bluuebunny/crossref_metadata_2025_split huggingface dataset:
SqueezeMeta, a highly portable, fully automatic metagenomic analysis pipeline
Authors: Tamames Javier , Puente-Sánchez Fernando 
Published: June 2018

AbstractThe improvement of sequencing technologies has allowed the generalization of metagenomic sequencing, which has become a standard procedure for analysing the structure and functionality of microbiomes. The bioinformatic analysis of the sequencing results poses a challenge because it involves many different complex steps. SqueezeMeta is a full automatic pipeline for metagenomics/metatranscriptomics, covering all steps of the analysis. SqueezeMeta includes multi-metagenome support allowing the co-assembly of related metagenomes and the retrieval of individual genomes via binning procedures. SqueezeMeta features several unique characteristics: Co-assembly procedure or co-assembly of unlimited number of metagenomes via merging of individual assembled metagenomes, both with read mapping for estimation of the abundances of genes in each metagenome. It also includes binning and bin checking for retrieving individual genomes. Internal checks for the assembly and binning steps inform about the consistency of contigs and bins. Also, the results are stored in a mySQL database, where they can be easily exported and shared, and can be inspected anywhere using a flexible web interface allowing the easy creation of complex queries.We illustrate the potential of SqueezeMeta by analyzing 32 gut metagenomes in a fully automatic way, allowing to retrieve several millions of genes and several hundreds of genomic bins.One of the motivations in the development of SqueezeMeta was producing a software capable to run in small desktop computers, thus being amenable to all users and all settings. We were also able to co-assemble two of these metagenomes and complete the full analysis in less than one day using a simple laptop computer, illustrating the capacity of SqueezeMeta to run without high-performance computing infrastructure. SqueezeMeta is a complete system covering all steps in the analysis of metagenomes and metatranscriptomes, capable to work even in scarcity of computational resources. It is therefore adequate for in-situ, real time analysis of metagenomes produced by nanopore sequencing.SqueezeMeta can be downloaded from https://github.com/jtamames/SqueezeMeta
Mind-wandering in Parkinson’s disease hallucinations reflects primary visual and default network coupling
Authors: Walpola Ishan C. , Muller Alana J. , Hall Julie M. , Andrews-Hanna Jessica R. , Irish Muireann , Lewis Simon J. G. , Shine James M. , O’Callaghan Claire 
Published: June 2018

AbstractA mismatch between top-down expectations and incoming sensory information is thought to be associated with hallucinations across a range of neuropsychiatric disorders. In Parkinson’s disease with visual hallucinations, abnormal activity within the default network, and its pattern of connectivity with early visual regions, has been identified as a potential pathological source of the internally generated expectations that override incoming sensory input. In the context of attention deficits and visual dysfunction, mental imagery and perceptual expectancies generated across the default network are suggested to exert excessive influence over earlier visual regions, leading to aberrant perceptual experiences. Whilst converging neuroimaging evidence has identified unconstrained default network activity in Parkinson’s disease with hallucinations, to date there has been a lack of behavioural evidence to confirm the consequences of an over-engaged default mode network – therefore the contributions it might make to hallucination phenomenology remain speculative. To address this, we administered a validated thought-sampling task to 38 Parkinson’s disease patients (18 with hallucinations; 20 without) and 40 controls, to test the hypothesis that individuals with hallucinations experience an increased frequency of mind-wandering – a form of spontaneous cognition strongly associated with mental imagery and default network activity. The neural correlates of mind-wandering frequency were examined in relation to resting-state functional connectivity. Our results showed that patients with hallucinations exhibited significantly higher mind-wandering frequencies compared to non-hallucinators, who in turn had reduced levels of mind-wandering relative to controls. Inter-network connectivity and seed-to-voxel analyses confirmed that increased mind-wandering in the hallucinating vs. non-hallucinating group was associated with greater coupling between the primary visual cortex and dorsal default network. Taken together, both elevated mind-wandering and increased default-visual network coupling emerged as a distinguishing feature of the hallucinatory phenotype. We propose that the finding of increased mind-wandering reflects unconstrained spontaneous thought and mental imagery, which in turn furnish the content of visual hallucinations. Our findings suggest that primary visual cortex to dorsal default network coupling may provide a neural substrate by which regions of the default network exert disproportionate influence over ongoing visual perception. These findings refine current models of visual hallucinations by identifying a specific cognitive phenomenon and neural substrate consistent with the top-down influences over perception that have been implicated in visual hallucinations.
Supporting progression to HE: the role of colleges and vocational courses
Authors: Gartland Clare Elizabeth , Smith Christine 
Published: June 2018

Purpose
Vocational courses in England support the progression to higher education (HE) of large numbers of young people from disadvantaged backgrounds, yet there is little research exploring the college experiences of these young people prior to entering university. The purpose of this paper is to consider the experiences of young people on Level 3 Business and Technology Education Council (BTEC) vocational courses in their progression to HE from differently positioned post-16 colleges in England.

Design/methodology/approach
A qualitative study was undertaken into the experiences of students on BTEC courses in four subject clusters (science, technology, engineering and maths, arts and humanities, social sciences and health) at both a Further Education College and a Sixth Form College in an area of multiple deprivation and low HE participation. Young people’s experiences of BTEC courses and the support and guidance they receive are explored through the conceptual lens of “possible selves” and using Bourdieu’s ideas of capital, habitus and field.

Findings
Pedagogies and practices on BTEC courses are found to support the development of relevant social and cultural capital and help young people formulate well-articulated “possible selves” as university students, even amongst students who previously had not considered university as an option. The findings illustrate how differently positioned colleges support students’ progression and identify challenges presented by an increasingly stratified and marketised system.

Originality/value
The study highlights the transformative potential of BTEC courses and their role in supporting progression to HE amongst young people from economically disadvantaged backgrounds. The current emphasis on standardisation and rigour as mechanisms to better equip students for HE neglects the unique contribution BTEC pedagogies and practices make to encouraging HE participation. A Bourdieusian and “possible selves” theoretical framework has provided new insights into these valuable learning processes.
Entrepreneurial orientation
Authors: Smith Brent , Jambulingam Thanigavelan 
Published: June 2018

Purpose
Scholarship in the entrepreneurship and marketing literatures has helped advance thinking about how health care organizations create value for companies and consumers. However, there is an ongoing need for empirical research; hence, the purpose of this paper is to examine how entrepreneurial orientation and customer orientation influence healthcare (retail pharmacy) industry performance.

Design/methodology/approach
Using a sample of the US retail pharmacies, the study applies partial least squares structural equation modeling to identify the direct and indirect effects of the entrepreneurial orientation constructs on company performance. The study also includes importance–performance analyses to prioritize for managers which orientations, dimensions and respective manifest items merit the most critical attention as contributors to pharmacy performance.

Findings
We find that the entrepreneurial orientation has a significant impact on customer orientation and company effectiveness. We also find that three dimensions – innovation, risk-taking, and proactiveness – exhibit stronger importance and performance than autonomy and competitive aggressiveness.

Research limitations/implications
While the present study employs data from firms of various sizes, it is limited to firms in the pharmacy industry. Although this study included established EO measures, one of the risk taking items was dropped from the final analysis. In certain research contexts, this result may or may not be consequential. Finally, this study employed nonfinancial measures for measuring performance. Using such measures is not uncommon and can offer insightful linkages to long-term organizational strategies in ways not afforded by conventional financial measures (Ittner and Larcker 2000); however, future research should, if possible, aim to capture financial and nonfinancial data.

Practical implications
In the dynamic healthcare environment, entrepreneurial pharmacies that have the ability to innovate, take risks and be proactive can provide superior customer orientation and hence better performance.

Social implications
Health care industry in general and pharmacies in particular have to be entrepreneurial to meet customer needs and hence the wellbeing of the society With the aging population and growth of complex diseases, pharmacies can provide better access to care delivery if they have entrepreneurial orientation.

Originality/value
In this study, partial least square modeling technique along with importance performance analysis was adopted for first time in this literature to identify key factors that contribute to EO. The findings will aid pharmacy managers to focus their initiatives on the three key dimensions to succeed in their retail pharmacy business.
The trade and income effects of RCEP: implications for China and Korea
Authors: Li Qiaomin , Moon Hee Cheol 
Published: June 2018

Purpose
The purpose of this paper is to simulate the effects of the Regional Comprehensive Economic Partnership (RCEP) on trade and income, with a particular interest in the effect on China and Korea.

Design/methodology/approach
This paper adopts a Computable General Equilibrium (CGE) model developed by Li et al. (2017) to simulate the effect of RCEP. The CGE model is grounded in the firm heterogeneity theory. Within this framework, the feature of dynamic movements of firms allows the CGE model to capture the extensive margin of trade increase. Aside from that, the CGE model separates foreign direct investment (FDI) from domestic investment, which helps to explain the effect of the removal of FDI barriers.

Findings
Results show that RCEP will increase trade of China by 1.5 percent. The income of China will increase by 2.5 percent. The trade increase of Korea will be $8bn, and its income will increase by 0.6 percent. In terms of welfare, China will gain $214bn and Korea will gain $23~35bn, taking 2~3 percent of Korea’s GDP. Also, the reduction of behind-the-border barriers presents very significant effects.

Originality/value
The main contribution of this paper is to quantitatively assess the potential effects of RCEP on trade and income. The positive findings would propel RCEP parties, especially China and Korea, to reach an agreement as soon as possible.
From “clientilism” to transformational leadership? An autoethnographic journey from Soviet Georgia to the UK
Authors: Beattie Liana 
Published: June 2018

Purpose
The purpose of this paper is to contribute to the ethnographic tradition in the educational leadership literature through providing an autoethnographic critical analysis of the idiosyncrasies of leadership across two different socio-political environments: a Soviet educational establishment and a contemporary UK higher education institution.

Design/methodology/approach
In a previous issue, Doloriert and Sambrook (2012) argued that autoethnographic approach could help to uncover some experiences and voices that previously were silenced due to the discomfort they caused. In response to this claim and with consideration of three epistemological possibilities of autoethnography as suggested by Doloriert and Sambrook (2012), the author uses narrative accounts of personal experiences of leadership in Soviet Georgia and in the UK as the main source of data in the attempt to demonstrate how the three epistemological positions overlap and complement each other in the context of a critical autoethnography.

Findings
The paper argues that autoethnographic approach can provide a unique opportunity for a simultaneous analysis of the particularities of leadership practice across different socio-political environments, whereas the “three positions” approach could be used as an expedient template for further exploration of educational leadership. The paper also suggests there are some parallels between current leadership practice in the UK higher education and Soviet system of “clientilism”.

Originality/value
This paper is one of the first attempts to use autoethnography as an analytical tool for comparing leadership patterns in two contrasting socio-political structures.
How CSR impact meaning of work and dysfunctional customer behavior
Authors: Kim Jiyoung , Kim Hae-Ryong , Lacey Russell , Suh Jaebeom 
Published: June 2018

Purpose
The purpose of this paper is to investigate how frontline service employees’ (FSEs) perceptions of corporate social responsibility (CSR) can enhance meaningful work perceptions as well as help alleviate FSEs’ perceptions of verbal dysfunctional customer behavior.

Design/methodology/approach
The conceptual model is empirically examined through a survey of 306 FSEs of a large insurance company in South Korea and tested via structural equation modeling.

Findings
The results indicate that FSEs’ perceptions of CSR are negatively related to their perceptions of verbal dysfunctional customer conduct, which in turn is shown to be directly linked to emotional exhaustion. FSEs’ CSR perceptions strengthen their view that they are performing meaningful work (i.e. perceived task significance), which in turn strengthens their job satisfaction.

Practical implications
CSR has a preventive effect on workplace stress reduction, as FSE perceptions of CSR may help them cope with the emotional fatigue of dealing with dysfunctional customer behavior. CSR also provides a needs fulfillment effect, as FSEs’ perceptions of CSR foster perceived task significance and helps reduce their emotional exhaustion from work.

Originality/value
This is the first study to examine the potential impact of CSR within the context of FSEs’ boundary spanning emotional labor.
SME ambidexterity during economic recessions: the role of managerial external capabilities
Authors: Alcalde-Heras Henar , Iturrioz-Landart Cristina , Aragon-Amonarriz Cristina 
Published: June 2018

PurposeMost literature on ambidexterity has focused on large firms and on the influence of internal issues in this strategy, that is, organizational structures, top management integration, or internal knowledge management processes (Lutbatkinet al., 2006; Chang et al., 2011; Lee and Huang, 2012). The purpose of this paper is to assess small- to medium-sized enterprises (SMEs)’ ambidexterity strategies during economic recession periods in comparison with those of large firms and identify the managerial external capabilities which are associated with the development of SMEs’ ambidexterity.Design/methodology/approachA multinomial logit model and a probit model are proposed and tested using data collected from 2,150 Spanish firms during the period of 2009-2013.FindingsThe data analysis reveals that SMEs develop more ambidextrous innovation strategies in recession periods than larger firms do. Moreover, two managerial external capabilities have been identified as drivers of SMEs’ ambidextrous behavior in crisis periods: first, the capability of top management to anticipate scenarios; and second, the capacity to acquire adequate external resources through co-operation.Practical implicationsThe results show that SME managers wanting to develop ambidextrous strategies in recession periods have to forecast scenarios in terms of innovation difficulties and strengthen their resources through co-operation. Implementation of public policy is encouraged to support these capabilities, thus enhancing SME sustainability in uncertain contexts.Originality/valuePrior studies have paid little attention to the role of external capabilities. Although their role was revealed as a relevant dimension in the study of SME ambidexterity in adverse contexts by Caoet al.(2010), it remained underexplored. This paper aims to fill this gap.
Public–Private Partnerships and the Design Process: Consequences for Architects and City Building
Authors: van den Hurk Martijn , Siemiatycki Matti 
Published: June 2018

AbstractGovernments are increasingly using public–private partnerships (PPPs) to deliver public infrastructures and facilities. The prime motivation to embark on these partnerships is often to deliver products and services on time and on budget. It is generally assumed that by transferring project risks and responsibilities to private‐sector actors, governments can achieve better value for money. This article provides a novel perspective on the standards applied in PPP endeavors as it examines the tensions between the public management rationale behind value for money on the one hand, and conceptions of design and city building on the other. We focus on planning practice in the Canadian province of Ontario to show that governments apply different understandings of value in PPPs which, in turn, affect the way the design process is run. Architects, who are used to playing the role of master builder in a traditional public infrastructure project, are shifted into a less influential position and struggle with their new role. Furthermore, a different set of priorities applies in the new procurement process. The increasing use of PPPs can thus have significant consequences for city building.
Surgery in ovarian cancer – Brazilian Society of Surgical Oncology consensus
Authors: Tsunoda AT , Ribeiro R , Reis RJ , da Cunha Andrade CEM , Moretti Marques R , Baiocchi G , Fin F , Zanvettor PH , Falcao D , Batista TP , Azevedo BRB , Guitmann G , Pessini SA , Nunes JS , Campbell LM , Linhares JC , Carneiro V , Coimbra FJF 
Published: June 2018

Surgical management in epithelial ovarian cancer (EOC) has a significant impact in overall survival and progression‐free survival. The Brazilian Society of Surgical Oncology (BSSO) supported a taskforce of experts to reach a consensus: experienced and specialised trained surgeons, in cancer centres, provide the best EOC surgery. Laparoscopic and/or radiological staging prognosticates the possibility of complete cytoreduction (CC0) and helps to reduce unnecessary laparotomies. Surgical techniques were reviewed. Multidisciplinary input is essential for treatment planning. Quality assurance criteria are proposed and require national consensus. Genetic testing is mandatory. This consensus states the final recommendations from BSSO for management of EOC.Tweetable abstractBrazilian Society of Surgical Oncology consensus for surgery in epithelial ovarian cancer patients.
Would an RRS by any other name sound as RAD?
Authors: Campbell Erin O. , Brunet Bryan M. T. , Dupuis Julian R. , Sperling Felix A. H. 
Published: June 2018

Abstract

Sampling markers throughout a genome with restriction enzymes emerged in the 2000s as reduced representation shotgun sequencing (RRS). Rapid advances in sequencing technology have since spurred modifications of RRS, giving rise to many derivatives with unique names, such as restriction site‐associated DNA sequencing (RADseq). But naming conventions have often been more creative than consistent and criteria for recognizing unique methods have been unclear, resulting in a proliferation of names characterized by ambiguity.

We give an overview of methodological and etymological relationships among 36 restriction enzyme‐based methods, and survey the consistency of references to five prominent methods in the literature.

We identified several instances of methodological convergence, and note that many published derivatives have modified only minor elements of parent protocols. Misattribution through ambiguous or inconsistent literature references was observed in 8.4% of journal articles citing the original one and two‐enzyme RADseq and GBS, as well as SBG publications.

The rapid expansion of names associated with derivative protocols is confusing and, in many cases, unwarranted. We urge greater restraint in naming derivative methods and suggest general guidelines for naming that promote a balance between clarity, descriptiveness, and recognition of scientific innovation.
Chains of Love? Global Production and the Firm‐Level Diffusion of Labor Standards
Authors: Malesky Edmund J. , Mosley Layna 
Published: June 2018

AbstractUnder what conditions does the global economy serve as a means for the diffusion of labor standards and practices? We anticipate variation among internationally engaged firms in their propensity to improve labor standards. Upgrading is most likely when a firm's products exhibit significant cross‐market differences in markups, making accessing high‐standards overseas markets particularly profitable. Additionally, upgrading is more likely when lead firms attach a high salience to labor standards. Therefore, while participation in global production induces “trading up” behaviors among firms overall, the effect strength varies across industries. We test our expectations via a survey experiment, which queries foreign firms operating in Vietnam about their willingness to invest in labor‐related upgrading. We find strong evidence for the effect of markups on upgrading choices and suggestive evidence for the saliency mechanism.