bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pisces: An Accurate and Versatile Variant Caller for Somatic and Germline Next-Generation Sequencing Data
Authors: Dunn Tamsen , Berry Gwenn , Emig-Agius Dorothea , Jiang Yu , Lei Serena , Iyer Anita , Udar Nitin , Chuang Han-Yu , Hegarty Jeff , Dickover Michael , Klotzle Brandy , Robbins Justin , Bibikova Marina , Peeters Marc , Strömberg Michael 
Published: March 2018

AbstractMotivationNext-Generation Sequencing (NGS) technology is transitioning quickly from research labs to clinical settings. The diagnosis and treatment selection for many acquired and autosomal conditions necessitate a method for accurately detecting somatic and germline variants, suitable for the clinic.ResultsWe have developed Pisces, a rapid, versatile and accurate small variant calling suite designed for somatic and germline amplicon sequencing applications. Pisces accuracy is achieved by four distinct modules, the Pisces Read Stitcher, Pisces Variant Caller, the Pisces Variant Quality Recalibrator, and the Pisces Variant Phaser. Each module incorporates a number of novel algorithmic strategies aimed at reducing noise or increasing the likelihood of detecting a true variant.AvailabilityPisces is distributed under an open source license and can be downloaded from https://github.com/Illumina/Pisces. Pisces is available on the BaseSpace™ SequenceHub as part of the TruSeq Amplicon workflow and the Illumina Ampliseq Workflow. Pisces is distributed on Illumina sequencing platforms such as the MiSeq™, and is included in the Praxis™ Extended RAS Panel test which was recently approved by the FDA for the detection of multiple RAS gene mutations.Contactpisces@illumina.comSupplementary informationSupplementary data are available online.
EPA-ng: Massively Parallel Evolutionary Placement of Genetic Sequences
Authors: Barbera Pierre , Kozlov Alexey M. , Czech Lucas , Morel Benoit , Darriba Diego , Flouri Tomáš , Stamatakis Alexandros 
Published: March 2018

AbstractNext Generation Sequencing (NGS) technologies have led to a ubiquity of molecular sequence data. This data avalanche is particularly challenging in metagenetics, which focuses on taxonomic identification of sequences obtained from diverse microbial environments. To achieve this, phylogenetic placement methods determine how these sequences fit into an evolutionary context. Previous implementations of phylogenetic placement algorithms, such as the Evolutionary Placement Algorithm (EPA) included in RAxML, or pplacer, are being increasingly used for this purpose. However, due to the steady progress in NGS technologies, the current implementations face substantial scalability limitations. Here we present EPA-ng, a complete reimplementation of the EPA that is substantially faster, offers a distributed memory parallelization, and integrates concepts from both, RAxML-EPA, and pplacer. EPA-ng can be executed on standard shared memory, as well as on distributed memory systems (e.g., computing clusters). To demonstrate the scalability of EPA-ng we placed 1 billion metagenetic reads from the Tara Oceans Project onto a reference tree with 3,748 taxa in just under 7 hours, using 2,048 cores. Our performance assessment shows that EPA-ng outperforms RAxML-EPA and pplacer by up to a factor of 30 in sequential execution mode, while attaining comparable parallel efficiency on shared memory systems. We further show that the distributed memory parallelization of EPA-ng scales well up to 3,520 cores. EPA-ng is available under the AGPLv3 license: https://github.com/Pbdas/epa-ng
A structural mechano-chemical model for dynamic instability of microtubule
Authors: Stewman Shannon F. , Ma Ao 
Published: March 2018

AbstractMicrotubules are a major component of the cytoskeleton and vital to numerous cellular processes. The central dogma of microtubules is that all their functions are driven by dynamic instability; understanding its key phenomena (i.e. catastrophe, rescue, pause, differential behaviors at the plus and minus ends) distilled from a myriad of experiments under a consistent and unified scheme, however, has been unattainable. Here, we present a novel statistical-physics-based model uniquely constructed from conformational states deduced from existing tubulin structures, with transitions between them controlled by steric constraints and mechanical energy of the microtubule lattice. This mechano-chemical model allows, for the first time, all the key phenomena of dynamic instability to be coherently reproduced by the corresponding kinetic simulations. Long-puzzling phenomena, such as aging, small GTP-cap size, fast catastrophe upon dilution and temperature-induced ribbon-to-tube transition of GMPCPP-tubulins, robustly emerge and thus can be understood with confidence.
Dosage sensitivity of X-linked genes in human embryonic single cells
Authors: Yang Jian-Rong , Chen Xiaoshu 
Published: March 2018

ABSTRACTFifty years ago, Susumu Ohno proposed that the expression levels of X-linked genes have doubled as dosage compensation for autosomal genes due to degeneration of Y-linked homologs during evolution of mammalian sex chromosomes. Recent studies have nevertheless shown that the X to autosome expression ratio equals ~1 in haploid human parthenogenetic embryonic stem (pES) cells and ~0.5 in diploid pES cells, thus refuting Ohno’s hypothesis. Here, by reanalyzing a RNA-seq-based single-cell transcriptome dataset of human embryos (Petropoulos, et al. 2016), we found that from the 8-cell stage until the time-point just prior to implantation, the expression levels of X-linked genes are not two-fold upregulated in male cells and gradually decrease from two-fold in female cells. This observation suggests that the expression levels of X-linked genes are imbalanced, with autosomal genes starting from the early 8-cell stage, and that the dosage conversion is fast, such that the X:AA expression ratio reaches ~0.5 in no more than a week. Additional analyses of gene expression noise further suggest that the dosage sensitivity of X-linked genes is weaker than that of autosomal genes in differentiated female cells, which contradicts a key assumption of Ohno’s hypothesis. Moreover, the dosage-sensitive housekeeping genes are preferentially located on autosomes, implying selection against X-linkage for dosage-sensitive genes. Our results collectively suggest an alternative to Ohno’s hypothesis that X-linked genes are less likely to be dosage sensitive than autosomal genes.
Branch-recombinant Gaussian processes for analysis of perturbations in biological time series
Authors: Penfold Christopher A. , Sybirna Anastasiya , Reid John , Huang Yun , Wernisch Lorenz , Ghahramani Zoubin , Grant Murray , Surani M. Azim 
Published: March 2018

AbstractMotivationA common class of behaviour encountered in the biological sciences involves branching and recombination. During branching, a statistical process bifurcates resulting in two or more potentially correlated processes that may under-go further branching; the contrary is true during recombination, where two or more statistical processes converge into one. A key objective is to identify the time of this bifurcation (branch time) from time series measurements e.g., comparing a control time series with a perturbed time series. Whilst statistical treatments for the two branch (control versus treatment) case exists, the ability to infer more complex branching structure from time series data remains open. Gaussian processes (GPs) represents an ideal framework for such analysis, allowing for nonlinear regression that includes a rigorous treatment of uncertainty. Currently, however, GP models only exist for two-branch systems. Here we highlight how arbitrarily complex branching processes can be built using the correct composition of covariance functions within a GP framework, thus outlining a general framework for the treatment of branching and recombination in the form of branch-recombinant Gaussian processes (B-RGPs). We first demonstrate the performance of B-RGPs compared to a variety of existing regression approaches, and demonstrate robustness to model misspecification. B-RGPs are then used to investigate the branching patterns ofArabidopsis thalianagene expression following inoculation with the hemibotrophic bacteria,Pseudomonas syringae DC3000, and a disarmed mutant strain, hrpA. By grouping genes according to the number of branches, we could naturally separate out genes involved in basal immune response from those subverted by the virulent strain, and show enrichment for targets of pathogen protein effectors. Finally, we identify two early branching genes WRKY11 and WRKY17, and showed that groups of genes that branched at similar times to WRKY11/17 were enriched for W-box binding motifs, and overrepresented for genes differentially expressed in WRKY11/17 knockouts, suggesting that branch time could be used for identifying direct and indirect binding targets of key transcription factors.Software is available from:https://github.com/cap76/BranchingGPs.
Chinese learner in a linguistically challenged environment – an exploratory study
Authors: Wong Grace , Dellaportas Steven , Cooper Barry J. 
Published: March 2018

Purpose
The purpose of this paper is to explore the implications for student learning when accounting education is delivered in the student’s non-native language. It examines the impact on learning arising from the different components of English language competencies, namely, listening, reading, writing, and speaking.

Design/methodology/approach
The data are drawn from focus group interviews with students from Mainland China undertaking an accounting degree in Australia.

Findings
The findings indicate that students relied primarily on their reading instead of listening to seek understanding, and in turn, writing was considered less important compared to listening and reading. Notably, speaking was overlooked by many students as it was considered the least important skill necessary to achieve success as a student and to be a competent practitioner. Students developed a misconception that the quality of oral communication required of accountants in practice is unimportant.

Practical implications
The findings will assist accounting educators and the accounting profession in designing and implementing appropriate instructional strategies and assessment tasks for international students. One suggestion includes a more balanced weighting between written and oral assessment.

Originality/value
Few studies have specifically explored the impact of English language on learning accounting. While some studies examine specific aspects of language as a unitary concept, little has been reported on the impact of all components of the language skill-set on student learning.
The role of trip purpose and hotel star rating on guests’ satisfaction and WOM
Authors: Rajaguru Rajesh , Hassanli Najmeh 
Published: March 2018

PurposeThis paper aims to understand how guests’ trip purpose and hotel star rating influence the effects of the value for money perceived at hotels and service quality on guest satisfaction and word of mouth (WOM) recommendation.Design/methodology/approachUsing TripAdvisor, 25 Singaporean hotels were randomly selected for the study, which yielded hotel reviews from 2,040 respondents. Hierarchical and logistic regression analysis was conducted to investigate the relationships proposed in the study.FindingsResults indicate significant differences between leisure and business guests’ perception of value for money and service quality at hotels with various star ratings. While perceived value for money and service quality were found as significant predictors for both leisure and business guests’ satisfaction and WOM, the effects were moderated by the hotel star rating. Despite the significant effect of hotel star rating on guest satisfaction, the study found no significant relationships between hotel star rating and WOM for leisure and business guests.Practical implicationsThe findings suggest that managers in the hotel industry should understand the purpose of guests’ trip and offer services based on their expectations. As the star rating of a hotel creates certain expectations for both leisure and business guests, providing an appropriate level of services and assuring value for money in accordance with the hotel rating contributes to guest satisfaction and WOM recommendation.Originality/valueThis study contributes to the hospitality literature by investigating how hotel star rating moderates the relationship of value for money and service quality on leisure and business guests’ satisfaction and WOM recommendation.
Executive chefs’ calling: effect on engagement, work-life balance and life satisfaction
Authors: Cain Lisa , Busser James , Kang Hee Jung (Annette) 
Published: March 2018

PurposeThis paper aims to understand the relationships among calling, employee engagement, work-life balance and life satisfaction for executive chefs based on role theory and spillover theory.Design/methodology/approachSurveys were completed by members of the American Culinary Federation in North America, the Nevada Restaurant Association and attendees at the ChefConnect Annual Conference. The data were analysed with confirmatory factor analysis and structural equation modelling.FindingsAll relationships in the model were significantly positive except for calling to life satisfaction. Importantly work-life balance was a significant mediator between calling and life satisfaction as well as for employee engagement and life satisfaction.Research limitations/implicationsThe research provides a more comprehensive framework for hospitality scholars to understand the outcomes of work as a calling through meaningfulness. The sample of executive chef limits generalizability.Practical implicationsThe identification of a calling through in-depth interviews is recommended. Once recognized, managers should further foster chef’s passion through employee engagement facilitated by workplace autonomy and continuing education and work-life balance supported with human resource management practices including time off for critical life events. This will allow calling to flourish, increase life satisfaction and reduce the likelihood of turnover and burnout.Originality/valueOutcomes reveal the complexity of the relationship between calling and life satisfaction. Contrary to previous findings, the presence of positive work-life balance was critical to attain life satisfaction, even when work was viewed as a calling.
Evaluating hotel guest technologies: does home matter?
Authors: Beldona Srikanth , Schwartz Zvi , Zhang Xian 
Published: March 2018

PurposeWith the advent of the smart home, where connectivity is facilitated by the internet of things, the provision of guest technologies in hotel service delivery has acquired greater significance. This ubiquity of technology implies that hotels need to view their technological offerings as facilitating guest’s broader lifestyles, and not just services in isolated spaces. This study aims to examine the role of “home” as a socio-technological unit, and how customers’ ownership of technologies at home affects evaluations of guest technologies at hotels.Design/methodology/approachData are collected from a sample of US lodging consumers using Amazon’s Mechanical Turk. Partial least squares, which is a component-based structural equation modeling technique with SmartPLS 3.2, is used to test the hypotheses and meet the study’s objectives.FindingsThe findings show that hotel guest technologies should be of a higher standard than those at home, for guests to be satisfied with them. This relationship was robust across all hotel types, and both leisure and business visitation. Also, satisfaction with guest technologies has a relatively stronger impact on customer satisfaction in mid-scale and economy hotels compared to that in upscale and luxury hotels.Research limitations/implicationsBy empirically validating “home” as a frame of reference in the evaluations of hospitality experiences, it opens up the potential for future research to study how home affects the evaluation of the hospitality experience as a whole.Practical implicationsHotels need to identify viable technologies that have the potential to become mainstream, and be ahead of customers in the technology adoption curve.Originality/valueThis study is the first to look at home as a conceptual entity that is integral to hospitality using a socio-psychological lens, and evaluates its impact on evaluations of guest technologies at hotels.
Exploring the MICE industry career path
Authors: Wang Mingsheng , Luo Qiuju 
Published: March 2018

PurposeThis paper aims to explain and resolve the paradoxical situation in China regarding how it is difficult to get an offer of employment in China while people are unwilling to pursue or embark on a career in the Meetings, Incentives, Conventions and Exhibitions (MICE) industry. Therefore, the MICE industry career path should be carefully explored.Design/methodology/approachThe paper used semi-structured interviews with more than 30 representative managers from key MICE companies, a social community perspective and conceptions of the social world combined with the traditional career-ladder model.FindingsThe study’s key findings are: a general career path exists in the MICE industry in China; there are three main types of career paths and two different kinds of promotion mechanisms, which vary according to the type of ownership, scale or other characteristics of companies; and a feedback mechanism, linking social-world events and social community characteristics, affects individual employees and their career paths in the MICE industry, leading to promotion in or retreat from the industry. Typically, the mechanism fits high-level employees better than the freshmen, which leads to high turnover in the MICE labor market.Practical implicationsThis paper provides a better understanding of MICE industry and facilitates people’s employment choices.Originality/valueThis paper provide a new social community perspective for exploring the MICE career path; there are also significant practical implications for MICE elites, which present a new framework for future research and industry applications.
Big data and predictive analytics in humanitarian supply chains
Authors: Dubey Rameshwar , Luo Zongwei , Gunasekaran Angappa , Akter Shahriar , Hazen Benjamin T. , Douglas Matthew A. 
Published: March 2018

PurposeThe purpose of this paper is to understand how big data and predictive analytics (BDPA), as an organizational capability, can improve both visibility and coordination in humanitarian supply chains.Design/methodology/approachThe authors conceptualize a research model grounded in contingent resource-based view where the authors propose that BDPA capabilities affect visibility and coordination under the moderating effect of swift trust. Using ordinary least squares regression, the authors test the hypotheses using survey data collected from informants at 205 international non-government organizations.FindingsThe results indicate that BDPA has a significant influence on visibility and coordination. Further, the results suggest that swift trust does not have an amplifying effect on the relationships between BDPA and visibility and coordination. However, the mediation test suggests that swift trust acts as a mediating construct. Hence, the authors argue that swift trust is not the condition for improving coordination among the actors in humanitarian supply chains.Research limitations/implicationsThe major limitation of the study is that the authors have used cross-sectional survey data to test the research hypotheses. Following Guide and Ketokivi (2015), the authors present arguments on how to address the limitations of cross-sectional data or use of longitudinal data that can address common method bias or endogeneity-related problems.Practical implicationsManagers can use this framework to understand: first, how organizational resources can be used to create BDPA, and second, how BDPA can help build swift trust and be used to improve visibility and coordination in the humanitarian supply chain.Originality/valueThis is the first research that has empirically tested the anecdotal and conceptual evidence. The findings make notable contributions to existing humanitarian supply chain literature and may be useful to managers who are contemplating the use of BDPA to improve disaster-relief-related activities.
Big data analytics and demand forecasting in supply chains: a conceptual analysis
Authors: Hofmann Erik , Rutschmann Emanuel 
Published: March 2018

Purpose
Demand forecasting is a challenging task that could benefit from additional relevant data and processes. The purpose of this paper is to examine how big data analytics (BDA) enhances forecasts’ accuracy.

Design/methodology/approach
A conceptual structure based on the design-science paradigm is applied to create categories for BDA. Existing approaches from the scientific literature are synthesized with industry knowledge through experience and intuition. Accordingly, a reference frame is developed using three steps: description of conceptual elements utilizing justificatory knowledge, specification of principles to explain the interplay between elements, and creation of a matching by conducting investigations within the retail industry.

Findings
The developed framework could serve as a guide for meaningful BDA initiatives in the supply chain. The paper illustrates that integration of different data sources in demand forecasting is feasible but requires data scientists to perform the job, an appropriate technological foundation, and technology investments.

Originality/value
So far, no scientific work has analyzed the relation of forecasting methods to BDA; previous works have described technologies, types of analytics, and forecasting methods separately. This paper, in contrast, combines insights and provides advice on how enterprises can employ BDA in their operational, tactical, or strategic demand plans.
Practitioners understanding of big data and its applications in supply chain management
Authors: Brinch Morten , Stentoft Jan , Jensen Jesper Kronborg , Rajkumar Christopher 
Published: March 2018

Purpose
Big data poses as a valuable opportunity to further improve decision making in supply chain management (SCM). However, the understanding and application of big data seem rather elusive and only partially explored. The purpose of this paper is to create further guidance in understanding big data and to explore applications from a business process perspective.

Design/methodology/approach
This paper is based on a sequential mixed-method. First, a Delphi study was designed to gain insights regarding the terminology of big data and to identify and rank applications of big data in SCM using an adjusted supply chain operations reference (SCOR) process framework. This was followed by a questionnaire-survey among supply chain executives to elucidate the Delphi study findings and to assess the practical use of big data.

Findings
First, big data terminology seems to be more about data collection than of data management and data utilization. Second, the application of big data is most applicable for logistics, service and planning processes than of sourcing, manufacturing and return. Third, supply chain executives seem to have a slow adoption of big data.

Research limitations/implications
The Delphi study is explorative by nature and the questionnaire-survey rather small in scale; therefore, findings have limited generalizability.

Practical implications
The findings can help supply chain managers gain a clearer understanding of the domain of big data and guide them in where to deploy big data initiatives.

Originality/value
This study is the first to assess big data in the SCOR process framework and to rank applications of big data as a mean to guide the SCM community to where big data is most beneficial.