bluuebunny/crossref_metadata_2025_split huggingface dataset:
Goalkeeper game: a new assessment instrument in neurology showed higher predictive power than moca for gait performance in people with parkinson’s disease
Authors: Stern Rafael B. , d’Alencar Matheus , Uscapi Yanina L. , Gubitoso Marco D. , Roque Antonio C. , Helene André F. , Piemonte Maria Elisa P. 
Published: August 2018

ObjectiveTo investigate the use of the Goalkeeper Game (GG) to assess gait automaticity decline under dual task conditions in people with Parkinson’s disease (PPD) and compare its predictive power with the one of the MoCA test.Materials and Methods74 PPD (H&Y stages: 23 in stage 1; 31 in stage 2; 20 in stage 3), without dementia (MoCA cut-off 23), tested in ON period with dopaminergic medication were submitted to single individual cognitive/motor evaluation sessions. The tests applied were: MoCA, GG, dynamic gait index (DGI) task and timed up and go test (TUG) under single and dual-task (DT) conditions. GG test resulted in 9 measures extracted via a statistical model. The predictive power of the GG measures and the MoCA score with respect to gait performance, as assessed by DGI and DT-TUG, were compared.ResultsThe predictive models based on GG measures and MoCA score obtained, respectively, sensitivities of 65% and 56% for DGI scores and 59% and 57% for DT-TUG cost at a 50% specificity. GG application proved to be feasible and aroused more motivation in PPDs than MoCa.ConclusionGG, a friendly and ludic game, was able to reach a good power of gait performance prediction in people at initial and intermediate stages of PD evolution.
Why do phylogenomic analyses of early animal evolution continue to disagree? Sites in different structural environments yield different answers
Authors: Pandey Akanksha , Braun Edward L. 
Published: August 2018

AbstractPhylogenomics has revolutionized the study of evolutionary relationships. However, genome-scale data have not been able to resolve all relationships in the tree of life. This could reflect the poor-fit of the models used to analyze heterogeneous datasets; that heterogeneity is likely to have many explanations. However, it seems reasonable to hypothesize that the different patterns of selection on proteins based on their structures might represent a source of heterogeneity. To test that hypothesis, we developed an efficient pipeline to divide phylogenomic datasets that comprise proteins into subsets based on secondary structure and relative solvent accessibility. We then tested whether amino acids in different structural environments had different signals for the deepest branches in the metazoan tree of life. Sites located in different structural environments did support distinct tree topologies. The most striking difference in phylogenetic signal reflected relative solvent accessibility; analyses of sites on the surface of proteins yielded a tree that placed ctenophores sister to all other animals whereas sites buried inside proteins yielded a tree with a sponge-ctenophore clade. These differences in phylogenetic signal were not ameliorated when we repeated our analyses using the site-heterogeneous CAT model, a mixture model that is often used for analyses of protein datasets. In fact, analyses using the CAT model actually resulted in rearrangements that are unlikely to represent evolutionary history. These results provide striking evidence that it will be necessary to achieve a better understanding the constraints due to protein structure to improve phylogenetic estimation.
The dimensions of species diversity
Authors: Larcombe Matthew J. , Jordan Gregory J. , Bryant David , Higgins Steven I. 
Published: August 2018

ABSTRACTDiversification processes underpin the patterns of species diversity that fascinate biologists. Two competing hypotheses disagree about the effect of competition on these processes. The bounded hypothesis suggests that species diversity is limited (bounded) by competition between species for finite niche space, while the unbounded hypothesis proposes that evolution and ecological opportunity associated with speciation, render competition unimportant. We use phylogenetically structured niche modelling, to show that processes consistent with both these diversification models have driven species accumulation in conifers. In agreement with the bounded hypothesis, niche competition constrained diversification, and in line with the unbounded hypothesis, niche evolution and partitioning promoted diversification. We then analyse niche traits to show that these diversification enhancing and inhibiting processes can occur simultaneously on different niche dimensions. Together these results suggests a new hypothesis for lineage diversification based on the multi-dimensional nature of ecological niches that accommodates both bounded and unbounded diversification processes.
Heat Shock Factor 1 Drives Intergenic Association of Its Target Gene Loci Upon Heat Shock
Authors: Chowdhary Surabhi , Kainth Amoldeep S. , Pincus David , Gross David S. 
Published: August 2018

ABSTRACTTranscriptional induction ofHeat Shock Protein(HSP) genes in yeast is accompanied by dynamic changes in their 3D structure and spatial organization, yet the molecular basis for these phenomena remains unknown. Using chromosome conformation capture and single cell imaging, we show that genes transcriptionally activated by Heat Shock Factor 1 (Hsf1) specifically interact across chromosomes and coalesce into diffraction-limited intranuclear foci. Genes activated by the alternative stress regulators Msn2 and Msn4, in contrast, do not interact among themselves nor with Hsf1 targets. Likewise, constitutively expressed genes, even those interposed betweenHSPgenes, show no detectable interaction. Hsf1 forms discrete subnuclear puncta when stress-activated, and these puncta dissolve in concert with transcriptional attenuation, paralleling the kinetics ofHSPgene coalescence and dissolution. Nuclear Hsf1 and RNA Pol II are both necessary for intergenicHSPgene interactions, while DNA-bound Hsf1 is necessary and sufficient to drive coalescence of a heterologous gene. Our findings demonstrate that Hsf1 can dynamically restructure the yeast genome.
Translocation and duplication from CRISPR-Cas9 editing inArabidopsis thaliana
Authors: Lynagh Peter G. , Inagaki Soichi , Amundson Kirk R. , Marimuthu Mohan P.A. , Pike Brett Randolph , Henry Isabelle M. , Tan Ek Han , Comai Luca 
Published: August 2018

AbstractCut DNA ends in plants may recombine to form novel molecules. We asked whether CRISPR-Cas9 expression in plants could induce nonhomologous recombination between diverse and heterologous broken DNA ends. We induced two breaks separated by 2.3 or by 8.5 kilobases leading to duplication of the intervening DNA and meiotic transmission of the 2.3kb duplication. Two or more dsDNA breaks in nonhomologous chromosomes led to ligation of breakpoints consistent with chromosome arm translocations. Screening 881 primary transformants we obtained 195 PCR products spanning independent, expected translocation junctions involving ends produced by cutting different loci. Sequencing indicated a true positive rate of 84/91 and demonstrated the occurrence of different junction alleles. A majority of the resulting structures would be deleterious and none were transmitted meiotically. Ligation of interchromosomal, heterologous dsDNA ends suggest that the CRISPR-Cas9 can be used to engineer plant genes and chromosomes in vivo.Significance StatementWe explored how genome editing tools such as CRISPR-Cas9 could provide new ways to tailor novel genomic combinations and arrangements. We show that distant cut ends often precisely come together, that cuts in different chromosomes can result in translocations, and that two cuts within a chromosome often result in the duplication of the intervening segment. Formation of multiple structures with precise junctions will enable engineered rearrangements that can be predicted with accuracy.
Characterization for Drought Tolerance and Physiological Efficiency in Novel Cytoplasmic Male Sterile Sources of Sunflower (Helianthus annuus L.)
Authors: Tyagi Vikrant , Kaur Gurpreet , Kaushik Prashant , Dhillon Satwinder Kaur 
Published: August 2018

Abstract:Sunflower is sensitive to drought and its hybrids have a limited cytoplasmic diversity. The wild cytoplasmic sources of sunflower are not well exploited to their potential for drought tolerance and hybrid development. In this respect, we carried out a Line × Tester based genetic study using 19 sunflower genotypes representing, 13 cytoplasmic male sterile (CMS) lines from wild and conventional sources, 2 maintainer lines, and 4 restorer lines. The CMS and maintainer lines were crossed with restorer lines to develop sixty one-way F1 hybrids. The parents and their hybrids were evaluated under two water regimes viz., normal irrigated and water stress. A total of twelve important plant descriptors were studied over a period of two years. The significant differences were observed between parents and hybrids in both water regimes. Hybrids were higher in average values for all the descriptors than parents. The role of female parent was more prominent in the expression of traits in hybrids as compared to male parents. The CMS sources varied significantly regarding seed yield per plant and other physiological traits. Proline content was three times higher in parents and their hybrids under water stress, and it was not correlated with any other descriptor. Accession CMS-PKU-2A was identified as the best general combiner for leaf area and specific leaf weight. Whereas, CMS-234A was the best general combiner for biological yield and photosynthetic efficiency under both the conditions. The cross combinations CMS-ARG-2A × RCR-8297, CMS-234A × P124R, and CMS-38A × P124R were found significant for biological yield, seed yield and oil content under both environments. Overall, this study provides useful information about the cytoplasmic effects on important sunflower traits and drought stress tolerance when used in the different combinations.
Dual role for fungal-specific outer kinetochore proteins during cell cycle and development in Magnaporthe oryzae
Authors: Shah Hiral , Rawat Kanika , Ashar Harsh , Patkar Rajesh , Manjrekar Johannes 
Published: August 2018

AbstractThe outer kinetochore DASH/DAM complex ensures proper spindle structure and chromosome segregation. While DASH complex protein requirement diverges among different yeasts, its role in filamentous fungi has not been investigated so far. We studied the dynamics and role of middle (Mis12) and outer (Dam1 and Ask1) kinetochore proteins in the filamentous fungal pathogen, Magnaporthe oryzae, which undergoes multiple cell cycle linked developmental transitions. Both Dam1 and Ask1, unlike Mis12, were recruited to the nucleus specifically during mitosis. While Dam1 was not required for viability, loss of its function (dam1Δ mutant) delayed mitotic progression, resulting in impaired conidial and hyphal development in Magnaporthe. Intriguingly, both Dam1 and Ask1 also localised to the hyphal tips, in the form of punctae oscillating back and forth from the growing ends, suggesting that Magnaporthe DASH complex proteins may play a non-canonical role in polarised growth during interphase, in addition to their function in nuclear segregation during mitosis. Impaired appressorial (infection structure) development and function in the dam1Δ mutant suggest that fungus-specific Dam1 complex proteins could be an attractive target for a novel anti-fungal strategy.Summary StatementDASH complex proteins are differentially recruited to the nucleus during cell division and are intriguingly involved in polarised growth during development and differentiation in the rice blast fungus.
Evolution of mating types in finite populations: the precarious advantage of being rare
Authors: Czuppon Peter , Rogers David W. 
Published: August 2018

AbstractSexually reproducing populations with self-incompatibility bear the cost of limiting potential mates to individuals of a different type. Rare mating types escape this cost since they are unlikely to encounter incompatible partners, leading to the deterministic prediction of continuous invasion by new mutants and an ever increasing number of types. However, rare types are also at an increased risk of being lost by random drift. Calculating the number of mating types that a population can maintain requires consideration of both the deterministic advantages and the stochastic risks. By comparing the relative importance of selection and drift, we show that a population of sizeNcan maintain a maximum of approximatelyN1/3mating types for intermediate population sizes while for largeNwe derive a formal estimate. Although the number of mating types in a population is quite stable, the rare type advantage promotes turnover of types. We derive explicit formulas for both the invasion and turnover probabilities in finite populations.
Development of Coupling Controlled Polymerizations by Adapter-ligation in Mate-pair Sequencing for Detection of Various Genomic Variants in One Single Assay
Authors: Dong Zirui , Zhao Xia , Li Qiaoling , Yang Zhenjun , Xi Yang , Alexeev Andrei , Shen Hanjie , Wang Ou , Ruan Jie , Ren Han , Wei Hanmin , Qi Xiaojuan , Li Jiguang , Zhu Xiaofan , Zhang Yanyan , Dai Peng , Kong Xiangdong , Kirkconnell Killeen , Alferov Oleg , Giles Shane , Yamtich Jennifer , Kermani Bahram G. , Dong Chao , Liu Pengjuan , Mi Zilan , Zhang Wenwei , Xu Xun , Drmanac Radoje , Choy Kwong Wai , Jiang Yuan 
Published: August 2018

AbstractThe diversity of disease presentations warrants one single assay for detection and delineation of various genomic disorders. Herein, we describe a gel-free and biotin-capture-free mate-pair method through coupling Controlled Polymerizations by Adapter-Ligation (CP-AL). We first demonstrated the feasibility and ease-of-use in monitoring DNA nick-translation and primer extension by limiting the nucleotide input. By coupling these two controlled polymerizations by a reported non-conventional adapter ligation reaction 3’ branch ligation, we evidenced that CP-AL significantly increased DNA-circularization efficiency (by 4-fold) and was applicable for different sequencing methods but at a faction of current cost. Its advantages were further demonstrated by fully elimination of small-insert-contaminated (by 39.3-fold) with a ~50% increment of physical coverage, and producing uniform genome/exome coverage and the lowest chimeric rate. It achieved single-nucleotide variants detection with sensitivity and specificity up to 97.3 and 99.7%, respectively, compared with data from small-insert libraries. In addition, this method can provide a comprehensive delineation of structural rearrangements, evidenced by a potential diagnosis in a patient with oligo-atheno-terato-spermia. Moreover, it enables accurate mutation identification by integration of genomic variants from different aberration types. Overall, it provides a potential single-integrated solution for detecting various genomic variants, facilitating a genetic diagnosis in human diseases.
Deep attention networks reveal the rules of collective motion in zebrafish
Authors: Heras Francisco J.H. , Romero-Ferrero Francisco , Hinz Robert C. , Polavieja Gonzalo G. de 
Published: August 2018

AbstractA variety of simple models has been proposed to understand the collective motion of animals. These models can be insightful but lack important elements necessary to predict the motion of each individual in the collective. Adding more detail increases predictability but can make models too complex to be insightful. Here we report that deep attention networks can obtain in a data-driven way a model of collective behavior that is simultaneously predictive and insightful thanks to an organization in modules. The model obtains that interactions between two zebrafish, Danio rerio, in a large groups of 60-100, can be approximately be described as repulsive, attractive or as alignment, but only when moving slowly. At high velocities, interactions correspond only to alignment or alignment mixed with repulsion at close distances. The model also shows that each zebrafish decides where to move by aggregating information from the group as a weighted average over neighbours. Weights are higher for neighbours that are close, in a collision path or moving faster in frontal and lateral locations. These weights effectively select 5 relevant neighbours on average, but this number is dynamical, changing between a single neighbour to up to 12, often in less than a second. Our results suggest that each animal in a group decides by dynamically selecting information from the group.HighlightsAt 30 days postfertilization, zebrafish, Danio rerio, can move in very cohesive and predictable large groupsDeep attention networks obtain a predictive and understadable model of collective motionWhen moving slowly, interations between pairs of zebrafish have clear components of repulsion, attraction and alignmentWhen moving fast, interactions correspond to alignment and a mixture of alignment and repulsion at close distancesZebrafish turn left or right depending on a weighted average of interaction information with other fish, with weights higher for close fish, those in a collision path or those moving fast in front or to the sidesAggregation is dynamical, oscillating between 1 and 12 neighbouring fish, with 5 on average
Environmental programming of adult foraging behavior in C. elegans
Authors: Pradhan Sreeparna , Quilez Sabrina , Homer Kai , Hendricks Michael 
Published: August 2018

AbstractForaging strategies must be tuned to the availability and distribution of resources in the environment. This can occur over generations and lead to genetic differences in foraging behavior, or it can occur on shorter time scales within an individual’s life span. Both genetic and experience-based strategies must be implemented by neural circuits that respond to environmental cues and track internal states, and the analysis of such circuits provides insight into the neural basis of complex decision making. In C. elegans, between-strain genetic differences and within-strain plasticity in foraging has been observed. Most individual changes in foraging are short-term, based on experience over several hours. Here, we tested if developmental experience could permanently alter foraging. We found that in wild strains that are normally highly exploratory, early-life starvation leads to “cautious” foraging behavior in which exploration is reduced. We characterize the behavioral bases for these strategies and identify changes in the dynamics of a locomotory circuit involved in navigation. Overall, we show that some C. elegans strains exhibit adaptive tuning of their foraging behavior based on early-life experience, and this is associated with changes in a core navigation circuit.
gFACs: Filtering, Analysis, and Conversion to Unify Genome Annotations Across Alignment and Gene Prediction Frameworks
Authors: Caballero Madison , Wegrzyn Jill 
Published: August 2018

AbstractPublished genome annotations are filled with erroneous gene models that represent issues associated with frame, start side identification, splice sites, and related structural features. The source of these inconsistencies can often be traced to translated text file formats designed to describe long read alignments and predicted gene structures. The majority of gene prediction frameworks do not provide downstream filtering to remove problematic gene annotations, nor do they represent these annotations in a format consistent with current file standards. In addition, these frameworks lack consideration for functional attributes, such as the presence or absence of protein domains which can be used for gene model validation. To provide oversight to the increasing number of published genome annotations, we present gFACs as a software package to filter, analyze, and convert predicted gene models and alignments. gFACs operates across a wide range of alignment, analysis, and gene prediction software inputs with a flexible framework for defining gene models with reliable structural and functional attributes. gFACs supports common downstream applications, including genome browsers and generates extensive details on the filtering process, including distributions that can be visualized to further assess the proposed gene space.
Gridlock from Diagnosis to Treatment of Multidrug Resistant Tuberculosis (MDR-TB) in Tanzania: Patients’ Perspectives from the Focus Group Discussion
Authors: Mpagama Stellah G , Mangi Ezekiel , Mbelele Peter M , Chongolo Anna M , Kibiki Gibson S , Heysell Scott K 
Published: August 2018

AbstractIntroductionMolecular diagnostics have revolutionized the diagnosis of multidrug resistant tuberculosis (MDR-TB). Yet in Tanzania we found delay in diagnosis with more than 70% of MDR-TB patients having history of several previous treatment courses for TB signaling complications of prior missed diagnosis. We aimed to explore patients’ viewpoints and experiences with personal and socio-behavioral obstacles from MDR-TB diagnosis to treatment in an attempt to understand these prior findings.MethodsThe study was conducted in December 2016 with MDR-TB patients admitted at Kibong’oto Infectious Diseases Hospital. We used semi-structured interviews and focus group discussion to examine patients’ views and experiences during MDR-TB diagnosis. Groups were sex aggregated to allow free interaction and to gauge gender specific issues in the social and behavioral contexts. The discussion – explored patients’ delivery factors that were impacting delay from MDR-TB diagnosis to treatment. Iterative data collection and analysis was applied with data, codes and categories being compared and refined.ResultsForty-five MDR-TB patients participated in 6 focus group discussions. Challenges and barriers contributing to the delay from MDR-TB diagnosis to treatment were as follows: 1) The general population had differing understanding of MDR-TB that led to seeking services from traditional healers; 2) Also socio-economic adversity made health-seeking behavior difficult and often unproductive; 3) In the health system, challenges included inadequacy of MDR-TB diagnostic centers, lack of knowledge on behalf of health care providers to consider MDR-TB and order appropriate diagnostics; 4) Insufficiency in the specimen referral system for early diagnosis of MDR-TB. Non-adherence of TB patients to first-line anti-TB drugs prior to MDR-TB diagnosis given the multitude of barriers discussed was coupled with both intentional and unintentional non-adherence of health care providers to international standards of TB care.ConclusionPatient-centered strategies bridging communities and the health system are urgently required for optimum MDR-TB control in Tanzania.