bluuebunny/crossref_metadata_2025_split huggingface dataset:
Allele-Specific Quantification of Structural Variations in Cancer Genomes
Authors: Li Yang , Zhou Shiguo , Schwartz David C. , Ma Jian 
Published: April 2016

AbstractOne of the hallmarks of cancer genome is aneuploidy, resulting in abnormal copy numbers of alleles. Structural variations (SVs) can further modify the aneuploid cancer genomes into a mixture of rearranged genomic segments with extensive range of somatic copy number alterations (CNAs). Indeed, aneuploid cancer genomes have significantly higher rate of CNAs and SVs. However, although methods have been developed to identify SVs and allele-specific copy number of genome (ASCNG) separately, no existing algorithm can simultaneously analyze SVs and ASCNG. Such integrated approach is particularly important to fully understand the complexity of cancer genomes. Here we introduce a new algorithm called Weaver to provide allele-specific quantification of SVs and CNAs in aneuploid cancer genomes. Weaver uses a probabilistic graphical model by utilizing cancer whole genome sequencing data to simultaneously estimate the digital copy number and inter-connectivity of SVs. Our simulation evaluation, comparison with single-molecule Optical Mapping analysis, and real data applications (including MCF-7, HeLa, and TCGA whole genome sequencing samples) demonstrated that Weaver is highly accurate and can greatly refine the analysis of complex cancer genome structure.
Concordance Among Indices of Intrinsic Brain Function: Insights from Inter-Individual Variation and Temporal Dynamics
Authors: Yan Chao-Gan , Yang Zhen , Colcombe Stanley J. , Zuo Xi-Nian , Milham Michael P. 
Published: April 2016

ABSTRACTVarious resting-state fMRI (R-fMRI) measures have been developed to characterize intrinsic brain activity. While each of these measures has gained a growing presence in the literature, questions remain regarding the common and unique aspects these indices capture. The present work provided a comprehensive examination of inter-individual variation and intra-individual temporal variation for commonly used measures, including fractional amplitude of low frequency fluctuations, regional homogeneity, voxel-mirrored homotopic connectivity, network centrality and global signal correlation. Regardless of whether examining intra-individual or inter-individual variation, we found that these definitionally distinct R-fMRI indices tend to exhibit a relatively high degree of covariation, which doesn’t exist in phase randomized surrogate data. As a measure of intrinsic brain function, concordance for R-fMRI indices was negatively correlated with age across individuals (i.e., concordance among functional indices decreased with age). To understand the functional significance of concordance, we noted that higher concordance was generally associated with higher strengths of R-fMRI indices, regardless of whether looking through the lens of inter-individual (i.e., high vs. low concordance participants) or intra-individual (i.e., high vs. low concordance states identified via temporal dynamic analyses) differences. We also noted a linear increase in functional concordance together with the R-fMRI indices through the scan, which may suggest a decrease in arousal. The current study demonstrated an enriched picture regarding the relationship among the R-fMRI indices, as well as provided new insights in examining dynamic states within and between individuals.
Reversible Polymorphism-Aware Phylogenetic Models and their Application to Tree Inference
Authors: Schrempf Dominik , Minh Bui Quang , De Maio Nicola , von Haeseler Arndt , Kosiol Carolin 
Published: April 2016

AbstractWe present a reversible Polymorphism-Aware Phylogenetic Model (revPoMo) for species tree estimation from genome-wide data. revPoMo enables the reconstruction of large scale species trees for many within-species samples. It expands the alphabet of DNA substitution models to include polymorphic states, thereby, naturally accounting for incomplete lineage sorting. We implemented revPoMo in the maximum likelihood software IQ-TREE. A simulation study and an application to great apes data show that the runtimes of our approach and standard substitution models are comparable but that revPoMo has much better accuracy in estimating trees, divergence times and mutation rates. The advantage of revPoMo is that an increase of sample size per species improves estimations but does not increase runtime. Therefore, revPoMo is a valuable tool with several applications, from speciation dating to species tree reconstruction.
Variation and evolution of the glutamine-rich repeat region of Drosophila Argonaute-2
Authors: Palmer William H , Obbard Darren J 
Published: April 2016

AbstractRNA interference pathways mediate multiple biological processes through Argonaute-family proteins, which bind small RNAs as guides to silence complementary target nucleic acids. In insects and crustaceans,Argonaute-2silences viral nucleic acids, and therefore acts as a primary effector of innate antiviral immunity. Although the function of the major ofArgonaute-2domains, which are conserved across most Argonaute-family proteins, are known, many invertebrateArgonaute-2homologs contain a glutamine-rich repeat (GRR) region of unknown function at the N-terminus. Here we combine long-read amplicon sequencing of Drosophila Genetic Reference Panel (DGRP) lines with publicly available sequence data from many insect species to show that this region evolves extremely rapidly and is hypervariable within species. We identify distinct GRR haplotype groups inD. melanogaster, and suggest that one of these haplotype groups has recently risen to high frequency in North American populations. Finally, we use published data from genome-wide association studies of viral resistance inD. melanogasterto test whether GRR haplotypes are associated with survival after virus challenge. We find a marginally significant association with survival after challenge with Drosophila C Virus in the DGRP, but we were unable to replicate this finding using lines from the Drosophila Synthetic Population Resource panel.
Comparing online and in-store risks in multichannel shopping
Authors: BEZES Christophe 
Published: April 2016

PurposeThis paper compares empirically the nature, level and influence of perceived risks involved in a retailer’s website and stores, as multichannel shoppers will do when deciding which distribution channel to buy in.Design/methodology/approachThe research design uses an online survey of 1,015 multichannel customers that was drawn from the behavioural databases of a French multichannel retailer.FindingsOverall risk as well as risks associated with logistics, psychological and performance are higher and more dissuasive for an online purchase; however, financial, time and transaction risks tend predominantly or exclusively to discourage in-store purchasing. Customers’ familiarity with the channel seems to make them more vigilant.Research limitations/implicationsThe concept of risk, and especially financial risk, is variable among researchers, making it more difficult to undertake comparative studies on e-commerce than on stores or products.Practical implicationsRetailers should not look merely to the salience of an isolated risk factor but rather should consider its actual impact on their customers’ final decision. Nonetheless, retailers will find it more difficult to reduce perceived risk on-line than in-store.Originality/valueBy focussing on a multichannel retailer’s website and stores and comparing the effects of six types of risk on the purchase attitudes of its multichannel shoppers, this study is distinct from most single-channel studies, which have examined risk inherent in Internet purchasing, handled risk on an experimental website and explored in-store risk. Moreover, the study focuses on the risks entailed by the purchase channel rather than those related to particular products or brands.
Impact of environment on performance measurement design and processing in retailing
Authors: Harrauer Verena , Schnedlitz Peter 
Published: April 2016

Purpose
By focusing on the interface between information dissemination and interpretation at the retail sales floor, the paper aims to open up new practice theory contribution on management control and performance measurement used in complex environments.

Design/methodology/approach
Problem-centered qualitative interviews in two different contexts (U.S. and Europe) build the methodological approach. 22 interviewees were selected from various retail sectors and hierarchy levels with the focus on store management. Following content analysis procedures, data was coded according to contingency theoretical underpinnings.

Findings
Environment shapes corporate processes as well as retail management in multiple ways. By studying fast fashion industries, we found similarities in retail management in all researched settings. First, we present relevant operational performance metrics in the retailing context. Second, we see that store managers aim to optimize processes and generate efficient and effective practices to maximize store performance. Third, information and task overload are reasons for neglecting performance information. As a consequence, managers call for decision facilitating tools, e.g. dashboards, to reduce information complexity.

Originality/value
Widely accepted in contingency literature, environmental aspects influence business activities and performance outcomes. However, evaluating research studies that deal with performance measurement in retailing contexts reveals contradicting results. With the focus on larger retail companies with multibranch and department structures in two different national contexts we can unravel different perspectives on environment in operational retail settings for the first time.
The multi-channel impact on the sales forces management.
Authors: Lapoule Paul , Colla Enrico  Bruno 
Published: April 2016

Purpose
The primary objective of this qualitative research is to gain a deeper understanding of the multi-channel impact on the role of sales forces and the way in which they are managed in a B2B context.

Design/methodology/approach
The authors compare the conclusion of their literature review with an analysis of the sales strategy of a leading cosmetic brand. They conducted their study by applying a multi-method qualitative research approach, which includes semi-structured interviews with managers and a research action performed by accompanying five salespeople on visits to their professional clients.

Findings
The results suggest that the development of a multi-channel context encourages salespeople to focus less on sales and order taking and more on advising clients about how best to develop their businesses. The multi-channel evolution seems to have enabled a transition of the role of sales people from a sales function to a function of a provider of personalized advice in the fields of business development, team management, salon promotions and merchandising.

Research limitations/implications
The quest for coherence, particularly at the international level, would justify a broadening of our study to include the impact of multi-channels sales on the market positioning of the brand and of other brands in different industrial sectors.

Practical implications
The expansion of the multi-channel sales approach implies that managers are obliged to seek a convergence, or at least a degree of coherence between the different channels. This strategy can be used to promote an effective integration of channels at the international level into a single, reliable distribution system that avoids all forms of cannibalization.
The Omni-channel strategy implies shifting the emphasis in the channel and moving from a focus on direct sales to the professional client (“selling-in”) to a stress on direct sales to the end user (“selling-out”).

Originality/value
This article provides an original analytical approach to highlighting training methods and systems of remuneration that will help sales forces to manage the inter-channel migration of their customers. Salespeople will then be able to view the future Omni-channel context as an opportunity to improve the status of their role.
Mapping the field of educational administration research: a journal citation network analysis
Authors: Wang Yinying , Bowers Alex J. 
Published: April 2016

PurposeThe purpose of this study is to uncover how knowledge is exchanged and disseminated in the educational administration research literature through the journal citation network.Design/methodology/approachDrawing upon social network theory and citation network studies in other disciplines, we constructed an educational administration journal citation network by extracting all 157,372 citations from 5,359 journal articles in 30 educational administration journals from 2009 to 2013. We then performed social network analysis to visualize the network structure by journal clusters, and quantified journal prominence and interdisciplinarity by calculating Freeman indegree and betweenness, respectively. In addition to journal-to-journal citations, we examined the sources of non-journal citations by citation counts.FindingsThe results of journal prominence, interdisciplinarity, and eight journal clusters in the citation network indicate that educational administration, as a porous field, intimately interacts with the sub-fields of education (e.g., urban education and teacher education), other disciplines (e.g., economics, human resources, sociology, and psychology), and the research internationally. In addition to journals as the knowledge source (45.29%), we also found books (31.08%) and reports (14.98%) are important citation sources in the educational administration research literature. The most cited books and reports shed light on the knowledge base in the theory, research, and practice of educational administration.Originality/valueThe results of this by far the largest-scale study of educational administration journals present abundant evidence that educational administration is a porous field. This study also presents social network analysis as an alternative method to evaluate journal influence in the educational administration field.
Educational leadership effectiveness: a Rasch analysis
Authors: Sinnema Claire , Ludlow Larry , Robinson Viviane 
Published: April 2016

PurposeThe purposes of this study are, firstly, to establish the psychometric properties of the ELP tool, and, secondly, to test, using a Rasch item response theory analysis, the hypothesized progression of challenge presented by the items included in the tool.Design/methodology/approachData were collected at two time points through a survey of the educational leadership practices of school principals (n = 148) and their teachers (n = 5,425). The survey comprised seven effectiveness scales relating to school-wide dimensions of leadership, and one scale relating to the effectiveness of individual principals’ leadership. We undertook validation of the hypothesized structure of the eight ELP scales using the Rasch rating scale model.FindingsWe established constructs that underpin leadership practices that are more and less effectively performed and determined the nature of their progression from those that are relatively routine through those that are more rigorous and challenging to enact. Furthermore, a series of analyses suggest strong goodness-of-model fit, unidimensionality, and invariance across time and educator group for the eight ELP scalesResearch limitations/implicationsThis study focused on experienced principals - future studies could usefully include school leaders who are new to their role or compare leadership patterns of higher and lower performing schools. A useful future direction would be to investigate the predictive validity of the ELP tool.Practical implicationsOriginality/valueThis study reveals the ELP is a useful tool both for diagnosing leadership effectiveness and, given that it is essentially stable over time, may prove useful for charting the effectiveness of leadership development interventions.
Compressive sensing for noisy solder joint imagery based on convex optimization
Authors: Zhao Huihuang , Chen Jianzhen , Xu Shibiao , Wang Ying , Qiao Zhijun 
Published: April 2016

Purpose
The purpose of this paper is to develop a compressive sensing (CS) algorithm for noisy solder joint imagery compression and recovery. A fast gradient-based compressive sensing (FGbCS) approach is proposed based on the convex optimization. The proposed algorithm is able to improve performance in terms of peak signal noise ratio (PSNR) and computational cost.

Design/methodology/approach
Unlike traditional CS methods, the authors first transformed a noise solder joint image to a sparse signal by a discrete cosine transform (DCT), so that the reconstruction of noisy solder joint imagery is changed to a convex optimization problem. Then, a so-called gradient-based method is utilized for solving the problem. To improve the method efficiency, the authors assume the problem to be convex with the Lipschitz gradient through the replacement of an iteration parameter by the Lipschitz constant. Moreover, a FGbCS algorithm is proposed to recover the noisy solder joint imagery under different parameters.

Findings
Experiments reveal that the proposed algorithm can achieve better results on PNSR with fewer computational costs than classical algorithms like Orthogonal Matching Pursuit (OMP), Greedy Basis Pursuit (GBP), Subspace Pursuit (SP), Compressive Sampling Matching Pursuit (CoSaMP) and Iterative Re-weighted Least Squares (IRLS). Convergence of the proposed algorithm is with a faster rate O(k*k) instead of O(1/k).

Practical implications
This paper provides a novel methodology for the CS of noisy solder joint imagery, and the proposed algorithm can also be used in other imagery compression and recovery.

Originality/value
According to the CS theory, a sparse or compressible signal can be represented by a fewer number of bases than those required by the Nyquist theorem. The new development might provide some fundamental guidelines for noisy imagery compression and recovering.
Entrepreneurship success factors: an empirical investigation in Sri Lanka
Authors: Lussier Robert N , Bandara Chamara , Marom Shaike 
Published: April 2016

Purpose
To investigate small business success versus failure prediction variables in the emerging market of Sri Lanka.

Design/methodology/approach
Survey research was used to collect data in Sri Lanka with a sample size of 450 small businesses (200 failed and 250 successful) based on 10 of the 15 Lussier success versus failure prediction model variables.

Findings
The results reveal significant differences between all 10 successful and failed variables tested.

Practical implications
The findings indicate that small business owners and managers can benefit from starting their business with adequate capital, by maintaining good records with financial control, having prior business and management experience, developing a business plan, having higher levels of education, being able to staff the business, starting the business during the early stages of the product life cycle, having partners, and having marketing expertise.

Originality/value
This is the first major small business success versus failure study conducted in Sri Lanka. Results support the Lussier model’s validity in Sri Lanka, reinforcing its global validity and moving toward a theory; while demonstrating similarity to those in other economies. There is no accepted theory of success vs failure, thus this study is a foundation for further research and comparisons between developed countries and emerging markets.
Potential preventive effects of proactive therapy on sensitization in moderate to severe childhood atopic dermatitis: A randomized, investigator‐blinded, controlled study
Authors: Fukuie Tatsuki , Hirakawa Satoshi , Narita Masami , Nomura Ichiro , Matsumoto Kenji , Tokura Yoshiki , Ohya Yukihiro 
Published: April 2016

AbstractProactive therapy for atopic dermatitis (AD) effectively prevents exacerbation. However, its role in preventing subsequent sensitization to allergens has not been prospectively studied. We investigated whether proactive therapy for AD can effectively impact immunological parameters in a randomized, investigator‐blinded, parallel group study. Thirty patients aged 3 months to 7 years with moderate to severe AD who had undergone an AD educational program were allocated to a proactive treatment group or a reactive treatment group. During the disease control period, patients in the proactive group performed intermittent preventive application of topical corticosteroid for 1 year. Changes in the severity scoring, quality of life measures and immunological parameters (serum thymus and activation regulated chemokine [TARC], total immunoglobulin E [IgE] and house dust mite‐specific IgE levels) were evaluated and compared between the proactive and reactive treatment groups. Although the average topical corticosteroid ointment use per day in both groups was not significantly different, the severity and quality of life scores were significantly lower in the proactive group than in the reactive group at the final visit. In addition, compared with baseline levels, serum TARC levels remained significantly lower during proactive therapy, while house dust mite‐specific IgE levels were significantly increased only in the reactive group. The results suggest that in addition to controlling the severity of AD, intermittent preventive administration of topical corticosteroids may prevent an increase in aeroallergen‐specific IgE levels in patients with childhood AD. The use of TARC levels as a biomarker for AD remission is also supported.
Gluten‐Free Precooked Rice‐Yellow Pea Pasta: Effect of Extrusion‐Cooking Conditions on Phenolic Acids Composition, Selected Properties and Microstructure
Authors: Bouasla Abdallah , Wójtowicz Agnieszka , Zidoune Mohammed Nasereddine , Olech Marta , Nowak Renata , Mitrus Marcin , Oniszczuk Anna 
Published: April 2016

AbstractRice/yellow pea flour blend (2/1 ratio) was used to produce gluten‐free precooked pasta using a single‐screw modified extrusion‐cooker TS‐45. The effect of moisture content (28%, 30%, and 32%) and screw speed (60, 80, and 100 rpm) on some quality parameters was assessed. The phenolic acids profile and selected pasta properties were tested, like pasting properties, water absorption capacity, cooking loss, texture characteristics, microstructure, and sensory overall acceptability. Results indicated that dough moisture content influenced all tested quality parameters of precooked pasta except firmness. Screw speed showed an effect only on some quality parameters. The extrusion‐cooking process at 30% of dough moisture with 80 rpm is appropriate to obtain rice‐yellow pea precooked pasta with high content of phenolics and adequate quality. These pasta products exhibited firm texture, low stickiness, and regular and compact interne structure confirmed by high score in sensory overall acceptability.