bluuebunny/crossref_metadata_2025_split huggingface dataset:
The rhythms of predictive coding: pre-stimulus phase modulates the influence of shape perception on luminance judgments
Authors: Han Biao , VanRullen Rufin 
Published: June 2016

AbstractPredictive coding is an influential model emphasizing interactions between feedforward and feedback signals. Here, we investigated its temporal dynamics. Two gray disks with different versions of the same stimulus, one enabling predictive feedback (a 3D-shape) and one impeding it (random-lines), were simultaneously presented on the left and right of fixation. Human subjects judged the luminance of the two disks while EEG was recorded. Independently of the spatial response (left/right), we found that the choice of 3D-shape or random-lines as the brighter disk (our measure of post-stimulus predictive coding efficiency on each trial) fluctuated along with the pre-stimulus phase of two spontaneous oscillations: a ~5Hz oscillation in contralateral frontal electrodes and a ~16Hz oscillation in contralateral occipital electrodes. This pattern of results demonstrates that predictive coding is a rhythmic process, and suggests that it could take advantage of faster oscillations in low-level areas and slower oscillations in high-level areas.
When is a bacterial “virulence factor” really virulent?
Authors: Granato Elisa T. , Harrison Freya , Kümmerli Rolf , Ross-Gillespie Adin 
Published: June 2016

ABSTRACTBacterial traits that contribute to disease are termed ‘virulence factors’ and there is much interest in therapeutic approaches that disrupt such traits. However, ecological theory predicts disease severity to be multifactorial and context dependent, which might complicate our efforts to identify the most generally important virulence factors. Here, we use meta-analysis to quantify disease outcomes associated with one well-studied virulence factor – pyoverdine, an iron-scavenging compound secreted by the opportunistic pathogenPseudomonas aeruginosa. Consistent with ecological theory, we found that the effect of pyoverdine, albeit frequently contributing to disease, varied considerably across infection models. In many cases its effect was relatively minor, suggesting that pyoverdine is rarely essential for infections. Our work demonstrates the utility of meta-analysis as a tool to quantify variation and overall effects of purported virulence factors across different infection models. This standardised approach will help us to evaluate promising targets for anti-virulence approaches.
Imputation-based fine-mapping suggests that most QTL in an outbredchickenAdvanced Intercross Line are due to multiple, linked loci
Authors: Brandt Monika , Ahsan Muhammad , Honaker Christa F. , Siegel Paul B. , Carlborg Örjan 
Published: June 2016

AbstractThe Virginiachickenlines have been divergently selected for juvenile body-weight for more than 50 generations. Today, the high-and low-weight lines show a 12-fold difference for the selected trait, 56-day body-weight. These lines provide unique opportunities to study the genetic architecture of long-term, single-trait selection. Previously, several Quantitative Trait Loci (QTL) contributing to weight differences between the lines were mapped in an F2-cross between them, and these were later replicated and fine-mapped in a nine-generation advanced intercross of them. Here, we explore the possibility to further increase the fine-mapping resolution of these QTL via a pedigree-based imputation strategy that aims to better capture the haplotype-diversity in the divergently selected, but outbred, founder lines. The founders of the intercross were high-density genotyped, and then pedigree-based imputation was used to assign genotypes throughout the pedigree. Imputation increased the marker-density 20-fold in the selected QTL, providing 6911 markers for the subsequent analysis. Both single-marker association and multi-marker backward-elimination analyses were used to detect associations to 56-day body-weight. The approach revealed several statistically and population-structure independent associations and increased the resolution of most QTL. Further, most QTL were also found to contain multiple independent associations, implying a complex underlying architecture due to the combined effects of multiple, linked loci on independent haplotypes that still segregate in the selected lines.Article summaryAfter 50 generations of bi-directional selection, the Virginia chicken lines display a 12-fold difference in bodyweight at 56 days of age. Birds from the high and low selected lines were crossed to found an Advanced Intercross Line, which has been maintained for 9 generations. Using high-density genotypes of the founders, we imputed genotypes in intercross birds that were only genotyped for a sparse set of markers. Using single and multi-marker association analyses, we replicated nine known body-weight QTL. Multiple statistically independent associations were revealed in eight of the QTL, suggesting that most are caused by multiple linked loci.
Variable species densities are induced by volume exclusion interactions upon domain growth
Authors: Ross Robert J. H. , Yates C. A. , Baker R. E. 
Published: June 2016

AbstractIn this work we study the effect of domain growth on spatial correlations in agent populations containing multiple species. This is important as heterogenous cell populations are ubiquitous during the embryonic development of many species. We have previously shown that the long term behaviour of an agent population depends on the way in which domain growth is implemented. We extend this work to show that, depending on the way in which domain growth is implemented, different species dominate in multispecies simulations. Continuum approximations of the lattice-based model that ignore spatial correlations cannot capture this behaviour, while those that explicitly account for spatial correlations can. The results presented here show that the precise mechanism of domain growth can determine the long term behaviour of multispecies populations, and in certain circumstances, establish spatially varying species densities.
NR1H3p.Arg415Gln Is Not Associated To Multiple Sclerosis Risk
Authors:   The International Multiple Sclerosis Genetics Consortium, Cotsapas Chris 
Published: June 2016

AbstractA recent study by Wanget alclaims the low-frequency variantNR1H3p.Arg415Gln is pathological for multiple sclerosis and determines a patient’s likelihood of primary progressive disease. We sought to replicate this finding in the International MS Genetics Consortium (IMSGC) patient collection, which is 13-fold larger than the collection of Wanget al, but we find no evidence that this variant is associated either with MS or disease subtype. Wanget alalso report a common variant association in the region, which we show captures the association the IMSGC reported in 2013. Therefore, we conclude that the reported low-frequency association is a false positive, likely generated by insufficient sample size. The claim ofNR1H3mutations describing a Mendelian form of MS - of which no examples exist - can therefore not be substantiated by data.
iCAVE: an open source tool for immersive 3D visualization of complex biomolecular interaction networks
Authors: Liluashvili Vaja , Kalayci Selim , Flouder Eugene , Wilson Manda , Gabow Aaron , Gümü Zeynep H. 
Published: June 2016

AbstractVisualizations of biomolecular networks assist in systems-level data exploration in myriad cellular processes in health and disease. While these networks are increasingly informed by data generated from high-throughout (HT) experiments, current tools do not adequately scale with concomitant increase in their size and complexity. We present an open-source software platform, interactome-CAVE, (iCAVE), that leverages stereoscopic (3D) immersive display technologies for visualizing complex biomolecular interaction networks. Users can explore networks (i) in 3D in any computer and (ii) inimmersive3D in any computer with an appropriate graphics card as well as in CAVE environments. iCAVE includes new 3D network layout algorithms in addition to extensions of known 2D network layout, clustering and edge-bundling algorithms to the 3D space, to assist in understanding the underlying structures in large, dense, layered or clustered networks. Users can perform simultaneous queries of several databases within iCAVE or visualize their own networks (e.g. disease, drug, protein, metabolite, phenotype, genotype) utilizing directionality, weight or other properties by using different property settings. iCAVE has modular structure to allow rapid development by the addition of algorithms, datasets or features without affecting other parts of the code. Overall, iCAVE is a freely available open source tool to help gain novel insights from complex HT datasets.
Direct coevolutionary couplings reflect biophysical residue interactions in proteins
Authors: Coucke Alice , Uguzzoni Guido , Oteri Francesco , Cocco Simona , Monasson Remi , Weigt Martin 
Published: June 2016

AbstractCoevolution of residues in contact imposes strong statistical constraints on the sequence variability between homologous proteins. Direct-Coupling Analysis (DCA), a global statistical inference method, successfully models this variability across homologous protein families to infer structural information about proteins. For each residue pair, DCA infers 21×21 matrices describing the coevolutionary coupling for each pair of amino acids (or gaps). To achieve the residue-residue contact prediction, these matrices are mapped onto simple scalar parameters; the full information they contain gets lost. Here, we perform a detailed spectral analysis of the coupling matrices resulting from 70 protein families, to show that they contain quantitative information about the physico-chemical properties of amino-acid interactions. Results for protein families are corroborated by the analysis of synthetic data from lattice-protein models, which emphasizes the critical effect of sampling quality and regularization on the biochemical features of the statistical coupling matrices.
The population dynamics of a bacterial pathogen after host re-infection affects the founding population size
Authors: Jiang Gaofei , Peyraud Rémi , Remigi Philippe , Guidot Alice , Berthomé Richard , Ding Wei , Jousset Alexandre , Genin Stéphane , Peeters Nemo 
Published: June 2016

AbstractIn natura, many organisms face multiple infections by pathogens. The ability of a pathogen to reinfect an already-infected host affects the genetic makeup of the pathogen population at the end of the infectious cycle. Despite the likely prevalence of this situation, the population dynamics of pathogens during multiple infections over time is still poorly understood. Here we combined theoretical and empirical investigations of the founding population size, a critical driver of the evolution of pathogens, in a setting allowing for multiple and subsequent re-infections. Using the soil-borne bacterial pathogen Ralstonia solanacearum and tomato as its host, we first assessed the strength of the host infection bottleneck, and showed that both the host barrier and the immune system work additively to constrain the infection. Then, by increasing the temperature, we experimentally demonstrated that the increased pathogen proliferation within the host reduces the contribution of subsequent re-infection leading to a lower founding population size. Our study highlights the importance of within-host pathogen proliferation in determining founding population size – and thus bacterial genetic diversity during epidemics – for pathosystems where multiple re-infections occur. Under current global changes, our work notably predicts that an increased temperature provided this increase has a beneficial impact on pathogen growth, should decrease the founding population size and as a consequence potentially lower the diversity of the infecting and transmitted pathogen population.Significance StatementFounder population size is a major determinant of pathogen evolution, yet we still have limited insights into effective populations in natural settings. Most studies have considered infection as a single event, followed by pathogen growth in the host. But, in natura, organisms typically face multiple infections by several co-exisiting pathogen strains. Therefore, effective population size will depend on the timing and relative growth rate of the different infecting strains. In this work, we predict and experimentally show that both priority effects and within-host competition determines effective founding size, with an over-contribution of fast-growing and early infecting genotypes. This work sheds a new light on the ecological and evolutionary pressures affecting infection dynamics in realistic conditions.
Reuse of scientific data in academic publications
Authors: He Lin , Nahar Vinita 
Published: June 2016

Purpose
– In recent years, a large number of data repositories have been built and used. However, the extent to which scientific data are re-used in academic publications is still unknown. The purpose of this paper is to explore the functions of re-used scientific data in scholarly publication in different fields.

Design/methodology/approach
– To address these questions, the authors identified 827 publications citing resources in the Dryad Digital Repository indexed by Scopus from 2010 to 2015.

Findings
– The results show that: the number of citations to scientific data increases sharply over the years, but mainly from data-intensive disciplines, such as agricultural, biology science, environment science and medicine; the majority of citations are from the originating articles; and researchers tend to reuse data produced by their own research groups.

Research limitations/implications
– Dryad data may be re-used without being formally cited.

Originality/value
– The conservatism in data sharing suggests that more should be done to encourage researchers to re-use other’s data.
Testing the stability of “wisdom of crowds” judgments of search results over time and their similarity with the search engine rankings
Authors: Zhitomirsky-Geffet Maayan , Bar-Ilan Judit , Levene Mark 
Published: June 2016

Purpose– One of the under-explored aspects in the process of user information seeking behaviour is influence of time on relevance evaluation. It has been shown in previous studies that individual users might change their assessment of search results over time. It is also known that aggregated judgements of multiple individual users can lead to correct and reliable decisions; this phenomenon is known as the “wisdom of crowds”. The purpose of this paper is to examine whether aggregated judgements will be more stable and thus more reliable over time than individual user judgements.Design/methodology/approach– In this study two simple measures are proposed to calculate the aggregated judgements of search results and compare their reliability and stability to individual user judgements. In addition, the aggregated “wisdom of crowds” judgements were used as a means to compare the differences between human assessments of search results and search engine’s rankings. A large-scale user study was conducted with 87 participants who evaluated two different queries and four diverse result sets twice, with an interval of two months. Two types of judgements were considered in this study: relevance on a four-point scale, and ranking on a ten-point scale without ties.Findings– It was found that aggregated judgements are much more stable than individual user judgements, yet they are quite different from search engine rankings.Practical implications– The proposed “wisdom of crowds”-based approach provides a reliable reference point for the evaluation of search engines. This is also important for exploring the need of personalisation and adapting search engine’s ranking over time to changes in users preferences.Originality/value– This is a first study that applies the notion of “wisdom of crowds” to examine an under-explored in the literature phenomenon of “change in time” in user evaluation of relevance.
The structuring of information through search: sorting waste with Google
Authors: Haider Jutta 
Published: June 2016

Purpose– The purpose of this paper is to explore informational structures producing and organising the construction of waste sorting in Sweden. It shows how the issue is constructed by it being searched for in Google and how this contributes to the specific informational texture of waste sorting in Sweden. It is guided by the following questions: who are the main actors and which are the central topics featuring in Google results on popular, suggested searches for waste sorting in Sweden? What do the link relations between these tell the author about the issue space that is formed around waste sorting in Sweden? How is the construction of the notions of waste sorting and waste shaped in the information available through Google’s features for related and other relevant searches?Design/methodology/approach– Waste sorting is discussed as a practice structured along moral rules and as a classification exercise. The study brings together two types of material, results from searches carried out in Google and lists of Google query suggestions for relevant search terms. These are analysed with a mixed method approach, uniting quantitative network analysis and qualitative content analysis of query suggestions. A sociomaterial approach theoretically grounds the analysis.Findings– Waste sorting in Sweden emerges as an issue that is characterised by dense networks of rules and regulation, focused in public authorities and government agencies, which in turn address consumers, waste management businesses and other authorities. Search engine use and waste sorting in Sweden are shown to be joined together in various mundane everyday life practices and practices of governance that become visible through the search engine in form of search results and suggested searches. The search engine is shown to work as a fluid classification system, which is also created and shaped by its use.Originality/value– The study offers a novel methodological approach to studying the informational structures of an issue and of its shaping through it being searched for. The sociomaterially grounded analysis of Google as a fluid classification system is original.
Impact of exchange rate movement and macro-economic factors on exports of software and services from India
Authors: Upadhyay Parijat , Ghosh Roy Saikat 
Published: June 2016

Purpose
– The information technology (IT) sector in India is the leading exporter from the service sector domain and also is a significant contributor to the overall export kitty of India. The IT sector’s contribution in total Indian exports (merchandise plus services) increased from less than 4 percent in FY1998-1999 to about 25 percent in FY2011-2012 as per IT industry nodal body National Association of Software and Services Companies and the central bank of the country, the Reserve Bank of India (RBI). As this industry earns most of its revenue in foreign currencies it is exposed to the foreign exchange risks. The purpose of this paper is to validate the macro-economic theory that depreciation in domestic currency boosts export as it makes domestic good and services cheaper and appreciation in domestic currency deters export as it makes domestic good and services costlier. The authors are validating this theory for Indian rupee and keeping software services export in the focus.

Design/methodology/approach
– In this study the authors have done the multiple regression analysis on the obtained time-series data. The research was totally based on the secondary data from Quarter1 (April-June) of FY 2000-2001 to Quarter4 (January-March) of FY 2011-2012. It comprises of data for 48 consecutive quarters. The authors have taken the growth rate, so the final data set consist of data of 47 quarters. The main source of data are published data by RBI. Data have been collected for export of software services, merchandise export, real effective exchange rate, US-dollar-Indian rupee exchange rate, gross domestic product of India and selected countries.

Findings
– Data analysis leads the authors to the following findings: real effective exchange rate has no significant impact on software services export; US-dollar-Indian rupee exchange rate has no significant impact on software services export; external gross domestic product growth has no significant impact on software services export; and gross domestic product growth of India has no significant impact on software services export. The results obtained from multiple regression analysis are also supported by the results obtained from Granger Causality test. It does not identify any single factor as a major cause of software export. Results shows that the external GDP is having the statistically significant impact on the software export but the low value of R2 denotes that the impact is very low.

Originality/value
– There are no published studies available which has attempted similar kind of an approach to study using aggregated export data and other macro-economic variables like real effective exchange rate (REER) and GDP growth rate. All previous literatures used REER to measure the impact of the exchange rate on export.
Benchmarking operating room departments in the Netherlands
Authors: van Veen-Berkx Elizabeth , de Korne Dirk F. , Olivier Olivier S. , Bal Roland A. , Kazemier Geert 
Published: June 2016

Purpose– Benchmarking is increasingly considered a useful management instrument to improve performance in healthcare. The purpose of this paper is to assess if a nationwide long-term benchmarking collaborative between operating room (OR) departments of university medical centres in the Netherlands leads to benefits in OR management and to evaluate if the initiative meets the requirements of the 4P-model.Design/methodology/approach– The evaluation was based on the 4P-model (purposes, performance indicators, participating organisations, performance management system), developed in former studies. A mixed-methods design was applied, consisting of document study, observations, interviews as well as analysing OR performance data using SPSS statistics.Findings– Collaborative benchmarking has benefits different from mainly performance improvement and identification of performance gaps. It is interesting that, since 2004, the OR benchmarking initiative still endures after already existing for ten years. A key benefit was pointed out by all respondents as “the purpose of networking”, on top of the purposes recognised in the 4P-model. The networking events were found to make it easier for participants to contact and also visit one another. Apparently, such informal contacts were helpful in spreading knowledge, sharing policy documents and initiating improvement. This benchmark largely met all key conditions of the 4P-model.Research limitations/implications– The current study has the limitations accompanied with any qualitative research and particularly related to interviewing. Qualitative research findings must be viewed within the context of the conducted case study. The experiences in this university hospital context in the Netherlands might not be transferable to other (general) hospital settings or other countries. The number of conducted interviews is restricted; nevertheless, all other data sources are extensive.Originality/value– A collaborative approach in benchmarking can be effective because participants use its knowledge-sharing infrastructure which enables operational, tactical and strategic learning. Organisational learning is to the advantage of overall OR management. Benchmarking seems a useful instrument in enabling hospitals to learn from each other, to initiate performance improvements and catalyse knowledge-sharing.