bluuebunny/crossref_metadata_2025_split huggingface dataset:
MINT: A multivariate integrative method to identify reproducible molecular signatures across independent experiments and platforms
Authors: Rohart F. , Eslami A. , Matigian N. , Bougeard S. , Lê Cao K-A. 
Published: August 2016

AbstractBackgroundMolecular signatures identified from high-throughput transcriptomic studies often have poor reliability and fail to reproduce across studies. One solution is to combine independent studies into a single integrative analysis, additionally increasing sample size. However, the different protocols and technological platforms across transcriptomic studies produce unwanted systematic variation that strongly confounds the integrative analysis results. When studies aim to discriminate an outcome of interest, the common approach is a sequential two-step procedure; unwanted systematic variation removal techniques are applied prior to classification methods.ResultsTo limit the risk of overfitting and over-optimistic results of a two-step procedure, we developed a novel multivariate integration method,MINT, that simultaneously accounts for unwanted systematic variation and identifies predictive gene signatures with greater reproducibility and accuracy. In two biological examples on the classification of three human cell types and four subtypes of breast cancer, we combined high-dimensional microarray and RNA-seq data sets and MINT identified highly reproducible and relevant gene signatures predictive of a given phenotype. MINT led to superior classification and prediction accuracy compared to the existing sequential two-step procedures.ConclusionsMINTis a powerful approach and the first of its kind to solve the integrative classification framework in a single step by combining multiple independent studies.MINTis computationally fast as part of the mixOmics R CRAN package, available athttp://www.mixOmics.org/mixMINT/andhttp://cran.r-project.org/web/packages/mixOmics/.
Opponent surrounds explain diversity of contextual phenomena across visual modalities
Authors: Mély David A. , Serre Thomas 
Published: August 2016

AsbtractContext is known to affect how a stimulus is perceived. A variety of illusions have been attributed to contextual processing — from orientation tilt effects to chromatic induction phenomena, but their neural underpinnings remain poorly understood. Here, we present a recurrent network model of classical and extra-classical receptive fields that is constrained by the anatomy and physiology of the visual cortex. A key feature of the model is the postulated existence of two spatially disjoint near-vs. far-extra-classical regions with complementary facilitatory and suppressive contributions to the classical receptive field. The model accounts for a variety of contextual illusions, reveals commonalities between seemingly disparate phenomena, and helps organize them into a novel taxonomy. It explains how center-surround interactions may shift from attraction to repulsion in tilt effects, and from contrast to assimilation in induction phenomena. The model further explains enhanced perceptual shifts generated by a class of patterned background stimuli that activate the two opponent extra-classical regions cooperatively. Overall, the ability of the model to account for the variety and complexity of contextual illusions provides computational evidence for a novel canonical circuit that is shared across visual modalities.
SNP analysis implicates role of cytosine methylation in introducing consequential mutations inVibrio choleraegenomes
Authors: Sharda Mohak , Seshasayee Aswin Sai Narain , Khedkar Supriya 
Published: August 2016

AbstractEpigenetic modifications play a key role in gene regulation and in recognition of self DNA in bacteria. In-spite of their positive role in cell survival, modifications like cytosine methylation incur a mutational cost. Cytosine methylation, specifically 5-methylcytosine, is prone to hydrolytic deamination which leads to C → T and G → A transitions. Here, we first study the abundance of mutagenic cytosine methylation target motifs and show that bacteria likeVibrio choleraemight use motif avoidance as a strategy to minimize the mutational effect of deamination of methylated cytosine. Second by performing SNP analysis on whole genome sequence data fromVibrio choleraepatient isolates we show a) high abundance of cytosine methylation-dependent mutations in the cytosine methylation target motif RCCGGY, b) 95% of these C → T and G → A transitions in the coding region lead to non-synonymous substitutions and c) many of these transitions are associated with membrane proteins and are implicated in virulence. Thus, our SNP analysis ofV. choleraegenomes implicates the role of cytosine methylation in generating genotypic diversity with adaptive potential.
Information theory and the phenotypic complexity of evolutionary adaptations and innovations
Authors: Wagner Andreas 
Published: August 2016

AbstractTwo main lines of research link information theory to evolutionary biology. The first focuses on organismalphenotypes, and on the information that organisms acquire about their environment. The second connects information-theoretic concepts togenotypicchange. The genotypic and phenotypic level can be linked by experimental high-throughput genotyping and computational models of genotype-phenotype relationships. I here use a simple information-theoretic framework to compute a phenotype’s information content (its phenotypic complexity), and the information gain or change that comes with a new phenotype. I apply this framework to experimental data on DNA-binding phenotypes of multiple transcription factors. Low phenotypic complexity is associated with a biological system’s ability to discover novel phenotypes in evolution. I show that DNA duplications lower phenotypic complexity, which illustrates how information theory can help explain why gene duplications accelerate evolutionary adaptation. I also demonstrate that with the right experimental design, sequencing data can be used to infer the information gain associated with novel evolutionary adaptations, for example in laboratory evolution experiments. Information theory can help quantify the evolutionary progress embodied in the discovery of novel adaptive phenotypes.
Rhythmic entrainment source separation: Optimizing analyses of neural responses to rhythmic sensory stimulation
Authors: Cohen Michael X , Gulbinaite Rasa 
Published: August 2016

AbstractThe so-called steady-state evoked potentials (SSEPs) are rhythmic brain responses to rhythmic sensory stimulation, and are often used to study perceptual and attentional processes. We present a data analysis method for maximizing the signal-to-noise ratio of the narrow-band steady-state response in the frequency and time-frequency domains. The method, termed rhythmic entrainment source separation (RESS), is based on denoising source separation approaches that take advantage of the simultaneous but differential projection of neural activity to many non-invasively placed electrodes or sensors. Our approach is a combination and extension of existing multivariate source separation methods. We demonstrate that RESS performs well on both simulated and empirical data, and outperforms conventional SSEP analysis methods based on selecting electrodes with the strongest SSEP response. We also discuss the potential confound of overfitting—whereby the filter captures noise in absence of a signal. Matlab scripts are available to replicate and extend our simulations and methods. We conclude with some practical advice for optimizing SSEP data analyses and interpreting the results.
OrchID: a Generalized Framework for Taxonomic Classification of Images Using Evolved Artificial Neural Networks
Authors: Pereira Serrano , Gravendeel Barbara , Wijntjes Patrick , Vos Rutger A. 
Published: August 2016

ABSTRACTTaxonomic expertise for the identification of species is rare and costly. On-going advances in computer vision and machine learning have led to the development of numerous semi- and fully automated species identification systems. However, these systems are rarely agnostic to specific morphology, rarely can perform taxonomic “approximation” (by which we mean partial identification at least to higher taxonomic level if not to species), and frequently rely on costly scientific imaging technologies. We present a generic, hierarchical identification system for automated taxonomic approximation of organisms from images. We assessed the effectiveness of this system using photographs of slipper orchids (Cypripedioideae), for which we implemented image pre-processing, segmentation, and colour and shape feature extraction algorithms to obtain digital phenotypes for 116 species. The identification system trained on these digital phenotypes uses a nested hierarchy of artificial neural networks for pattern recognition and automated classification that mirrors the Linnean taxonomy, such that user-submitted photos can be assigned a genus, section, and species classification by traversing this hierarchy. Performance of the identification system varied depending on photo quality, number of species included for training, and desired taxonomic level for identification. High quality photos were scarce for some taxa and were under-represented in the training set, resulting in imbalanced network training. The image features used for training were sufficient to reliably identify photos to the correct genus but less so to the correct section and species. The outcomes of this project include a library of feature extraction algorithms calledImgPheno,a collection of scripts for neural network training calledNBClassify,a library for evolutionary optimization of artificial neural network construction calledAI::FANN::Evolvingand a planned web application calledOrchIDfor identification of user-submitted images. All project outcomes are open source and freely available.
Prevalence of Congenital Amusia
Authors: Peretz Isabelle , Vuvan Dominique T. 
Published: August 2016

AbstractCongenital amusia (commonly known as tone-deafness) is a lifelong musical disorder that should affect 4% of the population according to a single estimate based on a single test from 1980. Here we present the first large-based measure of prevalence with a sample of 20,000 participants that does not rely on self-referral. On the basis of three objective tests and a questionnaire, we show that (a) the prevalence of congenital amusia is only 1.5% with slightly more females than males, unlike other developmental disorders where males often predominate; (b) self-disclosure is a reliable index of congenital amusia, that suggests that congenital amusia is hereditary with 46% first-degree relatives similarly affected; c) that the deficit is not attenuated by musical training and d) it emerges in relative isolation from other cognitive disorder except for spatial orientation problems. Hence, we suggest that congenital amusia is likely to result from genetic variations that affect musical abilities specifically.
Debunking myths about soft leadership and exploring it to achieve organizational excellence and effectiveness
Authors: Rao M.S. 
Published: August 2016

Purpose
The purpose of this paper is to debunk myths about soft leadership.

Design/methodology/approach
The paper distinguishes soft leadership from other leadership styles.

Findings
It calls for companies exploring this new leadership perspective to achieve organizational excellence and effectiveness; and countries to achieve peace and prosperity.

Practical implications
This new leadership perspective can be adopted by leaders for companies and countries.

Social implications
The social implications of this research suggests that leaders can improve employees’ performance and productivity by treating them as partners.

Originality/value
It defines and explains soft leadership with four OB models. It unfolds that it is the age of partnership, not followership. It unveils that employees prefer to work in an egalitarian set up. They appreciate leaders with an integrative, participative, collaborative, and relationship-oriented leadership mindset.
Design and modeling adsorption kinetics of methylene blue on zeolite adsorbents and clay
Authors: Lamia Maaza , Fatiha Djafri , Mohammed Bouchekara , Mustapha Djebbar , Ayada Djafri 
Published: August 2016

Purpose
The purpose of this paper is to examine the batch adsorption system of a cationic dye (methylene blue, widely used in various sectors) on two adsorbents; ZSM-5 zeolite which was prepared with the molar composition: 0.2057 Na2O-0.00266 Al2O3-SiO2-0.68 (pyrrolidine)-40 H2O-0.12 H2SO4.

Design/methodology/approach
By the hydrothermal synthesis method, and the purified clay and is analyzed by IR and DRX method.

Findings
For this, the authors conducted a parametric study of adsorption and effect of several important parameters on the adsorption of BM on the material used, in particular, the contact time (equilibrium is established after 120 min), different concentrations of adsorbents, different masses, the pH and temperature. The experiments demonstrated the crucial role of these parameters. A kinetic study was done and kinetic models were applied to the experimental results such as the pseudo-first order, pseudo-second order.

Originality/value
This work is original.
Colour gamut with easy sources of natural dyes
Authors: Tayade Priti B. , Adivarekar Ravindra V. 
Published: August 2016

Purpose
In nature, thousands of different colours and shades exist. Basic set of dyes, namely, yellow, red, blue and green are necessary for a complete colour gamut. Creating a complete gamut with natural dyes with one common extraction and application procedure is not exploited hitherto. The paper aims to discuss this issue.

Design/methodology/approach
In this study, an attempt was made to create a complete colour gamut with easily available natural dyes with one common extraction and application procedure.

Findings
Silk fabrics were dyed using various natural dyes alone and in combination to yield various shades, namely, yellow, red, green, blue. Pre-mordanting of silk fabrics was carried out with mordants, namely, alum, ferrous sulphate, copper sulphate, stannous chloride, potassium dichromate followed by dyeing. The fastness properties and colour strength values of all the shades obtained were determined.

Originality/value
Creating a complete gamut with natural dyes with one common extraction and application procedure is not exploited hitherto.
The impact of external social and internal personal forces on consumers’ brand community engagement on Facebook
Authors: Simon Carina , Brexendorf Tim Oliver , Fassnacht Martin 
Published: August 2016

Purpose
Consumer engagement has been designated as an approach to describing online interactions that more comprehensively reflects the nature of consumers’ interactive relationships in online brand communities. This paper aims to explore consumers’ brand community engagement in the context of Facebook brand pages. This research puts forth the hypothesis that consumers’ brand community engagement on Facebook is dependent upon two overarching themes: external social forces and internal personal forces.

Design/methodology/approach
Based on social impact theory, social identity theory and social exchange theory, a conceptual research model is developed and empirically tested through structural equation modelling using cross-sectional data of 460 Facebook brand fans.

Findings
The empirical results suggest that internal personal forces primarily positively influence brand community engagement, while external social forces can even impact consumers’ brand community engagement negatively.

Research limitations/implications
Future research should test and validate the proposed model for specific categories and brands.

Practical implications
This paper offers help to online brand marketers to trigger meaningful engagement of consumers in a brand community on Facebook.

Originality/value
This paper examines the consumer engagement construct from a behavioural perspective in a defined social media context and highlights the peculiarities of online brand communities on Facebook that distinguish them from traditional brand communities. The research uses a strong theoretical foundation to develop a model that investigates the prevalent variables that influence consumers’ brand community engagement on Facebook.
Ponds, Power and Institutions: The Everyday Governance of Accessing Urban Water Bodies in a Small Bengali City
Authors: Cornea Natasha , Zimmer Anna , Véron René 
Published: August 2016

AbstractWhile researchers in the growing field of urban political ecology have given significant attention to the fragmented hydroscape that characterizes access to drinking water in the global South, so far the (re)production of other urban waters and its related power relations have been underexplored. This article seeks to contribute to filling this gap by exploring the everyday negotiations over access to urban water bodies, in particular ponds. These are understood as a composite resource that is simultaneously water, land and public space. This analysis draws on a case study from a small city in West Bengal, India, and is based primarily on data from open interviews with different actors with a stake in urban ponds. The article demonstrates that in a context of ambiguity of the statutory governance regime and fragmented control, the (re)production of the pondscape is embedded within complex relationships of power whereby social marginalization can be offset at least momentarily by local institutions such as neighbourhood clubs and political parties.
Self‐administration of injectable contraceptives: a systematic review
Authors: Kim CR , Fønhus MS , Ganatra B 
Published: August 2016

BackgroundThe contraceptive injectable is a safe and effective method that is used worldwide. With the variety of injectable delivery systems, there is potential for administration by the woman herself. Self‐administration of the contraceptive injectable is the subject of this systematic review.ObjectivesTo assess how effective and safe the contraceptive injectable method is when women themselves perform/administer it, compared with when the usual healthcare providers administer it.Search strategyWe searched PubMed, Popline, Cochrane, CINAHL, and Embase for articles with subject headings or text words related to ‘self‐administration’ and ‘contraception’.Selection criteriaStudies that compared the administration of the contraceptive injectable by the woman herself versus administration by the healthcare provider were included. Outcomes of interest were continuation rates, safety, and the women's overall satisfaction with the contraceptive provider and method.Data collection and analysisWe undertook data extraction, descriptive analysis, and assessment of risk of bias.Main resultsThree studies met the inclusion criteria. The best available evidence shows that there may be little or no difference in continuation rates when women self‐administer contraceptive injections (326 per 1000 women; 95% CI 192–554 per 1000 women) compared with administration by healthcare providers (304 per 1000 women). Safety was not estimable as no serious adverse events were reported in any of the studies. With regards to overall satisfaction towards the provider and the method, the effect of the intervention was uncertain.Authors’ conclusionsFindings suggest that with appropriate information and training the provision of contraceptive injectables for the woman to self‐administer at home can be an option in some contexts.Tweetable abstractThis review assessed the continuation rates and safety of self‐administration of the contraceptive injection.
Are there really two cultures? A pilot study on the application of qualitative and quantitative methods in political science
Authors: KUEHN DAVID , ROHLFING INGO 
Published: August 2016

AbstractIn their 2012 publication A Tale of Two Cultures, Gary Goertz and James Mahoney argue that empirical research in the social sciences aiming at causal inference can be differentiated into a qualitative and a quantitative methodological culture. The two cultures differ fundamentally in how researchers approach and implement empirical studies. The argument is well laid out and comprehensively illustrated, but the empirical validity of the two cultures hypothesis has not yet been evaluated systematically. This note introduces a research project that aims to test the two cultures hypothesis via an empirical analysis of how qualitative and quantitative methods are applied. To determine whether there is a qualitative and quantitative method culture, the researchers initially sampled 30 articles from three journals (Comparative Political Studies, European Journal of Political Research, World Politics) in the 2008–2012 period. Based on this dataset, no evidence was found for the existence of coherent systems of methods practices in political science.
Decreasing Malpractice Claims by Reducing Preventable Perinatal Harm
Authors: Riley William , Meredith Les W. , Price Rebecca , Miller Kristi K. , Begun James W. , McCullough Mac , Davis Stanley 
Published: August 2016

ObjectiveTo evaluate the association of improved patient safety practices with medical malpractice claims and costs in the perinatal units of acute care hospitals.Data SourcesMalpractice and harm data from participating hospitals; litigation records and medical malpractice claims data from American Excess Insurance Exchange, RRG, whose data are managed by Premier Insurance Management Services, Inc. (owned by Premier Inc., a health care improvement company).Study DesignA quasi‐experimental prospective design to compare baseline and postintervention data. Statistical significance tests for differences were performed using chi‐square, Wilcoxon signed‐rank test, and t‐test.Data CollectionClaims data were collected and evaluated by experienced senior claims managers through on‐site claim audits to evaluate claim frequency, severity, and financial information. Data were provided to the analyzing institution through confidentiality contracts.Principal FindingsThere is a significant reduction in the number of perinatal malpractice claims paid, losses paid, and indemnity payments (43.9 percent, 77.6 percent, and 84.6 percent, respectively) following interventions to improve perinatal patient safety and reduce perinatal harm. This compares with no significant reductions in the nonperinatal claims in the same hospitals during the same time period.ConclusionsThe number of perinatal malpractice claims and dollar amount of claims payments decreased significantly in the participating hospitals, while there was no significant decrease in nonperinatal malpractice claims activity in the same hospitals.