bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interpreting Wide-Band Neural Activity Using Convolutional Neural Networks
Authors: Frey Markus , Tanni Sander , Perrodin Catherine , O’Leary Alice , Nau Matthias , Kelly Jack , Banino Andrea , Bendor Daniel , Doeller Christian F. , Barry Caswell 
Published: December 2019

AbstractRapid progress in technologies such as calcium imaging and electrophysiology has seen a dramatic increase in the size and extent of neural recordings. Even so, interpretation of this data often depends on manual operations and requires considerable knowledge about the nature of the representation. Decoding provides a means to infer the information content of such recordings but typically requires highly processed data and prior knowledge of the encoding scheme. Here, we developed a deep-learning-framework able to decode sensory and behavioural variables directly from wide-band neural data. The network requires little user input and generalizes across stimuli, behaviours, brain regions, and recording techniques. Once trained, it can be analysed to determine elements of the neural code that are informative about a given variable. We validated this approach using data from rodent auditory cortex and hippocampus, identifying a novel representation of head direction encoded by putative CA1 interneurons.
Negros Bleeding-heartGallicolumba keayiprefers dense understorey vegetation and dense canopy cover, and species distribution modelling shows little remaining suitable habitat
Authors: Mynott Holly , Abrahams Mark , Kerhoas Daphne 
Published: December 2019

AbstractThe Philippines is a global biodiversity hotspot, with a large number of Threatened bird species, one of which is the Critically Endangered Negros Bleeding-heartGallicolumba keayi. The aim of this study was to investigate the habitat preference of the Negros Bleeding-heart and undertake species distribution modelling to locate areas of conservation importance based on identified suitable habitat. A survey of 94 point counts was undertaken and eight camera traps were deployed from May to August 2018 in the Northwest Panay Peninsula Natural Park, Panay, Philippines. Habitat variables (canopy cover, understorey cover, ground cover, altitude, presence of rattan and pandan, tree diameter at breast height and branching architecture) were measured in 93 5 m-radius quadrats. To identify areas of potentially suitable habitat for the Negros Bleeding-heart, species distribution modelling was undertaken in MaxEnt using tree cover and altitude data on Panay and Negros. Using a Generalised Linear Model, Negros Bleeding-heart presence was found to be significantly positively associated with high understorey cover and dense canopy cover. Species distribution modelling showed that the Northwest Panay Peninsula Natural Park is currently the most effectively located protected area for Negros Bleeding-heart conservation, while protected areas in Negros require further protection. It is imperative that protection is continued in the Northwest Panay Peninsula Natural Park, and more survey effort is needed to identify other critical Negros Bleeding-heart populations, around which deforestation and hunting ban enforcement is strongly recommended.
A multi-dimensional, time-lapse, high content screening platform applied to schistosomiasis drug discovery
Authors: Chen Steven , Suzuki Brian M , Dohrmann Jakob , Singh Rahul , Arkin Michelle R , Caffrey Conor R 
Published: December 2019

AbstractApproximately 10% of the world’s population is at risk of schistosomiasis, a disease of poverty caused by the Schistosoma parasite. To facilitate drug discovery for this complex flatworm, we developed an automated high-content screen to quantify the multidimensional responses of Schistosoma mansoni post-infective larvae (somules) to chemical insult. We describe an integrated platform to process worms at scale, collect time-lapsed, bright-field images, segment highly variable and touching worms, and then store, visualize, and query dynamic phenotypes. To demonstrate the methodology, we treated somules with seven drugs that generated diverse responses and evaluated 45 static and kinetic response descriptors relative to concentration and time. For compound screening, we used the Mahalanobis distance to compare multidimensional phenotypic effects induced by 1,323 approved drugs. Overall, we characterize both known anti-schistosomals and identify new bioactives. Apart from facilitating drug discovery, the multidimensional quantification provided by this platform will allow mapping of chemistry to phenotype.
Nearly unbiased estimator ofNe/Nbased on kinship relationships
Authors: Akita Tetsuya 
Published: December 2019

AbstractThis study develops a nearly unbiased estimator of the ratio of the contemporary effective mother size to the census size in a population, as a proxy of the ratio of contemporary effective size to census size (Ne/N). The proposed estimator is based on both known mother–offspring (MO) and maternal-sibling (MS) relationships observed within the same cohort, in which sampled individuals in the cohort probably share MO relationships with sampled mothers. The rationale is that the frequency of MO and MS pairs contains information regarding the contemporary effective mother size and the (mature) census size, respectively. Therefore, the estimator can be obtained only from genetic data. Moreover, We also evaluate the performance of the estimator by running an individual-based model. The results of this study provide the following: i) parameter range for satisfying the unbiasedness, and ii) guidance for sample sizes to ensure the required accuracy and precision, especially when the order of the ratio is available. Furthermore, the results demonstrate the usefulness of a sibship assignment method for genetic monitoring, providing insights for interpreting environmental and/or anthropological factors fluctuatingNe/N, especially in the context of conservation biology and wildlife management.
The neural representation of visually evoked emotion is high-dimensional, categorical, and distributed across transmodal brain regions
Authors: Horikawa Tomoyasu , Cowen Alan S. , Keltner Dacher , Kamitani Yukiyasu 
Published: December 2019

SummaryCentral to our subjective lives is the experience of different emotions. Recent behavioral work mapping emotional responses to 2185 videos found that people experience upwards of 27 distinct emotions occupying a high-dimensional space, and that emotion categories, more so than affective dimensions (e.g., valence), organize self-reports of subjective experience. Here, we sought to identify the neural substrates of this high-dimensional space of emotional experience using fMRI responses to all 2185 videos. Our analyses demonstrated that (1) dozens of video-evoked emotions were accurately predicted from fMRI patterns in multiple brain regions with different regional configurations for individual emotions, (2) emotion categories better predicted cortical and subcortical responses than affective dimensions, outperforming visual and semantic covariates in transmodal regions, and (3) emotion-related fMRI responses had a cluster-like organization efficiently characterized by distinct categories. These results support an emerging theory of the high-dimensional emotion space, illuminating its neural foundations distributed across transmodal regions.
Syntrophy via interspecies H2transfer betweenChristensenellaandMethanobrevibacterunderlies their global co-occurrence in the human gut
Authors: Ruaud Albane , Esquivel-Elizondo Sofia , de la Cuesta-Zuluaga Jacobo , Waters Jillian L. , Angenent Largus T. , Youngblut Nicholas D. , Ley Ruth E. 
Published: December 2019

AbstractAcross human populations, 16S rRNA gene-based surveys of gut microbiomes have revealed that the bacterial familyChristensenellaceae and the archaeal familyMethanobacteriaceaeco-occur and are enriched in individuals with a lean, compared to an obese, BMI. Whether these association patterns reflect interactions between metabolic partners remains to be ascertained, as well as whether these associations play a role in the lean host phenotype with which they associate. Here, we validated previously reported co-occurrence patterns of the two families, and their association with a lean BMI, with a meta-analysis of 1,821 metagenomes derived from 10 independent studies. Furthermore, we report positive associations at the genus and species level betweenChristensenellaspp. andMethanobrevibacter smithii,the most abundant methanogen of the human gut. By co-culturing threeChristensenellaspp. WithM. smithii,we show thatChristensenellaspp. efficiently support the ofM. smithiivia H2production, far better thanBacteroides thetaiotaomicron.C. minutaforms flocs colonized byM. smithiieven when H2is in excess. In culture withC. minuta, H2consumption byM. smithiishifts the metabolic output ofC. minuta’s fermentation towards acetate rather than butyrate. Together, these results indicate that the widespread co-occurrence of these microbiota is underpinned by both physical and metabolic interactions. Their combined metabolic activity may provide insights into their association with a lean host BMI.ImportanceThe human gut microbiome is made of trillions of microbial cells, most of which areBacteria, with a subset ofArchaea. The bacterial familyChristensenellaceaeand the archaeal familyMethanobacteriaceaeare widespread in human guts. They correlate with each other and with a lean body type. Whether species of these two families interact, and how they affect the body type, are unanswered questions. Here, we showed that species within these families correlate with each other across people. We also demonstrated that particular species of these two families grow together in dense flocs, wherein the bacteria provide hydrogen gas to the archaea, which then make methane. When the archaea are present, the ratio of bacterial products (which are nutrients for humans) is changed. These observations indicate when these species grow together, their products have the potential to affect the physiology of their human host.
Framework to simulate gene regulatory networks with stochastic molecular kinetics and to infer steady-state network structure
Authors: Hettich Johannes , Gebhardt J. Christof M. 
Published: December 2019

AbstractBackgroundThe temporal progression of many fundamental processes in cells and organisms, including homeostasis, differentiation and development, are governed by gene regulatory networks (GRNs). GRNs balance fluctuations in the output of their genes, which trace back to the stochasticity of molecular interactions. Although highly desirable to understand life processes, predicting the temporal progression of gene products within a GRN is challenging when considering stochastic events such as transcription factor – DNA interactions or protein production and degradation.ResultsWe report CaiNet, a fast computer-aided interactive network simulation environment optimized to set up, simulate and infer GRNs at molecular detail. In our approach, we consider each network element to be isolated from other elements during small time intervals, after which we synchronize molecule numbers between all network elements. Thereby, the temporal behaviour of network elements is decoupled and can be treated by local stochastic or deterministic solutions. We demonstrate the working principle of the modular approach of CaiNet with a repressive gene cascade comprising four genes. By considering a deterministic time evolution within each time interval for all elements, our method approaches the solution of the system of deterministic differential equations associated with the GRN. By allowing genes to stochastically switch between on and off states or by considering stochastic production of gene outputs, we are able to include increasing levels of stochastic detail and approximate the solution of a Gillespie simulation. Notably, our modular approach further allows for a simple consideration of deterministic delays. We further infer relevant regulatory connections and steady-state parameters of a GRN of up to ten genes from steady-state measurements by identifying each gene of the network with a single perceptron in an artificial neuronal network and using a gradient decent method originally designed to train recurrent neural networks.ConclusionCaiNet constitutes a user-friendly framework to simulate GRNs at molecular detail and to infer the topology and steady-state parameters of GRNs. Thus, it should prove helpful to analyze or predict the temporal progression of reaction networks or GRNs in cellular and organismic biology. CaiNet is freely available at https://gitlab.com/GebhardtLab/CaiNet.
Multiple requirements for Rab GTPases in the development ofDrosophilatracheal dorsal branches and terminal cells
Authors: Best Benedikt T. , Leptin Maria 
Published: December 2019

AbstractThe tracheal epithelium in fruit fly larvae is a popular model for multi- and unicellular migration and morphogenesis. Like all epithelial cells, tracheal cells use Rab GTPases to organise their internal membrane transport, resulting in the specific localisation or secretion of proteins on the apical or basal membrane compartments. Some contributions of Rabs to junctional remodelling and governance of tracheal lumen contents are known, but it is reasonable to assume that they play important further roles in morphogenesis. This pertains in particular to terminal tracheal cells, specialised branch-forming cells that drastically reshape both their apical and basal membrane during the larval stages. We performed a loss-of-function screen in the tracheal system, knocking down endogenously tagged alleles of 26 Rabs by targeting the tag via RNAi. This revealed that at least 14 Rabs are required to ensure proper cell fate specification and migration of the dorsal branches, as well as their epithelial fusion with the contralateral dorsal branch. The screen implicated four Rabs in the subcellular morphogenesis of terminal cells themselves. Further tests suggested residual gene function after knockdown, leading us to discuss the limitations of this approach. We conclude that more Rabs than identified here may be important for tracheal morphogenesis, and that the tracheal system offers great opportunities for studying several Rabs that have barely been characterised so far.
Kinetic study of extrusion cooking of corn-rice flour blend fortified with nutraceutical concentrates with respect to various physical parameters
Authors: Kour Jasmeet , Singh Sukhcharn , Saxena Dharmesh C. 
Published: December 2019

PurposeThe purpose of this paper is to investigate the effect of residence time distribution in extruders along with the incorporation of nutraceuticals on the final quality of the products with respect to several pivotal responses.Design/methodology/approachCorn–rice flour blend fortified with isolated nutraceutical concentrates at two (low and high) levels was extruded at barrel temperature (110°C), screw speed (260 rpm) and feed moisture (17 percent). Extrudates were collected at an interval of 24 s followed by analysis for radial expansion (RE), bulk density (BD), water absorption index (WAI), sensory score (SS), textural hardness, colorimetric values (L*,a* andb*) and color difference (E).FindingsThe entire data were fitted to zero- and first-order kinetic models. There was a gradual decrease in RE, SS andL* value, whereas an increase in BD, textural hardness anda* value of extrudates fortified with the three nutraceutical concentrates was observed with the successive time interval of 24 s along with a more pronounced effect on color difference (E) observed during the last stages of extrusion time. The zero-order kinetic model was well fitted for BD anda* value, whereas the first-order kinetic model showed better results for RE, WAI, SS, textural hardness,L* value,a* value andb* value of fortified extrudates.Originality/valueNutraceuticals likeβ-glucans, lignans andγoryzanol exhibit numerous health-beneficial effects. This study analyzes the kinetics of changes in various responses of extrudates fortified with these nutraceutical concentrates during extrusion.
How does the quality of public education influence the citizens’ willingness to support it? Evidence from a comparative survey of 27 countries
Authors: Habibov Nazim , Auchynnikava Alena , Luo Rong 
Published: December 2019

PurposeThe purpose of this paper is to empirically test two opposing theoretical hypotheses from research literature: low quality of public education boosts support for public education; and low quality of public education weakens support for public education.Design/methodology/approachThe authors use microdata from 27 post-communist countries over a period of five years. This study uses two outcome variables in order to capture the level of support for public education: the willingness to elevate investments in public education to an important policy priority; and the willingness to pay more taxes to improve public healthcare. A series of logistic regressions is used to find how the outcome variable is influenced by six dimensions of the quality of the public education system.FindingsThe main finding is that a lower quality of public education strengthens the willingness of citizens to make investments into public education by: making it a political priority for the government; and through a professed increased willingness to pay more taxes towards improving public education. These findings remain valid for both years of investigation and for both EU and non-EU samples. In contrast, the authors could not find support for the hypothesis that postulates that a lower quality of public education will reduce support for public education.Research limitations/implicationsThe main implication of these findings is that despite the increases in availability of private schooling opportunities, the citizens of post-communist countries have not abandoned their support for public education. Even if citizens of post-communist countries believe that public education is no longer of an appropriately high quality, they continue to support the provision of resources to it in order to improve on the current situation.Practical implicationsThe current low quality of public education can be seen as providing an impetus for encouraging support for public education.Social implicationsIn terms of policy-making, the findings demonstrate the opportunity to shore up public support for further reforms in public- education in post-communist countries.Originality/valueThe current education policy research literature is silent about the direction of the effect of low quality public education on the willingness to provide support for public education. Against this background, this is the first study which empirically tested whether quality of public education affect willingness to support it. Covering a period of five years, the authors test the above-postulated hypotheses using a diverse sample of 27 post-communist countries.
First-home buyers and herding behavior in Surabaya, Indonesia
Authors: Susanto Sofian Arif , Njo Anastasia 
Published: December 2019

Purpose
This study aims to determine the causality of herding which was traced down to social and normative influences from first-home buyers represented by undergraduate students.

Design/methodology/approach
The Perception Alignment Hypothesis was used in this experimental research, and was conducted on a sample of 125 undergraduates studying finance representing first-home buyers. The experiment provides the subjects property brochures in Surabaya to appraise a value that they see fit for purchase. The subjects were given both social- and normative-induced treatments separately using information cascade, and their valuation shifts were recorded. Their valuations were then divided into three sections under the treatment groups, consisting of initial, “social’ and “normative’ valuations.

Findings
In contrast to previous findings, the results showed that first-home buyers succumbed to both social and normative influences, causing them to herd. Further analysis of the credibility of information was conducted and it showed that the undergraduates were only prone to social influence, whereas other aspects regarding normative influences must be further researched.

Practical implications
The decline of homeownership on a global scale is concerning, especially when 60% of the market represents young adults under the age of 35. This implies that both the government and property developers may need to enact strict measures to regulate property purchases.

Originality/value
This is the first experimental study on herding of Surabaya, Indonesia, mainly focusing on human behavior and information cascade. Thus, this study could be a viable reflection to future policies in Indonesia being made to answer actual demands in the residential market.
Selling places: a community-based model for promoting local food. The case of Rhondda Cynon Taf
Authors: Bowen Robert , Bennett Sophie 
Published: December 2019

Purpose
This paper aims to evaluate how places approach the promotion of local food products and what it means to produce, consume and support local produce in a rural region.

Design/methodology/approach
The study uses a participatory action-reflective approach through a series of three focus groups held over consecutive weeks with nine participants. This included local food producers, artists and community members, with data collected through focus group discussions, reflective video diaries and a questionnaire. The research was conducted in Rhondda Cynon Taf, Wales, a region with entrepreneurial potential but lacking a reputation for food.

Findings
Findings demonstrate confused perceptions of local identity, leading to a clichéd image of the region. As such, an origin brand may do little to enhance the value of local produce or increase economic prosperity in places that lack an established identity. Places with a more recognised reputation for food, such as Wales, could benefit from an origin brand, similar to Brittany.

Originality/value
The study extends the academic understanding of place branding by investigating the value of using origin branding in promoting food products. The context of a lesser-known region highlights the importance of awareness and reputation for the successful implementation of the brand. Additionally, the unique community-led action-reflective methodology provides a holistic model in exploring the effective development of the brand.