bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sequence database versioning for command line and Galaxy bioinformatics servers
Authors: Dooley Damion M. , Petkau Aaron J. , Van Domselaar Gary , Hsiao William W.L. 
Published: December 2015

Abstract
Motivation: There are various reasons for rerunning bioinformatics tools and pipelines on sequencing data, including reproducing a past result, validation of a new tool or workflow using a known dataset, or tracking the impact of database changes. For identical results to be achieved, regularly updated reference sequence databases must be versioned and archived. Database administrators have tried to fill the requirements by supplying users with one-off versions of databases, but these are time consuming to set up and are inconsistent across resources. Disk storage and data backup performance has also discouraged maintaining multiple versions of databases since databases such as NCBI nr can consume 50 Gb or more disk space per version, with growth rates that parallel Moore's law.
Results: Our end-to-end solution combines our own Kipper software package—a simple key-value large file versioning system—with BioMAJ (software for downloading sequence databases), and Galaxy (a web-based bioinformatics data processing platform). Available versions of databases can be recalled and used by command-line and Galaxy users. The Kipper data store format makes publishing curated FASTA databases convenient since in most cases it can store a range of versions into a file marginally larger than the size of the latest version.
Availability and implementation: Kipper v1.0.0 and the Galaxy Versioned Data tool are written in Python and released as free and open source software available at https://github.com/Public-Health-Bioinformatics/kipper and https://github.com/Public-Health-Bioinformatics/versioned_data, respectively; detailed setup instructions can be found at https://github.com/Public-Health-Bioinformatics/versioned_data/blob/master/doc/setup.md
Contact: Damion.Dooley@Bccdc.Ca or William.Hsiao@Bccdc.Ca
Supplementary information: Supplementary data are available at Bioinformatics online.
INSECT 2.0: a web-server for genome-wide cis-regulatory modules prediction
Authors: Parra R. Gonzalo , Rohr Cristian O. , Koile Daniel , Perez-Castro Carolina , Yankilevich Patricio 
Published: December 2015

Abstract
INSECT is a user-friendly web server to predict the occurrence of Cis-Regulatory Modules (CRMs), which control gene expression. Here, we present a new release of INSECT which includes several new features, such as whole genome analysis, nucleosome occupancy predictions, and which provides additional links to third-party functional tools that complement user capabilities, CRM analysis and hypothesis construction. Improvements in the core implementation have led to a faster and more efficient tool. In addition, this new release introduces a new interface designed for a more integrative and dynamic user experience.
Availability and implementation: http://bioinformatics.ibioba-mpsp-conicet.gov.ar/INSECT2
Contact: pyankilevich@ibioba-mpsp-conicet.gov.ar
Rolling out lean production systems: a knowledge-based perspective
Authors: Secchi Raffaele , Camuffo Arnaldo 
Published: December 2015

Purpose– Adopting a knowledge-based perspective, the purpose of this paper is to investigate the roll-out process of lean production systems and explores the dimensions that might enhance or hinder its performance. It develops a framework to understand and design lean roll-out processes, identifying the research dimensions/design variables to classify and interpret such processes.Design/methodology/approach– This exploratory multiple case study analyses seven lean roll-out processes in multinational companies’ plants. An original data set, developed on the basis of a purposely design research protocol, was built through two rounds of plant visits and structured interviews. The cross-case analysis compares and contrasts the lean roll-out processes according to the research dimensions constituting the framework.Findings– The effectiveness and the efficiency of the lean roll-out processes: first, negatively co-vary with the degree of lean knowledge codification; second, positively co-vary with the degree of autonomy of the plant; third, positively co-vary with the degree of contextual ambidexterity. Moreover, lean roll-out processes characterized by principles-based knowledge replication strategy, plant autonomy and contextual ambidexterity are comparatively more effective and efficient.Research limitations/implications– This is an exploratory qualitative study that develops propositions potentially testable in larger scale, more analytical research.Practical implications– This study provides a tentative roadmap to successfully approach the roll-out of lean production systems in complex organizations.Originality/value– This study challenges the current theory and practice which implicitly assumes that lean roll-outs take place linearly, cascading a set of predefined lean operations practices. Instead, the authors show that a less codified, more decentralized and contextually ambidextrous approach might be more effective.
Sustainable supply management as a purchasing capability
Authors: Dabhilkar Mandar , Bengtsson Lars , Lakemond Nicolette 
Published: December 2015

Purpose
– The purpose of this paper is to use the relative power and total interdependence concepts as an intervening theoretical lens to explain why and how sustainable supply management (SSM) initiatives by manufacturing firms differ across the Kraljic matrix according to purchasing capability.

Design/methodology/approach
– Tested hypotheses by subjecting survey data from 338 manufacturers on buyer-supplier relationships in Europe and North America to regression analysis.

Findings
– Shows three situations where relative power and total interdependence determine the effectiveness of purchasing capabilities. First, sustainability programs impact supplier compliance in all Kraljic categories but bottleneck items. Second, there are significant trade-offs between lower cost and higher social and environmental supplier compliance for noncritical components. Third, strategic alignment of sustainability objectives between corporate and supply function levels only leads to improved financial performance for strategic components.

Research limitations/implications
– Further research could take power and dependence into account to explain when and how purchasing capabilities focussed on sustainability can be achieved.

Practical implications
– Shows how supply strategists could devise-tailored approaches for different purchasing categories with respect to power and dependence when pursuing economic, social and environmental objectives in combination – the triple bottom line – along their supply chains.

Originality/value
– Illustrates and provides a theoretical explanation for why SSM is a purchasing capability that must vary across purchasing categories defined by different situations of power and dependence.
Borrowing tools from the public library
Authors: Söderholm Jonas 
Published: December 2015

Purpose
– The purpose of this paper is to investigate tool lending library patrons’ perception of their tool borrowing, in order to explore the role of a public lending service in the context of their lives. It addresses the research question, why do patrons borrow tools from the library?

Design/methodology/approach
– A case study was conducted, consisting of semi-structured interviews with patrons of a tool lending library. Led by a phenomenographic approach, the interviews focused on participants’ recounted experiences. Transcripts were structured into major categories and underlying themes. Findings were discussed from a perspective taking departure in Wiegand’s notion of “the library in the life of the user,” and summarized with regards to sustainable community development.

Findings
– Participants are found to talk about their tool borrowing from two main viewpoints. First, reasons for making the decision. This involves weighing practical considerations, e.g., cost, storage, access, and frequency of use. It also includes ideological motivations, and sympathy with the concept. Second, effects of their borrowing, interpreted as how it enables them. This enablement includes inspiration, learning, support to self-employment, and strengthening of community. Patrons focus on local aspects of social and economic development, rather than global or environmental motivations.

Research limitations/implications
– A single and in part unique setting was studied. The findings provide foundation for a developed discussion on the societal role of public libraries providing “non-traditional” materials such as tools, with particular regards to community settings and sustainability.

Originality/value
– Addresses knowledge gaps on borrowing and tool lending libraries.
Third-party classification
Authors: Klimaszewski Cheryl 
Published: December 2015

Purpose– The purpose of this paper is to foreground the ways in which material objects emerged as a kind of classificatory force during a visit to a local museum in rural Romania. It considers ways in which classification both influences and is influenced by the spatio-temporal assemblages of things.Design/methodology/approach– Visual and textual ethnographic field data collected to document the museum tour are interpreted using a phenomenological approach. Jane Bennett’s agency of assemblage is used to contextualize these instants of interruption within the space/time arrangements of objects within the museum.Findings– The “marginal” category of translator commentary emerged during data coding to reveal “instants of interruption.” These instants exhibited classificatory tendencies that revealed relationships between seemingly disparate elements. As such, the translator acted as a kind of third-party classificatory force that illuminated how relationships between physical assemblages of things in the world can act as a force for new knowledge production.Originality/value– This paper contributes to the literature on social classification and document theory by revealing how alternative approaches to classification can open up additional avenues for research and knowledge discovery.
Transgender information behaviour
Authors: Pohjanen Aira Maria , Kortelainen Terttu Anna Maarit 
Published: December 2015

Purpose
– The purpose of this paper is to explore information behaviour and the information barriers transgendered people encounter. This study produces new information about the information needs in the construction of the transgendered identity, the changing of the information needs during this phase, utilized information sources, information sharing and barriers encountered in the information behaviour displayed by transgendered people.

Design/methodology/approach
– Semi-structured interviews were used to explore the information behaviour of 12 transgendered participants. This study represents a phenomenological-hermeneutic approach. A qualitative content analysis was used in analysing the data with categories derived from previous research and research questions.

Findings
– Serendipity played an important role at the beginning of the participants’ information seeking phase: the young individual would not have terms corresponding to his or her experience because of the invisibility of the transgender phenomenon in the culture. The barriers to seeking information were psychological, demographic, role-related or interpersonal, environmental or source characteristic. Fear was apparent as a barrier in the surrounding culture often caused by expectations, attitudes in the family environment and people around. Source characteristic barriers were related to the lack of terms and vocabulary required to seek information and also the lack of the information itself. Information about transgender and gender minorities was essential in building up a clear gender identity, and the most relevant information sources of this sort of information this were other transgendered people and the experience-based information they had shared.

Originality/value
– The information behaviour of transgendered people has not been previously studied. In this study a model of information behaviour and information barriers was made. The model includes individual’s information practices, sources of information and also the barriers affecting information behaviour.
Language in the information-seeking context
Authors: Sabbar Carol , Xie Iris 
Published: December 2015

Purpose– The purpose of this paper is to specifically investigate information seeking strategies that are used by scholars in the USA conducting research in languages other than English and the types of shifts that scholars make between strategies in planned, disruptive, and problematic situations.Design/methodology/approach– Interviews and research diaries were employed to gather information from 16 subjects using seven different languages across seven disciplines. Grounded theory and the constant comparative method were used to analyze types of strategies and types of shifts between strategies.Findings– This study identified four formal system strategies, seven informal resource strategies, four interactive human strategies, and one hybrid strategy. Subjects in the study selected informal resource and interactive human strategies more often as initial strategies while informal resource strategies are used as final strategies. Moreover, the findings presented a variety of shifts between strategies in planned, disruptive, and problematic situations.Research limitations/implications– Theoretically, this study introduces a new conceptual model – the information triangle – which facilitates the classification of strategies used by scholars throughout an information seeking task as well as the characterization of the shifts between strategies. Practically, this paper discusses implications for system designers, publishers, and support providers to better meet the needs of this specific group. A primary limitation is related to isolating the variables of language, culture, and geography from other possible factors such as domain knowledge, system knowledge, or limitations of the systems being used.Originality/value– This study fills a gap in current research in relation to how language plays a role in the selection of and shifts between information seeking strategies used by scholars who rely on sources that are not in English.
The functional requirements for community information
Authors: Hider Philip 
Published: December 2015

Purpose
– The purpose of this paper is to consider the nature of community information (CI) and proposes a data model, based on the entity-relationship approach adopted in the Functional Requirements for Bibliographic Records (FRBR), which may assist with the development of future metadata standards for CI systems.

Design/methodology/approach
– The two main data structure standards for CI, namely the element set developed by the Alliance of Information and Referral Systems (AIRS) and the MARC21 Format for CI, are compared by means of a mapping exercise, after which an entity-relationship data model is constructed, at a conceptual level, based on the definitions of CI found in the literature.

Findings
– The AIRS and MARC21 data structures converge to a fair degree, with MARC21 providing for additional detail in several areas. However, neither structure is systematically and unambiguously defined, suggesting the need for a data model. An entity-relationship data modelling approach, similar to that taken in FRBR, yielded a model that could be used as the basis for future standards development and research. It was found to effectively cover both the AIRS and MARC21 element sets.

Originality/value
– No explicit data model exists for CI, and there has been little discussion reported about what data elements are required to support CI seeking.
Relaxing effect of a new ruthenium complex nitric oxide donor on airway smooth muscle of an experimental model of asthma in rats
Authors: Castro Patrícia Ferreira da Silva , de Andrade Daniela Lobo , Reis Carolina de Fátima , Costa Sérgio Henrique Nascente , Batista Aline Carvalho , da Silva Roberto Santana , Rocha Matheus Lavorenti 
Published: December 2015

SummaryNO is a potent bronchodilator and NO‐donor compounds have demonstrated clinical significance for obstructive airway diseases. This study evaluated the relaxation mechanisms of two NO donors, a ruthenium compound (TERPY), and sodium nitroprusside (SNP), in rat tracheas with ovalbumin‐induced asthma (OVA group) and in another control group. The effect of TERPY and SNP was evaluated in tracheal rings in an isolated organ chamber. The contribution of K+ channels, sGC/cGMP pathway, phosphodiesterases, and extra and intracellular Ca2+ sources were analyzed. The TERPY and SNP‐induced tracheal smooth muscle relaxation in both groups. However, the maximum effect induced by TERPY was higher than that of SNP in both control (110.2 ± 3.2% vs 68.3 ± 3.1%, P < 0.001) and OVA groups (106.1 ± 1.5% vs 49.9 ± 2.7%, P < 0.001). In the control group, TERPY relaxation was induced by the activation of K+ channels and reduction of the calcium influx, while in the OVA group, these same effects were also brought about by TERPY, but with participation of the sGC/cGMP pathway. In both groups, SNP‐induced relaxation occurred through the activation of K+ channels, sGC/cGMP pathway and reduction of calcium influx. However, the activation of sGC pathway and reticular Ca2+‐ATPase seemed to be reduced in the OVA group. Furthermore, TERPY is capable of reversing the contraction of carbachol in asthmatic bronchioles. Finally, TERPY and SNP relaxation mechanisms were modified by asthma. SNP presented less relaxation than TERPY, which induced full relaxation with greater participation of K+ and Ca2+ fluxes through the membrane, thereby making TERPY a promising drug for reversing the narrowing of airways.
A Wider Range of Friends: Multi‐speed Organising during the 2015 Labour Leadership Contest
Authors: Garland Jessica 
Published: December 2015

AbstractThe British Labour party's recent adoption of a partially open primary for the selection of its leader conforms to a trend seen across many European political parties of increasing rights and privileges in internal party decision‐making and expanding opportunities for more loosely affiliated supporters to participate in party activity. This dual trend can be seen as a response to changes in the membership environment, greater individualisation of political participation and growth in social movement politics and online activism. Yet as much as parties are responding to a changed membership environment, they are also driving that change, increasingly blurring the distinction between members and supporters. This article examines the recent impact of this change within the British Labour party and argues that, in line with Susan Scarrow's theory of ‘multi‐speed’ membership, the Labour party's experiment in expanding affiliation options has led directly to a tension in locating the source of authority within the party, creating a challenge for its new leader in accommodating his new supporters within his party's representative traditions.
Risk of postnatal depression or suicide after in vitro fertilisation treatment: a nationwide case–control study
Authors: Vikström J , Sydsjö G , Hammar M , Bladh M , Josefsson A 
Published: December 2015

ObjectiveTo examine whether women who undergo in vitro fertilisation (IVF) treatment are at greater risk of postnatal suicide or postnatal depression (PND) requiring psychiatric care, compared with women who conceive spontaneously.DesignCase–control study using data from national registers.SettingSweden during the period 2003–2009.PopulationCases were 3532 primiparous women who had given birth following IVF treatment. An aged‐matched control group of 8553 mothers was randomly selected from the medical birth register.MethodsLogistic regression analyses were performed with PND as the outcome, and with known risk factors of PND as well as IVF/spontaneous birth as covariates.Main outcome measuresPostnatal depression (PND), defined as diagnoses F32–F39 of the tenth edition of the International Classification of Diseases (ICD–10), within 12 months of childbirth.ResultsInitial analyses showed that PND was more common in the control group than in the IVF group (0.8 versus 0.4%; P = 0.04); however, these differences disappeared when confounding factors were controlled for. A history of any psychiatric illness (P = 0.000; odds ratio, OR = 25.5; 95% confidence interval, 95% CI = 11.7–55.5), any previous affective disorder (P = 0.000; OR = 26.0; 95% CI = 10.5–64.0), or specifically a personality disorder (P = 0.028; OR = 3.8; 95% CI = 1.2–12.7) increased the risk of PND. No woman in either group committed suicide during the first year after childbirth.ConclusionsWhereas mothers who receive IVF treatment are not at increased risk of PND, the risk is increased among mothers with a history of mental illness.Tweetable abstractA Swedish study on 3532 women showed that IVF treatment does not increase the risk of postnatal depression.
Effects of Advice on Effectiveness and Efficiency of Tax Planning Tasks
Authors: Pinto Odette M. 
Published: December 2015

AbstractSupervisory advice is generally given to tax professionals in public accounting firms before they commence tax planning tasks. The objectives of giving advice are to achieve effectiveness and efficiency in tax planning, as well as for training tax professionals. An experiment with 54 tax professionals, from accounting firms across Canada, was conducted to determine the effects of supervisory advice on effectiveness and efficiency in performing tax planning tasks of different complexity. Advice results in lower effectiveness in lower‐complexity tasks, as evidenced by more technically inadequate tax plans, signs of confusion and overdetermined solutions (i.e., unnecessary information in the tax plans). In higher‐complexity cases, the results suggest a limited improvement in effectiveness, as evidenced by more technically adequate plans, but at a cost of limiting insightful judgment. On the other hand, advice results in limited gains in efficiency for both the lower and higher‐complexity tasks. This study extends the advice and tax literatures by investigating the role of advice in the performance of tax planning tasks of different complexity, which has not been examined in other research. This study also contributes to tax practice, as public accounting firms should consider the limited gains in efficiency with the decrease in effectiveness for lower‐complexity tasks and the potential to limit insightful judgment for higher complexity tasks. The results of this study suggest that firms face trade‐offs in achieving efficiency, effectiveness and the training objective.