bluuebunny/crossref_metadata_2025_split huggingface dataset:
The effects of a 6-week core exercises on swimming performance of national level swimmers
Authors: Karpiński Jakub , Rejdych Wojciech , Brzozowska Dominika , Gołaś Artur , Sadowski Wojciech , Swinarew Andrzej , Stachura Alicja , Gupta Subir , Stanula Arkadiusz 
Published: December 2019

AbstractThe aim of this study was to assess the impact of a 6-week specialized training program aimed at strengthening core muscles to improve the effectiveness of selected elements of a swimming race in group of elite polish swimmers. Sixteen male national and international level swimmers (21.6 ± 2.2 years) participated in the research. The competitors were randomly assigned to 1 of 2 groups before the data collection process: an experimental (EG, n = 8) and control (CG, n = 8) group. Both groups of swimmers carried out the same training program in the water environment (volume and intensity), while swimmers from EG additionally carried out the specific core muscle training. The task of the swimmers was an individual swim of 50 meters freestyle, during which the kinematic parameters of start, turn and swimming techniques were recorded using the video camera system. In both groups a minor increase in the flight phase was observed during the start (EG=0.06 m, 1.8%; p=0.088; CG = 0.08 m, 2.7%; p=0.013). The time of the distance 5 m after the turn and the recorded average speed of swimming this distance in EG statistically significant improved accordingly 0.1 s (−28.6%; p<0.001) and 3.56 m·s-1(23.2%; p=0.001). In EG, a statistically significant improvement in 50-m freestyle performance was observed by 0.3 s (−1.2%, p = 0.001). The results of the research show that the implementation of isolated strength of the stabilizing muscles seems to be a valuable addition to the standard training of swimmers.
Comparison of alternative models of human movement and the spread of disease
Authors: Bjørnstad Ottar N. , Grenfell Bryan T. , Viboud Cecile , King Aaron A. 
Published: December 2019

AbstractPredictive models for the spatial spread of infectious diseases has received much attention in recent years as tools for the management of infectious diseas outbreaks. Prominently, various versions of the so-called gravity model, borrowed from transportation theory, have been used. However, the original literature suggests that the model has some potential misspecifications inasmuch as it fails to capture higher-order interactions among population centers. The fields of economics, geography and network sciences holds alternative formulations for the spatial coupling within and among conurbations. These includes Stouffer’s rank model, Fotheringham’s competing destinations model and the radiation model of Simini et al. Since the spread of infectious disease reflects mobility through the filter of age-specific susceptibility and infectivity and since, moreover, disease may alter spatial behavior, it is essential to confront with epidemiological data on spread. To study their relative merit we, accordingly, fit variants of these models to the uniquely detailed dataset of prevaccination measles in the 954 cities and towns of England and Wales over the years 1944-65 and compare them using a consistent likelihood framework. We find that while the gravity model is a reasonable first approximation, both Stouffer’s rank model, an extended version of the radiation model and the Fotheringham competing destinations model provide significantly better fits, Stouffer’s model being the best. Through a new method of spatially disaggregated likelihoods we identify areas of relatively poorer fit, and show that it is indeed in densely-populated conurbations that higher order spatial interactions are most important. Our main conclusion is that it is premature to narrow in on a single class of models for predicting spatial spread of infectious disease. The supplemental materials contain all code for reproducing the results and applying the methods to other data sets.Author summaryThe ability to predict how infectious disease will spread is of great importance in the face of the numerous emergent and re-emergent pathogens that currently threatening human well-being. We identified a variety of alternative models that predict human mobility as as a function of population distribution across a landscape. These consider some models that account for pair-wise interactions between population centers, as well as some that allow for higher-order interactions. We trained the models using a uniquely rich spatiotemporal data set on pre-vaccination measles in England and wales (1944-65), which comprises more than a million records from 954 cities and towns. Likelihood rankings of the different models reveal strong evidence for higher-order interactions in the form of competition among cities as destinations for travelers and, thus, dilution of spatial transmission. The currently most commonly used so-called ‘gravity’ models were far from the best in capturing spatial disease dynamics.
Self-organization in brain tumors: how cell morphology and cell density influence glioma pattern formation
Authors: Jamous Sara , Comba Andrea , Lowenstein Pedro , Motsch Sebastien 
Published: December 2019

AbstractModeling cancer cells is essential to better understand the dynamic nature of brain tumors and glioma cells, including their invasion of normal brain. Our goal is to study how the morphology of the glioma cell influences the formation of patterns of collective behavior such as flocks (cells moving in the same direction) or streams (cells moving in opposite direction) referred to asoncostream. We have observed experimentally that the presence of oncostreams correlates with tumor progression. We propose an original agent-based model that considers each cell as an ellipsoid. We show that stretching cells from round to ellipsoid increases stream formation.A systematic numerical investigation of the model was implemented in ℝ2. We deduce a phase diagram identifying key regimes for the dynamics (e.g. formation of flocks, streams, scattering). Moreover, we study the effect of cellular density and show that, in contrast to classical models of flocking, increasing cellular density reduces the formation of flocks. We observe similar patterns in ℝ3with the noticeable difference that stream formation is more ubiquitous compared to flock formation.Author summarySelf-organization is the formation of large-scale multicellular patterns that result exclusively from the interactions amongst constituent single cells. To establish the existence of self-organization in brain tumors we used agent-based modeling based on data extracted from static and dynamic genetically engineered mouse glioma models. Implementation of our model in ℝ2identifies the dynamics that lead to formation of flocks (cells moving in a single direction), streams (cells moving in two directions), and cells moving as swarms or scattering. Increasing cellular density reduced formation of flocks and increased the formation of streams both in ℝ2and in ℝ3. These results demonstrate the detailed mechanism leading to self-organization in brain tumors. As increasing density of oncostreams correlates with tumor malignancy, we establish a pathophysiological link between self-organization of glioma tumors and glioma malignancy. We propose the dismantling of oncostreams as a new therapeutic approach to the treatment of brain tumors.
TRA1: a locus responsible for controllingAgrobacterium-mediated transformability in barley
Authors: Orman-Ligeza Beata , Harwood Wendy , Hedley Pete E. , Hinchcliffe Alison , Macaulay Malcolm , Uauy Cristobal , Trafford Kay 
Published: December 2019

AbstractIn barley (Hordeum vulgareL.),Agrobacterium-mediated transformation efficiency is highly dependent on genotype with very few cultivars being amenable to transformation. Golden Promise is the cultivar most widely used for barley transformation and developing embryos are the most common donor tissue. We tested whether barley mutants with abnormally large embryos were more or less amenable to transformation and discovered that mutant M1460 had a transformation efficiencies similar to that of Golden Promise. The large-embryo phenotype of M1460 is due to mutation at theLYS3locus. There are three other barley lines with independent mutations at the sameLYS3locus, and one of these, Risø1508 has an identical missense mutation to that in M1460. However, none of thelys3mutants except M1460 were transformable showing that the locus responsible for transformation efficiency,TRA1, was notLYS3but another locus unique to M1460. To identifyTRA1, we generated a mapping population by crossing M1460 to the cultivar Optic, which is recalcitrant to transformation. After four rounds of backcrossing to Optic, plants were genotyped and their progeny were tested for transformability. Some of the progeny lines were transformable at high efficiencies similar to those seen for the parent M1460 and some were not transformable, like Optic. A region on chromosome 2H inherited from M1460 is present in transformable lines only. We propose that one of the 225 genes in this region isTRA1.
Adding insult to injury: Effects of chronic oxybenzone exposure and elevated temperature on two reef-building corals
Authors: Wijgerde Tim , van Ballegooijen Mike , Nijland Reindert , van der Loos Luna , Kwadijk Christiaan , Osinga Ronald , Murk Albertinka , Slijkerman Diana 
Published: December 2019

AbstractWe studied the effect of chronic oxybenzone exposure and elevated temperature on coral health. Microcolonies ofStylophora pistillataandAcropora tenuiswere cultured in 20 flow-through aquaria, of which 10 were exposed to oxybenzone at a field-relevant concentration of ~0.06 μg L−1at 26 °C. After two weeks, half of the corals experienced a heat wave culminating at 33 °C. AllS. pistillatacolonies survived the heat wave, although heat reduced growth and zooxanthellae density, irrespective of oxybenzone.A. tenuissurvival was reduced to 0% at 32 °C, and oxybenzone accelerated mortality. Oxybenzone and heat significantly reduced photosynthetic yield in both species, causing a 5% and 22−33% decrease, respectively. In addition, combined oxybenzone and temperature stress altered the abundance of five bacterial families in the microbiome ofS. pistillata. Our results suggest that oxybenzone adds insult to injury by further weakening corals in the face of global warming.Highlights➢Chronic effect study on corals combining oxybenzone and elevated temperature➢Oxybenzone affected photosystem II of coral photosymbionts and altered coral microbiome➢Temperature effects were stronger than oxybenzone effects➢Sensitivities were species-dependent➢Oxybenzone adds insult to injury by weakening corals in the face of global warming
Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird-of-paradise
Authors: Peona Valentina , Blom Mozes P.K. , Xu Luohao , Burri Reto , Sullivan Shawn , Bunikis Ignas , Liachko Ivan , Jønsson Knud A. , Zhou Qi , Irestedt Martin , Suh Alexander 
Published: December 2019

AbstractGenome assemblies are currently being produced at an impressive rate by consortia and individual laboratories. The low costs and increasing efficiency of sequencing technologies have opened up a whole new world of genomic biodiversity. Although these technologies generate high-quality genome assemblies, there are still genomic regions difficult to assemble, like repetitive elements and GC-rich regions (genomic “dark matter”). In this study, we compare the efficiency of currently used sequencing technologies (short/linked/long reads and proximity ligation maps) and combinations thereof in assembling genomic dark matter starting from the same sample. By adopting different de-novo assembly strategies, we were able to compare each individual draft assembly to a curated multiplatform one and identify the nature of the previously missing dark matter with a particular focus on transposable elements, multi-copy MHC genes, and GC-rich regions. Thanks to this multiplatform approach, we demonstrate the feasibility of producing a high-quality chromosome-level assembly for a non-model organism (paradise crow) for which only suboptimal samples are available. Our approach was able to reconstruct complex chromosomes like the repeat-rich W sex chromosome and several GC-rich microchromosomes. Telomere-to-telomere assemblies are not a reality yet for most organisms, but by leveraging technology choice it is possible to minimize genome assembly gaps for downstream analysis. We provide a roadmap to tailor sequencing projects around the completeness of both the coding and non-coding parts of the genomes.
HyPo: Super Fast & Accurate Polisher for Long Read Genome Assemblies
Authors: Kundu Ritu , Casey Joshua , Sung Wing-Kin 
Published: December 2019

ABSTRACTEfforts towards making population-scale long read genome assemblies (especially human genomes) viable have intensified recently with the emergence of many fast assemblers. The reliance of these fast assemblers on polishing for the accuracy of assemblies makes it crucial. We present HyPo–aHybridPolisher–that utilises short as well as long reads within a single run to polish a long read assembly of small and large genomes. It exploits unique genomic kmers to selectively polish segments of contigs using partial order alignment of selective read-segments. As demonstrated on human genome assemblies, Hypo generates significantly more accurate polished assemblies in about one-third time with about half the memory requirements in comparison to Racon (the widely used polisher currently).
A neurocomputational model for intrinsic reward
Authors: Chew Benjamin , Blain Bastien , Dolan Raymond J , Rutledge Robb B 
Published: December 2019

SUMMARYStandard economic indicators provide an incomplete picture of what we value both as individuals and as a society. Furthermore, canonical macroeconomic measures, such as GDP, do not account for non-market activities (e.g., cooking, childcare) that nevertheless impact well-being. Here, we introduce a computational tool that measures the affective value of experiences (e.g., playing a musical instrument without errors). We go on to validate this tool with neural data, using fMRI to measure neural activity in male and female human subjects performing a reinforcement learning task that incorporated periodic ratings of subjective affective state. Learning performance determined level of payment (i.e., extrinsic reward). Crucially, the task also incorporated a skilled performance component (i.e., intrinsic reward) which did not influence payment. Both extrinsic and intrinsic rewards influenced affective dynamics, and their relative influence could be captured in our computational model. Individuals for whom intrinsic rewards had a greater influence on affective state than extrinsic rewards had greater ventromedial prefrontal cortex (vmPFC) activity for intrinsic than extrinsic rewards. Thus, we show that computational modelling of affective dynamics can index the subjective value of intrinsic relative to extrinsic rewards, a ‘computational hedonometer’ that reflects both behavior and neural activity that quantifies the affective value of experience.SIGNIFICANCE STATEMENTTraditional economic indicators are increasingly recognized to provide an incomplete picture of what we value as a society. Standard economic approaches struggle to accurately assign values to non-market activities that nevertheless may be intrinsically rewarding, prompting a need for new tools to measure what really matters to individuals. Using a combination of neuroimaging and computational modeling, we show that despite their lack of instrumental value, intrinsic rewards influence subjective affective state and ventromedial prefrontal cortex activity. The relative degree to which extrinsic and intrinsic rewards influence affective state is predictive of their relative impacts on neural activity, confirming the utility of our approach for measuring the affective value of experiences and other non-market activities in individuals.
X-ray 3D imaging of gene expression in whole-mount murine brain by microCT, implication for functional analysis of tRNA endonuclease 54 gene mutated in pontocerebellar hypoplasia
Authors: Ermakova Olga , Orsini Tiziana , Fruscoloni Paolo , Chiani Francesco , Gambadoro Alessia , Putti Sabrina , Cirilli Maurizio , Mezzi Alessio , Kaciulis Saulius , Raspa Marcello , Scavizzi Ferdinando , Tocchini-Valentini Glauco P. 
Published: December 2019

AbstractAcquisition of detailed structural and molecular information from intact biological samples, while preserving cellular three-dimensional structures, still represents a challenge for biological studies aiming to unravel system functions. Here we describe a novel X-ray-based methodology for analysis of gene expression pattern in intact murine brain ex vivo by microCT. The method relays on detection of bromine molecules in the products of enzymatic reaction generated by theβ-galactosidase (lacZ) gene reporter. To demonstrate the feasibility of the method, the analysis of the expression pattern of tRNA endonuclease 54 (Tsen54)-lacZ reporter gene in the whole-mount murine brain in semi-quantitative manner is performed. Mutations in Tsen54 gene causes pontocerebellar hypoplasia (PCH), severe neurodegenerative disorder with both mental and motor deficits. Comparing relative levels of Tsen54 gene expression, we have demonstrated that highest Tsen54 expression observed in anatomical brain substructures important for the normal motor and memory functions in mice. In the forebrain strong expression in perirhinal, retrosplenial and secondary motor areas was observed. In olfactory area Tsen54 is highly expressed in the nucleus of the lateral olfactory tract, anterior olfactory and bed nuclei, while in hypothalamus in lateral mammillary nucleus and preoptic area. In hindbrain Tsen54 is expressed in the reticular, cuneate and trigeminal nuclei of medulla, and in pontine gray of pons and in cerebellum, in the molecular and Purkinje cell layers. Delineating anatomical brain regions in which Tsen54 is strongly expressed will allow functionally address the role Tsen54 gene in normal physiology and in PCH disease.Significance StatementCharacterization of gene expression pattern in the brain of model organisms is critical for unravelling the gene function in normal physiology and disease. It is performed by optical imaging of the two-dimensional brain sections which then assembled in volume images. Here we applied microCT platform, which allows three-dimensional imaging of non transparent samples, for analysis of gene expression. This method based on detection by X-ray the bromine molecules presented in the products generated by enzymatic activity of b-galactosidase reporter gene. With this method we identify anatomical brain substructures in which Tsen54 gene, mutated in pontocerebellar hypoplasia disease, is expressed.
Modulation of Yorkie activity by alternative splicing is required for developmental stability
Authors: Srivastava Diwas , de Toledo Marion , Manchon Laurent , Tazi Jamal , Juge François 
Published: December 2019

AbstractThe mechanisms that contribute to developmental stability are barely known. Here we show that alternative splicing ofyorkie(yki) is required for developmental stability inDrosophila. Yki encodes the effector of the Hippo pathway that has a central role in controlling organ growth and regeneration. We identify the splicing factor B52 as necessary for inclusion ofykialternative exon 3 that encodes one of the two WW domains of Yki protein. B52 depletion favors expression of Yki1 isoform carrying a single WW domain, and reduces growth in part through modulation ofykialternative splicing. Compared to the canonical Yki2 isoform containing two WW domains, Yki1 isoform has reduced transcriptional and growth-promoting activities, decreased binding to PPxY-containing partners, and lacks the ability to bridge two proteins containing PPxY motifs. Yet, Yki1 and Yki2 interact similarly with transcription factors and can thus competein vivo. Strikingly, flies deprived from Yki1 isoform exhibit increased fluctuating wing asymmetry, a signal of increased developmental noise. Our results identifyykialternative splicing as a new level of control of the Hippo pathway and provide the first experimental evidence that alternative splicing participates in developmental robustness.
Non-similar solution of Casson nanofluid with variable viscosity and variable thermal conductivity
Authors: Bisht Ankita , Sharma Rajesh 
Published: December 2019

Purpose
The purpose of this study is to provide a numerical investigation of Casson nanofluid along a vertical nonlinear stretching sheet with variable thermal conductivity and viscosity.

Design/methodology/approach
The boundary-layer equations are presented in the dimensionless form using proper non-similar transformations. The subsequent non-dimensional nonlinear partial differential equations are solved using the implicit finite difference technique. To linearize the nonlinear terms present in these equations, the quasilinearization technique is used.

Findings
The investigation showed graphically the temperature, velocity and nanoparticle volume fraction for particular included physical parameters. It is observed that the velocity profile decreases with an increase in the values of Casson fluid parameter while increases with an increase in the viscosity variation parameter. The temperature profile enhances for large values of velocity variation parameter and thermal conductivity parameter while it reduces for large values of thermal buoyancy parameter. Further, the Nusselt number and skin-friction coefficient are introduced which are helpful in determining the physical aspects of Casson nanofluid flow.

Practical implications
The immediate control of heat transfer in the industrial system is crucial because of increasing energy prices. Recently, nanotechnology is proposed to control the heat transfer phenomenon. Ongoing research in complex nanofluid has been fruitful in various applications such as solar thermal collectors, nuclear reactors, electronic equipment and diesel–electric conductor. A reasonable amount of nanoparticle when added to the base fluid in solar thermal collectors serves to deeper absorption of incident radiation, and hence it upgrades the efficiency of the solar thermal collectors.

Originality/value
The non-similar solution of Casson nanofluid due to a vertical nonlinear stretching sheet with variable viscosity and thermal conductivity is discussed in this work.