bluuebunny/crossref_metadata_2025_split huggingface dataset:
VSIM: Visualization and simulation of variants in personal genomes with an application to premarital testing
Authors: Althagafi Azza , Hoehndorf Robert 
Published: January 2019

AbstractBackgroundInterpretation of personal genomics data, for example in genetic counseling, is challenging due to the complexity of the data and the amount of background knowledge required for its interpretation. This background knowledge is distributed across several databases. Further information about genomic features can also be predicted through machine learning methods. Making this information accessible more easily has the potential to improve interpretation of variants in personal genomes.ResultsWe have developed VSIM, a web application for the interpretation and visualization of variants in personal genome sequences. VSIM identifies disease variants related to Mendelian, complex, and digenic disease as well as pharmacogenomic variants in personal genomes and visualizes them using a webserver. VSIM can further be used to simulate populations of children based on two parent genomes, and can be applied to support premarital genetic counseling. We make VSIM available as source code as well as through a container that can be installed easily in network environments in which genomic data is specially protected. VSIM and related documentation is freely available athttps://github.com/bio-ontology-research-group/VSIM.ConclusionsVSIM is a software that provides a web-based interface to variant interpretation in genetic counseling. VSIM can also be used for premarital genetic screening by simulating a population of children and analyze the disorder they might be carrying.
tealeaves: an R package for modelling leaf temperature using energy budgets
Authors: Muir Christopher. D. 
Published: January 2019

AbstractPlants must regulate leaf temperature to optimize photosynthesis, control water loss, and prevent damage caused by overheating or freezing. Physical models of leaf energy budgets calculate the energy fluxes and leaf temperatures for given a set leaf and environmental parameters. These models can provide deep insight into the variation in leaf form and function, but there are few computational tools available to use these models. Here I introduce a new R package calledtealeavesto make complex leaf energy budget models accessible to a broader array of plant scientists. This package enables novice users to start modelling leaf energy budgets quickly while allowing experts customize their parameter settings. The code is open source, freely available, and readily integrates with other R tools for scientific computing. This paper describes the current functionality oftealeaves, but new features will be added in future releases. This software tool will advance new research on leaf thermal physiology to advance our understanding of basic and applied plant science.
Robust taxonomic classification of uncharted microbial sequences and bins with CAT and BAT
Authors: Meijenfeldt F.A. Bastiaan von , Arkhipova Ksenia , Cambuy Diego D. , Coutinho Felipe H. , Dutilh Bas E. 
Published: January 2019

ABSTRACTCurrent-day metagenomics increasingly requires taxonomic classification of long DNA sequences and metagenome-assembled genomes (MAGs) of unknown microorganisms. We show that the standard best-hit approach often leads to classifications that are too specific. We present tools to classify high-quality metagenomic contigs (Contig Annotation Tool, CAT) and MAGs (Bin Annotation Tool, BAT) and thoroughly benchmark them with simulated metagenomic sequences that are classified against a reference database where related sequences are increasingly removed, thereby simulating increasingly unknown queries. We find that the query sequences are correctly classified at low taxonomic ranks if closely related organisms are present in the reference database, while classifications are made higher in the taxonomy when closely related organisms are absent, thus avoiding spurious classification specificity. In a real-world challenge, we apply BAT to over 900 MAGs from a recent rumen metagenomics study and classified 97% consistently with prior phylogeny-based classifications, but in a fully automated fashion.
Elite status talks, but how loudly and why? Exploring elite CSR micro-politics
Authors: Heath Robert L. , Waymer Damion 
Published: January 2019

PurposeThe purpose of this paper is to investigate the proactive role elite organizations play within-network corporate social responsibility (CSR) performance by determining whether organizations can be identified that serve as aspirational CSR role models. The assumption is that elite CSR performance inspires and challenges other in-network actors to raise their standards in order to be legitimate, and resource rewardable.Design/methodology/approachThree cases are discussed to exemplify elite CSR: historical: recognizing the value of embracing a trend in improved standards of meatpacking, Armour Meatpacking campaigned for sanitary meatpacking and implemented strategic change; global energy: Chevron Corporation conducts “business in a socially and environmentally responsible manner, respecting the law and universal human rights to benefit the communities where we work”; and non-profit: “Elite” universities’ CSR standards attract bright faculty and students and build beneficial relationships with industry, government and peers.FindingsElite institutions raise CSR standards by using issue trends to guide strategic change that can performatively demonstrate the societal value of proactive leadership that elevates standards and increases the reward value to communities and organizations that is achieved by adopting higher standards.Research limitations/implicationsThrough micro-politics that increase CSR social productivity, elite CSR standards earn rewards for exemplary organizations and subsequently raise standards for in-network organizations to, in turn, achieve the license to operate.Practical implicationsDiscussions of CSR should consider the influences that establish CSR standards. To that end, this paper offers the explanatory power of a micro-political, societal productivity approach to CSR based on the pragmatic/moral resource dependency paradigm.Social implicationsThe paper reasons that higher CSR standards result when NGO stakeholder critics and/or government agencies exert micro-political pressure. In response to such pressure, elite organizations, those that are or can meet those higher CSR standards, proactively demonstrate how higher CSR standards can accrue resources that benefit them and society. Elite CSR performance challenges other in-network actors to raise standards in order to be legitimate, that is resource rewardable.Originality/valueBecause elite organizations understand the reward advantage of higher levels of CSR, they proactively elevate the discuss of standards and advantages for achieving them, and penalties for falling short.
Lean as a learning system: What do organizations need to do to get the transformational benefits from Toyota’s method?
Authors: Ballé Michael , Chaize Jacques , Jones Daniel 
Published: January 2019

Purpose
The creators of the “lean” approach share their extensive experience, highlighting how organizations can reap the benefits of Toyota’s approach.

Design/methodology/approach
Based on the authors expertise and 30 plus years of experience developing and implementing the “lean” approach.

Findings
A shift is required in leaders, away from a chain of command to a chain of help. Type IV learning is required where everyone, including the “leaders”, explores, learns, and figures out, experientially, one change at a time.

Originality/value
The paper provides a succinct summary of the need for a mind-set shift in leaders if they are to create a truly lean culture in their organization. They call for leaders to start a cognitive revolution, rather than look to “bolt on” lean to existing organizational practices.
Zero rating and end-users’ freedom of choice: an economic analysis
Authors: Jaunaux Laure , Lebourges Marc 
Published: January 2019

PurposeAccording to European Union Open Internet Regulation, commercial practices of internet access service providers (IASP) should not restrict end-users’ choice regarding services, applications or contents. This paper aims to analyze the effects of Zero Rating (ZR) on freedom of choice translating this regulatory criterion into a formal expression: providing a ZR offer on a content or application provider (CAP) restricts end-users’ choice if it reduces the volume or provision of others usages.Design/methodology/approachThe analysis is made in two steps. First, the authors assess the direct effect of introducing zero rating on non-ZR usages, all other things equal. Second, the paper studies the knock-on effect of ZR on IASP offers and the supply of CAP.FindingsIn the short term, zero rating does not restrict end-users’ choice increasing both ZR and non-ZR usages. In the long term, in the case of pure ZR, IASPs may adapt their offer to support ZR costs impacting negatively other usages. However, in practice, these effects are compensated or diluted by competitive forces or if the ZR traffic is small relatively to the data allowance. In the case of SD, the CAP covers the cost which prevents cross-subsidies and protects freedom of choice if SD is open to all CAPs.Originality/valueThe economic literature on zero rating is scarce and assesses this practice from the general economic criterion of social or consumer welfare. This paper is the first one to use economic analysis to analyze whether Zero Rating is compatible with the EU regulatory criterion of freedom of choice.
Hidden patterns
Authors: Collins Regina , Steffen-Fluhr Nancy 
Published: January 2019

PurposeThe purpose of this paper is to describe how one group of ADVANCE Project researchers investigated faculty co-authorship networks to identify relationships between women’s positions in these networks, their research productivity and their advancement at the university – and to make those relationships transparent.Design/methodology/approachMultiple methods for capturing faculty network data were evaluated, including collecting self-reported data and mining bibliometric data from various web-based sources. Faculty co-authorship networks were subsequently analyzed using several methodologies including social network analysis (SNA), network visualizations and the Kaplan–Meier product limit estimator.FindingsResults suggest that co-authorship provides an important way for faculty to signal the value of their work, meaning that co-authoring with many others may be beneficial to productivity and promotion. However, patterns of homophily indicate that male faculty tend to collaborate more with other men, reducing signaling opportunities for women. Visualizing these networks can assist faculty in finding and connecting with new collaborators and can provide administrators with unique views of the interactions within their organizations. Finally, Kaplan–Meier survival studies showed longitudinal differences in the retention and advancement of faculty based on gender.Originality/valueTogether, these findings begin to shed light on subtle differences that, over time, may account for the significant gender disparities at STEM institutions, patterns which should be investigated and addressed by administrators. Lessons learned, as well as the novel use of SNA and Kaplan–Meier in investigating gender differences in STEM faculty, provide important findings for other researchers seeking to conduct similar studies at their own institutions.
CO2 emissions from facility services
Authors: Pelzeter Andrea , Sigg René 
Published: January 2019

Purpose
The purpose of this paper is identification of a methodology to determine CO2 emissions through facility services on an approximate and sufficiently accurate basis. This methodology is to be used by German practitioners for request for proposals (RFPs) and offers of facility services.

Design/methodology/approach
In accordance with ISO 14067, a matrix of CO2-relevant modules for the representation of CO2 emissions from facility services is developed. Key figures for energy consumption, transport and equipment manufacture and use are used in a case study.

Findings
For a transparent CO2 assessment of facility services, the following modules are required: work clothing, devices, vehicles (service personnel), supplies, transportation of personnel and overhead (vehicles and office space). In the case study, facility services account for about 30 per cent of the CO2 emissions originating from the use of the building.

Research limitations/implications
The methodology developed is also applicable to other services. Prior to that, however, the investigation of additional facility services (catering or security) and an extension to other types of facilities is required (office building, hospital, etc.).

Practical implications
The developed methodology allows transparent competition for low-carbon services concepts, for example, in RFP procedures for facility services.

Social implications
CO2-optimised facility services increase the demand for low-emission operating equipment and resources. They therefore have an indirect influence on the development of a low-carbon economy.

Originality/value
To date, there has not been a methodology that supports a transparent and practical summary of the service-related CO2 emissions associated with the resources used in facility services.
Grade point average vs competencies: which are most influential for employability?
Authors: Freire-Seoane Maria Jesus , Pais-Montes Carlos , Lopez-Bermúdez Beatriz 
Published: January 2019

Purpose
The purpose of this paper is to measure the combined influence that soft skills and Graduate Point Average (GPA) achievements have on the employability of higher education (HE) graduates, and the possible mitigating effects that score attainments have on some ex ante issues, like the gender asymmetries existing in labour market, or the great difference between some knowledge fields, regarding their unemployment rates.

Design/methodology/approach
The methodology used is a probit model, performed on a sample of 1,054 HE graduates, coming from a middle-sized European university.

Findings
The results show: a clear positive influence of the GPA on job finding odds; that some generic competencies improve this probabilities but another ones act as penalties; and that GPA and systemic competencies enhancement initiatives (at an individual level or at HE policy institutions level) could act as attenuators for the gender inequality or for the low recruitment perspectives existing on some knowledge fields like humanities or social sciences.

Originality/value
A wide scientific literature can be currently found on generic competencies and their influence on the employability odds, but the results regarding GPA attainments are still too heterogeneous and scarcely explored. On the other hand, there’s a non-solved controversy in the literature about the influence of the GPA results on the odds that a HE graduate has to obtain a job: do GPA signal correctly the best candidates? Do current employers prefer competencies scores over GPA attainments? This paper will contribute to clarify these questions.
Experiences of internet users regarding cyberhate
Authors: Celik Serkan 
Published: January 2019

PurposeThe purpose of this paper is to explore internet users’ experiences of cyberhate in the aspects of ethnicity, religion, sexual preference and political perspective.Design/methodology/approachResearchers employed an exploratory survey method to examine internet users’ experiences of cyberhate. The participants of the study were determined by purposive sampling methods to attain maximum variety among internet users with high-level digital literacy skills. The data were collected from 355 internet users affiliated with two universities in Turkey and the USA using a personal data form and a survey (Cyberhate Experience Survey) of which reliability and validity indexes were ensured.FindingsThe results indicated that participants have observed and experienced cyberhate at different levels targeting their ethnic, religious, gender-based and political identities. The findings also pointed out that gender, income and socio-political identities are significant variables on exposure to cyberhate regardless of cultural and educational boundaries. The majority of survey respondents reported that they had encountered cyberhate mostly on social media platforms.Social implicationsThe findings of the study imply that to address the hate speech problem comprehensively, the author must enlighten people, change their way of thinking and broaden their perspectives by using measures such as intercultural dialogue, critical thinking, media literacy, education on tolerance and diversity.Originality/valueThis research was intended to contribute into the need to elaborate on various aspects of cyberhate, which is shared by academics, thinkers, journalists and educators. It may also serve to clarify how frequently internet users encounter hateful content and harassment online, which can have social consequences and influence young people’s trust to other people.
Student voice: perceptions of fair treatment in a Foundations program
Authors: Gallagher Kay 
Published: January 2019

PurposeThe purpose of this paper is to investigate why beginning university Emirati students might believe they are unfairly treated by their instructors. By understanding student perceptions, the learning needs of such students can be better catered for, and learning outcomes enhanced.Design/methodology/approachAn interpretivist approach was taken to investigate a finding from a standardized survey of student satisfaction which showed that students felt they were treated unfairly by their instructors. Focus group interviews were used to uncover the possible reasons why students believed they received unfair treatment.FindingsInterpersonal or interactional unfairness is the type of unfair treatment most often cited by the Foundation students who participated in this study, indicative of the importance of interpersonal relations in the United Arab Emirates (UAE) higher education teaching and learning environment.Research limitations/implicationsAlthough the study is situated within one Foundations program in the UAE, the imperative for instructors to build positive interpersonal relationships with beginning students is highlighted, as well as the need for curricular transparency and ongoing moderation of grading practices, and the importance of informing students about these practices.Practical implicationsThe imperative of building positive pedagogical relationships with beginning university Arab Gulf students is highlighted, as well as the need for transparent practices such as moderation of grades, and explicitly informing students about fair practices.Social implicationsDrawing on data from faculty instructors, the paper suggests that a deeper, macrosystemic level of educational unfairness may also be at play: that is, the unfairness inherent in the hegemony of English, and the disconnect between the quality of the state school system and the demands of university. Until these educational issues are addressed, perceptions of unfair treatment in Foundations programs in the Gulf are likely to continue.Originality/valueAs higher education continues to undergo expansion and transformation in the UAE, increasing numbers of academic staff from around the world migrate there, and thousands of Gulf students continue to emigrate to study overseas. This paper contributes important insights into Gulf students’ perceptions.
Organizational constraints as root causes of role conflict
Authors: Gilbert Marie-Hélène , Dextras-Gauthier Julie , Fournier Pierre-Sébastien , Côté André , Auclair Isabelle , Knani Mouna 
Published: January 2019

PurposeThe purpose of this paper is to gain a better understanding of the difficulties encountered in the hybrid roles of physician−managers (P−Ms), examine the impact of organizational constraints on the role conflicts experienced by P−Ms and explore the different ways their two roles are integrated.Design/methodology/approachA qualitative approach was adopted, using six focus groups made up of clinical co-managers, medical directors and P−Ms. In all, 43 different people were interviewed to obtain their perceptions of the day-to-day realities of the role of the P−M. The data collected were subsequently validated.FindingsAlthough the expectations of the different groups involved regarding the role of P−Ms are well understood and shared, there are significant organizational constraints affecting what P−Ms are able to do in their day-to-day activities, and these constraints can result in role conflicts for the people involved. Such constraints also affect the ways P−Ms integrate the two roles. The authors identify three role hybridization profiles.Practical implicationsThe results afford a better understanding of how organizational constraints might be used as levers of organizational change to achieve a better hybridization of the dual roles of P−Ms.Originality/valueThis paper seeks to reach beyond a simple identification of constraints affecting the dual roles of P−Ms by analyzing how such constraints impact on these professionals’ day-to-day activities. Results also enable us to further refine Katz and Kahn’s (1966) role model, in addition to identifying hybridization profiles.
Using dispute settlement partnerships for capacity building
Authors: Bahri Amrita , Ali Toufiq 
Published: January 2019

Purpose
World Trade Organisation grants rights to its members, and WTO Dispute Settlement Understanding (DSU) provides a rule-oriented consultative and judicial mechanism to protect these rights in cases of WTO-incompatible trade infringements. However, the DSU participation benefits come at a cost. These costs are acutely formidable for least developing countries (LDCs) which have small market size and trading stakes. No LDC has ever filed a WTO compliant, with the only exception of India-Battery dispute filed by Bangladesh against India. This paper aims to look at the experience of how Bangladesh – so far the only LDC member that has filed a formal WTO complaint – persuaded India to withdraw anti-dumping duties India had imposed on the import of acid battery from Bangladesh.

Design/methodology/approach
The investigation is grounded on practically informed findings gathered through authors’ work experience and several semi-structured interviews and discussions which the authors have conducted with government representatives from Bangladesh, government and industry representatives from other developing countries, trade lawyers and officials based in Geneva and Brussels, and civil society organisations.

Findings
The discussion provides a sound indication of the participation impediments that LDCs can face at WTO DSU and the ways in which such challenges can be overcome with the help of resources available at the domestic level. It also exemplifies how domestic laws and practices can respond to international legal instruments and impact the performance of an LDC at an international adjudicatory forum.

Originality/value
Except one book chapter and a working paper, there is no literature available on this matter. This investigation is grounded on practically informed findings gathered with the help of original empirical research conducted by the authors.