bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic surveillance for hypervirulence and multi-drug resistance in invasive Klebsiella pneumoniae from south and southeast Asia
Authors: Wyres Kelly L , Nguyen To N T , Lam Margaret M C , Judd Louise M , van Vinh Chau Nguyen , Dance David A B , Ip Margaret , Karkey Abhilasha , Ling Clare L , Miliya Thyl , Newton Paul N , Nguyen Lan , Sengduangphachanh Amphone , Turner Paul , Veeraraghavan Balaji , Vinh Phat Voong , Vongsouvath Manivanh , Thomson Nicholas R , Baker Stephen , Holt Kathryn E 
Published: February 2019

BackgroundK. pneumoniae is a leading cause of blood stream infection (BSI). Strains producing extended spectrum beta-lactamases (ESBLs) or carbapenemases are considered global priority pathogens for which new treatment and prevention strategies are urgently required, due to severely limited therapeutic options. South and Southeast Asia are major hubs for antimicrobial resistant (AMR) K. pneumoniae, and also for the characteristically antimicrobial sensitive, community-acquired ‘hypervirulent’ strains. The emergence of hypervirulent AMR strains and lack of data on exopolysaccharide diversity pose a challenge for K. pneumoniae BSI control strategies worldwide.MethodsWe conducted a retrospective genomic epidemiology study of 365 BSI K. pneumoniae from seven major healthcare facilities across South and Southeast Asia, extracting clinically relevant information (AMR, virulence, K and O antigen loci) using Kleborate.FindingsK. pneumoniae BSI isolates were highly diverse, comprising 120 multi-locus sequence types (STs) and 63 K-loci. ESBL and carbapenemase gene frequencies were 47% and 17%, respectively. The aerobactin synthesis locus (iuc), associated with hypervirulence, was detected in 28% of isolates. Importantly, 7% of isolates harboured iuc plus ESBL and/or carbapenemase genes. The latter represent genotypic AMR-virulence convergence, which is generally considered a rare phenomenon but was particularly common amongst South Asian BSI (17%). Of greatest concern, we identified seven novel plasmids carrying both iuc and AMR genes, raising the prospect of co-transfer of these phenotypes amongst K. pneumoniae.InterpretationSouth and Southeast Asia are high-risk regions for the emergence of AMR and convergent AMR-hypervirulent K. pneumoniae. Enhanced surveillance efforts, reporting STs, AMR and virulence information are urgently required to monitor this public health threat.FundingThis work was supported by the Wellcome Trust (grant #206194 to Wellcome Sanger Institute) and the Bill and Melinda Gates Foundation, Seattle (grant OPP1175797 to KEH). KEH is supported by a Senior Medical Research Fellowship from the Viertel Foundation of Australia. DAB and PNN are supported by the Wellcome Trust.
SCINA: Semi-Supervised Analysis of Single Cells in silico
Authors: Zhang Ze , Danni Luo M.S. , Zhong Xue , Choi Jin Huk , Ma Yuanqing , Mahrt Elena , Guo Wei , Stawiski Eric W , Wang Stacy , Modrusan Zora , Seshagiri Somasekar , Kapur Payal , Wang Xinlei , Hon Gary C. , Brugarolas James , Wang Tao 
Published: February 2019

ABSTRACTAdvances in single-cell RNA sequencing (scRNA-Seq) have allowed for comprehensive analyses of single cell data. However, current analyses of scRNA-Seq data usually start from unsupervised clustering or visualization. These methods ignore the prior knowledge of transcriptomes and of the probable structures of the data. Moreover, cell identification heavily relies on subjective and inaccurate human inspection afterwards. We reversed this paradigm and developed SCINA, a semi-supervised model, for analyses of scRNA-Seq and flow cytometry/CyTOF data, and other data of similar format, by automatically exploiting previously established gene signatures using an expectation-maximization (EM) algorithm. We applied SCINA on a wide range of datasets, and showed its accuracy, stableness and efficiency exceeded most popular unsupervised approaches. Notably, SCINA discovered an intermediate stage of oligodendrocyte from mouse brain scRNA-Seq data. SCINA also detected immune cell population shifting in Stk4 knock-out mouse cytometry data. Finally, SCINA identified a new kidney tumor clade with similarity to FH-deficient tumors from bulk tumor data. Overall, SCINA provides both methodological advances and biological insights from perspectives different from traditional analytical methods.
A rare SMAD9 mutation identifies the BMP signalling pathway as a potential osteoanabolic target
Authors: Gregson Celia L , Bergen Dylan , Leo Paul , Sessions Richard B. , Wheeler Lawrie , Hartley April , Youlten Scott , Croucher Peter I , McInerney-Leo Aideen M. , Fraser William , Tang Jonathan C.Y. , Anderson Lisa , Marshall Mhairi , Sergot Leon , Paternoster Lavinia , Davey-Smith George ,   The AOGC Consortium, Brown Matthew A , Hammond Chrissy , Kemp John P , Tobias Jon H , Duncan Emma L 
Published: February 2019

AbstractTo identify targets for novel anabolic medicines for osteoporosis, we recruited a large cohort with unexplained high bone mass (HBM). Exome sequencing identified a rare (minor allele frequency 0.0014) missense mutation in SMAD9 (c.65T>C, p.Leu22Pro) segregating with HBM in an autosomal dominant family. The same mutation was identified in another two unrelated individuals with HBM. In-silico protein modelling predicts the mutation severely disrupts the MH1 DNA-binding domain of SMAD9. Affected individuals have bone mineral density [BMD] Z-Scores +3 to +5, with increased volumetric cortical and trabecular BMD, increased cortical thickness, and low/normal bone turnover. Fractures and nerve compressions are not seen. Both genome-wide, and gene-based association testing of heel estimated-BMD in >362,924 UK-Biobank British subjects showed strong associations with SMAD9 (PGWAS=6×10−16; PGENE =8×10−17). Smad9 is highly expressed in murine osteocytes and zebrafish bone tissue. Our findings support SMAD9 as a novel HBM gene, and a potential novel osteoanabolic target.
Microporous scaffolds drive assembly and maturation of progenitors into β-cell clusters
Authors: Youngblood Richard L. , Sampson Joshua P. , Lebioda Kimberly R. , Spicer Graham , Shea Lonnie D. 
Published: February 2019

AbstractHuman pluripotent stem cells (hPSCs) represent a promising cell source for the development of β-cells for use in therapies for type 1 diabetes. Current culture approaches provide the signals to drive differentiation towards β-cells, with the cells spontaneously assembling into clusters. Herein, we adapted the current culture systems to cells seeded on microporous biomaterials, with the hypothesis that the pores can guide the assembly into β-cell clusters of defined size that can enhance maturation. The microporous scaffold culture allows hPSC-derived pancreatic progenitors to form clusters at a consistent size as cells undergo differentiation to immature β-cells. By modulating the scaffold pore sizes, we observed 250-425 µm pore size scaffolds significantly enhance insulin expression and key β-cell maturation markers compared to suspension cultures. Furthermore, when compared to suspension cultures, the scaffold culture showed increased insulin secretion in response to glucose stimulus indicating the development of functional β-cells. In addition, scaffolds facilitated cell-cell interactions enabled by the scaffold design and cell-mediated matrix deposition of extracellular matrix (ECM) proteins associated with the basement membrane of islet cells. We further investigated the influence of ECM on cell development by incorporating an ECM matrix on the scaffold prior to cell seeding; however, their presence did not further enhance maturation. These results suggest the microporous scaffold culture facilitates 3D cluster formation, supports cell-cell interactions, and provides a matrix similar to a basement membrane to drive in vitro hPSC-derived β-cell maturation and demonstrates the feasibility of these scaffolds as a biomanufacturing platform.
OxyR senses reactive sulfane sulfur and activates genes for its removal in
Escherichia coli
Authors: Hou Ningke , Yan Zhenzhen , Fan Kaili , Li Huanjie , Zhao Rui , Xia Yongzhen , Liu Huaiwei , Xun Luying 
Published: February 2019

AbstractReactive sulfane sulfur species such as hydrogen polysulfide and organic persulfide are newly recognized as normal cellular components, involved in signaling and protecting cells from oxidative stress. Their production is extensively studied, but their removal is less characterized. Herein, we showed that reactive sulfane sulfur is toxic at high levels, and it is mainly removed via reduction by thioredoxin and glutaredoxin with the release of H2S in Escherichia coli. OxyR is best known to respond to H2O2, and it also played an important role in responding to reactive sulfane sulfur under both aerobic and anaerobic conditions. It was modified by hydrogen polysulfide to OxyR C199-SSH, which activated the expression of thioredoxin 2 and glutaredoxin 1. This is a new type of OxyR modification. Bioinformatics analysis showed that OxyRs are widely present in bacteria, including strict anaerobic bacteria. Thus, the OxyR sensing of reactive sulfane sulfur may represent a conserved mechanism for bacteria to deal with sulfane sulfur stress.
Identification of Microbiota-Induced Gene Expression Changes in theDrosophila melanogasterHead
Authors: Keith Scott A. , Eutsey Rory , Lee Heewook , Solomon Brad , Oliver Stacie , Kingsford Carl , Hiller N. Luisa , McCartney Brooke M. 
Published: February 2019

ABSTRACTSymbiotic microorganisms exert multifaceted impacts on the physiology of their animal hosts. Recent discoveries have shown the gut microbiota influence host brain function and behavior, but the host and microbial molecular factors required to actuate these effects are largely unknown. To uncover molecular mechanisms that underlie the gut-microbiota-brain axis, we usedDrosophila melanogasterand its bacterial microbiota as a model to identify microbiota-dependent gene expression changes in the host brain and head. Specifically, we employed RNA-seq and nanoString nCounter technology to identifyDrosophilagenes that exhibit altered transcript levels in fly heads upon elimination of the microbiota. The identified genes, some of which exhibited sex-specific differences, have demonstrated or inferred functional roles in the immune response, metabolism, neuronal activity, and stress resistance. Overall, this study reveals microbiota-responsive genes in the fly head, an anatomical structure not previously investigated in this context. Our results serve as a foundation for future investigations of how microbe-driven gene expression changes impactDrosophilabiology.
An oomycete RXLR effector triggers antagonistic plant hormone crosstalk to suppress host immunity
Authors: Anderson Ryan , Deb Devdutta , Withers John , He Sheng Yang , McDowell John 
Published: February 2019

ABSTRACTUnderstanding the mechanisms through which pathogens alter plant cell networks is essential for understanding plant-pathogen interactions and will inform efforts to reduce crop diseases. Oomycetes secrete diverse effector proteins into plant cells. The mechanisms through which these effectors promote virulence are largely unknown. We show that the HaRxL10 effector protein from the Arabidopsis thaliana pathogen Hyaloperonospora arabidopsidis (Hpa) targets a transcriptional repressor (JAZ3) involved in jasmonic acid (JA) signalling. This manipulation activates a regulatory cascade that inhibits salicylic acid (SA) signalling, which normally restricts Hpa infection. This virulence mechanism is functionally equivalent to but mechanistically distinct from activation of the antagonistic JA-SA hormone crosstalk by the bacterial JA-mimicking toxin coronatine and by bacterial Type III effectors. These results reveal a key role for JAZ3 in plant immunity and emphasize that JA-SA crosstalk is an Achilles’ heel in the plant immune system, vulnerable to manipulation by diverse microbes.
Autism spectrum disorders in high secure psychiatric care: a review of literature, future research and clinical directions
Authors: Murphy David , Allely Clare 
Published: February 2019

Purpose
The purpose of this paper is to review available literature targeting the assessment and management of individuals with an autism spectrum disorder (ASD) admitted to high secure psychiatric care (HSPC). Key areas of examination include the prevalence of ASD in HSPC, how individuals with an ASD differ from other patient groups in clinical and cognitive characteristics, the views of staff regarding patients with an ASD, an exploration of the experiences and quality of life of patients with an ASD, as well as treatment and interventions.

Design/methodology/approach
A review of the published literature.

Findings
Although individuals with an ASD comprise a relatively small proportion of the total HSPC cohort, they appear to be over represented relative to the general population prevalence. Several research projects suggest that individuals with an ASD present with difficulties and needs different to other patient groups, as well as being viewed by staff as potentially vulnerable and requiring a different care approach. Individuals with an ASD report both positive and negative aspects to life in HSPC.

Practical implications
Suggestions are made with regard to how individuals with an ASD might be better managed in HSPC. Following the spirit of various pieces of government legislation such as the Autism Act (2009) and the Equalities Act (2010) the role of a specialist ASD HSPC service is proposed.

Originality/value
This paper provides a detailed review of the research to date exploring the assessment and management of individuals with an ASD detained in HSPC. It outlines key research findings, highlights limitations with it and provides a personal perspective on future research and clinical targets.
Skill mapping for blue-collar employees and organisational performance
Authors: Mittal Amit , Dhiman Rahul , Lamba Parmod 
Published: February 2019

Purpose
The purpose of this paper is to explore the skill mapping process in a manufacturing organization and to examine its relationship with the select performance indicators, such as quality and defects. This paper also explores the role of the supervisor in the whole process of skill mapping of the blue-collar employees.

Design/methodology/approach
The study uses a case-based approach and the company selected is Mahindra and Mahindra Ltd, Swaraj Division, located in Phase 4, Industrial Area, Mohali (Punjab). The qualitative aspect of the paper is based on ten semi-structured interviews of the senior-level managers. These interviews are conducted in order to understand the role of the supervisor in skill mapping process and its relationship with the organizational performance. The quantitative aspect is based on the regression analysis to find out the impact of skill index on select performance indicators.

Findings
The results of the study indicate that the role of the supervisor in performance appraisal is very important in the whole process of skill mapping. Swaraj is an example where a robust skill mapping process for blue-collar employees have supported the business in improving the skill of employees and consequently supporting the business to perform well on key deliverables, such as better quality and less defects. The select variables are inter-correlated and variations in the select organizational performance indicators (production and defects) are due to variations in the skill index of the blue-collar employees in the manufacturing organization. The performance indicators of the manufacturing organization in terms of manufacturing defects have declined and also the production has increased, which is a good indicator for the organization.

Practical implications
The present study is of interest to researchers who are trying to understand the system for skill mapping and utilization of appraisal inputs in improving organizational performance.

Originality/value
To the authors’ best knowledge, this paper is one of the first to address the skill mapping process in a manufacturing organization especially for the blue-collar employees.
Induction motors broken rotor bars detection using RPVM and neural network
Authors: Bensaoucha Saddam , Bessedik Sid Ahmed , Ameur Aissa , Teta Ali 
Published: February 2019

Purpose
The purpose of this study aims to focus on the detection and identification of the broken rotor bars (BRBs) of a squirrel cage induction motor (SCIM). The presented diagnosis technique is based on artificial neural networks (NNs) that use as inputs the results of the spectral analysis using the fast Fourier transform (FFT) of the reduced Park’s vector modulus (RPVM), along with the load values in which the motor operates.

Design/methodology/approach
First, this paper presents a comparative study between FFT applied on Hilbert modulus, Park’s vector modulus and RPVM to extract feature frequencies of BRB faults. Moreover, the extracted features of FFT applied to RPVM and the load values were selected as NNs’ inputs for the detection of the number of BRBs.

Findings
The obtained simulation results using MATLAB (Matrix Laboratory) environment show the effectiveness and accuracy of the proposed NNs based approach.

Originality/value
The current paper presents a novel diagnostic method for BRBs’ fault detection in SCIM, based on the combination between the signal processing analysis (FFT of RPVM) and artificial intelligence (NNs).
“Superdiversity”: a new paradigm for inclusion in a transnational world
Authors: Ozkazanc-Pan Banu 
Published: February 2019

PurposeTransnational migration has become a defining feature of many societies across the globe. This paper focuses on contributions to diversity theorizing and research available from “superdiversity”, an analytic framework derived from transnational migration studies. “Superdiversity” speaks to the novel social transformations taking place globally and provides new opportunities, albeit with critique, for conceptualizing and studying people, difference and inclusion. The purpose of this paper is to provide innovative ways to rethink hallmark concepts of diversity scholarship by offering new insights about the role of nation-states, the concept of difference and inclusion in the midst of mobility.Design/methodology/approachThe paper relies upon transnational migration studies as an emergent field of inquiry about societal level changes brought upon by the ongoing movement of people. The social, cultural and political transformations growing out of transnational migration are used to theorize new directions for diversity research in the context of management and organization studies. By relying on “superdiversity” and its mobility-based ontology, epistemology and methodology, the paper proposes new ways to think about and carry out research on difference and inclusion.FindingsDeploying the analytic framework of “superdiversity,” the paper offers “belonging” as the new conversation on inclusion and proposes mobile methods as a means to study mobile subjects/objects. In addition, it discusses how the ongoing transformative societal changes by way of transnational migration impact the ways in which the author theorizes and carry out diversity research. Questions and concerns around ethics, (in)equality and representation are considered vital to future research in/around diversity.Originality/valueExtensive changes in societies emerging out of ongoing encounters between/among different kinds of people have taken shape by way of transnational migration. As a result, emergent and novel notions of difference have been forged in a transnational manner across social fields. By examining these transformations, the paper provides new directions and challenges for diversity scholarship in the context of rising societal tensions and rhetoric around difference and “belonging” in nation-states. It also provides alternative considerations for understanding and theorizing inclusion in diversity research.
The changer and the changed
Authors: Laursen Sandra L. , De Welde Kristine 
Published: February 2019

PurposeThe purpose of this paper is to examine the evolving theories of change of the US National Science Foundation’s (NSF) ADVANCE program to increase the representation of women on academic faculties in science, technology, engineering and mathematics (STEM). ADVANCE supports efforts to transform the cultures and structures of US institutions of higher education by removing gendered barriers to STEM faculty women’s employment, advancement and success, and by developing change strategies that others may adopt.Design/methodology/approachThe empirical study is based on qualitative, longitudinal analysis of nine requests for proposals (RfPs) for the ADVANCE program (2001–2016), complemented by historical analysis of funded ADVANCE projects using public records.FindingsThe analysis identifies changes over time that suggest shifts in NSF’s rationale and theory of change for ADVANCE. Increased guidance directs how institutions should best undertake change, document outcomes and share best practices. The RfPs reveal growing attention to equity, rather than simply to representation, and to intersectionality – how gender, race, social class and other identities intersect to produce disparate experiences and outcomes for individuals differently positioned in social systems. Gendered organizations theory helps to place these experiences and outcomes in a structural context. Iterative processes of organizational learning are postulated to account for these changes over time.Originality/valueWhile many studies have examined ADVANCE projects’ activities and outcomes, none have examined the premises and design of the ADVANCE program itself. This analysis offers insight into how the ADVANCE RfP has driven innovation and learning about transformative institutional change to advance gender equity in STEM.
Ostracizing targets of workplace sexual harassment before and after the #MeToo movement
Authors: Brown Stephanie E.V. , Battle Jericka S. 
Published: February 2019

Purpose
The purpose of this paper is to explore the connections between sexual harassment and ostracism both before and after the modern day #MeToo movement. It outlines how the birth of the #MeToo movement lessened the impact of ostracism, empowering victims to report their abusers.

Design/methodology/approach
This paper provides an overview of the ostracism literature, and discusses why ostracism has historically prevented individuals from disclosing workplace abuse. It also examines recent and historical cases of sexual harassment where ostracism has both inhibited targets of sexual harassment from reporting and harmed those who stood up for their right not to be harassed.

Findings
Both purposeful and non-purposeful ostracism have negative impacts on employees and organizations as a whole, and the fear of ostracism prevented many from disclosing harassment and abuse in the workplace. The #MeToo movement, by nature, is antithetical to ostracism by building community and freeing people to seek justice. This paper makes practical recommendations for organizations that wish to help prevent ostracism as a response to workplace sexual harassment disclosure.

Research limitations/implications
Both purposeful and non-purposeful ostracism have negative impacts on employees and organizations as a whole, and the fear of ostracism prevent many from disclosing harassment and abuse in the workplace. The #MeToo movement by nature is antithetical to ostracism, building community and freeing people to seek justice. This paper makes practical recommendations for organizations that wish to prevent ostracism as a response to workplace sexual harassment disclosure. Additionally, it provides future research directions to explore the empirical link between the disclosure of sexual harassment and ostracism.

Originality/value
This paper analyzes a crucial barrier to reporting sexual harassment. It both examines the consequences of ostracism and highlights how the threat of ostracism can be overcome through intentional organizational efforts.