bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic and epidemiological evidence of a dominant Panton-Valentine leucocidin-positive Methicillin Resistant Staphylococcus aureus lineage in Sri Lanka with spread to the United Kingdom and Australia
Authors: McTavish S.M. , Snow S.J. , Cook E.C. , Pichon B. , Coleman S. , Coombs G.W. , Pang S. , Arias C.A. , Díaz L. , Boldock E. , Davies S. , Udukala M. , Kearns A. , Siribaddana S. , de Silva T.I. 
Published: January 2019

AbstractObjectiveTo undertake the first detailed genomic analysis of methicillin-resistant Staphylococcus aureus (MRSA) isolated in Sri Lanka.MethodsA prospective observational study was performed on 94 MRSA isolates collected over a four month period from the Anuradhapura Teaching Hospital, Sri Lanka. Screening for mecA, mecC and the Panton-Valentine leucocidin (PVL)-associated lukS-PV/lukF-PV genes and molecular characterisation by spa typing was undertaken. Whole genome sequencing (WGS) and phylogenetic analysis was performed on selected multilocus sequence type (MLST) clonal complex 5 (CC5) isolates from Sri Lanka, England, Australia and Argentina.ResultsAll 94 MRSA harboured the mecA gene. Nineteen spa types associated with nine MLST clonal complexes were identified. Most isolates were from skin and soft tissue infections (76.9%), with the remainder causing more invasive disease. Sixty two (65.9%) of isolates were PVL positive with the majority (56 isolates; 90.3%) belonging to a dominant CC5 lineage. This lineage, PVL-positive ST5-MRSA-IVc, was associated with community and hospital-onset infections. Based on WGS, representative PVL-positive ST5-MRSA-IVc isolates from Sri Lanka, England and Australia formed a single phylogenetic clade, suggesting wide geographical circulation.ConclusionsWe present the most detailed genomic analysis of MRSA isolated in Sri Lanka to date. The analysis identified a PVL-positive ST5-MRSA-IVc that dominates MRSA clinical infections in Sri Lanka. Furthermore, transmission of the strain has occurred in the United Kingdom and Australia.
Repetitive mild concussion in subjects with a vulnerable cholinergic system: lasting cholinergic-attentional impairments in CHT+/- mice
Authors: Cherian Ajeesh Koshy , Tronson Natalie C. , Parikh Vinay , Kucinski Aaron , Blakely Randy D. , Sarter Martin 
Published: January 2019

AbstractPrevious research emphasized the impact of traumatic brain injury on cholinergic systems and associated cognitive functions. Here we addressed the converse question: Because of the available evidence indicating cognitive and neuronal vulnerabilities in humans expressing low-capacity cholinergic systems or with declining cholinergic systems, do injuries cause more severe cognitive decline in such subjects, and what cholinergic mechanisms contribute to such a vulnerability? Using mice heterozygous for the choline transporter (CHT+/- mice) as a model for a limited cholinergic capacity, we investigated the cognitive and neuronal consequences of repeated, mild concussion injuries (rmCc). Following five rmCc, and compared with WT mice, CHT+/- mice exhibited severe and lasting impairments in sustained attention performance, consistent with effects of cholinergic losses on attention. However, rmCc did not affect the integrity of neuronal cell bodies and did not alter the density of cortical synapses. As a cellular mechanism potentially responsible for the attentional impairment in CHT+/- mice, we found that rmCc nearly completely attenuated performance-associated, CHT-mediated choline transport. These results predict that subjects with an already vulnerable cholinergic system will experience severe and lasting cognitive-cholinergic effects following even relatively mild injuries. If confirmed in humans, such subjects may be excluded from, or receive special protection against, activities involving injury risk. Moreover, the treatment and long-term outcome of traumatic brain injuries may benefit from determining the status of cholinergic systems and associated cognitive functions.
First complete genome sequences of Zika virus from Midwest Brazil, 2015
Authors: Vieira Carla Julia da Silva Pessoa , Machado Laís Ceschini , Pena Lindomar José , Bronzoni Roberta Vieira de Morais , Wallau Gabriel da Luz 
Published: January 2019

AbstractZika virus (ZIKV) has been intensively studied in Brazil since 2015-2016 epidemics, but little is known about the virus in Midwest region of the country. We report here two ZIKV complete genomes, which were isolated during arboviral surveillance in Sinop city, southern border of the Amazonian forest, Midwest Brazil, 2015.
HMGB1 orchestrates uterine macrophage trafficking to safeguard embryo implantation
Authors: Aikawa Shizu , Deng Wenbo , Liang Xiaohuan , Yuan Jia , Bartos Amanda , Sun Xiaofei , Dey Sudhansu K 
Published: January 2019

AbstractA reciprocal communication between the implantation-competent blastocyst and the receptive uterus is essential to implantation. Blastocyst implantation is considered to be a regulated proinflammatory response in the uterus, however the underlining mechanism remains elusive. Here, we provide genetic evidence that High-mobility group protein Box-1 (HMGB1), expressed in uterine cell nuclei, restricts inflammatory responses during the periimplantation period. Conditional deletion of uterineHmgb1by using aPgr-Credriver (Pgrcre/+Hmgb1f/f) shows substantial infertility because of defective implantation and subsequent adverse ripple effects. These mice accumulate and retain an increased number of macrophages in the stroma on day 4 of pregnancy with a unique enrichment of macrophages in the stroma encircling the blastocyst on day 5, evoking inflammatory responses. These results are in contrast to previous findings that HMBG1 is an internal alarmin. In search for the mechanism, we found thatHmgb1-deleted stromal cells show reduced activation of PR and decreasedHoxa10expression, providing evidence that PR and Hoxa10 mediated regression of inflammation is mediated by HMGB1. In addition, levels of two macrophage attractants CSF1 and CCL2 are elevated in the stroma and in vitro studies show that CSF1 specifically attracts macrophages which is abrogated if challenged with a CSF1 receptor antagonist. The results suggest thatHmgb1contributes to successful blastocyst implantation by regulating macrophage trafficking in the stroma to prevent excessive inflammatory responses.
Mapping viscosity in discrete subcellular locations with a BODIPY based fluorescent probe
Authors: Pytowski Lior , Foley Alex C. , Hernández Zayra E. , Moon Niall , Donohoe Timothy J. , Vaux David J. 
Published: January 2019

AbstractNumerous cellular processes, including enzyme behaviour, signalling, and protein folding and transport are highly influenced by the local microviscosity environment within living cells. Molecular rotors are fluorescent molecules that respond to the viscosity of their environment through changes in both the intensity and lifetime of their fluorescence. We have synthesised a novel benzyl-guanine derivatized boron-dipyrromethene (BODIPY) molecular rotor that is a substrate for the SNAP-tag targeting system (named BG-BODIPY), allowing us to target the rotor to discrete locations within the living cell. We demonstrate that BG-BODIPY reports viscosity, and that this can be measured either through fluorescence lifetime or intensity ratiometric measurements. The relative microviscosities within the ER, Golgi, mitochondrial matrix, peroxisomes, lysosomes, cytoplasm, and nucleoplasm were significantly different. Additionally, this approach permitted fluorescence lifetime imaging microscopy (FLIM) to determine the absolute viscosity within both mitochondria and stress granules, showcasing BG-BODIPY’s usefulness in studying both membrane-bound and membraneless organelles. These results highlight targeted BG-BODIPY’s broad usefulness for making measurements of cellular viscosity both with FLIM and conventional ratiometric confocal microscopy, the latter option greatly extending the accessibility of the technique although limited to relative meassurements.Statement of SignificanceLocal viscosity affects molecular behaviour from diffusion and conformational changes to enzyme kinetics and has important implications for cell and tissue function. Mechanical methods for measurement of viscosity average over large volumes and long times and are thus unsuitable for rapid changes on small scales that are biologically relevant. This paper reports a novel optical fluorescence method using genome edited cells to deliver a viscosity reporter to tightly defined locations inside living cells, from which non-destructive organelle-specific measurements can be repeatedly made. The local viscosity of seven separate organelles in living cultured human cells is shown for the first time, together with the viscosity behaviour of a membraneless organelle as it is induced in cells by stress.
The GRASP domain in Golgi Reassembly and Stacking Proteins: differences and similarities between lower and higher Eukaryotes
Authors: Mendes Luís F. S. , Fontana Natália A. , Oliveira Carolina G. , Freire Marjorie C. L. C , Lopes José L. S. , Melo Fernando A. , Costa-Filho Antonio J. 
Published: January 2019

ABSTRACTThe Golgi complex is part of the endomembrane system and is responsible for receiving transport cargos from the endoplasmic reticulum and for sorting and targeting them to their final destination. To perform its function in higher eukaryotic cells, the Golgi needs to be correctly assembled as a flatted membrane sandwich kept together by a protein matrix. The correct mechanism controlling the Golgi cisternae assembly is not yet known, but it is already accepted that the Golgi Reassembly and Stacking Protein (GRASP) is a main component of the Golgi protein matrix. Unlike mammalian cells, which have two GRASP genes, lower eukaryotes present only one gene and distinct Golgi cisternae assembly. In this study, we performed a set of biophysical studies to get insights on both human GRASP55 and GRASP65 and compare them with GRASPs from lower eukaryotes (S. cerevisiae and C. neoformans). Our data suggest that both human GRASPs are essentially different from each other and GRASP65 is more similar to the subgroup of GRASPs from lower eukaryotes. GRASP55 is present mainly in the Golgi medial and trans faces, which are absent in both funguses, while GRASP65 is located in the cis-Golgi. We suggest that the GRASP65 gene is more ancient and the paralogue GRASP55 might have appeared latter in evolution, together with the medial and trans Golgi faces in mammalians.
Transcriptional analysis shows a robust host response toToxoplasma gondiiduring early and late chronic infection in both male and female mice
Authors: Garfoot Andrew L. , Cervantes Patrick W. , Knoll Laura J. 
Published: January 2019

ABSTRACTThe long-term host effects caused by the protozoan parasiteToxoplasma gondiiare poorly understood. RNA-seq analysis previously determined that the host response in the brain was higher and more complex at 28 versus 10 days postinfection. Here, we analyzed the host transcriptional profile of age-and sex-matched mice during early (21 and 28 days) and late (3 and 6 months) chronic infection. We found that a majority of the host genes which increase in abundance at day 21 postinfection are still increased 6 months postinfection for both male and female mice. While most of the differentially expressed genes were similar between sexes, females have far fewer genes that are significantly less abundant, which may lead to the slight increased cyst burden in males. Transcripts for C-X-C Motif Chemokine Ligand 13 (CXCL13) and a C-C Motif Chemokine Receptor 2 (CCR2) were significantly higher in females compared to males during infection. AsT. gondiichronic infection and profilin (PRF) confer resistance toListeria monocytogenesinfection in a CCR2 dependent manner, the sex specific difference in CCR2 expression lead us to re-test the protection of PRF in both sexes. Chronic infection as well as PRF were nearly as effective at reducing the bacterial burden in male versus female mice. These data show that most of the differentially express host genes are similar between males and females, important differences exist leading us to emphasize the inclusion of both sexes for future studies.
GenomegaMap: within-species genome-widedN/dSestimation from over 10,000 genomes
Authors: Wilson Daniel J. ,   The CRyPTIC Consortium
Published: January 2019

ABSTRACTThedN/dSratio provides evidence of adaptation or functional constraint in protein-coding genes by quantifying the relative excess or deficit of amino acid-replacing versus silent nucleotide variation. Inexpensive sequencing promises a better understanding of parameters such asdN/dS, but analysing very large datasets poses a major statistical challenge. Here I introduce genomegaMap for estimating within-species genome-wide variation indN/dS, and I apply it to 3,979 genes across 10,209 tuberculosis genomes to characterize the selection pressures shaping this global pathogen. GenomegaMap is a phylogeny-free method that addresses two major problems with existing approaches: (i) it is fast no matter how large the sample size and (ii) it is robust to recombination, which causes phylogenetic methods to report artefactual signals of adaptation. GenomegaMap uses population genetics theory to approximate the distribution of allele frequencies under general, parent-dependent mutation models. Coalescent simulations show that substitution parameters are well-estimated even when genomegaMap’s simplifying assumption of independence among sites is violated. I demonstrate the ability of genomegaMap to detect genuine signatures of selection at antimicrobial resistance-conferring substitutions inM. tuberculosisand describe a novel signature of selection in the cold-shock DEAD-box protein A genedeaD/csdA. The genomegaMap approach helps accelerate the exploitation of big data for gaining new insights into evolution within species.
Genome-wide epistasis and co-selection study using mutual information
Authors: Pensar Johan , Puranen Santeri , MacAlasdair Neil , Kuronen Juri , Tonkin-Hill Gerry , Pesonen Maiju , Arnold Brian , Xu Yingying , Sipola Aleksi , Sánchez-Busó Leonor , Lees John A , Chewapreecha Claire , Bentley Stephen D , Harris Simon R , Parkhill Julian , Croucher Nicholas J , Corander Jukka 
Published: January 2019

ABSTRACTDiscovery of polymorphisms under co-selective pressure or epistasis has received considerable recent attention in population genomics. Both statistical modeling of the population level co-variation of alleles across the chromosome and model-free testing of dependencies between pairs of polymorphisms have been shown to successfully uncover patterns of selection in bacterial populations. Here we introduce a model-free method, SpydrPick, whose computational efficiency enables analysis at the scale of pan-genomes of many bacteria. SpydrPick incorporates an efficient correction for population structure, which is demonstrated to maintain a very low rate of false positive findings among those SNP pairs highlighted to deviate significantly from the null hypothesis of neutral co-evolution in simulated data. We also introduce a new type of visualization of the results similar to the Manhattan plots used in genome-wide association studies, which enables rapid exploration of the identified signals of co-evolution. Application of the method to large population genomic data sets of two major human pathogens,Streptococcus pneumoniaeandNeisseria meningitidis, revealed both previously identified and novel putative targets of co-selection related to virulence and antibiotic resistance, highlighting the potential of this approach to drive molecular discoveries, even in the absence of phenotypic data.
Quality management practices in SMEs: a comparative study between India and Namibia
Authors: Chakraborty Ayon , Mutingi Michael , Vashishth Abhishek 
Published: January 2019

Purpose
Small- and medium-sized enterprises (SMEs) have now become an important part of economy for not only developed nations but also for emerging economies. Irrespective of the benefits that can be derived, SMEs in emerging economies still lack the will to implement quality management (QM) practices. Using a comparative study, the purpose of this paper is to understand the status of QM practices in SMEs of emerging economies.

Design/methodology/approach
A survey-based approach was adopted to understand the established QM practices in the SMEs. A survey instrument was designed by reviewing the literature on QM initiatives in SMEs. A sample of 270 SMEs across Southern India and 189 SMEs in Namibia was selected through stratified random sampling technique.

Findings
The overall response rate was 19.52 percent for India and 26.46 percent for Namibia, respectively. There were similarities and differences in responses from SMEs in both countries. Similarities are in terms of limited implementation of QM practices, and also less use of tools and techniques. Reasons for not implementing include unknown to the authors, and the high cost of training. Differences emerged in the type of market (Indian SMEs catering to one major customer), CSFs and business performance indicators. It was interesting to find that management commitment and involvement do not have a major influence as CSF for SMEs in both the countries.

Originality/value
The research is the first attempt in bringing a comparative study about QM practices in SMEs from developing countries. The insights will help emerging economies to develop policies for education and training, and thus facilitate implementation of QM practices in SMEs.
Effect of stearic acid coating on anti-oxidation property of Sn-Ag-Cu solder powder
Authors: Peng Fen , Liu Wensheng , Huang Yufeng , Tang Siwei , Liang Chaoping , Ma Yunzhu 
Published: January 2019

Purpose
The purpose of this study is to develop a monolayer surface coating of stearic acid on Sn-Ag-Cu solder powder to limit oxidation.

Design/methodology/approach
Stearic acid was adsorbed onto Sn-Ag-Cu solder powder through liquid-phase adsorption. The isotherm of adsorption was measured and then the microstructure of coated powder was characterized by scanning electron microscopy, transmission electron microscopy, X-ray photoelectron spectroscopy and Fourier-transform infrared spectroscopy.

Findings
The adsorption isotherm of stearic acid on the powder was “H” type, which revealed the layer-by-layer adsorption on non-porous surface. When the concentration of solution was in the range of 0.001-0.006 mol/L, with an adsorption amount of 0.12 ± 0.1 mg/g, monolayer stearic acid covered the solder powder completely. Uniform and integrated self-assembled monolayer coating was formed through hydrogen bonds between the oxygen ions in surface lattice of Sn3.0Ag0.5Cu solder powder and the —O—H hydroxyl group of stearic acid. The maximum angle of stability of coated powder also reduced by 2.87° compared with that of non-coated powder. The increase rate of oxygen content of coated powder was much slower than that of non-coated powder when they were exposed to humid air.

Originality/value
As a result, oxidation of fine solder powder was effectively limited. Essentially, this method can also be applied to the coating of other types of solder powder and has reference significance to other coating by liquid-phase method.
Measurement and regulation of saturated vapour height level in VPS chamber
Authors: Livovsky Lubomir , Pietrikova Alena 
Published: January 2019

Purpose
The purpose of this paper is to investigate measurement and regulation of saturated vapour height level in vapour phase soldering (VPS) chamber based on parallel plate capacitor and retaining a stable saturated vapour level above the boiling fluid, regardless of the quantity and size of assembled components.

Design/methodology/approach
Development and realisation of capacitance sensor that sensitively senses the maximum height level of saturated vapour above the boiling fluid in the VPS chamber was achieved. Methodology of measurement is based on capacitor change from single air to a parallel plate, filled with two dielectric environments in a stacked configuration: condensed fluid and vapour (air).

Findings
An easy air plate capacitor immersed in the saturated vapour above the boiling fluid can serve as a parallel plate capacitor owing to the conversion of the air to the parallel plate capacitor. A thin film of fluid between the two capacitor plates corresponds to the height of the saturated vapour, which changes the capacity of the parallel plate capacitor.

Originality/value
Introducing the capacitive sensor directly into the VPS work space allows to achieve a constant height level of saturated vapour. Based on the capacity change, it is possible to control the heating power. There is a lack of information regarding measurement of stable height of vapour in the industry, and the present article shows how to easily improve the way to regulate the bandwidth of saturated vapour in the VPS process.
Getting chased up the mountain: High elevation may limit performance and fitness characters in a montane insect
Authors: Dahlhoff Elizabeth P. , Dahlhoff Victoria C. , Grainger Corrine A. , Zavala Nicolas A. , Otepola‐Bello Dami , Sargent Brynn A. , Roberts Kevin T. , Heidl Sarah J. , Smiley John T. , Rank Nathan E. 
Published: January 2019

Abstract

Climate change is expected to shift species distributions as populations grow in favourable habitats and decline in harsh ones. Montane animals escape warming conditions at low elevation by moving upslope, but may be physiologically constrained by conditions there. Effects of elevation were studied for montane populations of the leaf beetle Chrysomela aeneicollis, where allele frequencies at nuclear genes and the mitochondrion vary along latitudinal and altitudinal gradients.

A population presence survey conducted along a steep altitudinal transect (1,600–3,800 m) from 1981 to 2018 revealed that populations expand to low elevation following wet winters and retreat during drought. Quantitative surveys of a 45‐site population network conducted from 2012 to 2018 along multiple altitudinal transects show that when beetles are abundant, population size peaks at 3,135 m, highest altitude populations are at the southern edge of the range, and populations decline and extirpate during drought, especially at low elevation.

To examine effects of elevation on measures of performance and fitness, beetles from a genetically introgressed population (Bishop Creek) were examined. In nature, fecundity of females transplanted along natural altitudinal transects was measured, as was thorax cytochrome c oxidase (CytOx) activity. To examine effects of environmental hypoxia independent of other factors limiting persistence at high elevation, development rate and activity of malate dehydrogenase (MDH) were measured for larvae reared under otherwise common garden conditions at low (1,250 m) and high (3,800 m) elevation.

In nature, fecundity declined with increasing elevation, independent of air temperature. CytOx activity was higher at high than low elevation, especially for individuals possessing genotypes of southern origin. Laboratory‐reared larvae with southern mitochondrial haplotypes developed equally well at both elevations, but larvae with northern haplotypes developed more slowly at high elevation. MDH activity showed a similar pattern, suggesting that slower development rates at high elevation may be due to reduction in metabolic rate.

These findings suggest that physiological effects of environmental hypoxia may contribute to other factors known to restrict insects’ ability to persist at high elevation, ultimately disrupting associated ecological communities. However, some populations may possess genetic variation that allows for local adaption to high elevation.

A plain language summary is available for this article.