bluuebunny/crossref_metadata_2025_split huggingface dataset:
Core Genome Multi Locus Sequence Typing and Single Nucleotide Polymorphism Analysis in the Epidemiology of Brucella melitensis Infections
Authors: Janowicz Anna , Massis Fabrizio De , Ancora Massimo , Cammà Cesare , Patavino Claudio , Battisti Antonio , Prior Karola , Harmsen Dag , Scholz Holger , Zilli Katiuscia , Sacchini Lorena , Giannatale Elisabetta Di , Garofolo Giuliano 
Published: April 2018

AbstractThe use of whole genome sequencing (WGS) using next generation sequencing (NGS) technology has become a widely accepted method for microbiology laboratories in the application of molecular typing for outbreak tracing and genomic epidemiology. Several studies demonstrated the usefulness of WGS data analysis through Single Nucleotide Polymorphism (SNP) calling from a reference sequence analysis for Brucella melitensis, whereas gene-by-gene comparison through core-genome Multilocus Sequence Typing (cgMLST) has not been explored so far. The current study developed an allele-based method cgMLST and compared its performance to the genome-wide SNP approach and the traditional MLVA on a defined sample collection. The dataset comprised of 37 epidemiologically linked animal cases of brucellosis as well as 71 epidemiologically unrelated human and animal isolates collected in Italy. The cgMLST scheme generated in this study contained 2,687 targets of the B. melitensis 16M reference genome (75.4% of the complete genome). We established the potential criteria necessary for inclusion of an isolate into a brucellosis outbreak cluster to be ≤4 loci in the cgMLST and ≤10 in WGS SNP analysis. CgMLST and SNP analysis provided much higher phylogenetic distance resolution than MLVA, particularly for strains belonging to the same lineage thus allowing diverse and unrelated genotypes to be identified with greater confidence. The application of this cgMLST scheme to the characterization of B. melitensis strains provided insights into the epidemiology of this pathogen and it is a candidate to be a benchmark tool for outbreak investigations in human and animal brucellosis.
Effect of stimulus polarity on detection thresholds in cochlear implant users: relationships with average threshold, gap detection, and rate discrimination
Authors: Carlyon Robert P. , Cosentino Stefano , Deeks John M. , Parkinson Wendy , Arenberg Julie A. 
Published: April 2018

AbstractPrevious psychophysical and modelling studies suggest that cathodic stimulation by a cochlear implant (CI) may preferentially activate the peripheral processes of the auditory nerve, whereas anodic stimulation may preferentially activate the central axons. Because neural degeneration typically starts with loss of the peripheral processes, lower thresholds for cathodic than for anodic stimulation may indicate good local neural survival. We measured thresholds for 99-pulse-per-second trains of triphasic (TP) pulses where the central high-amplitude phase was either anodic (TP-A) or cathodic (TP-C). Thresholds were obtained in monopolar mode from four or five electrodes and a total of eight ears from subjects implanted with the Advanced Bionics CI. When between–subject differences were removed, there was a modest but significant correlation between the polarity effect (TP-C threshold minus TP-A threshold) and the average of TP-C and TP-A thresholds, consistent with the hypothesis that a large polarity effect corresponds to good neural survival. When data were averaged across electrodes for each subject, relatively low thresholds for TP-C correlated with a high “upper limit” (the pulse rate up to which pitch continues to increase) from a previous study [Cosentino S, Carlyon RP, Deeks JM, Parkinson W, Bierer JA (2016) Rate discrimination, gap detection and ranking of temporal pitch in cochlear implant users. J Assoc Otolaryngol 17:371– 382]. Overall the results provide modest indirect support for the hypothesis that the polarity effect provides an estimate of local neural survival.
Nucleolar stress causes the entry into replicative senescence in budding yeast
Authors: Morlot Sandrine , Jia Song , Léger-Silvestre Isabelle , Matifas Audrey , Gadal Olivier , Charvin Gilles 
Published: April 2018

SummaryThe accumulation of Extrachromosomal rDNA Circles (ERCs) and their asymmetric segregation upon division have been hypothesized to be responsible for replicative senescence in mother yeasts and rejuvenation in daughter cells. However, it remains unclear by which molecular mechanisms ERCs would trigger the irreversible cell cycle slow-down leading to cell death. We show that ERCs accumulation is concomitant with a nucleolar stress, characterized by a massive accumulation of pre-rRNAs in the nucleolus, leading to a loss of nucleus-to-cytoplasm ratio, decreased growth rate and cell-cycle slow-down. This nucleolar stress, observed in old mothers, is not inherited by rejuvenated daughters. Unlike WT, in the long-lived mutant fob1∆, a majority of cells is devoid of nucleolar stress and does not experience replicative senescence before death. Our study provides a unique framework to order the successive steps that govern the transition to replicative senescence and highlights the causal role of nucleolar stress in cellular aging.
Leveraging DNA methylation quantitative trait loci to characterize the relationship between methylomic variation, gene expression and complex traits
Authors: Hannon Eilis , Gorrie-Stone Tyler J , Smart Melissa C , Burrage Joe , Hughes Amanda , Bao Yanchun , Kumari Meena , Schalkwyk Leonard C , Mill Jonathan 
Published: April 2018

ABSTRACTCharacterizing the complex relationship between genetic, epigenetic and transcriptomic variation has the potential to increase understanding about the mechanisms underpinning health and disease phenotypes. In this study, we describe the most comprehensive analysis of common genetic variation on DNA methylation (DNAm) to date, using the Illumina EPIC array to profile samples from the UK Household Longitudinal study. We identified 12,689,548 significant DNA methylation quantitative trait loci (mQTL) associations (P < 6.52x10-14) occurring between 2,907,234 genetic variants and 93,268 DNAm sites, including a large number not identified using previous DNAm-profiling methods. We demonstrate the utility of these data for interpreting the functional consequences of common genetic variation associated with > 60 human traits, using Summary data–based Mendelian Randomization (SMR) to identify 1,662 pleiotropic associations between 36 complex traits and 1,246 DNAm sites. We also use SMR to characterize the relationship between DNAm and gene expression, identifying 6,798 pleiotropic associations between 5,420 DNAm sites and the transcription of 1,702 genes. Our mQTL database and SMR results are available via a searchable online database (http://www.epigenomicslab.com/online-data-resources/) as a resource to the research community.
Hierarchical Cognition causes Task Related Deactivations but not just in Default Mode Regions
Authors: Farooqui Ausaf A , Manly Tom 
Published: April 2018

AbstractThe well-known deactivation of the Default Mode Network (DMN) during external tasks is usually thought to reflect the suppression of internally directed mental activity during external attention. In 3 experiments with human participants we organized sequences of task events identical in their attentional and control demands into larger task episodes. We found that DMN deactivation across such sequential events was never constant, but was maximum at the beginning of the episode, then decreased gradually across the episode, reaching baseline towards episode completion, with the final event of the episode eliciting an activation. Crucially, this pattern of activity was not limited to a fixed set of DMN regions but, across experiments, was shown by a variable set of regions expected to be uninvolved in processing the ongoing task. This change in deactivation across sequential but identical events showed that the deactivation cannot be related to attentional/control demands which were constant across the episode, instead it has to be related to some episode related load that was maximal at the beginning and then decreased gradually as parts of the episode got executed. We argue that this load resulted from cognitive programs through which the entire episode was hierarchically executed as one unit. At the beginning of task episodes, programs related to their entire duration is assembled, causing maximal deactivation. As execution proceeds, elements within the program related to the completed parts of the episode dismantle, thereby decreasing the program load and causing a decrease in deactivation.Significance StatementWe prepare breakfasts and write emails, and not individually execute their many component acts. The current study suggests that cognitive entities that enable such hierarchical execution of goal-directed behavior may cause the ubiquitously seen deactivation during external task execution. Further, while this deactivation has previously been associated with a defined set of the so called default mode regions, current study demonstrates that deactivation is shown by any region not currently involved in task execution, and in certain task episodes can even include attention related fronto-parietal regions as well as primary sensory and motor regions.
FAVITES: simultaneous simulation of transmission networks, phylogenetic trees, and sequences
Authors: Moshiri Niema , Ragonnet-Cronin Manon , Wertheim Joel O. , Mirarab Siavash 
Published: April 2018

AbstractMotivationThe ability to simulate epidemics as a function of model parameters allows insights that are unobtainable from real datasets. Further, reconstructing transmission networks for fast-evolving viruses like HIV may have the potential to greatly enhance epidemic intervention, but transmission network reconstruction methods have been inadequately studied, largely because it is difficult to obtain “truth” sets on which to test them and properly measure their performance.ResultsWe introduce FAVITES, a robust framework for simulating realistic datasets for epidemics that are caused by fast-evolving pathogens like HIV. FAVITES creates a generative model to produce contact networks, transmission networks, phylogenetic trees, and sequence datasets, and to add error to the data. FAVITES is designed to be extensible by dividing the generative model into modules, each of which is expressed as a fixed API that can be implemented using various models. We use FAVITES to simulate HIV datasets and study the realism of the simulated datasets. We then use the simulated data to study the impact of the increased treatment efforts on epidemiological outcomes. We also study two transmission network reconstruction methods and their effectiveness in detecting fast-growing clusters.Availability and implementationFAVITES is available at https://github.com/niemasd/FAVITES, and a Docker image can be found on DockerHub (https://hub.docker.com/r/niemasd/favites).
Linking protean career orientation to well-being: the role of psychological capital
Authors: Li Yongzhan 
Published: April 2018

PurposeThe purpose of this paper is to examine the effects of protean career orientation (PCO) and psychological capital (PsyCap) on well-being among knowledge workers.Design/methodology/approachThe author adopted a two-wave cross-lagged design. In total, 518 knowledge workers at three enterprises in China were sampled to complete the Direnzoet al.’s (2015) Protean Career Orientation Questionnaire, Luthanset al.’s (2007) Psychological Capacity Questionnaire, and Ryff and Keyes’ (1995) Psychological Well-Being Scale. The main statistical methods involved descriptive statistics, structural equation modeling, and bootstrapping analysis.FindingsThe findings of the study were as follows: PCO positively predicted PsyCap among knowledge workers; both PCO and PsyCap positively contributed to knowledge workers’ well-being; and knowledge workers’ PsyCap partially mediated the relationship between their PCO and well-being.Originality/valueRare empirical studies were conducted on the relationship between PCO and psychological well-being. The previous findings are inconsistent on whether PCO is an antecedent of PsyCap, or PsyCap is an antecedent of PCO. The author conducted a cross-lagged survey to examine the above relationships; to certain extent, the present study addresses the research gap and contributes to the burgeoning literature.
Governance structures, cash holdings and firm value on the Ghana Stock Exchange
Authors: Asante-Darko Disraeli , Adu Bonsu Bright , Famiyeh Samuel , Kwarteng Amoako , Goka Yayra 
Published: April 2018

Purpose
There is an existing relationship among shareholders, boards of directors and management of companies. Corporate governance practices of companies are expected to ensure that this relationship maximises the wealth of shareholders. Differences exist among corporate governance of companies listed on the Ghana Stock Exchange. Companies, for purposes of liquidity, hold cash, but cash holdings also add to the cost of financing, according to working capital theories. The study, thus, sought to examine the relationship between corporate governance practices, ownership structure, cash holdings and firm value.

Design/methodology/approach
The study deployed the seemingly unrelated regression to reduce the problem of multicollinearity resulting from the strong relationship between cash reserves and some control variables.

Findings
The study found no significant relationship between board size and firm value. Similar findings were also made on the relationship between proportion of non-executive directors on the board and firm value. However, firms audited by the big four audit firms are valued higher by the capital market. Cash holdings of firms negatively affect performance, and this is statistically significant. A positive relationship arises between a firm’s cash holdings and its value as a result of debt financing, even though this is not significant.

Originality/value
The study is the first of its kind that deploys Tobin’s Q as a measure of firms’ value to reflect investors’ valuation of firms in Ghana. The study is also the first of its kind to test the interactive effect of debt financing and cash holdings on firm value in Ghana.
Master degree under crisis
Authors: Khalifa Bayan , Dukhan Osama , Mouselli Sulaiman 
Published: April 2018

PurposeThe purpose of this paper is to explore why students decide to enrol in a business postgraduate programme at Damascus University in the current Syrian crisis.Design/methodology/approachExploration of students’ motives was generated in this study using semi-structured interviews. On the basis of saturation sampling, 11 interviews took place in the leading Syrian university providing postgraduate programmes, Damascus University.FindingsThe results from the interviews indicate the existence of six different motives for students to enrol in a postgraduate study: self-motives, professional motives, social motives, academic motives, lack of vision, and delaying military service, which is directly caused by the current war conditions in Syria.Practical implicationsUnderstanding postgraduates’ motives is essential at the national level, the institutional level, and also at the individual level to make better future plans related to opening new programmes or altering admission criteria. Recommendations to higher education policy makers are highlighted in the study.Originality/valueThe majority of previous studies concentrate on students’ motives to pursue postgraduate studies during financial crisis. However, very little is known on why students decide to enrol in a business postgraduate programme in a war context.
Strengthening school management committees: a framework for process and outcome
Authors: Adil Nauman , Rashidi Zaki , Frooghi Reema 
Published: April 2018

Purpose
The purpose of this paper is to analyze the existing mechanism of school management committees (SMCs) and to propose an improved framework for strengthening its process and outcomes. In 2005, the Education and Literacy department, Government of Sindh decentralizes the administrative and operational authorities to school level in the form of SMCs. These committees have been vested with several roles and responsibilities in accordance with the objective of SMCs set in by government in assistance with different international donor agencies.

Design/methodology/approach
The purposively selected respondent that includes 35 stakeholders among which 25 stakeholders has been interviewed individually while other ten has been interviewed in the form of two focused groups consisting of five members each. The findings based on the interviews are analyzed using the thematic analysis. This study analyzes the formation of SMCs, roles and responsibilities of members, Allocation SMC funds and its utilization methods. The study includes the challenges faced by these committees in school administration and operations with their recommendations for overcoming such challenges. Some common challenges include limited financial resources, interference of landlords and potential people of the community, limited administrative authorities and lack of interest of government toward government schools.

Findings
The recommendations have been categorized into three broad themes: strengthening of mechanism, strengthening through functions, roles and responsibilities and revising SMC fund allocation and its utilization.

Originality/value
The study proposed an improved framework for strengthening the process and outcomes of SMC.
Examining the relationship between school principals’ instructional leadership behaviors, teacher self-efficacy, and collective teacher efficacy
Authors: Cansoy Ramazan , Parlar Hanifi 
Published: April 2018

PurposeThe purpose of this paper is to examine the relationship between school principals’ instructional leadership behaviors, teacher self-efficacy, and collective teacher efficacy.Design/methodology/approachThe participants were a total of 427 teachers working in elementary, middle, and high schools located in the Cekmekoy district of Istanbul. The data were gathered through the “Effective School Leadership Scale,” the “Teacher Self-Efficacy Scale,” and the “Collective Efficacy Scale.” Arithmetic mean, Pearson product-moment correlation coefficient, and multiple linear regression analysis were used in the data analysis.FindingsThe results revealed positive and significant relationships between school leadership, teacher self-efficacy, and collective teacher efficacy. In addition, effective school leadership behaviors and teacher self-efficacy perceptions were found to be positive and significant predictors of collective teacher efficacy perceptions.Originality/valueSchool principals can implement practices to enhance teachers’ competence, to make them feel more effective and competent as a group. In this sense, teachers who do not feel competent can be guided by those who have more experience in the profession. Additionally, opportunities through which they can experience success can be created for these teachers.
Marketisation, managerialism and high-stake testing
Authors: Mutereko Sybert 
Published: April 2018

Purpose
Using a South African district of education as a case study, the purpose of this paper is to explore how high-stake assessments informed by marketisation and managerialism have been embedded in the South African education system.

Design/methodology/approach
This papers draws on data that were collected through a mixed method approach in the secondary schools of the uMgungundlovu District, which is in Kwazulu-Natal province (KZN) in the eastern part of South Africa. This paper emerged from multiple sources of data, that is, from documents, interviews, questionnaires, and observation as well as secondary sources.

Findings
The paper demonstrates how the pincer movement of markets and managerialism have used high-stake testing as a mechanism of performativity. It illustrates how test scores are published in newspapers to provide consumers with information that is needed for full participation in the marketised education system.

Practical implications
The insights from this paper have profound implications for school managers and policy makers. While high-stake tests are logically consistent and theoretically defensible, overdependence on them portends the replacement of traditional values of schools by the market value of the education.

Originality/value
The study contributes profound insights into how the high-stake testing serves the purpose of social control and subjugation mechanisms for students, schools, and teachers by the state and the invisible arm of the markets. The problem with the use of high-stakes testing as performativity mechanisms is not just that they hinders learning and teaching, but it changes the work of schools and teachers who are at the chalkface of education system.
Training autonomous managers for a dynamic environment
Authors: Santos M. Valle , Mayoral Rosa M. 
Published: April 2018

PurposeThe purpose of this paper is to explore self-regulated learning among university students, the role played by motivation and its impact on academic performance. This paper presents a teaching strategy aimed at self-regulation which draws on the educational value provided by the evaluation system.Design/methodology/approachThis research includes a quantitative analysis to examine the dependency relation between self-regulation, motivational orientation and academic performance. The impact of the teaching strategy on the relation between self-regulation and academic performance is also explored.FindingsThe findings indicate that self-regulation is closely linked to motivational orientation and is a determining factor in academic performance. In addition, implementing a teaching strategy focussing on self-regulation alters said relation.Practical implicationsThis research reflects the value of fostering the level of student self-regulation with a view to enhancing not only their current learning, but also the self-directed learning that will ensure professional success. The research also evidences the potential of the evaluation system for encouraging the development of self-regulation.Originality/valueThe conclusions to emerge from this research will help educators gain an awareness of the usefulness of strengthening student self-regulation and the potential offered by the evaluation system as a teaching resource. This research also merges extremely interesting elements – student self-regulation and the evaluation system – which to date have not been explored jointly.