bluuebunny/crossref_metadata_2025_split huggingface dataset:
VADR: validation and annotation of virus sequence submissions to GenBank
Authors: Schäffer Alejandro A , Hatcher Eneida L , Yankie Linda , Shonkwiler Lara , Brister J Rodney , Karsch-Mizrachi Ilene , Nawrocki Eric P 
Published: November 2019

AbstractBackgroundGenBank contains over 3 million viral sequences. The National Center for Biotechnology Information (NCBI) previously made available a tool for validating and annotating influenza virus sequences that is used to check submissions to GenBank. Before this project, there was no analogous tool in use for non-influenza viral sequence submissions.ResultsWe developed a system called VADR (Viral Annotation DefineR) that validates and annotates viral sequences in GenBank submissions. The annotation system is based on the analysis of the input nucleotide sequence using models built from curated RefSeqs. Hidden Markov models are used to classify sequences by determining the RefSeq they are most similar to, and feature annotation from the RefSeq is mapped based on a nucleotide alignment of the full sequence to a covariance model. Predicted proteins encoded by the sequence are validated with nucleotide-to-protein alignments using BLAST. The system identifies 43 types of “alerts” that (unlike the previous BLAST-based system) provide deterministic and rigorous feedback to researchers who submit sequences with unexpected characteristics. VADR has been integrated into GenBank’s submission processing pipeline allowing for viral submissions passing all tests to be accepted and annotated automatically, without the need for any human (GenBank indexer) intervention. Unlike the previous submission-checking system, VADR is freely available (https://github.com/nawrockie/vadr) for local installation and use. VADR has been used for Norovirus submissions since May 2018 and for Dengue virus submissions since January 2019. Other viruses with high numbers of submissions will be added incrementally.ConclusionVADR improves the speed with which non-flu virus submissions to GenBank can be checked and improves the content and quality of the GenBank annotations. The availability and portability of the software allow researchers to run the GenBank checks prior to submitting their viral sequences, and thereby gain confidence that their submissions will be accepted immediately without the need to correspond with GenBank staff. Reciprocally, the adoption of VADR frees GenBank staff to spend more time on services other than checking routine viral sequence submissions.
Zygotic pioneer factor activity of Odd-paired/Zic is necessary for establishing theDrosophilaSegmentation Network
Authors: Soluri Isabella V. , Zumerling Lauren M. , Payan Parra Omar A. , Clark Eleanor G. , Blythe Shelby A. 
Published: November 2019

AbstractBecause regulatory networks of transcription factors drive embryonic patterning, it is possible that chromatin accessibility states impact how networks interact with information encoded in DNA. To determine the interplay between chromatin states and regulatory network function, we performed ATAC seq onDrosophilaembryos over the period spanning the establishment of the segmentation network, from zygotic genome activation to gastrulation. Chromatin accessibility states are dynamic over this period, and establishment of the segmentation network requires maturation of the ground chromatin state. Elimination of all maternal patterning information allows identification of patterning-dependent and -independent dynamic chromatin regions. A significant proportion of patterning-dependent accessibility stems from pioneer activity of the pair-rule factor Odd-paired (opa). Whileopais necessary to drive late opening of segmentation network cis-regulatory elements, competence foropato pioneer is regulated over time. These results indicate that dynamic systems for chromatin regulation directly impact the interpretation of embryonic patterning information.
A multiple-trait Bayesian Lasso for genome-enabled analysis and prediction of complex traits
Authors: Gianola Daniel , Fernando Rohan L. 
Published: November 2019

1AbstractA multiple-trait Bayesian LASSO (MBL) for genome-based analysis and prediction of quantitative traits is presented and applied to two real data sets. The data-generating model is a multivariate linear Bayesian regression on possibly a huge number of molecular markers, and with a Gaussian residual distribution posed. Each (one per marker) of theT× 1 vectors of regression coefficients (T: number of traits) is assigned the sameT–variate Laplace prior distribution, with a null mean vector and unknown scale matrixΣ. The multivariate prior reduces to that of the standard univariate Bayesian LASSO whenT= 1. The covariance matrix of the residual distribution is assigned a multivariate Jeffreys prior andΣis given an inverse-Wishart prior. The unknown quantities in the model are learned using a Markov chain Monte Carlo sampling scheme constructed using a scale-mixture of normal distributions representation. MBL is demonstrated in a bivariate context employing two publicly available data sets using a bivariate genomic best linear unbiased prediction model (GBLUP) for benchmarking results. The first data set is one where wheat grain yields in two different environments are treated as distinct traits. The second data set comes from genotypedPinustrees with each individual was measured for two traits, rust bin and gall volume. In MBL, the bivariate marker effects are shrunk differentially, i.e., “short” vectors are more strongly shrunk towards the origin than in GBLUP; conversely, “long” vectors are shrunk less. A predictive comparison was carried out as well where, in wheat, the comparators of MBL where bivariate GBLUP and bivariate Bayes Cπ, a variable selection procedure. A training-testing layout was used, with 100 random reconstructions of training and testing sets. For the wheat data, all methods produced similar predictions. InPinus, MBL gave better predictions that either a Bayesian bivariate GBLUP or the single trait Bayesian LASSO. MBL has been implemented in the Julia language package JWAS and is now available for the scientific community to explore with different traits, species and environments. It is well known that there is no universally best prediction machine and MBL represents a new piece in the armamentarium for genome-enabled analysis and prediction of complex traits.
The transition state and regulation of γ-TuRC-mediated microtubule nucleation revealed by single molecule microscopy
Authors: Thawani Akanksha , Rale Michael J , Coudray Nicolas , Bhabha Gira , Stone Howard A , Shaevitz Joshua W , Petry Sabine 
Published: November 2019

AbstractDetermining how microtubules (MTs) are nucleated is essential for understanding how the cytoskeleton assembles. While the MT nucleator, γ-tubulin ring complex (γ-TuRC) has been identified, precisely how γ-TuRC nucleates a MT remains poorly understood. Here we developed a single molecule assay to directly visualize nucleation of a MT from purifiedXenopus laevisγ-TuRC. We reveal a high γ-/αβ-tubulin affinity, which facilitates assembly of a MT from γ-TuRC. Whereas spontaneous nucleation requires assembly of 8 αβ-tubulins, nucleation from γ-TuRC occurs efficiently with a cooperativity of 4 αβ-tubulin dimers. This is distinct from pre-assembled MT seeds, where a single dimer is sufficient to initiate growth. A computational model predicts our kinetic measurements and reveals the rate-limiting transition where laterally-associated αβ-tubulins drive γ-TuRC into a closed conformation. Putative activation domain of CDK5RAP2, NME7 and TPX2 do not enhance γ-TuRC-mediated nucleation, while XMAP215 drastically increases the nucleation efficiency by strengthening the longitudinal γ-/αβ-tubulin interaction.
Odd-paired is a late-acting pioneer factor coordinating with Zelda to broadly regulate gene expression in early embryos
Authors: Koromila Theodora , Gao Fan , Iwasaki Yasuno , He Peng , Pachter Lior , Gergen J. Peter , Stathopoulos Angelike 
Published: November 2019

ABSTRACTPioneer factors such as Zelda help initiate zygotic transcription inDrosophilaearly embryos, but whether other factors support this dynamic process is unclear. Odd-paired (Opa), a zinc-finger transcription factor expressed at cellularization, controls transition of genes from pair-rule to segmental patterns along the anterior-posterior axis. Finding that Opa also regulates late expression through enhancersog_Distal,along the dorso-ventral axis, we hypothesized that Opa acts as a general timing factor. Chromatin-immunoprecipitation (ChIP-seq) confirmed Opain vivobinding tosog_Distalbut also identified widespread binding throughout the genome, comparable to Zelda. Furthermore, chromatin assays (ATAC-seq) demonstrate that Opa, like Zelda, influences chromatin accessibility genome-wide, suggesting both are pioneer factors with common as well as distinct targets. Lastly, embryos lackingopaexhibit widespread, late patterning defects spanning both axes. Collectively, these data suggest Opa, a general timing factor and likely a late-acting pioneer factor, heralds in a secondary wave of zygotic gene expression.
Low redundancy and complementarity shape ecosystem functioning in a low‐diversity ecosystem
Authors: Henderson Christopher J. , Gilby Ben L. , Schlacher Thomas A. , Connolly Rod M. , Sheaves Marcus , Maxwell Paul S. , Flint Nicole , Borland Hayden P. , Martin Tyson S. H. , Olds Andrew D. 
Published: November 2019

Abstract

Ecosystem functioning is positively linked to biodiversity on land and in the sea. In high‐diversity systems (e.g. coral reefs), species coexist by sharing resources and providing similar functions at different temporal or spatial scales. How species combine to deliver the ecological function they provide is pivotal for maintaining the structure, functioning and resilience of some ecosystems, but the significance of this is rarely examined in low‐diversity systems such as estuaries.

We tested whether an ecological function is shaped by biodiversity in a low‐diversity ecosystem by measuring the consumption of carrion by estuarine scavengers. Carrion (e.g. decaying animal flesh) is opportunistically fed on by a large number of species across numerous ecosystems. Estuaries were chosen as the model system because carrion consumption is a pivotal ecological function in coastal seascapes, and estuaries are thought to support diverse scavenger assemblages, which are modified by changes in water quality and the urbanization of estuarine shorelines.

We used baited underwater video arrays to record scavengers and measure the rate at which carrion was consumed by fish in 39 estuaries across 1,000 km of coastline in eastern Australia.

Carrion consumption was positively correlated with the abundance of only one species, yellowfin bream Acanthopagrus australis, which consumed 58% of all deployed carrion. The consumption of carrion by yellowfin bream was greatest in urban estuaries with moderately hardened shorelines (20%–60%) and relatively large subtidal rock bars (>0.1 km2).

Our findings demonstrate that an ecological function can be maintained across estuarine seascapes despite both limited redundancy (i.e. dominated by one species) and complementarity (i.e. there is no spatial context where the function is delivered significantly when yellowfin bream are not present) in the functional traits of animal assemblages. The continued functioning of estuaries, and other low‐diversity ecosystems, might therefore not be tightly linked to biodiversity, and we suggest that the preservation of functionally dominant species that maintain functions in these systems could help to improve conservation outcomes for coastal seascapes.
Interactive range‐limit theory (iRLT): An extension for predicting range shifts
Authors: Sirén Alexej P. K. , Morelli Toni Lyn 
Published: November 2019

AbstractA central theme of range‐limit theory (RLT) posits that abiotic factors form high‐latitude/altitude limits, whereas biotic interactions create lower limits. This hypothesis, often credited to Charles Darwin, is a pattern widely assumed to occur in nature. However, abiotic factors can impose constraints on both limits and there is scant evidence to support the latter prediction. Deviations from these predictions may arise from correlations between abiotic factors and biotic interactions, as a lack of data to evaluate the hypothesis, or be an artifact of scale. Combining two tenets of ecology—niche theory and predator–prey theory—provides an opportunity to understand how biotic interactions influence range limits and how this varies by trophic level.We propose an expansion of RLT, interactive RLT (iRLT), to understand the causes of range limits and predict range shifts. Incorporating the main predictions of Darwin's hypothesis, iRLT hypothesizes that abiotic and biotic factors can interact to impact both limits of a species’ range. We summarize current thinking on range limits and perform an integrative review to evaluate support for iRLT and trophic differences along range margins, surveying the mammal community along the boreal‐temperate and forest‐tundra ecotones of North America.Our review suggests that range‐limit dynamics are more nuanced and interactive than classically predicted by RLT. Many (57 of 70) studies indicate that biotic factors can ameliorate harsh climatic conditions along high‐latitude/altitude limits. Conversely, abiotic factors can also mediate biotic interactions along low‐latitude/altitude limits (44 of 68 studies). Both scenarios facilitate range expansion, contraction or stability depending on the strength and the direction of the abiotic or biotic factors. As predicted, biotic interactions most often occurred along lower limits, yet there were trophic differences. Carnivores were only limited by competitive interactions (n = 25), whereas herbivores were more influenced by predation and parasitism (77%; 55 of 71 studies). We highlight how these differences may create divergent range patterns along lower limits.We conclude by (a) summarizing iRLT; (b) contrasting how our model system and others fit this hypothesis and (c) suggesting future directions for evaluating iRLT.
Stigma, trauma and sexuality: the experiences of women hospitalised with serious mental illness
Authors: Frieh Emma C. 
Published: November 2019

AbstractWomen with serious mental illness (SMI) occupy a social position in which their experiences are simultaneously influenced by stigmatisation, institutionalisation and gendered dimensions of trauma and power. Women with SMI are stigmatised in society, pushed to the margins and left vulnerable to victimisation and rejection, particularly if hospitalised in psychiatric institutions. Using modified labelling theory, I investigate how women hospitalised with SMI, especially those who have histories of sexual abuse and trauma, experience sexuality and perceive men and masculinity. I extend modified labelling theory by empirically analysing the role of social status and power in the labelling process. Specifically, I focus on gender, and analyse interviews with 55 women in US psychiatric hospitals, focusing on gendered experiences of trauma, stigma and attitudes about sexuality. I show how trauma increases the salience of stigma and potential for retraumatisation, both of which are amplified by the institutional setting. I find meaningful differences in the narratives of women who have experienced trauma and those who have not. Modified labelling theory helps explain how labelling can perpetuate self‐stigma, which threatens women's self‐esteem, safety and trust in others. The intersection of these experiences extends modified labelling theory and may have profound implications for recovery.
Detecting Accounting Fraud in Publicly Traded U.S. Firms Using a Machine Learning Approach
Authors: BAO YANG , KE BIN , LI BIN , YU Y. JULIA , ZHANG JIE 
Published: November 2019

ABSTRACTWe develop a state‐of‐the‐art fraud prediction model using a machine learning approach. We demonstrate the value of combining domain knowledge and machine learning methods in model building. We select our model input based on existing accounting theories, but we differ from prior accounting research by using raw accounting numbers rather than financial ratios. We employ one of the most powerful machine learning methods, ensemble learning, rather than the commonly used method of logistic regression. To assess the performance of fraud prediction models, we introduce a new performance evaluation metric commonly used in ranking problems that is more appropriate for the fraud prediction task. Starting with an identical set of theory‐motivated raw accounting numbers, we show that our new fraud prediction model outperforms two benchmark models by a large margin: the Dechow et al. logistic regression model based on financial ratios, and the Cecchini et al. support‐vector‐machine model with a financial kernel that maps raw accounting numbers into a broader set of ratios.
Ethyl‐N‐dodecanoyl‐l‐arginate hydrochloride combats pathogens with low‐resistance generation by membrane attack and modifies gut microbiota structure
Authors: Shao Ting , Fan Tingting , Tang Wenshu , Sun Yanting , Gao Song , Chen Huang , Sun Zhenliang , Liu Mingyao , Yi Zhengfang 
Published: November 2019

SummaryEthyl‐N‐dodecanoyl‐l‐arginate hydrochloride (LAE, ethyl lauroyl arginate HCl) is a cationic surfactant used as a food preservative with broad‐spectrum antibacterial activities. However, its resistance development, influences on gut microbiome and molecular target are unclear. In this study, bacteria were stimulated by LAE for 30 days to test the bacterial resistance. Several infected animal models were used to evaluate the antibacterial effect of LAE in vivo. Mice were orally treated with LAE to test its effect on animal growth. The influence of LAE on mice gut microbiome was analysed by 16S rDNA sequencing. The results indicated that Escherichia coli did not develop resistance to LAE. LAE significantly combats bacterial infection in mice, ducklings and piglets. Moreover, LAE promotes mouse weight gain without changing body composition or reducing animal vitality, and induces lower hepatotoxicity than ampicillin. In the mouse gut microbiome assessment and characterization, LAE modifies host gut microbiota structure. Mechanistically, LAE specifically binds to acidic phospholipids including phosphatidylserine, depolarizes the membrane and disrupts the bacterial membrane followed by bacterial growth inhibition. This study investigates the molecular mechanism of LAE as well as its antibacterial functions in poultry and livestock. Our data suggest LAE is a potential antibacterial agent in animal health.
Debt Covenant Restriction, Financial Misreporting, and Auditor Monitoring*
Authors: Pittman Jeffrey , Zhao Yuping 
Published: November 2019

ABSTRACTTheory suggests that financial report‐based debt covenants engender incentives for the manager to relax covenant constraints through accounting choices in order to avoid costly covenant violations. Prior studies directly testing this hypothesis in the context of financial misreporting fail to find consistent evidence. Using a more refined measure of debt covenant restriction, we find that debt covenant restriction is positively associated with the probability of financial statement misstatements. This positive association is driven by performance covenants rather than capital covenants and is more consistent with the manager striving to avoid a “false‐positive” violation than to delay the violation. Our results also imply that managers resort to both income‐increasing and non–income‐increasing misreporting to relieve covenant constraints and rely more on the latter when faced with greater earnings management constraints. Additionally, the auditor charges higher audit fees to firms with more binding covenants even outside the violation state, and audit fees increase with constraints relative to both performance and capital covenants, reflecting greater financial reporting risk and bankruptcy risk, respectively. Within capital covenants, we find some evidence of even higher audit fees for tighter intangible‐inclusive versus intangible‐exclusive capital covenants. Lastly, our evidence suggests that the positive association between covenant constraints and misreporting is attenuated when the auditor has more experience with debt covenants, has greater bargaining power over the client, or faces greater litigation risk.
Adaptive evolution and response to phytoplasma: A genome‐wide study of TCP transcription factors in Sesamum indicum L.
Authors: Parakkunnel Ramya , Bindhani Nirupama , Purru Supriya , Lakhanpaul Suman , Venkataramanna Bhat Kangila 
Published: November 2019

AbstractIntraspecific divergence study of TCP (teosinte branched [TB1], cycloidea [CYC] and proliferating cell factors [PCF]) transcription factors was conducted in Indian and Chinese varieties including landraces of sesame to understand the effects of breeding and adaptive selection on genomic architecture. The varieties included “Swetha,” a pedigree selection and “Zhongzhi‐13,” a space mutant; whereas the landraces studied were “Baizhima” and “Mishouzhima” adapted to widely different ecological niches. “Swetha” the Indian variety contained 33 TCP genes, including 14 Class‐I and 19 Class‐II genes, whereas “Zhongzhi‐13” the RefSeq variety contained 13 Class‐I and 15 Class‐II genes. Sixteen Class‐I genes and six CYC genes were common in both the landraces whereas an additional gene variant was found in “Baizhima.” Class‐II TCP genes were found more conserved within species while Class‐I genes differed widely within and across species. A cluster of 12 Class‐I genes was found unique to the Chinese genotypes, whereas two of the Class‐I genes in landrace “Baizhima” were found more similar to the Indian variety “Swetha” genes. A varied number of retrocopies and retropseudogenes were also found among Class‐I TCPs, due to insertion of TY1/Copia transposons. A number of active TY1/Copia retrotransposons containing “chimeric retrogenes” with multiple introns were discovered in sesame. One set involved “SiwTCP3” from “Swetha” and its homologues from the landraces with a mutation in the conserved Cys‐20 residue which abolished the redox sensitivity whereas the second set was present only in the landraces without the above mutation. None of the “Zhongzhi‐13” genes contained TY1/Copia insertions. Transposon insertions resulted in heavy methylation of unique genes in “Swetha” while methylation spread was noticed in the upstream and downstream regulatory regions. Although CIN‐TCPs were established as preferred binding partners of phytoplasma effectors, we found many mutations in the functional domains which altered the protein folding mechanisms among the protein homologues, with one set reported unique in the Chinese varieties. More duplication was noted in the CIN‐TCP's of “Swetha” whereas multiple exons and exon fusions resulted in the acquisition of novel functions for sesame TCP genes. The insertions, deletions and the duplications acquired through genome evolution under marginal environment conditions altered the binding abilities of CIN‐TCP transcription factors which ultimately resulted in variable response to sesame phyllody caused by phytoplasma.