bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Bayesian Perspective on Accumulation in the Magnitude System
Authors: Martin Benoît , Wiener Martin , van Wassenhove Virginie 
Published: January 2017

ABSTRACTSeveral theoretical and empirical work posit the existence of a common magnitude system in the brain. Such a proposal implies that manipulating stimuli in one magnitude dimension (e.g. duration in time) should interfere with the subjective estimation of another magnitude dimension (e.g. size in space). Here, we asked whether a generalized Bayesian magnitude estimation system would sample sensory evidence using a common, amodal prior. Two psychophysical experiments separately tested participants on their perception of duration, surface, and numerosity when the non-target magnitude dimensions and the rate of sensory evidence accumulation were manipulated. First, we found that duration estimation was resilient to changes in surface and numerosity, whereas lengthening (shortening) the duration yielded under- (over-) estimations of surface and numerosity. Second, the perception of surface and numerosity were affected by changes in the rate of sensory evidence accumulation, whereas duration was not. Our results suggest that a generalized magnitude system based on Bayesian computations would minimally necessitate multiple priors.
Modelling haplotypes with respect to reference cohort variation graphs
Authors: Rosen Yohei , Eizenga Jordan , Paten Benedict 
Published: January 2017

AbstractCurrent statistical models of haplotypes are limited to panels of haplotypes whose genetic variation can be represented by arrays of values at linearly ordered bi- or multiallelic loci. These methods cannot model structural variants or variants that nest or overlap. A variation graph is a mathematical structure that can encode arbitrarily complex genetic variation. We present the first haplotype model that operates on a variation graph-embedded population reference cohort. We describe an algorithm to calculate the likelihood that a haplotype arose from this cohort through recombinations and demonstrate time complexity linear in haplotype length and sublinear in population size. We furthermore demonstrate a method of rapidly calculating likelihoods for related haplotypes. We describe mathematical extensions to allow modelling of mutations. This work is an essential step forward for clinical genomics and genetic epidemiology since it is the first haplotype model which can represent all sorts of variation in the population.
Interactive effects of shifting body size and feeding adaptation drive interaction strengths of protist predators under warming
Authors: Fussmann K. E. , Rosenbaum B. , Brose U. , Rall B.C. 
Published: January 2017

AbstractGlobal change is heating up ecosystems fuelling biodiversity loss and species extinctions. High-trophic-level predators are especially prone to extinction due to an energetic mismatch between increasing feeding rates and metabolism with warming. Different adaptation mechanisms such as decreasing body size to reduce energy requirements (morphological response) as well as direct effects of adaptation to feeding parameters (physiological response) have been proposed to overcome this problem. Here, we use protist-bacteria microcosm experiments to show how those adaptations may have the potential to buffer the impact of warming on predator-prey interactions. After adapting the ciliate predatorTetrahymena pyriformisto three different temperatures (15°C, 20°C and 25°C) for approximately 20 generations we conducted functional response experiments on bacterial prey along an experimental temperature gradient (15°C, 20°C and 25°C). We found an increase of maximum feeding rates and half-saturation densities with rising experimental temperatures. Adaptation temperature had on average slightly negative effects on maximum feeding rates, but maximum feeding rates increased more strongly with rising experimental temperature in warm adapted predators than in cold adapted predators. There was no effect of adaptation temperature on half-saturation densities characterising foraging efficiency. Besides the mixed response in functional response parameters, predators also adapted by decreasing body size. As smaller predators need less energy to fulfil their energetic demands, maximum feeding rates relative to the energetic demands increased slightly with increased adaptation temperature. Accordingly, predators adapted to 25°C showed the highest feeding rates at 25°C experimental temperature, while predators adapted to 15°C showed the highest maximum feeding rate at 15°C. Therefore, adaptation to different temperatures potentially avoids an energetic mismatch with warming. Especially a shift in body size with warming additionally to an adaptation of physiological parameters potentially helps to maintain a positive energy balance and prevent predator extinction with rising temperatures.
Comparison and Characterisation of Mutation Calling from Whole Exome and RNA Sequencing Data for Liver and Muscle Tissue in Lactating Holstein Cows Divergent for Fertility
Authors: Moran Bruce , Butler Stephen T. , Creevey Christopher J. 
Published: January 2017

AbstractWhole exome sequencing has had low uptake in livestock species, despite allowing accurate analysis of single nucleotide variant (SNV) mutations. Transcriptomic data in the form of RNA sequencing has been generated for many livestock species and also represents a source of mutational information. However, there is little information on the accuracy of using this data for the identification of SNVs. We generated a bovine exome capture design and used it to sequence and call mutations from a lactating dairy cow model genetically divergent for fertility (Fert+, n=8; Fert-, n=8). We compared mutations called from liver and muscle transcriptomes from the same animals. Our exome capture demonstrated 99.1% coverage of the exome design of 56.7MB, whereas transcriptomes covered 55 and 46.5% of the exome, or 24.4 and 20.7MB, in liver and muscle respectively after filtering. We found that specificity of SNVs in the transcriptome data is approximately 75% following basic hard-filtering, and could be increased to above 80% by increasing the minimum threshold of reads covering SNVs, but this effect was negated in more highly covered SNVs. RNA-DNA differences, SNVs found in transcriptome but not exome, were discovered and shown to have significantly increased levels of transition mutations in both tissues. Functional annotation of non-synonymous SNVs specific to the high and low fertility phenotypes identified immune response-related genes, supporting previous work that has identified differential expression in the same genes. Publically available RNAseq data may be analysed in a similar way to further increase the utility of this resource.SummaryThe exome and transcriptome both relate to the same protein-coding regions of the genome. There has been sparse research on characterising mutations in RNA and DNA within the same individuals. Here we characterise the similarities in our Holstein dairy cow animal model. We offer practical and biological results indicating that RNA sequencing is a useful proxy of exome sequencing, itself shown to be applicable to this livestock species using a previously untested commercial application. This potentially unlocks public RNA sequencing data for further analysis, also indicating that RNA-DNA differences may associate with transcriptomic divergence.
A new and accurate continuum description of moving fronts
Authors: Johnston S T , Baker R E , Simpson M J 
Published: January 2017

AbstractProcesses that involve moving fronts of populations are prevalent in ecology and cell biology. A common approach to describe these processes is a lattice-based random walk model, which can include mechanisms such as crowding, birth, death, movement and agent-agent adhesion. However, these models are generally analytically intractable and it is computationally expensive to perform sufficiently many realisations of the model to obtain an estimate of average behaviour that is not dominated by random fluctuations. To avoid these issues, both mean-field and corrected mean-field continuum descriptions of random walk models have been proposed. However, both continuum descriptions are inaccurate outside of limited parameter regimes, and corrected mean-field descriptions cannot be employed to describe moving fronts. Here we present an alternative description in terms of the dynamics of groups of contiguous occupied lattice sites and contiguous vacant lattice sites. Our description provides an accurate prediction of the average random walk behaviour in all parameter regimes. Critically, our description accurately predicts the persistence or extinction of the population in situations where previous continuum descriptions predict the opposite outcome. Furthermore, unlike traditional mean-field models, our approach provides information about the spatial clustering within the population and, subsequently, the moving front.
Unraveling the population history of Indian Siddis
Authors: Das Ranajit , Upadhyai Priyanka 
Published: January 2017

AbstractThe Siddis are a unique Indian tribe of African, South Asian and European ancestry. While their ancestral origins have been traced to the Bantu populations from sub-Saharan Africa, their population history has remained an enigmatic question. Here, we have traced the biogeographical origin of the Siddis employing an admixture based algorithm, Geographical Population Structure (GPS). We evaluated 14 Siddi genomes in reference to 5 African populations from the 1000 Genomes project and 7 Bantu populations from the Human Genome Diversity project. GPS assigned the Siddi genomes to west Zambia and the present-day border between Zimbabwe and northeastern Botswana, overlapping with one of the principal areas of secondary Bantu settlement in Africa, ~1700 years before present (YBP). This is concordant with the secondary Bantu dispersal route from the east African Bantu center that brought the African ancestors of the Siddis to settlement sites in southeast Africa, from where they were disseminated to India, by the Portuguese. Our results also suggest that while the Siddi genomes are significantly different from that of the Bantus, they displayed the highest genomic proximity to the Luhyas and North-East Bantus from Kenya, and that ancestral Siddis are likely to have split from the Luhyas, ~2700 YBP, in congruence with known Bantu expansion and population migration routes. Together with historical, linguistic and anthropological evidences our findings shine light on the genetic relatedness between populations, fine-scale population structure and recapitulate the population history of the Siddis, in the ethnohistorical context of India.
A portable system for metagenomic analyses using nanopore-based sequencer and laptop computers can realize rapid on-site determination of bacterial compositions
Authors: Mitsuhashi Satomi , Kryukov Kirill , Nakagawa So , Takeuchi Junko S , Shiraishi Yoshiki , Asano Koichiro , Imanishi Tadashi 
Published: January 2017

AbstractWe developed a portable system for metagenomic analyses consisting of nanopore technology-based sequencer, MinION, and laptop computers, and assessed its potential ability to determine bacterial compositions rapidly. We tested our protocols using mock bacterial community that contained equimolar 16S rDNA and a pleural effusion from a patient with empyema for time effectiveness and accuracy. MinION sequencing targeting 16S rDNA detected all of 20 bacteria present in the mock bacterial community. Time course analysis indicated that sequence data obtained during the first 5-minute sequencing were enough to detect all 20 bacteria species in the mock sample and determine their compositions with sufficient accuracy. Additionally, using a clinical sample extracted from the pleural effusion of a patient with empyema, we could identify major bacteria in a pleural effusion by rapid sequencing and analysis. All of these results are comparable to or even better than the conventional 16S rDNA sequencing results using IonPGM sequencer. Our results suggest that rapid sequencing and bacterial composition determination is possible within 2 hours.Our integrative system is applicable to rapid diagnostic tests for infectious diseases in near future.
Epidemiological and ecological determinants of Zika virus transmission in an urban setting
Authors: Lourenço J , Maia de Lima M , Faria NR , Walker A , Kraemer MUG , Villabona-Arenas CJ , Lambert B , Marques de Cerqueira E , Pybus OG , Alcantara LCJ , Recker M 
Published: January 2017

AbstractZika has emerged as a global public health concern. Although its rapid geographic expansion can be attributed to the success of itsAedesmosquito vectors, local epidemiological drivers are still poorly understood. The city of Feira de Santana played a pivotal role in the early phases of the Chikungunya and Zika epidemics in Brazil. Here, using a climate-driven transmission model, we show that low Zika observation rates and a high vectorial capacity in this region were responsible for a high attack rate during the 2015 outbreak and the subsequent decline in cases in 2016, when the epidemic was peaking in the rest of the country. Our projections indicate that the balance between the loss of herd-immunity and the frequency of viral re-importation will dictate the transmission potential of Zika in this region in the near future. Sporadic outbreaks are expected but unlikely to be detected under current surveillance systems.
The burden of dengue fever and chikungunya in southern coastal Ecuador: Epidemiology, clinical presentation, and phylogenetics from the first two years of a prospective study
Authors: Stewart-Ibarra Anna M. , Ryan Sadie J. , Kenneson Aileen , King Christine A. , Abbott Mark , Barbachano-Guerrero Arturo , Beltrán-Ayala Efraín , Borbor-Cordova Mercy J. , Cárdenas Washington B. , Cueva Cinthya , Finkelstein Julia L. , Lupone Christina D. , Jarman Richard G. , Berry Irina Maljkovic , Mehta Saurabh , Polhemus Mark , Silva Mercy , Endy Timothy P. 
Published: January 2017

AbstractHere we report the findings from the first two years of an arbovirus surveillance study conducted in Machala, Ecuador, a dengue endemic region (2014-2015). Patients with suspected dengue virus (DENV) infections (index cases, n=324) were referred from five Ministry of Health clinical sites. A subset of DENV positive index cases (n = 44) were selected, and individuals from the index household and four neighboring homes within 200-meters were recruited (n = 400). Individuals who entered the study, other than index cases, are referred to as associates. In 2014, 70.9% of index cases and 35.6% of associates had acute or recent DENV infections. In 2015, 28.3% of index cases and 12.8% of associates had acute or recent DENV infections. For every DENV infection captured by passive surveillance, we detected an additional three acute or recent DENV infections in associates. Of associates with acute DENV infections, 68% reported dengue-like symptoms, with the highest prevalence of symptomatic acute infections in children under 10 years of age. The first chikungunya virus (CHIKV) infections were detected on epidemiological week 12 in 2015. 43.1% of index cases and 3.5% of associates had acute CHIKV infections. No Zika virus infections were detected. Phylogenetic analyses of isolates of DENV from 2014 revealed genetic relatedness and shared ancestry of DENV1, DENV2 and DENV4 genomes from Ecuador with those from Venezuela and Colombia, indicating presence of viral flow between Ecuador and surrounding countries. Enhanced surveillance studies, such as this, provide high-resolution data on symptomatic and inapparent infections across the population.
Revisiting suppression of interspecies hybrid male lethality inCaenorhabditisnematodes
Authors: Ryan Lauren E. , Haag Eric S. 
Published: January 2017

AbstractWithin the nematode genusCaenorhabditis,C. briggsaeandC. nigoniare among the most closely related species known. They differ in sexual mode, withC. nigoniretaining the ancestral XO male-XX female outcrossing system, whileC. briggsaefemales recently evolved self-fertility and an XX-biased sex ratio. Wild-typeC. briggsaeandC. nigonican produce fertile hybrid XX female progeny, but XO progeny are either 100% inviable (whenC. briggsaeis the mother) or viable but sterile (whenC. nigoniis the mother). A recent study provided evidence suggesting that loss of theCbr-him-8meiotic regulator inC. briggsaehermaphrodites allowed them to produce viable and fertile hybrid XO male progeny when mated toC. nigoni. Because such males would be useful for a variety of genetic experiments, we sought to verify this result. Preliminary crosses with wild-typeC. briggsaehermaphrodites occasionally produced fertile males, but they could not be confirmed to be interspecies hybrids. Using an RNA interference protocol that eliminates any possibility of self-progeny inCbr-him-8hermaphrodites, we find sterile males bearing theC. nigoniX chromosome, but no fertile males bearing theC. briggsaeX, as in wild-type crosses. Our results suggest that the apparent rescue of XO hybrid viability and fertility is due to incomplete purging of self-sperm prior to mating.
Critical success factors for eLearning in Saudi Arabian universities
Authors: Alhabeeb Abdullah , Rowley Jennifer 
Published: January 2017

PurposeThe purpose of this paper is to offer insights into the development of eLearning systems and the perceptions of key players in the management of eLearning systems in three large universities in Saudi Arabia. It establishes the relative importance of different factors and compares these findings with studies conducted elsewhere in the world.Design/methodology/approachDesk research was conducted to gather a profile of the eLearning initiatives in the participating universities. Structured interviews were conducted with senior managers with responsibility for implementing and promoting eLearning in their universities. The interview protocol prompted discussion of the importance of the following sets of factors in the success and acceptance of eLearning: student characteristics, instructor characteristics, learning environment, instructional design, and support. Interviews were transcribed and analysed using thematic analysis.FindingsSupported by the Saudi Government, the three universities in this study have been developing their eLearning services. The two most important groups of critical success factors in this process were regarded as those related to student and instructor characteristics. Further analysis within each group of factors suggested that participants regarded instructor knowledge with learning technologies and student knowledge of computer systems, and technical infrastructure as important facilitators of success. Amongst instructional design factors, clarity of learning objectives and content quality were regarded as important. Insights are offered as to the reasons for these selections.Originality/valueThis study furthers earlier research on eLearning managers’ views and contributes to understanding of eLearning and its management in the Middle East.
Fast fashion environments: consumer’s heaven or retailer’s nightmare?
Authors: Cook Sasikarn Chatvijit , Yurchisin Jennifer 
Published: January 2017

Purpose
The current research explored both pre-purchase and post-purchase factors of consumer behaviour. Specifically, the purpose of this paper is to investigate the relationships that may exist among consumers’ perceptions of perishability, scarcity, low price, attitudes, impulse buying, post-purchase emotions, and product returns within the context of the fast fashion environments.

Design/methodology/approach
A total of 246 usable questionnaires completed by female undergraduate students, who made purchases and product returns at fast fashion retailers, were analysed in SPSS and AMOS 23.0. Structural equation modelling was employed to test the hypotheses.

Findings
Consumers who are attracted to scarcity due to limited supply and scarcity due to time, referred to as perceived perishability, have a positive attitude towards the fast fashion retailers in which products are presented in scarce environments. Likewise, consumers have a positive attitude towards fast fashion retailers due to low priced merchandises they offer. Consequently, consumers who have a positive attitude towards the fast fashion retailers are likely to purchase products from them impulsively. Moreover, impulse buying behaviour positively influenced some negative post-purchase emotional responses, which in turn positively influenced product returns in the fast fashion environments.

Research limitations/implications
The results of the current study contribute to a greater understanding of apparel-related consumer behaviour in general. A theory formation of fast fashion consumer behaviour from acquisition to disposal can be drawn from the results of this study. Because some fast fashion retailers do sell clothing for both men and women, researchers could compare the responses of males and females to examine differences in consumer behaviour related to demographic characteristics. In the future, an examination of actual emotional responses and return behaviour would be beneficial for a more complete understanding of post-purchase consumer behaviour.

Practical implications
Fast fashion retailers could use this information to carefully design shopping environments that induce impulse buying behaviour because it may result in product returns. Fast fashion retailers need to understand the causes of the return behaviour, whether consumer related or product related, to better meet the needs of their target market. Return policies must be considered.

Originality/value
This research is the first to examine the impact of negative emotions following consumers’ impulse buying on product returns in the fast fashion retail environments.
Prominent retailing authors and institutions: 2009-2015
Authors: Ketron Seth , Runyan Rodney , Farris II M. Theodore 
Published: January 2017

Purpose
The current work reviews all retailing articles published in four prominent retailing journals – Journal of Retailing, Journal of Retailing and Consumer Services, International Journal of Retail & Distribution Management, and International Review of Retail, Distribution and Consumer Research – in the 2009-2015 period, picking up where Runyan and Hyun (2009) left off. The purpose of this paper is to identify leading authors and institutions in retailing research based on overall impact.

Design/methodology/approach
Content analysis/literature review/descriptive research.

Findings
In total, 1,392 articles were published during this time period, and through a procedure of weights and adjustments for author count, journal impact, journal quality, and journal publishing opportunity, the findings reveal that research collaboration is highly prevalent, as evidenced by the high number of multi-authored papers and cross-university/international partnerships. Additionally, some authors and institutions remain influential, while others have emerged as highly influential in the last seven years. This shows the dynamic nature of the field and the need to remain active in quality publishing.

Research limitations/implications
Scholars must understand that several factors influence impact judgments, which cannot be assessed using raw counts alone. Journal quality, impact, and publishing opportunity as well as author counts are important elements to consider.

Originality/value
These reviews are vital to the field in that they provide status updates on scholarship, so these reviews should be done periodically. Additionally, the findings in this paper provide a more holistic understanding of research impact and permit better assessment for scholars and administrators.