Choi, AH & Ben-Nissan, B 2018, Anatomy, Modeling and Biomaterial Fabrication for Dental and Maxillofacial Applications, Bentham Science Publishers. View description>>
For example, by integrating computerized modeling with medical imaging, it
would be possible to determine the ... of this computerized modeling
methodology will have innumerable applications in both dentistry and in oral and
maxillofacial ...
This easy-to-follow applied book expands upon the authors’ prior work on semiparametric regression to include the use of R software. In 2003, authors Ruppert and Wand co-wrote Semiparametric Regression with R.J. Carroll, which introduced the techniques and benefits of semiparametric regression in a concise and user-friendly fashion. Fifteen years later, semiparametric regression is applied widely, powerful new methodology is continually being developed, and advances in the R computing environment make it easier than ever before to carry out analyses.
Semiparametric Regression with R introduces the basic concepts of semiparametric regression with a focus on applications and R software. This volume features case studies from environmental, economic, financial, and other fields. The examples and corresponding code can be used or adapted to apply semiparametric regression to a wide range of problems. It contains more than fifty exercises, and the accompanying HRW package contains all datasets and scripts used in the book, as well as some useful R functions.
This book is suitable as a textbook for advanced undergraduates and graduate students, as well as a guide for statistically-oriented practitioners, and could be used in conjunction with Semiparametric Regression. Readers are assumed to have a basic knowledge of R and some exposure to linear models. For the underpinning principles, calculus-based probability, statistics, and linear algebra are desirable.
Scammell, H 2018, Interplay of Quantum and Statistical Fluctuations in Critical Quantum Matter, Springer. View description>>
This book explores critical phenomena in highly correlated quantum matter.
Aneece, IP, Thenkabail, PS, Lyon, JG, Huete, A & Slonecker, T 2018, 'Spaceborne Hyperspectral EO-1 Hyperion Data Pre-Processing' in Fundamentals, Sensor Systems, Spectral Libraries, and Data Mining for Vegetation, CRC Press, pp. 251-272. View/Download from: Publisher's site
Awasthi, R, Singh, AK, Mishra, G, Maurya, A, Chellappan, DK, Gupta, G, Hansbro, PM & Dua, K 2018, 'An Overview of Circular RNAs' in Advances in Experimental Medicine and Biology, Springer Singapore, Germany, pp. 3-14. View/Download from: Publisher's site View description>>
Circular RNAs (cirRNAs) are long, noncoding endogenous RNA molecules and covalently closed continuous loop without 5′–3′ polarity and polyadenylated tail which are largely concentrated in the nucleus. CirRNA regulates gene expression by modulating microRNAs and functions as potential biomarker. CirRNAs can translate in vivo to link between their expression and disease. They are resistant to RNA exonuclease and can convert to the linear RNA by microRNA which can then act as competitor to endogenous RNA. This chapter summarizes the evolutionary conservation and expression of cirRNAs, their identification, highlighting various computational approaches on cirRNA, and translation with a focus on the breakthroughs and the challenges in this new field.
Brodersen, KE, Kühl, M, Nielsen, DA, Pedersen, O & Larkum, AWD 2018, 'Rhizome, Root/Sediment Interactions, Aerenchyma and Internal Pressure Changes in Seagrasses' in Seagrasses of Australia, Springer International Publishing, Germany, pp. 393-418. View/Download from: Publisher's site View description>>
Choi, AH, Akyol, S, Bendavid, A & Ben-Nissan, B 2018, 'Nanobioceramic thin films: Surface modifications and cellular responses on titanium implants' in Titanium in Medical and Dental Applications, Elsevier, pp. 147-173. View/Download from: Publisher's site View description>>
Choi, AH, Conway, RC, Cazalbou, S & Ben-Nissan, B 2018, 'Maxillofacial bioceramics in tissue engineering: Production techniques, properties, and applications' in Fundamental Biomaterials: Ceramics, Elsevier, pp. 63-93. View/Download from: Publisher's site View description>>
Bioceramics prior to the 1970s were employed as implants to perform singular and biologically inert roles. The limitations with these synthetic materials as tissue substitutes were emphasized with the growing realization that the cells and tissues of the body perform many other vital regulatory and metabolic roles. Since then, the demands of bioceramics have changed, from maintaining an essentially physical function without eliciting a host response to providing a more positive interaction with the host. This has been accompanied by increasing demands on medical devices that they not only improve the quality of life but also extend its duration. More importantly, the exciting and potential opportunities associated with the use of nanobioceramics as body interactive materials, helping the body to heal, or promoting the regeneration of tissues, thus restoring physiological functions. This review covers the type of bioceramics currently used in maxillofacial surgery as well as their production methods and properties. The bioceramics covered include glass ceramics, bioglass, alumina, PSZ and zirconia, and calcium phosphate materials.
Choi, AH, Heness, G & Ben-Nissan, B 2018, 'Using finite element analysis to understand the mechanical properties of ceramic matrix composites' in Advances in Ceramic Matrix Composites, Elsevier, The Netherlands, pp. 375-400. View/Download from: Publisher's site View description>>
Cranfield, CG, Kloda, A, Nikolaev, YA, Martinac, AD, Ridone, P, Bavi, N, Bavi, O, Petrov, E, Battle, AR, Nomura, T, Rohde, PR, Nakayama, Y, Rosholm, KR, Cox, CD, Baker, MA & Martinac, B 2018, 'Mechanosensitivity of Ion Channels' in Encyclopedia of Biophysics, Springer Berlin Heidelberg, pp. 1-11. View/Download from: Publisher's site
Forbes, S & Ueland, M 2018, 'Time Since Death in Bioarchaeology and Human Osteology' in Smith, C (ed), Encyclopedia of Global Archaeology, Springer International Publishing, pp. 1-6. View/Download from: Publisher's site View description>>
Time since death (TSD) is defined as the time frame between death and discovery of an organism. When estimated in an archaeological context, this time frame may be referred to as time since deposition and in a forensic context can be termed postmortem interval. Time since death cannot be established with certainty and for this reason is provided as an estimate of the range of time encompassing the period when death occurred. A shorter postmortem interval is typically associated with a narrower time range, while a longer postmortem interval has a broader time range and includes a wider margin of error. Presently, there is no single indicator which provides a reliable or accurate measure of the time since death of an organism.
Gupta, V & Reddy, CRK 2018, 'A simple protocol for a rapid and consistent production of a large number of viable protoplasts from the Ulvophycean species' in Protocols for Macroalgae Research, CRC Press, pp. 129-138. View/Download from: Publisher's site
Huete, A, Koedsin, W & Wu, J 2018, 'Hyperspectral Applications to Landscape Phenology' in Advanced Applications in Remote Sensing of Agricultural Crops and Natural Vegetation, CRC Press, pp. 131-144. View/Download from: Publisher's site
Johnson, A & Dubey, JP 2018, 'Foodborne Disease Handbook, Second Edition' in Foodborne Disease Handbook: Volume II: Viruses, Parasites, Pathogens, and HACCP, CRC Press, Boca Raton, pp. 389-405. View/Download from: Publisher's site View description>>
The diagnosis of toxoplasmosis usually is based on one or more of the following: clinical signs, parasite isolation, antibody detection, cell-mediated responses, and antigen detection. However, the detection of Toxoplasma gondii DNA by polymerase chain reaction for diagnosis has become widespread. The clinical diagnosis of toxoplasmosis in humans is complicated due to the vast range and variation in degree of severity of symptoms. The most characteristic feature of acquired toxoplasmosis in the immunoincompetent host is central nervous system involvement. Along with the loss and reduction in quality of human life, toxoplasmosis causes great financial loss in the agricultural industry. Many serological tests have been used for the detection of immunoglobulin G T. gondii antibodies: Sabin-Feldman dye test, indirect hemagglutination, complement fixation, modified agglutination test, latex agglutination, indirect fluorescent antibody, and enzyme-linked immunosorbent assay. The diagnosis of toxoplasmosis has been confirmed by direct immunohistological detection of the parasite in tissue.
Kumar, M, Contreras-Porcia, L, Kumar, NM & Ralph, PJ 2018, 'Quantification and localization of reactive oxygen species in marine macrophytes' in Protocols for Macroalgae Research, CRC Press, pp. 267-277. View/Download from: Publisher's site
Larkum, AWD, Pernice, M, Schliep, M, Davey, P, Szabo, M, Raven, JA, Lichtenberg, M, Brodersen, KE & Ralph, PJ 2018, 'Photosynthesis and Metabolism of Seagrasses' in Seagrasses of Australia, Springer International Publishing, Switzerland, pp. 315-342. View/Download from: Publisher's site View description>>
Larkum, AWD, Waycott, M & Conran, JG 2018, 'Evolution and Biogeography of Seagrasses' in Seagrasses of Australia, Springer International Publishing, Switzerland, pp. 3-29. View/Download from: Publisher's site
Morgan, RM, French, JC & Meakin, GE 2018, 'Understanding forensic trace evidence' in Routledge Handbook of Crime Science, Routledge, pp. 393-407. View/Download from: Publisher's site
Mousley, JA & Matthews, C 2018, 'AUSTRALIA: Mathematics and its Teaching in Australia' in Series on Mathematics Education, WORLD SCIENTIFIC, pp. 113-155. View/Download from: Publisher's site
Murray, S & Hallegraeff, G 2018, 'Harmful Algae Introductions: Vectors of Transfer, Mitigation, and Management' in Shumway, S, Burkholder, JA & Morton, S (eds), Harmful Algal Blooms A Compendium Desk Reference, Wiley, USA, pp. 493-506. View/Download from: Publisher's site View description>>
Sophisticated molecular tools are now available to identify new introductions and range expansions, or the new blooming of previously unnoticed cryptic species of harmful algae. With the growing awareness of the problem of introduced marine pests in the past 30 years, a number of national and international regulations have been developed to reduce the risk of transfer of nonindigenous organisms. Determining whether a phytoplankton species has invasive characteristics is important for developing policy, management, and research responses to species with harmful impacts. While prediction of the impact of global climate change on marine harmful algal bloom (HAB) is fraught with difficulties, range expansion of warm‐water species at the expense of cold‐water species that are driven poleward is expected. Extensively researched ballast water treatment technologies serve as a guide toward suitable emergency treatment technologies to curb unwanted HAB translocations.
Ralph, PJ, Crosswell, JR, Cannard, T & Steven, ADL 2018, 'Estimating Seagrass Blue Carbon and Policy Implications: The Australian Perspective' in Seagrasses of Australia, Springer International Publishing, Switzerland, pp. 743-758. View/Download from: Publisher's site
Robertson, J & Roux, C 2018, 'From Crime Scene to Laboratory' in Roux, C (ed), Forensic Examination of Fibres: Third Edition, CRC Press, USA, pp. 99-144.
Rossy, Q, Décary-Hétu, D, Delémont, O & Mulone, M 2018, 'The Routledge International Handbook of Forensic Intelligence and Criminology' in Rossy, Q, Décary-Hétu, D, Delémont, O & Mulone, M (eds), The Routledge International Handbook of Forensic Intelligence and Criminology, Routledge, USA, pp. 65-76. View/Download from: Publisher's site View description>>
Schlögl, E 2018, 'Arbitrage-Free Interpolation in Models of Market Observable Interest Rates' in Sandmann, K & Schonbucher, PJ (eds), Advances in Finance and Stochastics: essays in honour of Dieter Sondermann, Springer-Verlag Berlin Heidelberg, Berlin, Germany, pp. 197-218. View description>>
Models which postulate lognormal dynamics for interest rates which are
compounded according to market conventions, such as forward LIBOR or forward
swap rates, can be constructed initially in a discrete tenor framework.
Interpolating interest rates between maturities in the discrete tenor structure
is equivalent to extending the model to continuous tenor. The present paper
sets forth an alternative way of performing this extension; one which preserves
the Markovian properties of the discrete tenor models and guarantees the
positivity of all interpolated rates.
Seymour, JR, Laverock, B, Nielsen, DA, Trevathan-Tackett, SM & Macreadie, PI 2018, 'The Microbiology of Seagrasses' in Seagrasses of Australia, Springer International Publishing, pp. 343-392. View/Download from: Publisher's site View description>>
Shimoni, O & Valenzuela, S 2018, 'Nanotechnology in Biology and Medicine' in Vo-Dinh, T (ed), Nanotechnology in Biology and Medicine: Methods, Devices, and Applications, CRC Press, USA, pp. 84-99. View/Download from: Publisher's site
Thenkabail, PS, Lyon, JG & Huete, A 2018, 'Advances in Hyperspectral Remote Sensing of Vegetation and Agricultural Crops' in Fundamentals, Sensor Systems, Spectral Libraries, and Data Mining for Vegetation, CRC Press, pp. 3-37. View/Download from: Publisher's site
Thenkabail, PS, Lyon, JG & Huete, A 2018, 'Fifty Years of Advances in Hyperspectral Remote Sensing of Agriculture and Vegetation—Summary, Insights, and Highlights of Volume II' in Hyperspectral Indices and Image Classifications for Agriculture and Vegetation, CRC Press, pp. 251-286. View/Download from: Publisher's site
Thenkabail, PS, Lyon, JG & Huete, A 2018, 'Fifty Years of Advances in Hyperspectral Remote Sensing of Agriculture and Vegetation—Summary, Insights, and Highlights of Volume III' in Biophysical and Biochemical Characterization and Plant Species Studies, CRC Press, pp. 303-341. View/Download from: Publisher's site
Thenkabail, PS, Lyon, JG & Huete, A 2018, 'Fifty Years of Advances in Hyperspectral Remote Sensing of Agriculture and Vegetation—Summary, Insights, and Highlights of Volume IV' in Advanced Applications in Remote Sensing of Agricultural Crops and Natural Vegetation, CRC Press, pp. 339-378. View/Download from: Publisher's site
Thenkabail, PS, Lyon, JG & Huete, A 2018, 'Fifty-Years of Advances in Hyperspectral Remote Sensing of Agriculture and Vegetation—Summary, Insights, and Highlights of Volume I' in Fundamentals, Sensor Systems, Spectral Libraries, and Data Mining for Vegetation, CRC Press, pp. 395-436. View/Download from: Publisher's site
Wang, T, Liu, Y, Su, D & Wang, G 2018, '1D and 2D Flexible Carbon Matrix Materials for Lithium–Sulfur Batteries' in Flexible Energy Conversion and Storage Devices, Wiley, pp. 127-153. View/Download from: Publisher's site
Wilkinson, S & Torpy, F 2018, 'Living Green Roofs' in Charlesworth, SM & Booth, CA (eds), Urban Pollution, Wiley, New York, pp. 131-145. View/Download from: Publisher's site View description>>
There are increasing challenges for urban settlements in both developed and developing countries. This chapter explores the relationship between urban development, pollution, and green roofs as a valuable, contributory means of mitigating the effects of urban pollution using examples from two major Australian cities, Melbourne and Sydney. Pollution in urban environments can affect soil, water, and air, with the latter having the greatest effect on human health, well‐being, and longevity. All cities are characterised by intense energy using activities and heat‐retaining materials such as concrete and bitumen. These factors combine to create the ‘urban heat island effect’. Green roofs are versatile and can be used on flat and pitched roof designs. Green roofs have multiple benefits collectively or individually. Three different types of rooftop garden beds were used to provide three illustrative case studies.
Abdul Halim, MF, Rodriguez, R, Stoltzfus, JD, Duggin, IG & Pohlschroder, M 2018, 'Conserved residues are critical for Haloferax volcanii archaeosortase catalytic activity: Implications for convergent evolution of the catalytic mechanisms of non‐homologous sortases from archaea and bacteria', Molecular Microbiology, vol. 108, no. 3, pp. 276-287. View/Download from: Publisher's site View description>>
Proper protein anchoring is key to the biogenesis of prokaryotic cell surfaces, dynamic, resilient structures that play crucial roles in various cell processes. A novel surface protein anchoring mechanism in Haloferax volcanii depends upon the peptidase archaeosortase A (ArtA) processing C-termini of substrates containing C-terminal tripartite structures and anchoring mature substrates to the cell membrane via intercalation of lipid-modified C-terminal amino acid residues. While this membrane protein lacks clear homology to soluble sortase transpeptidases of Gram-positive bacteria, which also process C-termini of substrates whose C-terminal tripartite structures resemble those of ArtA substrates, archaeosortases do contain conserved cysteine, arginine and arginine/histidine/asparagine residues, reminiscent of His-Cys-Arg residues of sortase catalytic sites. The study presented here shows that ArtAWT -GFP expressed in trans complements ΔartA growth and motility phenotypes, while alanine substitution mutants, Cys173 (C173A), Arg214 (R214A) or Arg253 (R253A), and the serine substitution mutant for Cys173 (C173S), fail to complement these phenotypes. Consistent with sortase active site replacement mutants, ArtAC173A -GFP, ArtAC173S -GFP and ArtAR214A -GFP cannot process substrates, while replacement of the third residue, ArtAR253A -GFP retains some processing activity. These findings support the view that similarities between certain aspects of the structures and functions of the sortases and archaeosortases are the result of convergent evolution.
Achlatis, M, Pernice, M, Green, K, Guagliardo, P, Kilburn, MR, Hoegh-Guldberg, O & Dove, S 2018, 'Single-cell measurement of ammonium and bicarbonate uptake within a photosymbiotic bioeroding sponge', The ISME Journal, vol. 12, no. 5, pp. 1308-1318. View/Download from: Publisher's site View description>>
Some of the most aggressive coral-excavating sponges host intracellular dinoflagellates from the genus Symbiodinium, which are hypothesized to provide the sponges with autotrophic energy that powers bioerosion. Investigations of the contribution of Symbiodinium to host metabolism and particularly inorganic nutrient recycling are complicated, however, by the presence of alternative prokaryotic candidates for this role. Here, novel methods are used to study nutrient assimilation and transfer within and between the outer-layer cells of the Indopacific bioeroding sponge Cliona orientalis. Combining stable isotope labelling, transmission electron microscopy (TEM) and nanoscale secondary ion mass spectrometry (NanoSIMS), we visualize and measure metabolic activity at the individual cell level, tracking the fate of 15N-ammonium and 13C-bicarbonate within the intact holobiont. We found strong uptake of both inorganic sources (especially 13C-bicarbonate) by Symbiodinium cells. Labelled organic nutrients were translocated from Symbiodinium to the Symbiodinium-hosting sponge cells within 6 h, and occasionally to other sponge cells within 3 days. By contrast, prokaryotic symbionts were not observed to participate in inorganic nutrient assimilation in the outer layers of the sponge. Our findings strongly support the metabolic interaction between the sponge and dinoflagellates, shedding light on the ecological advantages and adaptive capacity of photosymbiotic bioeroding sponges in oligotrophic marine habitats.
Adamala, S & Srivastava, A 2018, 'Comparative evaluation of daily evapotranspiration using artificial neural network and variable infiltration capacity models', Agricultural Engineering International: CIGR Journal, vol. 20, no. 1, pp. 32-39. View description>>
Evapotranspiration is a key variable for hydrologic, climatic and agricultural studies. Accurate quantification of this variable is the most important for irrigation management and crop productivity. With the availability of only meteorological data in climatic stations, reference gross evapotranspiration (ETo) estimation is becoming a challenging task. Hence, there is a scope to estimate the ETo using various physical and empirical methods. Among physical methods, FAO-56 Penman Monteith (PM) method is the best and Artificial Neural Network (ANN) model is an accurate empirical method. Further, ETo can also be estimated using a water budget approach i.e. variable infiltration capacity (VIC) model, which accounts for the sub-grid variability of land use, land cover and soil moisture accurately. In this study, the ETo was estimated by two different methods, namely, VIC and ANN for Mohanpur climatic location in India. The results of VIC-ETo showed the correlation coefficient, r = 0.853, coefficient of determination, R2 = 0.727 and index of agreement, d = 0.924; while ANN models with the FAO-56 PM method were in better agreement with r = 0.999, R2 = 0.998 and d = 0.999. Hence, it is concluded that the ANN showed better results as compared to VIC model for ETo estimation in Mohanpur climatic location.
Agbowuro, AA, Huston, WM, Gamble, AB & Tyndall, JDA 2018, 'Proteases and protease inhibitors in infectious diseases', Medicinal Research Reviews, vol. 38, no. 4, pp. 1295-1331. View/Download from: Publisher's site View description>>
There are numerous proteases of pathogenic organisms that are currently targeted for therapeutic intervention along with many that are seen as potential drug targets. This review discusses the chemical and biological makeup of some key druggable proteases expressed by the five major classes of disease causing agents, namely bacteria, viruses, fungi, eukaryotes, and prions. While a few of these enzymes including HIV protease and HCV NS3-4A protease have been targeted to a clinically useful level, a number are yet to yield any clinical outcomes in terms of antimicrobial therapy. A significant aspect of this review discusses the chemical and pharmacological characteristics of inhibitors of the various proteases discussed. A total of 25 inhibitors have been considered potent and safe enough to be trialed in humans and are at different levels of clinical application. We assess the mechanism of action and clinical performance of the protease inhibitors against infectious agents with their developmental strategies and look to the next frontiers in the use of protease inhibitors as anti-infective agents.
Agbowuro, AA, Mazraani, R, McCaughey, LC, Huston, WM, Gamble, AB & Tyndall, JDA 2018, 'Stereochemical basis for the anti-chlamydial activity of the phosphonate protease inhibitor JO146', Tetrahedron, vol. 74, no. 12, pp. 1184-1190. View/Download from: Publisher's site View description>>
The data presented here is related to the article titled, "Using handwriting to infer a writer's country of origin for forensic intelligence purposes" (Agius et al., 2017) [1]. This article reports original writer, spatial and construction characteristic data for thirty-seven English Australian writers and thirty-seven Vietnamese writers. All of these characteristics were coded and recorded in Microsoft Excel 2013 (version 15.31). The construction characteristics coded were only extracted from seven characters, which were: 'g', 'h', 'th', 'M', '0', '7' and '9'. The coded format of the writer, spatial and construction characteristics is made available in this Data in Brief in order to allow others to perform statistical analyses and modelling to investigate whether there is a relationship between the handwriting features and the nationality of the writer, and whether the two nationalities can be differentiated. Furthermore, to employ mathematical techniques that are capable of characterising the extracted features from each participant.
Forensic science has traditionally focused the majority of its resources and objectives towards addressing Court-related questions. However, this view restricts the contribution of forensic science to one process and results in a loss of information as the investigative and intelligence roles are largely neglected. A forensic science discipline suffering from this imbalance is handwriting examination, which may be characterised as a time consuming and subjective process that is mostly carried out towards the end of the investigation for the purpose of judicial proceedings. Individual and habitual characteristics are the major handwriting features exploited, however alternate information concerning the author's native language could potentially be used as a key element in an intelligence framework. This research focussed on the detection of characteristics that differentiate Vietnamese and English Australian writers based on their English handwriting. The study began with the extraction of handwriting characteristics from the writing of people from the two populations. The data was analysed using a logistic regression model and a classification and regression tree (CRT). Each recognised four class characteristics that were capable of distinguishing between the two nationalities. The logistic regression and CRT models were both capable of correctly predicting 93% of cases. Their predictive capabilities were then tested and supported using blind exemplars in order to mirror casework settings. It appeared that when using their respective class characteristics, the two models were capable of differentiating English Australians from Vietnamese in the data set. This proof of concept research demonstrated the plausibility of exploiting this additional information from a handwriting trace and taking advantage of it in an intelligence-led framework.
Ahmed, Z, Pauszek, SJ, Ludi, A, LaRocco, M, Khan, E, Afzal, M, Arshed, MJ, Farooq, U, Arzt, J, Bertram, M, Brito, B, Naeem, K, Abubakar, M & Rodriguez, LL 2018, 'Genetic diversity and comparison of diagnostic tests for characterization of foot‐and‐mouth disease virus strains from Pakistan 2008–2012', Transboundary and Emerging Diseases, vol. 65, no. 2, pp. 534-546. View/Download from: Publisher's site View description>>
We report the laboratory analysis of 125 clinical samples from suspected cases of foot-and-mouth disease (FMD) in cattle and Asian buffalo collected in Pakistan between 2008 and 2012. Of these samples, 89 were found to contain viral RNA by rRT-PCR, of which 88 were also found to contain infectious FMD virus (FMDV) by virus isolation (VI), with strong correlation between these tests (κ = 0.96). Samples that were VI-positive were serotyped by antigen detection ELISA (Ag-ELISA) and VP1 sequence acquisition and analysis. Sequence data identified FMDV serotypes A (n = 13), O (n = 36) and Asia-1 (n = 41), including three samples from which both serotypes Asia-1 and O were detected. Serotype A viruses were classified within three different Iran-05 sublineages: HER-10, FAR-11 and ESF-10. All serotype Asia-1 were within Group VII (Sindh-08 lineage), in a genetic clade that differs from viruses isolated prior to 2010. All serotypes O were classified as PanAsia-2 within two different sublineages: ANT-10 and BAL-09. Using VP1 sequencing as the gold standard for serotype determination, the overall sensitivity of Ag-ELISA to correctly determine serotype was 74%, and serotype-specific sensitivity was 8% for serotype A, 88% for Asia-1 and 89% for O. Serotype-specific specificity was 100% for serotype A, 93% for Asia-1 and 94% for O. Interestingly, 12 of 13 serotype A viruses were not detected by Ag-ELISA. This study confirms earlier accounts of regional genetic diversity of FMDV in Pakistan and highlights the importance of continued validation of diagnostic tests for rapidly evolving pathogens such as FMDV.
Ajani, PA, Kahlke, T, Siboni, N, Carney, R, Murray, SA & Seymour, JR 2018, 'The Microbiome of the Cosmopolitan Diatom Leptocylindrus Reveals Significant Spatial and Temporal Variability', Frontiers in Microbiology, vol. 9. View/Download from: Publisher's site
Ajani, PA, Larsson, ME, Woodcock, S, Rubio, A, Farrell, H, Brett, S & Murray, SA 2018, 'Bloom drivers of the potentially harmful dinoflagellate Prorocentrum minimum (Pavillard) Schiller in a south eastern temperate Australian estuary', Estuarine, Coastal and Shelf Science, vol. 215, pp. 161-171. View/Download from: Publisher's site
Ajani, PA, McGinty, N, Finkel, ZV & Irwin, AJ 2018, 'Phytoplankton Realized Niches Track Changing Oceanic Conditions at a Long-Term Coastal Station off Sydney Australia', Frontiers in Marine Science, vol. 5, pp. 1-12. View/Download from: Publisher's site
Ajani, PA, Verma, A, Lassudrie, M, Doblin, MA & Murray, SA 2018, 'A new diatom species P. hallegraeffii sp. nov. belonging to the toxic genus Pseudo-nitzschia (Bacillariophyceae) from the East Australian Current', PLOS ONE, vol. 13, no. 4, pp. e0195622-e0195622. View/Download from: Publisher's site View description>>
A new species belonging to the toxin producing diatom genus Pseudo-nitzschia, P. hallegraeffii sp. nov., is delineated and described from the East Australian Current (EAC). Clonal cultures were established by single cell isolation from phytoplankton net hauls collected as part of a research expedition in the EAC region in 2016 on the RV Investigator. Cultures were assessed for their morphological and genetic characteristics, their sexual compatibility with other Pseudo-nitzschia species, and their ability to produce domoic acid. Light and transmission electron microscopy revealed cells which differed from their closest relatives by their cell width, rows of poroids, girdle band structure and density of band straie. Phylogenetic analyses based on sequencing of nuclear-encoded ribosomal deoxyribonucleic acid (rDNA) regions showed this novel genotype clustered within the P. delicatissima complex, but formed a discrete clade from its closest relatives P. dolorosa, P. simulans, P. micropora and P. delicatissima. Complementary base changes (CBCs) were observed in the secondary structure of the 3' nuclear ribosomal transcribed spacer sequence region (ITS2) between P. hallegraeffii sp. nov. and its closest related taxa, P. simulans and P. dolorosa. Under laboratory conditions, and in the absence of any zooplankton cues, strains of P. hallegraeffii sp. nov. did not produce domoic acid (DA) and were not sexually compatible with any other Pseudo-nitzschia clones tested. A total of 18 Pseudo-nitzschia species, including three confirmed toxigenic species (P. cuspidata, P. multistriata and P. australis) have now been unequivocally confirmed from eastern Australia.
Al-Asfi, M, McNevin, D, Mehta, B, Power, D, Gahan, ME & Daniel, R 2018, 'Assessment of the Precision ID Ancestry panel', International Journal of Legal Medicine, vol. 132, no. 6, pp. 1581-1594. View/Download from: Publisher's site View description>>
Al-Badri, G & Castorina, A 2018, 'Insights into the Role of Neuroinflammation in the Pathogenesis of Multiple Sclerosis', Journal of Functional Morphology and Kinesiology, vol. 3, no. 1, pp. 13-13. View/Download from: Publisher's site View description>>
Multiple sclerosis (MS) is a devastating disease, and with the increasing number of cases each year, it is becoming a significant socioeconomic burden for the affected people and the entire community. The aetiology of MS is largely unknown, but genetic susceptibility, exposure to infections and/or environmental toxicants are recognised as risk factors. MS is characterised by the appearance of lesions/plaques in the central nervous system, caused by destruction of the myelin sheet by auto-reactive T cells. Symptoms range from mild impairment of daily motor functions to severe sensory and cognitive disabilities necessitating mobility assistance, medical and support from caregivers. Due to the progressive nature of the disease, MS is gaining more attention and research to better understand its multifaceted pathogenesis. In the present review, we focus on some of the latest research related to the neuroinflammatory component of the disease, since it appears to play a critical role in MS pathogenesis. The goal is to shed more light on this specific domain of MS, in an attempt to assist in the identification of novel treatment trajectories and management plans.
Alfeus, M, Grasselli, M & Schlögl, E 2018, 'A Consistent Stochastic Model of the Term Structure of Interest Rates for Multiple Tenors', Journal of Economic Dynamics and Control, vol. 114. View/Download from: Publisher's site View description>>
Explicitly taking into account the risk incurred when borrowing at a shorter
tenor versus lending at a longer tenor ('roll-over risk'), we construct a
stochastic model framework for the term structure of interest rates in which a
frequency basis (i.e. a spread applied to one leg of a swap to exchange one
floating interest rate for another of a different tenor in the same currency)
arises endogenously. This rollover risk consists of two components, a credit
risk component due to the possibility of being downgraded and thus facing a
higher credit spread when attempting to roll over short-term borrowing, and a
component reflecting the (systemic) possibility of being unable to roll over
short-term borrowing at the reference rate (e.g., LIBOR) due to an absence of
liquidity in the market. The modelling framework is of 'reduced form' in the
sense that (similar to the credit risk literature) the source of credit risk is
not modelled (nor is the source of liquidity risk). However, the framework has
more structure than the literature seeking to simply model a different term
structure of interest rates for each tenor frequency, since relationships
between rates for all tenor frequencies are established based on the modelled
roll-over risk. We proceed to consider a specific case within this framework,
where the dynamics of interest rate and roll-over risk are driven by a
multifactor Cox/Ingersoll/Ross-type process, show how such model can be
calibrated to market data, and used for relative pricing of interest rate
derivatives, including bespoke tenor frequencies not liquidly traded in the
market.
Almohaywi, B, Taunk, A, Wenholz, D, Nizalapur, S, Biswas, N, Ho, K, Rice, S, Iskander, G, Black, D, Griffith, R & Kumar, N 2018, 'Design and Synthesis of Lactams Derived from Mucochloric and Mucobromic Acids as Pseudomonas aeruginosa Quorum Sensing Inhibitors', Molecules, vol. 23, no. 5, pp. 1106-1106. View/Download from: Publisher's site View description>>
Bacterial infections, particularly hospital-acquired infections caused by Pseudomonas aeruginosa, have become a global threat with a high mortality rate. Gram-negative bacteria including P. aeruginosa employ N-acyl homoserine lactones (AHLs) as chemical signals to regulate the expression of pathogenic phenotypes through a mechanism called quorum sensing (QS). Recently, strategies targeting bacterial behaviour or QS have received great attention due to their ability to disarm rather than kill pathogenic bacteria, which lowers the evolutionary burden on bacteria and the risk of resistance development. In the present study, we report the design and synthesis of N-alkyl- and N-aryl 3,4 dichloro- and 3,4-dibromopyrrole-2-one derivatives through the reductive amination of mucochloric and mucobromic acid with aliphatic and aromatic amines. The quorum sensing inhibition (QSI) activity of the synthesized compounds was determined against a P. aeruginosa MH602 reporter strain. The phenolic compounds exhibited the best activity with 80% and 75% QSI at 250 µM and were comparable in activity to the positive control compound Fu-30. Computational docking studies performed using the LasR receptor protein of P. aeruginosa suggested the importance of hydrogen bonding and hydrophobic interactions for QSI.
Alqudah, A, McKinley, MC, McNally, R, Graham, U, Watson, CJ, Lyons, TJ & McClements, L 2018, 'Risk of pre-eclampsia in women taking metformin: a systematic review and meta-analysis', Diabetic Medicine, vol. 35, no. 2, pp. 160-172. View/Download from: Publisher's site View description>>
AIMS:To perform meta-analyses of studies evaluating the risk of pre-eclampsia in high-risk insulin-resistant women taking metformin prior to, or during pregnancy. METHODS:A search was conducted of the Medline, EMBASE, Web of Science and Scopus databases. Both randomized controlled trials and prospective observational cohort studies of metformin treatment vs. placebo/control or insulin either prior to or during pregnancy were selected. The main outcome measure was the incidence of pre-eclampsia in each treatment group. RESULTS:Overall, in five randomized controlled trials comparing metformin treatment (n = 611) with placebo/control (n = 609), no difference in the risk of pre-eclampsia was found [combined/pooled risk ratio (RR), 0.86 (95% CI 0.33-2.26); P = 0.76; I2 = 66%]. Meta-analysis of four cohort studies again showed no significant effect [RR, 1.21 (95% CI 0.56-2.61); P = 0.62; I2 = 30%]. A meta-analysis of eight randomized controlled trials comparing metformin (n = 838) with insulin (n = 836), however, showed a reduced risk of pre-eclampsia with metformin [RR, 0.68 (95% CI 0.48-0.95); P = 0.02; I2 = 0%]. No heterogeneity was present in the metformin vs. insulin analysis of randomized controlled trials, whereas high levels of heterogeneity were present in studies comparing metformin with placebo/control. Pre-eclampsia was a secondary outcome in most of the studies. The mean weight gain from time of enrolment to delivery was lower in the metformin group (P = 0.05, metformin vs. placebo; P = 0.004, metformin vs. insulin). CONCLUSIONS:In studies randomizing pregnant women to glucose-lowering therapy, metformin was associated with lower gestational weight gain and a lower risk of pre-eclampsia compared with insulin.
The real power of calculus is revealed when it is applied to actual physical problems. In this paper, we present a calculus inspired physics experiment suitable for high school and undergraduate programs. A model for the theory of the terminal velocity of a falling body subject to a resistive force is developed and its validity tested in an experiment of a falling magnet in a column of self-induced eddy currents. The presented method combines multiple physics concepts such as 1D kinematics, classical mechanics, electromagnetism and non-trivial mathematics. It offers the opportunity for lateral as well as project-based learning.
Andersson, J, Fuller, MA, Wood, K, Holt, SA & Köper, I 2018, 'A tethered bilayer lipid membrane that mimics microbial membranes', Physical Chemistry Chemical Physics, vol. 20, no. 18, pp. 12958-12969. View/Download from: Publisher's site View description>>
This work presents a self-assembled lipid bilayer architecture mimicking the outer membrane of Gram negative bacteria.
Angeloski, A, Gentle, AR, Scott, JA, Cortie, MB, Hook, JM, Westerhausen, MT, Bhadbhade, M, Baker, AT & McDonagh, AM 2018, 'From Lead(II) Dithiocarbamate Precursors to a Fast Response PbS Positive Temperature Coefficient Thermistor', Inorganic Chemistry, vol. 57, no. 4, pp. 2132-2140. View/Download from: Publisher's site
Antonosyan, DA, Solntsev, AS & Sukhorukov, AA 2018, 'Photon-pair generation in a quadratically nonlinear parity-time symmetric coupler', Photonics Research, vol. 6, no. 4, pp. A6-A6. View/Download from: Publisher's site
Archer, MS, Jones, SD & Wallman, JF 2018, 'Delayed reception of live blowfly (Calliphora vicina and Chrysomya rufifacies) larval samples: implications for minimum postmortem interval estimates', Forensic Sciences Research, vol. 3, no. 1, pp. 27-39. View/Download from: Publisher's site View description>>
Arias, M, Vink, J, de Gasperin, F, Salas, P, Oonk, JBR, van Weeren, RJ, van Amesfoort, AS, Anderson, J, Beck, R, Bell, ME, Bentum, MJ, Best, P, Blaauw, R, Breitling, F, Broderick, JW, Brouw, WN, Brüggen, M, Butcher, HR, Ciardi, B, de Geus, E, Deller, A, van Dijk, PCG, Duscha, S, Eislöffel, J, Garrett, MA, Grießmeier, JM, Gunst, AW, van Haarlem, MP, Heald, G, Hessels, J, Hörandel, J, Holties, HA, van der Horst, AJ, Iacobelli, M, Juette, E, Krankowski, A, van Leeuwen, J, Mann, G, McKay-Bukowski, D, McKean, JP, Mulder, H, Nelles, A, Orru, E, Paas, H, Pandey-Pommier, M, Pandey, VN, Pekal, R, Pizzo, R, Polatidis, AG, Reich, W, Röttgering, HJA, Rothkaehl, H, Schwarz, DJ, Smirnov, O, Soida, M, Steinmetz, M, Tagger, M, Thoudam, S, Toribio, MC, Vocks, C, van der Wiel, MHD, Wijers, RAMJ, Wucknitz, O, Zarka, P & Zucca, P 2018, 'Low-frequency radio absorption in Cassiopeia A', Astronomy & Astrophysics, vol. 612, pp. A110-A110. View/Download from: Publisher's site View description>>
Context.Cassiopeia A is one of the best-studied supernova remnants. Its bright radio and X-ray emission is due to shocked ejecta. Cas A is rather unique in that the unshocked ejecta can also be studied: through emission in the infrared, the radio-active decay of44Ti, and the low-frequency free-free absorption caused by cold ionised gas, which is the topic of this paper.Aims.Free-free absorption processes are affected by the mass, geometry, temperature, and ionisation conditions in the absorbing gas. Observations at the lowest radio frequencies can constrain a combination of these properties.Methods.We used Low Frequency Array (LOFAR) Low Band Antenna observations at 30–77 MHz and Very Large Array (VLA)L-band observations at 1–2 GHz to fit for internal absorption as parametrised by the emission measure. We simultaneously fit multiple UV-matched images with a common resolution of 17″ (this corresponds to 0.25 pc for a source at the distance of Cas A). The ample frequency coverage allows us separate the relative contributions from the absorbing gas, the unabsorbed front of the shell, and the absorbed back of the shell to the emission spectrum. We explored the effects that a temperature lower than the ~100–500 K proposed from infrared observations and a high degree of clumping can have on the derived physical properties of the unshocked material, such as its mass and density. We also compiled integrated radio flux density measurements, fit for the absorption processes that occur in the radio band, and considered their effect on the secular decline of the source.Results.We find a mass in the unshocked ejecta ofM= 2.95 ± 0.48M⊙for an assumed gas temperatureofT
Asatryan, AA & Novikov, A 2018, 'Anderson localization of classical waves in weakly scattering one-dimensional Levy lattices', Physical Review B, vol. 98, no. 23, pp. 235144-1-235144-8. View/Download from: Publisher's site
Assadi, MHN, Fronzi, M, Ford, M & Shigeta, Y 2018, 'High-performance Na ion cathodes based on the ubiquitous and reversible O redox reaction', Journal of Materials Chemistry A, vol. 6, no. 47, pp. 24120-24127. View/Download from: Publisher's site View description>>
We identified high capacity, high voltage and low-strain Na cathode materials that rely on the reversible oxygen redox reaction.
Awasthi, R, Rathbone, MJ, Hansbro, PM, Bebawy, M & Dua, K 2018, 'Therapeutic prospects of microRNAs in cancer treatment through nanotechnology', Drug Delivery and Translational Research, vol. 8, no. 1, pp. 97-110. View/Download from: Publisher's site View description>>
MicroRNAs (miRNAs) represent a new class of diagnostic and prognostic biomarker as well as new therapeutic targets in cancer therapy. miRNAs are gaining significant interest due to extensive advancements in knowledge since their discovery and, more recently, their translational application as therapeutic moieties and targets in the management of disease. miRNAs used in the treatment of cancer would position them as a new class of emerging therapeutic agents. Indeed, numerous candidate miRNAs have been identified as having therapeutic application in the treatment of cancer, but there is still much to learn about how to transform these into effective, patient-compliant, and targeted drug delivery systems. In this mini review, we discuss the utility and potential of nanotechnology in miRNA formulation and delivery with particular emphasis on cancer, including their role in conferring multidrug resistance and metastatic capacity. This review benefits both the formulation and biological scientists in understanding and exploring the new vistas of miRNA delivery using nanotechnology in the cancer clinically.
Awasthi, R, Roseblade, A, Hansbro, PM, Rathbone, MJ, Dua, K & Bebawy, M 2018, 'Nanoparticles in Cancer Treatment: Opportunities and Obstacles', Current Drug Targets, vol. 19, no. 14, pp. 1696-1709. View/Download from: Publisher's site
Baek, J-S, Tan, CH, Ng, NKJ, Yeo, YP, Rice, SA & Loo, SCJ 2018, 'A programmable lipid-polymer hybrid nanoparticle system for localized, sustained antibiotic delivery to Gram-positive and Gram-negative bacterial biofilms', Nanoscale Horizons, vol. 3, no. 3, pp. 305-311. View/Download from: Publisher's site View description>>
Lipid-polymer hybrid nanoparticle enhances antibiotic efficacy through localised, sustained delivery to bacterial biofilms.
Baffour, B, Silva, D, Veiga, A, Sexton, C & Brown, JJ 2018, 'Small area estimation strategy for the 2011 Census in England and Wales', Statistical Journal of the IAOS, vol. 34, no. 3, pp. 395-407. View/Download from: Publisher's site View description>>
Baines, KJ, Wright, TK, Gibson, PG, Powell, H, Hansbro, PM & Simpson, JL 2018, 'Azithromycin treatment modifies airway and blood gene expression networks in neutrophilic COPD', ERJ Open Research, vol. 4, no. 4, pp. 00031-2018. View/Download from: Publisher's site View description>>
Long-term, low-dose azithromycin reduces exacerbation frequency in chronic obstructive pulmonary disease (COPD), yet the mechanism remains unclear. This study characterised genome-wide gene expression changes in patients with neutrophilic COPD following long-term, low-dose azithromycin treatment.Patients with neutrophilic COPD (>61% or >162×104 cells per mL sputum neutrophils) were randomised to receive either azithromycin or placebo for 12 weeks. Sputum and blood were obtained before and after 12 weeks of treatment. Gene expression was defined using microarrays. Networks were analysed using the Search Tool for the Retrieval of Interacting Gene database.In sputum, 403 genes were differentially expressed following azithromycin treatment (171 downregulated and 232 upregulated), and three following placebo treatment (one downregulated and two upregulated) compared to baseline (adjusted p<0.05 by paired t-test, fold-change >1.5). In blood, 138 genes were differentially expressed with azithromycin (121 downregulated and 17 upregulated), and zero with placebo compared to baseline (adjusted p<0.05 by paired t-test, fold-change >1.3). Network analysis revealed one key network in both sputum (14 genes) and blood (46 genes), involving interferon-stimulated genes, human leukocyte antigens and genes regulating T-cell responses.Long-term, low-dose azithromycin is associated with downregulation of genes regulating antigen presentation, interferon and T-cell responses, and numerous inflammatory pathways in the airways and blood of neutrophilic COPD patients.
Bajpai, VK, Alam, MB, Quan, KT, Ju, M-K, Majumder, R, Shukla, S, Huh, YS, Na, M, Lee, SH & Han, Y-K 2018, 'Attenuation of inflammatory responses by (+)-syringaresinol via MAP-Kinase-mediated suppression of NF-κB signaling in vitro and in vivo', Scientific Reports, vol. 8, no. 1. View/Download from: Publisher's site View description>>
AbstractWe examined the anti-inflammatory effects of (+)-syringaresinol (SGRS), a lignan isolated from Rubia philippinensis, in lipopolysaccharide (LPS)-stimulated RAW 264.7 cells using enzyme-based immuno assay, Western blotting, and RT-PCR analyses. Additionally, in vivo effects of SGRS in the acute inflammatory state were examined by using the carrageenan-induced hind paw edema assay in experimental mice. As a result, treatment with SGRS (25, 50, and 100 μM) inhibited protein expression of lipopolysaccharide-stimulated inducible nitric oxide synthase (iNOS), cyclooxygenase-2 (COX-2), and nuclear factor kappa B (NF-κB) as well as production of nitric oxide (NO), prostaglandin E2 (PGE2), tumor necrosis factor-alpha (TNF-α), interleukin-1beta (IL-1β), and interleukin-6 (IL-6) induced by LPS. Moreover, SGRS also reduced LPS-induced mRNA expression levels of iNOS and COX-2, including NO, PGE2, TNF-α, IL-1β, and IL-6 cytokines in a dose-dependent fashion. Furthermore, carrageenan-induced paw edema assay validated the in vivo anti-edema effect of SGRS. Interestingly, SGRS (30 mg/kg) suppressed carrageenan-induced elevation of iNOS, COX-2, TNF-α, IL-1β, and IL-6 mRNA levels as well as COX-2 and NF-κB protein levels, suggesting SGRS may possess anti-inflammatory activities.
Bajpai, VK, Majumder, R, Rather, IA, Nam, G-J & Park, Y-H 2018, 'Molecular Characterization of Lactobacillus plantarum YML016 with Anti-Diabetic, Anti-Melanogenic and Anti-Viral Efficacy', National Academy Science Letters, vol. 41, no. 5, pp. 301-305. View/Download from: Publisher's site
Land‐based plants and ocean‐dwelling microbial phototrophs known as phytoplankton, are together responsible for almost all global primary production. Habitat warming associated with anthropogenic climate change has detrimentally impacted marine primary production, with the effects observed on regional and global scales. In contrast to slower‐growing higher plants, there is considerable potential for phytoplankton to evolve rapidly with changing environmental conditions. The energetic constraints associated with adaptation in phytoplankton are not yet understood, but are central to forecasting how global biogeochemical cycles respond to contemporary ocean change. Here, we demonstrate a number of potential trade‐offs associated with high‐temperature adaptation in a tropical microbial eukaryote, Amphidinium massartii (dinoflagellate). Most notably, the population became high‐temperature specialized (higher fitness within a narrower thermal envelope and higher thermal optimum), and had a greater nutrient requirement for carbon, nitrogen and phosphorus. Evidently, the energetic constraints associated with living at elevated temperature alter competiveness along other environmental gradients. While high‐temperature adaptation led to an irreversible change in biochemical composition (i.e., an increase in fatty acid saturation), the mechanisms underpinning thermal evolution in phytoplankton remain unclear, and will be crucial to understanding whether the trade‐offs observed here are species‐specific or are representative of the evolutionary constraints in all phytoplankton.
Baldeaux, J, Ignatieva, K & Platen, E 2018, 'Detecting money market bubbles', Journal of Banking & Finance, vol. 87, pp. 369-379. View/Download from: Publisher's site
Bao, G, Wong, K-L, Jin, D & Tanner, PA 2018, 'A stoichiometric terbium-europium dyad molecular thermometer: energy transfer properties', Light: Science & Applications, vol. 7, no. 1, pp. 1-10. View/Download from: Publisher's site View description>>
AbstractThe optical thermometer has shown great promise for use in the fields of aeronautical engineering, environmental monitoring and medical diagnosis. Self-referencing lanthanide thermo-probes distinguish themselves because of their accuracy, calibration, photostability, and temporal dimension of signal. However, the use of conventional lanthanide-doped materials is limited by their poor reproducibility, random distance between energy transfer pairs and interference by energy migration, thereby restricting their utility. Herein, a strategy for synthesizing hetero-dinuclear complexes that comprise chemically similar lanthanides is introduced in which a pair of thermosensitive dinuclear complexes, cycTb-phEu and cycEu-phTb, were synthesized. Their structures were geometrically optimized with an internuclear distance of approximately 10.6Å. The sensitive linear temperature-dependent luminescent intensity ratios of europium and terbium emission over a wide temperature range (50–298K and 10–200K, respectively) and their temporal dimension responses indicate that both dinuclear complexes can act as excellent self-referencing thermometers. The energy transfer from Tb3+ to Eu3+ is thermally activated, with the most important pathway involving the 7F1 Eu3+J-multiplet at room temperature. The energy transfer from the antenna to Eu3+ was simulated, and it was found that the most important ligand contributions to the rate come from transfers to the Eu3+ upper states rather than direct ligand–metal transfer to 5D1 or 5D0. As the first molecular-based thermometer with clear validation of the metal ratio and a fixed distance between the metal pairs, these dinuclear complexes can be used a...
Bao, G, Zha, S, Liu, Z, Fung, Y-H, Chan, C-F, Li, H, Chu, P-H, Jin, D, Tanner, PA & Wong, K-L 2018, 'Reversible and Sensitive Hg2+ Detection by a Cell-Permeable Ytterbium Complex', Inorganic Chemistry, vol. 57, no. 1, pp. 120-128. View/Download from: Publisher's site View description>>
A cell-permeable ytterbium complex shows reversible binding with Hg2+ in aqueous solution and in vitroby off-on visible and NIR emission. The fast response and 150 nM sensitivity of Hg2+ detection is based upon FRET and the lanthanide antenna effect. The reversible Hg2+ detection can be performed in vitro, and the binding mechanism is suggested by NMR employing the motif structure in a La complex and by DFT calculations.
Bao, W, Liu, L, Wang, C, Choi, S, Wang, D & Wang, G 2018, 'Facile Synthesis of Crumpled Nitrogen-Doped MXene Nanosheets as a New Sulfur Host for Lithium-Sulfur Batteries', Advanced Energy Materials, vol. 8, no. 13, pp. 1702485-1702485. View/Download from: Publisher's site View description>>
Barraza Bernadas, V, Grings, F, Restrepo-Coupe, N & Huete, A 2018, 'Comparison of the performance of latent heat flux products over southern hemisphere forest ecosystems: estimating latent heat flux error structure using in situ measurements and the triple collocation method', International Journal of Remote Sensing, vol. 39, no. 19, pp. 6300-6315. View/Download from: Publisher's site View description>>
Barry, SE, Ellis, M, Yang, Y, Guan, G, Wang, X, Britton, WJ & Saunders, BM 2018, 'Identification of a plasma microRNA profile in untreated pulmonary tuberculosis patients that is modulated by anti-mycobacterial therapy', Journal of Infection, vol. 77, no. 4, pp. 341-348. View/Download from: Publisher's site View description>>
microRNA expression profiles are of interest as a biomarker of tuberculosis (TB). How anti-TB therapy effects miRNA profiles is unknown and was examined.We identified 87 plasma miRNAs that were significantly modified in an exploratory group of 19 Chinese pulmonary TB (PTB) patients compared to 14 healthy controls. We selected 10 of these miRNAs for analysis in a cohort of 100 PTB patients prior to, and at one, two and six months during treatment.Five miRNAs were differentially expressed in PTB patients compared to controls at diagnosis; miRs -29a and -99b were up-regulated, whilst miRs -21, -146a and -652 were down-regulated. A combination of 5 miRNA distinguished TB from healthy controls with a sensitivity of 94%, a specificity of 88%, and an AUC of 0.976. Within one month of treatment, significant changes in miRs -29a, -99b, -26a and 146a levels occurred in successfully treated patients, although not all miRNAs returned to baseline by treatment completion.A 5-miRNA signature shows potential for development as a novel biomarker for TB disease with potential to predict response to treatment. The failure of all miRNA to return to baseline levels may reflect ongoing remodelling in the lung parenchyma that continues after completion of anti-TB therapy.
Batmunkh, M, Shrestha, A, Bat‐Erdene, M, Nine, MJ, Shearer, CJ, Gibson, CT, Slattery, AD, Tawfik, SA, Ford, MJ, Dai, S, Qiao, S & Shapter, JG 2018, 'Electrocatalytic Activity of a 2D Phosphorene‐Based Heteroelectrocatalyst for Photoelectrochemical Cells', Angewandte Chemie International Edition, vol. 57, no. 10, pp. 2644-2647. View/Download from: Publisher's site View description>>
Research into efficient synthesis, fundamental properties, and potential applications of phosphorene is currently the subject of intense investigation. Herein, solution-processed phosphorene or few-layer black phosphorus (FL-BP) sheets are prepared using a microwave exfoliation method and used in photoelectrochemical cells. Based on experimental and theoretical (DFT) studies, the FL-BP sheets are found to act as catalytically active sites and show excellent electrocatalytic activity for triiodide reduction in dye-sensitized solar cells. Importantly, the device fabricated based on the newly designed cobalt sulfide (CoSx ) decorated nitrogen and sulfur co-doped carbon nanotube heteroelectrocatalyst coated with FL-BP (FL-BP@N,S-doped CNTs-CoSx ) displayed an impressive photovoltaic efficiency of 8.31 %, outperforming expensive platinum based cells. This work paves the way for using phosphorene-based electrocatalysts for next-generation energy-storage systems.
Batmunkh, M, Shrestha, A, Bat‐Erdene, M, Nine, MJ, Shearer, CJ, Gibson, CT, Slattery, AD, Tawfik, SA, Ford, MJ, Dai, S, Qiao, S & Shapter, JG 2018, 'Electrocatalytic Activity of a 2D Phosphorene‐Based Heteroelectrocatalyst for Photoelectrochemical Cells', Angewandte Chemie, vol. 130, no. 10, pp. 2674-2677. View/Download from: Publisher's site View description>>
AbstractResearch into efficient synthesis, fundamental properties, and potential applications of phosphorene is currently the subject of intense investigation. Herein, solution‐processed phosphorene or few‐layer black phosphorus (FL‐BP) sheets are prepared using a microwave exfoliation method and used in photoelectrochemical cells. Based on experimental and theoretical (DFT) studies, the FL‐BP sheets are found to act as catalytically active sites and show excellent electrocatalytic activity for triiodide reduction in dye‐sensitized solar cells. Importantly, the device fabricated based on the newly designed cobalt sulfide (CoSx) decorated nitrogen and sulfur co‐doped carbon nanotube heteroelectrocatalyst coated with FL‐BP (FL‐BP@N,S‐doped CNTs‐CoSx) displayed an impressive photovoltaic efficiency of 8.31 %, outperforming expensive platinum based cells. This work paves the way for using phosphorene‐based electrocatalysts for next‐generation energy‐storage systems.
Been, F, O'Brien, J, Lai, FY, Morelato, M, Vallely, P, McGowan, J, van Nuijs, ALN, Covaci, A & Mueller, JF 2018, 'Analysis of N,N-dimethylamphetamine in wastewater - a pyrolysis marker and synthesis impurity of methamphetamine', Drug Testing and Analysis, vol. 10, no. 10, pp. 1590-1598. View/Download from: Publisher's site View description>>
The increased availability of high purity crystalline methamphetamine (MA) in Australia raised concerns because of high dosages and its potential consumption through inhalation. The present work investigates the possibility of using wastewater levels of N,N-dimethylamphetamine (DMA), a pyrolysis by-product, as an indirect indicator of MA smoking. A dedicated liquid chromatography quadrupole-time-of-flight mass spectrometry (LC-QToF-MS) method was set up to detect and quantify DMA in wastewater samples. Wastewater samples were collected from 8 locations across Australia during the period 2011-2016. Data about the abundance of DMA in MA seizures as well as in residues from drug paraphernalia were obtained from forensic laboratories in Australia. DMA/MA ratios measured in wastewater ranged from 0.0001 to 0.09 (median 0.007). DMA/MA ratios in bulk seizures are generally below 0.0025, with a median value of 0.0004, whilst residues in paraphernalia ranged from 0.031 to 3.37. DMA/MA ratios in wastewater decreased between 2011 and 2016, in parallel to an increase in MA loads. Furthermore, wastewater analyses highlighted a strong positive correlation between DMA/MA ratios and per capita MA use (Pearson's correlation ρ= 0.61, p-value <0.001). Nonetheless, geographical specificities could be highlighted between the investigated locations. The obtained data could help authorities detect hot spots of drug use as well as to plan specific intervention campaigns to tackle the issue. In future, simultaneous analysis of DMA and MA in both wastewater and seizures could improve our understanding about MA use and its consumption patterns.
Behrendt, L, Raina, J-B, Lutz, A, Kot, W, Albertsen, M, Halkjær-Nielsen, P, Sørensen, SJ, Larkum, AWD & Kühl, M 2018, 'In situ metabolomic- and transcriptomic-profiling of the host-associated cyanobacteria Prochloron and Acaryochloris marina', The ISME Journal, vol. 12, no. 2, pp. 556-567. View/Download from: Publisher's site View description>>
The tropical ascidian Lissoclinum patella hosts two enigmatic cyanobacteria: (1) the photoendosymbiont Prochloron spp., a producer of valuable bioactive compounds and (2) the chlorophyll-d containing Acaryochloris spp., residing in the near-infrared enriched underside of the animal. Despite numerous efforts, Prochloron remains uncultivable, restricting the investigation of its biochemical potential to cultivation-independent techniques. Likewise, in both cyanobacteria, universally important parameters on light-niche adaptation and in situ photosynthetic regulation are unknown. Here we used genome sequencing, transcriptomics and metabolomics to investigate the symbiotic linkage between host and photoendosymbiont and simultaneously probed the transcriptional response of Acaryochloris in situ. During high light, both cyanobacteria downregulate CO2 fixing pathways, likely a result of O2 photorespiration on the functioning of RuBisCO, and employ a variety of stress-quenching mechanisms, even under less stressful far-red light (Acaryochloris). Metabolomics reveals a distinct biochemical modulation between Prochloron and L. patella, including noon/midnight-dependent signatures of amino acids, nitrogenous waste products and primary photosynthates. Surprisingly, Prochloron constitutively expressed genes coding for patellamides, that is, cyclic peptides of great pharmaceutical value, with yet unknown ecological significance. Together these findings shed further light on far-red-driven photosynthesis in natural consortia, the interplay of Prochloron and its ascidian partner in a model chordate photosymbiosis and the uncultivability of Prochloron.The ISME Journal advance online publication, 31 October 2017; doi:10.1038/ismej.2017.192.
Benson, N, Oliveria Dos Santos, R, Griffiths, K, Cole, N, Doble, P, Roux, C & Blanes, L 2018, 'Erratum to “The development of a stabbing machine for forensic textile damage analysis” [FSI (2017) 132–139]>', Forensic Science International, vol. 285, pp. 161-161. View/Download from: Publisher's site
Berger, B, Berger, C, Heinrich, J, Niederstätter, H, Hecht, W, Hellmann, A, Rohleder, U, Schleenbecker, U, Morf, N, Freire-Aradas, A, McNevin, D, Phillips, C & Parson, W 2018, 'Dog breed affiliation with a forensically validated canine STR set', Forensic Science International: Genetics, vol. 37, pp. 126-134. View/Download from: Publisher's site View description>>
We tested a panel of 13 highly polymorphic canine short tandem repeat (STR) markers for dog breed assignment using 392 dog samples from the 23 most popular breeds in Austria, Germany, and Switzerland. This STR panel had originally been selected for canine identification. The dog breeds sampled in this study featured a population frequency ≥1% and accounted for nearly 57% of the entire pedigree dog population in these three countries. Breed selection was based on a survey comprising records for nearly 1.9 million purebred dogs belonging to more than 500 different breeds. To derive breed membership from STR genotypes, a range of algorithms were used. These methods included discriminant analysis of principal components (DAPC), STRUCTURE, GeneClass2, and the adegenet package for R. STRUCTURE analyses suggested 21 distinct genetic clusters. Differentiation between most breeds was clearly discernable. Fourteen of 23 breeds (61%) exhibited maximum mean cluster membership proportions of more than 0.70 with a highest value of 0.90 found for Cavalier King Charles Spaniels. Dogs of only 6 breeds (26%) failed to consistently show only one major cluster. The DAPC method yielded the best assignment results in all 23 declared breeds with 97.5% assignment success. The frequency-based assignment test also provided a high success rate of 87%. These results indicate the potential viability of dog breed prediction using a well-established and sensitive set of 13 canine STR markers intended for forensic routine use.
Berhane, AM, Jeong, K-Y, Bradac, C, Walsh, M, Englund, D, Toth, M & Aharonovich, I 2018, 'Photophysics of GaN single-photon emitters in the visible spectral range', Physical Review B, vol. 97, no. 16. View/Download from: Publisher's site
Berry, T, Dutta, D, Chen, R, Leong, A, Wang, H, Donald, WA, Parviz, M, Cornell, B, Willcox, M, Kumar, N & Cranfield, CG 2018, 'Lipid Membrane Interactions of the Cationic Antimicrobial Peptide Chimeras Melimine and Cys-Melimine', Langmuir, vol. 34, no. 38, pp. 11586-11592. View/Download from: Publisher's site View description>>
Melimine and its derivatives are synthetic chimeric antimicrobial agents based on protamine and melittin. The binding of solubilized melimine and its derivative, with a cysteine on N-terminus, (cys-melimine) on tethered bilayer lipid membranes (tBLMs) was examined using ac electrical impedance spectroscopy. The addition of melimine and cys-melimine initially increased membrane conduction, which subsequently falls over time. The results were obtained for tBLMs comprising zwitterionic phosphatidylcholine, anionic phosphatidylglycerol, or tBLMs made using purified lipids from Escherichia coli. The effect on conduction is more marked with the cysteine variant than the noncysteine variant. The variation in membrane conduction most probably arises from individual melimines inducing increased ionic permeability, which is then reduced as the melimines aggregate and phase-separate within the membrane. The actions of these antimicrobials are modeled in terms of altering the critical packing parameter (CPP) of the membranes. The variations in the peptide length of cys-melimine were compared with a truncated version of the peptide, cys-mel4. The results suggest that the smaller molecule impacts the membrane by a mechanism that increases the average CPP, reducing membrane conduction. Alternatively, an uncharged alanine-replacement version of melimine still produced an increase in membrane conduction, further supporting the CPP model of geometry-induced toroidal pore alterations. All the data were then compared to their antimicrobial effectiveness for the Gram-positive and Gram-negative strains of bacteria, and their fusogenic properties were examined using dynamic light scattering in 1-oleoyl-2-hydroxy- sn-glycero-3-phosphocholine lipid spheroids. We conclude that a degree of correlation exists between the antimicrobial effectiveness of the peptides studied here and their modulation of membrane conductivity.
Bertram, MR, Delgado, A, Pauszek, SJ, Smoliga, GR, Brito, B, Stenfeldt, C, Hartwig, EJ, Jumbo, SD, Abdoulmoumini, M, Oliva Marie, AA, Salhine, R, Rodriguez, LL, Garabed, R & Arzt, J 2018, 'Effect of vaccination on cattle subclinically infected with foot-and-mouth disease virus in Cameroon', Preventive Veterinary Medicine, vol. 155, pp. 1-10. View/Download from: Publisher's site View description>>
Foot-and-mouth disease (FMD) is one of the most contagious and economically important livestock diseases worldwide. Four serotypes of FMD virus (FMDV; O, A, SAT1, SAT2) circulate in Cameroon, and a trivalent inactivated vaccine against the three most common serotypes (O, A, SAT2) was recently introduced in 2014. The objective of this study was to characterize vaccine performance in cattle under natural hyperendemic conditions in the Adamawa region of Cameroon. Vaccinated cattle (n = 50) and non-vaccinated controls (n = 100) were monitored by serum and oropharyngeal fluid (OPF) sample collection through a 12-month period. Anti-FMDV non-structural protein (anti-NSP) seroprevalence increased from 59.3% (89/150) at the beginning of the study to 85.8% (103/120) at the end of the study, and FMDV RNA was found in 28% (42/150) of animals overall, despite detection of clinical signs of FMD in only 6 non-vaccinated animals. Viral sequence analysis indicated that subclinical infections of FMDV serotypes O and A were present within the study herds during the study period, which was reflected by an overall increase of anti-NSP seroprevalence during the study. There was no association between vaccination status and seroconversion or prevalence of FMDV RNA in OPF. Younger cattle had higher odds of detection of FMDV RNA in OPF, but older animals were more likely to be seropositive. This study suggests vaccination of herds previously exposed to FMDV may help to limit clinical signs and reduce economic losses caused by FMDV. These findings also suggest that subclinical circulation of FMDV occurs in hyperendemic regions regardless of vaccination.
Bertram, MR, Vu, LT, Pauszek, SJ, Brito, BP, Hartwig, EJ, Smoliga, GR, Hoang, BH, Phuong, NT, Stenfeldt, C, Fish, IH, Hung, VV, Delgado, A, VanderWaal, K, Rodriguez, LL, Long, NT, Dung, DH & Arzt, J 2018, 'Lack of Transmission of Foot-and-Mouth Disease Virus From Persistently Infected Cattle to Naïve Cattle Under Field Conditions in Vietnam', Frontiers in Veterinary Science, vol. 5. View/Download from: Publisher's site
Beutier, H, Hechler, B, Godon, O, Wang, Y, Gillis, CM, de Chaisemartin, L, Gouel-Chéron, A, Magnenat, S, Macdonald, LE, Murphy, AJ, Chollet-Martin, S, Longrois, D, Gachet, C, Bruhns, P & Jönsson, F 2018, 'Platelets expressing IgG receptor FcγRIIA/CD32A determine the severity of experimental anaphylaxis', Science Immunology, vol. 3, no. 22. View/Download from: Publisher's site View description>>
Platelet-derived serotonin contributes to FcγRIIA/CD32A-induced IgG-dependent anaphylaxis.
Bhandari, S, Bannister, KW, Murphy, T, Bell, M, Raja, W, Marvil, J, Hancock, PJ, Whiting, M, Flynn, CM, Collier, JD, Kaplan, DL, Allison, JR, Anderson, C, Heywood, I, Hotan, A, Hunstead, R, Lee-Waddell, K, Madrid, JP, McConnell, D, Popping, A, Rhee, J, Sadler, E & Voronkov, MA 2018, 'A pilot survey for transients and variables with the Australian Square Kilometre Array Pathfinder', Monthly Notices of the Royal Astronomical Society, vol. 478, no. 2, pp. 1784-1794. View/Download from: Publisher's site View description>>
Bharatula, LD, Marsili, E, Rice, S & Kwan, JJ 2018, 'The effects of high intensity focused ultrasound on biofilms formed by Pseudomonas aeruginosa', The Journal of the Acoustical Society of America, vol. 143, no. 3_Supplement, pp. 1928-1928. View/Download from: Publisher's site View description>>
Bacterial infections are increasingly difficult to treat due to their growing resistance to antibiotics. Most of these bacterial infections form a biofilm that limits the effectiveness of the antibiotic. Biofilms are microbial cells that are protected by a self-generated matrix of extracellular polymeric substances. In addition to their intrinsic antibiotic resistance, these biofilms are able to respond to the stresses from the antibiotic by inducing drug resistance mechanisms. Currently, the strategy to combat drug resistance is to develop novel drugs, however, the rate of drug development is being surpassed by the rate of drug resistance. There is therefore a need for alternative means in enhancing the efficacy of current drug therapeutics. We propose to use of high intensity focused ultrasound (HIFU) to disrupt the biofilm and promote drug penetration. However, the effects of HIFU on these bacterial communities remain unknown. Here we report on microstructural changes within biofilms formed by Pseudomonas aeruginosa due to exposure to HIFU at 500 kHz center frequency. Changes to the biofilm were nondestructively measured through impedance spectroscopy and confocal microscopy. Biofilms were shown to induce cavitation (as measured by a passive cavitation detector) at relatively low pressure amplitudes suggesting the presence of cavitation nuclei within the extracellular matrix.
Bhullar, KS, Lagarón, NO, McGowan, EM, Parmar, I, Jha, A, Hubbard, BP & Rupasinghe, HPV 2018, 'Kinase-targeted cancer therapies: progress, challenges and future directions', Molecular Cancer, vol. 17, no. 1. View/Download from: Publisher's site
Bihana, S, Dhiman, A, Singh, G & Satija, S 2018, 'Gas chromatography-mass spectroscopy analysis of bioactive compounds in the whole plant parts of ethanolic extract of Asclepias Curassavica L.', International Journal of Green Pharmacy, vol. 12, no. 2, pp. 107-114. View description>>
Objective: The present study was carried out to cultivate Asclepias curassavica and explore the phytoconstituents of ethanolic extract of A. curassavica whole part using gas chromatography-mass spectroscopy (GC-MS). This research may be useful for constituent(s)-based pharmacological activity. Materials and Methods: 5 g of powdered plant material was taken in a spotless, level container and soaked in 80 ml of ethanol, and extraction was done by hot extraction method. The glass container with extract was sealed and kept aside for few hours. It was then filtered through Whatman filter paper No.42. Ethanolic extract of A. curassavica was further undertaken for GC-MS analysis. Result: The ethanolic extract of the whole plant of A. curassavica revealed the presence of 49 diverse phytochemical compounds. Several of these phytoconstituents are reported to possess pharmacological potential. Conclusion: A. curassavica L. has been successfully cultivated, authenticated, and used for the identification of its organic chemical components by GC-MS. Pesticide residues may have an adverse effect on the food chain, and the concentration should be within permissible range for safe human consumption of any herbal drug product. A. curassavica has been observed as a tremendous source of many important phytochemicals, especially glycosidal, alkaloids, steroidal, and terpenoidal compounds. There were no pesticidal residues found in the tested plant drug. Therefore, it may be explored for the production of natural medicinal formulations in pharmaceutical drug industries including anticancer drugs, antibacterial, antimicrobial, antiasthmatics, urine acidifiers, and antimicrobial on account of its potential antioxidant activity.
Billatos, E, Faiz, A, Gesthalter, Y, LeClerc, A, Alekseyev, YO, Xiao, X, Liu, G, ten Hacken, NHT, Heijink, IH, Timens, W, Brandsma, CA, Postma, DS, van den Berge, M, Spira, A & Lenburg, ME 2018, 'Impact of acute exposure to cigarette smoke on airway gene expression', Physiological Genomics, vol. 50, no. 9, pp. 705-713. View/Download from: Publisher's site View description>>
Background: Understanding effects of acute smoke exposure (ASE) on airway epithelial gene expression and their relationship with the effects of chronic smoke exposure may provide biological insights into the development of smoking-related respiratory diseases. Methods: Bronchial airway epithelial cell brushings were collected from 63 individuals without recent cigarette smoke exposure and before and 24 h after smoking three cigarettes. RNA from these samples was profiled on Affymetrix Human Gene 1.0 ST microarrays. Results: We identified 91 genes differentially expressed 24 h after ASE (false discovery rate < 0.25). ASE induced genes involved in xenobiotic metabolism, oxidative stress, and inflammation and repressed genes related to cilium morphogenesis and cell cycle. While many genes altered by ASE are altered similarly in chronic smokers, metallothionein genes are induced by ASE and suppressed in chronic smokers. Metallothioneins are also suppressed in current and former smokers with lung cancer relative to those without lung cancer. Conclusions: Acute exposure to as little as three cigarettes and chronic smoking induce largely concordant changes in airway epithelial gene expression. Differences in short-term and long-term effects of smoking on metallothionein expression and their relationship to lung cancer requires further study given these enzymes’ role in the oxidative stress response.
Bishop, DP, Grossgarten, M, Dietrich, D, Vennemann, A, Cole, N, Sperling, M, Wiemann, M, Doble, PA & Karst, U 2018, 'Correction: Quantitative imaging of translocated silver following nanoparticle exposure by laser ablation-inductively coupled plasma-mass spectrometry', Analytical Methods, vol. 10, no. 8, pp. 926-926. View/Download from: Publisher's site View description>>
Correction for ‘Quantitative imaging of translocated silver following nanoparticle exposure by laser ablation-inductively coupled plasma-mass spectrometry’ by David P. Bishop et al., Anal. Methods, 2018, DOI: 10.1039/c7ay02294h.
Bishop, DP, Grossgarten, M, Dietrich, D, Vennemann, A, Cole, N, Sperling, M, Wiemann, M, Doble, PA & Karst, U 2018, 'Quantitative imaging of translocated silver following nanoparticle exposure by laser ablation-inductively coupled plasma-mass spectrometry', Analytical Methods, vol. 10, no. 8, pp. 836-840. View/Download from: Publisher's site View description>>
We demonstrate the use of LA-ICP-MS for determining the location and quantification of silver in a rat spleen following nanoparticle exposure.
Bishop, DP, Hare, DJ, Clases, D & Doble, PA 2018, 'Applications of liquid chromatography-inductively coupled plasma-mass spectrometry in the biosciences: A tutorial review and recent developments', TrAC Trends in Analytical Chemistry, vol. 104, pp. 11-21. View/Download from: Publisher's site View description>>
Diamond is an ideal material for a broad range of current and emerging applications in tribology, quantum photonics, high-power electronics, and sensing. However, top-down processing is very challenging due to its extreme chemical and physical properties. Gas-mediated electron beam-induced etching (EBIE) has recently emerged as a minimally invasive, facile means to dry etch and pattern diamond at the nanoscale using oxidizing precursor gases such as O2 and H2O. Here we explain the roles of oxygen and hydrogen in the etch process and show that oxygen gives rise to rapid, isotropic etching, while the addition of hydrogen gives rise to anisotropic etching and the formation of topographic surface patterns. We identify the etch reaction pathways and show that the anisotropy is caused by preferential passivation of specific crystal planes. The anisotropy can be controlled by the partial pressure of hydrogen and by using a remote RF plasma source to radicalize the precursor gas. It can be used to manipulate the geometries of topographic surface patterns as well as nano- and microstructures fabricated by EBIE. Our findings constitute a comprehensive explanation of the anisotropic etch process and advance present understanding of electron-surface interactions.
Blackman, CJ, Gleason, SM, Cook, AM, Chang, Y, Laws, CA & Westoby, M 2018, 'The links between leaf hydraulic vulnerability to drought and key aspects of leaf venation and xylem anatomy among 26 Australian woody angiosperms from contrasting climates', Annals of Botany, vol. 122, no. 1, pp. 59-67. View/Download from: Publisher's site
Blas Achic, BG, Wang, T, Su, Y, Kipnis, V, Dodd, K & Carroll, RJ 2018, 'Categorizing a continuous predictor subject to measurement error', Electronic Journal of Statistics, vol. 12, no. 2, pp. 4032-4056. View/Download from: Publisher's site
Bodachivskyi, I, Kuzhiumparambil, U & Williams, DBG 2018, 'Acid-Catalyzed Conversion of Carbohydrates into Value-Added Small Molecules in Aqueous Media and Ionic Liquids', ChemSusChem, vol. 11, no. 4, pp. 642-660. View/Download from: Publisher's site View description>>
Biomass is the only realistic major alternative source (to crude oil) of hydrocarbon substrates for the commercial synthesis of bulk and fine chemicals. Within biomass, terrestrial sources are the most accessible, and therein lignocellulosic materials are most abundant. Although lignin shows promise for the delivery of certain types of organic molecules, cellulose is a biopolymer with significant potential for conversion into high-volume and high-value chemicals. This review covers the acid-catalyzed conversion of lower value (poly)carbohydrates into valorized organic building-block chemicals (platform molecules). It focuses on those conversions performed in aqueous media or ionic liquids to provide the reader with a perspective on what can be considered a best case scenario, that is, that the overall process is as sustainable as possible.
Bogema, DR, Micallef, ML, Liu, M, Padula, MP, Djordjevic, SP, Darling, AE & Jenkins, C 2018, 'Analysis of Theileria orientalis draft genome sequences reveals potential species-level divergence of the Ikeda, Chitose and Buffeli genotypes', BMC Genomics, vol. 19, no. 1, pp. 298-298. View/Download from: Publisher's site View description>>
Theileria orientalis (Apicomplexa: Piroplasmida) has caused clinical disease in cattle of Eastern Asia for many years and its recent rapid spread throughout Australian and New Zealand herds has caused substantial economic losses to production through cattle deaths, late term abortion and morbidity. Disease outbreaks have been linked to the detection of a pathogenic genotype of T. orientalis, genotype Ikeda, which is also responsible for disease outbreaks in Asia. Here, we sequenced and compared the draft genomes of one pathogenic (Ikeda) and two apathogenic (Chitose, Buffeli) isolates of T. orientalis sourced from Australian herds.Using de novo assembled sequences and a single nucleotide variant (SNV) analysis pipeline, we found extensive genetic divergence between the T. orientalis genotypes. A genome-wide phylogeny reconstructed to address continued confusion over nomenclature of this species displayed concordance with prior phylogenetic studies based on the major piroplasm surface protein (MPSP) gene. However, average nucleotide identity (ANI) values revealed that the divergence between isolates is comparable to that observed between other theilerias which represent distinct species. Analysis of SNVs revealed putative recombination between the Chitose and Buffeli genotypes and also between Australian and Japanese Ikeda isolates. Finally, to inform future vaccine studies, dN/dS ratios and surface location predictions were analysed. Six predicted surface protein targets were confirmed to be expressed during the piroplasm phase of the parasite by mass spectrometry.We used whole genome sequencing to demonstrate that the T. orientalis Ikeda, Chitose and Buffeli variants show substantial genetic divergence. Our data indicates that future researchers could potentially consider disease-associated Ikeda and closely related genotypes as a separate species from non-pathogenic Chitose and Buffeli.
Boonyaratanakornkit, V, Hamilton, N, Márquez-Garbán, DC, Pateetin, P, McGowan, EM & Pietras, RJ 2018, 'Extranuclear signaling by sex steroid receptors and clinical implications in breast cancer', Molecular and Cellular Endocrinology, vol. 466, pp. 51-72. View/Download from: Publisher's site View description>>
Booth, DJ & Sear, J 2018, 'Coral expansion in Sydney and associated coral-reef fishes', Coral Reefs, vol. 37, no. 4, pp. 995-995. View/Download from: Publisher's site
Booth, DJ, Beretta, GA, Brown, L & Figueira, WF 2018, 'Predicting Success of Range-Expanding Coral Reef Fish in Temperate Habitats Using Temperature-Abundance Relationships', Frontiers in Marine Science, vol. 5. View/Download from: Publisher's site View description>>
An 18-year database of coral reef fish expatriation poleward in South East Australia was
used to estimate persistence of coal reef fish recruits on temperate reefs. Surveys have
identified over 150 coral reef fish species recruiting to temperate reefs at latitudes of
34◦S (Sydney) and 60 species to 37◦S (Merimbula) with 20 and 5 species respectively
overwintering in at least 1 year over the study duration. We developed indices of
vulnerability of key species to drops in water temperatures, by relating drops in
abundances of species to temperature drops. Twenty species were ranked according
to their temperature vulnerability. Overall, the families Chaetodontidae (butterflyfishes),
Acanthuridae (surgeonfishes), Labridae (wrasses) and Pomacetnridae (damselfishes) had
similar cold-water tolerance. However, there was considerable variability within families,
for instance in the Pomacentridae, species from the genus Abudefduf appeared to
have better cold-temperature tolerance than the other species. Predicted minimum
overwintering temperature varied from 15.6◦C to 19.8◦C, with some species showing
lower Tzero at Merimbula, the more poleward location. There was general concordance
between a species’ tolerance to cold-water and its tendency to occur as an overwinter
but also notable exceptions. So while this work demonstrates the potential utility of
tolerance to seasonal temperature drops as a means to predict range expansion
capacity of vagrant species, the exceptional cases serve to highlight alternative factors.
Specifically, tolerance to seasonal cooling of water is not the only important factor
when predicting the range expansion capacity of a species. Factors affecting the
general abundance of the vagrants, such as habitat suitability and competitor/predator
environments will also be critical where overwinter survival becomes a lottery.
Borovkov, K, Mishura, Y, Novikov, A & Zhitlukhin, M 2018, 'New and refined bounds for expected maxima of fractional Brownian motion', Statistics & Probability Letters, vol. 137, pp. 142-147. View/Download from: Publisher's site View description>>
Bouman, HA, Platt, T, Doblin, M, Figueiras, FG, Gudmundsson, K, Gudfinnsson, HG, Huang, B, Hickman, A, Hiscock, M, Jackson, T, Lutz, VA, Mélin, F, Rey, F, Pepin, P, Segura, V, Tilstone, GH, van Dongen-Vogels, V & Sathyendranath, S 2018, 'Photosynthesis–irradiance parameters of marine phytoplankton: synthesis of a global data set', Earth System Science Data, vol. 10, no. 1, pp. 251-266. View/Download from: Publisher's site View description>>
Abstract. The photosynthetic performance of marine phytoplankton varies in response to a variety of factors, environmental and taxonomic. One of the aims of the MArine primary Production: model Parameters from Space (MAPPS) project of the European Space Agency is to assemble a global database of photosynthesis–irradiance (P-E) parameters from a range of oceanographic regimes as an aid to examining the basin-scale variability in the photophysiological response of marine phytoplankton and to use this information to improve the assignment of P-E parameters in the estimation of global marine primary production using satellite data. The MAPPS P-E database, which consists of over 5000 P-E experiments, provides information on the spatio-temporal variability in the two P-E parameters (the assimilation number, PmB, and the initial slope, αB, where the superscripts B indicate normalisation to concentration of chlorophyll) that are fundamental inputs for models (satellite-based and otherwise) of marine primary production that use chlorophyll as the state variable. Quality-control measures consisted of removing samples with abnormally high parameter values and flags were added to denote whether the spectral quality of the incubator lamp was used to calculate a broad-band value of αB. The MAPPS database provides a photophysiological data set that is unprecedented in number of observations and in spatial coverage. The database will be useful to a variety of research communities, including marine ecologists, biogeochemical modellers, remote-sensing scientists and algal physiologists. The compiled data are available at https://doi.org/10.1594/PANGAEA.874087 (Bouman et al., 2017).
Boussarie, G, Bakker, J, Wangensteen, OS, Mariani, S, Bonnin, L, Juhel, J-B, Kiszka, JJ, Kulbicki, M, Manel, S, Robbins, WD, Vigliola, L & Mouillot, D 2018, 'Environmental DNA illuminates the dark diversity of sharks', Science Advances, vol. 4, no. 5, pp. eaap9661-eaap9661. View/Download from: Publisher's site View description>>
Environmental DNA reveals unsuspected shark diversity and calls for monitoring and protection of residual populations.
Bradbury, P, Traini, D, Ammit, AJ, Young, PM & Ong, HX 2018, 'Repurposing of statins via inhalation to treat lung inflammatory conditions', Advanced Drug Delivery Reviews, vol. 133, pp. 93-106. View/Download from: Publisher's site
Bradfield, LA, Hart, G & Balleine, BW 2018, 'Inferring action-dependent outcome representations depends on anterior but not posterior medial orbitofrontal cortex', Neurobiology of Learning and Memory, vol. 155, pp. 463-473. View/Download from: Publisher's site View description>>
Although studies examining orbitofrontal cortex (OFC) often treat it as though it were functionally homogeneous, recent evidence has questioned this assumption. Not only are the various subregions of OFC (lateral, ventral, and medial) hetereogeneous, but there is further evidence of heterogeneity within those subregions. For example, several studies in both humans and monkeys have revealed a functional subdivision along the anterior-posterior gradient of the medial OFC (mOFC). Given our previous findings suggesting that, in rats, the mOFC is responsible for inferring the likelihood of unobservable action outcomes (Bradfield, Dezfouli, van Holstein, Chieng, & Balleine, 2015), and given the anterior nature of the placements of our prior manipulations, we decided to assess whether the rat mOFC also differs in connection and function along its anteroposterior axis. We first used retrograde tracing to compare the density of efferents from mOFC to several structures known to contribute to goal-directed action: the mediodorsal thalamus, basolateral amygdala, posterior dorsomedial striatum, nucleus accumbens core and ventral tegmental area. We then compared the functional effects of anterior versus posterior mOFC excitotoxic lesions on tests of Pavlovian-instrumental transfer, instrumental outcome devaluation and outcome-specific reinstatement. We found evidence that the anterior mOFC had greater connectivity with the accumbens core and greater functional involvement in goal-directed action than the posterior mOFC. Consistent with previous findings across species, therefore, these results suggest that the anterior and posterior mOFC of the rat are indeed functionally distinct, and that it is the anterior mOFC that is particularly critical for inferring unobservable action outcomes.
Bradfield, LA, Matamales, M & Bertran-Gonzalez, J 2018, 'The Thalamostriatal Pathway and the Hierarchical Control of Action', Neuron, vol. 100, no. 3, pp. 521-523. View/Download from: Publisher's site
Bradley, DJ, Gladstone, W & Gribben, PE 2018, 'Relationships between the spread of Caulerpa filiformis and fish communities on temperate rocky reefs', Journal of Fish Biology, vol. 93, no. 1, pp. 12-20. View/Download from: Publisher's site View description>>
The previously sub-dominant native marine macrophyte Caulerpa filiformis is now dominant on many sub-tidal rocky reefs in New South Wales (NSW), Australia and is expanding its distribution. As C. filiformis is highly chemically defended and structurally different to co-occurring habitat-forming macrophytes, two key attributes that govern fish assemblages, we hypothesized that fish assemblages, particularly herbivorous fishes, would be different at sites where C. filiformis occurred from where it was previously absent and within sites, fish community structure would be correlated to the cover of C. filiformis. We investigated these hypotheses by determining reef-associated fish assemblage attributes (assemblage structure, species richness, total abundance, Shannon-Weiner diversity, abundance of herbivorous species) along transects within sites where C. filiformis was present and absent. Surprisingly, despite large patches and very high densities of C. filiformis on the reefs we sampled, at larger spatial scales (i.e., among sites) no fish assemblage metrics differed between sites with large stands of C. filiformis and sites without the alga. Moreover the abundance of one dominant herbivore, the rock cale Aplodactylus lophodon, was greater at sites within large beds of C. filiformis. At smaller spatial scales, however, i.e. within sites where C. filiformis was present, fish assemblages did vary as a function of C. filiformis cover along transects, although this was not consistent across sampling times. Overall, our results suggest that the potential effects of the spread of this alga on faunal communities warrants further investigation.
Bramucci, AR, Labeeuw, L, Orata, FD, Ryan, EM, Malmstrom, RR & Case, RJ 2018, 'The Bacterial Symbiont Phaeobacter inhibens Shapes the Life History of Its Algal Host Emiliania huxleyi', Frontiers in Marine Science, vol. 5. View/Download from: Publisher's site View description>>
Braun, M, Kirkup, L & Chadwick, S 2018, 'The impact of inquiry orientation and other elements of cultural framework on student engagement in first year laboratory programs', International Journal of Innovation in Science and Mathematics Education, vol. 26, no. 4, pp. 30-48. View description>>
Inquiry-oriented approaches to learning have gradually entered science laboratory programs, aiming to deliver an authentic experience of doing science, enhance student engagement with the material, and bring greater emphasis on generic skills underpinning graduate attributes. Although such approaches have demonstrated pedagogical advantages and improved student engagement, it is not clear how the advantages should be weighted against other elements of what may be regarded as the laboratory program's cultural framework. We analysed two large-enrolment introductory tertiary programs: physics and chemistry at the University of Technology Sydney. The programs differed in the level of inquiry orientation but also in approaches to design, logistics and relevancy. We found that, based on student survey responses, the putative advantages of a deeper inquiry orientation in the physics laboratory were insufficient to compensate for the apparent advantages arising from the other elements of the cultural framework in the chemistry laboratory.
We report on the first demonstration of FNDs containing either silicon or nitrogen vacancy color centers for multi-color bio-imaging.
Bray, K, Kato, H, Previdi, R, Sandstrom, R, Ganesan, K, Ogura, M, Makino, T, Yamasaki, S, Magyar, AP, Toth, M & Aharonovich, I 2018, 'Single crystal diamond membranes for nanoelectronics', Nanoscale, vol. 10, no. 8, pp. 4028-4035. View/Download from: Publisher's site View description>>
Single crystal, nanoscale diamond membranes are highly sought after for a variety of applications including nanophotonics, nanoelectronics and quantum information science.
Bray, K, Regan, B, Trycz, A, Previdi, R, Seniutinas, G, Ganesan, K, Kianinia, M, Kim, S & Aharonovich, I 2018, 'Single Crystal Diamond Membranes and Photonic Resonators Containing Germanium Vacancy Color Centers', ACS Photonics, vol. 5, no. 12, pp. 4817-4822. View/Download from: Publisher's site View description>>
Brito, B, Pauszek, SJ, Hartwig, EJ, Smoliga, GR, Vu, LT, Dong, PV, Stenfeldt, C, Rodriguez, LL, King, DP, Knowles, NJ, Bachanek-Bankowska, K, Long, NT, Dung, DH & Arzt, J 2018, 'A traditional evolutionary history of foot-and-mouth disease viruses in Southeast Asia challenged by analyses of non-structural protein coding sequences', Scientific Reports, vol. 8, no. 1, pp. 6472-6472. View/Download from: Publisher's site View description>>
AbstractRecombination of rapidly evolving RNA-viruses provides an important mechanism for diversification, spread, and emergence of new variants with enhanced fitness. Foot-and-mouth disease virus (FMDV) causes an important transboundary disease of livestock that is endemic to most countries in Asia and Africa. Maintenance and spread of FMDV are driven by periods of dominance of specific viral lineages. Current understanding of the molecular epidemiology of FMDV lineages is generally based on the phylogenetic relationship of the capsid-encoding genes, with less attention to the process of recombination and evolution of non-structural proteins. In this study, the putative recombination breakpoints of FMDVs endemic to Southeast Asia were determined using full-open reading frame sequences. Subsequently, the lineages’ divergence times of recombination-free genome regions were estimated. These analyses revealed a close relationship between two of the earliest endemic viral lineages that appear unrelated when only considering the phylogeny of their capsid proteins. Contrastingly, one lineage, named O/CATHAY, known for having a particular host predilection (pigs) has evolved independently. Additionally, intra-lineage recombination occurred at different breakpoints compared to the inter-lineage process. These results provide new insights about FMDV recombination patterns and the evolutionary interdependence of FMDV serotypes and lineages.
Brito, B, Pauszek, SJ, Hartwig, EJ, Smoliga, GR, Vu, LT, Vu, PP, Stenfeldt, C, Rodriguez, LL, King, DP, Knowles, NJ, Bachanek-Bankowska, K, Long, NT, Dung, H & Arzt, J 2018, 'A56 Evolutionary analyses of foot-and-mouth disease virus in Southeast Asia using whole-genome sequences', Virus Evolution, vol. 4, no. suppl_1. View/Download from: Publisher's site
Brito, BP, Mohapatra, JK, Subramaniam, S, Pattnaik, B, Rodriguez, LL, Moore, BR & Perez, AM 2018, 'Dynamics of widespread foot‐and‐mouth disease virus serotypes A, O and Asia‐1 in southern Asia: A Bayesian phylogenetic perspective', Transboundary and Emerging Diseases, vol. 65, no. 3, pp. 696-710. View/Download from: Publisher's site View description>>
Foot-and-mouth disease (FMD) is, arguably, the animal disease with the most devastating global economic impact owing in part, to the severe trade restrictions imposed upon affected countries and regions. South Asia is one of the regions where widespread lineages of the FMDV virus (FMDV) have emerged. Here, we performed an integrative phylogenetic analysis of all FMDV serotypes (A, O and Asia-1) circulating in southern Asia, including viral sequences collected until 2013. Our results describe the occurrence of FMD caused by different serotypes and lineages, focusing in the cycles where a specific lineage predominates within a region for a protracted period and then are rapidly or progressively replaced by an emergent or re-emergent strain that is introduced from an adjacent region. Transmission between the two main regions in southern Asia (the Indian subcontinent and the region comprised by Afghanistan, Iran and Pakistan) has been limited. Results of time divergence estimation of lineages that currently circulate in this region indicate that the most recent common ancestor of endemic lineages are: 1992 [1989-1995] for lineage O/PanAsia; 1997 [1995-1999] for PanAsia2; 2001 [1998-2004] for O/Ind2001; 2001 [2000-2002] for A/Iran-05; 1990 [1988-1991] for A/G-18 (G-VII); 2003 [2000-2006] for Asia-1 Sindh08 and 2002 [1999-2004] for Asia-1 G-VIII. We estimated the mean of the overall substitution rate of the VP1 coding region (substitution/site/year) for serotype O (5.95 × 10-3 ), serotype A (1.19 × 10-2 ) and serotype Asia-1 (3.08 × 10-3 ). The potential factors driving the lineage turnover are discussed. Our results provide insights into the ecological and evolutionary factors driving the emergence of FMDV.
Broderick, JW, Fender, RP, Miller-Jones, JCA, Trushkin, SA, Stewart, AJ, Anderson, GE, Staley, TD, Blundell, KM, Pietka, M, Markoff, S, Rowlinson, A, Swinbank, JD, van der Horst, AJ, Bell, ME, Breton, RP, Carbone, D, Corbel, S, Eislöffel, J, Falcke, H, Grießmeier, J-M, Hessels, JWT, Kondratiev, VI, Law, CJ, Molenaar, GJ, Serylak, M, Stappers, BW, van Leeuwen, J, Wijers, RAMJ, Wijnands, R, Wise, MW & Zarka, P 2018, 'LOFAR 150-MHz observations of SS 433 and W 50', Monthly Notices of the Royal Astronomical Society, vol. 475, no. 4, pp. 5360-5377. View/Download from: Publisher's site View description>>
SummaryThe seagrass rhizosphere harbors dynamic microenvironments, where plant‐driven gradients of O2 and dissolved organic carbon form microhabitats that select for distinct microbial communities. To examine how seagrass‐mediated alterations of rhizosphere geochemistry affect microbial communities at the microscale level, we applied 16S rRNA amplicon sequencing of artificial sediments surrounding the meristematic tissues of the seagrass Zostera muelleri together with microsensor measurements of the chemical conditions at the basal leaf meristem (BLM). Radial O2 loss (ROL) from the BLM led to ∼ 300 µm thick oxic microzones, wherein pronounced decreases in H2S and pH occurred. Significantly higher relative abundances of sulphate‐reducing bacteria were observed around the meristematic tissues compared to the bulk sediment, especially around the root apical meristems (RAM; ∼ 57% of sequences). Within oxic microniches, elevated abundances of sulphide‐oxidizing bacteria were observed compared to the bulk sediment and around the RAM. However, sulphide oxidisers within the oxic microzone did not enhance sediment detoxification, as rates of H2S re‐oxidation here were similar to those observed in a pre‐sterilized root/rhizome environment. Our results provide novel insights into how chemical and microbiological processes in the seagrass rhizosphere modulate plant‐microbe interactions potentially affecting seagrass health.
Brown, MV, van de Kamp, J, Ostrowski, M, Seymour, JR, Ingleton, T, Messer, LF, Jeffries, T, Siboni, N, Laverock, B, Bibiloni-Isaksson, J, Nelson, TM, Coman, F, Davies, CH, Frampton, D, Rayner, M, Goossen, K, Robert, S, Holmes, B, Abell, GCJ, Craw, P, Kahlke, T, Sow, SLS, McAllister, K, Windsor, J, Skuza, M, Crossing, R, Patten, N, Malthouse, P, van Ruth, PD, Paulsen, I, Fuhrman, JA, Richardson, A, Koval, J, Bissett, A, Fitzgerald, A, Moltmann, T & Bodrossy, L 2018, 'Systematic, continental scale temporal monitoring of marine pelagic microbiota by the Australian Marine Microbial Biodiversity Initiative', Scientific Data, vol. 5, no. 1, pp. 180130-180130. View/Download from: Publisher's site View description>>
AbstractSustained observations of microbial dynamics are rare, especially in southern hemisphere waters. The Australian Marine Microbial Biodiversity Initiative (AMMBI) provides methodologically standardized, continental scale, temporal phylogenetic amplicon sequencing data describing Bacteria, Archaea and microbial Eukarya assemblages. Sequence data is linked to extensive physical, biological and chemical oceanographic contextual information. Samples are collected monthly to seasonally from multiple depths at seven sites: Darwin Harbour (Northern Territory), Yongala (Queensland), North Stradbroke Island (Queensland), Port Hacking (New South Wales), Maria Island (Tasmania), Kangaroo Island (South Australia), Rottnest Island (Western Australia). These sites span ~30° of latitude and ~38° longitude, range from tropical to cold temperate zones, and are influenced by both local and globally significant oceanographic and climatic features. All sequence datasets are provided in both raw and processed fashion. Currently 952 samples are publically available for bacteria and archaea which include 88,951,761 bacterial (72,435 unique) and 70,463,079 archaeal (24,205 unique) 16 S rRNA v1-3 gene sequences, and 388 samples are available for eukaryotes which include 39,801,050 (78,463 unique) 18 S rRNA v4 gene sequences.
Buchmann, JP, Fourment, M & Holmes, EC 2018, 'The Biological Object Notation (BON): a structured file format for biological data', Scientific Reports, vol. 8, no. 1. View/Download from: Publisher's site View description>>
AbstractThe large size and high complexity of biological data can represent a major methodological challenge for the analysis and exchange of data sets between computers and applications. There has also been a substantial increase in the amount of metadata associated with biological data sets, which is being increasingly incorporated into existing data formats. Despite the existence of structured formats based on XML, biological data sets are mainly formatted using unstructured file formats, and the incorporation of metadata results in increasingly complex parsing routines such that they become more error prone. To overcome these problems, we present the “biological object notation” (BON) format, a new way to exchange and parse nearly all biological data sets more efficiently and with less error than other currently available formats. Based on JavaScript Object Notation (JSON), BON simplifies parsing by clearly separating the biological data from its metadata and reduces complexity compared to XML based formats. The ability to selectively compress data up to 87% compared to other file formats and the reduced complexity results in improved transfer times and less error prone applications.
Burgess, JK, Ketheson, A, Faiz, A, Limbert Rempel, KA, Oliver, BG, Ward, JPT & Halayko, AJ 2018, 'Phenotype and Functional Features of Human Telomerase Reverse Transcriptase Immortalized Human Airway Smooth Muscle Cells from Asthmatic and Non-Asthmatic Donors', Scientific Reports, vol. 8, no. 1, pp. 805-805. View/Download from: Publisher's site View description>>
AbstractAsthma is an obstructive respiratory disease characterised by chronic inflammation with airway hyperresponsiveness. In asthmatic airways, there is an increase in airway smooth muscle (ASM) cell bulk, which differs from non-asthmatic ASM in characteristics. This study aimed to assess the usefulness of hTERT immortalisation of human ASM cells as a research tool. Specifically we compared proliferative capacity, inflammatory mediator release and extracellular matrix (ECM) production in hTERT immortalised and parent primary ASM cells from asthmatic and non-asthmatic donors. Our studies revealed no significant differences in proliferation, IL-6 and eotaxin-1 production, or CTGF synthesis between donor-matched parent and hTERT immortalised ASM cell lines. However, deposition of ECM proteins fibronectin and fibulin-1 was significantly lower in immortalised ASM cells compared to corresponding primary cells. Notably, previously reported differences in proliferation and inflammatory mediator release between asthmatic and non-asthmatic ASM cells were retained, but excessive ECM protein deposition in asthmatic ASM cells was lost in hTERT ASM cells. This study shows that hTERT immortalised ASM cells mirror primary ASM cells in proliferation and inflammatory profile characteristics. Moreover, we demonstrate both strengths and weaknesses of this immortalised cell model as a representation of primary ASM cells for future asthma pathophysiological research.
Burke, C, Burnard, D, Polkinghorne, A, Webb, J & Huston, W 2018, 'Cloacal and Ocular Microbiota of the Endangered Australian Northern Quoll', Microorganisms, vol. 6, no. 3, pp. 68-68. View/Download from: Publisher's site View description>>
The Australian northern quoll is an important predatory marsupial carnivore that is currently endangered due to inappropriate fire regimes, predation, and the spread of invasive cane toads. The microbiota of Australian marsupials has not been extensively studied, but is thought to play a role in their health. This study provides an initial characterization of the cloacal microbiota of the northern quoll, as well as other marsupials including possums and kangaroos which were opportunistically sampled. The northern quoll cloaca microbiota was dominated by Enterococcus and Lactobacillus and had a relatively high proportion of members of the Proteobacteria phylum, which has been observed in other carnivorous marsupials. The diversity and structure of the microbiota was not influenced by presence of Chlamydiales which are intracellular bacteria and potential pathogens. The microbiota of the other marsupials was quite varied, which may be related to their health status. Characterization of the northern quoll microbiota will help to better understand the biology of this endangered animal.
Butterworth, NJ, Byrne, PG, Keller, PA & Wallman, JF 2018, 'Body Odor and Sex: Do Cuticular Hydrocarbons Facilitate Sexual Attraction in the Small Hairy Maggot Blowfly?', Journal of Chemical Ecology, vol. 44, no. 3, pp. 248-256. View/Download from: Publisher's site
Calarco, L, Barratt, J & Ellis, J 2018, 'Genome Wide Identification of Mutational Hotspots in the Apicomplexan Parasite Neospora caninum and the Implications for Virulence', Genome Biology and Evolution, vol. 10, no. 9, pp. 2417-2431. View/Download from: Publisher's site
Camp, EF, Schoepf, V & Suggett, DJ 2018, 'How can “Super Corals” facilitate global coral reef survival under rapid environmental and climatic change?', Global Change Biology, vol. 24, no. 7, pp. 2755-2757. View/Download from: Publisher's site View description>>
Coral reefs are in a state of rapid global decline via environmental and climate change, and efforts have intensified to identify or engineer coral populations with increased resilience. Concurrent with these efforts has been increasing use of the popularized term "Super Coral" in both popular media and scientific literature without a unifying definition. However, how this subjective term is currently applied has the potential to mislead inference over factors contributing to coral survivorship, and the future trajectory of coral reef form and functioning. Here, we discuss that the information required to support a single definition does not exist, and in fact may never be appropriate, i.e. "How Super is Super"? Instead, we advocate caution of this term, and suggest a workflow that enables contextualization and clarification of superiority to ensure that inferred or asserted survivorship is appropriate into future reef projections. This is crucial to robustly unlock how "Super Corals" can be integrated into the suite of management options required to facilitate coral survival under rapid environmental and climate change.
Camp, EF, Schoepf, V, Mumby, PJ & Suggett, DJ 2018, 'Editorial: The Future of Coral Reefs Subject to Rapid Climate Change: Lessons From Natural Extreme Environments', Frontiers in Marine Science, vol. 5. View/Download from: Publisher's site
Camp, EF, Schoepf, V, Mumby, PJ, Hardtke, LA, Rodolfo-Metalpa, R, Smith, DJ & Suggett, DJ 2018, 'The Future of Coral Reefs Subject to Rapid Climate Change: Lessons from Natural Extreme Environments', Frontiers in Marine Science, vol. 5. View/Download from: Publisher's site
Canfield, PJ, Blake, IM, Cai, Z-L, Luck, IJ, Krausz, E, Kobayashi, R, Reimers, JR & Crossley, MJ 2018, 'A new fundamental type of conformational isomerism', Nature Chemistry, vol. 10, no. 6, pp. 615-624. View/Download from: Publisher's site View description>>
Isomerism is a fundamental chemical concept, reflecting the fact that the arrangement of atoms in a molecular entity has a profound influence on its chemical and physical properties. Here we describe a previously unclassified fundamental form of conformational isomerism through four resolved stereoisomers of a transoid (BF)O(BF)-quinoxalinoporphyrin. These comprise two pairs of enantiomers that manifest structural relationships not describable within existing IUPAC nomenclature and terminology. They undergo thermal diastereomeric interconversion over a barrier of 104 ± 2 kJ mol-1, which we term 'akamptisomerization'. Feasible interconversion processes between conceivable synthesis products and reaction intermediates were mapped out by density functional theory calculations, identifying bond-angle inversion (BAI) at a singly bonded atom as the reaction mechanism. We also introduce the necessary BAI stereodescriptors parvo and amplo. Based on an extended polytope formalism of molecular structure and stereoisomerization, BAI-driven akamptisomerization is shown to be the final fundamental type of conformational isomerization.
Canfield, PJ, Blake, IM, Cai, Z-L, Luck, IJ, Krausz, E, Kobayashi, R, Reimers, JR & Crossley, MJ 2018, 'Publisher Correction: A new fundamental type of conformational isomerism', Nature Chemistry, vol. 10, no. 9, pp. 989-989. View/Download from: Publisher's site
Carroll, R, Su, Y & Reedy, J 2018, 'Clustering in General Measurement Error Models', Statistica Sinica, vol. 28, no. 4, pp. 2337-2351. View/Download from: Publisher's site View description>>
Carstensen, A, Herdean, A, Schmidt, SB, Sharma, A, Spetea, C, Pribil, M & Husted, S 2018, 'The Impacts of Phosphorus Deficiency on the Photosynthetic Electron Transport Chain', Plant Physiology, vol. 177, no. 1, pp. 271-284. View/Download from: Publisher's site
Carter, DJ, Brown, J & Saunders, C 2018, 'The Patient’s Voice: Australian Health Care Quality and Safety Regulation From the Perspective of the Public', Journal of Law and Medicine, vol. 25, no. 2, pp. 408-428. View description>>
The quality and safety of health care is a topic of permanent debate in the field of health services policy and regulation. Often absent from this debate, however, are the views and values of the public. These are excluded by a dominant narrative of health care regulation which understands the regulation of quality and safety in health care as principally a technical and instrumental undertaking. This approach constrains the application of law and legal regulation, devaluing their normative and expressive function in this field. In-part as a form of corrective, we offer an analysis based on recent survey data, of the attitudes and perceptions held by the Australian public towards stakeholder responsibility for, and the regulation of, health care quality and safety.
Casey, E, Ribaux, O & Roux, C 2018, 'Digital transformations and the viability of forensic science laboratories: Crisis-opportunity through decentralisation', Forensic Science International, vol. 289, pp. e24-e25. View/Download from: Publisher's site
Cendes, Y, Prasad, P, Rowlinson, A, Wijers, RAMJ, Swinbank, JD, Law, CJ, van der Horst, AJ, Carbone, D, Broderick, JW, Staley, TD, Stewart, AJ, Huizinga, F, Molenaar, G, Alexov, A, Bell, ME, Coenen, T, Corbel, S, Eislöffel, J, Fender, R, Grießmeier, J-M, Jonker, P, Kramer, M, Kuniyoshi, M, Pietka, M, Stappers, B, Wise, M & Zarka, P 2018, 'RFI flagging implications for short-duration transients', Astronomy and Computing, vol. 23, pp. 103-114. View/Download from: Publisher's site View description>>
Chadwick, S, de la Hunty, M & Baker, A 2018, 'Developing Awareness of Professional Behaviors and Skills in the First-Year Chemistry Laboratory', Journal of Chemical Education, vol. 95, no. 6, pp. 947-953. View/Download from: Publisher's site View description>>
Students in first-year chemistry classes come from a variety of backgrounds, with many students unaware of the qualities and behaviors of a professional scientist. Throughout their degree, students will gradually develop their cognitive skills, but they may not be adequately taught or assessed on their professional behavioral skills as a scientist until late in the undergraduate course. By assessing the professional skills of students in first-year chemistry practical classes, this innovation commenced the development of students’ professional identity from the beginning of their university experience. The skills that were assessed included preparedness, cooperation in the group activities, working safely in the laboratory, and time management. By engaging students with professional behaviors and what it means to be a scientist during their first semester, students can potentially carry this through their whole undergraduate degree. This task was received positively by students and staff with over 50% of students believing it increased their confidence in the laboratory. Staff also saw a significant improvement in student behavior and engagement because of this task.
The primary aims of fingermark detection research are to improve the quality and increase the rate of detection of identifiable impressions. This is usually performed through the development of new methods and technologies to provide alternatives to or improve current procedures. While research of this nature is important to pursue, it fails to address the underlying question related to the factors that affect the detection of a latent fingermark. There has been significant research that has examined the differences between techniques, donors and fingermark age, as well as the composition of latent fingermarks. However, they tend not to focus on determining how these factors influence the quality of the developed mark. This study involved the development and evaluation of over 14,000 natural fingermarks deposited on a variety of surfaces to examine the effect of substrate, age, donor variability (both inter- and intra-), depletions and type of finger on fingermark development. Fingermarks were deposited on four substrates (two non-porous and two porous) and developed with either indanedione-zinc (IND-Zn) or cyanoacrylate followed by rhodamine 6G staining (CA+R6G). Three independent assessors graded each mark on the quality of development using an absolute scale proposed by the UK Centre for Applied Science and Technology (CAST). The data generated from these assessments were then analysed for trends or other useful insights. The results from this work reaffirm that individual substrate characteristics (and the choice of development technique) play a significant role in determining the number and quality of marks developed. It was found that fingermarks were more likely to be detected on porous substrates and to also be of a higher quality than on non-porous. The effect of fingermark donor variability was also explored, with significant differences observed between donors and within donors. This research shows that current detection techniques do not detect all av...
Chartrand, KM, Szabó, M, Sinutok, S, Rasheed, MA & Ralph, PJ 2018, 'Living at the margins – The response of deep-water seagrasses to light and temperature renders them susceptible to acute impacts', Marine Environmental Research, vol. 136, pp. 126-138. View/Download from: Publisher's site View description>>
Seagrasses inhabit environments where light varies at different timescales, nonetheless are acutely sensitive to reductions in light beyond some conditional bounds. Two tropical deep-water seagrasses, Halophila decipiens and Halophila spinulosa, from the Great Barrier Reef were tested for their response to defined light and temperature regimes to identify their growth requirements and potential thresholds of mortality. Species were exposed to two light intensities, saturating (75 μmol photons m-2 s-1) and limiting (25 μmol photons m-2 s-1) light and two temperature treatments (26 °C and 30 °C) over a four-week period. Wavelength-specific parameters of PSII photochemistry were evaluated for seagrass leaves, as well as shoot density, gas exchange, and pigment content. Both species were sustained under saturating light levels (3.2 mol photons m-2 d-1) while limiting light led to decreased shoot density for H. decipiens and H. spinulosa after two and four weeks, respectively. Wavelength-specific photochemistry was also affected under light-limiting treatments for both species while the functional absorption cross section was highly conserved. Photoacclimation and physiological adjustments by either species was not adequate to compensate for reduced irradiance suggesting these plants reside at the margins of their functional limits. As such, relatively short periods of light attenuating events, like dredging or flood plumes, may be detrimental to deep-water seagrass populations.
Chellappan, DK, Hansbro, PM, Dua, K, Hsu, A, Gupta, G, Ng, ZY, Wong, J-Y, Chellian, J & Panneerselvam, J 2018, 'Vesicular Systems Containing Curcumin and Their Applications in Respiratory Disorders – A Mini Review', Pharmaceutical Nanotechnology, vol. 5, no. 4, pp. 250-254. View/Download from: Publisher's site View description>>
Vesicular systems like nanotechnology and liposomes are gaining tremendous attention lately in the field of respiratory diseases. These formulations enhance bioavailability of the drug candidate, which could be achieved through a novel drug delivery mechanism. Moreover, the therapeutic potential achieved through these systems is highly controllable over long durations of time providing better efficacy and patient compliance.The objective of this paper is to review the recent literature on vesicular drug delivery systems containing curcumin.We have collated and summarized various recent attempts made to develop different controlled release drug delivery systems containing curcumin which would be of great interest for herbal, formulation and biological scientists. There are several vesicular nanotechnological techniques involving curcumin which have been studied recently, targeting pulmonary diseases.Different vesicular systems containing curcumin are being studied for their therapeutic potential in different respiratory diseases. There has been a renewed interest in formulations containing curcumin recently, primarily owing to the broad spectrum therapeutic potential of this miracle substance. Various types of formulations, containing curcumin, targeting different bodily systems have recently emerged and, nevertheless, the search for newer frontiers with this drug goes on.This mini review, in this direction, tries to highlight the key research interventions employing vesicular systems of drug delivery with curcumin.
Chellappan, DK, Ng, ZY, Wong, J-Y, Hsu, A, Wark, P, Hansbro, N, Taylor, J, Panneerselvam, J, Madheswaran, T, Gupta, G, Bebawy, M, Hansbro, PM & Dua, K 2018, 'Immunological axis of curcumin-loaded vesicular drug delivery systems', Future Medicinal Chemistry, vol. 10, no. 8, pp. 839-844. View/Download from: Publisher's site View description>>
Several vesicular systems loaded with curcumin have found their way in the therapeutic applications of several diseases, primarily acting through their immunological pathways. Such systems use particles at a nanoscale range, bringing about their intended use through a range of complex mechanisms. Apart from delivering drug substances into target tissues, these vesicular systems also effectively overcome problems like insolubility and unequal drug distribution. Several mechanisms are explored lately by different workers, and interest over vesicular curcumin has been renewed in the past decade. This commentary discusses several immunological targets in which curcumin is employed in a vesicular form.
Chellappan, DK, Sivam, NS, Teoh, KX, Leong, WP, Fui, TZ, Chooi, K, Khoo, N, Yi, FJ, Chellian, J, Cheng, LL, Dahiya, R, Gupta, G, Singhvi, G, Nammi, S, Hansbro, PM & Dua, K 2018, 'Gene therapy and type 1 diabetes mellitus', Biomedicine & Pharmacotherapy, vol. 108, pp. 1188-1200. View/Download from: Publisher's site
AbstractMultiphoton fluorescence microscopy (MPM), using near infrared excitation light, provides increased penetration depth, decreased detection background, and reduced phototoxicity. Using stimulated emission depletion (STED) approach, MPM can bypass the diffraction limitation, but it requires both spatial alignment and temporal synchronization of high power (femtosecond) lasers, which is limited by the inefficiency of the probes. Here, we report that upconversion nanoparticles (UCNPs) can unlock a new mode of near-infrared emission saturation (NIRES) nanoscopy for deep tissue super-resolution imaging with excitation intensity several orders of magnitude lower than that required by conventional MPM dyes. Using a doughnut beam excitation from a 980 nm diode laser and detecting at 800 nm, we achieve a resolution of sub 50 nm, 1/20th of the excitation wavelength, in imaging of single UCNP through 93 μm thick liver tissue. This method offers a simple solution for deep tissue super resolution imaging and single molecule tracking.
Chen, C-H 2018, 'Travel Time Prediction Based on Data Feature Selection and Data Clustering Methods', IEICE Transactions on Information and Systems, vol. E102-D, no. 7, pp. 1374-1383. View/Download from: Publisher's site View description>>
In recent years, governments applied intelligent transportation system (ITS) technique to provide several convenience services (e.g., garbage truck app) for residents. This study proposes a garbage truck fleet management system (GTFMS) and data feature selection and data clustering methods for travel time prediction. A GTFMS includes mobile devices (MD), on-board units, fleet management server, and data analysis server (DAS). When user uses MD to request the arrival time of garbage truck, DAS can perform the procedure of data feature selection and data clustering methods to analyses travel time of garbage truck. The proposed methods can cluster the records of travel time and reduce variation for the improvement of travel time prediction. After predicting travel time and arrival time, the predicted information can be sent to user’s MD. In experimental environment, the results showed that the accuracies of previous method and proposed method are 16.73% and 85.97%, respectively. Therefore, the proposed data feature selection and data clustering methods can be used to predict stop-to-stop travel time of garbage truck.
Chen, F, Ji, S, Liu, Q, Wang, H, Liu, H, Brett, DJL, Wang, G & Wang, R 2018, 'Rational Design of Hierarchically Core-Shell Structured Ni3S2@NiMoO4 Nanowires for Electrochemical Energy Storage', Small, vol. 14, no. 27, pp. 1800791-1800791. View/Download from: Publisher's site View description>>
Rational design and controllable synthesis of nanostructured materials with unique microstructure and excellent electrochemical performance for energy storage are crucially desired. In this paper, a facile method is reported for general synthesis of hierarchically core-shell structured Ni3 S2 @NiMoO4 nanowires (NWs) as a binder-free electrode for asymmetric supercapacitors. Due to the intimate contact between Ni3 S2 and NiMoO4 , the hierarchical structured electrodes provide a promising unique structure for asymmetric supercapacitors. The as-prepared binder-free Ni3 S2 @NiMoO4 electrode can significantly improve the electrical conductivity between Ni3 S2 and NiMoO4 , and effectively avoid the aggregation of NiMoO4 nanosheets, which provide more active space for storing charge. The Ni3 S2 @NiMoO4 electrode presents a high areal capacity of 1327.3 µAh cm-2 and 67.8% retention of its initial capacity when current density increases from 2 to 40 mA cm-2 . In a two-electrode Ni3 S2 @NiMoO4 //active carbon cell, the active materials deliver a high energy density of 121.5 Wh kg-1 at a power density of 2.285 kW kg-1 with excellent cycling stability.
Chen, H 2018, 'Gold nanoparticles improve metabolic profile of mice fed a high-fat diet', J Nanobiotechnology, vol. 16. View description>>
BACKGROUND:
Obesity is a high risk for multiple metabolic disorders due to excessive influx of energy, glucose and lipid, often from a western based diet. Low-grade inflammation plays a key role in the progression of such metabolic disorders. The anti-inflammatory property of gold compounds has been used in treating rheumatoid arthritis in the clinic. Previously we found that pure gold nanoparticles (AuNPs, 21 nm) also possess anti-inflammatory effects on the retroperitoneal fat tissue following intraperitoneal injection, by downregulating tumor necrosis factor (TNF) α. However, whether such an effect can change the risk of metabolic disorders in the obese has not been well studied. The study employed C57BL/6 mice fed a pellet high fat diet (HFD, 43% as fat) that were treated daily with AuNPs [low (HFD-LAu) or high (HFD-HAu) dose] via intraperitoneal injection for 9 weeks. In the in vitro study, RAW264.7 macrophages and 3T3-L1 adipocytes were cultured with low and high concentrations of AuNPs alone or together.
RESULTS:
The HFD-fed mice showed a significant increase in fat mass, glucose intolerance, dyslipidemia, and liver steatosis. The HFD-LAu group showed an 8% reduction in body weight, ameliorated hyperlipidemia, and normal glucose tolerance; while the HFD-HAu group had a 5% reduction in body weight with significant improvement in their glucose intolerance and hyperlipidemia. The underlying mechanism may be attributed to a reduction in adipose and hepatic local proinflammatory cytokine production, e.g. TNFα. In vitro studies of co-cultured murine RAW264.7 macrophage and 3T3-L1 adipocytes supported this proposed mechanism.
CONCLUSION:
AuNPs demonstrate a promising profile for potential management of obesity related glucose and lipid disorders and are useful as a research tool for the study of biological mechanisms.
AbstractThere is a need for pharmaceutical agents that can reduce neuronal loss and improve functional deficits following traumatic brain injury (TBI). Previous research suggests that oxidative stress and mitochondrial dysfunction play a major role in neuronal damage after TBI. Therefore, this study aimed to investigate two drugs known to have antioxidant effects, L-carnitine and exendin-4, in rats with moderate contusive TBI. L-carnitine (1.5 mM in drinking water) or exendin-4 (15 µg/kg/day, ip) were given immediately after the injury for 2 weeks. Neurological function and brain histology were examined (24 h and 6 weeks post injury). The rats with TBI showed slight sensory, motor and memory functional deficits at 24 h, but recovered by 6 weeks. Both treatments improved sensory and motor functions at 24 h, while only exendin-4 improved memory. Both treatments reduced cortical contusion at 24 h and 6 weeks, however neither affected gliosis and inflammatory cell activation. Oxidative stress was alleviated and mitochondrial reactive oxygen species was reduced by both treatments, however only mitochondrial functional marker protein transporter translocase of outer membrane 20 was increased at 24 h post injury. In conclusion, L-carnitine and exendin-4 treatments immediately after TBI can improve neurological functional outcome and tissue integrity by reducing oxidative stress.
Chen, H, Li, G, Chan, YL, Chapman, DG, Sukjamnong, S, Nguyen, T, Annissa, T, McGrath, KC, Sharma, P & Oliver, BG 2018, 'Maternal E-Cigarette Exposure in Mice Alters DNA Methylation and Lung Cytokine Expression in Offspring', American Journal of Respiratory Cell and Molecular Biology, vol. 58, no. 3, pp. 366-377. View/Download from: Publisher's site View description>>
E-cigarette usage is increasing, especially among the young, with both the general population and physicians perceiving them as a safe alternative to tobacco smoking. Worryingly, e-cigarettes are commonly used by pregnant women. As nicotine is known to adversely affect children in utero, we hypothesized that nicotine delivered via e-cigarettes would negatively affect lung development. To test this, we developed a mouse model of maternal e-vapor (nicotine and nicotine-free) exposure and investigated the impact on the growth and lung inflammation in both offspring and mothers. Female Balb/c mice were exposed to e-fluid vapor containing nicotine (18 mg/ml nicotine E-cigarette [E-cig18], equivalent to two cigarettes per treatment, twice daily,) or nicotine free (E-cig0 mg/ml) from 6 weeks before mating until pups weaned. Male offspring were studied at Postnatal Day (P) 1, P20, and at 13 weeks. The mothers were studied when the pups weaned. In the mothers' lungs, e-cigarette exposure with and without nicotine increased the proinflammatory cytokines IL-1β, IL-6, and TNF-α. In adult offspring, TNF-α protein levels were increased in both E-cig18 and E-cig0 groups, whereas IL-1β was suppressed. This was accompanied by global changes in DNA methylation. In this study, we found that e-cigarette exposure during pregnancy adversely affected maternal and offspring lung health. As this occurred with both nicotine-free and nicotine-containing e-vapor, the effects are likely due to by-products of vaporization rather than nicotine.
Chen, H, Li, G, Chan, YL, Nguyen, T, van Reyk, D, Saad, S & Oliver, BG 2018, 'Modulation of neural regulators of energy homeostasis, and of inflammation, in the pups of mice exposed to e-cigarettes', Neuroscience Letters, vol. 684, pp. 61-66. View/Download from: Publisher's site View description>>
BACKGROUND:Maternal smoking can lead to perturbations in central metabolic regulators such as neuropeptide Y (NPY) and pro-opiomelanocortin (POMC) signalling components in offspring. With the growing interest in e-cigarettes as a tobacco replacement, this short report assessed central metabolic regulation in offspring of mouse dams exposed to e-cigarettes. We examined the impact of continuous use of e-cigarettes, and e-cigarette replacement of tobacco cigarettes during pregnancy. Supplementation of an antioxidant l-carnitine was also co-used with tobacco cigarette in the mother to determine whether the impact of maternal tobacco smoking was oxidative stress driven. METHODS:Balb/c mice were exposed to either nicotine-containing (E-cig18) or nicotine-free (E-cig0) e-cigarette aerosols or tobacco smoke (SE) prior to mating and until their pups were weaned. After mating, two SE sub-groups were changed to E-cig18 exposure (Replacement), or supplementation l-carnitine while SE was continued. Male offspring were studied at weaning age. RESULTS:The offspring of E-cig0 dams were the heaviest with the most body fat. Replacing SE with E-cig18 during pregnancy resulted in offspring with significantly less body fat. E-cig0 offspring had significantly increased mRNA expression of brain NPY and iNOS. Maternal SE upregulated mRNA expression of NPY, NPY Y1 receptor, POMC downstream components, and iNOS expression, which were normalised in Replacement offspring, but only partially normalised with maternal L-carnitine supplementation during gestation and lactation. CONCLUSIONS:Maternal exposure to either tobacco and nicotine-free e-cigarettes lead to disturbances in the level of central homeostatic control markers in offspring, suggesting that maternal exposure to e-cigarettes is not without risks.
Chen, H, McGowan, EM, Ren, N, Lal, S, Nassif, N, Shad-Kaneez, F, Qu, X & Lin, Y 2018, 'Nattokinase: A Promising Alternative in Prevention and Treatment of Cardiovascular Diseases', Biomarker Insights, vol. 13, pp. 117727191878513-117727191878513. View/Download from: Publisher's site View description>>
Cardiovascular disease (CVD) is the leading cause of death in the world and our approach to the control and management of CVD mortality is limited. Nattokinase (NK), the most active ingredient of natto, possesses a variety of favourable cardiovascular effects and the consumption of Natto has been linked to a reduction in CVD mortality. Recent research has demonstrated that NK has potent fibrinolytic activity, antihypertensive, anti-atherosclerotic, and lipid-lowering, antiplatelet, and neuroprotective effects. This review covers the major pharmacologic effects of NK with a focus on its clinical relevance to CVD. It outlines the advantages of NK and the outstanding issues pertaining to NK pharmacokinetics. Available evidence suggests that NK is a unique natural compound that possesses several key cardiovascular beneficial effects for patients with CVD and is therefore an ideal drug candidate for the prevention and treatment of CVD. Nattokinase is a promising alternative in the management of CVD.
Chen, H, Ng, JPM, Bishop, DP, Milthorpe, BK & Valenzuela, SM 2018, 'Gold nanoparticles as cell regulators: beneficial effects of gold nanoparticles on the metabolic profile of mice with pre-existing obesity', Journal of Nanobiotechnology, vol. 16, no. 1. View/Download from: Publisher's site
Chen, S, Lin, Y, Zhong, S, An, H, Lu, Y, Yin, M, Liang, W & McGowan, EM 2018, 'Anti-MUC1 CAR-T cells combined with PD-1 knockout engineered T cells for patients with non-small cell lung cancer (NSCLC): A pilot study', Annals of Oncology, vol. 29, pp. x11-x11. View/Download from: Publisher's site
Chen, WY & Wand, MP 2018, 'Factor graph fragmentization of expectation propagation', Journal of the Korean Statistical Society, vol. 49, pp. 722-756. View/Download from: Publisher's site View description>>
Expectation propagation is a general approach to fast approximate inference
for graphical models. The existing literature treats models separately when it
comes to deriving and coding expectation propagation inference algorithms. This
comes at the cost of similar, long-winded algebraic steps being repeated and
slowing down algorithmic development. We demonstrate how factor graph
fragmentization can overcome this impediment. This involves adoption of the
message passing on a factor graph approach to expectation propagation and
identification of factor graph sub-graphs, which we call fragments, that are
common to wide classes of models. Key fragments and their corresponding
messages are catalogued which means that their algebra does not need to be
repeated. This allows compartmentalization of coding and efficient software
development.
Chen, Y, Choi, S, Su, D, Gao, X & Wang, G 2018, 'Self-standing sulfur cathodes enabled by 3D hierarchically porous titanium monoxide-graphene composite film for high-performance lithium-sulfur batteries', Nano Energy, vol. 47, pp. 331-339. View/Download from: Publisher's site View description>>
Chen, Y, Duong, HTT, Wen, S, Mi, C, Zhou, Y, Shimoni, O, Valenzuela, SM & Jin, D 2018, 'Exonuclease III-Assisted Upconversion Resonance Energy Transfer in a Wash-Free Suspension DNA Assay', Analytical Chemistry, vol. 90, no. 1, pp. 663-668. View/Download from: Publisher's site View description>>
Sensitivity is the key in optical detection of low-abundant analytes, such as circulating RNA or DNA. The enzyme Exonuclease III (Exo III) is a useful tool in this regard; its ability to recycle target DNA molecules results in markedly improved detection sensitivity. Lower limits of detection may be further achieved if the detection background of autofluorescence can be removed. Here we report an ultrasensitive and specific method to quantify trace amounts of DNA analytes in a wash-free suspension assay. In the presence of target DNA, the Exo III recycles the target DNA by selectively digesting the dye-tagged sequence-matched probe DNA strand only, so that the amount of free dye removed from the probe DNA is proportional to the number of target DNAs. Remaining intact probe DNAs are then bound onto upconversion nanoparticles (energy donor), which allows for upconversion luminescence resonance energy transfer (LRET) that can be used to quantify the difference between the free dye and tagged dye (energy acceptor). This scheme simply avoids both autofluorescence under infrared excitation and many tedious washing steps, as the free dye molecules are physically located away from the nanoparticle surface, and as such they remain "dark" in suspension. Compared to alternative approaches requiring enzyme-assisted amplification on the nanoparticle surface, introduction of probe DNAs onto nanoparticles only after DNA hybridization and signal amplification steps effectively avoids steric hindrance. Via this approach, we have achieved a detection limit of 15 pM in LRET assays of human immunodeficiency viral DNA.
Does modelling stochastic interest rates, beyond stochastic volatility, improve pricing performance on long-dated commodity derivatives? To answer this question, we consider futures price models for commodity derivatives that allow for stochastic volatility and stochastic interest rates and a correlation structure between the underlying variables. We examine the empirical pricing performance of these models on pricing long-dated crude oil derivatives. Estimating the model parameters from historical crude oil futures prices and option prices, we find that stochastic interest rate models improve pricing performance on long-dated crude oil derivatives, when the interest rate volatility is relatively high. Furthermore, increasing the model dimensionality does not tend to improve the pricing performance on long-dated crude oil option prices, but it matters for long-dated futures prices. We also find empirical evidence for a negative correlation between crude oil futures prices and interest rates that contributes to improving fit to long-dated crude oil option prices.
Cheung, EYY, Gahan, ME & McNevin, D 2018, 'Prediction of biogeographical ancestry in admixed individuals', Forensic Science International: Genetics, vol. 36, pp. 104-111. View/Download from: Publisher's site
Cheung, EYY, Gahan, ME & McNevin, D 2018, 'Predictive DNA analysis for biogeographical ancestry', Australian Journal of Forensic Sciences, vol. 50, no. 6, pp. 1-8. View/Download from: Publisher's site View description>>
Cheung, S, Wu, D, Daly, HC, Busschaert, N, Morgunova, M, Simpson, JC, Scholz, D, Gale, PA & O'Shea, DF 2018, 'Real-Time Recording of the Cellular Effects of the Anion Transporter Prodigiosin', Chem, vol. 4, no. 4, pp. 879-895. View/Download from: Publisher's site
Chew, SC, Yam, JKH, Matysik, A, Seng, ZJ, Klebensberger, J, Givskov, M, Doyle, P, Rice, SA, Yang, L & Kjelleberg, S 2018, 'Matrix Polysaccharides and SiaD Diguanylate Cyclase Alter Community Structure and Competitiveness of Pseudomonas aeruginosa during Dual-Species Biofilm Development with Staphylococcus aureus', mBio, vol. 9, no. 6. View/Download from: Publisher's site View description>>
Bacteria in natural and engineered environments form biofilms that include many different species. Microorganisms rely on a number of different strategies to manage social interactions with other species and to access resources, build biofilm consortia, and optimize growth. For example,
Pseudomonasaeruginosa
and
Staphylococcus aureus
are biofilm-forming bacteria that coinfect the lungs of cystic fibrosis patients and diabetic and chronic wounds.
P. aeruginosa
is known to antagonize
S. aureus
growth. However, many of the factors responsible for mixed-species interactions and outcomes such as infections are poorly understood. Biofilm bacteria are encased in a self-produced extracellular matrix that facilitates interspecies behavior and biofilm development. In this study, we examined the poorly understood roles of the major matrix biopolymers and their regulators in mixed-species biofilm interactions and development.
Chilambi, GS, Gao, IH, Yoon, BK, Park, S, Kawakami, LM, Ravikumar, V, Chan-Park, MB, Cho, N-J, Bazan, GC, Kline, KA, Rice, SA & Hinks, J 2018, 'Membrane adaptation limitations inEnterococcus faecalisunderlie sensitivity and the inability to develop significant resistance to conjugated oligoelectrolytes', RSC Advances, vol. 8, no. 19, pp. 10284-10293. View/Download from: Publisher's site View description>>
COEs are emerging antimicrobials to combat drug resistant infections and to which bacteria develop only limited resistance.
Choi, JP, Wang, R, Yang, X, Wang, X, Wang, L, Ting, KK, Foley, M, Cogger, V, Yang, Z, Liu, F, Han, Z, Liu, R, Baell, J & Zheng, X 2018, 'Ponatinib (AP24534) inhibits MEKK3-KLF signaling and prevents formation and progression of cerebral cavernous malformations', Science Advances, vol. 4, no. 11. View/Download from: Publisher's site View description>>
Ponatinib, a cancer drug, inhibits occurrence and growth of cerebral cavernous malformation in mouse models.
Choi, S, Su, D, Shin, M, Park, S & Wang, G 2018, 'Pomegranate‐Structured Silica/Sulfur Composite Cathodes for High‐Performance Lithium–Sulfur Batteries', Chemistry – An Asian Journal, vol. 13, no. 5, pp. 568-576. View/Download from: Publisher's site View description>>
AbstractPorous materials have many structural advantages for energy storage and conversion devices such as rechargeable batteries, supercapacitors, and fuel cells. When applied as a host material in lithium‐sulfur batteries, porous silica materials with a pomegranate‐like architecture can not only act as a buffer matrix for accommodating a large volume change of sulfur, but also suppress the polysulfide shuttle effect. The porous silica/sulfur composite cathodes exhibit excellent electrochemical performances including a high specific capacity of 1450 mA h g−1, a reversible capacity of 82.9 % after 100 cycles at a rate of C/2 (1 C=1672 mA g−1) and an extended cyclability over 300 cycles at 1 C‐rate. Furthermore, the high polysulfide adsorption property of porous silica has been proven by ex‐situ analyses, showing a relationship between the surface area of silica and polysulfide adsorption ability. In particular, the modified porous silica/sulfur composite cathode, which is treated by a deep‐lithiation process in the first discharge step, exhibits a highly reversible capacity of 94.5 % at 1C‐rate after 300 cycles owing to a formation of lithiated‐silica frames and stable solid‐electrolyte‐interphase layers.
Choi, V, Cobbin, D & Walsh, S 2018, 'Does Modern Research Concerning Chinese Medicine Acupoints Relate to Original Prescriptions? If Not, Why Not?', Medical Acupuncture, vol. 30, no. 6. View/Download from: Publisher's site
Christenson, SA, van den Berge, M, Faiz, A, Inkamp, K, Bhakta, N, Bonser, LR, Zlock, LT, Barjaktarevic, IZ, Barr, RG, Bleecker, ER, Boucher, RC, Bowler, RP, Comellas, AP, Curtis, JL, Han, MK, Hansel, NN, Hiemstra, PS, Kaner, RJ, Krishnanm, JA, Martinez, FJ, O’Neal, WK, Paine, R, Timens, W, Wells, JM, Spira, A, Erle, DJ & Woodruff, PG 2018, 'An airway epithelial IL-17A response signature identifies a steroid-unresponsive COPD patient subgroup', Journal of Clinical Investigation, vol. 129, no. 1, pp. 169-181. View/Download from: Publisher's site View description>>
BACKGROUND:Chronic obstructive pulmonary disease (COPD) is a heterogeneous smoking-related disease characterized by airway obstruction and inflammation. This inflammation may persist even after smoking cessation and responds variably to corticosteroids. Personalizing treatment to biologically similar "molecular phenotypes" may improve therapeutic efficacy in COPD. IL-17A is involved in neutrophilic inflammation and corticosteroid resistance, and thus may be particularly important in a COPD molecular phenotype. METHODS:We generated a gene expression signature of IL-17A response in bronchial airway epithelial brushings from smokers with and without COPD (n = 238), and validated it using data from 2 randomized trials of IL-17 blockade in psoriasis. This IL-17 signature was related to clinical and pathologic characteristics in 2 additional human studies of COPD: (a) SPIROMICS (n = 47), which included former and current smokers with COPD, and (b) GLUCOLD (n = 79), in which COPD participants were randomized to placebo or corticosteroids. RESULTS:The IL-17 signature was associated with an inflammatory profile characteristic of an IL-17 response, including increased airway neutrophils and macrophages. In SPIROMICS the signature was associated with increased airway obstruction and functional small airways disease on quantitative chest CT. In GLUCOLD the signature was associated with decreased response to corticosteroids, irrespective of airway eosinophilic or type 2 inflammation. CONCLUSION:These data suggest that a gene signature of IL-17 airway epithelial response distinguishes a biologically, radiographically, and clinically distinct COPD subgroup that may benefit from personalized therapy. TRIAL REGISTRATION:ClinicalTrials.gov NCT01969344. FUNDING:Primary support from the NIH, grants K23HL123778, K12HL11999, U19AI077439, DK072517, U01HL137880, K24HL137013 and R01HL121774 and contracts HHSN268200900013C, HHSN268200900014C, HHSN268200900015C, HHSN268200900016C, HHSN2682...
Cinner, JE, Maire, E, Huchery, C, MacNeil, MA, Graham, NAJ, Mora, C, McClanahan, TR, Barnes, ML, Kittinger, JN, Hicks, CC, D’Agata, S, Hoey, AS, Gurney, GG, Feary, DA, Williams, ID, Kulbicki, M, Vigliola, L, Wantiez, L, Edgar, GJ, Stuart-Smith, RD, Sandin, SA, Green, A, Hardt, MJ, Beger, M, Friedlander, AM, Wilson, SK, Brokovich, E, Brooks, AJ, Cruz-Motta, JJ, Booth, DJ, Chabanet, P, Gough, C, Tupper, M, Ferse, SCA, Sumaila, UR, Pardede, S & Mouillot, D 2018, 'Gravity of human impacts mediates coral reef conservation gains', Proceedings of the National Academy of Sciences, vol. 115, no. 27, pp. E6116-E6125. View/Download from: Publisher's site View description>>
SignificanceMarine reserves that prohibit fishing are a critical tool for sustaining coral reef ecosystems, yet it remains unclear how human impacts in surrounding areas affect the capacity of marine reserves to deliver key conservation benefits. Our global study found that only marine reserves in areas of low human impact consistently sustained top predators. Fish biomass inside marine reserves declined along a gradient of human impacts in surrounding areas; however, reserves located where human impacts are moderate had the greatest difference in fish biomass compared with openly fished areas. Reserves in low human-impact areas are required for sustaining ecological functions like high-order predation, but reserves in high-impact areas can provide substantial conservation gains in fish biomass.
Clark, JS, Poore, AGB & Doblin, MA 2018, 'Shaping up for stress: Physiological flexibility is key to survivorship in a habitat-forming macroalga', Journal of Plant Physiology, vol. 231, pp. 346-355. View/Download from: Publisher's site View description>>
Organisms from all domains of life can have highly variable morphologies, with this plasticity suggested to increase fitness and survivability under stressful conditions. Predicting how organisms will adapt to environmental change requires an understanding of how variable morphologies perform under environmental stress. Morphological plasticity has been documented within marine macroalgae inhabiting environmental gradients, however the functional consequences of this variation has been rarely tested. In this study, form-function was assessed in the habitat-forming, intertidal macroalga Hormosira banksii. Morphological variation was quantified on two spatial scales (tidal gradient versus latitudinal gradient) and the performance tested (relative water content and photosynthetic efficiency) of morphological variants during heat and desiccation stress. At regional scales, individuals at the warm distributional edge were overall smaller in size, and had smaller vesicles (higher surface area to volume ratio; SA:VOL) than those from central populations. At local scales, individuals high on the shore were generally shorter and had larger vesicles than those low on the shore. Vesicle morphology (SA:VOL) was found to predict relative water content and photosynthetic performance during desiccation and rehydration. Differences in SA:VOL of vesicles between heights on the shore may reflect water requirements needed to maintain tissue hydration for photosynthesis during low tide. Warm-edge populations showed increased thermal sensitivity as indicated by decreased photosynthetic yield of PSII and delays in recovery after desiccation. Sensitivities to higher temperatures amongst warm-edge populations are potentially due to smaller fluctuations in regional temperatures as well as their morphology. This study provides a mechanistic understanding of the morphological variation among H. banksii populations. It suggests that H. banksii has a high degree of morphological plasticity r...
Clarke, C, Liu, D, Wang, F, Liu, Y, Chen, C, Ton-That, C, Xu, X & Jin, D 2018, 'Large-scale dewetting assembly of gold nanoparticles for plasmonic enhanced upconversion nanoparticles', Nanoscale, vol. 10, no. 14, pp. 6270-6276. View/Download from: Publisher's site View description>>
The integrated methods of core shell upconversion nanoparticle synthesis, thermal annealing and gold dewetting produce gold-decorated upconversion nanoparticles with enhanced emission.
Claywell, BC, Dinh, V, Fourment, M, McCoy, CO & Matsen IV, FA 2018, 'A Surrogate Function for One-Dimensional Phylogenetic Likelihoods', Molecular Biology and Evolution, vol. 35, no. 1, pp. 242-246. View/Download from: Publisher's site View description>>
Cohen, A, Zinger, A, Tiberti, N, Grau, GER & Combes, V 2018, 'Differential plasma microvesicle and brain profiles of microRNA in experimental cerebral malaria', Malaria Journal, vol. 17, no. 1, pp. 192-192. View/Download from: Publisher's site View description>>
Cerebral malaria (CM) is a fatal complication of Plasmodium infection, mostly affecting children under the age of five in the sub-Saharan African region. CM pathogenesis remains incompletely understood, although sequestered infected red blood cells, inflammatory cells aggregating in the cerebral blood vessels, and the microvesicles (MV) that they release in the circulation, have been implicated. Plasma MV numbers increase in CM patients and in the murine model, where blocking their release, genetically or pharmacologically, protects against brain pathology, suggesting a role of MV in CM neuropathogenesis. In this work, the microRNA (miRNA) cargo of MV is defined for the first time during experimental CM with the overarching hypothesis that this characterization could help understand CM pathogenesis.The change in abundance of miRNA was studied following infection of CBA mice with Plasmodium berghei ANKA strain (causing experimental CM), and Plasmodium yoelii, which causes severe malaria without cerebral complications, termed non-CM (NCM). miRNA expression was analyzed using microarrays to compare MV from healthy (NI) and CM mice, yielding several miRNA of interest. The differential expression profiles of these selected miRNA (miR-146a, miR-150, miR-193b, miR-205, miR-215, miR-467a, and miR-486) were analyzed in mouse MV, MV-free plasma, and brain tissue by quantitative reverse transcription PCR (RT-qPCR). Two miRNA-miR-146a and miR-193b-were confirmed as differentially abundant in MV from CM mice, compared with NCM and NI mice. These miRNA have been shown to play various roles in inflammation, and their dysregulation during CM may be critical for triggering the neurological syndrome via regulation of their potential downstream targets.These data suggest that, in the mouse model at least, miRNA may have a regulatory role in the pathogenesis of severe malaria.
Cole, JM, Gong, Y, McCree-Grey, J, Evans, PJ & Holt, SA 2018, 'Modulation of N3 and N719 dye···TiO2 Interfacial Structures in Dye-Sensitized Solar Cells As Influenced by Dye Counter Ions, Dye Deprotonation Levels, and Sensitizing Solvent', ACS Applied Energy Materials, vol. 1, no. 6, pp. 2821-2831. View/Download from: Publisher's site
Collier, JD, Tingay, SJ, Callingham, JR, Norris, RP, Filipović, MD, Galvin, TJ, Huynh, MT, Intema, HT, Marvil, J, O’Brien, AN, Roper, Q, Sirothia, S, Tothill, NFH, Bell, ME, For, B-Q, Gaensler, BM, Hancock, PJ, Hindson, L, Hurley-Walker, N, Johnston-Hollitt, M, Kapińska, AD, Lenc, E, Morgan, J, Procopio, P, Staveley-Smith, L, Wayth, RB, Wu, C, Zheng, Q, Heywood, I & Popping, A 2018, 'High-resolution Observations of Low-luminosity Gigahertz-Peaked Spectrum and Compact Steep Spectrum Sources', Monthly Notices of the Royal Astronomical Society, vol. 477, no. 1, pp. 78-592. View/Download from: Publisher's site View description>>
Colusso, AV, McDonagh, AM, Gentle, A & Cortie, MB 2018, 'Photomechanical photochromism in a cetyltrimethylammonium isopolytungstate', RSC Advances, vol. 8, no. 34, pp. 18776-18783. View/Download from: Publisher's site View description>>
The photochromic properties of a hybrid compound comprised of the surfactant cation cetyltrimethylammonium [(C16H33)N(CH3)3]+ and the isopolytungstate anion [H2W12O40]6− is investigated.
Cooper, ER, McGrath, KCY, Li, X & Heather, AK 2018, 'Androgen Bioassay for the Detection of Nonlabeled Androgenic Compounds in Nutritional Supplements', International Journal of Sport Nutrition and Exercise Metabolism, vol. 28, no. 1, pp. 10-18. View/Download from: Publisher's site View description>>
Both athletes and the general population use nutritional supplements. Athletes often turn to supplements hoping that consuming the supplement will help them be more competitive and healthy, while the general population hopes to improve body image or vitality. While many supplements contain ingredients that may have useful properties, there are supplements that are contaminated with compounds that are banned for use in sport or have been deliberately adulterated to fortify a supplement with an ingredient that will produce the advertised effect. In the present study, we have used yeast cell and mammalian cell androgen bioassays to characterize the androgenic bioactivity of 112 sports supplements available from the Australian market, either over the counter or via the Internet. All 112 products did not declare an androgen on the label as an included ingredient. Our findings show that six out of 112 supplements had strong androgenic bioactivity in the yeast cell bioassay, indicating products spiked or contaminated with androgens. The mammalian cell bioassay confirmed the strong androgenic bioactivity of five out of six positive supplements. Supplement 6 was metabolized to weaker androgenic bioactivity in the mammalian cells. Further to this, Supplement 6 was positive in a yeast cell progestin bioassay. Together, these findings highlight that nutritional supplements, taken without medical supervision, could expose or predispose users to the adverse consequences of androgen abuse. The findings reinforce the need to increase awareness of the dangers of nutritional supplements and highlight the challenges that clinicians face in the fast-growing market of nutritional supplements.
Copeland, E, Leonard, K, Carney, R, Kong, J, Forer, M, Naidoo, Y, Oliver, BGG, Seymour, JR, Woodcock, S, Burke, CM & Stow, NW 2018, 'Chronic Rhinosinusitis: Potential Role of Microbial Dysbiosis and Recommendations for Sampling Sites', Frontiers in Cellular and Infection Microbiology, vol. 8, pp. 1-14. View/Download from: Publisher's site
Cortie, MB, Cortie, DL & Timchenko, V 2018, 'Heat transfer from nanoparticles for targeted destruction of infectious organisms', International Journal of Hyperthermia, vol. 34, no. 2, pp. 157-167. View/Download from: Publisher's site View description>>
Whereas the application of optically or magnetically heated nanoparticles to destroy tumours is now well established, the extension of this concept to target pathogens has barely begun. Here we examine the challenge of targeting pathogens by this means and, in particular, explore the issues of power density and heat transfer. Depending on the rate of heating, either hyperthermia or thermoablation may occur. This division of the field is fundamental and implies very different sources of excitation and heat transfer for the two modes, and different strategies for their clinical application. Heating by isolated nanoparticles and by agglomerates of nanoparticles is compared: hyperthermia is much more readily achieved with agglomerates and for large target volumes, a factor which favours magnetic excitation and moderate power densities. In contrast, destruction of planktonic pathogens is best achieved by localised thermoablation and very high power density, a scenario that is best delivered by pulsed optical excitation.
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 2018, 'DSYB catalyses the key step of dimethylsulfoniopropionate biosynthesis in many phytoplankton', Nature Microbiology, vol. 3, no. 4, pp. 430-439. View/Download from: Publisher's site View description>>
Dimethylsulfoniopropionate (DMSP) is a globally important organosulfur molecule and the major precursor for dimethyl sulfide. These compounds are important info-chemicals, key nutrients for marine microorganisms, and are involved in global sulfur cycling, atmospheric chemistry and cloud formation1-3. DMSP production was thought to be confined to eukaryotes, but heterotrophic bacteria can also produce DMSP through the pathway used by most phytoplankton 4 , and the DsyB enzyme catalysing the key step of this pathway in bacteria was recently identified 5 . However, eukaryotic phytoplankton probably produce most of Earth's DMSP, yet no DMSP biosynthesis genes have been identified in any such organisms. Here we identify functional dsyB homologues, termed DSYB, in many phytoplankton and corals. DSYB is a methylthiohydroxybutryate methyltransferase enzyme localized in the chloroplasts and mitochondria of the haptophyte Prymnesium parvum, and stable isotope tracking experiments support these organelles as sites of DMSP synthesis. DSYB transcription levels increased with DMSP concentrations in different phytoplankton and were indicative of intracellular DMSP. Identification of the eukaryotic DSYB sequences, along with bacterial dsyB, provides the first molecular tools to predict the relative contributions of eukaryotes and prokaryotes to global DMSP production. Furthermore, evolutionary analysis suggests that eukaryotic DSYB originated in bacteria and was passed to eukaryotes early in their evolution.
Cwiklinski, K, Jewhurst, H, McVeigh, P, Barbour, T, Maule, AG, Tort, J, O'Neill, SM, Robinson, MW, Donnelly, S & Dalton, JP 2018, 'Infection by the Helminth Parasite Fasciola hepatica Requires Rapid Regulation of Metabolic, Virulence, and Invasive Factors to Adjust to Its Mammalian Host', Molecular & Cellular Proteomics, vol. 17, no. 4, pp. 792-809. View/Download from: Publisher's site View description>>
The parasite Fasciola hepatica infects a broad range of mammals with impunity. Following ingestion of parasites (metacercariae) by the host, newly excysted juveniles (NEJ) emerge from their cysts, rapidly penetrate the duodenal wall and migrate to the liver. Successful infection takes just a few hours and involves negotiating hurdles presented by host macromolecules, tissues and micro-environments, as well as the immune system. Here, transcriptome and proteome analysis of ex vivo F. hepatica metacercariae and NEJ reveal the rapidity and multitude of metabolic and developmental alterations that take place in order for the parasite to establish infection. We found that metacercariae despite being encased in a cyst are metabolically active, and primed for infection. Following excystment, NEJ expend vital energy stores and rapidly adjust their metabolic pathways to cope with their new and increasingly anaerobic environment. Temperature increases induce neoblast proliferation and the remarkable up-regulation of genes associated with growth and development. Cysteine proteases synthesized by gastrodermal cells are secreted to facilitate invasion and tissue degradation, and tegumental transporters, such as aquaporins, are varied to deal with osmotic/salinity changes. Major proteins of the total NEJ secretome include proteases, protease inhibitors and anti-oxidants, and an array of immunomodulators that likely disarm host innate immune effector cells. Thus, the challenges of infection by F. hepatica parasites are met by rapid metabolic and physiological adjustments that expedite tissue invasion and immune evasion; these changes facilitate parasite growth, development and maturation. Our molecular analysis of the critical processes involved in host invasion has identified key targets for future drug and vaccine strategies directed at preventing parasite infection.
Da Costa, GS, Soria, R, Farrell, SA, Bayliss, D, Bessell, MS, Vogt, FPA, Zhou, G, Points, SD, Beers, TC, López-Sánchez, ÁR, Bannister, KW, Bell, M, Hancock, PJ, Burlon, D, Gaensler, BM, Sadler, EM, Tingay, S, Keller, SC, Schmidt, BP & Tisserand, P 2018, 'SMSS J130522.47−293113.0: a high-latitude stellar X-ray source with pc-scale outflow relics?', Monthly Notices of the Royal Astronomical Society, vol. 477, no. 1, pp. 766-779. View/Download from: Publisher's site View description>>
Dachian, S, Kordzakhia, N, Kutoyants, YA & Novikov, A 2018, 'Estimation of cusp location of stochastic processes: a survey', Statistical Inference for Stochastic Processes, vol. 21, no. 2, pp. 345-362. View/Download from: Publisher's site View description>>
Dai, S, Tymchenko, M, Xu, Z-Q, Tran, TT, Yang, Y, Ma, Q, Watanabe, K, Taniguchi, T, Jarillo-Herrero, P, Aharonovich, I, Basov, DN, Tao, TH & Alù, A 2018, 'Internal Nanostructure Diagnosis with Hyperbolic Phonon Polaritons in Hexagonal Boron Nitride', Nano Letters, vol. 18, no. 8, pp. 5205-5210. View/Download from: Publisher's site View description>>
Imaging materials and inner structures with resolution below the diffraction limit has become of fundamental importance in recent years for a wide variety of applications. We report subdiffractive internal structure diagnosis of hexagonal boron nitride by exciting and imaging hyperbolic phonon polaritons. On the basis of their unique propagation properties, we are able to accurately locate defects in the crystal interior with nanometer resolution. The precise location, size, and geometry of the concealed defects are reconstructed by analyzing the polariton wavelength, reflection coefficient, and their dispersion. We have also studied the evolution of polariton reflection, transmission, and scattering as a function of defect size and photon frequency. The nondestructive high-precision polaritonic structure diagnosis technique introduced here can be also applied to other hyperbolic or waveguide systems and may be deployed in the next-generation biomedical imaging, sensing, and fine structure analysis.
Daines, AM, Robinson, H, Glenny, M, Williams, DBG & Hinkley, SFR 2018, 'Linear and macrocyclic water soluble polyacylhydrazones and their utilisation in coatings', Progress in Organic Coatings, vol. 121, pp. 38-44. View/Download from: Publisher's site View description>>
The spatial distributions of organism abundance and diversity are often heterogeneous. This includes the sub-centimetre distributions of microbes, which have 'hotspots' of high abundance, and 'coldspots' of low abundance. Previously we showed that 300 μl abundance hotspots, coldspots and background regions were distinct at all taxonomic levels. Here we build on these results by showing taxonomic micropatches within these 300 μl microscale hotspots, coldspots and background regions at the 1 μl scale. This heterogeneity among 1 μl subsamples was driven by heightened abundance of specific genera. The micropatches were most pronounced within hotspots. Micropatches were dominated by Pseudomonas, Bacteroides, Parasporobacterium and Lachnospiraceae incertae sedis, with Pseudomonas and Bacteroides being responsible for a shift in the most dominant genera in individual hotspot subsamples, representing up to 80.6% and 47.3% average abundance, respectively. The presence of these micropatches implies the ability these groups have to create, establish themselves in, or exploit heterogeneous microenvironments. These genera are often particle-associated, from which we infer that these micropatches are evidence for sub-millimetre aggregates and the aquatic polymer matrix. These findings support the emerging paradigm that the microscale distributions of planktonic microbes are numerically and taxonomically heterogeneous at scales of millimetres and less. We show that microscale microbial hotspots have internal structure within which specific local nutrient exchanges and cellular interactions might occur.
In this study we investigated the effect of light-limitation (∼20 μmol photons m-2 s-1) on the southern hemisphere seagrass, Zostera muelleri. RNA sequencing, chlorophyll fluorometry and HPLC techniques were used to investigate how the leaf-specific transcriptome drives changes in photosynthesis and photo-pigments in Z. muelleri over 6 days. 1593 (7.51%) genes were differentially expressed on day 2 and 1481 (6.98%) genes were differentially expressed on day 6 of the experiment. Differential gene expression correlated with significant decreases in rETRMax, Ik, an increase in Yi (initial photosynthetic quantum yield of photosystem II), and significant changes in pigment composition. Regulation of carbohydrate metabolism was observed along with evidence that abscisic acid may serve a role in the low-light response of this seagrass. This study provides a novel understanding of how Z. muelleri responds to light-limitation in the marine water column and provides potential molecular markers for future conservation monitoring efforts.
Davies, CH, Ajani, P, Armbrecht, L, Atkins, N, Baird, ME, Beard, J, Bonham, P, Burford, M, Clementson, L, Coad, P, Crawford, C, Dela-Cruz, J, Doblin, MA, Edgar, S, Eriksen, R, Everett, JD, Furnas, M, Harrison, DP, Hassler, C, Henschke, N, Hoenner, X, Ingleton, T, Jameson, I, Keesing, J, Leterme, SC, James McLaughlin, M, Miller, M, Moffatt, D, Moss, A, Nayar, S, Patten, NL, Patten, R, Pausina, SA, Proctor, R, Raes, E, Robb, M, Rothlisberg, P, Saeck, EA, Scanes, P, Suthers, IM, Swadling, KM, Talbot, S, Thompson, P, Thomson, PG, Uribe-Palomino, J, van Ruth, P, Waite, AM, Wright, S & Richardson, AJ 2018, 'A database of chlorophyll a in Australian waters', Scientific Data, vol. 5, no. 1. View/Download from: Publisher's site View description>>
AbstractChlorophyll a is the most commonly used indicator of phytoplankton biomass in the marine environment. It is relatively simple and cost effective to measure when compared to phytoplankton abundance and is thus routinely included in many surveys. Here we collate 173, 333 records of chlorophyll a collected since 1965 from Australian waters gathered from researchers on regular coastal monitoring surveys and ocean voyages into a single repository. This dataset includes the chlorophyll a values as measured from samples analysed using spectrophotometry, fluorometry and high performance liquid chromatography (HPLC). The Australian Chlorophyll a database is freely available through the Australian Ocean Data Network portal (https://portal.aodn.org.au/). These data can be used in isolation as an index of phytoplankton biomass or in combination with other data to provide insight into water quality, ecosystem state, and relationships with other trophic levels such as zooplankton or fish.
Dawson, A, Huston, W, Kawaguchi, S, King, C, Cropp, R, Wild, S, Eisenmann, P, Townsend, K & Bengtson Nash, S 2018, 'Uptake and Depuration Kinetics Influence Microplastic Bioaccumulation and Toxicity in Antarctic Krill (Euphausia superba)', Environmental Science & Technology, vol. 52, no. 5, pp. 3195-3201. View/Download from: Publisher's site
Dawson, A, Poulsen, A, Huston, W & Bengtson Nash, S 2018, 'Expression of common biomarkers in Antarctic krill (Euphausia superba) exposed to an organochlorine contaminant', Polar Biology, vol. 41, no. 3, pp. 505-513. View/Download from: Publisher's site View description>>
Dawson, AL, Kawaguchi, S, King, CK, Townsend, KA, King, R, Huston, WM & Bengtson Nash, SM 2018, 'Turning microplastics into nanoplastics through digestive fragmentation by Antarctic krill', Nature Communications, vol. 9, no. 1. View/Download from: Publisher's site View description>>
AbstractMicroplastics (plastics <5 mm diameter) are at the forefront of current environmental pollution research, however, little is known about the degradation of microplastics through ingestion. Here, by exposing Antarctic krill (Euphausia superba) to microplastics under acute static renewal conditions, we present evidence of physical size alteration of microplastics ingested by a planktonic crustacean. Ingested microplastics (31.5 µm) are fragmented into pieces less than 1 µm in diameter. Previous feeding studies have shown spherical microplastics either; pass unaffected through an organism and are excreted, or are sufficiently small for translocation to occur. We identify a new pathway; microplastics are fragmented into sizes small enough to cross physical barriers, or are egested as a mixture of triturated particles. These findings suggest that current laboratory-based feeding studies may be oversimplifying interactions between zooplankton and microplastics but also introduces a new role of Antarctic krill, and potentially other species, in the biogeochemical cycling and fate of plastic.
De Puysseleyr, K, Kieckens, E, De Puysseleyr, L, Van den Wyngaert, H, Ahmed, B, Van Lent, S, Creasy, HH, Myers, GSA & Vanrompay, D 2018, 'Development of aChlamydia suis-specific antibody enzyme-linked immunosorbent assay based on the use of a B-cell epitope of the polymorphic membrane protein C', Transboundary and Emerging Diseases, vol. 65, no. 2, pp. e457-e469. View/Download from: Publisher's site View description>>
Chlamydia suis infections lead to economic loss in the pork industry. Chlamydia suis infections could be successfully treated with tetracyclines until the appearance of a tetracycline resistant phenotype, which was acquired via horizontal gene transfer of the tet(C) gene. Given the importance of C. suis as a swine pathogen and as a recently emerged tetracycline resistant pathogen with zoonotic potential, our aim was to develop a sensitive C. suis-specific antibody ELISA based on the polymorphic membrane proteins (Pmps). Chlamydia Pmps are important virulence factors and candidate antigens for serodiagnosis. We identified nine Pmps (PmpA to I) in C. suis strain MD56 using a recently developed Hidden-Markov model. PmpC was the most promising candidate for the development of a C. suis-specific antibody ELISA as the protein was absent in C. abortus, C. pecorum and C. psittaci which also infect pigs and as the protein contained C. suis-specific amino acid regions, absent in C. trachomatis PmpC. We identified an immunodominant B-cell epitope in C. suis PmpC using experimental porcine sera. The sensitivity and specificity of the PmpC ELISA was compared to the complement fixation test (CFT) and to a recombinant MOMP ELISA using experimental sera. The PmpC ELISA detected all positive control sera and was in contrast to CFT and the rMOMP ELISA 100% C. suis specific as positive control sera against other Chlamydia species did not react in the PmpC ELISA. The test was successfully validated using slaughterhouse sera and sera from clinically affected pigs. The PmpC ELISA could assist in diminishing the spread of C. suis infections in the pork industry.
de Vries, M, Faiz, A, Woldhuis, RR, Postma, DS, de Jong, TV, Sin, DD, Bossé, Y, Nickle, DC, Guryev, V, Timens, W, van den Berge, M & Brandsma, C-A 2018, 'Lung tissue gene-expression signature for the ageing lung in COPD', Thorax, vol. 73, no. 7, pp. 609-617. View/Download from: Publisher's site View description>>
IntroductionCOPD is a chronic, progressive, inflammatory disease of the lungs and the third leading cause of death worldwide. The current knowledge of the pathophysiology of COPD is limited and novel insights in underlying disease mechanisms are urgently needed. Since there are clear parallels between ageing and COPD, we investigated genes underlying lung ageing in general and abnormal lung ageing in COPD.MethodsWhole genome mRNA profiling was performed on lung tissue samples (n=1197) and differential gene expression with increasing age was analysed using an adjusted linear regression model. Subsequent pathway analysis was performed using GeneNetwork and the gene-expression signature was compared with lung ageing in the Genotype-Tissue Expression (GTEx) project. In a subset of patients with COPD (n=311) and non-COPD controls (n=270), we performed an interaction analysis between age and COPD to identify genes differentially expressed with age in COPD compared with controls, followed by gene set enrichment pathway analysis.ResultsWe identified a strong gene-expression signature for lung ageing with 3509 differentially expressed genes, of which 33.5% were found nominal significant in the GTEx project. Interestingly, we foundEDA2Ras a strong candidate gene for lung ageing. The age*COPD interaction analysis revealed 69 genes significantly differentially expressed with age between COPD and controls.ConclusionsOur study indicates that processes related to lung development, cell-cell contacts, calcium signalling and immune responses are involved in lung ageing in general. Pathways related to extracellular matrix, mammalian target of rapamycin signalling, splicing of introns and exons and the ribosome complex are prop...
Dean, S, Walsh, S, Williams, C, Zaslawski, C, Morgan, A & Levett-Jones, T 2018, 'The mystery shopper student learning experience in undergraduate health education: A case study', Nurse Education Today, vol. 70, no. 2018, pp. 69-76. View/Download from: Publisher's site
Muon spin rotation/relaxation measurements show clear evidence for magnetism in 2.2 nm gold nanoparticles capped with butanethiol. At low temperatures (1.8 K), there is significant spin relaxation which decreases as a function of both the applied longitudinal magnetic field and increasing temperature. The results indicate that there are spatially inhomogeneous electronic moments that fluctuate with a wide distribution of correlation times. Possible explanations are discussed.
DeMaere, MZ & Darling, AE 2018, 'bin3C : Exploiting Hi-C sequencing data to accurately resolve metagenome-assembled genomes (MAGs)', Genome Biology, vol. 20. View/Download from: Publisher's site View description>>
AbstractMost microbes inhabiting the planet cannot be easily grown in the lab. Metagenomic techniques provide a means to study these organisms, and recent advances in the field have enabled the resolution of individual genomes from metagenomes, so-called Metagenome Assembled Genomes (MAGs). In addition to expanding the catalog of known microbial diversity, the systematic retrieval of MAGs stands as a tenable divide and conquer reduction of metagenome analysis to the simpler problem of single genome analysis. Many leading approaches to MAG retrieval depend upon time-series or transect data, whose effectiveness is a function of community complexity, target abundance and depth of sequencing. Without the need for time-series data, promising alternative methods are based upon the high-throughput sequencing technique called Hi-C.The Hi-C technique produces read-pairs which capture in-vivo DNA-DNA proximity interactions (contacts). The physical structure of the community modulates the signal derived from these interactions and a hierarchy of interaction rates exists (īntra-chromosomal > Inter-chromosomal > Inter-cellular).We describe an unsupervised method that exploits the hierarchical nature of Hi-C interaction rates to resolve MAGs from a single time-point. As a quantitative demonstration, next, we validate the method against the ground truth of a simulated human faecal microbiome. Lastly, we directly compare our method against a recently announced proprietary service ProxiMeta, which also performs MAG retrieval using Hi-C data.bin3C has been implemented as a simple open-source pipeline and makes use of the unsupervised community detection algorithm Infomap (https://github.com/cerebis/bin3C).
DeMaere, MZ & Darling, AE 2018, 'Sim3C: simulation of Hi-C and Meta3C proximity ligation sequencing technologies', GigaScience, vol. 7, no. 2, pp. 1-12. View/Download from: Publisher's site View description>>
Chromosome conformation capture (3C) and Hi-C DNA sequencing methods have rapidly advanced our understanding of the spatial organization of genomes and metagenomes. Many variants of these protocols have been developed, each with their own strengths. Currently there is no systematic means for simulating sequence data from this family of sequencing protocols, potentially hindering the advancement of algorithms to exploit this new datatype.We describe a computational simulator that, given simple parameters and reference genome sequences, will simulate Hi-C sequencing on those sequences. The simulator models the basic spatial structure in genomes that is commonly observed in Hi-C and 3C datasets, including the distance-decay relationship in proximity ligation, differences in the frequency of interaction within and across chromosomes, and the structure imposed by cells. A means to model the 3D structure of randomly generated topologically associating domains is provided. The simulator considers several sources of error common to 3C and Hi-C library preparation and sequencing methods, including spurious proximity ligation events and sequencing error.We have introduced the first comprehensive simulator for 3C and Hi-C sequencing protocols. We expect the simulator to have use in testing of Hi-C data analysis algorithms, as well as more general value for experimental design, where questions such as the required depth of sequencing, enzyme choice, and other decisions can be made in advance in order to ensure adequate statistical power with respect to experimental hypothesis testing.
Deplazes, E 2018, 'Molecular simulations of venom peptide‐membrane interactions: Progress and challenges', Peptide Science, vol. 110, no. 3, pp. e24060-e24060. View/Download from: Publisher's site View description>>
AbstractBecause of their wide range of biological activities venom peptides are a valuable source of lead molecules for the development of pharmaceuticals, pharmacological tools and insecticides. Many venom peptides work by modulating the activity of ion channels and receptors or by irreversibly damaging cell membranes. In many cases, the mechanism of action is intrinsically linked to the ability of the peptide to bind to or partition into membranes. Thus, understanding the biological activity of these venom peptides requires characterizing their membrane binding properties. This review presents an overview of the recent developments and challenges in using biomolecular simulations to study venom peptide‐membrane interactions. The review is focused on (i) gating modifier peptides that target voltage‐gated ion channels, (ii) venom peptides that inhibit mechanosensitive ion channels, and (iii) pore‐forming venom peptides. The methods and approaches used to study venom peptide‐membrane interactions are discussed with a particular focus on the challenges specific to these systems and the type of questions that can (and cannot) be addressed using state‐of‐the‐art simulation techniques. The review concludes with an outlook on future aims and directions in the field.
At the 2017 meeting of the Australian Society for Biophysics, we presented the combined results from two recent studies showing how hydronium ions (H3O+) modulate the structure and ion permeability of phospholipid bilayers. In the first study, the impact of H3O+ on lipid packing had been identified using tethered bilayer lipid membranes in conjunction with electrical impedance spectroscopy and neutron reflectometry. The increased presence of H3O+ (i.e. lower pH) led to a significant reduction in membrane conductivity and increased membrane thickness. A first-order explanation for the effect was assigned to alterations in the steric packing of the membrane lipids. Changes in packing were described by a critical packing parameter (CPP) related to the interfacial area and volume and shape of the membrane lipids. We proposed that increasing the concentraton of H3O+ resulted in stronger hydrogen bonding between the phosphate oxygens at the water–lipid interface leading to a reduced area per lipid and slightly increased membrane thickness. At the meeting, a molecular model for these pH effects based on the result of our second study was presented. Multiple μs-long, unrestrained molecular dynamic (MD) simulations of a phosphatidylcholine lipid bilayer were carried out and showed a concentration dependent reduction in the area per lipid and an increase in bilayer thickness, in agreement with experimental data. Further, H3O+ preferentially accumulated at the water–lipid interface, suggesting the localised pH at the membrane surface is much lower than the bulk bathing solution. Another significant finding was that the hydrogen bonds formed by H3O+ ions with lipid headgroup oxygens are, on average, shorter in length and longer-lived than the ones formed in bulk water. In addition, the H3O+ ions resided for longer periods in association with the carbonyl oxygens than with either phosphate oxygen in lipids. In summary, the MD simulations support a model where the hydrogen bon...
This work studies the mechanisms by which hydronium ions modulate the structure of phospholipid bilayers.
Deppeler, S, Petrou, K, Schulz, KG, Westwood, K, Pearce, I, McKinlay, J & Davidson, A 2018, 'Ocean acidification of a coastal Antarctic marine microbial community reveals a critical threshold for CO<sub>2</sub> tolerance in phytoplankton productivity', Biogeosciences, vol. 15, no. 1, pp. 209-231. View/Download from: Publisher's site View description>>
Abstract. High-latitude oceans are anticipated to be some of the first regions affected by ocean acidification. Despite this, the effect of ocean acidification on natural communities of Antarctic marine microbes is still not well understood. In this study we exposed an early spring, coastal marine microbial community in Prydz Bay to CO2 levels ranging from ambient (343 µatm) to 1641 µatm in six 650 L minicosms. Productivity assays were performed to identify whether a CO2 threshold existed that led to a change in primary productivity, bacterial productivity, and the accumulation of chlorophyll a (Chl a) and particulate organic matter (POM) in the minicosms. In addition, photophysiological measurements were performed to identify possible mechanisms driving changes in the phytoplankton community. A critical threshold for tolerance to ocean acidification was identified in the phytoplankton community between 953 and 1140 µatm. CO2 levels ≥ 1140 µatm negatively affected photosynthetic performance and Chl a-normalised primary productivity (csGPP14C), causing significant reductions in gross primary production (GPP14C), Chl a accumulation, nutrient uptake, and POM production. However, there was no effect of CO2 on C : N ratios. Over time, the phytoplankton community acclimated to high CO2 conditions, showing a down-regulation of carbon concentrating mechanisms (CCMs) and likely adjusting other intracellular processes. Bacterial abundance initially increased in CO2 treatments ≥ 953 µatm (days 3–5), yet gross bacterial production (GBP14C) remained unchanged and cell-specific bacterial productivity (csBP14C) was reduced. Towards the end of the experiment, GBP14C and csBP14C markedly increased across all treatments regardless of CO2 availability. This coincided with increased organic matter availability (POC and PON) combined with improved efficiency of carbon uptake. Changes in phytoplankton community production could have negative effects on the Antarctic food web...
Deutscher, AT, Burke, CM, Darling, AE, Riegler, M, Reynolds, OL & Chapman, TA 2018, 'Near full-length 16S rRNA gene next-generation sequencing revealed Asaia as a common midgut bacterium of wild and domesticated Queensland fruit fly larvae', Microbiome, vol. 6, no. 1. View/Download from: Publisher's site View description>>
BACKGROUND:Gut microbiota affects tephritid (Diptera: Tephritidae) fruit fly development, physiology, behavior, and thus the quality of flies mass-reared for the sterile insect technique (SIT), a target-specific, sustainable, environmentally benign form of pest management. The Queensland fruit fly, Bactrocera tryoni (Tephritidae), is a significant horticultural pest in Australia and can be managed with SIT. Little is known about the impacts that laboratory-adaptation (domestication) and mass-rearing have on the tephritid larval gut microbiome. Read lengths of previous fruit fly next-generation sequencing (NGS) studies have limited the resolution of microbiome studies, and the diversity within populations is often overlooked. In this study, we used a new near full-length (> 1300 nt) 16S rRNA gene amplicon NGS approach to characterize gut bacterial communities of individual B. tryoni larvae from two field populations (developing in peaches) and three domesticated populations (mass- or laboratory-reared on artificial diets). RESULTS:Near full-length 16S rRNA gene sequences were obtained for 56 B. tryoni larvae. OTU clustering at 99% similarity revealed that gut bacterial diversity was low and significantly lower in domesticated larvae. Bacteria commonly associated with fruit (Acetobacteraceae, Enterobacteriaceae, and Leuconostocaceae) were detected in wild larvae, but were largely absent from domesticated larvae. However, Asaia, an acetic acid bacterium not frequently detected within adult tephritid species, was detected in larvae of both wild and domesticated populations (55 out of 56 larval gut samples). Larvae from the same single peach shared a similar gut bacterial profile, whereas larvae from different peaches collected from the same tree had different gut bacterial profiles. Clustering of the Asaia near full-length sequences at 100% similarity showed that the wild flies from different locations had different Asaia strains. CONCLUSIONS:Variation in the gut bac...
Devadas, R, Huete, AR, Vicendese, D, Erbas, B, Beggs, PJ, Medek, D, Haberle, SG, Newnham, RM, Johnston, FH, Jaggard, AK, Campbell, B, Burton, PK, Katelaris, CH, Newbigin, E, Thibaudon, M & Davies, JM 2018, 'Dynamic ecological observations from satellites inform aerobiology of allergenic grass pollen', Science of The Total Environment, vol. 633, pp. 441-451. View/Download from: Publisher's site View description>>
Allergic diseases, including respiratory conditions of allergic rhinitis (hay fever) and asthma, affect up to 500 million people worldwide. Grass pollen are one major source of aeroallergens globally. Pollen forecast methods are generally site-based and rely on empirical meteorological relationships and/or the use of labour-intensive pollen collection traps that are restricted to sparse sampling locations. The spatial and temporal dynamics of the grass pollen sources themselves, however, have received less attention. Here we utilised a consistent set of MODIS satellite measures of grass cover and seasonal greenness (EVI) over five contrasting urban environments, located in Northern (France) and Southern Hemispheres (Australia), to evaluate their utility for predicting airborne grass pollen concentrations. Strongly seasonal and pronounced pollinating periods, synchronous with satellite measures of grass cover greenness, were found at the higher latitude temperate sites in France (46-50° N. Lat.), with peak pollen activity lagging peak greenness, on average by 2-3weeks. In contrast, the Australian sites (34-38° S. Lat.) displayed pollinating periods that were less synchronous with satellite greenness measures as peak pollen concentrations lagged peak greenness by as much as 4 to 7weeks. The Australian sites exhibited much higher spatial and inter-annual variations compared to the French sites and at the Sydney site, broader and multiple peaks in both pollen concentrations and greenness data coincided with flowering of more diverse grasses including subtropical species. Utilising generalised additive models (GAMs) we found the satellite greenness data of grass cover areas explained 80-90% of airborne grass pollen concentrations across the three French sites (p<0.001) and accounted for 34 to 76% of grass pollen variations over the two sites in Australia (p<0.05). Our results demonstrate the potential of satellite sensing to augment forecast models of grass pollen aer...
Diaz, D, Care, A & Sunna, A 2018, 'Bioengineering Strategies for Protein-Based Nanoparticles', Genes, vol. 9, no. 7, pp. 370-370. View/Download from: Publisher's site View description>>
In recent years, the practical application of protein-based nanoparticles (PNPs) has expanded rapidly into areas like drug delivery, vaccine development, and biocatalysis. PNPs possess unique features that make them attractive as potential platforms for a variety of nanobiotechnological applications. They self-assemble from multiple protein subunits into hollow monodisperse structures; they are highly stable, biocompatible, and biodegradable; and their external components and encapsulation properties can be readily manipulated by chemical or genetic strategies. Moreover, their complex and perfect symmetry have motivated researchers to mimic their properties in order to create de novo protein assemblies. This review focuses on recent advances in the bioengineering and bioconjugation of PNPs and the implementation of synthetic biology concepts to exploit and enhance PNP’s intrinsic properties and to impart them with novel functionalities.
Dickel, C, Wesdorp, JJ, Langford, NK, Peiter, S, Sagastizabal, R, Bruno, A, Criger, B, Motzoi, F & DiCarlo, L 2018, 'Chip-to-chip entanglement of transmon qubits using engineered measurement fields', Physical Review B, vol. 97, no. 6. View/Download from: Publisher's site View description>>
Dietrich, A, Bürk, M, Steiger, ES, Antoniuk, L, Tran, TT, Nguyen, M, Aharonovich, I, Jelezko, F & Kubanek, A 2018, 'Observation of Fourier transform limited lines in hexagonal boron nitride', Physical Review B, vol. 98, no. 8. View/Download from: Publisher's site View description>>
Dinh, V, Darling, AE & Matsen IV, FA 2018, 'Online Bayesian Phylogenetic Inference: Theoretical Foundations via Sequential Monte Carlo', Systematic Biology, vol. 67, no. 3, pp. 503-517. View/Download from: Publisher's site
Doble, PA & Miklos, GLG 2018, 'Distributions of manganese in diverse human cancers provide insights into tumour radioresistance', Metallomics, vol. 10, no. 9, pp. 1191-1210. View/Download from: Publisher's site View description>>
We show that measuring manganese levels in tumours of cancer patients is predictive for their radiation treatment.
Donovan, C, Starkey, MR, Kim, RY, Rana, BMJ, Barlow, JL, Jones, B, Haw, TJ, Mono Nair, P, Budden, K, Cameron, GJM, Horvat, JC, Wark, PA, Foster, PS, McKenzie, ANJ & Hansbro, PM 2018, 'Roles for T/B lymphocytes and ILC2s in experimental chronic obstructive pulmonary disease', Journal of Leukocyte Biology, vol. 105, no. 1, pp. 143-150. View/Download from: Publisher's site View description>>
AbstractPulmonary inflammation in chronic obstructive pulmonary disease (COPD) is characterized by both innate and adaptive immune responses; however, their specific roles in the pathogenesis of COPD are unclear. Therefore, we investigated the roles of T and B lymphocytes and group 2 innate lymphoid cells (ILC2s) in airway inflammation and remodelling, and lung function in an experimental model of COPD using mice that specifically lack these cells (Rag1−/− and Rorafl/flIl7rCre [ILC2-deficient] mice). Wild-type (WT) C57BL/6 mice, Rag1−/−, and Rorafl/flIl7rCre mice were exposed to cigarette smoke (CS; 12 cigarettes twice a day, 5 days a week) for up to 12 weeks, and airway inflammation, airway remodelling (collagen deposition and alveolar enlargement), and lung function were assessed. WT, Rag1−/−, and ILC2-deficient mice exposed to CS had similar levels of airway inflammation and impaired lung function. CS exposure increased small airway collagen deposition in WT mice. Rag1−/− normal air- and CS-exposed mice had significantly increased collagen deposition compared to similarly exposed WT mice, which was associated with increases in IL-33, IL-13, and ILC2 numbers. CS-exposed Rorafl/flIl7rCre mice were protected from emphysema, but had increased IL-33/IL-13 expression and collagen deposition compared to WT CS-exposed mice. T/B lymphocytes and ILC2s play roles in airway collagen deposition/fibrosis, but not inflammation, in experimental COPD.T/B lymphocytes and ILC2s play roles in airway fibrosis but not inflammation in a mouse model of experimental COPD.
Douglas, A, Torpy, F, Surawski, N & Irga, P 2018, 'Mapping Urban Aerosolized Fungi: Predicting Spatial and Temporal Indoor Concentrations', Human Ecology Review, vol. 24, no. 2, pp. 81-103. View/Download from: Publisher's site
Dowse, R, Melvold, J & McGrath, K 2018, 'Students guiding students: Integrating student peer review into a large first year science subject. A Practice Report', Student Success, vol. 9, no. 3, pp. 79-86. View/Download from: Publisher's site View description>>
Learning how to give and receive peer review is a skill that science students need support in developing. We included student peer review in an assessment for a large first year science subject. Class time was dedicated to introducing and developing peer review skills and increasing engagement among students and between students and teachers. Students worked in pairs, small groups, and facilitated group discussions and were encouraged to learn from each other. The student peer review exercise provided students with the opportunity to reflect on and improve their work prior to submission. Survey results showed 78% of students agreed that peer review developed their ability to give constructive feedback. Training and resources provision for the teaching staff was crucial to the integration of peer review activities. Supported teaching staff were able to engage with and support the students, and the students valued this engagement and guidance.
Doyle, LE, Williams, RBH, Rice, SA, Marsili, E & Lauro, FM 2018, 'Draft Genome Sequence of Enterobacter sp. Strain EA-1, an Electrochemically Active Microorganism Isolated from Tropical Sediment', Genome Announcements, vol. 6, no. 9. View/Download from: Publisher's site View description>>
ABSTRACTEnterobacter
sp. strain EA-1 is an electrochemically active bacterium isolated from tropical sediment in Singapore. Here, the annotated draft genome assembly of the bacterium is reported. Whole-genome comparison indicates that
Enterobacter
sp. EA-1, along with a previously sequenced
Enterobacter
isolate from East Asia, forms a distinct clade within the
Enterobacter
genus.
Drake, JE, Tjoelker, MG, Vårhammar, A, Medlyn, BE, Reich, PB, Leigh, A, Pfautsch, S, Blackman, CJ, López, R, Aspinwall, MJ, Crous, KY, Duursma, RA, Kumarathunge, D, De Kauwe, MG, Jiang, M, Nicotra, AB, Tissue, DT, Choat, B, Atkin, OK & Barton, CVM 2018, 'Trees tolerate an extreme heatwave via sustained transpirational cooling and increased leaf thermal tolerance', Global Change Biology, vol. 24, no. 6, pp. 2390-2402. View/Download from: Publisher's site
Dua, K, Awasthi, R, Madan, JR, Chellappan, DK, Nalluri, BN, Gupta, G, Bebawy, M & Hansbro, PM 2018, 'Novel drug delivery approaches in treating pulmonary fibrosis', Panminerva Medica, vol. 60, no. 4, pp. 238-240. View/Download from: Publisher's site
Dua, K, Awasthi, R, Madan, JR, Chellappan, DK, Nalluri, BN, Gupta, G, Bebawy, M & Hansbro, PM 2018, 'Novel drug delivery approaches in treating pulmonary fibrosis', PANMINERVA MEDICA, vol. 60, no. 4, pp. 238-240. View/Download from: Publisher's site
Dua, K, Bebawy, M, Awasthi, R, Tekade, RK, Tekade, M, Gupta, G, De Jesus Andreoli Pinto, T & Hansbro, PM 2018, 'Application of Chitosan and its Derivatives in Nanocarrier Based Pulmonary Drug Delivery Systems', Pharmaceutical Nanotechnology, vol. 5, no. 4, pp. 243-249. View/Download from: Publisher's site View description>>
The respiratory tract as a non-invasive route of drug administration is gaining increasing attention in the present time on achieving both local and the systemic therapeutic effects. Success in achieving pulmonary delivery, requires overcoming barriers including mucociliary clearance and uptake by macrophages. An effective drug delivery system delivers the therapeutically active moieties at the right time and rate to target sites. A major limitation associated with most of the currently available conventional and controlled release drug delivery devices is that not all the drug candidates are well absorbed uniformly locally or systemically.We searched and reviewed the literature focusing on chitosan and chitosan derivative based nanocarrier systems used in pulmonary drug delivery. We focused on the applications of chitosan in the development of nanoparticles for this purpose.Chitosan, a natural linear bio-polyaminosaccharide is central in the development of novel drug delivery systems (NDDS) including nanoparticles for use in the treatment of various respiratory diseases. It achieves this through its unique properties of biodegradability, biocompatibility, mucoadhesivity and its ability to enhance macromolecule permeation across membranes. It also achieves sustained and targeted effects, primary requirements for an effective pulmonary drug delivery system. This review highlights the applications and importance of chitosan with special emphasis on nanotechnology, employed in the management of respiratory diseases such as asthma, Chronic Obstructive Pulmonary Disease (COPD), lung cancer and pulmonary fibrosis.This review will be of interest to both the biological and formulation scientists as it provides a summary on the utility of chitosan in pulmonary drug delivery systems. At present, there are no patented chitosan based controlled release products available for pulmonary drug delivery and so this area has enormous potential in the field of respiratory science.
Dua, K, Chellappan, DK, Singhvi, G, de Jesus Andreoli Pinto, T, Gupta, G & Hansbro, PM 2018, 'Targeting microRNAs using nanotechnology in pulmonary diseases', Panminerva Medica, vol. 60, no. 4, pp. 230-232. View/Download from: Publisher's site
Dua, K, de Jesus Andreoli Pinto, T, Chellappan, DK, Gupta, G, Bebawy, M & Hansbro, PM 2018, 'Advancements in nano drug delivery systems: a challenge for biofilms in respiratory diseases', Panminerva Medica, vol. 60, no. 1, pp. 35-36. View/Download from: Publisher's site
Dua, K, Hansbro, NG, Foster, PS & Hansbro, PM 2018, 'Targeting MicroRNAs: Promising Future Therapeutics in the Treatment of Allergic Airway Disease', Critical Reviews in Eukaryotic Gene Expression, vol. 28, no. 2, pp. 125-127. View/Download from: Publisher's site
Dua, K, Rapalli, VK, Shukla, SD, Singhvi, G, Shastri, MD, Chellappan, DK, Satija, S, Mehta, M, Gulati, M, Pinto, TDJA, Gupta, G & Hansbro, PM 2018, 'Multi-drug resistant Mycobacterium tuberculosis & oxidative stress complexity: Emerging need for novel drug delivery approaches', Biomedicine & Pharmacotherapy, vol. 107, pp. 1218-1229. View/Download from: Publisher's site
Duan, J, Jiang, L, Guo, X, Chen, S, Wang, G & Zhao, C 2018, 'Mxene‐Directed Dual Amphiphilicity at Liquid, Solid, and Gas Interfaces', Chemistry – An Asian Journal, vol. 13, no. 24, pp. 3850-3854. View/Download from: Publisher's site View description>>
AbstractMXenes represent a category of two‐dimensional functional nanomaterials with remarkable structural and chemical properties, which have been manipulated into different architectures for versatile applications. These manipulation processes generally take place at the interfaces between liquid, solid, and gas; and therefore, the investigation of the interfacial property of MXenes is the key. Here we show that MXenes exhibit amphiphilic behaviours at interfaces. Different from common amphiphiles, MXenes have the dual function of both colloidal and molecular activities owing to their two abrupt structural length scales: their large lateral sheet size allows for behaving like colloidal amphiphiles for creating emulsions, while their small sheet thickness allows for serving as molecular amphiphiles for dispersing solid substances. Further, such dual colloidal‐molecular amphiphility has driven MXenes to accumulate at the interfaces of water and nitrogen gas, and the assembly into thin film electrodes for electrochemical energy storage. All these findings open up enormous opportunities for processing various MXenes‐related functional materials and devices.
Dubey, BN, Bashary, R, Mehta, M, Satija, S, Khurana, N, Sharma, N & Khatik, GL 2018, 'Identification of possible molecular targets of potential anti-Alzheimer drugs by predicting their binding affinities using molecular docking technique', International Journal of Green Pharmacy, vol. 12, no. 2, pp. 16-21. View description>>
Objective: The objective of this study was to study the newly selected drug molecule for Alzheimer’s disease (AD) which is under clinical trial. Methods: The structures were drawn using ChemBioDraw 2D software on the basis of the 1EVE receptor by changing the ligands. Afterward, they were converted to 3D structures using the same ChemBioDraw 3D software in which they were subjected to energy minimization using the MM2 menu and then saved as pdb extension files which can be accessed using the ADT interface. AutoDock Vina (ADT) 1.5.6 software version was used for molecular docking study. Results: The selected molecules which are under clinical trial for AD were analyzed by molecular modeling software for identification of activity on different targets. This revealed that three drugs Etozolate, PBT2, and scyllo-Inositol have shown interactions with the 1EVE receptors (acetylcholine esterase) among studied proteins. Conclusion: The study has been done by docking, each drug with its original and by cross docking them with different another receptor to determine on what receptor each drug has the greatest affinity. Among these ligands, Etozolate, PTB2, and scyllo-Inositol showed the maximum activity against the 1EVE protein (acetylcholine esterase) with the binding affinities of −8.2, −8.0, and −5.9 Kcal\ mol, respectively. This helps in identifying the best possible molecular target for the AD.
Duong, HNM, Nguyen, MAP, Kianinia, M, Abe, H, Ohshima, T, Watanabe, K, Taniguchi, T, Edgar, JH, Aharonovich, I & Toth, M 2018, 'Effects of high energy electron irradiation on quantum emitters in hexagonal boron nitride', ACS Applied Materials and Interfaces, vol. 10, no. 29, pp. 24886-24891. View/Download from: Publisher's site View description>>
Hexagonal Boron Nitride (hBN) mono and multilayers are promising hosts for
room temperature single photon emitters (SPEs). In this work we explore high
energy (~ MeV) electron irradiation as a means to generate stable SPEs in hBN.
We investigate four types of exfoliated hBN flakes - namely, high purity
multilayers, isotopically pure hBN, carbon rich hBN multilayers and monolayered
material - and find that electron irradiation increases emitter concentrations
dramatically in all samples. Furthermore, the engineered emitters are located
throughout hBN flakes (not only at flake edges or grain boundaries), and do not
require activation by high temperature annealing of the host material after
electron exposure. Our results provide important insights into controlled
formation of hBN SPEs and may aid in identification of their crystallographic
origin.
Duong, HTT, Chen, Y, Tawfik, SA, Wen, S, Parviz, M, Shimoni, O & Jin, D 2018, 'Systematic investigation of functional ligands for colloidal stable upconversion nanoparticles', RSC Advances, vol. 8, no. 9, pp. 4842-4849. View/Download from: Publisher's site View description>>
Here we quantitatively investigate the competitive adsorption of polymers bearing phosphate, carboxylic acid and sulphonic acid anchoring groups onto the surface of UCNPs and study their binding strength to identify the best conjugation strategy.
Duong, NMH, Xu, Z-Q, Kianinia, M, Su, R, Liu, Z, Kim, S, Bradac, C, Li, L-J, Solntsev, A, Liu, J & Aharonovich, I 2018, 'Enhanced Emission from WSe2 Monolayers Coupled to Circular Bragg Gratings', ACS Photonics, vol. 5, pp. 3950-3955. View/Download from: Publisher's site View description>>
Two-dimensional transition-metal dichalcogenides (TMDC) are of great interest
for on-chip nanophotonics due to their unique optoelectronic properties. Here,
we propose and realize coupling of tungsten diselenide (WSe2) monolayers to
circular Bragg grating structures to achieve enhanced emission. The interaction
between WSe2 and the resonant mode of the structure results in Purcell-enhanced
emission, while the symmetric geometrical structure improves the directionality
of the out-coupling stream of emitted photons. Furthermore, this hybrid
structure produces a record high contrast of the spin valley readout (> 40%)
revealed by the polarization resolved photoluminescence (PL) measurements. Our
results are promising for on-chip integration of TMDC monolayers with optical
resonators for nanophotonic circuits.
Dyda, A, Stelzer-Braid, S, Adam, D, Chughtai, AA & MacIntyre, CR 2018, 'The association between acute flaccid myelitis (AFM) and Enterovirus D68 (EV-D68) – what is the evidence for causation?', Eurosurveillance, vol. 23, no. 3. View/Download from: Publisher's site View description>>
BackgroundEnterovirus D68 (EV-D68) has historically been a sporadic disease, causing occasional small outbreaks of generally mild infection. In recent years, there has been evidence of an increase in EV-D68 infections globally. Large outbreaks of EV-D68, with thousands of cases, occurred in the United States, Canada and Europe in 2014. The outbreaks were associated temporally and geographically with an increase in clusters of acute flaccid myelitis (AFM). Aims: We aimed to evaluate a causal association between EV-D68 and AFM. Methods: Using data from the published and grey literature, we applied the Bradford Hill criteria, a set of nine principles applied to examine causality, to evaluate the relationship between EV-D68 and AFM. Based on available evidence, we defined the Bradford Hill Criteria as being not met, or met minimally, partially or fully. Results: Available evidence applied to EV-D68 and AFM showed that six of the Bradford Hill criteria were fully met and two were partially met. The criterion of biological gradient was minimally met. The incidence of EV-D68 infections is increasing world-wide. Phylogenetic epidemiology showed diversification from the original Fermon and Rhyne strains since the year 2000, with evolution of a genetically distinct outbreak strain, clade B1. Clade B1, but not older strains, is associated with AFM and is neuropathic in animal models. Conclusion: While more research is needed on dose–response relationship, application of the Bradford Hill criteria supported a causal relationship between EV-D68 and AFM.
Eapen, MS, Hansbro, PM, Larsson‑Callerfelt, A-K, Jolly, MK, Myers, S, Sharma, P, Jones, B, Rahman, MA, Markos, J, Chia, C, Larby, J, Haug, G, Hardikar, A, Weber, HC, Mabeza, G, Cavalheri, V, Khor, YH, McDonald, CF & Sohal, SS 2018, 'Chronic Obstructive Pulmonary Disease and Lung Cancer: Underlying Pathophysiology and New Therapeutic Modalities', Drugs, vol. 78, no. 16, pp. 1717-1740. View/Download from: Publisher's site View description>>
Chronic obstructive pulmonary disease (COPD) and lung cancer are major lung diseases affecting millions worldwide. Both diseases have links to cigarette smoking and exert a considerable societal burden. People suffering from COPD are at higher risk of developing lung cancer than those without, and are more susceptible to poor outcomes after diagnosis and treatment. Lung cancer and COPD are closely associated, possibly sharing common traits such as an underlying genetic predisposition, epithelial and endothelial cell plasticity, dysfunctional inflammatory mechanisms including the deposition of excessive extracellular matrix, angiogenesis, susceptibility to DNA damage and cellular mutagenesis. In fact, COPD could be the driving factor for lung cancer, providing a conducive environment that propagates its evolution. In the early stages of smoking, body defences provide a combative immune/oxidative response and DNA repair mechanisms are likely to subdue these changes to a certain extent; however, in patients with COPD with lung cancer the consequences could be devastating, potentially contributing to slower postoperative recovery after lung resection and increased resistance to radiotherapy and chemotherapy. Vital to the development of new-targeted therapies is an in-depth understanding of various molecular mechanisms that are associated with both pathologies. In this comprehensive review, we provide a detailed overview of possible underlying factors that link COPD and lung cancer, and current therapeutic advances from both human and preclinical animal models that can effectively mitigate this unholy relationship.
Eapen, MS, Kota, A, Vindin, H, McAlinden, KD, Xenaki, D, Oliver, BG, Deshpande, DA, Sohal, SS & Sharma, P 2018, 'Apoptosis signal-regulating kinase 1 inhibition attenuates human airway smooth muscle growth and migration in chronic obstructive pulmonary disease', Clinical Science, vol. 132, no. 14, pp. 1615-1627. View/Download from: Publisher's site View description>>
Increased airway smooth muscle (ASM) mass is observed in chronic obstructive pulmonary disease (COPD), which is correlated with disease severity and negatively affects lung function in these patients. Thus, there is clear unmet clinical need for finding new therapies which can target airway remodeling and disease progression in COPD. Apoptosis signal-regulating kinase 1 (ASK1) is a ubiquitously expressed mitogen-activated protein kinase (MAPK) kinase kinase (MAP3K) activated by various stress stimuli, including reactive oxygen species (ROS), tumor necrosis factor (TNF)-α, and lipopolysaccharide (LPS) and is known to regulate cell proliferation. ASM cells from COPD patients are hyperproliferative to mitogens in vitro. However, the role of ASK1 in ASM growth is not established. Here, we aim to determine the effects of ASK1 inhibition on ASM growth and pro-mitogenic signaling using ASM cells from COPD patients. We found greater expression of ASK1 in ASM bundles of COPD lung when compared with non-COPD. Pre-treatment of ASM cells with highly selective ASK1 inhibitor, TC ASK 10 resulted in a dose-dependent reduction in mitogen (FBS, PDGF, and EGF; 72 h)-induced ASM growth as measured by CyQUANT assay. Further, molecular targetting of ASK1 using siRNA in ASM cells prevented mitogen-induced cell growth. In addition, to anti-mitogenic potential, ASK1 inhibitor also prevented TGFβ1-induced migration of ASM cells in vitro. Immunoblotting revealed that anti-mitogenic effects are mediated by C-Jun N-terminal kinase (JNK) and p38MAP kinase-signaling pathways as evident by reduced phosphorylation of downstream effectors JNK1/2 and p38MAP kinases, respectively, with no effect on extracellular signal-regulated kinase (ERK) 1/2 (ERK1/2). Collectively, these findings establish the anti-mitogenic effect of ASK1 inhibition and identify a novel pathway that can be targetted to reduce or prevent excessive ASM mass in COPD.
Egilmezer, E, Walker, GJ, Bakthavathsalam, P, Peterson, JR, Gooding, JJ, Rawlinson, W & Stelzer-Braid, S 2018, 'Systematic review of the impact of point-of-care testing for influenza on the outcomes of patients with acute respiratory tract infection', Reviews in Medical Virology, vol. 28, no. 5, pp. e1995-e1995. View/Download from: Publisher's site View description>>
Acute respiratory tract infections are a major cause of morbidity and mortality and represent a significant burden on the health care system. Laboratory testing is required to definitively distinguish infecting influenza virus from other pathogens, resulting in prolonged emergency department (ED) visits and unnecessary antibiotic use. Recently available rapid point-of-care tests (POCT) may allow for appropriate use of antiviral and antibiotic treatments and decrease patient lengths of stay. We undertook a systematic review to assess the effect of POCT for influenza on three outcomes: (1) antiviral prescription, (2) antibiotic prescription, and (3) patient length of stay in the ED. The databases Medline and Embase were searched using MeSH terms and keywords for influenza, POCT, antivirals, antibiotics, and length of stay. Amongst 245 studies screened, 30 were included. The majority of papers reporting on antiviral prescription found that a positive POCT result significantly increased use of antivirals for influenza compared with negative POCT results and standard supportive care. A positive POCT result also led to decreased antibiotic use. The results of studies assessing the effect of POCT on ED length of stay were not definitive. The studies assessed in this systematic review support the use of POCT for diagnosis of influenza in patients suffering an acute respiratory infection. Diagnosis using POCT may lead to more appropriate prescription of treatments for infectious agents. Further studies are needed to assess the effect of POCT on the length of stay in ED.
Elbadawi, C, Queralt, RT, Xu, Z-Q, Bishop, J, Ahmed, T, Kuriakose, S, Walia, S, Toth, M, Aharonovich, I & Lobo, CJ 2018, 'Encapsulation-Free Stabilization of Few-Layer Black Phosphorus', ACS Applied Materials & Interfaces, vol. 10, no. 29, pp. 24327-24331. View/Download from: Publisher's site View description>>
Under ambient conditions and in H2O and O2 environments, reactive oxygen species (ROS) cause immediate degradation of the mobility of few-layer black phosphorus (FLBP). Here, we show that FLBP degradation can be prevented by maintaining the temperature in the range ∼125-300 °C during ROS exposure. FLBP devices maintained at elevated temperature show no deterioration of electrical conductance, in contrast to the immediate degradation of pristine FLBP held at room temperature. Our results constitute the first demonstration of stable FLBP in the presence of ROS without requiring encapsulation or a protective coating. The stabilization method will enable applications based on the surface properties of intrinsic FLBP.
El-Sayed, H, Sankar, S, Daraghmi, Y-A, Tiwari, P, Rattagan, E, Mohanty, M, Puthal, D & Prasad, M 2018, 'Accurate Traffic Flow Prediction in Heterogeneous Vehicular Networks in an Intelligent Transport System Using a Supervised Non-Parametric Classifier', Sensors, vol. 18, no. 6, pp. 1696-1696. View/Download from: Publisher's site View description>>
Heterogeneous vehicular networks (HETVNETs) evolve from vehicular ad hoc networks (VANETs), which allow vehicles to always be connected so as to obtain safety services within intelligent transportation systems (ITSs). The services and data provided by HETVNETs should be neither interrupted nor delayed. Therefore, Quality of Service (QoS) improvement of HETVNETs is one of the topics attracting the attention of researchers and the manufacturing community. Several methodologies and frameworks have been devised by researchers to address QoS-prediction service issues. In this paper, to improve QoS, we evaluate various traffic characteristics of HETVNETs and propose a new supervised learning model to capture knowledge on all possible traffic patterns. This model is a refinement of support vector machine (SVM) kernels with a radial basis function (RBF). The proposed model produces better results than SVMs, and outperforms other prediction methods used in a traffic context, as it has lower computational complexity and higher prediction accuracy.
El-Sayed, H, Sankar, S, Prasad, M, Puthal, D, Gupta, A, Mohanty, M & Lin, C-T 2018, 'Edge of Things: The Big Picture on the Integration of Edge, IoT and the Cloud in a Distributed Computing Environment', IEEE Access, vol. 6, pp. 1706-1717. View/Download from: Publisher's site View description>>
Ewans, LJ, Schofield, D, Shrestha, R, Zhu, Y, Gayevskiy, V, Ying, K, Walsh, C, Lee, E, Kirk, EP, Colley, A, Ellaway, C, Turner, A, Mowat, D, Worgan, L, Freckmann, M-L, Lipke, M, Sachdev, R, Miller, D, Field, M, Dinger, ME, Buckley, MF, Cowley, MJ & Roscioli, T 2018, 'Whole-exome sequencing reanalysis at 12 months boosts diagnosis and is cost-effective when applied early in Mendelian disorders', Genetics in Medicine, vol. 20, no. 12, pp. 1564-1574. View/Download from: Publisher's site View description>>
PURPOSE:Whole-exome sequencing (WES) has revolutionized Mendelian diagnostics, however, there is no consensus on the timing of data review in undiagnosed individuals and only preliminary data on the cost-effectiveness of this technology. We aimed to assess the utility of WES data reanalysis for diagnosis in Mendelian disorders and to analyze the cost-effectiveness of this technology compared with a traditional diagnostic pathway. METHODS:WES was applied to a cohort of 54 patients from 37 families with a variety of Mendelian disorders to identify the genetic etiology. Reanalysis was performed after 12 months with an improved WES diagnostic pipeline. A comparison was made between costs of a modeled WES pathway and a traditional diagnostic pathway in a cohort with intellectual disability (ID). RESULTS:Reanalysis of WES data at 12 months improved diagnostic success from 30 to 41% due to interim publication of disease genes, expanded phenotype data from referrer, and an improved bioinformatics pipeline. Cost analysis on the ID cohort showed average cost savings of US$586 (AU$782) for each additional diagnosis. CONCLUSION:Early application of WES in Mendelian disorders is cost-effective and reanalysis of an undiagnosed individual at a 12-month time point increases total diagnoses by 11%.
Faiz, A, Heijink, IH, Vermeulen, CJ, Guryev, V, van den Berge, M, Nawijn, MC & Pouwels, SD 2018, 'Cigarette smoke exposure decreases CFLAR expression in the bronchial epithelium, augmenting susceptibility for lung epithelial cell death and DAMP release', Scientific Reports, vol. 8, no. 1, pp. 12426-12426. View/Download from: Publisher's site View description>>
AbstractCigarette smoking is a major risk factor for the inflammatory disease, chronic obstructive pulmonary disease (COPD). The mechanism by which cigarette smoke (CS) induces chronic lung inflammation is still largely unknown. We hypothesize that immunogenic airway epithelial cell death is involved in the initiation of the inflammatory response. We previously identified CFLAR, the gene encoding the cell death regulator protein c-FLIP, to be associated with CS-induced release of damage-associated molecular patterns (DAMPs). Here, we investigated the effect of CS on expression levels of CFLAR in bronchial biopsies from smokers and non-smokers and CFLAR transcript isoform-expression in a dataset of air-liquid interface-differentiated bronchial epithelial cells. Furthermore, CFLAR was down-regulated by siRNA in lung epithelial A549 cells, followed by investigation of the effects on apoptosis, necrosis and DAMP release. CS exposure significantly decreased CFLAR expression in bronchial epithelial cells. Moreover, we observed a shift in relative abundance of the isoforms c-FLIPS and c-FLIPL transcripts in bronchial biopsies of current smokers compared to non-smokers, consistent with a shift towards necroptosis. In vitro, down-regulation of CFLAR increased apoptosis at baseline as well as CS extract-induced necrosis and DAMP release. In conclusion, CS exposure decreases CFLAR expression, which might increase susceptibility to immunogenic cell death.
Faiz, A, Weckmann, M, Tasena, H, Vermeulen, CJ, Van den Berge, M, ten Hacken, NHT, Halayko, AJ, Ward, JPT, Lee, TH, Tjin, G, Black, JL, Haghi, M, Xu, C-J, King, GG, Farah, CS, Oliver, BG, Heijink, IH & Burgess, JK 2018, 'Profiling of healthy and asthmatic airway smooth muscle cells following interleukin-1β treatment: a novel role for CCL20 in chronic mucus hypersecretion', European Respiratory Journal, vol. 52, no. 2, pp. 1800310-1800310. View/Download from: Publisher's site View description>>
Chronic mucus hypersecretion (CMH) contributes to the morbidity and mortality of asthma, and remains uncontrolled by current therapies in the subset of patients with severe, steroid-resistant disease. Altered cross-talk between airway epithelium and airway smooth muscle cells (ASMCs), driven by pro-inflammatory cytokines such as interleukin (IL)-1β, provides a potential mechanism that influences CMH. This study investigated mechanisms underlying CMH by comparing IL-1β-induced gene expression profiles between asthma and control-derived ASMCs and the subsequent paracrine influence on airway epithelial mucus production in vitroIL-1β-treated ASMCs from asthmatic patients and healthy donors were profiled using microarray analysis and ELISA. Air-liquid interface (ALI)-cultured CALU-3 and primary airway epithelial cells were treated with identified candidates and mucus production assessed.The IL-1β-induced CCL20 expression and protein release was increased in ASMCs from moderate compared with mild asthmatic patients and healthy controls. IL-1β induced lower MIR146A expression in asthma-derived ASMCs compared with controls. Decreased MIR146A expression was validated in vivo in bronchial biopsies from 16 asthmatic patients versus 39 healthy donors. miR-146a-5p overexpression abrogated CCL20 release in ASMCs. CCL20 treatment of ALI-cultured CALU-3 and primary airway epithelial cells induced mucus production, while CCL20 levels in sputum were associated with increased levels of CMH in asthmatic patients.Elevated CCL20 production by ASMCs, possibly resulting from dysregulated expression of the anti-inflammatory miR-146a-5p, may contribute to enhanced mucus production in asthma.
Faiz, MB, Amal, R, Marquis, CP, Harry, EJ, Sotiriou, GA, Rice, SA & Gunawan, C 2018, 'Nanosilver and the microbiological activity of the particulate solids versus the leached soluble silver', Nanotoxicology, vol. 12, no. 3, pp. 263-273. View/Download from: Publisher's site View description>>
Nanosilver (Ag NPs) is currently one of the most commercialized antimicrobial nanoparticles with as yet, still unresolved cytotoxicity origins. To date, research efforts have mostly described the antimicrobial contribution from the leaching of soluble silver, while the undissolved solid Ag particulates are often considered as being microbiologically inert, serving only as source of the cytotoxic Ag ions. Here, we show the rapid stimulation of lethal cellular oxidative stress in bacteria by the presence of the undissolved Ag particulates. The cytotoxicity characteristics are distinct from those arising from the leached soluble Ag, the latter being locked in organic complexes. The work also highlights the unique oxidative stress-independent bacterial toxicity of silver salt. Taken together, the findings advocate that future enquiries on the antimicrobial potency and also importantly, the environmental and clinical impact of Ag NPs use, should pay attention to the potential bacterial toxicological responses to the undissolved Ag particulates, rather than just to the leaching of soluble silver. The findings also put into question the common use of silver salt as model material for evaluating bacterial toxicity of Ag NPs.
Faizi, M, Zavřel, T, Loureiro, C, Červený, J & Steuer, R 2018, 'A model of optimal protein allocation during phototrophic growth', Biosystems, vol. 166, pp. 26-36. View/Download from: Publisher's site
FALLETTA, J & WOODCOCK, S 2018, 'A SIMULATION STUDY OF TEXAS HOLD ’EM POKER: WHAT TAYLOR SWIFT UNDERSTANDS AND JAMES BOND DOESN’T', The ANZIAM Journal, vol. 60, no. 1, pp. 55-64. View/Download from: Publisher's site View description>>
Recent years have seen a large increase in the popularity of Texas hold ’em poker. It is now the most commonly played variant of the game, both in casinos and through online platforms. In this paper, we present a simulation study for games of Texas hold ’em with between two and 23 players. From these simulations, we estimate the probabilities of each player having been dealt the winning hand. These probabilities are calculated conditional on both partial information (that is, the player only having knowledge of his/her cards) and also on fuller information (that is, the true probabilities of each player winning given knowledge of the cards dealt to each player). Where possible, our estimates are compared to exact analytic results and are shown to have converged to three significant figures.With these results, we assess the poker strategies described in two recent pieces of popular culture. In comparing the ideas expressed in Taylor Swift’s song, New Romantics, and the betting patterns employed by James Bond in the 2006 film, Casino Royale, we conclude that Ms Swift demonstrates a greater understanding of the true probabilities of winning a game of Texas hold ’em poker.
Fan, X, McLaughlin, C, Ravasini, J, Robinson, C & George, AM 2018, 'Zeolite protects mice from iron‐induced damage in a mouse model trial', FEBS Open Bio, vol. 8, no. 11, pp. 1773-1781. View/Download from: Publisher's site View description>>
Farjana, SH, Huda, N & Mahmud, MAP 2018, 'Life-Cycle environmental impact assessment of mineral industries', IOP Conference Series: Materials Science and Engineering, vol. 351, pp. 012016-012016. View/Download from: Publisher's site
Farjana, SH, Huda, N & Parvez Mahmud, MA 2018, 'Environmental impact assessment of european non-ferro mining industries through life-cycle assessment', IOP Conference Series: Earth and Environmental Science, vol. 154, pp. 012019-012019. View/Download from: Publisher's site
Farjana, SH, Huda, N, Mahmud, MAP & Lang, C 2018, 'Comparative life-cycle assessment of uranium extraction processes', Journal of Cleaner Production, vol. 202, pp. 666-683. View/Download from: Publisher's site
Farjana, SH, Huda, N, Mahmud, MAP & Lang, C 2018, 'Towards sustainable TiO2 production: An investigation of environmental impacts of ilmenite and rutile processing routes in Australia', Journal of Cleaner Production, vol. 196, pp. 1016-1025. View/Download from: Publisher's site
Farjana, SH, Huda, N, Mahmud, MAP & Saidur, R 2018, 'Solar industrial process heating systems in operation – Current SHIP plants and future prospects in Australia', Renewable and Sustainable Energy Reviews, vol. 91, pp. 409-419. View/Download from: Publisher's site
Farjana, SH, Huda, N, Mahmud, MAP & Saidur, R 2018, 'Solar process heat in industrial systems – A global review', Renewable and Sustainable Energy Reviews, vol. 82, pp. 2270-2286. View/Download from: Publisher's site
Farooq, A, Ashraf, MA, Rasheed, A, Khan, JU & Irshad, F 2018, 'Development of a novel method for natural dyeing of cotton fabrics using ultrasonic radiations and acacia bark', Journal of Natural Fibers, vol. 15, no. 5, pp. 680-686. View/Download from: Publisher's site
Farooq, U, Ahmed, Z, Naeem, K, Bertram, M, Brito, B, Stenfeldt, C, Pauszek, SJ, LaRocco, M, Rodriguez, L & Arzt, J 2018, 'Characterization of naturally occurring, new and persistent subclinical foot‐and‐mouth disease virus infection in vaccinated Asian buffalo in Islamabad Capital Territory, Pakistan', Transboundary and Emerging Diseases, vol. 65, no. 6, pp. 1836-1850. View/Download from: Publisher's site
Farrell, H, Ajani, P, Murray, S, Baker, P, Webster, G, Brett, S & Zammit, A 2018, 'Diarrhetic Shellfish Toxin Monitoring in Commercial Wild Harvest Bivalve Shellfish in New South Wales, Australia', Toxins, vol. 10, no. 11, pp. 446-446. View/Download from: Publisher's site View description>>
An end-product market survey on biotoxins in commercial wild harvest shellfish (Plebidonax deltoides, Katelysia spp., Anadara granosa, Notocallista kingii) during three harvest seasons (2015–2017) from the coast of New South Wales, Australia found 99.38% of samples were within regulatory limits. Diarrhetic shellfish toxins (DSTs) were present in 34.27% of 321 samples but only in pipis (P. deltoides), with two samples above the regulatory limit. Comparison of these market survey data to samples (phytoplankton in water and biotoxins in shellfish tissue) collected during the same period at wild harvest beaches demonstrated that, while elevated concentrations of Dinophysis were detected, a lag in detecting bloom events on two occasions meant that wild harvest shellfish with DSTs above the regulatory limit entered the marketplace. Concurrently, data (phytoplankton and biotoxin) from Sydney rock oyster (Saccostrea glomerata) harvest areas in estuaries adjacent to wild harvest beaches impacted by DSTs frequently showed elevated Dinophysis concentrations, but DSTs were not detected in oyster samples. These results highlighted a need for distinct management strategies for different shellfish species, particularly during Dinophysis bloom events. DSTs above the regulatory limit in pipis sampled from the marketplace suggested there is merit in looking at options to strengthen the current wild harvest biotoxin management strategies.
Farrell, H, Baker, P, Webster, G, Jansson, E, Szabo, E & Zammit, A 2018, 'An assessment of potential heavy metal contaminants in bivalve shellfish from aquaculture zones along the coast of New South Wales, Australia', Food Protection Trends, vol. 38, no. 1, pp. 18-25. View description>>
Evaluation of shellfish aquaculture for potential contaminants is essential for consumer confidence and safety. Every three years, between 1999 and 2014, bivalve shellfish from aquaculture zones in up to 31 estuaries across 2,000 km of Australia's east coast were tested for cadmium, copper, lead, mercury, selenium and zinc. Inorganic arsenic was included in the analyses in 2002, and total arsenic was used as a screen for the inorganic form in subsequent years. Concentrations of inorganic arsenic, cadmium, lead and mercury were low and did not exceed maximum limits mandated in the Australia New Zealand Food Standards Code. As maximum limits have not been assigned to copper, selenium and zinc, accepted international dietary guidelines were used as a benchmark. Dietary exposure assessments for these elements demonstrated that shellfish from the aquaculture areas investigated do not present a food safety risk. Continued surveillance is essential, given increasing pressure on Australia's coastal resources.
Faunce, TA, Prest, J, Su, D, Hearne, SJ & Iacopi, F 2018, 'On-grid batteries for large-scale energy storage: Challenges and opportunities for policy and technology', MRS Energy & Sustainability, vol. 5, no. 1. View/Download from: Publisher's site View description>>
ABSTRACT
Feit, B, Gordon, CE, Webb, JK, Jessop, TS, Laffan, SW, Dempster, T & Letnic, M 2018, 'Invasive cane toads might initiate cascades of direct and indirect effects in a terrestrial ecosystem', Biological Invasions, vol. 20, no. 7, pp. 1833-1847. View/Download from: Publisher's site View description>>
Feng, Y, Rudd, R, Baker, C, Mashalaba, Q, Mavuso, M & Schlögl, E 2018, 'Quantifying the Model Risk Inherent in the Calibration and Recalibration of Option Pricing Models', Risks, vol. 9, no. 1, pp. 13-13. View/Download from: Publisher's site View description>>
We focus on two particular aspects of model risk: the inability of a chosen
model to fit observed market prices at a given point in time (calibration
error) and the model risk due to recalibration of model parameters (in
contradiction to the model assumptions). In this context, we follow the
approach of Glasserman and Xu (2014) and use relative entropy as a pre-metric
in order to quantify these two sources of model risk in a common framework, and
consider the trade-offs between them when choosing a model and the frequency
with which to recalibrate to the market. We illustrate this approach applied to
the models of Black and Scholes (1973) and Heston (1993), using option data for
Apple (AAPL) and Google (GOOG). We find that recalibrating a model more
frequently simply shifts model risk from one type to another, without any
substantial reduction of aggregate model risk. Furthermore, moving to a more
complicated stochastic model is seen to be counterproductive if one requires a
high degree of robustness, for example as quantified by a 99 percent quantile
of aggregate model risk.
Fernandez-Rojo, MA, Deplazes, E, Pineda, SS, Brust, A, Marth, T, Wilhelm, P, Martel, N, Ramm, GA, Mancera, RL, Alewood, PF, Woods, GM, Belov, K, Miles, JJ, King, GF & Ikonomopoulou, MP 2018, 'Gomesin peptides prevent proliferation and lead to the cell death of devil facial tumour disease cells', Cell Death Discovery, vol. 4, no. 1. View/Download from: Publisher's site View description>>
AbstractThe Tasmanian devil faces extinction due to devil facial tumour disease (DFTD), a highly transmittable clonal form of cancer without available treatment. In this study, we report the cell-autonomous antiproliferative and cytotoxic activities exhibited by the spider peptide gomesin (AgGom) and gomesin-like homologue (HiGom) in DFTD cells. Mechanistically, both peptides caused a significant reduction at G0/G1 phase, in correlation with an augmented expression of the cell cycle inhibitory proteins p53, p27, p21, necrosis, exacerbated generation of reactive oxygen species and diminished mitochondrial membrane potential, all hallmarks of cellular stress. The screening of a novel panel of AgGom-analogues revealed that, unlike changes in the hydrophobicity and electrostatic surface, the cytotoxic potential of the gomesin analogues in DFTD cells lies on specific arginine substitutions in the eight and nine positions and alanine replacement in three, five and 12 positions. In conclusion, the evidence supports gomesin as a potential antiproliferative compound against DFTD disease.
Firasat, S, Kaul, H, Ashfaq, UA & Idrees, S 2018, 'In silico analysis of five missense mutations in CYP1B1 gene in Pakistani families affected with primary congenital glaucoma', International Ophthalmology, vol. 38, no. 2, pp. 807-814. View/Download from: Publisher's site
Fish, I, Stenfeldt, C, Pauszek, SJ, Brito, BP, Hartwig, EJ, Smoliga, G, Rodriguez, LL & Arzt, J 2018, 'A55 Foot-and-mouth disease virus undergoes abundant viral genomic changes at distinct stages of infection of cattle', Virus Evolution, vol. 4, no. suppl_1. View/Download from: Publisher's site
Flaherty, BR, Talundzic, E, Barratt, J, Kines, KJ, Olsen, C, Lane, M, Sheth, M & Bradbury, RS 2018, 'Restriction enzyme digestion of host DNA enhances universal detection of parasitic pathogens in blood via targeted amplicon deep sequencing', Microbiome, vol. 6, no. 1. View/Download from: Publisher's site
For, B-Q, Staveley-Smith, L, Hurley-Walker, N, Franzen, T, Kapińska, AD, Filipović, MD, Collier, JD, Wu, C, Grieve, K, Callingham, JR, Bell, ME, Bernardi, G, Bowman, JD, Briggs, F, Cappallo, RJ, Deshpande, AA, Dwarakanath, KS, Gaensler, BM, Greenhill, LJ, Hancock, P, Hazelton, BJ, Hindson, L, Johnston-Hollitt, M, Kaplan, DL, Lenc, E, Lonsdale, CJ, McKinley, B, McWhirter, SR, Mitchell, DA, Morales, MF, Morgan, E, Morgan, J, Oberoi, D, Offringa, A, Ord, SM, Prabu, T, Procopio, P, Shankar, NU, Srivani, KS, Subrahmanyan, R, Tingay, SJ, Wayth, RB, Webster, RL, Williams, A, Williams, CL & Zheng, Q 2018, 'A multifrequency radio continuum study of the Magellanic Clouds – I. Overall structure and star formation rates', Monthly Notices of the Royal Astronomical Society, vol. 480, no. 2, pp. 2743-2756. View/Download from: Publisher's site View description>>
Time-resolved phylogenetic methods use information about the time of sample collection to estimate the rate of evolution. Originally, the models used to estimate evolutionary rates were quite simple, assuming that all lineages evolve at the same rate, an assumption commonly known as the molecular clock. Richer and more complex models have since been introduced to capture the phenomenon of substitution rate variation among lineages. Two well known model extensions are the local clock, wherein all lineages in a clade share a common substitution rate, and the uncorrelated relaxed clock, wherein the substitution rate on each lineage is independent from other lineages while being constrained to fit some parametric distribution. We introduce a further model extension, called the flexible local clock (FLC), which provides a flexible framework to combine relaxed clock models with local clock models. We evaluate the flexible local clock on simulated and real datasets and show that it provides substantially improved fit to an influenza dataset. An implementation of the model is available for download from https://www.github.com/4ment/flc.
Fourment, M, Claywell, BC, Dinh, V, McCoy, C, Matsen IV, FA & Darling, AE 2018, 'Effective Online Bayesian Phylogenetics via Sequential Monte Carlo with Guided Proposals', Systematic Biology, vol. 67, no. 3, pp. 490-502. View/Download from: Publisher's site View description>>
Modern infectious disease outbreak surveillance produces continuous streams of sequence data which require phylogenetic analysis as data arrives. Current software packages for Bayesian phylogenetic inference are unable to quickly incorporate new sequences as they become available, making them less useful for dynamically unfolding evolutionary stories. This limitation can be addressed by applying a class of Bayesian statistical inference algorithms called sequential Monte Carlo (SMC) to conduct online inference, wherein new data can be continuously incorporated to update the estimate of the posterior probability distribution. In this article, we describe and evaluate several different online phylogenetic sequential Monte Carlo (OPSMC) algorithms. We show that proposing new phylogenies with a density similar to the Bayesian prior suffers from poor performance, and we develop "guided" proposals that better match the proposal density to the posterior. Furthermore, we show that the simplest guided proposals can exhibit pathological behavior in some situations, leading to poor results, and that the situation can be resolved by heating the proposal density. The results demonstrate that relative to the widely used MCMC-based algorithm implemented in MrBayes, the total time required to compute a series of phylogenetic posteriors as sequences arrive can be significantly reduced by the use of OPSMC, without incurring a significant loss in accuracy.
Fowler, AM, Chick, RC & Stewart, J 2018, 'Patterns and drivers of movement for a coastal benthopelagic fish, Pseudocaranx georgianus, on Australia’s southeast coast', Scientific Reports, vol. 8, no. 1. View/Download from: Publisher's site View description>>
AbstractKnowledge of connectivity and population structure is integral to the sustainable management of fished populations, yet such information is unavailable for many species over scales relevant to their exploitation. We examined broad-scale patterns and drivers of adult movement for a putatively mobile carangid (Pseudocaranx georgianus) on Australia’s southeast coast using an angler tag-recapture dataset. More than 6300 individuals were tagged and released across 1007 km of coastline, with anglers recapturing 157 (2.48%) individuals during a 14-year period. Median distance moved was 5 km and a substantial proportion of individuals (19%) were recaptured at their release location. Recapture latitude was also strongly predicted by release latitude (r2 = 0.87). However, a broad range of movements were observed (0–508 km), with 6% of individuals moving further than 100 km. Most individuals recaptured in areas now designated as Marine Protected Areas (MPAs) were originally released in the same area (79.2%). Larger body size, longer periods at liberty, and releases during Spring all positively influenced distance moved. Results support restricted movement over an intermediate scale, punctuated by occasional large movements. Our findings suggest adult movement of P. georgianus in southeastern Australia primarily occurs over smaller distances than the current spatial scale of management.
Fowler, AM, Jørgensen, A, Svendsen, JC, Macreadie, PI, Jones, DOB, Boon, AR, Booth, DJ, Brabant, R, Callahan, E, Claisse, JT, Dahlgren, TG, Degraer, S, Dokken, QR, Gill, AB, Johns, DG, Leewis, RJ, Lindeboom, HJ, Linden, O, May, R, Murk, AJ, Ottersen, G, Schroeder, DM, Shastri, SM, Teilmann, J, Todd, V, Van Hoey, G, Vanaverbeke, J & Coolen, JWP 2018, 'Environmental benefits of leaving offshore infrastructure in the ocean', Frontiers in Ecology and the Environment, vol. 16, no. 10, pp. 571-578. View/Download from: Publisher's site View description>>
The removal of thousands of structures associated with oil and gas development from the world's oceans is well underway, yet the environmental impacts of this decommissioning practice remain unknown. Similar impacts will be associated with the eventual removal of offshore wind turbines. We conducted a global survey of environmental experts to guide best decommissioning practices in the North Sea, a region with a substantial removal burden. In contrast to current regulations, 94.7% of experts (36 out of 38) agreed that a more flexible case‐by‐case approach to decommissioning could benefit the North Sea environment. Partial removal options were considered to deliver better environmental outcomes than complete removal for platforms, but both approaches were equally supported for wind turbines. Key considerations identified for decommissioning were biodiversity enhancement, provision of reef habitat, and protection from bottom trawling, all of which are negatively affected by complete removal. We provide recommendations to guide the revision of offshore decommissioning policy, including a temporary suspension of obligatory removal.
Fowler, AM, Parkinson, K & Booth, DJ 2018, 'New poleward observations of 30 tropical reef fishes in temperate southeastern Australia', Marine Biodiversity, vol. 48, no. 4, pp. 2249-2254. View/Download from: Publisher's site View description>>
Fransen, J, Baxter-Jones, A & Woodcock, S 2018, 'Responding to the Commentary on the Article: “Improving the Prediction of Maturity From Anthropometric Variables Using a Maturity Ratio”', Pediatric Exercise Science, vol. 30, no. 2, pp. 311-313. View/Download from: Publisher's site
Fransen, J, Bush, S, Woodcock, S, Novak, A, Deprez, D, Baxter-Jones, ADG, Vaeyens, R & Lenoir, M 2018, 'Improving the Prediction of Maturity From Anthropometric Variables Using a Maturity Ratio', Pediatric Exercise Science, vol. 30, no. 2, pp. 296-307. View/Download from: Publisher's site View description>>
Purpose:This study aimed to improve the prediction accuracy of age at peak height velocity (APHV) from anthropometric assessment using nonlinear models and a maturity ratio rather than a maturity offset.Methods:The dataset used to develop the original prediction equations was used to test a new prediction model, utilizing the maturity ratio and a polynomial prediction equation. This model was then applied to a sample of male youth academy soccer players (n = 1330) to validate the new model in youth athletes.Results:A new equation was developed to estimate APHV more accurately than the original model (new model: Akaike information criterion: −6062.1,R2 = 90.82%; original model: Akaike information criterion = 3048.7,R2 = 88.88%) within a general population of boys, particularly with relatively high/low APHVs. This study has also highlighted the successful application of the new model to estimate APHV using anthropometric variables in youth athletes, thereby supporting the use of this model in sports talent identification and development.Conclusion:This study argues that this newly developed equation should become standard practice for the estimation of maturity from anthropometric variables in boys from both a general and an athletic population.
French, J, Arscott, E, Morgan, R & Meakin, G 2018, 'Reply to letter to the editor: Response to “A study of the perception of verbal expressions of the strength of evidence”', Science & Justice, vol. 58, no. 4, pp. 299-299. View/Download from: Publisher's site
Fricker, M, Goggins, BJ, Mateer, S, Jones, B, Kim, RY, Gellatly, SL, Jarnicki, AG, Powell, N, Oliver, BG, Radford-Smith, G, Talley, NJ, Walker, MM, Keely, S & Hansbro, PM 2018, 'Chronic cigarette smoke exposure induces systemic hypoxia that drives intestinal dysfunction', JCI Insight, vol. 3, no. 3. View/Download from: Publisher's site View description>>
Crohn's disease (CD) is a chronic inflammatory disease of the gastrointestinal tract (GIT). Cigarette smoke (CS) exposure and chronic obstructive pulmonary disease (COPD) are risk factors for CD, although the mechanisms involved are poorly understood. We employed a mouse model of CS-induced experimental COPD and clinical studies to examine these mechanisms. Concurrent with the development of pulmonary pathology and impaired gas exchange, CS-exposed mice developed CD-associated pathology in the colon and ileum, including gut mucosal tissue hypoxia, HIF-2 stabilization, inflammation, increased microvasculature, epithelial cell turnover, and decreased intestinal barrier function. Subsequent smoking cessation reduced GIT pathology, particularly in the ileum. Dimethyloxaloylglycine, a pan-prolyl hydroxylase inhibitor, ameliorated CS-induced GIT pathology independently of pulmonary pathology. Prior smoke exposure exacerbated intestinal pathology in 2,4,6-trinitrobenzenesulfonic acid-induced (TNBS-induced) colitis. Circulating vascular endothelial growth factor, a marker of systemic hypoxia, correlated with CS exposure and CD in mice and humans. Increased mucosal vascularisation was evident in ileum biopsies from CD patients who smoke compared with nonsmokers, supporting our preclinical data. We provide strong evidence that chronic CS exposure and, for the first time to our knowledge, associated impaired gas exchange cause systemic and intestinal ischemia, driving angiogenesis and GIT epithelial barrier dysfunction, resulting in increased risk and severity of CD.
Fronzi, M, Assadi, MHN & Ford, MJ 2018, 'Ab Initio Investigation of Water Adsorption and Hydrogen Evolution on Co9S8 and Co3S4 Low-Index Surfaces', ACS Omega, vol. 3, no. 9, pp. 12215-12228. View/Download from: Publisher's site View description>>
Fronzi, M, Tawfik, SA, Stampfl, C & Ford, MJ 2018, 'Magnetic properties of stoichiometric and defective Co9S8', Physical Chemistry Chemical Physics, vol. 20, no. 4, pp. 2356-2362. View/Download from: Publisher's site View description>>
Our theoretical investigation confirms the antiferromagnetic nature of pentlandite Co9S8 and predicts a change in the local magnetic properties upon sulfur vacancy formation.
Fujimoto, R, Uezono, K, Ishikura, S, Osabe, K, Peacock, WJ & Dennis, ES 2018, 'Recent research on the mechanism of heterosis is important for crop and vegetable breeding systems', Breeding Science, vol. 68, no. 2, pp. 145-158. View/Download from: Publisher's site
Fujise, L, Nitschke, MR, Frommlet, JC, Serôdio, J, Woodcock, S, Ralph, PJ & Suggett, DJ 2018, 'Cell Cycle Dynamics of Cultured Coral Endosymbiotic Microalgae ( Symbiodinium ) Across Different Types (Species) Under Alternate Light and Temperature Conditions', Journal of Eukaryotic Microbiology, vol. 65, no. 4, pp. 505-517. View/Download from: Publisher's site
Funari, R, Bhalla, N, Chu, K-Y, Söderström, B & Shen, AQ 2018, 'Nanoplasmonics for Real-Time and Label-Free Monitoring of Microbial Biofilm Formation', ACS Sensors, vol. 3, no. 8, pp. 1499-1509. View/Download from: Publisher's site
Fung, E, Yang, X, Newton, PJ, Ferguson, C, Gastelurrutia, P, Lupón, J, Bayés-Genís, A, Jha, S & Macdonald, PS 2018, 'Letter by Fung et al Regarding Article, “Frailty and Clinical Outcomes in Heart Failure: A Systematic Review and Meta-analysis”', Journal of the American Medical Directors Association, vol. 19, no. 12, pp. 1143-1146. View/Download from: Publisher's site
Gai, S, Yang, G, Yang, P, He, F, Lin, J, Jin, D & Xing, B 2018, 'Recent advances in functional nanomaterials for light–triggered cancer therapy', Nano Today, vol. 19, pp. 146-187. View/Download from: Publisher's site View description>>
Gale, PA & Caltagirone, C 2018, 'Fluorescent and colorimetric sensors for anionic species', Coordination Chemistry Reviews, vol. 354, pp. 2-27. View/Download from: Publisher's site
Gale, PA, Howe, ENW, Wu, X & Spooner, MJ 2018, 'Anion receptor chemistry: Highlights from 2016', Coordination Chemistry Reviews, vol. 375, pp. 333-372. View/Download from: Publisher's site
Gali, M & Arnold, M 2018, 'Recurrent approach to effective material properties with application to anisotropic binarized random fields', Phys. Rev. B, vol. 99, no. 5, p. 054210. View/Download from: Publisher's site View description>>
Building on the foundation work of Brown, Milton and Torquato, we present a
tractable approach to analyse the effective permittivity of anisotropic
two-phase structures. This methodology accounts for successive dipolar
interactions, providing a recurrent series expansion of the effective
permittivity to arbitrary order. Within this framework, we also demonstrate a
progressive method to determine tight bounds that converge towards the exact
solution. We illustrate the utility of these methods by using ensemble
averaging to determine the micro-structural parameters of anisotropic level-cut
Gaussian fields. We find that the depolarization factor of these structures is
equivalent to that of an isolated ellipse with the same stretchingratio, and
discuss the contribution of the fourth order term to the exact anisotropy.
Galvin, TJ, Seymour, N, Marvil, J, Filipović, MD, Tothill, NFH, McDermid, RM, Hurley-Walker, N, Hancock, PJ, Callingham, JR, Cook, RH, Norris, RP, Bell, ME, Dwarakanath, KS, For, B, Gaensler, BM, Hindson, L, Johnston-Hollitt, M, Kapińska, AD, Lenc, E, McKinley, B, Morgan, J, Offringa, AR, Procopio, P, Staveley-Smith, L, Wayth, RB, Wu, C & Zheng, Q 2018, 'The spectral energy distribution of powerful starburst galaxies – I. Modelling the radio continuum', Monthly Notices of the Royal Astronomical Society, vol. 474, no. 1, pp. 779-799. View/Download from: Publisher's site View description>>
Gan, R, Zhang, Y, Shi, H, Yang, Y, Eamus, D, Cheng, L, Chiew, FHS & Yu, Q 2018, 'Use of satellite leaf area index estimating evapotranspiration and gross assimilation for Australian ecosystems', Ecohydrology, vol. 11, no. 5, pp. e1974-e1974. View/Download from: Publisher's site
Gao, J, Wu, S, Tan, F, Tian, H, Liu, J & Lu, GQM 2018, 'Nanoengineering of amino - functionalized mesoporous silica nanospheres as nanoreactors', Progress in Natural Science: Materials International, vol. 28, no. 2, pp. 242-245. View/Download from: Publisher's site
Garrastazu Pereira, G, Rawling, T, Pozzoli, M, Pazderka, C, Chen, Y, Dunstan, C, Murray, M & Sonvico, F 2018, 'Nanoemulsion-Enabled Oral Delivery of Novel Anticancer ω-3 Fatty Acid Derivatives', Nanomaterials, vol. 8, no. 10, pp. 825-825. View/Download from: Publisher's site View description>>
Lipid-based drugs are emerging as an interesting class of novel anticancer drugs with the potential to target specific cancer cell metabolic pathways linked to their proliferation and invasiveness. In particular, ω-3 polyunsaturated fatty acids (PUFA) derivatives such as epoxides and their bioisosteres have demonstrated the potential to suppress growth and promote apoptosis in triple-negative human breast cancer cells MDA-MB-231. In this study, 16-(4′-chloro-3′-trifluorophenyl)carbamoylamino]hexadecanoic acid (ClFPh-CHA), an anticancer lipid derived from ω-3,17,18-epoxyeicosanoic acid, was formulated as a stable nanoemulsion with size around 150 nm and narrow droplet size distribution (PDI < 0.200) through phase-inversion emulsification process followed by high pressure homogenization in view of an oral administration. The ClFPh-CHA-loaded nanoemulsions were able to significantly decrease the relative tumor volume in mice bearing an intramammary tumor xenograft at all doses tested (2.5, 10 and 40 mg/kg) after 32 days of daily oral administration. Furthermore, absolute tumor weight was decreased to 50% of untreated control at 10 and 40 mg/kg, while intraperitoneal administration could achieve a significant reduction only at the highest dose of 40 mg/kg. Results suggest that oral administration of ClFPh-CHA formulated as a nanoemulsion has a sufficient bioavailability to provide an anticancer effect in mice and that the activity is at least equal if not superior to that obtained by a conventional parenteral administration of equivalent doses of the same drug.
Gellert, K & Schlogl, E 2018, 'Parameter Learning and Change Detection Using a Particle Filter With Accelerated Adaptation', Risks, vol. 9, no. 12, pp. 228-228. View/Download from: Publisher's site View description>>
This paper presents the construction of a particle filter, which incorporates elements inspired by genetic algorithms, in order to achieve accelerated adaptation of the estimated posterior distribution to changes in model parameters. Specifically, the filter is designed for the situation where the subsequent data in online sequential filtering does not match the model posterior filtered based on data up to a current point in time. The examples considered encompass parameter regime shifts and stochastic volatility. The filter adapts to regime shifts extremely rapidly and delivers a clear heuristic for distinguishing between regime shifts and stochastic volatility, even though the model dynamics assumed by the filter exhibit neither of those features.
Gennarino, VA, Palmer, EE, McDonell, LM, Wang, L, Adamski, CJ, Koire, A, See, L, Chen, C-A, Schaaf, CP, Rosenfeld, JA, Panzer, JA, Moog, U, Hao, S, Bye, A, Kirk, EP, Stankiewicz, P, Breman, AM, McBride, A, Kandula, T, Dubbs, HA, Macintosh, R, Cardamone, M, Zhu, Y, Ying, K, Dias, K-R, Cho, MT, Henderson, LB, Baskin, B, Morris, P, Tao, J, Cowley, MJ, Dinger, ME, Roscioli, T, Caluseriu, O, Suchowersky, O, Sachdev, RK, Lichtarge, O, Tang, J, Boycott, KM, Holder, JL & Zoghbi, HY 2018, 'A Mild PUM1 Mutation Is Associated with Adult-Onset Ataxia, whereas Haploinsufficiency Causes Developmental Delay and Seizures', Cell, vol. 172, no. 5, pp. 924-936.e11. View/Download from: Publisher's site View description>>
Geoghegan, J, Pirotta, V, Harvey, E, Smith, A, Buchmann, J, Ostrowski, M, Eden, J-S, Harcourt, R & Holmes, E 2018, 'Virological Sampling of Inaccessible Wildlife with Drones', Viruses, vol. 10, no. 6, pp. 300-300. View/Download from: Publisher's site View description>>
There is growing interest in characterizing the viromes of diverse mammalian species, particularly in the context of disease emergence. However, little is known about virome diversity in aquatic mammals, in part due to difficulties in sampling. We characterized the virome of the exhaled breath (or blow) of the Eastern Australian humpback whale (Megaptera novaeangliae). To achieve an unbiased survey of virome diversity, a meta-transcriptomic analysis was performed on 19 pooled whale blow samples collected via a purpose-built Unmanned Aerial Vehicle (UAV, or drone) approximately 3 km off the coast of Sydney, Australia during the 2017 winter annual northward migration from Antarctica to northern Australia. To our knowledge, this is the first time that UAVs have been used to sample viruses. Despite the relatively small number of animals surveyed in this initial study, we identified six novel virus species from five viral families. This work demonstrates the potential of UAVs in studies of virus disease, diversity, and evolution.
Giardina, M, Cheong, S, Marjo, CE, Clode, PL, Guagliardo, P, Pickford, R, Pernice, M, Seymour, JR & Raina, J-B 2018, 'Quantifying Inorganic Nitrogen Assimilation by Synechococcus Using Bulk and Single-Cell Mass Spectrometry: A Comparative Study', Frontiers in Microbiology, vol. 9. View/Download from: Publisher's site View description>>
Microorganisms drive most of the major biogeochemical cycles in the ocean, but the rates at which individual species assimilate and transform key elements is generally poorly quantified. One of these important elements is nitrogen, with its availability limiting primary production across a large proportion of the ocean. Nitrogen uptake by marine microbes is typically quantified using bulk-scale approaches, such as Elemental Analyzer-Isotope Ratio Mass Spectrometry (EA-IRMS), which averages uptake over entire communities, masking microbial heterogeneity. However, more recent techniques, such as secondary ion mass spectrometry (SIMS), allow for elucidation of assimilation rates at the scale at which they occur: the single-cell level. Here, we combine and compare the application of bulk (EA-IRMS) and single-cell approaches (NanoSIMS and Time-of-Flight-SIMS) for quantifying the assimilation of inorganic nitrogen by the ubiquitous marine primary producer Synechococcus. We aimed to contrast the advantages and disadvantages of these techniques and showcase their complementarity. Our results show that the average assimilation of 15N by Synechococcus differed based on the technique used: values derived from EA-IRMS were consistently higher than those derived from SIMS, likely due to a combination of previously reported systematic depletion as well as differences in sample preparation. However, single-cell approaches offered additional layers of information, whereby NanoSIMS allowed for the quantification of the metabolic heterogeneity among individual cells and ToF-SIMS enabled identification of nitrogen assimilation into peptides. We suggest that this coupling of stable isotope-based approaches has great potential to elucidate the metabolic capacity and heterogeneity of microbial cells in natural environments.
Giffard, PM, Andersson, P, Wilson, J, Buckley, C, Lilliebridge, R, Harris, TM, Kleinecke, M, O’Grady, K-AF, Huston, WM, Lambert, SB, Whiley, DM & Holt, DC 2018, 'CtGEM typing: Discrimination of Chlamydia trachomatis ocular and urogenital strains and major evolutionary lineages by high resolution melting analysis of two amplified DNA fragments', PLOS ONE, vol. 13, no. 4, pp. e0195454-e0195454. View/Download from: Publisher's site View description>>
Gill, GK, Singh, A, Lal, UR, Kaur, H, Mehta, M, Satija, S & Mahajan, S 2018, 'Effect of fermentation on chemical changes in Vitis vinifera fruits used in alcoholic ayurvedic formulation', International Journal of Green Pharmacy, vol. 12, no. 2, pp. 29-34. View description>>
Background: Arishtas are weakly alcoholic Ayurvedic formulations prepared by fermenting the decoction of medicinal plants in an airtight sealed vessels. The presence of Vitis vinifera is considered essential to initiate the fermentation process. The fruits of V. vinifera were reported to have different polar components such as phenolics, phenolic acids, flavonoids, and flavonoid glycosides. Literature has mentioned the impact of fermentation in altering the chemical skeleton of molecules. Materials and Methods: Considering this fact, the present study was designed to understand the possible impact of fermentation on the chemical profile of V. vinifera by reversed-phase high-performance liquid chromatography (RP-HPLC) studies. Both fermented and non-fermented extract of V. vinifera was prepared by the traditional method and analyzed for chemical changes by RP-HPLC-ultraviolet method. Results and Conclusions: It was observed that the chromatogram of non-fermented extract of V. vinifera showed comparatively very few peaks as compared to the chromatogram of its fermented extract. This is probably due to the fact that the large molecular weight polyphenolics particularly flavonoid glycosides and tannins are hydrolyzed during ferat mention and degraded into small molecules of phenolics or phenolic acids. This change will modify significantly the biological activity of the fermented extracts and the final Ayurvedic formulation, particularly fermented biomedicine like Arishtas.
Gillis, CM & Reber, LL 2018, 'Un nouveau modèle de souris pour comprendre le rôle des neutrophiles', médecine/sciences, vol. 34, no. 4, pp. 339-343. View/Download from: Publisher's site View description>>
Les polynucléaires neutrophiles jouent un rôle important dans les défenses contre les pathogènes et la réponse inflammatoire. L’utilisation de souris déficientes en ces cellules a permis de démontrer que les neutrophiles peuvent également participer aux réponses immunitaires adaptatives et à la résolution de l’inflammation. Nous décrivons ici un nouveau modèle d’étude, les souris PMNDTR, qui permet une élimination sélective des neutrophiles par injection de toxine diphtérique, et qui a déjà conduit à la mise en évidence d’un rôle protecteur des neutrophiles dans le choc endotoxinique. Ses principaux avantages par rapport à d’autres modèles couramment utilisés sont décrits.
Gissibl, A, Care, A, Parker, LM, Iqbal, S, Hobba, G, Nevalainen, H & Sunna, A 2018, 'Microwave pretreatment of paramylon enhances the enzymatic production of soluble β-1,3-glucans with immunostimulatory activity', Carbohydrate Polymers, vol. 196, pp. 339-347. View/Download from: Publisher's site
Glastras, SJ, Chen, H, Pollock, CA & Saad, S 2018, 'Maternal obesity increases the risk of metabolic disease and impacts renal health in offspring', Bioscience Reports, vol. 38, no. 2. View/Download from: Publisher's site View description>>
Obesity, together with insulin resistance, promotes multiple metabolic abnormalities and is strongly associated with an increased risk of chronic disease including type 2 diabetes (T2D), hypertension, cardiovascular disease, non-alcoholic fatty liver disease (NAFLD) and chronic kidney disease (CKD). The incidence of obesity continues to rise in astronomical proportions throughout the world and affects all the different stages of the lifespan. Importantly, the proportion of women of reproductive age who are overweight or obese is increasing at an alarming rate and has potential ramifications for offspring health and disease risk. Evidence suggests a strong link between the intrauterine environment and disease programming. The current review will describe the importance of the intrauterine environment in the development of metabolic disease, including kidney disease. It will detail the known mechanisms of fetal programming, including the role of epigenetic modulation. The evidence for the role of maternal obesity in the developmental programming of CKD is derived mostly from our rodent models which will be described. The clinical implication of such findings will also be discussed.
Gleason, SM, Stephens, AEA, Tozer, WC, Blackman, CJ, Butler, DW, Chang, Y, Cook, AM, Cooke, J, Laws, CA, Rosell, JA, Stuart, SA & Westoby, M 2018, 'Shoot growth of woody trees and shrubs is predicted by maximum plant height and associated traits', Functional Ecology, vol. 32, no. 2, pp. 247-259. View/Download from: Publisher's site View description>>
AbstractThe rate of elongation and thickening of individual branches (shoots) varies across plant species. This variation is important for the outcome of competition and other plant–plant interactions. Here, we compared rates of shoot growth across 44 species from tropical, warm temperate and cool temperate forests of eastern Australia.Shoot growth rate was found to correlate with a suite of traits including the potential height of the species, xylem‐specific conductivity, leaf size, leaf area per xylem cross‐section (LA/XA), twig diameter (at 40 cm length), wood density and modulus of elasticity.Within this suite of traits, maximum plant height was the clearest correlate of growth rates, explaining 50%–67% of the variation in growth overall (p < .0001), and 23%–32% of the variation (p < .05) in growth when holding the influence of the other traits constant. Structural equation models suggest that traits associated with “hydraulics,” “biomechanics” and the “leaf economics spectrum” represent three clearly separated axes of variation, with the hydraulic axis exhibiting the strongest alignment with height and largest independent contribution to growth (in the case of branch thickening). However, most of the capacity of these axes to predict growth was also associated with maximum height, presumably reflecting coordinated selection on multiple traits that together influence life histories.Growth rates were not strongly correlated with leaf nitrogen or leaf mass per unit leaf area.Correlations between growth and maximum height arose both across latitude (47%, p < .0001) and from within‐site differences be...
Gloag, L, Benedetti, TM, Cheong, S, Li, Y, Chan, X, Lacroix, L, Chang, SLY, Arenal, R, Florea, I, Barron, H, Barnard, AS, Henning, AM, Zhao, C, Schuhmann, W, Gooding, JJ & Tilley, RD 2018, 'Three‐Dimensional Branched and Faceted Gold–Ruthenium Nanoparticles: Using Nanostructure to Improve Stability in Oxygen Evolution Electrocatalysis', Angewandte Chemie International Edition, vol. 57, no. 32, pp. 10241-10245. View/Download from: Publisher's site View description>>
AbstractAchieving stability with highly active Ru nanoparticles for electrocatalysis is a major challenge for the oxygen evolution reaction. As improved stability of Ru catalysts has been shown for bulk surfaces with low‐index facets, there is an opportunity to incorporate these stable facets into Ru nanoparticles. Now, a new solution synthesis is presented in which hexagonal close‐packed structured Ru is grown on Au to form nanoparticles with 3D branches. Exposing low‐index facets on these 3D branches creates stable reaction kinetics to achieve high activity and the highest stability observed for Ru nanoparticle oxygen evolution reaction catalysts. These design principles provide a synthetic strategy to achieve stable and active electrocatalysts.
Gloag, L, Benedetti, TM, Cheong, S, Marjo, CE, Gooding, JJ & Tilley, RD 2018, 'Cubic-Core Hexagonal-Branch Mechanism To Synthesize Bimetallic Branched and Faceted Pd–Ru Nanoparticles for Oxygen Evolution Reaction Electrocatalysis', Journal of the American Chemical Society, vol. 140, no. 40, pp. 12760-12764. View/Download from: Publisher's site
Godecke, E, Rai, T, Cadilhac, DA, Armstrong, E, Middleton, S, Ciccone, N, Whitworth, A, Rose, ML, Holland, A, Ellery, F, Hankey, GJ & Bernhardt, J 2018, 'Statistical analysis plan (SAP) for the Very Early Rehabilitation in Speech (VERSE) after stroke trial: an international 3-arm clinical trial to determine the effectiveness of early, intensive, prescribed, direct aphasia therapy', International Journal of Stroke, vol. 13, no. 8, pp. 863-880. View/Download from: Publisher's site View description>>
Background Limited evidence exists to support very early intensive aphasia rehabilitation after stroke. VERSE is a PROBE trial designed to determine whether two types of intensive aphasia therapy, beginning within 14 days of acute stroke, provide greater therapeutic and cost-effectiveness than usual care. Objective To publish the detailed statistical analysis plan for the VERSE trial prior to unblinding. This statistical analysis plan was based on the published and registered VERSE trial protocol and was developed by the blinded steering committee and management team, led by the trial statistician. This plan was developed using outcome measures and trial data collection forms. Results The VERSE statistical analysis plan is consistent with reporting standards for clinical trials and provides for clear and open reporting. Conclusions Publication of a statistical analysis plan serves to reduce potential trial reporting bias and outlines transparent pre-specified analyses. Australian New Zealand Clinical Trials Registry (ANZCTR) Registration number: ACTRN12613000776707; Universal Trial Number (UTN) is U1111-1145-4130.
Goodswen, SJ, Kennedy, PJ & Ellis, JT 2018, 'A Gene-Based Positive Selection Detection Approach to Identify Vaccine Candidates Using Toxoplasma gondii as a Test Case Protozoan Pathogen', Frontiers in Genetics, vol. 9. View/Download from: Publisher's site View description>>
Over the last two decades, various in silico approaches have been developed and refined that attempt to identify protein and/or peptide vaccines candidates from informative signals encoded in protein sequences of a target pathogen. As to date, no signal has been identified that clearly indicates a protein will effectively contribute to a protective immune response in a host. The premise for this study is that proteins under positive selection from the immune system are more likely suitable vaccine candidates than proteins exposed to other selection pressures. Furthermore, our expectation is that protein sequence regions encoding major histocompatibility complexes (MHC) binding peptides will contain consecutive positive selection sites. Using freely available data and bioinformatic tools, we present a high-throughput approach through a pipeline that predicts positive selection sites, protein subcellular locations, and sequence locations of medium to high T-Cell MHC class I binding peptides. Positive selection sites are estimated from a sequence alignment by comparing rates of synonymous (dS) and non-synonymous (dN) substitutions among protein coding sequences of orthologous genes in a phylogeny. The main pipeline output is a list of protein vaccine candidates predicted to be naturally exposed to the immune system and containing sites under positive selection. Candidates are ranked with respect to the number of consecutive sites located on protein sequence regions encoding MHCI-binding peptides. Results are constrained by the reliability of prediction programs and quality of input data. Protein sequences from Toxoplasma gondii ME49 strain (TGME49) were used as a case study. Surface antigen (SAG), dense granules (GRA), microneme (MIC), and rhoptry (ROP) proteins are considered worthy T. gondii candidates. Given 8263 TGME49 protein sequences processed anonymously, the top 10 predicted candidates were all worthy candidates. In particular, the top ten included ROP5 and...
Goodwin, C, Higgins, D, Tobe, SS, Austin, J, Wotherspoon, A, Gahan, ME & McNevin, D 2018, 'Singleplex quantitative real-time PCR for the assessment of human mitochondrial DNA quantity and quality', Forensic Science, Medicine and Pathology, vol. 14, no. 1, pp. 70-75. View/Download from: Publisher's site View description>>
Mitochondrial DNA (mtDNA) can provide a means for forensic identity testing when genotyping of nuclear DNA (nuDNA) targets is not possible due to degradation or lack of template. For degraded samples, an indication of the quantity and quality of mtDNA is essential to allow selection of appropriately sized targets for hypervariable region (HVR) analysis, which may conserve sample and resources. Three human-specific mtDNA targets of increasing length (86, 190 and 452 base pairs) were amplified by singleplex quantitative real-time PCR (qPCR), capable of providing an index of mtDNA degradation from fragment length information. Quantification was achieved by preparation of a standard curve for each target, using a purified mtDNA standard containing all three targets of interest, which produced a linear, accurate and precise result from 1×108 to 10 copies. These novel assays demonstrated excellent sensitivity, specificity and reproducibility in line with the minimum information for qPCR experiments (MIQE) guidelines. Further, a separate inhibition control reaction was included to guide sample clean-up and ensure the validity of degradation assays. This protocol assists the selection and analysis of appropriately sized targets to maximize the chance of obtaining an informative result in downstream assays like sequencing.
Gorlach, MA, Dobrykh, DA, Slobozhanyuk, AP, Belov, PA & Lapine, M 2018, 'Nonlinear symmetry breaking in photometamaterials', Physical Review B, vol. 97, no. 11. View/Download from: Publisher's site View description>>
Grüning, B, Dale, R, Sjödin, A, Chapman, BA, Rowe, J, Tomkins-Tinch, CH, Valieris, R & Köster, J 2018, 'Bioconda: sustainable and comprehensive software distribution for the life sciences', Nature Methods, vol. 15, no. 7, pp. 475-476. View/Download from: Publisher's site
Gu, H, Kononov, A, Memar, J & Zinder, Y 2018, 'Efficient Lagrangian heuristics for the two-stage flow shop with job dependent buffer requirements', Journal of Discrete Algorithms, vol. 52-53, pp. 143-155. View/Download from: Publisher's site View description>>
Guan, M, Zhou, Z, Mei, L, Zheng, H, Ren, W, Wang, L, Du, Y, Jin, D & Zhou, J 2018, 'Direct cation exchange of surface ligand capped upconversion nanocrystals to produce strong luminescence', Chemical Communications, vol. 54, no. 69, pp. 9587-9590. View/Download from: Publisher's site View description>>
We develop a facile and rapid cation exchange method for upconversion nanocrystals (UCNCs) without removing surface ligands.
Gunawan, D, Dang, K-D, Quiroz, M, Kohn, R & Tran, M-N 2018, 'Subsampling Sequential Monte Carlo for Static Bayesian Models', Statistics and Computing, vol. 30, no. 6, pp. 1741-1758. View/Download from: Publisher's site View description>>
We show how to speed up Sequential Monte Carlo (SMC) for Bayesian inference
in large data problems by data subsampling. SMC sequentially updates a cloud of
particles through a sequence of distributions, beginning with a distribution
that is easy to sample from such as the prior and ending with the posterior
distribution. Each update of the particle cloud consists of three steps:
reweighting, resampling, and moving. In the move step, each particle is moved
using a Markov kernel; this is typically the most computationally expensive
part, particularly when the dataset is large. It is crucial to have an
efficient move step to ensure particle diversity. Our article makes two
important contributions. First, in order to speed up the SMC computation, we
use an approximately unbiased and efficient annealed likelihood estimator based
on data subsampling. The subsampling approach is more memory efficient than the
corresponding full data SMC, which is an advantage for parallel computation.
Second, we use a Metropolis within Gibbs kernel with two conditional updates. A
Hamiltonian Monte Carlo update makes distant moves for the model parameters,
and a block pseudo-marginal proposal is used for the particles corresponding to
the auxiliary variables for the data subsampling. We demonstrate both the
usefulness and limitations of the methodology for estimating four generalized
linear models and a generalized additive model with large datasets.
Gunduz, O, Yetmez, M, Ekren, N, Kilic, O, Ben Nissan, B & Oktar, FN 2018, 'Microstructural and Mechanical Properties of Nano-Yttria-Oxide Doped Hydroxyapatite Composites', Materials Science Forum, vol. 923, pp. 89-92. View/Download from: Publisher's site View description>>
Nowadays hydroxyapatite (HA) bioceramics are very important because increasing traffic accidents and ageing of the population. They can be produced from synthetic or natural sources with different production methods. The biggest negative issue of HA is being very brittle and unstable under pressure. Various materials are added for restoring these weaknesses, but there is not so much studies adding nano-ingredients for restoring the mechanical properties of HA. In this study, 5-10% nano-yittria-oxide is added to bovine derived HA (BHA) and to commercial synthetic (CSHA) as a control group. Physical and mechanical properties are examined. Results show that adding of nano-ingredients are really helping to mechanical properties of HA.
Guo, X, Li, K, Bao, W, Zhao, Y, Xu, J, Liu, H & Wang, G 2018, 'Highly Reversible Lithium Polysulfide Semiliquid Battery with Nitrogen‐Rich Carbon Fiber Electrodes', Energy Technology, vol. 6, no. 2, pp. 251-256. View/Download from: Publisher's site View description>>
Guo, X, Zhang, J, Song, J, Wu, W, Liu, H & Wang, G 2018, 'MXene encapsulated titanium oxide nanospheres for ultra-stable and fast sodium storage', Energy Storage Materials, vol. 14, pp. 306-313. View/Download from: Publisher's site View description>>
Guo, Y, Seo, DH, Hong, J, Su, D, Wang, H, Zheng, J, Li, X, Murphy, AB & Ostrikov, KK 2018, 'Controlling the adsorption behavior of hydrogen at the interface of polycrystalline CVD graphene', International Journal of Hydrogen Energy, vol. 43, no. 41, pp. 18735-18744. View/Download from: Publisher's site View description>>
Gupta, G, Chellappan, DK, de Jesus Andreoli Pinto, T, Hansbro, PM, Bebawy, M & Dua, K 2018, 'Tumor suppressor role of miR-503', Panminerva Medica, vol. 60, no. 1, pp. 17-24. View/Download from: Publisher's site View description>>
MicroRNAs (miRNAs) are non-coding RNAs of around 20-25 nucleotides in length with highly conserved characteristics. They moderate post-transcriptional silencing by precisely combining with 3' untranslated regions (UTRs) of target mRNAs at a complementary site. miR‑503, an associate of the "canonical" miRNA-16 family, is expressed in numerous types of tumors such as breast cancer, prostate cancer, lung cancer, colorectal cancer, hepatocellular carcinoma, glioblastoma and several others. There is convincing evidence to show that miR‑503 functions as a tumor suppressor gene through its effects on target genes that regulate cell proliferation, migration, and invasion in tumor cells. In this current assessment, we discuss the biology and tumor suppressor role of miR‑503 in different cancers and elaborate on its mechanism of action.
Gupta, V, Trivedi, N, Simoni, S & Reddy, CRK 2018, 'Marine macroalgal nursery: A model for sustainable production of seedlings for large scale farming', Algal Research, vol. 31, pp. 463-468. View/Download from: Publisher's site
Gushchin, A, Kordzakhia, N & Novikov, A 2018, 'Translation invariant statistical experiments with independent increments', Statistical Inference for Stochastic Processes, vol. 21, no. 2, pp. 363-383. View/Download from: Publisher's site View description>>
Gutiérrez Moreno, JJ, Fronzi, M, Lovera, P, O’Riordan, A & Nolan, M 2018, 'Stability of Adsorbed Water on TiO2–TiN Interfaces. A First-Principles and Ab Initio Thermodynamics Investigation', The Journal of Physical Chemistry C, vol. 122, no. 27, pp. 15395-15408. View/Download from: Publisher's site View description>>
Regulation of the PI-3 kinase (PI3K)/Akt signalling pathway is essential for maintaining the integrity of fundamental cellular processes, cell growth, survival, death and metabolism, and dysregulation of this pathway is implicated in the development and progression of cancers. Receptor tyrosine kinases (RTKs) are major upstream regulators of PI3K/Akt signalling. The phosphatase and tensin homologue (PTEN), a well characterised tumour suppressor, is a prime antagonist of PI3K and therefore a negative regulator of this pathway. Loss or inactivation of PTEN, which occurs in many tumour types, leads to overactivation of RTK/PI3K/Akt signalling driving tumourigenesis. Cellular PTEN levels are tightly regulated by a number of transcriptional, post-transcriptional and post-translational regulatory mechanisms. Of particular interest, transcription of the PTEN pseudogene, PTENP1, produces sense and antisense transcripts that exhibit post-transcriptional and transcriptional modulation of PTEN expression respectively. These additional levels of regulatory complexity governing PTEN expression add to the overall intricacies of the regulation of RTK/PI-3 K/Akt signalling. This review will discuss the regulation of oncogenic PI3K signalling by PTEN (the regulator) with a focus on the modulatory effects of the sense and antisense transcripts of PTENP1 on PTEN expression, and will further explore the potential for new therapeutic opportunities in cancer treatment.
Hall, P, Johnstone, IM, Ormerod, JT, Wand, MP & Yu, JCF 2018, 'Fast and Accurate Binary Response Mixed Model Analysis via Expectation Propagation', Journal of the American Statistical Association, vol. 115, no. 532, pp. 1902-1916. View/Download from: Publisher's site View description>>
Expectation propagation is a general prescription for approximation of
integrals in statistical inference problems. Its literature is mainly concerned
with Bayesian inference scenarios. However, expectation propagation can also be
used to approximate integrals arising in frequentist statistical inference. We
focus on likelihood-based inference for binary response mixed models and show
that fast and accurate quadrature-free inference can be realized for the probit
link case with multivariate random effects and higher levels of nesting. The
approach is supported by asymptotic theory in which expectation propagation is
seen to provide consistent estimation of the exact likelihood surface.
Numerical studies reveal the availability of fast, highly accurate and scalable
methodology for binary mixed model analysis.
Hamidian, M & Hall, RM 2018, 'The AbaR antibiotic resistance islands found in Acinetobacter baumannii global clone 1 – Structure, origin and evolution', Drug Resistance Updates, vol. 41, pp. 26-39. View/Download from: Publisher's site View description>>
In multiply resistant Acinetobacter baumannii, complex transposons located in the chromosomal comM gene carry antibiotic and heavy metal resistance determinants. For one type, known collectively as AbaR, the ancestral form, AbaR0, entered a member of global clone 1 (GC1) in the mid 1970s and continued to evolve in situ forming many variants. In AbaR0, antibiotic and mercuric ion resistance genes are located between copies of a cadmium-zinc resistance transposon, Tn6018, and this composite transposon is in a class III transposon, Tn6019, carrying arsenate/arsenite resistance genes and five tni transposition genes. The antibiotic resistance genes in the AbaR0 and derived AbaR3 configurations are aphA1b, blaTEM, catA1, sul1, tetA(A), and cassette-associated aacC1 and aadA1 genes. These genes are in a specific arrangement of fragments from well-known transposons, e.g. Tn1, Tn1721, Tn1696 and Tn2670, that arose in an IncM1 plasmid. All known GC1 lineage 1 isolates carry AbaR0 or AbaR3, which arose around 1990, or a variant derived from one of them. Variants arose via deletions caused by one of three internal IS26s, by recombination between duplicate copies of sul1 or Tn6018, or by gene cassette addition or replacement. A few GC2 isolates also carry an AbaR island with different cassette-associated genes, aacA4 and oxa20.
Circular RNAs (cirRNAs) are long, noncoding endogenous RNA molecules and covalently closed continuous loop without 5′–3′ polarity and polyadenylated tail which are largely concentrated in the nucleus. CirRNA regulates gene expression by modulating microRNAs and functions as potential biomarker. CirRNAs can translate in vivo to link between their expression and disease. They are resistant to RNA exonuclease and can convert to the linear RNA by microRNA which can then act as competitor to endogenous RNA. This chapter summarizes the evolutionary conservation and expression of cirRNAs, their identification, highlighting various computational approaches on cirRNA, and translation with a focus on the breakthroughs and the challenges in this new field.
Hare, DJ, Cardoso, BR, Szymlek-Gay, EA & Biggs, B-A 2018, 'Neurological effects of iron supplementation in infancy: finding the balance between health and harm in iron-replete infants', The Lancet Child & Adolescent Health, vol. 2, no. 2, pp. 144-156. View/Download from: Publisher's site View description>>
Iron mediates many biochemical processes in neural networks that proliferate during brain development. Insufficient iron causes irreversible neurodevelopmental deficits, and most high-income countries recommend that infants older than 4-6 months receive additional iron via food fortification or supplementation to prevent iron-deficiency anaemia. Now that the prevalence of iron-deficiency anaemia in children has decreased to less than 10% in most developed countries, concerns that the recommended intakes far exceed those required to prevent iron-deficiency anaemia have been raised, and emerging evidence suggests that iron overexposure could be linked to adverse outcomes later in life. In this Viewpoint, we discuss the importance of iron for neurodevelopment, investigate the biochemical markers used to assess iron stores, summarise the disparity in public health policies among high-income countries, and discuss the potential association between iron overexposure and adverse neurological outcomes later in life. We present a case for new studies to establish the optimal amount of iron that both prevents deficiency and reduces the potential risk of long-term negative health outcomes.
Hart, G, Bradfield, LA & Balleine, BW 2018, 'Prefrontal Corticostriatal Disconnection Blocks the Acquisition of Goal-Directed Action', The Journal of Neuroscience, vol. 38, no. 5, pp. 1311-1322. View/Download from: Publisher's site View description>>
The acquisition of goal-directed action requires encoding of the association between an action and its specific consequences or outcome. At a neural level, this encoding has been hypothesized to involve a prefrontal corticostriatal circuit involving the projection from the prelimbic cortex (PL) to the posterior dorsomedial striatum (pDMS); however, no direct evidence for this claim has been reported. In a series of experiments, we performed functional disconnection of this pathway using targeted lesions of the anterior corpus callosum to disrupt contralateral corticostriatal projections with asymmetrical lesions of the PL and/or pDMS to block plasticity in this circuit in rats. We first demonstrated that unilaterally blocking the PL input to the pDMS prevented the phosphorylation of extracellular signal-related kinase/mitogen activated protein kinase (pERK/pMAPK) induced by instrumental training. Next, we used a full bilateral disconnection of the PL from the pDMS and assessed goal-directed action using an outcome-devaluation test. Importantly, we found evidence that rats maintaining an ipsilateral and/or contralateral connection between the PL and the pDMS were able to acquire goal-directed actions. In contrast, bilateral PL–pDMS disconnection abolished the acquisition of goal-directed actions. Finally, we used a temporary pharmacological disconnection to disrupt PL inputs to the pDMS by infusing the NMDA antagonistdl-2-amino-5-phosphonopentanoic acid into the pDMS during instrumental training and found that this manipulation also disrupted goal-directed learning. These results establish that, in rats, the acquisition of new goal-directed actions depends on a prefrontal–corticostriatal circuit involving a connection between the PL and the pDMS.SIGNIFICANCE STATEMENTIt has been hypothesized that the prelimbic cortex (PL) and posterior dorsomedial striatum (pDMS) in rodents interact in a corticostr...
Hart, G, Bradfield, LA, Fok, SY, Chieng, B & Balleine, BW 2018, 'The Bilateral Prefronto-striatal Pathway Is Necessary for Learning New Goal-Directed Actions', Current Biology, vol. 28, no. 14, pp. 2218-2229.e7. View/Download from: Publisher's site View description>>
The acquisition of new goal-directed actions requires the encoding of action-outcome associations. At a neural level, this encoding has been hypothesized to involve a prefronto-striatal circuit extending between the prelimbic cortex (PL) and the posterior dorsomedial striatum (pDMS); however, no research identifying this pathway with any precision has been reported. We started by mapping the prelimbic input to the dorsal and ventral striatum using a combination of retrograde and anterograde tracing with CLARITY and established that PL-pDMS projections share some overlap with projections to the nucleus accumbens core (NAc) in rats. We then tested whether each of these pathways were functionally required for goal-directed learning; we used a pathway-specific dual-virus chemogenetic approach to selectively silence pDMS-projecting or NAc-projecting PL neurons during instrumental training and tested rats for goal-directed action. We found that silencing PL-pDMS projections abolished goal-directed learning, whereas silencing PL-NAc projections left goal-directed learning intact. Finally, we used a three-virus approach to silence bilateral and contralateral pDMS-projecting PL neurons and again blocked goal-directed learning. These results establish that the acquisition of new goal-directed actions depends on the bilateral PL-pDMS pathway driven by intratelencephalic cortical neurons.
Hartigan, J, MacNamara, S & Leslie, LM 2018, 'Comparing precipitation and temperature trends between inland and coastal locations', ANZIAM Journal, vol. 60, pp. C109-C126. View/Download from: Publisher's site View description>>
Motivated by the Millennium Drought and the current drought over much of southern and eastern Australia, this detailed statistical study compares trends in annual wet season precipitation and temperature between a coastal site (Newcastle) and an inland site (Scone). Bootstrap permutation tests reveal Scone precipitation has decreased significantly over the past 40 years (p-value=0.070) whereas Newcastle has recorded little to no change (p-value=0.800). Mean maximum and minimum temperatures for Newcastle have increased over the past 40 years (p-values of 0.002 and 0.015, respectively) while the mean maximum temperature for Scone has increased (p-value = 0.058) and the mean minimum temperature has remained stable. This suggests mean temperatures during the wet season for both locations are increasing. Considering these trends along with those for precipitation, water resources in the Hunter region will be increasingly strained as a result of increased evaporation with either similar or less precipitation falling in the region. Wavelet analysis reveals that both sites have similar power spectra for precipitation and mean maximum temperature with a statistically significant signal in the two to seven year period, typically indicative of the El-Nino Southern Oscillation climate driver. The El-Nino Southern Oscillation also drives the Newcastle mean minimum temperature, whereas the Scone power spectra has no indication of a definitive driver for mean minimum temperature.
References R. A., R. L. Kitching, F. Chiew, L. Hughes, P. C. D. Newton, S. S. Schuster, A. Tait, and P. Whetton. Climate change 2014: Impacts, adaptation, and vulnerability. Part B: Regional aspects. Contribution of Working Group II to the Fifth Assessment of the Intergovernmental Panel on Climate Change. Technical report, Intergovernmental Panel on Climate Change, 2014. URL https://www.ipcc.ch/report/ar5/wg2/. Bureau of Meteorology. Climate Glossary-Dro...
Hartjes, FJ, Vonk, JM, Faiz, A, Hiemstra, PS, Lapperre, TS, Kerstjens, HAM, Postma, DS & van den Berge, M 2018, 'Predictive value of eosinophils and neutrophils on clinical effects of ICS in COPD', Respirology, vol. 23, no. 11, pp. 1023-1031. View/Download from: Publisher's site View description>>
BACKGROUND AND OBJECTIVE:Inflammation is present to a variable degree and composition in patients with COPD. This study investigates associations between both eosinophils and neutrophils in blood, sputum, airway wall biopsies and bronchoalveolar lavage (BAL) and their potential use as biomarkers for clinical response to inhaled corticosteroids (ICS). METHODS:In total, 114 steroid-naïve COPD patients of the Groningen Leiden Universities Corticosteroids in Obstructive Lung Disease (GLUCOLD) study using ICS or placebo during 30-month follow-up were included. Cell counts in blood, sputum, biopsies and BAL were evaluated at baseline. In addition, at baseline, 6 and 30 months, forced expiratory flow in 1 s (FEV1 ), residual volume/total lung capacity (hyperinflation) and Clinical COPD Questionnaire were evaluated. RESULTS:Cross-sectional analyses at baseline showed that higher blood eosinophils were significantly associated with higher eosinophil counts in sputum, biopsies and BAL. However, blood neutrophils did not significantly correlate with neutrophil counts in the other compartments. Baseline eosinophils and neutrophils, in whichever compartment measured, did not predict longitudinal FEV1 changes. Higher baseline biopsy eosinophils were associated with an increase in symptoms during 6- and 30-month ICS treatment. In addition, higher biopsy neutrophils were associated with a more marked reduction in hyperinflation during 6-month ICS treatment compared with placebo. CONCLUSION:Our findings indicate that blood eosinophils reflect eosinophils in other compartments, in contrast to neutrophils, in ICS-naïve COPD patients. Both baseline eosinophils and neutrophils do not predict ICS-induced lung function changes over a period of 6-30 months. The associations of biopsy eosinophils with worsening respiratory symptoms and biopsy neutrophils with improvement in hyperinflation during ICS treatment deserve further investigation.
Hassan, KA, Liu, Q, Elbourne, LDH, Ahmad, I, Sharples, D, Naidu, V, Chan, CL, Li, L, Harborne, SPD, Pokhrel, A, Postis, VLG, Goldman, A, Henderson, PJF & Paulsen, IT 2018, 'Pacing across the membrane: the novel PACE family of efflux pumps is widespread in Gram-negative pathogens', Research in Microbiology, vol. 169, no. 7-8, pp. 450-454. View/Download from: Publisher's site
Haw, TJ, Starkey, MR, Pavlidis, S, Fricker, M, Arthurs, AL, Mono Nair, P, Liu, G, Hanish, I, Kim, RY, Foster, PS, Horvat, JC, Adcock, IM & Hansbro, PM 2018, 'Toll-like receptor 2 and 4 have Opposing Roles in the Pathogenesis of Cigarette Smoke-induced Chronic Obstructive Pulmonary Disease', American Journal of Physiology-Lung Cellular and Molecular Physiology, vol. 314, no. 2, pp. ajplung.00154.2-ajplung.00154.2. View/Download from: Publisher's site
He, H, Howard, CB, Chen, Y, Wen, S, Lin, G, Zhou, J, Thurecht, KJ & Jin, D 2018, 'Bispecific Antibody-Functionalized Upconversion Nanoprobe', Analytical Chemistry, vol. 90, no. 5, pp. 3024-3029. View/Download from: Publisher's site View description>>
Upconversion nanoparticles (UCNPs) are new optical probes for biological applications. For specific biomolecular recognition to be realized for diagnosis and imaging, the key lies in developing a stable and easy-to-use bioconjugation method for antibody modification. Current methods are not yet satisfactory regarding conjugation time, stability, and binding efficiency. Here, we report a facile and high-yield approach based on a bispecific antibody (BsAb) free of chemical reaction steps. One end of the BsAb is designed to recognize methoxy polyethylene glycol-coated UCNPs, and the other end of the BsAb is designed to recognize the cancer antigen biomarker. Through simple vortexing, BsAb-UCNP nanoprobes form within 30 min and show higher (up to 54%) association to the target than that of the traditional UCNP nanoprobes in the ELISA-like assay. We further demonstrate its successful binding to the cancer cells with high efficiency and specificity for background-free fluorescence imaging under near-infrared excitation. This method suggests a general approach broadly suitable for functionalizing a range of nanoparticles to specifically target biomolecules.
Paper-based lateral flow assays, though being low-cost and widely used for rapid in vitro diagnostics, are indicative and do not provide sufficient sensitivity for the detection and quantification of low abundant biomarkers for early stage cancer diagnosis. Here, we design a compact device to create a focused illumination spot with high irradiance, which activates a range of highly doped 50 nm upconversion nanoparticles (UCNPs) to produce orders of magnitude brighter emissions. The device employs a very low-cost laser diode, simplified excitation, and collection optics and permits a mobile phone camera to record the results. Using highly erbium ion (Er3+)-doped and thulium ion (Tm3+)-doped UCNPs as two independent reporters on two-color lateral flow strips, new records of limit of detection (LOD), 89 and 400 pg/mL, have been achieved for the ultrasensitive detection of prostate specific antigen (PSA) and ephrin type-A receptor 2 (EphA2) biomarkers, respectively, without crosstalk. The technique and device presented in this work suggests a broad scope of low-cost, rapid, and quantitative lateral flow assays in early detection of bioanalytes.
Heffernan, AL & Hare, DJ 2018, 'Tracing Environmental Exposure from Neurodevelopment to Neurodegeneration', Trends in Neurosciences, vol. 41, no. 8, pp. 496-501. View/Download from: Publisher's site View description>>
Interplay between genetic and environmental factors during critical time windows can have effects that span from neurodevelopment to neurodegeneration. We present the concept of the 'neuroexposome', emphasizing the brain's distinctive response to environmental exposure, and how current 'omics' sciences can inform on both disease pathogenesis and future public health policies.
Hing, ML, Klanten, OS, Dowton, M, Brown, KR & Wong, MYL 2018, 'Repeated cyclone events reveal potential causes of sociality in coral-dwelling Gobiodon fishes', PLOS ONE, vol. 13, no. 9, pp. e0202407-e0202407. View/Download from: Publisher's site
Høj, L, Levy, N, Baillie, BK, Clode, PL, Strohmaier, RC, Siboni, N, Webster, NS, Uthicke, S & Bourne, DG 2018, 'Crown-of-Thorns Sea Star Acanthaster cf. solaris Has Tissue-Characteristic Microbiomes with Potential Roles in Health and Reproduction', Applied and Environmental Microbiology, vol. 84, no. 13. View/Download from: Publisher's site View description>>
ABSTRACT
Outbreaks of coral-eating crown-of-thorns sea stars (CoTS;
Acanthaster
species complex) cause substantial coral loss; hence, there is considerable interest in developing prevention and control strategies. We characterized the microbiome of captive CoTS and assessed whether dysbiosis was evident in sea stars during a disease event. Most tissue types had a distinct microbiome. The exception was female gonads, in which the microbiomes were highly variable among individuals. Male gonads were dominated (>97% of reads) by a single
Mollicutes
-related operational taxonomic unit (OTU). Detailed phylogenetic and microscopy analysis demonstrated the presence of a novel
Spiroplasma
-related bacterium in the spermatogenic layer. Body wall samples had high relative abundance (43 to 64% of reads) of spirochetes, likely corresponding to subcuticular symbionts reported from many echinoderms. Tube feet were characterized by
Hyphomonadaceae
(24 to 55% of reads). Pyloric cecal microbiomes had high alpha diversity, comprising many taxa commonly found in gastrointestinal systems. The order
Oceanospirillales
(genera
Endozoicomonas
and
Kistimonas
) was detected in all tissues. A microbiome shift occurred in diseased individuals although differences between tissue types were...
Ho-Le, TP, Pham, HM, Center, JR, Eisman, JA, Nguyen, HT & Nguyen, TV 2018, 'Prediction of changes in bone mineral density in the elderly: contribution of “osteogenomic profile”', Archives of Osteoporosis, vol. 13, no. 1. View/Download from: Publisher's site View description>>
The contribution of genetic variants to longitudinal bone loss has not been well documented. We constructed an "osteogenomic profile" based on 62 BMD-associated genetic variants and showed that the profile was significantly associated with bone loss, independently from baseline BMD and age. The osteogenomic profile can help predict bone loss in an individual.The rate of longitudinal bone loss (ΔBMD) is a risk factor for fracture. The variation in ΔBMD is partly determined by genetic factors. This study sought to define the association between an osteogenomic profile and ΔBMD.The osteogenomic profile was created from 62 BMD-associated SNPs from genome-wide association studies (GWAS) that were genotyped in 1384 elderly men and women aged 60+ years. Weighted genetic risk scores (GRS) were constructed for each individual by summing the products of the number of risk alleles and the sex-specific regression coefficients [associated with BMD from GWAS]. ΔBMD, expressed as annual percent change-in-BMD, was determined by linear regression analysis for each individual who had had at least two femoral neck BMD measurements.The mean ΔBMD was - 0.65% (SD 1.64%) for women and - 0.57% (SD 1.40%) for men, and this difference was not statistically significant (P = 0.32). In women, each unit increase in GRS was associated with 0.21% (SE 0.10) higher ΔBMD at the femoral neck (P = 0.036), and this association was independent of baseline BMD and age. In logistic regression analysis, each unit increase of GRS was associated with 41% odds (95%CI: 1.07-1.87) of rapid bone loss (ΔBMD ≤ - 1.2%/year; mean of rapid loss group = - 2.2%/year). There was no statistically significant association between ΔBMD and GRS in men.We conclude that the osteogenomic profile constructed from BMD-associated genetic variants is modestly associated with long-term changes in femoral neck BMD in women, but not in men.
AbstractThis study sought to define the sex-difference in trabecular and cortical bone parameters in Vietnamese individuals. The study involved 1404 women and 864 men aged between 20 and 86 years who were recruited from Ho Chi Minh City, Vietnam. Trabecular and cortical volumetric BMD were measured at the proximal tibia and proximal radius at 4%, 38%, and 66% points, using a peripheral quantitative computed tomography XCT2000 (Stratec, Germany). Polar strength strain index was estimated from cortical bone parameters. Changes in bone parameters were assessed by the multiple linear regression model. Among individuals aged 20–39 years, women had significantly lower peak trabecular BMD at both the radius (40%) and tibia (16%) than men, but the age-related reduction in trabecular BMD were similar between two sexes. For cortical BMD, peak values in women and men were comparable, but the age-related diminution was greater in women than men. At any age, polar strength strain index in women was lower than men, and the difference was mainly attributable to cortical bone area and total bone mass. We conclude that in the elderly, sex-related difference in trabecular BMD is originated during growth, but sex-related difference in cortical BMD is determined by differential age-related bone loss.
Hoseini, SJ, Bahrami, M, Maddahfar, M, Hashemi Fath, R & Roushani, M 2018, 'Polymerization of graphene oxide nanosheet by using of aminoclay: Electrocatalytic activity of its platinum nanohybrids', Applied Organometallic Chemistry, vol. 32, no. 1, pp. e3894-e3894. View/Download from: Publisher's site
Hoseini, SJ, Bahrami, M, Sadri, N, Aramesh, N, Fard, ZS, Iran, HR, Agahi, BH, Maddahfar, M, Dehghani, M, Arabi, AZB, Heidari, N, Fard, SFH & Moradi, Z 2018, 'Multi-metal nanomaterials obtained from oil/water interface as effective catalysts in reduction of 4-nitrophenol', Journal of Colloid and Interface Science, vol. 513, pp. 602-616. View/Download from: Publisher's site
Hsieh, M-H, Huang, P-T, Liou, H-H, Liang, P-H, Chen, P-M, Holt, SA, Yu, IF, James, M, Shiau, Y-S, Lee, M-T, Lin, T-L & Lou, K-L 2018, 'The Penetration Depth for Hanatoxin Partitioning into the Membrane Hydrocarbon Core Measured with Neutron Reflectivity', Langmuir, vol. 34, no. 30, pp. 9036-9046. View/Download from: Publisher's site
Hu, P, Chen, H, McGowan, EM, Ren, N, Xu, M & Lin, Y 2018, 'Assessment of FGFR1 Over-Expression and Over-Activity in Lung Cancer Cells: A Toolkit for Anti-FGFR1 Drug Screening', Human Gene Therapy Methods, vol. 29, no. 1, pp. 30-43. View/Download from: Publisher's site View description>>
Lung cancer, mainly caused by smoking, is one of the most prevalent diseases in China resulting in high mortality rates. The increasing incidence of chronic disease due to lung cancer places a huge burden on the welfare and cost to the Chinese society. Amplification of the fibroblast growth factor receptor 1 (FGFR1) is associated with high incidence and mortality in lung cancer patients. FGFR1 signaling is implicated in oncogenic traits such as proliferation, cell survival, angiogenesis and migration. Targeting the FGFR1 and its ligand basic FGF (bFGF) is a key step forward in developing new therapies for this crippling disease. Lung adenocarcinoma is the most common subtype of non-small cell lung cancer. In this study A549, a lung adenocarcinoma cell line widely used in vitro as a model for drug metabolism and as a transfection host, was used to study FGFR1. Here we describe a stable lentiviral FGFR1 overexpression system in lung cancer cells for the study of anti-lung cancer drug candidates targeting FGFR1. Ligand binding to FGFR1 activates the PI3K/Akt/mTOR signaling pathway and increases adhesion, invasion and migration in this model. Using a unique FGF monoclonal antibody developed in our laboratory we effectively blocked the overactive PI3K pathway abrogating the negative metastatic signaling pathways in lung cancer cells. Importantly, this model provides an effective and simple screening kit for anti-FGF1 drug compounds for lung cancer treatment and a tool for understanding the molecular mechanisms of the FGFR1 signaling pathway in lung cancer. Furthermore, this toolkit based on a FGFR1 lentiviral construct model is transferrable to study FGFR1 signaling in any type of cancer cell.
Huang, Y-H & Hwang, FJ 2018, 'Global optimization for the three-dimensional open-dimension rectangular packing problem', Engineering Optimization, vol. 50, no. 10, pp. 1789-1809. View/Download from: Publisher's site
Hughes, DJ, Campbell, DA, Doblin, MA, Kromkamp, JC, Lawrenz, E, Moore, CM, Oxborough, K, Prášil, O, Ralph, PJ, Alvarez, MF & Suggett, DJ 2018, 'Roadmaps and Detours: Active Chlorophyll-a Assessments of Primary Productivity Across Marine and Freshwater Systems', Environmental Science & Technology, vol. 52, no. 21, pp. 12039-12054. View/Download from: Publisher's site View description>>
Assessing phytoplankton productivity over space and time remains a core goal for oceanographers and limnologists. Fast Repetition Rate fluorometry (FRRf) provides a potential means to realize this goal with unprecedented resolution and scale yet has not become the "go-to" method despite high expectations. A major obstacle is difficulty converting electron transfer rates to equivalent rates of C-fixation most relevant for studies of biogeochemical C-fluxes. Such difficulty stems from methodological inconsistencies and our limited understanding of how the electron requirement for C-fixation (Φe,C) is influenced by the environment and by differences in the composition and physiology of phytoplankton assemblages. We outline a "roadmap" for limiting methodological bias and to develop a more mechanistic understanding of the ecophysiology underlying Φe,C. We 1) re-evaluate core physiological processes governing how microalgae invest photosynthetic electron transport-derived energy and reductant into stored carbon versus alternative sinks. Then, we 2) outline steps to facilitate broader uptake and exploitation of FRRf, which could transform our knowledge of aquatic primary productivity. We argue it is time to 3) revise our historic methodological focus on carbon as the currency of choice, to 4) better appreciate that electron transport fundamentally drives ecosystem biogeochemistry, modulates cell-to-cell interactions, and ultimately modifies community biomass and structure.
Hughes, DJ, Varkey, D, Doblin, MA, Ingleton, T, Mcinnes, A, Ralph, PJ, van Dongen‐Vogels, V & Suggett, DJ 2018, 'Impact of nitrogen availability upon the electron requirement for carbon fixation in Australian coastal phytoplankton communities', Limnology and Oceanography, vol. 63, no. 5, pp. 1891-1910. View/Download from: Publisher's site View description>>
AbstractNitrogen (N) availability affects phytoplankton photosynthetic performance and regulates marine primary production (MPP) across the global coast and oceans. Bio‐optical tools including Fast Repetition Rate fluorometry (FRRf) are particularly well suited to examine MPP variability in coastal regions subjected to dynamic spatio‐temporal fluctuations in nutrient availability. FRRf determines photosynthesis as an electron transport rate through Photosystem II (ETRPSII), requiring knowledge of an additional parameter, the electron requirement for carbon fixation (KC), to retrieve rates of CO2‐fixation. KC strongly depends upon environmental conditions regulating photosynthesis, yet the importance of N‐availability to this parameter has not been examined. Here, we use nutrient bioassays to isolate how N (relative to other macronutrients P, Si) regulates KC of phytoplankton communities from the Australian coast during summer, when N‐availability is often highly variable. KC consistently responded to N‐amendment, exhibiting up to a threefold reduction and hence an apparent increase in the efficiency with which electrons were used to drive C‐fixation. However, the process driving this consistent reduction was dependent upon initial conditions. When diatoms dominated assemblages and N was undetectable (e.g., post bloom), KC decreased predominantly via a physiological adjustment of the existing community to N‐amendment. Conversely, for mixed assemblages, N‐addition achieved a similar reduction in KC through a change in community structure toward diatom domination. We generate new understanding and parameteriza...
Huque, MH, Anderson, C, Walton, R, Woolford, S & Ryan, L 2018, 'Smooth individual level covariates adjustment in disease mapping', Biometrical Journal, vol. 60, no. 3, pp. 597-615. View/Download from: Publisher's site
Huynh, TT, Lem, LLC, Kuramata, A, Phillips, MR & Ton-That, C 2018, 'Kinetics of charge carrier recombination in β−Ga2O3 crystals', Physical Review Materials, vol. 2, no. 10. View/Download from: Publisher's site View description>>
Hwang, FJ & Lin, BMT 2018, 'Survey and extensions of manufacturing models in two-stage flexible flow shops with dedicated machines', Computers & Operations Research, vol. 98, pp. 103-112. View/Download from: Publisher's site View description>>
This study considers the manufacturing environments in which $m+1$ machines are configured as two-stage flexible flow shops with dedicated machines (F2DM). The F2DM scheduling problems arise naturally from practical production and fabrication systems, and they are classified into two categories, whose machine settings are antithetical to each other. In model 1, a single common bottleneck machine is installed at stage 1 and m parallel dedicated machines comprise stage 2. The second model has the m dedicated machines at stage 1 and the bottleneck machine at stage 2. Categorizing the literature according to the performance metrics, we survey the existing research results of the two models and propose several new solution procedures with improved computational complexity. The complexity results are summarized, and suggestions are made for future research.
Imkamp, K, Berg, M, Vermeulen, CJ, Heijink, IH, Guryev, V, Kerstjens, HAM, Koppelman, GH, van den Berge, M & Faiz, A 2018, 'Nasal epithelium as a proxy for bronchial epithelium for smoking-induced gene expression and expression Quantitative Trait Loci', Journal of Allergy and Clinical Immunology, vol. 142, no. 1, pp. 314-317.e15. View/Download from: Publisher's site
Indigo, N, Smith, J, Webb, JK & Phillips, B 2018, 'Not such silly sausages: Evidence suggests northern quolls exhibit aversion to toads after training with toad sausages', Austral Ecology, vol. 43, no. 5, pp. 592-601. View/Download from: Publisher's site View description>>
Irga, PJ, Barker, K & Torpy, FR 2018, 'Conservation mycology in Australia and the potential role of citizen science', Conservation Biology, vol. 32, no. 5, pp. 1031-1037. View/Download from: Publisher's site View description>>
Fungi are undoubtedly important for ecosystem functioning; however, they have been omitted or given scant attention in most biodiversity policy documents, management plans, and formal conservation schedules throughout the world. This oversight may be due to a general lack of awareness in the scientific community and compounded by a scarcity of mycology-associated curricula at the tertiary level and a lack of mycologists in research institutions. Although molecular techniques advance the systematic cataloging of fungi and facilitate insights into fungal communities, the scarcity of professional mycologists in the environmental sciences hampers conservation efforts. Conversely, citizen science initiatives are making significant contributions to the mycology discipline by increasing awareness and extending the scope of fungal surveys. Future research by professional and amateur mycologists into the distribution of fungi and their function in ecosystems will help identify wider and more effective conservation goals.
Irga, PJ, Pettit, TJ & Torpy, FR 2018, 'The phytoremediation of indoor air pollution: a review on the technology development from the potted plant through to functional green wall biofilters', Reviews in Environmental Science and Bio/Technology, vol. 17, no. 2, pp. 395-415. View/Download from: Publisher's site View description>>
Poor indoor air quality is a health problem of escalating magnitude, as communities become increasingly urbanised and people’s behaviours change, lending to lives spent almost exclusively in indoor environments. The accumulation of, and continued exposure to, indoor air pollution has been shown to result in detrimental health outcomes. Particulate matter penetrating into the building, volatile organic compounds (VOCs) outgassing from synthetic materials and carbon dioxide from human respiration are the main contributors to these indoor air quality concerns. Whilst a range of physiochemical methods have been developed to remove contaminants from indoor air, all methods have high maintenance costs. Despite many years of study and substantial market demand, a well evidenced procedure for indoor air bioremediation for all applications is yet to be developed. This review presents the main aspects of using horticultural biotechnological tools for improving indoor air quality, and explores the history of the technology, from the humble potted plant through to active botanical biofiltration. Regarding the procedure of air purification by potted plants, many researchers and decades of work have confirmed that the plants remove CO2 through photosynthesis, degrade VOCs through the metabolic action of rhizospheric microbes, and can sequester particulate matter through a range of physical mechanisms. These benefits notwithstanding, there are practical barriers reducing the value of potted plants as standalone air cleaning devices. Recent technological advancements have led to the development of active botanical biofilters, or functional green walls, which are becoming increasingly efficient and have the potential for the functional mitigation of indoor air pollutant concentrations.
Isaacs, SR, Kim, KW, Cheng, JX, Bull, RA, Stelzer-Braid, S, Luciani, F, Rawlinson, WD & Craig, ME 2018, 'Amplification and next generation sequencing of near full-length human enteroviruses for identification and characterisation from clinical samples', Scientific Reports, vol. 8, no. 1, pp. 11889-11889. View/Download from: Publisher's site View description>>
AbstractMore than 100 different enterovirus (EV) genotypes infect humans and contribute to substantial morbidity. However, current methods for characterisation of full-length genomes are based on Sanger sequencing of short genomic regions, which are labour-intensive and do not enable comprehensive characterisation of viral populations. Here, we describe a simple and sensitive protocol for the amplification and sequencing of near full-length genomes of human EV species using next generation sequencing. EV genomes were amplified from 89% of samples tested, with Ct values ranging between 15.7 and 39.3. These samples included 7 EV-A genotypes (CVA2, 5–7, 10, 16 and EV71), 19 EV-B genotypes (CVA9, CVB1-6, ECHO3, 4, 6, 7, 9, 11, 16, 18, 25, 29, 30, and EV69), 3 EV-C genotypes (CVA19 and PV2, 3) and 1 EV-D genotype (EV70). We characterised 70 EVs from 58 clinical stool samples and eight reference strains, with a minimum of 100X depth. We found evidence of co-infection in four clinical specimens, each containing two distinct EV genotypes (CVB3/ECHO7, CVB3/ECHO18 and ECHO9/30). Characterisation of the complete genome provided conclusive genotyping of EVs, which can be applied to investigate the intra-host virus evolution of EVs, and allows further identification and investigation of EV outbreaks.
Ishikawa, AA, Bordin, DM, de Campos, EG, Blanes, L, Doble, P & De Martinis, BS 2018, 'A Gas Chromatography–Mass Spectrometry Method for Toxicological Analysis of MDA, MDEA and MDMA in Vitreous Humor Samples from Victims of Car Accidents', Journal of Analytical Toxicology, vol. 42, no. 9, pp. 661-666. View/Download from: Publisher's site View description>>
Vitreous humor (VH) shows excellent potential as a matrix of choice for postmortem analytical toxicology due to the ease of sampling and low metabolic activity. This study demonstrates a simple and rapid analytical method to identify and quantify 3,4-methylenedioxyamphetamine, 3,4-methylenedioxymethamphetamine and 3,4-methylenedioxy-ethylamphetamine in VH. Samples were collected with a simple eye puncture procedure, followed by liquid-liquid extraction and derivatization with heptafluorobutyric anhydride and analysis via gas chromatography-mass spectrometry. The accuracy of the method ranged 97-103%, intra-assay precision was between 4.54 and 9.14% relative standard deviation (RSD) and interassay precision ranged from 6.92 to 10.59% RSD. Limits of detection and quantification ranged from 1.0 to 2.5 ng/mL and 10 ng/mL, respectively. The validated method was successfully applied to detect methylenedioxyamphetamine derivatives in VH samples collected from victims of fatal car crashes.
Islam, MM, Jelocnik, M, Huston, WM, Timms, P & Polkinghorne, A 2018, 'Characterization of the In Vitro Chlamydia pecorum Response to Gamma Interferon', Infection and Immunity, vol. 86, no. 4. View/Download from: Publisher's site View description>>
ABSTRACTChlamydia pecorum
is an important intracellular bacterium that causes a range of diseases in animals, including a native Australian marsupial, the koala. In humans and animals, a gamma interferon (IFN-γ)-mediated immune response is important for the control of intracellular bacteria. The present study tested the hypotheses that
C. pecorum
can escape IFN-γ-mediated depletion of host cell tryptophan pools. In doing so, we demonstrated that, unlike
Chlamydia trachomatis
,
C. pecorum
is completely resistant to IFN-γ in human epithelial cells. While the growth of
C. pecorum
was inhibited in tryptophan-deficient medium, it could be restored by the addition of kynurenine, anthranilic acid, and indole, metabolites that could be exploited by the gene products of the
C. pecorum
tryptophan biosynthesis operon. We also found that expression of
trp
genes was detectable only when
C. pecorum
was grown in tryptophan-free medium, with gene repression occurring in response to the addition of kynurenine, anthranilic acid, and indole. When grown in bovine kidney epithelial cells, bovine IFN-γ also failed to restrict the growth of
C. pecorum
, ...
Jaffar, J, Yang, S-H, Kim, SY, Kim, H-W, Faiz, A, Chrzanowski, W & Burgess, JK 2018, 'Greater cellular stiffness in fibroblasts from patients with idiopathic pulmonary fibrosis', American Journal of Physiology-Lung Cellular and Molecular Physiology, vol. 315, no. 1, pp. L59-L65. View/Download from: Publisher's site View description>>
Idiopathic pulmonary fibrosis (IPF) is a lethal lung disease involving degenerative breathing capacity. Fibrotic disease is driven by dysregulation in mechanical forces at the organ, tissue, and cellular level. While it is known that, in certain pathologies, diseased cells are stiffer than healthy cells, it is not known if fibroblasts derived from patients with IPF are stiffer than their normal counterparts. Using IPF patient-derived cell cultures, we measured the stiffness of individual lung fibroblasts via high-resolution force maps using atomic force microscopy. Fibroblasts from patients with IPF were stiffer and had an augmented cytoskeletal response to transforming growth factor-β1 compared with fibroblasts from donors without IPF. The results from this novel study indicate that the increased stiffness of lung fibroblasts of IPF patients may contribute to the increased rigidity of fibrotic lung tissue.
Jenkins, C, Jelocnik, M, Micallef, ML, Galea, F, Taylor–Brown, A, Bogema, DR, Liu, M, O’Rourke, B, Chicken, C, Carrick, J & Polkinghorne, A 2018, 'An epizootic of Chlamydia psittaci equine reproductive loss associated with suspected spillover from native Australian parrots', Emerging Microbes & Infections, vol. 7, no. 1, pp. 1-13. View/Download from: Publisher's site View description>>
Chlamydia psittaci is an avian pathogen capable of spill-over infections to humans. A parrot C. psittaci strain was recently detected in an equine reproductive loss case associated with a subsequent cluster of human C. psittaci infections. In this study, we screened for C. psittaci in cases of equine reproductive loss reported in regional New South Wales, Australia during the 2016 foaling season. C. psittaci specific-PCR screening of foetal and placental tissue samples from cases of equine abortion (n = 161) and foals with compromised health status (n = 38) revealed C. psittaci positivity of 21.1% and 23.7%, respectively. There was a statistically significant geographical clustering of cases ~170 km inland from the mid-coast of NSW (P < 0.001). Genomic analysis and molecular typing of C. psittaci positive samples from this study and the previous Australian equine index case revealed that the equine strains from different studs in regional NSW were clonal, while the phylogenetic analysis revealed that the C. psittaci strains from both Australian equine disease clusters belong to the parrot-associated 6BC clade, again indicative of spill-over of C. psittaci infections from native Australian parrots. The results of this work suggest that C. psittaci may be a more significant agent of equine reproductive loss than thought. A range of studies are now required to evaluate (a) the exact role that C. psittaci plays in equine reproductive loss; (b) the range of potential avian reservoirs and factors influencing infection spill-over; and
Jessop, TS, Webb, J, Dempster, T, Feit, B & Letnic, M 2018, 'Interactions between corticosterone phenotype, environmental stressor pervasiveness and irruptive movement-related survival', Journal of Experimental Biology, vol. 221, no. 24. View/Download from: Publisher's site View description>>
Animals use irruptive movement to avoid exposure to stochastic and pervasive environmental stressors that impact fitness. Beneficial irruptive movements transfer individuals from high-stress areas (conferring low fitness) to alternate localities that may improve survival or reproduction. However, being stochastic, environmental stressors can limit an animal's preparatory capacity to enhance irruptive movement performance. Thus individuals must rely on standing, or rapidly induced, physiological and behavioural responses. Rapid elevation of glucocorticoid hormones in response to environmental stressors are widely implicated in adjusting physiological and behaviour processes that could influence irruptive movement capacity. However, there remains little direct evidence to demonstrate that corticosterone regulated movement performance, nor the interaction with the pervasiveness of environmental stress, confers adaptive movement outcomes. Here we compared how movement-related survival of cane toads (Rhinella marina) varied with three different experimental corticosterone phenotypes across four increments of increasing environmental stressor pervasiveness (i.e. distance from water in a semi-arid landscape). Our results indicated that toads with phenotypically increased corticosterone levels attained higher movement-related survival compared to individuals with control or lowered corticosterone phenotypes. However, the effects of corticosterone phenotypes on movement-related survival to some extent co-varied with stressor pervasiveness. Thus our study demonstrates how the interplay among an individual's corticosterone phenotype and movement capacity alongside the arising costs of movement and the pervasiveness of the environmental stressor can affect survival outcomes.
The objectives of this short report are to: (i) explore #Frailty Twitter activity over a six-month period; and (ii) provide a snapshot Twitter content analysis of #Frailty usage.A mixed-method study was conducted to explore Twitter data related to frailty. The primary search term was #Frailty. Objective 1: data were collected using Symplur analytics, including variables for total number of tweets, unique tweeters (users) and total number of impressions. Objective 2: a retrospectively conducted snapshot content analysis of 1500 #Frailty tweets was performed using TweetReach™ .Over a six-month period (1 January 2017-31 June 2017), there was a total of 6545 #Frailty tweets, generating 14.8 million impressions across 3986 participants. Of the 1500 tweets (814 retweets; 202 replies; 484 original tweets), 56% were relevant to clinical frailty. The main contributors ('who') were as follows: the public (29%), researchers (25%), doctors (21%), organisations (18%) and other allied health professionals (7%). Tweet main message intention ('what') was public health/advocacy (41%), social communication (28%), research-based evidence/professional education (24%), professional opinion/case studies (15%) and general news/events (7%).Twitter is increasingly being used to communicate about frailty. It is important that thought leaders contribute to the conversation. There is potential to leverage Twitter to promote and disseminate frailty-related knowledge and research.
Jin, D & Cao, J 2018, '“Perspective” – A new approach to serve our Light community', Light: Science & Applications, vol. 7, no. 1. View/Download from: Publisher's site
Jin, D, Xi, P, Wang, B, Zhang, L, Enderlein, J & van Oijen, AM 2018, 'Nanoparticles for super-resolution microscopy and single-molecule tracking', Nature Methods, vol. 15, no. 6, pp. 415-423. View/Download from: Publisher's site View description>>
We review the use of luminescent nanoparticles in super-resolution imaging and single-molecule tracking, and showcase novel approaches to super-resolution imaging that leverage the brightness, stability, and unique optical-switching properties of these nanoparticles. We also discuss the challenges associated with their use in biological systems, including intracellular delivery and molecular targeting. In doing so, we hope to provide practical guidance for biologists and continue to bridge the fields of super-resolution imaging and nanoparticle engineering to support their mutual advancement.
Johansen, MD, de Silva, K, Plain, KM, Begg, DJ, Whittington, RJ & Purdie, AC 2018, 'Sheep and cattle exposed to Mycobacterium avium subspecies paratuberculosis exhibit altered total serum cholesterol profiles during the early stages of infection', Veterinary Immunology and Immunopathology, vol. 202, pp. 164-171. View/Download from: Publisher's site
Johansen, MD, Hortle, E, Kasparian, JA, Romero, A, Novoa, B, Figueras, A, Britton, WJ, de Silva, K, Purdie, AC & Oehlers, SH 2018, 'Analysis of mycobacterial infection-induced changes to host lipid metabolism in a zebrafish infection model reveals a conserved role for LDLR in infection susceptibility', Fish & Shellfish Immunology, vol. 83, pp. 238-242. View/Download from: Publisher's site
Johansen, MD, Kasparian, JA, Hortle, E, Britton, WJ, Purdie, AC & Oehlers, SH 2018, 'Mycobacterium marinum infection drives foam cell differentiation in zebrafish infection models', Developmental & Comparative Immunology, vol. 88, pp. 169-172. View/Download from: Publisher's site
Johnson, L, Tan, S, Jenkins, E, Wood, B & Marks, DC 2018, 'Characterization of biologic response modifiers in the supernatant of conventional, refrigerated, and cryopreserved platelets', Transfusion, vol. 58, no. 4, pp. 927-937. View/Download from: Publisher's site
Jolly, CJ, Kelly, E, Gillespie, GR, Phillips, B & Webb, JK 2018, 'Out of the frying pan: Reintroduction of toad-smart northern quolls to southern Kakadu National Park', Austral Ecology, vol. 43, no. 2, pp. 139-149. View/Download from: Publisher's site View description>>
Jolly, CJ, Webb, JK & Phillips, BL 2018, 'The perils of paradise: an endangered species conserved on an island loses antipredator behaviours within 13 generations', Biology Letters, vol. 14, no. 6, pp. 20180222-20180222. View/Download from: Publisher's site View description>>
When imperilled by a threatening process, the choice is often made to conserve threatened species on offshore islands that typically lack the full suite of mainland predators. While keeping the species extant, this releases the conserved population from predator-driven natural selection. Antipredator traits are no longer maintained by natural selection and may be lost. It is implicitly assumed that such trait loss will happen slowly, but there are few empirical tests. In Australia, northern quolls (
Dasyurus hallucatus
) were moved onto a predator-free offshore island in 2003 to protect the species from the arrival of invasive cane toads on the mainland. We compared the antipredator behaviours of wild-caught quolls from the predator-rich mainland with those from this predator-free island. We compared the responses of both wild-caught animals and their captive-born offspring, to olfactory cues of two of their major predators (feral cats and dingoes). Wild-caught, mainland quolls recognized and avoided predator scents, as did their captive-born offspring. Island quolls, isolated from these predators for only 13 generations, showed no recognition or aversion to these predators. This study suggests that predator aversion behaviours can be lost very rapidly, and that this may make a population unsuitable for reintroduction to a predator-rich mainland.
Jowett, LA, Howe, ENW, Wu, X, Busschaert, N & Gale, PA 2018, 'New Insights into the Anion Transport Selectivity and Mechanism of Tren‐based Tris‐(thio)ureas', Chemistry – A European Journal, vol. 24, no. 41, pp. 10475-10487. View/Download from: Publisher's site View description>>
AbstractThe anion transport properties of a series of previously reported tren‐based anionophores have been revisited using new assays designed to measure anion uniport. This study provides new insights into the transport mechanism and selectivity of this important class of transporters. Specifically, we report the chloride and nitrate transport selectivity of these systems and quantify sulfate transport to determine EC50 values for sulfate transport for the first time. Two new assays were developed to study bicarbonate transport allowing accurate quantification of chloride/bicarbonate exchange.
Kabakova, IV, Azuri, I, Chen, Z, Nayak, PK, Snaith, HJ, Kronik, L, Paterson, C, Bakulin, AA & Egger, DA 2018, 'The Effect of Ionic Composition on Acoustic Phonon Speeds in Hybrid Perovskites from Brillouin Spectroscopy and Density Functional Theory', Journal of Materials Chemistry C, vol. 6, no. 15, pp. 3861-3868. View/Download from: Publisher's site View description>>
Hybrid organic-inorganic perovskites (HOIPs) have recently emerged as highly
promising solution-processable materials for photovoltaic (PV) and other
optoelectronic devices. HOIPs represent a broad family of materials with
properties highly tuneable by the ions that make up the perovskite structure as
well as their multiple combinations. Interestingly, recent high-efficiency PV
devices using HOIPs with substantially improved long-term stability have used
combinations of different ionic compositions. The structural dynamics of these
systems are unique for semiconducting materials and are currently argued to be
central to HOIPs stability and charge-transport properties. Here, we studied
the impact of ionic composition on phonon speeds of HOIPs from Brillouin
spectroscopy experiments and density functional theory calculations for
FAPbBr$_3$, MAPbBr$_3$, MAPbCl$_3$, and the mixed halide
MAPbBr$_{1.25}$Cl$_{1.75}$. Our results show that the acoustic phonon speeds
can be strongly modified by ionic composition, which we explain by analysing
the lead-halide sublattice in detail. The vibrational properties of HOIPs are
therefore tuneable by using targeted ionic compositions in the perovskite
structure. This tuning can be rationalized with non-trivial effects, for
example, considering the influence of the shape and dipole moment of organic
cations. This has an important implication to further improvements in the
stability and charge-transport properties of these systems.
Kahlke, T, Jumppanen, P, Westram, R, Abell, GCG & Bodrossy, L 2018, 'ProbeSpec: batch specificity testing and visualization of oligonucleotide probe sets implemented in ARB', F1000Research, vol. 7, pp. 1901-1901. View/Download from: Publisher's site View description>>
High-throughput molecular methods such as quantitative polymerase chain reaction (qPCR) and environmental microarrays are cost-effective methods for semi-quantitative assessment of bacterial community structure and the identification of specific target organisms. Both techniques rely on short nucleotide sequences, so-called oligonucleotide probes, which require high specificity to the organisms in question to avoid cross-hybridization with non-target taxa. However, designing oligonucleotide probes for novel taxa or marker genes that show sufficient phylogenetic sensitivity and specificity is often time- and labor-intensive, as each probe has to be in-silico tested for its specificity and sensitivity. Here we present ProbeSpec, to our knowledge the first batch sensitivity and specificity estimation and visualization tool for oligonucleotide probes integrated into the widely used ARB software. Using ProbeSpec’s interactive “mismatch threshold” and “clade marked threshold” we were able to reduce the development time of highly specific probes for a recently published environmental oligonucleotide microarray from several months to one week.
Kanniah, KD, Tan, KP, Cracknell, AP, Huete, AR, Idris, NH, Lau, AMS, Abd Rahman, MZ, Rasib, AW & Ahmad, A 2018, 'Assessment of biophysical properties of Royal Belum tropical forest, Malaysia', Singapore Journal of Tropical Geography, vol. 39, no. 1, pp. 90-106. View/Download from: Publisher's site View description>>
Karacan, I, Gunduz, O, Ozyegin, LS, Gökce, H, Ben-Nissan, B, Akyol, S & Oktar, FN 2018, 'The natural nano-bioceramic powder production from organ pipe red coral (Tubipora musica) by a simple chemical conversion method', Journal of the Australian Ceramic Society, vol. 54, no. 2, pp. 317-329. View/Download from: Publisher's site View description>>
Karami, A, Karbalaei, S, Ebrahimi, M, Ismail, A, Jahromi, MF, Simpson, SL, Eghtesadi Araghi, P, Lim, RP & Liang, JB 2018, 'Changes in nutritional values induced by butachlor in juvenile diploid and triploid Clarias gariepinus', International Journal of Environmental Science and Technology, vol. 15, no. 10, pp. 2117-2128. View/Download from: Publisher's site View description>>
Kaur, A, Shimoni, O & Wallach, M 2018, 'Novel screening test for celiac disease using peptide functionalised gold nanoparticles', World Journal of Gastroenterology, vol. 24, no. 47, pp. 5379-5390. View/Download from: Publisher's site View description>>
AIM:To develop a screening test for celiac disease based on the coating of gold nanoparticles with a peptide sequence derived from gliadin, the protein that triggers celiac disease. METHODS:20 nm gold nanoparticles were first coated with NeutrAvidin. A long chain Polyethylene glycol (PEG) linker containing Maleimide at the Ω-end and Biotin group at the α-end was used to ensure peptide coating to the gold nanoparticles. The maleimide group with the thiol (-SH) side chain reacted with the cysteine amino acid in the peptide sequence and the biotinylated and PEGylated peptide was added to the NeutrAvidin coated gold nanoparticles. The peptide coated gold nanoparticles were then converted into a serological assay. We used the peptide functionalised gold nanoparticle-based assay on thirty patient serum samples in a blinded assessment and compared our results with the previously run serological and pathological tests on these patients. RESULTS:A stable colloidal suspension of peptide coated gold nanoparticles was obtained without any aggregation. An absorbance peak shift as well as color change was caused by the aggregation of gold nanoparticles following the addition of anti-gliadin antibody to peptide coated nanoparticles at levels associated with celiac disease. The developed assay has been shown to detect anti-gliadin antibody not only in quantitatively spiked samples but also in a small-scale study on real non-hemolytic celiac disease patient's samples. CONCLUSION:The study demonstrates the potential of gold nanoparticle-peptide based approach to be adapted for developing a screening assay for celiac disease diagnosis. The assay could be a part of an exclusion based diagnostic strategy and prove particularly useful for testing high celiac disease risk populations.
KC, R, Shukla, SD, Gautam, SS, Hansbro, PM & O’Toole, RF 2018, 'The role of environmental exposure to non‐cigarette smoke in lung disease', Clinical and Translational Medicine, vol. 7, no. 1, pp. 1-12. View/Download from: Publisher's site View description>>
AbstractChronic exposure to household indoor smoke and outdoor air pollution is a major contributor to global morbidity and mortality. The majority of these deaths occur in low and middle‐income countries. Children, women, the elderly and people with underlying chronic conditions are most affected. In addition to reduced lung function, children exposed to biomass smoke have an increased risk of developing lower respiratory tract infections and asthma‐related symptoms. In adults, chronic exposure to biomass smoke, ambient air pollution, and opportunistic exposure to fumes and dust are associated with an increased risk of developing chronic bronchitis, chronic obstructive pulmonary disease (COPD), lung cancer and respiratory infections, including tuberculosis. Here, we review the evidence of prevalence of COPD in people exposed to non‐cigarette smoke. We highlight mechanisms that are likely involved in biomass‐smoke exposure‐related COPD and other lung diseases. Finally, we summarize the potential preventive and therapeutic strategies for management of COPD induced by non‐cigarette smoke exposure.
Kelly, E, Phillips, BL & Webb, JK 2018, 'Taste overshadows less salient cues to elicit food aversion in endangered marsupial', Applied Animal Behaviour Science, vol. 209, pp. 83-87. View/Download from: Publisher's site View description>>
Fingermarks can be exploited for both their ridge detail and touch DNA. One-step luminescent cyanoacrylate (CA) fuming techniques used for fingermark enhancement, such as PolyCyano UV (Foster+Freeman Ltd) and Lumicyano™ (Crime Science Technology), claim to be compatible with DNA analysis as they reduce the need for post-staining to increase contrast of the developed fingermark. The aim of this study was to determine the impact that these one-step luminescent cyanoacrylates have on DNA analysis and how they compare to conventional CA techniques. Four donors each deposited five sets of natural fingermarks, to which a known amount of washed saliva cells was dispensed onto half of each set of fingermarks. Each set was treated with either a conventional CA technique or a one-step luminescent CA technique prior to collection and processing of DNA, with one set left as a non-fumed control. It was found that DNA was still recoverable and detectable following each of the treatments. Lumicyano™ had a similar impact on DNA profiles as conventional CA fuming and with post-stain, however, the degradation effect of PolyCyano UV on DNA was greater than the conventional treatments. For quantities of DNA such as that from touch DNA, the use of PolyCyano UV to enhance fingermarks may impact subsequent DNA analysis by causing allele drop out at larger fragment sizes.
Kim, ASI & Wand, MP 2018, 'On expectation propagation for generalised, linear and mixed models', Australian & New Zealand Journal of Statistics, vol. 60, no. 1, pp. 75-102. View/Download from: Publisher's site View description>>
Kim, JS, Staicu, A-M, Maity, A, Carroll, RJ & Ruppert, D 2018, 'Additive Function-on-Function Regression', Journal of Computational and Graphical Statistics, vol. 27, no. 1, pp. 234-244. View/Download from: Publisher's site View description>>
We study additive function-on-function regression where the mean response at a particular time point depends on the time point itself, as well as the entire covariate trajectory. We develop a computationally efficient estimation methodology based on a novel combination of spline bases with an eigenbasis to represent the trivariate kernel function. We discuss prediction of a new response trajectory, propose an inference procedure that accounts for total variability in the predicted response curves, and construct pointwise prediction intervals. The estimation/inferential procedure accommodates realistic scenarios, such as correlated error structure as well as sparse and/or irregular designs. We investigate our methodology in finite sample size through simulations and two real data applications. Supplementary Material for this article is available online.
Kim, M, Brodersen, KE, Szabó, M, Larkum, AWD, Raven, JA, Ralph, PJ & Pernice, M 2018, 'Low oxygen affects photophysiology and the level of expression of two-carbon metabolism genes in the seagrass Zostera muelleri', Photosynthesis Research, vol. 136, no. 2, pp. 147-160. View/Download from: Publisher's site View description>>
Seagrasses are a diverse group of angiosperms that evolved to live in shallow coastal waters, an environment regularly subjected to changes in oxygen, carbon dioxide and irradiance. Zostera muelleri is the dominant species in south-eastern Australia, and is critical for healthy coastal ecosystems. Despite its ecological importance, little is known about the pathways of carbon fixation in Z. muelleri and their regulation in response to environmental changes. In this study, the response of Z. muelleri exposed to control and very low oxygen conditions was investigated by using (i) oxygen microsensors combined with a custom-made flow chamber to measure changes in photosynthesis and respiration, and (ii) reverse transcription quantitative real-time PCR to measure changes in expression levels of key genes involved in C4 metabolism. We found that very low levels of oxygen (i) altered the photophysiology of Z. muelleri, a characteristic of C3 mechanism of carbon assimilation, and (ii) decreased the expression levels of phosphoenolpyruvate carboxylase and carbonic anhydrase. These molecular-physiological results suggest that regulation of the photophysiology of Z. muelleri might involve a close integration between the C3 and C4, or other CO2 concentrating mechanisms metabolic pathways. Overall, this study highlights that the photophysiological response of Z. muelleri to changing oxygen in water is capable of rapid acclimation and the dynamic modulation of pathways should be considered when assessing seagrass primary production.
Kim, S, Fröch, JE, Christian, J, Straw, M, Bishop, J, Totonjian, D, Watanabe, K, Taniguchi, T, Toth, M & Aharonovich, I 2018, 'Photonic Crystal Cavities from Hexagonal Boron Nitride', Nature Communications, vol. 9, no. 1, pp. 2623-2623. View/Download from: Publisher's site View description>>
Development of scalable quantum photonic technologies requires on-chip
integration of components such as photonic crystal cavities and waveguides with
nonclassical light sources. Recently, hexagonal boron nitride (hBN) has emerged
as a promising platform for nanophotonics, following reports of hyperbolic
phonon-polaritons and optically stable, ultra-bright quantum emitters. However,
exploitation of hBN in scalable, on-chip nanophotonic circuits, quantum
information processing and cavity quantum electrodynamics (QED) experiments
requires robust techniques for the fabrication of monolithic optical
resonators. In this letter, we design and engineer high quality photonic
crystal cavities from hBN. We employ two approaches based on a focused ion beam
method and a minimally-invasive electron beam induced etching (EBIE) technique
to fabricate suspended two dimensional (2D) and one dimensional (1D) cavities
with quality (Q) factors in excess of 2,000. Subsequently, we show
deterministic, iterative tuning of individual cavities by direct-write,
single-step EBIE without significant degradation of the Q-factor. The
demonstration of tunable, high Q cavities made from hBN is an unprecedented
advance in nanophotonics based on van der Waals materials. Our results and hBN
processing methods open up promising new avenues for solid-state systems with
applications in integrated quantum photonics, polaritonics and cavity QED
experiments.
We propose and design photonic crystal cavities (PCCs) in hexagonal boron nitride (hBN) for diverse photonic and quantum applications. Two dimensional (2D) hBN flakes contain quantum emitters which are ultra-bright and photostable at room temperature. To achieve optimal coupling of these emitters to optical resonators, fabrication of cavities from hBN is therefore required to maximize the overlap between cavity optical modes and the emitters. Here, we design 2D and 1D PCCs using anisotropic indices of hBN. The influence of underlying substrates and material absorption are investigated, and spontaneous emission rate enhancements are calculated. Our results are promising for future quantum photonic experiments with hBN.
King, SR, Gentle, AR, Cortie, MB & McDonagh, AM 2018, 'On the Development of Optical Properties during Thermal Coarsening of Gold Nanoparticle Composites', The Journal of Physical Chemistry C, vol. 122, no. 22, pp. 12098-12105. View/Download from: Publisher's site View description>>
Klingberg, J, Shimmon, R, Philp, M, Tahtouh, M, Nic Daeid, N & Fu, S 2018, 'Evaluating the use of Differential Scanning Calorimetry for the analysis of illicit substances and their adulterants', Journal of Forensic Investigation, vol. 6, no. 1, pp. 8-8.
Knight, DA & Hansbro, PM 2018, 'Restricted access or access all areas? a new cadherin-like protein upregulated in the inflamed esophagus', Mucosal Immunology, vol. 11, no. 1, pp. 1-2. View/Download from: Publisher's site
Koolaji, N, Rawling, T, Bourget, K & Murray, M 2018, 'Carboxylate Analogues of Aryl-Urea-Substituted Fatty Acids That Target the Mitochondria in MDA-MB-231 Breast Cancer Cells to Promote Cell Death', ChemMedChem, vol. 13, no. 10, pp. 1036-1043. View/Download from: Publisher's site View description>>
Selective targeting of the tumor cell mitochondrion is a viable approach for the development of anticancer agents because the organelle is functionally different from the mitochondria of normal cells. We recently developed a novel aryl-urea fatty acid, 16({[4-chloro-3-(trifluoromethyl)phenyl]carbamoyl}amino)hexadecanoic acid (1) that was found to disrupt mitochondria and to activate apoptosis in MDA-MB-231 breast cancer cells. However, there is currently little information on the structural requirements for the activity of compound 1 analogues. The present study evaluated the role of the carboxylic acid group on the anticancer activity of 1. Bioisosteric replacement of the carboxylate in 1 maintained activity. Thus, like 1, the sulfonic acid analogue 1-SA and the oxo-thiadiazole analogue 1-OT were also found to target the mitochondrion and to activate cell killing capacity. The hydroxamic acid analogue 1-HA also killed MDA-MB-231 cells, but its onset of action was slower than that of 1-SA and 1-OT. In contrast, replacement of the carboxylate with non-bioisosteric amido and methylamido groups produced analogues that minimally altered mitochondrial function and showed little capacity to decrease tumor cell viability. These findings suggest that the carboxylate moiety in the novel mitochondrially targeted agent 1 is an important determinant of the kinetics and efficacy of anticancer cell activities of compound 1 analogues. Further development of carboxylate-modified analogues of aryl-urea fatty acids as potential anticancer agents could now be warranted.
Kordzakhia, NE, Kutoyants, YA, Novikov, AA & Hin, L-Y 2018, 'On limit distributions of estimators in irregular statistical models and a new representation of fractional Brownian motion', Statistics & Probability Letters, vol. 139, pp. 141-151. View/Download from: Publisher's site View description>>
Kota, A, Deshpande, DA, Haghi, M, Oliver, B & Sharma, P 2018, 'Autophagy and airway fibrosis: Is there a link?', F1000Research, vol. 6, pp. 409-409. View/Download from: Publisher's site View description>>
In the past decade, an emerging process named “autophagy” has generated intense interest in many chronic lung diseases. Tissue remodeling and fibrosis is a common feature of many airway diseases, and current therapies do not prevent or reverse these structural changes. Autophagy has evolved as a conserved process for bulk degradation and recycling of cytoplasmic components to maintain basal cellular homeostasis and healthy organelle populations in the cell. Furthermore, autophagy serves as a cell survival mechanism and can also be induced by chemical and physical stress to the cell. Accumulating evidence demonstrates that autophagy plays an essential role in vital cellular processes, including tissue remodeling. This review will discuss some of the recent advancements made in understanding the role of this fundamental process in airway fibrosis with emphasis on airway remodeling, and how autophagy can be exploited as a target for airway remodeling in asthma and chronic obstructive pulmonary disease.
Kramer, T, Noack, M, Reimers, JR, Reinefeld, A, Rodríguez, M & Yin, S 2018, 'Energy flow in the Photosystem I supercomplex: Comparison of approximative theories with DM-HEOM', Chemical Physics, vol. 515, pp. 262-271. View/Download from: Publisher's site View description>>
Krix, DW & Murray, BR 2018, 'Landscape variation in plant leaf flammability is driven by leaf traits responding to environmental gradients', Ecosphere, vol. 9, no. 2, pp. e02093-e02093. View/Download from: Publisher's site
Kroon, SJ, Ravel, J & Huston, WM 2018, 'Cervicovaginal microbiota, women's health, and reproductive outcomes', Fertility and Sterility, vol. 110, no. 3, pp. 327-336. View/Download from: Publisher's site View description>>
The human microbiome project has shown a remarkable diversity of microbial ecology within the human body. The vaginal microbiota is unique in that in many women it is most often dominated by Lactobacillus species. However, in some women it lacks Lactobacillus spp. and is comprised of a wide array of strict and facultative anaerobes, a state that broadly correlates with increased risk for infection, disease, and poor reproductive and obstetric outcomes. Interestingly, the level of protection against infection can also vary by species and strains of Lactobacillus, and some species although dominant are not always optimal. This factors into the risk of contracting sexually transmitted infections and possibly influences the occurrence of resultant adverse reproductive outcomes such as tubal factor infertility. The composition and function of the vaginal microbiota appear to play an important role in pregnancy and fertility treatment outcomes and future research in this field will shed further translational mechanistic understanding onto the interplay of the vaginal microbiota with women's health and reproduction.
Kumar, C, Verma, S, Singh, B, Haque, A, Satija, S & Vyas, M 2018, 'A review on conventional and modern techniques to develop Orodispersible films', Asian Journal of Pharmaceutics, vol. 12, pp. S433-S438. View description>>
Nowadays, solubility of active pharmaceutical ingredient (API) is one of the biggest challenges faced by the researchers during the development of pharmaceutical oral dosage form. Developing a new molecule is very expensive than formulating a dosage form of existing API. Orodispersible film (ODF) is one of the alternatives for the conventional dosage form as it dissolves and directly absorbed from the mouth. It is suitable for the delivery of poorly soluble drugs. It does not require water for the administration and gives quick absorption and high bioavailability. There are various techniques that can be used to improve the solubility of poorly soluble drugs in ODFs, namely, surfactants, superdisintegrants, and printing technology. Water-soluble polymers are used as the film former, but the different concentration and different combination of polymers and use of various additives like surfactant; superdisintegrants can show the significant effect on the solubility. It can be used for both local and systemic action. ODFs are gaining popularity and are widely accepted by the consumers, but it is still lacking in some areas due to the absence of pharmacopoeial specifications for disintegration, mechanical properties, etc.
Kumar, R, Arjuna, A, Diksha, Gupta, R, Mahajan, S, Satija, S & Mehta, M 2018, 'In vitro antioxidant and antimicrobial activity of polyherbal formulation', International Journal of Green Pharmacy, vol. 12, no. 2, pp. 80-84. View description>>
Context: Antioxidants play a major role in protecting the body against oxidative stress that is associated with many chronic diseases and disorders including chronic wounds. Plants are the richest source for antioxidant and are effective in the management of oxidative stress, caused by free radical damage. Wound healing and antimicrobial potential are also attributed to the antioxidant potential of drugs. Aim: The aim of this study is to carry out the antioxidant and antimicrobial activity of given polyherbal formulation (PHF) to correlate with the wound healing potential of the formulation. Materials and Methods: Antioxidant potential of the PHF was evaluated by the 2, 2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging method. Agar well diffusion method was used to determine its antimicrobial activity against the Escherichia coli, Pseudomonas aeruginosa, Proteus vulgaris, Klebsiella aerogenes. Results: Results of the study demonstrated that PHF exhibited significant antioxidant activity. Antibacterial activity of polyherbal formula was evaluated against the four pathogenic microorganisms in which it showed mild-to-moderate antimicrobial activity against the E. coli and K. aerogenes, while mild antimicrobial activity against the P. aeruginosa and P. vulgaris. Conclusion: Results of this study suggested that PHF can be used for the treatment of wound infections due to its marked antioxidant and antimicrobial activity.
Kumar, R, Kumar, R, Anand, A, Mahajan, R, Khatik, GL, Duggal, N, Mehta, M, Satija, S, Sharma, N & Khurana, N 2018, 'Potential of prediction of activity spectra of substances software to justify 3Rs ethics for in Vivo anti-Alzheimer’s studies of phytochemicals', International Journal of Green Pharmacy, vol. 12, no. 2, pp. 66-72. View description>>
Context: Alzheimer’s disease (AD) is a progressive neurodegenerative disorder having important concern in today’s society. The prediction of activity spectra of substances (PASS) software allows prediction of the pharmacological activity on behalf of canonical simplified molecular-input line-entry system (SMILES) of the substance. PASS predicted the activity of substances in two manners, i.e. probable activity (Pa) and probable inactivity. Objective: In this study, we elaborated the benefit of PASS to define 3Rs ethics (replacement, reduction, and refinement) in animal study for anti-Alzheimer’s activities of phytochemicals. Materials and Methods: Pa values of different phytochemicals important for AD predicted using PASS. For the prediction of activity in the different targets of AD, canonical SMILES of phytochemicals was obtained from PubChem website. Results and Discussion: Based on these Pa values predicted for different target sites of AD, screening of pharmacologically important phytochemicals was performed so that those phytochemicals can be further explored for in vivo pharmacological activity against AD to justify the 3Rs ethics. Conclusion: PASS online software provides an informative data to support the reported activities of the phytochemicals.
Kumari, N & Srivastava, A 2018, 'Harmonization and comparative evaluation of evapotranspiration estimates in data scarce conditions', Indian Journal of Ecology, vol. 45, no. 2, pp. 305-310. View description>>
For efficient irrigation water management and hydro-meteorological studies at both the field and catchment scales, a need exists to evaluate the existing évapotranspiration (ET) estimation methods under varied physiographical and data availability conditions. With the limited availability of meteorological variables at basin-scale in many remote areas, ET estimation is becoming a challenging task. There is a scope to test the ET methods by FAO-56 PM method, the benchmark method with Hargreaves raw model. All of them were inter-compared by taking its basin average. Further, FAO-56 PM and Hargreaves raw model were harmonized by daily and monthly correction factor (C, ) for five year period and was verified by using statistical indicators namely, index of agreement (d) and Pearson correlation coefficient (r) as well as graphical indicators. The harmonized estimators of less data intensive methods relative to FAO PM provides satisfactory results in all six stations after applying the correction factor.
Kuppusamy, R, Yasir, M, Berry, T, Cranfield, CG, Nizalapur, S, Yee, E, Kimyon, O, Taunk, A, Ho, KKK, Cornell, B, Manefield, M, Willcox, M, Black, DS & Kumar, N 2018, 'Design and synthesis of short amphiphilic cationic peptidomimetics based on biphenyl backbone as antibacterial agents', European Journal of Medicinal Chemistry, vol. 143, pp. 1702-1722. View/Download from: Publisher's site View description>>
Antimicrobial peptides (AMPs) and their synthetic mimics have received recent interest as new alternatives to traditional antibiotics in attempts to overcome the rise of antibiotic resistance in many microbes. AMPs are part of the natural defenses of most living organisms and they also have a unique mechanism of action against bacteria. Herein, a new series of short amphiphilic cationic peptidomimetics were synthesized by incorporating the 3'-amino-[1,1'-biphenyl]-3-carboxylic acid backbone to mimic the essential properties of natural AMPs. By altering hydrophobicity and charge, we identified the most potent analogue 25g that was active against both Gram-positive Staphylococcus aureus (MIC = 15.6 μM) and Gram-negative Escherichia coli (MIC = 7.8 μM) bacteria. Cytoplasmic permeability assay results revealed that 25g acts primarily by depolarization of lipids in cytoplasmic membranes. The active compounds were also investigated for their cytotoxicity to human cells, lysis of lipid bilayers using tethered bilayer lipid membranes (tBLMs) and their activity against established biofilms of S. aureus and E. coli.
Kuriakose, S, Ahmed, T, Balendhran, S, Collis, GE, Bansal, V, Aharonovich, I, Sriram, S, Bhaskaran, M & Walia, S 2018, 'Effects of plasma-treatment on the electrical and optoelectronic properties of layered black phosphorus', Applied Materials Today, vol. 12, pp. 244-249. View/Download from: Publisher's site View description>>
Kusrini, E, Hashim, F, Gunawan, C, Mann, R, Azmi, WNNWN & Amin, NM 2018, 'Anti-amoebic activity of acyclic and cyclic-samarium complexes on Acanthamoeba', Parasitology Research, vol. 117, no. 5, pp. 1409-1417. View/Download from: Publisher's site View description>>
This work investigated the anti-amoebic activity of two samarium (Sm) complexes, the acyclic complex [bis(picrato)(pentaethylene glycol)samarium(III)] picrate-referred to as [Sm(Pic)2(EO5)](Pic)-and the cyclic complex [bis(picrato)(18-crown-6)samarium(III)] picrate-referred to as [Sm(Pic)2(18C6)](Pic). Both Sm complexes caused morphological transformation of the protozoa Acanthamoeba from its native trophozoite form carrying a spine-like structure called acanthopodia, to round-shaped cells with loss of the acanthopodia structure, a trademark response to environmental stress. Further investigation, however, revealed that the two forms of the Sm complexes exerted unique cytotoxicity characteristics. Firstly, the IC50 of the acyclic complex (0.7 μg/mL) was ~ 10-fold lower than IC50 of the cyclic Sm complex (6.5 μg/mL). Secondly, treatment of the Acanthamoeba with the acyclic complex caused apoptosis of the treated cells, while the treatment with the cyclic complex caused necrosis evident by the leakage of the cell membrane. Both treatments induced DNA damage in Acanthamoeba. Finally, a molecular docking simulation revealed the potential capability of the acyclic complex to form hydrogen bonds with profilin-a membrane protein present in eukaryotes, including Acanthamoeba, that plays important roles in the formation and degradation of actin cytoskeleton. Not found for the cyclic complex, such potential interactions could be the underlying reason, at least in part, for the much higher cytotoxicity of the acyclic complex and also possibly, for the observed differences in the cytotoxicity traits. Nonetheless, with IC50 values of < 10 μg/mL, both the acyclic and cyclic Sm complexes feature a promising potential as cytotoxic agents to fight amoebic infections.
Kusrini, E, Wicaksono, B, Yulizar, Y, Prasetyanto, EA & Gunawan, C 2018, 'Textile Dye Removal from Aqueous Solution using Modified Graphite Waste/Lanthanum/Chitosan Composite', IOP Conference Series: Materials Science and Engineering, vol. 316, no. 1, pp. 012029-012029. View/Download from: Publisher's site View description>>
Kusrini, E, Wicaksono, W, Gunawan, C, Daud, NZA & Usman, A 2018, 'Kinetics, mechanism, and thermodynamics of lanthanum adsorption on pectin extracted from durian rind', Journal of Environmental Chemical Engineering, vol. 6, no. 5, pp. 6580-6588. View/Download from: Publisher's site View description>>
The rare-earth elements in aqueous waste streams have received great attention due to their potential to pollute the environment. Lanthanum is one of the most used rare-earth elements in industries and disposed as waste. Several efforts have been devoted to remove lanthanum from waste water systems. This study was focused on the adsorption of lanthanum from aqueous solutions by using pectin extracted from durian rind, which is home and industrial waste of durian fruit. Adsorption experiments were carried out in batch method, and the effects of contact time, initial concentration of lanthanum ion, pH of medium, pectin dosage, and temperature on the adsorption efficiency were investigated. The kinetics, mechanism, and thermodynamics of lanthanum adsorption on the pectin were also evaluated. The results demonstrated that the pectin as a cost-effective biosorbent could remove lanthanum with efficiency as high as 41.2 mg/g (at the optimum conditions: pH 4.0, 25 °C, 90 min). The adsorption process of lanthanum on the pectin is well described by either Freundlich or Temkin isotherm model, indicating that adsorption occurs mainly on multilayers and heterogeneous surfaces of pectin. Thermodynamic quantities suggested that the adsorption of lanthanum on the pectin was exothermic and spontaneous, and the reaction was feasible. We also showed that the spent adsorbent can be regenerated up to a limited number of times, upon strong base treatment.
Laiolo, L, Matear, R, Baird, ME, Soja-Woźniak, M & Doblin, MA 2018, 'Information content of in situ and remotely sensed chlorophyll-a: Learning from size-structured phytoplankton model', Journal of Marine Systems, vol. 183, pp. 1-12. View/Download from: Publisher's site View description>>
Lan, C, Peng, H, McGowan, EM, Hutvagner, G & Li, J 2018, 'An isomiR expression panel based novel breast cancer classification approach using improved mutual information', BMC Medical Genomics, vol. 11, no. S6, pp. 118-118. View/Download from: Publisher's site View description>>
BACKGROUND:Gene expression-based profiling has been used to identify biomarkers for different breast cancer subtypes. However, this technique has many limitations. IsomiRs are isoforms of miRNAs that have critical roles in many biological processes and have been successfully used to distinguish various cancer types. Biomarker isomiRs for identifying different breast cancer subtypes has not been investigated. For the first time, we aim to show that isomiRs are better performing biomarkers and use them to explain molecular differences between breast cancer subtypes. RESULTS:In this study, a novel method is proposed to identify specific isomiRs that faithfully classify breast cancer subtypes. First, as a null hypothesis method we removed the lowly expressed isomiRs from small sequencing data generated from diverse breast cancers types. Second, we developed an improved mutual information-based feature selection method to calculate the weight of each isomiR expression. The weight of isomiR measures the importance of a given isomiR in classifying breast cancer subtypes. The improved mutual information enables to apply the dataset in which the feature is continuous data and label is discrete data; whereby, the traditional mutual information cannot be applied in this dataset. Finally, the support vector machine (SVM) classifier is applied to find isomiR biomarkers for subtyping. CONCLUSIONS:Here we demonstrate that isomiRs can be used as biomarkers in the identification of different breast cancer subtypes, and in addition, they may provide new insights into the diverse molecular mechanisms of breast cancers. We have also shown that the classification of different subtypes of breast cancer based on isomiRs expression is more effective than using published gene expression profiling. The proposed method provides a better performance outcome than Fisher method and Hellinger method for discovering biomarkers to distinguish different breast cancer subtypes. This novel techniqu...
Larkin, BP, Glastras, SJ, Chen, H, Pollock, CA & Saad, S 2018, 'DNA methylation and the potential role of demethylating agents in prevention of progressive chronic kidney disease', The FASEB Journal, vol. 32, no. 10, pp. 5215-5226. View/Download from: Publisher's site View description>>
Chronic kidney disease (CKD) is a global epidemic, and its major risk factors include obesity and type 2 diabetes. Obesity not only promotes metabolic dysregulation and the development of diabetic kidney disease but also may independently lead to CKD by a variety of mechanisms, including endocrine and metabolic dysfunction, inflammation, oxidative stress, altered renal hemodynamics, and lipotoxicity. Deleterious renal effects of obesity can also be transmitted from one generation to the next, and it is increasingly recognized that offspring of obese mothers are predisposed to CKD. Epigenetic modifications are changes that regulate gene expression without altering the DNA sequence. Of these, DNA methylation is the most studied. Epigenetic imprints, particularly DNA methylation, are laid down during critical periods of fetal development, and they may provide a mechanism by which maternal-fetal transmission of chronic disease occurs. Our current review explores the evidence for the role of DNA methylation in the development of CKD, diabetic kidney disease, diabetes, and obesity. DNA methylation has been implicated in renal fibrosis-the final pathophysiologic pathway in the development of end-stage kidney disease-which supports the notion that demethylating agents may play a potential therapeutic role in preventing development and progression of CKD.-Larkin, B. P., Glastras, S. J., Chen, H., Pollock, C. A., Saad, S. DNA methylation and the potential role of demethylating agents in prevention of progressive chronic kidney disease.
Larkum, AWD, Ritchie, RJ & Raven, JA 2018, 'Living off the Sun: chlorophylls, bacteriochlorophylls and rhodopsins', Photosynthetica, vol. 56, no. SPECIAL ISSUE, pp. 11-43. View/Download from: Publisher's site
Larsson, M, Laczka, O, Harwood, D, Lewis, R, Himaya, S, Murray, S & Doblin, M 2018, 'Toxicology of Gambierdiscus spp. (Dinophyceae) from Tropical and Temperate Australian Waters', Marine Drugs, vol. 16, no. 1, pp. 7-7. View/Download from: Publisher's site View description>>
Ciguatera Fish Poisoning (CFP) is a human illness caused by the consumption of marine fish contaminated with ciguatoxins (CTX) and possibly maitotoxins (MTX), produced by species from the benthic dinoflagellate genus Gambierdiscus. Here, we describe the identity and toxicology of Gambierdiscus spp. isolated from the tropical and temperate waters of eastern Australia. Based on newly cultured strains, we found that four Gambierdiscus species were present at the tropical location, including G. carpenteri, G. lapillus and two others which were not genetically identical to other currently described species within the genus, and may represent new species. Only G. carpenteri was identified from the temperate location. Using LC-MS/MS analysis we did not find any characterized microalgal CTXs (P-CTX-3B, P-CTX-3C, P-CTX-4A and P-CTX-4B) or MTX-1; however, putative maitotoxin-3 (MTX-3) was detected in all species except for the temperate population of G. carpenteri. Using the Ca2+ influx SH-SY5Y cell Fluorescent Imaging Plate Reader (FLIPR) bioassay we found CTX-like activity in extracts of the unidentified Gambierdiscus strains and trace level activity in strains of G. lapillus. While no detectable CTX-like activity was observed in tropical or temperate strains of G. carpenteri, all species showed strong maitotoxin-like activity. This study, which represents the most comprehensive analyses of the toxicology of Gambierdiscus strains isolated from Australia to date, suggests that CFP in this region may be caused by currently undescribed ciguatoxins and maitotoxins.
Larsson, ME, Laczka, OF, Suthers, IM, Ajani, PA & Doblin, MA 2018, 'Hitchhiking in the East Australian Current: rafting as a dispersal mechanism for harmful epibenthic dinoflagellates', Marine Ecology Progress Series, vol. 596, pp. 49-60. View/Download from: Publisher's site
SummaryDinoflagellates of the genus Symbiodinium underpin the survival and ecological success of corals. The use of cultured strains has been particularly important to disentangle the complex life history of Symbiodinium and their contribution to coral host physiology. However, these cultures typically harbour abundant bacterial communities which likely play important, but currently unknown, roles in Symbiodinium biology. We characterized the bacterial communities living in association with a wide phylogenetic diversity of Symbiodinium cultures (18 types spanning 5 clades) to define the core Symbiodinium microbiome. Similar to other systems, bacteria were nearly two orders of magnitude more numerically abundant than Symbiodinium cells and we identified three operational taxonomic units (OTUs) which were present in all cultures. These represented the α‐proteobacterium Labrenzia and the γ‐proteobacteria Marinobacter and Chromatiaceae. Based on the abundance and functional potential of bacteria harboured in these cultures, their contribution to Symbiodinium physiology can no longer be ignored.
Lebender, LF, Prünte, L, Rumzhum, NN & Ammit, AJ 2018, 'Selectively targeting prostanoid E (EP) receptor-mediated cell signalling pathways: Implications for lung health and disease', Pulmonary Pharmacology & Therapeutics, vol. 49, pp. 75-87. View/Download from: Publisher's site View description>>
Arachidonic acid is metabolized by cyclooxygenases (COX-1 and COX-2) into various prostanoids which exert different functions in mammalian physiology. One of these prostanoids, prostaglandin E2 (PGE2), interacts with four different G protein-coupled receptors, named EP1, EP2, EP3 and EP4, to initiate different downstream signalling pathways. Prostanoid receptors are diversely expressed throughout different tissues all over the body and PGE2 is responsible for a large variety of beneficial and disadvantageous effects. We have recently achieved a greater understanding of the biology of prostanoid E receptors and the potential for specific drug targeting with the advent of potent and selective EP receptor agonists and antagonists. This has important implications for lung health and disease as PGE2-mediated EP receptor activation impacts upon migration of airway smooth muscle cells, airway microvascular leak, tone regulation of pulmonary blood vessels, mast cell degranulation, bronchodilatation, cough, angiogenesis and airway inflammation, to name a few. In this review, we overview the EP receptor family and the related signalling pathways, summarize a variety of EP1-4 receptor agonists and antagonists, provide an overview of pharmacological tools used to implicate EP receptor function in the context of respiratory health and disease and finally highlight some of the more selective pharmacological reagents that have recently been developed. The availability of selective pharmacological agonists and antagonists for the distinct EP receptors, as well as the development of specific prostanoid receptor knock-out mice, offer hitherto unattainable opportunities for achieving an in depth understanding of the role and function of PGE2 in respiratory disease and the exciting potential of targeting EP receptors more broadly.
Leclaire, NA, Li, M, Véron, AC, Neels, A, Heier, J, Reimers, JR & Nüesch, FA 2018, 'Cyanine platelet single crystals: growth, crystal structure and optical spectra', Physical Chemistry Chemical Physics, vol. 20, no. 46, pp. 29166-29173. View/Download from: Publisher's site View description>>
Micro transmittance spectroscopy of ultrathin crystalline organic salt semiconductors reveals strong low-energy and weak high-energy bands polarized along the crystallographic b- and c-axis. While the excitonic coupling pattern explains the occurrence of polarized bands, the observed intensities are opposite of expectations based on chromophore alignment within the crystal.
Lee, AS, White, E, Monahan, LG, Jensen, SO, Chan, R & van Hal, SJ 2018, 'Defining the Role of the Environment in the Emergence and Persistence of vanA Vancomycin-Resistant Enterococcus (VRE) in an Intensive Care Unit: A Molecular Epidemiological Study', Infection Control & Hospital Epidemiology, vol. 39, no. 6, pp. 668-675. View/Download from: Publisher's site View description>>
OBJECTIVETo describe the transmission dynamics of the emergence and persistence of vanA vancomycin-resistant enterococcus (VRE) in an intensive care unit (ICU) using whole-genome sequencing of patient and environmental isolates.DESIGNRetrospective cohort study.SETTINGICU in a tertiary referral center.PARTICIPANTSPatients admitted to the ICU over an 11-month period.METHODSVanA VRE isolated from patients (n=31) were sequenced using the Illumina MiSeq platform. Environmental samples from bed spaces, equipment, and waste rooms were collected. All vanA VRE-positive environmental samples (n=14) were also sequenced. Data were collected regarding patient ward and bed movements.RESULTSThe 31 patient vanA VRE isolates were from screening (n=19), urine (n=4), bloodstream (n=3), skin/wound (n=3), and intra-abdominal (n=2) sources. The phylogeny from sequencing data confirmed several VRE clusters, with 1 group accounting for 38 of 45 isolates (84%). Within this cluster, cross-transmission was extensive and complex across the ICU. Directionality indicated that colonized patients contaminated environmental sites. Similarly, environmental sources not only led to patient colonization but also to infection. Notably, shared equipment acted as a con...
Lees, T, Shad-Kaneez, F, Simpson, AM, Nassif, NT, Lin, Y & Lal, S 2018, 'Heart Rate Variability as a Biomarker for Predicting Stroke, Post-stroke Complications and Functionality', Biomarker Insights, vol. 13, pp. 117727191878693-117727191878693. View/Download from: Publisher's site View description>>
Background: Heart rate variability (HRV) is a non-invasive measure of the function of the autonomic nervous system, and its dynamic nature may provide a means through which stroke and its associated complications may be predicted, monitored, and managed. Objective: The objective of this review is to identify and provide a critique on the most recent uses of HRV in stroke diagnosis/management and highlight areas that warrant further research. Methods: The MEDLINE, CINAHL, and OVID MEDLINE databases were canvassed using a systematic search strategy, for articles investigating the use of HRV in stroke diagnosis and management. Initial paper selections were based on title alone, and final paper inclusion was informed by a full-text critical appraisal. Results: The systematic search returned 98 records, of which 51 were unique. Following screening, 22 records were included in the final systematic review. The included papers provided some information regarding predicting incident stroke, which largely seems to be best predicted by time- and frequency-domain HRV parameters. Furthermore, post-stroke complications and functionality are similarly predicted by time- and frequency-domain parameters, as well as non-linear parameters in some instances. Conclusions: Current research provides good evidence that HRV parameters may have utility as a biomarker for stroke and for post-stroke complications and/or functionality. Future research would benefit from the integration of non-linear, and novel parameters, the hybridisation of HRV parameters, and the expansion of the utilisation of predictive regression and hazard modelling.
Lenzini, F, Poddubny, AN, Titchener, J, Fisher, P, Boes, A, Kasture, S, Haylock, B, Villa, M, Mitchell, A, Solntsev, AS, Sukhorukov, AA & Lobino, M 2018, 'Direct characterization of a nonlinear photonic circuit’s wave function with laser light', Light: Science & Applications, vol. 7, no. 1, pp. 17143-17143. View/Download from: Publisher's site View description>>
AbstractIntegrated photonics is a leading platform for quantum technologies including nonclassical state generation1, 2, 3, 4, demonstration of quantum computational complexity5 and secure quantum communications6. As photonic circuits grow in complexity, full quantum tomography becomes impractical, and therefore an efficient method for their characterization7, 8 is essential. Here we propose and demonstrate a fast, reliable method for reconstructing the two-photon state produced by an arbitrary quadratically nonlinear optical circuit. By establishing a rigorous correspondence between the generated quantum state and classical sum-frequency generation measurements from laser light, we overcome the limitations of previous approaches for lossy multi-mode devices9, 10. We applied this protocol to a multi-channel nonlinear waveguide network and measured a 99.28±0.31% fidelity between classical and quantum characterization. This technique enables fast and precise evaluation of nonlinear quantum photonic networks, a crucial step towards complex, large-scale, device production.
Li, C, Zang, R, Li, P, Man, Z, Wang, S, Li, X, Wu, Y, Liu, S & Wang, G 2018, 'High Crystalline Prussian White Nanocubes as a Promising Cathode for Sodium‐ion Batteries', Chemistry – An Asian Journal, vol. 13, no. 3, pp. 342-349. View/Download from: Publisher's site View description>>
Prussian blue and its analogues (PBAs) have been recognized as one of the most promising cathode materials for room-temperature sodium-ion batteries (SIBs). Herein, we report high crystalline and Na-rich Prussian white Na2 CoFe(CN)6 nanocubes synthesized by an optimized and facile co-precipitation method. The influence of crystallinity and sodium content on the electrochemical properties was systematically investigated. The optimized Na2 CoFe(CN)6 nanocubes exhibited an initial capacity of 151 mA h g-1 , which is close to its theoretical capacity (170 mA h g-1 ). Meanwhile, the Na2 CoFe(CN)6 cathode demonstrated an outstanding long-term cycle performance, retaining 78 % of its initial capacity after 500 cycles. Furthermore, the Na2 CoFe(CN)6 Prussian white nanocubes also achieved a superior rate capability (115 mA h g-1 at 400 mA g-1 , 92 mA h g-1 at 800 mA g-1 ). The enhanced performances could be attributed to the robust crystal structure and rapid transport of Na ions through large channels in the open-framework. Most noteworthy, the as-prepared Na2 CoFe(CN)6 nanocubes are not only low-cost in raw materials but also contain a rich sodium content (1.87 Na ions per lattice unit cell), which will be favorable for full cell fabrication and large-scale electric storage applications.
Li, D, Wen, S, Sun, W, Zhang, J, Jin, D, Peng, C, Shen, M & Shi, X 2018, 'One-Step Loading of Gold and Gd2O3 Nanoparticles within PEGylated Polyethylenimine for Dual Mode Computed Tomography/Magnetic Resonance Imaging of Tumors', ACS Applied Bio Materials, vol. 1, no. 2, pp. 221-225. View/Download from: Publisher's site View description>>
We report here a facile method for one-step loading of gold (Au) and gadolinium oxide (Gd2O3) nanoparticles (NPs) within polyethylenimine (PEI) premodified with polyethtylene glycol (PEG) for dual mode computed tomography (CT) and magnetic resonance (MR) imaging of tumors. PEGylated PEI was used as a template to complex Au(III) and Gd(III) salts, followed by sodium borohydride reduction and acetylation of remaining PEI surface amines to generate the hybrid PEI@Au/Gd2O3 NPs. The hybrid NPs exhibit a remarkable colloidal stability and cytocompatibility and possess a high X-ray attenuation efficacy and r1 relaxivity, enabling their uses for dual mode CT/MR imaging of tumors.
Li, G, Saad, S, Oliver, B & Chen, H 2018, 'Heat or Burn? Impacts of Intrauterine Tobacco Smoke and E-Cigarette Vapor Exposure on the Offspring’s Health Outcome', Toxics, vol. 6, no. 3, pp. 43-43. View/Download from: Publisher's site View description>>
Maternal smoking during pregnancy leads to gestational complications and organ disorders in the offspring. As nicotine replacement therapy is often ineffective for smoking cessation, pregnant women turn to alternatives such as heat-not-burn tobacco and e-cigarettes. Recently, the popularly of e-cigarettes has been increasing especially among the youth and pregnant women, mainly due to the advertisements claiming their safety. This has even led to some clinicians recommending their use during pregnancy. E-cigarettes heat e-liquid to produce an aerosol (e-vapor), delivering flavorings and nicotine to the user. However, e-vapor also contains toxins such as formaldehyde along with heavy metals and carcinogenic nitrosamines. In addition, specific flavoring compounds such as diacetyl can be toxic themselves or decompose into toxic compounds such as benzaldehydes. These compounds can induce toxicity, inflammation and oxidative stress in the mothers and can accumulate in the developing fetus, affecting intrauterine development. Recent animal studies suggest that maternal e-vapor exposure during pregnancy could cause respiratory and neurological disorders in the offspring. This review will examine the available literature to shed light on the current understanding of this problem-to-be from lessons learned in animal models.
Li, H, Staudenmayer, J, Wang, T, Keadle, SK & Carroll, RJ 2018, 'Three‐part joint modeling methods for complex functional data mixed with zero‐and‐one–inflated proportions and zero‐inflated continuous outcomes with skewness', Statistics in Medicine, vol. 37, no. 4, pp. 611-626. View/Download from: Publisher's site View description>>
We take a functional data approach to longitudinal studies with complex bivariate outcomes. This work is motivated by data from a physical activity study that measured 2 responses over time in 5‐minute intervals. One response is the proportion of time active in each interval, a continuous proportions with excess zeros and ones. The other response, energy expenditure rate in the interval, is a continuous variable with excess zeros and skewness. This outcome is complex because there are 3 possible activity patterns in each interval (inactive, partially active, and completely active), and those patterns, which are observed, induce both nonrandom and random associations between the responses. More specifically, the inactive pattern requires a zero value in both the proportion for active behavior and the energy expenditure rate; a partially active pattern means that the proportion of activity is strictly between zero and one and that the energy expenditure rate is greater than zero and likely to be moderate, and the completely active pattern means that the proportion of activity is exactly one, and the energy expenditure rate is greater than zero and likely to be higher. To address these challenges, we propose a 3‐part functional data joint modeling approach. The first part is a continuation‐ratio model to reorder the ordinal valued 3 activity patterns. The second part models the proportions when they are in interval (0,1). The last component specifies the skewed continuous energy expenditure rate with Box‐Cox transformations when they are greater than zero. In this 3‐part model, the regression structures are specified as smooth curves measured at various time points with random effects that have a correlation structure. The smoothed random curves for each variable are summarized using a few important principal components, and the association of the 3 longitudinal components is modeled through the association of the principal component scores. The difficulties...
Li, L, Wang, Y, Arora, VK, Eamus, D, Shi, H, Li, J, Cheng, L, Cleverly, J, Hajima, T, Ji, D, Jones, C, Kawamiya, M, Li, W, Tjiputra, J, Wiltshire, A, Zhang, L & Yu, Q 2018, 'Evaluating Global Land Surface Models in CMIP5: Analysis of Ecosystem Water- and Light-Use Efficiencies and Rainfall Partitioning', Journal of Climate, vol. 31, no. 8, pp. 2995-3008. View/Download from: Publisher's site View description>>
AbstractWater and carbon fluxes simulated by 12 Earth system models (ESMs) that participated in phase 5 of the Coupled Model Intercomparison Project (CMIP5) over several recent decades were evaluated using three functional constraints that are derived from both model simulations, or four global datasets, and 736 site-year measurements. Three functional constraints are ecosystem water-use efficiency (WUE), light-use efficiency (LUE), and the partitioning of precipitation P into evapotranspiration (ET) and runoff based on the Budyko framework. Although values of these three constraints varied significantly with time scale and should be quite conservative if being averaged over multiple decades, the results showed that both WUE and LUE simulated by the ensemble mean of 12 ESMs were generally lower than the site measurements. Simulations by the ESMs were generally consistent with the broad pattern of energy-controlled ET under wet conditions and soil water-controlled ET under dry conditions, as described by the Budyko framework. However, the value of the parameter in the Budyko framework ω, obtained from fitting the Budyko curve to the ensemble model simulation (1.74), was larger than the best-fit value of ω to the observed data (1.28). Globally, the ensemble mean of multiple models, although performing better than any individual model simulations, still underestimated the observed WUE and LUE, and overestimated the ratio of ET to P, as a result of overestimation in ET and underestimation in gross primary production (GPP). The results suggest that future model development should focus on improving the algorithms of the partitioning of precipitation into ecosystem ET and runoff, and the coupling of water and carbon cycles for different land-use types.
Li, M, Cortie, DL, Liu, J, Yu, D, Islam, SMKN, Zhao, L, Mitchell, DRG, Mole, RA, Cortie, MB, Dou, S & Wang, X 2018, 'Ultra-high thermoelectric performance in graphene incorporated Cu2Se: Role of mismatching phonon modes', Nano Energy, vol. 53, pp. 993-1002. View/Download from: Publisher's site
Li, M, Reimers, JR, Dobson, JF & Gould, T 2018, 'Faraday cage screening reveals intrinsic aspects of the van der Waals attraction', Proceedings of the National Academy of Sciences, vol. 115, no. 44, pp. E10295-E10302. View/Download from: Publisher's site View description>>
Significance
How the van der Waals dispersion interaction relates to chemical electron-correlation effects presents a critical challenge to density functional theory development. Here, recently observed screening of the dispersion force between two insulating objects caused by the insertion of an intermediary graphene layer is explained in terms of Dobson’s general description of dispersion. This then provides a much-needed handle concerning how density functional approaches relate such long-range dispersion interactions to the subtleties of covalent bonding. Screening at intermediate distances appears to change the London expression from
r−6
to
r−7
, an effect that becomes antiscreening (dispersion enhancement) at distances shorter than van der Waals contact. This provides basic insight into modern revelations that dispersion forces can outcompete covalent forces to control chemical structure.
Li, Y, Shi, H, Zhou, L, Eamus, D, Huete, A, Li, L, Cleverly, J, Hu, Z, Harahap, M, Yu, Q, He, L & Wang, S 2018, 'Disentangling Climate and LAI Effects on Seasonal Variability in Water Use Efficiency Across Terrestrial Ecosystems in China', Journal of Geophysical Research: Biogeosciences, vol. 123, no. 8, pp. 2429-2443. View/Download from: Publisher's site View description>>
Li, Z, Liu, X, Causer, GL, Lin, K-W, Pong, P, Holt, SA, Klose, F & Li, YY 2018, 'Structural evolution of a Ni/NiOx based supercapacitor in cyclic charging-discharging: A polarized neutron and X-ray reflectometry study', Electrochimica Acta, vol. 290, pp. 118-127. View/Download from: Publisher's site
Liana, AE, Marquis, CP, Gunawan, C, Justin Gooding, J & Amal, R 2018, 'Antimicrobial activity of T4 bacteriophage conjugated indium tin oxide surfaces', Journal of Colloid and Interface Science, vol. 514, pp. 227-233. View/Download from: Publisher's site View description>>
We report the antimicrobial activity of bare and surface functionalized indium tin oxide (ITO) conjugated with T4 bacteriophage towards E. coli. A ∼ 103-fold reduction (99.9%) in the bacterial concentration was achieved within 2 h exposure of E. coli to the bare as well as the amine, carboxylic and methyl functionalized ITO/T4 surfaces. Despite the known differences in bacteriophage loading of these ITO/T4 systems, the almost identical extent of antimicrobial activity of all of the ITO/T4 systems resulted from the release of a comparable amount of infective T4 from the systems. As anticipated, a single dose of immobilized bacteriophage was sufficient to eliminate further surge of bacterial population. Upon the 2 h eradication of the '1st batch' of E. coli population, all of the ITO/T4 systems, each system with 102-fold more suspended bacteriophage (due to propagation of the phage at the expense of the '1st batch' E. coli death), reduced the '2nd batch' of E. coli concentration by ∼104-fold in just 30 min, suggesting the potential of immobilized bacteriophage systems as solution to the issues of antimicrobial agent depletion. All of the ITO/T4 systems maintained their antimicrobial activity in the presence of model food components. The antimicrobial activity was however, affected by pH; at pH 5 whereby the bacteria's growth was physiologically inhibited, generally no reduction in E. coli concentration was detected. The present work provides an understanding of the mode of antimicrobial activity exhibited by an immobilized bacteriophage based substrate and demonstrates efficacy in the presence of food components.
Liang, L, Carroll, R & Ma, Y 2018, 'Dimension reduction and estimation in the secondary analysis of case-control studies', Electronic Journal of Statistics, vol. 12, no. 1, pp. 1782-1821. View/Download from: Publisher's site View description>>
Liang, L, Ma, Y, Wei, Y & Carroll, RJ 2018, 'Semiparametrically Efficient Estimation in Quantile Regression of Secondary Analysis', Journal of the Royal Statistical Society Series B: Statistical Methodology, vol. 80, no. 4, pp. 625-648. View/Download from: Publisher's site View description>>
SummaryAnalysing secondary outcomes is a common practice for case–control studies. Traditional secondary analysis employs either completely parametric models or conditional mean regression models to link the secondary outcome to covariates. In many situations, quantile regression models complement mean-based analyses and provide alternative new insights on the associations of interest. For example, biomedical outcomes are often highly asymmetric, and median regression is more useful in describing the ‘central’ behaviour than mean regressions. There are also cases where the research interest is to study the high or low quantiles of a population, as they are more likely to be at risk. We approach the secondary quantile regression problem from a semiparametric perspective, allowing the covariate distribution to be completely unspecified. We derive a class of consistent semiparametric estimators and identify the efficient member. The asymptotic properties of the resulting estimators are established. Simulation results and a real data analysis are provided to demonstrate the superior performance of our approach with a comparison with the only existing approach so far in the literature.
Liao, Y, Ithurbide, S, de Silva, RT, Erdmann, S & Duggin, IG 2018, 'Archaeal cell biology: diverse functions of tubulin-like cytoskeletal proteins at the cell envelope', Emerging Topics in Life Sciences, vol. 2, no. 4, pp. 547-559. View/Download from: Publisher's site View description>>
The tubulin superfamily of cytoskeletal proteins is widespread in all three domains of life — Archaea, Bacteria and Eukarya. Tubulins build the microtubules of the eukaryotic cytoskeleton, whereas members of the homologous FtsZ family construct the division ring in prokaryotes and some eukaryotic organelles. Their functions are relatively poorly understood in archaea, yet these microbes contain a remarkable diversity of tubulin superfamily proteins, including FtsZ for division, a newly described major family called CetZ that is involved in archaeal cell shape control, and several other divergent families of unclear function that are implicated in a variety of cell envelope-remodelling contexts. Archaeal model organisms, particularly halophilic archaea such as Haloferax volcanii, have sufficiently developed genetic tools and we show why their large, flattened cells that are capable of controlled differentiation are also well suited to cell biological investigations by live-cell high-resolution light and electron microscopy. As most archaea only have a glycoprotein lattice S-layer, rather than a peptidoglycan cell wall like bacteria, the activity of the tubulin-like cytoskeletal proteins at the cell envelope is expected to vary significantly, and may involve direct membrane remodelling or directed synthesis or insertion of the S-layer protein subunits. Further studies of archaeal cell biology will provide fresh insight into the evolution of cells and the principles in common to their fundamental activities across the full spectrum of cellular life.
Lin, G & Jin, D 2018, 'Taking upconversion to lase in microcavity', Nature Nanotechnology, vol. 13, no. 7, pp. 534-536. View/Download from: Publisher's site
Lin, G, Baker, MAB, Hong, M & Jin, D 2018, 'The Quest for Optical Multiplexing in Bio-discoveries', Chem, vol. 4, no. 5, pp. 997-1021. View/Download from: Publisher's site
Lin, S, Li, J, Liu, Q, Huete, A & Li, L 2018, 'Effects of Forest Canopy Vertical Stratification on the Estimation of Gross Primary Production by Remote Sensing', Remote Sensing, vol. 10, no. 9, pp. 1329-1329. View/Download from: Publisher's site View description>>
Gross primary production (GPP) in forests is the most important carbon flux in terrestrial ecosystems. Forest ecosystems with high leaf area index (LAI) values have diverse species or complex forest structures with vertical stratifications that influence the carbon–water–energy cycles. In this study, we used three light use efficiency (LUE) GPP models and site-level experiment data to analyze the effects of the vertical stratification of dense forest vegetation on the estimates of remotely sensed GPP during the growing season of two forest sites in East Asia: Dinghushan (DHS) and Tomakomai (TMK). The results showed that different controlling environmental factors of the vertical layers, such as temperature and vapor pressure deficit (VPD), produce different responses for the same LUE value in the different sub-ecosystems (defined as the tree, shrub, and grass layers), which influences the GPP estimation. Air temperature and VPD play important roles in the effects of vertical stratification on the GPP estimates in dense forests, which led to differences in GPP uncertainties from −50% to 30% because of the distinct temperature responses in TMK. The unequal vertical LAI distributions in the different sub-ecosystems led to GPP variations of 1–2 gC/m2/day with uncertainties of approximately −30% to 20% because sub-ecosystems have unique absorbed fractions of photosynthetically active radiation (APAR) and LUE. A comparison with the flux tower-based GPP data indicated that the GPP estimations from the LUE and APAR values from separate vertical layers exhibited better model performance than those calculated using the single-layer method, with 10% less bias in DHS and more than 70% less bias in TMK. The precision of the estimated GPP in regions with thick understory vegetation could be effectively improved by considering the vertical variations in environmental parameters and the LAI values of different sub-ecosystems as separate factors when calculating the GPP o...
Litaker, RW, Fraga, S, Montresor, M, Brosnahan, M, Anderson, D, Hoppenrath, M, Murray, S, Wolny, J, John, U, Sampedro, N, Larsen, J & Calado, A 2018, 'A practical guide to the new nomenclature for species within the 'Alexandrium tamarense' species complex', Harmful algae news / Unesco; IOC; Intergovernmental Oceanographic Commission, vol. 61, pp. 13-15.
Liu, C, Liew, CW, Wong, YH, Tan, ST, Poh, WH, Manimekalai, MSS, Rajan, S, Xin, L, Liang, Z-X, Grüber, G, Rice, SA & Lescar, J 2018, 'Insights into Biofilm Dispersal Regulation from the Crystal Structure of the PAS-GGDEF-EAL Region of RbdA from Pseudomonas aeruginosa', Journal of Bacteriology, vol. 200, no. 3. View/Download from: Publisher's site View description>>
ABSTRACT
RbdA is a positive
r
egulator of
b
iofilm
d
ispersal of
Pseudomonas aeruginosa
. Its cytoplasmic region (cRbdA) comprises an N-terminal Per-ARNT-Sim (PAS) domain followed by a diguanylate cyclase (GGDEF) domain and an EAL domain, whose phosphodiesterase activity is allosterically stimulated by GTP binding to the GGDEF domain. We report crystal structures of cRbdA and of two binary complexes: one with GTP/Mg
2+
bound to the GGDEF active site and one with the EAL domain bound to the c-di-GMP substrate. These structures unveil a 2-fold symmetric dimer stabilized by a closely packed N-terminal PAS domain and a noncanonical EAL dimer. The autoinhibitory switch is formed by an α-helix (S-helix) immediately N-terminal to the GGDEF domain that interacts with the EAL dimerization helix (α
6-E
) of the other EAL monomer and maintains the protein in a locked conformation. We propose that local conformational changes in cRbdA upon GTP binding lead to a structure with the PAS domain and S-helix shifted away from the GGDEF-EAL domains, as suggested by small-angle X-ray scattering (SAXS) experiments. Domain reorientation should be facilitated by the presence of an α-helical lever (H-helix) that tethers the GGDEF and EAL regions, allowing the EAL domain to rearrange into an active dimeric conformation.
IMPORTANCE
Biofilm formation by bacterial pathogens increases resistance to antibiotics. RbdA positively regulates biofilm dispersal of
Pseu...
Liu, MY, Cokcetin, NN, Lu, J, Turnbull, L, Carter, DA, Whitchurch, CB & Harry, EJ 2018, 'Rifampicin-Manuka Honey Combinations Are Superior to Other Antibiotic-Manuka Honey Combinations in Eradicating Staphylococcus aureus Biofilms', Frontiers in Microbiology, vol. 8, pp. 1-12. View/Download from: Publisher's site View description>>
Chronic wound infections are a major burden to both society and the health care industry. Bacterial biofilms are the major cause of chronic wound infections and are notoriously recalcitrant to treatments with antibiotics, making them difficult to eradicate. Thus, new approaches are required to combat biofilms in chronic wounds. One possible approach is to use drug combination therapies. Manuka honey has potent broad-spectrum antibacterial activity and has previously shown synergistic activity in combination with antibiotics against common wound pathogens, including Staphylococcus aureus. In addition, manuka honey exhibits anti-biofilm activity, thereby warranting the investigation of its potential as a combination therapy with antibiotics for the topical treatment of biofilm-related infections. Here we report the first use of MacSynergy II to investigate the response of established S. aureus (strain NCTC 8325) biofilms to treatment by combinations of Medihoney (medical grade manuka honey) and conventional antibiotics that are used for preventing or treating infections: rifampicin, oxacillin, fusidic acid, clindamycin, and gentamicin. Using checkerboard microdilution assays, viability assays and MacSynergy II analysis we show that the Medihoney-rifampicin combination was more effective than combinations using the other antibiotics against established staphylococcal biofilms. Medihoney and rifampicin were strongly synergistic in their ability to reduce both biofilm biomass and the viability of embedded S. aureus cells at a level that is likely to be significant in vivo. Other combinations of Medihoney and antibiotic produced an interesting array of effects: Medihoney-fusidic acid treatment showed minor synergistic activity, and Medihoney-clindamycin, -gentamicin, and -oxacillin combinations showed overall antagonistic effects when the honey was used at sub-inhibitory concentration, due to enhanced biofilm formation at these concentrations which could not be counter...
Liu, SH, Bobb, JF, Claus Henn, B, Schnaas, L, Tellez‐Rojo, MM, Gennings, C, Arora, M, Wright, RO, Coull, BA & Wand, MP 2018, 'Modeling the health effects of time‐varying complex environmental mixtures: Mean field variational Bayes for lagged kernel machine regression', Environmetrics, vol. 29, no. 4. View/Download from: Publisher's site View description>>
There is substantial interest in assessing how exposure to environmental mixtures, such as chemical mixtures, affect child health. Researchers are also interested in identifying critical time windows of susceptibility to these complex mixtures. A recently developed method, called lagged kernel machine regression (LKMR), simultaneously accounts for these research questions by estimating effects of time-varying mixture exposures, and identifying their critical exposure windows. However, LKMR inference using Markov chain Monte Carlo methods (MCMC-LKMR) is computationally burdensome and time intensive for large datasets, limiting its applicability. Therefore, we develop a mean field variational Bayesian inference procedure for lagged kernel machine regression (MFVB-LKMR). The procedure achieves computational efficiency and reasonable accuracy as compared with the corresponding MCMC estimation method. Updating parameters using MFVB may only take minutes, while the equivalent MCMC method may take many hours or several days. We apply MFVB-LKMR to PROGRESS, a prospective cohort study in Mexico. Results from a subset of PROGRESS using MFVB-LKMR provide evidence of significant positive association between second trimester cobalt levels and z-scored birthweight. This positive association is heightened by cesium exposure. MFVB-LKMR is a promising approach for computationally efficient analysis of environmental health datasets, to identify critical windows of exposure to complex mixtures.
Liu, T, Zhang, W, McLean, P, Ueland, M, Forbes, SL & Su, SW 2018, 'Electronic Nose-Based Odor Classification using Genetic Algorithms and Fuzzy Support Vector Machines', International Journal of Fuzzy Systems, vol. 20, no. 4, pp. 1309-1320. View/Download from: Publisher's site View description>>
Llewelyn, J, Choyce, NC, Phillips, BL, Webb, JK, Pearson, DJ, Schwarzkopf, L & Shine, R 2018, 'Behavioural responses of an Australian colubrid snake (Dendrelaphis punctulatus) to a novel toxic prey item (the Cane Toad Rhinella marina)', Biological Invasions, vol. 20, no. 9, pp. 2507-2516. View/Download from: Publisher's site View description>>
Loyeung, B, Lee, J, Michaeil, C & Zaslawski, C 2018, 'An experimental study in distinguishing an authentic herbal substance from sham herbal substances', Complementary Therapies in Medicine, vol. 39, pp. 92-96. View/Download from: Publisher's site View description>>
An unblinded randomised trial can result in biased treatment effect estimates and lead to erroneous conclusions on the efficacy of the therapeutic intervention. Unlike pharmaceutical substances, Chinese herbal medicines have special characteristics including texture, colour, odour and taste as the origin of these constituents are different. In addition, its distinctive odour makes blinding of Chinese herbal medicine RCTs very difficult, as the placebo substance needs to match the special characteristics of the herbal substance being investigated. For these reasons, two studies were undertaken to evaluate whether a participant could distinguish a herbal intervention capsule (Ganopoly combination) when compared to three types of capsules containing culinary materials following a visual, odour and taste evaluation.Study One, was a pilot involving eleven participants (n = 11) while Study Two, involved eighty one participants (n = 81) and was conducted to make improvements on Study One. For both studies, participants were asked to identify which of four capsules were a herbal substance following a visual, smell and taste evaluation.For study One it was found that for both odour (p = .484) and visual appearance (p = .077) the number of participants selecting the herbal substance was not significantly different from what may have been selected by chance. This was not the case for taste where significantly more participants selected capsule B as the herbal substance (p = .004). For Study Two test it was found that all three evaluations for odour, visual appearance and taste significantly more participants selected the herbal substance (p < .0001 in all cases). This indicates that the participant guesses were not evenly distributed across the four choices and suggests a failure to blind.The failure to blind participants highlights the difficulties in preparing sham herbal substances that look, smell and taste like the real herbal substance.
Luong, S, Forbes, SL, Wallman, JF & Roberts, RG 2018, 'Monitoring the extent of vertical and lateral movement of human decomposition products through sediment using cholesterol as a biomarker', Forensic Science International, vol. 285, pp. 93-104. View/Download from: Publisher's site View description>>
Due to the lack of human decomposition research facilities available in different geographical regions, the extent of movement of human decomposition products from a cadaver into various sedimentary environments, in different climates, has not been able to be studied in detail. In our study, a human cadaver was placed on the surface of a designated plot at the Australian Facility for Taphonomic Experimental Research (AFTER), the only human decomposition facility in Australia, where the natural process of decomposition was allowed to progress over 14days in the Australian summer. Sediment columns (approximately 1m deep) were collected at lateral distances of 0.25m, 0.5m, 1.0m and 2.5m in each of four directions from the centre of the torso. Plot elevation and weather data were also collected. Each sediment column was subdivided, dried and homogenised. A sample was isolated from each sediment subdivision, extracted with hexane, and the hexane extract cleaned with citrate buffer (pH 3), filtered and spiked with cholesterol-D7 internal standard. After derivatisation with BSTFA+1% TMCS, cholesterol was monitored in the samples using targeted gas chromatography tandem mass spectrometry analysis. A positive result for decomposition products was given if the cholesterol abundance in the test sample was higher than that detected in the 'control' samples of a similar substrate type collected prior to cadaver placement. Within the confines of the experimental design and the measured parameters, lateral leaching was observed over distances of up to 2.5m from the centre of the torso, which was the maximum distance tested in the study. Vertical leaching was detected to depths of up to 49cm below the ground surface. Such data can aid the development of policies related to plot sizing and sediment renewal and regeneration at other human decomposition facilities and at cemeteries. The density and distribution of cholesterol surrounding the cadaver in this study can also help fore...
Luts, J, Wang, SSJ, Ormerod, JT & Wand, MP 2018, 'Semiparametric Regression Analysis via Infer.NET', Journal of Statistical Software, vol. 87, no. 2. View/Download from: Publisher's site
Luu, LDW, Octavia, S, Zhong, L, Raftery, MJ, Sintchenko, V & Lan, R 2018, 'Proteomic Adaptation of Australian EpidemicBordetella pertussis', PROTEOMICS, vol. 18, no. 8, pp. 1700237-1700237. View/Download from: Publisher's site
Ma, K, Zhang, F, Sayyadi, N, Chen, W, Anwer, AG, Care, A, Xu, B, Tian, W, Goldys, EM & Liu, G 2018, '“Turn-on” Fluorescent Aptasensor Based on AIEgen Labeling for the Localization of IFN-γ in Live Cells', ACS Sensors, vol. 3, no. 2, pp. 320-326. View/Download from: Publisher's site
Ma, T, Chen, L, Shi, M, Niu, J, Zhang, X, Yang, X, Zhanghao, K, Wang, M, Xi, P, Jin, D, Zhang, M & Gao, J 2018, 'Developing novel methods to image and visualize 3D genomes', Cell Biology and Toxicology, vol. 34, no. 5, pp. 367-380. View/Download from: Publisher's site View description>>
To investigate three-dimensional (3D) genome organization in prokaryotic and eukaryotic cells, three main strategies are employed, namely nuclear proximity ligation-based methods, imaging tools (such as fluorescence in situ hybridization (FISH) and its derivatives), and computational/visualization methods. Proximity ligation-based methods are based on digestion and re-ligation of physically proximal cross-linked chromatin fragments accompanied by massively parallel DNA sequencing to measure the relative spatial proximity between genomic loci. Imaging tools enable direct visualization and quantification of spatial distances between genomic loci, and advanced implementation of (super-resolution) microscopy helps to significantly improve the resolution of images. Computational methods are used to map global 3D genome structures at various scales driven by experimental data, and visualization methods are used to visualize genome 3D structures in virtual 3D space-based on algorithms. In this review, we focus on the introduction of novel imaging and visualization methods to study 3D genomes. First, we introduce the progress made recently in 3D genome imaging in both fixed cell and live cells based on long-probe labeling, short-probe labeling, RNA FISH, and the CRISPR system. As the fluorescence-capturing capability of a particular microscope is very important for the sensitivity of bioimaging experiments, we also introduce two novel super-resolution microscopy methods, SDOM and low-power super-resolution STED, which have potential for time-lapse super-resolution live-cell imaging of chromatin. Finally, we review some software tools developed recently to visualize proximity ligation-based data. The imaging and visualization methods are complementary to each other, and all three strategies are not mutually exclusive. These methods provide powerful tools to explore the mechanisms of gene regulation and transcription in cell nuclei.
Macha, I & Ben-Nissan, B 2018, 'Marine Skeletons: Towards Hard Tissue Repair and Regeneration', Marine Drugs, vol. 16, no. 7, pp. 225-225. View/Download from: Publisher's site View description>>
Musculoskeletal disorders in the elderly have significantly increased due to the increase in an ageing population. The treatment of these diseases necessitates surgical procedures, including total joint replacements such as hip and knee joints. Over the years a number of treatment options have been specifically established which are either permanent or use temporary natural materials such as marine skeletons that possess unique architectural structure and chemical composition for the repair and regeneration of bone tissue. This review paper will give an overview of presently used materials and marine structures for hard tissue repair and regeneration, drugs of marine origin and other marine products which show potential for musculoskeletal treatment.
Machaalani, R & Chen, H 2018, 'Brain derived neurotrophic factor (BDNF), its tyrosine kinase receptor B (TrkB) and nicotine', NeuroToxicology, vol. 65, pp. 186-195. View/Download from: Publisher's site View description>>
Nicotine is the major neurotoxicant in cigarettes that affects many transmitter systems within the brain as well as other factors, including the growth factors. Brain derived neurotrophic factor (BDNF), is the most abundant growth factor in the brain and plays a critical role in early new neuron differentiation, development and synapsis growth, and the survival of fully developed neurons and synaptic activity. Over the past 3 decades, data has emerged on the effects of nicotine and cigarette smoke exposure on the expression of BDNF and its primary specific receptor tyrosine kinase receptor B (TrkB). This review summarizes data regarding the changes in brain BDNF expression after nicotine or cigarette smoke exposure, and discusses their implications considering BDNF's functional roles.
MacMillan, CP, Birke, H, Chuah, A, Brill, E, Tsuji, Y, Ralph, J, Dennis, ES, Llewellyn, D & Pettolino, FA 2018, 'Correction to: Tissue and cell-specific transcriptomes in cotton reveal the subtleties of gene regulation underlying the diversity of plant secondary cell walls', BMC Genomics, vol. 19, no. 1. View/Download from: Publisher's site
Macreadie, PI, McLean, DL, Thomson, PG, Partridge, JC, Jones, DOB, Gates, AR, Benfield, MC, Collin, SP, Booth, DJ, Smith, LL, Techera, E, Skropeta, D, Horton, T, Pattiaratchi, C, Bond, T & Fowler, AM 2018, 'Eyes in the sea: Unlocking the mysteries of the ocean using industrial, remotely operated vehicles (ROVs)', Science of The Total Environment, vol. 634, pp. 1077-1091. View/Download from: Publisher's site View description>>
For thousands of years humankind has sought to explore our oceans. Evidence of this early intrigue dates back to 130,000BCE, but the advent of remotely operated vehicles (ROVs) in the 1950s introduced technology that has had significant impact on ocean exploration. Today, ROVs play a critical role in both military (e.g. retrieving torpedoes and mines) and salvage operations (e.g. locating historic shipwrecks such as the RMS Titanic), and are crucial for oil and gas (O&G) exploration and operations. Industrial ROVs collect millions of observations of our oceans each year, fueling scientific discoveries. Herein, we assembled a group of international ROV experts from both academia and industry to reflect on these discoveries and, more importantly, to identify key questions relating to our oceans that can be supported using industry ROVs. From a long list, we narrowed down to the 10 most important questions in ocean science that we feel can be supported (whole or in part) by increasing access to industry ROVs, and collaborations with the companies that use them. The questions covered opportunity (e.g. what is the resource value of the oceans?) to the impacts of global change (e.g. which marine ecosystems are most sensitive to anthropogenic impact?). Looking ahead, we provide recommendations for how data collected by ROVs can be maximised by higher levels of collaboration between academia and industry, resulting in win-win outcomes. What is clear from this work is that the potential of industrial ROV technology in unravelling the mysteries of our oceans is only just beginning to be realised. This is particularly important as the oceans are subject to increasing impacts from global change and industrial exploitation. The coming decades will represent an important time for scientists to partner with industry that use ROVs in order to make the most of these 'eyes in the sea'.
Maes, W, Huete, A, Avino, M, Boer, M, Dehaan, R, Pendall, E, Griebel, A & Steppe, K 2018, 'Can UAV-Based Infrared Thermography Be Used to Study Plant-Parasite Interactions between Mistletoe and Eucalypt Trees?', Remote Sensing, vol. 10, no. 12, pp. 2062-2062. View/Download from: Publisher's site View description>>
Some of the remnants of the Cumberland Plain woodland, an endangered dry sclerophyllous forest type of New South Wales, Australia, host large populations of mistletoe. In this study, the extent of mistletoe infection was investigated based on a forest inventory. We found that the mistletoe infection rate was relatively high, with 69% of the Eucalyptus fibrosa and 75% of the E. moluccana trees being infected. Next, to study the potential consequences of the infection for the trees, canopy temperatures of mistletoe plants and of infected and uninfected trees were analyzed using thermal imagery acquired during 10 flights with an unmanned aerial vehicle (UAV) in two consecutive summer seasons. Throughout all flight campaigns, mistletoe canopy temperature was 0.3–2 K lower than the temperature of the eucalypt canopy it was growing in, suggesting higher transpiration rates. Differences in canopy temperature between infected eucalypt foliage and mistletoe were particularly large when incoming radiation peaked. In these conditions, eucalypt foliage from infected trees also had significantly higher canopy temperatures (and likely lower transpiration rates) compared to that of uninfected trees of the same species. The study demonstrates the potential of using UAV-based infrared thermography for studying plant-water relations of mistletoe and its hosts.
Maestrini, L & Wand, MP 2018, 'Variational message passing for skew t regression', Stat, vol. 7, no. 1, pp. e196-e196. View/Download from: Publisher's site View description>>
Maheshwari, R, Sharma, P, Tekade, M, Atneriya, U, Dua, K, Hansbro, PM & Tekade, RK 2018, 'Microsponge Embedded Tablets for Sustained Delivery of Nifedipine', Pharmaceutical Nanotechnology, vol. 5, no. 3, pp. 192-202. View/Download from: Publisher's site View description>>
Nifedipine is a potential therapeutic agent for the treatment of cardiovascular disturbances, although it suffers from short half-life (t1/2, 2 hr).To address the problem, we first prepared nifedipine loaded sustained release microsponges and then formulated tablets for effective clinical application and patient compliance.Preparations of microsponges were carried out using different compositions of nifedipine and polymer (1:1, 1:2 and 1:3 % molar ratio) using emulsion solvent diffusion technique.The microsponges with molar ratio 1:3 (formulation code: MF-3) found optimized as revealed by analyzing surface morphology, better powder flow properties (angle of repose; 28.80 ± 0.9, Hausner ratio 1.15 ± 0.2, % compressibility 15.28 ± 0.5% and higher % drug content (80 ± 1.9 %). Different batches of tablets were then formulated incorporating MF-3 microsponges and different proportions (10-50 %) of microcrystalline cellulose and starch as additives. Among tablet formulations, batch composed of 48% of MF-3, 30% of MCC, 20 % of starch and 2 % of talc (TF-33), showed 92.73 ± 2.19 % drug release during 24 hr in vitro release study in comparison to other batches including commercial formulation which was found to be released completely in 20 hr. Further, stability analysis revealed good drug retention of loaded nifedipine as well as consistent in vitro release pattern over a period of 90 days at 40°C and 75% RH.The microsponge tablet delivery system was found to be superior concerning the therapeutic advantage as well as manufacturing feasibility of nifedipine.
Mahmood, A, Tabassum, H, Zhao, R, Guo, W, Aftab, W, Liang, Z, Sun, Z & Zou, R 2018, 'Fe2N/S/N Codecorated Hierarchical Porous Carbon Nanosheets for Trifunctional Electrocatalysis', Small, vol. 14, no. 49, pp. 1803500-1803500. View/Download from: Publisher's site
Mahmud, MAP, Huda, N, Farjana, SH & Lang, C 2018, 'Environmental sustainability assessment of hydropower plant in Europe using life cycle assessment', IOP Conference Series: Materials Science and Engineering, vol. 351, pp. 012006-012006. View/Download from: Publisher's site
Mai, HT, Tran, TS, Ho-Le, TP, Pham, TT, Center, JR, Eisman, JA & Nguyen, TV 2018, 'Low-trauma rib fracture in the elderly: Risk factors and mortality consequence', Bone, vol. 116, pp. 295-300. View/Download from: Publisher's site
Main, BJ & Rodgers, KJ 2018, 'Assessing the Combined Toxicity of BMAA and Its Isomers 2,4-DAB and AEG In Vitro Using Human Neuroblastoma Cells', Neurotoxicity Research, vol. 33, no. 1, pp. 33-42. View/Download from: Publisher's site View description>>
The non-protein amino acid (NPAA) ß-methylamino-L-alanine (BMAA) is produced by a diverse range of cyanobacteria, diatoms and dinoflagellates, and is present in both aquatic and terrestrial ecosystems globally. Exposure to BMAA has been implicated in the development of neurodegenerative diseases including amyotrophic lateral sclerosis (ALS), Alzheimer's disease (AD) and Parkinson's disease (PD). BMAA is often found in nature along with its structural isomers 2,4-diaminobutyric acid (2,4-DAB) and aminoethylglycine (AEG); however, the toxicity of these NPAAs in combination has not been examined. We have previously demonstrated that BMAA induces endoplasmic reticulum (ER) stress and increases caspase and cathepsin activity in human neuroblastoma cells (SH-SY5Y), effects consistent with proteotoxic stress due to disturbances in protein synthesis, folding or turnover. The current study investigates whether 2,4-DAB and AEG share a similar mechanism of toxicity to BMAA, and if simultaneous exposure of cells to BMAA and its isomers results in increased toxicity in vitro. We show that a 48-h treatment with both 500 μM BMAA and 2,4-DAB decreases cell viability in vitro whereas AEG was not cytotoxic under the same conditions. Treatment of SH-SY5Y cells with 2,4-DAB did not increase expression of ER stress markers. Combined treatment of cells with BMAA and 2,4-DAB resulted in increased caspase activity and increased apoptosis above that of BMAA or 2,4-DAB on their own. These results suggest that 2,4-DAB does not share the same mechanism of toxicity as BMAA but the presence of 2,4-DAB increases the toxicity of BMAA to human cells in vitro.
The emerging toxin β-methylamino-l-alanine (BMAA) has been linked to the development of a number of neurodegenerative diseases in humans including amyotrophic lateral sclerosis (ALS), Alzheimer's disease, and Parkinson's disease. BMAA has been found to be produced by a range of cyanobacteria, diatoms, and dinoflagellates worldwide, and is present in freshwater, saltwater, and terrestrial ecosystems. Surface scum samples were collected from waterways in rural and urban New South Wales, Australia and algal species identified. Reverse phase liquid chromatography-tandem mass spectrometry was used to analyse sixteen cyanobacterial scum for the presence of BMAA as well as its toxic structural isomer 2,4-diaminobutyric acid (2,4-DAB). BMAA was detected in ten of the samples analysed, and 2,4-DAB in all sixteen. The presence of these toxins in water used for agriculture raises concerns for public health and food security in Australia.
Main, BJ, Italiano, CJ & Rodgers, KJ 2018, 'Investigation of the interaction of β-methylamino-l-alanine with eukaryotic and prokaryotic proteins', Amino Acids, vol. 50, no. 3-4, pp. 397-407. View/Download from: Publisher's site View description>>
There is a strong body of evidence linking the non-protein amino acid (NPAA) β-methylamino-L-alanine (BMAA) to the development of a number of neurodegenerative diseases. BMAA has been found globally, is produced by a number of organisms including cyanobacteria, diatoms, and dinoflagellates; and has been shown to biomagnify through trophic levels. The role of BMAA in neurodegenerative disease is highlighted by its presence in the brains of a number of neurodegenerative disease patients, where it was found in a protein-bound form. We have previously shown that BMAA is bound to cell proteins, and results in the upregulation of the unfolded protein response, an endoplasmic reticulum stress response activated by the presence of misfolded proteins within the cell. Structurally aberrant proteins are features of a number of neurodegenerative diseases, and further investigation of how BMAA interacts with proteins is crucial to our understanding of its toxicity. Here we use radiolabelled BMAA to investigate the interaction and binding of BMAA to eukaryotic and prokaryotic proteins. We found differences in the presence and distribution of protein-bound BMAA between E. coli and neuroblastoma cells, with an increase in binding over time only seen in the eukaryotic cells. We also found that BMAA was unable to bind to pure proteins, or cell lysate in native or denaturing conditions, indicating that biological processing is required for BMAA to bind to proteins.
Maire, E, Villéger, S, Graham, NAJ, Hoey, AS, Cinner, J, Ferse, SCA, Aliaume, C, Booth, DJ, Feary, DA, Kulbicki, M, Sandin, SA, Vigliola, L & Mouillot, D 2018, 'Community-wide scan identifies fish species associated with coral reef services across the Indo-Pacific', Proceedings of the Royal Society B: Biological Sciences, vol. 285, no. 1883, pp. 20181167-20181167. View/Download from: Publisher's site View description>>
Determining whether many functionally complementary species or only a subset of key species are necessary to maintain ecosystem functioning and services is a critical question in community ecology and biodiversity conservation. Identifying such key species remains challenging, especially in the tropics where many species co-occur and can potentially support the same or different processes. Here, we developed a new community-wide scan (CWS) approach, analogous to the genome-wide scan, to identify fish species that significantly contribute, beyond the socio-environmental and species richness effects, to the biomass and coral cover on Indo-Pacific reefs. We found that only a limited set of species (51 out of approx. 400, approx. 13%), belonging to various functional groups and evolutionary lineages, are strongly and positively associated with fish biomass and live coral cover. Many of these species have not previously been identified as functionally important, and thus may be involved in unknown, yet important, biological mechanisms that help sustain healthy and productive coral reefs. CWS has the potential to reveal species that are key to ecosystem functioning and services and to guide management strategies as well as new experiments to decipher underlying causal ecological processes.
Maitre, M, Horder, M, Kirkbride, KP, Gassner, A-L, Weyermann, C, Roux, C & Beavis, A 2018, 'A forensic investigation on the persistence of organic gunshot residues', Forensic Science International, vol. 292, pp. 1-10. View/Download from: Publisher's site View description>>
Gunshot residues (GSR) are a potential form of forensic traces in firearm-related events. In most forensic laboratories, GSR analyses focus on the detection and characterisation of the inorganic components (IGSR), which are mainly particles containing mixtures of lead, barium and antimony originating from the primer. The increasing prevalence of heavy metal-free ammunition challenges the current protocols used for IGSR analysis. To provide complementary information to IGSR particles, the current study concentrated on the organic components (OGSR) arising from the combustion of the propellant. The study focused on four compounds well-known as being part of OGSR: ethylcentralite (EC), methylcentralite (MC), diphenylamine (DPA), N-nitrosodiphenylamine (N-nDPA). This study assessed the retention of these OGSR traces on a shooter's hands. The overall project aim was to provide appropriate information regarding OGSR persistence, which can be suitable to be integrated into the interpretation framework of OGSR as recommended by the recent ENFSI Guideline for Evaluative Reporting in Forensic Science. The persistence was studied through several intervals ranging from immediately after discharge to four hours and two ammunition calibres were chosen: .40 S&W calibre, used by the NSW Police Force; and .357 Magnum, which is frequently encountered in Australian casework. This study successfully detected the compounds of interest up to four hours after discharge. The trends displayed a large decrease in the amount detected during the first hour. A large variability was also observed due to numerous factors involved in the production, deposition and collection of OGSR.
Maitre, M, Kirkbride, KP, Horder, M, Roux, C & Beavis, A 2018, 'Thinking beyond the lab: organic gunshot residues in an investigative perspective', Australian Journal of Forensic Sciences, vol. 50, no. 6, pp. 1-7. View/Download from: Publisher's site View description>>
Maixner, F, Turaev, D, Cazenave-Gassiot, A, Janko, M, Krause-Kyora, B, Hoopmann, MR, Kusebauch, U, Sartain, M, Guerriero, G, O’Sullivan, N, Teasdale, M, Cipollini, G, Paladin, A, Mattiangeli, V, Samadelli, M, Tecchiati, U, Putzer, A, Palazoglu, M, Meissen, J, Lösch, S, Rausch, P, Baines, JF, Kim, BJ, An, H-J, Gostner, P, Egarter-Vigl, E, Malfertheiner, P, Keller, A, Stark, RW, Wenk, M, Bishop, D, Bradley, DG, Fiehn, O, Engstrand, L, Moritz, RL, Doble, P, Franke, A, Nebel, A, Oeggl, K, Rattei, T, Grimm, R & Zink, A 2018, 'The Iceman’s Last Meal Consisted of Fat, Wild Meat, and Cereals', Current Biology, vol. 28, no. 14, pp. 2348-2355.e9. View/Download from: Publisher's site View description>>
The history of humankind is marked by the constant adoption of new dietary habits affecting human physiology, metabolism, and even the development of nutrition-related disorders. Despite clear archaeological evidence for the shift from hunter-gatherer lifestyle to agriculture in Neolithic Europe [1], very little information exists on the daily dietary habits of our ancestors. By undertaking a complementary -omics approach combined with microscopy, we analyzed the stomach content of the Iceman, a 5,300-year-old European glacier mummy [2, 3]. He seems to have had a remarkably high proportion of fat in his diet, supplemented with fresh or dried wild meat, cereals, and traces of toxic bracken. Our multipronged approach provides unprecedented analytical depth, deciphering the nutritional habit, meal composition, and food-processing methods of this Copper Age individual.
Majeed, I, Manzoor, U, Kanodarwala, FK, Nadeem, MA, Hussain, E, Ali, H, Badshah, A, Stride, JA & Nadeem, MA 2018, 'Pd–Ag decorated g-C3N4 as an efficient photocatalyst for hydrogen production from water under direct solar light irradiation', Catalysis Science & Technology, vol. 8, no. 4, pp. 1183-1193. View/Download from: Publisher's site View description>>
Pd–Ag bimetallic and monometallic nanoparticles were decorated on g-C3N4 and evaluated for their ability to produce H2 through water splitting reactions.
Mallick, K, Toivonen, E, Trebs, I, Boegh, E, Cleverly, J, Eamus, D, Koivusalo, H, Drewry, D, Arndt, SK, Griebel, A, Beringer, J & Garcia, M 2018, 'Bridging Thermal Infrared Sensing and Physically‐Based Evapotranspiration Modeling: From Theoretical Implementation to Validation Across an Aridity Gradient in Australian Ecosystems', Water Resources Research, vol. 54, no. 5, pp. 3409-3435. View/Download from: Publisher's site View description>>
AbstractThermal infrared sensing of evapotranspiration (E) through surface energy balance (SEB) models is challenging due to uncertainties in determining the aerodynamic conductance (gA) and due to inequalities between radiometric (TR) and aerodynamic temperatures (T0). We evaluated a novel analytical model, the Surface Temperature Initiated Closure (STIC1.2), that physically integrates TR observations into a combined Penman‐Monteith Shuttleworth‐Wallace (PM‐SW) framework for directly estimating E, and overcoming the uncertainties associated with T0 and gA determination. An evaluation of STIC1.2 against high temporal frequency SEB flux measurements across an aridity gradient in Australia revealed a systematic error of 10–52% in E from mesic to arid ecosystem, and low systematic error in sensible heat fluxes (H) (12–25%) in all ecosystems. Uncertainty in TR versus moisture availability relationship, stationarity assumption in surface emissivity, and SEB closure corrections in E were predominantly responsible for systematic E errors in arid and semi‐arid ecosystems. A discrete correlation (r) of the model errors with observed soil moisture variance (r = 0.33–0.43), evaporative index (r = 0.77–0.90), and climatological dryness (r = 0.60–0.77) explained a strong association between ecohydrological extremes and TR
Manandhar, B, Paudel, KR, Sharma, B & Karki, R 2018, 'Phytochemical profile and pharmacological activity of Aegle marmelos Linn.', Journal of Integrative Medicine, vol. 16, no. 3, pp. 153-163. View/Download from: Publisher's site
Mann, G, Breitling, F, Vocks, C, Aurass, H, Steinmetz, M, Strassmeier, KG, Bisi, MM, Fallows, RA, Gallagher, P, Kerdraon, A, Mackinnon, A, Magdalenic, J, Rucker, H, Anderson, J, Asgekar, A, Avruch, IM, Bell, ME, Bentum, MJ, Bernardi, G, Best, P, Bîrzan, L, Bonafede, A, Broderick, JW, Brüggen, M, Butcher, HR, Ciardi, B, Corstanje, A, de Gasperin, F, de Geus, E, Deller, A, Duscha, S, Eislöffel, J, Engels, D, Falcke, H, Fender, R, Ferrari, C, Frieswijk, W, Garrett, MA, Grießmeier, J, Gunst, AW, van Haarlem, M, Hassall, TE, Heald, G, Hessels, JWT, Hoeft, M, Hörandel, J, Horneffer, A, Juette, E, Karastergiou, A, Klijn, WFA, Kondratiev, VI, Kramer, M, Kuniyoshi, M, Kuper, G, Maat, P, Markoff, S, McFadden, R, McKay-Bukowski, D, McKean, JP, Mulcahy, DD, Munk, H, Nelles, A, Norden, MJ, Orru, E, Paas, H, Pandey-Pommier, M, Pandey, VN, Pizzo, R, Polatidis, AG, Rafferty, D, Reich, W, Röttgering, H, Scaife, AMM, Schwarz, DJ, Serylak, M, Sluman, J, Smirnov, O, Stappers, BW, Tagger, M, Tang, Y, Tasse, C, ter Veen, S, Thoudam, S, Toribio, MC, Vermeulen, R, van Weeren, RJ, Wise, MW, Wucknitz, O, Yatawatta, S, Zarka, P & Zensus, JA 2018, 'Tracking of an electron beam through the solar corona with LOFAR', Astronomy & Astrophysics, vol. 611, pp. A57-A57. View/Download from: Publisher's site View description>>
The Sun’s activity leads to bursts of radio emission, among other phenomena. An example is type-III radio bursts. They occur frequently and appear as short-lived structures rapidly drifting from high to low frequencies in dynamic radio spectra. They are usually interpreted as signatures of beams of energetic electrons propagating along coronal magnetic field lines. Here we present novel interferometric LOFAR (LOw Frequency ARray) observations of three solar type-III radio bursts and their reverse bursts with high spectral, spatial, and temporal resolution. They are consistent with a propagation of the radio sources along the coronal magnetic field lines with nonuniform speed. Hence, the type-III radio bursts cannot be generated by a monoenergetic electron beam, but by an ensemble of energetic electrons with a spread distribution in velocity and energy. Additionally, the density profile along the propagation path is derived in the corona. It agrees well with three-fold coronal density model by (1961, ApJ, 133, 983).
Manshare, K, Anand, A, Mahajan, S, Satija, S, Sharma, N, Khurana, N, Duggal, N & Mehta, M 2018, 'Evaluation of nephroprotective activity of gallic acid in gentamicin-induced rat model of nephrotoxicity', International Journal of Green Pharmacy, vol. 12, no. 2, pp. 48-52. View description>>
Introduction: Renal damage due to gentamicin is associated with oxidative stress. Gallic acid is a phenolic compound that possesses antioxidant and anti-inflammatory properties. Hence, an attempt was made to explore the nephroprotective activity of gallic acid in gentamicin-induced nephrotoxicity. Materials and Methods: Wistar albino rats of either sex were used. Experimental nephrotoxicity was produced by intraperitoneal administration of gentamicin for 8 days. Rats were divided into five groups: Group I - normal control (normal Saline), Group II - gentamicin only treated group (100 mg/kg), Group III - gentamicin (s100 mg/kg) + Vitamin C (200 mg/kg), Group IV (treatment group) - gentamicin (100 mg/kg) + gallic acid (200 mg/kg), and Group V - gentamicin (100 mg/kg) + gallic acid (400 mg/kg). The period of drug administration was of 8 days, in which animals were treated with Vitamin C and gallic acid. After the treatment for 8 days, the animals were sacrificed for the investigation of biochemical parameters and histopathological examination. Results: Gentamicin-induced nephrotoxicity was successfully reproduced. Concurrent administration of gallic acid along with gentamicin significantly prevented the rise in level of serum creatinine, serum urea, blood urea nitrogen, and total protein. Administration of gallic acid also leads to increase glutathione and superoxide dismutase level in the kidney. Therefore, gallic acid had significantly prevented nephrotoxicity as compared to the group receiving gentamicin drug alone. Conclusion: These results showed that gallic acid is effective as nephroprotective agent.
Marsh, JW, Hayward, RJ, Shetty, AC, Mahurkar, A, Humphrys, MS & Myers, GSA 2018, 'Bioinformatic analysis of bacteria and host cell dual RNA-sequencing experiments', Briefings in Bioinformatics, vol. 19, no. 6, pp. 1115-1129. View/Download from: Publisher's site View description>>
Bacterial pathogens subvert host cells by manipulating cellular pathways for survival and replication; in turn, host cells respond to the invading pathogen through cascading changes in gene expression. Deciphering these complex temporal and spatial dynamics to identify novel bacterial virulence factors or host response pathways is crucial for improved diagnostics and therapeutics. Dual RNA sequencing (dRNA-Seq) has recently been developed to simultaneously capture host and bacterial transcriptomes from an infected cell. This approach builds on the high sensitivity and resolution of RNA sequencing technology and is applicable to any bacteria that interact with eukaryotic cells, encompassing parasitic, commensal or mutualistic lifestyles. Several laboratory protocols have been presented that outline the collection, extraction and sequencing of total RNA for dRNA-Seq experiments, but there is relatively little guidance available for the detailed bioinformatic analyses required. This protocol outlines a typical dRNA-Seq experiment, based on a Chlamydia trachomatis-infected host cell, with a detailed description of the necessary bioinformatic analyses with currently available software tools
Marsili, E, Kjelleberg, S & Rice, SA 2018, 'Mixed community biofilms and microbially influenced corrosion', Microbiology Australia, vol. 39, no. 3, pp. 152-152. View/Download from: Publisher's site View description>>
Metals are used in most marine infrastructures for energy extraction and production. Metal corrosion is a serious concern, due to the environmental, safety, and replacement costs associated with it. Microbially influenced corrosion (MIC) contributes to the overall corrosion process, through several chemical, electrochemical and biochemical mechanisms, particularly in the presence of microbial biofilms. In this short article, we discuss briefly recent advances in MIC research, comparing corrosion in single species and mixed species biofilms, and outline possible strategies for biofilm and corrosion control.
Mateer, SW, Mathe, A, Bruce, J, Liu, G, Maltby, S, Fricker, M, Goggins, BJ, Tay, HL, Marks, E, Burns, G, Kim, RY, Minahan, K, Walker, MM, Callister, RC, Foster, PS, Horvat, JC, Hansbro, PM & Keely, S 2018, 'IL-6 Drives Neutrophil-Mediated Pulmonary Inflammation Associated with Bacteremia in Murine Models of Colitis', The American Journal of Pathology, vol. 188, no. 7, pp. 1625-1639. View/Download from: Publisher's site View description>>
Inflammatory bowel disease (IBD) is associated with several immune-mediated extraintestinal manifestations. More than half of all IBD patients have some form of respiratory pathology, most commonly neutrophil-mediated diseases, such as bronchiectasis and chronic bronchitis. Using murine models of colitis, we aimed to identify the immune mechanisms driving pulmonary manifestations of IBD. We found increased neutrophil numbers in lung tissue associated with the pulmonary vasculature in both trinitrobenzenesulfonic acid- and dextran sulfate sodium-induced models of colitis. Analysis of systemic inflammation identified that neutrophilia was associated with bacteremia and pyrexia in animal models of colitis. We further identified IL-6 as a systemic mediator of neutrophil recruitment from the bone marrow of dextran sulfate sodium animals. Functional inhibition of IL-6 led to reduced systemic and pulmonary neutrophilia, but it did not attenuate established colitis pathology. These data suggest that systemic bacteremia and pyrexia drive IL-6 secretion, which is a critical driver for pulmonary manifestation of IBD. Targeting IL-6 may reduce neutrophil-associated extraintestinal manifestations in IBD patients.
Matis, PA, Donelson, JM, Bush, S, Fox, RJ & Booth, DJ 2018, 'Temperature influences habitat preference of coral reef fishes: Will generalists become more specialised in a warming ocean?', Global Change Biology, vol. 24, no. 7, pp. 3158-3169. View/Download from: Publisher's site View description>>
Climate change is expected to pose a significant risk to species that exhibit strong behavioural preferences for specific habitat types, with generalist species assumed to be less vulnerable. In this study, we conducted habitat choice experiments to determine how water temperature influences habitat preference for three common species of coral reef damselfish (Pomacentridae) that differ in their levels of habitat specialisation. The lemon damselfish Pomacentrus moluccensis, a habitat specialist, consistently selected complex coral habitat across all temperature treatments (selected based on local average seasonal temperatures naturally experienced in situ: ambient winter 22°C; ambient summer 28°C; and elevated 31°C). Unexpectedly, the neon damselfish Pomacentrus coelestis and scissortail sergeant Abudefduf sexfasciatus, both of which have more generalist habitat associations, developed strong habitat preferences (for complex coral and boulder habitat, respectively) at the elevated temperature treatment (31°C) compared to no single preferred habitat at 22°C or 28°C. The observed shifts in habitat preference with temperature suggest that we may be currently underestimating the vulnerability of some habitat generalists to climate change and highlight that the ongoing loss of complex live coral through coral bleaching could further exacerbate resource overlap and species competition in ways not currently considered in climate change models.
MATTHEWS, CE, KOZEY KEADLE, S, MOORE, SC, SCHOELLER, DS, CARROLL, RJ, TROIANO, RP & SAMPSON, JN 2018, 'Measurement of Active and Sedentary Behavior in Context of Large Epidemiologic Studies', Medicine & Science in Sports & Exercise, vol. 50, no. 2, pp. 266-276. View/Download from: Publisher's site
Matthews, JL, Oakley, CA, Lutz, A, Hillyer, KE, Roessner, U, Grossman, AR, Weis, VM & Davy, SK 2018, 'Partner switching and metabolic flux in a model cnidarian–dinoflagellate symbiosis', Proceedings of the Royal Society B: Biological Sciences, vol. 285, no. 1892, pp. 20182336-20182336. View/Download from: Publisher's site View description>>
Metabolite exchange is fundamental to the viability of the cnidarian–Symbiodiniaceae symbiosis and survival of coral reefs. Coral holobiont tolerance to environmental change might be achieved through changes in Symbiodiniaceae species composition, but differences in the metabolites supplied by different Symbiodiniaceae species could influence holobiont fitness. Using
13
C stable-isotope labelling coupled to gas chromatography–mass spectrometry, we characterized newly fixed carbon fate in the model cnidarian
Exaiptasia pallida
(Aiptasia) when experimentally colonized with either native
Breviolum minutum
or non-native
Durusdinium trenchii
. Relative to anemones containing
B. minutum
,
D. trenchii
-colonized hosts exhibited a 4.5-fold reduction in
13
C-labelled glucose and reduced abundance and diversity of
13
C-labelled carbohydrates and lipogenesis precursors, indicating symbiont species-specific modifications to carbohydrate availability and lipid storage. Mapping carbon fate also revealed significant alterations to host molecular signalling pathways. In particular,
D. trenchii-
colonized hosts exhibited a 40-fold reduction in
13
C-labelled
scyllo
-inositol, a potential interpartner signalling molecule in symbiosis specificity.
13
C-labelling also highlighted differential antioxidant- and ammonium-producing pathway activities, suggesting physiological responses to differe...
McCauley, JI, Winberg, PC, Meyer, BJ & Skropeta, D 2018, 'Effects of nutrients and processing on the nutritionally important metabolites of Ulva sp. (Chlorophyta)', Algal Research, vol. 35, pp. 586-594. View/Download from: Publisher's site View description>>
Background: Frailty is an independent predictor of mortality across many conditions. Reported rates of frailty in heart failure range from 15% to 74%. There are several instruments available to assess frailty; however, to date there has been no consensus on the most appropriate instrument for use in individuals with heart failure. Aims: To identify how frailty is assessed in individuals with heart failure and to elucidate which domains of frailty are most frequently assessed. Methods: Key electronic databases were searched (MEDLINE, COCHRANE Central and CINAHL) to identify studies that assessed frailty in individuals with heart failure using a formal frailty instrument. Results: Twenty studies published in 24 articles were included, for which a total of seven unique frailty instruments were identified. The most commonly used instrument was the Frailty Phenotype ( n= 11), with the majority of studies using a modified version of the Frailty Phenotype ( n= 8). The second most commonly used instrument identified was the Comprehensive Geriatric Assessment ( n= 4). Conclusion: There is an increasing interest in the assessment of frailty, but, to date, there is no frailty instrument validated specifically in the heart failure population.
McGrath, KCY, Gangoda, SVS, Li, X-H, McRobb, LS & Heather, AK 2018, 'Corrigendum to “Inhibitory Effect of a French Maritime Pine Bark Extract-Based Nutritional Supplement on TNF-α-Induced Inflammation and Oxidative Stress in Human Coronary Artery Endothelial Cells”', Evidence-Based Complementary and Alternative Medicine, vol. 2018, pp. 1-1. View/Download from: Publisher's site
McIlroy, DJ, Minahan, K, Keely, S, Lott, N, Hansbro, P, Smith, DW & Balogh, ZJ 2018, 'Reduced deoxyribonuclease enzyme activity in response to high postinjury mitochondrial DNA concentration provides a therapeutic target for Systemic Inflammatory Response Syndrome', Journal of Trauma and Acute Care Surgery, vol. 85, no. 2, pp. 354-358. View/Download from: Publisher's site View description>>
BACKGROUNDCell-free mitochondrial DNA (mtDNA) is proinflammatory and has been detected in high concentrations in trauma patients’ plasma. Deoxyribonuclease (DNAse) is the free plasma enzyme responsible for the digestion of extracellular DNA. The relationship between mtDNA and DNAse after major trauma is unknown. We hypothesized that DNAse activity would be elevated after injury and trauma surgery and would be associated with high concentrations of extracellular DNA.METHODSTwo-year prospective study was performed on 103 consecutive trauma patients (male, 81%; age, 38 years [interquartile range, 30–59 years]; injury severity score, 18 [interquartile range, 12–26 years]) who underwent standardized major orthopedic trauma surgical interventions. Blood was collected at five perioperative time points (preoperative, postoperative, 7 hours, 24 hours, and 3 days postoperatively). Healthy control subjects (n = 20) were also sampled. Cell-free mtDNA and nuclear DNA (nDNA) were measured using quantitative polymerase chain reaction. Deoxyribonuclease was also assayed in the same plasma samples.RESULTSIncreased levels of mtDNA (from preoperative 163 ± 86 ng/mL to 3 days 282 ± 201 ng/mL, p < 0.0001) and nDNA (from preoperative 28 ± 20 ng/mL to 3 days 37 ± 27 ng/mL, p < 0.05) were present in trauma patients at all perioperative time points compared with healthy controls (mtDNA: 4 ± 2 ng/mL; nDNA: 10 ± 5 ng/mL). Deoxyribonuclease activity was lower in the trauma cohort (from preoperative 0.06 ± 0.04U/mL to 3 days 0.08 ± 0.04U/mL, p < 0.0001) compared with healthy cont...
McIlroy, DJ, Minahan, K, Keely, S, Lott, N, Hansbro, P, Smith, DW & Balogh, ZJ 2018, 'Reduced deoxyribonuclease enzyme activity in response to high postinjury mitochondrial DNA concentration provides a therapeutic target for Systemic Inflammatory Response Syndrome.', J Trauma Acute Care Surg, vol. 85, no. 2, pp. 354-358. View/Download from: Publisher's site View description>>
BACKGROUND: Cell-free mitochondrial DNA (mtDNA) is proinflammatory and has been detected in high concentrations in trauma patients' plasma. Deoxyribonuclease (DNAse) is the free plasma enzyme responsible for the digestion of extracellular DNA. The relationship between mtDNA and DNAse after major trauma is unknown. We hypothesized that DNAse activity would be elevated after injury and trauma surgery and would be associated with high concentrations of extracellular DNA. METHODS: Two-year prospective study was performed on 103 consecutive trauma patients (male, 81%; age, 38 years [interquartile range, 30-59 years]; injury severity score, 18 [interquartile range, 12-26 years]) who underwent standardized major orthopedic trauma surgical interventions. Blood was collected at five perioperative time points (preoperative, postoperative, 7 hours, 24 hours, and 3 days postoperatively). Healthy control subjects (n = 20) were also sampled. Cell-free mtDNA and nuclear DNA (nDNA) were measured using quantitative polymerase chain reaction. Deoxyribonuclease was also assayed in the same plasma samples. RESULTS: Increased levels of mtDNA (from preoperative 163 ± 86 ng/mL to 3 days 282 ± 201 ng/mL, p < 0.0001) and nDNA (from preoperative 28 ± 20 ng/mL to 3 days 37 ± 27 ng/mL, p < 0.05) were present in trauma patients at all perioperative time points compared with healthy controls (mtDNA: 4 ± 2 ng/mL; nDNA: 10 ± 5 ng/mL). Deoxyribonuclease activity was lower in the trauma cohort (from preoperative 0.06 ± 0.04U/mL to 3 days 0.08 ± 0.04U/mL, p < 0.0001) compared with healthy controls (DNAse: 0.17 ± 0.03U/mL). There was no correlation between DNAse and perioperative DNA concentrations. Elevated mtDNA (but not nDNA) correlated with the development of systemic inflammatory response syndrome (SIRS) (p = 0.026) but not multiple organ failure. CONCLUSIONS: The significant perioperative elevation in plasma-free mtDNA concentration is associated with the development of SIRS. The fact that in...
McKinnon, J, Roy Chowdhury, P & Djordjevic, SP 2018, 'Genomic analysis of multidrug-resistant Escherichia coli ST58 causing urosepsis', International Journal of Antimicrobial Agents, vol. 52, no. 3, pp. 430-435. View/Download from: Publisher's site View description>>
Sequence type 58 (ST58) phylogroup B1 Escherichia coli have been isolated from a wide variety of mammalian and avian hosts but are not noted for their ability to cause serious disease in humans or animals. Here we determined the genome sequences of two multidrug-resistant E. coli ST58 strains from urine and blood of one patient using a combination of Illumina and Single Molecule, Real-Time (SMRT) sequencing. Both ST58 strains were clonal and were characterised as serotype O8:H25, phylogroup B1 and carried a complex resistance locus/loci (CRL) that featured an atypical class 1 integron with a dfrA5 (trimethoprim resistance) gene cassette followed by only 24 bp of the 3'-CS. CRL that carry this particular integron have been described previously in E. coli from cattle, pigs and humans in Australia. The integron abuts a copy of Tn6029, an IS26-flanked composite transposon encoding blaTEM, sul2 and strAB genes that confer resistance to ampicillin, sulfathiazole and streptomycin, respectively. The CRL resides within a novel Tn2610-like hybrid Tn1721/Tn21 transposon on an IncF, ColV plasmid (pSDJ2009-52F) of 138 553 bp that encodes virulence associated genes implicated in life-threatening extraintestinal pathogenic E. coli (ExPEC) infections. Notably, pSDJ2009-52F shares high sequence identity with pSF-088-1, a plasmid reported in an E. coli ST95 strain from a patient with blood sepsis from a hospital in San Francisco. These data suggest that extraintestinal infections caused by E. coli carrying ColV-like plasmids, irrespective of their phylogroup or ST, may pose a potential threat to human health, particularly to the elderly and immunocompromised.
McNevin, D 2018, 'Bayesian interpretation of discrete class characteristics', Forensic Science International, vol. 292, pp. 125-130. View/Download from: Publisher's site View description>>
Bayesian interpretation of forensic evidence has become dominated by the likelihood ratio (LR) with a large LR generally considered favourable to the prosecution hypothesis, HP, over the defence hypothesis, HD. However, the LR simply quantifies by how much the prior odds ratio of the probability of HP relative to HD has been improved by the forensic evidence to provide a posterior ratio. Because the prior ratio is mostly neglected, the posterior ratio is largely unknown, regardless of the LR used to improve it. In fact, we show that the posterior ratio will only favour HP when LR is at least as large as the number of things that could possibly be the source of that evidence, all being equally able to contribute. This restriction severely limits the value of evidence to the prosecution when only a single, discrete class characteristic is used to match a subset of these things to the evidence. The limitation can be overcome by examining more than one individual characteristic, as long as they are independent of each other, as they are for the genotypes at multiple loci combined for DNA evidence. We present a criterion for determining how many such characteristics are required. Finally, we conclude that a frequentist interpretation is inappropriate as a measure of the strength of forensic evidence precisely because it only estimates the denominator of the LR.
BACKGROUND:Bacterial filamentation occurs when rod-shaped bacteria grow without dividing. To identify genetically encoded inhibitors of division that promote filamentation, we used cell sorting flow cytometry to enrich filamentous clones from an inducible expression library, and then identified the cloned DNA with high-throughput DNA sequencing. We applied the method to an expression library made from fragmented genomic DNA of uropathogenic E. coli UTI89, which undergoes extensive reversible filamentation in urinary tract infections and might encode additional regulators of division. RESULTS:We identified 55 genomic regions that reproducibly caused filamentation when expressed from the plasmid vector, and then further localized the cause of filamentation in several of these to specific genes or sub-fragments. Many of the identified genomic fragments encode genes that are known to participate in cell division or its regulation, and others may play previously-unknown roles. Some of the prophage genes identified were previously implicated in cell division arrest. A number of the other fragments encoded potential short transcripts or peptides. CONCLUSIONS:The results provided evidence of potential new links between cell division and distinct cellular processes including central carbon metabolism and gene regulation. Candidate regulators of the UTI-associated filamentation response or others were identified amongst the results. In addition, some genomic fragments that caused filamentation may not have evolved to control cell division, but may have applications as artificial inhibitors. Our approach offers the opportunity to carry out in depth surveys of diverse DNA libraries to identify new genes or sequences encoding the capacity to inhibit division and cause filamentation.
Mehta, M, Garg, M, Dua, K & Satija, S 2018, 'Simultaneous HPTLC Densitometric Estimation of KBA and AKBA from Boswellia serrata', Current Analytical Chemistry, vol. 15, no. 1, pp. 84-91. View/Download from: Publisher's site View description>>
Background: Boswellic acids (BAs) are extracted from oleo gum of Boswellia serrata and
are utilized as potential anti-inflammatory, hypolipidemic, immunomodulatory and antitumor specialists.
The present examination was meant to assess KBA and AKBA in Boswellia serrata separate by
High-Performance Thin Layer Chromatography (HPTLC).Methods:The separation of bioactive compounds was performed utilizing mobile phase glacial acetic
acid, n-hexane, ethyl acetate and toluene (0.3: 1: 8: 2) (v/v/v/v) and distinguished at wavelength 254
nm. The technique was approved for linearity, precision, accuracy, limit of detection (LOD), limit of
quantification (LOQ), and so forth by International Conference on Harmonization guidelines.Results: The calibration range was observed to be 2- 14 μg/band for both the bioactive compounds.
KBA was isolated with an Rf estimation of 0.39 ± 0.02 and AKBA with an Rf estimation of
0.42 ± 0.02. The accuracy was seen to be as high as 99.17% and 97.42 for KBA and KBA, respectively.
The percentage RSD value for intra-day and between day varieties was under 2%. The system indicated
high affectability and specificity.Conclusion: The developed HPTLC method was simple, precise, robust, specific, rapid, and costeffective
and could be used for quality control analysis and quantification of KBA and AKBA in different
herbal formulations containing the plant species.
Mehta, M, Kalsi, V, Sharma, N, Khurana, N, Duggal, N, Khatik, GL, Singh, D, Mahajan, S, Singh, A, Satija, S, Gupta, R & Verma, S 2018, 'Pharmacognostic and pharmacological screening of Psidium guajava stem extract for its analgesic potential', International Journal of Green Pharmacy, vol. 12, no. 2, pp. 53-57. View description>>
Context: The search for biologically active compounds from natural source has always been of great interest to researchers looking for new source of drugs useful in infectious diseases. Higher plants have played a vital role as the source of important therapeutic agents. Objective: The present investigation was aimed to find novel analgesic agent from herbal origin. For the purpose, Psidium guajava stem extracts was screened for its analgesic potential. Materials and Methods: Animal model of acetic acid induced writhing was followed. Three different extracts were used to study the activity. Results: The methanolic extract at the dose tested was shown to possess analgesic activity. The significant reduction in acetic acid-induced writhings suggests that the analgesic effect may be peripherally mediated via the inhibition of synthesis and release of prostaglandins (PGs) and other endogenous substances. Discussion: The abdominal constriction response induced by acetic acid is a sensitive procedure to evaluate peripherally acting analgesics. In general acetic acid causes pain by liberating endogenous substances such as serotonin, histamine, PGs bradykinins and substance P, which stimulate nerve endings. Local peritoneal receptors are postulated to be involved in the abdominal constrictions response. Conclusion: It can be concluded that the crude extract of stem of P. guajava have given positive results for analgesic activity. These medicinal herbs may afford lead compounds which could be beneficial for future drug development.
Mehta, M, Neeta, Pandey, P, Mahajan, S & Satija, S 2018, 'Gastro retentive drug delivery systems: An overview', Research Journal of Pharmacy and Technology, vol. 11, no. 5, pp. 2157-2157. View/Download from: Publisher's site View description>>
Mehta, M, Shukla, B, Khurana, N, Arora, P, Sharma, N, Mahajan, S, Khatik, GL, Verma, S, Vyas, M & Satija, S 2018, 'Recent patent technologies of boswellic acids: A short review', Drug Invention Today, vol. 10, no. 8, pp. 1446-1449. View description>>
Boswellic acids (BAs) are pentacyclic triterpenoids and have potent biological properties that resulted in a number of protocols being developed for their synthesis. During the past 28 years (1990-2018), a number of synthetic BAs have been prepared. Both natural BAs and their synthetic derivatives can be used to treat various cancers as well as inflammatory diseases. This review covers patents on therapeutic activities of natural BAs and their synthetic derivatives published in past 28 years (1990-2018). BAs possess excellent anticancer and anti-inflammatory properties. A large number of BAs and their analogs have been prepared through modification at functional groups. Most importantly, the C-24 amide and amino derivatives demonstrated increased anticancer and anti-inflammatory activity compared with other BA derivatives. Furthermore, BAs have the potential to form conjugates with other anticancer drugs that will synergistically enhance their anticancer effects, and we believe that to get lead compounds, there needs to be a greater focus on the synthesis of halo derivatives of BAs.
Mena, J, Brito, B, Moreira, R, Tadich, T, González, I, Cruces, J, Ortega, R, van Bakel, H, Rathnasinghe, R, Pizarro-Lucero, J, Medina, R & Neira, V 2018, 'Reemergence of H3N8 Equine Influenza A virus in Chile, 2018', Transboundary and Emerging Diseases, vol. 65, no. 6, pp. 1408-1415. View/Download from: Publisher's site View description>>
A new outbreak of equine Influenza A virus (IAV) was reported in Chile in January 2018, 6 years after its last report in 2012. Equine IAV was detected by rtRT-PCR, followed by virus isolation and full genome sequencing. Genetic characterization of equine IAV classified the virus within clade 1 of the Florida sublineage. Although this is the same sublineage that caused an outbreak in Chile in 2012, the virus has a high similarity to other cocirculating viruses that were recently identified in Europe and Asia. The Chilean 2018 equine influenza (EI) outbreak was caused by an H3N8 strain circulating globally that spread through horse movements.
Miles, NG, Butler, GL, Diamond, SL, Bishop, DP, van der Meulen, DE, Reinfelds, I & Walsh, CT 2018, 'Combining otolith chemistry and telemetry to assess diadromous migration in pinkeye mullet, Trachystoma petardi (Actinopterygii, Mugiliformes)', Hydrobiologia, vol. 808, no. 1, pp. 265-281. View/Download from: Publisher's site View description>>
Mitchell, AB, Mourad, B, Buddle, L, Peters, MJ, Oliver, BGG & Morgan, LC 2018, 'Viruses in bronchiectasis: a pilot study to explore the presence of community acquired respiratory viruses in stable patients and during acute exacerbations', BMC Pulmonary Medicine, vol. 18, no. 1. View/Download from: Publisher's site
Mitchell, AB, Mourad, B, Morgan, LC, Oliver, BGG & Glanville, AR 2018, 'Transplanting the pulmonary virome: Dynamics of transient populations', The Journal of Heart and Lung Transplantation, vol. 37, no. 9, pp. 1111-1118. View/Download from: Publisher's site
Mitchell, AB, Tang, B, Shojaei, M, Barnes, LS, Nalos, M, Oliver, BG & McLean, AS 2018, 'A novel sampling method to detect airborne influenza and other respiratory viruses in mechanically ventilated patients: a feasibility study', Annals of Intensive Care, vol. 8, no. 1. View/Download from: Publisher's site View description>>
Respiratory viruses circulate constantly in the ambient air. The risk of opportunistic infection from these viruses can be increased in mechanically ventilated patients. The present study evaluates the feasibility of detecting airborne respiratory viruses in mechanically ventilated patients using a novel sample collection method involving ventilator filters.We collected inspiratory and expiratory filters from the ventilator circuits of mechanically ventilated patients in an intensive care unit over a 14-month period. To evaluate whether we could detect respiratory viruses collected in these filters, we performed a reverse transcription polymerase chain reaction on the extracted filter membrane with primers specific for rhinovirus, respiratory syncytial virus, influenza virus A and B, parainfluenza virus (type 1, 2 and 3) and human metapneumovirus. For each patient, we also performed a full virology screen (virus particles, antibody titres and virus-induced biomarkers) on respiratory samples (nasopharyngeal swab, tracheal aspirate or bronchoalveolar fluid) and blood samples.Respiratory viruses were detected in the ventilator filters of nearly half the patients in the study cohort (n = 33/70). The most common virus detected was influenza A virus (n = 29). There were more viruses detected in the inspiratory filters (n = 18) than in the expiratory filters (n = 15). A third of the patients with a positive virus detection in the ventilator filters had a hospital laboratory confirmed viral infection. In the remaining cases, the detected viruses were different from viruses already identified in the same patient, suggesting that these additional viruses come from the ambient air or from cross-contamination (staff or visitors). In patients in whom new viruses were detected in the ventilator filters, there was no evidence of clinical signs of an active viral infection. Additionally, the levels of virus-induced biomarker in these patients were not statistically different fro...
Moheimani, F, Koops, J, Williams, T, Reid, AT, Hansbro, PM, Wark, PA & Knight, DA 2018, 'Influenza A virus infection dysregulates the expression of microRNA-22 and its targets; CD147 and HDAC4, in epithelium of asthmatics', Respiratory Research, vol. 19, no. 1. View/Download from: Publisher's site View description>>
BACKGROUND:Specific microRNAs (miRNAs) play essential roles in airway remodeling in asthma. Infection with influenza A virus (IAV) may also magnify pre-existing airway remodeling leading to asthma exacerbation. However, these events remain to be fully defined. We investigated the expression of miRNAs with diverse functions including proliferation (miR-20a), differentiation (miR-22) or innate/adaptive immune responses (miR-132) in primary bronchial epithelial cells (pBECs) of asthmatics following infection with the H1N1 strain of IAV. METHODS:pBECs from subjects (n = 5) with severe asthma and non-asthmatics were cultured as submerged monolayers or at the air-liquid-interface (ALI) conditions and incubated with IAV H1N1 (MOI 5) for up to 24 h. Isolated miRNAs were subjected to Taqman miRNAs assays. We confirmed miRNA targets using a specific mimic and antagomir. Taqman mRNAs assays and immunoblotting were used to assess expression of target genes and proteins, respectively. RESULTS:At baseline, these miRNAs were expressed at the same level in pBECs of asthmatics and non-asthmatics. After 24 h of infection, miR-22 expression increased significantly which was associated with the suppression of CD147 mRNA and HDAC4 mRNA and protein expression in pBECs from non-asthmatics, cultured in ALI. In contrast, miR-22 remained unchanged while CD147 expression increased and HDAC4 remained unaffected in cells from asthmatics. IAV H1N1 mediated increases in SP1 and c-Myc transcription factors may underpin the induction of CD147 in asthmatics. CONCLUSION:The different profile of miR-22 expression in differentiated epithelial cells from non-asthmatics may indicate a self-defense mechanism against aberrant epithelial responses through suppressing CD147 and HDAC4, which is compromised in epithelial cells of asthmatics.
Moore, S, Sonar, K, Bharadwaj, P, Deplazes, E & Mancera, R 2018, 'Characterisation of the Structure and Oligomerisation of Islet Amyloid Polypeptides (IAPP): A Review of Molecular Dynamics Simulation Studies', Molecules, vol. 23, no. 9, pp. 2142-2142. View/Download from: Publisher's site View description>>
Human islet amyloid polypeptide (hIAPP) is a naturally occurring, intrinsically disordered protein whose abnormal aggregation into amyloid fibrils is a pathological feature in type 2 diabetes, and its cross-aggregation with amyloid beta has been linked to an increased risk of Alzheimer’s disease. The soluble, oligomeric forms of hIAPP are the most toxic to β-cells in the pancreas. However, the structure of these oligomeric forms is difficult to characterise because of their intrinsic disorder and their tendency to rapidly aggregate into insoluble fibrils. Experimental studies of hIAPP have generally used non-physiological conditions to prevent aggregation, and they have been unable to describe its soluble monomeric and oligomeric structure at physiological conditions. Molecular dynamics (MD) simulations offer an alternative for the detailed characterisation of the monomeric structure of hIAPP and its aggregation in aqueous solution. This paper reviews the knowledge that has been gained by the use of MD simulations, and its relationship to experimental data for both hIAPP and rat IAPP. In particular, the influence of the choice of force field and water models, the choice of initial structure, and the configurational sampling method used, are discussed in detail. Characterisation of the solution structure of hIAPP and its mechanism of oligomerisation is important to understanding its cellular toxicity and its role in disease states, and may ultimately offer new opportunities for therapeutic interventions.
Morelato, M, Broséus, J, De Grazia, A, Tahtouh, M, Esseiva, P & Roux, C 2018, 'Forensic drug intelligence and the rise of cryptomarkets. Part II: Combination of data from the physical and virtual markets', Forensic Science International, vol. 288, pp. 201-210. View/Download from: Publisher's site View description>>
Technology provides new ways to access customers and suppliers while enhancing the security of off-line criminal activity. Since the first cryptomarket, Silk Road, in 2011, cryptomarkets have transformed the traditional drug sale by facilitating the creation of a global network of vendors and buyers. Due to the fragmented nature of traces that result from illegal activities, combining the results of concurrent processes based on traces of different nature should provide supplementary benefit to understand the drug market. This article compares the data of the Australian virtual market (in particular data extracted from cryptomarkets) to the data related to traditional market descriptors, namely national seizures and arrests, prevalence data, shipping countries of seized post shipments as well as outcomes of specific surveys targeting users' behaviour online. Results revealed the domestic nature of the online illicit drug trade in Australia which is dominated by amphetamine-type substances (ATS), in particular methylamphetamine and cannabis. These illicit drugs were also the most seized drugs on the physical market. This article shows that the combination of different information offers a broader perspective of the illicit drug market in Australia and thus provides stronger arguments for policy makers. It also highlights the links between the virtual and physical markets.
Moreno-Torres, KI, Brito, BP, Branan, MA, Rodriguez, LL, Delgado, AH, Stenfeldt, C & Arzt, J 2018, 'Foot-and-Mouth Disease Infection Dynamics in Contact-Exposed Pigs Are Determined by the Estimated Exposure Dose', Frontiers in Veterinary Science, vol. 5, no. Jul. View/Download from: Publisher's site View description>>
The quantitative relationship between the exposure dose of foot-and-mouth disease virus (FMDV) and subsequent infection dynamics has been demonstrated through controlled inoculation studies in various species. However, similar quantitation of viral doses has not been achieved during contact exposure experiments due to the intrinsic difficulty of measuring the virus quantities exchanged between animals. In the current study, novel modeling techniques were utilized to investigate FMDV infection dynamics in groups of pigs that had been contact-exposed to FMDV-infected donors shedding varying levels of virus, as well as in pigs inoculated via the intra-oropharyngeal (IOP) route. Estimated virus exposure doses were modeled and were found to be statistically significantly associated with the dynamics of FMDV RNA detection in serum and oropharyngeal fluid (OPF), and with the time to onset of clinical disease. The minimum estimated shedding quantity in OPF that defined infectiousness of donor pigs was 6.55 log10 genome copy numbers (GCN)/ml (95% CI 6.11, 6.98), which delineated the transition from the latent to infectious phase of disease which occurred during the incubation phase. This quantity corresponded to a minimum estimated exposure dose of 5.07 log10 GCN/ml (95% CI 4.25, 5.89) in contact-exposed pigs. Thus, we demonstrated that a threshold quantity of FMDV detection in donor pigs was necessary in order to achieve transmission by direct contact. The outcomes from this investigation demonstrate that variability of infection dynamics which occurs during the progression of FMD in naturally exposed pigs can be partially attributed to variations in exposure dose. Moreover, these modeling approaches for dose-quantitation may be retrospectively applied to contact-exposure experiments or field scenarios. Hence, robust information could be incorporated into models used to evaluate FMD spread and control.
Moret, S, Scott, E, Barone, A, Liang, K, Lennard, C, Roux, C & Spindler, X 2018, 'Metal-Organic Frameworks for fingermark detection — A feasibility study', Forensic Science International, vol. 291, pp. 83-93. View/Download from: Publisher's site View description>>
Metal-Organic Frameworks (MOFs) are porous crystalline structures, currently used as sensors, separation membranes, and as catalysts. Due to their physicochemical and optical properties, they have been recently proposed for fingermark detection. This study further explored their potential for fingermark detection. Natural fingermarks, as well as charged and protein-enriched marks, were used to test the efficiency of the technique. Various parameters, such as precursor concentration, pH, immersion time and detection protocols, were investigated and optimised. The performance of the optimised MOF-based method was then compared to that of routinely used techniques. The results obtained indicated that MOFs can effectively detect fingermarks, especially protein-rich marks such as marks contaminated with body fluids. However, after comparison and evaluation against benchmark techniques, results were judged to be inferior to those from currently employed detection methods. However, with further research and optimisation MOFs may be promising as an alternative to current powder suspension techniques.
Moulder, D, Hatoum, D, Tay, E, Lin, Y & McGowan, E 2018, 'The Roles of p53 in Mitochondrial Dynamics and Cancer Metabolism: The Pendulum between Survival and Death in Breast Cancer?', Cancers, vol. 10, no. 6, pp. 189-189. View/Download from: Publisher's site View description>>
Abstract: Cancer research has been heavily geared towards genomic events in the development
and progression of cancer. In contrast, metabolic regulation, such as aberrant metabolism in
cancer, is poorly understood. Alteration in cellular metabolism was once regarded simply as a
consequence of cancer rather than as playing a primary role in cancer promotion and maintenance.
Resurgence of cancer metabolism research has identified critical metabolic reprogramming events
within biosynthetic and bioenergetic pathways needed to fulfill the requirements of cancer cell growth
and maintenance. The tumor suppressor protein p53 is emerging as a key regulator of metabolic
processes and metabolic reprogramming in cancer cells—balancing the pendulum between cell death
and survival. This review provides an overview of the classical and emerging non-classical tumor
suppressor roles of p53 in regulating mitochondrial dynamics: mitochondrial engagement in cell
death processes in the prevention of cancer. On the other hand, we discuss p53 as a key metabolic
switch in cellular function and survival. The focus is then on the conceivable roles of p53 in breast
cancer metabolism. Understanding the metabolic functions of p53 within breast cancer metabolism
will, in due course, reveal critical metabolic hotspots that cancers advantageously re-engineer for
sustenance. Illustration of these events will pave the way for finding novel therapeutics that target
cancer metabolism and serve to overcome the breast cancer burden.
Mukherjee, M, Hu, Y, Tan, CH, Rice, SA & Cao, B 2018, 'Engineering a light-responsive, quorum quenching biofilm to mitigate biofouling on water purification membranes', Science Advances, vol. 4, no. 12. View/Download from: Publisher's site View description>>
We engineered a light-responsive, quorum quenching biofilm and demonstrated its application in mitigating membrane biofouling.
Mukhopadhyay, U, Dehollain, JP, Reichl, C, Wegscheider, W & Vandersypen, LMK 2018, 'A 2x2 quantum dot array with controllable inter-dot tunnel couplings', Appl. Phys. Lett., vol. 112, no. 18, p. 183505. View/Download from: Publisher's site View description>>
The interaction between electrons in arrays of electrostatically defined
quantum dots is naturally described by a Fermi-Hubbard Hamiltonian. Moreover,
the high degree of tunability of these systems make them a powerful platform to
simulate different regimes of the Hubbard model. However, most quantum dot
array implementations have been limited to one-dimensional linear arrays. In
this letter, we present a square lattice unit cell of 2$\times$2 quantum dots
defined electrostatically in a AlGaAs/GaAs heterostructure using a double-layer
gate technique. We probe the properties of the array using nearby quantum dots
operated as charge sensors. We show that we can deterministically and
dynamically control the charge occupation in each quantum dot in the single- to
few-electron regime. Additionally, we achieve simultaneous individual control
of the nearest-neighbor tunnel couplings over a range 0-40~$\mu$eV. Finally, we
demonstrate fast ($\sim 1$~$\mu$s) single-shot readout of the spin state of
electrons in the dots, through spin-to-charge conversion via Pauli spin
blockade. These advances pave the way to analog quantum simulations in two
dimensions, not previously accessible in quantum dot systems.
In response to an increasing risk of property loss from wildfires at the urban–wildland interface, there has been growing interest around the world in the plant characteristics of urban gardens that can be manipulated to minimize the chances of property damage or destruction. To date, considerable discussion of this issue can be found in the ‘grey’ literature, covering garden characteristics such as the spatial arrangement of plants in relation to each other, proximity of plants to houses, plant litter and fuel reduction, and the use of low-flammability plants as green firebreaks [1,2,3,4]. Recently, scientific studies from a geographically wide range of fire-prone regions including Europe [5], the USA [6], Australia [7], South Africa [8], and New Zealand [9] have been explicitly seeking to quantify variation among plant species with respect to different aspects of their flammability and to identify low-flammability horticultural species appropriate for implementation as green firebreaks in urban landscapes. The future prospects of this scientific work will ultimately depend on how successfully the results are integrated into the broader context of garden design in fire-prone regions at the urban–wildland interface. Although modern design of urban gardens must consider more than just the issue of green firebreaks, we and others [10,11] believe that selection of low-flammability plants should be high on the priority list of plant selection criteria in fire-prone regions.
Murray, M, Gillani, TB, Ghassabian, S, Edwards, RJ & Rawling, T 2018, 'Differential effects of hepatic cirrhosis on the intrinsic clearances of sorafenib and imatinib by CYPs in human liver', European Journal of Pharmaceutical Sciences, vol. 114, pp. 55-63. View/Download from: Publisher's site View description>>
The tyrosine kinase inhibitors sorafenib and imatinib are important in the treatment of a range of cancers but adverse effects in some patients necessitate dosage modifications. CYP3A4 has a major role in the oxidation of sorafenib to its N-oxide and N-hydroxymethyl metabolites and also acts in concert with CYP2C8 to mediate imatinib N-demethylation. CYP3A4 expression and function are impaired in patients with advanced liver disease, whereas the functions of CYP2C enzymes are relatively preserved. We evaluated the biotransformation of sorafenib and imatinib in well-characterized microsomal fractions from 17 control subjects and 19 individuals with hepatic cirrhosis of varying severity. The principal findings were that liver disease impaired the microsomal oxidation of sorafenib to its major metabolites to 40-44% of control (P<0.01), whereas the N-demethylation of imatinib was relatively unimpaired. The impairments in sorafenib biotransformation were correlated with decreased serum albumin concentrations and increased serum bilirubin concentrations in patients with liver disease, but not with the overall grade of liver disease according to the Child-Pugh system. In contrast, there was no relationship between imatinib N-demethylation and clinicopathologic factors in liver disease patients. These findings were accounted for in terms of the differential roles of CYPs 3A4 and 2C8 in the intrinsic clearance of the drugs. CYP3A4 has the major role in the intrinsic clearance of sorafenib but plays a secondary role to CYP2C8 in the intrinsic clearance of imatinib. In agreement with these findings CYP2C protein expression and CYP2C8-mediated paclitaxel 6α-hydroxylation were unimpaired in cirrhotic livers. This information could be adapted in individualized approaches such as in vivo CYP3A4 phenotyping to optimize sorafenib safety and efficacy in cancer patients with liver dysfunction.
Musumeci, G, Leggio, G, Marzagalli, R, Al-Badri, G, Drago, F & Castorina, A 2018, 'Identification of Dysregulated microRNA Networks in Schwann Cell-Like Cultures Exposed to Immune Challenge: Potential Crosstalk with the Protective VIP/PACAP Neuropeptide System', International Journal of Molecular Sciences, vol. 19, no. 4, pp. 981-981. View/Download from: Publisher's site View description>>
Following peripheral nerve injury, dysregulations of certain non-coding microRNAs (miRNAs) occur in Schwann cells. Whether these alterations are the result of local inflammation and/or correlate with perturbations in the expression profile of the protective vasoactive intestinal peptide (VIP)/pituitary adenylate cyclase-activating polypeptide (PACAP) system is currently unknown. To address these issues, we aimed at profiling the expression of selected miRNAs in the rat RT4 Schwann cell line. Cells exposed to lipopolysaccharide (LPS), to mimic the local inflammatory milieu, were appraised by real-time qPCR, Western blot and ELISAs. We found that upon LPS treatment, levels of pro-inflammatory cytokines (IL-1β, -6, -18, -17A, MCP-1 and TNFα) increased in a time-dependent manner. Unexpectedly, the expression levels of VIP and PACAP were also increased. Conversely, levels of VPAC1 and VPAC2 receptors were reduced. Downregulated miRNAs included miR-181b, -145, -27a, -340 and -132 whereas upregulated ones were miR-21, -206, -146a, -34a, -155, -204 and -29a, respectively. Regression analyses revealed that a subset of the identified miRNAs inversely correlated with the expression of VPAC1 and VPAC2 receptors. In conclusion, these findings identified a novel subset of miRNAs that are dysregulated by immune challenge whose activities might elicit a regulatory function on the VIP/PACAP system.
Nair, PM, Starkey, MR, Haw, TJ, Ruscher, R, Liu, G, Maradana, MR, Thomas, R, O’Sullivan, BJ & Hansbro, PM 2018, 'RelB-Deficient Dendritic Cells Promote the Development of Spontaneous Allergic Airway Inflammation', American Journal of Respiratory Cell and Molecular Biology, vol. 58, no. 3, pp. 352-365. View/Download from: Publisher's site
Nazimi, L, Robbins, WD, Schilds, A & Huveneers, C 2018, 'Comparison of industry-based data to monitor white shark cage-dive tourism', Tourism Management, vol. 66, pp. 263-273. View/Download from: Publisher's site View description>>
Nedeljkovic, I, Carnero-Montoro, E, Lahousse, L, van der Plaat, DA, de Jong, K, Vonk, JM, van Diemen, CC, Faiz, A, van den Berge, M, Obeidat, M, Bossé, Y, Nickle, DC, Consortium, BIOS, Uitterlinden, AG, van Meurs, JJB, Stricker, BCH, Brusselle, GG, Postma, DS, Boezen, HM, van Duijn, CM & Amin, N 2018, 'Understanding the role of the chromosome 15q25.1 in COPD through epigenetics and transcriptomics', European Journal of Human Genetics, vol. 26, no. 5, pp. 709-722. View/Download from: Publisher's site View description>>
Chronic obstructive pulmonary disease (COPD) is a major health burden in adults and cigarette smoking is considered the most important environmental risk factor of COPD. Chromosome 15q25.1 locus is associated with both COPD and smoking. Our study aims at understanding the mechanism underlying the association of chromosome 15q25.1 with COPD through epigenetic and transcriptional variation in a population-based setting. To assess if COPD-associated variants in 15q25.1 are methylation quantitative trait loci, epigenome-wide association analysis of four genetic variants, previously associated with COPD (P < 5 × 10-8) in the 15q25.1 locus (rs12914385:C>T-CHRNA3, rs8034191:T>C-HYKK, rs13180:C>T-IREB2 and rs8042238:C>T-IREB2), was performed in the Rotterdam study (n = 1489). All four variants were significantly associated (P < 1.4 × 10-6) with blood DNA methylation of IREB2, CHRNA3 and PSMA4, of which two, including IREB2 and PSMA4, were also differentially methylated in COPD cases and controls (P < 0.04). Further additive and multiplicative effects of smoking were evaluated and no significant effect was observed. To evaluate if these four genetic variants are expression quantitative trait loci, transcriptome-wide association analysis was performed in 1087 lung samples. All four variants were also significantly associated with differential expression of the IREB2 3'UTR in lung tissues (P < 5.4 × 10-95). We conclude that regulatory mechanisms affecting the expression of IREB2 gene, such as DNA methylation, may explain the association between genetic variants in chromosome 15q25.1 and COPD, largely independent of smoking.
Nedeljkovic, I, Lahousse, L, Carnero-Montoro, E, Faiz, A, Vonk, JM, de Jong, K, van der Plaat, DA, van Diemen, CC, van den Berge, M, Obeidat, M, Bossé, Y, Nickle, DC, Consortium, BIOS, Uitterlinden, AG, van Meurs, JBJ, Stricker, BHC, Brusselle, GG, Postma, DS, Boezen, HM, van Duijn, CM & Amin, N 2018, 'COPD GWAS variant at 19q13.2 in relation with DNA methylation and gene expression', Human Molecular Genetics, vol. 27, no. 2, pp. 396-405. View/Download from: Publisher's site View description>>
Chronic obstructive pulmonary disease (COPD) is among the major health burdens in adults. While cigarette smoking is the leading risk factor, a growing number of genetic variations have been discovered to influence disease susceptibility. Epigenetic modifications may mediate the response of the genome to smoking and regulate gene expression. Chromosome 19q13.2 region is associated with both smoking and COPD, yet its functional role is unclear. Our study aimed to determine whether rs7937 (RAB4B, EGLN2), a top genetic variant in 19q13.2 region identified in genome-wide association studies of COPD, is associated with differential DNA methylation in blood (N = 1490) and gene expression in blood (N = 721) and lungs (N = 1087). We combined genetic and epigenetic data from the Rotterdam Study (RS) to perform the epigenome-wide association analysis of rs7937. Further, we used genetic and transcriptomic data from blood (RS) and from lung tissue (Lung expression quantitative trait loci mapping study), to perform the transcriptome-wide association study of rs7937. Rs7937 was significantly (FDR < 0.05) and consistently associated with differential DNA methylation in blood at 4 CpG sites in cis, independent of smoking. One methylation site (cg11298343-EGLN2) was also associated with COPD (P = 0.001). Additionally, rs7937 was associated with gene expression levels in blood in cis (EGLN2), 42% mediated through cg11298343, and in lung tissue, in cis and trans (NUMBL, EGLN2, DNMT3A, LOC101929709 and PAK2). Our results suggest that changes of DNA methylation and gene expression may be intermediate steps between genetic variants and COPD, but further causal studies in lung tissue should confirm this hypothesis.
Neshev, D & Aharonovich, I 2018, 'Optical metasurfaces: new generation building blocks for multi-functional optics', Light: Science & Applications, vol. 7, no. 1. View/Download from: Publisher's site View description>>
AbstractOptical metasurfaces (OMs) have emerged as promising candidates to solve the bottleneck of bulky optical elements. OMs offer a fundamentally new method of light manipulation based on scattering from resonant nanostructures rather than conventional refraction and propagation, thus offering efficient phase, polarization, and emission control. This perspective highlights state of the art OMs and provides a roadmap for future applications, including active generation, manipulation and detection of light for quantum technologies, holography and sensing.
New, EJ, Wimmer, VC & Hare, DJ 2018, 'Promises and Pitfalls of Metal Imaging in Biology', Cell Chemical Biology, vol. 25, no. 1, pp. 7-18. View/Download from: Publisher's site View description>>
A picture may speak a thousand words, but if those words fail to form a coherent sentence there is little to be learned. As cutting-edge imaging technology now provides us the tools to decipher the multitude of roles played by metals and metalloids in molecular, cellular, and developmental biology, as well as health and disease, it is time to reflect on the advances made in imaging, the limitations discovered, and the future of a burgeoning field. In this Perspective, the current state of the art is discussed from a self-imposed contrarian position, as we not only highlight the major advances made over the years but use them as teachable moments to zoom in on challenges that remain to be overcome. We also describe the steps being taken toward being able to paint a completely undisturbed picture of cellular metal metabolism, which is, metaphorically speaking, the Holy Grail of the discipline.
Newton, K, Jeffries, TC, Smith, RJ, Seymour, JR, Seuront, L & Mitchell, JG 2018, 'Taxonomic and metabolic shifts in the Coorong bacterial metagenome driven by salinity and external inputs', Journal of Oceanology and Limnology, vol. 36, no. 6, pp. 2033-2049. View/Download from: Publisher's site View description>>
Ng, ZY, Wong, J-Y, Panneerselvam, J, Madheswaran, T, Kumar, P, Pillay, V, Hsu, A, Hansbro, N, Bebawy, M, Wark, P, Hansbro, P, Dua, K & Chellappan, DK 2018, 'Assessing the potential of liposomes loaded with curcumin as a therapeutic intervention in asthma', Colloids and Surfaces B: Biointerfaces, vol. 172, pp. 51-59. View/Download from: Publisher's site
Nguyen, HT, Ma, X, Newbigin, E, Beggs, P, Davies, J & Huete, A 2018, 'Grassland Phenology and Meteorology Co-Influence Grass Pollen Counts in Victoria, Australia', ISEE Conference Abstracts, vol. 2018, no. 1. View/Download from: Publisher's site
Nguyen, LT, Chen, H, Mak, C, Zaky, A, Pollock, C & Saad, S 2018, 'SRT1720 attenuates obesity and insulin resistance but not liver damage in the offspring due to maternal and postnatal high-fat diet consumption', American Journal of Physiology-Endocrinology and Metabolism, vol. 315, no. 2, pp. E196-E203. View/Download from: Publisher's site View description>>
Recent studies indicate that sirtuin-1 (SIRT1), an important metabolic sensor and regulator of life span, plays a mechanistic role in maternal obesity-induced programming of metabolic disorders in the offspring. In this study we investigate whether SIRT1 activation in early childhood can mitigate metabolic disorders due to maternal and postnatal high-fat feeding in mice. Male offspring born to chow-fed (MC) or high fat diet-fed dams (MHF) were weaned onto postnatal chow or high-fat diet and treated with SRT1720 (25 mg/kg ip every 2 days) or vehicle control for 6 wk and examined for metabolic disorders. MHF exacerbated offspring body weight and insulin resistance in the offspring exposed to postnatal HFD (OHF). These metabolic changes were associated with reduced hepatic lipid droplet accumulation but increased plasma levels of alanine aminotransferase (ALT), a marker of liver damage. SRT1720 significantly decreased offspring body weight, adiposity, glucose intolerance, and hyperleptinemia due to OHF and reversed hyperinsulinemia and adipocyte hypertrophy due to the additive effects of MHF. Although SRT1720 suppresses liver lipogenesis, inflammation, and oxidative stress markers, it also reduces antioxidants and increased liver collagen deposition in OHF offspring independent of MHF. Hepatic steatosis was attenuated only in MC/OHF offspring in association with elevated plasma ALT levels. The study suggests that postnatal SRT1720 administration can mitigate obesity and insulin resistance in the offspring due to maternal and postnatal HFD exposure. However, the possibility of liver toxicity needs to be further examined.
Single-photon emitters in gallium nitride (GaN) are gaining interest as
attractive quantum systems due to the well-established techniques for growth
and nanofabrication of the host material, as well as its remarkable chemical
stability and optoelectronic properties. We investigate the nature of such
single-photon emitters in GaN with a systematic analysis of various samples
produced under different growth conditions. We explore the effect that
intrinsic structural defects (dislocations and stacking faults), doping and
crystal orientation in GaN have on the formation of quantum emitters. We
investigate the relationship between the position of the emitters (determined
via spectroscopy and photoluminescence measurements) and the location of
threading dislocations (characterised both via atomic force microscopy and
cathodoluminescence). We find that quantum emitters do not correlate with
stacking faults or dislocations; instead, they are more likely to originate
from point defects or impurities whose density is modulated by the local
extended defect density.
Electronic cigarette (e-cigarette) use is on the rise worldwide and is particularly attractive to young people and as a smoking substitute by pregnant woman. There is a perception in pregnant women and women of child-bearing age that the use of e-cigarettes (vaping) is safer than smoking tobacco cigarettes during pregnancy. However, there is little evidence to support this perception. Here, we examined the offspring from mouse dams that had been exposed during and after pregnancy to ambient air (sham) ( n = 8), e-cigarette aerosols with nicotine ( n = 8), or e-cigarette aerosols without nicotine ( n = 8). Offspring underwent cognitive testing at 12 weeks of age and epigenetic testing of brain tissues at 1 day, 20 days, and 13 weeks after birth. The findings showed deficits in short-term memory, reduced anxiety, and hyperactivity in offspring following maternal e-cigarette exposure using the novel object recognition and elevated plus maze tests. In addition, global DNA methylation was increased in the brains of offspring soon after birth. Using a quantitative-PCR array specific to chromatin modification enzymes on genomic DNA and histones,13 key genes were identified to be significantly altered in the offspring brains from the e-cigarette groups compared to the nonexposed groups. The changes to genes Aurka, Aurkb, Aurkc, Kdm5c, Kdm6b, Dnmt3a, Dnmt3b, and Atf2, all associated with modulating neurological activity, were validated using RT-qPCR. In conclusion, in a mouse model, maternal exposure to e-cigarette aerosols resulted in both cognitive and epigenetic changes in offspring. This suggests that the use of e-cigarettes during pregnancy may have hitherto undetected neurological consequences on newborns.
Ocean warming is resulting in increased occurrence of mass coral bleaching; a response in which the intracellular algal endosymbionts (Symbiodinium sp.) are expelled from the coral host due to physiological stress. This detrimental process is often attributed to overproduction of reactive oxygen species (ROS) that leak out of the endosymbionts and causes damage to the host cell, though direct evidence validating this link is limited. Here, for the first time, we used confocal microscopy and fluorescent dyes to investigate if endosymbiont ROS production significantly and predictably affects physiological parameters in its host cell. Heat treatment resulted in a 60% reduction in coral symbiont density, a ~70% increase in median endosymbiont ROS and a small reduction in photosystem efficiency (FV/FM, 11%), indicating absence of severe light stress. Notably, no other physiological parameters were affected in either endosymbionts or host cells, including reduced glutathione and ROS-induced lipid peroxidation. Taken together, the increase in endosymbiont ROS could not be linked to physiological damage in either partner, suggesting that oxidative stress is unlikely to have been the driver for symbiont expulsion in this study.
Nissen, G, Hollaender, H, Tang, FSM, Wegmann, M, Lunding, L, Vock, C, Bachmann, A, Lemmel, S, Bartels, R, Oliver, BG, Burgess, JK, Becker, T, Kopp, MV & Weckmann, M 2018, 'Tumstatin fragment selectively inhibits neutrophil infiltration in experimental asthma exacerbation', Clinical & Experimental Allergy, vol. 48, no. 11, pp. 1483-1493. View/Download from: Publisher's site
Nitschke, MR, Gardner, SG, Goyen, S, Fujise, L, Camp, EF, Ralph, PJ & Suggett, DJ 2018, 'Utility of Photochemical Traits as Diagnostics of Thermal Tolerance amongst Great Barrier Reef Corals', Frontiers in Marine Science, vol. 5, no. FEB. View/Download from: Publisher's site View description>>
Nixon, GL, McEntee, L, Johnson, A, Farrington, N, Whalley, S, Livermore, J, Natal, C, Washbourn, G, Bibby, J, Berry, N, Lestner, J, Truong, M, Owen, A, Lalloo, D, Charles, I & Hope, W 2018, 'Repurposing and Reformulation of the Antiparasitic Agent Flubendazole for Treatment of Cryptococcal Meningoencephalitis, a Neglected Fungal Disease', Antimicrobial Agents and Chemotherapy, vol. 62, no. 4. View/Download from: Publisher's site View description>>
ABSTRACT
Current therapeutic options for cryptococcal meningitis are limited by toxicity, global supply, and emergence of resistance. There is an urgent need to develop additional antifungal agents that are fungicidal within the central nervous system and preferably orally bioavailable. The benzimidazoles have broad-spectrum antiparasitic activity but also have
in vitro
antifungal activity that includes
Cryptococcus neoformans
. Flubendazole (a benzimidazole) has been reformulated by Janssen Pharmaceutica as an amorphous solid drug nanodispersion to develop an orally bioavailable medicine for the treatment of neglected tropical diseases such as onchocerciasis. We investigated the
in vitro
activity, the structure-activity-relationships, and both
in vitro
and
in vivo
pharmacodynamics of flubendazole for cryptococcal meningitis. Flubendazole has potent
in vitro
activity against
Cryptococcus neoformans
, with a modal MIC of 0.125 mg/liter using European Committee on Antimicrobial Susceptibility Testing (EUCAST) methodology. Computer models provided an insight into the residues responsible for the binding of flubendazole to cryptococcal β-tubulin. Rapid fungicidal activity was evident in a hollow-fiber infection model of cryptococcal meningitis. The solid drug nanodispersion was orally bioavailable in mice with higher drug exposure in the cerebrum. The maximal dose of flubendazole (12 mg/kg of body weight/day) orally resulted in an ∼2 log
10
...
Nolan, LM, Whitchurch, CB, Barquist, L, Katrib, M, Boinett, CJ, Mayho, M, Goulding, D, Charles, IG, Filloux, A, Parkhill, J & Cain, AK 2018, 'A global genomic approach uncovers novel components for twitching motility-mediated biofilm expansion in Pseudomonas aeruginosa', Microbial Genomics, vol. 4, no. 11. View/Download from: Publisher's site View description>>
Pseudomonas aeruginosa is an extremely successful pathogen able to cause both acute and chronic infections in a range of hosts, utilizing a diverse arsenal of cell-associated and secreted virulence factors. A major cell-associated virulence factor, the Type IV pilus (T4P), is required for epithelial cell adherence and mediates a form of surface translocation termed twitching motility, which is necessary to establish a mature biofilm and actively expand these biofilms. P. aeruginosa twitching motility-mediated biofilm expansion is a coordinated, multicellular behaviour, allowing cells to rapidly colonize surfaces, including implanted medical devices. Although at least 44 proteins are known to be involved in the biogenesis, assembly and regulation of the T4P, with additional regulatory components and pathways implicated, it is unclear how these components and pathways interact to control these processes. In the current study, we used a global genomics-based random-mutagenesis technique, transposon directed insertion-site sequencing (TraDIS), coupled with a physical segregation approach, to identify all genes implicated in twitching motility-mediated biofilm expansion in P. aeruginosa. Our approach allowed identification of both known and novel genes, providing new insight into the complex molecular network that regulates this process in P. aeruginosa. Additionally, our data suggest that the flagellum-associated gene products have a differential effect on twitching motility, based on whether components are intra- or extracellular. Overall the success of our TraDIS approach supports the use of this global genomic technique for investigating virulence genes in bacterial pathogens.
ABSTRACTVibrio vulnificus
, a ubiquitous inhabitant of coastal marine environments, has been isolated from a variety of sources. It is an opportunistic pathogen of both marine animals and humans. Here, the genome sequence of
V. vulnificus
Env1, an environmental isolate resistant to predation by the ciliate
Tetrahymena pyriformis
, is reported.
O’Neil, JD, Ammit, AJ & Clark, AR 2018, 'MAPK p38 regulates inflammatory gene expression via tristetraprolin: Doing good by stealth', The International Journal of Biochemistry & Cell Biology, vol. 94, pp. 6-9. View/Download from: Publisher's site View description>>
Tristetraprolin (TTP) is an RNA-destabilizing protein that exerts profound anti-inflammatory effects by inhibiting the expression of tumour necrosis factor and many other inflammatory mediators. The mitogen-activated protein kinase (MAPK) p38 signaling pathway controls the strength and duration of inflammatory responses by regulating both the expression and function of TTP. The kinase MK2 (MAPK activated kinase 2) is activated by MAPK p38, and in turn phosphorylates TTP at two critical serine residues. One consequence of these phosphorylations is the protection of TTP from proteasome-mediated degradation. Another consequence is the loss of mRNA destabilizing activity. The control of TTP expression and function by the MAPK p38 pathway provides an elegant mechanism for coupling the on and off phases of inflammatory responses, and dictating the precise kinetics of expression of individual inflammatory mediators.
O’Rourke, MB, Raymond, BBA, Djordjevic, SP & Padula, MP 2018, 'The Effect of Collimating Lens Focusing on Laser Beam Shape in Matrix Assisted Laser Desorption/Ionization Mass Spectrometry (MALDI-MS)', Journal of the American Society for Mass Spectrometry, vol. 29, no. 3, pp. 512-515. View/Download from: Publisher's site
Obeidat, M, Dvorkin-Gheva, A, Li, X, Bossé, Y, Brandsma, C-A, Nickle, DC, Hansbro, PM, Faner, R, Agusti, A, Paré, PD, Stampfli, MR & Sin, DD 2018, 'The Overlap of Lung Tissue Transcriptome of Smoke Exposed Mice with Human Smoking and COPD', Scientific Reports, vol. 8, no. 1. View/Download from: Publisher's site View description>>
AbstractGenome-wide mRNA profiling in lung tissue from human and animal models can provide novel insights into the pathogenesis of chronic obstructive pulmonary disease (COPD). While 6 months of smoke exposure are widely used, shorter durations were also reported. The overlap of short term and long-term smoke exposure in mice is currently not well understood, and their representation of the human condition is uncertain. Lung tissue gene expression profiles of six murine smoking experiments (n = 48) were obtained from the Gene Expression Omnibus (GEO) and analyzed to identify the murine smoking signature. The “human smoking” gene signature containing 386 genes was previously published in the lung eQTL study (n = 1,111). A signature of mild COPD containing 7 genes was also identified in the same study. The lung tissue gene signature of “severe COPD” (n = 70) contained 4,071 genes and was previously published. We detected 3,723 differentially expressed genes in the 6 month-exposure mice datasets (FDR <0.1). Of those, 184 genes (representing 48% of human smoking) and 1,003 (representing 27% of human COPD) were shared with the human smoking-related genes and the COPD severity-related genes, respectively. There was 4-fold over-representation of human and murine smoking-related genes (P = 6.7 × 10−26) and a 1.4 fold in the severe COPD -related genes (P = 2.3 × 10−12). There was no significant enrichment of the mice and human smoking-related genes in mild COPD signature. These data suggest that murine smoke models are strongly representative of molecular processes of human smoking but less of COPD.
O'Donoghue, SI, Baldi, BF, Clark, SJ, Darling, AE, Hogan, JM, Kaur, S, Maier-Hein, L, McCarthy, DJ, Moore, WJ, Stenau, E, Swedlow, JR, Vuong, J & Procter, JB 2018, 'Visualization of Biomedical Data', Annual Review of Biomedical Data Science, vol. 1, no. 1, pp. 275-304. View/Download from: Publisher's site View description>>
The rapid increase in volume and complexity of biomedical data requires changes in research, communication, and clinical practices. This includes learning how to effectively integrate automated analysis with high–data density visualizations that clearly express complex phenomena. In this review, we summarize key principles and resources from data visualization research that help address this difficult challenge. We then survey how visualization is being used in a selection of emerging biomedical research areas, including three-dimensional genomics, single-cell RNA sequencing (RNA-seq), the protein structure universe, phosphoproteomics, augmented reality–assisted surgery, and metagenomics. While specific research areas need highly tailored visualizations, there are common challenges that can be addressed with general methods and strategies. Also common, however, are poor visualization practices. We outline ongoing initiatives aimed at improving visualization practices in biomedical research via better tools, peer-to-peer learning, and interdisciplinary collaboration with computer scientists, science communicators, and graphic designers. These changes are revolutionizing how we see and think about our data.
Oh, B, Eade, T, Kneebone, A, Hruby, G, Lamoury, G, Pavlakis, N, Clarke, S, Zaslawski, C, Marr, I, Costa, D & Back, M 2018, 'Acupuncture in Oncology: The Effectiveness of Acupuncture May Not Depend on Needle Retention Duration', Integrative Cancer Therapies, vol. 17, no. 2, pp. 458-466. View/Download from: Publisher's site View description>>
Background. Guidelines surrounding optimum needle retention duration in acupuncture have not been established, despite a growing evidence base for acupuncture over recent decades. This retrospective study explored the effect of varying acupuncture needle retention durations in cancer patients. Method. Patients received either 2 (n = 35), 10 (n = 53), or 20 minutes (n = 54) of acupuncture once a week for 6 weeks. Outcomes of anxiety and depression, stress, fatigue, and quality of life (QOL), with the Hospital Anxiety and Depression Scale, Perceived Stress Scale, Functional Assessment of Cancer Therapy–Fatigue, and European Organization for Research and Treatment of Cancer Quality of Life, were measured at baseline and at 6 weeks following the intervention. Results. The mean age of participants was 58 years (n = 152). The majority were female, diagnosed with breast cancer. Depression, stress, fatigue, and QOL were significantly improved in all 3 groups at 6 weeks postintervention. No significant differences in all outcomes were found between the 3 groups (≤2 vs 10 minutes vs 20 minutes). There were no differences with the satisfaction of the acupuncture services and perceived efficacy of acupuncture among the 3 groups. More than 95% of participants indicated that they would recommend acupuncture to other cancer patients, friends, and their family members. Conclusion. The efficacy of acupuncture may not only depend on needle retention duration, but may also be associated with multiple factors. Considering the limitations of this study design, robust randomized controlled studies are warranted to confirm the findings.
Oh, B, Yeung, A, Klein, P, Larkey, L, Ee, C, Zaslawski, C, Knobf, T, Payne, P, Stener-Victorin, E, Lee, R, Choi, W, Chun, M, Bonucci, M, Lang, H-D, Pavlakis, N, Boyle, F, Clarke, S, Back, M, Yang, P, Wei, Y, Guo, X, Weng, C-H, Irwin, M, Elfiky, A & Rosenthal, D 2018, 'Accreditation Standard Guideline Initiative for Tai Chi and Qigong Instructors and Training Institutions', Medicines, vol. 5, no. 2, pp. 51-51. View/Download from: Publisher's site View description>>
Evidence of the health and wellbeing benefits of Tai Chi and Qigong (TQ) have emerged in the past two decades, but TQ is underutilized in modern health care in Western countries due to lack of promotion and the availability of professionally qualified TQ instructors. To date, there are no government regulations for TQ instructors or for training institutions in China and Western countries, even though TQ is considered to be a part of Traditional Chinese medicine that has the potential to manage many chronic diseases. Based on an integrative health care approach, the accreditation standard guideline initiative for TQ instructors and training institutions was developed in collaboration with health professionals, integrative medicine academics, Tai Chi and Qigong master instructors and consumers including public safety officers from several countries, such as Australia, Canada, China, Germany, Italy, Korea, Sweden and USA. In this paper, the rationale for organizing the Medical Tai Chi and Qigong Association (MTQA) is discussed and the accreditation standard guideline for TQ instructors and training institutions developed by the committee members of MTQA is presented. The MTQA acknowledges that the proposed guidelines are broad, so that the diversity of TQ instructors and training institutions can be integrated with recognition that these guidelines can be developed with further refinement. Additionally, these guidelines face challenges in understanding the complexity of TQ associated with different principles, philosophies and schools of thought. Nonetheless, these guidelines represent a necessary first step as primary resource to serve and guide health care professionals and consumers, as well as the TQ community.
Oh, H-S, Constancias, F, Ramasamy, C, Tang, PYP, Yee, MO, Fane, AG, McDougald, D & Rice, SA 2018, 'Biofouling control in reverse osmosis by nitric oxide treatment and its impact on the bacterial community', Journal of Membrane Science, vol. 550, pp. 313-321. View/Download from: Publisher's site View description>>
Ollivier, QR, Hammill, E, Booth, DJ, Madin, EMP, Hinchliffe, C, Harborne, AR, Lovelock, CE, Macreadie, PI & Atwood, TB 2018, 'Benthic meiofaunal community response to the cascading effects of herbivory within an algal halo system of the Great Barrier Reef', PLOS ONE, vol. 13, no. 3, pp. e0193932-e0193932. View/Download from: Publisher's site
Reproducibility has been one of the biggest hurdles faced when attempting to develop quantitative protocols for MALDI mass spectrometry. The heterogeneous nature of sample recrystallization has made automated sample acquisition somewhat “hit and miss” with manual intervention needed to ensure that all sample spots have been analyzed. In this review, we explore the last 30 years of literature and anecdotal evidence that has attempted to address and improve reproducibility in MALDI MS. Though many methods have been attempted, we have discovered a significant publication history surrounding the use of nitrocellulose as a substrate to improve homogeneity of crystal formation and therefore reproducibility. We therefore propose that this is the most promising avenue of research for developing a comprehensive and universal preparation protocol for quantitative MALDI MS analysis
O'Rourke, MB, Padula, MP, Smith, C, Youssef, P, Cordwell, S, Witting, P, Sutherland, G & Crossett, B 2018, 'Optimal Preparation of Formalin Fixed Samples for Peptide Based Matrix Assisted Laser Desorption/Ionization Mass Spectrometry Imaging Workflows', Journal of Visualized Experiments, no. 131. View/Download from: Publisher's site View description>>
The use of matrix-assisted laser desorption/ionization, mass spectrometry imaging (MALDI MSI) has rapidly expanded, since this technique analyzes a host of biomolecules from drugs and lipids to N-glycans. Although various sample preparation techniques exist, detecting peptides from formaldehyde preserved tissues remains one of the most difficult challenges for this type of mass spectrometric analysis. For this reason, we have created and optimized a robust methodology that preserves the spatial information contained within the sample, while eliciting the greatest number of ionizable peptides. We have also aimed to achieve this in a cost effective and simple way, thereby eliminating potential bias or preparation error, which can occur when using automated instrumentation. The end result is a reproducible and inexpensive protocol.
Osman, EO, Smith, DJ, Ziegler, M, Kürten, B, Conrad, C, El‐Haddad, KM, Voolstra, CR & Suggett, DJ 2018, 'Thermal refugia against coral bleaching throughout the northern Red Sea', Global Change Biology, vol. 24, no. 2, pp. e474-e484. View/Download from: Publisher's site View description>>
AbstractTropical reefs have been impacted by thermal anomalies caused by global warming that induced coral bleaching and mortality events globally. However, there have only been very few recordings of bleaching within the Red Sea despite covering a latitudinal range of 15° and consequently it has been considered a region that is less sensitive to thermal anomalies. We therefore examined historical patterns of sea surface temperature (SST) and associated anomalies (1982–2012) and compared warming trends with a unique compilation of corresponding coral bleaching records from throughout the region. These data indicated that the northern Red Sea has not experienced mass bleaching despite intensive Degree Heating Weeks (DHW) of >15°C‐weeks. Severe bleaching was restricted to the central and southern Red Sea where DHWs have been more frequent, but far less intense (DHWs <4°C‐weeks). A similar pattern was observed during the 2015–2016 El Niño event during which time corals in the northern Red Sea did not bleach despite high thermal stress (i.e. DHWs >8°C‐weeks), and bleaching was restricted to the central and southern Red Sea despite the lower thermal stress (DHWs < 8°C‐weeks). Heat stress assays carried out in the northern (Hurghada) and central (Thuwal) Red Sea on four key reef‐building species confirmed different regional thermal susceptibility, and that central Red Sea corals are more sensitive to thermal anomalies as compared to those from the north. Together, our data demonstrate that corals in the northern Red Sea have a much higher heat tolerance than their prevailing temperature regime would suggest. In contrast, corals from the central Red Sea are close to their thermal li...
Ozbek, B, Erdogan, B, Ekren, N, Oktar, FN, Akyol, S, Ben-Nissan, B, Sasmazel, HT, Kalkandelen, C, Mergen, A, Kuruca, SE, Ozen, G & Gunduz, O 2018, 'Production of the novel fibrous structure of poly(ε-caprolactone)/tri-calcium phosphate/hexagonal boron nitride composites for bone tissue engineering', Journal of the Australian Ceramic Society, vol. 54, no. 2, pp. 251-260. View/Download from: Publisher's site View description>>
Pagnucco, R & Phillips, ML 2018, 'Comparative effectiveness of natural by-products and synthetic sorbents in oil spill booms', Journal of Environmental Management, vol. 225, pp. 10-16. View/Download from: Publisher's site View description>>
Sorbent booms are considered a ‘first line of defence’ technology used for containing and minimizing the impacts of crude oil spills. Booms containing human hair waste as sorbent were compared to other natural sorbents, including cotton by-product, recycled cellulose, as well as booms containing synthetic polypropylene, in order to evaluate their effectiveness in adsorbing petroleum crude oil pollution, remaining buoyant, and adsorbing seawater. A series of oceanic mesocosm experiments were used to simulate oil spill pollution events and to test sorbent effectiveness. Hair by-product was found to be significantly better at adsorbing crude oil on average (i.e. 0.84 g of crude oil per 1 g of sorbent) than all other materials, although it had wider variation in adsorbency likely associated with the non-homogeneous nature of mixed human hair. Hair sorbent was also observed to be less naturally buoyant than other materials, potentially due to low surface tension or increased porosity.
Palmer, EE, Schofield, D, Shrestha, R, Kandula, T, Macintosh, R, Lawson, JA, Andrews, I, Sampaio, H, Johnson, AM, Farrar, MA, Cardamone, M, Mowat, D, Elakis, G, Lo, W, Zhu, Y, Ying, K, Morris, P, Tao, J, Dias, K-R, Buckley, M, Dinger, ME, Cowley, MJ, Roscioli, T, Kirk, EP, Bye, A & Sachdev, RK 2018, 'Integrating exome sequencing into a diagnostic pathway for epileptic encephalopathy: Evidence of clinical utility and cost effectiveness', Molecular Genetics & Genomic Medicine, vol. 6, no. 2, pp. 186-199. View/Download from: Publisher's site View description>>
Epileptic encephalopathies are a devastating group of neurological conditions in which etiological diagnosis can alter management and clinical outcome. Exome sequencing and gene panel testing can improve diagnostic yield but there is no cost-effectiveness analysis of their use or consensus on how to best integrate these tests into clinical diagnostic pathways.We conducted a retrospective cost-effectiveness study comparing trio exome sequencing with a standard diagnostic approach, for a well-phenotyped cohort of 32 patients with epileptic encephalopathy, who remained undiagnosed after "first-tier" testing. Sensitivity analysis was included with a range of commercial exome and multigene panels.The diagnostic yield was higher for the exome sequencing (16/32; 50%) than the standard arm (2/32; 6.2%). The trio exome sequencing pathway was cost-effective compared to the standard diagnostic pathway with a cost saving of AU$5,236 (95% confidence intervals $2,482; $9,784) per additional diagnosis; the standard pathway cost approximately 10 times more per diagnosis. Sensitivity analysis demonstrated that the majority of commercial exome sequencing and multigene panels studied were also cost-effective. The clinical utility of all diagnoses was reported.Our study supports the integration of exome sequencing and gene panel testing into the diagnostic pathway for epileptic encephalopathy, both in terms of cost effectiveness and clinical utility. We propose a diagnostic pathway that integrates initial rapid screening for treatable causes and comprehensive genomic screening. This study has important implications for health policy and public funding for epileptic encephalopathy and other neurological conditions.
Pamphlett, R, Bishop, DP, Kum Jew, S & Doble, PA 2018, 'Age-related accumulation of toxic metals in the human locus ceruleus', PLOS ONE, vol. 13, no. 9, pp. e0203627-e0203627. View/Download from: Publisher's site View description>>
Damage to the locus ceruleus has been implicated in the pathogenesis of a number of neurological conditions. Locus ceruleus neurons accumulate toxic metals such as mercury selectively, however, the presence of toxic metals in locus ceruleus neurons of people of different ages, and with a variety of disorders, is not known. To demonstrate at what age toxic metals are first detectable in the locus ceruleus, and to evaluate whether their presence is more common in certain clinicopathological conditions, we looked for these metals in 228 locus ceruleus samples. Samples were taken at coronial autopsies from individuals with a wide range of ages, pre-existing conditions and causes of death. Paraffin sections of pons containing the locus ceruleus were stained with silver nitrate autometallography, which indicates inorganic mercury, silver and bismuth within cells (termed autometallography-detected toxic metals, or AMG™). No locus ceruleus AMG neurons were seen in 38 individuals aged under 20 years. 47% of the 190 adults (ie, aged 20 years and over) had AMG locus ceruleus neurons. The proportion of adults with locus ceruleus AMG neurons increased during aging, except for a decreased proportion in the 90-plus years age group. No differences were found in the proportions of locus ceruleus AMG neurons between groups with different neurological, psychiatric, or other clinicopathological conditions, or among various causes of death. Elemental analysis with laser ablation-inductively coupled plasma-mass spectrometry was used to cross-validate the metals detected by AMG, by looking for silver, gold, bismuth, cadmium, chromium, iron, mercury, nickel, and lead in the locus ceruleus of ten individuals. This confirmed the presence of mercury in locus ceruleus samples containing AMG neurons, and showed cadmium, silver, lead, iron, and nickel in the locus ceruleus of some individuals. In conclusion, toxic metals stained by AMG (most likely inorganic mercury) appear in locus ceruleus ...
Pan, GJ, Rayner, BS, Zhang, Y, van Reyk, DM & Hawkins, CL 2018, 'A pivotal role for NF-κB in the macrophage inflammatory response to the myeloperoxidase oxidant hypothiocyanous acid', Archives of Biochemistry and Biophysics, vol. 642, pp. 23-30. View/Download from: Publisher's site View description>>
Atherosclerosis is characterised by the infiltration of macrophages at sites of inflammation within the vessel wall and the release of myeloperoxidase (MPO), which forms hypochlorous acid (HOCl) and hypothiocyanous acid (HOSCN). HOCl is a damaging oxidant implicated in the development of atherosclerosis. Preferential formation of HOSCN occurs under conditions where thiocyanate ions are elevated, as is the case in smokers. HOSCN reacts selectively with thiols, which can result in more enzyme inactivation and damage than HOCl at susceptible sites, which may contribute to atherosclerosis in smokers. In this study, we show that exposure of macrophages to HOSCN results in a time- and dose-dependent increase in the mRNA expression and release of pro-inflammatory cytokines and chemokines, including monocyte chemotactic protein 1, tumour necrosis factor alpha, and interleukins 6, 8 and 1β. At high oxidant concentrations (>200 μM), a significant loss of cellular thiols and increased cell death is observed. HOSCN-induced cytokine/chemokine expression and cell death were decreased on pharmacological inhibition of nuclear factor kappa B. These data highlight a pathway by which HOSCN could promote inflammation and the development of atherosclerosis, in the presence of supra-physiological levels of the precursor thiocyanate, which are achievable by cigarette smoking.
Pankratova, N, Cuartero, M, Jowett, LA, Howe, ENW, Gale, PA, Bakker, E & Crespo, GA 2018, 'Fluorinated tripodal receptors for potentiometric chloride detection in biological fluids', Biosensors and Bioelectronics, vol. 99, pp. 70-76. View/Download from: Publisher's site
Panth, N, Paudel, KR, Gong, D-S & Oak, M-H 2018, 'Vascular Protection by Ethanol Extract of Morus alba Root Bark: Endothelium-Dependent Relaxation of Rat Aorta and Decrease of Smooth Muscle Cell Migration and Proliferation', Evidence-Based Complementary and Alternative Medicine, vol. 2018, pp. 1-8. View/Download from: Publisher's site View description>>
Morus alba (white mulberry) is native to the northern part of Korea and popularly used as a traditional medicine due to its numerous health benefits against human’s disease. However, the possibility that M. alba may also affect the cardiovascular system remains unexplored. This study sought to investigate the vascular protective effects of the root bark extract of M. alba (MAE). Vascular reactivity was performed in organ baths using isolated rat thoracic aorta, while platelet derived growth factor (PDGF) induced proliferation and migration of vascular smooth muscle cells (VSMCs) were studied by 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium (MTS) and wound healing assay, respectively. MAE evoked a concentration dependent vasorelaxation following endothelium-dependent pathway. However, vessel relaxations in response to MAE were markedly reduced after endothelium removal; treatment of endothelial nitric oxide synthase inhibitor, guanylyl cyclase inhibitor, and nonspecific potassium channel inhibitor, however, was not altered by cyclooxygenase inhibitor. Furthermore, MAE also significantly blunted contractile response to vasoconstrictor agent, phenylephrine. Taken together, the current evidence revealed that MAE is a potent endothelium-dependent vasodilator and this effect was involved in, at least in part, nitric oxide cyclic-guanosine monophosphate (NO-cGMP) pathway in combination with potassium (K+) channel activation. Moreover, MAE inhibited proliferation and migration of VSMCs induced by PDGF. Therefore, MAE could be a promising candidate of natural medicine for preventing and controlling cardiovascular diseases linked with endothelial dysfunction.
Parker, LM, O'Connor, WA, Byrne, M, Dove, M, Coleman, RA, Pörtner, H-O, Scanes, E, Virtue, P, Gibbs, M & Ross, PM 2018, 'Ocean acidification but not warming alters sex determination in the Sydney rock oyster, Saccostrea glomerata', Proceedings of the Royal Society B: Biological Sciences, vol. 285, no. 1872, pp. 20172869-20172869. View/Download from: Publisher's site View description>>
Whether sex determination of marine organisms can be altered by ocean acidification and warming during this century remains a significant, unanswered question. Here, we show that exposure of the protandric hermaphrodite oyster,
Saccostrea glomerata
to ocean acidification, but not warming, alters sex determination resulting in changes in sex ratios. After just one reproductive cycle there were 16% more females than males. The rate of gametogenesis, gonad area, fecundity, shell length, extracellular pH and survival decreased in response to ocean acidification. Warming as a sole stressor slightly increased the rate of gametogenesis, gonad area and fecundity, but this increase was masked by the impact of ocean acidification at a level predicted for this century. Alterations to sex determination, sex ratios and reproductive capacity will have flow on effects to reduce larval supply and population size of oysters and potentially other marine organisms.
Parvez Mahmud, MA, Huda, N, Farjana, SH, Asadnia, M & Lang, C 2018, 'Recent Advances in Nanogenerator-Driven Self-Powered Implantable Biomedical Devices', Advanced Energy Materials, vol. 8, no. 2, pp. 1701210-1701210. View/Download from: Publisher's site
Parvez Mahmud, MA, Huda, N, Hisan Farjana, S & Lang, C 2018, 'Environmental profile evaluations of piezoelectric polymers using life cycle assessment', IOP Conference Series: Earth and Environmental Science, vol. 154, pp. 012017-012017. View/Download from: Publisher's site
Patel, NR, Padalia, H, Devadas, R, Huete, A, Senthil Kumar, A & Krishna Murthy, YVN 2018, 'Estimating Net Primary Productivity of Croplands in Indo-Gangetic Plains Using GOME-2 Sun-Induced Fluorescence and MODIS NDVI', Current Science, vol. 114, no. 06, pp. 1333-1333. View/Download from: Publisher's site View description>>
Pateras, A, Park, J, Ahn, Y, Tilka, JA, Holt, MV, Reichl, C, Wegscheider, W, Baart, TA, Dehollain, JP, Mukhopadhyay, U, Vandersypen, LMK & Evans, PG 2018, 'Mesoscopic Elastic Distortions in GaAs Quantum Dot Heterostructures', Nano Letters, vol. 18, no. 5, pp. 2780-2786. View/Download from: Publisher's site View description>>
Quantum devices formed in high-electron-mobility semiconductor heterostructures provide a route through which quantum mechanical effects can be exploited on length scales accessible to lithography and integrated electronics. The electrostatic definition of quantum dots in semiconductor heterostructure devices intrinsically involves the lithographic fabrication of intricate patterns of metallic electrodes. The formation of metal/semiconductor interfaces, growth processes associated with polycrystalline metallic layers, and differential thermal expansion produce elastic distortion in the active areas of quantum devices. Understanding and controlling these distortions present a significant challenge in quantum device development. We report synchrotron X-ray nanodiffraction measurements combined with dynamical X-ray diffraction modeling that reveal lattice tilts with a depth-averaged value up to 0.04° and strain on the order of 10-4 in the two-dimensional electron gas (2DEG) in a GaAs/AlGaAs heterostructure. Elastic distortions in GaAs/AlGaAs heterostructures modify the potential energy landscape in the 2DEG due to the generation of a deformation potential and an electric field through the piezoelectric effect. The stress induced by metal electrodes directly impacts the ability to control the positions of the potential minima where quantum dots form and the coupling between neighboring quantum dots.
Pathinayake, PS, Hsu, AC-Y, Waters, DW, Hansbro, PM, Wood, LG & Wark, PAB 2018, 'Understanding the Unfolded Protein Response in the Pathogenesis of Asthma', Frontiers in Immunology, vol. 9. View/Download from: Publisher's site
Paul, PK, Kumari, N, Panigrahi, N, Mishra, A & Singh, R 2018, 'Implementation of cell-to-cell routing scheme in a large scale conceptual hydrological model', Environmental Modelling & Software, vol. 101, pp. 23-33. View/Download from: Publisher's site
Poor air quality is an emerging world-wide problem, with most urban air pollutants arising from vehicular emissions. As such, localized high pollution environments, such as traffic tunnels pose a significant health risk. Phytoremediation, including the use of active (ventilated) green walls or botanical biofilters, is gaining recognition as a potentially effective method for air pollution control. Research to date has tested the capacity of these systems to remove low levels of pollutants from indoor environments. If botanical biofilters are to be used in highly polluted environments, the plants used in these systems must be resilient, however, this idea has received minimal research. Thus, testing was conducted to assess the hardiness of the vegetated component of a botanical biofilter to simulated street level air pollutant exposure. A range of morphological, physiological, and biochemical tests were conducted on 8 common green wall plant species prior to and post 5-week exposure to highly concentrated diesel fuel combustion effluent; as a pilot study to investigate viability in in situ conditions. The results indicated that species within the fig family were the most tolerant species of those assessed. It is likely that species within the fig family can withstand enhanced air pollutant conditions, potentially a result of its leaf morphology and physiology. Other species tested were all moderately tolerant to the pollution treatment. We conclude that most common green wall plant species have the capacity to withstand high pollutant environments, however, extended experimentation is needed to rule out potential long term effects along with potential decreases in filter efficiency from accumulative effects on the substrate.
Pech, M, Weckmann, M, König, IR, Franke, A, Heinsen, F-A, Oliver, B, Ricklefs, I, Fuchs, O, Rabe, K, Hansen, G, v. Mutius, E & Kopp, MV 2018, 'Rhinovirus infections change DNA methylation and mRNA expression in children with asthma', PLOS ONE, vol. 13, no. 11, pp. e0205275-e0205275. View/Download from: Publisher's site
Peng, D, Wu, C, Zhang, X, Yu, L, Huete, AR, Wang, F, Luo, S, Liu, X & Zhang, H 2018, 'Scaling up spring phenology derived from remote sensing images', Agricultural and Forest Meteorology, vol. 256-257, pp. 207-219. View/Download from: Publisher's site
Periyalil, HA, Wood, LG, Wright, TA, Karihaloo, C, Starkey, MR, Miu, AS, Baines, KJ, Hansbro, PM & Gibson, PG 2018, 'Obese asthmatics are characterized by altered adipose tissue macrophage activation', Clinical & Experimental Allergy, vol. 48, no. 6, pp. 641-649. View/Download from: Publisher's site
Petrou, K & Nielsen, DA 2018, 'Uptake of dimethylsulphoniopropionate (DMSP) by the diatom Thalassiosira weissflogii: a model to investigate the cellular function of DMSP', Biogeochemistry, vol. 141, no. 2, pp. 265-271. View/Download from: Publisher's site
Petrou, K, Nielsen, DA & Heraud, P 2018, 'Single-Cell Biomolecular Analysis of Coral Algal Symbionts Reveals Opposing Metabolic Responses to Heat Stress and Expulsion', Frontiers in Marine Science, vol. 5, no. MAR. View/Download from: Publisher's site View description>>
Pettit, T, Irga, PJ & Torpy, FR 2018, 'Functional green wall development for increasing air pollutant phytoremediation: Substrate development with coconut coir and activated carbon', Journal of Hazardous Materials, vol. 360, pp. 594-603. View/Download from: Publisher's site View description>>
Functional green walls are gaining attention due to their air cleaning abilities, however the air cleaning capacity of these systems may be improved through substrate modification. This experiment investigated the capacity of several green wall media to filter a range of air pollutants. Media, consisting of differently sized coconut husk-based substrates, and with different ratios of activated carbon were evaluated through the use of scaled down model 'cassettes'. Tests were conducted assessing each substrate's ability to filter particulate matter, benzene, ethyl acetate and ambient total VOCs. While the particle size of coconut husk did not influence removal efficiency, the addition of activated carbon to coconut husk media improved the removal efficiency for all gaseous pollutants. Activated carbon as a medium component, however, inhibited the removal efficiency of particulate matter. Once the substrate concentration of activated carbon approached ∼50%, its gas remediation capacity became asymptotic, suggesting that a 50:50 composite medium provided the best VOC removal. In full-scale botanical biofilter modules, activated carbon-based substrates increased benzene removal, yet decreased particulate matter removal despite the addition of plants. The findings suggest that medium design should be target pollutant dependent, while further work is needed to establish plant viability in activated carbon-based media.
Indoor air quality has become a growing concern due to the increasing proportion of time people spend indoors, combined with reduced building ventilation rates resulting from an increasing awareness of building energy use. It has been well established that potted-plants can help to phytoremediate a diverse range of indoor air pollutants. In particular, a substantial body of literature has demonstrated the ability of the potted-plant system to remove volatile organic compounds (VOCs) from indoor air. These findings have largely originated from laboratory scale chamber experiments, with several studies drawing different conclusions regarding the primary VOC removal mechanism, and removal efficiencies. Advancements in indoor air phytoremediation technology, notably active botanical biofilters, can more effectively reduce the concentrations of multiple indoor air pollutants through the action of active airflow through a plant growing medium, along with vertically aligned plants which achieve a high leaf area density per unit of floor space. Despite variable system designs, systems available have clear potential to assist or replace existing mechanical ventilation systems for indoor air pollutant removal. Further research is needed to develop, test and confirm their effectiveness and safety before they can be functionally integrated in the broader built environment. The current article reviews the current state of active air phytoremediation technology, discusses the available botanical biofiltration systems, and identifies areas in need of development.
Pham, TH & Wand, MP 2018, 'Generalised additive mixed models analysis via gammSlice', Australian & New Zealand Journal of Statistics, vol. 60, no. 3, pp. 279-300. View/Download from: Publisher's site View description>>
Phillips, S, Vodstrcil, LA, Huston, WM, Lawerence, A, Timms, P, Chen, MY, Worthington, K, McIver, R, Bradshaw, CS, Garland, SM, Tabrizi, SN & Hocking, JS 2018, 'Detection of Chlamydia trachomatis mRNA using digital PCR as a more accurate marker of viable organism', European Journal of Clinical Microbiology & Infectious Diseases, vol. 37, no. 11, pp. 2117-2122. View/Download from: Publisher's site View description>>
Spontaneous resolution of urogenital Chlamydia trachomatis (CT) without treatment has previously been described, but a limitation of these reports is that DNA or RNA-based amplification tests used do not differentiate between viable infection and non-viable DNA. We modified a previously published CT mRNA detection (omp2) method to differentiate between viable infection and non-viable DNA in a sample of CT DNA PCR positive women. We modified a CT mRNA detection (omp2) method from reverse transcriptase qPCR (RTqPCR) to digital PCR (dPCR) and evaluated it in samples from CT DNA positive women. Firstly, CT infected McCoy B cells treated with azithromycin in vitro identified detectable mRNA levels disappeared <2 days, while DNA persisted up to 6 days. We used 55 self-collected vaginal swabs from a cohort of women diagnosed as DNA positive for chlamydia obtained pre- and 7 days of post-azithromycin treatment. Concordance with DNA results was higher for dPCR than RTqPCR (74.5% versus 65.5%). At visit 1, there was a strong linear relationship between DNA and mRNA (r = 0.9, p < 0.000); 24 samples had both mRNA and DNA detected (82.8%) and 5 had only DNA detected with a potential false positive proportion of 17.2% (95%CI: 5.8, 35.8). At visit 2, there was poor correlation between DNA and mRNA (r = 0.14, p = 0.55); eight specimens had only DNA detected (42.1%; 95%CI: 20.25, 66.50) and one had mRNA detected. DNA detection methods alone may detect non-viable DNA. Consideration should be given to further develop mRNA assays as ancillary tests to improve detection of viable chlamydia.
Philp, M & Fu, S 2018, 'A review of chemical ‘spot’ tests: A presumptive illicit drug identification technique', Drug Testing and Analysis, vol. 10, no. 1, pp. 95-108. View/Download from: Publisher's site View description>>
Chemical 'spot' tests are a presumptive illicit drug identification technique commonly used by law enforcement, border security personnel, and forensic laboratories. The simplicity, low cost, and rapid results afforded by these tests make them particularly attractive for presumptive identification globally. In this paper, we review the development of these long-established methods and discuss color test recommendations and guidelines. A search of the scientific literature revealed the chemical reactions occurring in many color tests are either not actively investigated or reported as unknown. Today, color tests face many challenges, from the appearance of new psychoactive substances to concerns regarding selectivity, sensitivity, and safety. Advances in technology have seen color test reagents used in digital image color analysis, solid sensors, and microfluidic devices for illicit drug detection. This summarizes current research and suggests the future of presumptive color testing.
Philp, M, Shimmon, R, Tahtouh, M & Fu, S 2018, 'Color Spot Test As a Presumptive Tool for the Rapid Detection of Synthetic Cathinones', Journal of Visualized Experiments, vol. 2018, no. 132. View/Download from: Publisher's site View description>>
Synthetic cathinones are a large class of new psychoactive substances (NPS) that are increasingly prevalent in drug seizures made by law enforcement and other border protection agencies globally. Color testing is a presumptive identification technique indicating the presence or absence of a particular drug class using rapid and uncomplicated chemical methods. Owing to their relatively recent emergence, a color test for the specific identification of synthetic cathinones is not currently available. In this study, we introduce a protocol for the presumptive identification of synthetic cathinones, employing three aqueous reagent solutions: copper(II) nitrate, 2,9-dimethyl-1,10-phenanthroline (neocuproine) and sodium acetate. Small pin-head sized amounts (approximately 0.1-0.2 mg) of the suspected drugs are added to the wells of a porcelain spot plate, and each reagent is then added dropwise sequentially before heating on a hotplate. A color change from very light blue to yellow-orange after 10 min indicates the likely presence of synthetic cathinones. The highly stable and specific test reagent has the potential for use in the presumptive screening of unknown samples for synthetic cathinones in a forensic laboratory. However, the nuisance of an added heating step for the color change result limits the test to laboratory application and decreases the likelihood of an easy translation to field testing.
Pingle, H, Wang, P-Y, Cavaliere, R, Whitchurch, CB, Thissen, H & Kingshott, P 2018, 'Minimal attachment of Pseudomonas aeruginosa to DNA modified surfaces', Biointerphases, vol. 13, no. 6, pp. 06E405-06E405. View/Download from: Publisher's site View description>>
Extracellular deoxyribonucleic acid (eDNA) exists in biological environments such as those around medical implants since prokaryotic or eukaryotic cells can undergo processes such as autolysis, necrosis, and apoptosis. For bacteria, eDNA has been shown to be involved in biofilm formation and gene transfer and acts as a nutrient source. In terms of biofilm formation, eDNA in solution has been shown to be very important in increasing attachment; however, very little is known about the role played by surface immobilized eDNA in initiating bacterial attachment and whether the nature of a DNA layer (physically adsorbed or covalently attached, and molecular weight) influences biofilm formation. In this study, the authors shed light on the role that surface attached DNA plays in the early biofilm formation by using Si wafers (Si) and allylamine plasma polymer (AAMpp) coated Si wafers to adsorb and covalently immobilize salmon sperm DNA of three different molecular weights. Pseudomonas aeruginosa was chosen to study the bacterial interactions with these DNA functionalized surfaces. Characterization of surface chemistry and imaging of attached bacteria were performed via x-ray photoelectron spectroscopy (XPS), scanning electron microscopy, and epi-fluorescence microscopy. XPS results confirmed the successful grafting of DNA on the AAMpp and Si surfaces, and surprisingly the results showed that the surface attached DNA actually reduced initial bacterial attachment, which was contrary to the initial hypothesis. This adds speculation about the specific role played by DNA in the dynamics of how it influences biofilm formation, with the possibility that it could actually be used to make bacterial resistant surfaces.
Poddar, N, Sen, R & Martin, GJO 2018, 'Glycerol and nitrate utilisation by marine microalgae Nannochloropsis salina and Chlorella sp. and associated bacteria during mixotrophic and heterotrophic growth', Algal Research, vol. 33, pp. 298-309. View/Download from: Publisher's site
Portbury, SD, Hare, DJ, Bishop, DP, Finkelstein, DI, Doble, PA & Adlard, PA 2018, 'Trehalose elevates brain zinc levels following controlled cortical impact in a mouse model of traumatic brain injury', Metallomics, vol. 10, no. 6, pp. 846-853. View/Download from: Publisher's site View description>>
Zinc (Zn) deficiency is a clinical consequence of brain injury that can result in neuropathological outcomes that are exacerbated with age.
Pouwels, SD, Klont, F, Kwiatkowski, M, Wiersma, VR, Faiz, A, van den Berge, M, Horvatovich, P, Bischoff, R & ten Hacken, NHT 2018, 'Cigarette Smoking Acutely Decreases Serum Levels of the Chronic Obstructive Pulmonary Disease Biomarker sRAGE', American Journal of Respiratory and Critical Care Medicine, vol. 198, no. 11, pp. 1456-1458. View/Download from: Publisher's site
Prasansuklab, A, Theerasri, A, Payne, M, Ung, AT & Tencomnao, T 2018, 'Acid-base fractions separated from Streblus asper leaf ethanolic extract exhibited antibacterial, antioxidant, anti-acetylcholinesterase, and neuroprotective activities', BMC Complementary and Alternative Medicine, vol. 18, no. 1, pp. 223-223. View/Download from: Publisher's site View description>>
Streblus asper is a well-known plant native to Southeast Asia. Different parts of the plant have been traditionally used for various medicinal purposes. However, there is very little scientific evidence reporting its therapeutic benefits for potential treatment of Alzheimer's disease (AD). The study aimed to evaluate antibacterial, antioxidant, acetylcholinesterase (AChE) inhibition, and neuroprotective properties of S. asper leaf extracts with the primary objective of enhancing therapeutic applications and facilitating activity-guided isolation of the active chemical constituents.The leaves of S. asper were extracted in ethanol and subsequently fractionated into neutral, acid and base fractions. The phytochemical constituents of each fraction were analyzed using GC-MS. The antibacterial activity was evaluated using a broth microdilution method. The antioxidant activity was determined using DPPH and ABTS radical scavenging assays. The neuroprotective activity against glutamate-induced toxicity was tested on hippocampal neuronal HT22 cell line by evaluating the cell viability using MTT assay. The AChE inhibitory activity was screened by thin-layer chromatography (TLC) bioautographic method.The partition of the S. asper ethanolic leaf extract yielded the highest mass of phytochemical constitutions in the neutral fraction and the lowest in the basic fraction. Amongst the three fractions, the acidic fraction showed the strongest antibacterial activity against gram-positive bacteria. The antioxidant activities of three fractions were found in the order of acidic > basic > neutral, whereas the decreasing order of neuroprotective activity was neutral > basic > acidic. TLC bioautography revealed one component in the neutral fraction exhibited anti-AChE activity. While in the acid fraction, two components showed inhibitory activity against AChE. GC-MS analysis of three fractions showed the presence of major phytochemical constituents including terpenoids, steroids, phenol...
Precoda, K, Baird, AH, Madsen, A, Mizerek, T, Sommer, B, Su, SN & Madin, JS 2018, 'How does a widespread reef coral maintain a population in an isolated environment?', Marine Ecology Progress Series, vol. 594, pp. 85-94. View/Download from: Publisher's site
Prosser, C, Meyer, W, Ellis, J & Lee, R 2018, 'Evolutionary ARMS Race: Antimalarial Resistance Molecular Surveillance', Trends in Parasitology, vol. 34, no. 4, pp. 322-334. View/Download from: Publisher's site View description>>
Molecular surveillance of antimalarial drug resistance markers has become an important part of resistance detection and containment. In the current climate of multidrug resistance, including resistance to the global front-line drug artemisinin, there is a consensus to upscale molecular surveillance. The most salient limitation to current surveillance efforts is that skill and infrastructure requirements preclude many regions. This includes sub-Saharan Africa, where Plasmodium falciparum is responsible for most of the global malaria disease burden. New molecular and data technologies have emerged with an emphasis on accessibility. These may allow surveillance to be conducted in broad settings where it is most needed, including at the primary healthcare level in endemic countries, and extending to the village health worker.
Prosser, C, Meyer, W, Ellis, J & Lee, R 2018, 'Resistance screening and trend analysis of imported falciparum malaria in NSW, Australia (2010 to 2016)', PLOS ONE, vol. 13, no. 5, pp. e0197369-e0197369. View/Download from: Publisher's site View description>>
BACKGROUND:The World Health Organization currently recommends artemisinin (along with a partner drug) as the global frontline treatment for Plasmodium falciparum malaria. Artemisinin resistant P. falciparum are now found throughout the greater Mekong subregion of South East Asia. Several polymorphisms in the parasite's kelch gene have been demonstrated to confer artemisinin resistance. While genotypes within the greater Mekong subregion are thoroughly examined in the literature, P. falciparum populations within several areas that do not (yet) have endemic resistance are underrepresented. RESULTS:This investigation characterised the Pfkelch13 propeller domains from 153 blood samples of 140 imported cases of P. falciparum malaria in New South Wales from 2010 to 2016. A low level of propeller domain diversity was observed, including the C580Y coding mutation most strongly associated with artemisinin resistance in South East Asia. The resistance genotype was found in a sample originating in Papua New Guinea, where this mutation, or artemisinin treatment failure, have not been previously reported. Sequencing a panel of geographically informative polymorphisms within the organellar genomes identified the C580Y parasite as having Oceanic origins. Patient data analysis revealed that New South Wales, Australia, P. falciparum malaria cases often originated from regions with limited drug resistance screening. CONCLUSIONS:The C580Y finding from outside of the greater Mekong subregion supports the consensus to upscale molecular surveillance of artemisinin resistance outside of South East Asia. The genetic screening results identify a risk of importing resistant falciparum malaria to Australia, supporting an ongoing surveillance protocol to pre-empt treatment failure and contribute to global data gathering.
Pushpamalar, J, Langford, SJ, Ahmad, MB, Lim, YY & Hashim, K 2018, 'Eco-friendly smart hydrogels for soil conditioning and sustain release fertilizer', International Journal of Environmental Science and Technology, vol. 15, no. 10, pp. 2059-2074. View/Download from: Publisher's site
Quiroz, M, Villani, M, Kohn, R, Tran, M-N & Dang, K-D 2018, 'Subsampling MCMC - An introduction for the survey statistician', Sankhya A, vol. 80, pp. 33-69. View/Download from: Publisher's site View description>>
The rapid development of computing power and efficient Markov Chain Monte
Carlo (MCMC) simulation algorithms have revolutionized Bayesian statistics,
making it a highly practical inference method in applied work. However, MCMC
algorithms tend to be computationally demanding, and are particularly slow for
large datasets. Data subsampling has recently been suggested as a way to make
MCMC methods scalable on massively large data, utilizing efficient sampling
schemes and estimators from the survey sampling literature. These developments
tend to be unknown by many survey statisticians who traditionally work with
non-Bayesian methods, and rarely use MCMC. Our article explains the idea of
data subsampling in MCMC by reviewing one strand of work, Subsampling MCMC, a
so called pseudo-marginal MCMC approach to speeding up MCMC through data
subsampling. The review is written for a survey statistician without previous
knowledge of MCMC methods since our aim is to motivate survey sampling experts
to contribute to the growing Subsampling MCMC literature.
Rädecker, N, Raina, J-B, Pernice, M, Perna, G, Guagliardo, P, Kilburn, MR, Aranda, M & Voolstra, CR 2018, 'Corrigendum: Using Aiptasia as a Model to Study Metabolic Interactions in Cnidarian-Symbiodinium Symbioses', Frontiers in Physiology, vol. 9. View/Download from: Publisher's site View description>>
[This corrects the article on p. 214 in vol. 9, PMID: 29615919.].
Rädecker, N, Raina, J-B, Pernice, M, Perna, G, Guagliardo, P, Kilburn, MR, Aranda, M & Voolstra, CR 2018, 'Using Aiptasia as a Model to Study Metabolic Interactions in Cnidarian-Symbiodinium Symbioses', Frontiers in Physiology, vol. 9. View/Download from: Publisher's site
Raes, EJ, Bodrossy, L, van de Kamp, J, Bissett, A, Ostrowski, M, Brown, MV, Sow, SLS, Sloyan, B & Waite, AM 2018, 'Oceanographic boundaries constrain microbial diversity gradients in the South Pacific Ocean', Proceedings of the National Academy of Sciences, vol. 115, no. 35, pp. E8266-E8275. View/Download from: Publisher's site View description>>
Significance
High-resolution data covering marine microbes and microeukaryotes are sparse, even though these organisms control global biogeochemical cycles. Here we present a dataset describing the microbial pro- and eukaryotic diversity along a 7,000-km transect from the Antarctic ice edge to the equator in the South Pacific Ocean. We show that (
i
) temperature is not a primary driver of richness gradients, (
ii
) prokaryotic richness increases with productivity, and (
iii
) oceanographic features can structure the diversity of pro- and eukaryotes. Our data have given us a better understanding of how diversity relates to dissolved inorganic nitrogen and productivity as well as insights into the potential shifts in the geographical range of marine microbe communities in light of the rapidly changing climate.
Rafeek, AD, Choi, G & Evans, LA 2018, 'Morphological, spectroscopic and crystallographic studies of calcium phosphate bioceramic powders', Journal of the Australian Ceramic Society, vol. 54, no. 1, pp. 161-168. View/Download from: Publisher's site
Rahimi, E & Reimers, JR 2018, 'Molecular quantum cellular automata cell design trade-offs: latching vs. power dissipation', Physical Chemistry Chemical Physics, vol. 20, no. 26, pp. 17881-17888. View/Download from: Publisher's site View description>>
A new way of using molecules to enact switches in quantum cellular automata (QCA) is proposed, utilizing monostable molecules that neither provide latching nor consume power; properties are compared to those for conventional bistable switches that both latch and consume power.
Rahman, MA, Scott, JA, Gentle, A, Phillips, MR & Ton-That, C 2018, 'A facile method for bright, colour-tunable light-emitting diodes based on Ga-doped ZnO nanorods', Nanotechnology, vol. 29, no. 42, pp. 425707-425707. View/Download from: Publisher's site View description>>
Bottom-up fabrication of nanowire-based devices is highly attractive for oxide photonic devices because of high light extraction efficiency; however, unsatisfactory electrical injection into ZnO and poor carrier transport properties of nanowires severely limit their practical applications. Here, we demonstrate that ZnO nanorods doped with Ga donors by in situ dopant incorporation during vapour-solid growth exhibit superior optoelectronic properties that exceed those currently synthesised by chemical vapour deposition, and accordingly can be electrically integrated into Si-based photonic devices. Significantly, the doping method was found to improve the nanorod quality by decreasing the concentration of point defects. Light-emitting diodes (LEDs) fabricated from the Ga-doped ZnO nanorod/p-Si heterojunction display bright and colour-tunable electroluminescence (EL). These nanorod LEDs possess a dramatically enhanced performance and an order of magnitude higher EL compared with equivalent devices fabricated with undoped nanorods. These results point to an effective route for large-scale fabrication of conductive, single-crystalline ZnO nanorods for photonic and optoelectronic applications.
There are more than one million microbial cells in every drop of seawater, and their collective metabolisms not only recycle nutrients that can then be used by larger organisms but also catalyze key chemical transformations that maintain Earth’s habitability. Understanding how these microbes interact with each other and with multicellular hosts is critical to reliably quantify any functional aspect of their metabolisms and to predicting their outcomes on larger scales.
Raina, J-B, Eme, L, Pollock, FJ, Spang, A, Archibald, JM & Williams, TA 2018, 'Symbiosis in the microbial world: from ecology to genome evolution', Biology Open, vol. 7, no. 2. View/Download from: Publisher's site View description>>
ABSTRACTThe concept of symbiosis – defined in 1879 by de Bary as ‘the living together of unlike organisms’ – has a rich and convoluted history in biology. In part, because it questioned the concept of the individual, symbiosis fell largely outside mainstream science and has traditionally received less attention than other research disciplines. This is gradually changing. In nature organisms do not live in isolation but rather interact with, and are impacted by, diverse beings throughout their life histories. Symbiosis is now recognized as a central driver of evolution across the entire tree of life, including, for example, bacterial endosymbionts that provide insects with vital nutrients and the mitochondria that power our own cells. Symbioses between microbes and their multicellular hosts also underpin the ecological success of some of the most productive ecosystems on the planet, including hydrothermal vents and coral reefs. In November 2017, scientists working in fields spanning the life sciences came together at a Company of Biologists’ workshop to discuss the origin, maintenance, and long-term implications of symbiosis from the complementary perspectives of cell biology, ecology, evolution and genomics, taking into account both model and non-model organisms. Here, we provide a brief synthesis of the fruitful discussions that transpired.
Ranieri, MRM, Whitchurch, CB & Burrows, LL 2018, 'Mechanisms of biofilm stimulation by subinhibitory concentrations of antimicrobials', Current Opinion in Microbiology, vol. 45, pp. 164-169. View/Download from: Publisher's site View description>>
Biofilms are a typical mode of growth for most microorganisms and provide them with a variety of survival benefits. Biofilms can pose medical and industrial challenges due to their increased tolerance of antimicrobials and disinfectants. Exposure of bacteria to subinhibitory concentrations of those compounds can further exacerbate the problem, as they provoke physiological changes that lead to increased biofilm production and potential therapeutic failure. The protected niche of a biofilm provides conditions that promote selection for persisters and resistant mutants. In this review we discuss our current understanding of the mechanisms underlying biofilm stimulation in response to subinhibitory antimicrobials, and how we might exploit this 'anti-antibiotic' phenotype to treat biofilm-related infections and discover new compounds.
Rath, EM, Cheng, YY, Pinese, M, Sarun, KH, Hudson, AL, Weir, C, Wang, YD, Håkansson, AP, Howell, VM, Liu, GJ, Reid, G, Knott, RB, Duff, AP & Church, WB 2018, 'BAMLET kills chemotherapy-resistant mesothelioma cells, holding oleic acid in an activated cytotoxic state', PLOS ONE, vol. 13, no. 8, pp. e0203003-e0203003. View/Download from: Publisher's site
Raymond, BBA, Jenkins, C, Turnbull, L, Whitchurch, CB & Djordjevic, SP 2018, 'Extracellular DNA release from the genome-reduced pathogen Mycoplasma hyopneumoniae is essential for biofilm formation on abiotic surfaces', Scientific Reports, vol. 8, no. 1, pp. 10373-10373. View/Download from: Publisher's site View description>>
AbstractMycoplasma hyopneumoniae is an economically devastating, globally disseminated pathogen that can maintain a chronic infectious state within its host, swine. Here, we depict the events underpinning M. hyopneumoniae biofilm formation on an abiotic surface and demonstrate for the first time, biofilms forming on porcine epithelial cell monolayers and in the lungs of pigs, experimentally infected with M. hyopneumoniae. Nuclease treatment prevents biofilms forming on glass but not on porcine epithelial cells indicating that extracellular DNA (eDNA), which localises at the base of biofilms, is critical in the formation of these structures on abiotic surfaces. Subpopulations of M. hyopneumoniae cells, denoted by their ability to take up the dye TOTO-1 and release eDNA, were identified. A visually distinct sub-population of pleomorphic cells, that we refer to here as large cell variants (LCVs), rapidly transition from phase dark to translucent “ghost” cells. The translucent cells accumulate the membrane-impermeable dye TOTO-1, forming readily discernible membrane breaches immediately prior to lysis and the possible release of eDNA and other intracellular content (public goods) into the extracellular environment. Our novel observations expand knowledge of the lifestyles adopted by this wall-less, genome-reduced pathogen and provide further insights to its survival within farm environments and swine.
Mycoplasma hyopneumoniae, an agriculturally important porcine pathogen, disrupts the mucociliary escalator causing ciliostasis, loss of cilial function, and epithelial cell death within the porcine lung. Losses to swine production due to growth rate retardation and reduced feed conversion efficiency are severe, and antibiotics are used heavily to control mycoplasmal pneumonia. Notably, little is known about the repertoire of host receptors that M. hyopneumoniae targets to facilitate colonization. Here we show, for the first time, that actin exists extracellularly on porcine epithelial monolayers (PK-15) using surface biotinylation and 3D-Structured Illumination Microscopy (3D-SIM), and that M. hyopneumoniae binds to the extracellular β-actin exposed on the surface of these cells. Consistent with this hypothesis we show: (i) monoclonal antibodies that target β-actin significantly block the ability of M. hyopneumoniae to adhere and colonize PK-15 cells; (ii) microtiter plate binding assays show that M. hyopneumoniae cells bind to monomeric G-actin in a dose dependent manner; (iii) more than 100 M. hyopneumoniae proteins were recovered from affinity-chromatography experiments using immobilized actin as bait; and (iv) biotinylated monomeric actin binds directly to M. hyopneumoniae proteins in ligand blotting studies. Specifically, we show that the P97 cilium adhesin possesses at least two distinct actin-binding regions, and binds monomeric actin with nanomolar affinity. Taken together, these observations suggest that actin may be an important receptor for M. hyopneumoniae within the swine lung and will aid in the future development of intervention strategies against this devastating pathogen. Furthermore, our observations have wider implications for extracellular actin as an important bacterial receptor.
Raymond, BBA, Turnbull, L, Jenkins, C, Madhkoor, R, Schleicher, I, Uphoff, CC, Whitchurch, CB, Rohde, M & Djordjevic, SP 2018, 'Mycoplasma hyopneumoniae resides intracellularly within porcine epithelial cells', Scientific Reports, vol. 8, no. 1. View/Download from: Publisher's site View description>>
AbstractEnzootic pneumonia incurs major economic losses to pork production globally. The primary pathogen and causative agent, Mycoplasma hyopneumoniae, colonises ciliated epithelium and disrupts mucociliary function predisposing the upper respiratory tract to secondary pathogens. Alleviation of disease is reliant on antibiotics, vaccination, and sound animal husbandry, but none are effective at eliminating M. hyopneumoniae from large production systems. Sustainable pork production systems strive to lower reliance on antibiotics but lack of a detailed understanding of the pathobiology of M. hyopneumoniae has curtailed efforts to develop effective mitigation strategies. M. hyopneumoniae is considered an extracellular pathogen. Here we show that M. hyopneumoniae associates with integrin β1 on the surface of epithelial cells via interactions with surface-bound fibronectin and initiates signalling events that stimulate pathogen uptake into clathrin-coated vesicles (CCVs) and caveosomes. These early events allow M. hyopneumoniae to exploit an intracellular lifestyle by commandeering the endosomal pathway. Specifically, we show: (i) using a modified gentamicin protection assay that approximately 8% of M. hyopneumoniae cells reside intracellularly; (ii) integrin β1 expression specifically co-localises with the deposition of fibronectin precisely where M. hyopneumoniae cells assemble extracellularly; (iii) anti-integrin β1 antibodies block entry of M. hyopneumoniae into porcine cells; and (iv) M. hyopneumoniae survives phagolysosomal fusion, and resides within recycling endosomes that are trafficked to the cell membrane. Our data creates a paradigm shift by challenging the ...
Razavy, S, Gadau, M, Zhang, SP, Wang, FC, Bangrazi, S, Berle, C, Li, T, Li, WH & Zaslawski, C 2018, 'Anxiety related to De Qi psychophysical responses as measured by MASS: A sub-study embedded in a multisite randomised clinical trial', Complementary Therapies in Medicine, vol. 39, pp. 24-35. View/Download from: Publisher's site View description>>
Acupuncture has been broadly applied in the management of many diseases and conditions; however, its mechanism of action has been partially elucidated. Additionally, assessment of psychophysical responses in the acupuncture therapy is not common regarding anxiety disorder studies. Taken together, the therapeutic effect of acupuncture appears when De Qi psychophysical response is experienced following stimulation of the afferent sensory nerves. The present study investigates the level of anxiety perceived at different occasions in acupuncture and mock laser group. Furthermore, it examines the relationship between perceived De Qi psychophysical response and the level of anxiety experienced during administration of each intervention. The study was embedded in a two-arm parallel design multi-center, randomized clinical trial, the Tennis Elbow Acupuncture-International Study-China, Hong Kong, Australia, Italy. Participants' level of anxiety was measured using a validated instrument, the Massachusetts General Hospital Acupuncture Sensation Mood Scale. Ninety-six participants with Lateral Elbow Pain were randomly allocated into two groups; the acupuncture treatment group (n = 47) and the inactive mock laser control group (n = 49). Data were collected immediately following the interventions at the first and the ninth session within the clinical trial. Acupuncture with De Qi did not induce higher level of anxiety compared to prior administration of acupuncture. In fact, participants were more relaxed after receiving acupuncture than those who received mock laser. There was also a weak association between participants' perception of anxiety during acupuncture and the MASS De Qi Index in session nine only (p < 0.01). Further investigation of the result revealed weak positive correlation between anxiety perceived during administration of acupuncture and the following De Qi characteristics; 'soreness' (p < 0.01), 'Deep pressure' (p < 0.05), 'Heaviness' (p < 0.05), and 'Fullne...
Reid, AT, Veerati, PC, Gosens, R, Bartlett, NW, Wark, PA, Grainge, CL, Stick, SM, Kicic, A, Moheimani, F, Hansbro, PM & Knight, DA 2018, 'Persistent induction of goblet cell differentiation in the airways: Therapeutic approaches', Pharmacology & Therapeutics, vol. 185, pp. 155-169. View/Download from: Publisher's site
Reimers, JR 2018, 'How Equilibrium Gets Mimicked During Kinetic and Thermodynamic Control in Porphyrin and Phthalocyanine Self-Assembled Monolayers', Langmuir, vol. 34, no. 1, pp. 18-22. View/Download from: Publisher's site View description>>
The recent review of Hipps and Mazur is extended to consider the origins and significance of their conclusion that "surface structures vary with relative component concentration in a way that may mimic equilibria but is not". How this situation can arise during self-assembly is discussed, as well as a range of qualitative and quantitative observations and high-level free-energy calculations that document the effect for meso-tetraalkylporphyrins self-assembled monolayer (SAM) polymorphs. This leads to a discussion of modern challenges facing quantification of the effects caused by kinetic control, as well as to the usefulness of equilibrium mimicking in the design and synthesis of SAMs.
Reimers, JR, Sajid, A, Kobayashi, R & Ford, MJ 2018, 'Understanding and calibrating Density-Functional-Theory calculations describing the energy and spectroscopy of defect sites in hexagonal boron nitride', J. Chem. Theory Comput.2018, vol. 14, no. 3, pp. 1602-1613. View/Download from: Publisher's site View description>>
Defect states in 2D materials present many possible uses but both
experimental and computational characterization of their spectroscopic
properties is difficult. We provide and compare results from 13 DFT and ab
initio computational methods for up to 25 excited states of a paradigm system,
the VNCB defect in hexagonal boron nitride (h-BN). Studied include include: (i)
potentially catastrophic effects for computational methods arising from the
multi-reference nature of the closed-shell and open-shell states of the defect,
which intrinsically involves broken chemical bonds, (ii) differing results from
DFT and time-dependent DFT (TDDFT) calculations, (iii) comparison of cluster
models to periodic-slab models of the defect, (iv) the starkly differing
effects of nuclear relaxation on the various electronic states as broken bonds
try to heal that control the widths of photoabsorption and photoemission
spectra, (v) the effect of zero-point energy and entropy on free-energy
differences, (vi) defect-localized and conduction/valence band transition
natures, and (vii) strategies needed to ensure that the lowest-energy state of
a defect can be computationally identified.
Reimers, JR, Tawfik, SA & Ford, MJ 2018, 'Van der Waals forces control ferroelectric-antiferroelectric ordering in ABP2X6 laminar materials', Chemical Science, vol. 9, pp. 7620-7627. View/Download from: Publisher's site View description>>
We show how van der Waals (vdW) forces outcompete covalent and ionic forces
to control ferroelectric ordering in CuInP2S6 nanoflakes as well as in CuInP2S6
and CuBiP2Se6 crystals. While the self-assembly of these 2D layered materials
is clearly controlled by vdW effects, this result indicates that the internal
layer structure is also similarly controlled. Using up to 14 first-principles
computational methods, we predict that the bilayers of both materials should be
antiferroelectric. However, antiferroelectric nanoflakes and bulk materials are
shown to embody two fundamentally different types of inter-layer interactions,
with vdW forces strongly favouring one and strongly disfavouring the other
compared to ferroelectric ordering. Strong specific vdW interactions involving
the Cu atoms control this effect. Thickness-dependent significant cancellation
of these two large opposing vdW contributions results in a small net effect
that interacts with weak ionic contributions to control ferroelectric ordering.
Gene therapy is one treatment that may ultimately cure type 1 diabetes. We have previously shown that the introduction of furin-cleavable human insulin (INS-FUR) to the livers in several animal models of diabetes resulted in the reversal of diabetes and partial pancreatic transdifferentiation of liver cells. The present study investigated whether streptozotocin-diabetes could be reversed in FRG mice in which chimeric mouse-human livers can readily be established and, in addition, whether pancreatic transdifferentiation occurred in the engrafted human hepatocytes.Engraftment of human hepatocytes was confirmed by measuring human albumin levels. Following delivery of the empty vector or the INS-FUR vector to diabetic FRG mice, mice were monitored for weight and blood glucose levels. Intraperitoneal glucose tolerance tests (IPGTTs) were performed. Expression levels of pancreatic hormones and transcription factors were determined by a reverse transcriptase-polymerase chain reaction (RT-PCR) and immunohistochemistry.Diabetes was reversed for a period of 60 days (experimental endpoint) after transduction with INS-FUR. IPGTTs of the insulin-transduced animals were not significantly different from nondiabetic animals. Immunofluorescence microscopy revealed the expression of human albumin and insulin in transduced liver samples. Quantitative RT-PCR showed expression of human and mouse endocrine hormones and β-cell transcription factors, indicating partial pancreatic transdifferentiation of mouse and human hepatocytes. Nonfasting human C-peptide levels were significantly higher than mouse levels, suggesting that transdifferentiated human hepatocytes made a significant contribution to the reversal of diabetes.These data show that human hepatocytes can be induced to undergo partial pancreatic transdifferentiation in vivo, indicating that the technology holds promise for the treatment of type 1 diabetes.
Ren, W, Wen, S, Tawfik, SA, Su, QP, Lin, G, Ju, LA, Ford, MJ, Ghodke, H, van Oijen, AM & Jin, D 2018, 'Anisotropic functionalization of upconversion nanoparticles', Chemical Science, vol. 9, no. 18, pp. 4352-4358. View/Download from: Publisher's site View description>>
Ligand competition directs heterogeneous bio-chemistry surface and self-assembly for upconversion nanoparticles.
Ren, W, Zhou, Y, Wen, S, He, H, Lin, G, Liu, D & Jin, D 2018, 'DNA-mediated anisotropic silica coating of upconversion nanoparticles', Chemical Communications, vol. 54, no. 52, pp. 7183-7186. View/Download from: Publisher's site View description>>
We report a facile approach of using DNA molecules as switches to selectively activate silica coating onto specific facets of upconversion nanoparticles.
Reyna, J & Meier, P 2018, 'Learner-Generated Digital Media (LGDM) as an Assessment Tool in Tertiary Science Education: A Review of Literature', IAFOR Journal of Education, vol. 6, no. 3, pp. 93-109. View/Download from: Publisher's site View description>>
Learner-Generated Digital Media (LGDM) in tertiary science education focuses on research skills, inquiry, active learning, teamwork, and collaboration. LGDM across disciplines is under-theorised, under-researched, and only in its early development. This paper evaluates the research in the field of LGDM in tertiary science education. The literature review had four
stages – identification, screening, filtering, and selection of relevant scholarly research. Results showed that research in the field of LGDM assignments had been done without a systematic approach to designing, implementing, and evaluating the assessment task. Most studies neglected student digital media training and are characterised by a lack of compelling marking
rubrics or strategies to ensure efficient groupwork. Studies also lack rigorous methodologies for data capture to evaluate the intervention and they use small sample size cohorts and different digital media types that require different sets of production skills. With the empirical data available, validation of the benefits of LGDM assignments in science education is not
possible, and studies have limited scalability. These gaps in the literature create a need to develop theoretical models for the design, implementation, and evaluation of LGDM in the classroom. This paper discusses future research needs in this field and the implications for assessment design.
Reyna, J & Meier, P 2018, 'Using the Learner-Generated Digital Media (LGDM) Framework in Tertiary Science Education: A Pilot Study', Education Sciences, vol. 8, no. 3, pp. 106-106. View/Download from: Publisher's site View description>>
Learner-Generated Digital Media (LGDM) has become prevalent in higher education. Frameworks have been developed for video-making in the classroom that consider technical requirements, pedagogies, and the combination of both. However, missing is a practical model to guide academics and students on the implementation of LGDM assignments. This research aims to test a model to design, implement, and evaluate LGDM as an assessment tool. The model was built based on research gaps and it considers the following elements: (1) pedagogy, (2) student training, (3) hosting of videos, (4) marking schemes, (5) group contribution, (6) feedback, (7) reflection, and (8) evaluation. For this purpose, five science subjects (N = 270) were used to test the model as a guide to implementing LGDM assignments. Data was gathered using a validated 33-step questionnaire instrument. Additionally, group contributions were received using the SPARKPlus peer review application, and marks attained were gathered. Methodological triangulation of the datasets suggested that students have a positive attitude toward LGDM for science learning. Students enjoyed the group work and creativity, and they identified digital media support as a critical component of their learning experience. Preliminary data support using the LGDM framework to design digital media assignments for science education.
Reyna, J, Hanham, J & Meier, P 2018, 'The Internet explosion, digital media principles and implications to communicate effectively in the digital space', E-Learning and Digital Media, vol. 15, no. 1, pp. 36-52. View/Download from: Publisher's site View description>>
Being literate has traditionally meant being able to read and write using the media of the day. In the 21st century, being literate requires additional skills such as competence with digital media creation. Until recently, those who could afford and use equipment and applications to produce digital media content were typically developers and technicians. With the development of prosumer electronics, in conjunction with the use of mobile devices and tablets, a shift has occurred in the accessibility of these tools, becoming more affordable for the general population. Video sharing services, social software and Web 2.0 applications have made it possible to host a digital media ecosystem on the Internet, and this has led to the proliferation of User-Generated Content. These technological advances have changed how we communicate, socialise and learn. Effective communication using digital media is underpinned by a set of design principles which most students are not likely to be aware. This paper built on two previous papers on the Digital Media Literacy Framework and the Taxonomy of Digital Media types for teaching and learning. It argues the importance of digital media principles to develop effective communication in the digital space. Students now require knowledge of these principles, in conjunction with conceptual and functional skills, for effective communication in the digital space.
Reyna, J, Hanham, J & Meier, PC 2018, 'A framework for digital media literacies for teaching and learning in higher education', E-Learning and Digital Media, vol. 15, no. 4, pp. 176-190. View/Download from: Publisher's site View description>>
Across a broad range of subjects in higher education institutions, students are required to complete assessment tasks that involve the production of digital artefacts. Examples include podcasts, digital stories, animations, video and blended media. To produce effective digital artefacts, one must be digitally literate. This requires a certain set of technical, audio-visual, behavioural, critical and social skills. In this article, the authors propose a framework that can be used to develop digital media literacies and train students in digital media creation. The framework considers three interdependent domains: conceptual, functional and audio-visual. A series of examples will be provided to illustrate the importance and interdependent nature of these domains. Implications of the framework on student training are discussed.
Richier, S, Achterberg, EP, Humphreys, MP, Poulton, AJ, Suggett, DJ, Tyrrell, T & Moore, CM 2018, 'Geographical CO2 sensitivity of phytoplankton correlates with ocean buffer capacity', Global Change Biology, vol. 24, no. 9, pp. 4438-4452. View/Download from: Publisher's site View description>>
Accumulation of anthropogenic CO2 is significantly altering ocean chemistry. A range of biological impacts resulting from this oceanic CO2 accumulation are emerging, however, the mechanisms responsible for observed differential susceptibility between organisms and across environmental settings remain obscure. A primary consequence of increased oceanic CO2 uptake is a decrease in the carbonate system buffer capacity, which characterizes the system's chemical resilience to changes in CO2 , generating the potential for enhanced variability in pCO2 and the concentration of carbonate [CO32-], bicarbonate [HCO3-], and protons [H+ ] in the future ocean. We conducted a meta-analysis of 17 shipboard manipulation experiments performed across three distinct geographical regions that encompassed a wide range of environmental conditions from European temperate seas to Arctic and Southern oceans. These data demonstrated a correlation between the magnitude of natural phytoplankton community biological responses to short-term CO2 changes and variability in the local buffer capacity across ocean basin scales. Specifically, short-term suppression of small phytoplankton (<10 μm) net growth rates were consistently observed under enhanced pCO2 within experiments performed in regions with higher ambient buffer capacity. The results further highlight the relevance of phytoplankton cell size for the impacts of enhanced pCO2 in both the modern and future ocean. Specifically, cell size-related acclimation and adaptation to regional environmental variability, as characterized by buffer capacity, likely influences interactions between primary producers and carbonate chemistry over a range of spatio-temporal scales.
Richman, MB & Leslie, LM 2018, 'The 2015-2017 Cape Town Drought: Attribution and Prediction Using Machine Learning', Procedia Computer Science, vol. 140, pp. 248-257. View/Download from: Publisher's site View description>>
Cape Town was declared a disaster area after the worst drought in almost a century, following its driest three consecutive wet seasons (April 1-October 31), in 2015 -2017. Cape Town’s drought was extreme, with “zero day” water storage months away, causing severe water rationing to Cape Town’s ~3.8 million population. The crisis extended into surrounding farmlands, as agriculture is vital for the region’s economy. Possible drought causes are numerous and, aside from the decreasing wet season precipitation, the effects are exacerbated by the increasing population with associated water demand, greater agricultural acreage and land surface changes. As rainfall decreases, water management becomes critical, requiring predictions for future rainfall. Possible climate drivers associated with available Cape Town precipitation and temperature include: The Southern Annular Mode, Atlantic Meridional Mode, Indian Ocean Dipole, an Integrated Southern Hemisphere temperature index and several El Niño indices. Several variable selection techniques suggest signals in both the Atlantic and Indian Oceans contribute to Cape Town droughts. Machine learning techniques are applied to these drivers for the first time and provide encouraging predictive skill levels. Results suggest that machine learning holds promise for adapting to drought by managing water resources in Cape Town and, more generally for global locations depending solely on rainfall under a warming climate.
Ritchie, RJ, Larkum, AWD & Ribas, I 2018, 'Could photosynthesis function on Proxima Centauri b?', International Journal of Astrobiology, vol. 17, no. 2, pp. 147-176. View/Download from: Publisher's site View description>>
AbstractCould oxygenic and/or anoxygenic photosynthesis exist on planet Proxima Centauri b? Proxima Centauri (spectral type – M5.5 V, 3050 K) is a red dwarf, whereas the Sun is type G2 V (5780 K). The light regimes on Earth and Proxima Centauri b are compared with estimates of the planet's suitability for Chlorophylla(Chla) and Chld-based oxygenic photosynthesis and for bacteriochlorophyll (BChl)-based anoxygenic photosynthesis. Proxima Centauri b has low irradiance in the oxygenic photosynthesis range (400–749 nm: 64–132 µmol quanta m−2s−1). Much larger amounts of light would be available for BChl-based anoxygenic photosynthesis (350–1100 nm: 724–1538 µmol quanta m−2s−1). We estimated primary production under these light regimes. We used the oxygenic algaeSynechocystisPCC6803,Prochlorothrix hollandica,Acaryochloris marina,Chlorella vulgaris,Rhodomonassp. andPhaeodactylum tricornutumand the anoxygenic photosynthetic bacteriaRhodopseudomonas palustris(BChla),Afifella marina(BChla),Thermochromatium tepidum(BChla),Chlorobaculum tepidum(BChla + c) andBlastochloris viridis(BChlb) as representative photosynthetic organisms. Proxima Centauri b has only ≈3% of the PAR (400–700 nm) of Earth irradiance, but we found that potential gross photosynthesis (Pg) on Proxima Centauri b could be surprisingly high (ox...
Robertson, J & Roux, C 2018, 'The forensic scientist of the future – are universities prepared?', Australian Journal of Forensic Sciences, vol. 50, no. 4, pp. 305-306. View/Download from: Publisher's site
Rodgers, KJ, Main, BJ & Samardzic, K 2018, 'Cyanobacterial Neurotoxins: Their Occurrence and Mechanisms of Toxicity', Neurotoxicity Research, vol. 33, no. 1, pp. 168-177. View/Download from: Publisher's site View description>>
Cyanobacteria are some of the oldest organisms on earth, and have evolved to produce a battery of toxic metabolites, including hepatotoxins, dermatoxins, and neurotoxins. In this review, we focus on the occurrence and mechanisms of toxicity of a number of neurotoxins synthesised by these ancient photosynthetic prokaryotes. We discuss the evidence linking β-methylamino-L-alanine (BMAA), a non-protein amino acid, to an unusual neurological disease complex reported on the island of Guam in the 1950s, and how 60 years later, the role that BMAA plays in human disease is still unclear. There is now evidence that BMAA is also produced by some eukaryotes, and can bioaccumulate in food chains; this combined with higher frequency of cyanobacterial blooms globally, increases the potential for human exposure. Three BMAA isomers that often co-occur with BMAA have been identified, and the current knowledge on the toxicity of these molecules is presented. The acute alkaloid toxins; anatoxin-a, homoanatoxin-a and the saxitoxins, and the organophosphate neurotoxin anatoxin-a(S) are also discussed. In many cases, human exposure to a cocktail of cyanobacterial neurotoxins is likely; however, the implications of combined exposure to these toxins have not been fully explored. Increased understanding of the combined effects of cyanobacterial neurotoxins is required to fully understand how these molecules impact on human health.
Roediger, B, Lee, Q, Tikoo, S, Cobbin, JCA, Henderson, JM, Jormakka, M, O’Rourke, MB, Padula, MP, Pinello, N, Henry, M, Wynne, M, Santagostino, SF, Brayton, CF, Rasmussen, L, Lisowski, L, Tay, SS, Harris, DC, Bertram, JF, Dowling, JP, Bertolino, P, Lai, JH, Wu, W, Bachovchin, WW, Wong, JJ-L, Gorrell, MD, Shaban, B, Holmes, EC, Jolly, CJ, Monette, S & Weninger, W 2018, 'An Atypical Parvovirus Drives Chronic Tubulointerstitial Nephropathy and Kidney Fibrosis', Cell, vol. 175, no. 2, pp. 530-543.e24. View/Download from: Publisher's site View description>>
The occurrence of a spontaneous nephropathy with intranuclear inclusions in laboratory mice has puzzled pathologists for over 4 decades, because its etiology remains elusive. The condition is more severe in immunodeficient animals, suggesting an infectious cause. Using metagenomics, we identify the causative agent as an atypical virus, termed "mouse kidney parvovirus" (MKPV), belonging to a divergent genus of Parvoviridae. MKPV was identified in animal facilities in Australia and North America, is transmitted via a fecal-oral or urinary-oral route, and is controlled by the adaptive immune system. Detailed analysis of the clinical course and histopathological features demonstrated a stepwise progression of pathology ranging from sporadic tubular inclusions to tubular degeneration and interstitial fibrosis and culminating in renal failure. In summary, we identify a widely distributed pathogen in laboratory mice and establish MKPV-induced nephropathy as a new tool for elucidating mechanisms of tubulointerstitial fibrosis that shares molecular features with chronic kidney disease in humans.
Rohlfs, A-M, Williams, S, Rees, GN, Lim, RP, Werry, L & Mitrovic, SM 2018, 'Experimental dam releases stimulate respiration in an epilithic biofilm community', Hydrobiologia, vol. 820, no. 1, pp. 175-187. View/Download from: Publisher's site View description>>
Roux, C, Ribaux, O & CRISPINO, F 2018, 'Forensic science 2020 – the end of the crossroads?', Australian Journal of Forensic Sciences, vol. 50, no. 6, pp. 1-12. View/Download from: Publisher's site View description>>
Rumman, R, Atkin, OK, Bloomfield, KJ & Eamus, D 2018, 'Variation in bulk‐leaf 13C discrimination, leaf traits and water‐use efficiency–trait relationships along a continental‐scale climate gradient in Australia', Global Change Biology, vol. 24, no. 3, pp. 1186-1200. View/Download from: Publisher's site View description>>
AbstractLarge spatial and temporal gradients in rainfall and temperature occur across Australia. This heterogeneity drives ecological differentiation in vegetation structure and ecophysiology. We examined multiple leaf‐scale traits, including foliar 13C isotope discrimination (Δ13C), rates of photosynthesis and foliar N concentration and their relationships with multiple climate variables. Fifty‐five species across 27 families were examined across eight sites spanning contrasting biomes. Key questions addressed include: (i) Does Δ13C and intrinsic water‐use efficiency (WUEi) vary with climate at a continental scale? (ii) What are the seasonal and spatial patterns in Δ13C/WUEi across biomes and species? (iii) To what extent does Δ13C reflect variation in leaf structural, functional and nutrient traits across climate gradients? and (iv) Does the relative importance of assimilation and stomatal conductance in driving variation in Δ13C differ across seasons? We found that MAP, temperature seasonality, isothermality and annual temperature range exerted independent effects on foliar Δ13C/WUEi. Temperature‐related variables exerted larger effects than rainfall‐related variables. The relative importance of photosynthesis and stomatal conductance (gs) in determining Δ13C differed across seasons: Δ13C was more strongly regulated by gs during the dry‐season and by photosynthetic capacity during the wet‐season. Δ13C was most strongly correlated, inversely, with leaf mass area ratio among all leaf attributes considered. Leaf Nmass was significantly and positively correlated with MAP during dry‐ and wet‐seasons and...
Rust, L, Nizio, KD, Wand, MP & Forbes, SL 2018, 'Investigating the detection limits of scent-detection dogs to residual blood odour on clothing', Forensic Chemistry, vol. 9, pp. 62-75. View/Download from: Publisher's site View description>>
Rutting, S, Papanicolaou, M, Xenaki, D, Wood, LG, Mullin, AM, Hansbro, PM & Oliver, BG 2018, 'Dietary ω-6 polyunsaturated fatty acid arachidonic acid increases inflammation, but inhibits ECM protein expression in COPD', Respiratory Research, vol. 19, no. 1, pp. 211-211. View/Download from: Publisher's site View description>>
BACKGROUND:The obesity paradox in COPD describes protective effects of obesity on lung pathology and inflammation. However, the underlying relationships between obesity, diet and disease outcomes in COPD are not fully understood. In this study we measured the response to dietary fatty acids upon markers of inflammation and remodelling in human lung cells from people with and without COPD. METHODS:Pulmonary fibroblasts were challenged with ω-3 polyunsaturated fatty acids (PUFAs), ω-6 PUFAs, saturated fatty acids (SFAs) or the obesity-associated cytokine TNFα. After 48-72 h release of the pro-inflammatory cytokines interleukin (IL)-6 and CXCL8 was measured using ELISA and mRNA expression and deposition of the extracellular matrix (ECM) proteins fibronectin, type I collagen, tenascin and perlecan were measured using qPCR or ECM ELISA, respectively. RESULTS:Challenge with the ω-6 PUFA arachidonic acid (AA), but not ω-3 PUFAs or SFAs, resulted in increased IL-6 and CXCL8 release from fibroblasts, however IL-6 and CXCL8 release was reduced in COPD (n = 19) compared to non-COPD (n = 36). AA-induced cytokine release was partially mediated by downstream mediators of cyclooxygenase (COX)-2 in both COPD and non-COPD. In comparison, TNFα-induced IL-6 and CXCL8 release was similar in COPD and non-COPD, indicating a specific interaction of AA in COPD. In patients with or without COPD, regression analysis revealed no relationship between BMI and cytokine release. In addition, AA, but not SFAs or ω-3 PUFAs reduced the basal deposition of fibronectin, type I collagen, tenascin and perlecan into the ECM in COPD fibroblasts. In non-COPD fibroblasts, AA-challenge decreased basal deposition of type I collagen and perlecan, but not fibronectin and tenascin. CONCLUSIONS:This study shows that AA has disease-specific effects on inflammation and ECM protein deposition. The impaired response to AA in COPD might in part explain why obesity appears to have less detrimental effects in COPD, c...
Rutting, S, Xenaki, D, Lau, E, Horvat, J, Wood, LG, Hansbro, PM & Oliver, BG 2018, 'Dietary omega-6, but not omega-3, polyunsaturated or saturated fatty acids increase inflammation in primary lung mesenchymal cells', American Journal of Physiology-Lung Cellular and Molecular Physiology, vol. 314, no. 6, pp. L922-L935. View/Download from: Publisher's site View description>>
Obesity is an important risk factor for developing severe asthma. Dietary fatty acids, which are increased in sera of obese individuals and after high-fat meals, activate the innate immune system and induce inflammation. This study investigated whether dietary fatty acids directly cause inflammation and/or synergize with obesity-induced cytokines in primary human pulmonary fibroblasts in vitro. Fibroblasts were challenged with BSA-conjugated fatty acids [ω-6 polyunsaturated fatty acids (PUFAs) and ω-3 PUFAs or saturated fatty acids (SFAs)], with or without TNF-α, and release of the proinflammatory cytokines, IL-6 and CXCL8, was measured. We found that the ω-6 PUFA arachidonic acid (AA), but not ω-3 PUFAs or SFAs, upregulates IL-6 and CXCL8 release. Combined AA and TNF-α challenge resulted in substantially greater cytokine release than either alone, demonstrating synergy. Synergistic upregulation of IL-6, but not CXCL8, was mainly mediated via cyclooxygenase (COX). Inhibition of p38 MAPK reduced CXCL8 release, induced by AA and TNF-α alone, but not in combination. Synergistic CXCL8 release, following AA and TNF-α challenge, was not medicated via a single signaling pathway (MEK1, JNK, phosphoinositide 3-kinase, and NF-κB) nor by hyperactivation of NF-κB or p38. To investigate if these findings occur in other airway cells, effects of AA in primary human airway smooth muscle (ASM) cells and human bronchial epithelial cells were also investigated. We found proinflammatory effects in ASM cells but not epithelial cells. This study suggests that diets rich in ω-6 PUFAs might promote airway inflammation via multiple pathways, including COX-dependent and -independent pathways, and in an obese person, may lead to more severe airway inflammation.
Ruvindy, R, Bolch, CJ, MacKenzie, L, Smith, KF & Murray, SA 2018, 'qPCR Assays for the Detection and Quantification of Multiple Paralytic Shellfish Toxin-Producing Species of Alexandrium', Frontiers in Microbiology, vol. 9. View/Download from: Publisher's site View description>>
Paralytic shellfish toxin producing dinoflagellates have negatively impacted the shellfish aquaculture industry worldwide, including in Australia and New Zealand. Morphologically identical cryptic species of dinoflagellates that may differ in toxicity, in particular, species of the former Alexandrium tamarense species complex, co-occur in Australia, as they do in multiple regions in Asia and Europe. To understand the dynamics and the ecological drivers of the growth of each species in the field, accurate quantification at the species level is crucial. We have developed the first quantitative polymerase chain reaction (qPCR) primers for A. australiense, and new primers targeting A. ostenfeldii, A. catenella, and A. pacificum. We showed that our new primers for A. pacificum are more specific than previously published primer pairs. These assays can be used to quantify planktonic cells and cysts in the water column and in sediment samples with limits of detection of 2 cells/L for the A. catenella and A. australiense assays, 2 cells/L and 1 cyst/mg sediment for the A. pacificum assay, and 1 cells/L for the A. ostenfeldii assay, and efficiencies of >90%. We utilized these assays to discriminate and quantify co-occurring A. catenella, A. pacificum, and A. australiense in samples from the east coast of Tasmania, Australia.
Rychener, L, In-Albon, S, Djordjevic, SP, Chowdhury, PR, Nicholson, P, Ziech, RE, de Vargas, AC, Frey, J & Falquet, L 2018, 'Corrigendum: Clostridium chauvoei, an Evolutionary Dead-End Pathogen', Frontiers in Microbiology, vol. 9. View/Download from: Publisher's site View description>>
[This corrects the article on p. 1054 in vol. 8, PMID: 28649238.].
Saad, S, Al-Odat, I, Chan, YL, McGrath, KC, Pollock, CA, Oliver, BG & Chen, H 2018, 'Maternal L-carnitine supplementation improves glucose and lipid profiles in female offspring of dams exposed to cigarette smoke', Clinical and Experimental Pharmacology and Physiology, vol. 45, no. 7, pp. 694-703. View/Download from: Publisher's site View description>>
Sex differences in disease susceptibility due to maternal programming have been reported. We previously observed that maternal smoking induced renal disease and neurological changes are restricted to males, while both male and female offspring develop metabolic disorders. We have also found that maternal L-carnitine supplementation during gestation and lactation can significantly improve glucose intolerance and hyperlipidaemia in male offspring. This study aimed to determine whether such beneficial effects can also occur in female offspring. Balb/c female mice were exposed to cigarette smoke (SE) 6 weeks prior to gestation, during gestation and lactation. A subgroup of the SE dams was given L-carnitine (1.5 mmol/L in drinking water) during gestation and lactation. Female offspring were studied at 20 days (weaning) and 13 weeks (adulthood). Maternal smoking increased liver weight (%) and blood glucose levels at 20 days, as well as glucose intolerance and plasma triglycerides levels at adulthood (P < .05). The hepatic lipid metabolic marker adipose triglyceride lipase was downregulated in the SE offspring at 20 days (P < .05). At 13 weeks, the hepatic pro-inflammatory markers IL-1β and TNF-α mRNA expression were upregulated, while the anti-inflammatory marker IL-10 mRNA expression was downregulated in the SE offspring (P < .05). Liver fibrosis was apparent at 20 days and 13 weeks. Maternal L-carnitine supplementation either normalised or suppressed the detrimental effects induced by maternal smoke exposure (P < .05). We conclude that maternal L-carnitine supplementation improves metabolic parameters in the female offspring of SE dams.
Sablok, G, Hayward, RJ, Davey, PA, Santos, RP, Schliep, M, Larkum, A, Pernice, M, Dolferus, R & Ralph, PJ 2018, 'SeagrassDB: An open-source transcriptomics landscape for phylogenetically profiled seagrasses and aquatic plants', Scientific Reports, vol. 8, no. 1. View/Download from: Publisher's site View description>>
AbstractSeagrasses and aquatic plants are important clades of higher plants, significant for carbon sequestration and marine ecological restoration. They are valuable in the sense that they allow us to understand how plants have developed traits to adapt to high salinity and photosynthetically challenged environments. Here, we present a large-scale phylogenetically profiled transcriptomics repository covering seagrasses and aquatic plants. SeagrassDB encompasses a total of 1,052,262 unigenes with a minimum and maximum contig length of 8,831 bp and 16,705 bp respectively. SeagrassDB provides access to 34,455 transcription factors, 470,568 PFAM domains, 382,528 prosite models and 482,121 InterPro domains across 9 species. SeagrassDB allows for the comparative gene mining using BLAST-based approaches and subsequent unigenes sequence retrieval with associated features such as expression (FPKM values), gene ontologies, functional assignments, family level classification, Interpro domains, KEGG orthology (KO), transcription factors and prosite information. SeagrassDB is available to the scientific community for exploring the functional genic landscape of seagrass and aquatic plants at: http://115.146.91.129/index.php.
Sack, BK, Behet, M, Mikolajczak, S, Cardamone, H, Nguyen, T, Flannery, E, Vaughan, AM, Oliver, B, Vigdorovich, V, Carbonetti, S, Sather, N, Scholzen, A, Sauerwein, R & Kappe, SHI 2018, 'Antibodies targeting the intracellular liver stage malaria parasite after infection can be a potent means of reducing parasite liver burden', The Journal of Immunology, vol. 200, no. 1_Supplement, pp. 180.30-180.30. View/Download from: Publisher's site View description>>
AbstractMalaria is one of the oldest and deadliest diseases known to humans, and in 2017 an estimated 216 million people were infected with 445,000 succumbing to disease. Antibodies which block the skin-to-liver stages of malaria infection continue to be pursued due to their potential to stop infection prior to the progression to the disease and transmission-causing blood stages. Phase III clinical trials with a vaccine targeting the major sporozoite surface protein (circumsporozoite protein) have provided suboptimal efficacy in the field which must be improved before large scale use for malaria prevention and eradication. New antibody targets will likely be needed in order to provide complete, sterilizing protection. Thus far, the search has largely been limited to targeting surface and secreted proteins of the sporozoite, merozoite or gametocyte stages.Here, we present data demonstrating that antibodies which instead target the intracellular liver stage parasite after hepatocyte infection can be a potent means of limiting parasite liver infection in vivo. This was done in a rodent malaria model by targeting two different proteins found on the parasitophorous vacuole membrane that forms the border between parasite and host cytoplasm—indicating antibodies are entering the hepatocyte to mediate their effect. This phenomenon was also demonstrated using the most common human malaria species Plasmodium falciparum in humanized liver chimeric mice where human antibodies targeting the parasite periphery were able to potently reduce liver burden and parasite liver growth between days 5–6. These data present a new class of antibody targets for malaria and strongly argue for the inclusion of intracellular antigens in novel vaccine formulations.
Sajid, A, Reimers, JR & Ford, MJ 2018, 'Defect states in hexagonal boron nitride: Assignments of observed properties and prediction of properties relevant to quantum computation', Physical Review B, vol. 97, no. 6, p. 064101. View/Download from: Publisher's site View description>>
Key properties of nine possible defect sites in hexagonal boron nitride
(h-BN) are predicted using density-functional theory and are corrected by
applying results from high-level ab initio calculations. Observed h-BN
electron-paramagnetic resonance signals at 22.4, 20.83, and 352.70 MHz are
assigned to VN, CN, and VNO2B, respectively, while the observed photoemission
at 1.95 eV is assigned to VNCB. Detailed consideration of the available excited
states, allowed spin-orbit couplings, zero-field splitting, and optical
transitions are made for the two related defects VNCB and VBCN. VNCB is
proposed for realizing long-lived quantum memory in h-BN. VBCN is predicted to
have a triplet ground state, implying that spin initialization by optical means
is feasible and suitable optical excitations are identified, making this defect
of interest for possible quantum-qubit operations.
Sankaran, J, Karampatzakis, A, Rice, SA & Wohland, T 2018, 'Quantitative imaging and spectroscopic technologies for microbiology', FEMS Microbiology Letters, vol. 365, no. 9. View/Download from: Publisher's site View description>>
Satija, S, Kamboj, S, Kaur, J, Mahajan, S, Neeta, Sharma, N, Khurana, N, Vyas, M & Mehta, M 2018, 'Morphological and anatomical studies of stem of Ageratum conyzoides', International Journal of Green Pharmacy, vol. 12, no. 2, pp. 127-130. View description>>
Context: Ageratum conyzoides Linn. (Asteraceae) is an important medicinal plant used in African traditional medicine for healing mental and infectious disorders. Objective: The objective of this work was to contribute to the pharmacobotanical standardization of A. conyzoides. Materials and Methods: Cross sections of the stem were obtained, by hand, for microscopic characterization of the stem. Powder microscopical characteristics were studied by microscope and scanning electron microscopy. Macroscopic characters and physiochemical standards of drug were also studied through standard methods mentioned in the WHO. Results and Discussion: Morphology of A. conyzoides showed that the outer surface of the stem was light green and inner surface was cream white in color, having slight bitter taste, and aromatic odor. Acicular calcium oxalate, sclerenchyma, thin long fibers, and hexagonal cork cells were observed in powder microscopy. Scanning electron microscopy showed the arrangement of vascular tissue in transverse section of the stem. Conclusion: These anatomical features are useful for the diagnosis of the species and provide support to their quality control.
Satija, S, Kamboj, S, Kaur, J, Ripdaman, Vyas, M & Mehta, M 2018, 'Pharmacognostic and pharmacological screening of Ageratum conyzoides stem extract for its antianxiety potential', International Journal of Green Pharmacy, vol. 12, no. 2, pp. S414-S418. View description>>
Objective: The current study assessed the antianxiety potential of standardized stem extracts of Ageratum conyzoides. Materials and Methods: Methanol extract of A. conyzoides stem was prepared using Soxhlet apparatus. Phytochemical investigation was done using standard procedures. Fractionation of methanol extract was done using liquid-liquid extraction. Methanol extract and its fractions (ethyl acetate and butanol) were evaluated for antianxiety potential using elevated plus maze model. Results and Discussion: The methanol extract gave the yield of 12% w/w and its ethyl acetate and butanol fractions gave 5.03% w/w and 2.0% w/w, respectively. The methanol extract of A. conyzoides showed a significant increase in mean of a number of entries by mice in open arms and average time spent when compared to control group. Results revealed that ethyl acetate fraction was responsible for its anxiolytic effect. Conclusion: The present study validates the traditional claim of A. conyzoides as anxiolytic drug as methanol extract of stem produced a significant antianxiety effect.
Satija, S, Mahajan, S, Vyas, M & Mehta, M 2018, 'Pharmacognostic study of dioscorea villosa leaves', International Journal of Green Pharmacy, vol. 12, no. 2, pp. S428-S432. View description>>
Context: Yam (Dioscorea spp.) is an important edible tuber plant used for medicinal purposes to promote health and longevity in Chinese tradition. Steroidal saponins were reported to be the major physiologically active constituents in yams. Therefore, this study was designed to investigate its pharmacognostic characters for its standardization. Materials and Methods: Macroscopic, microscopic, and physiochemical evaluation of Dioscorea villosa was performed using standardized procedures as mentioned in the WHO guidelines. Thin-layer chromatography (TLC) was done to check the purity and identification of the drug. Results and Discussion: Morphology of D. villosa showed that the upper surface of leaves was green in color, having bitter taste and some characteristic odor. The presence of calcium oxalate crystal, thin long fibers, xylem vessels, and epidermal cells was observed in powder microscopy. Phytochemical analysis of crude extracts indicated the presence of alkaloids, glycosides, saponins, and flavonoids. The presence of saponins was also confirmed by foaming index. TLC was done for all the extracts which showed a number of spots indicating the presence of number of chemical constituents. Conclusion: All the above pharmacognostic parameters could be useful for the authentication and preparation of monograph for D. villosa.
Satija, S, Prince, Gupta, R, Mahajan, S, Sharma, N, Khurana, N, Kalsi, V, Duggal, N, Singh, A & Mehta, M 2018, 'Chromatographic fingerprinting, antioxidant, and anti-inflammatory potential of Dioscorea villosa (Wild Yam) leaves', International Journal of Green Pharmacy, vol. 12, no. 2, pp. 102-106. View description>>
Context: Free radicals have been implicated in a wide range diversity of diseases and ailments, and therefore, the compounds having the ability to scavenge these free radicals are under extensive investigation, of which Dioscorea species have been actively involved. Objective: The current study assessed the anti-inflammatory and antioxidant potential of standardized leaf extracts of Dioscorea villosa. Material and Methods: Anti-inflammatory activity was carried out using carrageenan-induced paw edema assay, and antioxidant activity was evaluated using 1,1-diphenyl-2-picrylhydrazyl radical scavenging assay. Chromatographic fingerprinting of the crude methanolic extract was carried out using high-performance liquid chromatography (HPLC) whereby diosgenin was used as a standard marker compound. Results: Among all the crude successive extracts, methanolic extract showed significant anti-inflammatory activity in comparison with the standard whereby the extract showed maximum inhibition of paw edema after 3 h of carrageenan injection. The aqueous extract showed noticeable antioxidant activity with the half maximal inhibitory concentration of 21.36 μg/ml. Discussion: The preliminary phytochemical screening showed the presence of flavonoids and tannins that may be responsible for the observed effect. In addition, the presence of steroids marks toward the observed anti-inflammatory activity. In addition, the extract showed noticeable levels of diosgenin, which were marked and quantified using HPLC. Conclusion: The results strongly support the ethnobotanical use of the plant.
Saunders, BM, Rudnicka, C, Filipovska, A, Davies, S, Ward, N, Hricova, J, Schlaich, MP & Matthews, VB 2018, 'Shining LIGHT on the metabolic role of the cytokine TNFSF14 and the implications on hepatic IL-6 production', Immunology and Cell Biology, vol. 96, no. 1, pp. 41-53. View/Download from: Publisher's site View description>>
The cytokine Tumor Necrosis Factor Superfamily member 14, TNFSF14 (or LIGHT), is a controversial player in numerous diseases. We investigated the role of endogenously expressed TNFSF14 in diet-induced obesity in vivo. Firstly, we studied the effects of Tnfsf14 ablation on the development of obesity, glucose intolerance, insulin resistance, steatosis, tissue inflammation, and mitochondrial respiration in the liver. Secondly, we examined the role of TNFSF14 expression in hematopoietic cells on obesity and insulin sensitivity. Male Tnfsf14 knockout (KO) and wild type mice were fed chow or high fat diet (HFD) for 12 weeks and were assessed for weight gain, glucose intolerance, insulin resistance, hepatosteatosis, mitochondrial dysfunction, and cytokine expression. Wild-type mice were also reconstituted with bone marrow cells from Tnfsf14 knockout mice and were fed chow or HFD for 12 weeks. These mice were examined for weight gain and insulin resistance. HFD fed mice had elevated circulating levels of serum TNFSF14. Liver and white adipose tissue are potential sources of this elevated TNFSF14. Tnfsf14 deficient mice displayed increased obesity, glucose intolerance, insulin resistance, hepatosteatosis, and mitochondrial dysfunction compared to control mice on a HFD. Hepatic cytokine profiling pointed to a potential novel role of decreased IL-6 in the metabolic disturbances in obesogenic Tnfsf14 knockout mice. Bone marrow cells from Tnfsf14 deficient mice appeared to promote diet-induced obesity, insulin resistance and reduced FGF21 levels in white adipose tissue and liver. Our novel data suggest that Tnfsf14 ablation exacerbates parameters of the metabolic syndrome under high fat feeding conditions and provides evidence to support the development of TNFSF14 agonists as potential therapeutics in diet-induced obesity.
Saunders, C, Brown, JJ, Carter, DJ & Lapkin, S 2018, 'Chronic disease management support in Australian workplaces-low base, rising need', Health Promotion Journal of Australia, vol. 29, no. 3, pp. 257-264. View/Download from: Publisher's site View description>>
Issue addressed
This study investigates the current nature, levels and perceived need for workplace support among mature age Australian workers with chronic illness.
Methods
A cross‐sectional population survey was conducted via a double opt‐in panel sample of Australian workers aged 45 years and older with one or more of six major chronic diseases (diabetes and/or chronic heart, kidney, lung, mental health and/or musculoskeletal conditions).
Results
Three hundred and fourteen respondents reported being in the workforce and having at least one of the chronic conditions under investigation, of which almost one third reported having more than one of the conditions. The findings reveal a number of considerable gaps in Australian workplace support for employees 45 years and older with chronic illness, including workplace flexibility, supportive policies and co‐worker support.
Conclusions
This research adds to a scarce existing literature base on workplace support for workers with chronic illness in Australia. Future research is needed to identify opportunities for effective public policy and implementation of workplace interventions to better support this cohort.
So what?
If timely progress is not made in this area, the projected increase in the aged population and scheduled public policy changes impacting retirement age will multiply potential adverse effects on the health of employees with chronic illness and Australia's labour market productivity.
Scanes, E, Kutti, T, Fang, JKH, Johnston, EL, Ross, PM & Bannister, RJ 2018, 'Mine Waste and Acute Warming Induce Energetic Stress in the Deep-Sea Sponge Geodia atlantica and Coral Primnoa resedeaformis; Results From a Mesocosm Study', Frontiers in Marine Science, vol. 5. View/Download from: Publisher's site
Scanes, E, Parker, LM, O’Connor, WA, Gibbs, MC & Ross, PM 2018, 'Copper and ocean acidification interact to lower maternal investment, but have little effect on adult physiology of the Sydney rock oyster Saccostrea glomerata', Aquatic Toxicology, vol. 203, pp. 51-60. View/Download from: Publisher's site
In this work, we introduce an elastic analog of the Purcell effect and show theoretically that spherical nanoparticles can serve as tunable and robust antennas for modifying the emission from localized elastic sources. This effect can be qualitatively described by introducing elastic counterparts of the familiar electromagnetic parameters: local density of elastic states, elastic Purcell factor, and effective volume of elastic modes. To illustrate our framework, we consider the example of a submicron gold sphere as a generic elastic GHz antenna and find that shear and mixed modes of low orders in such systems offer considerable elastic Purcell factors. This formalism opens pathways towards extended control over dissipation of vibrations in various optomechanical systems and contributes to closing the gap between classical and quantum-mechanical treatments of phonons localized in elastic nanoresonators.
Schofield, ZV, Croker, D, Robertson, AAB, Massey, NL, Donovan, C, Tee, E, Edwards, D, Woodruff, TM, Halai, R, Hansbro, PM & Cooper, MA 2018, 'Characterisation of small molecule ligands 4CMTB and 2CTAP as modulators of human FFA2 receptor signalling', Scientific Reports, vol. 8, no. 1. View/Download from: Publisher's site View description>>
AbstractShort chain fatty acids (SCFAs) are protective against inflammatory diseases. Free fatty acid receptor 2 (FFA2), is a target of SCFAs however, their selectivity for FFA2 over other FFA receptors is limited. This study aimed to functionally characterise 2-(4-chlorophenyl)-3-methyl-N-(thiazole-2-yl)butanamide (4CMTB) and 4-((4-(2-chlorophenyl)thiazole-2-yl)amino)-4oxo-3-phenylbutanoic acid (2CTAP), and their enantiomers, in modulating FFA2 activity. The racemic mixture (R/S) and its constituents (R-)and (S-) 4CMTB or 2CTAP were used to stimulate human (h)FFA2 in the absence or presence of acetate. Calcium ions (Ca2+), phosphorylated extracellular signal-regulated kinase 1 and 2 (pERK1/2) and cyclic adenosine monophosphate (cAMP) were measured.R/S-4CMTB is a functionally selective ago-allosteric ligand that enhances Ca2+response to acetate. BothR/S-4CMTB andS-4CMTB are more potent activators of pERK1/2 and inhibitors of forskolin-induced cAMP than acetate.S-4CMTB increased neutrophil infiltration in intestinal ischemia reperfusion injury (IRI). 2CTAP inhibited constitutive Ca2+levels, antagonised acetate-induced pERK1/2 and prevented damage following IRI. This study characterises enantiomers of functionally selective ligands for FFA2 in cells stably expressing hFFA2. It highlights the novel roles of selective FFA2 enantiomers 4CMTB and 2CTAP on Ca2+, pERK1/2 and cAMP and their roles as allosteric modulators which, may assist in efforts to design novel therapeutic agents for FFA2-driven inflammatory diseases.
Schrameyer, V, York, PH, Chartrand, K, Ralph, PJ, Kühl, M, Brodersen, KE & Rasheed, MA 2018, 'Contrasting impacts of light reduction on sediment biogeochemistry in deep- and shallow-water tropical seagrass assemblages (Green Island, Great Barrier Reef)', Marine Environmental Research, vol. 136, pp. 38-47. View/Download from: Publisher's site View description>>
Seagrass meadows increasingly face reduced light availability as a consequence of coastal development, eutrophication, and climate-driven increases in rainfall leading to turbidity plumes. We examined the impact of reduced light on above-ground seagrass biomass and sediment biogeochemistry in tropical shallow- (∼2 m) and deep-water (∼17 m) seagrass meadows (Green Island, Australia). Artificial shading (transmitting ∼10-25% of incident solar irradiance) was applied to the shallow- and deep-water sites for up to two weeks. While above-ground biomass was unchanged, higher diffusive O2 uptake (DOU) rates, lower O2 penetration depths, and higher volume-specific O2 consumption (R) rates were found in seagrass-vegetated sediments as compared to adjacent bare sand (control) areas at the shallow-water sites. In contrast, deep-water sediment characteristics did not differ between bare sand and vegetated sites. At the vegetated shallow-water site, shading resulted in significantly lower hydrogen sulphide (H2S) levels in the sediment. No shading effects were found on sediment biogeochemistry at the deep-water site. Overall, our results show that the sediment biogeochemistry of shallow-water (Halodule uninervis, Syringodium isoetifolium, Cymodocea rotundata and C. serrulata) and deep-water (Halophila decipiens) seagrass meadows with different species differ in response to reduced light. The light-driven dynamics of the sediment biogeochemistry at the shallow-water site could suggest the presence of a microbial consortium, which might be stimulated by photosynthetically produced exudates from the seagrass, which becomes limited due to lower seagrass photosynthesis under shaded conditions.
PAM Review is the peer-reviewed student research journal of the School of Mathematical and Physical Sciences at the University of Technology Sydney. It was born out of the desire to create a practical student centered, authentic learning experience in a highly theoretical course that is exciting and challenging and facilitates to promote the desired graduate attributes.
Schulte, J, Tiffen, B, Edwards, J, Abbott, S & Luca, E 2018, 'Shaping the Future of Academic Libraries: Authentic Learning for the Next Generation', College & Research Libraries, vol. 79, no. 5, pp. 685-696. View/Download from: Publisher's site View description>>
Schumann-Gillett, A, Mark, AE, Deplazes, E & O’Mara, ML 2018, 'A potential new, stable state of the E-cadherin strand-swapped dimer in solution', European Biophysics Journal, vol. 47, no. 1, pp. 59-67. View/Download from: Publisher's site View description>>
E-cadherin is a transmembrane glycoprotein that facilitates inter-cellular adhesion in the epithelium. The ectodomain of the native structure is comprised of five repeated immunoglobulin-like domains. All E-cadherin crystal structures show the protein in one of three alternative conformations: a monomer, a strand-swapped trans homodimer and the so-called X-dimer, which is proposed to be a kinetic intermediate to forming the strand-swapped trans homodimer. However, previous studies have indicated that even once the trans strand-swapped dimer is formed, the complex is highly dynamic and the E-cadherin monomers may reorient relative to each other. Here, molecular dynamics simulations have been used to investigate the stability and conformational flexibility of the human E-cadherin trans strand-swapped dimer. In four independent, 100 ns simulations, the dimer moved away from the starting structure and converged to a previously unreported structure, which we call the Y-dimer. The Y-dimer was present for over 90% of the combined simulation time, suggesting that it represents a stable conformation of the E-cadherin dimer in solution. The Y-dimer conformation is stabilised by interactions present in both the trans strand-swapped dimer and X-dimer crystal structures, as well as additional interactions not found in any E-cadherin dimer crystal structures. The Y-dimer represents a previously unreported, stable conformation of the human E-cadherin trans strand-swapped dimer and suggests that the available crystal structures do not fully capture the conformations that the human E-cadherin trans homodimer adopts in solution.
Synthesis of Co9S8, Ni3S2, Co and Ni nanowires by solventless thermolysis of a mixture of metal(ii) acetate and cysteine in vacuum is reported.
Scott, PD, Coleman, HM, Khan, S, Lim, R, McDonald, JA, Mondon, J, Neale, PA, Prochazka, E, Tremblay, LA, Warne, MSJ & Leusch, FDL 2018, 'Histopathology, vitellogenin and chemical body burden in mosquitofish (Gambusia holbrooki) sampled from six river sites receiving a gradient of stressors', Science of The Total Environment, vol. 616-617, pp. 1638-1648. View/Download from: Publisher's site View description>>
There are over 40,000 chemical compounds registered for use in Australia, and only a handful are monitored in the aquatic receiving environments. Their effects on fish species in Australia are largely unknown. Mosquitofish (Gambusia holbrooki) were sampled from six river sites in Southeast Queensland identified as at risk from a range of pollutants. The sites selected were downstream of a wastewater treatment plant discharge, a landfill, two agricultural areas, and two sites in undeveloped reaches within or downstream of protected lands (national parks). Vitellogenin analysis, histopathology of liver, kidney and gonads, morphology of the gonopodium, and chemical body burden were measured to characterize fish health. Concentrations of trace organic contaminants (TrOCs) in water were analyzed by in vitro bioassays and chemical analysis. Estrogenic, anti-estrogenic, anti-androgenic, progestagenic and anti-progestagenic activities and TrOCs were detected in multiple water samples. Several active pharmaceutical ingredients (APIs), industrial compounds, pesticides and other endocrine active compounds were detected in fish carcasses at all sites, ranging from <4-4700ng/g wet weight, including the two undeveloped sites. While vitellogenin protein was slightly increased in fish from two of the six sites, the presence of micropollutants did not cause overt sexual endocrine disruption in mosquitofish (i.e., no abnormal gonads or gonopodia). A correlation between lipid accumulation in the liver with total body burden warrants further investigation to determine if exposure to low concentrations of TrOCs can affect fish health and increase stress on organs such as the liver and kidneys via other mechanisms, including disruption of non-sexual endocrine axes involved in lipid regulation and metabolism.
Scudder, N, McNevin, D, Kelty, SF, Walsh, SJ & Robertson, J 2018, 'Forensic DNA phenotyping: Developing a model privacy impact assessment', Forensic Science International: Genetics, vol. 34, pp. 222-230. View/Download from: Publisher's site View description>>
Forensic scientists around the world are adopting new technology platforms capable of efficiently analysing a larger proportion of the human genome. Undertaking this analysis could provide significant operational benefits, particularly in giving investigators more information about the donor of genetic material, a particularly useful investigative lead. Such information could include predicting externally visible characteristics such as eye and hair colour, as well as biogeographical ancestry. This article looks at the adoption of this new technology from a privacy perspective, using this to inform and critique the application of a Privacy Impact Assessment to this emerging technology. Noting the benefits and limitations, the article develops a number of themes that would influence a model Privacy Impact Assessment as a contextual framework for forensic laboratories and law enforcement agencies considering implementing forensic DNA phenotyping for operational use.
Scudder, N, McNevin, D, Kelty, SF, Walsh, SJ & Robertson, J 2018, 'Massively parallel sequencing and the emergence of forensic genomics: Defining the policy and legal issues for law enforcement', Science & Justice, vol. 58, no. 2, pp. 153-158. View/Download from: Publisher's site View description>>
Use of DNA in forensic science will be significantly influenced by new technology in coming years. Massively parallel sequencing and forensic genomics will hasten the broadening of forensic DNA analysis beyond short tandem repeats for identity towards a wider array of genetic markers, in applications as diverse as predictive phenotyping, ancestry assignment, and full mitochondrial genome analysis. With these new applications come a range of legal and policy implications, as forensic science touches on areas as diverse as 'big data', privacy and protected health information. Although these applications have the potential to make a more immediate and decisive forensic intelligence contribution to criminal investigations, they raise policy issues that will require detailed consideration if this potential is to be realised. The purpose of this paper is to identify the scope of the issues that will confront forensic and user communities.
Seckiner, D, Mallett, X, Roux, C, Meuwly, D & Maynard, P 2018, 'Forensic image analysis – CCTV distortion and artefacts', Forensic Science International, vol. 285, pp. 77-85. View/Download from: Publisher's site
Segečová, A, Červený, J & Roitsch, T 2018, 'Advancement of the cultivation and upscaling of photoautotrophic suspension cultures using Chenopodium rubrum as a case study', Plant Cell, Tissue and Organ Culture (PCTOC), vol. 135, no. 1, pp. 37-51. View/Download from: Publisher's site
Like many organisms, bacteria regularly inhabit environments characterised by spatiotemporal heterogeneity in the availability of resources required for growth and energy generation, meaning they must either tune their metabolism to prevailing conditions or have the capacity to migrate to favourable microenvironments1. To achieve the latter, bacteria measure their resource landscape and suitably direct their locomotion using a behaviour called chemotaxis, which is the ability to guide movement up or down chemical gradients. The capacity to perform chemotaxis is widespread across the bacterial domain, although most of our understanding of this phenotype is derived from enteric bacteria2,3. In the ocean, marine bacteria are often motile4, and in fact capable of much higher swimming speeds5 and chemotactic precision6 than these enteric models for chemotaxis2. Here we discuss the underlying motives and purposes for bacterial chemotaxis in the ocean, by noting that marine bacteria experience a surprisingly heterogeneous chemical seascape7,8, whereby chemotaxis can provide substantial fitness advantages and even influence large-scale processes including marine ecosystem productivity, biogeochemical cycling and disease.
Seymour, JR, Barbasch, TA & Buston, PM 2018, 'Lunar cycles of reproduction in the clown anemonefish Amphiprion percula: individual-level strategies and population-level patterns', Marine Ecology Progress Series, vol. 594, pp. 193-201. View/Download from: Publisher's site
Shad, KF, Luqman, N, Simpson, AM & Lal, S 2018, 'Peripheral Biomarker for Vascular Disorders', Biomarker Insights, vol. 13, pp. 117727191881246-117727191881246. View/Download from: Publisher's site View description>>
Atherosclerosis is the underlying cause of most myocardial infarction (MI) and ischaemic stroke episodes. An early sign of atherosclerosis is hypertrophy of the arterial wall. It is known that increased intima media thickness (IMT) is a non-invasive marker of arterial wall alteration, which can easily be assessed in the carotid arteries by high-resolution B-mode ultrasound. Similarly, the other key element of MI and ischaemic strokes is the N-methyl-D-aspartate (NMDA) receptor which is an ionotropic glutamate receptor that mediates the vast majority of excitatory neurotransmission in the brain. NMDA activation requires the binding of both glutamate and a coagonist like D-serine to its glycine site. A special enzyme, serine racemase (SR), is required for the conversion of L-serine into D-serine, and alterations in SR activities lead to a variety of physiological and pathological conditions ranging from synaptic plasticity to ischemia, MI, and stroke. The amount of D-serine available for the activation of glutamatergic signalling is largely determined by SR and we have developed ways to estimate its levels in human blood samples and correlate it with the IMT. This research based short communication describes our pilot study, which clearly suggests that there is a direct relationship between the SR, D-serine, and IMT. In this article, we will discuss whether the activity of SR can determine the future consequences resulting from vascular pathologies such as MI and stroke.
Shah, JS, Gard, GB, Yang, J, Maidens, J, Valmadre, S, Soon, PS & Marsh, DJ 2018, 'Combining serum microRNA and CA-125 as prognostic indicators of preoperative surgical outcome in women with high-grade serous ovarian cancer', Gynecologic Oncology, vol. 148, no. 1, pp. 181-188. View/Download from: Publisher's site View description>>
The most widely used approach for the clinical management of women with high-grade serous ovarian cancer (HGSOC) is surgery, followed by platinum and taxane based chemotherapy. The degree of macroscopic disease remaining at the conclusion of surgery is a key prognostic factor determining progression free and overall survival. We sought to develop a non-invasive test to assist surgeons to determine the likelihood of achieving complete surgical resection. This knowledge could be used to plan surgical approaches for optimal clinical management.We profiled 170 serum microRNAs (miRNAs) using the Serum/Plasma Focus miRNA PCR panel containing locked nucleic acid (LNA) primers (Exiqon) in women with HGSOC (N=56) and age-matched healthy volunteers (N=30). Additionally, we measured serum CA-125 levels in the same samples. The HGSOC cohort was further classified based on the degree of macroscopic disease at the conclusion of surgery. Stepwise logistic regression was used to identify predictive markers.We identified a combination of miR-375 and CA-125 as the strongest discriminator of healthy versus HGSOC serum, with an area under the curve (AUC) of 0.956. The inclusion of miR-210 increased the AUC to 0.984; however, miR-210 was affected by hemolysis. The combination of miR-34a-5p and CA-125 was the strongest predictor of completeness of surgical resection with an AUC of 0.818.A molecular test incorporating circulating miRNA to predict completeness of surgical resection for women with HGSOC has the potential to contribute to planning for optimal patient management, ultimately improving patient outcome.
Shang, Y, Bao, G, Zhou, J, Wong, K, Yang, C & Jin, D 2018, 'Lanthanide-Doped Upconversion Luminescent Materials for Point of Care Diagnosis', Zhongguo Xitu Xuebao/Journal of the Chinese Rare Earth Society, vol. 36, no. 2, pp. 129-146. View/Download from: Publisher's site View description>>
Point of care (POC) diagnosis has attracted much research interest due to its rapid, specific and sensitive detection of biomarkers and pathogens. This decentralized diagnostic approach undoubtedly has huge advantage over laboratory testing at large hospitals or community laboratories regarding cost-effectiveness, healthcare delivery, especially with the emerging and spreading of smart technologies. Among all the materials for POC, lanthanides have become a rising star because of their excellent photophysical properties such as long life time, characteristic luminescence. Here, we focus on the wide-spread platforms of POC diagnostic devices and the applications of lanthanide upconverting materials in this field. With the market and social trend analysis, we will give our future perspective about the applications of lanthanide materials in POC.
Shannon, RM, Macquart, J-P, Bannister, KW, Ekers, RD, James, CW, Osłowski, S, Qiu, H, Sammons, M, Hotan, AW, Voronkov, MA, Beresford, RJ, Brothers, M, Brown, AJ, Bunton, JD, Chippendale, AP, Haskins, C, Leach, M, Marquarding, M, McConnell, D, Pilawa, MA, Sadler, EM, Troup, ER, Tuthill, J, Whiting, MT, Allison, JR, Anderson, CS, Bell, ME, Collier, JD, Gürkan, G, Heald, G & Riseley, CJ 2018, 'The dispersion–brightness relation for fast radio bursts from a wide-field survey', Nature, vol. 562, no. 7727, pp. 386-390. View/Download from: Publisher's site
Shastri, MD, Shukla, SD, Chong, WC, Dua, K, Peterson, GM, Patel, RP, Hansbro, PM, Eri, R & O’Toole, RF 2018, 'Role of Oxidative Stress in the Pathology and Management of Human Tuberculosis', Oxidative Medicine and Cellular Longevity, vol. 2018, pp. 1-10. View/Download from: Publisher's site View description>>
Tuberculosis (TB), caused by the bacteriumMycobacterium tuberculosis, is the leading cause of mortality worldwide due to a single infectious agent. The pathogen spreads primarily via aerosols and especially infects the alveolar macrophages in the lungs. The lung has evolved various biological mechanisms, including oxidative stress (OS) responses, to counteract TB infection.M. tuberculosisinfection triggers the generation of reactive oxygen species by host phagocytic cells (primarily macrophages). The development of resistance to commonly prescribed antibiotics poses a challenge to treat TB; this commonly manifests as multidrug resistant tuberculosis (MDR-TB). OS and antioxidant defense mechanisms play key roles during TB infection and treatment. For instance, several established first-/second-line antitubercle antibiotics are administered in an inactive form and subsequently transformed into their active form by components of the OS responses of both host (nitric oxide,S-oxidation) and pathogen (catalase/peroxidase enzyme, EthA). Additionally,M. tuberculosishas developed mechanisms to survive high OS burden in the host, including the increased bacterial NADH/NAD+ratio and enhanced intracellular survival (Eis) protein, peroxiredoxin, superoxide dismutases, and catalases. Here, we review the interplay between lung OS and its effects on both activation of antitubercle antibiotics and the strategies employed byM. tuberculosisthat are essential for survival of both drug-susceptible and drug-resistant bacterial subtypes. We then outline potential new therapies that are based on combining standard antitubercular antibiotics with adjuvant agents that could limit the ability ofM. tuberculosisto counter the host’s OS response.
She, L, Xue, Y, Yang, X, Guang, J, Li, Y, Che, Y, Fan, C & Xie, Y 2018, 'Dust Detection and Intensity Estimation Using Himawari-8/AHI Observation', Remote Sensing, vol. 10, no. 4, pp. 490-490. View/Download from: Publisher's site
Shen, J, Huete, A, Tran, NN, Devadas, R, Ma, X, Eamus, D & Yu, Q 2018, 'Diverse sensitivity of winter crops over the growing season to climate and land surface temperature across the rainfed cropland-belt of eastern Australia', Agriculture, Ecosystems & Environment, vol. 254, pp. 99-110. View/Download from: Publisher's site View description>>