bluuebunny/crossref_metadata_2025_split huggingface dataset:
IPCAPS: an R package for iterative pruning to capture population structure
Authors: Chaichoompu Kridsadakorn , Yazew Fentaw Abegaz , Tongsima Sissades , Shaw Philip James , Sakuntabhai Anavaj , Pereira Luísa , Van Steen Kristel 
Published: September 2017

AbstractBackgroundResolving population genetic structure is challenging, especially when dealing with closely related or geographically confined populations. Although Principal Component Analysis (PCA)-based methods and genomic variation with single nucleotide polymorphisms (SNPs) are widely used to describe shared genetic ancestry, improvements can be made especially when fine-scale population structure is the target.ResultsThis work presents an R package called IPCAPS, which uses SNP information for resolving possibly fine-scale population structure. The IPCAPS routines are built on the iterative pruning Principal Component Analysis (ipPCA) framework that systematically assigns individuals to genetically similar subgroups. In each iteration, our tool is able to detect and eliminate outliers, hereby avoiding severe misclassification errors.ConclusionsIPCAPS supports different measurement scales for variables used to identify substructure. Hence, panels of gene expression and methylation data can be accommodated as well. The tool can also be applied in patient sub-phenotyping contexts. IPCAPS is developed in R and is freely available frombio3.giga.ulg.ac.be/ipcaps
Rapid seasonal evolution in innate immunity of wildDrosophila melanogaster
Authors: Behrman Emily L. , Howick Virginia M. , Kapun Martin , Staubach Fabian , Bergland Alan O. , Petrov Dmitri A. , Lazzaro Brian P. , Schmidt Paul S. 
Published: September 2017

AbstractUnderstanding the rate of evolutionary change and the genetic architecture that facilitates rapid adaptation is a current challenge in evolutionary biology. Comparative studies show that genes with immune function are among the most rapidly evolving genes in a range of taxa. Here, we use immune defense in natural populations ofD. melanogasterto understand the rate of evolution in natural populations and the genetics underlying the rapid change. We probed the immune system using the natural pathogensEnterococcus faecalisandProvidencia rettgerito measure post-infection survival and bacterial load of wildD. melanogasterpopulations collected across seasonal time along a latitudinal transect on the eastern North America (Massachusetts, Pennsylvania, and Virginia). There are pronounced and repeatable changes in the immune response over approximately 10 generations between the spring and fall populations with a significant but less distinct difference among geographic locations. Genes with known immune function are not enriched among alleles that cycle with seasonal time, but the immune function of a subset of seasonally cycling alleles in immune genes was tested using reconstructed outbred populations. We find that flies containing seasonal alleles inThioester-containing protein 3 (Tep3)have different functional responses to infection and that epistatic interactions among seasonalTep3andDrosomycin-like 6 (Dro6)alleles produce the immune phenotypes observed in natural populations. This rapid, cyclic response to seasonal environmental pressure broadens our understanding of the complex ecological and genetic interactions determining the evolution of immune defense in natural populations.
A minimalist approach to protein identification
Authors: Sampath G. 
Published: September 2017

AbstractComputations on proteome sequence databases show that most proteins can be identified from a protein’s isoelectric point (IEP) and digitized linear sequence volume (equal to the total volume of its residues). This is illustrated with four proteomes:H. pylori(1553 proteins),E. coli(4306 proteins),S. cerevisiae(6721 proteins), andH. sapiens(20207 proteins); the identification rate exceeds 90% in all four cases for appropriate parameter values. IEP can be obtained with 1-d gel electrophoresis (GE), whose accuracy is better than 0.01. Linear protein sequence volumes of unbroken proteins can be obtained with a sub-nanometer diameter nanopore that can measure residue volume with a resolution of 0.07-0.1 nm3(Kennedy et al.,Nature Nanotech., 2016,11, 968-976; Dong et al.,ACS Nano, 2017, doi: 10.1021/acsnano.6b08452); the blockade current due to a translocating protein is roughly proportional to the volume it excludes in the pore. There is no need to identify any of the residues. More than 90% of all the proteins have estimated translocation times higher than 1 μs, which is within the time resolution of available detectors. This is a minimalist proteolysis-free GE-and nanopore-based single-molecule approach requires very small samples, is non-destructive (the sample can be recovered for reuse), and can be translated with currently available technology into a portable device for possible use in the field, an academic lab, or a pre-screening step preceding conventional mass spectrometry.
Researcher vs advocate: ethnographic-ethical dilemmas in feminist scholarship
Authors: Jain Tania 
Published: September 2017

PurposeThe purpose of this paper is to explore the nature of dilemmas that emerge at the theoretical and practical interfaces of ethnographic fieldwork and feminist advocacy. This is done by examining the researcher’s role in the field and the complex relationships between the researcher and the researched.Design/methodology/approachCritical self-reflections and autoethnographic analyses of fieldwork experiences in the author’s home country in South Asia are used to explore these dilemmas.FindingsUsing situated examples from a typical organisational setting involving both the oppressive and the oppressed, the researcher’s participant observation is found to be conflicted between critical participation and critical observation. Conscious and/or unconscious critical participation through enactment of feminist ethics by combining researcher and advocacy roles allows a route to assuage these conflicts. Practical strategies used to accomplish this are also discussed.Research limitations/implicationsAlthough the practical strategies discussed in this paper are culturally and organisationally specific and hence limited by them, it is hoped that suitable variants will emerge for readers from their discussion. Further research is needed to investigate the variety of ways in which the researcher-advocate positionality proposed in this paper can be strategically adopted conditional on cultural and organisational contexts, feminist research questions, and researchers’ abilities and constraints.Practical implicationsThis paper seeks to shed light on the dilemmas of feminist ethics faced by critical feminist researchers conducting ethnographic fieldwork. It also discusses ways to enable researchers to circumvent these dilemmas in both epistemologically productive ways by collecting rich data and in ontologically enriching ways by allowing some enactment of feminist ethics. To this end, a positionality of the feminist researcher-advocate is conceptualised that does not enforce constraints of extreme positionalities of either a conventional ethnographer or an action researcher.Social implicationsBesides illustrating the need to stretch beyond traditional boundaries of participant observation, the researcher-advocate positionality also allows feminist researchers to make small, but directly tangible impact towards gender equality in their field setting. Implications for researchers’ emotional, and cognitive safety are also discussed especially when they identify with one or more minority identities.Originality/valueThis paper contributes to discussions on the theory of methods by highlighting the benefits of enacting feminist ethics as a way of critical participation in research settings.
Meezan Bank: category leader in Islamic banking
Authors: Gul Rashid Amber , Usmani Obaid , Ejaz Lalarukh , Faraz Hasan 
Published: September 2017

Subject area
Islamic Banking has been in the limelight since the recession of 2008. Although around for a long time, it is enjoying a renaissance of sorts. This case provides an introduction.

Study level/applicability
EMBA and/or MBA introduction to banking, senior semester undergraduate, specialization in Islamic Banking.

Case overview
This case is written in the form of an interview with Meezan Bank, one of the leading financial institutions in the Islamic banking sector. It is based on primary as well as secondary data obtained via interviews and documentary analysis.

Expected learning outcomes
This is an analytical case and not a decision-making one. The main theme of the case revolves around analysing what Islamic banking is, the challenges that Meezan has faced, the pros and cons of doing business this way and the future issues it can face.

Supplementary materials
Teaching Notes are available for educators only. Please contact your library to gain login details or email support@emeraldinsight.com to request teaching notes.

Subject code
CSS 7: Management Science.
Storytelling and innovative behavior: an empirical study in a Brazilian group
Authors: D’Arrigo Fernanda Pauletto , Robini Eduardo , Larentis Fabiano , Camargo Maria Emilia , Schmiedgen Peter 
Published: September 2017

PurposeThe paper aims to identify the relationship between the use of storytelling and innovative work behavior (IWB) in organizations.Design/methodology/approachThe research took place in a human resource development (HRD) training session for leaders of Alpha Group. In this session, storytelling was adopted to discuss innovation and IWB. Following the training, the leaders completed a questionnaire about the effectiveness of the stories for the construction of knowledge and IWB. Data were collected from 97 leading sectors. Subsequently, data analysis was performed to identify correlations between the aspects.FindingsThe paper provides empirical insights about the use of storytelling, the effectiveness of the stories, as well as their relationship with the innovative behavior of sectors leaders in a Brazilian organization. It has identified the relation between effectiveness of stories and level of innovative behavior.Research limitations/implicationsOwing to the chosen research approach, the research results cannot be generalized. Because it is a study of a single organization, the results concern to the reality experienced in the organization studied. Therefore, researchers are encouraged to test this relationship in other organizations to contribute to the discussion and practice of innovation in HRD.Practical implicationsStories can contribute to innovative behavior, and innovative behavior contributes to helping understand the stories. HRD practitioners can provide the use of storytelling, combined with other forms of interventions, to enhance IWB to promote collaborative learning culture and work engagement.Originality/valuePrevious papers have identified the role of HRD in the development of IWB in organizations. Theoretically, previous papers have also highlighted that storytelling can be a tool for the development of innovative behavior. The paper empirically has tested these contributions, identifying emerging aspects of this relationship.
Does reflective supervision have a future in English local authority child and family social work?
Authors: Wilkins David 
Published: September 2017

Purpose
The purpose of this paper is to discuss the underlying assumption that social workers need reflective supervision specifically, as opposed to managerial or any other form of supervision or support, and to consider whether our focus on the provision of reflective supervision may be preventing us from thinking more broadly and creatively about what support local authority child and family social workers need and how best to provide it.

Design/methodology/approach
The paper provides an argument based on the author’s own research and a selective review of the literature.

Findings
Reflective supervision has no future in local authority child and family social work because: first, there is no clear understanding of what reflective supervision is; second, there is no clear evidence for its effectiveness; and third, sizeable proportion of local authority child and family social workers in England do not receive reflective supervision and many never have.

Originality/value
The paper challenges the received wisdom about the value of reflective supervision and advocates exploring alternative models for supporting best practice in child and family social work.
Does past failure inhibit future entrepreneurial intent? Evidence from Ghana
Authors: Acheampong George , Tweneboah-Koduah Ernest Yaw 
Published: September 2017

Purpose
The purpose of this paper is to examine the relationship between past entrepreneurial failure and future entrepreneurial intentions. It also considers the moderating role of past entrepreneurial failure on the relationship between attitude, subjective norms and perceived behavioural control (PBC) and entrepreneurial intentions.

Design/methodology/approach
Data from the Ghana Global Entrepreneurship Monitor Adult Population Survey (2013) are used to test the hypotheses developed after an extensive literature review. The empirical specification was estimated with a probit of standard form and marginal derivatives estimated for the purposes of interpretation.

Findings
The mean future entrepreneurial intent is 63.2 per cent of the sample with 75 per cent having failed in the past and 60 per cent never failed before. Also, only 20.9 per cent of the interviewed entrepreneurs have failed at a past entrepreneurial activity. Past entrepreneurial failure has a positive effect on future entrepreneurial intentions. The interaction between attitude and failure yields a positive effect on future entrepreneurial intentions. The same effects can be reported for the interactions between subjective norms and failure as well as PBC and failure.

Originality/value
In this study, the authors are able to show that the mean moderational effects are important but they can be deceptive. Rather, a decomposition helps the authors to disaggregate these effects to better understand the underlying mechanisms.
Novel insights on population and range edge dynamics using an unparalleled spatiotemporal record of species invasion
Authors: Grayson Kristine L. , Johnson Derek M. 
Published: September 2017

AbstractQuantifying the complex spatial dynamics taking place at range edges is critical for understanding future distributions of species, yet very few systems have sufficient data or the spatial resolution to empirically test these dynamics. This paper reviews how data from a large‐scale pest management programme have provided important contributions to the fields of population dynamics and invasion biology.The invasion of gypsy moth (Lymantria dispar) is well‐documented from its introduction near Boston, MassachusettsUSAin 1869 to its current extent of over 900,000 km2in Eastern North America. Over the past two decades, theUSDAForest Service Slow the Spread (STS) programme for managing the future spread of gypsy moth has produced unrivalled spatiotemporal data across the invasion front.TheSTSprogramme annually deploys a grid of 60,000–100,000 pheromone‐baited traps, currently extending from Minnesota to North Carolina. The data from this programme have provided the foundation for investigations of complex population dynamics and the ability to examine ecological hypotheses previously untestable outside of theoretical venues, particularly regarding invasive spread and Allee effects.This system provides empirical data on the importance of long‐distance dispersal and time‐lags on population establishment and spatial spread. Studies showing high rates of spatiotemporal variation of the range edge, from rapid spread to border stasis and even retraction, highlight future opportunities to test mechanisms that influence both invasive and native species ranges.TheSTStrap data have also created a unique opportunity to study low‐density population dynamics and quantify Allee effects with empirical data. Notable contributions include evidence for spatiotemporal variation in Allee effects, demonstrating empirical links between Allee effects and spatial spread, and testing mechanisms of population persistence and growth rates at range edges.There remain several outstanding questions in spatial ecology and population biology that can be tested within this system, such as the scaling of local ecological processes to large‐scale dynamics across landscapes. The gypsy moth is an ideal model of how important ecological questions can be answered by thinking more broadly about monitoring data.
Fundamental niche prediction of the pathogenic yeasts Cryptococcus neoformans and Cryptococcus gattii in Europe
Authors: Cogliati Massimo , Puccianti Erika , Montagna Maria T. , De Donno Antonella , Susever Serdar , Ergin Cagri , Velegraki Aristea , Ellabib Mohamed S. , Nardoni Simona , Macci Cristina , Trovato Laura , Dipineto Ludovico , Rickerts Volker , Akcaglar Sevim , Mlinaric‐Missoni Emilija , Bertout Sebastien , Vencà Ana C.F. , Sampaio Ana C. , Criseo Giuseppe , Ranque Stéphane , Çerikçioğlu Nilgün , Marchese Anna , Vezzulli Luigi , Ilkit Macit , Desnos‐Ollivier Marie , Pasquale Vincenzo , Polacheck Itzhack , Scopa Antonio , Meyer Wieland , Ferreira‐Paim Kennio , Hagen Ferry , Boekhout Teun , Dromer Françoise , Varma Ashok , Kwon‐Chung Kyung J. , Inácio Joäo , Colom Maria F. 
Published: September 2017

SummaryFundamental niche prediction of Cryptococcus neoformans and Cryptococcus gattii in Europe is an important tool to understand where these pathogenic yeasts have a high probability to survive in the environment and therefore to identify the areas with high risk of infection. In this study, occurrence data for C. neoformans and C. gattii were compared by MaxEnt software with several bioclimatic conditions as well as with soil characteristics and land use. The results showed that C. gattii distribution can be predicted with high probability along the Mediterranean coast. The analysis of variables showed that its distribution is limited by low temperatures during the coldest season, and by heavy precipitations in the driest season. C. neoformans var. grubii is able to colonize the same areas of C. gattii but is more tolerant to cold winter temperatures and summer precipitations. In contrast, the C. neoformans var. neoformans map was completely different. The best conditions for its survival were displayed in sub‐continental areas and not along the Mediterranean coasts. In conclusion, we produced for the first time detailed prediction maps of the species and varieties of the C. neoformans and C. gattii species complex in Europe and Mediterranean area.
Dissemination and loss of a biofilm‐related genomic island in marine Pseudoalteromonas mediated by integrative and conjugative elements
Authors: Wang Pengxia , Zeng Zhenshun , Wang Weiquan , Wen Zhongling , Li Jie , Wang Xiaoxue 
Published: September 2017

SummaryAcquisition of genomic islands (GIs) plays a central role in the diversification and adaptation of bacteria. Some GIs can be mobilized in trans by integrative and conjugative elements (ICEs) or conjugative plasmids if the GIs carry specific transfer‐related sequences. However, the transfer mechanism of GIs lacking such elements remains largely unexplored. Here, we investigated the transmissibility of a GI found in a coral‐associated marine bacterium. This GI does not carry genes with transfer functions, but it carries four genes required for robust biofilm formation. Notably, this GI is inserted in the integration site for SXT/R391 ICEs. We demonstrated that acquisition of an SXT/R391 ICE results in either a tandem GI/ICE arrangement or the complete displacement of the GI. The GI displacement by the ICE greatly reduces biofilm formation. In contrast, the tandem integration of the ICE with the GI in cis allows the GI to hijack the transfer machinery of the ICE to excise, transfer and re‐integrate into a new host. Collectively, our findings reveal that the integration of an ICE into a GI integration site enables rapid genome dynamics and a new mechanism by which SXT/R391 ICEs can augment genome plasticity.
Host‐microbe interaction in the gastrointestinal tract
Authors: Parker Aimée , Lawson Melissa A. E. , Vaux Laura , Pin Carmen 
Published: September 2017

SummaryThe gastrointestinal tract is a highly complex organ in which multiple dynamic physiological processes are tightly coordinated while interacting with a dense and extremely diverse microbial population. From establishment in early life, through to host‐microbe symbiosis in adulthood, the gut microbiota plays a vital role in our development and health. The effect of the microbiota on gut development and physiology is highlighted by anatomical and functional changes in germ‐free mice, affecting the gut epithelium, immune system and enteric nervous system. Microbial colonisation promotes competent innate and acquired mucosal immune systems, epithelial renewal, barrier integrity, and mucosal vascularisation and innervation. Interacting or shared signalling pathways across different physiological systems of the gut could explain how all these changes are coordinated during postnatal colonisation, or after the introduction of microbiota into germ‐free models. The application of cell‐based in‐vitro experimental systems and mathematical modelling can shed light on the molecular and signalling pathways which regulate the development and maintenance of homeostasis in the gut and beyond.
Genome‐wide analysis of bacterial determinants of plant growth promotion and induced systemic resistance by Pseudomonas fluorescens
Authors: Cheng Xu , Etalo Desalegn W. , van de Mortel Judith E. , Dekkers Ester , Nguyen Linh , Medema Marnix H. , Raaijmakers Jos M. 
Published: September 2017

SummaryPseudomonas fluorescens strain SS101 (Pf.SS101) promotes growth of Arabidopsis thaliana, enhances greening and lateral root formation, and induces systemic resistance (ISR) against the bacterial pathogen Pseudomonas syringae pv. tomato (Pst). Here, targeted and untargeted approaches were adopted to identify bacterial determinants and underlying mechanisms involved in plant growth promotion and ISR by Pf.SS101. Based on targeted analyses, no evidence was found for volatiles, lipopeptides and siderophores in plant growth promotion by Pf.SS101. Untargeted, genome‐wide analyses of 7488 random transposon mutants of Pf.SS101 led to the identification of 21 mutants defective in both plant growth promotion and ISR. Many of these mutants, however, were auxotrophic and impaired in root colonization. Genetic analysis of three mutants followed by site‐directed mutagenesis, genetic complementation and plant bioassays revealed the involvement of the phosphogluconate dehydratase gene edd, the response regulator gene colR and the adenylsulfate reductase gene cysH in both plant growth promotion and ISR. Subsequent comparative plant transcriptomics analyses strongly suggest that modulation of sulfur assimilation, auxin biosynthesis and transport, steroid biosynthesis and carbohydrate metabolism in Arabidopsis are key mechanisms linked to growth promotion and ISR by Pf.SS101.