that form complexes to coordinate cell cycle progression. Active CTU analogues also stimulated the phosphorylation and activation of the p38 MAP kinase signalling pathway in cells and both decreased proliferation (5-bromo-2'-deoxyuridine (brdU) incorporation) and activated apoptosis (executioner caspase-3/7 activity). These agents offer a new approach to target the cell cycle at multiple phases in order to efficiently prevent cancer cell expansion. Inclusion of the present structural information in drug design approaches could enhance the development of optimal analogues of aryl-urea fatty acids as potential anti-cancer agents.
Anand, A, Khurana, R, Wahal, N, Mahajan, S, Mehta, M, Satija, S, Sharma, N, Vyas, M & Khurana, N 2019, 'Vanillin: A comprehensive review of pharmacological activities', Plant Archives, vol. 19, pp. 1000-1004.
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Vanillin is the chief constituent of the vanilla bean extract obtained from the seed pods of Vanillus planifolia belonging to the family Orchidaceae. Nowadays, synthetic vanillin is being preferred as a flavouring agent in foods, beverages and pharmaceuticals. Chemically, it is a phenolic aldehyde with the molecular formula C8H8O3. Over years it has been used as a flavor in sweet foods like chocolates & ice creams, in cosmetics like perfumes, and in pharmaceuticals to mask the unpleasant odor and tastes in medicines. Also, vanillin-HCl is extensively used a visualizing agent in Thin Layer Chromatography. Quite recently, vanillin has been studied by researchers all over the world for its pharmacological effects. The compound has exhibited remarkable effects in treatment and management of several pathological conditions. This review focuses on the different reported pharmacological activities of vanillin.
Anantanawat, K, Pitsch, N, Fromont, C & Janitz, C 2019, 'High-throughput Quant-iT PicoGreen assay using an automated liquid handling system', BioTechniques, vol. 66, no. 6, pp. 290-294.
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Workflows in NGS facilities require high-standard practices and high-throughput pipelines to process the large number of samples received in a timely manner. Downstream protocols such as NGS library preparation require accurate estimation of nucleic acid concentrations, which can be achieved using fluorescent dye-based nucleic acid measurement. Here, we report a protocol for preparing a 384-well Quant-iT PicoGreen assay. The protocol allows the concentrations of 184 DNA samples to be measured simultaneously in duplicate in only 1 h using an Eppendorf epMotion 5075 liquid handling system. The advantages of this high-throughput approach include a reduction in both reagents (10x less reagents compared to a standard protocol) and time (3 h for 384 samples compared with 3 days).
Anderson, C, Hafen, R, Sofrygin, O & Ryan, L 2019, 'Comparing predictive abilities of longitudinal child growth models', Statistics in Medicine, vol. 38, no. 19, pp. 3555-3570.
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The Bill and Melinda Gates Foundation's Healthy Birth, Growth and Development knowledge integration project aims to improve the overall health and well‐being of children across the world. The project aims to integrate information from multiple child growth studies to allow health professionals and policy makers to make informed decisions about interventions in lower and middle income countries. To achieve this goal, we must first understand the conditions that impact on the growth and development of children, and this requires sensible models for characterising different growth patterns. The contribution of this paper is to provide a quantitative comparison of the predictive abilities of various statistical growth modelling techniques based on a novel leave‐one‐out validation approach. The majority of existing studies have used raw growth data for modelling, but we show that fitting models to standardised data provide more accurate estimation and prediction. Our work is illustrated with an example from a study into child development in a middle income country in South America.
Andersson, AJ, Venn, AA, Pendleton, L, Brathwaite, A, Camp, EF, Cooley, S, Gledhill, D, Koch, M, Maliki, S & Manfrino, C 2019, 'Ecological and socioeconomic strategies to sustain Caribbean coral reefs in a high-CO2 world', Regional Studies in Marine Science, vol. 29, pp. 100677-100677.
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© 2019 The Authors The Caribbean and Western Atlantic region hosts one of the world's most diverse geopolitical regions and a unique marine biota distinct from tropical seas in the Pacific and Indian Oceans. While this region varies in human population density, GDP and wealth, coral reefs, and their associated ecosystem services, are central to people's livelihoods. Unfortunately, the region's reefs have experienced extensive degradation over the last several decades. This degradation has been attributed to a combination of disease, overfishing, and multiple pressures from other human activities. Furthermore, the Caribbean region has experienced rapid ocean warming and acidification as a result of climate change that will continue and accelerate throughout the 21st century. It is evident that these changes will pose increasing threats to Caribbean reefs unless imminent actions are taken at the local, regional and global scale. Active management is required to sustain Caribbean reefs and increase their resilience to recover from acute stress events. Here, we propose local and regional solutions to halt and reverse Caribbean coral reef degradation under ongoing ocean warming and acidification. Because the Caribbean has already experienced high coral reef degradation, we suggest that this region may be suitable for more aggressive interventions that might not be suitable for other regions. Solutions with direct ecological benefits highlighted here build on existing knowledge of factors that can contribute to reef restoration and increased resilience in the Caribbean: (1)management of water quality, (2)reduction of unsustainable fishing practices, (3)application of ecological engineering, and (4)implementing marine spatial planning. Complementary socioeconomic and governance solutions include: (1)increasing communication and leveraging resources through the establishment of a regional reef secretariat, (2)incorporating reef health and sustainability goals into the bl...
Andrejic, OM, Vucic, RM, Pavlovic, M, McClements, L, Stokanovic, D, Jevtovic–Stoimenov, T & Nikolic, VN 2019, 'Association between Galectin-3 levels within central and peripheral venous blood, and adverse left ventricular remodelling after first acute myocardial infarction', Scientific Reports, vol. 9, no. 1.
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AbstractOur study investigates association between Galectin-3 levels and adverse left ventricular remodelling (LVR) at six months. Fifty-seven patients following first acute myocardial infarction (AMI) were enrolled in this study and blood samples collected on day 1 from the femoral vein and artery, the right atrium near the coronary sinus and the aortic root, and on day 30, from the cubital vein. Patients with LVESV ≥20% at six months, were included in the LVR group. On day 1, Galectin-3 plasma levels in the femoral vein (10.34 ng/ml ± 3.81 vs 8.22 ng/ml ± 2.34, p = 0.01), and near coronary sinus (10.7 ng/ml ± 3.97 vs 8.41 ng/ml ± 2.56, p = 0.007) were higher in the LVR group. Positive correlations between Galectin-3 levels from aortic root and coronary sinus, aortic root and femoral vein, and coronary sinus and femoral vein, were observed in both groups. On day 30, Galectin-3 concentration in the cubital vein was an independent risk factor of LVR six months post-AMI, demonstrating 1.5-fold increased risk. Day-30 Galectin-3 also showed positive correlations with echocardiography parameters indicative of diastolic and systolic dysfunction. Determining Galectin-3 plasma concentration on day 30 following AMI could have beneficial prognostic value in predicting LVR.
Angeloski, A, Cortie, MB, Scott, JA, Bordin, DM & McDonagh, AM 2019, 'Conversion of single crystals of a nickel(II) dithiocarbamate complex to nickel sulfide crystals', Inorganica Chimica Acta, vol. 487, pp. 228-233.
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© 2018 Elsevier B.V. Single crystals of bis(κ2S,S′-di(isopropyl)dithiocarbamato) nickel(II) were utilized as a single source precursor for the formation of NiS via thermolysis. The complex decomposed at ∼250 °C to form α-NiS exclusively with no β-NiS detected. Analysis of the thermolysis regime using in situ techniques showed that the thermolysis occurs in a single step with the major volatile side-products being isopropyl-isothiocyanate and carbon disulfide. The resultant NiS was examined using SEM and TEM to reveal a retention of precursor crystal edge-length and angle relationships.
Angeloski, A, Rawal, A, Bhadbhade, M, Hook, JM, Schurko, RW & McDonagh, AM 2019, 'An Unusual Mercury(II) Diisopropyldithiocarbamate Coordination Polymer', Crystal Growth & Design, vol. 19, no. 2, pp. 1125-1133.
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Arhin, SK, Zhao, J, Ji, X, Shi, C, Tang, J, Gu, Y, Xi, H, Cheng, J, Qu, X, Shi, H, Jin, XL & Lv, JQ 2019, 'Multiple facilitated glucose transporters SLC2As are required for normal mouse preimplantation embryo development', American Journal of Translational Research, vol. 11, no. 6, pp. 3412-3425.
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Background: Glucose metabolism is an essential energy source for mammalian preimplantation embryonic development. Therefore, we aimed to analyze the expression of all 12 known glucose transporters (facilitated solute carrier family 2, Slc2a) during early mouse embryo development. Methods: Gene and protein expression of Slc2a transporters in oocytes and embryos were assessed by the TaqMan gene expression assay and confocal immunofluorescence, respectively. Results: Except for Slc2a2, the other 11 Slc2a transcripts were detected in oocytes. Transcripts of Slc2a1, Slc2a3, Slc2a4, and Slc2a8 were the most enriched and detected in preimplantation embryos. The transcription of other Slc2a isoforms was barely detectable or absent after fertilization; however, they were detected in blastocysts, except for Slc2a10 and Slc2a13. Embryo culture in the simple defined medium caused a reduction in transcription of Slc2a1, Slc2a3, Slc2a4, and Slc2a8 in blastocyst; yet, amino acids partially reversed this impaired transcription of Slc2a1 and Slc2a4. SLC2A1 and SLC2A4 proteins were detected at all embryonic stages with nuclear accumulation in the embryos at the early cleavage stage. SLC2A3 and SLC2A8 were not detected in embryos until the eight-cell stage. The cellular membrane localization of SLC2A1, SLC2A3, and SLC2A8 occurred after compaction and was characterized in blastocysts. SLC2A4 was evenly distributed in the cytoplasm and nuclei without its characteristic membrane localization. Indinavir sulfate (a SLC2A4 inhibitor) decreased the rate of development and prevented glucose utilization in embryos after compaction. These inhibitory activities were partially reversed by exogenous insulin. Conclusion: The results unveil distinct expression patterns of individual Slc2a glucose transporters during early embryo development. Taken together, they provide novel insights into the understanding and management of glucose metabolic infertility in assisted-reproductive technologies (ART).
Armbrecht, LH, Coolen, MJL, Lejzerowicz, F, George, SC, Negandhi, K, Suzuki, Y, Young, J, Foster, NR, Armand, LK, Cooper, A, Ostrowski, M, Focardi, A, Stat, M, Moreau, JW & Weyrich, LS 2019, 'Ancient DNA from marine sediments: Precautions and considerations for seafloor coring, sample handling and data generation', Earth-Science Reviews, vol. 196, pp. 102887-102887.
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Arnold, MD 2019, 'Effective transport properties of conformal Voronoi-bounded columns via recurrent boundary element expansions', Journal of Applied Physics, vol. 126, no. 16, pp. 164307-164307.
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Effective transport properties of heterogeneous structures are predicted by
geometric microstructural parameters, but these can be difficult to calculate.
Here, a boundary element code with a recurrent series method accurately and
efficiently determines the high order parameters of polygonal and conformal
prisms in regular two-dimensional lattices and Voronoi tessellations (VT). This
reveals that proximity to simpler estimates is associated with: centroidal VT
(cf random VT), compactness, and VT structures (cf similarly compact
semi-regular lattices). An error in previously reported values for triangular
lattices is noted.
Arti, Kaur, A, Singh, M, Arora, S, Dhiman, S, Satija, S & Singh, TG 2019, 'Pharmacotherapy of amyotrophic lateral sclerosis: An insight', Plant Archives, vol. 19, pp. 1385-1397.
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Amyotrophic Lateral Sclerosis (ALS) is a neurodegenerative disease of motor neurons resulting in worsening of voluntary muscles and degeneration of motor neurons in the motor cortex brainstem and spinal cord. Pathogenetic mechanism of ALS includes involvement of mitochondrial dysfunction, glutamate excitotoxicity, oxidative stress and apoptosis showing that ALS is a multifactorial disease. Major symptoms include spasticity, cognitive impairment, malnutrition and muscle cramps. As ALS still remains fatal due to several complications involved, various advances have been made in modifying the disease course. Symptomatic treatment, due to complicated symptoms, and nutrition assessment and intervention, due to the involvement of malnutrition in patients has an important role in controlling the distress caused by the disease. This article reviews the current therapeutic approaches including recent advances in pharmacological treatment strategies along with nutrition and dietary supplements based on the potential to delay onset of disease, retard the progression of disease, extend the lifespan and improve the quality of life of patients.
Atto, B, Eapen, MS, Sharma, P, Frey, U, Ammit, AJ, Markos, J, Chia, C, Larby, J, Haug, G, Weber, HC, Mabeza, G, Tristram, S, Myers, S, Geraghty, DP, Flanagan, KL, Hansbro, PM & Sohal, SS 2019, 'New therapeutic targets for the prevention of infectious acute exacerbations of COPD: role of epithelial adhesion molecules and inflammatory pathways', Clinical Science, vol. 133, no. 14, pp. 1663-1703.
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AbstractChronic respiratory diseases are among the leading causes of mortality worldwide, with the major contributor, chronic obstructive pulmonary disease (COPD) accounting for approximately 3 million deaths annually. Frequent acute exacerbations (AEs) of COPD (AECOPD) drive clinical and functional decline in COPD and are associated with accelerated loss of lung function, increased mortality, decreased health-related quality of life and significant economic costs. Infections with a small subgroup of pathogens precipitate the majority of AEs and consequently constitute a significant comorbidity in COPD. However, current pharmacological interventions are ineffective in preventing infectious exacerbations and their treatment is compromised by the rapid development of antibiotic resistance. Thus, alternative preventative therapies need to be considered. Pathogen adherence to the pulmonary epithelium through host receptors is the prerequisite step for invasion and subsequent infection of surrounding structures. Thus, disruption of bacterial–host cell interactions with receptor antagonists or modulation of the ensuing inflammatory profile present attractive avenues for therapeutic development. This review explores key mediators of pathogen–host interactions that may offer new therapeutic targets with the potential to prevent viral/bacterial-mediated AECOPD. There are several conceptual and methodological hurdles hampering the development of new therapies that require further research and resolution.
Avent, I, Kinnane, AG, Jones, N, Petermann, I, Daniel, R, Gahan, ME & McNevin, D 2019, 'The QIAGEN 140-locus single-nucleotide polymorphism (SNP) panel for forensic identification using massively parallel sequencing (MPS): an evaluation and a direct-to-PCR trial', International Journal of Legal Medicine, vol. 133, no. 3, pp. 677-688.
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Massively parallel sequencing (MPS) of identity informative single-nucleotide polymorphisms (IISNPs) enables hundreds of forensically relevant markers to be analysed simultaneously. Generating DNA sequence data enables more detailed analysis including identification of sequence variations between individuals. The GeneRead DNAseq 140 IISNP MPS panel (QIAGEN) has been evaluated on both the MiSeq (Illumina) and Ion PGM™ (Applied Biosystems) MPS platforms using the GeneRead DNAseq Targeted Panels V2 library preparation workflow (QIAGEN). The aims of this study were to (1) determine if the GeneRead DNAseq panel is effective for identity testing by assessing deviation from Hardy-Weinberg (HWE) and pairwise linkage equilibrium (LE); (2) sequence samples with the GeneRead DNAseq panel on the Ion PGM™ using the QIAGEN workflow and assess specificity, sensitivity and accuracy; (3) assess the efficacy of adding biological samples directly to the GeneRead DNAseq PCR, without prior DNA extraction; and (4) assess the effect of varying coverage and allele frequency thresholds on genotype concordance. Analyses of the 140 SNPs for HWE and LE using Fisher's exact tests and the sequential Bonferroni correction revealed that one SNP was out of HWE in the Japanese population and five SNP combinations were commonly out of LE in 13 of 14 populations. The panel was sensitive down to 0.3125 ng of DNA input. A direct-to-PCR approach (without DNA extraction) produced highly concordant genotypes. The setting of appropriate allele frequency thresholds is more effective for reducing erroneous genotypes than coverage thresholds.
Ayres, DL, Cummings, MP, Baele, G, Darling, AE, Lewis, PO, Swofford, DL, Huelsenbeck, JP, Lemey, P, Rambaut, A & Suchard, MA 2019, 'BEAGLE 3: Improved Performance, Scaling, and Usability for a High-Performance Computing Library for Statistical Phylogenetics', Systematic Biology, vol. 68, no. 6, pp. 1052-1061.
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Abstract
BEAGLE is a high-performance likelihood-calculation library for phylogenetic inference. The BEAGLE library defines a simple, but flexible, application programming interface (API), and includes a collection of efficient implementations for calculation under a variety of evolutionary models on different hardware devices. The library has been integrated into recent versions of popular phylogenetics software packages including BEAST and MrBayes and has been widely used across a diverse range of evolutionary studies. Here, we present BEAGLE 3 with new parallel implementations, increased performance for challenging data sets, improved scalability, and better usability. We have added new OpenCL and central processing unit-threaded implementations to the library, allowing the effective utilization of a wider range of modern hardware. Further, we have extended the API and library to support concurrent computation of independent partial likelihood arrays, for increased performance of nucleotide-model analyses with greater flexibility of data partitioning. For better scalability and usability, we have improved how phylogenetic software packages use BEAGLE in multi-GPU (graphics processing unit) and cluster environments, and introduced an automated method to select the fastest device given the data set, evolutionary model, and hardware. For application developers who wish to integrate the library, we also have developed an online tutorial. To evaluate the effect of the improvements, we ran a variety of benchmarks on state-of-the-art hardware. For a partitioned exemplar analysis, we observe run-time performance improvements as high as 5.9-fold over our previous GPU implementation. BEAGLE 3 is free, open-source software licensed under the Lesser GPL and available at https://beagle-dev.github.io.
Backwell, A, Macrina, A, Schlögl, E & Skovmand, D 2019, 'Term Rates, Multicurve Term Structures and Overnight Rate Benchmarks: a Roll-Over Risk Approach'.
Bailey, RL, Dodd, KW, Gahche, JJ, Dwyer, JT, Cowan, AE, Jun, S, Eicher-Miller, HA, Guenther, PM, Bhadra, A, Thomas, PR, Potischman, N, Carroll, RJ & Tooze, JA 2019, 'Best Practices for Dietary Supplement Assessment and Estimation of Total Usual Nutrient Intakes in Population-Level Research and Monitoring', The Journal of Nutrition, vol. 149, no. 2, pp. 181-197.
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ABSTRACTThe use of dietary supplements (DS) is pervasive and can provide substantial amounts of micronutrients to those who use them. Therefore when characterizing dietary intakes, describing the prevalence of inadequacy or excess, or assessing relations between nutrients and health outcomes, it is critical to incorporate DS intakes to improve exposure estimates. Unfortunately, little is known about the best methods to assess DS, and the structure of measurement error in DS reporting. Several characteristics of nutrients from DS are salient to understand when comparing to those in foods. First, DS can be consumed daily or episodically, in bolus form and can deliver discrete and often very high doses of nutrients that are not limited by energy intakes. These characteristics contribute to bimodal distributions and distributions severely skewed to the right. Labels on DS often provide nutrient forms that differ from those found in conventional foods, and underestimate analytically derived values. Finally, the bioavailability of many nutrient-containing DS is not known and it may not be the same as the nutrients in a food matrix. Current methods to estimate usual intakes are not designed specifically to handle DS. Two temporal procedures are described to refer to the order that nutrient intakes are combined relative to usual intake procedures, referred to as a “shrinking” the distribution to remove random error. The “shrink then add” approach is preferable to the “add then shrink” approach when users and nonusers are combined for most research questions. Stratifying by DS before usual intake methods is another defensible option. This review describes how to incorporate nutrient intakes from DS to usual intakes from foods, and describes the available methods and fit-for-purpose of different analytical strategies to address research questions where total usual intakes are of interest at the group level for use in nutrition research and ...
Bakshi, HA, Mishra, V, Satija, S, Mehta, M, Hakkim, FL, Kesharwani, P, Dua, K, Chellappan, DK, Charbe, NB, Shrivastava, G, Rajeshkumar, S, Aljabali, AA, Al-Trad, B, Pabreja, K & Tambuwala, MM 2019, 'Dynamics of Prolyl Hydroxylases Levels During Disease Progression in Experimental Colitis', Inflammation, vol. 42, no. 6, pp. 2032-2036.
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Bannwarth, A, Morelato, M, Benaglia, L, Been, F, Esseiva, P, Delemont, O & Roux, C 2019, 'The use of wastewater analysis in forensic intelligence: drug consumption comparison between Sydney and different European cities', Forensic Sciences Research, vol. 4, no. 2, pp. 141-151.
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Bansal, R, Care, A, Lord, MS, Walsh, TR & Sunna, A 2019, 'Experimental and theoretical tools to elucidate the binding mechanisms of solid-binding peptides', New Biotechnology, vol. 52, pp. 9-18.
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Bao, G & Jin, D 2019, 'Nanoparticles give mice infrared vision', Nature Photonics, vol. 13, no. 5, pp. 304-305.
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© 2019, Springer Nature Limited. The injection of rare-earth-doped upconversion nanoparticles into the eyes of mice allows them to visualize near-infrared light with a wavelength of ~1 μm.
Bao, G, Wong, K & Tanner, PA 2019, 'A Reversible Rhodamine B Based pH Probe with Large Pseudo‐Stokes Shift', ChemPlusChem, vol. 84, no. 7, pp. 816-820.
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Bao, W, Shuck, CE, Zhang, W, Guo, X, Gogotsi, Y & Wang, G 2019, 'Boosting Performance of Na–S Batteries Using Sulfur-Doped Ti3C2Tx MXene Nanosheets with a Strong Affinity to Sodium Polysulfides', ACS Nano, vol. 13, no. 10, pp. 11500-11509.
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Barratt, JLN & Ellis, J 2019, 'Angiostrongylus cantonensis: a review of its distribution, molecular biology and clinical significance as a human pathogen – CORRIGENDUM', Parasitology, vol. 146, no. 10, pp. 1360-1360.
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Barratt, JLN, Lane, M, Talundzic, E, Richins, T, Robertson, G, Formenti, F, Pritt, B, Verocai, G, Nascimento de Souza, J, Mato Soares, N, Traub, R, Buonfrate, D & Bradbury, RS 2019, 'A global genotyping survey of Strongyloides stercoralis and Strongyloides fuelleborni using deep amplicon sequencing', PLOS Neglected Tropical Diseases, vol. 13, no. 9, pp. e0007609-e0007609.
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Strongyloidiasis is a neglected tropical disease caused by the human infective nematodes Strongyloides stercoralis, Strongyloides fuelleborni fuelleborni and Strongyloides fuelleborni kellyi. Previous large-scale studies exploring the genetic diversity of this important genus have focused on Southeast Asia, with a small number of isolates from the USA, Switzerland, Australia and several African countries having been genotyped. Consequently, little is known about the global distribution of geographic sub-variants of these nematodes and the genetic diversity that exists within the genus Strongyloides generally. We extracted DNA from human, dog and primate feces containing Strongyloides, collected from several countries representing all inhabited continents. Using a genotyping assay adapted for deep amplicon sequencing on the Illumina MiSeq platform, we sequenced the hyper-variable I and hyper-variable IV regions of the Strongyloides 18S rRNA gene and a fragment of the mitochondrial cytochrome c oxidase subunit 1 (cox1) gene from these specimens. We report several novel findings including unique S. stercoralis and S. fuelleborni genotypes, and the first identifications of a previously unknown S. fuelleborni infecting humans within Australia. We expand on an existing Strongyloides genotyping scheme to accommodate S. fuelleborni and these novel genotypes. In doing so, we compare our data to all 18S and cox1 sequences of S. fuelleborni and S. stercoralis available in GenBank (to our knowledge), that overlap with the sequences generated using our approach. As this analysis represents more than 1,000 sequences collected from diverse hosts and locations, representing all inhabited continents, it allows a truly global understanding of the population genetic structure of the Strongyloides species infecting humans, non-human primates, and domestic dogs.
Barratt, JLN, Park, S, Nascimento, FS, Hofstetter, J, Plucinski, M, Casillas, S, Bradbury, RS, Arrowood, MJ, Qvarnstrom, Y & Talundzic, E 2019, 'Genotyping genetically heterogeneousCyclospora cayetanensisinfections to complement epidemiological case linkage', Parasitology, vol. 146, no. 10, pp. 1275-1283.
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AbstractSexually reproducing pathogens such asCyclospora cayetanensisoften produce genetically heterogeneous infections where the number of unique sequence types detected at any given locus varies depending on which locus is sequenced. The genotypes assigned to these infections quickly become complex when additional loci are analysed. This genetic heterogeneity confounds the utility of traditional sequence-typing and phylogenetic approaches for aiding epidemiological trace-back, and requires new methods to address this complexity. Here, we describe an ensemble of two similarity-based classification algorithms, including a Bayesian and heuristic component that infer the relatedness ofC. cayetanensisinfections. The ensemble requires a set of haplotypes as input and assigns arbitrary distances to specimen pairs reflecting their most likely relationships. The approach was applied to data generated from a test cohort of 88 human fecal specimens containingC. cayetanensis, including 30 from patients whose infections were associated with epidemiologically defined outbreak clusters of cyclosporiasis. The ensemble assigned specimens to plausible clusters of genetically related infections despite their complex haplotype composition. These relationships were corroborated by a significant number of epidemiological linkages (P< 0.0001) suggesting the ensemble's utility for aiding epidemiological trace-back investigations of cyclosporiasis.
Barraza, V, Grings, F, Franco, M, Douna, V, Entekhabi, D, Restrepo-Coupe, N, Huete, A, Gassmann, M & Roitberg, E 2019, 'Estimation of latent heat flux using satellite land surface temperature and a variational data assimilation scheme over a eucalypt forest savanna in Northern Australia', Agricultural and Forest Meteorology, vol. 268, pp. 341-353.
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In this study, the performance of the combined-source variational data assimilation scheme (CS-VDA) is assessed in detail using in situ heat fluxes (i.e. sensible heat (H) and latent heat (LE)) collected at a Eucalypt forest savanna of Northern Australia (Howard Springs). The CS VDA scheme estimates surface turbulent heat fluxes via assimilation of sequences of land surface temperature (LST) and meteorological data into a surface energy balance model and a dynamic model. The main objectives of this paper were to extend previous studies to a semi-arid ecosystem and to evaluate the potential of using global meteorological forcing data (GMD) to drive the CS VDA model (rather than in-situ meteorological observations). In order to study the new errors associated with the use of GMD, the effects on LE of the uncertainty in air temperature and wind speed (the two key meteorological factors that controls the total estimation error) was quantitatively characterized. Using hourly in-situ measurements as inputs, the daily-averaged LE RMSEdaily was 54 W/m2, which agrees with the errors previously reported in the literature. As expected, replacing local meteorological data with GMD reduces the performance of the LE estimation (GMA: RMSEdaily = 82 W/m2, GLDAS: RMSEdaily = 151 W/m2). However, LE RMSE values at 8-day temporal scale for GMA are RMSE8-days = 32 W/m2, similar to those reported in this area for other models (MODIS (MOD16A2) and Breathing Earth System Simulator (BESS)). The error propagation analysis indicate that the CS VDA model is very sensitive to uncertainties in wind speed measurements. Moreover, there are large discrepancies between in situ and GMD wind speed. These two factors combined can explain the degradation in LE estimations. In this context, our study is a first step towards the characterization of an operational daily LE estimation scheme using hourly LST observations.
Bartlett, M, Wang, J, Hay, L & Pang, G 2019, 'Health service use in the older person with complex health needs', Australian Health Review, vol. 43, no. 1, pp. 62-62.
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Objective Effective health care for older people with complex health needs requires a diverse range of healthcare professionals working together. The Building Partnerships Framework of the New South Wales Agency for Clinical Innovation seeks to promote collaboration and integration among service providers. The aim of the present study was to inform implementation and evaluation of the Framework. Methods Data from the 45 and Up Study was linked with deaths and service data from hospitalisations and the Medicare Benefits Schedule (MBS). Participants with a hospitalisation for conditions representing ‘geriatric syndrome’ were allocated to a complex needs group; the remainder were allocated to a comparison group. Hospital admissions and MBS services use were modelled using log-linear Poisson regression. Results Multivariate analysis showed that the rate of hospitalisation in the 2 years following index admission for the complex needs group was 18% (95% confidence interval (CI) 1.12–1.24) greater than the comparison group and specialist physician attendance was 13% (95% CI 1.06 – 1.21) greater. The rate of general practitioner (GP) attendances was 2% (95% CI 0.97–1.07) greater in the complex needs group, but this was not statistically significant. Discussion The greater rates of hospitalisation and specialist service use, the absence of a similar finding for GP services and the prominence of the role of primary care in service integration literature, policy and strategy underscore the importance of careful planning, consultation and inclusiveness in the development and implementation of integrated care policy. What is known about the topic? Older people with complex health needs are significant consumers of primary and secondary health services and benefit from well-planned and coordinated care. What does this paper add? The findings presented here indicate that although hospitals and specialist physicians provide a significantly greater volume of services to ...
Bates, H, Zavafer, A, Szabó, M & Ralph, PJ 2019, 'A guide to Open-JIP, a low-cost open-source chlorophyll fluorometer', Photosynthesis Research, vol. 142, no. 3, pp. 361-368.
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Batmunkh, M, Vimalanathan, K, Wu, C, Bati, ASR, Yu, L, Tawfik, SA, Ford, MJ, Macdonald, TJ, Raston, CL, Priya, S, Gibson, CT & Shapter, JG 2019, 'Efficient Production of Phosphorene Nanosheets via Shear Stress Mediated Exfoliation for Low‐Temperature Perovskite Solar Cells', Small Methods, vol. 3, no. 5, pp. 1800521-1800521.
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AbstractA simple and fast “top‐down” protocol is introduced herein to prepare solution processable few‐layer phosphorene nanosheets using vortex fluidic mediated exfoliation under near‐infrared (NIR) pulsed laser irradiation. This novel shear‐exfoliation method requires short processing times and produces highly crystalline, atomically thin phosphorene nanosheets (4.3 ± 0.4 nm). The as‐prepared phosphorene nanosheets are used as an effective electron transporting material (ETM) for low‐temperature processed, planar n‐i‐p perovskite solar cells (PSCs). With the addition of phosphorene, the average power conversion efficiency (PCE) increases from 14.32% to 16.53% with a maximum PCE of 17.85% observed for the phosphorene incorporated PSCs which is comparable to the devices made using the traditional high‐temperature protocol. Experimental and theoretical (density‐functional theory) investigations reveal the PCE improvements are due to the high carrier mobility and suitable band energy alignment of the phosphorene. The work not only paves the way for novel synthesis of 2D materials, but also opens a new avenue in using phosphorene as an efficient ETM in photovoltaic devices.
Bawa, G, Mahajan, R, Mehta, M, Satija, S, Vyas, M, Sharma, N & Khurana, N 2019, 'Herbal drugs for the treatment of opioid withdrawal syndrome: A mini review', Plant Archives, vol. 19, pp. 1005-1011.
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Addiction to opioid drugs is the extensive medical and social burden of human life. Chronic usage of morphine in the severe pain has also been associated with its major drawback for development of dependence and tolerance. In different brain regions, there are various receptors which play important role in opioid withdrawal syndrome. The herbal drugs; like Nigella sativa, Withania somnifera, Aloe vera, Matricaria recutita, venlafaxine, curucumin play vital role to treat the abstinence syndrome. Most of the above mentioned drugs are related with some adverse effects. So there is need to develop some novel agents targeting the various mechanism underlying the opioid withdrawal, thereby providing significant relief from opioid withdrawal syndrome. In this review, we discussed the usefulness and limitations of various drug treatments for opioid withdrawal syndrome.
Bedward, TM, Xiao, L & Fu, S 2019, 'Application of Raman spectroscopy in the detection of cocaine in food matrices', Australian Journal of Forensic Sciences, vol. 51, no. 2, pp. 209-219.
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© 2017 Australian Academy of Forensic Sciences While modern methodologies for the smuggling of illicit substances often tend towards more elaborate inventions, the simple practice of concealing cocaine hydrochloride within food matrices is becoming increasingly popular. This study was conducted to develop and optimize a Raman spectroscopic method capable of identifying and quantifying cocaine hydrochloride concealed within food matrices. Samples of cocaine hydrochloride were concealed within baking powder, cake mix and white rum, with identification of the drug achieved through a combination of manual and automated detection methods and comparison with a digital spectral library. Principal component analysis (PCA) and partial least squares regression (PLSR) were employed to qualitatively and quantitatively examine the collected spectra, allowing for traces of cocaine hydrochloride found within each matrix to be identified and quantified. For each of the solid matrices, Raman spectroscopy enabled rapid, non-invasive, and unambiguous identification of the concealed drug. For the white rum samples, due to strong matrix interference, full spectrum matching was not possible, but presumptive identification of cocaine in the samples was achieved at 100%. No false positives or miss-identified samples were recorded, Results of the PLSR analysis showed potential, however difficulties in obtaining accurate concentrations served to limit the method’s use in quantitative analysis.
Beknazarova, M, Barratt, JLN, Bradbury, RS, Lane, M, Whiley, H & Ross, K 2019, 'Detection of classic and cryptic Strongyloides genotypes by deep amplicon sequencing: A preliminary survey of dog and human specimens collected from remote Australian communities', PLOS Neglected Tropical Diseases, vol. 13, no. 8, pp. e0007241-e0007241.
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Strongyloidiasis is caused by the human infective nematodes Strongyloides stercoralis, Strongyloides fuelleborni subsp. fuelleborni and Strongyloides fuelleborni subsp. kellyi. The zoonotic potential of S. stercoralis and the potential role of dogs in the maintenance of strongyloidiasis transmission has been a topic of interest and discussion for many years. In Australia, strongyloidiasis is prevalent in remote socioeconomically disadvantaged communities in the north of the continent. Being an isolated continent that has been separated from other regions for a long geological period, description of diversity of Australian Strongyloides genotypes adds to our understanding of the genetic diversity within the genus. Using PCR and amplicon sequencing (Illumina sequencing technology), we sequenced the Strongyloides SSU rDNA hyper-variable I and hyper-variable IV regions using Strongyloides-specific primers, and a fragment of the mtDNA cox1 gene using primers that are broadly specific for Strongyloides sp. and hookworms. These loci were amplified from DNA extracted from Australian human and dog faeces, and one human sputum sample. Using this approach, we confirm for the first time that potentially zoonotic S. stercoralis populations are present in Australia, suggesting that dogs represent a potential reservoir of human strongyloidiasis in remote Australian communities.
Belay, Y, Coetzee, L-C, Williams, DBG & Muller, A 2019, 'Synthesis of novel 1,2,3-triazole based polycarboxylic acid functionalised ligands for MOF systems', Tetrahedron Letters, vol. 60, no. 6, pp. 501-503.
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© 2019 Copper catalysed click reactions are excellent tools to generate various 1,2,3-triazole linked polytopic aromatic carboxylates. The general reaction route involves protection of the carboxylates before proceeding with the click reaction. These polycarboxylate azoles are conveniently prepared for potential utility as novel key building blocks for metal organic frameworks. In one case, the ligand crystallises into a solid structure containing 1D, 2D and 3D features, based on a zigzag 1D structure, a ‘chicken mesh’-like 2D structure and a 3D structure with very well-defined channels.
Bell, J, Nel, P & Stuart, B 2019, 'Non-invasive identification of polymers in cultural heritage collections: evaluation, optimisation and application of portable FTIR (ATR and external reflectance) spectroscopy to three-dimensional polymer-based objects', Heritage Science, vol. 7, no. 1.
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AbstractThe conservation of polymer-based cultural heritage is a major concern for collecting institutions internationally. Collections include a range of different polymers, each with its own degradation processes and preservation needs, however, they are frequently unidentified in collection catalogues. Fourier transform infrared (FTIR) spectroscopy is a useful analytical tool for identifying polymers, which is vital for determining storage, exhibition, loan and treatment conditions. Attenuated Total Reflection (ATR), and External Reflection (ER) are proven effective FTIR sampling techniques for polymer identification and are beginning to appear in conservation labs. This paper evaluates and optimises the application of these two FTIR techniques to three-dimensional plastic objects in the museum context. Elements of the FTIR measurement process are investigated for 15 common polymers found in museum collections using both authentic reference sheets, and case study objects to model for surface characteristics. Including: use of the ATR and ER modules, the difference between clamping and manually holding objects in contact with the ATR crystal, use of the Kramers–Kronig Transformation, signal-to-noise ratios for increasing number of co-added scans, resultant time taken to collect each measurement, associated professional, health and safety considerations, and the use and availability of reference materials for polymer identify verification. Utilising this information, a flowchart for applying FTIR spectroscopy to three-dimensional historic plastic objects during museum collection surveys is proposed to guide the conservation profession.
Bell, ME, Murphy, T, Hancock, PJ, Callingham, JR, Johnston, S, Kaplan, DL, Hunstead, RW, Sadler, EM, Croft, S, White, SV, Hurley-Walker, N, Chhetri, R, Morgan, JS, Edwards, PG, Rowlinson, A, Offringa, AR, Bernardi, G, Bowman, JD, Briggs, F, Cappallo, RJ, Deshpande, AA, Gaensler, BM, Greenhill, LJ, Hazelton, BJ, Johnston-Hollitt, M, Lonsdale, CJ, McWhirter, SR, Mitchell, DA, Morales, MF, Morgan, E, Oberoi, D, Ord, SM, Prabu, T, Shankar, NU, Srivani, KS, Subrahmanyan, R, Tingay, SJ, Wayth, RB, Webster, RL, Williams, A & Williams, CL 2019, 'The Murchison Widefield Array Transients Survey (MWATS). A search for low frequency variability in a bright Southern hemisphere sample', Monthly Notices of the Royal Astronomical Society, vol. 482, no. 2, pp. 2484-2501.
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Bennett, N, Woodcock, S, Pluss, MA, Bennett, KJM, Deprez, D, Vaeyens, R, Lenoir, M & Fransen, J 2019, 'Forecasting the development of explosive leg power in youth soccer players', Science and Medicine in Football, vol. 3, no. 2, pp. 131-137.
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Monitoring athletic development in youth soccer can help sporting professionals monitor athletic development and evaluate the effectiveness of training interventions. However, long-term follow up in talent development programmes in youth soccer is complicated. Therefore, the aim of this study was to forecast the developmental trajectories of explosive leg power in youth soccer players. Methods: Mixed effects regression models were used to forecast explosive leg power (countermovement (CMJ) and standing broad jump (SBJ)) in a longitudinal sample of 2201 youth soccer players from two high level Belgian acedemies and the Belgian National teams. Players were aged between 6 and 20 years (mean age = 13.04 ± 3.18 y) and were subdivided into three age cohorts (6–10, 11–15, and 16–20 y) for CMJ and two age cohorts (6–16, and 17–20 y) for SBJ. Results: This study was able to accurately forecast explosive leg power using different regression equations in each age cohort. Conclusions: Researchers, coaches, and sporting professionals can use these methods to either predict future explosive leg power from current performance measures, monitor the development of explosive leg power, or assess the effectiveness of training interactions aimed at altering predicted developmental trajectories.
Berlowitz, DJ, Schembri, R, Graco, M, Ross, JM, Ayas, N, Gordon, I, Lee, B, Graham, A, Cross, SV, McClelland, M, Kennedy, P, Thumbikat, P, Bennett, C, Townson, A, Geraghty, TJ, Pieri-Davies, S, Singhal, R, Marshall, K, Short, D, Nunn, A, Mortimer, D, Brown, D, Pierce, RJ & Cistulli, PA 2019, 'Positive airway pressure for sleep-disordered breathing in acute quadriplegia: a randomised controlled trial', Thorax, vol. 74, no. 3, pp. 282-290.
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RationaleHighly prevalent and severe sleep-disordered breathing caused by acute cervical spinal cord injury (quadriplegia) is associated with neurocognitive dysfunction and sleepiness and is likely to impair rehabilitation.ObjectiveTo determine whether 3 months of autotitrating CPAP would improve neurocognitive function, sleepiness, quality of life, anxiety and depression more than usual care in acute quadriplegia.Methods and measurementsMultinational, randomised controlled trial (11 centres) from July 2009 to October 2015. The primary outcome was neurocognitive (attention and information processing as measure with the Paced Auditory Serial Addition Task). Daytime sleepiness (Karolinska Sleepiness Scale) was a priori identified as the most important secondary outcome.Main results1810 incident cases were screened. 332 underwent full, portable polysomnography, 273 of whom had an apnoea hypopnoea index greater than 10. 160 tolerated at least 4 hours of CPAP during a 3-day run-in and were randomised. 149 participants (134 men, age 46±34 years, 81±57 days postinjury) completed the trial. CPAP use averaged 2.9±2.3 hours per night with 21% fully ‘adherent’ (at least 4 hours use on 5 days per week). Intention-to-treat analyses revealed no significant differences between groups in the Paced Auditory Serial Addition Task (mean improvement of 2.28, 95% CI −7.09 to 11.6; p=0.63). Controlling for premorbid intelligence, age and obstructive sleep apnoea severity (group effect −1.15, 95% CI −10 to 7.7) did not alter this finding. Sleepiness was significantly improved by CPAP on intention-to-treat analysis (mean difference −1.26, 95% CI −2.2 to –0.32; p=0.01).Conclusion<...
Bharatula, LD, Rice, S, Marsili, E & Kwan, JJ 2019, 'Acoustically stressing biofilms formed by Pseudomonas aeruginosa', The Journal of the Acoustical Society of America, vol. 146, no. 4_Supplement, pp. 3031-3031.
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Bacterial biofilms, the complex and dynamic assemblages of bacterial cells, have shown increased tolerance to antimicrobials compared to their planktonic counterparts. Altered metabolism and micro-environments, in addition to the self-generated extracellular polymeric substances (EPS), collectively help to protect the bacteria from the effect of antimicrobials, thereby increasing the necessity for novel treatment methods that are effective against biofilms. To address this, we have investigated the effect of high intensity focused ultrasound (HIFU) in killing or dispersing biofilms. HIFU reduces the total biofilm biomass without significant cell killing. To investigate the molecular mechanism of action of HIFU, we quantified the intracellular concentrations of cyclic di-GMP, which regulates the switch between biofilm and planktonic life-styles. Biofilms grown on polymeric sheets were exposed to HIFU at 0.5 MHz frequency and the c di-GMP concentration was characterized using confocal microscopy. Changes in the c di-GMP activity localized at the acoustic focus were observed as the biomass decreased. The mechanisms promoting these changes were further investigated by examining the shape of individual bacterial colony grown on agar plates. The observed effects were compared to sham (negative control) and c di-GMP overproducing mutant (positive control).
Bharatula, LD, Rice, S, Marsili, E & Kwan, JJ 2019, 'Sounding out bacteria: Microstructural effects of therapeutic ultrasound on bacterial biofilms', The Journal of the Acoustical Society of America, vol. 145, no. 3_Supplement, pp. 1894-1894.
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Treatment of chronic infections due to formation of bacterial biofilms are a huge risk due to the growing concerns with antimicrobial resistance. Biofilms grow in a complex and dynamic environment that weaken the effect of antimicrobials. Yet, the current strategy to tackle the problem is the development of novel drugs. However, the increasing prevalence of antimicrobial resistance suggests that an alternative treatment strategy without, or in synergy with, antibiotics is necessary to combat the biofilm infections. We and others have proposed high intensity focused ultrasound (HIFU) as a means to disrupt the biofilm matrix and improve therapy. Yet to date, there is limited knowledge on the cellular activity triggered by the biofilm-acoustic interactions. Here, we report the effect of HIFU at 500 kHz center frequency in absence of antibiotics or microbubbles on the microstructure of biofilms formed by Pseudomonas aeruginosa. Changes to the biofilm after acoustic exposure were characterized by confocal microscopy and electrochemical impedance spectroscopy. We observed a drop in the biomass at pressures where non-linear acoustics were dominant, and an increase in cellular activity. Our results suggest that there are acoustic bio-effects present in these bacteria that have not yet been reported.
Bharill, N, Patel, OP, Tiwari, A, Mu, L, Li, D-L, Mohanty, M, Kaiwartya, O & Prasad, M 2019, 'A Generalized Enhanced Quantum Fuzzy Approach for Efficient Data Clustering', IEEE Access, vol. 7, pp. 50347-50361.
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Billings, JL, Gordon, SL, Rawling, T, Doble, PA, Bush, AI, Adlard, PA, Finkelstein, DI & Hare, DJ 2019, 'l‐3,4‐dihydroxyphenylalanine (l‐DOPA) modulates brain iron, dopaminergic neurodegeneration and motor dysfunction in iron overload and mutant alpha‐synuclein mouse models of Parkinson's disease', Journal of Neurochemistry, vol. 150, no. 1, pp. 88-106.
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AbstractTreatment with the dopamine (DA) precursor l‐3,4‐dihydroxyphenylalanine (l‐DOPA) provides symptomatic relief arising from DA denervation in Parkinson's disease. Mounting evidence that DA autooxidation to neurotoxic quinones is involved in Parkinson's disease pathogenesis has raised concern about potentiation of oxidative stress by l‐DOPA. The rate of DA quinone formation increases in the presence of excess redox‐active iron (Fe), which is a pathological hallmark of Parkinson's disease. Conversely, l‐DOPA has pH‐dependent Fe‐chelating properties, and may act to ‘redox silence’ Fe and partially allay DA autoxidation. We examined the effects of l‐DOPA in three murine models of parkinsonian neurodegeneration: early‐life Fe overexposure in wild‐type mice, transgenic human (h)A53T mutant α‐synuclein (α‐syn) over‐expression, and a combined ‘multi‐hit’ model of Fe‐overload in hA53T mice. We found that l‐DOPA was neuroprotective and prevented age‐related Fe accumulation in the substantia nigra pars compacta (SN
Bilokur, M, Gentle, AR, Arnold, MD, Cortie, MB & Smith, GB 2019, 'High temperature optically stable spectrally-selective Ti1xAlxN-based multilayer coating for concentrated solar thermal applications', Solar Energy Materials and Solar Cells, vol. 200, pp. 109964-109964.
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© 2019 Elsevier B.V. Spectrally-selective solar absorbing coatings based on the Ti1-xAlxN system were deposited using DC magnetron sputtering. Due to their refractory nature and very suitable optical properties, these were considered for high temperature solar thermal energy conversion. The composition of Ti1-xAlxN, (effectively, the Ti/Al ratio) was optimized to achieve a maximized solar absorptance. The optimum composition was then tested in a tandem absorber which included anti-reflective layers. A stainless steel substrate was used in order to simulate service in parabolic trough-based power plants that use stainless steel pipe to carry the heat-transfer fluid. High temperature annealing of the stack caused structural modifications but the solar absorptance of 92% was retained even after annealing at 900 °C.
Biswal, JK, Ranjan, R, Subramaniam, S, Mohapatra, JK, Patidar, S, Sharma, MK, Bertram, MR, Brito, B, Rodriguez, LL, Pattnaik, B & Arzt, J 2019, 'Genetic and antigenic variation of foot-and-mouth disease virus during persistent infection in naturally infected cattle and Asian buffalo in India', PLOS ONE, vol. 14, no. 6, pp. e0214832-e0214832.
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The role of foot-and-mouth disease virus (FMDV) persistently infected ruminants in initiating new outbreaks remains controversial, and the perceived threat posed by such animals hinders international trade in FMD-endemic countries. In this study we report longitudinal analyses of genetic and antigenic variations of FMDV serotype O/ME-SA/Ind2001d sublineage during naturally occurring, persistent infection in cattle and buffalo at an organised dairy farm in India. The proportion of animals from which FMDV RNA was recovered was not significantly different between convalescent (post-clinical) and sub-clinically infected animals or between cattle and buffalo across the sampling period. However, infectious virus was isolated from a higher proportion of buffalo samples and for a longer duration compared to cattle. Analysis of the P1 sequences from recovered viruses indicated fixation of mutations at the rate of 1.816 x 10-2substitution/site/year (s/s/y) (95% CI 1.362-2.31 x 10-2 s/s/y). However, the majority of point mutations were transitional substitutions. Within individual animals, the mean dN/dS (ω) value for the P1 region varied from 0.076 to 0.357, suggesting the selection pressure acting on viral genomes differed substantially across individual animals. Statistical parsimony analysis indicated that all of the virus isolates from carrier animals originated from the outbreak virus. The antigenic relationship value as determined by 2D-VNT assay revealed fluctuation of antigenic variants within and between carrier animals during the carrier state which suggested that some carrier viruses had diverged substantially from the protection provided by the vaccine strain. This study contributes to understanding the extent of within-host and within-herd evolution that occurs during the carrier state of FMDV.
Black, HD, Xu, W, Hortle, E, Robertson, SI, Britton, WJ, Kaur, A, New, EJ, Witting, PK, Chami, B & Oehlers, SH 2019, 'The cyclic nitroxide antioxidant 4-methoxy-TEMPO decreases mycobacterial burden in vivo through host and bacterial targets', Free Radical Biology and Medicine, vol. 135, pp. 157-166.
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Boakes, RA, Fu, MX, Kendig, MD, Martire, SI & Rooney, KB 2019, 'Recovery from sucrose-induced metabolic and cognitive impairments in male rats', Obesity Research & Clinical Practice, vol. 13, no. 3, pp. 279-279.
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Bodachivskyi, I, Kuzhiumparambil, U & Bradley G. Williams, D 2019, 'High Yielding Acid‐Catalysed Hydrolysis of Cellulosic Polysaccharides and Native Biomass into Low Molecular Weight Sugars in Mixed Ionic Liquid Systems', ChemistryOpen, vol. 8, no. 10, pp. 1316-1324.
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AbstractIonic media comprising 1‐butyl‐3‐methylimidazolium chloride and the acidic deep eutectic solvent choline chloride/oxalic acid as co‐solvent‐catalyst, very efficiently convert various cellulosic substrates, including native cellulosic biomass, into water‐soluble carbohydrates. The optimum reaction systems yield a narrow range of low molecular weight carbohydrates directly from cellulose, lignocellulose, or algal saccharides, in high yields and selectivities up to 98 %. Cellulose possesses significant potential as a renewable platform from which to generate large volumes of green replacements to many petrochemical products. Within this goal, the production of low molecular weight saccharides from cellulosic substances is the key to success. Native cellulose and lignocellulosic feedstocks are less accessible for such transformations and depolymerisation of polysaccharides remains a primary challenge to be overcome. In this study, we identify the catalytic activity associated with selected deep eutectic solvents that favours the hydrolysis of polysaccharides and develop reaction conditions to improve the outcomes of desirable low molecular weight sugars. We successfully apply the chemistry to raw bulk, non‐pretreated cellulosic substances.
Bodachivskyi, I, Kuzhiumparambil, U & Williams, DBG 2019, 'A Systematic Study of Metal Triflates in Catalytic Transformations of Glucose in Water and Methanol: Identifying the Interplay of Brønsted and Lewis Acidity', ChemSusChem, vol. 12, no. 14, pp. 3208-3208.
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AbstractInvited for this month′s cover is the group of Prof. Bradley Williams at the University of Technology Sydney. The image depicts the manifold products that can be selected in transformations of glucose through manipulation of the Brønsted or Lewis acidity of the catalyst. The Full Paper itself is available at 10.1002/cssc.201900292.
Bodachivskyi, I, Kuzhiumparambil, U & Williams, DBG 2019, 'A Systematic Study of Metal Triflates in Catalytic Transformations of Glucose in Water and Methanol: Identifying the Interplay of Brønsted and Lewis Acidity', ChemSusChem, vol. 12, no. 14, pp. 3263-3270.
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AbstractThe specific type of acidity associated with the given metal trifloromethanesulfonates (Brønsted or Lewis acidity) dramatically influences the course of reactions, and it is possible to select for disaccharides, fructose, methyl glucosides, or methyl levulinate. Glucose is transformed into a range of value‐added molecules in water and methanol under the action of acidic metal triflates as catalysts, including their analogous Brønsted acid‐assisted or Brønsted base‐modified systems. A systematic study is presented of a range of metal triflates in methanol and water, pinning down the preferred conditions to select for each product.
Bodachivskyi, I, Kuzhiumparambil, U & Williams, DBG 2019, 'Acid‐Catalysed Conversion of Carbohydrates into Furan‐Type Molecules in Zinc Chloride Hydrate', ChemPlusChem, vol. 84, no. 4, pp. 352-357.
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AbstractAcid‐catalysed conversion of biomass, specifically cellulose, holds promise to create value‐added, renewable replacements for many petrochemical products. We investigated an unusual acid‐catalysed transformation of cellulose and cellobiose in the biphasic solvent system zinc chloride hydrate (ionic liquid)/anisole. Here, furyl hydroxymethyl ketone and furfural are obtained as major products, which are valuable but less commonly formed in high yields in transformations of cellulosic substrates. We explored this chemistry in small‐scale model reactions and applied the optimised methods to the conversion of cellulose in bench‐scale processes. The optimum reaction system and preferred reaction conditions are defined to select for highly desirable furanoid products in the highest known yields (up to 46 %) directly from cellulose or cellobiose. The method avoids the use of added catalysts: the ionic solvent zinc chloride hydrate possesses the intrinsic acidity required for the hydrolysis and chemical transformation steps. The process involves inexpensive media for the catalytic conversion of cellulose into high‐value products under mild processing conditions.
Bodachivskyi, I, Kuzhiumparambil, U & Williams, DBG 2019, 'Metal triflates are tunable acidic catalysts for high yielding conversion of cellulosic biomass into ethyl levulinate', Fuel Processing Technology, vol. 195, pp. 106159-106159.
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© 2019 Metal triflates and their mixtures with Brønsted acids are excellent catalysts for the selective and high yielding transformation of microcrystalline cellulose into ethyl levulinate, in ethanol, producing synergistic catalyst effects in some instances. The pretreatment of raw and unrefined cellulosic materials with a deep eutectic solvent enables similarly excellent catalysed conversion thereof into ethyl levulinate in superb yield (up to 75%) and selectivity (up to 88%). When using fermentation-derived ethanol, the product possesses 100% renewable content.
Bodachivskyi, I, Kuzhiumparambil, U & Williams, DBG 2019, 'The role of the molecular formula of ZnCl2·nH2O on its catalyst activity: a systematic study of zinc chloride hydrates in the catalytic valorisation of cellulosic biomass', Catalysis Science & Technology, vol. 9, no. 17, pp. 4693-4701.
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We show the efficient and direct transformation of a range of low value cellulosic substrates such as lignocellulose and algal biomass, into higher value chemicals, including low molecular weight reducing saccharides and furanoid products.
Bojer, MS, Wacnik, K, Kjelgaard, P, Gallay, C, Bottomley, AL, Cohn, MT, Lindahl, G, Frees, D, Veening, J, Foster, SJ & Ingmer, H 2019, 'SosA inhibits cell division in Staphylococcus aureus in response to DNA damage', Molecular Microbiology, vol. 112, no. 4, pp. 1116-1130.
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SummaryInhibition of cell division is critical for viability under DNA‐damaging conditions. DNA damage induces the SOS response that in bacteria inhibits cell division while repairs are being made. In coccoids, such as the human pathogen, Staphylococcus aureus, this process remains poorly studied. Here, we identify SosA as the staphylococcal SOS‐induced cell division inhibitor. Overproduction of SosA inhibits cell division, while sosA inactivation sensitizes cells to genotoxic stress. SosA is a small, predicted membrane protein with an extracellular C‐terminal domain in which point mutation of residues that are conserved in staphylococci and major truncations abolished the inhibitory activity. In contrast, a minor truncation led to SosA accumulation and a strong cell division inhibitory activity, phenotypically similar to expression of wild‐type SosA in a CtpA membrane protease mutant. This suggests that the extracellular C‐terminus of SosA is required both for cell division inhibition and for turnover of the protein. Microscopy analysis revealed that SosA halts cell division and synchronizes the cell population at a point where division proteins such as FtsZ and EzrA are localized at midcell, and the septum formation is initiated but unable to progress to closure. Thus, our findings show that SosA is central in cell division regulation in staphylococci.
Bonnin, L, Robbins, WD, Boussarie, G, Kiszka, JJ, Dagorn, L, Mouillot, D & Vigliola, L 2019, 'Repeated long-range migrations of adult males in a common Indo-Pacific reef shark', Coral Reefs, vol. 38, no. 6, pp. 1121-1132.
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© 2019, Springer-Verlag GmbH Germany, part of Springer Nature. The grey reef shark, Carcharhinus amblyrhynchos, is one of the most abundant coral reef sharks throughout the Indo-Pacific. However, this species has been critically impacted across its range, with well-documented population declines of > 90% attributed to human activities. A key knowledge gap in the successful implementation of grey reef shark conservation plans is the understanding of large-scale movement patterns, along with the associated biological and ecological drivers. To address this shortfall, we acoustically monitored 147 adult and juvenile grey reef sharks of all sexes for more than 2 yr across the New Caledonian archipelago, West Pacific. Here, we document multiple adult males undertaking return journeys of up to nearly 700 km in consecutive years. This constitutes the first evidence of repeated long-range migrations for this species. Although only a limited number of adult males were definitively tracked undertaking migrations, similar timing in changes in the detection patterns of a further 13 animals, mostly adult males, suggests this behavior may be more common than previously thought. The paucity of evidence for juvenile migrations and timing of adult movements suggest that mating is the motivation behind these migrations. Our results have important implications for management, given the potential of mature individuals to recurrently travel outside managed or protected areas. Future management of this species clearly needs to consider the importance of large-scale migratory behaviors when developing management plans.
Bonou, SAS, Sagbo, E, Aubry, C, Charvillat, C, Ben-Nissan, B & Cazalbou, S 2019, 'Conversion of snail shells (Achatina achatina) acclimatized in Benin to calcium phosphate for medical and engineering use', Journal of the Australian Ceramic Society, vol. 55, no. 4, pp. 1177-1186.
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Botté, ES, Nielsen, S, Abdul Wahab, MA, Webster, J, Robbins, S, Thomas, T & Webster, NS 2019, 'Changes in the metabolic potential of the sponge microbiome under ocean acidification', Nature Communications, vol. 10, no. 1.
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AbstractAnthropogenic CO2 emissions are causing ocean acidification, which can affect the physiology of marine organisms. Here we assess the possible effects of ocean acidification on the metabolic potential of sponge symbionts, inferred by metagenomic analyses of the microbiomes of two sponge species sampled at a shallow volcanic CO2 seep and a nearby control reef. When comparing microbial functions between the seep and control sites, the microbiome of the sponge Stylissa flabelliformis (which is more abundant at the control site) exhibits at the seep reduced potential for uptake of exogenous carbohydrates and amino acids, and for degradation of host-derived creatine, creatinine and taurine. The microbiome of Coelocarteria singaporensis (which is more abundant at the seep) exhibits reduced potential for carbohydrate import at the seep, but greater capacity for archaeal carbon fixation via the 3-hydroxypropionate/4-hydroxybutyrate pathway, as well as archaeal and bacterial urea production and ammonia assimilation from arginine and creatine catabolism. Together these metabolic features might contribute to enhanced tolerance of the sponge symbionts, and possibly their host, to ocean acidification.
Bouckaert, R, Vaughan, TG, Barido-Sottani, J, Duchêne, S, Fourment, M, Gavryushkina, A, Heled, J, Jones, G, Kühnert, D, De Maio, N, Matschiner, M, Mendes, FK, Müller, NF, Ogilvie, HA, du Plessis, L, Popinga, A, Rambaut, A, Rasmussen, D, Siveroni, I, Suchard, MA, Wu, C-H, Xie, D, Zhang, C, Stadler, T & Drummond, AJ 2019, 'BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis', PLOS Computational Biology, vol. 15, no. 4, pp. e1006650-e1006650.
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Elaboration of Bayesian phylogenetic inference methods has continued at pace in recent years with major new advances in nearly all aspects of the joint modelling of evolutionary data. It is increasingly appreciated that some evolutionary questions can only be adequately answered by combining evidence from multiple independent sources of data, including genome sequences, sampling dates, phenotypic data, radiocarbon dates, fossil occurrences, and biogeographic range information among others. Including all relevant data into a single joint model is very challenging both conceptually and computationally. Advanced computational software packages that allow robust development of compatible (sub-)models which can be composed into a full model hierarchy have played a key role in these developments. Developing such software frameworks is increasingly a major scientific activity in its own right, and comes with specific challenges, from practical software design, development and engineering challenges to statistical and conceptual modelling challenges. BEAST 2 is one such computational software platform, and was first announced over 4 years ago. Here we describe a series of major new developments in the BEAST 2 core platform and model hierarchy that have occurred since the first release of the software, culminating in the recent 2.5 release.
Bowman, S, McNevin, D, Venables, SJ, Roffey, P, Richardson, A & Gahan, ME 2019, 'Species identification using high resolution melting (HRM) analysis with random forest classification', Australian Journal of Forensic Sciences, vol. 51, no. 1, pp. 57-72.
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© 2017 Australian Academy of Forensic Sciences Species identification is an important facet of forensic investigation. In this study, human and non-human species (cow, chicken, pig, sheep, cat, dog, rabbit, fox, kangaroo and wombat) were assayed on the ViiA 7 Real-Time PCR System (Thermo Fisher Scientific) to rapidly screen for their species of origin using the high resolution melt (HRM) analysis targeting the 16S rRNA gene. Classification of HRM difference profiles using the onboard ViiA 7 software resulted in a classification accuracy of < 20%. Derivative profiles (temperature versus negative first derivative of fluorescence, –dF/dT) were classified using random forest algorithms supplemented by bagging and boosting, with either a randomly partitioned test set or a variety of folds of cross-classification, in addition to a range of trees and variables. Random forest classification with bagging conditions (constructed over 500 trees) was found to considerably outperform the ViiA 7 software for species differentiation with 100% classification accuracy for biological material from humans, domestic pets (cat and dog) and consumable meats (chicken and sheep) with an average classification accuracy of 70% across all species.
Bozier, J, Rutting, S, Xenaki, D, Peters, M, Adcock, I & Oliver, BG 2019, 'Heightened response to e-cigarettes in COPD', ERJ Open Research, vol. 5, no. 1, pp. 00192-2018.
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E-cigarettes induce greater inflammatory mediators from COPD lung cells; therefore, the risks of e-cigarette use in COPD might be greater than in people without COPD http://ow.ly/xmnN30nzDhX.
Bradac, C, Gao, W, Forneris, J, Trusheim, ME & Aharonovich, I 2019, 'Quantum nanophotonics with group IV defects in diamond', Nature Communications, vol. 10, no. 1.
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AbstractDiamond photonics is an ever-growing field of research driven by the prospects of harnessing diamond and its colour centres as suitable hardware for solid-state quantum applications. The last two decades have seen the field shaped by the nitrogen-vacancy (NV) centre with both breakthrough fundamental physics demonstrations and practical realizations. Recently however, an entire suite of other diamond defects has emerged—group IV colour centres—namely the Si-, Ge-, Sn- and Pb-vacancies. In this perspective, we highlight the leading techniques for engineering and characterizing these diamond defects, discuss the current state-of-the-art group IV-based devices and provide an outlook of the future directions the field is taking towards the realisation of solid-state quantum photonics with diamond.
Bradbury, P, Patel, BS, Cidem, A, Nader, CP, Oliver, BG & Ammit, AJ 2019, 'Prostaglandin E2, but not cAMP nor β2-agonists, induce tristetraprolin (TTP) in human airway smooth muscle cells', Inflammation Research, vol. 68, no. 5, pp. 369-377.
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Tristetraprolin (TTP) is an anti-inflammatory molecule known to post-transcriptionally regulate cytokine production and is, therefore, an attractive drug target for chronic respiratory diseases driven by inflammation, such as asthma and chronic obstructive pulmonary disease. Our recent in vitro studies in primary human airway smooth (ASM) cells have confirmed the essential anti-inflammatory role played by TTP as a critical partner in a cytokine regulatory network. However, several unanswered questions remain. While prior in vitro studies have suggested that TTP is regulated in a cAMP-mediated manner, raising the possibility that this may be one of the ways in which β2-agonists achieve beneficial effects beyond bronchodilation, the impact of β2-agonists on ASM cells is unknown. Furthermore, the effect of prostaglandin E2 (PGE2) on TTP expression in ASM cells has not been reported. We address this herein and reveal, for the first time, that TTP is not regulated by cAMP-activating agents nor following treatment with long-acting β2-agonists. However, PGE2 does induce TTP mRNA expression and protein upregulation in ASM cells. Although the underlying mechanism of action remains undefined, we can confirm that PGE2-induced TTP upregulation is not mediated via cAMP, or EP2/EP4 receptor activation, and occurred in a manner independent of the p38 MAPK-mediated pathway. Taken together, these data confirm that β2-agonists do not upregulate TTP in human ASM cells and indicate that another way in which PGE2 may achieve beneficial effects in asthma and COPD may be via upregulation of the master controller of inflammation-TTP.
Bradbury, P, Rumzhum, NN & Ammit, AJ 2019, 'EP2 and EP4 receptor antagonists: Impact on cytokine production and β2‐adrenergic receptor desensitization in human airway smooth muscle', Journal of Cellular Physiology, vol. 234, no. 7, pp. 11070-11077.
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AbstractProstaglandin E2 (PGE2) is a key prostanoid known to have both proinflammatory and anti‐inflammatory impact in the context of chronic respiratory diseases. We hypothesize that these opposing effects may be the result of different prostanoid E (EP) receptor‐mediated signaling pathways. In this study, we focus on two of the four EP receptors, EP2 and EP4, as they are known to induce cyclic adenosine monophosphate (cAMP)‐dependent signaling pathways. Using primary human airway smooth muscle (ASM) cells, we first focussed on the PGE2‐induced production of two cAMP‐dependent proinflammatory mediators: interleukin 6 (IL‐6) and cyclo‐oxygenase 2 production. We show that PGE2‐induced IL‐6 protein secretion occurs via an EP2‐mediated pathway, in a manner independent of receptor‐mediated effects on messenger RNA (mRNA) expression and temporal activation kinetics of the transcription factor cAMP response element binding. Moreover, stimulation of ASM with PGE2 did not establish a positive, receptor‐mediated, feedback loop, as mRNA expression for EP2 and EP4 receptors were not upregulated and receptor antagonists were without effect. Our studies revealed that the EP2, but not the EP4, receptor is responsible for β2‐adrenergic desensitization induced by PGE2. We demonstrate that PGE2‐induced heterologous receptor desensitization responsible for tachyphylaxis to short‐ (salbutamol) or long‐ (formoterol) β2‐agonists (measured by cAMP release) can be reversed by the EP2 receptor antagonist PF‐04418948. Importantly, this study highlights that inhibiting the EP2 receptor...
Bramucci, AR & Case, RJ 2019, 'Phaeobacter inhibens induces apoptosis-like programmed cell death in calcifying Emiliania huxleyi', Scientific Reports, vol. 9, no. 1.
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AbstractThe model coccolithophore,Emiliania huxleyi, forms expansive blooms dominated by the calcifying cell type, which produce calcite scales called coccoliths. Blooms last several weeks, after which the calcified algal cells rapidly die, descending into the deep ocean.E. huxleyibloom collapse is attributed toE. huxleyiviruses (EhVs) that infect and kill calcifying cells, while otherE. huxleyipathogens, such as bacteria belonging to the roseobacter clade, are overlooked. EhVs kill calcifyingE. huxleyiby inducing production of bioactive viral-glycosphingolipids (vGSLs), which trigger algal programmed cell death (PCD). The roseobacterPhaeobacter inhibenswas recently shown to interact with and kill the calcifying cell type ofE. huxleyi, but the mechanism of algal death remains unelucidated. Here we demonstrate thatP. inhibenskills calcifyingE. huxleyiby inducing a highly specific type of PCD called apoptosis-like-PCD (AL-PCD). Host death can successfully be abolished in the presence of a pan-caspase inhibitor, which prevents the activation of caspase-like molecules. This finding differentiatesP. inhibensand EhV pathogenesis ofE. huxleyi, by demonstrating that bacterial-induced AL-PCD requires active caspase-like molecules, while the viral pathogen does not. This is the first demonstration of a bacterium inducing AL-PCD in an algal host as a killing mechanism.
Bretherton, L, Poulton, AJ, Lawson, T, Rukminasari, N, Balestreri, C, Schroeder, D, Mark Moore, C & Suggett, DJ 2019, 'Day length as a key factor moderating the response of coccolithophore growth to elevated pCO2', Limnology and Oceanography, vol. 64, no. 3, pp. 1284-1296.
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AbstractThe fate of coccolithophores in the future oceans remains uncertain, in part due to key factors having not been standardized across experiments. A potentially moderating role for differences in day length (photoperiod) remains largely unexplored. We therefore cultured four different geographical isolates of the species Emiliania huxleyi, as well as two additional species, Gephyrocapsa oceanica (tropical) and Coccolithus braarudii (temperate), to test for interactive effects of pCO2 with the light : dark (L : D) cycle. We confirmed a general regulatory effect of photoperiod on the pCO2 response, whereby growth and particulate inorganic carbon and particulate organic carbon (PIC : POC) ratios were reduced with elevated pCO2 under 14 : 10 h L : D, but these reductions were dampened under continuous (24 h) light. The dynamics underpinning this pattern generally differed for the temperate vs. tropical isolates. Reductions in PIC : POC with elevated pCO2 for tropical taxa were largely through reduced calcification and enhanced photosynthesis under 14 : 10 h L : D, with differences dampened under continuous light. In contrast, reduced PIC : POC for temperate strains reflected increases of photosynthesis that outpaced increases in calcification rates under 14 : 10 h L : D, with both responses again dampened under continuous light. A multivariate analysis of 35 past studies of E. huxleyi further demonstrated that differences in photoperiod account for as much as 40% (strain B11/92) to 55% (strain NZEH) of the varian...
Brodersen, KE, Trevathan-Tackett, SM, Nielsen, DA, Connolly, RM, Lovelock, CE, Atwood, TB & Macreadie, PI 2019, 'Oxygen Consumption and Sulfate Reduction in Vegetated Coastal Habitats: Effects of Physical Disturbance', Frontiers in Marine Science, vol. 6, no. FEB.
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© 2019 Brodersen, Trevathan-Tackett, Nielsen, Connolly, Lovelock, Atwood and Macreadie. Vegetated coastal habitats (VCHs), such as mangrove forests, salt marshes and seagrass meadows, have the ability to capture and store carbon in the sediment for millennia, and thus have high potential for mitigating global carbon emissions. Carbon sequestration and storage is inherently linked to the geochemical conditions created by a variety of microbial metabolisms, where physical disturbance of sediments may expose previously anoxic sediment layers to oxygen (O 2 ), which could turn them into carbon sources instead of carbon sinks. Here, we used O 2 , hydrogen sulfide (H 2 S) and pH microsensors to determine how biogeochemical conditions, and thus aerobic and anaerobic metabolic pathways, vary across mangrove, salt marsh and seagrass sediments (case study from the Sydney area, Australia). We measured the biogeochemical conditions in the top 2.5 cm of surface (0-10 cm depth) and experimentally exposed deep sediments (> 50 cm depth) to simulate undisturbed and physically exposed sediments, respectively, and how these conditions may affect carbon cycling processes. Mangrove surface sediment exhibited the highest rates of O 2 consumption and sulfate (SO 42- ) reduction based on detailed microsensor measurements, with a diffusive O 2 uptake rate of 102 mmol O 2 m -2 d -1 and estimated sulfate reduction rate of 57 mmol S tot2- m -2 d -1 . Surface sediments (0-10 cm) across all the VCHs generally had higher O 2 consumption and estimated sulfate reduction rates than deeper layers (> 50 cm depth). O 2 penetration was < 4 mm for most sediments and only down to 1 mm depth in mangrove surface sediments, which correlated with a significantly higher percent organic carbon content (%C org ) within sediments originating from mangrove forests as compared to those from seagrass and salt marsh ecosystems. Additionally, pH dropped from 8.2 at the sediment/water interface to < 7-7.5 within th...
Brown, JJ, Sexton, C, Abbott, O & Smith, PA 2019, 'The framework for estimating coverage in the 2011 Census of England and Wales: Combining dual-system estimation with ratio estimation', Statistical Journal of the IAOS, vol. 35, no. 3, pp. 481-499.
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Dual-system estimation is a well-established approach for estimating an unknown population size from two independent but imperfect counts of the population. In this paper we develop the estimation framework for using a coverage survey and population census as the two sources and combining with ratio estimation to produce a set of population estimates. Adjustments are developed to correct for a failure of the key assumptions of homogeneity and independence that under-pin dual-system estimation using an external count of the number of households. The issue of over-count within the census is also discussed and a bootstrap approach to variance estimation is proposed. A comprehensive set of simulation results are presented to support the decision to implement the framework to estimate the population following the 2011 Census of England and Wales; and the implementation to the estimation of census coverage in 2011 is discussed.
Brown, P, Tan, A-C, El-Esawi, MA, Liehr, T, Blanck, O, Gladue, DP, Almeida, GMF, Cernava, T, Sorzano, CO, Yeung, AWK, Engel, MS, Chandrasekaran, AR, Muth, T, Staege, MS, Daulatabad, SV, Widera, D, Zhang, J, Meule, A, Honjo, K, Pourret, O, Yin, C-C, Zhang, Z, Cascella, M, Flegel, WA, Goodyear, CS, van Raaij, MJ, Bukowy-Bieryllo, Z, Campana, LG, Kurniawan, NA, Lalaouna, D, Hüttner, FJ, Ammerman, BA, Ehret, F, Cobine, PA, Tan, E-C, Han, H, Xia, W, McCrum, C, Dings, RPM, Marinello, F, Nilsson, H, Nixon, B, Voskarides, K, Yang, L, Costa, VD, Bengtsson-Palme, J, Bradshaw, W, Grimm, DG, Kumar, N, Martis, E, Prieto, D, Sabnis, SC, Amer, SEDR, Liew, AWC, Perco, P, Rahimi, F, Riva, G, Zhang, C, Devkota, HP, Ogami, K, Basharat, Z, Fierz, W, Siebers, R, Tan, K-H, Boehme, KA, Brenneisen, P, Brown, JAL, Dalrymple, BP, Harvey, DJ, Ng, G, Werten, S, Bleackley, M, Dai, Z, Dhariwal, R, Gelfer, Y, Hartmann, MD, Miotla, P, Tamaian, R, Govender, P, Gurney-Champion, OJ, Kauppila, JH, Zhang, X, Echeverría, N, Subhash, S, Sallmon, H, Tofani, M, Bae, T, Bosch, O, Cuív, PO, Danchin, A, Diouf, B, Eerola, T, Evangelou, E, Filipp, FV, Klump, H, Kurgan, L, Smith, SS, Terrier, O, Tuttle, N, Ascher, DB, Janga, SC, Schulte, LN, Becker, D, Browngardt, C, Bush, SJ, Gaullier, G, Ide, K, Meseko, C, Werner, GDA, Zaucha, J, Al-Farha, AA, Greenwald, NF, Popoola, SI, Rahman, MS, Xu, J, Yang, SY, Hiroi, N, Alper, OM, Baker, CI, Bitzer, M, Chacko, G, Debrabant, B, Dixon, R, Forano, E, Gilliham, M, Kelly, S, Klempnauer, K-H, Lidbury, BA, Lin, MZ, Lynch, I, Ma, W, Maibach, EW, Mather, DE, Nandakumar, KS, Ohgami, RS, Parchi, P, Tressoldi, P, Xue, Y, Armitage, C, Barraud, P, Chatzitheochari, S, Coelho, LP, Diao, J, Doxey, AC, Gobet, A, Hu, P, Kaiser, S, Mitchell, KM, Salama, MF, Shabalin, IG, Song, H, Stevanovic, D, Yadollahpour, A, Zeng, E, Zinke, K, Alimba, CG, Beyene, TJ, Cao, Z, Chan, SS, Gatchell, M, Kleppe, A, Piotrowski, M, Torga, G, Woldesemayat, AA, Cosacak, MI, Haston, S, Ross, SA, Williams, R, Wong, A, Abramowitz, MK, Effiong, A, Lee, S, Abid, MB, Agarabi, C, Alaux, C, Albrecht, DR, Atkins, GJ, Beck, CR, Bonvin, AMJJ, Bourke, E, Brand, T, Braun, RJ, Bull, JA, Cardoso, P, Carter, D, Delahay, RM, Ducommun, B, Duijf, PHG, Epp, T, Eskelinen, E-L, Fallah, M, Farber, DB, Fernandez-Triana, J, Feyerabend, F, Florio, T, Friebe, M, Furuta, S, Gabrielsen, M, Gruber, J, Grybos, M, Han, Q & et al. 2019, 'Large expert-curated database for benchmarking document similarity detection in biomedical literature search', Database, vol. 2019, pp. 1-66.
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Abstract
Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency–Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.
Bryant, C, Aleks Lau, KH, Vuckovic, S, Marsh-Wakefield, F, Kruzins, A, McGuire, H, Yang, S, Fazekas de St. Groth, B, Nassif, N, Byrne, SN, Gibson, J, Brown, C, Larsen, S, McCulloch, D, Boyle, R, Joshua, D & Ho, PJ 2019, 'Accumulation of CD69+ Terminal Effector CD8+ T cells occurs in the bone marrow of newly diagnosed Myeloma patients who lack protective clonal Vb expanded cytotoxic T cells', Clinical Lymphoma Myeloma and Leukemia, vol. 19, no. 10, pp. e29-e29.
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Buapet, P, Mohammadi, NS, Pernice, M, Kumar, M, Kuzhiumparambil, U & Ralph, PJ 2019, 'Excess copper promotes photoinhibition and modulates the expression of antioxidant-related genes in Zostera muelleri', Aquatic Toxicology, vol. 207, pp. 91-100.
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Budden, KF, Shukla, SD, Rehman, SF, Bowerman, KL, Keely, S, Hugenholtz, P, Armstrong-James, DPH, Adcock, IM, Chotirmall, SH, Chung, KF & Hansbro, PM 2019, 'Functional effects of the microbiota in chronic respiratory disease', The Lancet Respiratory Medicine, vol. 7, no. 10, pp. 907-920.
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The composition of the lung microbiome is increasingly well characterised, with changes in microbial diversity or abundance observed in association with several chronic respiratory diseases such as asthma, cystic fibrosis, bronchiectasis, and chronic obstructive pulmonary disease. However, the precise effects of the microbiome on pulmonary health and the functional mechanisms by which it regulates host immunity are only now beginning to be elucidated. Bacteria, viruses, and fungi from both the upper and lower respiratory tract produce structural ligands and metabolites that interact with the host and alter the development and progression of chronic respiratory diseases. Here, we review recent advances in our understanding of the composition of the lung microbiome, including the virome and mycobiome, the mechanisms by which these microbes interact with host immunity, and their functional effects on the pathogenesis, exacerbations, and comorbidities of chronic respiratory diseases. We also describe the present understanding of how respiratory microbiota can influence the efficacy of common therapies for chronic respiratory disease, and the potential of manipulation of the microbiome as a therapeutic strategy. Finally, we highlight some of the limitations in the field and propose how these could be addressed in future research.
Buis, R, Rust, L, Nizio, KD, Rai, T, Stuart, BH & Forbes, SL 2019, 'Investigating the Sensitivity of Cadaver- Detection Dogs to Aged, Diluted Decomposition Fluid', Journal of Forensic Identification, vol. 69, no. 3, pp. 367-377.
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Cadaver-detection dogs (also known as human remains detection dogs) are used worldwide to locate deceased victims and human remains. Ethical restrictions often prevent the dog handlers from using cadavers as training aids, resulting in a reliance on pseudo-scents or human tissues, such as blood, bone, and decomposition fluid. Often these aids must be re-used many times because of the difficulty in obtaining new materials. The aim of this study was to investigate the dogs' sensitivity to aged human decomposition fluid samples that are used as a training aid. Human decomposition fluid was collected and serially diluted to 1 part-per-trillion (10u) and aged up to two years. The samples were presented throughout the aging process to three police accredited cadaver-detectior. dog teams under standard indoor training conditions. The dogs were capable of detecting the oldest and lowest dilution levels of decomposition fluid samples. Ongoing training to retain this level of sensitivity is recommended. The results of these trials indicate human decomposition fluid is a valid training aid for cadaver-detection dogs.
Butcher, EV, van Oorschot, RAH, Morgan, RM & Meakin, GE 2019, 'Opportunistic crimes: Evaluation of DNA from regularly-used knives after a brief use by a different person', Forensic Science International: Genetics, vol. 42, pp. 135-140.
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When evaluating trace DNA recovered from evidential items in forensic casework, it is crucial to consider how the DNA got there, and such evaluative interpretations should ideally be informed by published experimental data. A key activity-level question is whether the DNA obtained comes from the regular user, the last user (ostensibly the user at the time of the crime) or from indirect transfer events. The aim of this experiment was to provide data to contribute to answering this question, particularly when considering opportunistic crimes, in which an offender might grab the nearest item at hand required for their purpose, e.g. a weapon or tool, and therefore only handle it very briefly. Volunteers ('regular users') used knives in a prescribed manner to simulate regular use (one user per knife); DNA recovery by mini-tapes from these knives gave ˜1-10 ng DNA, with <16% non-donor DNA from indirect transfer events. Different volunteers ('second users') then stabbed replicate sets of regularly-used knives into a foam block for either 2, 30 or 60 s (on different occasions), with each timeframe in triplicate, and DNA was recovered from the knife handles using mini-tapes. For knives regularly-used by three of the four volunteers, the ratios of regular user to second user DNA were approximately 4:1, 2:1 and 1:1 for durations of use by the second user of 2, 30 and 60 s, respectively. Analysis of the respective quantities of DNA showed that this trend resulted from a decrease in regular user DNA via transfer to the second user's hands, rather than an increase in DNA deposition from the second user. However, for knives regularly-used by the fourth volunteer, DNA from the regular user remained at significantly higher quantities than DNA from the second user and unknown sources, irrespective of duration of use by the second user. Furthermore, one volunteer deposited a similar amount of DNA through regular use as the amount of indirectly-transferred unknown DNA deposited by a...
Butterworth, NJ, Byrne, PG & Wallman, JF 2019, 'The Blow Fly Waltz: Field and Laboratory Observations of Novel and Complex Dipteran Courtship Behavior', Journal of Insect Behavior, vol. 32, no. 2, pp. 109-119.
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© 2019, Springer Science+Business Media, LLC, part of Springer Nature. Complex courtship has been well documented in the Diptera. However, studies have focused on a limited number of taxa and mostly using lab populations, where behavior can differ substantially compared to nature. To broaden our understanding of dipteran courtship, studies are required in a wider range of species, across both wild and captive populations. The blow flies (Diptera: Calliphoridae) include some of the most commonly encountered flies, yet courtship has been documented in less than 1% of species and is reported to be brief and simple throughout the family. To further investigate blow fly courtship, and to assess the effect of captivity on behavior, this study aimed to document the courtship of a habitat specialist that is endemic to Australasia, Chrysomya flavifrons. Video footage of wild and captive groups was recorded and analyzed using behavioral analysis software. The specific aims were 1) to quantify the behavioral sequences that constitute courtship and 2) to compare courtship between wild and captive flies. We found that the courtship behavior of Ch. flavifrons was complex and stereotyped, consisting of five discrete behaviors, which starkly contrasts with the simple courtship observed in most calliphorids. All of these stereotyped behaviors were observed in both wild and captive groups. However, the proportion of time males spent on these behaviors differed substantially. These findings highlight that blow fly courtship behavior may be more complex than currently perceived, and that careful consideration should be given to the influence of the laboratory environment in future studies of fly behavior.
Calarco, L & Ellis, J 2019, 'Annotating the ‘hypothetical’ in hypothetical proteins: In-silico analysis of uncharacterised proteins for the Apicomplexan parasite, Neospora caninum', Veterinary Parasitology, vol. 265, pp. 29-37.
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Neospora caninum is a parasite of veterinary and economic importance, affecting beef and dairy cattle industries globally. While this species has been recognised as a serious cause of disease in cattle and dogs for over 30 years, treatment and control options are still not available. Furthermore, whilst vaccination was identified as the most economic control strategy, vaccine discovery programs require new leads to investigate as vaccines. The current lack of gene annotation available for N. caninum, especially compared to the closely related model organism, Toxoplasma gondii, considerably hinders vaccine related research. Moreover, due to the high degree of similarity between the two organisms, a significant amount of gene annotation available for N. caninum stems from sequence homology between the species. However, there is a plethora of literature identifying conserved virulence factors between members of the Apicomplexa, which suggests that key players are contributing to successful parasite invasion, motility, and host cell attachment. In this study, bioinformatic approaches classified 125 uncharacterised proteins within the N. caninum genome, as transmembrane proteins with signal peptide sequences. Functional annotation assigned enriched gene ontologies for cell-adhesion, ATP binding, protein serine/threonine phosphatase complex, immune system process, antigen binding, and proteolysis. Additionally, 32 of these proteins were also identified as adhesins, or having adhesin-like properties, which were further characterised through the discovery of domains and gene ontology, to reveal their potential functional significance as virulence factors for N. caninum. This study identifies a new, small subset of proteins within N. caninum, that may be involved in host-cell interaction, parasite adhesion, and invasion, thereby implicating them as potential targets to exploit in the development of control options against the disease.
Caldwell, JD, Aharonovich, I, Cassabois, G, Edgar, JH, Gil, B & Basov, DN 2019, 'Photonics with hexagonal boron nitride', Nature Reviews Materials, vol. 4, no. 8, pp. 552-567.
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© 2019, Springer Nature Limited. For more than seven decades, hexagonal boron nitride (hBN) has been employed as an inert, thermally stable engineering ceramic; since 2010, it has also been used as the optimal substrate for graphene in nanoelectronic and optoelectronic devices. Recent research has revealed that hBN exhibits a unique combination of optical properties that enable novel (nano)photonic functionalities. Specifically, hBN is a natural hyperbolic material in the mid-IR range, in which photonic material options are sparse. Furthermore, hBN hosts defects that can be engineered to obtain room-temperature, single-photon emission; exhibits strong second-order nonlinearities with broad implications for practical devices; and is a wide-bandgap semiconductor well suited for deep UV emitters and detectors. Inspired by these promising attributes, research on the properties of hBN and the development of large-area bulk and thin-film growth techniques has dramatically expanded. This Review offers a snapshot of current research exploring the properties underlying the use of hBN for future photonics functionalities and potential applications, and covers some of the remaining obstacles.
CAMERON, G, Loering, S, Deshpande, A, Jiang, S, Molofsky, A, McKenzie, A, Hansbro, P & Starkey, M 2019, 'SAT-129 GROUP 2 INNATE LYMPHOID CELLS ARE REDUNDANT IN EXPERIMENTAL RENAL ISCHEMIA-REPERFUSION INJURY', Kidney International Reports, vol. 4, no. 7, pp. S59-S59.
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Cameron, GJM, Cautivo, KM, Loering, S, Jiang, SH, Deshpande, AV, Foster, PS, McKenzie, ANJ, Molofsky, AB, Hansbro, PM & Starkey, MR 2019, 'Group 2 Innate Lymphoid Cells Are Redundant in Experimental Renal Ischemia-Reperfusion Injury', Frontiers in Immunology, vol. 10, no. Mar.
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Acute kidney injury (AKI) can be fatal and is a well-defined risk factor for the development of chronic kidney disease. Group 2 innate lymphoid cells (ILC2s) are innate producers of type-2 cytokines and are critical regulators of homeostasis in peripheral organs. However, our knowledge of their function in the kidney is relatively limited. Recent evidence suggests that increasing ILC2 numbers by systemic administration of recombinant interleukin (IL)-25 or IL-33 protects against renal injury. Whilst ILC2s can be induced to protect against ischemic- or chemical-induced AKI, the impact of ILC2 deficiency or depletion on the severity of renal injury is unknown. Firstly, the phenotype and location of ILC2s in the kidney was assessed under homeostatic conditions. Kidney ILC2s constitutively expressed high levels of IL-5 and were located in close proximity to the renal vasculature. To test the functional role of ILC2s in the kidney, an experimental model of renal ischemia-reperfusion injury (IRI) was used and the severity of injury was assessed in wild-type, ILC2-reduced, ILC2-deficient, and ILC2-depleted mice. Surprisingly, there were no differences in histopathology, collagen deposition or mRNA expression of injury-associated (Lcn2), inflammatory (Cxcl1, Cxcl2, and Tnf) or extracellular matrix (Col1a1, Fn1) factors following IRI in the absence of ILC2s. These data suggest the absence of ILC2s does not alter the severity of renal injury, suggesting possible redundancy. Therefore, other mechanisms of type 2-mediated immune cell activation likely compensate in the absence of ILC2s. Hence, a loss of ILC2s is unlikely to increase susceptibility to, or severity of AKI.
Cameron, GJM, Jiang, SH, Loering, S, Deshpande, AV, Hansbro, PM & Starkey, MR 2019, 'Emerging therapeutic potential of group 2 innate lymphoid cells in acute kidney injury', The Journal of Pathology, vol. 248, no. 1, pp. 9-15.
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AbstractAcute kidney injury (AKI) remains a global challenge and, despite the availability of dialysis and transplantation, can be fatal. Those that survive an AKI are at increased risk of developing chronic kidney disease and end stage renal failure. Understanding the fundamental mechanisms underpinning the pathophysiology of AKI is critical for developing novel strategies for diagnosis and treatment. A growing body of evidence indicates that amplifying type 2 immunity may have therapeutic potential in kidney injury and disease. Of particular interest are the recently described subset of innate immune cells, termed group 2 innate lymphoid cells (ILCs). Group 2 ILCs are crucial tissue‐resident immune cells that maintain homeostasis and regulate tissue repair at multiple organ sites, including the kidney. They are critical mediators of type 2 immune responses following infection and injury. The existing literature suggests that activation of group 2 ILCs and production of a local type 2 immune milieu is protective against renal injury and associated pathology. In this review, we describe the emerging role for group 2 ILCs in renal homeostasis and repair. We provide an in‐depth discussion of the most recent literature that use preclinical models of AKI and assess the therapeutic effect of modulating group 2 ILC function. We debate the potential for targeting these cells as novel cellular therapies in AKI and discuss the implications for future studies and translation. Copyright © 2019 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Camp, EF, Edmondson, J, Doheny, A, Rumney, J, Grima, AJ, Huete, A & Suggett, DJ 2019, 'Mangrove lagoons of the Great Barrier Reef support coral populations persisting under extreme environmental conditions', Marine Ecology Progress Series, vol. 625, pp. 1-14.
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© The authors 2019. Global degradation of coral reefs has increased the urgency of identifying stress-tolerant coral populations, to enhance understanding of the biology driving stress tolerance, as well as identifying stocks of stress-hardened populations to aid reef rehabilitation. Surprisingly, scientists are continually discovering that naturally extreme environments house established coral populations adapted to grow within extreme abiotic conditions comparable to seawater conditions predicted over the coming century. Such environments include inshore mangrove lagoons that carry previously unrecognised ecosystem service value for corals, spanning from refuge to stress preconditioning. However, the existence of such hot-spots of resilience on the Great Barrier Reef (GBR) remains entirely unknown. Here we describe, for the first time, 2 extreme GBR mangrove lagoons (Woody Isles and Howick Island), exposing taxonomically diverse coral communities (34 species, 7 growth morphologies) to regular extreme low pH (<7.6), low oxygen (<1 mg l−1) and highly variable temperature range (>7°C) conditions. Coral cover was typically low (<5%), but highly patchy and included established colonies (>0.5 m diameter), with net photosynthesis and calcification rates of 2 dominant coral species (Acropora millepora, Porites lutea) reduced (20−30%), and respiration enhanced (11−35%), in the mangrove lagoon relative to adjacent reefs. Further analysis revealed that physiological plasticity (photosynthetic ‘strategy’) and flexibility of Symbiodiniaceae taxa associations appear crucial in supporting coral capacity to thrive from reef to lagoon. Prevalence of corals within these extreme conditions on the GBR (and elsewhere) increasingly challenge our understanding of coral resilience to stressors, and highlight the need to study unfavourable coral environments to better resolve mechanisms of stress tolerance.
Canonico, G, Buttigieg, PL, Montes, E, Muller-Karger, FE, Stepien, C, Wright, D, Benson, A, Helmuth, B, Costello, M, Sousa-Pinto, I, Saeedi, H, Newton, J, Appeltans, W, Bednaršek, N, Bodrossy, L, Best, BD, Brandt, A, Goodwin, KD, Iken, K, Marques, AC, Miloslavich, P, Ostrowski, M, Turner, W, Achterberg, EP, Barry, T, Defeo, O, Bigatti, G, Henry, L-A, Ramiro-Sánchez, B, Durán, P, Morato, T, Roberts, JM, García-Alegre, A, Cuadrado, MS & Murton, B 2019, 'Global Observational Needs and Resources for Marine Biodiversity', Frontiers in Marine Science, vol. 6, no. JUL.
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The diversity of life in the sea is critical to the health of ocean ecosystems that support living resources and therefore essential to the economic, nutritional, recreational, and health needs of billions of people. Yet there is evidence that the biodiversity of many marine habitats is being altered in response to a changing climate and human activity. Understanding this change, and forecasting where changes are likely to occur, requires monitoring of organism diversity, distribution, abundance, and health. It requires a minimum of measurements including productivity and ecosystem function, species composition, allelic diversity, and genetic expression. These observations need to be complemented with metrics of environmental change and socio-economic drivers. However, existing global ocean observing infrastructure and programs often do not explicitly consider observations of marine biodiversity and associated processes. Much effort has focused on physical, chemical and some biogeochemical measurements. Broad partnerships, shared approaches, and best practices are now being organized to implement an integrated observing system that serves information to resource managers and decision-makers, scientists and educators, from local to global scales. This integrated observing system of ocean life is now possible due to recent developments among satellite, airborne, and in situ sensors in conjunction with increases in information system capability and capacity, along with an improved understanding of marine processes represented in new physical, biogeochemical, and biological models.
Cao, J, Soiaporn, K, Carroll, RJ & Ruppert, D 2019, 'Modeling and Prediction of Multiple Correlated Functional Outcomes', Journal of Agricultural, Biological and Environmental Statistics, vol. 24, no. 1, pp. 112-129.
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We propose a copula-based approach for analyzing functional data with correlated multiple functional outcomes exhibiting heterogeneous shape characteristics. To accommodate the possibly large number of parameters due to having several functional outcomes, parameter estimation is performed in two steps: first, the parameters for the marginal distributions are estimated using the skew t family, and then the dependence structure both within and across outcomes is estimated using a Gaussian copula. We develop an estimation algorithm for the dependence parameters based on the Karhunen-Loève expansion and an EM algorithm that significantly reduces the dimension of the problem and is computationally efficient. We also demonstrate prediction of an unknown outcome when the other outcomes are known. We apply our methodology to diffusion tensor imaging data for multiple sclerosis (MS) patients with three outcomes and identify differences in both the marginal distributions and the dependence structure between the MS and control groups. Our proposed methodology is quite general and can be applied to other functional data with multiple outcomes in biology and other fields.
Cao, M, Ellis, JT, Marriott, D, Harkness, J & Stark, D 2019, 'Evaluation of the EasyScreen Protozoan Detection Kit for the diagnosis of Entamoeba histolytica', Pathology, vol. 51, no. 4, pp. 426-428.
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Cao, Y, Wang, L, Wang, C, Su, D, Liu, Y & Hu, X 2019, 'Photoelectrochemical determination of malathion by using CuO modified with a metal-organic framework of type Cu-BTC', Microchimica Acta, vol. 186, no. 7.
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A photoelectrochemical (PEC) sensor was constructed for the detection of non-electroactive malathion. It is based on the use of a hierarchical CuO material derived from a Cu-BTC metal-organic framework (where BTC stands for benzene-1,3,5-tricarboxylic acid). The modified CuO was obtained by calcination of Cu-BTC at a high temperature (300 °C) and possesses a high photocurrent conversion efficiency. Under irradiation with visible light and in the presence of malathion, the formation of the CuO-malathion complex on the CuO gave rise to an increase in steric hindrance. This results in a decrease in photocurrent. This novel PEC detection method has a lower detection limit of 8.6 × 10-11 mol L-1 and a wide linear range (1.0 × 10-10 ~ 1.0 × 10-5 mol L-1). Graphical abstract Schematic presentation of the Cu-BTC MOF derived photoelectrochemical sensor for non-electroactive malathion detection.
Caramori, G, Ruggeri, P, Mumby, S, Ieni, A, Lo Bello, F, Chimankar, V, Donovan, C, Andò, F, Nucera, F, Coppolino, I, Tuccari, G, Hansbro, PM & Adcock, IM 2019, 'Molecular links between COPD and lung cancer: new targets for drug discovery?', Expert Opinion on Therapeutic Targets, vol. 23, no. 6, pp. 539-553.
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INTRODUCTION:COPD and lung cancer are leading causes of morbidity and mortality worldwide, and they share a common environmental risk factor in cigarette smoke exposure and a genetic predisposition represented by their incidence in only a fraction of smokers. This reflects the ability of cigarette smoke to induce an inflammatory response in the airways of susceptible smokers. Moreover, COPD could be a driving factor in lung cancer, by increasing oxidative stress and the resulting DNA damage and repression of the DNA repair mechanisms, chronic exposure to pro-inflammatory cytokines, repression of innate immunity and increased cellular proliferation. Areas covered: We have focused our review on the potential pathogenic molecular links between tobacco smoking-related COPD and lung cancer and the potential molecular targets for new drug development by understanding the common signaling pathways involved in COPD and lung cancer. Expert commentary: Research in this field is mostly limited to animal models or small clinical trials. Large clinical trials are needed but mostly combined models of COPD and lung cancer are necessary to investigate the processes caused by chronic inflammation, including genetic and epigenetic alteration, and the expression of inflammatory mediators that link COPD and lung cancer, to identify new molecular therapeutic targets.
Cardona, T, Sánchez‐Baracaldo, P, Rutherford, AW & Larkum, AW 2019, 'Early Archean origin of Photosystem II', Geobiology, vol. 17, no. 2, pp. 127-150.
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AbstractPhotosystem II is a photochemical reaction center that catalyzes the light‐driven oxidation of water to molecular oxygen. Water oxidation is the distinctive photochemical reaction that permitted the evolution of oxygenic photosynthesis and the eventual rise of eukaryotes. At what point during the history of life an ancestral photosystem evolved the capacity to oxidize water still remains unknown. Here, we study the evolution of the core reaction center proteins of Photosystem II using sequence and structural comparisons in combination with Bayesian relaxed molecular clocks. Our results indicate that a homodimeric photosystem with sufficient oxidizing power to split water had already appeared in the early Archean about a billion years before the most recent common ancestor of all described Cyanobacteria capable of oxygenic photosynthesis, and well before the diversification of some of the known groups of anoxygenic photosynthetic bacteria. Based on a structural and functional rationale, we hypothesize that this early Archean photosystem was capable of water oxidation to oxygen and had already evolved protection mechanisms against the formation of reactive oxygen species. This would place primordial forms of oxygenic photosynthesis at a very early stage in the evolutionary history of life.
Cardoso, BR, Roberts, BR, Malpas, CB, Vivash, L, Genc, S, Saling, MM, Desmond, P, Steward, C, Hicks, RJ, Callahan, J, Brodtmann, A, Collins, S, Macfarlane, S, Corcoran, NM, Hovens, CM, Velakoulis, D, O’Brien, TJ, Hare, DJ & Bush, AI 2019, 'Supranutritional Sodium Selenate Supplementation Delivers Selenium to the Central Nervous System: Results from a Randomized Controlled Pilot Trial in Alzheimer’s Disease', Neurotherapeutics, vol. 16, no. 1, pp. 192-202.
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Insufficient supply of selenium to antioxidant enzymes in the brain may contribute to Alzheimer's disease (AD) pathophysiology; therefore, oral supplementation may potentially slow neurodegeneration. We examined selenium and selenoproteins in serum and cerebrospinal fluid (CSF) from a dual-dose 24-week randomized controlled trial of sodium selenate in AD patients, to assess tolerability, and efficacy of selenate in modulating selenium concentration in the central nervous system (CNS). A pilot study of 40 AD cases was randomized to placebo, nutritional (0.32 mg sodium selenate, 3 times daily), or supranutritional (10 mg, 3 times daily) groups. We measured total selenium, selenoproteins, and inorganic selenium levels, in serum and CSF, and compared against cognitive outcomes. Supranutritional selenium supplementation was well tolerated and yielded a significant (p < 0.001) but variable (95% CI = 13.4-24.8 μg/L) increase in CSF selenium, distributed across selenoproteins and inorganic species. Reclassifying subjects as either responsive or non-responsive based on elevation in CSF selenium concentrations revealed that responsive group did not deteriorate in Mini-Mental Status Examination (MMSE) as non-responsive group (p = 0.03). Pooled analysis of all samples revealed that CSF selenium could predict change in MMSE performance (Spearman's rho = 0.403; p = 0.023). High-dose sodium selenate supplementation is well tolerated and can modulate CNS selenium concentration, although individual variation in selenium metabolism must be considered to optimize potential benefits in AD. The Vel002 study is listed on the Australian and New Zealand Clinical Trials Registry ( http://www.anzctr.org.au /), ID: ACTRN12611001200976.
Carney, RL, Labbate, M, Siboni, N, Tagg, KA, Mitrovic, SM & Seymour, JR 2019, 'Urban beaches are environmental hotspots for antibiotic resistance following rainfall', Water Research, vol. 167, pp. 115081-115081.
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To reveal the occurrence and mechanisms for dispersal of antibiotic resistance (AbR) among the microbial assemblages inhabiting impacted coastal environments, we performed a weekly, two-year duration time-series study at two urban beaches between 2014 and 2016. We combined quantitative PCR and multiplex PCR/reverse line blot techniques to track patterns in the occurrence of 31 AbR genes, including genes that confer resistance to antibiotics that are critically important antimicrobials for human medicine. Patterns in the abundance of these genes were linked to specific microbial groups and environmental parameters by coupling qPCR and 16S rRNA amplicon sequencing data with network analysis. Up to 100-fold increases in the abundance of several AbR genes, including genes conferring resistance to quinolones, trimethoprim, sulfonamides, tetracycline, vancomycin and carbapenems, occurred following storm-water and modelled wet-weather sewer overflow events. The abundance of AbR genes strongly and significantly correlated with several potentially pathogenic bacterial OTUs regularly associated with wastewater infrastructure, such as Arcobacter, Acinetobacter, Aeromonas and Cloacibacterium. These high-resolution observations provide clear links between storm-water discharge and sewer overflow events and the occurrence of AbR in the coastal microbial assemblages inhabiting urban beaches, highlighting a direct mechanism for potentially significant AbR exposure risks to humans.
Carter, A, Richards, LJ, Apthorp, D, Azghadi, MR, Badcock, DR, Balleine, B, Bekkers, JM, Berk, M, Bourne, JA, Bradley, AP, Breakspear, M, Brichta, A, Carter, O, Castles, A, Chakli, K, Cohen-Woods, S, Conn, SJ, Cornish, J, Cornish, K, de Zubicaray, G, Egan, GF, Enticott, PG, Fitzgibbon, BM, Forlini, C, Fornito, A, Griffiths, L, Gullifer, J, Hall, W, Halliday, G, Hannan, AJ, Harrer, S, Harvey, A, Hatherly, C, Hickie, IB, Kennett, J, Kiernan, M, Kilpatrick, T, Kiral-Kornek, I, Korgaonkar, MS, Lawrence, AJ, Leventer, R, Levy, N, Licinio, J, Lovell, N, Mackellar, G, Malcolm, L, Mason, A, Mattingley, JB, Medland, SE, Michie, PT, Nithianantharajah, J, Parker, J, Payne, JM, Poole-Warren, L, Sah, P, Sarnyai, Z, Schofield, PR, Shimoni, O, Shum, DHK, Silk, T, Slee, M, Smith, AE, Soulis, T, Sriram, S, Stuart, GJ, Tapson, J, Thompson, MB, van Schaik, A, Vincent, NA, Vissel, B & Waters, A 2019, 'A Neuroethics Framework for the Australian Brain Initiative', Neuron, vol. 101, no. 3, pp. 365-369.
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Casey, E, Ribaux, O & Roux, C 2019, 'The Kodak Syndrome: Risks and Opportunities Created by Decentralization of Forensic Capabilities', Journal of Forensic Sciences, vol. 64, no. 1, pp. 127-136.
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AbstractForensic science laboratories are being challenged by the expanding decentralization of forensic capabilities, particularly for digital traces. This study recommends laboratories undertake digital transformations to capitalize on the decentralization movement, develop a more comprehensive understanding of crime and security‐relevant problems, and play a more central role in problem‐solving collaboratively with law enforcement organizations and other stakeholders. A framework for the bilateral transfer of information and knowledge is proposed to magnify the impact of forensic science laboratories on abating crime, strengthening security, and reinforcing the criminal justice system. To accomplish digital transformations, laboratories require personnel with different expertise, including investigative reasoning, knowledge codification, data analytics, and forensic intelligence. Ultimately, this study encourages managers, educators, researchers, and policymakers to look beyond the usefulness of forensic results for solving individual investigations, and to realize the value of combined forensic knowledge and intelligence for developing broader strategies to deal with crime in digitalized society.
Castorina, A, Vogiatzis, M, Kang, JWM & Keay, KA 2019, 'PACAP and VIP expression in the periaqueductal grey of the rat following sciatic nerve constriction injury', Neuropeptides, vol. 74, pp. 60-69.
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Nerve injuries often result in neuropathic pain with co-morbid changes in social behaviours, motivation, sleep-wake cycles and neuroendocrine function. In an animal model of neuropathic injury (CCI) similar co-morbid changes are evoked in a subpopulation (~30%) of injured rats. In addition to anatomical evidence of altered neuronal and glial function, the periaqueductal grey (PAG) of these rats shows evidence of cell death. These changes in the PAG may play a role in the disruption of the normal emotional coping responses triggered by nerve injury. Cell death can occur via a number of mechanisms, including the disruption of neuroprotective mechanisms. Pituitary adenylate cyclase activating polypeptide (PACAP) and vasoactive intestinal peptide (VIP) are two endogenous neuropeptides whose activities are tightly regulated by two receptors subtypes, namely the PAC1 and VPAC receptors. These peptides and their receptors exert robust neuroprotective roles. In these studies, we hypothesized that rats expressing disabilities following CCI showed altered expression of PACAP and VIP in the PAG. Rats were categorized as having either Pain alone, Transient or Persistent disability, based on changes in social behaviours pre- and post-CCI. Social interaction behavioural tested (BT), sham-injured and naïve untested rats were also included. For measurements of mRNA and protein expression we utilised micro-dissected PAGs blocks taken from each group. At the mRNA level, VIP was downregulated and PAC1 was upregulated in BT animals, whilst VPAC1 mRNA was specifically increased in the Pain alone group. Interestingly, protein levels of both PACAP and VIP were remarkably increased in the Persistent Disability group. Taken together, sciatic nerve CCI that triggers neuropathic pain and persistent disability results in abnormally increased VIP and PACAP expression in the PAG. Our data also suggest that these effects are likely to be governed by post-transcriptional mechanisms.
Castrogiovanni, P, Di Rosa, M, Ravalli, S, Castorina, A, Guglielmino, C, Imbesi, R, Vecchio, M, Drago, F, Szychlinska, M & Musumeci, G 2019, 'Moderate Physical Activity as a Prevention Method for Knee Osteoarthritis and the Role of Synoviocytes as Biological Key', International Journal of Molecular Sciences, vol. 20, no. 3, pp. 511-511.
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The purpose of this study was to investigate the influence of moderate physical activity (MPA) on the expression of osteoarthritis (OA)-related (IL-1β, IL-6, TNF-α, MMP-13) and anti-inflammatory and chondroprotective (IL-4, IL-10, lubricin) biomarkers in the synovium of an OA-induced rat model. A total of 32 rats were divided into four groups: Control rats (Group 1); rats performing MPA (Group 2); anterior cruciate ligament transection (ACLT)-rats with OA (Group 3); and, ACLT-rats performing MPA (Group 4). Analyses were performed using Hematoxylin & Eosin (H&E) staining, histomorphometry and immunohistochemistry. In Group 3, OA biomarkers were significantly increased, whereas, IL-4, IL-10, and lubricin were significantly lower than in the other experimental groups. We hypothesize that MPA might partake in rescuing type B synoviocyte dysfunction at the early stages of OA, delaying the progression of the disease.
Chahwan, B, Kwan, S, Isik, A, van Hemert, S, Burke, C & Roberts, L 2019, 'Gut feelings: A randomised, triple-blind, placebo-controlled trial of probiotics for depressive symptoms', Journal of Affective Disorders, vol. 253, pp. 317-326.
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BACKGROUND:Depression is the leading cause of disability worldwide; with evidence suggesting that decreased gut barrier function and inflammation are correlated with depressive symptoms. We conducted a clinical trial to determine the effect of consumption of probiotic supplements (Winclove's Ecologic® Barrier) on depressive symptoms in a sample of participants with mild to severe depression. METHOD:71 participants were randomly allocated to either probiotic or placebo, which was, consumed daily over eight weeks. Pre- and post-intervention measures of symptoms and vulnerability markers of depression as well as gut microbiota composition were compared. Clinical trial participants were also compared on psychological variables and gut microbiota composition to a non-depressed group (n = 20). RESULTS:All clinical trial participants demonstrated improvement in symptoms, suggesting non-specific therapeutic effects associated with weekly monitoring visits. Participants in the probiotic group demonstrated a significantly greater reduction in cognitive reactivity compared with the placebo group, particularly in the mild/moderate subgroup. Probiotics did not significantly alter the microbiota of depressed individuals, however, a significant correlation was found between Ruminococcus gnavus and one depression metric. LIMITATIONS:There was a high attrition rate, which may be attributed to weekly monitoring visits. Additionally, modulation of the gut microbiota may need more specific testing to distinguish subtle changes. CONCLUSIONS:While microbiota composition was similar between all groups, probiotics did affect a psychological variable associated with susceptibility to depression. Further research is needed to investigate how probiotics can be utilised to modify mental wellbeing, and whether they can act as an adjunct to existing treatments.
Chan, YL, Wang, B, Chen, H, Ho, KF, Cao, J, Hai, G, Jalaludin, B, Herbert, C, Thomas, PS, Saad, S & Oliver, BGG 2019, 'Pulmonary inflammation induced by low-dose particulate matter exposure in mice', American Journal of Physiology-Lung Cellular and Molecular Physiology, vol. 317, no. 3, pp. L424-L430.
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Air pollution is a ubiquitous problem and comprises gaseous and particulate matter (PM). Epidemiological studies have clearly shown that exposure to PM is associated with impaired lung function and the development of lung diseases, such as chronic obstructive pulmonary disease and asthma. To understand the mechanisms involved, animal models are often used. However, the majority of such models represent high levels of exposure and are not representative of the exposure levels in less polluted countries, such as Australia. Therefore, in this study, we aimed to determine whether low dose PM10 exposure has any detrimental effect on the lungs. Mice were intranasally exposed to saline or traffic-related PM10 (1μg or 5μg/day) for 3 wk. Bronchoalveolar lavage (BAL) and lung tissue were analyzed. PM10 at 1 μg did not significantly affect inflammatory and mitochondrial markers. At 5 μg, PM10 exposure increased lymphocytes and macrophages in BAL fluid. Increased NACHT, LRR and PYD domains-containing protein 3 (NLRP3) and IL-1β production occurred following PM10 exposure. PM10 (5 μg) exposure reduced mitochondrial antioxidant manganese superoxide (antioxidant defense system) and mitochondrial fusion marker (OPA-1), while it increased fission marker (Drp-1). Autophagy marker light-chain 3 microtubule-associated protein (LC3)-II and phosphorylated-AMPK were reduced, and apoptosis marker (caspase 3) was increased. No significant change of remodeling markers was observed. In conclusion, a subchronic low-level exposure to PM can have an adverse effect on lung health, which should be taken into consideration for the planning of roads and residential buildings.
Chellappan, DK, Sze Ning, QL, Su Min, SK, Bin, SY, Chern, PJ, Shi, TP, Ee Mei, SW, Yee, TH, Qi, OJ, Thangavelu, L, Rajeshkumar, S, Negi, P, Chellian, J, Wadhwa, R, Gupta, G, Collet, T, Hansbro, PM & Dua, K 2019, 'Interactions between microbiome and lungs: Paving new paths for microbiome based bio-engineered drug delivery systems in chronic respiratory diseases', Chemico-Biological Interactions, vol. 310, pp. 108732-108732.
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BACKGROUND:The human body is a home to thousands of microbiotas. It is defined as a community of symbiotic, commensal and pathogenic microorganisms that have existed in all exposed sites of the body, which have co-evolved with diet, lifestyle, genetic factors and immune factors. Human microbiotas have been studied for years on their effects with relation to health and diseases. METHODS:Relevant published studies, literature and reports were searched from accessible electronic databases and related institutional databases. We used keywords, viz; microbiome, microbiota, microbiome drug delivery and respiratory disease. Selected articles were carefully read through, clustered, segregated into subtopics and reviewed. FINDINGS:The traditional belief of sterile lungs was challenged by the emergence of culture-independent molecular techniques and the recently introduced invasive broncho-alveolar lavage (BAL) sampling method. The constitution of a lung microbiome mainly depends on three main ecological factors, which include; firstly, the immigration of microbes into airways, secondly, the removal of microbes from airways and lastly, the regional growth conditions. In healthy conditions, the microbial communities that co-exist in our lungs can build significant pulmonary immunity and could act as a barrier against diseases, whereas, in an adverse way, microbiomes may interact with other pathogenic bacteriomes and viromes, acting as a cofactor in inflammation and host immune responses, which may lead to the progression of a disease. Thus, the use of microbiota as a target, and as a drug delivery system in the possible modification of a disease state, has started to gain massive attention in recent years. Microbiota, owing to its unique characteristics, could serve as a potential drug delivery system, that could be bioengineered to suit the interest. The engineered microbiome-derived therapeutics can be delivered through BC, bacteriophage, bacteria-derived lipid vesicles a...
Chellappan, DK, Yee, NJ, Kaur Ambar Jeet Singh, BJ, Panneerselvam, J, Madheswaran, T, Chellian, J, Satija, S, Mehta, M, Gulati, M, Gupta, G & Dua, K 2019, 'Formulation and characterization of glibenclamide and quercetin-loaded chitosan nanogels targeting skin permeation', Therapeutic Delivery, vol. 10, no. 5, pp. 281-293.
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Aim: Our aim was to develop and characterize a nanogel formulation containing both glibenclamide and quercetin and to explore the permeation profile of this combination. Methods: Drug-loaded nanogel was prepared by ionic gelation. In addition, optimum encapsulation efficiencies of glibenclamide and quercetin were also obtained. The average nanoparticle size at optimum conditions was determined by Zetasizer. Results: The particle size of the nanogel was found to be 370.4 ± 4.78 nm with a polydispersity index of 0.528 ± 0.04, while the λ potential was positive in a range of 17.6 to 24.8 mV. The percentage cumulative drug release also showed favorable findings. Conclusion: The chitosan nanogel could be a potential alternative for delivering glibenclamide and quercetin through skin.
Chen, C, liu, Z & Jin, D 2019, 'Bypassing the limit in volumetric imaging of mesoscale specimens', Advanced Photonics, vol. 1, no. 02, pp. 1-1.
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Chen, C, Pistono, A, Ryan, S, Szkuta, B & Meakin, GE 2019, 'The effect of climatic simulations on DNA persistence on glass, cotton and polyester', Forensic Science International: Genetics Supplement Series, vol. 7, no. 1, pp. 274-276.
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© 2019 Elsevier B.V. It is important to understand the variables impacting DNA persistence when considering the recovery, and evaluative interpretation, of DNA evidence from crime scenes. Whilst it is known that temperature, humidity and UV affect DNA persistence, little research has been conducted to explore these effects in a combined and controlled manner. This study includes two experiments in which a climate chamber was used to simulate climatic conditions over a repeating 24-h period. Aliquots of ∼50 ng DNA were added to each substrate and DNA recovered at 0, 1, 3 and 7 days after deposition. Samples were run in triplicate, extracted and quantified. The first experiment investigated the effect of typical Southern English winter and summer days on DNA persistence on glass and cotton, with DNA being recovered by wet and dry swabs from glass and mini-tapes from cotton. The second experiment investigated the effect of typical Northern Italian winter and summer days on DNA persistence on cotton and polyester, with DNA being recovered by wet and moist swabs from both fabrics. Quantities of DNA on all substrates significantly declined over 7 days under summer conditions (p < 0.05), and more DNA tended to persist on the fabric substrates in both studies under conditions of winter than summer. These results contribute to our understanding of DNA persistence under different climatic conditions and will help inform investigators’ DNA recovery strategies.
Chen, C-H, Kung, H-Y & Hwang, F-J 2019, 'Deep Learning Techniques for Agronomy Applications', Agronomy, vol. 9, no. 3, pp. 142-142.
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This editorial introduces the Special Issue, entitled “Deep Learning (DL) Techniques for Agronomy Applications”, of Agronomy. Topics covered in this issue include three main parts: (I) DL-based image recognition techniques for agronomy applications, (II) DL-based time series data analysis techniques for agronomy applications, and (III) behavior and strategy analysis for agronomy applications. Three papers on DL-based image recognition techniques for agronomy applications are as follows: (1) “Automatic segmentation and counting of aphid nymphs on leaves using convolutional neural networks,” by Chen et al.; (2) “Estimating body condition score in dairy cows from depth images using convolutional neural networks, transfer learning, and model ensembling techniques,” by Alvarez et al.; and (3) “Development of a mushroom growth measurement system applying deep learning for image recognition,” by Lu et al. One paper on DL-based time series data analysis techniques for agronomy applications is as follows: “LSTM neural network based forecasting model for wheat production in Pakistan,” by Haider et al. One paper on behavior and strategy analysis for agronomy applications is as follows: “Research into the E-learning model of agriculture technology companies: analysis by deep learning,” by Lin et al.
Chen, D, Mu, Z, Zhou, Y, Fröch, JE, Rasmit, A, Diederichs, C, Zheludev, N, Aharonovich, I & Gao, W-B 2019, 'Optical Gating of Resonance Fluorescence from a Single Germanium Vacancy Color Center in Diamond', Physical Review Letters, vol. 123, no. 3.
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Scalable quantum photonic networks require coherent excitation of quantum emitters. However, many solid-state systems can undergo a transition to a dark shelving state that inhibits the resonance fluorescence. Here, we demonstrate that by a controlled gating using a weak nonresonant laser, the resonant fluorescence can be recovered and amplified for single germanium vacancies. Employing the gated resonance excitation, we achieve optically stable resonance fluorescence of germanium vacancy centers. Our results are pivotal for the deployment of diamond color centers as reliable building blocks for scalable solid-state quantum networks.
Chen, H & Lim, CED 2019, 'The efficacy of using acupuncture in managing polycystic ovarian syndrome', Current Opinion in Obstetrics & Gynecology, vol. 31, no. 6, pp. 428-432.
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Chen, H, Li, Y, Chen, Y, Li, Y, McGowan, E & Lin, Y 2019, 'Serglycin level in peripheral circulating blood cells has prognostic significance in patients with hepatocellular carcinoma', Annals of Oncology, vol. 30, pp. iv8-iv9.
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Chen, H, Steele, J, Li, G, Chan, Y, Oliver, B, Saad, S & Machaalani, R 2019, 'E-vapour inhalation – How does it affect memory?', IBRO Reports, vol. 6, pp. S208-S209.
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Chen, T, Liu, AB, Sun, S, Ajami, NJ, Ross, MC, Wang, H, Zhang, L, Reuhl, K, Kobayashi, K, Onishi, JC, Zhao, L & Yang, CS 2019, 'Green Tea Polyphenols Modify the Gut Microbiome in db/db Mice as Co‐Abundance Groups Correlating with the Blood Glucose Lowering Effect', Molecular Nutrition & Food Research, vol. 63, no. 8, pp. 1801064-1801064.
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ScopeThe effects of green tea polyphenols, Polyphenon E (PPE), and black tea polyphenols, theaflavins (TFs), on gut microbiota and development of diabetes in db/db mice are investigated and compared.Methods and resultsSupplementation of PPE (0.1%) in the diet of female db/db mice for 7 weeks decreases fasting blood glucose levels and mesenteric fat while increasing the serum level of insulin, possibly through protection against β‐cell damage. However, TFs are less or not effective. Microbiome analysis through 16S rRNA gene sequencing shows that PPE and TFs treatments significantly alter the bacterial community structure in the cecum and colon, but not in the ileum. The key bacterial phylotypes responding to the treatments are then clustered into 11 co‐abundance groups (CAGs). CAGs 6 and 7, significantly increased by PPE but not by TFs, are negatively associated with blood glucose levels. The operational taxonomic units in these CAGs are from two different phyla, Firmicutes and Bacteroidetes. CAG 10, decreased by PPE and TFs, is positively associated with blood glucose levels.ConclusionGut microbiota respond to tea polyphenol treatments as CAGs instead of taxa. Some of the CAGs associated with the blood glucose lowering effect are enriched by PPE, but not TFs.
Chen, X-X, Lin, X-Y, Wu, X, Gale, PA, Anslyn, EV & Jiang, Y-B 2019, 'Design of Chiral Supramolecular Polymers Exhibiting a Negative Nonlinear Response', The Journal of Organic Chemistry, vol. 84, no. 22, pp. 14587-14592.
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Chen, Y, Ju, LA, Zhou, F, Liao, J, Xue, L, Su, QP, Jin, D, Yuan, Y, Lu, H, Jackson, SP & Zhu, C 2019, 'An integrin αIIbβ3 intermediate affinity state mediates biomechanical platelet aggregation', Nature Materials, vol. 18, no. 7, pp. 760-769.
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Integrins are membrane receptors that mediate cell adhesion and mechanosensing. The structure-function relationship of integrins remains incompletely understood, despite the extensive studies carried out because of its importance to basic cell biology and translational medicine. Using a fluorescence dual biomembrane force probe, microfluidics and cone-and-plate rheometry, we applied precisely controlled mechanical stimulations to platelets and identified an intermediate state of integrin αIIbβ3 that is characterized by an ectodomain conformation, ligand affinity and bond lifetimes that are all intermediate between the well-known inactive and active states. This intermediate state is induced by ligand engagement of glycoprotein (GP) Ibα via a mechanosignalling pathway and potentiates the outside-in mechanosignalling of αIIbβ3 for further transition to the active state during integrin mechanical affinity maturation. Our work reveals distinct αIIbβ3 state transitions in response to biomechanical and biochemical stimuli, and identifies a role for the αIIbβ3 intermediate state in promoting biomechanical platelet aggregation.
Chen, Y, Toth, M & He, C 2019, 'Facile and fast fabrication of high structure-stable thin film nanocomposite membrane for potential application in solvent resistance nanofiltration', Applied Surface Science, vol. 496, pp. 143483-143483.
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Chen, Y, Zhang, W, Zhou, D, Tian, H, Su, D, Wang, C, Stockdale, D, Kang, F, Li, B & Wang, G 2019, 'Co–Fe Mixed Metal Phosphide Nanocubes with Highly Interconnected-Pore Architecture as an Efficient Polysulfide Mediator for Lithium–Sulfur Batteries', ACS Nano, vol. 13, no. 4, pp. 4731-4741.
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Lithium-sulfur (Li-S) batteries have been regarded as one of the most promising candidates for next-generation energy storage owing to their high energy density and low cost. However, the practical deployment of Li-S batteries has been largely impeded by the low conductivity of sulfur, the shuttle effect of polysulfides, and the low areal sulfur loading. Herein, we report the synthesis of uniform Co-Fe mixed metal phosphide (Co-Fe-P) nanocubes with highly interconnected-pore architecture to overcome the main bottlenecks of Li-S batteries. With the highly interconnected-pore architecture, inherently metallic conductivity, and polar characteristic, the Co-Fe-P nanocubes not only offer sufficient electrical contact to the insulating sulfur for high sulfur utilization and fast redox reaction kinetics but also provide abundant adsorption sites for trapping and catalyzing the conversion of lithium polysulfides to suppress the shuttle effect, which is verified by both the comprehensive experiments and density functional theory calculations. As a result, the sulfur-loaded Co-Fe-P (S@Co-Fe-P) nanocubes delivered a high discharge capacity of 1243 mAh g-1 at 0.1 C and excellent cycling stability for 500 cycles with an average capacity decay rate of only 0.043% per cycle at 1 C. Furthermore, the S@Co-Fe-P electrode showed a high areal capacity of 4.6 mAh cm-2 with superior stability when the sulfur loading was increased to 5.5 mg cm-2. More impressively, the prototype soft-package Li-S batteries based on S@Co-Fe-P cathodes also exhibited superior cycling stability with great flexibility, demonstrating their great potential for practical applications.
Cherk Yong, DO, Saker, SR, Wadhwa, R, Chellappan, DK, Madheswaran, T, Panneerselvam, J, Tambuwala, MM, Bakshi, HA, Kumar, P, Pillay, V, Gupta, G, Oliver, BG, Wark, P, Hsu, A, Hansbro, PM, Dua, K & Zeeshan, F 2019, 'Preparation, characterization and in-vitro efficacy of quercetin loaded liquid crystalline nanoparticles for the treatment of asthma', Journal of Drug Delivery Science and Technology, vol. 54, pp. 101297-101297.
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© 2019 Elsevier B.V. The present study aims to formulate quercetin loaded liquid crystalline nanoparticles (LCN) and surface modified liquid crystalline nanoparticles (sm-LCN) as well as investigate their anti-inflammatory activity in human primary bronchial epithelial cell line (BCi-NS1.1) induced with lipopolysaccharide (LPS). Quercetin LCN were prepared using ultrasonication method. The formulated LCNs and sm-LCNs were characterised in terms of particle size, zeta potential as well as the drug encapsulation efficiency. Furthermore, their morphology and in vitro release profile were also studied. In addition, the anti-inflammatory activity of quercetin LCN and sm-LCNs were evaluated by measuring the concentration of pro-inflammatory markers namely interleukin (IL)-1β, IL-6 and IL-8 in BCI-NS1.1 cell lines via cytometric bead array. The molecular mechanism inherent to the inclusion of quercetin into monoolein nanosystem and surface modification of the nanosystem with chitosan was elucidated via molecular mechanics simulations. Quercetin LCN and sm-LCN significantly (p < 0.05) decreased the production of IL-1β, IL-6 and IL-8 compared to LPS only group. Encapsulation of quercetin into LCN and sm-LCN further enhanced its anti-inflammatory activity compared to quercetin in dimethyl sulfoxide (DMSO). In addition to that, quercetin LCN and sm-LCN also exhibited comparable activity to fluticasone in terms of significantly (p < 0.05) reducing the production of IL-1β and IL-6. Quercetin loaded LCN and sm-LCN could be a potential therapeutic intervention for asthma as they are efficacious in suppressing the production of key pro-inflammatory cytokines associated with the development of asthma.
Cheung, EYY, Phillips, C, Eduardoff, M, Lareu, MV & McNevin, D 2019, 'Performance of ancestry-informative SNP and microhaplotype markers', Forensic Science International: Genetics, vol. 43, pp. 102141-102141.
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The use of microhaplotypes (MHs) for ancestry inference has added to an increasing number of ancestry-informative markers (AIMs) for forensic application that includes autosomal single nucleotide polymorphisms (SNPs) and insertions/deletions (indels). This study compares bi-allelic and tri-allelic SNPs as well as MH markers for their ability to differentiate African, European, South Asian, East Asian, and American population groups from the 1000 Genomes Phase 3 database. A range of well-established metrics were applied to rank each marker according to the population differentiation potential they measured. These comprised: absolute allele frequency differences (δ); Rosenberg's informativeness for (ancestry) assignment (In); the fixation index (FST); and the effective number of alleles (Ae). A panel consisting of all three marker types resulted in the lowest mean divergence per population per individual (MDPI = 2.16%) when selected by In. However, when marker types were not mixed, MHs were the highest performing markers by most metrics (MDPI < 4%) for differentiation between the five continental populations.
Chikoidze, E, Rogers, DJ, Teherani, FH, Rubio, C, Sauthier, G, Von Bardeleben, HJ, Tchelidze, T, Ton-That, C, Fellous, A, Bove, P, Sandana, EV, Dumont, Y & Perez-Tomas, A 2019, 'Puzzling robust 2D metallic conductivity in undoped β-Ga2O3 thin films', Materials Today Physics, vol. 8, pp. 10-17.
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© 2018 Elsevier Ltd Here, we report the analogy of an extremely stable topological-like ultra-wide bandgap insulator, a solid that is a pure insulator in its bulk but has a metallic conductive surface, presenting a two-dimensional conductive channel at its surface that challenges our current thinking about semiconductor conductivity engineering. Nominally undoped epitaxial β-Ga 2 O 3 thin films without any detectable defect (after a range of state-of-the-art techniques) showed the unexpectedly low resistivity of 3 × 10 −2 Ωcm which was found to be also resistant to high dose proton irradiation (2 MeV, 5 × 10 15 cm −2 dose) and was largely invariant (metallic) over the phenomenal temperature range of 2 K up to 850 K. The unique resilience and stability of the electrical properties under thermal and highly ionizing radiation stressing, combined with the extended transparency range (thanks to the ultra-wide bandgap) and the already known toughness under high electrical field could open up new perspectives for use as expanded spectral range transparent electrodes (e.g., for UV harvesting solar cells or UV LEDs/lasers) and robust Ohmic contacts for use in extreme environments/applications and for novel optoelectronic and power device concepts.
Chmelík, D, Hrouzek, P, Fedorko, J, Vu, DL, Urajová, P, Mareš, J & Červený, J 2019, 'Accumulation of cyanobacterial oxadiazine nocuolin A is enhanced by temperature shift during cultivation and is promoted by bacterial co-habitants in the culture', Algal Research, vol. 44, pp. 101673-101673.
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© 2019 Elsevier B.V. Proper setting of cultivation conditions is essential for production of high-value compounds in microbial biotechnology. The present study characterizes photoautotrophic growth and capacity to accumulate the antiproliferative secondary metabolite Nocuolin A (NoA) in cyanobacterium Nostoc sp. CCAP 1453/38. As the cyanobacterial culture was found to be non-axenic, the bacteria accompanying the culture were characterized, then the growth demands and NoA production in the Nostoc-bacterial consortium were determined, and finally an axenic strain was prepared. For the purposes of growth characterization, the culture was maintained in a quasi-continuous regime under various light intensities, temperatures, and inorganic carbon concentrations in a small-scale laboratory photobioreactor. The maximum biomass growth rate obtained was 0.10 h−1 (doubling time Dt = 6.93 h). Following optimal growth conditions were identified: temperature of 35 °C, light intensity 600 μmol(photons) m−2 s−1, and 2500 ppm CO2 in the sparging gas. As the temperature optima for the biomass production and for NoA accumulation differed, biphasic cultivation for maximal NoA yield was designed, leading to a three times more effective cultivation procedure compared to batch culture maintained at a temperature optimal for NoA production. The increased NoA accumulation at reduced temperature that correlated with enhanced expression of NoA biosynthetic genes after the temperature shift suggested its regulation occurs at the expression level. It has further been shown that NoA production is reduced in axenic culture, which indicates that it is also triggered by presence of bacteria. This study shows an example of how a biphasic cultivation mode with different temperatures can be used in high-value compound production processes. It also brings direct evidence that cyanobacterial strain axenization can lead to a rapid decrease in production of valuable compounds and that non-axenic strain...
Choi, S, Seo, DH, Kaiser, MR, Zhang, C, van der laan, T, Han, ZJ, Bendavid, A, Guo, X, Yick, S, Murdock, AT, Su, D, Lee, BR, Du, A, Dou, SX & Wang, G 2019, 'WO3 nanolayer coated 3D-graphene/sulfur composites for high performance lithium/sulfur batteries', Journal of Materials Chemistry A, vol. 7, no. 9, pp. 4596-4603.
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WO3/graphene composite minimizes the polysulfide dissolution problem in the lithium–sulfur (Li–S) battery systems while exhibiting an excellent battery performance.
Christensen, S, Halili, MA, Strange, N, Petit, GA, Huston, WM, Martin, JL & McMahon, RM 2019, 'Oxidoreductase disulfide bond proteins DsbA and DsbB form an active redox pair in Chlamydia trachomatis, a bacterium with disulfide dependent infection and development', PLOS ONE, vol. 14, no. 9, pp. e0222595-e0222595.
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Chlamydia trachomatis is an obligate intracellular bacterium with a distinctive biphasic developmental cycle that alternates between two distinct cell types; the extracellular infectious elementary body (EB) and the intracellular replicating reticulate body (RB). Members of the genus Chlamydia are dependent on the formation and degradation of protein disulfide bonds. Moreover, disulfide cross-linking of EB envelope proteins is critical for the infection phase of the developmental cycle. We have identified in C. trachomatis a homologue of the Disulfide Bond forming membrane protein Escherichia coli (E. coli) DsbB (hereafter named CtDsbB) and-using recombinant purified proteins-demonstrated that it is the redox partner of the previously characterised periplasmic oxidase C. trachomatis Disulfide Bond protein A (CtDsbA). CtDsbA protein was detected in C. trachomatis inclusion vacuoles at 20 h post infection, with more detected at 32 and similar levels at 44 h post infection as the developmental cycle proceeds. As a redox pair, CtDsbA and CtDsbB largely resemble their homologous counterparts in E. coli; CtDsbA is directly oxidised by CtDsbB, in a reaction in which both periplasmic cysteine pairs of CtDsbB are required for complete activity. In our hands, this reaction is slow relative to that observed for E. coli equivalents, although this may reflect a non-native expression system and use of a surrogate quinone cofactor. CtDsbA has a second non-catalytic disulfide bond, which has a small stabilising effect on the protein's thermal stability, but which does not appear to influence the interaction of CtDsbA with its partner protein CtDsbB. Expression of CtDsbA during the RB replicative phase and during RB to EB differentiation coincided with the oxidation of the chlamydial outer membrane complex (COMC). Together with our demonstration of an active redox pairing, our findings suggest a potential role for CtDsbA and CtDsbB in the critical disulfide bond formation step in...
Christensen, S, McMahon, RM, Martin, JL & Huston, WM 2019, 'Life inside and out: making and breaking protein disulfide bonds inChlamydia', Critical Reviews in Microbiology, vol. 45, no. 1, pp. 33-50.
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Disulphide bonds are widely used among all domains of life to provide structural stability to proteins and to regulate enzyme activity. Chlamydia spp. are obligate intracellular bacteria that are especially dependent on the formation and degradation of protein disulphide bonds. Members of the genus Chlamydia have a unique biphasic developmental cycle alternating between two distinct cell types; the extracellular infectious elementary body (EB) and the intracellular replicating reticulate body. The proteins in the envelope of the EB are heavily cross-linked with disulphides and this is known to be critical for this infectious phase. In this review, we provide a comprehensive summary of what is known about the redox state of chlamydial envelope proteins throughout the developmental cycle. We focus especially on the factors responsible for degradation and formation of disulphide bonds in Chlamydia and how this system compares with redox regulation in other organisms. Focussing on the unique biology of Chlamydia enables us to provide important insights into how specialized suites of disulphide bond (Dsb) proteins cater for specific bacterial environments and lifecycles.
Chughtai, AA, Stelzer-Braid, S, Rawlinson, W, Pontivivo, G, Wang, Q, Pan, Y, Zhang, D, Zhang, Y, Li, L & MacIntyre, CR 2019, 'Contamination by respiratory viruses on outer surface of medical masks used by hospital healthcare workers', BMC Infectious Diseases, vol. 19, no. 1.
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BACKGROUND:Medical masks are commonly used in health care settings to protect healthcare workers (HCWs) from respiratory and other infections. Airborne respiratory pathogens may settle on the surface of used masks layers, resulting in contamination. The main aim of this study was to study the presence of viruses on the surface of medical masks. METHODS:Two pilot studies in laboratory and clinical settings were carried out to determine the areas of masks likely to contain maximum viral particles. A laboratory study using a mannequin and fluorescent spray showed maximum particles concentrated on upper right, middle and left sections of the medical masks. These findings were confirmed through a small clinical study. The main study was then conducted in high-risk wards of three selected hospitals in Beijing China. Participants (n = 148) were asked to wear medical masks for a shift (6-8 h) or as long as they could tolerate. Used samples of medical masks were tested for presence of respiratory viruses in upper sections of the medical masks, in line with the pilot studies. RESULTS:Overall virus positivity rate was 10.1% (15/148). Commonly isolated viruses from masks samples were adenovirus (n = 7), bocavirus (n = 2), respiratory syncytial virus (n = 2) and influenza virus (n = 2). Virus positivity was significantly higher in masks samples worn for > 6 h (14.1%, 14/99 versus 1.2%, 1/49, OR 7.9, 95% CI 1.01-61.99) and in samples used by participants who examined > 25 patients per day (16.9%, 12/71 versus 3.9%, 3/77, OR 5.02, 95% CI 1.35-18.60). Most of the participants (83.8%, 124/148) reported at least one problem associated with mask use. Commonly reported problems were pressure on face (16.9%, 25/148), breathing difficulty (12.2%, 18/148), discomfort (9.5% 14/148), trouble communicating with the patient (7.4%, 11/148) and headache (6.1%, 9/148). CONCLUSION:Respiratory pathogens on the outer surface of the used medical masks may result in self-contamination. The risk is...
Chung, H-P, Lee, C-H, Huang, K-H, Yang, S-L, Wang, K, Solntsev, AS, Sukhorukov, AA, Setzpfandt, F & Chen, Y-H 2019, 'Broadband on-chip polarization mode splitters in lithium niobate integrated adiabatic couplers', Optics Express, vol. 27, no. 2, pp. 1632-1632.
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We report, to the best of our knowledge, the first broadband polarization mode splitter (PMS) based on the adiabatic light passage mechanism in the lithium niobate (LiNbO3) waveguide platform. A broad bandwidth of ~140 nm spanning telecom S, C, and L bands at polarization-extinction ratios (PER) of >20 dB and >18 dB for the TE and TM polarization modes, respectively, is found in a five-waveguide adiabatic coupler scheme whose structure is optimized by an adiabaticity engineering process in titanium-diffused LiNbO3 waveguides. When the five-waveguide PMS is integrated with a three-waveguide "shortcut to adiabaticity" structure, we realize a broadband, high splitting-ratio (ηc) mode splitter for spatial separation of TE- (H-) polarized pump (700-850 nm for ηc>99%), TM- (V-) polarized signal (1510-1630 nm for ηc>97%), and TE- (H-) polarized idler (1480-1650 nm for ηc>97%) modes. Such a unique integrated-optical device is of potential for facilitating the on-chip implementation of a pump-filtered, broadband tunable entangled quantum-state generator.
Clases, D, Fingerhut, S, Jeibmann, A, Sperling, M, Doble, P & Karst, U 2019, 'LA-ICP-MS/MS improves limits of detection in elemental bioimaging of gadolinium deposition originating from MRI contrast agents in skin and brain tissues', Journal of Trace Elements in Medicine and Biology, vol. 51, pp. 212-218.
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A novel analytical method to detect the retention of gadolinium from contrast agents for magnetic resonance imaging (MRI) in tissue samples of patients is presented. It is based on laser ablation - inductively coupled plasma - triple quadrupole - mass spectrometry (LA-ICP-MS/MS). Both Gd and P were monitored with a mass shift of +16, corresponding to mono-oxygenated species, as well as Zn, Ca, and Fe on-mass. This method resulted in a significantly reduced background and improved limits of detection not only for phosphorus, but also for gadolinium. These improvements were essential to perform elemental bioimaging with improved resolution of 5 μm x 5 μm, allowing the detection of small Gd deposits in fibrotic skin and brain tumour tissue with diameters of approximately 50 μm. Detailed analyses of these regions revealed that most Gd was accompanied with P and Ca, indicating co-precipitation.
Clases, D, Gonzalez de Vega, R, Adlard, PA & Doble, PA 2019, 'On-line reverse isotope dilution analysis for spatial quantification of elemental labels used in immunohistochemical assisted imaging mass spectrometry via LA-ICP-MS', Journal of Analytical Atomic Spectrometry, vol. 34, no. 2, pp. 407-412.
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We present a novel on-line isotope dilution analysis (IDA) approach for the quantification of isotopically enriched metal labels used in immunohistochemical assisted imaging mass spectrometry.
Clases, D, Gonzalez de Vega, R, Bishop, D & Doble, P 2019, 'SEC-ICP-MS and on-line isotope dilution analysis for characterisation and quantification of immunochemical assays', Analytical and Bioanalytical Chemistry, vol. 411, no. 16, pp. 3553-3560.
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This study presents a novel size exclusion chromatography-inductively coupled plasma-mass spectrometry (SEC-ICP-MS) method for the characterisation and quantification of immunoassays with lanthanide-labelled antibodies. SEC-ICP-MS in combination with a double isotope dilution approach enabled facile validation of the antibodies' integrity, the determination of the batch to batch labelling efficiency, monitoring of each labelling step, and quantification of the immunocomplexes after incubation with the target protein. The addition of oxygen into the dynamic reaction cell improved the detection of sulphur as a marker for the antibodies and target protein via mass-shifting (LOD = 3.7 ng/mL), whilst maintaining sufficient sensitivity for the analysis of the lanthanides. Ultra-high performance liquid chromatography (UHPLC) SEC ensured a rapid chromatographic method with separation times under 7 min of the labelled and unlabelled antibodies, the immunocomplexes, and the unconjugated polymer used to lanthanide-label the antibodies. SEC calibration estimated the molecular weights of all peaks and provided valuable insights in immunochemical reactions and the stoichiometry of the reactants and products. A novel on-line isotope dilution analysis (IDA) enabled absolute quantification of sulphur and lanthanide signals and the protein of interest. The chromatographic separation of immunocomplexes and labelled antibodies allowed the simultaneous determination of the antibody/metal stoichiometry and target protein concentration from a single mass flow chromatogram. An immunoglobulin protein was quantified after incubation with an 153Eu-labelled primary polyclonal antibody. The procedure was validated with direct labelling of the target protein with 156Gd for parallel, simultaneous quantification. The concentration determined via direct labelling of the protein deviated 1.9% from the immunochemical approach employing 153Eu-labelled polyclonal antibodies. Graphical abstract.
Cleverly, J, Eamus, D, Edwards, W, Grant, M, Grundy, MJ, Held, A, Karan, M, Lowe, AJ, Prober, SM, Sparrow, B & Morris, B 2019, 'TERN, Australia’s land observatory: addressing the global challenge of forecasting ecosystem responses to climate variability and change', Environmental Research Letters, vol. 14, no. 9, pp. 095004-095004.
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The global challenge of understanding and forecasting ecosystem responses to climate extremes and climate change is addressed in this review of research enabled through environmental research infrastructure (RI) provided by Australia's Terrestrial Ecosystem Research Network (TERN). Two primary climatic drivers of ecosystem structure and function in Australia are fire and aridity, to which Australian flora and fauna has shown marked adaptability. Australian vegetation shows resilience to climate extremes of flooding rains, droughts and heatwaves such that variability in primary productivity of Australian vegetation has a tangible effect on the global carbon cycle. Nonetheless, Australian flora and ecosystems could be vulnerable to projected climate change (e.g., to increasing vapour pressure deficit). Refugia are also vulnerable to climate change, with conditions in these areas already near the tipping point for a change in community composition. Ensuring genetic diversity during directional change in climate (e.g., increasing aridity) requires proactive approaches to conservation and restoration projects. To address these challenges, TERN provides environmental research infrastructure (RI) at three scales of observation: i) environmental monitoring using remote sensing techniques at a landscape and continental scale; ii) a spatially extensive network of ecosystem monitoring plots; and iii) intensely measured sites collecting detailed data on ecosystem processes. Through partnerships with international environmental RIs, TERN enables research that addresses global challenges, on the first steps toward the forecasting of ecosystem–climate interactions.
Clifton, J, Osman, EO, Suggett, DJ & Smith, DJ 2019, 'WITHDRAWN: Resolving conservation and development tensions in a small island state: A governance analysis of Curieuse Marine National Park, Seychelles', Marine Policy, pp. 103650-103650.
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Coil, DA, Jospin, G, Darling, AE, Wallis, C, Davis, IJ, Harris, S, Eisen, JA, Holcombe, LJ & O’Flynn, C 2019, 'Genomes from bacteria associated with the canine oral cavity: A test case for automated genome-based taxonomic assignment', PLOS ONE, vol. 14, no. 6, pp. e0214354-e0214354.
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Taxonomy for bacterial isolates is commonly assigned via sequence analysis. However, the most common sequence-based approaches (e.g. 16S rRNA gene-based phylogeny or whole genome comparisons) are still labor intensive and subjective to varying degrees. Here we present a set of 33 bacterial genomes, isolated from the canine oral cavity. Taxonomy of these isolates was first assigned by PCR amplification of the 16S rRNA gene, Sanger sequencing, and taxonomy assignment using BLAST. After genome sequencing, taxonomy was revisited through a manual process using a combination of average nucleotide identity (ANI), concatenated marker gene phylogenies, and 16S rRNA gene phylogenies. This taxonomy was then compared to the automated taxonomic assignment given by the recently proposed Genome Taxonomy Database (GTDB). We found the results of all three methods to be similar (25 out of the 33 had matching genera), but the GTDB approach required fewer subjective decisions, and required far less labor. The primary differences in the non-identical taxonomic assignments involved cases where GTDB has proposed taxonomic revisions.
Coleman, MA, Clark, JS, Doblin, MA, Bishop, MJ & Kelaher, BP 2019, 'Genetic differentiation between estuarine and open coast ecotypes of a dominant ecosystem engineer', Marine and Freshwater Research, vol. 70, no. 7, pp. 977-977.
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Temperate intertidal shores globally are often dominated by habitat-forming seaweeds, but our knowledge of these systems is heavily biased towards northern hemisphere species. Rocky intertidal shores throughout Australia and New Zealand are dominated by a single monotypic species, Hormosira banksii. This species plays a key role in facilitating biodiversity on both rocky shores and estuarine habitats, yet we know little about the processes that structure populations. Herein we characterise the genetic diversity and structure of Hormosira and demonstrate strong restrictions to gene flow over small spatial scales, as well as between estuarine and open coast populations. Estuarine ecotypes were often genetically unique from nearby open coast populations, possibly due to extant reduced gene flow between habitats, founder effects and coastal geomorphology. Deviations from random mating in many locations suggest complex demographic processes are at play within shores, including clonality in estuarine populations. Strong isolation by distance in Hormosira suggests that spatial management of intertidal habitats will necessitate a network of broad-scale protection. Understanding patterns of genetic diversity and gene flow in this important ecosystem engineer will enhance the ability to manage, conserve and restore this key species into the future.
Collins, PF, Yang, IA, Chang, Y-C & Vaughan, A 2019, 'Nutritional support in chronic obstructive pulmonary disease (COPD): an evidence update', Journal of Thoracic Disease, vol. 11, no. S17, pp. S2230-S2237.
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Collison, AM, Li, J, de Siqueira, AP, Lv, X, Toop, HD, Morris, JC, Starkey, MR, Hansbro, PM, Zhang, J & Mattes, J 2019, 'TRAIL signals through the ubiquitin ligase MID1 to promote pulmonary fibrosis', BMC Pulmonary Medicine, vol. 19, no. 1.
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BACKGROUND:Tumour necrosis factor-related apoptosis-inducing ligand (TRAIL) has previously been demonstrated to play a pro-inflammatory role in allergic airways disease and COPD through the upregulation of the E3 ubiquitin ligase MID1 and the subsequent deactivation of protein phosphatase 2A (PP2A). METHODS:Biopsies were taken from eight IPF patients presenting to the Second Affiliated Hospital of Jilin University, China between January 2013 and February 2014 with control samples obtained from resected lung cancers. Serum TRAIL, MID1 protein and PP2A activity in biopsies, and patients' lung function were measured. Wild type and TRAIL deficient Tnfsf10-/- BALB/c mice were administered bleomycin to induce fibrosis and some groups were treated with the FTY720 analogue AAL(s) to activate PP2A. Mouse fibroblasts were treated with recombinant TRAIL and fibrotic responses were assessed. RESULTS:TRAIL in serum and MID1 protein levels in biopsies from IPF patients were increased compared to controls. MID1 levels were inversely associated while PP2A activity levels correlated with DLco. Tnfsf10-/- and mice treated with the PP2A activator AAL(s) were largely protected against bleomycin-induced reductions in lung function and fibrotic changes. Addition of recombinant TRAIL to mouse fibroblasts in-vitro increased collagen production which was reversed by PP2A activation with AAL(s). CONCLUSION:TRAIL signalling through MID1 deactivates PP2A and promotes fibrosis with corresponding lung function decline. This may provide novel therapeutic targets for IPF.
Commault, AS, Fabris, M, Kuzhiumparambil, U, Adriaans, J, Pernice, M & Ralph, PJ 2019, 'Methyl jasmonate treatment affects the regulation of the 2-C-methyl-D-erythritol 4-phosphate pathway and early steps of the triterpenoid biosynthesis in Chlamydomonas reinhardtii', Algal Research, vol. 39, pp. 101462-101462.
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© 2019 Elsevier B.V. Terpenoids are a large and diverse class of naturally occurring metabolites serving many industrial applications and natural roles. Economically important terpenoids are often produced in low abundance from their natural sources, making their industrial-scale production challenging or uneconomical, therefore engineered microorganisms are frequently used as heterologous production platforms. Photosynthetic microorganisms, such as the green alga Chlamydomonas reinhardtii, represent promising systems to produce terpenoids in a cost-effective and sustainable manner, but knowledge about the regulation of their terpenoid metabolism remains limited. Here we report on the investigation of the phytohormone methyl jasmonate (MeJA) as elicitor of algal terpenoid synthesis. We treated C. reinhardtii cells in mid-exponential growth phase with three different concentrations of MeJA (0.05, 0.5 and 1 mM). The highest concentration of MeJA affected the photosynthetic activity of the cells, arrested the growth and up-regulated key genes of the 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway, leading to a significant increase in intermediates of this pathway, squalene and (S)-2,3-epoxysqualene, while the abundance of cycloartenol, and two main sterols (ergosterol and 7-dehydroporiferasterol) decreased. These data suggest the redirection of the carbon flux towards the synthesis of yet uncharacterised triterpenoid secondary metabolites upon MeJA treatment. Our results offer important new insights into the regulation of the triterpenoid metabolism in C. reinhardtii and raise important questions on hormonal signalling in microalgae. Phytohormone treatment is tested for the first time in algae, where it holds great potential for identifying key transcriptional regulators of the MEP pathway as targets for future metabolic engineering studies for improve production of high-value triterpenoids.
Cooke, I, Mead, O, Whalen, C, Boote, C, Moya, A, Ying, H, Robbins, S, Strugnell, JM, Darling, A, Miller, D, Voolstra, CR & Adamska, M 2019, 'Molecular techniques and their limitations shape our view of the holobiont', Zoology, vol. 137, pp. 125695-125695.
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It is now recognised that the biology of almost any organism cannot be fully understood without recognising the existence and potential functional importance of associated microbes. Arguably, the emergence of this holistic viewpoint may never have occurred without the development of a crucial molecular technique, 16S rDNA amplicon sequencing, which allowed microbial communities to be easily profiled across a broad range of contexts. A diverse array of molecular techniques are now used to profile microbial communities, infer their evolutionary histories, visualise them in host tissues, and measure their molecular activity. In this review, we examine each of these categories of measurement and inference with a focus on the questions they make tractable, and the degree to which their capabilities and limitations shape our view of the holobiont.
Cooper, EA, Bonne Lee, B & Muhlmann, M 2019, 'Outcomes following stoma formation in patients with spinal cord injury', Colorectal Disease, vol. 21, no. 12, pp. 1415-1420.
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AbstractAimThe formation of a diverting stoma of the bowel in patients with spinal cord injury (SCI) is a useful option in managing problems associated with prolonged bowel care, pressure ulcers and neurogenic bowel. This descriptive study examines surgical outcomes and the effect on an individual's health‐related quality of life (HrQoL) in this complex group of patients.MethodsData were retrospectively collected in all patients with SCI who underwent a diverting stoma at Prince of Wales Hospital, Sydney, between January 2013 and January 2018 via a self‐report questionnaire developed specifically for the study.ResultsForty‐three individuals were identified of whom 26 responded. 73% were men with a mean age of 45 years. The reasons for stoma formation included sacral pressure ulcer (50%), prolonged bowel care (35%), faecal incontinence (19%), constipation (8%), autonomic dysreflexia (8%), carer difficulties (8%) and haemorrhoids (4%). 76% of patients reported an improvement in HrQoL with 72% scoring their satisfaction with a stoma ≥ 8/10.ConclusionWhile stoma formation is often seen as a treatment of last resort, our study has shown that it is an effective management option for a number of conditions post‐SCI. It can improve HrQoL and has a high level of satisfaction amongst patients. Ideally, patients who could potentially benefit from a stoma should be identified early and receive appropriate education and counselling to help facilitate informed and timely decision‐making and reduce adverse bowel related impact on quality of li...
Corbit, L, Becchi, S & Kendig, M 2019, 'Experience-based changes to decision-making circuits and implications for behavioural control', IBRO Reports, vol. 6, pp. S35-S35.
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Cranfield, CG 2019, 'ABA/ASB Membrane Biophysics session II 2018', Biophysical Reviews, vol. 11, no. 3, pp. 281-282.
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Crispino, F, Roux, C, Delémont, O & Ribaux, O 2019, 'Is the (traditional) Galilean science paradigm well suited to forensic science?', WIREs Forensic Science, vol. 1, no. 6.
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AbstractFor more than 10 years, forensic science has been at best, criticized for its lack of scientific foundations and at worst, presented as an oxymoron. An exclusive focus on standard operating procedures and quality management could cause forensic science to fall short of addressing the epistemological issue initiated by judges. This is particularly so in rapidly changing times, including digital transformation of society and decentralization of forensic services. As a consequence, the present understanding of forensic science by both scientists and its stakeholders is questioned. It is argued that that forensic science fundamental principles and, more broadly, forensic science philosophy are pivotal to the reliable application of science to address security and justice questions.This article is categorized under:
Forensic Science in Action/Crime Scene Investigation > Epistemology and Method
Jurisprudence and Regulatory Oversight > Communication across Science and Law
Jurisprudence and Regulatory Oversight > Expert Evidence and Narrative
Cummins, ML, Reid, CJ, Roy Chowdhury, P, Bushell, RN, Esbert, N, Tivendale, KA, Noormohammadi, AH, Islam, S, Marenda, MS, Browning, GF, Markham, PF & Djordjevic, SP 2019, 'Whole genome sequence analysis of Australian avian pathogenic Escherichia coli that carry the class 1 integrase gene', Microbial Genomics, vol. 5, no. 2.
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Avian pathogenic Escherichia coli (APEC) cause widespread economic losses in poultry production and are potential zoonotic pathogens. Genome sequences of 95 APEC from commercial poultry operations in four Australian states that carried the class 1 integrase gene intI1, a proxy for multiple drug resistance (MDR), were characterized. Sequence types ST117 (22/95), ST350 (10/95), ST429 and ST57 (each 9/95), ST95 (8/95) and ST973 (7/95) dominated, while 24 STs were represented by one or two strains. FII and FIB repA genes were the predominant (each 93/95, 98 %) plasmid incompatibility groups identified, but those of B/O/K/Z (25/95, 26 %) and I1 (24/95, 25 %) were also identified frequently. Virulence-associated genes (VAGs) carried by ColV and ColBM virulence plasmids, including those encoding protectins [iss (91/95, 96 %), ompT (91/95, 96 %) and traT (90/95, 95 %)], iron-acquisition systems [sitA (88/95, 93 %), etsA (87/95, 92 %), iroN (84/95, 89 %) and iucD/iutA (84/95, 89 %)] and the putative avian haemolysin hylF (91/95, 96 %), featured prominently. Notably, mobile resistance genes conferring resistance to fluoroquinolones, colistin, extended-spectrum β-lactams and carbapenems were not detected in the genomes of these 95 APEC but carriage of the sulphonamide resistance gene, sul1 (59/95, 63 %), the trimethoprim resistance gene cassettes dfrA5 (48/95, 50 %) and dfrA1 (25/95, 27 %), the tetracycline resistance determinant tet(A) (51/95, 55 %) and the ampicillin resistance genes blaTEM-1A/B/C (48/95, 52 %) was common. IS26 (77/95, 81 %), an insertion element known to capture and mobilize a wide spectrum of antimicrobial resistance genes, was also frequently identified. These studies provide a baseline snapshot of drug-resistant APEC in Australia and their role in the carriage of ColV-like virulence plasmids.
Curson, ARJ, Williams, BT, Pinchbeck, BJ, Sims, LP, Martínez, AB, Rivera, PPL, Kumaresan, D, Mercadé, E, Spurgin, LG, Carrión, O, Moxon, S, Cattolico, RA, Kuzhiumparambil, U, Guagliardo, P, Clode, PL, Raina, J-B & Todd, JD 2019, 'Author Correction: DSYB catalyses the key step of dimethylsulfoniopropionate biosynthesis in many phytoplankton', Nature Microbiology, vol. 4, no. 3, pp. 540-542.
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In the version of this Letter originally published, the Methods incorrectly stated that all phytoplankton cultures were sampled in mid-exponential phase. The low-nitrogen cultures were sampled in early stationary phase and at the point at which Fv/Fm values decreased, to indicate that cultures were experiencing low-nitrogen conditions. All other phytoplankton cultures were sampled in exponential phase. Growth and Fv/Fm data are provided here on high- and low-nitrogen cultures (Figs 1, 2 and 3) to clarify and support this correction. The Methods also stated that cell counting was done using a Beckman Multisizer 3 Coulter Counter, but a CASY Model TT Cell Counter was used.
Curtis, EM, Knight, CA & Leigh, A 2019, 'Intracanopy adjustment of leaf-level thermal tolerance is associated with microclimatic variation across the canopy of a desert tree (Acacia papyrocarpa)', Oecologia, vol. 189, no. 1, pp. 37-46.
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Tree crowns are spatially heterogeneous, sometimes resulting in significant variation in microclimate across the canopy, particularly with respect to temperature. Yet it is not known whether such localised temperature variation equates to intracanopy variation in leaf-level physiological thermal tolerance. Here, we studied whether microclimate variation across the canopy of a dominant desert tree equated to localised variation in leaf thermal thresholds (T50) among four canopy positions: upper south, upper north, lower south, lower north. Principal component analysis was used to generate a composite climatic stress variable (CSTRESS) from canopy temperature, vapour pressure deficit, and relative humidity. We also determined the average number of days that maximum temperatures exceeded the air temperature equating to this species' critical threshold of 49 °C (AT49). To estimate how closely leaf temperatures track ambient temperature, we predicted the thermal time constant (τ) for leaves at each canopy position. We found that CSTRESS and AT49 were significantly greater in lower and north-facing positions in the canopy. Differences in wind speed with height resulted in significantly longer predicted τ for leaves positioned at lower, north-facing positions. Variation in these drivers was correlated with significantly higher T50 for leaves in these more environmentally stressful canopy positions. Our findings suggest that this species may optimise resources to protect against thermal damage at a whole-plant level. They also indicate that, particularly in desert environments with steep intracanopy microclimatic gradients, whole-plant carbon models could substantially under- or overestimate productivity under heat stress, depending on where in the canopy T50 is measured.
Cwiklinski, K, Donnelly, S, Drysdale, O, Jewhurst, H, Smith, D, De Marco Verissimo, C, Pritsch, IC, O'Neill, S, Dalton, JP & Robinson, MW 2019, 'The cathepsin-like cysteine peptidases of trematodes of the genus Fasciola', vol. 104, pp. 113-164.
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In this report, we review our present understanding of the cathepsin-like
cysteine peptidases of F. hepatica in the context of the parasite’s relationship with its mammalian host. Wehave integrated information gathered frombasic molecular biology/biochemical studies and experimental laboratory techniques with the emerging –omics technologies (genomics, transcriptomics and proteomics) and immunological advances to clarify the structural make-up of the peptidase families and to help our continual re-assessment of the role each peptidase plays in the virulence, pathogenicity and, indeed, in the lengthy rapport between parasite and host.
Dan, X, Wang, C, Xu, X, Liu, Y, Cheng, X, Fronzi, M, Bi, L & Zhao, XS 2019, 'Improving the sinterability of CeO2 by using plane-selective nanocubes', Journal of the European Ceramic Society, vol. 39, no. 14, pp. 4429-4434.
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© 2019 Elsevier Ltd CeO2 nanocubes with (100) surface orientation are successfully synthesized and found to facilitate the sinterability of CeO2 material. The CeO2 nanocubes show a much-improved sinterability relative to CeO2 nanoparticles prepared by the conventional citric-nitrate method. The nanocubes can be successfully sintered at a relatively low temperature of 1200 °C without using any sintering aids. In contrast, a pellet using conventional CeO2 nano-powder obtained from the conventional citric-nitrate method can be densified only after sintering at 1400 °C, which is 200 °C higher than that for the CeO2 nanocube sintering, although the starting particle size of both CeO2 samples is similar. Density functional theory indicates that the surface energy of the (100) plane is significantly higher than that of the (111) plane, which is the more typical surface presentation of conventional CeO2 particles. This high surface energy allows fast growth of the CeO2 nanocubes during sintering, contributing to their improved sinterability.
Danastas, K, Whittington, CM, Dowland, SN, Combes, V, Murphy, CR & Lindsay, LA 2019, 'Ovarian Hyperstimulation Reduces Vascular Endothelial Growth Factor-A During Uterine Receptivity', Reproductive Sciences, vol. 26, no. 2, pp. 259-268.
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The angiogenic factor vascular endothelial growth factor-A (VEGFA) plays a critical role during early pregnancy in many species including the rat, and any alterations in VEGFA levels can severely impact blastocyst implantation rates. The rat ovarian hyperstimulation (OH) model is useful in studying how the induction of superovulation affects VEGFA levels and endometrial receptivity to blastocyst implantation. The present study shows that the major isoform in the rat uterus, Vegf188, is reduced at the time of receptivity in OH compared to normal pregnancy, whereas there is no change in Vegf164 and Vegf120 messenger RNA (mRNA). The VEGFA receptor 2 (VEGFR2) protein levels are also reduced at the time of receptivity in OH. Our ovariectomy studies show that Vegf164, Vegf188, and Vegf120 are significantly decreased by estrogen, and, to a lesser extent progesterone, when compared to control animals. Although no change in the percentage of endometrial blood vessels was seen across all stages of pregnancy, at the time of receptivity in OH pregnancies, blood vessels were typically larger compared to other stages. The altered progesterone-estrogen ratio seen in OH, taken together with our ovariectomy studies, explains the changes to Vegfa mRNA in OH at the time of receptivity. Since VEGFA is important during implantation, the changes to Vegfa and VEGFR2 levels in the endometrium may help explain the observed lower endometrial receptivity following OH. This study aimed to analyse how ovarian hyperstimulation alters the levels of vascular endothleial growth factor and its major receptor, VEGFR2 in the uterus in a rat model.
Dang, KD, Quiroz, M, Kohn, R, Tran, MN & Villani, M 2019, 'Hamiltonian monte carlo with energy conserving subsampling', Journal of Machine Learning Research, vol. 20, pp. 1-31.
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Hamiltonian Monte Carlo (HMC) samples efficiently from high-dimensional posterior distributions with proposed parameter draws obtained by iterating on a discretized version of the Hamiltonian dynamics. The iterations make HMC computationally costly, especially in problems with large data sets, since it is necessary to compute posterior densities and their derivatives with respect to the parameters. Naively computing the Hamiltonian dynamics on a subset of the data causes HMC to lose its key ability to generate distant parameter proposals with high acceptance probability. The key insight in our article is that efficient subsampling HMC for the parameters is possible if both the dynamics and the acceptance probability are computed from the same data subsample in each complete HMC iteration. We show that this is possible to do in a principled way in a HMC-within-Gibbs framework where the subsample is updated using a pseudo marginal MH step and the parameters are then updated using an HMC step, based on the current subsample. We show that our subsampling methods are fast and compare favorably to two popular sampling algorithms that use gradient estimates from data subsampling. We also explore the current limitations of subsampling HMC algorithms by varying the quality of the variance reducing control variates used in the estimators of the posterior density and its gradients.
Darling, ES, McClanahan, TR, Maina, J, Gurney, GG, Graham, NAJ, Januchowski-Hartley, F, Cinner, JE, Mora, C, Hicks, CC, Maire, E, Puotinen, M, Skirving, WJ, Adjeroud, M, Ahmadia, G, Arthur, R, Bauman, AG, Beger, M, Berumen, ML, Bigot, L, Bouwmeester, J, Brenier, A, Bridge, TCL, Brown, E, Campbell, SJ, Cannon, S, Cauvin, B, Chen, CA, Claudet, J, Denis, V, Donner, S, Estradivari, Fadli, N, Feary, DA, Fenner, D, Fox, H, Franklin, EC, Friedlander, A, Gilmour, J, Goiran, C, Guest, J, Hobbs, J-PA, Hoey, AS, Houk, P, Johnson, S, Jupiter, SD, Kayal, M, Kuo, C-Y, Lamb, J, Lee, MAC, Low, J, Muthiga, N, Muttaqin, E, Nand, Y, Nash, KL, Nedlic, O, Pandolfi, JM, Pardede, S, Patankar, V, Penin, L, Ribas-Deulofeu, L, Richards, Z, Roberts, TE, Rodgers, KS, Safuan, CDM, Sala, E, Shedrawi, G, Sin, TM, Smallhorn-West, P, Smith, JE, Sommer, B, Steinberg, PD, Sutthacheep, M, Tan, CHJ, Williams, GJ, Wilson, S, Yeemin, T, Bruno, JF, Fortin, M-J, Krkosek, M & Mouillot, D 2019, 'Social–environmental drivers inform strategic management of coral reefs in the Anthropocene', Nature Ecology & Evolution, vol. 3, no. 9, pp. 1341-1350.
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de las Peñas, MLAN, Verzosa, DMB, Aberin, MAQ, Garces, LPDM, Francisco, FF, Bautista, EP, Tolentino, MAC & Tabares, WC 2019, 'Digital simulations for grade 7 to 10 mathematics', Philippine Journal of Science, vol. 148, no. 4, pp. 735-749.
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This article describes a Department of Science and Technology – Philippine Council for Industry, Energy and Emerging Technology (DOST-PCIEERD) project aimed to facilitate the implementation of the mathematical objectives raised by the Department of Education’s (DepEd) K to 12 program in the Philippines through the use of innovative digital technologies. In particular, a selection of application software (“apps”) were created for Grade 7 to 10 mathematics that covered topics indicated in the five strands outlined in the K to 12 program – namely (1) number, (2) geometry, (3) measurement, (4) patterns and algebra, and (5) statistics and probability. The design of the apps was informed by an amalgamated framework of the Cognitive Theory of Multimedia Learning (Mayer 2005) and Mathematical Theories of Representation (Goldin 1998). The design was informed by how students learn and how students learn mathematics. The project also aimed to design manipulable software that allows learners to construct and grapple with their mental representations of mathematical concepts. This paper describes a selection of the apps designed by the project and how their features were informed by the theoretical framework. It also presents results from pilot studies that demonstrate the apps’ potential to increase performance, facilitate conceptual development, and increase learners’ engagement.
de Lima Ribeiro, A, Artlett, C, Ajani, PA, Derkenne, C & Pask, H 2019, 'Impact of fluorescence on Raman remote sensing of temperature in natural water samples', Optics Express, vol. 27, no. 16, pp. 22339-22339.
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Deepika, Arora, S, Kaur, R, Singh, TG, Singh, M, Satija, S & Singh, R 2019, 'Prescribing pattern of antihypertensive drugs in a tertiary care hospital: A review', Plant Archives, vol. 19, pp. 1311-1316.
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Hypertension is one the leading cause of mortality in various developing countries like India. For the effective management of this lifestyle disorder a rational approach & measures are required to be taken by the health care professionals. In order to achieve this, prescription pattern analysis is a powerful tool which elaborated the trends of prescribing and their evaluation in reference to the standard treatment guidelines by the various health agencies. An ample of studies focusing on prescribing patterns of antihypertensive drugs was reviewed in this article. It has been concluded that most of the studies were showing that monotherapy including ACEIs (Angiotensin converting enzyme inhibitors) was first choice antihypertensive treatment. Additionally, ARBs (angiotensin receptor blockers) were the second most preferred class followed by CCBs (calcium channel blockers), Diuretics and BB (beta blockers). However, most of the studies have shown that the prescribing trends were according to the recommended guidelines but JNC 8 guidelines were not being completely followed. Due to persistent clinical challenges in the management of hypertension, we still require additional care & monitoring of the treatment patterns. So adoption of a rational approach aligned with standard treatment guidelines is essential which will not only fill the gaps in the clinical practice but also help in complete & effective management of this illness.
Dehollain, JP, Mukhopadhyay, U, Michal, VP, Wang, Y, Wunsch, B, Reichl, C, Wegscheider, W, Rudner, MS, Demler, E & Vandersypen, LMK 2019, 'Nagaoka ferromagnetism observed in a quantum dot plaquette', Nature, vol. 579, no. 7800, pp. 528-533.
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Engineered, highly-controllable quantum systems hold promise as simulators of
emergent physics beyond the capabilities of classical computers. An important
problem in many-body physics is itinerant magnetism, which originates purely
from long-range interactions of free electrons and whose existence in real
systems has been subject to debate for decades. Here we use a quantum simulator
consisting of a four-site square plaquette of quantum dots to demonstrate
Nagaoka ferromagnetism. This form of itinerant magnetism has been rigorously
studied theoretically but has remained unattainable in experiment. We load the
plaquette with three electrons and demonstrate the predicted emergence of
spontaneous ferromagnetic correlations through pairwise measurements of spin.
We find the ferromagnetic ground state is remarkably robust to engineered
disorder in the on-site potentials and can induce a transition to the low-spin
state by changing the plaquette topology to an open chain. This demonstration
of Nagaoka ferromagnetism highlights that quantum simulators can be used to
study physical phenomena that have not yet been observed in any system before.
The work also constitutes an important step towards large-scale quantum dot
simulators of correlated electron systems.
DeMaere, MZ & Darling, AE 2019, 'bin3C: exploiting Hi-C sequencing data to accurately resolve metagenome-assembled genomes', Genome Biology, vol. 20, no. 1, pp. 46-46.
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Dennis, L & Peacock, J 2019, 'Genes Directing Flower Development in Arabidopsis', The Plant Cell, vol. 31, no. 6, pp. 1192-1193.
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Deplazes, E, White, J, Murphy, C, Cranfield, CG & Garcia, A 2019, 'Competing for the same space: protons and alkali ions at the interface of phospholipid bilayers', Biophysical Reviews, vol. 11, no. 3, pp. 483-490.
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Maintaining gradients of solvated protons and alkali metal ions such as Na+ and K+ across membranes is critical for cellular function. Over the last few decades, both the interactions of protons and alkali metal ions with phospholipid membranes have been studied extensively and the reported interactions of these ions with phospholipid headgroups are very similar, yet few studies have investigated the potential interdependence between proton and alkali metal ion binding at the water-lipid interface. In this short review, we discuss the similarities between the proton-membrane and alkali ion-membrane interactions. Such interactions include cation attraction to the phosphate and carbonyl oxygens of the phospholipid headgroups that form strong lipid-ion and lipid-ion-water complexes. We also propose potential mechanisms that may modulate the affinities of these cationic species to the water-phospholipid interfacial oxygen moieties. This review aims to highlight the potential interdependence between protons and alkali metal ions at the membrane surface and encourage a more nuanced understanding of the complex nature of these biologically relevant processes.
Deschaseaux, E, O'Brien, J, Siboni, N, Petrou, K & Seymour, JR 2019, 'Shifts in dimethylated sulfur concentrations and microbiome composition in the red-tide causing dinoflagellate <i>Alexandrium minutum</i> during a simulated marine heatwave', Biogeosciences, vol. 16, no. 22, pp. 4377-4391.
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Abstract. The biogenic sulfur compounds dimethyl sulfide (DMS), dimethyl
sulfoniopropionate (DMSP) and dimethyl sulfoxide (DMSO) are produced and
transformed by diverse populations of marine microorganisms and have
substantial physiological, ecological and biogeochemical importance spanning
organism to global scales. Understanding the production and transformation
dynamics of these compounds under shifting environmental conditions is
important for predicting their roles in a changing ocean. Here, we report
the physiological and biochemical response of a robust strain of
Alexandrium minutum, a dinoflagellate with the highest reported intracellular DMSP content,
exposed to a 6 d increase in temperature mimicking mild and extreme
coastal marine heatwave conditions (+4 and +12 ∘C). Under mild temperature increases (+4 ∘C), A. minutum growth was
enhanced, with no measurable physiological stress response. However, under a
very acute increase in temperature (+12 ∘C) triggering thermal
stress, A. minutum growth declined, photosynthetic efficiency (FV∕FM) was
impaired, and enhanced oxidative stress was observed. These physiological
responses indicative of thermal stress were accompanied by increased DMS and
DMSO concentrations followed by decreased DMSP concentration. At this
temperature extreme, we observed a cascading stress response in A. minutum, which was
initiated 6 h after the start of the experiment by a spike in DMS and DMSO
concentrations and a rapid decrease in FV∕FM. This was followed by
an increase in reactive oxygen species (ROS) and an abrupt decline in DMS
and DMSO on day 2 of the experiment. A subsequent decrease in DMSP coupled
with a decline in the growth rate of both A. minutum and its associated total
bacterial assemblage coincided with a shift in the composition of the A. minutum
microbiome. Specifically, an increase in the relative abundance of the operational taxonomic units (OTUs)
matching Oceanicaulis (17.0 %), Phycisphaeraceae SM1A02 (8....
Dietrich, A, Bürk, M, Steiger, ES, Antoniuk, L, Tran, TT, Nguyen, M, Aharonovich, I, Jelezko, F & Kubanek, A 2019, 'Reply to “Comment on ‘Observation of Fourier transform limited lines in hexagonal boron nitride’”', Physical Review B, vol. 100, no. 4.
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© 2019 American Physical Society. In this Reply, we answer to the comments by Langbein [Phys. Rev. B 100, 047401 (2019)10.1103/PhysRevB.100.047401]. We disagree with the argument that our measured spectral shapes and the extracted linewidths are caused by temporal blinking. We give detailed information on our evaluation process to exclude blinking events. Beyond the question raised in the Comment, we analyze the influence of spectral diffusion. Although spectral diffusion is an ongoing limitation for defect centers in hexagonal boron nitride, we prove that it is not influencing our extracted linewidths.
Ding, B, Shao, S, Jiang, F, Dang, P, Sun, C, Huang, S, Ma, P, Jin, D, Kheraif, AAA & Lin, J 2019, 'MnO2-Disguised Upconversion Hybrid Nanocomposite: An Ideal Architecture for Tumor Microenvironment-Triggered UCL/MR Bioimaging and Enhanced Chemodynamic Therapy', Chemistry of Materials, vol. 31, no. 7, pp. 2651-2660.
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Copyright © 2019 American Chemical Society. Upconversion nanoparticles (UCNPs) and MnO 2 hybrid theranostic nanoplatform (UCMn) is highly desired; however, the rational design of such UCMn hybrid nanomaterials is still a great challenge. Herein, a simple and versatile strategy for the in situ growth of MnO 2 on the surfaces of UCNPs was reported using a sacrificial template method to construct an ideal MnO 2 -disguised and tumor microenvironment-triggered architecture. Such sophisticated architecture not only achieves activatable magnetic resonance imaging and restorable upconversion luminescence (UCL) imaging with over 100-fold enhancement of UCL in vivo but also significantly improves the efficiency of chemodynamic therapy (CDT) by glutathione depletion- and cisplatin-activation-enhanced • OH generation simultaneously. Additionally, the synergetic effect of CDT and chemotherapy presents excellent therapeutic effect in vivo as compared to either CDT or chemotherapy alone. We believe that the ideal design of the MnO 2 -disguised upconversion hybrid nanocomposite will provide more revelations on the future research on nanoscale theranostic systems.
Djordjevic, SP & Morgan, BS 2019, 'A One Health genomic approach to antimicrobial resistance is essential for generating relevant data for a holistic assessment of the biggest threat to public health', Microbiology Australia, vol. 40, no. 2, pp. 73-73.
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Antimicrobial resistance (AMR) threatens modern medicine as we know it. AMR infections may ultimately be untreatable and routine surgeries will become inherently risky1. By 2050 more people may die of drug-resistant infections (DRIs) every year than of cancer, which equates to more than 10 million annual deaths globally2 and the World Bank has estimated that AMR could cost the global economy $1 trillion every year after 2030. DRIs also lead to an increase in the length of hospital stays, the use of more toxic or costly antibiotics and an increased likelihood of death3. BRIC nations (Brazil, Russia, India, China) and socio-economically challenged countries and people who already have higher rates of infectious diseases will feel the greatest impact2. Indeed, AMR has been likened to the 2008 global financial crisis on an annual repeat cycle. That is because the effects of AMR are not just confined to the human medical sector. The veterinary sector is also reliant on the availability of antimicrobials to treat infectious diseases in companion and food-producing animals.
Djurichkovic, LD, Donelson, JM, Fowler, AM, Feary, DA & Booth, DJ 2019, 'The effects of water temperature on the juvenile performance of two tropical damselfishes expatriating to temperate reefs', Scientific Reports, vol. 9, no. 1.
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AbstractOcean warming associated with global climate change is already inducing geographic range shifts of marine species. Juvenile coral reef fishes transported into temperate latitudes (termed ‘vagrant’ fishes) can experience winter water temperatures below their normal thermal minimum. Such environmental extremes may increase energetic costs for such fishes, resulting in reduced performance, which may be the governing factor that limits the potential for poleward range expansion of such fishes. This study compared the juvenile physiological performance and behaviour of two congeneric tropical damselfishes which settle during austral summer months within temperate eastern Australia: Abudefduf vaigiensis have an extended southern range, and lower threshold survival temperature than the congeneric A. whitleyi. Physiological and behavioural performance parameters that may be affected by cooler temperature regimes at higher latitudes were measured in aquaria. Lower water temperature resulted in reduced growth rates, feeding rates, burst escape speed and metabolic rates of both species, with significantly reduced performance (up to six-fold reductions) for fishes reared at 18 °C relative to 22 °C and 26 °C. However, A. whitleyi exhibited lower growth rates than A. vaigiensis across all temperatures, and lower aerobic capacity at the lowest temperature (18 °C). This difference between species in growth and metabolic capacity suggests that the extended southern distribution and greater overwintering success of A. vaigiensis, in comparison to A. whitleyi is related to thermal performance parameters which are critical in maintaining individual health and survival. Our results support previous findings in the region that water temperature below 22 °C represents a critical physiol...
Donelson, JM, Sunday, JM, Figueira, WF, Gaitán-Espitia, JD, Hobday, AJ, Johnson, CR, Leis, JM, Ling, SD, Marshall, D, Pandolfi, JM, Pecl, G, Rodgers, GG, Booth, DJ & Munday, PL 2019, 'Understanding interactions between plasticity, adaptation and range shifts in response to marine environmental change', Philosophical Transactions of the Royal Society B: Biological Sciences, vol. 374, no. 1768, pp. 20180186-20180186.
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Climate change is leading to shifts in species geographical distributions, but populations are also probably adapting to environmental change at different rates across their range. Owing to a lack of natural and empirical data on the influence of phenotypic adaptation on range shifts of marine species, we provide a general conceptual model for understanding population responses to climate change that incorporates plasticity and adaptation to environmental change in marine ecosystems. We use this conceptual model to help inform where within the geographical range each mechanism will probably operate most strongly and explore the supporting evidence in species. We then expand the discussion from a single-species perspective to community-level responses and use the conceptual model to visualize and guide research into the important yet poorly understood processes of plasticity and adaptation.
This article is part of the theme issue ‘The role of plasticity in phenotypic adaptation to rapid environmental change’.
Donovan, C & Hansbro, PM 2019, 'TRPA1: A potential target for cold‐induced airway disease?', Respirology, vol. 24, no. 3, pp. 193-194.
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Dörk, T, Peterlongo, P, Mannermaa, A, Bolla, MK, Wang, Q, Dennis, J, Ahearn, T, Andrulis, IL, Anton-Culver, H, Arndt, V, Aronson, KJ, Augustinsson, A, Freeman, LEB, Beckmann, MW, Beeghly-Fadiel, A, Behrens, S, Bermisheva, M, Blomqvist, C, Bogdanova, NV, Bojesen, SE, Brauch, H, Brenner, H, Burwinkel, B, Canzian, F, Chan, TL, Chang-Claude, J, Chanock, SJ, Choi, J-Y, Christiansen, H, Clarke, CL, Couch, FJ, Czene, K, Daly, MB, dos-Santos-Silva, I, Dwek, M, Eccles, DM, Ekici, AB, Eriksson, M, Evans, DG, Fasching, PA, Figueroa, J, Flyger, H, Fritschi, L, Gabrielson, M, Gago-Dominguez, M, Gao, C, Gapstur, SM, García-Closas, M, García-Sáenz, JA, Gaudet, MM, Giles, GG, Goldberg, MS, Goldgar, DE, Guénel, P, Haeberle, L, Haiman, CA, Håkansson, N, Hall, P, Hamann, U, Hartman, M, Hauke, J, Hein, A, Hillemanns, P, Hogervorst, FBL, Hooning, MJ, Hopper, JL, Howell, T, Huo, D, Ito, H, Iwasaki, M, Jakubowska, A, Janni, W, John, EM, Jung, A, Kaaks, R, Kang, D, Kapoor, PM, Khusnutdinova, E, Kim, S-W, Kitahara, CM, Koutros, S, Kraft, P, Kristensen, VN, Kwong, A, Lambrechts, D, Marchand, LL, Li, J, Lindström, S, Linet, M, Lo, W-Y, Long, J, Lophatananon, A, Lubiński, J, Manoochehri, M, Manoukian, S, Margolin, S, Martinez, E, Matsuo, K, Mavroudis, D, Meindl, A, Menon, U, Milne, RL, Mohd Taib, NA, Muir, K, Mulligan, AM, Neuhausen, SL, Nevanlinna, H, Neven, P, Newman, WG, Offit, K, Olopade, OI, Olshan, AF, Olson, JE, Olsson, H, Park, SK, Park-Simon, T-W, Peto, J, Plaseska-Karanfilska, D, Pohl-Rescigno, E, Presneau, N, Rack, B, Radice, P, Rashid, MU, Rennert, G, Rennert, HS, Romero, A, Ruebner, M, Saloustros, E, Schmidt, MK, Schmutzler, RK, Schneider, MO, Schoemaker, MJ, Scott, C, Shen, C-Y, Shu, X-O, Simard, J, Slager, S, Smichkoska, S, Southey, MC, Spinelli, JJ, Stone, J, Surowy, H, Swerdlow, AJ, Tamimi, RM, Tapper, WJ, Teo, SH, Terry, MB, Toland, AE, Tollenaar, RAEM, Torres, D, Torres-Mejía, G, Troester, MA, Truong, T, Tsugane, S, Untch, M, Vachon, CM, Ouweland, AMWVD, Veen, EMV, Vijai, J, Wendt, C, Wolk, A, Yu, J-C, Zheng, W, Ziogas, A, Ziv, E, Balleine, R, Baxter, R, Braye, S, Carpenter, J, Dahlstrom, J, Forbes, J, Lee, CS, Marsh, D, Morey, A, Pathmanathan, N, Scott, R, Simpson, P, Spigelman, A, Wilcken, N, Yip, D, Zeps, N, Børresen-Dale, A-L, Grenaker Alnæs, GI, Sahlberg, KK, Ottestad, L, Kåresen, R, Schlichting, E, Holmen, MM, Sauer, T & et al. 2019, 'Two truncating variants in FANCC and breast cancer risk', Scientific Reports, vol. 9, no. 1.
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AbstractFanconi anemia (FA) is a genetically heterogeneous disorder with 22 disease-causing genes reported to date. In some FA genes, monoallelic mutations have been found to be associated with breast cancer risk, while the risk associations of others remain unknown. The gene for FA type C, FANCC, has been proposed as a breast cancer susceptibility gene based on epidemiological and sequencing studies. We used the Oncoarray project to genotype two truncating FANCC variants (p.R185X and p.R548X) in 64,760 breast cancer cases and 49,793 controls of European descent. FANCC mutations were observed in 25 cases (14 with p.R185X, 11 with p.R548X) and 26 controls (18 with p.R185X, 8 with p.R548X). There was no evidence of an association with the risk of breast cancer, neither overall (odds ratio 0.77, 95%CI 0.44–1.33, p = 0.4) nor by histology, hormone receptor status, age or family history. We conclude that the breast cancer risk association of these two FANCC variants, if any, is much smaller than for BRCA1, BRCA2 or PALB2 mutations. If this applies to all truncating variants in FANCC it would suggest there are differences between FA genes in their roles on breast cancer risk and demonstrates the merit of large consortia for clarifying risk associations of rare variants.
Douglas, ANJ, Irga, PJ & Torpy, FR 2019, 'Determining broad scale associations between air pollutants and urban forestry: A novel multifaceted methodological approach', Environmental Pollution, vol. 247, pp. 474-481.
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Global urbanisation has resulted in population densification, which is associated with increased air pollution, mainly from anthropogenic sources. One of the systems proposed to mitigate urban air pollution is urban forestry. This study quantified the spatial associations between concentrations of CO, NO₂, SO₂, and PM₁₀ and urban forestry, whilst correcting for anthropogenic sources and sinks, thus explicitly testing the hypothesis that urban forestry is spatially associated with reduced air pollution on a city scale. A Land Use Regression (LUR) model was constructed by combining air pollutant concentrations with environmental variables, such as land cover type and use, to develop predictive models for air pollutant concentrations. Traffic density and industrial air pollutant emissions were added to the model as covariables to permit testing of the main effects after correcting for these air pollutant sources. It was found that the concentrations of all air pollutants were negatively correlated with tree canopy cover and positively correlated with dwelling density, population density and traffic count. The LUR models enabled the establishment of a statistically significant spatial relationship between urban forestry and air pollution mitigation. These findings further demonstrate the spatial relationships between urban forestry and reduced air pollution on a city-wide scale, and could be of value in developing planning policies focused on urban greening.
Dua, K, Gupta, G, Chellappan, DK, Shukla, S & Hansbro, PM 2019, 'Targeting bacterial biofilms in pulmonary diseases in pediatric population', Minerva Pediatrica, vol. 71, no. 3.
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Dua, K, Malyla, V, Singhvi, G, Wadhwa, R, Krishna, RV, Shukla, SD, Shastri, MD, Chellappan, DK, Maurya, PK, Satija, S, Mehta, M, Gulati, M, Hansbro, N, Collet, T, Awasthi, R, Gupta, G, Hsu, A & Hansbro, PM 2019, 'Increasing complexity and interactions of oxidative stress in chronic respiratory diseases: An emerging need for novel drug delivery systems', Chemico-Biological Interactions, vol. 299, pp. 168-178.
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Oxidative stress is intensely involved in enhancing the severity of various chronic respiratory diseases (CRDs) including asthma, chronic obstructive pulmonary disease (COPD), infections and lung cancer. Even though there are various existing anti-inflammatory therapies, which are not enough to control the inflammation caused due to various contributing factors such as anti-inflammatory genes and antioxidant enzymes. This leads to an urgent need of novel drug delivery systems to combat the oxidative stress. This review gives a brief insight into the biological factors involved in causing oxidative stress, one of the emerging hallmark feature in CRDs and particularly, highlighting recent trends in various novel drug delivery carriers including microparticles, microemulsions, microspheres, nanoparticles, liposomes, dendrimers, solid lipid nanocarriers etc which can help in combating the oxidative stress in CRDs and ultimately reducing the disease burden and improving the quality of life with CRDs patients. These carriers improve the pharmacokinetics and bioavailability to the target site. However, there is an urgent need for translational studies to validate the drug delivery carriers for clinical administration in the pulmonary clinic.
Dua, K, Wadhwa, R, Singhvi, G, Rapalli, V, Shukla, SD, Shastri, MD, Gupta, G, Satija, S, Mehta, M, Khurana, N, Awasthi, R, Maurya, PK, Thangavelu, L, S, R, Tambuwala, MM, Collet, T, Hansbro, PM & Chellappan, DK 2019, 'The potential of siRNA based drug delivery in respiratory disorders: Recent advances and progress', Drug Development Research, vol. 80, no. 6, pp. 714-730.
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AbstractLung diseases are the leading cause of mortality worldwide. The currently available therapies are not sufficient, leading to the urgent need for new therapies with sustained anti‐inflammatory effects. Small/short or silencing interfering RNA (siRNA) has potential therapeutic implications through post‐transcriptional downregulation of the target gene expression. siRNA is essential in gene regulation, so is more favorable over other gene therapies due to its small size, high specificity, potency, and no or low immune response. In chronic respiratory diseases, local and targeted delivery of siRNA is achieved via inhalation. The effectual delivery can be attained by the generation of aerosols via inhalers and nebulizers, which overcomes anatomical barriers, alveolar macrophage clearance and mucociliary clearance. In this review, we discuss the different siRNA nanocarrier systems for chronic respiratory diseases, for safe and effective delivery. siRNA mediated pro‐inflammatory gene or miRNA targeting approach can be a useful approach in combating chronic respiratory inflammatory conditions and thus providing sustained drug delivery, reduced therapeutic dose, and improved patient compliance. This review will be of high relevance to the formulation, biological and translational scientists working in the area of respiratory diseases.
Duke, NC, Field, C, Mackenzie, JR, Meynecke, J-O & Wood, AL 2019, 'Rainfall and its possible hysteresis effect on the proportional cover of tropical tidal-wetland mangroves and saltmarsh–saltpans', Marine and Freshwater Research, vol. 70, no. 8, pp. 1047-1047.
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Mangrove–saltmarsh tidal wetlands are highly dynamic ecosystems, responding and adapting to climate and physical conditions at all spatial and temporal scales. Knowledge of the large-scale ecosystem processes involved and how they might be influenced by climate variables is highly relevant today. For tidal-wetland sites well within the latitudinal range of the mostly tropical mangrove communities, we confirm that average annual rainfall influences vegetative cover, as well as species composition and biomass of tidal wetlands. On the basis of 205 largely unmodified, tropical and subtropical estuaries of northern Australia, a sigmoidal relationship, with a centroid inflection point ~1368mm, was derived between rainfall and the relative amounts of high-biomass mangroves and low-biomass saltmarsh–saltpan vegetation. The presence and probability of observed combinations of these community types were quantified using the wetland cover index, which is the ratio of total mangrove area to that of mangroves plus intertidal saltmarsh and saltpans. Accordingly, periodic changes in rainfall trends are likely manifest as either encroachment or dieback of mangroves along the ecotones separating them from tidal saltmarsh–saltpans. Presented is a new conceptual framework and model that describes how such ecosystem-scale processes take place in tropical and subtropical tidal wetlands.
Dukic, E, Herdean, A, Cheregi, O, Sharma, A, Nziengui, H, Dmitruk, D, Solymosi, K, Pribil, M & Spetea, C 2019, 'K+ and Cl− channels/transporters independently fine-tune photosynthesis in plants', Scientific Reports, vol. 9, no. 1.
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AbstractIn variable light environments, plants adjust light use in photosynthetic electron transport and photoprotective dissipation in the thylakoid membrane. In this respect, roles of the K+/H+ antiporter KEA3, the Cl− channel/transporter CLCe and the voltage-dependent Cl− channel VCCN1 have been unraveled in Arabidopsis thaliana. Here we report that they independently adjust photosynthesis on the basis of analyses using single and higher order loss-of-function mutants. In short experiments of photosynthetic response on transition from dark to low light, we reveal a sequential functioning of VCCN1 and CLCe in the activation of photoprotection and of KEA3 in its downregulation to a low steady state while adjusting the electron transport. On transition from low to high light, VCCN1 accelerates the activation of photoprotection, whereas KEA3 slows it down on transition from high to low light. Based on parallel electrochromic band shift measurements, the mechanism behind is that VCCN1 builds up a pH gradient across the thylakoid membrane, whereas KEA3 dissipates this gradient, which affects photoprotection. CLCe regulates photosynthesis by a pH-independent mechanism likely involving Cl− homeostasis. Nevertheless, all genotypes grow well in alternating high and low light. Taken together, the three studied ion channels/transporters function independently in adjusting photosynthesis to the light environment.
Duong, NMH, Glushkov, E, Chernev, A, Navikas, V, Comtet, J, Nguyen, MAP, Toth, M, Radenovic, A, Tran, TT & Aharonovich, I 2019, 'Facile Production of Hexagonal Boron Nitride Nanoparticles by Cryogenic Exfoliation', Nano Letters, vol. 19, no. 8, pp. 5417-5422.
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Fluorescent nanoparticles with optically robust luminescence are imperative to applications in imaging and labeling. Here we demonstrate that hexagonal boron nitride (hBN) nanoparticles can be reliably produced using a scalable cryogenic exfoliation technique with sizes below 10 nm. The particles exhibit bright fluorescence generated by color centers that act as atomic-size quantum emitters. We analyze their optical properties, including emission wavelength, photon-statistics, and photodynamics, and show that they are suitable for far-field super-resolution fluorescence nanoscopy. Our results provide a foundation for exploration of hBN nanoparticles as candidates for bioimaging, labeling, as well as biomarkers that are suitable for quantum sensing.
Eapen, MS, Sharma, P, Gaikwad, AV, Lu, W, Myers, S, Hansbro, PM & Sohal, SS 2019, '<p>Epithelial–mesenchymal transition is driven by transcriptional and post transcriptional modulations in COPD: implications for disease progression and new therapeutics</p>', International Journal of Chronic Obstructive Pulmonary Disease, vol. Volume 14, pp. 1603-1610.
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COPD is a common and highly destructive disease with huge impacts on people and health services throughout the world. It is mainly caused by cigarette smoking though environmental pollution is also significant. There are no current treatments that affect the overall course of COPD; current drugs focus on symptomatic relief and to some extent reducing exacerbation rates. There is an urgent need for in-depth studies of the fundamental pathogenic mechanisms that underpin COPD. This is vital, given the fact that nearly 40%-60% of the small airway and alveolar damage occurs in COPD well before the first measurable changes in lung function are detected. These individuals are also at a high risk of lung cancer. Current COPD research is mostly centered around late disease and/or innate immune activation within the airway lumen, but the actual damage to the airway wall has early onset. COPD is the end result of complex mechanisms, possibly triggered through initial epithelial activation. To change the disease trajectory, it is crucial to understand the mechanisms in the epithelium that are switched on early in smokers. One such mechanism we believe is the process of epithelial to mesenchymal transition. This article highlights the importance of this profound epithelial cell plasticity in COPD and also its regulation. We consider that understanding early changes in COPD will open new windows for therapy.
Eapen, MS, Sharma, P, Moodley, YP, Hansbro, PM & Sohal, SS 2019, 'Dysfunctional Immunity and Microbial Adhesion Molecules in Smoking-induced Pneumonia', American Journal of Respiratory and Critical Care Medicine, vol. 199, no. 2, pp. 250-251.
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Eapen, MS, Sharma, P, Thompson, IE, Lu, W, Myers, S, Hansbro, PM & Sohal, SS 2019, 'Heparin-binding epidermal growth factor (HB-EGF) drives EMT in patients with COPD: implications for disease pathogenesis and novel therapies', Laboratory Investigation, vol. 99, no. 2, pp. 150-157.
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Chronic obstructive pulmonary disease (COPD) is a progressive and devastating chronic lung condition that has a significant global burden, both medically and financially. Currently there are no medications that can alter the course of disease. At best, the drugs in clinical practice provide symptomatic relief to suffering patients by alleviating acute exacerbations. Most of current clinical research activities are in late severe disease with lesser attention given to early disease manifestations. There is as yet, a lack of understanding of the underlying mechanisms of disease progression and the molecular switches that are involved in their manifestation. Small airway fibrosis and obliteration are known to cause fixed airflow obstruction in COPD, and the consequential damage to the lung has an early onset. So far, there is little evidence of the mechanisms that underlie this aspect of pathology. However, emerging research confirms that airway epithelial reprogramming or epithelial to mesenchymal transition (EMT) is a key mechanism that drives fibrotic remodelling changes in smokers and patients with COPD. A recent study by Lai et al. further highlights the importance of EMT in smoking-related COPD pathology. The authors identify HB-EGF, an EGFR ligand, as a key driver of EMT and a potential new therapeutic target for the amelioration of EMT and airway remodelling. There are also wider implications in lung cancer prophylaxis, which is another major comorbidity associated with COPD. We consider that improved molecular understanding of the intricate pathways associated with epithelial cell plasticity in smokers and patients with COPD will have major therapeutic implications.
Eggleton, BJ, Poulton, CG, Rakich, PT, Steel, MJ & Bahl, G 2019, 'Brillouin integrated photonics', Nature Photonics, vol. 13, no. 10, pp. 664-677.
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© 2019, Springer Nature Limited. A recent renaissance in Brillouin scattering research has been driven by the increasing maturity of photonic integration platforms and nanophotonics. The result is a new breed of chip-based devices that exploit acousto-optic interactions to create lasers, amplifiers, filters, delay lines and isolators. Here, we provide a detailed overview of Brillouin scattering in integrated waveguides and resonators, covering key concepts such as the stimulation of the Brillouin process, in which the optical field itself induces acoustic vibrations, the importance of acoustic confinement, methods for calculating and measuring Brillouin gain, and the diversity of materials platforms and geometries. Our Review emphasizes emerging applications in microwave photonics, signal processing and sensing, and concludes with a perspective for future directions.
Eijkelkamp, BA, Morey, JR, Neville, SL, Tan, A, Pederick, VG, Cole, N, Singh, PP, Ong, C-LY, Gonzalez de Vega, R, Clases, D, Cunningham, BA, Hughes, CE, Comerford, I, Brazel, EB, Whittall, JJ, Plumptre, CD, McColl, SR, Paton, JC, McEwan, AG, Doble, PA & McDevitt, CA 2019, 'Dietary zinc and the control of Streptococcus pneumoniae infection', PLOS Pathogens, vol. 15, no. 8, pp. e1007957-e1007957.
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Human zinc deficiency increases susceptibility to bacterial infection. Although zinc supplementation therapies can reduce the impact of disease, the molecular basis for protection remains unclear. Streptococcus pneumoniae is a major cause of bacterial pneumonia, which is prevalent in regions of zinc deficiency. We report that dietary zinc levels dictate the outcome of S. pneumoniae infection in a murine model. Dietary zinc restriction impacts murine tissue zinc levels with distribution post-infection altered, and S. pneumoniae virulence and infection enhanced. Although the activation and infiltration of murine phagocytic cells was not affected by zinc restriction, their efficacy of bacterial control was compromised. S. pneumoniae was shown to be highly sensitive to zinc intoxication, with this process impaired in zinc restricted mice and isolated phagocytic cells. Collectively, these data show how dietary zinc deficiency increases sensitivity to S. pneumoniae infection while revealing a role for zinc as a component of host antimicrobial defences.
Elbadawi, C, Fröch, JE, Aharonovich, I, Toth, M & Lobo, CJ 2019, 'One-Step Nanoscale Patterning of Silver Nanowire–Nitride Heterostructures Using Substrate-Assisted Chemical Etching', The Journal of Physical Chemistry C, vol. 123, no. 1, pp. 945-949.
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© 2018 American Chemical Society. Nanoscale etching and patterning of noble metals such as copper, silver, and gold are extremely difficult to achieve due to the low volatility of group 11 metal compounds. Here, we introduce a method of nanoscale chemical etching that involves reactions between H2O adsorbates and N radicals generated from electron-beam-induced etching (EBIE) of a hexagonal boron nitride or AlN substrate to achieve efficient and highly localized chemical etching of Ag nanowires and the underlying substrate. The volatilization of noble metal nanowires by radical species generated during EBIE of the underlying substrate represents a new class of EBIE reactions, which we term "substrate-assisted chemical etching".
Elise, S, Bailly, A, Urbina-Barreto, I, Mou-Tham, G, Chiroleu, F, Vigliola, L, Robbins, WD & Bruggemann, JH 2019, 'An optimised passive acoustic sampling scheme to discriminate among coral reefs’ ecological states', Ecological Indicators, vol. 107, pp. 105627-105627.
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© 2019 The Authors In the present era of rapid global change, innovative monitoring methods can greatly enhance our ability to detect ecological disturbances and prioritise conservation areas in a timely and cost-effective manner. While Passive Acoustic Monitoring (PAM) has recently emerged as a promising tool for monitoring ecological states in marine environments, the specifics of how to apply this method remains poorly defined. In this study we examined how different combinations of sampling settings (frequency bandwidth, time of sampling (day/night), and sample duration) influenced the ability of two acoustic indices, the Sound Pressure Level (SPL) and the Acoustic Complexity Index (ACI), to discriminate different ecological states (ecostates) of coral reefs. We applied an iterative approach to select the most efficient and consistent combinations of sampling settings to use for these two acoustic indices, depending on the stability of their discriminating power across different time scales (successive days, moon phases, and seasons), and the minimum sampling effort required for reliable ecostate assessment. The ability of SPL and ACI to discriminate ecostate-specific soundscapes was more stable and required less sampling effort at nighttime. For indices calculated in the higher frequency band (>2 kHz), very short recording times (≤20 min divided into 5 s samples) were sufficient to discriminate ecostates, whereas longer recording times (≥200 min divided into 5 min samples) were necessary when using indices calculated in the lower frequency bands (<1 kHz). An optimised sampling scheme, i.e. the group of the five best combinations of settings to discern among coral reef ecostates, was determined at Reunion Island, Indian Ocean, then tested at New Caledonia, Pacific Ocean. Here, the classifications obtained through visual surveys and with the optimised acoustic sampling scheme were congruent. The concordance of our results with visual fish counts confirms the p...
Ende, JA, Ahmadzad, S, Christensen, JM, Oliver, B, Estephan, T, Alvarado, R, Rimmer, J & Harvey, RJ 2019, 'Isolated respiratory epithelials cell in suspension exhibiting ciliary activity', ASVIDE, vol. 6, pp. 62-62.
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Ende, JA, Ahmadzada, S, Christensen, JM, Oliver, B, Estepha, T, Alvarado, R, Rimmer, J & Harvey, RJ 2019, 'An ALI culture well with well-differentiated respiratory epithelium demonstrating coordinated ciliary activity and mucociliary clearance', ASVIDE, vol. 6, pp. 64-64.
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Ende, JA, Ahmadzada, S, Christensen, JM, Oliver, B, Estephan, T, Alvarado, R, Rimmer, J & Harvey, RJ 2019, 'An ALI culture well exhibiting well-differentiated respiratory epithelium with ciliary activity', ASVIDE, vol. 6, pp. 63-63.
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Ernst, A, Fung, J, Singh, G & Zinder, Y 2019, 'Flexible flow shop with dedicated buffers', Discrete Applied Mathematics, vol. 261, pp. 148-163.
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© 2018 Elsevier B.V. A two-stage flexible flow shop is considered, where first- and second-stage machines form disjoint pairs, each with a buffer. The buffer capacity varies from pair to pair, and the buffer requirement varies from job to job. Each job is to be assigned to a pair of machines for processing and uses the required amount of buffer from the start till the end of its processing. Operations have equal duration. It is shown that, unless P=NP, no polynomial-time algorithm guarantees a makespan less than 4∕3 of the optimal. The paper presents two integer linear programs, compared by means of computational experiments. Both approaches utilise as a subroutine the developed polynomial-time algorithm for the case of equal buffers.
Espinoza-Vergara, G, Noorian, P, Silva-Valenzuela, CA, Raymond, BBA, Allen, C, Hoque, MM, Sun, S, Johnson, MS, Pernice, M, Kjelleberg, S, Djordjevic, SP, Labbate, M, Camilli, A & McDougald, D 2019, 'Vibrio cholerae residing in food vacuoles expelled by protozoa are more infectious in vivo', Nature Microbiology, vol. 4, no. 12, pp. 2466-2474.
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Eun-Sol Oh, J, Walsh, S & Zaslawski, C 2019, 'A snapshot of Chinese Medicine practice in Australia over a 10 year period (2006–2016): Moving towards integrative clinical care', Advances in Integrative Medicine, vol. 6, pp. S35-S35.
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Ewans, LJ, Colley, A, Gaston-Massuet, C, Gualtieri, A, Cowley, MJ, McCabe, MJ, Anand, D, Lachke, SA, Scietti, L, Forneris, F, Zhu, Y, Ying, K, Walsh, C, Kirk, EP, Miller, D, Giunta, C, Sillence, D, Dinger, M, Buckley, M & Roscioli, T 2019, 'Pathogenic variants in PLOD3 result in a Stickler syndrome-like connective tissue disorder with vascular complications', Journal of Medical Genetics, vol. 56, no. 9, pp. 629-638.
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BackgroundPathogenic PLOD3 variants cause a connective tissue disorder (CTD) that has been described rarely. We further characterise this CTD and propose a clinical diagnostic label to improve recognition and diagnosis of PLOD3-related disease.MethodsReported PLOD3 phenotypes were compared with known CTDs utilising data from three further individuals from a consanguineous family with a homozygous PLOD3 c.809C>T; p.(Pro270Leu) variant. PLOD3 mRNA expression in the developing embryo was analysed for tissue-specific localisation. Mouse microarray expression data were assessed for phylogenetic gene expression similarities across CTDs with overlapping clinical features.ResultsKey clinical features included ocular abnormalities with risk for retinal detachment, sensorineural hearing loss, reduced palmar creases, finger contractures, prominent knees, scoliosis, low bone mineral density, recognisable craniofacial dysmorphisms, developmental delay and risk for vascular dissection. Collated clinical features showed most overlap with Stickler syndrome with variable features of Ehlers-Danlos syndrome (EDS) and epidermolysis bullosa (EB). Human lysyl hydroxylase 3/PLOD3 expression was localised to the developing cochlea, eyes, skin, forelimbs, heart and cartilage, mirroring the clinical phenotype of this disorder.ConclusionThese data are consistent with pathogenic variants in PLOD3 resulting in a clinically distinct Stickler-like syndrome with vascular complications and variable features of EDS and EB. Early identification of PLOD3 variants would improve monit...
Facey, JA, Apte, SC & Mitrovic, SM 2019, 'A Review of the Effect of Trace Metals on Freshwater Cyanobacterial Growth and Toxin Production', Toxins, vol. 11, no. 11, pp. 643-643.
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Cyanobacterial blooms are becoming more common in freshwater systems, causing ecological degradation and human health risks through exposure to cyanotoxins. The role of phosphorus and nitrogen in cyanobacterial bloom formation is well documented and these are regularly the focus of management plans. There is also strong evidence that trace metals are required for a wide range of cellular processes, however their importance as a limiting factor of cyanobacterial growth in ecological systems is unclear. Furthermore, some studies have suggested a direct link between cyanotoxin production and some trace metals. This review synthesises current knowledge on the following: (1) the biochemical role of trace metals (particularly iron, cobalt, copper, manganese, molybdenum and zinc), (2) the growth limitation of cyanobacteria by trace metals, (3) the trace metal regulation of the phytoplankton community structure and (4) the role of trace metals in cyanotoxin production. Iron dominated the literature and regularly influenced bloom formation, with 15 of 18 studies indicating limitation or colimitation of cyanobacterial growth. A range of other trace metals were found to have a demonstrated capacity to limit cyanobacterial growth, and these metals require further study. The effect of trace metals on cyanotoxin production is equivocal and highly variable. Better understanding the role of trace metals in cyanobacterial growth and bloom formation is an essential component of freshwater management and a direction for future research.
Facey, JA, Steele, JR, Violi, JP, Mitrovic, SM & Cranfield, C 2019, 'An examination of microcystin-LR accumulation and toxicity using tethered bilayer lipid membranes (tBLMs)', Toxicon, vol. 158, pp. 51-56.
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Microcystin-LR (MC-LR) is a potent cyanobacterial toxin responsible for animal and human poisonings worldwide. MC-LR is found in organisms throughout the foodweb, however there is conjecture regarding whether it biomagnifies. Few studies have investigated how MC-LR interacts with lipid membranes, a determinant of biomagnification potential. We tested whether 1 μM MC-LR irreversibly associates with lipid bilayers or causes the creation of pore defects upon short and long-term exposure. Using tethered bilayer lipid membranes (tBLMs), we observed an increase in membrane conduction in tBLMs, representing an interaction of microcystin-LR with the lipid bilayer and a change in membrane packing properties. However, there were minimal changes in membrane capacitance upon short and long-term exposure, and MC-LR exhibited a rapid off-rate. Upon 24 h exposure to the toxin, no lipophilic multimeric complexes were detected capable of altering the toxin's off-rate. There was no evidence of the creation of new pores. This study demonstrates that MC-LR does not irreversibly imbed itself into lipids membranes after short or long-term exposure and suggests MC-LR does not biomagnify through the food web via lipid storage.
Faiz, A, Steiling, K, Roffel, MP, Postma, DS, Spira, A, Lenburg, ME, Borggrewe, M, Eijgenraam, TR, Jonker, MR, Koppelman, GH, Pouwels, SD, Liu, G, Alekseyev, YO, Lam, S, Hiemstra, PS, Sterk, PJ, Timens, W, Brandsma, C-A, Heijink, IH & van den Berge, M 2019, 'Effect of long-term corticosteroid treatment on microRNA and gene-expression profiles in COPD', European Respiratory Journal, vol. 53, no. 4, pp. 1801202-1801202.
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The aim was to investigate whether microRNA (miRNA) expression is modulated by inhaled corticosteroid (ICS) treatmentWe performed genome-wide miRNA analysis on bronchial biopsies of 69 moderate/severe chronic obstructive pulmonary disease (COPD) patients at baseline and after 6- and 30-month treatment with the ICS fluticasone propionate or placebo. The effect of ICS on miRNA expression was validated in differentiated primary bronchial epithelial cultures, and functional studies were conducted in BEAS-2B cells. MiRNAs affected by ICS and their predicted targets were compared to an independent miRNA dataset of bronchial brushings from COPD patients and healthy controls.Treatment with ICS for both 6 and 30 months significantly altered the expression of four miRNAs, including miR-320d, which was increased during ICS treatment compared with placebo. The ICS-induced increase of miR-320d was confirmed in primary airway epithelial cells. MiR-320d negatively correlated targets were enriched for pro-inflammatory genes and were increased in the bronchial brushes of patients with lower lung function in the independent dataset. Overexpression of miR-320d in BEAS-2B cells dampened cigarette smoke extract-induced pro-inflammatory activity via inhibition of nuclear factor-κB.Collectively, we identified miR-320d as a novel mediator of ICS, regulating the pro-inflammatory response of the airway epithelium.
Faiz, A, van den Berge, M, Vermeulen, CJ, ten Hacken, NHT, Guryev, V & Pouwels, SD 2019, 'AGER expression and alternative splicing in bronchial biopsies of smokers and never smokers', Respiratory Research, vol. 20, no. 1.
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Cigarette smoking is one of the major risk factors for the development of chronic obstructive pulmonary disease (COPD). Evidence is accumulating that Receptor for Advanced Glycation-End products (RAGE)-signaling is a key pathway in the pathophysiology of COPD. To date, it is unknown how smoking affects RAGE expression. In the current study, we investigated the effect of smoking on AGER, the gene encoding RAGE, expression and on alternative splicing of AGER. To this end, we conducted RNA-Seq on bronchial biopsies for asymptomatic smokers (n = 36) and never smokers (n = 40). Total AGER gene expression was accessed using DESeq2, while alternative splicing was investigated by measuring the number of specific split reads spanning exon-exon junctions and the total split reads. One of the major isoforms of RAGE is endogenous soluble (es) RAGE, an anti-inflammatory decoy receptor, making up for approximately 10% of the total amount of soluble (s)RAGE. We found that smokers show decreased total gene expression of AGER in bronchial biopsies, while the relative abundance of the esRAGE isoform is increased. Furthermore, no difference in the serum levels of total sRAGE were observed between smokers and non-smokers. Our data indicates that smoking initiates a protective anti-inflammatory mechanism with decreased expression of the pro-inflammatory gene AGER and increased relative abundance of the anti-inflammatory isoform esRAGE.
Fan, X, McLaughlin, C, Robinson, C, Ravasini, J, Schelch, K, Johnson, T, Zandwijk, N, Reid, G & George, AM 2019, 'Zeolites ameliorate asbestos toxicity in a transgenic model of malignant mesothelioma', FASEB BioAdvances, vol. 1, no. 9, pp. 550-560.
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Fang, G, Lu, H, Law, A, Gallego-Ortega, D, Jin, D & Lin, G 2019, 'Gradient-sized control of tumor spheroids on a single chip', Lab on a Chip, vol. 19, no. 24, pp. 4093-4103.
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Gradient-sized spheroids can be simultaneously generated on a single chip using a liquid-dome method assisted by the surface tension. The facile method can be used for investigation of the size-dependent behaviors of spheroids in biomedical research.
Farjana, SH, Huda, N & Mahmud, MAP 2019, 'Life cycle analysis of copper-gold-lead-silver-zinc beneficiation process', Science of The Total Environment, vol. 659, pp. 41-52.
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Farjana, SH, Huda, N & Mahmud, MAP 2019, 'Life cycle assessment of cobalt extraction process', Journal of Sustainable Mining, vol. 18, no. 3, pp. 150-161.
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Farjana, SH, Huda, N, Mahmud, MAP & Lang, C 2019, 'A global life cycle assessment of manganese mining processes based on EcoInvent database', Science of The Total Environment, vol. 688, pp. 1102-1111.
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Farjana, SH, Huda, N, Mahmud, MAP & Lang, C 2019, 'Impact analysis of gold silver refining processes through life-cycle assessment', Journal of Cleaner Production, vol. 228, pp. 867-881.
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Farjana, SH, Huda, N, Mahmud, MAP & Lang, C 2019, 'Life-cycle assessment of solar integrated mining processes: A sustainable future', Journal of Cleaner Production, vol. 236, pp. 117610-117610.
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Fergie, N, Todd, N, McClements, L, McAuley, D, O'Kane, C & Krasnodembskaya, A 2019, 'Hypercapnic acidosis induces mitochondrial dysfunction and impairs the ability of mesenchymal stem cells to promote distal lung epithelial repair', The FASEB Journal, vol. 33, no. 4, pp. 5585-5598.
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Ferreira, MA, Gamazon, ER, Al-Ejeh, F, Aittomäki, K, Andrulis, IL, Anton-Culver, H, Arason, A, Arndt, V, Aronson, KJ, Arun, BK, Asseryanis, E, Azzollini, J, Balmaña, J, Barnes, DR, Barrowdale, D, Beckmann, MW, Behrens, S, Benitez, J, Bermisheva, M, Białkowska, K, Blomqvist, C, Bogdanova, NV, Bojesen, SE, Bolla, MK, Borg, A, Brauch, H, Brenner, H, Broeks, A, Burwinkel, B, Caldés, T, Caligo, MA, Campa, D, Campbell, I, Canzian, F, Carter, J, Carter, BD, Castelao, JE, Chang-Claude, J, Chanock, SJ, Christiansen, H, Chung, WK, Claes, KBM, Clarke, CL, Adlard, J, Ahmed, M, Barwell, J, Brady, A, Brewer, C, Cook, J, Davidson, R, Donaldson, A, Eason, J, Eeles, R, Evans, DG, Gregory, H, Hanson, H, Henderson, A, Hodgson, S, Izatt, L, Kennedy, MJ, Lalloo, F, Miller, C, Morrison, PJ, Ong, K-R, Perkins, J, Porteous, ME, Rogers, MT, Side, LE, Snape, K, Walker, L, Harrington, PA, Arnold, N, Auber, B, Bogdanova-Markov, N, Borde, J, Caliebe, A, Ditsch, N, Dworniczak, B, Engert, S, Faust, U, Gehrig, A, Hahnen, E, Hauke, J, Hentschel, J, Herold, N, Honisch, E, Just, W, Kast, K, Larsen, M, Lemke, J, Nguyen, HP, Niederacher, D, Ott, C-E, Platzer, K, Pohl-Rescigno, E, Ramser, J, Rhiem, K, Steinemann, D, Sutter, C, Varon-Mateeva, R, Wang-Gohrke, S, Weber, BHF, Prieur, F, Pujol, P, Sagne, C, Sevenet, N, Sobol, H, Sokolowska, J, Stoppa-Lyonnet, D, Venat-Bouvet, L, Couch, FJ, Cox, A, Cross, SS, Czene, K, Daly, MB, de la Hoya, M, Dennis, J, Devilee, P, Diez, O, Dörk, T, Dunning, AM, Dwek, M, Eccles, DM, Ejlertsen, B, Ellberg, C, Engel, C, Eriksson, M, Fasching, PA, Fletcher, O, Flyger, H, Friedman, E, Frost, D, Gabrielson, M, Gago-Dominguez, M, Ganz, PA, Gapstur, SM, Garber, J, García-Closas, M, García-Sáenz, JA, Gaudet, MM, Giles, GG, Glendon, G, Godwin, AK, Goldberg, MS, Goldgar, DE, González-Neira, A, Greene, MH, Gronwald, J, Guénel, P, Haiman, CA, Hall, P, Hamann, U, He, W, Heyworth, J, Hogervorst, FBL, Hollestelle, A, Hoover, RN, Hopper, JL, Hulick, PJ, Humphreys, K, Imyanitov, EN, Balleine, R, Baxter, R, Braye, S, Carpenter, J, Dahlstrom, J, Forbes, J, Lee, SC, Marsh, D, Morey, A, Pathmanathan, N, Simpson, P, Spigelman, A, Wilcken, N, Yip, D, Heemskerk-Gerritsen, BAM, Rookus, MA, Seynaeve, CM, van der Baan, FH, van der Hout, AH, van der Kolk, LE, van der Luijt, RB, van Deurzen, CHM, van Doorn, HC, van Engelen, K, van Hest, L, van Os, TAM & et al. 2019, 'Genome-wide association and transcriptome studies identify target genes and risk loci for breast cancer', Nature Communications, vol. 10, no. 1.
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AbstractGenome-wide association studies (GWAS) have identified more than 170 breast cancer susceptibility loci. Here we hypothesize that some risk-associated variants might act in non-breast tissues, specifically adipose tissue and immune cells from blood and spleen. Using expression quantitative trait loci (eQTL) reported in these tissues, we identify 26 previously unreported, likely target genes of overall breast cancer risk variants, and 17 for estrogen receptor (ER)-negative breast cancer, several with a known immune function. We determine the directional effect of gene expression on disease risk measured based on single and multiple eQTL. In addition, using a gene-based test of association that considers eQTL from multiple tissues, we identify seven (and four) regions with variants associated with overall (and ER-negative) breast cancer risk, which were not reported in previous GWAS. Further investigation of the function of the implicated genes in breast and immune cells may provide insights into the etiology of breast cancer.
Figlioli, G, Bogliolo, M, Catucci, I, Caleca, L, Lasheras, SV, Pujol, R, Kiiski, JI, Muranen, TA, Barnes, DR, Dennis, J, Michailidou, K, Bolla, MK, Leslie, G, Aalfs, CM, Balleine, R, Baxter, R, Braye, S, Carpenter, J, Dahlstrom, J, Forbes, J, Lee, CS, Marsh, D, Morey, A, Pathmanathan, N, Scott, R, Simpson, P, Spigelman, A, Wilcken, N, Yip, D, Zeps, N, Adank, MA, Adlard, J, Agata, S, Cadoo, K, Agnarsson, BA, Ahearn, T, Aittomäki, K, Ambrosone, CB, Andrews, L, Anton-Culver, H, Antonenkova, NN, Arndt, V, Arnold, N, Aronson, KJ, Arun, BK, Asseryanis, E, Auber, B, Auvinen, P, Azzollini, J, Balmaña, J, Barkardottir, RB, Barrowdale, D, Barwell, J, Beane Freeman, LE, Beauparlant, CJ, Beckmann, MW, Behrens, S, Benitez, J, Berger, R, Bermisheva, M, Blanco, AM, Blomqvist, C, Bogdanova, NV, Bojesen, A, Bojesen, SE, Bonanni, B, Borg, A, Brady, AF, Brauch, H, Brenner, H, Brüning, T, Burwinkel, B, Buys, SS, Caldés, T, Caliebe, A, Caligo, MA, Campa, D, Campbell, IG, Canzian, F, Castelao, JE, Chang-Claude, J, Chanock, SJ, Claes, KBM, Clarke, CL, Collavoli, A, Conner, TA, Cox, DG, Cybulski, C, Czene, K, Daly, MB, de la Hoya, M, Devilee, P, Diez, O, Ding, YC, Dite, GS, Ditsch, N, Domchek, SM, Dorfling, CM, dos-Santos-Silva, I, Durda, K, Dwek, M, Eccles, DM, Ekici, AB, Eliassen, AH, Ellberg, C, Eriksson, M, Evans, DG, Fasching, PA, Figueroa, J, Flyger, H, Foulkes, WD, Friebel, TM, Friedman, E, Gabrielson, M, Gaddam, P, Gago-Dominguez, M, Gao, C, Gapstur, SM, Garber, J, García-Closas, M, García-Sáenz, JA, Gaudet, MM, Gayther, SA, Belotti, M, Bertrand, O, Birot, A-M, Buecher, B, Caputo, S, Dupré, A, Fourme, E, Gauthier-Villars, M, Golmard, L, Le Mentec, M, Moncoutier, V, de Pauw, A, Saule, C, Boutry-Kryza, N, Calender, A, Giraud, S, Léone, M, Bressac-de-Paillerets, B, Caron, O, Guillaud-Bataille, M, Bignon, Y-J, Uhrhammer, N, Bonadona, V, Lasset, C, Berthet, P, Castera, L, Vaur, D, Bourdon, V, Noguès, C, Noguchi, T, Popovici, C, Remenieras, A, Sobol, H, Coupier, I, Pujol, P, Adenis, C, Dumont, A, Révillion, F, Muller, D, Barouk-Simonet, E, Bonnet, F, Bubien, V, Longy, M, Sevenet, N, Gladieff, L, Guimbaud, R, Feillel, V, Toulas, C, Dreyfus, H, Leroux, CD, Peysselon, M, Rebischung, C, Legrand, C, Baurand, A, Bertolone, G, Coron, F, Faivre, L, Jacquot, C, Lizard, S, Kientz, C, Lebrun, M, Prieur, F, Fert-Ferrer, S, Mari, V, Vénat-Bouvet, L, Bézieau, S & et al. 2019, 'The FANCM:p.Arg658* truncating variant is associated with risk of triple-negative breast cancer', npj Breast Cancer, vol. 5, no. 1.
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AbstractBreast cancer is a common disease partially caused by genetic risk factors. Germline pathogenic variants in DNA repair genes BRCA1, BRCA2, PALB2, ATM, and CHEK2 are associated with breast cancer risk. FANCM, which encodes for a DNA translocase, has been proposed as a breast cancer predisposition gene, with greater effects for the ER-negative and triple-negative breast cancer (TNBC) subtypes. We tested the three recurrent protein-truncating variants FANCM:p.Arg658*, p.Gln1701*, and p.Arg1931* for association with breast cancer risk in 67,112 cases, 53,766 controls, and 26,662 carriers of pathogenic variants of BRCA1 or BRCA2. These three variants were also studied functionally by measuring survival and chromosome fragility in FANCM−/− patient-derived immortalized fibroblasts treated with diepoxybutane or olaparib. We observed that FANCM:p.Arg658* was associated with increased risk of ER-negative disease and TNBC (OR = 2.44, P = 0.034 and OR = 3.79; P = 0.009, respectively). In a country-restricted analysis, we confirmed the associations detected for FANCM:p.Arg658* and found that also FANCM:p.Arg1931* was associated with ER-negative breast cancer risk (OR = 1.96; P = 0.006). The functional results indicated that all three variants were deleterious affecting cell survival and chromosome stability with FANCM:p.Arg658* causing more severe phenotypes. In conclusion, we confirmed that the two rare FANCM d...
Figueira, WF, Curley, B & Booth, DJ 2019, 'Can temperature-dependent predation rates regulate range expansion potential of tropical vagrant fishes?', Marine Biology, vol. 166, no. 6.
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© 2019, Springer-Verlag GmbH Germany, part of Springer Nature. The effect of temperature on predator–prey dynamics has the potential to be an important factor regulating ecological interactions and is becoming increasingly common due to climate-change-driven range shifts and species introductions. Here, we use mesocosm experiments to evaluate the thermal sensitivity of burst swimming (a proxy for prey escape ability) and mortality rates of cohorts of introduced tropical and resident temperate marine fishes in the presence of a local temperate predator. Increasing temperature (17–21–25 °C) resulted in a reduction in predation rates (by Hypoplectrodes maccullochi, family Serranidae) on the tropical prey species (Abudefduf vaigiensis, family Pomacentridae) which were more warm adapted, whereas predation rates on the temperate prey species (Atypichthys strigatus, family Kyphosidae) remained unchanged over the 17–21 °C range (25 °C not tested). These changes were linearly related to predator–prey burst swimming ratios, which decreased with increasing temperature for the tropical prey but remained largely unchanged for the temperate prey. By demonstrating the temperature sensitivity of predator–prey interactions, our work highlights the importance of linking physiology with ecology to understand the consequences of climate-driven range shifts and species introductions.
Filippini, G, Bugnot, AB, Johnston, EL, Ruszczyk, J, Potts, J, Scanes, P, Ferguson, A, Ostrowski, M, Varkey, D & Dafforn, KA 2019, 'Sediment bacterial communities associated with environmental factors in Intermittently Closed and Open Lakes and Lagoons (ICOLLs)', Science of The Total Environment, vol. 693, pp. 133462-133462.
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Intermittently Closed and Open Lakes and Lagoons (ICOLLS) are important coastal systems that are periodically separated from the ocean by a sand barrier or a berm. In urban ICOLLs, continuous inputs of organic material and nutrients into coastal lagoons are contributing to eutrophic conditions that, together with natural environmental factors have implications for the resident sediment bacterial communities. We used molecular tools to investigate the ecological communities of four ICOLLs; Narrabeen, Dee Why, Curl Curl and Manly in Sydney, Australia, which have been subjected to increasing pressure from anthropogenic activities over the last century. We used targeted gene sequencing of the prokaryotic 16S ribosomal RNA gene to describe the bacterial diversity and community structure and discuss differences with respect to environmental factors at the ICOLL scale (e.g. size, shape, normalised N loading) and site scale (e.g. water and sediment quality) within each lagoon. Due to differences in hydrological patterns, we expected that sediment bacterial communities would be more heterogenous in displacement-dominated lagoons (Curl Curl and Manly) than the mixing-dominated lagoons (Narrabeen and Dee Why). Interestingly, we did not find strong relationships between the main bacterial groups and distance from the lagoon entrance (used as a proxy for salinity and silt) in the displacement-dominated lagoons. Moreover, we found that α diversity was highest in Narrabeen and Manly lagoons despite differences in lagoon size and shape. Furthermore, while bacterial community structure was similar in Curl Curl and Dee Why, communities in Manly and Narrabeen differed along temperature/TOC and salinity/silt gradients respectively. In Manly lagoon, we found relatively more anaerobic bacteria such as Epsilonbactereota which is involved in the oxidation and reduction of sulfur compounds. Moreover, we identified several bacterial taxa (including sulfur metabolising Chlorobiaceae) relat...
Findlay, AD, Foot, JS, Buson, A, Deodhar, M, Jarnicki, AG, Hansbro, PM, Liu, G, Schilter, H, Turner, CI, Zhou, W & Jarolimek, W 2019, 'Identification and Optimization of Mechanism-Based Fluoroallylamine Inhibitors of Lysyl Oxidase-like 2/3', Journal of Medicinal Chemistry, vol. 62, no. 21, pp. 9874-9889.
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Fisher, A, Wangpraseurt, D, Larkum, AWD, Johnson, M, Kühl, M, Chen, M, Wong, HL & Burns, BP 2019, 'Correlation of bio-optical properties with photosynthetic pigment and microorganism distribution in microbial mats from Hamelin Pool, Australia', FEMS Microbiology Ecology, vol. 95, no. 1.
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Microbial mats and stromatolites are widespread in Hamelin Pool, Shark Bay, however the phototrophic capacity of these systems is unknown. This study has determined the optical properties and light-harvesting potential of these mats with light microsensors. These characteristics were linked via a combination of 16S rDNA sequencing, pigment analyses and hyperspectral imaging. Local scalar irradiance was elevated over the incident downwelling irradiance by 1.5-fold, suggesting light trapping and strong scattering by the mats. Visible light (400-700 nm) penetrated to a depth of 2 mm, whereas near-infrared light (700-800 nm) penetrated to at least 6 mm. Chlorophyll a and bacteriochlorophyll a (Bchl a) were found to be the dominant photosynthetic pigments present, with BChl a peaking at the subsurface (2-4 mm). Detailed 16S rDNA analyses revealed the presence of putative Chl f-containing Halomicronema sp. and photosynthetic members primarily decreased from the mat surface down to a depth of 6 mm. Data indicated high abundances of some pigments and phototrophic organisms in deeper layers of the mats (6-16 mm). It is proposed that the photosynthetic bacteria present in this system undergo unique adaptations to lower light conditions below the mat surface, and that phototrophic metabolisms are major contributors to ecosystem function.
Fleming, C, Gunawan, C, Golzan, M, Torpy, F, Irga, P & Mcgrath, K 2019, 'Investigating the effects of air pollutant nanoparticles on the onset or progression of Alzheimer's disease', IBRO Reports, vol. 6, pp. S329-S330.
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Fourment, M & Darling, AE 2019, 'Evaluating probabilistic programming and fast variational Bayesian inference in phylogenetics', PeerJ, vol. 7, pp. e8272-e8272.
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Recent advances in statistical machine learning techniques have led to the creation of probabilistic programming frameworks. These frameworks enable probabilistic models to be rapidly prototyped and fit to data using scalable approximation methods such as variational inference. In this work, we explore the use of the Stan language for probabilistic programming in application to phylogenetic models. We show that many commonly used phylogenetic models including the general time reversible substitution model, rate heterogeneity among sites, and a range of coalescent models can be implemented using a probabilistic programming language. The posterior probability distributions obtained via the black box variational inference engine in Stan were compared to those obtained with reference implementations of Markov chain Monte Carlo (MCMC) for phylogenetic inference. We find that black box variational inference in Stan is less accurate than MCMC methods for phylogenetic models, but requires far less compute time. Finally, we evaluate a custom implementation of mean-field variational inference on the Jukes–Cantor substitution model and show that a specialized implementation of variational inference can be two orders of magnitude faster and more accurate than a general purpose probabilistic implementation.
Fritz, A, Hofmann, P, Majda, S, Dahms, E, Dröge, J, Fiedler, J, Lesker, TR, Belmann, P, DeMaere, MZ, Darling, AE, Sczyrba, A, Bremges, A & McHardy, AC 2019, 'CAMISIM: simulating metagenomes and microbial communities', Microbiome, vol. 7, no. 1.
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BACKGROUND:Shotgun metagenome data sets of microbial communities are highly diverse, not only due to the natural variation of the underlying biological systems, but also due to differences in laboratory protocols, replicate numbers, and sequencing technologies. Accordingly, to effectively assess the performance of metagenomic analysis software, a wide range of benchmark data sets are required. RESULTS:We describe the CAMISIM microbial community and metagenome simulator. The software can model different microbial abundance profiles, multi-sample time series, and differential abundance studies, includes real and simulated strain-level diversity, and generates second- and third-generation sequencing data from taxonomic profiles or de novo. Gold standards are created for sequence assembly, genome binning, taxonomic binning, and taxonomic profiling. CAMSIM generated the benchmark data sets of the first CAMI challenge. For two simulated multi-sample data sets of the human and mouse gut microbiomes, we observed high functional congruence to the real data. As further applications, we investigated the effect of varying evolutionary genome divergence, sequencing depth, and read error profiles on two popular metagenome assemblers, MEGAHIT, and metaSPAdes, on several thousand small data sets generated with CAMISIM. CONCLUSIONS:CAMISIM can simulate a wide variety of microbial communities and metagenome data sets together with standards of truth for method evaluation. All data sets and the software are freely available at https://github.com/CAMI-challenge/CAMISIM.
Fröch, JE, Hwang, Y, Kim, S, Aharonovich, I & Toth, M 2019, 'Photonic Nanostructures from Hexagonal Boron Nitride', Advanced Optical Materials, vol. 7, no. 4, pp. 1801344-1801344.
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© 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim Growing interest in devices based on layered van der Waals (vdW) materials is motivating the development of new nanofabrication methods. Hexagonal boron nitride (hBN) is one of the most promising materials for studies of quantum photonics and phonon polaritonics. A promising nanofabrication process used to fabricate several hBN photonic devices using a hybrid reactive ion etching (RIE) and electron beam-induced etching (EBIE) technique is reported in detail here. The shortcomings and benefits of RIE and EBIE are highlighted and the utility of the hybrid approach for the fabrication of suspended and supported device structures with nanoscale features and highly vertical sidewalls are demonstrated. Functionality of the fabricated devices is proven by measurements of high-quality cavity optical modes (Q ≈ 1500). This nanofabrication approach constitutes an advance toward an integrated, monolithic quantum photonics platform based on hBN and other layered vdW materials.
Fröch, JE, Kim, S, Mendelson, N, Kianinia, M, Toth, M & Aharonovich, I 2019, 'Coupling hBN quantum emitters to 1D photonic crystal cavities'.
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Quantum photonics technologies require a scalable approach for integration of
non-classical light sources with photonic resonators to achieve strong light
confinement and enhancement of quantum light emission. Point defects from
hexagonal Boron Nitride (hBN) are amongst the front runners for single photon
sources due to their ultra bright emission, however, coupling of hBN defects to
photonic crystal cavities has so far remained elusive. Here we demonstrate
on-chip integration of hBN quantum emitters with photonic crystal cavities from
silicon nitride (Si3N4) and achieve experimentally measured Q-factor of 3,300
for hBN/Si3N4 hybrid cavities. We observed 9-fold photoluminescence enhancement
of a hBN single photon emission at room temperature. Our work paves the way
towards hybrid integrated quantum photonics with hBN, and outlines an excellent
path for further development of cavity quantum electrodynamic experiments and
on-chip integration of 2D materials.
Fronzi, M, Assadi, MHN & Hanaor, DAH 2019, 'Theoretical insights into the hydrophobicity of low index CeO2 surfaces', Applied Surface Science, vol. 478, pp. 68-74.
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© 2019 The hydrophobicity of CeO 2 surfaces is examined here. Since wettability measurements are extremely sensitive to experimental conditions, we propose a general approach to obtain contact angles between water and ceria surfaces of specified orientations based on density functional calculations. In particular, we analysed the low index surfaces of this oxide to establish their interactions with water. According to our calculations, the CeO 2 (111) surface was the most hydrophobic with a contact angle of Θ = 112.53° followed by (100) with Θ = 93.91°. The CeO 2 (110) surface was, on the other hand, mildly hydrophilic with Θ = 64.09°. By combining our calculations with an atomistic thermodynamic approach, we found that the O terminated (100) surface was unstable unless fully covered by molecularly adsorbed water. We also identified a strong attractive interaction between the hydrogen atoms in water molecules and surface oxygen, which gives rise to the hydrophilic behaviour of (110) surfaces. Interestingly, the adsorption of water molecules on the lower-energy (111) surface stabilises oxygen vacancies, which are expected to enhance the catalytic activity of this plane. The findings here shed light on the origin of the intrinsic wettability of rare earth oxides in general and CeO 2 surfaces in particular and also explain why CeO 2 (100) surface properties are so critically dependant on applied synthesis methods.
Fu, L, Chung, R & Shi, B 2019, 'Upconversion Nanoparticle-Based Strategy for Crossing the Blood-Brain Barrier to Treat the Central Nervous System Disease', pp. 263-282.
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Fu, S, Stove, C & Elliott, S 2019, 'Editorial: Advances in Analytical Methods for Drugs of Abuse Testing', Frontiers in Chemistry, vol. 7, pp. 589-589.
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Funari, R, Ripa, R, Söderström, B, Skoglund, U & Shen, AQ 2019, 'Detecting Gold Biomineralization by Delftia acidovorans Biofilms on a Quartz Crystal Microbalance', ACS Sensors, vol. 4, no. 11, pp. 3023-3033.
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Gahan, ME, Bowman, S, Chevalier, R, Rossi, R, Nelson, M, Roffey, P, Xu, B, Power, D & McNevin, D 2019, 'Bacillus species at the Canberra Airport: A comparison of real-time polymerase chain reaction and massively parallel sequencing for identification', Forensic Science International, vol. 295, pp. 169-178.
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Anthrax, caused by the Gram-positive, spore forming bacterium Bacillus anthracis, is a disease with naturally occurring outbreaks in many parts of the world, primarily in domestic and wild herbivores. Due to the movement of people and stock, B. anthracis could, however, be at transportation hubs including airports. The continuous threat to national and international security from a biological agent release, or hoax attack, is a very real concern. Sensitive, robust and rapid (hours-day) methods to identify biological agents, including B. anthracis, and distinguish pathogenic from non-pathogenic species, is an essential cornerstone to national security. The aim of this project was to determine the presence of Bacillus species at the Canberra Airport using two massively parallel sequencing (MPS) approaches and compare with previous results using real-time polymerase chain reaction (qPCR). Samples were collected daily for seven days each month from August 2011-July 2012 targeting movement of people, luggage and freight into and out of the Canberra Airport. Extracted DNA was analysed using qPCR specific for B. anthracis. A subset of samples was analysed using two MPS approaches. Approach one, using the Ion PGM™ (Thermo Fisher Scientific; TFS) and an in-house assay, targeted the two B. anthracis virulence plasmids (cya and capB genes) and a single conserved region of the 16S rRNA gene. Approach two, using the Ion S5™ (TFS) and the commercial Ion 16S™ Metagenomics Kit (TFS), targeted multiple regions within the bacterial 16S rRNA gene. Overall there was consistency between the two MPS approaches and between MPS and qPCR, however, MPS was more sensitive, particularly for plasmid detection. Whilst the broad-range 16S genomic target(s) used in both MPS approaches in this study was able to generate a metagenomic fingerprint of the bacterial community at the Canberra Airport, it could not resolve Bacillus species beyond the level of the Bacillus cereus group. The inclusion o...
Gale, PA & Gibb, BC 2019, 'Editorial: a methods article', Supramolecular Chemistry, vol. 31, no. 5, pp. 296-296.
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Gan, W, Tserkezis, C, Cai, Q, Falin, A, Mateti, S, Nguyen, M, Aharonovich, I, Watanabe, K, Taniguchi, T, Huang, F, Song, L, Kong, L, Chen, Y & Li, LH 2019, 'Atomically Thin Boron Nitride as an Ideal Spacer for Metal-Enhanced Fluorescence', ACS Nano, vol. 13, no. 10, pp. 12184-12191.
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Ganesan, M, Trivedi, N, Gupta, V, Madhav, SV, Radhakrishna Reddy, C & Levine, IA 2019, 'Seaweed resources in India – current status of diversity and cultivation: prospects and challenges', Botanica Marina, vol. 62, no. 5, pp. 463-482.
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Abstract
Seaweeds are an integral part of coastal ecosystems and offer invaluable ecosystem services supporting the life of many marine forms. The economic value of seaweeds significantly contributes to the sustainable development of rural coastal regions. Seaweeds are consumed as food in some Asian countries, but their utilization for production of phycocolloids is widespread across the globe, with an estimated value of more than one billion US$. In India, seaweeds have been utilized exclusively for the production of phycocolloids but recently they are used for the production of plant growth stimulants for agricultural applications. The domestic agar and alginate industry totally depends on the supplies from natural seaweed beds with some occasional imports. The recent success achieved in both upstream and downstream technologies in production and processing of seaweeds has boosted the prospects for commercialization of seaweed resources in the country. The present article briefly appraises the current status of Indian seaweed resources and their utilization, as well as developments in seaweed farming technologies, the status of seaweed industry and recent efforts to transform seaweed farming into a social enterprise. It also highlights the challenges encountered for mainstreaming these resources so as to evolve into a marine industry.
Gao, X, Feng, J, Su, D, Ma, Y, Wang, G, Ma, H & Zhang, J 2019, 'In-situ exfoliation of porous carbon nitride nanosheets for enhanced hydrogen evolution', Nano Energy, vol. 59, pp. 598-609.
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© 2019 Elsevier Ltd The development of water splitting technology is severely impeded by the limited strategies for preparing efficient photocatalyst with optimal structure. Herein, a facile structure and doping engineering strategy is proposed to obtain the atomic-thin mesoporous graphite carbon nitride (g-C 3 N 4 ) nanosheets with a large specific surface area of 212.5 m 2 g −1 , an ultra-large pore volume of 1.55 cm 3 g −1 , high C and O contents of ∼51.4 and 4.8% via an acid-assisted exfoliation route without any hard templates. The theoretical calculation reveals that the introduction of additional C/O atoms into g-C 3 N 4 matrix would boost the charge transfer rate and charge separation efficiency due to the enhanced electronic polarization effect (Bader Charge) and shortened bond lengths. Additionally, the electronic conductivity is demonstrated to be enhanced due to the formation of delocalized π-bonding both experimentally and theoretically. The synergic contribution of textural and electronic features renders an excellent photoelectrochemical (PEC) performance with 50–60 times larger photocurrent in comparison with the pristine g-C 3 N 4 and high hydrogen evolution rates of 830.1 and 115.5 μmol g −1 h −1 under the solar- and visible-light irradiation, respectively. This in-situ exfoliation approach demonstrates a facile yet efficient method to synthesize highly porous carbon nitride materials with optimal structure and composition for efficient water splitting.
Gao, X, Zhou, D, Chen, Y, Wu, W, Su, D, Li, B & Wang, G 2019, 'Strong charge polarization effect enabled by surface oxidized titanium nitride for lithium-sulfur batteries', Communications Chemistry, vol. 2, no. 1.
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AbstractThe commercialization of high-energy-density and low-cost lithium-sulfur batteries has been severely impeded by capacity fading and electrochemical polarization. Here we report a strategy to entrap polysulfides and boost the cathodic redox kinetics by embedding the surface oxidized quantum-dot-size TiN (TiN-O) within the highly ordered mesoporous carbon matrix. While the carbon scaffold offers sufficient electrical contact to the insulate sulfur, benefiting the full usage of sulfur and physical confinement of polysulfides. The surface oxygen renders TiN-O with a strong charge polarization effect for polysulfides via S-O-Ti bond as verified experimentally and theoretically. The suppressed shuttle effect and high lithium ion diffusion coefficient (7.9 × 10−8 cm2 s−1) lead to a high capacity of 1264 mA h g−1 at 0.2 C with a negligible capacity fading rate of 0.06% per cycle. Additionally, TiN-O based prototype soft-package cells also exhibit excellent cycling stability with flexibility, demonstrating their potential for practical applications.
Garcia, A, Lev, B, Hossain, KR, Gorman, A, Diaz, D, Pham, THN, Cornelius, F, Allen, TW & Clarke, RJ 2019, 'Cholesterol depletion inhibits Na+,K+-ATPase activity in a near-native membrane environment', Journal of Biological Chemistry, vol. 294, no. 15, pp. 5956-5969.
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Cholesterol's effects on Na+,K+-ATPase reconstituted in phospholipid vesicles have been extensively studied. However, previous studies have reported both cholesterol-mediated stimulation and inhibition of Na+,K+-ATPase activity. Here, using partial reaction kinetics determined via stopped-flow experiments, we studied cholesterol's effect on Na+,K+-ATPase in a near-native environment in which purified membrane fragments were depleted of cholesterol with methyl-β-cyclodextrin (mβCD). The mβCD-treated Na+,K+-ATPase had significantly reduced overall activity and exhibited decreased observed rate constants for ATP phosphorylation (ENa3 + → E2P, i.e. phosphorylation by ATP and Na+ occlusion from the cytoplasm) and K+ deocclusion with subsequent intracellular Na+ binding (E2K2 + → E1Na3 +). However, cholesterol depletion did not affect the observed rate constant for K+ occlusion by phosphorylated Na+,K+-ATPase on the extracellular face and subsequent dephosphorylation (E2P → E2K2 +). Thus, partial reactions involving cation binding and release at the protein's intracellular side were most dependent on cholesterol. Fluorescence measurements with the probe eosin indicated that cholesterol depletion stabilizes the unphosphorylated E2 state relative to E1, and the cholesterol depletion-induced slowing of ATP phosphorylation kinetics was consistent with partial conversion of Na+,K+-ATPase into the E2 state, requiring a slow E2 → E1 transition before the phosphorylation. Molecular dynamics simulations of Na+,K+-ATPase in membranes with 40 mol % cholesterol revealed cholesterol interaction sites that differ markedly among protein conformations. They further indicated state-dependent effects on membrane shape, with the E2 state being likely disfavored in cholesterol-rich bilayers relative to the E1P state because of a greater hydrophobic mismatch. In summary, cholesterol extraction from membranes significantly decreases Na+,K+-ATPase steady-state activity.
Garcia, A, Zou, H, Hossain, KR, Xu, QH, Buda, A & Clarke, RJ 2019, 'Polar Interactions Play an Important Role in the Energetics of the Main Phase Transition of Phosphatidylcholine Membranes', ACS Omega, vol. 4, no. 1, pp. 518-527.
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© 2019 American Chemical Society. Conformational changes of membrane proteins are accompanied by deformation in the surrounding lipid bilayer. To gain insight into the energetics of membrane deformation, the phase behavior of dimyristoylphosphatidylcholine (DMPC) membranes in the presence of the dipole potential, d, modifiers was investigated by differential scanning calorimetry. 7-Ketocholesterol, which weakens d and reduces membrane-perpendicular dipole-dipole repulsion, causes a discrete second peak on the high-temperature side of the main transition, whereas 6-ketocholestanol, which strengthens d and increases membrane-perpendicular dipole-dipole repulsion, merely produces a shoulder. Measurements on pure DMPC vesicles showed that the observed temperature profile could not be explained by a single endothermic process, that is, breaking of van der Waals forces between hydrocarbon chains alone. Removal of NaCl from the buffer caused an increase in the main transition temperature and the appearance of an obvious shoulder, implicating polar interactions. Consideration of the phosphatidylcholine (PC) head group dipole moment indicates direct interactions between PC dipoles that are unlikely to account for the additional process. It seems more likely that the breaking of an in-plane hydrogen-bonded network consisting of hydrating water dipoles together with zwitterionic lipid head groups is responsible. The evidence presented supports the idea that the breaking of van der Waals forces between lipid tails required for the main phase transition of PC membranes is coupled to partial breaking of a hydrogen-bonded network at the membrane surface.
Gassner, A-L, Manganelli, M, Werner, D, Rhumorbarbe, D, Maitre, M, Beavis, A, Roux, CP & Weyermann, C 2019, 'Secondary transfer of organic gunshot residues: Empirical data to assist the evaluation of three scenarios', Science & Justice, vol. 59, no. 1, pp. 58-66.
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© 2018 The Chartered Society of Forensic Sciences The present study aimed at providing data to assess the secondary transfer of organic gunshot residues (OGSR). Three scenarios were evaluated in controlled conditions, namely displacing a firearm from point A to point B, a simple handshake and an arrest involving handcuffing on the ground. Specimens were collected from the firearm, the hands of the shooter and the non-shooter undergoing the secondary transfer in order to compare the amounts detected. Secondary transfer was observed for the three scenarios, but to a different extent. It was found that displacing a firearm resulted in secondary transfer in <50% of the experiments. The firearm also had an influence, as contrary to the pistol, no secondary OGSR were detected using the revolver. Shaking the hand of the shooter also transferred OGSR to the non-shooter's hand. In that case, the amount of OGSR was generally higher on the shooter than on the non-shooter. Finally, the largest secondary transfer was observed after the arrest with handcuffing with positive results in all cases using the pistol. In that scenario, the amounts on the shooter and the non-shooter were in the same range. This study highlights that the secondary transfer must be taken into account in the interpretation of OGSR. Indeed, an individual's hands might be contaminated by handling a firearm or having physical contact with a shooter.
Gaw, S, Harford, A, Pettigrove, V, Sevicke‐Jones, G, Manning, T, Ataria, J, Cresswell, T, Dafforn, KA, Leusch, FDL, Moggridge, B, Cameron, M, Chapman, J, Coates, G, Colville, A, Death, C, Hageman, K, Hassell, K, Hoak, M, Gadd, J, Jolley, DF, Karami, A, Kotzakoulakis, K, Lim, R, McRae, N, Metzeling, L, Mooney, T, Myers, J, Pearson, A, Saaristo, M, Sharley, D, Stuthe, J, Sutherland, O, Thomas, O, Tremblay, L, Wood, W, Boxall, ABA, Rudd, MA & Brooks, BW 2019, 'Towards Sustainable Environmental Quality: Priority Research Questions for the Australasian Region of Oceania', Integrated Environmental Assessment and Management, vol. 15, no. 6, pp. 917-935.
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ABSTRACTEnvironmental challenges persist across the world, including the Australasian region of Oceania, where biodiversity hotspots and unique ecosystems such as the Great Barrier Reef are common. These systems are routinely affected by multiple stressors from anthropogenic activities, and increasingly influenced by global megatrends (e.g., the food–energy–water nexus, demographic transitions to cities) and climate change. Here we report priority research questions from the Global Horizon Scanning Project, which aimed to identify, prioritize, and advance environmental quality research needs from an Australasian perspective, within a global context. We employed a transparent and inclusive process of soliciting key questions from Australasian members of the Society of Environmental Toxicology and Chemistry. Following submission of 78 questions, 20 priority research questions were identified during an expert workshop in Nelson, New Zealand. These research questions covered a range of issues of global relevance, including research needed to more closely integrate ecotoxicology and ecology for the protection of ecosystems, increase flexibility for prioritizing chemical substances currently in commerce, understand the impacts of complex mixtures and multiple stressors, and define environmental quality and ecosystem integrity of temporary waters. Some questions have specific relevance to Australasia, particularly the uncertainties associated with using toxicity data from exotic species to protect unique indigenous species. Several related priority questions deal with the theme of how widely international ecotoxicological data and databases can be applied to regional ecosystems. Other timely questions, which focus on improving predictive chemistry and toxicology tools and techniques, will be important to answer several of the priority questions identified here. Another important question raised was how to protect local cultural and socia...
Gemikonakli, G, Keay, KA, Kendig, MD, Kang, JWM, Corbit, LH & Mor, D 2019, 'Altered monoamine levels in the dorsal striatum of the rat are associated with alterations in behavioural selection and motivation following peripheral nerve injury and acute stress', European Journal of Neuroscience, vol. 50, no. 5, pp. 2786-2800.
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AbstractChronic neuropathic pain and psychological stress interact to compromise goal‐directed control over behaviour following mild psychological stress. The dorsomedial (DMS) and dorsolateral (DLS) striatum in the rat are crucial for the expression of goal‐directed and habitual behaviours, respectively. This study investigated whether changes in monoamine levels in the DMS and DLS following nerve injury and psychological stress reflect these behavioural differences. Neuropathic pain was induced by a chronic constriction injury (CCI) of the sciatic nerve in Sprague–Dawley rats. Acute stress was induced using a 15‐min restraint. Behavioural flexibility was assessed using the outcome devaluation paradigm. Noradrenaline, serotonin, dopamine and associated metabolites were measured bilaterally from the DLS and DMS. In uninjured rats, restraint increased dopaminergic markers in the left and serotonergic markers in the right of both the DMS and DLS, indicating a possible left hemisphere‐mediated dominance. CCI led to a slightly different lateralised effect, with a larger effect in the DMS than in the DLS. Individual differences in behavioural flexibility following CC...
Georgevsky, D, Retsas, S, Raoufi, N, Shimoni, O & Golzan, SM 2019, 'A longitudinal assessment of retinal function and structure in the APP/PS1 transgenic mouse model of Alzheimer’s disease', Translational Neurodegeneration, vol. 8, no. 1.
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Abstract
Background
A great body of evidence suggests that there are retinal functional and structural changes that occur in Alzheimer’s disease (AD). However, whether such changes are primary or secondary remains to be elucidated. We studied a range of retinal functional and structural parameters in association with AD- specific pathophysiological markers in the double transgenic APP/PS1 and control mice across age.
Methods
Electroretinogram (ERG) and optical coherence tomography (OCT) was performed in APP/PS1 and wild type (WT) control mice every 3 months from 3 to 12 months of age. For functional assessment, the a- and b-wave of the ERG, amplitude of oscillatory potentials (OP) and the positive scotopic threshold response (pSTR) were quantified at each time point. For structural assessment, the inner and outer retinal thickness was segmented and measured from OCT scans. Episodic memory was evaluated at 6, 9 and 12 months of age using the novel object recognition test. Amyloid beta (Aβ) distribution in the hippocampus and the retina were visualised at 3, 6 and 12 months of age. Inter- and intra- group analysis was performed to study rate of change for each parameter between the two groups.
Results
Inter-group analysis revealed a significant difference in b-wave and OPs of APP/PS1 compared to WT controls starting from 3 months (p < 0.001). There was also a significant difference in the amplitude of pSTR between the two groups starting from 6 months (p < 0.001). Furthermore, a significant difference in the inner retinal thickness, between the two...
Gerace, D, Martiniello-Wilks, R, Habib, R & Simpson, AM 2019, 'Luciferase-based reporting of suicide gene activity in murine mesenchymal stem cells', PLOS ONE, vol. 14, no. 7, pp. e0220013-e0220013.
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Due to their ease of isolation, gene modification and tumor-homing properties, mesenchymal stem cells (MSCs) are an attractive cellular vehicle for the delivery of toxic suicide genes to a variety of cancers in pre-clinical models. In addition, the incorporation of suicide genes in stem cell-derived cell replacement therapies improves their safety profile by permitting graft destruction in the event of unexpected tumorigeneses or unwanted differentiation. Due to the functional requirement of ATP for the Firefly luciferase gene Luc2 to produce light, luciferase-based reporting of cytotoxicity can be engineered into potential cell therapies. Consequently, we nucleofected mammalian expression plasmids containing both the Luc2 and the yeast fusion cytosine deaminase uracil phosphoribosyltransferase (CDUPRT) genes for expression in murine MSCs to assess luciferase as a reporter of suicide gene cytotoxicity, and MSC as vehicles of suicide gene therapy. In vitro bioluminescence imaging (BLI) showed that following the addition of the non-toxic prodrug fluorocytosine (5-FC), CDUPRT-expressing MSCs displayed enhanced cytotoxicity in comparison to Luc2 reporter MSC controls. This study demonstrates the utility of luciferase as a reporter of CDUPRT-mediated cytotoxicity in murine MSC using BLI.
Gerace, D, Martiniello-Wilks, R, Habib, R, Ren, B, Nassif, NT, O’Brien, BA & Simpson, AM 2019, 'Ex Vivo Expansion of Murine MSC Impairs Transcription Factor-Induced Differentiation into Pancreatic β-Cells', Stem Cells International, vol. 2019, pp. 1-15.
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Combinatorial gene and cell therapy as a means of generating surrogate β-cells has been investigated for the treatment of type 1 diabetes (T1D) for a number of years with varying success. One of the limitations of current cell therapies for T1D is the inability to generate sufficient quantities of functional transplantable insulin-producing cells. Due to their impressive immunomodulatory properties, in addition to their ease of expansion and genetic modification ex vivo, mesenchymal stem cells (MSCs) are an attractive alternative source of adult stem cells for regenerative medicine. To overcome the aforementioned limitation of current therapies, we assessed the utility of ex vivo expanded bone marrow-derived murine MSCs for their persistence in immune-competent and immune-deficient animal models and their ability to differentiate into surrogate β-cells. CD45-/Ly6+ murine MSCs were isolated from the bone marrow of nonobese diabetic (NOD) mice and nucleofected to express the bioluminescent protein, Firefly luciferase (Luc2). The persistence of a subcutaneous (s.c.) transplant of Luc2-expressing MSCs was assessed in immune-competent (NOD) (n=4) and immune-deficient (NOD/Scid) (n=4) animal models of diabetes. Luc2-expressing MSCs persisted for 2 and 12 weeks, respectively, in NOD and NOD/Scid mice. Ex vivo expanded MSCs were transduced with the HMD lentiviral vector (MOI = 10) to express furin-cleavable ...
Ghassabian, S, Gillani, TB, Rawling, T, Crettol, S, Nair, PC & Murray, M 2019, 'Sorafenib N-Oxide Is an Inhibitor of Human Hepatic CYP3A4', The AAPS Journal, vol. 21, no. 2.
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The multi-kinase inhibitor sorafenib (SOR) is clinically important in the treatment of hepatocellular and renal cancers and undergoes CYP3A4-dependent oxidation in liver to the pharmacologically active N-oxide metabolite (SNO). There have been reports that kinase inhibitors such as SOR may precipitate pharmacokinetic interactions with coadministered drugs that compete for CYP3A4-mediated biotransformation, but these occur non-uniformly in patients. Clinical evidence also indicates that SNO accumulates in serum of some patients during prolonged SOR therapy. In this study undertaken in hepatic microsomes from individual donors, we assessed the possibility that SNO might contribute to pharmacokinetic interactions mediated by SOR. Enzyme kinetics of CYP3A4-mediated midazolam 1'-hydroxylation in individual human hepatic microsomes were analyzed by non-linear regression and appropriate replots. Thus, SNO and SOR were linear-mixed inhibitors of microsomal CYP3A4 activity (Kis 15 ± 4 and 33 ± 14 μM, respectively). To assess these findings, further molecular docking studies of SOR and SNO with the 1TQN crystal structure of CYP3A4 were undertaken. SNO elicited a larger number of interactions with key amino acid residues located in substrate recognition sequences of the enzyme. In the optimal docking pose, the N-oxide moiety of SNO was also found to interact directly with the heme moiety of CYP3A4. These findings suggest that SNO could contribute to pharmacokinetic interactions involving SOR, perhaps in individuals who produce high circulating concentrations of the metabolite.
Giannopoulos, S, Samardzic, K, Raymond, BBA, Djordjevic, SP & Rodgers, KJ 2019, 'L-DOPA causes mitochondrial dysfunction in vitro: A novel mechanism of L-DOPA toxicity uncovered', The International Journal of Biochemistry & Cell Biology, vol. 117, pp. 105624-105624.
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In Parkinson's disease (PD), as in many other neurodegenerative disorders, mitochondrial dysfunction, protein misfolding, and proteotoxic stress underly the disease process. For decades, the primary symptomatic treatment for PD has been the dopamine precursor L-DOPA (Levodopa). L-DOPA however can initiate protein misfolding through its ability to mimic the protein amino acid L-tyrosine, resulting in random errors in aminoacylation and L-DOPA becoming mistakenly inserted into the polypeptide chain of proteins in place of L-tyrosine. In the present study we examined the impact that the generation of DOPA-containing proteins had on human neuroblastoma cell (SH-SY5Y) function in vitro. We showed that even in the presence of antioxidants there was a significant accumulation of cytosolic ubiquitin in DOPA-treated cells, an upregulation in the endosomal-lysosomal degradation system, deleterious changes to mitochondrial morphology and a marked decline in mitochondrial function.The effects of L-DOPA on mitochondrial function were not observed with D-DOPA, the stereoisomer of L-DOPA that cannot be inserted into proteins so did not result from oxidative stress. We could fully protect against these effects by co-treatment with L-tyrosine, supporting the view that misincorporation of L-DOPA into proteins contributed to these cytotoxic effects, leading us to suggest that co-treatment with L-tyrosine could be beneficial therapeutically.
Gibb, BC & Gale, PA 2019, '2019 Sessler Early Career Researcher Prize', Supramolecular Chemistry, vol. 31, no. 9, pp. 607-607.
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Gill, AJ, Lim, G, Cheung, VKY, Andrici, J, Perry-Keene, JL, Paik, J, Sioson, L, Clarkson, A, Sheen, A, Luxford, C, Elston, MS, Meyer-Rochow, GY, Nano, MT, Kruijff, S, Engelsman, AF, Sywak, M, Sidhu, SB, Delbridge, LW, Robinson, BG, Marsh, DJ, Toon, CW, Chou, A & Clifton-Bligh, RJ 2019, 'Parafibromin-deficient (HPT-JT Type, CDC73 Mutated) Parathyroid Tumors Demonstrate Distinctive Morphologic Features', American Journal of Surgical Pathology, vol. 43, no. 1, pp. 35-46.
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The gene CDC73 (previously known as HRPT2) encodes the protein parafibromin. Biallelic mutation of CDC73 is strongly associated with malignancy in parathyroid tumors. Heterozygous germline mutations cause hyperparathyroidism jaw tumor syndrome,which is associated with a high life-time risk of parathyroid carcinoma. Therefore loss of parafibromin expression by immunohistochemistry may triage genetic testing for hyperparathyroidism jaw tumor syndrome and be associated with malignant behavior in atypical parathyroid tumors. We share our experience that parafibromin-negative parathyroid tumors show distinctive morphology. We searched our institutional database for parathyroid tumors demonstrating complete loss of nuclear expression of parafibromin with internal positive controls. Forty-three parafibromin-negative tumors from 40 (5.1%) of 789 patients undergoing immunohistochemistry were identified. Thirty-three (77%) were external consultation cases; the estimated incidence in unselected tumors was 0.19%. Sixteen (37.2%) fulfilled World Health Organization 2017 criteria for parathyroid carcinoma and 63% had serum calcium greater than 3mmol/L. One of 27 (3.7%) noninvasive but parafibromin-negative tumors subsequently metastasized. Parafibromin-negative patients were younger (mean, 36 vs. 63 y; P<0.001) and had larger tumors (mean, 3.04 vs. 0.62 g; P<0.001). Not all patients had full testing, but 26 patients had pathogenic CDC73 mutation/deletions confirmed in tumor (n=23) and/or germline (n=16). Parafibromin-negative tumors demonstrated distinctive morphology including extensive sheet-like rather than acinar growth, eosinophilic cytoplasm, nuclear enlargement with distinctive coarse chromatin, perinuclear cytoplasmic clearing, a prominent arborizing vasculature, and, frequently, a thick capsule. Microcystic change was found in 21 (48.8%). In conclusion, there are previously unrecognized morphologic clues to parafibromin loss/CDC73 mutation in parathyroid tumors which,...
Gissibl, A, Care, A, Sun, A, Hobba, G, Nevalainen, H & Sunna, A 2019, 'Development of screening strategies for the identification of paramylon-degrading enzymes', Journal of Industrial Microbiology and Biotechnology, vol. 46, no. 6, pp. 769-781.
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Abstract
Enzymatic degradation of the β-1,3-glucan paramylon could enable the production of bioactive compounds for healthcare and renewable substrates for biofuels. However, few enzymes have been found to degrade paramylon efficiently and their enzymatic mechanisms remain poorly understood. Thus, the aim of this work was to find paramylon-degrading enzymes and ways to facilitate their identification. Towards this end, a Euglena gracilis-derived cDNA expression library was generated and introduced into Escherichia coli. A flow cytometry-based screening assay was developed to identify E. gracilis enzymes that could hydrolyse the fluorogenic substrate fluorescein di-β-d-glucopyranoside in combination with time-saving auto-induction medium. In parallel, four amino acid sequences of potential E. gracilis β-1,3-glucanases were identified from proteomic data. The open reading frame encoding one of these candidate sequences (light_m.20624) was heterologously expressed in E. coli. Finally, a Congo Red dye plate assay was developed for the screening of enzyme preparations potentially able to degrade paramylon. This assay was validated with enzymes assumed to have paramylon-degrading activity and then used to identify four commercial preparations with previously unknown paramylon degradation ability.
Gissibl, A, Sun, A, Care, A, Nevalainen, H & Sunna, A 2019, 'Bioproducts From Euglena gracilis: Synthesis and Applications', Frontiers in Bioengineering and Biotechnology, vol. 7.
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Gleason, FH, Larkum, AWD, Raven, JA, Manohar, CS & Lilje, O 2019, 'Ecological implications of recently discovered and poorly studied sources of energy for the growth of true fungi especially in extreme environments', Fungal Ecology, vol. 39, pp. 380-387.
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© 2018 Rhodopsin transmembrane proton pumps (fuelled by visible light which is absorbed by retinal (carotenoid) chromophores) exist in all three domains of living species and in all groups of true fungi studied. Light driven proton and sodium pumps are likely to be essential for some marine fungi, especially hypersaline tolerant and endolithic species. Rhodopsin macromolecular machines, using visible light, drive metabolic reactions in addition to those provided by aerobic respiration, providing extra energy needed for the maintenance and growth of fungi, especially in euphotic environments where oxygen concentration is limited. In addition, dissimilatory nitrate and metal oxide reduction can provide sources of energy for fungi in the absence of oxygen, for example, in fungal species growing in marine sediments. Finally, the oxidation of elemental sulphur, iron and manganese can be a source of energy. Some fungi are, therefore, lithotrophs and photoheterotrophs. The ecological implications of these latter processes are discussed.
Gloag, L, Mehdipour, M, Chen, D, Tilley, RD & Gooding, JJ 2019, 'Advances in the Application of Magnetic Nanoparticles for Sensing', Advanced Materials, vol. 31, no. 48, pp. 1904385-1904385.
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AbstractMagnetic nanoparticles (MNPs) are of high significance in sensing as they provide viable solutions to the enduring challenges related to lower detection limits and nonspecific effects. The rapid expansion in the applications of MNPs creates a need to overview the current state of the field of MNPs for sensing applications. In this review, the trends and concepts in the literature are critically appraised in terms of the opportunities and limitations of MNPs used for the most advanced sensing applications. The latest progress in MNP sensor technologies is overviewed with a focus on MNP structures and properties, as well as the strategies of incorporating these MNPs into devices. By looking at recent synthetic advancements, and the key challenges that face nanoparticle‐based sensors, this review aims to outline how to design, synthesize, and use MNPs to make the most effective and sensitive sensors.
GOH, CJ, PARK, D, LEE, JS, DAVEY, PA, PERNICE, M, RALPH, PJ & HAHN, Y 2019, 'Zostera virus T – a novel virus of the genus Tepovirus identified in the eelgrass, Zostera muelleri', Acta virologica, vol. 63, no. 04, pp. 366-372.
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Analysis of a transcriptome dataset obtained from tissue samples of the eelgrass Zostera muelleri, an aquatic flowering plant species of the family Zosteraceae, yielded three genome sequence contigs of a novel RNA virus. Sequence comparison and phylogenetic analysis revealed that the novel RNA virus, named Zostera virus T (ZoVT), belongs to the genus Tepovirus of the family Betaflexiviridae. The three genome contigs of ZoVT showed 88.2‒97.2% nucleotide sequence identity to each other, indicating that they descended from a common ancestor. The ZoVT genome contains three open reading frames (ORFs): ORF1 encodes a 1816 amino acid (aa) replicase (REP) with RNA-dependent RNA polymerase (RdRp) activity; ORF2, a 398 aa movement protein (MP); and ORF3, a 240 aa coat protein (CP). The phylogenetic analysis using REP sequences of ZoVT and other Betaflexiviridae viruses showed that Prunus virus T is the closest known virus to ZoVT, whereas potato virus T, the type species of the genus Tepovirus, is the second closest virus. Genome sequences of ZoVT, which is the third tepovirus species identified to date, may be useful for investigating the evolution and molecular biology of tepoviruses. Keywords: Zostera virus T; Tepovirus; Betaflexiviridae; eelgrass; Zostera muelleri.
González de Vega, R, Clases, D, Fernández-Sánchez, ML, Eiró, N, González, LO, Vizoso, FJ, Doble, PA & Sanz-Medel, A 2019, 'MMP-11 as a biomarker for metastatic breast cancer by immunohistochemical-assisted imaging mass spectrometry', Analytical and Bioanalytical Chemistry, vol. 411, no. 3, pp. 639-646.
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MMP-11 is a member of the matrix metalloproteinase family (MMPs) which are overexpressed in cancer cells, stromal cells and the adjacent microenvironment. The MMP protein family encompasses zinc-dependent endopeptidases that degrade the extracellular matrix (ECM), facilitating the breakdown of the basal membrane and matrix connective tissues. This function is believed to be important in cancer development and metastasis. This paper investigated a gold nanoparticle-based immunohistochemical assay to visualise the distribution of MMP-11 in human breast cancer tissues from eight patients with and without metastases by employing laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS). The expression of MMP-11 was increased and more heterogeneous in metastatic specimens compared to non-metastatic tumour samples. These findings demonstrate that imaging breast tumours by LA-ICP-MS may be a useful tool to aid the prognosis and treatment of breast cancer. As an example, samples of two patients are presented who were diagnosed with matching characteristics and grades of breast cancer. Although both patients had a similar prognosis and treatment, only one developed metastases.
Gonzalez-Bayon, R, Shen, Y, Groszmann, M, Zhu, A, Wang, A, Allu, AD, Dennis, ES, Peacock, WJ & Greaves, IK 2019, 'Senescence and Defense Pathways Contribute to Heterosis', Plant Physiology, vol. 180, no. 1, pp. 240-252.
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Abstract
Hybrids are used extensively in agriculture due to their superior performance in seed yield and plant growth, yet the molecular mechanisms underpinning hybrid performance are not well understood. Recent evidence has suggested that a decrease in basal defense response gene expression regulated by reduced levels of salicylic acid (SA) may be important for vigor in certain hybrid combinations. Decreasing levels of SA in the Arabidopsis (Arabidopsis thaliana) accession C24 through the introduction of the SA catabolic enzyme salicylate1 hydroxylase (NahG) increases plant size, phenocopying the large-sized C24/Landsberg erecta (Ler) F1 hybrids. C24♀ × Ler♂ F1 hybrids and C24 NahG lines shared differentially expressed genes and pathways associated with plant defense and leaf senescence including decreased expression of SA biosynthetic genes and SA response genes. The expression of TL1 BINDING TRANSCRIPTION FACTOR1, a key regulator in resource allocation between growth and defense, was decreased in both the F1 hybrid and the C24 NahG lines, which may promote growth. Both C24 NahG lines and the F1 hybrids showed decreased expression of the key senescence-associated transcription factors WRKY53, NAC-CONTAINING PROTEIN29, and ORESARA1 with a delayed onset of senescence compared to C24 plants. The delay in senescence resulted in an extension of the photosynthetic period in the leaves of F1 hybrids compared to the parental lines, potentially allowing each leaf to contribute more resources toward growth.
Gottscholl, A, Kianinia, M, Soltamov, V, Bradac, C, Kasper, C, Krambrock, K, Sperlich, A, Toth, M, Aharonovich, I & Dyakonov, V 2019, 'Room Temperature Initialisation and Readout of Intrinsic Spin Defects in a Van der Waals Crystal', Nature Materials (2020), vol. 19, no. 5, pp. 540-545.
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Optically addressable spins in widebandgap semiconductors have become one of
the most prominent platforms for exploring fundamental quantum phenomena. While
several candidates in 3D crystals including diamond and silicon carbide have
been extensively studied, the identification of spindependent processes in
atomically thin 2D materials has remained elusive. Although optically
accessible spin states in hBN are theoretically predicted, they have not yet
been observed experimentally. Here, employing rigorous electron paramagnetic
resonance techniques and photoluminescence spectroscopy, we identify
fluorescence lines in hexagonal boron nitride associated with a particular
defect, the negatively charged boron vacancy and determine the parameters of
its spin Hamiltonian. We show that the defect has a triplet ground state with a
zero field splitting of 3.5 GHz and establish that the centre exhibits
optically detected magnetic resonance at room temperature. We also demonstrate
the spin polarization of this centre under optical pumping, which leads to
optically induced population inversion of the spin ground state a prerequisite
for coherent spin manipulation schemes. Our results constitute a leap forward
in establishing two dimensional hBN as a prime platform for scalable quantum
technologies, with extended potential for spin based quantum information and
sensing applications, as our ODMR studies on hBN NV diamonds hybrid structures
show.
Gough, R, Ellis, J & Stark, D 2019, 'Comparison and Recommendations for Use of Dientamoeba fragilis Real-Time PCR Assays', Journal of Clinical Microbiology, vol. 57, no. 5.
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Dientamoeba fragilis
is a gastrointestinal trichomonad parasite whose pathogenicity is yet to be determined. The difficulty involved in microscopically diagnosing
D. fragilis
in feces led to the development of real-time PCR methodologies for the detection of
D. fragilis
in stool samples.
Gow, I, Millar, D, Ellis, J, Melki, J & Stark, D 2019, 'Semi-Quantitative, Duplexed qPCR Assay for the Detection of Leishmania spp. Using Bisulphite Conversion Technology', Tropical Medicine and Infectious Disease, vol. 4, no. 4, pp. 135-135.
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Leishmaniasis is caused by the flagellated protozoan Leishmania, and is a neglected tropical disease (NTD), as defined by the World Health Organisation (WHO). Bisulphite conversion technology converts all genomic material to a simplified form during the lysis step of the nucleic acid extraction process, and increases the efficiency of multiplex quantitative polymerase chain reaction (qPCR) reactions. Through utilization of qPCR real-time probes, in conjunction with bisulphite conversion, a new duplex assay targeting the 18S rDNA gene region was designed to detect all Leishmania species. The assay was validated against previously extracted DNA, from seven quantitated DNA and cell standards for pan-Leishmania analytical sensitivity data, and 67 cutaneous clinical samples for cutaneous clinical sensitivity data. Specificity was evaluated by testing 76 negative clinical samples and 43 bacterial, viral, protozoan and fungal species. The assay was also trialed in a side-by-side experiment against a conventional PCR (cPCR), based on the Internal transcribed spacer region 1 (ITS1 region). Ninety-seven percent of specimens from patients that previously tested positive for Leishmania were positive for Leishmania spp. with the bisulphite conversion assay, and a limit of detection (LOD) of 10 copies per PCR was achieved, while the LOD of the ITS1 methodology was 10 cells/1000 genomic copies per PCR. This method of rapid, accurate and simple detection of Leishmania can lead to improved diagnosis, treatment and public health outcomes.
Goyen, S, Camp, EF, Fujise, L, Lloyd, A, Nitschke, MR, LaJeunensse, T, Kahlke, T, Ralph, PJ & Suggett, D 2019, 'Mass coral bleaching of P. versipora in Sydney Harbour driven by the 2015–2016 heatwave', Coral Reefs, vol. 38, no. 4, pp. 815-830.
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© 2019, Springer-Verlag GmbH Germany, part of Springer Nature. High-latitude coral communities are distinct from their tropical counterparts, and how they respond to recent heat wave events that have decimated tropical reefs remains unknown. In Australia, the 2016 El Niño resulted in the largest global mass coral bleaching event to date, reaching as far south as Sydney Harbour (~ 34°S). Coral bleaching was observed for the first time (affecting ca., 60% of all corals) as sea surface temperatures in Sydney Harbour remained > 2 °C above the long-term mean summer maxima, enabling us to examine whether high-latitude corals bleached in a manner described for tropical corals. Responses of the geographically cosmopolitan Plesiastrea versipora and southerly restricted Coscinaraea mcneilli were contrasted across two harbour sites, both in situ and among samples-maintained ex situ in aquaria continually supplied with Sydney Harbour seawater. While both coral taxa hosted the same species of microalgal endosymbiont (Breviolum spp; formerly clade B), only P. versipora bleached both in situ and ex situ via pronounced losses of endosymbiont cells. Both species displayed very different metabolic responses (growth, photosynthesis, respiration and calcification) and bleaching susceptibilities under elevated temperatures. Bacterial microbiome profiling, however, revealed a convergence of bacterial community composition across coral species throughout the bleaching. Corals species found in temperate regions, including the generalist P. versipora, will therefore likely be highly susceptible to future change as heat waves grow in frequency and severity unless their thermal thresholds increase. Our observations provide further evidence that high-latitude systems are susceptible to community reorganisation under climate change.
Goyen, S, Camp, EF, Fujise, L, Lloyd, A, Nitschke, MR, LaJeunesse, TC, Kahlke, T, Ralph, PJ & Suggett, D 2019, 'Correction to: Mass coral bleaching of P. versipora in Sydney Harbour driven by the 2015–2016 heatwave', Coral Reefs, vol. 38, no. 4, pp. 877-877.
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Graco, M, Schembri, R, Ross, J, Green, SE, Booker, L, Cistulli, PA, Ayas, NT, Berlowitz, DJ, Lee, B, Graham, A, Cross, SV, McClelland, M, Thumbikat, P, Bennett, C, Townson, A, Geraghty, TJ, Pieri-Davies, S, Singhal, R, Marshall, K, Short, D, Nunn, A & Brown, D 2019, 'Continuous Positive Airway Pressure Use for Obstructive Sleep Apnea in Acute, Traumatic Tetraplegia', Archives of Physical Medicine and Rehabilitation, vol. 100, no. 12, pp. 2276-2282.
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Gramaglia, I, Velez, J, Chang, Y-S, Caparros-Wanderley, W, Combes, V, Grau, G, Stins, MF & van der Heyde, HC 2019, 'Citrulline protects mice from experimental cerebral malaria by ameliorating hypoargininemia, urea cycle changes and vascular leak', PLOS ONE, vol. 14, no. 3, pp. e0213428-e0213428.
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Clinical and model studies indicate that low nitric oxide (NO) bioavailability due in part to profound hypoargininemia contributes to cerebral malaria (CM) pathogenesis. Protection against CM pathogenesis may be achieved by altering the diet before infection with Plasmodium falcIParum infection (nutraceutical) or by administering adjunctive therapy that decreases CM mortality (adjunctive therapy). This hypothesis was tested by administering citrulline or arginine in experimental CM (eCM). We report that citrulline injected as prophylaxis immediately post infection (PI) protected virtually all mice by ameliorating (i) hypoargininemia, (ii) urea cycle impairment, and (iii) disruption of blood brain barrier. Citrulline prophylaxis inhibited plasma arginase activity. Parasitemia was similar in citrulline- And vehicle control-groups, indicating that protection from pathogenesis was not due to decreased parasitemia. Both citrulline and arginine administered from day 1 PI in the drinking water significantly protected mice from eCM. These observations collectively indicate that increasing dietary citrulline or arginine decreases eCM mortality. Citrulline injected IP on day 4 PI with quinine-injected IP on day 6 PI partially protected mice from eCM; citrulline plus scavenging of superoxide with pegylated superoxide dismutase and pegylated catalase protected all recIPients from eCM. These findings indicate that ameliorating hypoargininemia with citrulline plus superoxide scavenging decreases eCM mortality.
Gray, CM, Carroll, RJ, Lentjes, MAH & Keogh, RH 2019, 'Correcting for measurement error in fractional polynomial models using Bayesian modelling and regression calibration, with an application to alcohol and mortality', Biometrical Journal, vol. 61, no. 3, pp. 558-573.
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AbstractExposure measurement error can result in a biased estimate of the association between an exposure and outcome. When the exposure–outcome relationship is linear on the appropriate scale (e.g. linear, logistic) and the measurement error is classical, that is the result of random noise, the result is attenuation of the effect. When the relationship is non‐linear, measurement error distorts the true shape of the association. Regression calibration is a commonly used method for correcting for measurement error, in which each individual's unknown true exposure in the outcome regression model is replaced by its expectation conditional on the error‐prone measure and any fully measured covariates. Regression calibration is simple to execute when the exposure is untransformed in the linear predictor of the outcome regression model, but less straightforward when non‐linear transformations of the exposure are used. We describe a method for applying regression calibration in models in which a non‐linear association is modelled by transforming the exposure using a fractional polynomial model. It is shown that taking a Bayesian estimation approach is advantageous. By use of Markov chain Monte Carlo algorithms, one can sample from the distribution of the true exposure for each individual. Transformations of the sampled values can then be performed directly and used to find the expectation of the transformed exposure required for regression calibration. A simulation study shows that the proposed approach performs well. We apply the method to investigate the relationship between usual alcohol intake and subsequent all‐cause mortality using an error model that adjusts for the episodic nature of alcohol consumption.
Gray, R, Jones, HA, Hitchcock, JN, Hardwick, L, Pepper, D, Lugg, A, Seymour, JR & Mitrovic, SM 2019, 'Mitigation of cold‐water thermal pollution downstream of a large dam with the use of a novel thermal curtain', River Research and Applications, vol. 35, no. 7, pp. 855-866.
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AbstractHypolimnial releases from dams during periods of thermal stratification modify the downstream riverine thermal regime by decreasing water temperature and reducing natural diel thermal variability. This cold‐water thermal pollution in rivers can persist for hundreds of kilometres downstream of dams and impact important ecological processes such as fish spawning. To mitigate this problem, a first‐of‐its‐kind thermal curtain was fitted to the large bottom release Burrendong Dam on the Macquarie River, Australia. The thermal curtain acts by directing warmer, near‐surface epilimnial water to the low‐level hypolimnial offtake. This study aimed to test the efficacy of the thermal curtain by measuring temperatures before and after the curtains installation, quantifying the magnitude and extent of cold‐water thermal pollution along the Macquarie River downstream of Burrendong Dam. Epilimnial releases with use of the curtain increased diel temperature ranges and the mean monthly water temperature below the dam. Epilimnial releases with use of the curtain increased diel temperature ranges from 0.9°C to 2.5°C and reduced the difference between the mean monthly water temperature of an upstream control and a downstream site by up to 3.5°C. A comparison of the monthly temperature means along the river, indicated that thermal recovery, whereby temperatures returned to within the natural range of upstream temperatures occurred 45 km downstream of the dam during summer when the thermal curtain was deployed, compared with approximately 200 km prior to deployment of the curtain. Our study suggests that the use of thermal curtains can reduce cold‐water thermal pollution and improve ecological outcomes for river ecosystems downstream of dams.
Green, TJ, Siboni, N, King, WL, Labbate, M, Seymour, JR & Raftos, D 2019, 'Simulated Marine Heat Wave Alters Abundance and Structure of Vibrio Populations Associated with the Pacific Oyster Resulting in a Mass Mortality Event', Microbial Ecology, vol. 77, no. 3, pp. 736-747.
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Marine heat waves are predicted to become more frequent and intense due to anthropogenically induced climate change, which will impact global production of seafood. Links between rising seawater temperature and disease have been documented for many aquaculture species, including the Pacific oyster Crassostrea gigas. The oyster harbours a diverse microbial community that may act as a source of opportunistic pathogens during temperature stress. We rapidly raised the seawater temperature from 20 °C to 25 °C resulting in an oyster mortality rate of 77.4%. Under the same temperature conditions and with the addition of antibiotics, the mortality rate was only 4.3%, strongly indicating a role for bacteria in temperature-induced mortality. 16S rRNA amplicon sequencing revealed a change in the oyster microbiome when the temperature was increased to 25 °C, with a notable increase in the proportion of Vibrio sequences. This pattern was confirmed by qPCR, which revealed heat stress increased the abundance of Vibrio harveyi and Vibrio fortis by 324-fold and 10-fold, respectively. Our findings indicate that heat stress-induced mortality of C. gigas coincides with an increase in the abundance of putative bacterial pathogens in the oyster microbiome and highlights the negative consequences of marine heat waves on food production from aquaculture.
Gu, Y, Guo, Z, Yuan, W, Kong, M, Liu, Y, Liu, Y, Gao, Y, Feng, W, Wang, F, Zhou, J, Jin, D & Li, F 2019, 'High-sensitivity imaging of time-domain near-infrared light transducer', Nature Photonics, vol. 13, no. 8, pp. 525-531.
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© 2019, The Author(s), under exclusive licence to Springer Nature Limited. The optically transparent biological window in the near-infrared (NIR) spectral range allows deep-tissue excitation and the detection of fluorescence signals1,2. Spectrum-domain discrimination of NIR contrast agents via an upconversion or downshifting scheme requires sufficient (anti-) Stokes shift to separate excitation and fluorescence emission. Here, we report a time-domain (τ) scheme in which about 5,000 ytterbium signal transducers are condensed within an optically inert and biocompatible CaF2 shell (2.3 nm), which forms a 14.5 nm τ-dot. Because of the long-lived and spectrally narrowly defined excited state of pure ytterbium ions, the NIR τ-dot can convert the NIR pulsed excitation into long-decaying luminescence with an efficiency approaching 100%. Within a safe injection dosage of 13 μg g−1, an excitation power density of 1.1 mW cm−2 was sufficient to image organs with a signal-to-noise ratio of >9. The high brightness of τ-dots further allows long-term in vivo passive targeting and dynamic tracking in a tumour-bearing mouse model.
Gulzar, A, Xu, J, Wang, C, He, F, Yang, D, Gai, S, Yang, P, Lin, J, Jin, D & Xing, B 2019, 'Tumour microenvironment responsive nanoconstructs for cancer theranostic', Nano Today, vol. 26, pp. 16-56.
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© 2019 Elsevier Ltd The tumour mass is made up of not only of a heterogeneous population of cancer cells nonetheless also a mixture of resident as well as the infiltrating host cells, secreted factors besides extracellular matrix proteins, together recognized as the tumour microenvironment (TME). Tumour development is overwhelmingly affected through the dealings of cancer cells with their environment which eventually conclude whether the primary tumour is eliminated, metastasizes or creates dormant micro metastases. The TME may perhaps shape therapeutic responses as well as resistance. Some inimitable features of TME, for example vascular abnormalities, hypoxia, acidic pH and glutathione (GSH) are comparative to normal tissue. Several types of cells, together with tumour cells, macrophages, immune and fibroblast cells are nourished by flawed blood vessels in the solid tumour. To dispense anticancer agents to tumour sites nanovehicles can be competent carts. For augmented therapeutic efficacy, TME is the key for designing of nanoparticles (NPs). In this review, we will discuss the TME and summarize the current advancement in several nano-formulations for cancer therapy, with an extraordinary stress on TME-responsive ones. Scheme 1 highlights several TME modulation tactics with positive cancer therapeutic competence. The design of nanoconstructs and future challenges, consideration and opportunities are also discussed in detail. We have confidence in that these modulation approaches of TME tender a reliable opportunity for the practical translation of nanoparticle formulas into clinic.
Gunawan, C, Lord, MS, Lovell, E, Wong, RJ, Jung, MS, Oscar, D, Mann, R & Amal, R 2019, 'Oxygen-Vacancy Engineering of Cerium-Oxide Nanoparticles for Antioxidant Activity', ACS Omega, vol. 4, no. 5, pp. 9473-9479.
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To address an important challenge in the engineering of antioxidant nanoparticles, the present work devised a surface-to-bulk migration of oxygen vacancies in the oxygen radical-scavenging cerium-oxide nanoparticles. The study highlights the significance of surface oxygen vacancies in the intended cellular internalization and, subsequently, the radical scavenging activity of the nanoparticles inside the cells. The findings advise future development of therapeutic antioxidant nanomaterials to also include engineering of the particles for enhanced surface defects not only for the accessibility of their oxygen vacancies but also, equally important, rendering them bioavailable for cellular uptake.
Guo, J, Huo, J, Liu, Y, Wu, W, Wang, Y, Wu, M, Liu, H & Wang, G 2019, 'Nitrogen‐Doped Porous Carbon Supported Nonprecious Metal Single‐Atom Electrocatalysts: from Synthesis to Application', Small Methods, vol. 3, no. 9, pp. 1900159-1900159.
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AbstractNonprecious metal single‐atom materials have attracted extensive attention in the field of electrocatalysis due to their low cost, high reactivity, high selectivity, and high atomic utilization. However, the high surface energy of a single atom causes agglomeration during preparation and catalytic measurement, resulting in damage to the catalytic sites. The strong interaction between substrate and monoatoms is the key factor to prevent the aggregation of individual metal atoms, and the geometry and electronic structure of the catalysts can be adjusted to optimize the catalytic activity. Due to the hierarchically pores, high specific surface area, and defect effect, nitrogen‐doped porous carbon (NPC) has been widely studied as an ideal nonprecious metal single‐atom support, which synergistically enhance the electrocatalytic performance toward oxygen reduction reaction, oxygen evolution reaction, hydrogen evolution reaction, carbon dioxide reduction reaction, and nitrogen reduction reaction with non‐noble metal single atoms. This review summarizes the controllable synthesis, characterization, theoretical calculation, and application of M (M = Co, Fe, Ni, Cu, Zn, Mo, etc.) single atoms on nitrogen‐doped porous carbon. Finally, the future development and challenges of nitrogen‐doped porous carbon supported nonprecious metal single‐atom electrocatalysts for practical commercialization are concluded.
Guo, X, Zhang, J, Zhao, Y, Sun, B, Liu, H & Wang, G 2019, 'Ultrathin Porous NiCo2O4 Nanosheets for Lithium–Oxygen Batteries: An Excellent Performance Deriving from an Enhanced Solution Mechanism', ACS Applied Energy Materials, vol. 2, no. 6, pp. 4215-4223.
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© Copyright 2019 American Chemical Society. Lithium-oxygen batteries are of interest for long-range electric vehicles owing to their high theoretical energy density. However, the poor cycling performance and low round-trip efficiency deriving from the sluggish oxygen reduction reaction (ORR) and oxygen evolution reaction (OER) kinetics severely impede their practical application. Ingenious design of cathode catalysts is imperative to overcome these challenges. Here, we report ultrathin porous NiCo2O4 nanosheets with abundant oxygen vaccines as an efficient cathode catalyst toward both OER and ORR for Li-O2 batteries. From combined theoretical calculation with experimental results, a unique enhanced solution mechanism is proposed in the ether-based electrolyte system. Benefiting from the porous 2D architecture of the cathode and the hierarchical toroidal products, the Li-O2 batteries using NiCo2O4 cathodes deliver a high discharge capacity of 16 400 mAh g-1 at 200 mA g-1 and an excellent cycling performance up to 150 cycles with a restricted capacity of 1000 mAh g-1.
Gupta, A, Martinez-Lopez, C, Curran, JM & Almirall, JR 2019, 'Multi-element comparisons of tapes evidence using dimensionality reduction for calculating likelihood ratios', Forensic Science International, vol. 301, pp. 426-434.
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Gupta, V, Kumar, R, Kumar, R, Mahajan, R, Mehta, M, Satija, S, Vyas, M, Khurana, N & Sharma, N 2019, 'Pharmacological actions of sinomenium acutum : A brief review', Plant Archives, vol. 19, pp. 1732-1736.
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Sinomenine is an alkaloid, found in the roots of the Sinomenium acutum, which is a popular Chinese medicinal plant. It contains alkaloids, sterols, and phospholipids. Sinomenine have a great therapeutic benefit in rheumatic disease due to its analgesic, anti-arrhythmic and anti-inflammatory property. It is a morphinan derivative which is related to opioids such as levorphenol. It is reported to have activity against oligomeric Aβ protein, that support its neuroprotective potential, specifically to hippocampal cells. It also possesses anti-inflammatory effect against various neurological disorders. The current review mainly focuses on the action of sinomenine on immune system, cardiovascular system, and nervous system.
Gutiérrez Moreno, JJ, Fronzi, M, Lovera, P, O’Riordan, A, Ford, MJ, Li, W & Nolan, M 2019, 'Structure, stability and water adsorption on ultra-thin TiO2 supported on TiN', Physical Chemistry Chemical Physics, vol. 21, no. 45, pp. 25344-25361.
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Water adsorbs dissociatively on O-defective ultra-thin TiO1.75 supported on TiN. The Ti3+ states reduce the energy gap compared to TiO2.
Hamedi-Shahraki, S, Eshraghian, M-R, Yekaninejad, M-S, Nikoobakht, M, Rasekhi, A, Chen, H & Pakpour, A 2019, 'Health-related quality of life and medication adherence in elderly patients with epilepsy', Neurologia i Neurochirurgia Polska, vol. 53, no. 2, pp. 123-130.
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OBJECTIVE:Considering the high prevalence of epilepsy in the elderly and the importance of maximising their quality of life (QoL), this study aimed to investigate the relationship between medication adherence and QoL, and the mediating effects of medication adherence on the association between serum antiepileptic drug (AED) level and seizure severity with QoL in elderly epileptics. METHODS:In a longitudinal study, 766 elderly patients with epilepsy who were prescribed a minimum of one antiepileptic drug were selected by convenience sampling method. A Medication Adherence Report Scale (MARS-5) questionnaire was completed at the baseline. Seizure severity and QoL were assessed after six months using the Liverpool Seizure Severity Scale (LSSS) and the QoL in Epilepsy (QOLIE-31) questionnaires respectively. Serum level of AED was also measured at six-month follow-up. RESULTS:Medication adherence was significantly correlated with both seizure severity (β = -0.33, p < 0.0001) and serum AED level (β = 0.29, p < 0.0001) after adjusting for demographic and clinical characteristics. Neither QoL nor its sub-classes were correlated with seizure severity. In addition, a significant correlation was not observed between serum AED level and QoL. However, medication adherence was significantly correlated with QoL (β = 0.30, p < 0.0001). The mediating effects of medication adherence on the association between serum AED level (Z = 3.39, p < 0.001) and seizure severity (Z = -3.47, p < 0.001) with QoL were supported by the Sobel test. CONCLUSION:This study demonstrates that medication adherence has a beneficial impact on QoL in elderly epileptics. Therefore, adherence to treatment should be monitored to improve their QoL.
Han, N, Wei, Q, Tian, H, Zhang, S, Zhu, Z, Liu, J & Liu, S 2019, 'Highly Stable Dual‐Phase Membrane Based on Ce0.9Gd0.1O2–δ—La2NiO4+δ for Oxygen Permeation under Pure CO2 Atmosphere', Energy Technology, vol. 7, no. 5, pp. 1800701-1800701.
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Dense oxygen ion–conducting ceramic membranes with CO2 resistance can promote many advanced applications such as membrane reactors for green chemical synthesis and oxy‐fuel combustion for clean energy delivery. The state‐of‐the‐art perovskite oxide membranes are characterized by their high O2 flux but low stability in a CO2‐containing atmosphere. To solve this problem, dual‐phase membranes have captured the imagination of researchers. Herein, a novel dual‐phase hollow fiber membrane with a composition of 40 wt% Ce0.9Gd0.1O2–δ (GDC)–60 wt% La2NiO4+δ (LNO) is developed via a combined phase inversion sintering process. During the high temperature treatment, La‐doping behavior is observed with La leaching out from the LNO phase and diffusing into the GDC phase. This dual phase membrane displays the O2 flux of 1.47 at 950 °C, which is reduced by 10% to 1.31 mL min−1 cm−2 when the sweep gas is switched from helium to pure CO2. Such minor O2 flux reduction is due to the strong CO2 adsorption on membrane surface occupying the O2 vacancies without permanent membrane damage, which is fully eliminated by an inert gas purge. Such a robust dual‐phase membrane exhibits the potential to overcome the low stability problem under the CO2‐containing atmosphere.
Han, R, Khan, MH, Angeloski, A, Casillas, G, Yoon, CW, Sun, X & Huang, Z 2019, 'Hexagonal Boron Nitride Nanosheets Grown via Chemical Vapor Deposition for Silver Protection', ACS Applied Nano Materials, vol. 2, no. 5, pp. 2830-2835.
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Hardy, S, Mabotuwana, NS, Murtha, LA, Coulter, B, Bezenilla, SS, Al-Omary, MS, Senanayake, T, Loering, S, Rech, CLS, Starkey, M, Lee, RJ, Rainer, P, Hansbro, PM & Boyle, AJ 2019, 'P6296The role of extracellular matrix protein 1 (ECM1) - a novel link between inflammation and cardiac fibrosis', European Heart Journal, vol. 40, no. Supplement_1.
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Abstract
Introduction
Cardiac fibrosis is a severe consequence of cardiovascular disease and aging, in which we currently have no effective treatments. The mechanisms underpinning the development of cardiac fibrosis remains poorly understood. Our preliminary data suggested extracellular matrix protein 1 (ECM1) is involved in cardiac fibrosis. We therefore aimed to investigate the role of ECM1 in several fibrotic cardiac diseases.
Methods
Young and ageing (3m/18m) male C57BL/6 mice, and primary mouse cardiac fibroblast (cFB) cultures, commercial human cardiac fibroblasts (Hu-cFB), human coronary artery endothelial cell (HCAEC)/smooth muscle cell (HCASMC), and human cardiac myocyte (HCM) cell lines were used. Young mice were subject to myocardial infarction (MI, 3-day/28-day, n=6/6), or pressure overload (TAC, 3-day/13-week, n=4/4). Left ventricle (LV) was collected at all time-points, and at 18m (ageing; n=3). Spleen and bone marrow was extracted from young control mice. Hu-cFB cells were treated with recombinant ECM1 (20ng/ml) for either 10, 30 or 50 min, or 48h. Immunoblotting was conducted on all samples, qPCR on LV tissue only, density gradient centrifugation and multicolour flow cytometry coupled with fluorescent ECM1 mRNA in-situ hybridisation (FISH-Flow) on bone marrow cells.
Results
ECM1 expression was upregulated in ageing LV (mRNA 2.2±0.1-fold, p=0.0002; protein 2.0-fold, p=0.0006), day-3 post-MI (mRNA, 4.9±2.0-fold, p=0.004; protein, 3.0-fold, p=0.004), a trend of ECM1 upregulation was observed at day-28 post-MI (mRNA, 13.2±12.0-fold, p=0.003; protein, 1.8-fold, p=0.2), but no c...
Hardy, S, Mabotuwana, NS, Murtha, LA, Coulter, B, Bezenilla, SS, Al-Omary, MS, Senanayake, T, Loering, S, Rech, CLS, Starkey, M, Lee, RJ, Rainer, P, Hansbro, PM & Boyle, AJ 2019, 'The role of extracellular matrix protein 1 (ECM1) - a novel link between inflammation and cardiac fibrosis', EUROPEAN HEART JOURNAL, vol. 40, pp. 3900-3900.
Hardy, SA, Mabotuwana, NS, Murtha, LA, Coulter, B, Sanchez-Bezanilla, S, Al-Omary, MS, Senanayake, T, Loering, S, Starkey, M, Lee, RJ, Rainer, PP, Hansbro, PM & Boyle, AJ 2019, 'Novel role of extracellular matrix protein 1 (ECM1) in cardiac aging and myocardial infarction', PLOS ONE, vol. 14, no. 2, pp. e0212230-e0212230.
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INTRODUCTION:The prevalence of heart failure increases in the aging population and following myocardial infarction (MI), yet the extracellular matrix (ECM) remodeling underpinning the development of aging- and MI-associated cardiac fibrosis remains poorly understood. A link between inflammation and fibrosis in the heart has long been appreciated, but has mechanistically remained undefined. We investigated the expression of a novel protein, extracellular matrix protein 1 (ECM1) in the aging and infarcted heart. METHODS:Young adult (3-month old) and aging (18-month old) C57BL/6 mice were assessed. Young mice were subjected to left anterior descending artery-ligation to induce MI, or transverse aortic constriction (TAC) surgery to induce pressure-overload cardiomyopathy. Left ventricle (LV) tissue was collected early and late post-MI/TAC. Bone marrow cells (BMCs) were isolated from young healthy mice, and subject to flow cytometry. Human cardiac fibroblast (CFb), myocyte, and coronary artery endothelial & smooth muscle cell lines were cultured; human CFbs were treated with recombinant ECM1. Primary mouse CFbs were cultured and treated with recombinant angiotensin-II or TGF-β1. Immunoblotting, qPCR and mRNA fluorescent in-situ hybridization (mRNA-FISH) were conducted on LV tissue and cells. RESULTS:ECM1 expression was upregulated in the aging LV, and in the infarct zone of the LV early post-MI. No significant differences in ECM1 expression were found late post-MI or at any time-point post-TAC. ECM1 was not expressed in any resident cardiac cells, but ECM1 was highly expressed in BMCs, with high ECM1 expression in granulocytes. Flow cytometry of bone marrow revealed ECM1 expression in large granular leucocytes. mRNA-FISH revealed that ECM1 was indeed expressed by inflammatory cells in the infarct zone at day-3 post-MI. ECM1 stimulation of CFbs induced ERK1/2 and AKT activation and collagen-I expression, suggesting a pro-fibrotic role. CONCLUSIONS:ECM1 expression is in...
Hare, DJ, Braat, S, Cardoso, BR, Morgan, C, Szymlek-Gay, EA & Biggs, B-A 2019, 'Health outcomes of iron supplementation and/or food fortification in iron-replete children aged 4–24 months: protocol for a systematic review and meta-analysis', Systematic Reviews, vol. 8, no. 1.
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Abstract
Background
Direct supplementation or food fortification with iron are two public health initiatives intended to reduce the prevalence of iron deficiency (ID) and iron deficiency anaemia (IDA) in 4–24-month-old infants. In most high-income countries where IDA prevalence is < 15%, the recommended daily intake levels of iron from supplements and/or consumption of fortified food products are at odds with World Health Organisation (WHO) guidelines that recommend shorter-term (3 months/year) supplementation only in populations with IDA prevalence > 40%. Emerging concerns about delayed neurological effects of early-life iron overexposure have raised questions as to whether recommended guidelines in high-income countries are unnecessarily excessive. This systematic review will gather evidence from supplementation/fortification trials, comparing health outcomes in studies where iron-replete children did or did not receive additional dietary iron; and determine if replete children at study outset were not receiving additional iron show changes in haematological indices of ID/IDA over the trial duration.
Methods
We will perform a systematic review of the literature, including all studies of iron supplementation and/or fortification, including study arms with confirmed iron-replete infants at the commencement of the trial. This includes both dietary iron intervention or placebo/average dietary intakes. One reviewer will conduct searches in electronic databases of published and ongoing trials (Medline, Web of Science, Scopus, CENTRAL, EBSCO [e.g. CINAHL Complete, Food Science and Technology Abstracts], Embase, ClinicalTrials.gov, ClinicalTrialsRegister.eu and who.it/trialsearch), digital theses and dissertations (WorldCat, Ne...
Harrison, JA, Kelso, C, Padula, MP, Nicholson, GM & Beck, JL 2019, 'Structural characterization of protein toxins from Australian snake venoms using native mass spectrometry', Toxicon, vol. 158, pp. S43-S43.
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Harvey, KL, Jarocki, VM, Charles, IG & Djordjevic, SP 2019, 'The Diverse Functional Roles of Elongation Factor Tu (EF-Tu) in Microbial Pathogenesis', Frontiers in Microbiology, vol. 10.
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Elongation factor thermal unstable Tu (EF-Tu) is a G protein that catalyzes the binding of aminoacyl-tRNA to the A-site of the ribosome inside living cells. Structural and biochemical studies have described the complex interactions needed to effect canonical function. However, EF-Tu has evolved the capacity to execute diverse functions on the extracellular surface of both eukaryote and prokaryote cells. EF-Tu can traffic to, and is retained on, cell surfaces where can interact with membrane receptors and with extracellular matrix on the surface of plant and animal cells. Our structural studies indicate that short linear motifs (SLiMs) in surface exposed, non-conserved regions of the molecule may play a key role in the moonlighting functions ascribed to this ancient, highly abundant protein. Here we explore the diverse moonlighting functions relating to pathogenesis of EF-Tu in bacteria and examine putative SLiMs on surface-exposed regions of the molecule.
Häußler, S, Benedikter, J, Bray, K, Regan, B, Dietrich, A, Twamley, J, Aharonovich, I, Hunger, D & Kubanek, A 2019, 'Diamond photonics platform based on silicon vacancy centers in a single-crystal diamond membrane and a fiber cavity', Physical Review B, vol. 99, no. 16.
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© 2019 American Physical Society. We realize a potential platform for an efficient spin-photon interface, namely negatively-charged silicon-vacancy centers in a diamond membrane coupled to the mode of a fully-tunable, fiber-based, optical resonator. We demonstrate that introducing the thin (∼200nm), single crystal diamond membrane into the mode of the resonator does not change the cavity properties, which is one of the crucial points for an efficient spin-photon interface. In particular, we observe constantly high Finesse values of up to 3000 and a linear dispersion in the presence of the membrane. We observe cavity-coupled fluorescence from an ensemble of SiV- centers with an enhancement factor of ∼1.9. Furthermore from our investigations we extract the ensemble absorption and extrapolate an absorption cross section of (2.9±2)×10-12cm2 for a single SiV- center, much higher than previously reported.
Hayman, TJ, Hsu, AC, Kolesnik, TB, Dagley, LF, Willemsen, J, Tate, MD, Baker, PJ, Kershaw, NJ, Kedzierski, L, Webb, AI, Wark, PA, Kedzierska, K, Masters, SL, Belz, GT, Binder, M, Hansbro, PM, Nicola, NA & Nicholson, SE 2019, 'RIPLET, and not TRIM25, is required for endogenous RIG‐I‐dependent antiviral responses', Immunology & Cell Biology, vol. 97, no. 9, pp. 840-852.
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AbstractThe innate immune system is our first line of defense against viral pathogens. Host cell pattern recognition receptors sense viral components and initiate immune signaling cascades that result in the production of an array of cytokines to combat infection. Retinoic acid–inducible gene‐I (RIG‐I) is a pattern recognition receptor that recognizes viral RNA and, when activated, results in the production of type I and III interferons (IFNs) and the upregulation of IFN‐stimulated genes. Ubiquitination of RIG‐I by the E3 ligases tripartite motif‐containing 25 (TRIM25) and Riplet is thought to be requisite for RIG‐I activation; however, recent studies have questioned the relative importance of these two enzymes for RIG‐I signaling. In this study, we show that deletion of Trim25 does not affect the IFN response to either influenza A virus (IAV), influenza B virus, Sendai virus or several RIG‐I agonists. This is in contrast to deletion of either Rig‐i or Riplet, which completely abrogated RIG‐I‐dependent IFN responses. This was consistent in both mouse and human cell lines, as well as in normal human bronchial cells. With most of the current TRIM25 literature based on exogenous expression, these findings provide critical evidence that Riplet, and not TRIM25, is required endogenously for the ubiquitination of RIG‐I. Despite this, loss of TRIM25 results in greater susceptibility to IAV infection in vivo, suggesting that it may have an alternative role in host antiviral defense. This study refines our understanding of RIG‐I signaling in viral infections and will inform future studies in the field.
Hayward, RJ, Marsh, JW, Humphrys, MS, Huston, WM & Myers, GSA 2019, 'Early Transcriptional Landscapes of Chlamydia trachomatis-Infected Epithelial Cells at Single Cell Resolution', Frontiers in Cellular and Infection Microbiology, vol. 9.
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Chlamydia are Gram-negative obligate intracellular bacterial pathogens responsible for a variety of disease in humans and animals worldwide. Chlamydia trachomatis causes trachoma in disadvantaged populations, and is the most common bacterial sexually transmitted infection in humans, causing reproductive tract disease. Antibiotic therapy successfully treats diagnosed chlamydial infections, however asymptomatic infections are common. High-throughput transcriptomic approaches have explored chlamydial gene expression and infected host cell gene expression. However, these were performed on large cell populations, averaging gene expression profiles across all cells sampled and potentially obscuring biologically relevant subsets of cells. We generated a pilot dataset, applying single cell RNA-Seq (scRNA-Seq) to C. trachomatis infected and mock-infected epithelial cells to assess the utility, pitfalls and challenges of single cell approaches applied to chlamydial biology, and to potentially identify early host cell biomarkers of chlamydial infection. Two hundred sixty-four time-matched C. trachomatis-infected and mock-infected HEp-2 cells were collected and subjected to scRNA-Seq. After quality control, 200 cells were retained for analysis. Two distinct clusters distinguished 3-h cells from 6- and 12-h. Pseudotime analysis identified a possible infection-specific cellular trajectory for Chlamydia-infected cells, while differential expression analyses found temporal expression of metallothioneins and genes involved with cell cycle regulation, innate immune responses, cytoskeletal components, lipid biosynthesis and cellular stress. We find that changes to the host cell transcriptome at early times of C. trachomatis infection are readily discernible by scRNA-Seq, supporting the utility of single cell approaches to identify host cell biomarkers of chlamydial infection, and to further deconvolute the complex host response to infection.
He, P, Smith, A, Gelissen, IC & Ammit, AJ 2019, 'The effect of statins and the synthetic LXR agonist T0901317 on expression of ABCA1 transporter protein in human lung epithelial cell lines in vitro', Pharmacological Reports, vol. 71, no. 6, pp. 1219-1226.
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BACKGROUND: The pathogenesis of chronic obstructive pulmonary disease (COPD) is associated with dyslipidemia, an established co-morbidity. Statins treat hypercholesterolemia, but more recently have been trailed in the setting of COPD for their potential anti-inflammatory benefits. The outcomes of prospective trials however have been inconsistent. Thus, we hypothesize that the variation in results may have been due to statin-induced downregulation of ATP-binding cassette transporter A1 (ABCA1), thereby reducing cholesterol export. This study aims to elucidate whether statin treatment in a cellular model of COPD leads to a decrease in ABCA1 protein expression. METHODS: To mimic the inflammatory environment of COPD, two commonly used lung epithelial cell lines (BEAS-2B and A549) were treated with tumor necrosis factor (TNF), and co-treated with cholesterol/25-hydroxycholesterol (25-OH) to mimic dyslipidemia. ABCA1 protein was detected by Western Blotting. RESULTS: We unexpectedly showed that statins did not affect ABCA1 expression. However, the LXR agonist T0901317 significantly increased ABCA1 expression in both cell lines, while TNF, cholesterol or 25-OH induced ABCA1 protein upregulation in BEAS-2B cells, indicating cell line differences in response. There was also evidence of synergistic impacts of combined treatments on ABCA1 upregulation in BEAS-2B cells. CONCLUSION: Statins did not have an impact on ABCA1 expression in lung epithelial cell lines, disproving our original hypothesis. However, we showed for the first time, the effect of the inflammatory cytokine TNF, cholesterol/25-OH, statins and the LXR agonist T0901317 on expression of ABCA1 transporter protein in human lung epithelial cell lines in vitro. We hope that these in vitro studies may prove beneficial for addressing dyslipidemia in COPD in the future.
Hewson, I, Sullivan, B, Jackson, EW, Xu, Q, Long, H, Lin, C, Quijano Cardé, EM, Seymour, J, Siboni, N, Jones, MRL & Sewell, MA 2019, 'Perspective: Something Old, Something New? Review of Wasting and Other Mortality in Asteroidea (Echinodermata)', Frontiers in Marine Science, vol. 6.
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Hing, ML, Klanten, OS, Wong, MYL & Dowton, M 2019, 'Drivers of sociality in Gobiodon fishes: An assessment of phylogeny, ecology and life-history', Molecular Phylogenetics and Evolution, vol. 137, pp. 263-273.
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What drives the evolution of sociality in animals? Many robust studies in terrestrial organisms have pointed toward various kinship-based, ecological and life-history traits or phylogenetic constraint which have played a role in the evolution of sociality. These traits are not mutually exclusive and the exact combination of traits is likely taxon-specific. Phylogenetic comparative analyses have been instrumental in identifying social lineages and comparing various traits with non-social lineages to give broad evolutionary perspectives on the development of sociality. Few studies have attempted this approach in marine vertebrate systems. Social marine fishes are particularly interesting because many have a pelagic larval phase and non-conventional life-history strategies (e.g. bi-directional sex-change) not often observed in terrestrial animals. Such strategies provide novel insights into terrestrially-derived theories of social evolution. Here, we assess the strength of the phylogenetic signal of sociality in the Gobiodon genus with Pagel's lambda and Blomberg's K parameters. We found some evidence of a phylogenetic signal of sociality, but factors other than phylogenetic constraint also have a strong influence on the extant social state of each species. We then use phylogenetic generalized least squares analyses to examine several ecological and life-history traits that may have influenced the evolution of sociality in the genus. We found an interaction of habitat size and fish length was the strongest predictor of sociality. Sociality in larger species was more dependent on coral size than in smaller species, but smaller species were more social overall, regardless of coral size. Finally, we comment on findings regarding the validity of the species G. spilophthalmus which arose during the course of our research. These findings in a group of marine fishes add a unique perspective on the evolution of sociality to the excellent terrestrial work conducted in this f...
Hitchcock, JN & Mitrovic, SM 2019, 'Microplastic pollution in estuaries across a gradient of human impact', Environmental Pollution, vol. 247, pp. 457-466.
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Microplastic (MP) pollution is an emerging issue in aquatic sciences. Little comparative information currently exists about the problem in coastal systems exposed to different levels of human impact. Here we report a year-long study on the abundance of MP in the water column of three estuaries on the east-coast of Australia. The estuaries are subject to different scales of human impact; the Clyde estuary has little human modification, the Bega estuary has a small township and single wastewater treatment works discharging to its waters, and the Hunter estuary which has multiple townships, multiple wastewater treatment plants, and heavy industry. MP abundance followed an expected pattern with the lowest abundance in the low-impact Clyde estuary (98 part. m3), moderate levels of MP in the moderately impacted Bega estuary (246 part. m3), and high MP abundance in the highly impacted Hunter estuary (1032 part. m3). The majority of particles were <200 μm and fragment-like rather than fiber-like. MP abundance was positively related to maximum antecedent rainfall in the Bega estuary, however there are no clear environmental factors that could explain MP variation in the other systems. MP were generally higher in summer and following freshwater inflow events. On the Hunter estuary MP abundance was at times as high as zooplankton abundance, and within the range of numbers reported in other highly impacted systems globally. The results confirm that higher levels of human impact lead to greater plastic pollution and highlight the need to examine aquatic ecosystems under a range of conditions in order to adequately characterize the extent of MP pollution in rivers and coastal systems.
Hogan, AL, Don, EK, Rayner, SL, Lee, A, Laird, AS, Watchon, M, Winnick, C, Tarr, IS, Morsch, M, Fifita, JA, Gwee, SSL, Formella, I, Hortle, E, Yuan, KC, Molloy, MP, Williams, KL, Nicholson, GA, Chung, RS, Blair, IP & Cole, NJ 2019, 'Expression of ALS/FTD-linked mutant CCNF in zebrafish leads to increased cell death in the spinal cord and an aberrant motor phenotype', Human Molecular Genetics, vol. 28, no. 4, pp. 698-698.
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Hoppenrath, M, Kretzschmar, AL, Kaufmann, MJ & Murray, SA 2019, 'Morphological and molecular phylogenetic identification and record verification of Gambierdiscus excentricus (Dinophyceae) from Madeira Island (NE Atlantic Ocean)', Marine Biodiversity Records, vol. 12, no. 1.
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Hoppstädter, J & Ammit, AJ 2019, 'Role of Dual-Specificity Phosphatase 1 in Glucocorticoid-Driven Anti-inflammatory Responses', Frontiers in Immunology, vol. 10.
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Glucocorticoids (GCs) potently inhibit pro-inflammatory responses and are widely used for the treatment of inflammatory diseases, such as allergies, autoimmune disorders, and asthma. Dual-specificity phosphatase 1 (DUSP1), also known as mitogen-activated protein kinase (MAPK) phosphatase-1 (MKP-1), exerts its effects by dephosphorylation of MAPKs, i.e., extracellular-signal-regulated kinase (ERK), p38, and c-Jun N-terminal kinase (JNK). Endogenous DUSP1 expression is tightly regulated at multiple levels, involving both transcriptional and post-transcriptional mechanisms. DUSP1 has emerged as a central mediator in the resolution of inflammation, and upregulation of DUSP1 by GCs has been suggested to be a key mechanism of GC actions. In this review, we discuss the impact of DUSP1 on the efficacy of GC-mediated suppression of inflammation and address the underlying mechanisms.
Hortle, E, Johnson, KE, Johansen, MD, Nguyen, T, Shavit, JA, Britton, WJ, Tobin, DM & Oehlers, SH 2019, 'Thrombocyte Inhibition Restores Protective Immunity to Mycobacterial Infection in Zebrafish', The Journal of Infectious Diseases, vol. 220, no. 3, pp. 524-534.
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Abstract
Background
Infection-induced thrombocytosis is a clinically important complication of tuberculosis infection. Recent studies have highlighted the utility of aspirin as a host-directed therapy modulating the inflammatory response to infection but have not investigated the possibility that the effect of aspirin is related to an antiplatelet mode of action.
Methods
In this study, we utilize the zebrafish-Mycobacterium marinum model to show mycobacteria drive host hemostasis through the formation of granulomas. Treatment of infected zebrafish with aspirin markedly reduced mycobacterial burden. This effect is reproduced by treatment with platelet-specific glycoprotein IIb/IIIa inhibitors demonstrating a detrimental role for infection-induced thrombocyte activation.
Results
We find that the reduction in mycobacterial burden is dependent on macrophages and granuloma formation, providing the first in vivo experimental evidence that infection-induced platelet activation compromises protective host immunity to mycobacterial infection.
Conclusions
Our study illuminates platelet activation as an efficacious target of aspirin, a widely available and affordable host-directed therapy candidate for tuberculosis.
Hortle, E, Starrs, L, Brown, FC, Jane, SM, Curtis, DJ, McMorran, BJ, Foote, SJ & Burgio, G 2019, 'KCC1 Activation protects Mice from the Development of Experimental Cerebral Malaria', Scientific Reports, vol. 9, no. 1.
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AbstractPlasmodium falciparum malaria causes half a million deaths per year, with up to 9% of this mortality caused by cerebral malaria (CM). One of the major processes contributing to the development of CM is an excess of host inflammatory cytokines. Recently K+ signaling has emerged as an important mediator of the inflammatory response to infection; we therefore investigated whether mice carrying an ENU induced activation of the electroneutral K+ channel KCC1 had an altered response to Plasmodium berghei. Here we show that Kcc1M935K/M935K mice are protected from the development of experimental cerebral malaria, and that this protection is associated with an increased CD4+ and TNFa response. This is the first description of a K+ channel affecting the development of experimental cerebral malaria.
Hossain, KR & Clarke, RJ 2019, 'General and specific interactions of the phospholipid bilayer with P-type ATPases', Biophysical Reviews, vol. 11, no. 3, pp. 353-364.
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Protein structure and function are modulated via interactions with their environment, representing both the surrounding aqueous media and lipid membranes that have an active role in shaping the structural topology of membrane proteins. Compared to a decade ago, there is now an abundance of crystal structural data on membrane proteins, which together with their functional studies have enhanced our understanding of the salient features of lipid-protein interactions. It is now important to recognize that membrane proteins are regulated by both (1) general lipid-protein interactions, where the general physicochemical properties of the lipid environment affect the conformational flexibility of a membrane protein, and (2) by specific lipid-protein interactions, where lipid molecules directly interact via chemical interactions with specific lipid-binding sites located on the protein. However, due to local differences in membrane composition, thickness, and lipid packing, local membrane physical properties and hence the associated lipid-protein interactions also differ due to membrane location, even for the same protein. Such a phenomenon has been shown to be true for one family of integral membrane ion pumps, the P2-type adenosine triphosphatases (ATPases). Despite being highly homologous, individual members of this family have distinct structural and functional activity and are an excellent candidate to highlight how the local membrane physical properties and specific lipid-protein interactions play a vital role in facilitating the structural rearrangements of these proteins necessary for their activity. Hence in this review, we focus on both the general and specific lipid-protein interactions and will mostly discuss the structure-function relationships of the following P2-type ATPases, Na+,K+-ATPase (NKA), gastric H+,K+-ATPase (HKA), and sarco(endo)plasmic reticulum Ca2+-ATPase (SERCA), in concurrence with their lipid environment.
Hossain, KR, Turkewitz, DR, Holt, SA, Herson, L, Brown, LJ, Cornell, BA, Curmi, PMG & Valenzuela, SM 2019, 'A conserved GXXXG motif in the transmembrane domain of CLIC proteins is essential for their cholesterol-dependant membrane interaction', Biochimica et Biophysica Acta (BBA) - General Subjects, vol. 1863, no. 8, pp. 1243-1253.
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BACKGROUND:Sterols have been reported to modulate conformation and hence the function of several membrane proteins. One such group is the Chloride Intracellular Ion Channel (CLIC) family of proteins. The CLIC protein family consists of six evolutionarily conserved protein members in vertebrates. These proteins exist as both monomeric soluble proteins and as membrane bound proteins. To date, the structure of their membrane-bound form remains unknown. In addition to several studies indicating cellular redox environment and pH as facilitators of CLIC1 insertion into membranes, we have also demonstrated that the spontaneous membrane insertion of CLIC1 is regulated by membrane cholesterol. METHOD:We have performed Langmuir-film, Impedance Spectroscopy and Molecular Docking Simulations to study the role of this GXXXG motif in CLIC1 interaction with cholesterol. RESULTS:Unlike CLIC1-wild-type protein, the G18A and G22A mutants, that form part of the GXXXG motif, showed much slower initial kinetics and lower ion channel activity compared to the native protein. This difference can be attributed to the significantly reduced membrane interaction and insertion rate of the mutant proteins and/or slower formation of the final membrane configuration of the mutant proteins once in the membrane. CONCLUSION:In this study, our findings uncover the identification of a GXXXG motif in CLIC1, which likely serves as the cholesterol-binding domain, that facilitates the protein's membrane interaction and insertion. Furthermore, we were able to postulate a model by which CLIC1 can autonomously insert into membranes to form functional ion channels. GENERAL SIGNIFICANCE:Members of the CLIC family of proteins demonstrate unusual structural and dual functional properties - as ion channels and enzymes. Elucidating how the CLIC proteins' interact with membranes, thus allowing them to switch between their soluble and membrane form, will provide key information as to a mechanism of moonlighting ac...
Howe, ENW & Gale, PA 2019, 'Fatty Acid Fueled Transmembrane Chloride Transport', Journal of the American Chemical Society, vol. 141, no. 27, pp. 10654-10660.
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Hu, M, Schulze, KE, Ghildyal, R, Henstridge, DC, Kolanowski, JL, New, EJ, Hong, Y, Hsu, AC, Hansbro, PM, Wark, PAB, Bogoyevitch, MA & Jans, DA 2019, 'Respiratory syncytial virus co-opts host mitochondrial function to favour infectious virus production', eLife, vol. 8.
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Although respiratory syncytial virus (RSV) is responsible for more human deaths each year than influenza, its pathogenic mechanisms are poorly understood. Here high-resolution quantitative imaging, bioenergetics measurements and mitochondrial membrane potential- and redox-sensitive dyes are used to define RSV’s impact on host mitochondria for the first time, delineating RSV-induced microtubule/dynein-dependent mitochondrial perinuclear clustering, and translocation towards the microtubule-organizing centre. These changes are concomitant with impaired mitochondrial respiration, loss of mitochondrial membrane potential and increased production of mitochondrial reactive oxygen species (ROS). Strikingly, agents that target microtubule integrity the dynein motor protein, or inhibit mitochondrial ROS production strongly suppresses RSV virus production, including in a mouse model with concomitantly reduced virus-induced lung inflammation. The results establish RSV’s unique ability to co-opt host cell mitochondria to facilitate viral infection, revealing the RSV-mitochondrial interface for the first time as a viable target for therapeutic intervention.
Hu, P, Hu, S, Huang, Y, Reimers, JR, Rappe, AM, Li, Y, Stroppa, A & Ren, W 2019, 'Bioferroelectric Properties of Glycine Crystals', The Journal of Physical Chemistry Letters, vol. 10, no. 6, pp. 1319-1324.
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Biological ferroelectric materials have great potential in biosensing and disease diagnosis and treatment. Glycine crystals form the simplest bioferroelectric materials, and here we investigate the polarizations of its β- and γ-phases. Using density functional theory, we predict that glycine crystals can develop polarizations even larger than those of conventional inorganic ferroelectrics. Further, using systematic molecular dynamics simulations utilizing polarized crystal charges, we predict the Curie temperature of γ-glycine to be 630 K, with a required coercive field to switch its polarization states of 1 V·nm-1, consistent with experimental evidence. This work sheds light on the microscopic mechanism of electric dipole ordering in biomaterials, helping in the material design of novel bioferroelectrics.
Hundal, AK, Agarwal, A, Jameel, M, Chen, J-Y, Li, J-L, Jones, L, Kaur, N, Langford, S & Gupta, A 2019, 'Improvement of the optoelectronic and photovoltaic properties of a cyanopyrid-2,6-dione-based donor via molecular engineering', Dyes and Pigments, vol. 170, pp. 107661-107661.
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Hurley-Walker, N, Filipović, MD, Gaensler, BM, Leahy, DA, Hancock, PJ, Franzen, TMO, Offringa, AR, Callingham, JR, Hindson, L, Wu, C, Bell, ME, For, B-Q, Johnston-Hollitt, M, Kapińska, AD, Morgan, J, Murphy, T, McKinley, B, Procopio, P, Staveley-Smith, L, Wayth, RB & Zheng, Q 2019, 'New candidate radio supernova remnants detected in the GLEAM survey over 345° <l< 60°, 180° <l< 240°', Publications of the Astronomical Society of Australia, vol. 36.
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AbstractWe have detected 27 new supernova remnants (SNRs) using a new data release of the GLEAM survey from the Murchison Widefield Array telescope, including the lowest surface brightness SNR ever detected, G 0.1 – 9.7. Our method uses spectral fitting to the radio continuum to derive spectral indices for 26/27 candidates, and our low-frequency observations probe a steeper spectrum population than previously discovered. None of the candidates have coincidentWISEmid-IR emission, further showing that the emission is non-thermal. Using pulsar associations we derive physical properties for six candidate SNRs, finding G 0.1 – 9.7 may be younger than 10 kyr. Sixty per cent of the candidates subtend areas larger than 0.2 deg2on the sky, compared to < 25% of previously detected SNRs. We also make the first detection of two SNRs in the Galactic longitude range 220°–240°.
Hurley-Walker, N, Gaensler, BM, Leahy, DA, Filipović, MD, Hancock, PJ, Franzen, TMO, Offringa, AR, Callingham, JR, Hindson, L, Wu, C, Bell, ME, For, B-Q, Johnston-Hollitt, M, Kapińska, AD, Morgan, J, Murphy, T, McKinley, B, Procopio, P, Staveley-Smith, L, Wayth, RB & Zheng, Q 2019, 'Candidate radio supernova remnants observed by the GLEAM survey over 345° <l< 60° and 180° <l< 240°', Publications of the Astronomical Society of Australia, vol. 36.
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AbstractWe examined the latest data release from the GaLactic and Extragalactic All-sky Murchison Widefield Array (GLEAM) survey covering 345° <l< 60° and 180° <l< 240°, using these data and that of theWidefield Infrared Survey Explorerto follow up proposed candidate Supernova Remnant (SNR) from other sources. Of the 101 candidates proposed in the region, we are able to definitively confirm ten as SNRs, tentatively confirm two as SNRs, and reclassify five as Hiiregions. A further two are detectable in our images but difficult to classify; the remaining 82 are undetectable in these data. We also investigated the 18 unclassified Multi-Array Galactic Plane Imaging Survey (MAGPIS) candidate SNRs, newly confirming three as SNRs, reclassifying two as Hiiregions, and exploring the unusual spectra and morphology of two others.
Hurley-Walker, N, Hancock, PJ, Franzen, TMO, Callingham, JR, Offringa, AR, Hindson, L, Wu, C, Bell, ME, For, B-Q, Gaensler, BM, Johnston-Hollitt, M, Kapińska, AD, Morgan, J, Murphy, T, McKinley, B, Procopio, P, Staveley-Smith, L, Wayth, RB & Zheng, Q 2019, 'GaLactic and Extragalactic All-sky Murchison Widefield Array (GLEAM) survey II: Galactic plane 345° <l< 67°, 180° <l< 240°', Publications of the Astronomical Society of Australia, vol. 36.
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AbstractThis work makes available a further$2\,860~\text{deg}^2$of the GaLactic and Extragalactic All-sky Murchison Widefield Array (GLEAM) survey, covering half of the accessible galactic plane, across 20 frequency bands sampling 72–231 MHz, with resolution$4\,\text{arcmin}-2\,\text{arcmin}$. Unlike previous GLEAM data releases, we used multi-scaleCLEANto better deconvolve large-scale galactic structure. For the galactic longitude ranges$345^\circ < l < 67^\circ$,$180^\circ < l < 240^\circ$, we provide a compact source catalogue of 22 037 components selected from a 60-MHz bandwidth image centred at 200 MHz, with RMS noise$\approx10-20\,\text{mJy}\,\text{beam}^{-1}$
Hurtado Silva, M, Berry, I, Strange, N, Djordjevic, S & Padula, M 2019, 'Terminomics Methodologies and the Completeness of Reductive Dimethylation: A Meta-Analysis of Publicly Available Datasets', Proteomes, vol. 7, no. 2, pp. 11-11.
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Methods for analyzing the terminal sequences of proteins have been refined over the previous decade; however, few studies have evaluated the quality of the data that have been produced from those methodologies. While performing global N-terminal labelling on bacteria, we observed that the labelling was not complete and investigated whether this was a common occurrence. We assessed the completeness of labelling in a selection of existing, publicly available N-terminomics datasets and empirically determined that amine-based labelling chemistry does not achieve complete labelling and potentially has issues with labelling amine groups at sequence-specific residues. This finding led us to conduct a thorough review of the historical literature that showed that this is not an unexpected finding, with numerous publications reporting incomplete labelling. These findings have implications for the quantitation of N-terminal peptides and the biological interpretations of these data.
Hurtado-McCormick, V, Kahlke, T, Petrou, K, Jeffries, T, Ralph, PJ & Seymour, JR 2019, 'Regional and Microenvironmental Scale Characterization of the Zostera muelleri Seagrass Microbiome', Frontiers in Microbiology, vol. 10.
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Seagrasses are globally distributed marine plants that represent an extremely valuable component of coastal ecosystems. Like terrestrial plants, seagrass productivity and health are likely to be strongly governed by the structure and function of the seagrass microbiome, which will be distributed across a number of discrete microenvironments within the plant, including the phyllosphere, the endosphere and the rhizosphere, all different in physical and chemical conditions. Here we examined patterns in the composition of the microbiome of the seagrass Zostera muelleri, within six plant-associated microenvironments sampled across four different coastal locations in New South Wales, Australia. Amplicon sequencing approaches were used to characterize the diversity and composition of bacterial, microalgal, and fungal microbiomes and ultimately identify “core microbiome” members that were conserved across sampling microenvironments. Discrete populations of bacteria, microalgae and fungi were observed within specific seagrass microenvironments, including the leaves and roots and rhizomes, with “core” taxa found to persist within these microenvironments across geographically disparate sampling sites. Bacterial, microalgal and fungal community profiles were most strongly governed by intrinsic features of the different seagrass microenvironments, whereby microscale differences in community composition were greater than the differences observed between sampling regions. However, our results showed differing strengths of microbial preferences at the plant scale, since this microenvironmental variability was more pronounced for bacteria than it was for microalgae and fungi, suggesting more specific interactions between the bacterial consortia and the seagrass host, and potentially implying a highly specialized coupling between seagrass and bacterial metabolism and ecology. Due to their persistence within a given seagrass microenvironment, acro...
Huston, W 2019, 'Spotlight on…Wilhelmina M. Huston', FEMS Microbiology Letters, vol. 366, no. 20.
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Huston, WM, Coers, J & Garzino-Demo, A 2019, 'Fresh faces and new approaches at Pathogens and Disease', Pathogens and Disease, vol. 77, no. 1.
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Huston, WM, Cranfield, CG, Forbes, SL & Leigh, A 2019, 'A sponsorship action plan for increasing diversity in STEMM', Ecology and Evolution, vol. 9, no. 5, pp. 2340-2345.
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There are numerous structural and cultural barriers to the progression of women and marginalized groups to leadership in academia, especially in Science, Technology, Engineering, Mathematics and Medicine (STEMM). A range of interventions have been described to address this inequity, with varying success. Here, we suggest that sponsorship could be one effective intervention and propose an institutional action plan to implement a sponsorship program in academia. We outline why sponsorship could be an effective strategy, especially if implemented through a deliberate program by an institution. We then detail the three components of an action plan to be considered in implementation: the elements of the program, the activities that sponsorship in academia likely encompasses, and the selection of sponsors and protégés. The plan could also be enacted by academic leadership in the absence of an institutional program and could serve as a guide to individuals in academia aspiring to address diversity and inclusion in STEMM.
Idowu, O, Semple, KT, Ramadass, K, O'Connor, W, Hansbro, P & Thavamani, P 2019, 'Beyond the obvious: Environmental health implications of polar polycyclic aromatic hydrocarbons', Environment International, vol. 123, pp. 543-557.
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The genotoxic, mutagenic and carcinogenic effects of polar polycyclic aromatic hydrocarbons (polar PAHs) are believed to surpass those of their parent PAHs; however, their environmental and human health implications have been largely unexplored. Oxygenated PAHs (oxy-PAHs) is a critical class of polar PAHs associated with carcinogenic effects without enzymatic activation. They also cause an upsurge in reactive oxygen species (ROS) in living cells. This results in oxidative stress and other consequences, such as abnormal gene expressions, altered protein activities, mutagenesis, and carcinogenesis. Similarly, some nitrated PAHs (N-PAHs) are probable human carcinogens as classified by the International Agency for Research on Cancer (IARC). Heterocyclic PAHs (polar PAHs containing nitrogen, sulphur and oxygen atoms within the aromatic rings) have been shown to be potent endocrine disruptors, primarily through their estrogenic activities. Despite the high toxicity and enhanced environmental mobility of many polar PAHs, they have attracted only a little attention in risk assessment of contaminated sites. This may lead to underestimation of potential risks, and remediation end points. In this review, the toxicity of polar PAHs and their associated mechanisms of action, including their role in mutagenic, carcinogenic, developmental and teratogenic effects are critically discussed. This review suggests that polar PAHs could have serious toxicological effects on human health and should be considered during risk assessment of PAH-contaminated sites. The implications of not doing so were argued and critical knowledge gaps and future research requirements discussed.
Iikawa, F, Hernández-Mínguez, A, Aharonovich, I, Nakhaie, S, Liou, Y-T, Lopes, JMJ & Santos, PV 2019, 'Acoustically modulated optical emission of hexagonal boron nitride layers', Applied Physics Letters, vol. 114, no. 17, pp. 171104-171104.
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We investigate the effect of surface acoustic waves on the atomic-like optical emission from defect centers in hexagonal boron nitride layers deposited on the surface of a LiNbO3 substrate. The dynamic strain field of the surface acoustic waves modulates the emission lines resulting in intensity variations as large as 50% and oscillations of the emission energy with an amplitude of almost 1 meV. From a systematic study of the dependence of the modulation on the acoustic wave power, we determine a hydrostatic deformation potential of about 40 meV/% for defect centers in this two-dimensional material. Furthermore, we show that the dynamic piezoelectric field of the acoustic wave could contribute to the stabilization of the optical properties of these emission centers. Our results show that surface acoustic waves are a powerful tool to modulate and control the electronic states of two-dimensional materials.
Imkamp, K, Bernal, V, Grzegorzcyk, M, Horvatovich, P, Vermeulen, CJ, Heijink, IH, Guryev, V, Kerstjens, HAM, van den Berge, M & Faiz, A 2019, 'Gene network approach reveals co-expression patterns in nasal and bronchial epithelium', Scientific Reports, vol. 9, no. 1.
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AbstractNasal gene expression profiling is a new approach to investigate the airway epithelium as a biomarker to study the activity and treatment responses of obstructive pulmonary diseases. We investigated to what extent gene expression profiling of nasal brushings is similar to that of bronchial brushings. We performed genome wide gene expression profiling on matched nasal and bronchial epithelial brushes from 77 respiratory healthy individuals. To investigate differences and similarities among regulatory modules, network analysis was performed on correlated, differentially expressed and smoking-related genes using Gaussian Graphical Models. Between nasal and bronchial brushes, 619 genes were correlated and 1692 genes were differentially expressed (false discovery rate <0.05, |Fold-change|>2). Network analysis of correlated genes showed pro-inflammatory pathways to be similar between the two locations. Focusing on smoking-related genes, cytochrome-P450 pathway related genes were found to be similar, supporting the concept of a detoxifying response to tobacco exposure throughout the airways. In contrast, cilia-related pathways were decreased in nasal compared to bronchial brushes when focusing on differentially expressed genes. Collectively, while there are substantial differences in gene expression between nasal and bronchial brushes, we also found similarities, especially in the response to the external factors such as smoking.
Indigo, N, Smith, J, Webb, JK & Phillips, BL 2019, 'Bangers and cash: Baiting efficiency in a heterogeneous population', Wildlife Society Bulletin, vol. 43, no. 4, pp. 669-677.
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ABSTRACTUptake of baits is a key variable in management actions aimed at the vaccination, training, or control of many vertebrate species. Increasingly, however, it is apparent that individuals of the target species vary in their likelihood of taking baits. To optimize a baiting program, knowledge on the rate of bait uptake, how this rate changes with bait availability, and the proportion of the target population that will take a bait is required. The invasive cane toad (Rhinella marina) in Australia is a major threat to northern quolls (Dasyurus hallucatus), which are poisoned when they attack this novel toxic prey item. Conditioned‐taste‐aversion baits (cane toad sausages) can be delivered in the field to train northern quolls to avoid toads. We conducted a large‐scale field trial among 11 sites across one large property in Western Australia from 19–26 July 2017. We used camera traps and statistical modelling to estimate the proportion of baitable animals in the population, their encounter rate with baits, and survival rate of baits in the environment. Population estimates varied at each site from 2.5 to 16.8 quolls per site, resulting in a range among sites of 0.7–4.6 baits available/individual. Approximately 64% of individual quolls were bait‐susceptible. Both encounter rate and bait survival were low, resulting in our baiting regime treating <30% of the bait‐susceptible population. Using our model parameters, we estimate that we would need to increase our bait density 6‐fold to treat all bait‐susceptible individuals in the population. Without accounting for heterogeneity in bait‐susceptibility, our model would suggest we would need a 10‐fold increase in bait density. Thus, accounting for heterogeneity provides a more efficient baiting design. Data and models such as ours provide wildlife managers with information critical to informed decision‐making and are fundamental ...
Insuasty, A, Maniam, S & Langford, SJ 2019, 'Recent Advances in the Core‐Annulation of Naphthalene Diimides', Chemistry – A European Journal, vol. 25, no. 29, pp. 7058-7073.
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AbstractThis review focuses on describing all known synthetic strategies leading to core‐annulation of naphthalene diimides (NDIs). Strategies presented involve the formation of four‐, five‐ and six‐membered ring annulations bearing different heteroatomic and carbocyclic derivatives, including annulenes. The core‐annulation method opens the possibility for obtaining designer molecules with tuneable electronic characteristics such as a reduced energy band gap, and enhanced intermolecular overlap of π‐systems that improve electronic coupling between molecules—which is highly desirable for charge transport properties summarised in the final pages for applications in electronic devices such as organic field‐effect transistors (OFETs) and organic photovoltaic (OPV) cells. Molecular recognition in pH and fluoride sensing, or as a DNA probe, are some of additional applications of core‐annulated NDIs presented here. Additionally, recent advances in core modification of NDIs are presented, opening an entire new chemical avenue to be explored. Finally, the outlook on the future prospect of annulated NDIs in various applications is summarised.
Irga, PJ, Pettit, T, Irga, RF, Paull, NJ, Douglas, ANJ & Torpy, FR 2019, 'Does plant species selection in functional active green walls influence VOC phytoremediation efficiency?', Environmental Science and Pollution Research, vol. 26, no. 13, pp. 12851-12858.
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Volatile organic compounds (VOCs) are of public concern due to their adverse health effects. Botanical air filtration is a promising technology for reducing indoor air contaminants, but the underlying mechanisms are not fully understood. This study assessed active botanical biofilters for their single-pass removal efficiency (SPRE) for benzene, ethyl acetate and ambient total volatile organic compounds (TVOCs), at concentrations of in situ relevance. Biofilters containing four plant species (Chlorophytum orchidastrum, Nematanthus glabra, Nephrolepis cordifolia 'duffii' and Schefflera arboricola) were compared to discern whether plant selection influenced VOC SPRE. Amongst all tested plant species, benzene SPREs were between 45.54 and 59.50%, with N. glabra the most efficient. The botanical biofilters removed 32.36-91.19% of ethyl acetate, with C. orchidastrum and S. arboricola recording significantly higher ethyl acetate SPREs than N. glabra and N. cordifolia. These findings thus indicate that plant type influences botanical biofilter VOC removal. It is proposed that ethyl acetate SPREs were dependent on hydrophilic adsorbent sites, with increasing root surface area, root diameter and root mass all associated with increasing ethyl acetate SPRE. The high benzene SPRE of N. glabra is likely due to the high wax content in its leaf cuticles. The SPREs for the relatively low levels of ambient TVOCs were consistent amongst plant species, providing no evidence to suggest that in situ TVOC removal is influenced by plant choice. Nonetheless, as inter-species differences do exist for some VOCs, botanical biofilters using a mixture of plants is proposed.
Jain, D, Ghonse, SS, Trivedi, T, Fernandes, GL, Menezes, LD, Damare, SR, Mamatha, SS, Kumar, S & Gupta, V 2019, 'CO2 fixation and production of biodiesel by Chlorella vulgaris NIOCCV under mixotrophic cultivation', Bioresource Technology, vol. 273, pp. 672-676.
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Jaramillo-Madrid, AC, Ashworth, J, Fabris, M & Ralph, PJ 2019, 'Phytosterol biosynthesis and production by diatoms (Bacillariophyceae)', Phytochemistry, vol. 163, pp. 46-57.
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Diatoms are abundant unicellular marine photosynthetic algae that have genetically diversified their physiology and metabolism while adapting to numerous environments. The metabolic repertoire of diatoms presents opportunities to characterise the biosynthesis and production of new and potentially valuable microalgal compounds, including sterols. Sterols of plant origin, known as phytosterols, have been studied for health benefits including demonstrated cholesterol-lowering properties. In this review we summarise sterol diversity, the unique metabolic features of sterol biosynthesis in diatoms, and prospects for the extraction of diatom phytosterols in comparison to existing sources. We also review biotechnological efforts to manipulate diatom biosynthesis, including culture conditions and avenues for the rational engineering of metabolism and cellular regulation.
Jarocki, V 2019, 'Mycoplasma hyopneumoniae' proteases: Investigating their role in pathogenesis and chronic infection', Journal and Proceedings of the Royal Society of New South Wales, vol. 152, no. 471/472, pp. 145-146.
Jarocki, VM, Raymond, BBA, Tacchi, JL, Padula, MP & Djordjevic, SP 2019, 'Mycoplasma hyopneumoniae surface-associated proteases cleave bradykinin, substance P, neurokinin A and neuropeptide Y', Scientific Reports, vol. 9, no. 1.
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AbstractMycoplasma hyopneumoniae is an economically-devastating and geographically-widespread pathogen that colonises ciliated epithelium, and destroys mucociliary function. M. hyopneumoniae devotes ~5% of its reduced genome to encode members of the P97 and P102 adhesin families that are critical for colonising epithelial cilia, but mechanisms to impair mucociliary clearance and manipulate host immune response to induce a chronic infectious state have remained elusive. Here we identified two surface exposed M. hyopneumoniae proteases, a putative Xaa-Pro aminopeptidase (MHJ_0659; PepP) and a putative oligoendopeptidase F (MHJ_0522; PepF), using immunofluorescence microscopy and two orthogonal proteomic methodologies. MHJ_0659 and MHJ_0522 were purified as polyhistidine fusion proteins and shown, using a novel MALDI-TOF MS assay, to degrade four pro-inflammatory peptides that regulate lung homeostasis; bradykinin (BK), substance P (SP), neurokinin A (NKA) and neuropeptide Y (NPY). These findings provide insight into the mechanisms used by M. hyopneumoniae to influence ciliary beat frequency, impair mucociliary clearance, and initiate a chronic infectious disease state in swine, features that are a hallmark of disease caused by this pathogen.
Jarocki, VM, Reid, CJ, Chapman, TA & Djordjevic, SP 2019, 'Escherichia coli ST302: Genomic Analysis of Virulence Potential and Antimicrobial Resistance Mediated by Mobile Genetic Elements', Frontiers in Microbiology, vol. 10.
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aEPEC are associated with persistent diarrhea, and diarrheal outbreaks in both humans and animals worldwide. They are differentiated from typical EPEC by the lack of bundle-forming pili, and from EHEC by the lack of phage-mediated stx toxins. However, phylogenetic analyses often associate aEPEC with EHEC, promoting the hypothesis that aEPEC are the progenitors of EHEC, which is supported by aEPEC conversion to EHEC by stx-carrying phages. While aEPEC can cause disease outright, the potential to acquire stx, one of the most potent bacterial toxins known, merits close monitoring. Escherichia coli ST302 (O108:H9, O182:H9, O45:H9) are aEPEC that have been isolated from diarrheic human, pig and rabbit hosts, as well as in healthy pigs, however, no study to date has focused on E. coli ST302 strains. Through WGS and hybrid assembly we present the first closed chromosome, and two circularized plasmids of an ST302 strain - F2_18C, isolated from a healthy pig in Australia. A phylogenetic analysis placed E. coli ST302 strains in proximity to EHEC ST32 (O145:H28) strains. Public databases were interrogated for WGSs of E. coli ST302 strains and short-read gene screens were used to compare their virulence-associated gene (VAG) and antimicrobial resistance gene (ARG) cargo. E. coli ST302 strains carry diverse VAGs, including those that typically associated with extraintestinal pathogenic E. coli (ExPEC). Plasmid comparisons showed that pF2_18C_FIB shared homology with EHEC virulence plasmids such as pO103 while pF2_18C_HI2 is a large multidrug resistance IncHI2:ST3 plasmid. A comparison of 33 HI2:ST3 plasmids demonstrated that those of Australian origin have not acquired resistances to extended-spectrum beta-lactams, colistin, fosfomycin or rifampicin, unlike those originating from Asia. F2_18C was shown to carry two additional pathogenicity islands - ETT2, and the STEC-associated PAI CL 3, plasmid-associated heavy metal resistance genes, as well as several unoccupied stx-phage...
Jarocki, VM, Steele, JR, Widjaja, M, Tacchi, JL, Padula, MP & Djordjevic, SP 2019, 'Formylated N-terminal methionine is absent from the Mycoplasma hyopneumoniae proteome: Implications for translation initiation', International Journal of Medical Microbiology, vol. 309, no. 5, pp. 288-298.
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N-terminal methionine excision (NME) is a proteolytic pathway that cleaves the N-termini of proteins, a process that influences where proteins localise in the cell and their turnover rates. In bacteria, protein biosynthesis is initiated by formylated methionine start tRNA (fMet-tRNAfMet). The formyl group is attached by formyltransferase (FMT) and is subsequently removed by peptide deformylase (PDF) in most but not all proteins. Methionine aminopeptidase then cleaves deformylated methionine to complete the process. Components of NME, particularly PDF, are promising therapeutic targets for bacterial pathogens. In Mycoplasma hyopneumoniae, a genome-reduced, major respiratory pathogen of swine, pdf and fmt are absent from its genome. Our bioinformatic analysis uncovered additional enzymes involved in formylated N-terminal methionine (fnMet) processing missing in fourteen mycoplasma species, including M. hyopneumoniae but not in Mycoplasma pneumoniae, a major respiratory pathogen of humans. Consistent with our bioinformatic studies, an analysis of in-house tryptic peptide libraries confirmed the absence of fnMet in M. hyopneumoniae proteins but, as expected fnMet peptides were detected in the proteome of M. pneumoniae. Additionally, computational molecular modelling of M. hyopneumoniae translation initiation factors reveal structural and sequence differences in areas known to interact with fMet-tRNAfMet. Our data suggests that some mycoplasmas have evolved a translation process that does not require fnMet.
Jaspers, C, Fraune, S, Arnold, AE, Miller, DJ, Bosch, TCG & Voolstra, CR 2019, 'Resolving structure and function of metaorganisms through a holistic framework combining reductionist and integrative approaches', Zoology, vol. 133, pp. 81-87.
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Current research highlights the importance of associated microbes in contributing to the functioning, health, and even adaptation of their animal, plant, and fungal hosts. As such, we are witnessing a shift in research that moves away from focusing on the eukaryotic host sensu stricto to research into the complex conglomerate of the host and its associated microorganisms (i.e., microbial eukaryotes, archaea, bacteria, and viruses), the so-called metaorganism, as the biological entity. While recent research supports and encourages the adoption of such an integrative view, it must be understood that microorganisms are not involved in all host processes and not all associated microorganisms are functionally important. As such, our intention here is to provide a critical review and evaluation of perspectives and limitations relevant to studying organisms in a metaorganism framework and the functional toolbox available to do so. We note that marker gene-guided approaches that primarily characterize microbial diversity are a first step in delineating associated microbes but are not sufficient to establish proof of their functional relevance. More sophisticated tools and experiments are necessary to reveal the specific functions of associated microbes. This can be accomplished through the study of metaorganisms in less complex environments, the targeted manipulation of microbial associates, or work at the mechanistic level with the toolbox available in model systems. We conclude that the metaorganism framework is a powerful new concept to help provide answers to longstanding biological questions such as the evolution and ecology of organismal complexity and the importance of organismal symbioses to ecosystem functioning. The intricacy of the metaorganism requires a holistic framework combining reductionist and integrative approaches to resolve the structure and function of its member species and to disclose the various roles that microorganisms play in the biology of th...
Jean-Richard-dit-Bressel, P, Ma, C, Bradfield, LA, Killcross, S & McNally, GP 2019, 'Punishment insensitivity emerges from impaired contingency detection, not aversion insensitivity or reward dominance', eLife, vol. 8.
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Our behaviour is shaped by its consequences – we seek rewards and avoid harm. It has been reported that individuals vary markedly in their avoidance of detrimental consequences, that is in their sensitivity to punishment. The underpinnings of this variability are poorly understood; they may be driven by differences in aversion sensitivity, motivation for reward, and/or instrumental control. We examined these hypotheses by applying several analysis strategies to the behaviour of rats (n = 48; 18 female) trained in a conditioned punishment task that permitted concurrent assessment of punishment, reward-seeking, and Pavlovian fear. We show that punishment insensitivity is a unique phenotype, unrelated to differences in reward-seeking and Pavlovian fear, and due to a failure of instrumental control. Subjects insensitive to punishment are afraid of aversive events, they are simply unable to change their behaviour to avoid them.
Jerotic, D, Matic, M, Suvakov, S, Vucicevic, K, Damjanovic, T, Savic-Radojevic, A, Pljesa-Ercegovac, M, Coric, V, Stefanovic, A, Ivanisevic, J, Jelic-Ivanovic, Z, McClements, L, Dimkovic, N & Simic, T 2019, 'Association of Nrf2, SOD2 and GPX1 Polymorphisms with Biomarkers of Oxidative Distress and Survival in End-Stage Renal Disease Patients', Toxins, vol. 11, no. 7, pp. 431-431.
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The oxidative stress response via Nuclear factor (erythroid-derived 2)-like 2 (Nrf2) interlinks inflammation- and metabolism-related pathways in chronic kidney disease. We assessed the association between polymorphisms in Nrf2, superoxide dismutase (SOD2), glutathione peroxidase (GPX1), and the risk of end-stage renal disease (ESRD). The modifying effect of these polymorphisms on both oxidative phenotype and ESRD prognosis, both independently and/or in combination with the glutathione S-transferase M1 (GSTM1) deletion polymorphism, was further analyzed. Polymorphisms in Nrf2 (rs6721961), SOD2 (rs4880), GPX1 (rs1050450), and GSTM1 were determined by PCR in 256 ESRD patients undergoing hemodialysis and 374 controls. Byproducts of oxidative stress were analyzed spectrophotometically or by ELISA. Time-to-event modeling was performed to evaluate overall survival and cardiovascular survival. The SOD2 Val/Val genotype increased ESRD risk (OR = 2.01, p = 0.002), which was even higher in combination with the GPX1 Leu/Leu genotype (OR = 3.27, p = 0.019). Polymorphism in SOD2 also showed an effect on oxidative phenotypes. Overall survival in ESRD patients was dependent on a combination of the Nrf2 (C/C) and GPX1 (Leu/Leu) genotypes in addition to a patients’ age and GSTM1 polymorphism. Similarly, the GPX1 (Leu/Leu) genotype contributed to longer cardiovascular survival. Conclusions: Our results show that SOD2, GPX1, and Nrf2 polymorphisms are associated with ESRD development and can predict survival.
Jian, X, Wang, H, Rao, G, Jiang, L, Wang, H, Subramaniyam, CM, Mahmood, A, Zhang, W, Xiang, Y, Dou, SX, Zhou, Z, Hui, D, Kalantar-Zadeh, K & Mahmood, N 2019, 'Self-tunable ultrathin carbon nanocups as the electrode material of sodium-ion batteries with unprecedented capacity and stability', Chemical Engineering Journal, vol. 364, pp. 578-588.
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Jo, Y, Johir, MAH, Cho, Y, Naidu, G, Rice, SA, McDougald, D, Kandasamy, J, Vigneswaran, S & Sun, S 2019, 'A comparative study on nitric oxide and hypochlorite as a membrane cleaning agent to minimise biofilm growth in a membrane bioreactor (MBR) process', Biochemical Engineering Journal, vol. 148, pp. 9-15.
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© 2019 Elsevier B.V. Reverse osmosis concentrates (ROC) produced from water reclamation plants can threaten the environment if it is not appropriately treated before discharge. A membrane bioreactor (MBR) process to treat ROC was used in this project. In an MBR, fouling is an essential and inevitable phenomenon which leads to higher operational and capital costs. A comparative study on chemical cleaning, such as sodium hypochlorite (NaOCl) and nitric oxide (NO), was experimentally evaluated together with the influence of filtration flux. Exposure to a low concentration of NO reduced biofilms in an MBR system. NO treatment delayed the formation of new biofilm biomass on the membrane. NO also showed good performance in reducing membrane fouling and had no adverse effect on activated sludge and the environment. In MBR, the bacterial community was dominated by Proteobacteria (61%), with Alpha and Beta-proteobacteria representing approximately 54% of the community. After NO treatment, the relative abundance of the Proteobacteria decreased to 44%, and this was also reflected in a reduction in Alpha and Beta-proteobacteria, to 30% and 5% respectively. Thus, NO treatment resulted in the decrease of the relative biofilms associated with reduced MBR performance.
Johansen, MD, de Silva, K, Plain, KM, Whittington, RJ & Purdie, AC 2019, 'Mycobacterium avium subspecies paratuberculosis is able to manipulate host lipid metabolism and accumulate cholesterol within macrophages', Microbial Pathogenesis, vol. 130, pp. 44-53.
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Johnson, G, Taylor, B, Robbins, W, Franklin, E, Toonen, R, Bowen, B & Choat, J 2019, 'Diversity and Structure of Parrotfish Assemblages across the Northern Great Barrier Reef', Diversity, vol. 11, no. 1, pp. 14-14.
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The structure and dynamics of coral reef environments vary across a range of spatial scales, with patterns of associated faunal assemblages often reflecting this variability. However, delineating drivers of biological variability in such complex environments has proved challenging. Here, we investigated the assemblage structure and diversity of parrotfishes—a common and ecologically important group—across 6° of latitude on the Northern Great Barrier Reef (GBR), Australia. Parrotfish abundance and biomass were determined from stereo-video surveys across 82 sites spanning 31 reefs and assessed against geographic, biophysical, and management-related factors in a multivariate framework to determine major drivers and associated scales of assemblage structure. Large cross-shelf variation in parrotfish assemblages pervaded along the entire Northern GBR, with distinct assemblages associated with sheltered and exposed reefs. Species abundances and diversity generally decreased with decreasing latitude. The gradient of explicit predator biomass associated with management zoning had no effect on parrotfish assemblage structure, but was positively correlated with parrotfish diversity. Our results highlight the ubiquitous presence of cross-shelf variation, where the greatest differences in parrotfish community composition existed between sheltered (inner and mid shelf) and exposed (outer shelf) reef systems. Prior attempts to explain linkages between parrotfishes and fine-scale biophysical factors have demonstrated parrotfishes as habitat generalists, but recent developments in nutritional ecology suggest that their cross-shelf variation on the GBR is likely reflective of benthic resource distribution and species-specific feeding modes.
Johnson, L, Cameron, M, Waters, L, Padula, MP & Marks, DC 2019, 'The impact of refrigerated storage of UVC pathogen inactivated platelet concentrates on in vitro platelet quality parameters', Vox Sanguinis, vol. 114, no. 1, pp. 47-56.
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Background and ObjectivesRefrigeration (cold‐storage) of pathogen inactivated (PI) platelet components may increase the shelf‐life and safety profile of platelet components, compared to conventional room‐temperature (RT) storage. Whilst there is substantial knowledge regarding the impact of these individual treatments on platelets, the combined effect has not been assessed.Materials and methodsUsing a pool‐and‐split study design, paired buffy‐coat derived platelets in 70% platelet additive solution (SSP+; MacoPharma) were left untreated or PI‐treated using the THERAFLEX UV‐Platelets System (UVC; MacoPharma). Units from each pair were split and stored at room temperature (20–24°C) or cold‐stored (2–6°C) to yield RT, cold, RT‐UVC and cold‐UVC study groups (n = 8 in each group). In vitro quality and function was tested over 9 days.ResultsCold‐storage of UVC‐treated platelets reduced glycolytic metabolism (glucose consumption and lactate production) compared to RT‐Zootaxa, vol. 4612, no. 4, pp. 595-595.
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New Caledonia is described as one of Earth’s key biodiversity hotspots, with high species endemism, particularly for plants and vertebrate animals (Myers et al. 2000; Kier et al. 2009). The distinct biodiversity of this country has been attributed to the Gondwanan origins of the New Caledonian archipelago, its relative isolation from neighbouring countries (such as Australia) and the stability of its climate. These factors are suggested to have led to the accumulation of many Gondwanan species, with few instances of extinction, which has allowed for marked species diversification (Espeland & Murienne 2011).
Jolly, CJ, Lee, Q, Padula, MP, Pinello, N, Williams, SH, O’Rourke, MB, Fumagalli, MJ, Orkin, JD, Shaban, B, Brenner, O, Weninger, W, de Souza, WM, Melin, AD, Wong, JJ-L, Crim, MJ, Monette, S & Roediger, B 2019, 'MKPV (aka MuCPV) and related chapparvoviruses are nephro-tropic and encode novel accessory proteins p15 and NS2'.
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AbstractMouse kidney parvovirus (MKPV) is a member of the provisionalChapparvovirusgenus that causes renal disease in immune-compromised mice, with a disease course reminiscent of polyomavirus-associated nephropathy in immune-suppressed kidney transplant patients. Here we map four MKPV transcripts, created by alternative splicing, to a common transcription initiation region, and use mass spectrometry to identify “p10” and “p15” as novel chapparvovirus accessory proteins produced in MKPV-infected kidneys. p15 and a splicing-dependent putative accessory protein NS2 are conserved in all near-complete tetrapod chapparvovirus genomes currently available (from mammals, birds and a reptile). In contrast, p10 may be encoded only by viruses with >60% amino acid identity to MKPV. We show that MKPV is kidney-tropic and that the bat chapparvovirus DrPV-1 and a non-human primate chapparvovirus, CKPV, are also found in the kidneys of their hosts. We propose, therefore, that chapparvoviruses with >60% VP1 amino acid identity to MKPV be classified into a genus dubbedNephroparvovirus, which is consistent with nomenclature for the genusErythroparvovirus.
Jolly, CJ, Webb, JK, Gillespie, GR, Hughes, NK & Phillips, BL 2019, 'Bias averted: personality may not influence trappability', Behavioral Ecology and Sociobiology, vol. 73, no. 9.
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© 2019, Springer-Verlag GmbH Germany, part of Springer Nature. Abstract: If bold animals are more likely to be trapped than shy animals, we take a biased sample of personalities—a problem for behavioural research. Such a bias is problematic, also, for population estimation using mark-recapture models that assume homogeneity in detection probabilities. In this study, we investigated whether differences in boldness result in differences in detection probability in a native Australian rodent, the grassland melomys (Melomys burtoni). During a mark-recapture study of this species, we used modified open field tests to assess the boldness (via emergence, and interaction with a novel object) of melomys trapped on the last night of four trapping nights in each of two trapping sessions. Despite melomys showing repeatable variation in these behavioural traits, neither boldness nor emergence latency had an effect on detection probability, and we found no evidence that detection probability varied between individuals. This result suggests that any neophobia is experienced and resolved in individuals of this species on a scale of minutes, rather than the hours across which traps are made available each night. Our work demonstrates that personality-caused sampling bias may not be inevitable, even in situations where animals are required to respond to novelty to be detected, such as in baited traps. Heterogeneity in personality does not inevitably lead to heterogeneity in detection probability. Significance statement: Historically, passive traps were assumed a non-biased means of sampling animal populations. Increasingly behavioural ecologists suggest that personality traits, particularly individual boldness, may influence behaviour and, as a consequence, could result in sampling bias. Here, we present a comprehensive example of when animal personality has no effect on detection probability. Despite having distinct personalities, detection probabilities of a native Australian ro...
Jones, MWM, Phillips, NW, Abbey, B, Hare, DJ, van Riessen, GA, Vine, DJ, de Jonge, MD & McColl, G 2019, 'Simultaneous nanostructure and chemical imaging of intact whole nematodes', Chemical Communications, vol. 55, no. 8, pp. 1052-1055.
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Accurately locating biologically relevant elements at high resolution: simultaneous ptychography and fluorescence imaging of large specimens comes of age.
Jones, PM, Mazzio, E, Soliman, K & George, AM 2019, 'In Silico Investigation of the Binding of MCoTI-II Plant Defense Knottin to the γ-NGF Serine Protease of the 7S Nerve Growth Factor Complex and Biological Activity of Its NGF Mimetic Properties', The Journal of Physical Chemistry B, vol. 123, no. 43, pp. 9104-9110.
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Jönsson, F, de Chaisemartin, L, Granger, V, Gouel-Chéron, A, Gillis, CM, Zhu, Q, Dib, F, Nicaise-Roland, P, Ganneau, C, Hurtado-Nedelec, M, Paugam-Burtz, C, Necib, S, Keita-Meyer, H, Le Dorze, M, Cholley, B, Langeron, O, Jacob, L, Plaud, B, Fischler, M, Sauvan, C, Guinnepain, M-T, Montravers, P, Aubier, M, Bay, S, Neukirch, C, Tubach, F, Longrois, D, Chollet-Martin, S & Bruhns, P 2019, 'An IgG-induced neutrophil activation pathway contributes to human drug-induced anaphylaxis', Science Translational Medicine, vol. 11, no. 500.
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Co-existence of drug-specific IgE and IgG antibodies aggravates neuromuscular-blocking agent-induced anaphylaxis in humans.
Jowett, LA & Gale, PA 2019, 'Supramolecular methods: the chloride/nitrate transmembrane exchange assay', Supramolecular Chemistry, vol. 31, no. 5, pp. 297-312.
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Jung, JY, Kang, P-W, Kim, E, Chacon, D, Beck, D & McNevin, D 2019, 'Ancestry informative markers (AIMs) for Korean and other East Asian and South East Asian populations', International Journal of Legal Medicine, vol. 133, no. 6, pp. 1711-1719.
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Inference of ancestry from biological evidence can provide investigative information, especially for unknown DNA donors. Although tools for predicting ancestry have been developing, ancestry research focusing on populations relevant for South Korea is not common and markers are seldom chosen specifically to differentiate Koreans from other East Asian and South East Asian populations. Here, we report ancestry informative markers (AIMs) for distinguishing six East/South East Asian regional populations: China, Japan, Indonesia, Philippines, South Korea and Thailand. Individual genotypes from these six populations were available in PanSNPdb: The HUGO Pan-Asian SNP Database. To select AIMs, we calculated four population divergence metrics for each SNP: Nei's FST, Rosenberg's Informativeness (In), the average absolute allele frequency difference between populations (δFmean) and the maximum allele frequency difference between populations (δFmax). Based on these values, we selected 100 single nucleotide polymorphisms (SNPs) for distinguishing the six populations, 13 of which exhibited large allele frequency differences between Koreans and non-Koreans. To assess the performance of the AIMs, we performed principal coordinates analysis (PCoA) on the individuals from all six populations and inferred ancestral population clusters using the STRUCTURE program. In conclusion, we found that the selected AIMs can be applied to distinguish the six East/South East Asian groups and we suggest the markers in this study will be helpful to establish ancestry panels for Korea and neighbouring populations.
Kamachi, K, Otsuka, N, Fumimoto, R, Ozawa, K, Yao, S-M, Chiang, C-S, Luu, LDW, Lan, R, Shibayama, K & Watanabe, M 2019, 'A novel multilocus variable-number tandem repeat analysis for Bordetella parapertussis', Journal of Medical Microbiology, vol. 68, no. 11, pp. 1671-1676.
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Kanodarwala, FK, Moret, S, Spindler, X, Lennard, C & Roux, C 2019, 'Nanoparticles used for fingermark detection—A comprehensive review', WIREs Forensic Science, vol. 1, no. 5.
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AbstractNanoparticles (NPs) have been used in numerous fields such as medicine, imaging, and electronics to cite just a few. In forensic science, NPs have been researched specifically for the detection of fingermarks. Their small size, surface functionalization ability, and luminescence properties can potentially lead to better resolution, increased sensitivity, and selectivity. This paper offers an extensive review of the various NP types investigated over the past three decades. NPs are sorted into seven categories, namely metal, metal oxide, quantum dots (QDs), carbon dots (C‐dots), silica (SiO2), and upconverters NPs (UCNPs) as well as a miscellaneous section. Each type is discussed in details from a critical viewpoint. The most promising NP types are also identified.This article is categorized under:
Forensic Chemistry and Trace Evidence > Fingermarks and Other Marks
Karacan, I, Ben-Nissan, B, Wang, HA, Juritza, A, Swain, MV, Müller, WH, Chou, J, Stamboulis, A, Macha, IJ & Taraschi, V 2019, 'Mechanical testing of antimicrobial biocomposite coating on metallic medical implants as drug delivery system', Materials Science and Engineering: C, vol. 104, no. 109757, pp. 109757-109757.
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Kaufer, A, Barratt, J, Stark, D & Ellis, J 2019, 'The complete coding region of the maxicircle as a superior phylogenetic marker for exploring evolutionary relationships between members of the Leishmaniinae', Infection, Genetics and Evolution, vol. 70, pp. 90-100.
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The mitochondrial DNA (mtDNA) is a potentially valuable phylogenetic marker given its presence across all eukaryotic taxa and its relative conservation in structure and sequence. In trypanosomatids, a homologue of the mtDNA referred to as the maxicircle DNA, is located within a specialised structure in the single mitochondrion of the trypanosomatids called the kinetoplast; a high molecular weight network of DNA composed of thousands of catenated minicircles and a smaller number of larger maxicircles. Unique to the kinetoplastid protists, the maxicircle component of this complex network could represent a desirable target for taxonomic inquiry that may also facilitate exploration of the evolutionary history of this important group of parasites. The aim of this study was to investigate the phylogenetic value of the trypanosomatid maxicircle for these applications. Maxicircle sequences were obtained either by assembling raw sequence data publicly accessible in online databases (i.e., NCBI), or by amplification of novel maxicircle sequences from trypanosomatid DNA using long-range (LR) PCR with subsequent Illumina sequencing. This procedure facilitated the generation of nearly complete maxicircle sequences (i.e., excluding the divergent region) for numerous dixenous and monoxenous trypanosomatid species. Annotation of each maxicircle sequence confirmed that their structure was conserved across all taxa examined. Phylogenetic analyses confirmed that Z. australiensis showed a greater genetic relatedness with the dixenous trypanosomatids of the genera Leishmania and Endotrypanum, as opposed to members of the monoxenous genera Crithidia and Leptomonas. Additionally, molecular clock analysis supported that the dixenous Leishmaniinae appeared approximately 75 million years ago during the breakup of Gondwana. In line with previous studies, our results support the Supercontinents hypothesis regarding the origin of dixenous Leishmaniinae. Ultimately, we demonstrate that the ma...
Kaufer, A, Ellis, J & Stark, D 2019, 'Identification of Clinical Infections of Leishmania Imported into Australia: Revising Speciation with Polymerase Chain Reaction-RFLP of the Kinetoplast Maxicircle', The American Journal of Tropical Medicine and Hygiene, vol. 101, no. 3, pp. 590-601.
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Kaufer, Stark & Ellis 2019, 'Evolutionary Insight into the Trypanosomatidae Using Alignment-Free Phylogenomics of the Kinetoplast', Pathogens, vol. 8, no. 3, pp. 157-157.
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Advancements in next-generation sequencing techniques have led to a substantial increase in the genomic information available for analyses in evolutionary biology. As such, this data requires the exponential growth in bioinformatic methods and expertise required to understand such vast quantities of genomic data. Alignment-free phylogenomics offer an alternative approach for large-scale analyses that may have the potential to address these challenges. The evolutionary relationships between various species within the trypanosomatid family, specifically members belonging to the genera Leishmania and Trypanosoma have been extensively studies over the last 30 years. However, there is a need for a more exhaustive analysis of the Trypanosomatidae, summarising the evolutionary patterns amongst the entire family of these important protists. The mitochondrial DNA of the trypanosomatids, better known as the kinetoplast, represents a valuable taxonomic marker given its unique presence across all kinetoplastid protozoans. The aim of this study was to validate the reliability and robustness of alignment-free approaches for phylogenomic analyses and its applicability to reconstruct the evolutionary relationships between the trypanosomatid family. In the present study, alignment-free analyses demonstrated the strength of these methods, particularly when dealing with large datasets compared to the traditional phylogenetic approaches. We present a maxicircle genome phylogeny of 46 species spanning the trypanosomatid family, demonstrating the superiority of the maxicircle for the analysis and taxonomic resolution of the Trypanosomatidae.
Kaur, S, Sharma, N, Vyas, M, Mahajan, R, Satija, S, Mehta, M & Khurana, N 2019, 'A review on pharmacological activities of betaine', Plant Archives, vol. 19, pp. 1021-1034.
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Betaine is an important phytoconstituent found in plant Beta vulgaris. It is found abundantly in various common foods like beets, spinach and cereals, whereas wheat is its major source in human diet. Chemically, betaine is termed as trimethylglycine. It plays an important physiological role in the body. It has found to be a an organis osmolyte and it participates in methionine-homocysteine cycle as a methyl group donor due to which it possesses many physiological activities. It has widely been studied for its promising antioxidant properties, neuroprotective effects, anti-Inflammatory effects, inhibition of NF-κB signaling pathway, inhibition of NLRP3 inflammasome activation, regulating energy metabolism to relieve chronic inflammation, mitigation of endoplasmic reticulum stress and apoptosis, canonical and noncanonical inflammasome-mediated processing of IL-1β, against neurodegenerative diseases, anticonvulsant effects, reducing the total homocysteine content in brain and its role in performance and action. The present article firstly aims to review the pharmacological effects including neuroprotective effects, physiological effects of betaine including effects on performance and human body composition, secondly to study the safety concerns of betaine and its future prospects.
Keadle, S, Kravitz, E, Matthews, CE, Tseng, M & Carroll, RJ 2019, 'Development And Testing Of An Integrated Score For Physical Behaviors', Medicine & Science in Sports & Exercise, vol. 51, no. 6S, pp. 164-164.
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KEADLE, SK, KRAVITZ, ES, MATTHEWS, CE, TSENG, M & CARROLL, RJ 2019, 'Development and Testing of an Integrated Score for Physical Behaviors', Medicine & Science in Sports & Exercise, vol. 51, no. 8, pp. 1759-1766.
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ABSTRACT
Purpose
Interest in a variety of physical behaviors (e.g., exercise, sitting time, sleep) in relation to health outcomes creates a need for new statistical approaches to analyze the joint effects of these distinct but inter-related physical behaviors. We developed and tested an integrated physical behavior score (PBS).
Methods
National Institutes of Health-American Association of Retired Persons Diet and Health Study participants (N = 163,016) completed a questionnaire (2004–2006) asking about time spent in five exercise and nonexercise physical activities, two sedentary behaviors (television and nontelevision), and sleep. In half of the sample, we used shape-constrained additive regression to model the relationship between each behavior and survival. Maximum logit scores from each of the eight behavior-survival functions were summed to produce a PBS that was proportionally rescaled to range from 0 to 100. We examined predictive validity of the PBS in the other half-sample using Cox Proportional Hazards models after adjustment for covariates for all-cause and cause-specific mortality.
Results
In the testing sample, over an average of 6.6 yr of follow-up, 8732 deaths occurred. We found a strong graded decline in risk of all-cause mortality across quintiles of PBS (Q5 vs Q1 hazard ratio [95% CI] = 0.53 [0.49, 0.57]). Risk estimates for the PBS were higher than any of the components in isolation. Results were similar but stronger for cardiovascular disease (Q5 vs Q1 = 0.42 [0.39, 0.48]) and other mortality (Q5 vs Q1 = 0.42 [0.36, 0.48]). The relationship between PBS and mortality was observed in stratif...
Keenan, CR, Iannarella, N, Garnham, AL, Brown, AC, Kim, RY, Horvat, JC, Hansbro, PM, Nutt, SL & Allan, RS 2019, 'Polycomb repressive complex 2 is a critical mediator of allergic inflammation', JCI Insight, vol. 4, no. 10.
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Strategies that intervene with the development of immune-mediated diseases are urgently needed, as current treatments mostly focus on alleviating symptoms rather than reversing the disease. Targeting enzymes involved in epigenetic modifications to chromatin represents an alternative strategy that has the potential to perturb the function of the lymphocytes that drive the immune response. Here, we report that 2 major epigenetic silencing pathways are increased after T cell activation. By specific inactivation of these molecules in the T cell compartment in vivo, we demonstrate that the polycomb repressive complex 2 (PRC2) is essential for the generation of allergic responses. Furthermore, we show that small-molecule inhibition of the PRC2 methyltransferase, enhancer of zeste homolog 2 (Ezh2), reduces allergic inflammation in mice. Therefore, by systematically surveying the pathways involved in epigenetic gene silencing we have identified Ezh2 as a target for the suppression of allergic disease.
Kendig, M, Westbrook, RF & Morris, MJ 2019, 'Adiposity and spatial memory impairments are determined by the pattern of access to high-fat, high-sugar ‘cafeteria’ diet in rats', Obesity Research & Clinical Practice, vol. 13, no. 3, pp. 284-285.
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Kendig, MD & Morris, MJ 2019, 'Fizzing out: No effect of acute carbohydrate consumption on mood', Neuroscience & Biobehavioral Reviews, vol. 104, pp. 56-57.
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Kendig, MD, Martire, SI, Boakes, RA & Rooney, KB 2019, 'Metabolic improvement from switching to saccharin or water following chronic consumption by rats of 10% sucrose solution', Obesity Research & Clinical Practice, vol. 13, no. 1, pp. 89-90.
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Keshvardoust, P, Huron, VAA, Clemson, M, Constancias, F, Barraud, N & Rice, SA 2019, 'Biofilm formation inhibition and dispersal of multi-species communities containing ammonia-oxidising bacteria', npj Biofilms and Microbiomes, vol. 5, no. 1.
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AbstractDespite considerable research, the biofilm-forming capabilities of Nitrosomonas europaea are poorly understood for both mono and mixed-species communities. This study combined biofilm assays and molecular techniques to demonstrate that N. europaea makes very little biofilm on its own, and relies on the activity of associated heterotrophic bacteria to establish a biofilm. However, N. europaea has a vital role in the proliferation of mixed-species communities under carbon-limited conditions, such as in drinking water distribution systems, through the provision of organic carbon via ammonia oxidation. Results show that the addition of nitrification inhibitors to mixed-species nitrifying cultures under carbon-limited conditions disrupted biofilm formation and caused the dispersal of pre-formed biofilms. This dispersal effect was not observed when an organic carbon source, glucose, was included in the medium. Interestingly, inhibition of nitrification activity of these mixed-species biofilms in the presence of added glucose resulted in increased total biofilm formation compared to controls without the addition of nitrification inhibitors, or with only glucose added. This suggests that active AOB partially suppress or limit the overall growth of the heterotrophic bacteria. The experimental model developed here provides evidence that ammonia-oxidising bacteria (AOB) are involved in both the formation and maintenance of multi-species biofilm communities. The results demonstrate that the activity of the AOB not only support the growth and biofilm formation of heterotrophic bacteria by providing organic carbon, but also restrict and limit total biomass in mixed community systems.
Khatami, M, Salehipour, A & Hwang, FJ 2019, 'Makespan minimization for the m-machine ordered flow shop scheduling problem', Computers & Operations Research, vol. 111, pp. 400-414.
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Kim, JH, Kim, H, Kang, D, Lim, YK, Ajani, P, Jung, SW & Baek, SH 2019, 'Field application and validity of a red-tide acoustic sensing system (RASS) for monitoring and alerting of harmful algal blooms (HABs) in Korean coastal waters', Journal of Applied Phycology, vol. 31, no. 6, pp. 3737-3748.
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Kim, M, Pernice, M, Watson-Lazowski, A, Guagliardo, P, Kilburn, MR, Larkum, AWD, Raven, JA & Ralph, PJ 2019, 'Effect of reduced irradiance on 13C uptake, gene expression and protein activity of the seagrass Zostera muelleri', Marine Environmental Research, vol. 149, pp. 80-89.
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Photosynthesis in the seagrass Zostera muelleri remains poorly understood. We investigated the effect of reduced irradiance on the incorporation of 13C, gene expression of photosynthetic, photorespiratory and intermediates recycling genes as well as the enzymatic content and activity of Rubisco and PEPC within Z. muelleri. Following 48 h of reduced irradiance, we found that i) there was a ∼7 fold reduction in 13C incorporation in above ground tissue, ii) a significant down regulation of photosynthetic, photorespiratory and intermediates recycling genes and iii) no significant difference in enzyme activity and content. We propose that Z. muelleri is able to alter its physiology in order to reduce the amount of C lost through photorespiration to compensate for the reduced carbon assimilation as a result of reduced irradiance. In addition, the first estimated rate constant (Kcat) and maximum rates of carboxylation (Vcmax) of Rubisco is reported for the first time for Z. muelleri.
Kim, S, Duong, NMH, Nguyen, M, Lu, T-J, Kianinia, M, Mendelson, N, Solntsev, A, Bradac, C, Englund, DR & Aharonovich, I 2019, 'Integrated on chip platform with quantum emitters in layered materials', Advanced Optical Materials, vol. 7, no. 23.
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Integrated quantum photonic circuitry is an emerging topic that requires
efficient coupling of quantum light sources to waveguides and optical
resonators. So far, great effort has been devoted to engineering on-chip
systems from three-dimensional crystals such as diamond or gallium arsenide. In
this study, we demonstrate room temperature coupling of quantum emitters
embedded within a layered hexagonal boron nitride to an on-chip aluminium
nitride waveguide. We achieved 1.2% light coupling efficiency of the device and
realise transmission of single photons through the waveguide. Our results serve
as a foundation for the integration of layered materials with on-chip
components and for the realisation of integrated quantum photonic circuitry.
Kim, S, Fröch, JE, Gardner, A, Li, C, Aharonovich, I & Solntsev, AS 2019, 'Second-harmonic generation in multilayer hexagonal boron nitride flakes', Optics Letters, vol. 44, no. 23, pp. 5792-5792.
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In this Letter, we report the second-harmonic generation (SHG) from thick hexagonal boron nitride (hBN) flakes with approximately 109-111 layers. The resulting effective second-order susceptibility is similar to previously reported few-layer experiments. This confirms that thick hBN flakes can serve as a platform for nonlinear optics, which is useful because thick flakes are easy to exfoliate while retaining a large size. We also show spatial second-harmonic maps revealing that SHG remains a useful tool for the characterization of the layer structure, even in the case of a large number of layers.
Kim, SW, Sampayo, EM, Sommer, B, Sims, CA, Gómez‐Cabrera, MDC, Dalton, SJ, Beger, M, Malcolm, HA, Ferrari, R, Fraser, N, Figueira, WF, Smith, SDA, Heron, SF, Baird, AH, Byrne, M, Eakin, CM, Edgar, R, Hughes, TP, Kyriacou, N, Liu, G, Matis, PA, Skirving, WJ & Pandolfi, JM 2019, 'Refugia under threat: Mass bleaching of coral assemblages in high‐latitude eastern Australia', Global Change Biology, vol. 25, no. 11, pp. 3918-3931.
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AbstractEnvironmental anomalies that trigger adverse physiological responses and mortality are occurring with increasing frequency due to climate change. At species' range peripheries, environmental anomalies are particularly concerning because species often exist at their environmental tolerance limits and may not be able to migrate to escape unfavourable conditions. Here, we investigated the bleaching response and mortality of 14 coral genera across high‐latitude eastern Australia during a global heat stress event in 2016. We evaluated whether the severity of assemblage‐scale and genus‐level bleaching responses was associated with cumulative heat stress and/or local environmental history, including long‐term mean temperatures during the hottest month of each year (SSTLTMAX), and annual fluctuations in water temperature (SSTVAR) and solar irradiance (PARZVAR). The most severely‐bleached genera included species that were either endemic to the region (Pocillopora aliciae) or rare in the tropics (e.g. Porites heronensis). Pocillopora spp., in particular, showed high rates of immediate mortality. Bleaching severity of Pocillopora was high where SSTLTMAX was low or PARZVAR was high, whereas bleaching severity of Porites was directly associated with cumulative heat stress. While many tropical Acropora species are extremely vulnerable to bleaching, the Acropora species common at high latitudes, such as A. glauca and A. solitaryensis, showed little incidence of bleaching and immediate mortality. Two other regionally‐abundant genera, Goniastrea and Turbinari...
King, AT, Hiscocks, HG, Matesic, L, Bhadbhade, M, Bishop, R & Ung, AT 2019, 'Formation of an unexpected 3,3-diphenyl-3H-indazole through a facile intramolecular [2 + 3] cycloaddition of the diazo intermediate', Beilstein Journal of Organic Chemistry, vol. 15, pp. 1347-1354.
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The one-pot reaction of 2,6-bis(diphenylmethyl)-4-methoxyaniline with tert-butylnitrite, BTEAC and DABSO in the presence of CuCl2 provided an unexpected 3H-indazole product 8. The structure of the compound was determined by HRMS, IR, NMR and further confirmed by single crystal X-ray crystallography. The compound crystallises in the triclinic P-1 space group, with unit cell parameters a = 9.2107 (4), b = 10.0413 (5), c = 14.4363 (6) Å, α = 78.183 (2), β = 87.625 (2), γ = 71.975 (2)°. The formation of 8 proceeded through a facile intramolecular [2 + 3] cycloaddition of the diazo intermediate 9. The molecules of 8 are organised by edge–face Ar–H···π, face–face π···π, and bifurcated OCH2–H···N interactions. In addition to these, there are Ar–H···H–Ar close contacts, (edge–edge and surrounding inversion centres) arranged as infinite tapes along the a direction.
King, DJM, Cheung, STY, Humphry-Baker, SA, Parkin, C, Couet, A, Cortie, MB, Lumpkin, GR, Middleburgh, SC & Knowles, AJ 2019, 'High temperature, low neutron cross-section high-entropy alloys in the Nb-Ti-V-Zr system', Acta Materialia, vol. 166, pp. 435-446.
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© 2019 Acta Materialia Inc. High-entropy alloys (HEAs) with high melting points and low thermal neutron cross-section are promising new cladding materials for generation III+ and IV power reactors. In this study a recently developed high throughput computational screening tool Alloy Search and Predict (ASAP) has been used to identify the most likely candidate single-phase HEAs with low thermal neutron cross-section, from over a million four-element equimolar combinations. The selected NbTiVZr HEA was further studied by density functional theory (DFT) for moduli and lattice parameter, and by CALPHAD to predict phase formation with temperature. HEAs of NbTiVZr x (x = 0.5, 1, 2) were produced experimentally, with Zr varied as the dominant cross-section modifier. Contrary to previous experimental work, these HEAs were demonstrated to constitute a single-phase HEA system; a result obtained using a faster cooling rate following annealing at 1200 °C. However, the beta (BCC) matrix decomposed following aging at 700 °C, into a combination of nano-scale beta, alpha (HCP) and C15 Laves phases.
King, WL, Jenkins, C, Go, J, Siboni, N, Seymour, JR & Labbate, M 2019, 'Characterisation of the Pacific Oyster Microbiome During a Summer Mortality Event', Microbial Ecology, vol. 77, no. 2, pp. 502-512.
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The Pacific oyster, Crassostrea gigas, is a key commercial species that is cultivated globally. In recent years, disease outbreaks have heavily impacted C. gigas stocks worldwide, with many losses incurred during summer. A number of infectious agents have been associated with these summer mortality events, including viruses (particularly Ostreid herpesvirus 1, OsHV-1) and bacteria; however, cases where no known aetiological agent can be identified are common. In this study, we examined the microbiome of disease-affected and disease-unaffected C. gigas during a 2013-2014 summer mortality event in Port Stephens (Australia) where known oyster pathogens including OsHV-1 were not detected. The adductor muscle microbiomes of 70 C. gigas samples across 12 study sites in the Port Stephens estuary were characterised using 16S rRNA (V1-V3 region) amplicon sequencing, with the aim of comparing the influence of spatial location and disease state on the oyster microbiome. Spatial location was found to be a significant determinant of the disease-affected oyster microbiome. Furthermore, microbiome comparisons between disease states identified a significant increase in rare operational taxonomic units (OTUs) belonging to Vibrio harveyi and an unidentified member of the Vibrio genus in the disease-affected microbiome. This is indicative of a potential role of Vibrio species in oyster disease and supportive of previous culture-based examination of this mortality event.
King, WL, Jenkins, C, Seymour, JR & Labbate, M 2019, 'Oyster disease in a changing environment: Decrypting the link between pathogen, microbiome and environment', Marine Environmental Research, vol. 143, pp. 124-140.
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Shifting environmental conditions are known to be important triggers of oyster diseases. The mechanism(s) behind these synergistic effects (interplay between host, environment and pathogen/s) are often not clear, although there is evidence that shifts in environmental conditions can affect oyster immunity, and pathogen growth and virulence. However, the impact of shifting environmental parameters on the oyster microbiome and how this affects oyster health and susceptibility to infectious pathogens remains understudied. In this review, we summarise the major diseases afflicting oysters with a focus on the role of environmental factors that can catalyse or amplify disease outbreaks. We also consider the potential role of the oyster microbiome in buffering or augmenting oyster disease outbreaks and suggest that a deeper understanding of the oyster microbiome, its links to the environment and its effect on oyster health and disease susceptibility, is required to develop new frameworks for the prevention and management of oyster diseases.
King, WL, Siboni, N, Kahlke, T, Green, TJ, Labbate, M & Seymour, JR 2019, 'A New High Throughput Sequencing Assay for Characterizing the Diversity of Natural Vibrio Communities and Its Application to a Pacific Oyster Mortality Event', Frontiers in Microbiology, vol. 10, pp. 2907-2907.
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The Vibrio genus is notable for including several pathogens of marine animals and humans, yet characterization of Vibrio diversity using routine 16S rRNA sequencing methods is often constrained by poor resolution beyond the genus level. Here, a new high throughput sequencing approach targeting the heat shock protein (hsp60) as a phylogenetic marker was developed to more precisely discriminate members of the Vibrio genus in environmental samples. The utility of this new assay was tested using mock communities constructed from known dilutions of Vibrio isolates. Relative to standard and Vibrio-specific 16S rRNA sequencing assays, the hsp60 assay delivered high levels of fidelity with the mock community composition at the species level, including discrimination of species within the Vibrio harveyi clade. This assay was subsequently applied to characterize Vibrio community composition in seawater and delivered substantially improved taxonomic resolution of Vibrio species compared to 16S rRNA analysis. Finally, this assay was applied to examine patterns in the Vibrio community within oysters during a Pacific oyster mortality event. In these oysters, the hsp60 assay identified species-level Vibrio community shifts prior to disease onset, pinpointing V. harveyi as a putative pathogen. Given that shifts in the Vibrio community can precede, cause, and follow disease onset in numerous marine organisms, there is a need for an accurate high throughput assay for defining Vibrio community composition in natural samples. This Vibrio-centric hsp60 sequencing assay offers the potential for precise high throughput characterization of Vibrio diversity, providing an enhanced platform for dissecting Vibrio dynamics in the environment.
King, WL, Siboni, N, Williams, NLR, Kahlke, T, Nguyen, KV, Jenkins, C, Dove, M, O’Connor, W, Seymour, JR & Labbate, M 2019, 'Variability in the Composition of Pacific Oyster Microbiomes Across Oyster Families Exhibiting Different Levels of Susceptibility to OsHV-1 μvar Disease', Frontiers in Microbiology, vol. 10, no. Mar.
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Oyster diseases are a major impediment to the profitability and growth of the oyster aquaculture industry. In recent years, geographically widespread outbreaks of disease caused by ostreid herpesvirus-1 microvariant (OsHV-1 μvar) have led to mass mortalities among Crassostrea gigas, the Pacific Oyster. Attempts to minimize the impact of this disease have been largely focused on breeding programs, and although these have shown some success in producing oyster families with reduced mortality, the mechanism(s) behind this protection is poorly understood. One possible factor is modification of the C. gigas microbiome. To explore how breeding for resistance to OsHV-1 μvar affects the oyster microbiome, we used 16S rRNA amplicon sequencing to characterize the bacterial communities associated with 35 C. gigas families, incorporating oysters with different levels of susceptibility to OsHV-1 μvar disease. The microbiomes of disease-susceptible families were significantly different to the microbiomes of disease-resistant families. OTUs assigned to the Photobacterium, Vibrio, Aliivibrio, Streptococcus, and Roseovarius genera were associated with low disease resistance. In partial support of this finding, qPCR identified a statistically significant increase of Vibrio-specific 16S rRNA gene copies in the low disease resistance families, possibly indicative of a reduced host immune response to these pathogens. In addition to these results, examination of the core microbiome revealed that each family possessed a small core community, with OTUs assigned to the Winogradskyella genus and the Bradyrhizobiaceae family consistent members across most disease-resistant families. This study examines patterns in the microbiome of oyster families exhibiting differing levels of OsHV-1 μvar disease resistance and reveals some key bacterial taxa that may provide a protective or detrimental role in OsHV-1 μvar disease outbreaks.
Klingberg, J, Cawley, A, Shimmon, R & Fu, S 2019, 'Collision-Induced Dissociation Studies of Synthetic Opioids for Non-targeted Analysis', Frontiers in Chemistry, vol. 7.
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The continual introduction of a large number of new psychoactive substances, along with the large turnover of these substances, necessitates the development of non-targeted detection strategies to keep pace with the ever-changing drug market. The production of certified reference materials often lags behind the introduction of new substances to the market, therefore these detection strategies need to be able to function without relying on reference materials or library spectra. Synthetic opioids have recently emerged as a drug class of particular concern due to the health issues caused by their incredibly high potency. A common method which has been used for non-targeted analysis in the past involves the identification of common product ions formed as a result of the fragmentation of the parent molecule. These common fragments can then potentially be used as markers to indicate the presence of a particular class of compounds within a sample. In this study, standards of a number of different synthetic opioids, including 14 fentanyl derivatives, 7 AH series opioids, 4 U series opioids, 4 W series opioids and MT-45, were subjected to collision-induced dissociation studies to determine how the compounds fragment. The spectra obtained from these studies included a number of diagnostic fragments common to the different opioid classes that, when used in combination, show potential for use as class predictors. By using simple data processing techniques, such as extracted ion chromatograms, these diagnostic product ions identified can be applied to a non-targeted screening workflow.
Kloten, V, Neumann, MHD, Di Pasquale, F, Sprenger-Haussels, M, Shaffer, JM, Schlumpberger, M, Herdean, A, Betsou, F, Ammerlaan, W, af Hällström, T, Serkkola, E, Forsman, T, Lianidou, E, Sjöback, R, Kubista, M, Bender, S, Lampignano, R, Krahn, T & Schlange, T 2019, 'Multicenter Evaluation of Circulating Plasma MicroRNA Extraction Technologies for the Development of Clinically Feasible Reverse Transcription Quantitative PCR and Next-Generation Sequencing Analytical Work Flows', Clinical Chemistry, vol. 65, no. 9, pp. 1132-1140.
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Abstract
BACKGROUND
In human body fluids, microRNA (miRNA) can be found as circulating cell-free miRNA (cfmiRNA), as well as secreted into extracellular vesicles (EVmiRNA). miRNAs are being intensively evaluated as minimally invasive liquid biopsy biomarkers in patients with cancer. The growing interest in developing clinical assays for circulating miRNA necessitates careful consideration of confounding effects of preanalytical and analytical parameters.
METHODS
By using reverse transcription quantitative real-time PCR and next-generation sequencing (NGS), we compared extraction efficiencies of 5 different protocols for cfmiRNA and 2 protocols for EVmiRNA isolation in a multicentric manner. The efficiency of the different extraction methods was evaluated by measuring exogenously spiked cel-miR-39 and 6 targeted miRNAs in plasma from 20 healthy individuals.
RESULTS
There were significant differences between the tested methods. Although column-based extraction methods were highly effective for the isolation of endogenous miRNA, phenol extraction combined with column-based miRNA purification and ultracentrifugation resulted in lower quality and quantity of isolated miRNA. Among all extraction methods, the ubiquitously expressed miR-16 was represented with high abundance when compared with other targeted miRNAs. In addition, the use of miR-16 as an endogenous control for normalization of quantification cycle values resulted in a decreased variability of column-based cfmiRNA extraction methods. Cluster analysis of normalized NGS counts clearly indicated a method-dependent bias.
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Knight, S, Leigh, A, Davila, YC, Martin, LJ & Krix, DW 2019, 'Calibrating assessment literacy through benchmarking tasks', Assessment & Evaluation in Higher Education, vol. 44, no. 8, pp. 1121-1132.
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In calibration tasks students assess exemplar texts using criteria against which their own work will be assessed. Typically these tasks are used in the context of training for peer assessment. Little research has been conducted on the benefits of calibration tasks, such as benchmarking, as learning opportunities in their own right. This paper examines a dataset from a long-running benchmarking task ( 500 students per semester, for four semesters). We investigate the relationship of benchmarking performance to other student outcomes, including ability to self-assess accurately. We show that students who complete the benchmarking perform better, that there is a relationship between benchmarking performance and self-assessment performance, and that students appreciate the support for learning that benchmarking tasks provide. We discuss implications for teaching and learning flagging the potential of calibration tasks as an under-explored tool.
Knobel, Z, Ueland, M, Nizio, KD, Patel, D & Forbes, SL 2019, 'A comparison of human and pig decomposition rates and odour profiles in an Australian environment', Australian Journal of Forensic Sciences, vol. 51, no. 5, pp. 557-572.
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© 2018 Australian Academy of Forensic Sciences Cadaver-detection dogs are trained to locate victim remains; however, their training is challenging owing to limited access to human remains. Animal analogues, such as pigs, are typically used as alternative training aids. This project aimed to compare the visual decomposition and volatile organic compound (VOC) profile of human and pig remains in an Australian environment, to determine the suitability of pig remains as human odour analogues for cadaver-detection dog training. Four human cadavers and four pig carcasses were placed in an outdoor environment at the Australian Facility for Taphonomic Experimental Research (AFTER) across two seasons. Decomposition was monitored progressively in summer and winter. VOCs were collected onto sorbent tubes and analysed using comprehensive two-dimensional gas chromatography – time-of-flight mass spectrometry. Visual observations highlighted the differences in decomposition rates, with pig remains progressing through all stages of decomposition, and human remains undergoing differential decomposition and mummification. Chemical and statistical analysis highlighted variations in the composition and abundance of VOCs over time between the odour profiles. This study concluded that the visual decomposition and VOC profile of pig and human remains was dissimilar. However, in cooler conditions the results from each species became more comparable, especially during the early stages of decomposition.
Kolesik, P, Butterworth, N, Lemmon, J, Gibson, T & Wallman, JF 2019, 'First gall midge (Diptera: Cecidomyiidae) known to feed on plant family Atherospermataceae: a new species of Asphondylia damaging the endangered Australian tree Daphnandra johnsonii', Austral Entomology, vol. 58, no. 2, pp. 317-323.
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AbstractA new gall midge, here named Asphondylia daphnandrae Kolesik sp. nov., is described and a segment of its cytochrome oxidase unit I mitochondrial gene is sequenced. Asphondylia daphnandrae is significant as the first gall midge known to feed on a plant from the family Atherospermataceae (Laurales). The host plant tree Daphnandra johnsonii is endemic to the Illawarra region, New South Wales, Australia, and is currently threatened with extinction. Larvae of the new species of gall midge were found feeding inside deformed fruits, impeding the sexual reproduction of this endangered plant species.
Kravitz, ES & Carroll, RJ 2019, 'Re‐evaluating composite scores: Adaptive Lasso variable selection for non‐linear models', Stat, vol. 8, no. 1.
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In nutrition, epidemiology, and other public health fields, composite scores are a common tool used to assess a health behaviour. These composite scores compare an individual's health behaviour to an idealized standard and provide a number, often between 0 and 100, to indicate their compliance to a health behaviour. Crucially, this measure of health behaviour is applied across populations (gender, smoking status, etc.) and health outcomes (colon cancer, breast cancer, etc.) to create a single interpretable score. One such composite score is the 2005 Healthy Eating Index that breaks diet into 12 components and evaluates nutritional intake by adherence to these components. We provide a general method that can be used to reassess the importance of these 12 components using flexible non‐linear models, across populations and diseases, based on an asymptotic least squares approximation. We establish oracle properties of this variable selection technique in our context, which is different from the usual one population and one disease context. Although our methods are motivated by the Healthy Eating Index, they are broad enough to be applied to any composite score and a broad range of non‐linear models.
Kretzschmar, AL, Larsson, ME, Hoppenrath, M, Doblin, MA & Murray, SA 2019, 'Characterisation of Two Toxic Gambierdiscus spp. (Gonyaulacales, Dinophyceae) from the Great Barrier Reef (Australia): G. lewisii sp. nov. and G. holmesii sp. nov.', Protist, vol. 170, no. 6, pp. 125699-125699.
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Kretzschmar, AL, Verma, A, Kohli, G & Murray, S 2019, 'Development of a quantitative PCR assay for the detection and enumeration of a potentially ciguatoxin-producing dinoflagellate, Gambierdiscus lapillus (Gonyaulacales, Dinophyceae)', PLOS ONE, vol. 14, no. 11, pp. e0224664-e0224664.
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Ciguatera fish poisoning (CFP) is an illness contracted through the ingestion of seafood containing ciguatoxins. It is prevalent in tropical regions worldwide, including in Australia. Ciguatoxins are produced by some species of Gambierdiscus. Therefore, screening of Gambierdiscus species identification through quantitative PCR (qPCR), along with the determination of species toxicity, can be useful in monitoring potential ciguatera risk in these regions. In Australia, CFP is prevalent in tropical Queensland and increasingly in sub-tropical regions of Australia, but has a report rate of approximately 10%. Yet the identity, distribution and abundance of ciguatoxin producing Gambierdiscus spp. is largely unknown. In this study, we developed a rapid qPCR assay to quantify the presence and abundance of Gambierdiscus lapillus, a likely ciguatoxic species first described from Australia. We assessed the specificity and efficiency of the qPCR assay. The assay was tested on 25 environmental samples from the Heron Island reef in the southern Great Barrier Reef, a ciguatera endemic region, to determine the presence and patchiness of this species across samples from Chnoospora sp., Padina sp. and Sargassum sp. macroalgal hosts.
Krix, DW, Phillips, ML & Murray, BR 2019, 'Relationships among leaf flammability attributes and identifying low-leaf-flammability species at the wildland–urban interface', International Journal of Wildland Fire, vol. 28, no. 4, pp. 295-295.
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Leaf flammability is a multidimensional plant functional trait with emerging importance for wildfire risk management. Understanding relationships among leaf flammability attributes not only provides information about the properties of leaves as fuels in the wildland–urban interface (WUI), it can also offer an effective way to identify low-leaf-flammability species. We examined relationships between leaf ignitibility, sustainability and combustibility among 60 plant species of the WUI of eastern Australia. We found that leaf ignitibility and sustainability worked in opposition to each other as dimensions of flammability. Species with leaves that were slow to ignite were those with leaves that sustained burning for the longest, whereas species with leaves that were fast to ignite had leaves that burned for the shortest periods of time. Low leaf combustibility was related to short leaf burning sustainability but not to ignitibility. We created an overall leaf flammability index (OLFI) to rank species on emergent properties of ignitibility, sustainability and combustibility attributes in combination. We found that low-leaf-flammability species with low OLFI values had small leaf area, high leaf mass per area and high leaf water content. Our findings have implications for species selection for green firebreaks in the WUI.
Kumar, R, Kumar, R, Sharma, N, Vyas, M, Mahajan, S, Satija, S, Singh, SK, Khursheed, R, Mehta, M, Khurana, S & Khurana, N 2019, 'Fisetin: A phytochemical with various pharmacological activities', Plant Archives, vol. 19, pp. 1012-1016.
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Flavonoids are the plant secondary metabolites which work as growth hormone as well as defence mechanism for the plants. These are well known for their antioxidant properties and are part of our daily food. Fisetin is one of the polyphenolic flavonol, present in various fruits and vegetables. Fisetin is reported to have various pharmacological properties. Strawberries have the maximum concentration of fisetin. Despite having various pharmacological properties, low oral bioavailability and high lipophilicity meared its use. In this review we tried to collect the information regarding the various pharmacological properties and its developed formulations to improve its bioavailability.
Kumar, R, Kumar, R, Sharma, N, Vyas, M, Mahajan, S, Satija, S, Singh, SK, Mehta, M & Khurana, N 2019, 'Genetics of Parkinson's disease: How close and how far we are?', Plant Archives, vol. 19, pp. 1017-1021.
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Parkinson's disease (PD) is one of the neuronal disorder in which there is continuous degeneration of the neurons occur. It is an age related disorder, so the most effected peoples are those who are 60 or above 60years of age. The main neurons involved in PD are the dopaminergic neurons, specifically present in the substantia nigra pars compacta. It is known that, at the time of diagnosis of PD or appearance of its symptoms, 80% of the dopaminergic neurons got deteriorated. The major symptoms of PD are tremors, rigidity, akinesia and postural instability. There are various etiological factors which are responsible for the development of the PD and among them, genetic factor considered to be one of main factor involved in this condition. The major genes which are involved in PD are SNCA, PARK1, PARK 2 and DJ-1. Whenever, any mutation occurs in these genes, it alters the protein expression which ultimately leads to the dysfunction of the neuronal cell organelles. There is aggregation of the α-synuclein protein occurs due to the mutation of these genes. In the present review, we reviewed the available information regarding the genetic of the PD and try to conclude about its present status.
Kusuma, KD, Griffith, R, Harry, EJ, Bottomley, AL & Ung, AT 2019, 'Analysis of FtsZ Crystal Structures Towards a New Target for Antibiotics', Australian Journal of Chemistry, vol. 72, no. 3, pp. 184-193.
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The bacterial cell division protein FtsZ is conserved in most bacteria and essential for viability. There have been concerted efforts in developing inhibitors that target FtsZ as potential antibiotics. Key to this is an in-depth understanding of FtsZ structure at the molecular level across diverse bacterial species to ensure inhibitors have high affinity for the FtsZ target in a variety of clinically relevant pathogens. In this study, we show that FtsZ structures differ in three ways: (1) the H7 helix curvature; (2) the dimensions of the interdomain cleft; and (3) the opening/closing mechanism of the interdomain cleft, whereas no differences were observed in the dimensions of the nucleotide-binding pocket and T7 loop. Molecular dynamics simulation may suggest that there are two possible mechanisms for the process of opening and closing of the interdomain cleft on FtsZ structures. This discovery highlights significant differences between FtsZ structures at the molecular level and this knowledge is vital in assisting the design of potent FtsZ inhibitors.
Kusuma, KD, Payne, M, Ung, AT, Bottomley, AL & Harry, EJ 2019, 'FtsZ as an Antibacterial Target: Status and Guidelines for Progressing This Avenue', ACS Infectious Diseases, vol. 5, no. 8, pp. 1279-1294.
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The disturbing increase in the number of bacterial pathogens that are resistant to multiple, or sometimes all, current antibiotics highlights the desperate need to pursue the discovery and development of novel classes of antibacterials. The wealth of knowledge available about the bacterial cell division machinery has aided target-driven approaches to identify new inhibitor compounds. The main division target being pursued is the highly conserved and essential protein FtsZ. Despite very active research on FtsZ inhibitors for several years, this protein is not yet targeted by any commercial antibiotic. Here, we discuss the suitability of FtsZ as an antibacterial target for drug development and review progress achieved in this area. We use hindsight to highlight the gaps that have slowed progress in FtsZ inhibitor development and to suggest guidelines for concluding that FtsZ is actually the target of these molecules, a key missing link in several studies. In moving forward, a multidisciplinary, communicative, and collaborative process, with sharing of research expertise, is critical if we are to succeed.
Kysenius, K, Hilton, JB, Paul, B, Hare, DJ & Crouch, PJ 2019, 'Anatomical redistribution of endogenous copper in embryonic mice overexpressing SOD1', Metallomics, vol. 11, no. 1, pp. 141-150.
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Detailed quantitativein situimaging of embryonic mice reveals overt Cu redistribution associated with SOD1-overexpression.
Kysenius, K, Paul, B, Hilton, JB, Liddell, JR, Hare, DJ & Crouch, PJ 2019, 'A versatile quantitative microdroplet elemental imaging method optimised for integration in biochemical workflows for low-volume samples', Analytical and Bioanalytical Chemistry, vol. 411, no. 3, pp. 603-616.
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Laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) analysis of μ-droplets is becoming an attractive alternative for detecting and quantifying elements in biological samples. With minimal sample preparation required and detection limits comparable to solution nebulisation ICP-MS, μ-droplets have substantial advantages over traditional elemental detection, particularly for low volumes, such as aliquots taken from samples required for multiple independent biochemical assays, or fluids and tissues where elements of interest exist at native concentrations not suited to the necessary dilution steps required for solution nebulisation ICP-MS. However, the characteristics of μ-droplet residue deposition are heavily dependent on the matrix, and potential effects on signal suppression or enhancement have not been fully characterised. We present a validated and flexible high-throughput method for quantification of elements in μ-droplets using LA-ICP-MS imaging and matrix-matched external calibrants. Imaging the entire μ-droplet area removes analytical uncertainty arising from the often-heterogenous distribution when compared to radial or bisecting line scans that capture only a small portion of the droplet residue. We examined the effects of common matrices found in a standard biochemistry workflow, including native protein and salt contents, as well as reagents used in typical preparation steps for concurrent biochemical assays, such as total protein quantification and enzyme activity assays. We found that matrix composition results in systemic, concentration-dependent signal enhancement and suppression for carbon, whereas high sodium content has a specific space-charge-like suppression effect on high masses. We confirmed the accuracy of our method using both a certified serum standard (Seronorm™ L1) and independent measurements of analysed samples by solution nebulisation ICP-MS, then tested the specificity and reproducibility by examining spinal cord ...
Lau, A, Kong, FYS, Huston, W, Chow, EPF, Fairley, CK & Hocking, JS 2019, 'Factors associated with anorectal Chlamydia trachomatis or Neisseria gonorrhoeae test positivity in women: a systematic review and meta-analysis', Sexually Transmitted Infections, vol. 95, no. 5, pp. 361-367.
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ObjectivesThere has been considerable discussion about anorectal Chlamydia trachomatis (CT) in women, with some calling for anorectal CT screening, but little about anorectal Neisseria gonorrhoeae (NG). Given that urogenital NG is more strongly associated with pelvic inflammatory disease, this is an evidence gap. This systematic review and meta-analysis investigates the associations between anorectal CT in women and CT positivity at other sites (urogenital/oropharyngeal) and with anal intercourse, and compares these with anorectal NG within the same study populations.MethodsElectronic databases were searched for English-language studies published to October 2018 using the following terms: (“Chlamydia” OR “Chlamydia trachomatis”) AND ((“anal” OR “rect*” OR “anorect*”) OR (“extra?genital” OR “multi?site”)). Studies were included if anorectal NG data were available. Random-effects meta-analyses calculated pooled estimates; heterogeneity was investigated using meta-regression.Results25 studies were eligible. Anorectal CT positivity ranged from 0% to 17.5%, with a summary estimate of 8.0% (95% CI 7.0 to 9.1; I2=88.5%). Anorectal NG positivity ranged from 0% to 17.0%, with a summary estimate of 2.1% (95% CI 1.6 to 2.8; I2=92.7%). The association between urogenital and anorectal positivity was stronger for NG than CT (summary prevalence ratio (PR)=89.3 (95% CI 53.1 to 150.3; I2=80.1%), PR=32.2 (95% CI 25.6 to 40.7; I2=70.3%), respectively), and between oropharyngeal and anorectal positivity it was stronger for NG than CT (PR=34.8 (95% CI 10.2 to 118.2; I2=89.9%), PR=8.8 (95% CI 6.8 to 11.5; I2=58.1%),...
Lawson, CA, Possell, M, Seymour, JR, Raina, J-B & Suggett, DJ 2019, 'Coral endosymbionts (Symbiodiniaceae) emit species-specific volatilomes that shift when exposed to thermal stress', Scientific Reports, vol. 9, no. 1.
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AbstractBiogenic volatile organic compounds (BVOCs) influence organism fitness by promoting stress resistance and regulating trophic interactions. Studies examining BVOC emissions have predominantly focussed on terrestrial ecosystems and atmospheric chemistry – surprisingly, highly productive marine ecosystems remain largely overlooked. Here we examined the volatilome (total BVOCs) of the microalgal endosymbionts of reef invertebrates, Symbiodiniaceae. We used GC-MS to characterise five species (Symbiodinium linucheae, Breviolum psygmophilum, Durusdinium trenchii, Effrenium voratum, Fugacium kawagutii) under steady-state growth. A diverse range of 32 BVOCs were detected (from 12 in D. trenchii to 27 in S. linucheae) with halogenated hydrocarbons, alkanes and esters the most common chemical functional groups. A thermal stress experiment on thermally-sensitive Cladocopium goreaui and thermally-tolerant D. trenchii significantly affected the volatilomes of both species. More BVOCs were detected in D. trenchii following thermal stress (32 °C), while fewer BVOCs were recorded in stressed C. goreaui. The onset of stress caused dramatic increases of dimethyl-disulfide (98.52%) in C. goreaui and nonanoic acid (99.85%) in D. trenchii. This first volatilome analysis of Symbiodiniaceae reveals that both species-specificity and environmental factors govern the composition of BVOC emissions among the Symbiodiniace...
Leahy, DA, Hopkins, AM, Norris, RP, Marvil, J, Collier, JD, Taylor, EN, Allison, JR, Anderson, C, Bell, M, Bilicki, M, Bland-Hawthorn, J, Brough, S, Brown, MJI, Driver, S, Gurkan, G, Harvey-Smith, L, Heywood, I, Holwerda, BW, Liske, J, Lopez-Sanchez, AR, McConnell, D, Moffett, A, Owers, MS, Pimbblet, KA, Raja, W, Seymour, N, Voronkov, MA & Wang, L 2019, 'ASKAP commissioning observations of the GAMA 23 field', Publications of the Astronomical Society of Australia, vol. 36.
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AbstractWe have observed the G23 field of the Galaxy AndMass Assembly (GAMA) survey using the Australian Square Kilometre Array Pathfinder (ASKAP) in its commissioning phase to validate the performance of the telescope and to characterise the detected galaxy populations. This observation covers ~48 deg2 with synthesised beam of 32.7 arcsec by 17.8 arcsec at 936MHz, and ~39 deg2 with synthesised beam of 15.8 arcsec by 12.0 arcsec at 1320MHz. At both frequencies, the root-mean-square (r.m.s.) noise is ~0.1 mJy/beam. We combine these radio observations with the GAMA galaxy data, which includes spectroscopy of galaxies that are i-band selected with a magnitude limit of 19.2. Wide-field Infrared Survey Explorer (WISE) infrared (IR) photometry is used to determine which galaxies host an active galactic nucleus (AGN). In properties including source counts, mass distributions, and IR versus radio luminosity relation, the ASKAP-detected radio sources behave as expected. Radio galaxies have higher stellar mass and luminosity in IR, optical, and UV than other galaxies. We apply optical and IR AGN diagnostics and find that they disagree for ~30% of the galaxies in our sample. We suggest possible causes for the disagreement. Some cases can be explained by optical extinction of the AGN, but for more than half of the cases we do not find a clear explanation. Radio sources aremore likely (~6%) to have an AGN than radio quiet galaxies (~1%), but the majority of AGN are not detected in radio at this sensitivity.
Lee, C-H, Kang, TH, Godon, O, Watanabe, M, Delidakis, G, Gillis, CM, Sterlin, D, Hardy, D, Cogné, M, Macdonald, LE, Murphy, AJ, Tu, N, Lee, J, McDaniel, JR, Makowski, E, Tessier, PM, Meyer, AS, Bruhns, P & Georgiou, G 2019, 'An engineered human Fc domain that behaves like a pH-toggle switch for ultra-long circulation persistence', Nature Communications, vol. 10, no. 1.
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AbstractThe pharmacokinetic properties of antibodies are largely dictated by the pH-dependent binding of the IgG fragment crystallizable (Fc) domain to the human neonatal Fc receptor (hFcRn). Engineered Fc domains that confer a longer circulation half-life by virtue of more favorable pH-dependent binding to hFcRn are of great therapeutic interest. Here we developed a pH Toggle switch Fc variant containing the L309D/Q311H/N434S (DHS) substitutions, which exhibits markedly improved pharmacokinetics relative to both native IgG1 and widely used half-life extension variants, both in conventional hFcRn transgenic mice and in new knock-in mouse strains. engineered specifically to recapitulate all the key processes relevant to human antibody persistence in circulation, namely: (i) physiological expression of hFcRn, (ii) the impact of hFcγRs on antibody clearance and (iii) the role of competing endogenous IgG. DHS-IgG retains intact effector functions, which are important for the clearance of target pathogenic cells and also has favorable developability.
Lee, C-H, Kang, TH, Godon, O, Watanabe, M, Delidakis, G, Gillis, CM, Sterlin, D, Hardy, D, Cogné, M, Macdonald, LE, Murphy, AJ, Tu, N, Lee, J, McDaniel, JR, Makowski, E, Tessier, PM, Meyer, AS, Bruhns, P & Georgiou, G 2019, 'Publisher Correction: An engineered human Fc domain that behaves like a pH-toggle switch for ultra-long circulation persistence', Nature Communications, vol. 10, no. 1.
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An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Lee, PLT, Kanodarwala, FK, Lennard, C, Spindler, X, Spikmans, V, Roux, C & Moret, S 2019, 'Latent fingermark detection using functionalised silicon oxide nanoparticles: Method optimisation and evaluation', Forensic Science International, vol. 298, pp. 372-383.
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The application of nanoparticles for latent fingermark detection has been reported in the literature over the past two decades. One of the nanoparticles that shows promise to become a routine technique is functionalised silicon oxide nanoparticles (SiO2 NPs). In a recent optimisation of the technique, the use of carboxyl-functionalised SiO2 NPs doped with luminescent ruthenium complex was proposed as a breakthrough for latent fingermark detection. In this study, the aforementioned functionalised SiO2 NPs were extensively evaluated. Modification and optimisation of the original detection parameters were performed to enhance detection quality and improve applicability. Various detection parameters were evaluated and assessed. A lower concentration of the functionalised nanoparticles used in the colloidal dispersion was determined to offer improved detection effectiveness. A combination of increased bath temperature and reduced immersion time was found to produce good overall results. A set of modified detection parameters was suggested for the use of the functionalised SiO2 NPs to detect latent fingermarks. Performance of the modified detection parameters was compared against that of the published detection method. Comparison experiments were carried out on fingermark specimens deposited on aluminium foil, transparent polypropylene plastic and green polyethylene plastic. Three donors (weak, average and strong) and two age intervals (ten days and three months) were considered in the comparison study. Evaluation of the results suggested that the overall performance of the modified method for latent fingermark detection was superior to that obtained using the previously published detection parameters.
Lee, U, Garcia, TP, Carroll, RJ, Gilbreath, KR & Wu, G 2019, 'Analysis of repeated measures data in nutrition research.', Front Biosci (Landmark Ed), vol. 24, no. 8, pp. 1377-1389.
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Amino acid nutrition studies often involve repeated measures data. An example is that the concentrations of plasma citrulline in steers are repeatedly measured from the same animals. The standard repeated measures ANOVA method does not detect significant time changes in the concentrations of plasma citrulline within 6 hours after steers consumed rumen-protected citrulline, while a graphical analysis indicates that there exists a time effect. Here we describe three mixed model analyses that capture the time effect in a statistically significant way, while accounting for the correlations of measurements over time from the same steers. First, we allow flexible variance-covariance structures on our model. Second, we use baseline measurements as a covariate in our model. Third, we use percent-change from baseline as a data normalization method. In our data analysis, all these three approaches can lead to meaningful statistical results that oral administration of rumen-protected citrulline enhances the concentrations of plasma citrulline over time in ruminants. This supports the notion that rumen-protected citrulline can bypass the rumen to effectively enter the blood circulation.
LEES, T, ELLIOTT, JL, GUNNING, S, NEWTON, PJ, RAI, T & LAL, S 2019, 'A systematic review of the current evidence regarding interventions for anxiety, PTSD, sleepiness and fatigue in the law enforcement workplace', Industrial Health, vol. 57, no. 6, pp. 655-667.
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Leggat, WP, Camp, EF, Suggett, DJ, Heron, SF, Fordyce, AJ, Gardner, S, Deakin, L, Turner, M, Beeching, LJ, Kuzhiumparambil, U, Eakin, CM & Ainsworth, TD 2019, 'Rapid Coral Decay Is Associated with Marine Heatwave Mortality Events on Reefs', Current Biology, vol. 29, no. 16, pp. 2723-2730.e4.
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Severe marine heatwaves have recently become a common feature of global ocean conditions due to a rapidly changing climate [1, 2]. These increasingly severe thermal conditions are causing an unprecedented increase in the frequency and severity of mortality events in marine ecosystems, including on coral reefs [3]. The degradation of coral reefs will result in the collapse of ecosystem services that sustain over half a billion people globally [4, 5]. Here, we show that marine heatwave events on coral reefs are biologically distinct to how coral bleaching has been understood to date, in that heatwave conditions result in an immediate heat-induced mortality of the coral colony, rapid coral skeletal dissolution, and the loss of the three-dimensional reef structure. During heatwave-induced mortality, the coral skeletons exposed by tissue loss are, within days, encased by a complex biofilm of phototrophic microbes, whose metabolic activity accelerates calcium carbonate dissolution to rates exceeding accretion by healthy corals and far greater than has been documented on reefs under normal seawater conditions. This dissolution reduces the skeletal density and hardness and increases porosity. These results demonstrate that severe-heatwave-induced mortality events should be considered as a distinct biological phenomenon from bleaching events on coral reefs. We also suggest that such heatwave mortality events, and rapid reef decay, will become more frequent as the intensity of marine heatwaves increases and provides further compelling evidence for the need to mitigate climate change and instigate actions to reduce marine heatwaves.
Leggio, GM, Di Marco, R, Gulisano, W, D’Ascenzo, M, Torrisi, SA, Geraci, F, Lavanco, G, Dahl, K, Giurdanella, G, Castorina, A, Aitta-aho, T, Aceto, G, Bucolo, C, Puzzo, D, Grassi, C, Korpi, ER, Drago, F & Salomone, S 2019, 'Dopaminergic-GABAergic interplay and alcohol binge drinking', Pharmacological Research, vol. 141, pp. 384-391.
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The dopamine D3 receptor (D3R), in the nucleus accumbens (NAc), plays an important role in alcohol reward mechanisms. The major neuronal type within the NAc is the GABAergic medium spiny neuron (MSN), whose activity is regulated by dopaminergic inputs. We previously reported that genetic deletion or pharmacological blockade of D3R increases GABAA α6 subunit in the ventral striatum. Here we tested the hypothesis that D3R-dependent changes in GABAA α6 subunit in the NAc affect voluntary alcohol intake, by influencing the inhibitory transmission of MSNs. We performed in vivo and ex vivo experiments in D3R knockout (D3R -/-) mice and wild type littermates (D3R +/+). Ro 15-4513, a high affinity α6-GABAA ligand was used to study α6 activity. At baseline, NAc α6 expression was negligible in D3R+/+, whereas it was robust in D3R-/-; other relevant GABAA subunits were not changed. In situ hybridization and qPCR confirmed α6 subunit mRNA expression especially in the NAc. In the drinking-in-the-dark paradigm, systemic administration of Ro 15-4513 inhibited alcohol intake in D3R+/+, but increased it in D3R-/-; this was confirmed by intra-NAc administration of Ro 15-4513 and furosemide, a selective α6-GABAA antagonist. Whole-cell patch-clamp showed peak amplitudes of miniature inhibitory postsynaptic currents in NAc medium spiny neurons higher in D3R-/- compared to D3R+/+; Ro 15-4513 reduced the peak amplitude in the NAc of D3R-/-, but not in D3R+/+. We conclude that D3R-dependent enhanced expression of α6 GABAA subunit inhibits voluntary alcohol intake by increasing GABA inhibition in the NAc.
Lehmann, DM, Krishnakumar, K, Batres, MA, Hakola-Parry, A, Cokcetin, N, Harry, E & Carter, DA 2019, 'A cost-effective colourimetric assay for quantifying hydrogen peroxide in honey', Access Microbiology, vol. 1, no. 10.
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Honey is a natural product with many beneficial properties including antimicrobial action. Production of hydrogen peroxide (H2O2) in diluted honey is central to this action. Here, we describe an optimized method for measuring levels of H2O2 in honey. This method is based on established methods, with the level of dilution, the time between dilution and reading the assay, and aeration of the samples during the assay identified as critical points for ensuring reliability and reproducibility. The method is cost-effective and easy to perform using common laboratory equipment. Using this method, we quantified the hydrogen peroxide content of five different, unprocessed polyfloral honeys collected in NC, USA. Our results show that H2O2 production by these honeys varies greatly, with some samples producing negligible levels of H2O2. We assessed the effect of colour on the assay by measuring the recovery of spiked H2O2 from light and dark honey and from serially diluted dark corn syrup, and found the amount of H2O2 that could be detected was lower in dark corn syrup and darker honey samples.
Lekamge, S, Miranda, AF, Trestrail, C, Pham, B, Ball, AS, Shukla, R & Nugegoda, D 2019, 'The Toxicity of Nonaged and Aged Coated Silver Nanoparticles to Freshwater Alga Raphidocelis subcapitata', Environmental Toxicology and Chemistry, vol. 38, no. 11, pp. 2371-2382.
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AbstractThe transformation of coated silver nanoparticles (AgNPs) and their impacts on aquatic organisms require further study. The present study investigated the role of aging on the transformation of differently coated AgNPs and their sublethal effects on the freshwater alga Raphidocelis subcapitata. The stability of AgNPs was evaluated over 32 d, and the results indicated that transformation of AgNPs occurred during the incubation; however, coating‐specific effects were observed. Fresh AgNPs increased reactive oxygen species (ROS) formation, whereas aged AgNPs induced excessive ROS generation compared with their fresh counterparts. Increased ROS levels caused increased lipid peroxidation (LPO) in treatment groups exposed to both fresh and aged NPs, although LPO was comparatively higher in algae exposed to aged AgNPs. The observed increase in catalase (CAT) activity of algal cells was attributed to early stress responses induced by excessive intracellular ROS generation, and CAT levels were higher in the aged NP treatment groups. In conclusion, AgNPs increased ROS levels and LPO in algae and caused the activation of antioxidant enzymes such as CAT. Overall, the results suggest that aging and coating of AgNPs have major impacts on AgNP transformation in media and their effects on algae. Environ Toxicol Chem 2019;38:2371–2382. © 2019 SETAC
Lema, KA, Constancias, F, Rice, SA & Hadfield, MG 2019, 'High bacterial diversity in nearshore and oceanic biofilms and their influence on larval settlement by Hydroides elegans (Polychaeta)', Environmental Microbiology, vol. 21, no. 9, pp. 3472-3488.
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© 2019 Society for Applied Microbiology and John Wiley & Sons Ltd. Settlement of many benthic marine invertebrates is stimulated by bacterial biofilms, although it is not known if patterns of settlement reflect microbial communities that are specific to discrete habitats. Here, we characterized the taxonomic and functional gene diversity (16S rRNA gene amplicon and metagenomic sequencing analyses), as well as the specific bacterial abundances, in biofilms from diverse nearby and distant locations, both inshore and offshore, and tested them for their ability to induce settlement of the biofouling tubeworm Hydroides elegans, an inhabitant of bays and harbours around the world. We found that compositions of the bacterial biofilms were site specific, with the greatest differences between inshore and offshore sites. Further, biofilms were highly diverse in their taxonomic and functional compositions across inshore sites, while relatively low diversity was found at offshore sites. Hydroides elegans settled on all biofilms tested, with settlement strongly correlated with bacterial abundance. Bacterial density in biofilms was positively correlated with biofilm age. Our results suggest that the localized distribution of H. elegans is not determined by ‘selection’ to locations by specific bacteria, but it is more likely linked to the prevailing local ecology and oceanographic features that affect the development of dense biofilms and the occurrence of larvae.
Levin, LA, Bett, BJ, Gates, AR, Heimbach, P, Howe, BM, Janssen, F, McCurdy, A, Ruhl, HA, Snelgrove, P, Stocks, KI, Bailey, D, Baumann-Pickering, S, Beaverson, C, Benfield, MC, Booth, DJ, Carreiro-Silva, M, Colaço, A, Eblé, MC, Fowler, AM, Gjerde, KM, Jones, DOB, Katsumata, K, Kelley, D, Le Bris, N, Leonardi, AP, Lejzerowicz, F, Macreadie, PI, McLean, D, Meitz, F, Morato, T, Netburn, A, Pawlowski, J, Smith, CR, Sun, S, Uchida, H, Vardaro, MF, Venkatesan, R & Weller, RA 2019, 'Global Observing Needs in the Deep Ocean', Frontiers in Marine Science, vol. 6, no. May.
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© 2019 Levin, Bett, Gates, Heimbach, Howe, Janssen, McCurdy, Ruhl, Snelgrove, Stocks, Bailey, Baumann-Pickering, Beaverson, Benfield, Booth, Carreiro-Silva, Colaço, Eblé, Fowler, Gjerde, Jones, Katsumata, Kelley, Le Bris, Leonardi, Lejzerowicz, Macreadie, McLean, Meitz, Morato, Netburn, Pawlowski, Smith, Sun, Uchida, Vardaro, Venkatesan and Weller. The deep ocean below 200 m water depth is the least observed, but largest habitat on our planet by volume and area. Over 150 years of exploration has revealed that this dynamic system provides critical climate regulation, houses a wealth of energy, mineral, and biological resources, and represents a vast repository of biological diversity. A long history of deep-ocean exploration and observation led to the initial concept for the Deep-Ocean Observing Strategy (DOOS), under the auspices of the Global Ocean Observing System (GOOS). Here we discuss the scientific need for globally integrated deep-ocean observing, its status, and the key scientific questions and societal mandates driving observing requirements over the next decade. We consider the Essential Ocean Variables (EOVs) needed to address deep-ocean challenges within the physical, biogeochemical, and biological/ecosystem sciences according to the Framework for Ocean Observing (FOO), and map these onto scientific questions. Opportunities for new and expanded synergies among deep-ocean stakeholders are discussed, including academic-industry partnerships with the oil and gas, mining, cable and fishing industries, the ocean exploration and mapping community, and biodiversity conservation initiatives. Future deep-ocean observing will benefit from the greater integration across traditional disciplines and sectors, achieved through demonstration projects and facilitated reuse and repurposing of existing deep-sea data efforts. We highlight examples of existing and emerging deep-sea methods and technologies, noting key challenges associated with data volume, preservation, ...
Li, A, Geyer, FC, Blecua, P, Lee, JY, Selenica, P, Brown, DN, Pareja, F, Lee, SSK, Kumar, R, Rivera, B, Bi, R, Piscuoglio, S, Wen, HY, Lozada, JR, Gularte-Mérida, R, Cavallone, L, Aghmesheh, M, Amor, D, Andrews, L, Antill, Y, Balleine, R, Beesley, J, Blackburn, A, Bogwitz, M, Brown, M, Burgess, M, Burke, J, Butow, P, Caldon, L, Campbell, I, Christian, A, Clarke, C, Cohen, P, Crook, A, Cui, J, Cummings, M, Dawson, S-J, De Fazio, A, Delatycki, M, Dobrovic, A, Dudding, T, Duijf, P, Edkins, E, Edwards, S, Farshid, G, Fellows, A, Field, M, Flanagan, J, Fong, P, Forbes, J, Forrest, L, Fox, S, French, J, Friedlander, M, Ortega, DG, Gattas, M, Giles, G, Gill, G, Gleeson, M, Greening, S, Haan, E, Harris, M, Hayward, N, Hickie, I, Hopper, J, Hunt, C, James, P, Jenkins, M, Kefford, R, Kentwell, M, Kirk, J, Kollias, J, Lakhani, S, Lindeman, G, Lipton, L, Lobb, L, Lok, S, Macrea, F, Mann, G, Marsh, D, McLachlan, S-A, Meiser, B, Milne, R, Nightingale, S, O’Connell, S, Pachter, N, Patterson, B, Phillips, K, Saleh, M, Salisbury, E, Saunders, C, Saunus, J, Scott, C, Scott, R, Sexton, A, Shelling, A, Simpson, P, Spigelman, A, Spurdle, M, Stone, J, Taylor, J, Thorne, H, Trainer, A, Trench, G, Tucker, K, Visvader, J, Walker, L, Wallis, M, Williams, R, Winship, I, Wu, K, Young, MA, Rezoug, Z, Nguyen-Dumont, T, Peterlongo, P, Tondini, C, Terkelsen, T, Rønlund, K, Boonen, SE, Mannerma, A, Winqvist, R, Janatova, M, Rajadurai, P, Xia, B, Norton, L, Robson, ME, Ng, P-S, Looi, L-M, Southey, MC, Weigelt, B, Soo-Hwang, T, Tischkowitz, M, Foulkes, WD & Reis-Filho, JS 2019, 'Publisher Correction: Homologous recombination DNA repair defects in PALB2-associated breast cancers', npj Breast Cancer, vol. 5, no. 1.
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An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Li, A, Geyer, FC, Blecua, P, Lee, JY, Selenica, P, Brown, DN, Pareja, F, Lee, SSK, Kumar, R, Rivera, B, Bi, R, Piscuoglio, S, Wen, HY, Lozada, JR, Gularte-Mérida, R, Cavallone, L, Rezoug, Z, Nguyen-Dumont, T, Peterlongo, P, Tondini, C, Terkelsen, T, Rønlund, K, Boonen, SE, Mannerma, A, Winqvist, R, Janatova, M, Rajadurai, P, Xia, B, Norton, L, Robson, ME, Ng, P-S, Looi, L-M, Southey, MC, Weigelt, B, Soo-Hwang, T, Tischkowitz, M, Foulkes, WD, Reis-Filho, JS, Aghmesheh, M, Amor, D, Andrews, L, Antill, Y, Balleine, R, Beesley, J, Blackburn, A, Bogwitz, M, Brown, M, Burgess, M, Burke, J, Butow, P, Caldon, L, Campbell, I, Christian, A, Clarke, C, Cohen, P, Crook, A, Cui, J, Cummings, M, Dawson, S-J, De Fazio, A, Delatycki, M, Dobrovic, A, Dudding, T, Duijf, P, Edkins, E, Edwards, S, Farshid, G, Fellows, A, Field, M, Flanagan, J, Fong, P, Forbes, J, Forrest, L, Fox, S, French, J, Friedlander, M, Ortega, DG, Gattas, M, Giles, G, Gill, G, Gleeson, M, Greening, S, Haan, E, Harris, M, Hayward, N, Hickie, I, Hopper, J, Hunt, C, James, P, Jenkins, M, Kefford, R, Kentwell, M, Kirk, J, Kollias, J, Lakhani, S, Lindeman, G, Lipton, L, Lobb, L, Lok, S, Macrea, F, Mann, G, Marsh, D, McLachlan, S-A, Meiser, B, Milne, R, Nightingale, S, O’Connell, S, Pachter, N, Patterson, B, Phillips, K, Saleh, M, Salisbury, E, Saunders, C, Saunus, J, Scott, C, Scott, R, Sexton, A, Shelling, A, Simpson, P, Spigelman, A, Spurdle, M, Stone, J, Taylor, J, Thorne, H, Trainer, A, Trench, G, Tucker, K, Visvader, J, Walker, L, Wallis, M, Williams, R, Winship, I, Wu, K & Young, MA 2019, 'Homologous recombination DNA repair defects in PALB2-associated breast cancers', npj Breast Cancer, vol. 5, no. 1.
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AbstractMono-allelic germline pathogenic variants in the Partner And Localizer of BRCA2 (PALB2) gene predispose to a high-risk of breast cancer development, consistent with the role of PALB2 in homologous recombination (HR) DNA repair. Here, we sought to define the repertoire of somatic genetic alterations in PALB2-associated breast cancers (BCs), and whether PALB2-associated BCs display bi-allelic inactivation of PALB2 and/or genomic features of HR-deficiency (HRD). Twenty-four breast cancer patients with pathogenic PALB2 germline mutations were analyzed by whole-exome sequencing (WES, n = 16) or targeted capture massively parallel sequencing (410 cancer genes, n = 8). Somatic genetic alterations, loss of heterozygosity (LOH) of the PALB2 wild-type allele, large-scale state transitions (LSTs) and mutational signatures were defined. PALB2-associated BCs were found to be heterogeneous at the genetic level, with PIK3CA (29%), PALB2 (21%), TP53 (21%), and NOTCH3 (17%) being the genes most frequently affected by somatic mutations. Bi-allelic PALB2 inactivation was found in 16 of the 24 cases (67%), either through LOH (n = 11) or second somatic mutations (n = 5) of the wild-type allele. High LST scores were found in all 12 PALB2-associated BCs with bi-allelic PALB2 inactivation sequenced by WES, of which eight displayed the HRD-related mutational signature 3. In addition, bi-allelic inactivation of PALB2 w...
Li, C, Xu, Z-Q, Mendelson, N, Kianinia, M, Toth, M & Aharonovich, I 2019, 'Purification of single-photon emission from hBN using post-processing treatments', Nanophotonics, vol. 8, no. 11, pp. 2049-2055.
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Abstract
Single-photon emitters (SPEs) in hexagonal boron nitride (hBN) are promising components for on-chip quantum information processing. Recently, large-area hBN films prepared by chemical vapor deposition (CVD) were found to host uniform, high densities of SPEs. However, the purity of these emitters has, to date, been low, hindering their applications in practical devices. In this work, we present two methods for post-growth processing of hBN, which significantly improve SPEs in hBN films that had been transferred from substrates used for CVD. The emitters exhibit high photon purities in excess of 90% and narrow linewidths of ~3 nm at room temperature. Our work lays a foundation for producing high-quality emitters in an ultra-compact two-dimensional material system and paves the way for deployment of hBN SPEs in scalable on-chip photonic and quantum devices.
Li, D, Roca, M, Yuecel, R & Lorenz, A 2019, 'Immediate visualization of recombination events and chromosome segregation defects in fission yeast meiosis', Chromosoma, vol. 128, no. 3, pp. 385-396.
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Li, G, Chan, YL, Nguyen, LT, Mak, C, Zaky, A, Anwer, AG, Shi, Y, Nguyen, T, Pollock, CA, Oliver, BG, Saad, S & Chen, H 2019, 'Impact of maternal e‐cigarette vapor exposure on renal health in the offspring', Annals of the New York Academy of Sciences, vol. 1452, no. 1, pp. 65-77.
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AbstractMaternal smoking during pregnancy is a significant risk factor of renal pathology in the offspring. E‐cigarettes are perceived to be a safe option and are increasingly used by pregnant women either continuously during pregnancy or as a replacement for tobacco cigarettes. This study aimed to determine the effects of replacing tobacco cigarettes with e‐cigarettes during pregnancy, and continuous e‐cigarette use during pregnancy on the offspring's kidneys. Female Balb/c mice were exposed to either air (sham) or tobacco cigarette smoke (SE) for 6 weeks prior to mating, during gestation and lactation. A subset of the “SE group” received e‐cigarette vapor (containing nicotine) after mating until pups weaned. Additional female mice were continuously exposed to e‐vapor (either with or without nicotine) for 6 weeks prior to mating until pups weaned. Kidneys and urine from the male offspring were assessed at postnatal day 1, day 20 (weaning), and 13 weeks of age (adulthood). E‐cigarette replacement was less detrimental to renal development and albuminuria than continuous SE during pregnancy. However, continuous e‐vapor exposure during pregnancy increased markers of oxidative stress, inflammation, and fibrosis in the adult offspring, independent of nicotine. E‐cigarette use during pregnancy confers future risk to the offspring's kidneys.
Li, G, Chan, YL, Sukjamnong, S, Anwer, AG, Vindin, H, Padula, M, Zakarya, R, George, J, Oliver, BG, Saad, S & Chen, H 2019, 'A Mitochondrial Specific Antioxidant Reverses Metabolic Dysfunction and Fatty Liver Induced by Maternal Cigarette Smoke in Mice', Nutrients, vol. 11, no. 7, pp. 1669-1669.
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Maternal smoking leads to glucose and lipid metabolic disorders and hepatic damage in the offspring, potentially due to mitochondrial oxidative stress. Mitoquinone mesylate (MitoQ) is a mitochondrial targeted antioxidant with high bioavailability. This study aimed to examine the impact of maternal cigarette smoke exposure (SE) on offspring’s metabolic profile and hepatic damage, and whether maternal MitoQ supplementation during gestation can affect these changes. Female Balb/c mice (eight weeks) were either exposed to air or SE for six weeks prior to mating and throughout gestation and lactation. A subset of the SE dams were supplied with MitoQ in the drinking water (500 µmol/L) during gestation and lactation. Intraperitoneal glucose tolerance test was performed in the male offspring at 12 weeks and the livers and plasma were collected at 13 weeks. Maternal SE induced glucose intolerance, hepatic steatosis, mitochondrial oxidative stress and related damage in the adult offspring. Maternal MitoQ supplementation reduced hepatic mitochondrial oxidative stress and improved markers of mitophagy and mitochondrial biogenesis. This may restore hepatic mitochondrial health and was associated with an amelioration of glucose intolerance, hepatic steatosis and pathological changes induced by maternal SE. MitoQ supplementation may potentially prevent metabolic dysfunction and hepatic pathology induced by intrauterine SE.
Li, J, Zhao, Y, Coleman, P, Chen, J, Ting, KK, Choi, JP, Zheng, X, Vadas, MA & Gamble, JR 2019, 'Low fluid shear stress conditions contribute to activation of cerebral cavernous malformation signalling pathways', Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease, vol. 1865, no. 11, pp. 165519-165519.
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Cerebral cavernous malformations (CCMs) are vascular malformations that cause hemorrhagic stroke. CCMs can arise from loss-of-function mutations in any one of CCM1 (KRIT1), CCM2 or CCM3 (PDCD10). Despite the mutation being in all endothelial cells the CCM lesions develop primarily in the regions with low fluid shear stress (FSS). Here we investigated the role of FSS in the signalling pathways associated with loss of function of CCM genes. We performed transcriptomic analysis on CCM1 or CCM2-silenced endothelial cells subjected to various FSS. The results showed 1382 genes were deregulated under low FSS, whereas only 29 genes were deregulated under high FSS. Key CCM downstream signalling pathways, including increased KLF2/4 expression, actin cytoskeleton reorganization, TGF-β and toll-like receptor signalling pathways and also oxidative stress pathways, were all highly upregulated but only under low FSS. We also show that the key known phenotypes of CCM lesions such as disrupted endothelial cell junction, increased inflammatory response/oxidative stress and elevated RhoA-ROCK activity, are only exhibited in monolayers of CCM-silenced endothelial cells subjected to low FSS. Our data establishes that shear stress acts as a previously unappreciated but important regulator for CCM gene function and may determine the site of CCM lesion development.
Li, P, Guo, X, Wang, S, Zang, R, Li, X, Man, Z, Li, P, Liu, S, Wu, Y & Wang, G 2019, 'Two-dimensional Sb@TiO2−x nanoplates as a high-performance anode material for sodium-ion batteries', Journal of Materials Chemistry A, vol. 7, no. 6, pp. 2553-2559.
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Two-dimensional Sb@TiO2−x nanoplates with abundant voids deliver high reversible capacity, excellent rate capability and stable cycling performance.
Li, T, Xu, J, Wang, C, Wu, W, Su, D & Wang, G 2019, 'The latest advances in the critical factors (positive electrode, electrolytes, separators) for sodium-sulfur battery', Journal of Alloys and Compounds, vol. 792, pp. 797-817.
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© 2019 The sodium-sulfur (Na/S) batteries have caused widespread concern owing to the advantages of low cost and high energy density, these advantages make them promising in the large-scale energy storage system. But the research progress in this field is still at the beginning stage and confronts with tough challenges, for example, the low sulfur conductivity and polysulfide shuttle effect. Considering Na/S battery is a complicated system whose reaction mechanism between sulfur and sodium is different from the operating temperatures, positive electrode hosts and electrolytes, thus a comprehensive understanding about the electrochemistry of the Na/S batteries that operating in high-temperature, intermediate-temperature and room-temperature is necessary. In addition, the critical factors (positive electrodes, electrolytes, separators) associated with the development of high energy density and high performance Na/S battery, it also need to be analysed for the successful application in the near future. In this review, the working methods of high-temperature Na/S (HT-Na/S) battery, intermediate-temperature Na/S (IT-Na/S) battery and room-temperature Na/S (RT-Na/S) battery will be compared, and also focus on the latest progress of positive electrodes, electrolytes and separators in Na/S batteries. Finally, we provide an outlook on the state of the art for the production of more efficient and reliable Na/S batteries with rational technique.
Li, VWH, Toogood, H, Ryan, S & Meakin, GE 2019, 'The effects of various household cleaning methods on DNA persistence on mugs and knives', Forensic Science International: Genetics Supplement Series, vol. 7, no. 1, pp. 277-278.
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© 2019 Elsevier B.V. With the prevalence of forensic science in popular media, offenders are becoming more forensically aware and can employ precautionary methods, such as cleaning used items or rubbing away fingermarks, to reduce their traces left at a crime scene. This study examined the effects of various cleaning methods on DNA persistence on commonly encountered casework exhibits, specifically knives and mugs. Aliquots of acellular DNA were added to the knife handles or mug rims, allowed to dry, and then the substrates were either sampled directly or were cleaned and then sampled. The plastic- and wood-handled knives were cleaned with a cloth in a sink of water, diluted dish washing liquid or diluted household bleach, whereas the ceramic, glass and steel mugs were cleaned with a dry or wet cloth, or by wiping with a cloth after applying a cleaning product (dish washing liquid or household bleach spray) directly into the mug and then rinsing it with water. DNA samples were collected with wet and dry swabs, in triplicate, and extracted and quantified. In both experiments, DNA was not detected on items after cleaning with dish washing liquid or household bleach, irrespective of the differences in amounts of DNA initially deposited, substrates, and cleaning methods. Even without a cleaning product, rubbing with a dry cloth decreased DNA recovery from the mugs, regardless of the mug substrate. These results contribute to our understanding of the impact of various cleaning methods on DNA recovery at the crime scene and will help inform DNA recovery strategies.
Li, X, Wang, S, Tang, X, Zang, R, Li, P, Li, P, Man, Z, Li, C, Liu, S, Wu, Y & Wang, G 2019, 'Porous Na3V2(PO4)3/C nanoplates for high-performance sodium storage', Journal of Colloid and Interface Science, vol. 539, pp. 168-174.
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Sodium super-ionic conductor (NASICON) structured Na3V2(PO4)3 (NVP), a promising cathode material for sodium-ion batteries (SIBs), benefits by its unique three-dimensional (3D) channel structure. However, the inherent characteristics of NVP (such as low electrical conductivity) usually lead to inferior rate and long-cycling performance, which miss the requirements of practical application in electrical energy storage systems (ESSs). Herein, we propose the synthesis of porous high-crystalline Na3V2(PO4)3/C nanoplates (NVP/C-P) via hydrothermal method and post-calcination. The porous nanoplate structure provides increased specific surface area and shortened diffusion pathway for ion/electron transport. Consequently, NVP/C-P cathodes exhibit a high specific capacity (117 mAh g-1, 0.2 C), exceptional rate performance (76.5 mAh g-1, 100 C) and long cyclic stability (10,000 cycles).
Liang, J, Mondal, AK, Wang, D & Iacopi, F 2019, 'Graphene‐Based Planar Microsupercapacitors: Recent Advances and Future Challenges', Advanced Materials Technologies, vol. 4, no. 1, pp. 1800200-1800200.
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© 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim The continuous development of integrated electronics such as maintenance-free biosensors, remote and mobile environmental sensors, wearable personal electronics, nanorobotics etc. and their continued miniaturization has led to an increasing demand for miniaturized energy storage units. Microsupercapacitors with graphene electrodes hold great promise as miniaturized, integrated power sources thanks to their fast charge/discharge rates, superior power performance, and long cycling stability. In addition, planar interdigitated electrodes also have the capability to reduce ion diffusion distances leading to a greatly improved electrochemical performance. Either as standalone power sources or complementing energy harvesting units, it is expected that graphene-based microsupercapacitors will play a key role as miniaturized power sources in electronic microsystems. This review highlights the recent development, challenges, and perspectives in this area, with an emphasis on the link between material and geometry design of planar graphene-based electrodes and their electrochemical performance and integrability.
Liang, L, Ma, Y & Carroll, RJ 2019, 'A semiparametric efficient estimator in case-control studies for gene–environment independent models', Journal of Multivariate Analysis, vol. 173, pp. 38-50.
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© 2019 Elsevier Inc. Case-controls studies are popular epidemiological designs for detecting gene–environment interactions in the etiology of complex diseases, where the genetic susceptibility and environmental exposures may often be reasonably assumed independent in the source population. Various papers have presented analytical methods exploiting gene–environment independence to achieve better efficiency, all of which require either a rare disease assumption or a distributional assumption on the genetic variables. We relax both assumptions. We construct a semiparametric estimator in case-control studies exploiting gene–environment independence, while the distributions of genetic susceptibility and environmental exposures are both unspecified and the disease rate is assumed unknown and is not required to be close to zero. The resulting estimator is semiparametric efficient and its superiority over prospective logistic regression, the usual analysis in case-control studies, is demonstrated in various numerical illustrations.
Lim, CED, Ng, RWC, Cheng, NCL, Zhang, GS & Chen, H 2019, 'Acupuncture for polycystic ovarian syndrome', Cochrane Database of Systematic Reviews, vol. 7, no. 7.
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BACKGROUND:Polycystic ovarian syndrome (PCOS) is characterised by the clinical signs of oligo-amenorrhoea, infertility and hirsutism. Conventional treatment of PCOS includes a range of oral pharmacological agents, lifestyle changes and surgical modalities. Beta-endorphin is present in the follicular fluid of both normal and polycystic ovaries. It was demonstrated that the beta-endorphin levels in ovarian follicular fluid of otherwise healthy women who were undergoing ovulation were much higher than the levels measured in plasma. Given that acupuncture impacts on beta-endorphin production, which may affect gonadotropin-releasing hormone (GnRH) secretion, it is postulated that acupuncture may have a role in ovulation induction via increased beta-endorphin production effecting GnRH secretion. This is an update of our previous review published in 2016. OBJECTIVES:To assess the effectiveness and safety of acupuncture treatment for oligo/anovulatory women with polycystic ovarian syndrome (PCOS) for both fertility and symptom control. SEARCH METHODS:We identified relevant studies from databases including the Gynaecology and Fertility Group Specialised Register, CENTRAL, MEDLINE, Embase, PsycINFO, CNKI, CBM and VIP. We also searched trial registries and reference lists from relevant papers. CENTRAL, MEDLINE, Embase, PsycINFO, CNKI and VIP searches are current to May 2018. CBM database search is to November 2015. SELECTION CRITERIA:We included randomised controlled trials (RCTs) that studied the efficacy of acupuncture treatment for oligo/anovulatory women with PCOS. We excluded quasi- or pseudo-RCTs. DATA COLLECTION AND ANALYSIS:Two review authors independently selected the studies, extracted data and assessed risk of bias. We calculated risk ratios (RR), mean difference (MD), standardised mean difference (SMD) and 95% confidence intervals (CIs). Primary outcomes were live birth rate, multiple pregnancy rate and ovulation rate, and secondary outcomes were clinical pregna...
Lin, Y, Ghazanfar, S, Wang, KYX, Gagnon-Bartsch, JA, Lo, KK, Su, X, Han, Z-G, Ormerod, JT, Speed, TP, Yang, P & Yang, JYH 2019, 'scMerge leverages factor analysis, stable expression, and pseudoreplication to merge multiple single-cell RNA-seq datasets', Proceedings of the National Academy of Sciences, vol. 116, no. 20, pp. 9775-9784.
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Concerted examination of multiple collections of single-cell RNA sequencing (RNA-seq) data promises further biological insights that cannot be uncovered with individual datasets. Here we present scMerge, an algorithm that integrates multiple single-cell RNA-seq datasets using factor analysis of stably expressed genes and pseudoreplicates across datasets. Using a large collection of public datasets, we benchmark scMerge against published methods and demonstrate that it consistently provides improved cell type separation by removing unwanted factors; scMerge can also enhance biological discovery through robust data integration, which we show through the inference of development trajectory in a liver dataset collection.
Lin, Y, He, P, Hu, P, Chen, H, Chen, Y & McGowan, E 2019, 'Low level of centromere-associated protein E promotes growth of hepatocellular carcinoma and is associated with adverse clinical features', Annals of Oncology, vol. 30, pp. iv9-iv9.
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Lin, Y, Yin, H, An, H, Zhou, C, Zhou, L, Chen, S & McGowan, E 2019, 'Chemokine receptor CCR2b expressing anti-Tn-MUC1 CAR-T cells enhanced anti-breast cancer activity', Annals of Oncology, vol. 30, no. Supplement 11, pp. xi12-xi12.
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Background: Enhanced anti-tumour activity is required for eradication of solid tumours by CART cells. One possibility of enhancing anti-tumour activity is by programming CART cells to express chemokine receptors that match chemokines produced either by the tumours or tumour-associated cells, thereby improving the infiltrating capacity of the CART cells. In this study, we engineered CCR2b expressing anti-Tn-MUC1 CAR T cells for the treatment of breast cancer.
Methods: Anti-Tn-MUC1-CARs were constructed using the SM3 scFv. Following lenti-MUC1 CAR retroviral transduction, efficiency of transgenic expression was assessed by flow cytometry. CCR2b expressing anti-Tn-MUC1 CAR T cells were prepared using PLV-CAR-5E5-CCR2b lentivirus. The susceptibility of MCF-7 cells to either anti-MUC1 CART or CCR2b expressing anti-MUC1 CART cell-mediated lysis was assessed using in vitro killing assays. For cytolytic analysis, CART-cells were cocultured 10:1 (effector:target) ratio with MCF-7 cells. The effects of CCR2b expressing CART cells on anti-tumour activity and infiltration were also assessed in an in vivo murine xenograft model.
Results: Activated T cells co-modified with both CCR2b and anti-MUC1-CAR had greater anti-tumour activity both in vivo and in vitro. When the effector / target cell ratio was 10, the killing rates of CART and CART-CCR2b were 56.9% and 83.9%, respectively. Tumour size was significantly smaller (P < 0.001) in the CAR-CCR2b group compared to the CAR alone group. At day 7 post-injection of CART cells, the infiltrated T cells was significantly increased (~2 folds) in the CAR-CCR2b group compared with the CART only group.
Conclusions: Our data demonstrated that the anti-tumour activity of the CCR2b expressing anti-Tn-MUC1 CART cells is 1.5 times more potent than CART cells without CCR2b. Augmentation of tumour suppression was also demonstrated in vivo in a murine xenograft model. These pre-clinical results show translational potential to the clinic for tr...
Liu, DL, Wang, B, Evans, J, Ji, F, Waters, C, Macadam, I, Yang, X & Beyer, K 2019, 'Propagation of climate model biases to biophysical modelling can complicate assessments of climate change impact in agricultural systems', International Journal of Climatology, vol. 39, no. 1, pp. 424-444.
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Regional climate model (RCM) simulations are being increasingly used for climate change impact assessments, but their application is challenging due to considerable biases inherited from global climate model (GCM) simulations and generated from dynamical downscaling processes. This study assesses the biases in NARCliM (NSW and ACT regional climate modelling) simulations and quantifies the consequence of the climate biases in the downstream assessment of climate change impact on wheat crop system, using the Agricultural Production System sIMulator (APSIM). Results showed that post‐processing bias‐corrected temperature and rainfall data from NARCliM had small annual mean biases but large biases in the crop growing season (CGS). During the CGS, the mean bias error of rainfall was generally positive for rainfall probability and negative for intensity, which subsequently resulted in APSIM simulating negative biases for runoff and deep drainage and positive bias in soil evaporation. Bias in soil water balance and water availability resulted in less plant transpiration and less N uptake, ultimately, leading to large negative biases in crop yields. A simple bias correction of the simulated crop yield driven by RCMs could result in a largely consistent distribution with those generated with APSIM simulations forced by observed climate. Our results showed that RCM simulation biases could confound with the climate change signal and produced an unreliable estimate of the effects of the changes in climate and farm management variables on crop yields. The results suggested that RCM simulations with the current bias correction on the RCM‐simulated outputs applied on an annual basis were inadequate for climate change assessments which involve biophysical models. Our study highlights the need for improved RCM simulations by eliminating the systemic biases associated with rainfall characteristics, although suitable post‐processing bias correction on a seasonal or monthly b...
Liu, F, Nattestad, A, Naficy, S, Han, R, Casillas, G, Angeloski, A, Sun, X & Huang, Z 2019, 'Fluorescent Carbon‐ and Oxygen‐Doped Hexagonal Boron Nitride Powders as Printing Ink for Anticounterfeit Applications', Advanced Optical Materials, vol. 7, no. 24, pp. 1901380-1901380.
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AbstractIncreasing demands for optical anticounterfeiting technology require the development of versatile luminescent materials with tunable photoluminescence properties. Herein, a number of fluorescent carbon‐ and oxygen‐doped hexagonal boron nitride (denoted as BCNO) phosphors are found to offer a such high‐tech anticounterfeiting solution. These multicolor BCNO powders, developed in a two‐step process with controlled annealing and oxidation, feature rod‐like particle shape, with varied luminescence properties. Studies of the optical properties of BCNO, along with other characterization, provide insight into this underexplored material. Anticounterfeiting applications are demonstrated with printed patterns which are indistinguishable to the naked eye under visible light but become highly discernible under UV irradiation. The fabricated patterns are demonstrated to be both chemically stable in corrosive environments and physically robust in mechanical bending testing. These properties render BCNO as promising and versatile anticounterfeiting material a wide variety of environments.
Liu, G, Cooley, MA, Jarnicki, AG, Borghuis, T, Nair, PM, Tjin, G, Hsu, AC, Haw, TJ, Fricker, M, Harrison, CL, Jones, B, Hansbro, NG, Wark, PA, Horvat, JC, Argraves, WS, Oliver, BG, Knight, DA, Burgess, JK & Hansbro, PM 2019, 'Fibulin-1c regulates transforming growth factor–β activation in pulmonary tissue fibrosis', JCI Insight, vol. 4, no. 16.
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Liu, G, Mateer, SW, Hsu, A, Goggins, BJ, Tay, H, Mathe, A, Fan, K, Neal, R, Bruce, J, Burns, G, Minahan, K, Maltby, S, Fricker, M, Foster, PS, Wark, PAB, Hansbro, PM & Keely, S 2019, 'Platelet activating factor receptor regulates colitis-induced pulmonary inflammation through the NLRP3 inflammasome', Mucosal Immunology, vol. 12, no. 4, pp. 862-873.
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Extra-intestinal manifestations (EIM) are common in inflammatory bowel disease (IBD). One such EIM is sub-clinical pulmonary inflammation, which occurs in up to 50% of IBD patients. In animal models of colitis, pulmonary inflammation is driven by neutrophilic infiltrations, primarily in response to the systemic bacteraemia and increased bacterial load in the lungs. Platelet activating factor receptor (PAFR) plays a critical role in regulating pulmonary responses to infection in conditions, such as chronic obstructive pulmonary disease and asthma. We investigated the role of PAFR in pulmonary EIMs of IBD, using dextran sulfate sodium (DSS) and anti-CD40 murine models of colitis. Both models induced neutrophilic inflammation, with increased TNF and IL-1β levels, bacterial load and PAFR protein expression in mouse lungs. Antagonism of PAFR decreased lung neutrophilia, TNF, and IL-1β in an NLRP3 inflammasome-dependent manner. Lipopolysaccharide from phosphorylcholine (ChoP)-positive bacteria induced NLRP3 and caspase-1 proteins in human alveolar epithelial cells, however antagonism of PAFR prevented NLRP3 activation by ChoP. Amoxicillin reduced bacterial populations in the lungs and reduced NLRP3 inflammasome protein levels, but did not reduce PAFR. These data suggest a role for PAFR in microbial pattern recognition and NLRP3 inflammasome signaling in the lung.
Liu, L, Zhang, X, Liu, Y, Zhang, L, Zheng, J, Wang, J, Hansbro, PM, Wang, L, Wang, G & Hsu, AC-Y 2019, 'Chitinase-like protein YKL-40 correlates with inflammatory phenotypes, anti-asthma responsiveness and future exacerbations', Respiratory Research, vol. 20, no. 1.
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BACKGROUND:Asthma is a heterogeneous chronic airway disease, which may be classified into different phenotypes. YKL-40 is a chitin-binding glycoprotein with unclear functions, but its expression is associated with inflammation and tissue remodeling. However, few studies have explored whether YKL-40 is associated with inflammatory phenotypes of asthma. METHODS:The study had two parts. Study I (n = 115) was a one-year prospective cohort designed to explore the relationship of serum YKL-40 levels with inflammatory phenotypes of asthma at baseline, and during exacerbations. Study II (n = 62) was a four-week prospective cohort designed to define whether serum YKL-40 levels could predict responses to a fixed anti-asthma regimen. YKL-40, IL-6 and CCL22 levels were detected using ELISA, and a sputum inflammatory panel (including IL-1β, IL-5, IL-8 and TNF-α) was assessed using Luminex-based MILLIPLEX assay. RESULTS:Study I: Serum YKL-40 levels in non-eosinophilic asthma (NEA) i.e. neutrophilic (47.77 [29.59, 74.97] ng/mL, n = 40) and paucigranulocytic (47.36 [28.81, 61.68] ng/mL, n = 31) were significantly elevated compared with eosinophilic asthma (31.05 [22.41, 51.10] ng/mL, n = 44) (P = 0.015). Serum YKL-40levels positively correlated with blood neutrophils, sputum IL-1β and plasma IL-6 but negatively correlated with serum IgE and blood eosinophils (all P ≤ 0.05). Baseline YKL-40 levels predicted moderate to severe exacerbations within a one-year period (aOR = 4.13, 95% CI = [1.08, 15.83]). Study II: Serum YKL-40 was an independent biomarker of negative responses to anti-asthma regimens (adjusted Odds Ratio [aOR] = 0.82, 95% CI = [0.71, 0.96]. CONCLUSIONS:These studies show that YKL-40 is a non-type 2 inflammatory signature for NEA, which could predict responsiveness or insensitivity to anti-asthma medications and more exacerbations. Further studies are needed to assess whether monitoring YKL-40 levels could provide potential implications for clinical relevance.
Liu, P & Separovic, F 2019, 'Membrane biophysics session', Biophysical Reviews, vol. 11, no. 3, pp. 283-284.
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Liu, S, Li, P, Umezawa, N, Zhou, W, Abe, H & Wang, G 2019, 'Constructing Sn(ii)-doped SrNb2O6 for visible light response driven H2 and O2 evolution from water', Catalysis Science & Technology, vol. 9, no. 14, pp. 3619-3622.
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A wide band-gap photocatalyst SrNb2O6 was adjusted to response to visible light in H2 and O2 evolution due to the new electron state in its band gap created by the Sn(ii) dopant.
Liu, T, Zhang, W, Ye, L, Ueland, M, Forbes, SL & Su, SW 2019, 'A novel multi-odour identification by electronic nose using non-parametric modelling-based feature extraction and time-series classification', Sensors and Actuators B: Chemical, vol. 298, pp. 126690-126690.
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© 2019 Elsevier B.V. The electronic nose (e-nose) is an olfaction system that consists of an array of chemical sensors and effective machine learning algorithms for the detection of various target odours. Feature extraction and classification methods are of great importance in improving the performance of the e-nose system. In this paper, a novel odour identification method is presented. Firstly, we use the kernel-based system modelling approach to extract odour features. Its solution is a series of finite impulse responses which containing discriminant information of different odours. In addition, a parameter optimisation method based on normalised mean square error and information entropy is proposed to optimise the kernel function. The entropy is effective in preventing the finite impulse responses from overfitting. Multi-odour classification is achieved based on Gaussian mixture density hidden Markov model (GMM-HMM) considering the characteristic of the extracted features. Also, parameter selection for GMM-HMM is realised according to BIC index and cross-validation. Then, we validate the performance of the proposed feature extraction method in resistance to noise and compare it with other existed features. The modelling-based feature reached the highest performance even without applying any filtering or smoothing techniques. Finally, we compare the proposed combination of feature extraction and classification algorithms with other approaches. The proposed method outperformed other approaches reaching 93.56% in sensitivity and 98.71% in specificity. The results demonstrate that the proposed method is applicable in e-nose-based odour identification.
Lockwood, TE, Talebi, M, Minett, A, Mills, S, Doble, PA & Bishop, DP 2019, 'Micro solid-phase extraction for the analysis of per- and polyfluoroalkyl substances in environmental waters', Journal of Chromatography A, vol. 1604, pp. 460495-460495.
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Growing concern over the environmental and health impacts of per- and polyfluoroalkyl substances (PFASs) has led to the development of increasingly stringent regulatory guidelines. To meet these guidelines for the determination of PFASs in surface-water, solid-phase extraction (SPE) is commonly implemented for clean-up and pre-concentration of samples. In this paper a micro-SPE method for the clean-up and pre-concentration of PFASs from surface-water was developed. A micro-SPE packing phase was created to retain 13 long and short chain PFAS after examining combinations of four 3 µm particle size sorbents, with the optimal phase consisting of a 50:50 mixture of C18 and aminopropyl silica. Micro-SPE achieved similar results to conventional SPE methods while reducing sample preparation time to 5 min and using only 2 mL of sample. The method was validated using spiked recoveries (100 ng L-1) from PFAS contaminated surface-water samples with recoveries ranging from 86% to 111% and relative standard deviations below 18%. Concentrations of the PFASs in the samples ranged from below the limit of quantification to 898 ± 15 ng L-1. Automation of sample preparation, including the micro-SPE extraction, was also demonstrated. These results show the potential for automated micro-SPE to replace conventional SPE, with the decreases in sample preparation time, sample and solvent volumes crucial for incorporation into routine analyses in commercial laboratories.
Lohr, KE, Camp, EF, Kuzhiumparambil, U, Lutz, A, Leggat, W, Patterson, JT & Suggett, DJ 2019, 'Resolving coral photoacclimation dynamics through coupled photophysiological and metabolomic profiling', Journal of Experimental Biology, vol. 222, no. Pt 8.
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Corals continuously adjust to short term variation in light availability on shallow reefs. Long-term light alterations can also occur due to natural and anthropogenic stressors, as well as management interventions such as coral transplantation. Although short term photophysiological responses are relatively well-understood in corals, little information is available regarding photoacclimation dynamics over weeks of altered light availability. We coupled photophysiology and metabolomic profiling to explore changes that accompany longer-term photoacclimation in a key Great Barrier Reef coral species (Acropora muricata). High (HL) and low light (LL) acclimated corals were collected from the reef and reciprocally exposed to high and low light ex situ. Rapid light curves using Pulse Amplitude Modulation (PAM) fluorometry revealed photophysiological acclimation of LL to HL and HL to LL shifted corals within 21 days. A subset of colonies sampled at 7 and 21 days for untargeted LC-MS and GC-MS metabolomic profiling revealed metabolic reorganization before acclimation was detected using PAM fluorometry. Metabolomic shifts were more pronounced for LL to HL treated corals than their HL to LL counterparts. Compounds driving metabolomic separation between HL-exposed and LL control colonies included amino acids, organic acids, fatty acids and sterols. Reduced glycerol and campesterol suggest decreased translocation of photosynthetic products from symbiont to host in LL to HL shifted corals, with concurrent increases in fatty acid abundance indicating reliance on stored lipids for energy. We discuss how these data provide novel insight into environmental regulation of metabolism and implications for management strategies that drive rapid changes in light availability.
Lohr, KE, Khattri, RB, Guingab-Cagmat, J, Camp, EF, Merritt, ME, Garrett, TJ & Patterson, JT 2019, 'Metabolomic profiles differ among unique genotypes of a threatened Caribbean coral', Scientific Reports, vol. 9, no. 1.
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AbstractGlobal threats to reefs require urgent efforts to resolve coral attributes that affect survival in a changing environment. Genetically different individuals of the same coral species are known to exhibit different responses to the same environmental conditions. New information on coral physiology, particularly as it relates to genotype, could aid in unraveling mechanisms that facilitate coral survival in the face of stressors. Metabolomic profiling detects a large subset of metabolites in an organism, and, when linked to metabolic pathways, can provide a snapshot of an organism’s physiological state. Identifying metabolites associated with desirable, genotype-specific traits could improve coral selection for restoration and other interventions. A key step toward this goal is determining whether intraspecific variation in coral metabolite profiles can be detected for species of interest, however little information exists to illustrate such differences. To address this gap, we applied untargeted 1H-NMR and LC-MS metabolomic profiling to three genotypes of the threatened coral Acropora cervicornis. Both methods revealed distinct metabolite “fingerprints” for each genotype examined. A number of metabolites driving separation among genotypes were identified or putatively annotated. Pathway analysis suggested differences in protein synthesis among genotypes. For the first time, these data illustrate intraspecific variation in metabolomic profiles for corals in a common garden. Our results contribute to the growing body of work on coral metabolomics and suggest future work could identify specific links between phenotype and metabolite profile in corals.
López-Campos, G, Bonner, E & McClements, L 2019, 'An Integrative Biomedical Informatics Approach to Elucidate the Similarities Between Pre-Eclampsia and Hypertension.', MedInfo, vol. 264, pp. 988-992.
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Pre-eclampsia is a pregnancy condition affecting 5-10% of pregnancies, and it is the leading cause of death in pregnancy associated with increased risk of cardiovascular disease later in life. Despite research, the pathogenesis of pre-eclampsia is still poorly understood. In this paper, we investigate the overlapping pathogenic mechanisms between pre-eclampsia and adult hypertension using an integrative biomedical informatics strategy that combined text mining techniques to identify genes and proteins, with geneset analyses, generating knowledge on the pathways and mechanisms involved in these conditions. We identified several overlapping pathogenic pathways/systems including metabolic pathways, developmental biology pathways, immune system, haemostasis, tyrosine kinase pathways, extracellular matrix and oxidative stress pathways. This bioinformatics approach could be applied for investigating mechanistic pathways of other disorders.
Lu, J, Cokcetin, NN, Burke, CM, Turnbull, L, Liu, M, Carter, DA, Whitchurch, CB & Harry, EJ 2019, 'Honey can inhibit and eliminate biofilms produced by Pseudomonas aeruginosa', Scientific Reports, vol. 9, no. 1.
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AbstractChronic wound treatment is becoming increasingly difficult and costly, further exacerbated when wounds become infected. Bacterial biofilms cause most chronic wound infections and are notoriously resistant to antibiotic treatments. The need for new approaches to combat polymicrobial biofilms in chronic wounds combined with the growing antimicrobial resistance crisis means that honey is being revisited as a treatment option due to its broad-spectrum antimicrobial activity and low propensity for bacterial resistance. We assessed four well-characterised New Zealand honeys, quantified for their key antibacterial components, methylglyoxal, hydrogen peroxide and sugar, for their capacity to prevent and eradicate biofilms produced by the common wound pathogen Pseudomonas aeruginosa. We demonstrate that: (1) honey used at substantially lower concentrations compared to those found in honey-based wound dressings inhibited P. aeruginosa biofilm formation and significantly reduced established biofilms; (2) the anti-biofilm effect of honey was largely driven by its sugar component; (3) cells recovered from biofilms treated with sub-inhibitory honey concentrations had slightly increased tolerance to honey; and (4) honey used at clinically obtainable concentrations completely eradicated established P. aeruginosa biofilms. These results, together with their broad antimicrobial spectrum, demonstrate that manuka honey-based wound dressings are a promising treatment for infected chronic wounds, including those with P. aeruginosa biofilms.
Luo, Z, Neville, SL, Campbell, R, Morey, JR, Menon, S, Thomas, M, Eijkelkamp, BA, Ween, MP, Huston, WM, Kobe, B & McDevitt, CA 2019, 'Structure and Metal Binding Properties of Chlamydia trachomatis YtgA', Journal of Bacteriology, vol. 202, no. 1.
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Chlamydia trachomatis
is the most common bacterial sexually transmitted infection in developed countries, with an estimated global prevalence of 4.2% in the 15- to 49-year age group. Although infection is asymptomatic in more than 80% of infected women, about 10% of cases result in serious disease. Infection by
C. trachomatis
is dependent on the ability to acquire essential nutrients, such as the transition metal iron, from host cells. In this study, we show that iron is the most abundant transition metal in
C. trachomatis
and report the structural and biochemical properties of the iron-recruiting protein YtgA. Knowledge of the high-resolution structure of YtgA will provide a platform for future structure-based antimicrobial design approaches.
Luu, LDW 2019, 'Pathogen adaptation to vaccination: the Australian Bordetella pertussis story', Microbiology Australia.
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Lyu, X, Wang, X & Leslie, LM 2019, 'The Dependence of Northwest Pacific Tropical Cyclone Intensification Rates on Environmental Factors', Advances in Meteorology, vol. 2019, pp. 1-18.
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The Northwest Pacific tropical cyclone (TC) intensification is classified into rapid intensification (RI), normal intensification (NI), and slow intensification (SI) categories. The initial location and intensity, the preceding intensity change, the motion direction, the occurrence month, and the intensification duration time are all found to differ for RI cases compared with NI and SI cases. The dependence of RI, NI, and SI on environmental conditions is further examined statistically by using the intensification rates of named TCs, for the 21-year period 1995–2015, obtained from JTWC best track data, and the environmental conditions derived from the ERA-Interim reanalysis data and GODAS high-resolution global ocean analysis data. It was found that deep-layer and upper-mid vertical wind shear (VWS), upper-level outflow, sea surface temperature (SST), and ocean heat content (OHC) are statistically different among RI, NI, and SI both before and during intensification. RI is enhanced by weaker and decreasing VWS, warmer oceans, and stronger and increasing outflow. In contrast, SI typically occurs with larger and increasing VWS, cooler oceans, and weaker, static outflow. The impacts of low-level VWS and net moisture inflow are only significantly different between RI and SI and between NI and SI, but not between RI and NI. Another key finding is that increased upper-level outflow and decreased VWS are important precursors and hence are possible predictors, of RI onset. The direction of upper-level outflow affects TC intensification, with NW and NE outflow being more favorable for TC RI than SE and SW outflow.
Ma, B, Huang, Y, Nie, Z, Qiu, X, Su, D, Wang, G, Yuan, J, Xie, X & Wu, Z 2019, 'Facile synthesis of Camellia oleifera shell-derived hard carbon as an anode material for lithium-ion batteries', RSC Advances, vol. 9, no. 35, pp. 20424-20431.
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Bio-waste Camellia oleifera shells (COS) are converted into porous carbon by a two-step method.
Ma, K, Liu, G-J, Yan, L, Wen, S, Xu, B, Tian, W, Goldys, EM & Liu, G 2019, 'AIEgen based poly(L-lactic-co-glycolic acid) magnetic nanoparticles to localize cytokine VEGF for early cancer diagnosis and photothermal therapy', Nanomedicine, vol. 14, no. 9, pp. 1191-1201.
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Aim: We demonstrated a novel theranostic system for simultaneous photothermal therapy and magnetic resonance imaging applicable to early diagnostics and treatment of cancer cells. Materials & methods: Oleic acid-Fe3O4 and triphenylamine-divinylanthracene-dicyano were loaded to the poly(L-lactic-co-glycolic acid) nanoparticles (NPs) on which anti-VEGF antibodies were modified to form anti-VEGF/OA-Fe3O4/triphenylamine-divinylanthracene-dicyano@poly(L-lactic-co-glycolic acid) NPs. The 1H nuclear magnetic resonance (NMR), mass spectra, fluorescence, UV absorption, dynamic light scattering, transmission electron microscope and inductively coupled plasma mass spectrometry tests were used to characterize the NPs, and the bioimaging was illustrated by confocal laser scanning microscope (CLSM) and in vivo MRI animal experiment. Results: This system was capable to recognize the overexpressed VEGF-A as low as 68 pg/ml in different cell lines with good selectivity and photothermal therapy effect. Conclusion: These ultrasensitive theranostic NPs were able to identify tumor cells by fluorescence imaging and MRI, and destroy tumors under near infrared illumination.
Ma, S, Zhu, L, Zhang, Z, Tsai, C-L & Carroll, RJ 2019, 'A robust and efficient approach to causal inference based on sparse sufficient dimension reduction', The Annals of Statistics, vol. 47, no. 3, pp. 1505-1535.
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© Institute of Mathematical Statistics, 2019. A fundamental assumption used in causal inference with observational data is that treatment assignment is ignorable given measured confounding variables. This assumption of no missing confounders is plausible if a large number of baseline covariates are included in the analysis, as we often have no prior knowledge of which variables can be important confounders. Thus, estimation of treatment effects with a large number of covariates has received considerable attention in recent years. Most existing methods require specifying certain parametric models involving the outcome, treatment and confounding variables, and employ a variable selection procedure to identify confounders. However, selection of a proper set of confounders depends on correct specification of the working models. The bias due to model misspecification and incorrect selection of confounding variables can yield misleading results. We propose a robust and efficient approach for inference about the average treatment effect via a flexible modeling strategy incorporating penalized variable selection. Specifically, we consider an estimator constructed based on an efficient influence function that involves a propensity score and an outcome regression. We then propose a new sparse sufficient dimension reduction method to estimate these two functions without making restrictive parametric modeling assumptions. The proposed estimator of the average treatment effect is asymptotically normal and semiparametrically efficient without the need for variable selection consistency. The proposed methods are illustrated via simulation studies and a biomedical application.
Ma, X, Huete, A & Tran, NN 2019, 'Interaction of Seasonal Sun-Angle and Savanna Phenology Observed and Modelled using MODIS', Remote Sensing, vol. 11, no. 12, pp. 1398-1398.
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Remote sensing of phenology usually works at the regional and global scales, which imposes considerable variations in the solar zenith angle (SZA) across space and time. Variations in SZA alters the shape and profile of the surface reflectance and vegetation index (VI) time series, but this effect on remote-sensing-derived vegetation phenology has not been adequately evaluated. The objective of this study is to understand the behaviour of VIs response to SZA, and to further improve the interpretation of satellite observed vegetation dynamics, across space and time. In this study, the sensitivity of two widely used VIs—the normalised difference vegetation index (NDVI) and the enhanced vegetation index (EVI)—to SZA was investigated at four northern Australian savanna sites, over a latitudinal distance of 9.8° (~1100 km). Complete time series of surface reflectances, as acquired with different SZA configurations, were simulated using Bidirectional Reflectance Distribution Function (BRDF) parameters provided by MODerate Resolution Imaging Spectroradiometer (MODIS). The sun-angle dependency of the four phenological transition dates were assessed. Results showed that while NDVI was very sensitive to SZA, such sensitivity was nearly absent for EVI. A negative correlation was also observed between NDVI sensitivity to SZA and vegetation cover, with sensitivity declining to the same level as EVI when vegetation cover was high. Different sun-angle configurations resulted in considerable variations in the shape and magnitude of the phenological profiles. The sensitivity of VIs to SZA was generally greater during the dry season (with only active trees present) than in the wet season (with both active trees and grasses), thus, the sun-angle effect on VIs was phenophase-dependent. The sun-angle effect on NDVI time series resulted in considerable differences in the phenological metrics across different sun-angle configurations. Across four sites, the sun-angle effect cau...
Macaulay, M & Rognon, P 2019, 'Shear-induced diffusion in cohesive granular flows: effect of enduring clusters', Journal of Fluid Mechanics, vol. 858.
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We investigate the effect of intergranular cohesive forces on the properties of self-diffusion in dense granular flows. The study is based on a series of simulated plane shear flows at different inertial and cohesion numbers, in which transverse diffusivities are measured. Results evidence an increase in diffusivity by up to two orders of magnitude when introducing cohesion. This strong effect is analysed using the Green–Kubo framework, expressing the diffusivity in terms of instantaneous grain velocity fluctuations and their time correlation. This analysis shows that cohesion, by forming enduring clusters in the flow, enhances the velocity fluctuations and their time persistence, which both contribute to enhancing grain mixing and self-diffusion.
Macha, IJ, Ben-Nissan, B, Vilchevskaya, EN, Morozova, AS, Abali, BE, Müller, WH & Rickert, W 2019, 'Drug Delivery From Polymer-Based Nanopharmaceuticals—An Experimental Study Complemented by Simulations of Selected Diffusion Processes', Frontiers in Bioengineering and Biotechnology, vol. 7.
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The success of medical therapy depends on the correct amount and the appropriate delivery of the required drugs for treatment. By using biodegradable polymers a drug delivery over a time span of weeks or even months is made possible. This opens up a variety of strategies for better medication. The drug is embedded in a biodegradable polymer (the "carrier") and injected in a particular position of the human body. As a consequence of the interplay between the diffusion process and the degrading polymer the drug is released in a controlled manner. In this work we study the controlled release of medication experimentally by measuring the delivered amount of drug within a cylindrical shell over a long time interval into the body fluid. Moreover, a simple continuum model of the Fickean type is initially proposed and solved in closed-form. It is used for simulating some of the observed release processes for this type of carrier and takes the geometry of the drug container explicitly into account. By comparing the measurement data and the model predictions diffusion coefficients are obtained. It turns out that within this simple model the coefficients change over time. This contradicts the idea that diffusion coefficients are constants independent of the considered geometry. The model is therefore extended by taking an additional absorption term into account leading to a concentration dependent diffusion coefficient. This could now be used for further predictions of drug release in carriers of different shape. For a better understanding of the complex diffusion and degradation phenomena the underlying physics is discussed in detail and even more sophisticated models involving different degradation and mass transport phenomena are proposed for future work and study.
Macha, IJ, Karacan, I, Ben-Nissan, B, Cazalbou, S & Müller, WH 2019, 'Development of antimicrobial composite coatings for drug release in dental, orthopaedic and neural prostheses applications', SN Applied Sciences, vol. 1, no. 1.
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While one of the major clinical and scientific challenges in the management of implant-related infections and post-operative complications after surgery is the application of new techniques, a new approach is pertinent in the design of medical implants to reduce bacterial infections. We have designed and tested antibiotic-containing biocomposite thin films of polylactic acid (PLA), and coralline-derived hydroxyapatite (HAp) as controlled drug delivery systems for the treatment of dental, orthopaedic and neural implant-related post-operative infections. These films can be applied to complicated designs of dental, miniaturized neural devices, cochlear or total hip replacement (THR) implants by spray or dip-coating techniques. Current results reveal that the devices could release antibiotic in a controlled manner to prevent significantly bacterial growth and biofilm production. Hydroxyapatite within the composites controls the release rate and also supplies minerals, such as calcium Ca2+ and phosphate PO42− ions, which are essential minerals for bone tissue regeneration. It is concluded from the physical, mechanical and biological properties that these coatings and devices could easily be utilized in a wide range of biomedical applications.
Machaalani, R, Thawley, M, Huang, J & Chen, H 2019, 'Effects of prenatal cigarette smoke exposure on BDNF, PACAP, microglia and gliosis expression in the young male mouse brainstem', NeuroToxicology, vol. 74, pp. 40-46.
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Cigarette smoke exposure during pregnancy into infancy affects brain growth and development in both short and long term (into adulthood). Using a mouse model of pre- into post- natal cigarette smoke exposure (SE), we aimed to determine the effects on brain derived neurotrophic factor (BDNF) and its receptor TrkB, neuropeptide pituitary adenylate cyclase activating polypeptide (PACAP) and its receptor PAC1, and astrocyte (GFAP) and microglia (Iba-1) immunohistochemical expression, in seven nuclei of the medulla and the facial (FAC) nucleus of the pons. Male pups of dams exposed to two cigarettes (nicotine <1.2 mg, CO <15 mg) twice daily for six weeks prior to mating, during gestation and lactation (n = 5; SE), were compared to pups exposed to air under the same condition (n = 5; SHAM) at postnatal day 20. Expression changes were only evident for BDNF, TrkB and PAC1 and included decreased BDNF in the hypoglossal (XII) nucleus and nucleus of the solitary tract (NTS), increased TrkB in XII but decreased TrkB in the FAC, and increased PAC1 in 4 nuclei of the medulla including the NTS. These results suggest that the effect of SE on the brainstem are region and marker selective, affecting regions of respiratory control (XII and NTS), and restricted to the BDNF system and PAC1, with no effect on activation states of astrocytes or microglia.
Maciuca, IE, Cummins, ML, Cozma, AP, Rimbu, CM, Guguianu, E, Panzaru, C, Licker, M, Szekely, E, Flonta, M, Djordjevic, SP & Timofte, D 2019, 'Genetic Features of mcr-1 Mediated Colistin Resistance in CMY-2-Producing Escherichia coli From Romanian Poultry', Frontiers in Microbiology, vol. 10.
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Colistin is a last resort antibiotic used for the treatment of human infections associated with carbapenemase-producing Enterobacteriales. Here, we evaluated the occurrence of mcr-1 and -2 plasmid-mediated colistin resistance in colistin and/or carbapenem resistant human clinical Enterobacteriales and other gram-negative bacteria (n = 543) as well as third generation cephalosporin-resistant (3GCR) Escherichia coli isolates from poultry abattoir workers (n = 15) and poultry fecal samples (n = 92) collected from two geographically separate abattoirs in Romania. which revealed that mcr-1 was present within four sequence types (STs): ST744 (n = 7), ST57 (n = 7), ST156 (n = 2), and ST10 (n = 1). Within STs, serotypes were conserved and, notably, all except one of the mcr-1-positive isolates were found to exhibit fluoroquinolone-resistance (FQR) associated SNPs in both gyrA and parC. While there were variations in genotypes, all isolates belonging to ST744, ST57, and ST156 were rich in resistance determinants, carrying aminoglycoside-modifying enzymes genes, sulfonamide resistance gene bla TEM- 1 as well as bla CMY- 2 AmpC β-lactamase resistance genes. They also exhibited high similarity in carriage of virulence genes; ST10, however, only carried the mcr-1 gene. Whole genome sequencing (WGS) analysis also revealed that although the mcr-1 gene was identified in a diverse population of E. coli, two STs (ST57 and ST744) predominated and interestingly, were found in isolates across both abattoirs providing evidence for clonal transmission. Also, two main genomic contexts of mcr-1 isolates were revealed with all ST57 isolates harboring the mcr-1 gene between two copies of ISApl1 (or the Tn6330 transposon) whilst a common mcr-1 containing scaffold, highly similar to IncX type mcr-1-bearing plasmids (pWI2-mcr, Accession number: LT838201), was present among mcr-1 isolates of varying phylogenetic backgrounds (ST10, ST744 and ST156). The high prevalence of the mcr-1 gene in poul...
Macreadie, PI, Atwood, TB, Seymour, JR, Fontes, MLS, Sanderman, J, Nielsen, DA & Connolly, RM 2019, 'Vulnerability of seagrass blue carbon to microbial attack following exposure to warming and oxygen', Science of The Total Environment, vol. 686, pp. 264-275.
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Seagrass meadows store globally-significant quantities of organic 'blue' carbon. These blue carbon stocks are potentially vulnerable to anthropogenic stressors (e.g. coastal development, climate change). Here, we tested the impact of oxygen exposure and warming (major consequences of human disturbance) on rates of microbial carbon break-down in seagrass sediments. Active microbes occurred throughout seagrass sediment profiles, but deep, ancient sediments (~5000 yrs. old) contained only 3% of the abundance of active microbes as young, surface sediments (<2 yrs. old). Metagenomic analysis revealed that microbial community structure and function changed with depth, with a shift from proteobacteria and high levels of genes involved in sulfur cycling in the near surface samples, to a higher proportion of firmicutes and euraracheota and genes involved in methanogenesis at depth. Ancient carbon consisted almost entirely (97%) of carbon considered 'thermally recalcitrant', and therefore presumably inaccessible to microbial attack. Experimental warming had little impact on carbon; however, exposure of ancient sediments to oxygen increased microbial abundance, carbon uptake and sediment carbon turnover (34-38 fold). Overall, this study provides detailed characterization of seagrass blue carbon (chemical stability, age, associated microbes) and suggests that environmental disturbances that expose coastal sediments to oxygen (e.g. dredging) have the capacity to diminish seagrass sediment carbon stocks by facilitating microbial remineralisation.
Mahmood, A, Li, S, Ali, Z, Tabassum, H, Zhu, B, Liang, Z, Meng, W, Aftab, W, Guo, W, Zhang, H, Yousaf, M, Gao, S, Zou, R & Zhao, Y 2019, 'Ultrafast Sodium/Potassium-Ion Intercalation into Hierarchically Porous Thin Carbon Shells', Advanced Materials, vol. 31, no. 2, pp. 1805430-1805430.
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Mahmud, MAP, Huda, N, Farjana, SH & Lang, C 2019, 'A strategic impact assessment of hydropower plants in alpine and non-alpine areas of Europe', Applied Energy, vol. 250, pp. 198-214.
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Mahmud, MAP, Huda, N, Farjana, SH & Lang, C 2019, 'Techno-Economic Operation and Environmental Life-Cycle Assessment of a Solar PV-Driven Islanded Microgrid', IEEE Access, vol. 7, pp. 111828-111839.
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Mai, HT, Tran, TS, Ho-Le, TP, Center, JR, Eisman, JA & Nguyen, TV 2019, 'Two-Thirds of All Fractures Are Not Attributable to Osteoporosis and Advancing Age: Implications for Fracture Prevention', The Journal of Clinical Endocrinology & Metabolism, vol. 104, no. 8, pp. 3514-3520.
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Abstract
Context
Although bone mineral density (BMD) is strongly associated with fracture and postfracture mortality, the burden of fractures attributable to low BMD has not been investigated.
Objectives
We sought to estimate the population attributable fraction of fractures and fracture-related mortality that can be attributed to low BMD.
Design and Setting
This study is a part of an ongoing population-based prospective cohort study, the Dubbo Osteoporosis Epidemiology study. In total, 3700 participants aged ≥50 years participated in the study. Low-trauma fracture was ascertained by X-ray reports, and mortality was ascertained from the Birth, Death and Marriage Registry.
Results
Overall, 21% of women and 11% of men had osteoporotic BMD. In univariable analysis, 21% and 16% of total fractures in women and men, respectively, were attributable to osteoporosis. Osteoporosis combined with advancing age (>70 years) accounted for 34% and 35% of fractures in women and men, respectively. However, these two factors accounted for ∼60% of hip fractures. About 99% and 66% of postfracture mortality in women and men, respectively, were attributable to advancing age, osteoporosis, and fracture; however, most of the attributable proportion was accounted for by advancing age.
Conclusions
A substantial health care burden of fracture is on people ...
Maitre, M, Chadwick, S, Kirkbride, KP, Gassner, A-L, Weyermann, C, Beavis, A & Roux, C 2019, 'An investigation on the secondary transfer of organic gunshot residues', Science & Justice, vol. 59, no. 3, pp. 248-255.
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Gunshot residues (GSR) are an important forensic trace in firearm-related events. Currently, routine GSR analyses focus on the detection and characterisation of the inorganic components (IGSR). The increasing prevalence of heavy metal-free ammunition challenges these current protocols and there is an increasing interest in how the organic components of GSR (OGSR) can provide complementary information. Similar to the situation with IGSR, OGSR compounds originally deposited on the shooter during the firing process may further be transferred onto another individual or surface. Hence, the aim of this study was to provide additional information regarding the risk of a secondary transfer of OGSR. Two scenarios were investigated, the first one related to the arrest process and the possibilities of a secondary transfer arising between a shooter onto a non-shooter (e.g. between a police officer and a person of interest (POI)). The second scenario concerned the transfer of OGSR onto the non-shooter after handling a firearm for few minutes without discharging it. One calibre was chosen, the .40 S&W calibre, used by several Australian State police forces. A secondary transfer was observed in all cases for the two scenarios investigated, for three compounds of interest: ethylcentralite (EC), diphenylamine (DPA), N-nitrosodiphenylamine (N-nDPA). The firearm handling scenario resulted in a larger secondary transfer to that of the arrest scenario. Overall, the amounts of OGSR detected on the non-shooter were generally lower than that detected on the shooter and controls after the arrest scenario. The results of this study provide complementary knowledge about OGSR, which can be further used to improve the current practice and the interpretation of OGSR evidence. In particular, it highlights that the secondary transfer proposition must be considered during the interpretation of forensic findings, especially when small amounts of OGSR target compounds are detected.
Maity, AK, Carroll, RJ & Mallick, BK 2019, 'Integration of Survival and Binary Data for Variable Selection and Prediction: A Bayesian Approach', Journal of the Royal Statistical Society Series C: Applied Statistics, vol. 68, no. 5, pp. 1577-1595.
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Summary
We consider the problem where the data consist of a survival time and a binary outcome measurement for each individual, as well as corresponding predictors. The goal is to select the common set of predictors which affect both the responses, and not just one of them. In addition, we develop a survival prediction model based on data integration. The paper is motivated by the Cancer Genomic Atlas databank, which is currently the largest genomics and transcriptomics database. The data contain cancer survival information along with cancer stages for each patient. Furthermore, it contains reverse phase protein array measurements for each individual, which are the predictors associated with these responses. The biological motivation is to identify the major actionable proteins associated with both survival outcomes and cancer stages. We develop a Bayesian hierarchical model to model jointly the survival time and the classification of the cancer stages. Moreover, to deal with the high dimensionality of the reverse phase protein array measurements, we use a shrinkage prior to identify significant proteins. Simulations and Cancer Genomic Atlas data analysis show that the joint integrated modelling approach improves survival prediction.
Majumder, R, Sutcliffe, B, Taylor, PW & Chapman, TA 2019, 'Next-Generation Sequencing reveals relationship between the larval microbiome and food substrate in the polyphagous Queensland fruit fly', Scientific Reports, vol. 9, no. 1.
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AbstractInsects typically host substantial microbial communities (the ‘microbiome’) that can serve as a vital source of nutrients and also acts as a modulator of immune function. While recent studies have shown that diet is an important influence on the gut microbiome, very little is known about the dynamics underpinning microbial acquisition from natural food sources. Here, we addressed this gap by comparing the microbiome of larvae of the polyphagous fruit fly Bactrocera tryoni (‘Queensland fruit fly’) that were collected from five different fruit types (sapodilla [from two different localities], hog plum, pomegranate, green apple, and quince) from North-east to South-east Australia. Using Next-Generation Sequencing on the Illumina MiSeq platform, we addressed two questions: (1) what bacterial communities are available to B. tryoni larvae from different host fruit; and (2) how does the microbiome vary between B. tryoni larvae and its host fruit? The abundant bacterial taxa were similar for B. tryoni larvae from different fruit despite significant differences in the overall microbial community compositions. Our study suggests that the bacterial community structure of B. tryoni larvae is related less to the host fruit (diet) microbiome and more to vertical transfer of the microbiome during egg laying. Our findings also suggest that geographic location may play a quite limited role in structuring of larval microbiomes. This is the first study to use Next-Generation Sequencing to analyze the microbiome of B. tryoni larvae together with the host fruit, an approach that has enabled greatly increased resolution of relationships between the insect’s microbiome and that of the surrounding host tissues.
Man, Z, Li, P, Zhou, D, Zang, R, Wang, S, Li, P, Liu, S, Li, X, Wu, Y, Liang, X & Wang, G 2019, 'High-performance lithium–organic batteries by achieving 16 lithium storage in poly(imine-anthraquinone)', Journal of Materials Chemistry A, vol. 7, no. 5, pp. 2368-2375.
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The Li/PIAQ cell exhibits excellent electrochemical performances with a 16 Li-storage mechanism based on DFT calculations and experimental investigations.
Mantri, VA, Ganesan, M, Gupta, V, Krishnan, P & Siddhanta, AK 2019, 'An overview on agarophyte trade in India and need for policy interventions', Journal of Applied Phycology, vol. 31, no. 5, pp. 3011-3023.
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Marino, G, Solntsev, AS, Xu, L, Gili, VF, Carletti, L, Poddubny, AN, Rahmani, M, Smirnova, DA, Chen, H, Lemaître, A, Zhang, G, Zayats, AV, Angelis, CD, Leo, G, Sukhorukov, AA & Neshev, DN 2019, 'Spontaneous photon-pair generation at the nanoscale', Optica, vol. 6, no. 11, pp. 1416-1422.
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Optical nanoantennas have shown a great capacity for efficient extraction of
photons from the near to the far-field, enabling directional emission from
nanoscale single-photon sources. However, their potential for the generation
and extraction of multi-photon quantum states remains unexplored. Here we
demonstrate experimentally the nanoscale generation of two-photon quantum
states at telecommunication wavelengths based on spontaneous parametric
down-conversion in an optical nanoantenna. The antenna is a crystalline AlGaAs
nanocylinder, possessing Mie-type resonances at both the pump and the bi-photon
wavelengths and when excited by a pump beam generates photonpairs with a rate
of 35 Hz. Normalized to the pump energy stored by the nanoantenna, this rate
corresponds to 1.4 GHz/Wm, being one order of magnitude higher than
conventional on-chip or bulk photon-pair sources. Our experiments open the way
for multiplexing several antennas for coherent generation of multi-photon
quantum states with complex spatial-mode entanglement and applications in
free-space quantum communications and sensing.
Marlton, F, Checchia, S & Daniels, J 2019, 'Revealing phase boundaries by weighted parametric structural refinement', Journal of Synchrotron Radiation, vol. 26, no. 5, pp. 1638-1643.
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Parametric Rietveld refinement from powder diffraction data has been utilized in a variety of situations to understand structural phase transitions of materials in situ. However, when analysing data from lower-resolution two-dimensional detectors or from samples with overlapping Bragg peaks, such transitions become difficult to observe. In this study, a weighted parametric method is demonstrated whereby the scale factor is restrained via an inverse tan function, making the phase boundary composition a refinable parameter. This is demonstrated using compositionally graded samples within the lead-free piezoelectric (BiFeO3)
x
(Bi0.5K0.5TiO3)
y
(Bi0.5Na0.5TiO3)1–x–y
and (Bi0.5Na0.5TiO3)
x
(BaTiO3)1–x
systems. This has proven to be an effective method for diffraction experiments with relatively low resolution, weak peak splitting or compositionally complex multiphase samples.
Marlton, F, Ivashko, O, Zimmerman, MV, Gutowski, O, Dippel, A-C & Jørgensen, MRV 2019, 'A simple correction for the parallax effect in X-ray pair distribution function measurements', Journal of Applied Crystallography, vol. 52, no. 5, pp. 1072-1076.
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Total scattering and pair distribution function (PDF) analysis has created new insights that traditional powder diffraction methods have been unable to achieve in understanding the local structures of materials exhibiting disorder or complex nanostructures. Care must be taken in such analyses as subtle and discrete features in the PDF can easily be artefacts generated in the measurement process, which can result in unphysical models and interpretation. The focus of this study is an artefact called the parallax effect, which can occur in area detectors with thick detection layers during the collection of X-ray PDF data. This effect results in high-Q peak offsets, which subsequently cause an r-dependent shift in the PDF peak positions in real space. Such effects should be accounted for if a truly accurate model is to be achieved, and a simple correction that can be conducted via a Rietveld refinement against the reference data is proposed.
Marsh, DJ & Dickson, K-A 2019, 'Writing Histone Monoubiquitination in Human Malignancy—The Role of RING Finger E3 Ubiquitin Ligases', Genes, vol. 10, no. 1, pp. 67-67.
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There is growing evidence highlighting the importance of monoubiquitination as part of the histone code. Monoubiquitination, the covalent attachment of a single ubiquitin molecule at specific lysines of histone tails, has been associated with transcriptional elongation and the DNA damage response. Sites function as scaffolds or docking platforms for proteins involved in transcription or DNA repair; however, not all sites are equal, with some sites resulting in actively transcribed chromatin and others associated with gene silencing. All events are written by E3 ubiquitin ligases, predominantly of the RING (really interesting new gene) finger type. One of the most well-studied events is monoubiquitination of histone H2B at lysine 120 (H2Bub1), written predominantly by the RING finger complex RNF20-RNF40 and generally associated with active transcription. Monoubiquitination of histone H2A at lysine 119 (H2AK119ub1) is also well-studied, its E3 ubiquitin ligase constituting part of thePolycomb Repressor Complex 1 (PRC1), RING1B-BMI1, associated with transcriptional silencing. Both modifications are activated as part of the DNA damage response. Histone monoubiquitination is a key epigenomic event shaping the chromatin landscape of malignancy and influencing how cells respond to DNA damage. This review discusses a number of these sites and the E3 RING finger ubiquitin ligases that write them.
Marsh, JW, Hayward, RJ, Shetty, A, Mahurkar, A, Humphrys, MS & Myers, GSA 2019, 'Dual RNA-Seq of Chlamydia and Host Cells', Methods in Molecular Biology, vol. 2042, pp. 123-135.
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During the infection of a host cell by a bacterial pathogen, a cascading series of gene expression changes occurs as each organism manipulates or responds to the other via defense or survival strategies. Unraveling this complex interplay is key for our understanding of bacterial virulence and host response pathways for the development of novel therapeutics. Dual RNA sequencing (dual RNA-Seq) has recently been developed to simultaneously capture host and bacterial transcriptomes from an infected cell. Leveraging the sensitivity and resolution allowed by RNA-seq, dual RNA-Seq can be applied to any bacteria-eukaryotic host interaction. We pioneered dual RNA-Seq to simultaneously capture Chlamydia and host expression profiles during an in vitro infection as proof of principle. Here we provide a detailed laboratory protocol and bioinformatics analysis guidelines for dual RNA-seq experiments focusing on Chlamydia as the organism of interest.
Marshall, HM, Vaughan, A & Yang, IA 2019, 'Personalised multidisciplinary management for patients with chronic obstructive pulmonary disease (COPD)', Journal of Thoracic Disease, vol. 11, no. S17, pp. S2115-S2116.
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Marsh-Wakefield, F, Kruzins, A, McGuire, HM, Yang, S, Bryant, C, Fazekas de St. Groth, B, Nassif, N, Byrne, SN, Gibson, J, Brown, C, Larsen, S, McCulloch, D, Boyle, R, Clark, G, Joshua, D, Ho, PJ & Vuckovic, S 2019, 'Mass Cytometry Discovers Two Discrete Subsets of CD39−Treg Which Discriminate MGUS From Multiple Myeloma', Frontiers in Immunology, vol. 10.
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Multiple Myeloma (MM) is preceded by the clinically stable condition monoclonal gammopathy of undetermined significance (MGUS). Critical immune events that discriminate MGUS from newly diagnosed MM (ND)MM patients remain unknown, but may involve changes in the regulatory T cell (Treg) compartment that favor myeloma growth. To address this possibility, we used mass cytometry and the unsupervised clustering algorithm Flow self-organizing map (FlowSOM) to interrogate the distribution of multiple subsets within CD25+CD127low/negTreg in matched bone marrow (BM) and peripheral blood (PB) of MGUS and NDMM patients. Both mass cytometry and flow cytometry confirmed a trend toward prevalence of CD39-Treg within the Treg compartment in BM and PB of NDMM patients compared to CD39-Treg in MGUS patients. FlowSOM clustering displayed a phenotypic organization of Treg into 25 metaclusters that confirmed Treg heterogeneity. It identified two subsets which emerged within CD39-Treg of NDMM patients that were negligible or absent in CD39-Treg of MGUS patients. One subset was found in both BM and PB which phenotypically resembled activated Treg based on CD45RO, CD49d, and CD62L expression; another subset resembled BM-resident Treg based on its tissue-resident CD69+CD62L-CD49d- phenotype and restricted location within the BM. Both subsets co-expressed PD-1 and TIGIT, but PD-1 was expressed at higher levels on BM-resident Treg than on activated Treg. Within BM, both subsets had limited Perforin and Granzyme B production, whilst activated Treg in PB acquired high Perforin and Granzyme B production. In conclusion, the use of mass cytometry and FlowSOM clustering discovered two discrete subsets of CD39-Treg which are discordant in MGUS and NDMM patients and may be permissive of myeloma growth which warrants further study. Understanding the regulatory properties of these subsets may also advance MGUS and MM diagnosis, prognosis, and therapeutic implications for MM patients.
Maynard, P, Skinner, K, Bolton, M & Moret, S 2019, 'Potential application of liquid dye penetrants for serial number restoration on firearms', Australian Journal of Forensic Sciences, vol. 51, no. 6, pp. 674-684.
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Maynard-Casely, HE, Booth, N, Leung, AE, Stuart, BH & Thomas, PS 2019, 'Potential of neutron powder diffraction for the study of solid triacylglycerols', Food Structure, vol. 22, pp. 100124-100124.
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© 2019 We present a high-resolution neutron powder diffraction study of the triclinic β form of tripalmitin as well as in situ crystallisation experiments, monitored with neutron diffraction, conducted over three different cooling rates. We use the results from the high-resolution study to anticipate if neutron diffraction could be beneficial in differentiating the polymorphism in triacylglycerol systems. We extend on this to present analysis of a diffraction pattern of cocoa butter, to establish the potential for neutron diffraction to study the (hydrogenous) forms of triacylglycerols used in food production.
Mazraani, R, Timms, P, Hill, PC, Suaalii-Sauni, T, Niupulusu, T, Temese, SVA, Iosefa-Siitia, L, Auvaa, L, Tapelu, SA, Motu, MF, Righarts, A, Walsh, MS, Rombauts, L, Allan, JA, Horner, P & Huston, WM 2019, 'Evaluation of a PGP3 ELISA for surveillance of the burden of Chlamydia infection in women from Australia and Samoa', Pathogens and Disease, vol. 77, no. 3.
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ABSTRACT
Serological assays can be used to investigate the population burden of infection and potentially sequelae from Chlamydia. We investigated the PGP3 ELISA as a sero-epidemiological tool for infection or sub-fertility in Australian and Samoan women. The PGP3 ELISA absorbance levels were compared between groups of women with infertility, fertile, and current chlamydial infections. In the Australian groups, women with chlamydial tubal factor infertility had significantly higher absorbance levels in the PGP3 ELISA compared to fertile women (P < 0.0001), but not when compared to women with current chlamydial infection (P = 0.44). In the Samoan study, where the prevalence of chlamydial infections is much higher there were significant differences in the PGP3 ELISA absorbance levels between chlamydial sub-fertile women and fertile women (P = 0.003). There was no difference between chlamydial sub-fertile women and women with a current infection (P = 0.829). The results support that the PGP3 assay is effective for sero-epidemiological analysis of burden of infection, but not for evaluation of chlamydial pathological sequelae such as infertility.
McAlinden, KD, Deshpande, DA, Ghavami, S, Xenaki, D, Sohal, SS, Oliver, BG, Haghi, M & Sharma, P 2019, 'Autophagy Activation in Asthma Airways Remodeling', American Journal of Respiratory Cell and Molecular Biology, vol. 60, no. 5, pp. 541-553.
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Current asthma therapies fail to target airway remodeling which correlates with asthma severity driving disease progression that ultimately leads to loss of lung function. Macroautophagy (here after autophagy) is a fundamental cell recycling mechanism in all eukaryotic cells; emerging evidence suggests that it is dysregulated in asthma. We investigated the interrelationship between autophagy and airway remodeling and assessed preclinical efficacy of a known autophagy inhibitor in murine models of asthma. Human asthmatic and non-asthmatic lung tissues were histologically evaluated and were immuno-stained for key autophagy markers. The percent area of positive staining was quantified in the epithelium and airway smooth muscle (ASM) bundles using ImageJ software. Furthermore, autophagy inhibitor chloroquine (CQ) was tested (i.n.) in prophylactic (3-week) and treatment (5-week) models of allergic asthma in mice. Human asthmatic tissues showed greater tissue inflammation and demonstrated hallmark features of airway remodeling displaying thickened epithelium (p<0.001) and reticular basement membrane (p<0.0001), greater lamina propria depth (p<0.005), and increase in ASM bundles (p<0.001) with higher expression of Beclin1 (p<0.01) and ATG5 (p<0.05) along with reduced p62 (p<0.05) compared to non-asthmatic controls. Beclin1 expression was significantly higher in asthmatic epithelium and ciliated cells (p<0.05) suggesting potential role of ciliophagy in asthma. Murine asthma models demonstrated effective preclinical efficacy (reduced key features of allergic asthma: airway inflammation, AHR and airway remodeling) of autophagy inhibitor CQ. Our data demonstrates cell-context dependent, and selective activation of autophagy in structural cells in asthma. Further, this pathway can be effectively targeted to ameliorate airway remodeling in asthma.
McAllum, EJ & Hare, DJ 2019, 'From niche methods to necessary tools: The growing importance of analytical atomic spectrometry in metal imaging in neuroscience', Spectrochimica Acta Part B: Atomic Spectroscopy, vol. 156, pp. 20-32.
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© 2019 Visualizing the highly compartmentalized distribution of metals in the brain has grown from a handful of analytical method development laboratories to now being an integral part of contemporary neuroscience and medical research. The burgeoning interest in mapping metals in the brain has been spurred on by an increasing appreciation of the role minor and trace elements play in normal neural function, ageing, neuroinflammation, and as a potential causative factor in a range of neurological disorders. Advances in technology, development of versatile imaging protocols, and an array of data analysis resources have all contributed to the current status of quantitative metal imaging as an invaluable, and often envied tool in the modern neuroscience laboratory. Atomic mass spectrometry and emission spectroscopy methods cover a broad range of applications that span macro, micro, and nanoscale imaging. Most importantly, increasing awareness of the capabilities of metal imaging has gradually captured the attention of neuroscientists, resulting in a shift in focus from traditional method development and optimization to use as a routine analytical technique in broader studies of brain function and disease. We reflect on the history and growth of metal imaging within the neurosciences, discuss how it has contributed to recent advances in our understanding of the brain and neurological disorders, appraise the challenges and limitations that remain unaddressed, and speculate on the future roles metal imaging will have in neuroscience research over the next decade.
McCabe, MJ, Gauthier, M-EA, Chan, C-L, Thompson, TJ, De Sousa, SMC, Puttick, C, Grady, JP, Gayevskiy, V, Tao, J, Ying, K, Cipponi, A, Deng, N, Swarbrick, A, Thomas, ML, Lord, RV, Johns, AL, Kohonen-Corish, M, O’Toole, SA, Clark, J, Mueller, SA, Gupta, R, McCormack, AI, Dinger, ME, Cowley, MJ, Aghmesheh, M, Amor, D, Andrews, L, Antill, Y, Armitage, S, Arnold, L, Balleine, R, Bastick, P, Beesley, J, Beilby, J, Bennett, I, Blackburn, A, Bogwitz, M, Botes, L, Brennan, M, Brown, M, Buckley, M, Burgess, M, Burke, J, Butow, P, Caldon, L, Callen, D, Campbell, I, Chauhan, D, Chauhan, M, Chenevix-Trench, G, Christian, A, Clarke, C, Cohen, P, Colley, A, Crook, A, Cui, J, Culling, B, Cummings, M, Dawson, S-J, deFazio, A, Delatycki, M, Dickson, R, Dixon, J, Dobrovic, A, Dudding, T, Edkins, T, Edwards, S, Eisenbruch, M, Farshid, G, Fellows, A, Fenton, G, Field, M, Flanagan, J, Fong, P, Forrest, L, Fox, S, French, J, Friedlander, M, Gaff, C, Ortega, DG, Gattas, M, George, P, Giles, G, Gill, G, Greening, S, Haan, E, Harris, M, Hart, S, Hayward, N, Heiniger, L, Hopper, J, Hunt, C, James, P, Jenkins, M, Kefford, R, Kidd, A, Kirk, J, Koehler, J, Kollias, J, Lakhani, S, Lindeman, G, Lipton, L, Lobb, L, Mann, G, Marsh, D, McLachaln, SA, Meiser, B, Milne, R, Nightingale, S, O’Connell, S, O’Sullivan, S, Pachter, N, Patterson, B, Phillips, K, Pieper, E, Rickard, E, Robinson, B, Saleh, M, Salisbury, E, Sambrook, J, Saunders, C, Saunus, J, Scott, E, Scott, C, Scott, R, Sexton, A, Shelling, A, Simpson, P, Southey, M, Spurdle, A, Taylor, J, Thorne, H, Trainer, A, Tucker, K, Visvader, J, Walker, L, Williams, R, Winship, I & Young, M-A 2019, 'Development and validation of a targeted gene sequencing panel for application to disparate cancers', Scientific Reports, vol. 9, no. 1.
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AbstractNext generation sequencing has revolutionised genomic studies of cancer, having facilitated the development of precision oncology treatments based on a tumour’s molecular profile. We aimed to develop a targeted gene sequencing panel for application to disparate cancer types with particular focus on tumours of the head and neck, plus test for utility in liquid biopsy. The final panel designed through Roche/Nimblegen combined 451 cancer-associated genes (2.01 Mb target region). 136 patient DNA samples were collected for performance and application testing. Panel sensitivity and precision were measured using well-characterised DNA controls (n = 47), and specificity by Sanger sequencing of the Aryl Hydrocarbon Receptor Interacting Protein (AIP) gene in 89 patients. Assessment of liquid biopsy application employed a pool of synthetic circulating tumour DNA (ctDNA). Library preparation and sequencing were conducted on Illumina-based platforms prior to analysis with our accredited (ISO15189) bioinformatics pipeline. We achieved a mean coverage of 395x, with sensitivity and specificity of >99% and precision of >97%. Liquid biopsy revealed detection to 1.25% variant allele frequency. Application to head and neck tumours/cancers resulted in detection of mutations aligned to published databases. In conclusion, we have developed an analytically-validated panel for application to cancers of disparate types with utility in liquid biopsy.
McCambridge, AB, Zaslawski, C & Bradnam, LV 2019, 'Investigating the mechanisms of acupuncture on neural excitability in healthy adults', NeuroReport, vol. 30, no. 2, pp. 71-76.
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Acupuncture is gaining interest as a potential treatment modality for various neurological conditions. Yet, the underlying mechanisms and efficacy on brain function are not well understood. Therefore, this study investigated the previously proposed hypothesis that acupuncture suppresses motor cortex excitability using transcranial magnetic stimulation (TMS) in healthy adults. The study was randomised, sham-controlled, and double-blinded. Single and paired-pulse TMS was delivered before, during, immediately after, and 30 min after removal of the needle. Acupuncture to the right Hegu acupoint (LI-4) of the hand was delivered by an experienced acupuncturist using standardised manipulations. A disposable (0.22×30 mm, Hwato) needle was used for verum stimulation (penetrating) and a Park retractable needle for sham (nonpenetrating). The peak-to-peak amplitude of TMS-induced motor-evoked potentials was recorded from two intrinsic hand muscles. Needling sensations were quantified using the Massachusett's acupuncture sensation scale. Participant needling sensations were not different between verum or sham acupuncture (P>0.54). Corticomotor excitability, intracortical inhibition, and intracortical facilitation were not modulated by verum or sham acupuncture during, immediately after, or 30 min after, recorded from a local or distant hand muscle to the needling site (all P>0.075). Contrary to previous studies, manual acupuncture did not affect motor cortex excitability in healthy adults. Because of the increasing popularity of acupuncture therapy, further research using patient populations should be considered.
McCaughey, EJ, Butler, JE, McBain, RA, Boswell-Ruys, CL, Hudson, AL, Gandevia, SC & Lee, BB 2019, 'Abdominal Functional Electrical Stimulation to Augment Respiratory Function in Spinal Cord Injury', Topics in Spinal Cord Injury Rehabilitation, vol. 25, no. 2, pp. 105-111.
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Background: Functional electrical stimulation (FES) is the application of electrical pulses to a nerve to achieve a functional muscle contraction. Surface electrical stimulation of the nerves that innervate the abdominal muscles, termed abdominal FES, can cause the abdominal muscles to contract, even when paralysed after spinal cord injury. As the abdominal muscles are the major expiratory muscles, and commonly partially or completely paralysed in tetraplegia, abdominal FES offers a promising method of improving respiratory function for this patient group. Objective: The aim of the article is to provide readers with a better understanding of how abdominal FES can be used to improve the health of the spinal cord–injured population. Methods: A narrative review of the abdominal FES literature was performed. Results: Abdominal FES can achieve an immediate effective cough in patients with tetraplegia, while the repeated application over 6 weeks of abdominal FES can improve unassisted respiratory function. Ventilator duration and tracheostomy cannulation time can also be reduced with repeated abdominal FES. Conclusion: Abdominal FES is a noninvasive method to achieve functional improvements in cough and respiratory function in acute and chronically injured people with tetraplegia. Potential practical outcomes of this include reduced ventilation duration, assisted tracheostomy decannulation, and a reduction in respiratory complications. All of these outcomes can contribute to reduced morbidity and mortality, improved quality of life, and significant potential cost savings for local health care providers.
McCauley, JI, Winberg, PC, Meyer, BJ & Skropeta, D 2019, 'Corrigendum to “Effects of nutrients and processing on the nutritionally important metabolites of Ulva sp. (Chlorophyta)” [Algal Res. 35 (November 2018) 586–594]', Algal Research, vol. 40, pp. 101478-101478.
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© 2019 Elsevier B.V. The authors wish to make the following corrigendum. Venus Shell Systems (VSS) provided the Ulva sp. used in this study. They are listed under the author affiliations, as well as in the Methods Section 2.1 as having provided the samples. To further clarify the involvement of the company we wish to make the following changes to the Conflicts of interest section. The company Venus Shell Systems (VSS), listed in the author affiliations, provided the cultivated Ulva sp. used in this study, obtained using a proprietary culture system. The authors declare that there was no significant financial support that could have influenced the outcome of the project. The research is free of bias and was conducted ethically in accord with the University of Wollongong's policy on external research collaboration. The authors would like to apologise for any inconvenience caused.
McClements, L, Annett, S, Yakkundi, A, O’Rourke, M, Valentine, A, Moustafa, N, Alqudah, A, Simões, BM, Furlong, F, Short, A, McIntosh, SA, McCarthy, HO, Clarke, RB & Robson, T 2019, 'FKBPL and its peptide derivatives inhibit endocrine therapy resistant cancer stem cells and breast cancer metastasis by downregulating DLL4 and Notch4', BMC Cancer, vol. 19, no. 1.
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BACKGROUND:Optimising breast cancer treatment remains a challenge. Resistance to therapy is a major problem in both ER- and ER+ breast cancer. Tumour recurrence after chemotherapy and/or targeted therapy leads to more aggressive tumours with enhanced metastatic ability. Self-renewing cancer stem cells (CSCs) have been implicated in treatment resistance, recurrence and the development of metastatic disease. METHODS:In this study, we utilised in vitro, in vivo and ex vivo breast cancer models using ER+ MCF-7 and ER- MDA-MB-231 cells, as well as solid and metastatic breast cancer patient samples, to interrogate the effects of FKBPL and its peptide therapeutics on metastasis, endocrine therapy resistant CSCs and DLL4 and Notch4 expression. The effects of FKBPL overexpression or peptide treatment were assessed using a t-test or one-way ANOVA with Dunnett's multiple comparison test. RESULTS:We demonstrated that FKBPL overexpression or treatment with FKBPL-based therapeutics (AD-01, pre-clinical peptide /ALM201, clinical peptide) inhibit i) CSCs in both ER+ and ER- breast cancer, ii) cancer metastasis in a triple negative breast cancer metastasis model and iii) endocrine therapy resistant CSCs in ER+ breast cancer, via modulation of the DLL4 and Notch4 protein and/or mRNA expression. AD-01 was effective at reducing triple negative MDA-MB-231 breast cancer cell migration (n ≥ 3, p < 0.05) and invasion (n ≥ 3, p < 0.001) and this was translated in vivo where AD-01 inhibited breast cancer metastasis in MDA-MB-231-lucD3H1 in vivo model (p < 0.05). In ER+ MCF-7 cells and primary breast tumour samples, we demonstrated that ALM201 inhibits endocrine therapy resistant mammospheres, representative of CSC content (n ≥ 3, p < 0.05). Whilst an in vivo limiting dilution assay, using SCID mice, demonstrated that ALM201 alone or in combination with tamoxifen was very effective at delaying tumour recurrence by 12 (p < 0.05) or 21 days (p < 0.001), respectively, by reducing the number o...
McInnes, AS, Laczka, OF, Baker, KG, Larsson, ME, Robinson, CM, Clark, JS, Laiolo, L, Alvarez, M, Laverock, B, Kremer, CT, van Sebille, E & Doblin, MA 2019, 'Live cell analysis at sea reveals divergent thermal performance between photosynthetic ocean microbial eukaryote populations', The ISME Journal, vol. 13, no. 5, pp. 1374-1378.
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Experimentation at sea provides insight into which traits of ocean microbes are linked to performance in situ. Here we show distinct patterns in thermal tolerance of microbial phototrophs from adjacent water masses sampled in the south-west Pacific Ocean, determined using a fluorescent marker for reactive oxygen species (ROS). ROS content of pico-eukaryotes was assessed after 1, 5 and 25 h of incubation along a temperature gradient (15.6-32.1 °C). Pico-eukaryotes from the East Australian Current (EAC) had relatively constant ROS and showed greatest mortality after 25 h at 7 °C below ambient, whereas those from the Tasman Sea had elevated ROS in both warm and cool temperature extremes and greatest mortality at temperatures 6-10 °C above ambient, interpreted as the outcome of thermal stress. Tracking of water masses within an oceanographic circulation model showed populations had distinct thermal histories, with EAC pico-eukaryotes experiencing higher average temperatures for at least 1 week prior to sampling. While acclimatization and community assembly could both influence biological responses, this study clearly demonstrates that phenotypic divergence occurs along planktonic drift trajectories.
McLean, MW & Wand, MP 2019, 'Variational Message Passing for Elaborate Response Regression Models', Bayesian Analysis, vol. 14, no. 2, pp. 371-398.
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McNevin, D 2019, 'Response to: Biedermann & Hicks (2019), Commentary on “Dennis McNevin, Bayesian interpretation of discrete class characteristics, Forensic Science International, 292 (2018) 125–130”', Forensic Science International, vol. 298, pp. e1-e2.
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McNevin, D, Wright, K, Chaseling, J & Barash, M 2019, 'Commentary on: Bright et al. (2018) Internal validation of STRmix™ – a multi laboratory response to PCAST, Forensic Science International: Genetics, 34: 11–24', Forensic Science International: Genetics, vol. 41, pp. e14-e17.
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Medek, DE, Simunovic, M, Erbas, B, Katelaris, CH, Lampugnani, ER, Huete, A, Beggs, PJ & Davies, JM 2019, 'Enabling self-management of pollen allergies: a pre-season questionnaire evaluating the perceived benefit of providing local pollen information', Aerobiologia, vol. 35, no. 4, pp. 777-782.
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© 2019, Springer Nature B.V. The Australian AusPollen Partnership provides respiratory allergy patients with accurate, relevant and localised pollen information via smartphone Apps. This study aims to evaluate public perceptions of need and benefit of providing local pollen information. Individuals aged 18 years and older were contacted through AusPollen Smartphone Apps (Brisbane, Sydney, Canberra and Melbourne), Australian Society for Clinical Immunology and Allergy, Asthma Australia and social media. A pilot questionnaire was developed in consultation with partner organisations, including select questions drawn from the National Young People and Asthma Survey. The questionnaire consisted of four sections: participant demographics, allergic rhinitis and asthma symptoms, symptom management and App utility. One hundred and twenty-seven people completed the survey, of whom 53% had access to local pollen information. Most (97%) participants without access to local pollen information indicated that they wanted such a service. Pollen information was most commonly perceived by participants to be useful for prevention and avoidance as well as preparation and planning. This preliminary study identified a public demand for local pollen information. Users identified practical ways in which pollen information assisted them. Publicised pollen concentrations and forecasts have the potential to improve awareness of allergy triggers and empower patient self-management, reducing symptoms and burden of disease.
Mehta, M, Deeksha, Sharma, N, Vyas, M, Khurana, N, Maurya, PK, Singh, H, Andreoli de Jesus, TP, Dureja, H, Chellappan, DK, Gupta, G, Wadhwa, R, Collet, T, Hansbro, PM, Dua, K & Satija, S 2019, 'Interactions with the macrophages: An emerging targeted approach using novel drug delivery systems in respiratory diseases', Chemico-Biological Interactions, vol. 304, pp. 10-19.
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Macrophages are considered as the most flexible cells of the hematopoietic system that are distributed in the tissues to act against pathogens and foreign particles. Macrophages are essential in maintaining homeostatic tissue processes, repair and immunity. Also, play important role in cytokine secretion and signal transduction of the infection so as to develop acquired immunity. Accounting to their involvement in pathogenesis, macrophages present a therapeutic target for the treatment of inflammatory respiratory diseases. This review focuses on novel drug delivery systems (NDDS) including nanoparticles, liposomes, dendrimers, microspheres etc that can target alveolar macrophage associated with inflammation, intracellular infection and lung cancer. The physiochemical properties and functional moieties of the NDDS attributes to enhanced macrophage targeting and uptake. The NDDS are promising for sustained drug delivery, reduced therapeutic dose, improved patient compliance and reduce drug toxicity. Further, the review also discuss about modified NDDS for specificity to the target and molecular targeting via anti-microbial peptides, kinases, NRF-2 and phosphodiesterase.
Mehta, M, Deeksha, Tewari, D, Gupta, G, Awasthi, R, Singh, H, Pandey, P, Chellappan, DK, Wadhwa, R, Collet, T, Hansbro, PM, Kumar, SR, Thangavelu, L, Negi, P, Dua, K & Satija, S 2019, 'Oligonucleotide therapy: An emerging focus area for drug delivery in chronic inflammatory respiratory diseases', Chemico-Biological Interactions, vol. 308, pp. 206-215.
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Oligonucleotide-based therapies are advanced novel interventions used in the management of various respiratory diseases such as asthma and Chronic Obstructive Pulmonary Disease (COPD). These agents primarily act by gene silencing or RNA interference. Better methodologies and techniques are the need of the hour that can deliver these agents to tissues and cells in a target specific manner by which their maximum potential can be reached in the management of chronic inflammatory diseases. Nanoparticles play an important role in the target-specific delivery of drugs. In addition, oligonucleotides also are extensively used for gene transfer in the form of polymeric, liposomal and inorganic carrier materials. Therefore, the current review focuses on various novel dosage forms like nanoparticles, liposomes that can be used efficiently for the delivery of various oligonucleotides such as siRNA and miRNA. We also discuss the future perspectives and targets for oligonucleotides in the management of respiratory diseases.
Mendelson, N, Xu, Z-Q, Tran, TT, Kianinia, M, Scott, J, Bradac, C, Aharonovich, I & Toth, M 2019, 'Engineering and Tuning of Quantum Emitters in Few-Layer Hexagonal Boron Nitride', ACS Nano, vol. 13, no. 3, pp. 3132-3140.
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Quantum technologies require robust and photostable single photon emitters (SPEs). Hexagonal boron nitride (hBN) has recently emerged as a promising candidate to host bright and optically stable SPEs operating at room temperature. However, the emission wavelength of the fluorescent defects in hBN has, to date, been shown to be uncontrolled, with a widespread of zero phonon line (ZPL) energies spanning a broad spectral range (hundreds of nanometers), which hinders the potential development of hBN-based devices and applications. Here we demonstrate chemical vapor deposition growth of large-area, few-layer hBN films that host large quantities of SPEs: ∼100-200 per 10 × 10 μm2. More than 85% of the emitters have a ZPL at (580 ± 10) nm, a distribution that is an order of magnitude narrower than reported previously. Furthermore, we demonstrate tuning of the ZPL wavelength using ionic liquid devices over a spectral range of up to 15 nm-the largest obtained to date from any solid-state SPE. The fabricated devices illustrate the potential of hBN for the development of hybrid quantum nanophotonic and optoelectronic devices based on two-dimensional materials.
Menictas, M, Nolan, TH, Simpson, DG & Wand, MP 2019, 'Streamlined Variational Inference for Higher Level Group-Specific Curve Models', Statistical Modelling: An International Journal.
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A two-level group-specific curve model is such that the mean response of each
member of a group is a separate smooth function of a predictor of interest. The
three-level extension is such that one grouping variable is nested within
another one, and higher level extensions are analogous. Streamlined variational
inference for higher level group-specific curve models is a challenging
problem. We confront it by systematically working through two-level and then
three-level cases and making use of the higher level sparse matrix
infrastructure laid down in Nolan and Wand (2018). A motivation is analysis of
data from ultrasound technology for which three-level group-specific curve
models are appropriate. Whilst extension to the number of levels exceeding
three is not covered explicitly, the pattern established by our systematic
approach sheds light on what is required for even higher level group-specific
curve models.
Meunier, V, Bonnet, S, Pernice, M, Benavides, M, Lorrain, A, Grosso, O, Lambert, C & Houlbrèque, F 2019, 'Bleaching forces coral’s heterotrophy on diazotrophs and Synechococcus', The ISME Journal, vol. 13, no. 11, pp. 2882-2886.
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Meyer, S, Clarke, C, dos Santos, RO, Bishop, D, Krieger, MA & Blanes, L 2019, 'Developing self-generated calibration curves using a capillary-driven wax-polyester lab on a chip device and thermal gates', Microchemical Journal, vol. 146, pp. 708-712.
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© 2019 Elsevier B.V. Here we describe the development of a capillary-driven wax-polyester lab on a chip device and the concept of thermal gates to create self-generated calibration curves. The devices were fabricated by printing a wax pattern on a polyester film, and laminating two mirrored layers together. Victoria Blue R and a diluent of methanol/water (1:1) were placed in separate wells, and capillary forces drove the reagents through three additional mixing wells, resulting in respective dilutions of 50%, 25% and 12.5% of the original dye concentration (100%). A photo was taken after the capillary action ceased, and the color brightness of the four different concentrations was used for the creation of a calibration curve, resulting in a coefficient of determination of 0.99. The chip was readily adapted to include an additional channel to perform chemical reactions with KOH to increase the available detection options. The chip designs required up to three reagents to be simultaneously added, with any discrepancies in the synchronization of reagent addition leading to irreproducible results. To overcome these synchronization discrepancies, thermal gates were added by printing 0.15 mm wax barriers across the channel inlets to prevent liquid movement. These gates were simultaneously opened to allow the solutions to flow by applying heat, controlled by an Arduino-based instrument controller, through bent copper filaments positioned adjacent to the barriers for 380 milliseconds.
Mi, C, Zhou, J, Wang, F & Jin, D 2019, 'Thermally enhanced NIR–NIR anti-Stokes emission in rare earth doped nanocrystals', Nanoscale, vol. 11, no. 26, pp. 12547-12552.
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Surface phonons enhancing the one-photon anti-Stokes fluorescence has been demonstrated in rare earth doped nanocrystals.
Mi, C, Zhou, J, Wang, F, Lin, G & Jin, D 2019, 'Ultrasensitive Ratiometric Nanothermometer with Large Dynamic Range and Photostability', Chemistry of Materials, vol. 31, no. 22, pp. 9480-9487.
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Copyright © 2019 American Chemical Society. Thermally responsive fluorescent nanoparticles can be constructed to allow robust, rapid, and noninvasive temperature measurements. Furthermore, due to their tiny size, they can be used to detect temperature changes at the nanoscale. In this way, such sensors are ideally suited to emerging applications including intracellular temperature sensing and microelectronics failure diagnostics. Despite their potential, current nanothermometers still suffer from limited sensitivity, dynamic range, and stability. By introducing thermal enhanced anti-Stokes emission from a pair of lanthanide ions, ytterbium and neodymium, we show an increase of more than 1 order of magnitude in both the sensitivity and the dynamic range when compared to conventional ytterbium and erbium-codoped nanothermometers. Here, we report heterogeneous temperature-responsive nanoparticles with a new record of sensitivity (9.6%/K at room temperature and above 2.3%/K at elevated temperatures up to 413 K) that can be used for ratiometric thermometry. The heterogeneous nanostructure design shows that the thermal responses can be fine-tuned by the controlled growth of nanoparticles. The stability of the ultrasensitive nanothermometers has enabled long-term noncontact monitoring of local heat dissipation of a microelectronic device.
Mohd Yusop, AY, Xiao, L & Fu, S 2019, 'Data on the optimisation and validation of a liquid chromatography-high-resolution mass spectrometry (LC-HRMS) to establish the presence of phosphodiesterase 5 (PDE5) inhibitors in instant coffee premixes', Data in Brief, vol. 25, pp. 104234-104234.
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This paper presents the data on the optimisation and validation of a liquid chromatography-high-resolution mass spectrometry (LC-HRMS) to establish the presence of phosphodiesterase 5 (PDE5) inhibitors and their analogues as adulterants in instant coffee premixes. The method development data covered chromatographic optimisation for better analyte separation and isomeric resolution, mass spectrometry optimisation for high sensitivity and sample preparation optimisation for high extraction recovery (RE) and low matrix effect (ME). The validation data covered specificity, linearity, range, accuracy, limit of detection, limit of quantification, precisions, ME, and RE. The optimisation and validation data presented here is related to the article: "Determination of phosphodiesterase 5 (PDE5) inhibitors in instant coffee premixes using liquid chromatography-high-resolution mass spectrometry (LC-HRMS)" Mohd Yusop et al., 2019.
Mohd Yusop, AY, Xiao, L & Fu, S 2019, 'Determination of phosphodiesterase 5 (PDE5) inhibitors in instant coffee premixes using liquid chromatography-high-resolution mass spectrometry (LC-HRMS)', Talanta, vol. 204, pp. 36-43.
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As a widely consumed beverage, coffee tends to be a target for intentional adulteration. This study describes the application of modified quick, easy, cheap, effective, rugged, and safe (QuEChERS) coupled to liquid chromatography-high-resolution mass spectrometry (LC-HRMS) for simultaneous screening, identification, and quantification of undeclared phosphodiesterase 5 (PDE5) inhibitors in instant coffee premixes (ICPs). The mass spectrometer was operated in auto MS/MS acquisition for simultaneous MS and MS/MS experiments. Qualitative establishments from the suspected-target screening and targeted identification processes led to an unambiguous analyte assignment from the protonated molecule ([M+H]+) precursor ion which is subsequently used for quantification of 23 targeted PDE5 inhibitors. The analytical method validation covered specificity, linearity, range, accuracy, limit of detection (LOD), limit of quantification (LOQ), precisions, matrix effect (ME), and extraction recovery (RE). The specificity was established using the optimised chromatographic separation as well as the distinguishable [M+H]+ precursor ion. The linearity of each target analyte was demonstrated with a coefficient of determination (r2) of >0.9960 over the expected range of sample concentrations. The accuracy ranged from 88.1%–119.3% with LOD and LOQ of <70 ng/mL and 80 ng/mL, respectively. Excellent precisions were established within 0.4%–9.1% of the relative standard deviation. An insignificant ME within −5.2% to +8.7% was achieved using three different strategies of chromatography, sample extraction, and sample dilution. The RE was good for all target analytes within 84.7%–123.5% except for N-desethylacetildenafil at low (53.8%) and medium (65.1%) quality control levels. The method was successfully applied to 25 samples of ICPs where 17 of them were found to be adulterated with PDE5 inhibitors and their analogues. Further quantification revealed the total amount of these adulterants range...
Monahan, LG, DeMaere, MZ, Cummins, ML, Djordjevic, SP, Roy Chowdhury, P & Darling, AE 2019, 'High contiguity genome sequence of a multidrug-resistant hospital isolate of Enterobacter hormaechei', Gut Pathogens, vol. 11, no. 1.
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Background:Enterobacter hormaechei is an important emerging pathogen and a key member of the highly diverse Enterobacter cloacae complex. E. hormaechei strains can persist and spread in nosocomial environments, and often exhibit resistance to multiple clinically important antibiotics. However, the genomic regions that harbour resistance determinants are typically highly repetitive and impossible to resolve with standard short-read sequencing technologies. Results:Here we used both short- and long-read methods to sequence the genome of a multidrug-resistant hospital isolate (C15117), which we identified as E. hormaechei. Hybrid assembly generated a complete circular chromosome of 4,739,272 bp and a fully resolved plasmid of 339,920 bp containing several antibiotic resistance genes. The strain also harboured a 34,857 bp repeat encoding copper resistance, which was present in both the chromosome and plasmid. Long reads that unambiguously spanned this repeat were required to resolve the chromosome and plasmid into separate replicons. Conclusion:This study provides important insights into the evolution and potential spread of antimicrobial resistance in a nosocomial E. hormaechei strain. More broadly, it further exemplifies the power of long-read sequencing technologies, particularly the Oxford Nanopore platform, for the characterisation of bacteria with complex resistance loci and large repeat elements.
Monterroso, B, Zorrilla, S, Sobrinos-Sanguino, M, Robles-Ramos, MÁ, Alfonso, C, Söderström, B, Meiresonne, NY, Verheul, J, den Blaauwen, T & Rivas, G 2019, 'The Bacterial DNA Binding Protein MatP Involved in Linking the Nucleoid Terminal Domain to the Divisome at Midcell Interacts with Lipid Membranes', mBio, vol. 10, no. 3.
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The division of an
E. coli
cell into two daughter cells with equal genomic information and similar size requires duplication and segregation of the chromosome and subsequent scission of the envelope by a protein ring, the Z-ring. MatP is a DNA binding protein that contributes both to the positioning of the Z-ring at midcell and the temporal control of nucleoid segregation. Our integrated
in vivo
and
in vitro
analysis provides evidence that MatP can interact with lipid membranes reproducing the phospholipid mixture in the
E. coli
inner membrane, without concomitant recruitment of the short DNA sequences specifically targeted by MatP. This observation strongly suggests that the membrane may play a role in the regulation of the function and localization of MatP, which could be relevant for the coordination of the two fundamental processes in which this protein participates, nucleoid segregation and cell division.
Moodley, YP, Corte, TJ, Oliver, BG, Glaspole, IN, Livk, A, Ito, J, Peters, K, Lipscombe, R, Casey, T & Tan, DBA 2019, 'Analysis by proteomics reveals unique circulatory proteins in idiopathic pulmonary fibrosis', Respirology, vol. 24, no. 11, pp. 1111-1114.
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Moore, LR, Huang, T, Ostrowski, M, Mazard, S, Kumar, SS, Gamage, HKAH, Brown, MV, Messer, LF, Seymour, JR & Paulsen, IT 2019, 'Unicellular Cyanobacteria Are Important Components of Phytoplankton Communities in Australia’s Northern Oceanic Ecoregions', Frontiers in Microbiology, vol. 9, no. Jan.
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The tropical marine environments of northern Australia encompasses a diverse range of geomorphological and oceanographic conditions and high levels of productivity and nitrogen fixation. However, efforts to characterize phytoplankton assemblages in these waters have been restricted to studies using microscopic and pigment analyses, leading to the current consensus that this region is dominated by large diatoms, dinoflagellates, and the marine cyanobacterium Trichodesmium. During an oceanographic transect from the Arafura Sea through the Torres Strait to the Coral Sea, we characterized prokaryotic and eukaryotic phytoplankton communities in surface waters using a combination of flow cytometry and Illumina based 16S and 18S ribosomal RNA amplicon sequencing. Similar to observations in other marine regions around Australian, phytoplankton assemblages throughout this entire region were rich in unicellular picocyanobacterial primary producers while picoeukaryotic phytoplankton formed a consistent, though smaller proportion of the photosynthetic biomass. Major taxonomic groups displayed distinct biogeographic patterns linked to oceanographic and nutrient conditions. Unicellular picocyanobacteria dominated in both flow cytometric abundance and carbon biomass, with members of the Synechococcus genus dominating in the shallower Arafura Sea and Torres Strait where chlorophyll a was relatively higher (averaging 0.4 ± 0.2 mg m-3), and Prochlorococcus dominating in the oligotrophic Coral Sea where chlorophyll a averaged 0.13 ± 0.07 mg m-3. Consistent with previous microscopic and pigment-based observations, we found from sequence analysis that a variety of diatoms (Bacillariophyceae) exhibited high relative abundance in the Arafura Sea and Torres Strait, while dinoflagellates (Dinophyceae) and prymnesiophytes (Prymnesiophyceae) were more abundant in the Coral Sea. Ordination analysis identified temperature, nutrient concentrations and water depth as key drivers of the region'...
Morelato, M, Franscella, D, Esseiva, P & Broséus, J 2019, 'When does the cutting of cocaine and heroin occur? The first large-scale study based on the chemical analysis of cocaine and heroin seizures in Switzerland', International Journal of Drug Policy, vol. 73, pp. 7-15.
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BACKGROUND:Illicit drug profiling can provide knowledge about illicit drug markets, informing on the level of distribution and its evolution in space and time. Illicit drug profiling is usually limited to impurities originally present in the illicit drug (e.g. alkaloids, co-extracted compounds or by-products). However, the benefit of a comprehensive analysis of cutting agents in drug seizures for law enforcement agencies, intelligence and health policy has not been thoroughly investigated in the literature and is the focus of this research. AIM:This research aims at assessing when and how cutting (i.e. adulteration and dilution) occurs in the supply chain by analysing cocaine and heroin seizures made between 2006 and 2015 in Switzerland. METHODS:Cocaine and heroin seizures made along the supply chain by law enforcement agencies in the Western region of Switzerland were investigated for adulteration and dilution. A total number of 7841 cocaine and 3476 heroin specimens coming from 1341 and 721 seizures, respectively, were analysed. RESULTS:The results show that, for both illicit drugs, adulteration and/or dilution occur before arrival into Switzerland as well as in Switzerland. While cocaine is adulterated and diluted, heroin is only adulterated. Interestingly, the same mixture of adulterants (i.e. caffeine-paracetamol) is used to cut heroin at each step in the supply chain. CONCLUSION:Gaining knowledge about adulteration and dilution at different stages in the supply chain enhances our understanding of drug markets. It also highlights differences along the supply chain and in the distribution of both drugs in Switzerland.
Moret, S, Lee, PLT, de la Hunty, M, Spindler, X, Lennard, C & Roux, C 2019, 'Single metal deposition versus physical developer: A comparison between two advanced fingermark detection techniques', Forensic Science International, vol. 294, pp. 103-112.
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Single metal deposition (SMD II) is a fingermark detection technique based on the use of colloidal gold. The technique has been simplified and optimised over the years to become more reliable, sensitive and user-friendly. Physical developer (PD) is a well-established detection method based on silver deposition from a redox solution. This study presents an extensive comparison of SMD II against PD for fingermark detection on porous substrates. The two techniques were compared as (i) standalone methods, (ii) in sequence after the application of routine amino acids reagents (1,2-indanedione/zinc followed by ninhydrin), and (iii) after the substrates have been wet. More than 1000 fingermark specimens were processed. Overall, the performance of SMD II was judged to be inferior to that of PD; therefore, SMD II cannot be recommended as a valid replacement for fingermark detection on porous substrates. Indanedione/zinc and ninhydrin application negatively impacts on SMD II performance and the technique gave inconsistent results across the selected range of porous substrates. Moreover, the detected fingermarks lacked contrast making their visualisation difficult. However, even if PD remains the technique of choice, SMD II showed significant potential. It proved to be less affected by donor variability and it can be applied on both porous and non-porous substrates. It did not lead to uncontrolled background staining that commonly occurs with PD. If contrast and consistency issues can be addressed in future research, SMD II may become a viable alternative to PD.
Mostyn, SN, Rawling, T, Mohammadi, S, Shimmon, S, Frangos, ZJ, Sarker, S, Yousuf, A, Vetter, I, Ryan, RM, Christie, MJ & Vandenberg, RJ 2019, 'Development of an N-Acyl Amino Acid That Selectively Inhibits the Glycine Transporter 2 To Produce Analgesia in a Rat Model of Chronic Pain', Journal of Medicinal Chemistry, vol. 62, no. 5, pp. 2466-2484.
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Inhibitors that target the glycine transporter 2, GlyT2, show promise as analgesics, but may be limited by their toxicity through complete or irreversible binding. Acyl-glycine inhibitors, however, are selective for GlyT2 and have been shown to provide analgesia in animal models of pain with minimal side effects, but are comparatively weak GlyT2 inhibitors. Here, we modify the simple acyl-glycine by synthesizing lipid analogues with a range of amino acid head groups in both l- and d-configurations, to produce nanomolar affinity, selective GlyT2 inhibitors. The potent inhibitor oleoyl-d-lysine (33) is also resistant to degradation in both human and rat plasma and liver microsomes, and is rapidly absorbed following an intraperitoneal injection to rats and readily crosses the blood-brain barrier. We demonstrate that 33 provides greater analgesia at lower doses, and does not possess the severe side effects of the very slowly reversible GlyT2 inhibitor, ORG25543 (2).
Mostyn, SN, Wilson, KA, Schumann-Gillett, A, Frangos, ZJ, Shimmon, S, Rawling, T, Ryan, RM, O'Mara, ML & Vandenberg, RJ 2019, 'Identification of an allosteric binding site on the human glycine transporter, GlyT2, for bioactive lipid analgesics', eLife, vol. 8.
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The treatment of chronic pain is poorly managed by current analgesics, and there is a need for new classes of drugs. We recently developed a series of bioactive lipids that inhibit the human glycine transporter GlyT2 (SLC6A5) and provide analgesia in animal models of pain. Here, we have used functional analysis of mutant transporters combined with molecular dynamics simulations of lipid-transporter interactions to understand how these bioactive lipids interact with GlyT2. This study identifies a novel extracellular allosteric modulator site formed by a crevice between transmembrane domains 5, 7, and 8, and extracellular loop 4 of GlyT2. Knowledge of this site could be exploited further in the development of drugs to treat pain, and to identify other allosteric modulators of the SLC6 family of transporters.
Mote, S, Schönberg, CHL, Samaai, T, Gupta, V & Ingole, B 2019, 'A new clionaid sponge infests live corals on the west coast of India (Porifera, Demospongiae, Clionaida)', Systematics and Biodiversity, vol. 17, no. 2, pp. 190-206.
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Mowe, MAD, Song, Y, Sim, DZH, Lu, J, Mitrovic, SM, Tan, HTW & Yeo, DCJ 2019, 'Comparative study of six emergent macrophyte species for controlling cyanobacterial blooms in a tropical reservoir', Ecological Engineering, vol. 129, pp. 11-21.
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© 2019 Elsevier B.V. Interactions between macrophytes and phytoplankton have been studied extensively in temperate water bodies, but far less attention has been paid to those for emergent macrophytes in the tropics. We investigated the effects of six emergent macrophyte species (Brachiaria mutica, Ipomoea aquatica, Sphagneticola trilobata, Ludwigia adscendens, Pandanus amaryllifolius and Persicaria barbata) on the phytoplankton community of a tropical reservoir using ex situ experiments with multiple planting densities (Treatment 1: 0.108, Treatment 2: 0.24, Treatment 3: 0.40, Treatment 4: 0.58 g dry weight L −1 ) in 100-L mesocosms. Chlorophyll a (as a proxy of total phytoplankton biomass) and phytoplankton community structure were examined. The initial phytoplankton community (average chlorophyll a: 20.36 ± 0.69 µg L −1 ) was dominated by cyanobacteria: Planktolyngybya, Pseudanabaena and Cylindrospermopsis (average relative biovolume 0.68 ± 0.03). Over four weeks, L. adscendens (Treatments 3 and 4) and P. barbata (Treatments 2 to 4) significantly reduced chlorophyll a concentrations by 3.29–6.69 µg L −1 compared to the controls. Comparing species effects over four weeks for Treatment 4, P. barbata significantly lowered chlorophyll a concentrations compared to I. aquatica while there were no significant differences between all other species. All treatments of L. adscendens and P. barbata significantly reduced the relative biovolume of cyanobacteria in the phytoplankton communities by 0.19–0.39 compared to the controls. The highest-density treatments of all six macrophyte species led to significant shifts in the phytoplankton community structure by reducing the relative abundance of filamentous cyanobacteria (Planktolyngbya, Pseudanabaena) and/or increasing the relative abundance of cryptomonads (Chroomonas, Rhodomonas). This study shows the potential of emergent macrophyte species, especially L. adscendens and P. barbata, to reduce total phytoplankton biomass a...
Müller, S, Zavřel, T & Červený, J 2019, 'Towards a quantitative assessment of inorganic carbon cycling in photosynthetic microorganisms', Engineering in Life Sciences, vol. 19, no. 12, pp. 955-967.
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AbstractPhotosynthetic organisms developed various strategies to mitigate high light stress. For instance, aquatic organisms are able to spend excessive energy by exchanging dissolved CO2 (dCO2) and bicarbonate () with the environment. Simultaneous uptake and excretion of the two carbon species is referred to as inorganic carbon cycling. Often, inorganic carbon cycling is indicated by displacements of the extracellular dCO2 signal from the equilibrium value after changing the light conditions. In this work, we additionally use (i) the extracellular pH signal, which requires non‐ or weakly‐buffered medium, and (ii) a dynamic model of carbonate chemistry in the aquatic environment to detect and quantitatively describe inorganic carbon cycling. Based on simulations and experiments in precisely controlled photobioreactors, we show that the magnitude of the observed dCO2 displacement crucially depends on extracellular pH level and buffer concentration. Moreover, we find that the dCO2 displacement can also be caused by simultaneous uptake of both dCO2 and (no inorganic carbon cycling). In a next step, the dynamic model of carbonate chemistry allows for a quantitative assessment of cellular dCO2, , and H+ exchange rates from the measured dCO
Murray, M, Gillani, TB, Rawling, T & Nair, PC 2019, 'Inhibition of Hepatic CYP2D6 by the Active N-Oxide Metabolite of Sorafenib', The AAPS Journal, vol. 21, no. 6.
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The multikinase inhibitor sorafenib (SOR) is used to treat patients with hepatocellular and renal carcinomas. SOR undergoes CYP-mediated biotransformation to a pharmacologically active N-oxide metabolite (SNO) that has been shown to accumulate to varying extents in individuals. Kinase inhibitors like SOR are frequently coadministered with a range of other drugs to improve the efficacy of anticancer drug therapy and to treat comorbidities. Recent evidence has suggested that SNO is more effective than SOR as an inhibitor of CYP3A4-mediated midazolam 1'-hydroxylation. CYP2D6 is also reportedly inhibited by SOR. The present study assessed the possibility that SNO might contribute to CYP2D6 inhibition. The inhibition kinetics of CYP2D6-mediated dextromethorphan O-demethylation were analyzed in human hepatic microsomes, with SNO found to be ~ 19-fold more active than SOR (Kis 1.8 ± 0.3 μM and 34 ± 11 μM, respectively). Molecular docking studies of SOR and SNO were undertaken using multiple crystal structures of CYP2D6. Both molecules mediated interactions with key amino acid residues in putative substrate recognition sites of CYP2D6. However, a larger number of H-bonding interactions was noted between the N-oxide moiety of SNO and active site residues that account for its greater inhibition potency. These findings suggest that SNO has the potential to contribute to pharmacokinetic interactions involving SOR, perhaps in those individuals in whom SNO accumulates.
Murray, SA, Ruvindy, R, Kohli, GS, Anderson, DM & Brosnahan, ML 2019, 'Evaluation of sxtA and rDNA qPCR assays through monitoring of an inshore bloom of Alexandrium catenella Group 1', Scientific Reports, vol. 9, no. 1.
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AbstractAlexandrium catenella (formerly A. tamarense Group 1, or A. fundyense) is the leading cause of Paralytic Shellfish Poisoning in North and South America, Europe, Africa, Australia and Asia. The quantification of A.catenella via sxtA, a gene involved in Paralytic Shellfish Toxin synthesis, may be a promising approach, but has not been evaluated in situ on blooms of A. catenella, in which cell abundances may vary from not detectable to in the order of 106 cells L−1. In this study, we compared sxtA assay performance to a qPCR assay targeted to a species-specific region of ribosomal DNA (rDNA) and an established fluorescent in situ hybridization (FISH) microscopy method. Passing-Bablok regression analyses revealed the sxtA assay to overestimate abundances when <5 cell equivalents A. catenella DNA were analysed, but otherwise was closer to microscopy estimates than the rDNA assay, which overestimated abundance across the full range of concentrations analysed, indicative of a copy number difference between the bloom population and a culture used for assay calibration a priori. In contrast, the sxtA assay performed more consistently, indicating less copy number variation. The sxtA assay was generally reliable, fast and effective in quantifying A. catenella and was predictive of PST contamination of shellfish.
Nader, CP, Cidem, A, Verrills, NM & Ammit, AJ 2019, 'Protein phosphatase 2A (PP2A): a key phosphatase in the progression of chronic obstructive pulmonary disease (COPD) to lung cancer', Respiratory Research, vol. 20, no. 1.
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AbstractLung cancer (LC) has the highest relative risk of development as a comorbidity of chronic obstructive pulmonary disease (COPD). The molecular mechanisms that mediate chronic inflammation and lung function impairment in COPD have been identified in LC. This suggests the two diseases are more linked than once thought. Emerging data in relation to a key phosphatase, protein phosphatase 2A (PP2A), and its regulatory role in inflammatory and tumour suppression in both disease settings suggests that it may be critical in the progression of COPD to LC. In this review, we uncover the importance of the functional and active PP2A holoenzyme in the context of both diseases. We describe PP2A inactivation via direct and indirect means and explore the actions of two key PP2A endogenous inhibitors, cancerous inhibitor of PP2A (CIP2A) and inhibitor 2 of PP2A (SET), and the role they play in COPD and LC. We explain how dysregulation of PP2A in COPD creates a favourable inflammatory micro-environment and promotes the initiation and progression of tumour pathogenesis. Finally, we highlight PP2A as a druggable target in the treatment of COPD and LC and demonstrate the potential of PP2A re-activation as a strategy to halt COPD disease progression to LC. Although further studies are required to elucidate if PP2A activity in COPD is a causal link for LC progression, studies focused on the potential of PP2A reactivating agents to reduce the risk of LC formation in COPD patients will be pivotal in improving clinical outcomes for both COPD and LC patients in the future.
Nair, PM, Starkey, MR, Haw, TJ, Liu, G, Collison, AM, Mattes, J, Wark, PA, Morris, JC, Verrills, NM, Clark, AR, Ammit, AJ & Hansbro, PM 2019, 'Enhancing tristetraprolin activity reduces the severity of cigarette smoke‐induced experimental chronic obstructive pulmonary disease', Clinical & Translational Immunology, vol. 8, no. 10.
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AbstractObjectiveChronic obstructive pulmonary disease (COPD) is a progressive disease that causes significant mortality and morbidity worldwide and is primarily caused by the inhalation of cigarette smoke (CS). Lack of effective treatments for COPD means there is an urgent need to identify new therapeutic strategies for the underlying mechanisms of pathogenesis. Tristetraprolin (TTP) encoded by the Zfp36 gene is an anti‐inflammatory protein that induces mRNA decay, especially of transcripts encoding inflammatory cytokines, including those implicated in COPD.MethodsHere, we identify a novel protective role for TTP in CS‐induced experimental COPD using Zfp36aa/aa mice, a genetically modified mouse strain in which endogenous TTP cannot be phosphorylated, rendering it constitutively active as an mRNA‐destabilising factor. TTP wild‐type (Zfp36+/+) and Zfp36aa/aa active C57BL/6J mice were exposed to CS for four days or eight weeks, and the impact on acute inflammatory responses or chronic features of COPD, respectively, was assessed.ResultsAfter four days of CS exposure, Zfp36aa/aa mice had reduced numbers of airway neutrophils and lymphocytes and mRNA expression levels of cytokines compared to wild‐type controls. After eight weeks, Zfp36aa/aa mice had reduced pulmonary inflammation, airway remodelling and emphysema‐like alveolar enlargement, and lung function was improved. We then used pharmacological treatments in vivo (protein phosphatase 2A activator, AAL(S), and t...
Nascimento, FS, Barta, JR, Whale, J, Hofstetter, JN, Casillas, S, Barratt, J, Talundzic, E, Arrowood, MJ & Qvarnstrom, Y 2019, 'Mitochondrial Junction Region as Genotyping Marker for Cyclospora cayetanensis', Emerging Infectious Diseases, vol. 25, no. 7, pp. 1314-1319.
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Cyclosporiasis is an infection caused by Cyclospora cayetanensis, which is acquired by consumption of contaminated fresh food or water. In the United States, cases of cyclosporiasis are often associated with foodborne outbreaks linked to imported fresh produce or travel to disease-endemic countries. Epidemiologic investigation has been the primary method for linking outbreak cases. A molecular typing marker that can identify genetically related samples would be helpful in tracking outbreaks. We evaluated the mitochondrial junction region as a potential genotyping marker. We tested stool samples from 134 laboratory-confirmed cases in the United States by using PCR and Sanger sequencing. All but 2 samples were successfully typed and divided into 14 sequence types. Typing results were identical among samples within each epidemiologically defined case cluster for 7 of 10 clusters. These findings suggest that this marker can distinguish between distinct case clusters and might be helpful during cyclosporiasis outbreak investigations.
Naser, IB, Hoque, MM, Faruque, SN, Kamruzzaman, M, Yamasaki, S & Faruque, SM 2019, 'Vibrio cholerae strains with inactivated cqsS gene overproduce autoinducer-2 which enhances resuscitation of dormant environmental V. cholerae', PLOS ONE, vol. 14, no. 10, pp. e0223226-e0223226.
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BACKGROUND:Toxigenic Vibrio cholerae resides in aquatic reservoirs of cholera-endemic areas mostly in a dormant form known as conditionally viable environmental cells (CVEC) in which the bacteria remain embedded in an exopolysaccharide matrix, and fail to grow in routine bacteriological culture. The CVEC can be resuscitated by supplementing culture media with either of two autoinducers CAI-1 and AI-2, which are signal molecules controlling quorum sensing, a regulatory network of bacterial gene expression dependent on cell density. This study investigated possible existence of variant strains that overproduce AIs, sufficient to resuscitate CVEC in environmental waters. METHODS:Environmental V. cholerae isolates and Tn insertion mutants of a V. cholerae strain C6706 were screened for production of AIs using bioluminescent reporter strains. Relevant mutations in environmental strains which overproduced AI-2 were characterized by nucleotide sequencing and genetic complementation studies. Effect of AIs produced in culture supernatants of relevant strains on reactivation of CVEC in water was determined by resuscitation assays. RESULTS:Two of 54 environmental V. cholerae isolates were found to overproduce AI-2. Screening of a Tn-insertion library of V. cholerae strain C6706, identified a mutant which overproduced AI-2, and carried Tn insertion in the cqsS gene. Nucleotide sequencing also revealed mutations inactivating the cqsS gene in environmental isolates which overproduced AI-2, and this property was reversed when complemented with a wild type cqsS gene. Culture of river water samples supplemented with spent medium of these mutants resuscitated dormant V. cholerae cells in water. SIGNIFICANCE:V. cholerae strains with inactivated cqsS gene may offer a convenient source of AI-2 in enhanced assays for monitoring bacteriological quality of water. The results also suggest a potential role of naturally occurring cqsS mutants in the environmental biology of V. cholerae. Fu...
Nasiri, N, Jin, D & Tricoli, A 2019, 'Nanoarchitechtonics of Visible‐Blind Ultraviolet Photodetector Materials: Critical Features and Nano‐Microfabrication', Advanced Optical Materials, vol. 7, no. 2, pp. 1800580-1800580.
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AbstractAccurate measurement of ultraviolet radiation is key to many technologies including wearable devices for skin cancer prevention, optical communication systems, and missile launch detection. Nanostructuring of wide bandgap semiconductors, such as GaN, ZnO, and SiC, promises some benefits over established commercial solutions relying on n–p type Si‐homojunction technology. In the past decade, a variety of carefully nanostructured architectures have been demonstrated as efficient designs for visible‐blind UV photodetectors featuring superior detectivity, thermal stability, robust radiation hardness, and very low operation bias and power consumption. Here, a comprehensive review of the latest achievements on ultraviolet photodetector materials is presented, with focus on the multiscale engineering of composition and nano‐microscale morphology. The review concludes with a critical assessment and comparison of state‐of‐the‐art devices aiming to provide guidelines and research directions for the next generation of UV photodetector materials.
Nelz, R, Radtke, M, Slablab, A, Kianinia, M, Li, C, Xu, Z-Q, Bradac, C, Aharonovich, I & Neu, E 2019, 'Near-field energy transfer between a luminescent 2D material and color centers in diamond', Advanced Quantum Technologies, vol. 3, no. 2.
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Energy transfer between fluorescent probes lies at the heart of many
applications ranging from bio-sensing and -imaging to enhanced photo-detection
and light harvesting. In this work, we study F\'orster resonance energy
transfer (FRET) between shallow defects in diamond --- nitrogen-vacancy (NV)
centers --- and atomically-thin, two-dimensional materials --- tungsten
diselenide (WSe$_2$). By means of fluorescence lifetime imaging, we demonstrate
the occurrence of FRET in the WSe$_2$/NV system. Further, we show that in the
coupled system, NV centers provide an additional excitation pathway for WSe$_2$
photoluminescence. Our results constitute the first step towards the
realization of hybrid quantum systems involving single-crystal diamond and
two-dimensional materials that may lead to new strategies for studying and
controlling spin transfer phenomena and spin valley physics.
Ng, SW, Chan, Y, Chellappan, DK, Madheswaran, T, Zeeshan, F, Chan, YL, Collet, T, Gupta, G, Oliver, BG, Wark, P, Hansbro, N, Hsu, A, Hansbro, PM, Dua, K & Panneerselvam, J 2019, 'Molecular modulators of celastrol as the keystones for its diverse pharmacological activities', Biomedicine & Pharmacotherapy, vol. 109, pp. 1785-1792.
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In the recent years, much attention has been focused on identifying bioactive compounds from medicinal plants that could be employed in therapeutics, which is attributed to their potent pharmacological actions and better toxicological profile. One such example that has come into the light with considerable interest is the pentacyclic triterpenoid, celastrol, which has been found to provide substantial therapeutic properties in a variety of diseases. In an effort to further accelerate its potential to be utilized in clinical practice in the future; along with advancing technologies in the field of drug discovery and development, different researchers have been investigating on the various mechanisms and immunological targets of celastrol that underlie its broad spectrum of pharmacological properties. In this review, we have collated the various research findings related to the molecular modulators responsible for different pharmacological activities shown by celastrol. Our review will be of interest to the herbal, biological, molecular scientist and by providing a quick snapshot about celastrol giving a new direction in the area of herbal drug discovery and development.
Nguyen, L, Mak, C, Chen, H, Zaky, A, Wong, M, Pollock, C & Saad, S 2019, 'SIRT1 Attenuates Kidney Disorders in Male Offspring Due to Maternal High-Fat Diet', Nutrients, vol. 11, no. 1, pp. 146-146.
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Maternal obesity has been associated with kidney disorders in male offspring. Our previous studies have demonstrated that Sirtuin (SIRT)1, an essential regulator of metabolic stress responses, is suppressed in the offspring as the result of maternal high-fat diet (HFD) consumption, which is likely to underpin the adverse metabolic and renal outcomes. To examine if SIRT1 overexpression or activation early in life can protect the offspring kidney, wild-type (WT) and transgenic (Tg) offspring were born to the same diet-induced obese female C57BL/6 mice through breeding with hemizygous SIRT1-transgenic (Tg) male mice and examined for renal pathological changes. In separate experiments, SIRT1 activator SRT1720 (25 mg/kg/2 days i.p) was administrated in WT offspring over 6 weeks of postnatal high-fat diet exposure. The results show that offspring born to obese dams have increased kidney weight, higher levels of renal triglycerides, and increased expression of oxidative stress, inflammatory, and fibrotic markers, as well as increased albuminuria compared to offspring of control dams. Both SIRT1 overexpression and SRT1720 treatment attenuated renal lipid contents and expression of lipogenesis, oxidative stress, and inflammatory markers; however, fibrosis was modestly reduced and albuminuria was not affected. The findings suggest that SIRT1 therapy can ameliorate some pathological mechanisms of kidney programming due to maternal obesity but may not be sufficient to prevent the resulting chronic kidney injury.
Nguyen, LN, Labeeuw, L, Commault, AS, Emmerton, B, Ralph, PJ, Johir, MAH, Guo, W, Ngo, HH & Nghiem, LD 2019, 'Validation of a cationic polyacrylamide flocculant for the harvesting fresh and seawater microalgal biomass', Environmental Technology & Innovation, vol. 16, pp. 100466-100466.
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© 2019 Elsevier B.V. A simple, efficient, and fast settling flocculation technique to harvest microalgal biomass was demonstrated using a proprietary cationic polyacrylamide flocculant for a freshwater (Chlorella vulgaris) and a marine (Phaeodactylum tricornutum) microalgal culture at their mid-stationary growth phase. The optimal flocculant doses were 18.9 and 13.7 mg/g of dry algal biomass for C. vulgaris and P. tricornutum, respectively (equivalent to 7 g per m3 of algal culture for both species). The obtained optimal dose was well corroborated with changes in cell surface charge, and culture solution optical density and turbidity. At the optimal dose, charge neutralization of 64 and 86% was observed for C. vulgaris and P. tricornutum algal cells, respectively. Algae recovery was independent of the culture solution pH in the range of pH 6 to 9. Algal biomass recovery was achieved of 100 and 90% for C vulgaris and P. tricornutum respectively, and over 98% medium recovery was achievable by simple decanting.
Nguyen, LT, Chen, H, Zaky, A, Pollock, C & Saad, S 2019, 'SIRT1 overexpression attenuates offspring metabolic and liver disorders as a result of maternal high‐fat feeding', The Journal of Physiology, vol. 597, no. 2, pp. 467-480.
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Key points
Maternal high‐fat diet (MHF) consumption led to metabolic and liver disorders in male offspring, which are associated with reduced sirtuin (SIRT)1 expression and activity in the offspring liver
SIRT1 overexpression in MHF offspring reduced their body weight and adiposity and normalized lipid metabolic markers in epididymal and retroperitoneal adipose tissues
SIRT1 overexpression in MHF offspring improved glucose tolerance, as well as systemic and hepatic insulin sensitivity
SIRT1 overexpression ameliorated MHF‐induced lipogenesis, oxidative stress and fibrogenesis in the liver of offspring.
AbstractMaternal obesity can increase the risk of metabolic disorders in the offspring. However, the underlying mechanism responsible for this is not clearly understood. Previous evidence implied that sirtuin (SIRT)1, a potent regulator of energy metabolism and stress responses, may play an important role. In the present study, we have shown, in C57BL/6 mice, that maternal high‐fat diet (HFD) consumption can induce a pre‐diabetic and non‐alcoholic fatty liver disease phenotype in the offspring, associated with reduced SIRT1 expression in the hypothalamus, white adipose tissues (WAT) and liver. Importantly, the overexpression of SIRT1 in these offspring significantly attenuated the excessive accumulation of epididymal (Epi) white adipose tissue (WAT) and retroperitoneal (Rp)WAT (P < 0.001), glucose intolerance and insulin resistance (both P < 0.05) at weaning age. These changes were associated with the suppression of peroxisome proliferator‐activated receptor gamma (...
Nguyen, M, Nikolay, N, Bradac, C, Kianinia, M, Ekimov, EA, Mendelson, N, Benson, O & Aharonovich, I 2019, 'Photodynamics and quantum efficiency of germanium vacancy color centers in diamond', Advanced Photonics, vol. 1, no. 06, pp. 1-1.
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Nguyen, T, Li, GE, Chen, H, Cranfield, CG, McGrath, KC & Gorrie, CA 2019, 'Neurological Effects in the Offspring After Switching From Tobacco Cigarettes to E-Cigarettes During Pregnancy in a Mouse Model', Toxicological Sciences, vol. 172, no. 1, pp. 191-200.
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Abstract
Maternal smoking is currently a public health concern and has been associated with a number of complications in the offspring. E-cigarettes are gaining popularity as a “safer” alternative to tobacco cigarettes during pregnancy, however, there are a limited number of studies to suggest that it is actually “safe.” Balb/C female mice were exposed to ambient air (n = 8; Sham), or tobacco cigarette smoke (n = 8; SE) before gestation, during gestation and lactation. A third group was exposed to cigarette smoke before gestation followed by e-cigarette aerosols during gestation and lactation (n = 8; Switch). Male offspring (12-week old, n = 10–14/group) underwent behavioral assessments to investigate short-term memory, anxiety, and activity using the novel object recognition and elevated plus maze tests. Brains were collected at postnatal day (P)1, P20, and Week 13 for global DNA methylation, epigenetic gene expression, and neuronal cell counts. The offspring from mothers switching to e-cigarettes exhibited no change in exploration/activity but showed a decrease in global DNA methylation, Aurora Kinase (Aurk) A and AurkB gene expression and a reduction in neuronal cell numbers in the cornu ammonis 1 region of the dorsal hippocampus compared with the SE group. Continuous tobacco cigarette smoke exposure during pregnancy resulted in marked neurological deficits in the offspring. Switching to e-cigarettes during pregnancy reduced these neurological deficits compared with cigarette smoke exposure. However, neurological changes were still observed, so we therefore conclude that e-cigarette use during pregnancy is not advised.
Nikolay, N, Mendelson, N, Özelci, E, Sontheimer, B, Böhm, F, Kewes, G, Toth, M, Aharonovich, I & Benson, O 2019, 'Direct measurement of quantum efficiency of single-photon emitters in hexagonal boron nitride', Optica, vol. 6, no. 8, pp. 1084-1084.
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© 2019 Optical Society of America. Single-photon emitters (SPEs) in two-dimensional materials are promising candidates for the future generation of quantum photonic technologies. In this work, we experimentally determine the quantum efficiency (QE) of SPEs in few-layer hexagonal boron nitride (h-BN). We employ a metal hemisphere that is attached to the tip of an atomic force microscope to directly measure the lifetime variation of the SPEs as the tip approaches the h-BN. This technique enables nondestructive, yet direct and absolute measurement of the QE of SPEs. We find that the emitters exhibit very high QEs approaching (87 ± 7)% at wavelengths of ≈580 nm, which is among the highest QEs recorded for a solid-state SPE.
Nikolay, N, Mendelson, N, Sadzak, N, Böhm, F, Tran, TT, Sontheimer, B, Aharonovich, I & Benson, O 2019, 'Very Large and Reversible Stark-Shift Tuning of Single Emitters in Layered Hexagonal Boron Nitride', Physical Review Applied, vol. 11, no. 4.
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Nixon, B, Johnston, SD, Skerrett-Byrne, DA, Anderson, AL, Stanger, SJ, Bromfield, EG, Martin, JH, Hansbro, PM & Dun, MD 2019, 'Modification of Crocodile Spermatozoa Refutes the Tenet That Post-testicular Sperm Maturation Is Restricted To Mammals*', Molecular & Cellular Proteomics, vol. 18, pp. S58-S76.
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Competition to achieve paternity has contributed to the development of a multitude of elaborate male reproductive strategies. In one of the most well-studied examples, the spermatozoa of all mammalian species must undergo a series of physiological changes, termed capacitation, in the female reproductive tract prior to realizing their potential to fertilize an ovum. However, the evolutionary origin and adaptive advantage afforded by capacitation remains obscure. Here, we report the use of comparative and quantitative proteomics to explore the biological significance of capacitation in an ancient reptilian species, the Australian saltwater crocodile (Crocodylus porosus). Our data reveal that exposure of crocodile spermatozoa to capacitation stimuli elicits a cascade of physiological responses that are analogous to those implicated in the functional activation of their mammalian counterparts. Indeed, among a total of 1119 proteins identified in this study, we detected 126 that were differentially phosphorylated (± ≥1.2 fold-change) in capacitated versus non-capacitated crocodile spermatozoa. Notably, this subset of phosphorylated proteins shared substantial evolutionary overlap with those documented in mammalian spermatozoa, and included key elements of signal transduction, metabolic and cellular remodeling pathways. Unlike mammalian sperm, however, we noted a distinct bias for differential phosphorylation of serine (as opposed to tyrosine) residues, with this amino acid featuring as the target for ~80% of all changes detected in capacitated spermatozoa. Overall, these results indicate that the phenomenon of sperm capacitation is unlikely to be restricted to mammals and provide a framework for understanding the molecular changes in sperm physiology necessary for fertilization.
Nixon, B, Johnston, SD, Skerrett-Byrne, DA, Anderson, AL, Stanger, SJ, Bromfield, EG, Martin, JH, Hansbro, PM & Dun, MD 2019, 'Modification of Crocodile Spermatozoa Refutes the Tenet That Post-testicular Sperm Maturation Is Restricted To Mammals.', Mol Cell Proteomics, vol. 18 Suppl 1, pp. S58-S76.
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Competition to achieve paternity has contributed to the development of a multitude of elaborate male reproductive strategies. In one of the most well-studied examples, the spermatozoa of all mammalian species must undergo a series of physiological changes, termed capacitation, in the female reproductive tract before realizing their potential to fertilize an ovum. However, the evolutionary origin and adaptive advantage afforded by capacitation remains obscure. Here, we report the use of comparative and quantitative proteomics to explore the biological significance of capacitation in an ancient reptilian species, the Australian saltwater crocodile (Crocodylus porosus,). Our data reveal that exposure of crocodile spermatozoa to capacitation stimuli elicits a cascade of physiological responses that are analogous to those implicated in the functional activation of their mammalian counterparts. Indeed, among a total of 1119 proteins identified in this study, we detected 126 that were differentially phosphorylated (± 1.2 fold-change) in capacitated versus, noncapacitated crocodile spermatozoa. Notably, this subset of phosphorylated proteins shared substantial evolutionary overlap with those documented in mammalian spermatozoa, and included key elements of signal transduction, metabolic and cellular remodeling pathways. Unlike mammalian sperm, however, we noted a distinct bias for differential phosphorylation of serine (as opposed to tyrosine) residues, with this amino acid featuring as the target for ∼80% of all changes detected in capacitated spermatozoa. Overall, these results indicate that the phenomenon of sperm capacitation is unlikely to be restricted to mammals and provide a framework for understanding the molecular changes in sperm physiology necessary for fertilization.
Noisang, C, Prosser, C, Meyer, W, Chemoh, W, Ellis, J, Sawangjaroen, N & Lee, R 2019, 'Molecular detection of drug resistant malaria in Southern Thailand', Malaria Journal, vol. 18, no. 1.
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BACKGROUND:Drug resistance within the major malaria parasites Plasmodium vivax and Plasmodium falciparum threatens malaria control and elimination in Southeast Asia. Plasmodium vivax first-line treatment drug is chloroquine together with primaquine, and the first-line treatment for P. falciparum malaria is artemisinin in combination with a partner drug. Plasmodium vivax and P. falciparum parasites resistant to their respective first-line therapies are now found within Southeast Asia. The resistance perimeters may include high transmission regions of Southern Thailand which are underrepresented in surveillance efforts. METHODS:This study investigated blood samples from malaria centres in Southern Thailand. Genetic loci associated with drug resistance were amplified and sequenced. Drug resistance associated genes Pvmdr1, Pvcrt-o, Pvdhfr, and Pvdhps were characterized for 145 cases of P. vivax malaria, as well as the artemisinin resistance-associated Pfkelch13 gene from 91 cases of P. falciparum malaria. RESULTS:Plasmodium vivax samples from Southern Thai provinces showed numerous chloroquine and antifolate resistance-associated mutations, including SNP and Pvcrt-o K10-insertion combinations suggestive of chloroquine resistant P. vivax phenotypes. A high proportion of the C580Y coding mutation (conferring artemisinin resistance) was detected in P. falciparum samples originating from Ranong and Yala (where the mutation was previously unreported). CONCLUSIONS:The results demonstrate a risk of chloroquine and antifolate resistant P. vivax phenotypes in Southern Thailand, and artemisinin resistant P. falciparum observed as far south as the Thai-Malaysian border region. Ongoing surveillance of antimalarial drug resistance markers is called for in Southern Thailand to inform case management.
Nolan, LM, Turnbull, L, Katrib, M, Osvath, SR, Losa, D, Lazenby, JJ & Whitchurch, CB 2019, 'Pseudomonas aeruginosa is capable of natural transformation in biofilms'.
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AbstractNatural transformation is a mechanism that enables competent bacteria to acquire naked, exogenous DNA from the environment. It is a key process that facilitates the dissemination of antibiotic resistance and virulence determinants throughout bacterial populations. Pseudomonas aeruginosa is an opportunistic Gram-negative pathogen that produces large quantities of extracellular DNA (eDNA) that is required for biofilm formation. P. aeruginosa has a remarkable level of genome plasticity and diversity that suggests a high degree of horizontal gene transfer and recombination but is thought to be incapable of natural transformation. Here we show that P. aeruginosa possesses homologs of all proteins known to be involved in natural transformation in other bacterial species. We found that P. aeruginosa in biofilms is competent for natural transformation of both genomic and plasmid DNA. Furthermore, we demonstrate that type IV pili (T4P) facilitate but are not absolutely essential for natural transformation in P. aeruginosa.
Nolan, M & Fronzi, M 2019, 'Activation of CO2 at chromia-nanocluster-modified rutile and anatase TiO2', Catalysis Today, vol. 326, pp. 68-74.
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© 2018 Elsevier B.V. Converting CO2 to fuels is required to enable the production of sustainable fuels and to contribute to alleviating CO2 emissions. In considering conversion of CO2, the initial step of adsorption and activation by the catalyst is crucial. In addressing this difficult problem, we have examined how nanoclusters of reducible metal oxides supported on TiO2 can promote CO2 activation. In this paper we present density functional theory (DFT) simulations of CO2 activation on heterostructures composed of clean or hydroxylated extended rutile and anatase TiO2 surfaces modified with chromia nanoclusters. The heterostructures show non-bulk Cr and O sites in the nanoclusters and an upshifted valence band edge that is dominated by Cr 3d- O 2p interactions. We show that the supported chromia nanoclusters can adsorb and activate CO2 and that activation of CO2 is promoted whether the TiO2 support is oxidised or hydroxylated. Reduced heterostructures, formed by removal of oxygen from the chromia nanocluster, also promote CO2 activation. In the strong CO2 adsorption modes, the molecule bends giving O–C–O angles of 127 - 132° and elongation of C–O distances up to 1.30 Å; no carbonates are formed. The electronic properties show a strong CO2–Cr–O interaction that drives the interaction of CO2 with the nanocluster and induces the structural distortions. These results highlight that a metal oxide support modified with reducible metal oxide nanoclusters can activate CO2, thus helping to overcome difficulties associated with the difficult first step in CO2 conversion.
Nolan, TH, Menictas, M & Wand, MP 2019, 'Streamlined Computing for Variational Inference with Higher Level Random Effects', Journal of Machine Learning Research, vol. 21, pp. 1-62.
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We derive and present explicit algorithms to facilitate streamlined computing
for variational inference for models containing higher level random effects.
Existing literature, such as Lee and Wand (2016), is such that streamlined
variational inference is restricted to mean field variational Bayes algorithms
for two-level random effects models. Here we provide the following extensions:
(1) explicit Gaussian response mean field variational Bayes algorithms for
three-level models, (2) explicit algorithms for the alternative variational
message passing approach in the case of two-level and three-level models, and
(3) an explanation of how arbitrarily high levels of nesting can be handled
based on the recently published matrix algebraic results of the authors. A
pay-off from (2) is simple extension to non-Gaussian response models. In
summary, we remove barriers for streamlining variational inference algorithms
based on either the mean field variational Bayes approach or the variational
message passing approach when higher level random effects are present.
O’Rourke, MB, Town, SEL, Dalla, PV, Bicknell, F, Koh Belic, N, Violi, JP, Steele, JR & Padula, MP 2019, 'What is Normalization? The Strategies Employed in Top-Down and Bottom-Up Proteome Analysis Workflows', Proteomes, vol. 7, no. 3, pp. 29-29.
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The accurate quantification of changes in the abundance of proteins is one of the main applications of proteomics. The maintenance of accuracy can be affected by bias and error that can occur at many points in the experimental process, and normalization strategies are crucial to attempt to overcome this bias and return the sample to its regular biological condition, or normal state. Much work has been published on performing normalization on data post-acquisition with many algorithms and statistical processes available. However, there are many other sources of bias that can occur during experimental design and sample handling that are currently unaddressed. This article aims to cast light on the potential sources of bias and where normalization could be applied to return the sample to its normal state. Throughout we suggest solutions where possible but, in some cases, solutions are not available. Thus, we see this article as a starting point for discussion of the definition of and the issues surrounding the concept of normalization as it applies to the proteomic analysis of biological samples. Specifically, we discuss a wide range of different normalization techniques that can occur at each stage of the sample preparation and analysis process.
Obeidat, M, Faiz, A, Li, X, van den Berge, M, Hansel, NN, Joubert, P, Hao, K, Brandsma, C-A, Rafaels, N, Mathias, R, Ruczinski, I, Beaty, TH, Barnes, KC, Man, SFP, Paré, PD & Sin, DD 2019, 'The pharmacogenomics of inhaled corticosteroids and lung function decline in COPD', European Respiratory Journal, vol. 54, no. 6, pp. 1900521-1900521.
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Inhaled corticosteroids (ICS) are widely prescribed for patients with chronic obstructive pulmonary disease (COPD), yet have variable outcomes and adverse reactions, which may be genetically determined. The primary aim of the study was to identify the genetic determinants for forced expiratory volume in 1 s (FEV1) changes related to ICS therapy.In the Lung Health Study (LHS)-2, 1116 COPD patients were randomised to the ICS triamcinolone acetonide (n=559) or placebo (n=557) with spirometry performed every 6 months for 3 years. We performed a pharmacogenomic genome-wide association study for the genotype-by-ICS treatment effect on 3 years of FEV1 changes (estimated as slope) in 802 genotyped LHS-2 participants. Replication was performed in 199 COPD patients randomised to the ICS, fluticasone or placebo.A total of five loci showed genotype-by-ICS interaction at p<5×10−6; of these, single nucleotide polymorphism (SNP) rs111720447 on chromosome 7 was replicated (discovery p=4.8×10−6, replication p=5.9×10−5) with the same direction of interaction effect. ENCODE (Encyclopedia of DNA Elements) data revealed that in glucocorticoid-treated (dexamethasone) A549 alveolar cell line, glucocorticoid receptor binding sites were located near SNP rs111720447. In stratified analyses of LHS-2, genotype at SNP rs111720447 was significantly associated with rate of FEV1 decline in patients taking ICS (C allele β 56.36 mL·year−1, 95% CI 29.96–82.76 mL·year−1) and in patients who were assigned to placebo, although the relationship was weaker and in the opposite direction to that in the ICS group (C allele β −27.57 mL·year−1, 95% CI −53.27– −1.87 mL·year−1).The study uncovered genetic factors associated with FEV...
Ockelford, A, Woodcock, S & Haynes, H 2019, 'The impact of inter‐flood duration on non‐cohesive sediment bed stability', Earth Surface Processes and Landforms, vol. 44, no. 14, pp. 2861-2871.
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AbstractLimited field and flume data suggests that both uniform and graded beds appear to progressively stabilize when subjected to inter‐flood flows as characterized by the absence of active bedload transport. Previous work has shown that the degree of bed stabilization scales with duration of inter‐flood flow, however, the sensitivity of this response to bed surface grain size distribution has not been explored. This article presents the first detailed comparison of the dependence of graded bed stability on inter‐flood flow duration. Sixty discrete experiments, including repetitions, were undertaken using three grain size distributions of identical D50 (4.8 mm); near‐uniform (σg = 1.13), unimodal (σg = 1.63) and bimodal (σg = 2.08). Each bed was conditioned for between 0 (benchmark) and 960 minutes by an antecedent shear stress below the entrainment threshold of the bed (τ*c50). The degree of bed stabilization was determined by measuring changes to critical entrainment thresholds and bedload flux characteristics.Results show that (i) increasing inter‐flood duration from 0 to 960 minutes increases the average threshold shear stress of the D50 by up to 18%; (ii) bedload transport rates were reduced by up to 90% as inter‐flood duration increased from 0 to 960 minutes; (iii) the rate of response to changes in inter‐flood duration in both critical shear stress and bedload transport rate is non‐linear and is inversely proportional to antecedent duration; (iv) there is a grade dependent response to changes in critical shear stress where the magnitude of response in uniform beds is up to twice that of the graded beds; and (v) there is a ...
Oliver, B, Tonga, K, Darley, D, Rutting, S, Zhang, X, Chen, H & Wang, G 2019, 'COPD treatment choices based on blood eosinophils: are we there yet?', Breathe, vol. 15, no. 4, pp. 318-323.
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Eosinophils are increasingly being recognised as an important characteristic feature of COPD. Patients with COPD and eosinophilic inflammation tend to respond to steroid therapy; however, many questions remain regarding the optimum measurement. Eosinophilic inflammation may be defined based on various sampling techniques, including eosinophil levels in blood, sputum, bronchoalveolar lavage or biopsy, which leads to inconsistencies in its definition. Blood eosinophils may increase in conjunction with sputum eosinophils during COPD exacerbations and therefore may be a good surrogate marker of airway eosinophilic inflammation. However, the timing of the blood eosinophil measurement, the stability of the eosinophil count and the threshold used in different studies are variable. The use of blood eosinophil count to direct biological therapies in COPD has also had variable outcomes. Eosinophilic inflammation has an important role in COPD management; however, its use as the optimum biomarker still needs further investigation.Key pointsEosinophilia may play a significant role in the pathogenesis of COPD.Eosinophilic inflammation in COPD can be steroid responsive; however, eosinophilic inflammation is variable, and caution needs to be taken with measurements and the thresholds used.The long-term effects of reducing eosinophil levels in COPD is unclear.Educational aimsTo explore current knowledge of eosinophils in COPD.To explore the relationship between eosinophilia and corticosteroid use.To understand the limitations of assessing and u...
Ong, J, Faiz, A, Timens, W, van den Berge, M, Terpstra, MM, Kok, K, van den Berg, A, Kluiver, J & Brandsma, CA 2019, 'Marked TGF-β-regulated miRNA expression changes in both COPD and control lung fibroblasts', Scientific Reports, vol. 9, no. 1.
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AbstractCOPD is associated with disturbed tissue repair, possibly due to TGF-β-regulated miRNA changes in fibroblasts. Our aim was to identify TGF-β-regulated miRNAs and their differential regulation and expression in COPD compared to control fibroblasts. Small RNA sequencing was performed on TGF-β-stimulated and unstimulated lung fibroblasts from 15 COPD patients and 15 controls. Linear regression was used to identify TGF-β-regulated and COPD-associated miRNAs. Interaction analysis was performed to compare miRNAs that responded differently to TGF-β in COPD and control. Re-analysis of previously generated Ago2-IP data and Enrichr were used to identify presence and function of potential target genes in the miRNA-targetome of lung fibroblasts. In total, 46 TGF-β-regulated miRNAs were identified in COPD and 86 in control fibroblasts (FDR < 0.05). MiR-27a-5p was the most significantly upregulated miRNA. MiR-148b-3p, miR-589-5p and miR-376b-3p responded differently to TGF-β in COPD compared to control (FDR < 0.25). MiR-660-5p was significantly upregulated in COPD compared to control (FDR < 0.05). Several predicted targets of miR-27a-5p, miR-148b-3p and miR-660-5p were present in the miRNA-targetome, and were mainly involved in the regulation of gene transcription. In conclusion, altered TGF-β-induced miRNA regulation and differential expression of miR-660-5p in COPD fibroblasts, may represent one of the mechanisms underlying aberrant tissue repair and remodelling in COPD.
Ong, J, van den Berg, A, Faiz, A, Boudewijn, I, Timens, W, Vermeulen, C, Oliver, B, Kok, K, Terpstra, M, van den Berge, M, Brandsma, C-A & Kluiver, J 2019, 'Current Smoking is Associated with Decreased Expression of miR-335-5p in Parenchymal Lung Fibroblasts', International Journal of Molecular Sciences, vol. 20, no. 20, pp. 5176-5176.
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Cigarette smoking causes lung inflammation and tissue damage. Lung fibroblasts play a major role in tissue repair. Previous studies have reported smoking-associated changes in fibroblast responses and methylation patterns. Our aim was to identify the effect of current smoking on miRNA expression in primary lung fibroblasts. Small RNA sequencing was performed on lung fibroblasts from nine current and six ex-smokers with normal lung function. MiR-335-5p and miR-335-3p were significantly downregulated in lung fibroblasts from current compared to ex-smokers (false discovery rate (FDR) <0.05). Differential miR-335-5p expression was validated with RT-qPCR (p-value = 0.01). The results were validated in lung tissue from current and ex-smokers and in bronchial biopsies from non-diseased smokers and never-smokers (p-value <0.05). The methylation pattern of the miR-335 host gene, determined by methylation-specific qPCR, did not differ between current and ex-smokers. To obtain insights into the genes regulated by miR-335-5p in fibroblasts, we overlapped all proven miR-335-5p targets with our previously published miRNA targetome data in lung fibroblasts. This revealed Rb1, CARF, and SGK3 as likely targets of miR-335-5p in lung fibroblasts. Our study indicates that miR-335-5p downregulation due to current smoking may affect its function in lung fibroblasts by targeting Rb1, CARF and SGK3.
Ong, M, Cheng, J, Jin, X, Lao, W, Johnson, M, Tan, Y & Qu, X 2019, 'Paeoniflorin extract reverses dexamethasone-induced testosterone over-secretion through downregulation of cytochrome P450 17A1 expression in primary murine theca cells', Journal of Ethnopharmacology, vol. 229, pp. 97-103.
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ETHNOPHARMACOLOGICAL RELEVANCE:Polycystic Ovarian Syndrome (PCOS) is a complex endocrine and reproductive disorder. A main hallmark includes increased androgen production. The root of Paeonia lactiflora Pall. (Bai Shao) is used in Chinese herbal medicine for reproductive disorders, however its effects and mechanisms on ovarian theca cells has not yet been fully elucidated. AIM OF THE STUDY:The aim of this study was to evaluate effect of paeoniflorin extract (PFE), the main constituents of Bai Shao, on androgen production in ovarian theca cells. MATERIALS AND METHODS:Primary murine theca cells were treated with concentrations of PFE (1-100 µg/mL) in the presence of dexamethasone (10 µM) with media-only treated cells used as the control. After 24 h, culture media was collected for biochemistry assays of testosterone and progesterone. Expression of key steroidogenic enzymes, cholesterol side-chain cleavage (CYP11A1) and 17α-hydroxylase (CYP17A1) was characterized using immunofluorescence staining, immunoblotting and qRT-PCR. RESULTS:Dexamethasone significantly enhanced testosterone secretion (P < 0.05 vs. the control cells). PFE reversed over-production of testosterone induced by dexamethasone in a dose-dependent manner. The treatment with PFE also normalized production of progesterone in dexamethasone-treated cells. Expression of CYP11A1 and CYP17A1 in the theca cells were visualised by immunofluorescence staining. All doses of PFE significantly inhibited CYP17A1 expression detected by immunoblotting, but only 100 µg/mL of PFE downregulated CYP11A1 expression and reduced CYP11A1 significantly in dexamethasone-treated theca cells. CONCLUSIONS:PFE may reduce over-secretion of testosterone in theca cells through downregulation of CYP17A1 and CYP11A1. These findings provide scientific evidence to treat ovarian hyperandrogenism with the root of Paeonia lactiflora Pall.
Onić, D, Filipović, MD, Bojičić, I, Hurley-Walker, N, Arbutina, B, Pannuti, TG, Maitra, C, Urošević, D, Haberl, F, Maxted, N, Wong, GF, Rowell, G, Bell, ME, Callingham, JR, Dwarakanath, KS, For, B-Q, Hancock, PJ, Hindson, L, Johnston-Hollitt, M, Kapińska, AD, Lenc, E, McKinley, B, Morgan, J, Offringa, AR, Porter, LE, Procopio, P, Staveley-Smith, L, Wayth, RB, Wu, C & Zheng, Q 2019, 'Murchison Widefield Array and XMM-Newton observations of the Galactic supernova remnant G5.9+3.1', A, vol. 625, p. A93.
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In this paper we discuss the radio continuum and X-ray properties of the
so-far poorly studied Galactic supernova remnant (SNR) G5.9+3.1. We present the
radio spectral energy distribution (SED) of the Galactic SNR G5.9+3.1 obtained
with the Murchison Widefield Array (MWA). Combining these new observations with
the surveys at other radio continuum frequencies, we discuss the integrated
radio continuum spectrum of this particular remnant. We have also analyzed an
archival XMM-Newton observation, which represents the first detection of X-ray
emission from this remnant. The SNR SED is very well explained by a simple
power-law relation. The synchrotron radio spectral index of G5.9+3.1, is
estimated to be 0.42$\pm$0.03 and the integrated flux density at 1GHz to be
around 2.7Jy. Furthermore, we propose that the identified point radio source,
located centrally inside the SNR shell, is most probably a compact remnant of
the supernova explosion. The shell-like X-ray morphology of G5.9+3.1 as
revealed by XMM-Newton broadly matches the spatial distribution of the radio
emission, where the radio-bright eastern and western rims are also readily
detected in the X-ray while the radio-weak northern and southern rims are weak
or absent in the X-ray. Extracted MOS1+MOS2+PN spectra from the whole SNR as
well as the north, east, and west rims of the SNR are fit successfully with an
optically thin thermal plasma model in collisional ionization equilibrium with
a column density N_H~0.80x$10^{22}$ cm$^{-2}$ and fitted temperatures spanning
the range kT~0.14-0.23keV for all of the regions. The derived electron number
densities n_e for the whole SNR and the rims are also roughly comparable
(ranging from ~$0.20f^{-1/2}$ cm$^{-3}$ to ~$0.40f^{-1/2}$ cm$^{-3}$, where f
is the volume filling factor). We also estimate the swept-up mass of the X-ray
emitting plasma associated with G5.9+3.1 to be ~$46f^{-1/2}M_{\odot}$.
O'Rourke, MB & Padula, MP 2019, 'An Inexpensive, simple calibration method for MALDI TOF/TOF systems', Journal of Mass Spectrometry, vol. 54, no. 12, pp. 1003-1007.
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AbstractThe array of analytes that can be measured by MADLI MS has created an equally vast range of calibration mixtures. The inherent problem with this is that acquiring all of them at commercial rates can be prohibitively expensive. With this in mind, we have created a low‐cost alternative to the most commonly used peptide calibrants.We were able to achieve an overall 78 ppm mass accuracy across a mass range of 900 to 2500 Da which was comparable to the mass accuracy achievable with commercial peptide mixes and hence has become a viable alternative.
O'Rourke, MB, Smith, CC, Tse, BCY, Sutherland, GT, Crossett, B & Padula, MP 2019, '‘What did I do wrong?’ An empirical evaluation of sample preparation methodologies in matrix-assisted laser desorption/ionization-mass spectrometry imaging', Future Science OA, vol. 5, no. 4.
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Aim: This guide aims to broaden the uptake of MALDI-MSI biomedical research by removing the initial ‘lag phase’ associated with empirical determination in sample preparation and data analysis. Methods: Samples from several tissue types were prepared for lipid, protein and peptide MSI analysis. Broadly, samples were cryo sectioned, mounted onto conductive MALDI slides and sublimed with an analyte specific matrix, recrystallised and analyzed in a Bruker UltrafleXtreme MALDI TOF/TOF. Results/conclusion: Here we present a general guide that serves as the first comprehensive, explanatory index for curation and verification of both sample preparation and data generation during the MALDI-MSI process.
Paijmans, KC, Booth, DJ & Wong, MYL 2019, 'Towards an ultimate explanation for mixed‐species shoaling', Fish and Fisheries, vol. 20, no. 5, pp. 921-933.
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AbstractThe formation of social groups has important impacts on fitness for many animal species, with differences in group compositions resulting in a range of fitness outcomes for individuals. Recent interest in mixed‐species grouping, which extends from a large body of literature invested in understanding single‐species grouping, highlights novel complexities of group formation which relate to phenotypic, behavioural and physiological differences that naturally exist between species. Among fishes, mixed‐species shoaling is a common form of social grouping behaviour displayed across a range of marine and freshwater ecosystems. Research explaining mixed‐species shoaling shows some overlap with explanations for single‐species shoaling; however, it also demonstrates that distinct differences between species give rise to unique cost‐benefit trade‐offs which need to be incorporated into conceptual models of mixed‐species shoaling behaviour. Unique predation related trade‐offs may arise from inefficiency of the confusion effect, variation in vigilance between species and unequal species‐preferences shown by predators, whilst unique foraging‐related trade‐offs may arise from diet partitioning, variations in foraging behaviour and differences in competitive abilities between species. We review the literature on fitness outcomes associated with mixed‐species shoaling and present a new theoretical framework to explain the cost‐benefit trade‐offs for individuals within mixed‐species shoals. The framework incorporates both trade‐offs arising from differences between species and those arising from group size, the former having been largely ignored due to a focus on single‐species shoaling. Our framework is designed to inform future research striving to explain mixed‐species shoaling behaviour.
Palmer, SR, Ren, Z, Hwang, G, Liu, Y, Combs, A, Söderström, B, Lara Vasquez, P, Khosravi, Y, Brady, LJ, Koo, H & Stoodley, P 2019, 'Streptococcus mutans yidC1 and yidC2 Impact Cell Envelope Biogenesis, the Biofilm Matrix, and Biofilm Biophysical Properties', Journal of Bacteriology, vol. 201, no. 1.
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YidC proteins are membrane-localized chaperone insertases that are universally conserved in all bacteria and are traditionally studied in the context of membrane protein insertion and assembly. Both YidC paralogs of the cariogenic pathogen
Streptococcus mutans
are required for proper envelope biogenesis and full virulence, indicating that these proteins may also contribute to optimal biofilm formation in streptococci. Here, we show that the deletion of either
yidC
results in changes to the structure and physical properties of the EPS matrix produced by
S. mutans
, ultimately impairing optimal biofilm development, diminishing its mechanical stability, and facilitating its removal. Importantly, the universal conservation of bacterial
yidC
orthologs, combined with our findings, provide a rationale for YidC as a possible drug target for antibiofilm therapies.
Pamphlett, R, Kum Jew, S, Doble, PA & Bishop, DP 2019, 'Elemental Analysis of Aging Human Pituitary Glands Implicates Mercury as a Contributor to the Somatopause', Frontiers in Endocrinology, vol. 10, no. JUN.
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Background: Growth hormone levels often decline on aging, and this "somatopause" is associated with muscle and bone loss, visceral adiposity and impaired cardiovascular function. Mercury has been detected in human pituitary glands, so to see if mercury could play a part in the somatopause we measured the proportion of people at different ages who had mercury in their anterior pituitary cells. Materials and methods: Paraffin sections of pituitary glands taken at autopsy from 94 people between the ages of 2 and 99 years were stained for inorganic mercury using autometallography. Pituitary mercury content was classified as none, low (<30% of cells) or high (>30% of cells) in increasing two-decade age groups. Autometallography combined with immunohistochemistry determined which hormone-producing cells contained mercury. Laser ablation-inductively coupled plasma-mass spectrometry was used to confirm the presence of mercury. Results: The proportion of people with low-content pituitary mercury remained between 33 and 42% at all ages. The proportion of people with high-content mercury increased with increasing age, from 0% of people in the 2-20 year group to a peak of 50% of people in the 61-80 years group, followed by a fall to 35% of people in the 81-99 years group. Mercury, when present, was found always in somatotrophs, occasionally in corticotrophs, rarely in thyrotrophs and gonadotrophs, and never in lactotrophs. Laser ablation-inductively coupled plasma-mass spectrometry detected mercury in regions of pituitaries that stained with autometallography. Conclusions: The proportion of people with mercury in their anterior pituitary cells, mostly somatotrophs, increases with aging, suggesting that mercury toxicity could be one factor contributing to the decline in growth hormone levels found in advancing age.
Panigrahi, R, Oh, H, Sharma, V, Lee, KWK, Rice, SA, Cohn, D & Ramanujan, RV 2019, 'Remote control of biofouling by heating PDMS/MnZn ferrite nanocomposites with an alternating magnetic field', Journal of Chemical Technology & Biotechnology, vol. 94, no. 8, pp. 2713-2720.
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AbstractBACKGROUNDThe accumulation of unwanted microorganisms on wetted surfaces, leading to surface damage and contamination, is a common and significant global issue.RESULTSHerein, we report a novel technique where the growth of microorganisms can be readily controlled by coating the surfaces with a polydimethylsiloxane (PDMS)/Mn0.8Zn0.2Fe2O4 (manganese‐zinc ferrite) nanocomposite followed by applying alternating magnetic field (AMF). The PDMS/MnZn ferrite nanocomposite is light weight and thermally stable (up to ∼ 330 °C) that can form a flexible coating. PDMS also provides hydrophobicity, which is further enhanced by the addition of Mn and Zn. The improved hydrophobicity makes the coated surface less susceptible to biofilm formation. When external AMF was applied to nanocomposites containing various MnZn ferrite nanoparticle loads of 10%, 20% and 30%, the temperature of the surface of nanocomposites reached to 80, 120 and 160 °C, respectively. Successful biofilm deactivation was achieved by heating the nanocomposites via AMF application, as shown in the biofilm test where up to ∼ 70% of the Pseudomonas aeruginosa PAO1 biofilm cells were killed when the AMF was applied for 20 min to the nanocomposites containing 30% nanoparticles.CONCLUSIONCoating the surface with PDMS/MnZn ferrite nanocomposites followed by applying external AMF can be an effective way to remove biofilm remotely in a wide range of applications. © 2019 Society of Chemical Industry
Parameshwaran, K, Sharma, P, Rajendra, S, Stelzer-Braid, S, Xuan, W & Rawlinson, WD 2019, 'Circulating human papillomavirus DNA detection in Barrett's dysplasia and esophageal adenocarcinoma', Diseases of the Esophagus, vol. 32, no. 12, pp. 1-6.
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SUMMARY
There is evidence to suggest that human papillomaviruses (HPV) are associated with Barrett's dysplasia and esophageal adenocarcinoma. In other HPV-linked cancers such as cervical and oropharyngeal cancer, circulating HPV DNA is a potential biomarker to assist in tumor diagnosis and management. This study aimed to determine whether circulating HPV DNA was detectable in patients with Barrett's dysplasia and esophageal adenocarcinoma, and if so, whether there is any correlation with esophageal tissue HPV status. Plasma from 138 patients representing esophageal adenocarcinoma (N = 41), Barrett's dysplasia (N = 48) and hospital controls (N = 49) were analyzed for the presence of circulating HPV DNA using droplet-digital PCR targeting the E7 gene of HPV types 16 and 18. Circulating HPV DNA was detected in 11/138 (8.0%) study subjects including 1/49 (2.0%) hospital controls, 4/48 (8.3%) Barrett's dysplasia patients, and 6/41 (14.6%) esophageal adenocarcinoma patients. Detection of circulating HPV DNA was higher in patients with HPV-positive esophageal tissue (6/35, 17.1%) compared to those with HPV-negative specimens (5/103; 4.9%) (OR = 4.06; 95% CI 1.15–14.25; P = 0.020). The highest rates of detection occurred in esophageal adenocarcinoma patients, particularly those with invasive tumors that had breached the esophageal submucosa, had regional lymph node involvement or metastatic disease. Circulating HPV DNA was detectable in a subset of Barrett's dysplasia and esophageal adenocarcinoma patients. Detection was associated with tissue HPV positivity and possibly disease severity.
Park, S-H, Park, S-H, Howe, ENW, Hyun, JY, Chen, L-J, Hwang, I, Vargas-Zuñiga, G, Busschaert, N, Gale, PA, Sessler, JL & Shin, I 2019, 'Determinants of Ion-Transporter Cancer Cell Death', Chem, vol. 5, no. 8, pp. 2079-2098.
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Parvez Mahmud, MA, Hossain, MJ, Nizami, MSH, Rahman, MS, Farjana, SH, Huda, N & Lang, C 2019, 'Advanced power routing framework for optimal economic operation and control of solar photovoltaic‐based islanded microgrid', IET Smart Grid, vol. 2, no. 2, pp. 242-249.
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© 2019 Institution of Engineering and Technology. All rights reserved. Energy sharing through a microgrid (MG) is essential for islanded communities to maximise the use of distributed energy resources (DERs) and battery energy storage systems (BESSs). Proper energy management and control strategies of such MGs can offer revenue to prosumers (active consumers with DERs) by routing excess energy to their neighbours and maintaining grid constraints at the same time. This paper proposes an advanced power-routing framework for a solarphotovoltaic (PV)-based islanded MG with a central storage system (CSS). An optimisation-based economic operation for the MG is developed that determines the power routing and energy sharing in the MG in the day-ahead stage. A modified droop controller-based real-time control strategy has been established that maintains the voltage constraints of the MG. The proposed power-routing framework is verified via a case study for a typical islanded MG. The outcome of the optimal economic operation and a controller verification of the proposed framework are presented to demonstrate the effectiveness of the proposed powerrouting framework. Results reveal that the proposed framework performs a stable control operation and provides a profit of 57 AU$/day at optimal conditions.
Pateras, A, Carnis, J, Mukhopadhyay, U, Richard, M-I, Leake, SJ, Schülli, TU, Reichl, C, Wegscheider, W, Dehollain, JP, Vandersypen, LMK & Evans, PG 2019, 'Electrode-induced lattice distortions in GaAs multi-quantum-dot arrays', Journal of Materials Research, vol. 34, no. 08, pp. 1291-1301.
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Abstract
Paull, NJ, Irga, PJ & Torpy, FR 2019, 'Active botanical biofiltration of air pollutants using Australian native plants', Air Quality, Atmosphere & Health, vol. 12, no. 12, pp. 1427-1439.
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© 2019, Springer Nature B.V. Air pollutants are of public concern due to their adverse health effects. Biological air filters have shown great promise for the bioremediation of air pollutants. Different plant species have previously been shown to significantly influence pollutant removal capacities, although the number of species tested to date is small. The aims of this paper were to determine the pollutant removal capacity of different Australian native species for their effect on active biowall particulate matter, volatile organic compounds and carbon dioxide removal, and to compare removal rates with previously tested ornamental species. The single-pass removal efficiency for PM and VOCs of native planted biofilters was determined with a flow-through chamber. CO2 removal was tested by a static chamber pull down study. The results indicated that the native species were not effective for CO2 removal likely due to their high light level requirements in conjunction with substrate respiration. Additionally, the native species had lower PM removal efficiencies compared to ornamental species, with this potentially being due to the ornamental species possessing advantageous leaf traits for increased PM accumulation. Lastly, the native species were found to have similar benzene removal efficiencies to ornamental species. As such, whilst the native species showed a capacity to phytoremediate air pollutants, ornamental species have a comparatively greater capacity to do so and are more appropriate for air filtration purposes in indoor circumstances. However, as Australian native plants have structural and metabolic adaptations that enhance their ability to tolerate harsh environments, they may find use in botanical biofilters in situations where common ornamental plants may be suitable, especially in the outdoor environment.
Pavasini, R, Serenelli, M, Celis-Morales, CA, Gray, SR, Izawa, KP, Watanabe, S, Colin-Ramirez, E, Castillo-Martínez, L, Izumiya, Y, Hanatani, S, Onoue, Y, Tsujita, K, Macdonald, PS, Jha, SR, Roger, VL, Manemann, SM, Sanchis, J, Ruiz, V, Bugani, G, Tonet, E, Ferrari, R, Volpato, S & Campo, G 2019, 'Grip strength predicts cardiac adverse events in patients with cardiac disorders: an individual patient pooled meta-analysis', Heart, vol. 105, no. 11, pp. 834-841.
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ObjectiveGrip strength is a well-characterised measure of weakness and of poor muscle performance, but there is a lack of consensus on its prognostic implications in terms of cardiac adverse events in patients with cardiac disorders.MethodsArticles were searched in PubMed, Cochrane Library, BioMed Central and EMBASE. The main inclusion criteria were patients with cardiac disorders (ischaemic heart disease, heart failure (HF), cardiomyopathies, valvulopathies, arrhythmias); evaluation of grip strength by handheld dynamometer; and relation between grip strength and outcomes. The endpoints of the study were cardiac death, all-cause mortality, hospital admission for HF, cerebrovascular accident (CVA) and myocardial infarction (MI). Data of interest were retrieved from the articles and after contact with authors, and then pooled in an individual patient meta-analysis. Univariate and multivariate logistic regression was performed to define predictors of outcomes.ResultsOverall, 23 480 patients were included from 7 studies. The mean age was 62.3±6.9 years and 70% were male. The mean follow-up was 2.82±1.7 years. After multivariate analysis grip strength (difference of 5 kg, 5× kg) emerged as an independent predictor of cardiac death (OR 0.84, 95% CI 0.79 to 0.89, p<0.0001), all-cause death (OR 0.87, 95% CI 0.85 to 0.89, p<0.0001) and hospital admission for HF (OR 0.88, 95% CI 0.84 to 0.92, p<0.0001). On the contrary, we did not find any relationship between grip strength and occurrence of MI or CVA.ConclusionIn patients with cardiac disorders, grip strength predicted cardiac death, all-cause death and hospital admission for HF.Trial registration numberCRD42015025280.
Pavlov, D, Gurbatov, S, Kudryashov, SI, Danilov, PA, Porfirev, AP, Khonina, SN, Vitrik, OB, Kulinich, SA, Lapine, M & Kuchmizhak, AA 2019, '10-million-elements-per-second printing of infrared-resonant plasmonic arrays by multiplexed laser pulses', Optics Letters, vol. 44, no. 2, pp. 283-283.
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Pavlov, D, Syubaev, S, Kuchmizhak, A, Gurbatov, S, Vitrik, O, Modin, E, Kudryashov, S, Wang, X, Juodkazis, S & Lapine, M 2019, 'Direct laser printing of tunable IR resonant nanoantenna arrays', Applied Surface Science, vol. 469, pp. 514-520.
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© 2018 We report on the application of direct femtosecond laser printing for manufacturing periodic nanoantenna structures with various geometry and period, printed on pure or alloyed noble metal films over a silica substrate. By varying applied pulse energy, we have realised a wide range of possible morphologies, from smooth nano-bumps to protruding nanojets with up to 1 μm height, and finally to through microholes. Using several pulse energy levels, we have printed periodic nanojet arrays with periods from 1.75 to 4 μm, and measured their IR reflection spectra. The resonance frequency and magnitude of the resulting absorbance were found to essentially depend on both the periodicity of the arrays and nanojet geometry. We explain these observations by considering nanojet-assisted plasmon excitation running along the nanojets and along the surface, and found a convincing agreement to the experiments. To this end, we have shown that the reported approach is suitable for designing structures with distinct IR resonances, tunable over a range of at least 2–6 μm. Finally, we have also applied direct laser printing to a variety of noble metal alloys, involving gold, silver and palladium in various combinations and compositions, and showed that nanojets can be reliably printed for such alloys, preserving their chemical composition and its homogeneous volumetric distribution.
Payne, M, Octavia, S, Luu, LDW, Sotomayor-Castillo, C, Wang, Q, Tay, ACY, Sintchenko, V, Tanaka, MM & Lan, R 2019, 'Enhancing genomics-based outbreak detection of endemic Salmonella enterica serovar Typhimurium using dynamic thresholds', Microbial Genomics, vol. 7, no. 6.
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Salmonella enterica
serovar Typhimurium is the leading cause of salmonellosis in Australia, and the ability to identify outbreaks and their sources is vital to public health. Here, we examined the utility of whole-genome sequencing (WGS), including complete genome sequencing with Oxford Nanopore technologies, in examining 105 isolates from an endemic multi-locus variable number tandem repeat analysis (MLVA) type over 5 years. The MLVA type was very homogeneous, with 90 % of the isolates falling into groups with a five SNP cut-off. We developed a new two-step approach for outbreak detection using WGS. The first clustering at a zero single nucleotide polymorphism (SNP) cut-off was used to detect outbreak clusters that each occurred within a 4 week window and then a second clustering with dynamically increased SNP cut-offs were used to generate outbreak investigation clusters capable of identifying all outbreak cases. This approach offered optimal specificity and sensitivity for outbreak detection and investigation, in particular of those caused by endemic MLVA types or clones with low genetic diversity. We further showed that inclusion of complete genome sequences detected no additional mutational events for genomic outbreak surveillance. Phylogenetic analysis found that the MLVA type was likely to have been derived recently from a single source that persisted over 5 years, and seeded numerous sporadic infections and outbreaks. Our findings suggest that SNP cut-offs for outbreak cluster detection and public-health surveillance should be based on the local diversity of the relevant strains over time. These f...
Pearse, R, Hitchcock, JN & Keane, H 2019, 'Gender, inter/disciplinarity and marginality in the social sciences and humanities: A comparison of six disciplines', Women's Studies International Forum, vol. 72, pp. 109-126.
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Pedersen, JL, Bokil, NJ & Saunders, BM 2019, 'Developing new TB biomarkers, are miRNA the answer?', Tuberculosis, vol. 118, pp. 101860-101860.
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Efforts to reduce the global TB burden are hindered by the lack of simple, reliable non-sputum based diagnostics. To date studies investigating the biomarker potential of circulating host proteins and mRNA have not shown sufficient diagnostic utility. Recently, there has been increasing interest in circulating miRNA as a biomarker of TB disease. This review examined all published miRNA-TB biomarker studies to determine if a reproducible miRNA signature of TB disease could be elucidated. From 15 miRNA profiling studies, 894 miRNA differentially expressed between TB patients and healthy controls were identified in at least one study. Of these, 143 miRNA were validated by qPCR with 53 differentially expressed between TB patients and controls. Interestingly, only 8 of these miRNA were identified in 2 or more studies, and no consensus on a reproducible miRNA signature for identification of TB disease could be identified. TB disease is clearly associated with a wide breadth of differentially expressed miRNA. This review highlights our recent progress and the multiple factors, including environment, source of tissue, ethnicity and extent of TB disease that may influence miRNA expression. Coordinated efforts are required to validate identified targets in multiple populations to progress miRNA biomarker development.
Peel, R, Ren, S, Hure, A, Evans, T, D'Este, CA, Abhayaratna, WP, Tonkin, AM, Hopper, I, Thrift, AG, Levi, CR, Sturm, J, Durrheim, D, Hung, J, Briffa, TG, Chew, DP, Anderson, P, Moon, L, McEvoy, M, Hansbro, PM, Newby, DA & Attia, JR 2019, 'Evaluating recruitment strategies for AUSPICE , a large Australian community‐based randomised controlled trial', Medical Journal of Australia, vol. 210, no. 9, pp. 409-415.
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OBJECTIVES:To examine the effectiveness of different strategies for recruiting participants for a large Australian randomised controlled trial (RCT), the Australian Study for the Prevention through Immunisation of Cardiovascular Events (AUSPICE). DESIGN, SETTING, PARTICIPANTS:Men and women aged 55-60 years with at least two cardiovascular risk factors (hypertension, hypercholesterolaemia, overweight/obesity) were recruited for a multicentre placebo-controlled RCT assessing the effectiveness of 23-valent pneumococcal polysaccharide vaccine (23vPPV) for preventing cardiovascular events. METHODS:Invitations were mailed by the Australian Department of Human Services to people in the Medicare database aged 55-60 years; reminders were sent 2 weeks later. Invitees could respond in hard copy or electronically. Direct recruitment was supplemented by asking invitees to extend the invitation to friends and family (snowball sampling) and by Facebook advertising. MAIN OUTCOME:Proportions of invitees completing screening questionnaire and recruited for participation in the RCT. RESULTS:21 526 of 154 992 invited people (14%) responded by completing the screening questionnaire, of whom 4725 people were eligible and recruited for the study. Despite the minimal study burden (one questionnaire, one clinic visit), the overall participation rate was 3%, or an estimated 10% of eligible persons. Only 16% of eventual participants had responded within 2 weeks of the initial invitation letter (early responders); early and late responders did not differ in their demographic or medical characteristics. Socio-economic disadvantage did not markedly influence response rates. Facebook advertising and snowball sampling did not increase recruitment. CONCLUSIONS:Trial participation rates are low, and multiple concurrent methods are needed to maximise recruitment. Social media strategies may not be successful in older age groups. TRIAL REGISTRATION:Australian New Zealand Clinical Trials Registry, A...
Peng, D, Zhang, H, Liu, L, Huang, W, Huete, AR, Zhang, X, Wang, F, Yu, L, Xie, Q, Wang, C, Luo, S, Li, C & Zhang, B 2019, 'Estimating the Aboveground Biomass for Planted Forests Based on Stand Age and Environmental Variables', Remote Sensing, vol. 11, no. 19, pp. 2270-2270.
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Measuring forest aboveground biomass (AGB) at local to regional scales is critical to understanding their role in regional and global carbon cycles. The Three-North Shelterbelt Forest Program (TNSFP) is the largest ecological restoration project in the world, and has been ongoing for over 40 years. In this study, we developed models to estimate the planted forest aboveground biomass (PF_AGB) for Yulin, a typical area in the project. Surface reflectances in the study area from 1978 to 2013 were obtained from Landsat series images, and integrated forest z-scores were constructed to measure afforestation and the stand age of planted forest. Normalized difference vegetation index (NDVI) was combined with stand age to develop an initial model to estimate PF_AGB. We then developed additional models that added environment variables to our initial model, including climatic factors (average temperature, total precipitation, and total sunshine duration) and a topography factor (slope). The model which combined the total precipitation and slope greatly improved the accuracy of PF_AGB estimation compared to the initial model, indicating that the environmental variables related to water distribution indirectly affected the growth of the planted forest and the resulting AGB. Afforestation in the study area occurred mainly in the early 1980s and early 21st century, and the PF_AGB in 2003 was 2.3 times than that of 1998, since the fourth term TNSFP started in 2000. The PF_AGB in 2013 was about 3.33 times of that in 2003 because many young trees matured. The leave-one-out cross-validation (LOOCV) approach showed that our estimated PF_AGB had a significant correlation with field-measured data (correlation coefficient (r) = 0.89, p < 0.001, root mean square error (RMSE) = 6.79 t/ha). Our studies provided a method to estimate long time series PF_AGB using satellite repetitive measures, particularly for arid or semi-arid areas.
Pereira, RRC, Scanes, E, Parker, L, Byrne, M, Cole, VJ & Ross, PM 2019, 'Restoring the flat oyster Ostrea angasi in the face of a changing climate', Marine Ecology Progress Series, vol. 625, pp. 27-39.
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Pérez-Tomás, A, Chikoidze, E, Dumont, Y, Jennings, MR, Russell, SO, Vales-Castro, P, Catalan, G, Lira-Cantú, M, Ton –That, C, Teherani, FH, Sandana, VE, Bove, P & Rogers, DJ 2019, 'Giant bulk photovoltaic effect in solar cell architectures with ultra-wide bandgap Ga2O3 transparent conducting electrodes', Materials Today Energy, vol. 14, pp. 100350-100350.
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© 2019 Elsevier Ltd The use of ultra-wide bandgap transparent conducting beta gallium oxide (β-Ga2O3) thin films as electrodes in ferroelectric solar cells is reported. In a new material structure for energy applications, we report a solar cell structure (a light absorber sandwiched in between two electrodes - one of them - transparent) which is not constrained by the Shockley–Queisser limit for open-circuit voltage (Voc) under typical indoor light. The solar blindness of the electrode enables a record-breaking bulk photovoltaic effect (BPE) with white light illumination (general use indoor light). This work opens up the perspective of ferroelectric photovoltaics which are not subject to the Shockley-Queisser limit by bringing into scene solar-blind conducting oxides.
Pernice, M & Hughes, DJ 2019, 'Forecasting global coral bleaching', Nature Climate Change, vol. 9, no. 11, pp. 803-804.
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Petroll, K, Care, A, Waterstraat, M, Bergquist, PL & Sunna, A 2019, 'Mixed-mode liquid chromatography for the rapid analysis of biocatalytic glucaric acid reaction pathways', Analytica Chimica Acta, vol. 1066, pp. 136-145.
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Petroll, K, Kopp, D, Care, A, Bergquist, PL & Sunna, A 2019, 'Tools and strategies for constructing cell-free enzyme pathways', Biotechnology Advances, vol. 37, no. 1, pp. 91-108.
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Petrou, K, Baker, KG, Nielsen, DA, Hancock, AM, Schulz, KG & Davidson, AT 2019, 'Acidification diminishes diatom silica production in the Southern Ocean', Nature Climate Change, vol. 9, no. 10, pp. 781-786.
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© 2019, The Author(s), under exclusive licence to Springer Nature Limited. Diatoms, large bloom-forming marine microorganisms, build frustules out of silicate, which ballasts the cells and aids their export to the deep ocean. This unique physiology forges an important link between the marine silicon and carbon cycles. However, the effect of ocean acidification on the silicification of diatoms is unclear. Here we show that diatom silicification strongly diminishes with increased acidity in a natural Antarctic community. Analyses of single cells from within the community reveal that the effect of reduced pH on silicification differs among taxa, with several species having significantly reduced silica incorporation at CO2 levels equivalent to those projected for 2100. These findings suggest that, before the end of this century, ocean acidification may influence the carbon and silicon cycle by both altering the composition of the diatom assemblages and reducing cell ballasting, which will probably alter vertical flux of these elements to the deep ocean.
Pettit, T, Bettes, M, Chapman, AR, Hoch, LM, James, ND, Irga, PJ & Torpy, FR 2019, 'The botanical biofiltration of VOCs with active airflow: is removal efficiency related to chemical properties?', Atmospheric Environment, vol. 214, pp. 116839-116839.
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© 2019 Elsevier Ltd Botanical biofiltration using active green walls is showing increasing promise as a viable method for the filtration of volatile organic compounds (VOCs) from ambient air; however there is a high level of heterogeneity reported amongst VOC removal efficiencies, and the reasons for these observations have yet to be explained. Comparisons of removal efficiencies amongst studies is also difficult due to the use of many different VOCs, and systems that have been tested under different conditions. The current work describes a procedure to determine whether some of these differences may be related to the chemical properties of the VOCs themselves. This work used an active green wall system to test the single pass removal efficiency (SPRE) of nine different VOCs (acetone, benzene, cyclohexane, ethanol, ethyl acetate, hexane, isopentane, isopropanol and toluene) and explored which chemical properties were meaningful predictor variables of their biofiltration efficiencies. Ethanol was removed most efficiently (average SPRE of 96.34% ± 1.61), while benzene was least efficiently removed (average SPRE of 19.76% ± 2.93). Multiple stepwise linear regression was used to determine that the dipole moment and molecular mass were significant predictors of VOC SPRE, in combination accounting for 54.6% of the variability in SPREs amongst VOCs. The octanol water partition coefficient, proton affinity, Henry's law constant and vapour pressure were not significant predictors of SPRE. The most influential predictor variable was the dipole moment, alone accounting for 49.8% of the SPRE variability. The model thus allows for an estimation of VOC removal efficiency based on a VOC's chemical properties, and supports the idea that system optimisation could be achieved through methods that promote both VOC partitioning into the biofilter's aqueous phase, and substrate development to enhance adsorption.'
Pettit, T, Irga, PJ & Torpy, FR 2019, 'The in situ pilot-scale phytoremediation of airborne VOCs and particulate matter with an active green wall', Air Quality, Atmosphere & Health, vol. 12, no. 1, pp. 33-44.
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© 2019, Springer Nature B.V. Atmospheric pollutant phytoremediation technologies, such as potted plants and green walls, have been thoroughly tested in lab-scale experiments for their potential to remove air pollutants. The functional value of these technologies, however, is yet to be adequately assessed in situ, in ‘high value’ environments, where pollutant removal will provide the greatest occupant health benefits. Air pollution in countries such as China is a significant public health issue, and efficient air pollution control technologies are needed. This work used pilot-scale trials to test the capacity of potted plants, a passive green wall and an active green wall (AGW) to remove particulate matter (PM) and total volatile organic compounds (TVOCs) from a room in a suburban residential house in Sydney, Australia, followed by an assessment of the AGW’s potential to remove these pollutants from a classroom in Beijing. In the residential room, compared to potted plants and the passive green wall, the AGW maintained TVOCs at significantly lower concentrations throughout the experimental period (average TVOC concentration 72.5% lower than the control), with a similar trend observed for PM. In the classroom, the AGW reduced the average TVOC concentration by ~ 28% over a 20-min testing period compared to levels with no green wall and a filtered HVAC system in operation. The average ambient PM concentration in the classroom with the HVAC system operating was 101.18 μg/m3, which was reduced by 42.6% by the AGW. With further empirical validation, AGWs may be implemented to efficiently clean indoor air through functional reductions in PM and TVOC concentrations.
Pettit, T, Irga, PJ, Surawski, NC & Torpy, FR 2019, 'An Assessment of the Suitability of Active Green Walls for NO2 Reduction in Green Buildings Using a Closed-Loop Flow Reactor', Atmosphere, vol. 10, no. 12, pp. 801-801.
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Nitrogen dioxide (NO2) is a common urban air pollutant that is associated with several adverse human health effects from both short and long term exposure. Additionally, NO2 is highly reactive and can influence the mixing ratios of nitrogen oxide (NO) and ozone (O3). Active green walls can filter numerous air pollutants whilst using little energy, and are thus a candidate for inclusion in green buildings, however, the remediation of NO2 by active green walls remains untested. This work assessed the capacity of replicate active green walls to filter NO2 at both ambient and elevated concentrations within a closed-loop flow reactor, while the concentrations of NO and O3 were simultaneously monitored. Comparisons of each pollutant’s decay rate were made for green walls containing two plant species (Spathiphyllum wallisii and Syngonium podophyllum) and two lighting conditions (indoor and ultraviolet). Biofilter treatments for both plant species exhibited exponential decay for the biofiltration of all three pollutants at ambient concentrations. Furthermore, both treatments removed elevated concentrations of NO and NO2, (average NO2 clean air delivery rate of 661.32 and 550.8 m3∙h−1∙m−3 of biofilter substrate for the respective plant species), although plant species and lighting conditions influenced the degree of NOx removal. Elevated concentrations of NOx compromised the removal efficiency of O3. Whilst the current work provided evidence that effective filtration of NOx is possible with green wall technology, long-term experiments under in situ conditions are needed to establish practical removal rates and plant health effects from prolonged exposure to air pollution.
Phillips, C, McNevin, D, Kidd, KK, Lagacé, R, Wootton, S, de la Puente, M, Freire-Aradas, A, Mosquera-Miguel, A, Eduardoff, M, Gross, T, Dagostino, L, Power, D, Olson, S, Hashiyada, M, Oz, C, Parson, W, Schneider, PM, Lareu, MV & Daniel, R 2019, 'MAPlex - A massively parallel sequencing ancestry analysis multiplex for Asia-Pacific populations', Forensic Science International: Genetics, vol. 42, pp. 213-226.
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Current forensic ancestry-informative panels are limited in their ability to differentiate populations in the Asia-Pacific region. MAPlex (Multiplex for the Asia-Pacific), a massively parallel sequencing (MPS) assay, was developed to improve differentiation of East Asian, South Asian and Near Oceanian populations found in the extensive cross-continental Asian region that shows complex patterns of admixture at its margins. This study reports the development of MAPlex; the selection of SNPs in combination with microhaplotype markers; assay design considerations for reducing the lengths of microhaplotypes while preserving their ancestry-informativeness; adoption of new population-informative multiple-allele SNPs; compilation of South Asian-informative SNPs suitable for forensic AIMs panels; and the compilation of extensive reference and test population genotypes from online whole-genome-sequence data for MAPlex markers. STRUCTURE genetic clustering software was used to gauge the ability of MAPlex to differentiate a broad set of populations from South and East Asia, the West Pacific regions of Near Oceania, as well as the other globally distributed population groups. Preliminary assessment of MAPlex indicates enhanced South Asian differentiation with increased divergence between West Eurasian, South Asian and East Asian populations, compared to previous forensic SNP panels of comparable scale. In addition, MAPlex shows efficient differentiation of Middle Eastern individuals from Europeans. MAPlex is the first forensic AIM assay to combine binary and multiple-allele SNPs with microhaplotypes, adding the potential to detect and analyze mixed source forensic DNA.
Phong Vo, HN, Le, GK, Hong Nguyen, TM, Bui, X-T, Nguyen, KH, Rene, ER, Vo, TDH, Thanh Cao, N-D & Mohan, R 2019, 'Acetaminophen micropollutant: Historical and current occurrences, toxicity, removal strategies and transformation pathways in different environments', Chemosphere, vol. 236, pp. 124391-124391.
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Pike, DA, Roznik, EA, Webb, JK & Shine, R 2019, 'Life history and ecology of the elegant snake-eyed skink (Cryptoblepharus pulcher) in south-eastern Australia', Australian Journal of Zoology, vol. 67, no. 1, pp. 51-51.
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Detailed information on life history and ecology is essential for successful conservation and management. However, we have relatively little detailed data on the life history and ecology of most small lizard species, relative to other vertebrates, especially those that have undergone recent taxonomic changes. We studied the ecology of the elegant snake-eyed skink (Cryptoblepharus pulcher), a lizard that occurs on trees, fences, walls, and rock outcroppings in eastern Australia that spans temperate to tropical environments. In our temperate-zone study population living in natural habitat, individuals are active year-round, and gravid females were found during the months of September through December. Sexual maturity is reached in 12 months, lifespan is at least three years, and clutch size is typically two eggs. In laboratory incubation experiments, larger eggs were more likely to hatch. Low incubation temperatures (averaging 23 ± 7.5°C versus high temperatures averaging 26 ± 7.5°C) increased incubation duration significantly (range 56–72 days versus 40–51 days) and reduced the body size of hatchlings significantly (17.8 mm versus 18.7 mm snout–vent length). Skinks sheltered beneath small rocks that were not shared simultaneously with predatory snakes, and that reached average temperatures that were up to 3°C warmer during the day than unused rocks. Preferred microhabitats include substrates of rock or soil, and the largest rocks were occasionally shared by up to four individuals of all body size/sex combinations (5.8% of observations were shared, 30.2% of individual rocks were shared). Our study expands upon knowledge of the widespread genus Cryptoblepharus by providing detailed life history and ecological information on C. pulcher that can serve as a baseline for future studies.
Pires da Silva, I, Wang, KYX, Wilmott, JS, Holst, J, Carlino, MS, Park, JJ, Quek, C, Wongchenko, M, Yan, Y, Mann, G, Johnson, DB, McQuade, JL, Rai, R, Kefford, RF, Rizos, H, Scolyer, RA, Yang, JYH, Long, GV & Menzies, AM 2019, 'Distinct Molecular Profiles and Immunotherapy Treatment Outcomes of V600E and V600K BRAF-Mutant Melanoma', Clinical Cancer Research, vol. 25, no. 4, pp. 1272-1279.
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Abstract
Purpose:
BRAF V600E and V600K melanomas have distinct clinicopathologic features, and V600K appear to be less responsive to BRAFi±MEKi. We investigated mechanisms for this and explored whether genotype affects response to immunotherapy.
Experimental Design:
Pretreatment formalin-fixed paraffin-embedded tumors from patients treated with BRAFi±MEKi underwent gene expression profiling and DNA sequencing. Molecular results were validated using The Cancer Genome Atlas (TCGA) data. An independent cohort of V600E/K patients treated with anti–PD-1 immunotherapy was examined.
Results:
Baseline tissue and clinical outcome with BRAFi±MEKi were studied in 93 patients (78 V600E, 15 V600K). V600K patients had numerically less tumor regression (median, −31% vs. −52%, P = 0.154) and shorter progression-free survival (PFS; median, 5.7 vs. 7.1 months, P = 0.15) compared with V600E. V600K melanomas had lower expression of the ERK pathway feedback regulator dual-specificity phosphatase 6, confirmed with TCGA data (116 V600E, 17 V600K). Pathway analysis showed V600K had lower expression of ERK and higher expression of PI3K-AKT genes than V600E. Higher mutational load was observed in V600K, with a higher proportion of mutations in PIK3R1 and tumor-suppressor genes. In patients treated with anti–PD-1, V600K (n = 19) had superior outcomes than V600E (n = 84), including response rate (53% vs. 29%, P = 0.059), PFS (median, 19 vs. 2.7 months, P = 0.049), and overall survival (20.4 vs. 11.7 months, P = 0.081).
Conclu...
Poerwoprajitno, AR, Gloag, L, Benedetti, TM, Cheong, S, Watt, J, Huber, DL, Gooding, JJ & Tilley, RD 2019, 'Formation of Branched Ruthenium Nanoparticles for Improved Electrocatalysis of Oxygen Evolution Reaction', Small, vol. 15, no. 17, pp. 1804577-1804577.
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AbstractBranched nanoparticles are one of the most promising nanoparticle catalysts as their branch sizes and surfaces can be tuned to enable both high activity and stability. Understanding how the crystallinity and surface facets of branched nanoparticles affect their catalytic performance is vital for further catalyst development. In this work, a synthesis is developed to form highly branched ruthenium (Ru) nanoparticles with control of crystallinity. It is shown that faceted Ru branched nanoparticles have improved stability and activity in the oxygen evolution reaction (OER) compared with polycrystalline Ru nanoparticles. This work achieves a low 180 mV overpotential at 10 mA cm−2 for hours, demonstrating that record‐high stability for Ru nanocrystals can be achieved while retaining high activity for OER. The superior electrocatalytic performance of faceted Ru branched nanoparticles is ascribed to the lower Ru dissolution rate under OER conditions due to low‐index facets on the branch surfaces.
Polikarpov, D, Liang, L, Care, A, Sunna, A, Campbell, D, Walsh, B, Balalaeva, I, Zvyagin, A, Gillatt, D & Guryev, E 2019, 'Functionalized Upconversion Nanoparticles for Targeted Labelling of Bladder Cancer Cells', Biomolecules, vol. 9, no. 12, pp. 820-820.
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Bladder cancer is the ninth most common cancer worldwide. Due to a high risk of recurrence and progression of bladder cancer, every patient needs long-term surveillance, which includes regular cystoscopy, sometimes followed by a biopsy of suspicious lesions or resections of recurring tumours. This study addresses the development of novel biohybrid nanocomplexes representing upconversion nanoparticles (UCNP) coupled to antibodies for photoluminescent (PL) detection of bladder cancer cells. Carrying specific antibodies, these nanoconjugates selectively bind to urothelial carcinoma cells and make them visible by emitting visible PL upon excitation with deeply penetrating near-infrared light. UCNP were coated with a silica layer and linked to anti-Glypican-1 antibody MIL38 via silica-specific solid-binding peptide. Conjugates have been shown to specifically attach to urothelial carcinoma cells with high expression of Glypican-1. This result highlights the potential of produced conjugates and conjugation technology for further studies of their application in the tumour detection and fluorescence-guided resection.
Pollier, J, Vancaester, E, Kuzhiumparambil, U, Vickers, CE, Vandepoele, K, Goossens, A & Fabris, M 2019, 'A widespread alternative squalene epoxidase participates in eukaryote steroid biosynthesis', Nature Microbiology, vol. 4, no. 2, pp. 226-233.
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Steroids are essential triterpenoid molecules that are present in all eukaryotes and modulate the fluidity and flexibility of cell membranes. Steroids also serve as signalling molecules that are crucial for growth, development and differentiation of multicellular organisms1-3. The steroid biosynthetic pathway is highly conserved and is key in eukaryote evolution4-7. The flavoprotein squalene epoxidase (SQE) catalyses the first oxygenation reaction in this pathway and is rate limiting. However, despite its conservation in animals, plants and fungi, several phylogenetically widely distributed eukaryote genomes lack an SQE-encoding gene7,8. Here, we discovered and characterized an alternative SQE (AltSQE) belonging to the fatty acid hydroxylase superfamily. AltSQE was identified through screening of a gene library of the diatom Phaeodactylum tricornutum in a SQE-deficient yeast. In accordance with its divergent protein structure and need for cofactors, we found that AltSQE is insensitive to the conventional SQE inhibitor terbinafine. AltSQE is present in many eukaryotic lineages but is mutually exclusive with SQE and shows a patchy distribution within monophyletic clades. Our discovery provides an alternative element for the conserved steroid biosynthesis pathway, raises questions about eukaryote metabolic evolution and opens routes to develop selective SQE inhibitors to control hazardous organisms.
Popovic, A, Morelato, M, Roux, C & Beavis, A 2019, 'Review of the most common chemometric techniques in illicit drug profiling', Forensic Science International, vol. 302, pp. 109911-109911.
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The information generated through drug profiling can be used to infer a common source between one or several seizures as well as drug trafficking routes to provide insights into drug markets. Although well established, it is time-consuming and ineffective to compare all drug profiles manually. In recent years, there has been a push to automate processes to enable a more efficient comparison of illicit drug specimens. Various chemometric methods have been employed to compare and interpret forensic case data promptly. The intelligence that is produced can be used by decision-makers to disrupt or reduce the impact of illicit drug markets. This review highlights the most common chemometric techniques used in drug profiling and more specifically, the most efficient comparison metrics and pattern recognition techniques outlined in the literature.
Popplewell, M, Reizes, J & Zaslawski, C 2019, 'A Novel Approach to Describing Traditional Chinese Medical Patterns: The “Traditional Chinese Medical Diagnostic Descriptor”', The Journal of Alternative and Complementary Medicine, vol. 25, no. 11, pp. 1121-1129.
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OBJECTIVES:In the first of a series of three articles by the present authors, diagnostic agreement between Traditional Chinese Medicine (TCM) practitioners was found to be low. This was the first time that TCM diagnoses had been evaluated with an open population of patients and this result is a cause of concern. In the second article, incorrect statistics were shown to have often been used to calculate chance-removed inter-rater agreement, and appropriate statistics such as Gwet's Agreement Coefficient 2 (AC2) was recommended for future studies. In this, the third article, a novel approach to recording TCM diagnostic patterns, the Traditional Chinese Medical Diagnostic Descriptor (TCMDD), is presented that allows chance-removed agreement calculation. An example of mapping TCM diagnostic patterns to the TCMDD format is given and diagnostic agreement is evaluated. Design, Settings, Subjects: The same 35 subjects used to report agreement in our first article were also diagnosed by additional practitioners using the TCMDD format during the same experimental sessions at the University of Technology, Sydney Clinic. TCM diagnoses from the first article were also mapped to the TCMDD format. OUTCOME MEASURES:Linearly weighted simple agreement and the AC2 statistic were utilized and all results compared. RESULTS:Linearly weighted simple agreement using the TCMDD and TCM mapped to TCMDD format averaged 0.80 ± 0.02 compared with 0.19 for TCM. TCMDD and TCM mapped to TCMDD chance-removed agreement, as calculated with AC2, ranged between 0.67 and 0.73 ± 0.03. CONCLUSIONS:The TCMDD allows the essence of diagnoses expressed by TCM practitioners to be appropriately compared. This was confirmed by the TCM mapped to TCMDD results. In both cases, simple agreement was significantly greater than that obtained with the TCM format. Chance-removed statistics and error estimates can be reliably calculated with the AC2 and the TCMDD in open populations.
Popplewell, M, Reizes, J & Zaslawski, C 2019, 'Appropriate Statistics for Determining Chance-Removed Interpractitioner Agreement', The Journal of Alternative and Complementary Medicine, vol. 25, no. 11, pp. 1115-1120.
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Fleiss' Kappa (FK) has been commonly, but incorrectly, employed as the "standard" for evaluating chance-removed inter-rater agreement with ordinal data. This practice may lead to misleading conclusions in inter-rater agreement research. An example is presented that demonstrates the conditions where FK produces inappropriate results, compared with Gwet's AC2, which is proposed as a more appropriate statistic. A novel format for recording a Chinese Medical (CM) diagnoses, called the Diagnostic System of Oriental Medicine (DSOM), was used to record and compare patient diagnostic data, which, unlike the contemporary CM diagnostic format, allows agreement by chance to be considered when evaluating patient data obtained with unrestricted diagnostic options available to diagnosticians.Five CM practitioners diagnosed 42 subjects drawn from an open population. Subjects' diagnoses were recorded using the DSOM format. All the available data were initially used to evaluate agreement. Then, the subjects were sorted into three groups to demonstrate the effects of differing data marginality on the calculated chance-removed agreement.Agreement between the practitioners for each subject was evaluated with linearly weighted simple agreement, FK and Gwet's AC2.In all cases, overall agreement was much lower with FK than Gwet's AC2. Larger differences occurred when the data were more free marginal. Inter-rater agreement determined with FK statistics is unlikely to be correct unless it can be shown that the data from which agreement is determined are, in fact, fixed marginal. It follows that results obtained on agreement between practitioners with FK are probably incorrect. It is shown that inter-rater agreement evaluated with AC2 statistic is an appropriate measure when fixed marginal data are neither expected nor guaranteed. The AC2 statistic should be used as the standard statistical approach for determining agreement between practitioners.
Popplewell, M, Reizes, J & Zaslawski, C 2019, 'Consensus in Traditional Chinese Medical Diagnosis in Open Populations', The Journal of Alternative and Complementary Medicine, vol. 25, no. 11, pp. 1109-1114.
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An acceptable level of diagnostic agreement is a prerequisite for consistent administration of treatment. It is critical for investigating effectiveness of different treatment approaches using multiple practitioners. To the best of our knowledge, no previous investigation of diagnostic consensus using open populations in Chinese medicine (CM) has been reported. Investigations restricted to individual medical conditions, such as have been usually studied, do not reveal any information as to what occurs in real world clinical settings. This knowledge gap led to the current study being conducted. Design/Location/Subjects/Interventions: Investigating diagnostic agreement specifically in Traditional Chinese Medicine (TCM) in an open population, two or three practitioners diagnosed 35 subjects at the University of Technology, Sydney (UTS), TCM clinic. The practitioners were restricted to a list of the 56 most frequently used TCM diagnoses at the UTS clinic. Up to three diagnostic patterns per subject could be selected, with nominated patterns scored between 1 and 5.Agreement was determined with two criteria, both expressed as simple percentages: pattern and linearly weighted agreements.The results showed that 23% of practitioners obtained pattern agreement, while 19% demonstrated weighted agreement.There appears to be very low diagnostic agreement between practitioners. This is an important finding. If unchallenged by further investigation, the recognition of such poor diagnostic consensus may lead to rejection of TCM theory before it has been adequately assessed. Diagnostic agreement must be improved so that future investigations into treatment effectiveness or mechanisms of action are made on a valid basis. Additionally, the current TCM diagnostic format must be altered to allow the application of chance-removed statistics or the calculation of a standard error with open populations. This article is the first of a series of three that report problems in TCM diagnosti...
Pouwels, SD, Klont, F, Kwiatkowski, M, Wiersma, VR, Faiz, A, van den Berge, M, Horvatovich, P, Bischoff, R & ten Hacken, NHT 2019, 'Reply to Biswas: Acute and Chronic Effects of Cigarette Smoking on sRAGE', American Journal of Respiratory and Critical Care Medicine, vol. 199, no. 6, pp. 806-807.
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Previdi, R, Levchenko, I, Arnold, M, Gali, M, Bazaka, K, Xu, S, Ostrikov, KK, Bray, K, Jin, D & Fang, J 2019, 'Plasmonic platform based on nanoporous alumina membranes: order control via self-assembly', Journal of Materials Chemistry A, vol. 7, no. 16, pp. 9565-9577.
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A novel approach to significantly enhance and comprehensively assess the level of nanochannel ordering in self-assembled nanoporous membranes is proposed and tested.
Prosser, C, Meyer, W, Ellis, J & Lee, R 2019, 'Traveller sentinels for global surveillance of malaria drug resistance and diagnostic test evasion', International Journal of Infectious Diseases, vol. 79, pp. 22-23.
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Raina, J-B, Fernandez, V, Lambert, B, Stocker, R & Seymour, JR 2019, 'The role of microbial motility and chemotaxis in symbiosis', Nature Reviews Microbiology, vol. 17, no. 5, pp. 284-294.
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Many symbiotic relationships rely on the acquisition of microbial partners from the environment. However, the mechanisms by which microbial symbionts find and colonize their hosts are often unknown. We propose that the acquisition of environmental symbionts often necessitates active migration and colonization by the symbionts through motility and chemotaxis. The pivotal role of these behaviours in the onset and maintenance of symbiotic interactions is well established in a small number of model systems but remains largely overlooked for the many symbioses that involve the recruitment of microbial partners from the environment. In this Review, we highlight when, where and how chemotaxis and motility can enable symbiont recruitment and propose that these symbiont behaviours are important across a wide range of hosts and environments.
Rajeshkumar, S, Menon, S, Venkat Kumar, S, Tambuwala, MM, Bakshi, HA, Mehta, M, Satija, S, Gupta, G, Chellappan, DK, Thangavelu, L & Dua, K 2019, 'Antibacterial and antioxidant potential of biosynthesized copper nanoparticles mediated through Cissus arnotiana plant extract', Journal of Photochemistry and Photobiology B: Biology, vol. 197, pp. 111531-111531.
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Ramarajan, M, Fabris, M, Abbriano, RM, Pernice, M & Ralph, PJ 2019, 'Novel endogenous promoters for genetic engineering of the marine microalga Nannochloropsis gaditana CCMP526', Algal Research, vol. 44, pp. 101708-101708.
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© 2019 Elsevier B.V. Nannochloropsis is a marine microalga from the Eustigmatophyceae stramenopile lineage that has been studied extensively due to a broad range of industrial applications, mostly related to their oil and pigment production. However, tools to genetically engineer members of this group, and therefore further understand and maximise their industrial potential are still limited. In order to expand the potential industrial uses of this organism, several molecular tools, including gene promoters of different strength, are needed. A comprehensive and diverse set of well-characterized promoters is key to a number of genetic engineering and synthetic biology applications, such as the assembly of complex biological functions or entire metabolic pathways. In this study, we measured the promoter activity of three endogenous constitutive promoters from N. gaditana genes EPPSII (Nga02101); HSP90 (Nga00934); ATPase (Nga06354.1) in driving the expression of a Sh ble- mVenus fluorescent reporter fusion protein. Through a combined approach that includes flow cytometry, RT-qPCR and immunoblotting, we profiled the activity of these promoters at both the transcript and protein level. Two promoters HSP90 (Nga00934) and EPPSII (Nga02101) outperformed the widely used β-tubulin promoter, exhibiting 4.5 and 3.1-fold higher mVenus fluorescence, respectively. A third promoter ATPase (Nga06354.1) was also able to drive the expression of transgenes, albeit at lower levels. We show that the new promoters identified in this study are valuable tools, which can be used for genetic engineering and functional genetics studies in N. gaditana.
Ramsahai, JM, Hansbro, PM & Wark, PAB 2019, 'Mechanisms and Management of Asthma Exacerbations', American Journal of Respiratory and Critical Care Medicine, vol. 199, no. 4, pp. 423-432.
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Acute asthma remains an important medical emergency, the most frequent cause of acute admissions in children and a major source of morbidity for adults with asthma. In all ages with asthma the presence of exacerbations is an important defining characteristic of asthma severity. In this review we will assess the epidemiology of acute asthma, the triggers of acute exacerbations and the mechanisms that underlie these exacerbations. We will also assess current treatments that prevent exacerbations, with an emphasis on the role of type 2 airway inflammation in the context of acute exacerbations and the novel treatments that effectively target this. Finally we will review current management strategies of the exacerbations themselves.
Rani, A, Viljoen, A, Johansen, MD, Kremer, L & Kumar, V 2019, 'Synthesis, anti-mycobacterial and cytotoxic evaluation of substituted isoindoline-1,3-dione-4-aminoquinolines coupled via alkyl/amide linkers', RSC Advances, vol. 9, no. 15, pp. 8515-8528.
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A series of secondary amine-substituted isoindoline-1,3-dione-4-aminoquinolines were prepared via microwave heating and assayed for their anti-mycobacterial activities.
Rathnayake, SNH, Van den Berge, M & Faiz, A 2019, 'Genetic profiling for disease stratification in chronic obstructive pulmonary disease and asthma', Current Opinion in Pulmonary Medicine, vol. 25, no. 3, pp. 317-322.
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PURPOSE OF REVIEW:In asthma and chronic obstructive pulmonary disease (COPD), the movement towards genetic profiling with a push towards 'personalized medicine' has been hindered by complex environment--gene interactions and lack of tools to identify clear causal genetic traits. In this review, we will discuss the need for genetic profiling in asthma and COPD, what methods are currently used in the clinics and the recent finding using new sequencing methods. RECENT FINDINGS:Over the past 10-15 years, genome-wide association studies analysis of common variants has provide little in the way of new genetic profiling markers for asthma and COPD. Whole exome/genome sequencing has provided a new method to identify lowly abundant alleles, which might have a much higher impact. Although, low population numbers due to high costs has hindered early studies, recent studies have reached genome wide significance. SUMMARY:The use of genetic profiling of COPD in the clinic is current limited to the identification of Alpha-1 antitrypsin deficiency, while being absent in asthma. Advances in sequencing technology provide new avenues to identify disease causes or therapy response altering variants that in the short-term will allow for the development of screening procedures for disease to identify patients at risk of developing asthma or COPD.
Rätsep, M, Linnanto, JM, Muru, R, Biczysko, M, Reimers, JR & Freiberg, A 2019, 'Absorption-emission symmetry breaking and the different origins of vibrational structures of the 1Qy and 1Qx electronic transitions of pheophytin a', The Journal of Chemical Physics, vol. 151, no. 16, pp. 165102-165102.
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The vibrational structure of the optical absorption and fluorescence spectra of the two lowest-energy singlet electronic states (Qy and Qx) of pheophytin a were carefully studied by combining low-resolution and high-resolution spectroscopy with quantum chemical analysis and spectral modeling. Large asymmetry was revealed between the vibrational structures of the Qy absorption and fluorescence spectra, integrally characterized by the total Huang-Rhys factor and reorganization energy in absorption of SvibA = 0.43 ± 0.06, λA = 395 cm−1 and in emission of SvibE = 0.35 ± 0.06, λE = 317 cm−1. Time-dependent density-functional theory using the CAM-B3LYP, ωB97XD, and MN15 functionals could predict and interpret this asymmetry, with the exception of one vibrational mode per model, which was badly misrep