bluuebunny/crossref_metadata_2025_split huggingface dataset:
HiMAP: robust Phylogenomics from Highly Multiplexed Amplicon sequencing
Authors: Dupuis Julian R. , Bremer Forest T. , Kauwe Angela , Jose Michael San , Leblanc Luc , Rubinoff Daniel , Geib Scott M. 
Published: November 2017

ABSTRACTHigh-throughput sequencing has fundamentally changed how molecular phylogenetic datasets are assembled, and phylogenomic datasets commonly contain 50-100-fold more loci than those generated using traditional Sanger-based approaches. Here, we demonstrate a new approach for building phylogenomic datasets using single tube, highly multiplexed amplicon sequencing, which we name HiMAP (Highly Multiplexed Amplicon-based Phylogenomics), and present bioinformatic pipelines for locus selection based on genomic and transcriptomic data resources and post-sequencing consensus calling and alignment. This method is inexpensive and amenable to sequencing a large number (hundreds) of taxa simultaneously, requires minimal hands-on time at the bench (<1/2 day), and data analysis can be accomplished without the need for read mapping or assembly. We demonstrate this approach by sequencing 878 amplicons in single reactions for 82 species of tephritid fruit flies across seven genera (384 individuals), including some of the most economically-important agricultural insect pests. The resulting dataset (>150,000 bp concatenated alignment) contained >40,000 phylogenetically informative characters, and although some discordance was observed between analyses, it provided unparalleled resolution of many phylogenetic relationships in this group. Most notably, we found high support for the generic status ofZeugodacusand the sister relationship betweenDacusandZeugodacus. We discuss HiMAP, with regard to its molecular and bioinformatic strengths, and the insight the resulting dataset provides into relationships of this diverse insect group.
Absence of receptor guanylyl cyclase C enhances ileal damage and reduces cytokine and antimicrobial peptide production during oralSalmonellaTyphimurium infection
Authors: Majumdar Shamik , Mishra Vishwas , Nandi Somesh , Abdullah Mudabir , Barman Anaxee , Raghavan Abinaya , Nandi Dipankar , Visweswariah Sandhya S. 
Published: November 2017

AbstractNon-typhoidalSalmonelladisease contributes towards significant morbidity and mortality across the world. Host factors including IFN-γ, TNF-α and gut microbiota, significantly influence the outcome ofSalmonellapathogenesis. However, the entire repertoire of host protective mechanisms contributing toSalmonellapathogenicity is not completely appreciated. Here, we have investigated the roles of receptor guanylyl cyclase C (GC-C) that is predominantly expressed in the intestine, and regulates intestinal cell proliferation and fluid-ion homeostasis. Mice deficient in GC-C (Gucy2c-/-) displayed accelerated mortality following infection via the oral route, in spite of possessing comparative systemicSalmonellainfection burden. Survival following intra-peritoneal infection remained similar, indicating that GC-C offered protection via a gut-mediated response. Serum cortisol was higher inGucy2c-/-mice, in comparison to wild type (Gucy2c+/+) mice, and an increase in infection-induced thymic atrophy, with loss in immature CD4+CD8+double positive thymocytes, was observed. Accelerated and enhanced damage in the ileum, including submucosal edema, epithelial cell damage, focal tufting and distortion of villus architecture, was seen inGucy2c-/-mice, concomitant with a larger number of ileal tissue-associated bacteria. Transcription of key mediators inSalmonella-induced inflammation (IL-22/Reg3β) were altered inGucy2c-/-mice in comparison toGucy2c+/+mice. A reduction in fecal Lactobacilli, which are protective against Salmonella infection, was observed inGucy2c-/-mice.Gucy2c-/-mice cohoused with wild type mice continued to show reduced Lactobacilli and increased susceptibility to infection. Our study therefore suggests that receptor GC-C confers a survival advantage during gut-mediatedS. Typhimurium pathogenesis, presumably by regulatingSalmonella-effectormechanisms and maintaining a beneficial microbiome.
Behavioral state-dependent lateralization of dorsal dentate gyrus c-Fos expression in mice
Authors: Jordan Jake T. , Shanley M. Regis , Pytte Carolyn L. 
Published: November 2017

AbstractHemispheric lateralization is a fundamental organizing principle of nervous systems across taxonomic groups with bilateral symmetry. The mammalian hippocampus is lateralized anatomically, physiologically, and chemically; however, functional asymmetries are not yet well understood. Imaging studies in humans have implicated the left and right hippocampus in specialized processing. However, it is not clear if lateralized activity occurs in the rodent hippocampus. c-Fos imaging in animals provides a measure of neuronal activity with a resolution at the level of single cells. The aim of this study was to determine whether lateralized activity-dependent c-Fos expression occurs in the rodent hippocampus. To understand functional lateralization of hippocampal processing, we compared interhemispheric expression of c-Fos in the dentate gyrus (DG), a structure involved in encoding new experiences, in mice that ran on a wheel, encoded a novel object, or remained in home cages. We found that wheel running induced the greatest amount of DG c-Fos expression in both hemispheres, with no difference between hemispheres. Object exploration resulted in left-lateralized DG c-Fos expression, whereas control mice were not lateralized. We then sought to determine whether differential consideration of hemispheres might influence the conclusions of a study by simulating common cell quantification methods. We found that different approaches led to different conclusions. These data demonstrate lateralization of neuronal activity in the mouse DG corresponding to the experience of the animal and show that differentially considering hemisphere leads to alternative conclusions.
Variational Autoencoder: An Unsupervised Model for Modeling and Decoding fMRI Activity in Visual Cortex
Authors: Han Kuan , Wen Haiguang , Shi Junxing , Lu Kun-Han , Zhang Yizhen , Liu Zhongming 
Published: November 2017

AbstractGoal-driven and feedforward-only convolutional neural networks (CNN) have been shown to be able to predict and decode cortical responses to natural images or videos. Here, we explored an alternative deep neural network, variational auto-encoder (VAE), as a computational model of the visual cortex. We trained a VAE with a five-layer encoder and a five-layer decoder to learn visual representations from a diverse set of unlabeled images. Inspired by the “free-energy” principle in neuroscience, we modeled the brain’s bottom-up and top-down pathways using the VAE’s encoder and decoder, respectively. Following such conceptual relationships, we used VAE to predict or decode cortical activity observed with functional magnetic resonance imaging (fMRI) from three human subjects passively watching natural videos. Compared to CNN, VAE resulted in relatively lower accuracies for predicting the fMRI responses to the video stimuli, especially for higher-order ventral visual areas. However, VAE offered a more convenient strategy for decoding the fMRI activity to reconstruct the video input, by first converting the fMRI activity to the VAE’s latent variables, and then converting the latent variables to the reconstructed video frames through the VAE’s decoder. This strategy was more advantageous than alternative decoding methods, e.g. partial least square regression, by reconstructing both the spatial structure and color of the visual input. Findings from this study support the notion that the brain, at least in part, bears a generative model of the visual world.
Theory of site-specific DNA-protein interactions in the presence of nucleosome roadblocks
Authors: Murugan R. 
Published: November 2017

AbstractWe show that nucleosomes can efficiently control the relative search times spent by transcription factors (TFs) on one- (1D) and three-dimensional (3D) diffusion routes towards locating their cognate sites on DNA. Our theoretical results suggest that the roadblock effects of nucleosomes are dependent on the relative position on DNA with respect to TFs and their cognate sites. Especially, nucleosomes exert maximum amount of hindrance to the 1D diffusion dynamics of TFs when they are positioned in between TFs and their cognate sites. The effective 1D diffusion coefficient (χTF) associated with the dynamics of TFs in the presence of nucleosome decreases with the free energy barrier (µ) associated the sliding dynamics of nucleosomes as . Subsequently the mean first passage time (ηL) that is required by TFs to scan L number of binding sites on DNA via 1D diffusion increases with μ as . When TFs move close to nucleosomes then they exhibit a typical sub-diffusive dynamics. Nucleosomes can enhance the search dynamics of TFs when TFs present in between nucleosomes and transcription factor binding sites (TFBS). The level of enhancement effects of nucleosomes seems to be much lesser than the level of retardation effects when nucleosomes present in between TFs and their cognate sites. These results suggest that nucleosome depleted regions around the cognate sites of TFs is mandatory for an efficient site-specific interactions of TFs with DNA. Remarkably the genome wide positioning pattern of TFs shows maximum at their specific binding sites and the positioning pattern of nucleosome shows minimum at the specific binding sites of TFs under in vivo conditions. This seems to be a consequence of increasing level of breathing dynamics of nucleosome cores and decreasing levels of fluctuations in the DNA binding domains of TFs as they move across TFBS. Since the extent of breathing dynamics of nucleosomes and fluctuations in the DBDs of TFs are directly linked with their respective 1D diffusion coefficients, the dynamics of TFs becomes slow as they approach their cognate sites so that TFs form tight site-specific complex. Whereas the dynamics of nucleosomes becomes rapid so that they pass through the cognate sites of TFs. Several in vivo datasets on genome wide positioning pattern of nucleosomes as well as TFs seem to agree well with our arguments. We further show that the condensed conformational state of DNA can significantly decrease the retarding effects of nucleosome roadblocks. The retarding effects of nucleosomes on the 1D diffusion dynamics of TFs can be nullified when the degree of condensation of the genomic DNA is such that it can permit a jump size associated with the dynamics of TFs beyond k > 150 bps.
Binless normalization of Hi-C data provides significant interaction and difference detection independently of resolution
Authors: Spill Yannick G. , Castillo David , Marti-Renom Marc A. 
Published: November 2017

Abstract3C-like experiments, such as 4C or Hi-C, have been fundamental in understanding genome organization. Thanks to these technologies, it is now known, for example, that Topologically Associating Domains (TADs) and chromatin loops are implicated in the dynamic interplay of gene activation and repression, and their disruption can have dramatic effects on embryonic development. To make their detection easier, scientists have endeavored into deeper sequencing to mechanically increase the chances to detect weaker signals such as chromatin loops. Part of this mindset can be attributed to the limitations of existing software: the analysis of Hi-C experiments is both statistically and computationally demanding. Here, we devise a new way to represent Hi-C data, which leads to a more detailed classification of paired-end reads and, ultimately, to a new normalization and interaction detection method. Unlike any other, Binless is resolution-agnostic, and adapts to the quality and quantity of available data. We demonstrate its capacities to call interactions and differences and make the software freely available.
Divalent metal cations potentiate the predatory capacity of amoeba forCryptococcus neoformans
Authors: Fu Man Shun , Casadevall Arturo 
Published: November 2017

AbstractAmong the best studied interaction between soil phagocytic predators and a human pathogenic fungus is that ofAcanthamoeba castellaniiandCryptococcus neoformans. The experimental conditions used in amoeba-fungal confrontation assays can have major effects on whether the fungus or the protozoan is ascendant in the interaction. In the presence of Mg2+and Ca2+in PBS,C. neoformanswas consistently killed when incubated withA. castellanii.A. castellaniisurvived better in the presence of Mg2+and Ca2+, even when incubated withC. neoformans. In the absence of Mg2+and Ca2+,C. neoformanssurvived when incubated withA. castellanii, and the percentage of dead amoeba was higher than when incubated without yeast cells. These results show that the presence of Mg2+and Ca2+can make a decisive contribution toward tilting the outcome of the interaction in favor of amoeba. Of the two metals Mg2+had a stronger effect than Ca2+. Cations enhancedA. castellaniiactivity againstC. neoformansthrough enhanced phagocytosis, which is the major mechanism for amoeba to kill fungal cells. We found no evidence that amoeba uses extracellular killing mechanisms in their interactions withC. neoformans. In summary, the presence of Mg2+and Ca2+enhanced cell adhesion on surface and motility of amoeba, thus increasing the chance for contact ofC. neoformansand the frequency of phagocytosis. Our findings imply that divalent cation concentration in soils could be an important variable for whether amoeba can controlC. neoformansin the environment.ImportanceGrazing of soil organisms by phagocytic predators such as amoeba is thought to select for traits that allow some of them to acquire the capacity for virulence in animals. Consequently, knowledge about the interactions between amoeba and soil microbes, such as pathogenic fungi, is important for understanding how virulence can emerge. We show that the interaction between amoeba and the pathogenic fungusC. neoformansis influenced by the presence of magnesium and calcium in the assay, which potentiate amoeba. The results may also have practical applications since enriching soils with divalent cations may reduceC. neoformansnumbers in contaminated soils.
Enhancing knowledge sharing in high-tech firms
Authors: Chiu Chou-Kang , Lin Chieh-Peng , Tsai Yuan-Hui , Teh Siew-Fong 
Published: November 2017

PurposeThe purpose of this paper is to explore the development of knowledge sharing from the perspectives of broaden-and-build theory and expectancy theory. Its research purpose is to understand how knowledge sharing is driven by such predictors as optimism, pessimism, and positive affect through their complex interactions with collectivism or power distance. In the proposed model of this study, knowledge sharing relates to optimism and pessimism via the partial mediation of positive affect. At the same time, the influence of optimism, pessimism, and positive affect on knowledge sharing are moderated by the national culture of collectivism and power distance, respectively.Design/methodology/approachThis study’s hypotheses were empirically tested using data from high-tech firms across Taiwan and Malaysia. Of the 550 questionnaires provided to the research participants, 397 usable questionnaires were collected (total response rate of 72.18 percent), with 237 usable questionnaires from Taiwanese employees and 160 usable questionnaires from Malaysian employees. The data from Taiwan and Malaysia were pooled and analyzed using: confirmatory factor analysis for verifying data validity, independent samplet-tests for verifying the consistency with previous literature regarding cultural differences, and hierarchical regression analysis for testing relational and moderating effects.FindingsThis study demonstrates the integrated application of the broaden-and-build theory and expectancy theory for understanding optimism, pessimism, and positive affect in the development of knowledge sharing. The test results confirm that positive affect partially mediates the relationship between optimism and knowledge sharing and fully mediates the relationship between pessimism and knowledge sharing. Moreover, collectivism and power distance have significant moderating effects on most of the model paths between knowledge sharing and its predictors except for the relationship between pessimism and knowledge sharing.Originality/valueThis study extends the expectancy theory to justify how optimistic and pessimistic expectations are stable traits that dominate the way employees share their knowledge sharing. This study shows how collectivism and power distance of Hofstede’s cultural framework can be blended with the broaden-and-build theory and expectancy theory to jointly explain knowledge sharing. Besides, this study provides additional support to the adaptation theory of well-being that suggests psychosocial interventions, which manage to enhance well-being by leveraging positive affect, hold the promise of reducing stressful symptoms and boosting psychological resources among employees.
A step‐wise approach to developing indicators to compare the performance of maternity units using hospital administrative data
Authors: Geary RS , Knight HE , Carroll FE , Gurol‐Urganci I , Morris E , Cromwell DA , van der Meulen JH 
Published: November 2017

Hospital administrative data are attractive for comparing performance of maternity units because of their often large sample sizes, lack of selection bias and the relatively low costs of accessing these data compared with conducting primary data collection. However, using administrative data to develop indicators can also present challenges including varying data quality, the limited detail on clinical risk factors and a lack of structural and user experience measures. This review illustrates how to develop performance indicators for maternity units using hospital administrative data, including methods to address the challenges that administrative data pose.Tweetable abstractHow to develop maternity indicators from administrative data.
Temporal Trends in Rainwater Tank Suicides in Rijeka, Croatia—A 30‐year Study
Authors: Ferenčić Antun , Šoša Ivan , Cuculic Drazen , Stemberga Valter , Byard Roger W. 
Published: November 2017

AbstractAlthough drowning in rainwater tanks is a generally rare phenomenon, this method for suicide has been observed in parts of Croatia. Review of autopsy records at the University of Rijeka, Croatia, was undertaken from 1987 to 2016 to examine this phenomenon. Of 469 drowning deaths, there were 35 suicides in rainwater tanks (7.5%). Overall drowning deaths showed no temporal trends. In contrast, suicidal drownings in rain water tanks showed a marked decline over the years, with 15 cases in 1987–1991, seven in 1992–1996, six in 1997–2001, six in 2002–2006, one in 2007–2011, and none in 2012–2016. Thus, suicidal drowning cases as a percentage of overall drownings dropped from 18% to zero (p<0.001). This study reports a very unusual method of suicide that may have occurred because of the ready availability of large water reservoirs in homes. The recent fall in numbers may relate to less reliance on domestic reservoirs of water.
The post‐politics of transport: establishing a new meeting ground for transport politics
Authors: Legacy Crystal 
Published: November 2017

AbstractThis paper brings together two disparate but critical bodies of literature about contemporary citizen participation in the Australian city: transport politics and post‐politics. The argument is advanced that state and citizen actor relations—as they exist in the governance and management of Australian urban transport—have taken on characteristics of post‐politics. By conceiving of citizen participation in this manner, new ways of understanding it are generated and it is possible to appreciate how such participation is shaped by state actors both across time and in response to the politicisation of transport proposals. The paper illustrates the extent to which citizen engagement has become a new focal point in transport politics, particularly given citizens' capacities to politicise proposals and transport trajectories. It achieves such ends by drawing upon key‐informant interviews conducted between 2013 and 2016 with public transport advocates, select resident groups, and local and state level planning officials from Melbourne, Australia.
Integrating evolutionary biology with digital arts to quantify ecological constraints on vision‐based behaviour
Authors: Bian Xue , Chandler Tom , Laird Warwick , Pinilla Angela , Peters Richard 
Published: November 2017

Abstract

Motion vision is crucial in the life of animals, in controlling locomotion, in foraging, for predator evasion and in communication. However, information on the conditions for motion vision in natural environments is limited. Advancing knowledge of the ecological limitations that affect functional behaviour requires novel methodologies.

To explore motion ecology in more detail we describe an innovative method that integrates evolutionary biology with digital arts. A visualization tool that simulates three spatial dimensions plus movement through time, 3D animation is an innovative approach to understand dynamic environments. Animal signalling systems have provided useful insights into ecological limitations on behaviour, and we demonstrate the utility of our approach by examining motion displays of lizards surrounded by plant motion noise.

The effectiveness of signals in noise was considered under different circumstances, and in each case, we had complete control over the simulations. We used these scenarios to both validate our approach and to demonstrate its potential. The relevance to motion signalling of prevailing wind and resultant plant motion is now well established and we begin by replicating this effect and illustrate how we can explore this in quantitative detail. We further demonstrate its utility by providing novel insights into the benefits of signalling in the right place and at the right time, by manipulating immediate signalling backgrounds, variation in signaller–plant distances and light environments. Each of these simulations provide opportunities for investigation that would be impossible in nature.

Systematic measurements of motion ecology in detail are now achievable. In addition to insights into the evolution of motion signals, 3D environmental reconstruction will provide a test bed for other topics in the field of motion ecology, and a resource to enhance public engagement with science.