bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Legacy of Sexual Ancestors in Phenotypic Variability, Gene Expression, and Homoeolog Regulation of Asexual Hybrids and Polyploids
Authors: Bartoš Oldřich , Röslein Jan , Kotusz Jan , Paces Jan , Pekárik Ladislav , Petrtýl Miloslav , Halačka Karel , Štefková Kašparová Eva , Mendel Jan , Boroń Alicja , Juchno Dorota , Leska Anna , Jablonska Olga , Benes Vladimir , Šídová Monika , Janko Karel 
Published: May 2019

AbstractHybridization and polyploidization are important evolutionary processes whose impacts range from the alteration of gene expression and phenotypic variation to the triggering of asexual reproduction. We investigated fishes of the Cobitis taenia-elongatoides hybrid complex, which allowed us to disentangle the direct effects of both processes, due to the co-occurrence of parental species with their diploid and triploid hybrids. Employing morphological, ecological, and RNAseq approaches, we investigated the molecular determinants of hybrid and polyploid forms.In contrast with other studies, hybridization and polyploidy induced relatively very little transgressivity. Instead, Cobitis hybrids appeared intermediate with a clear effect of genomic dosing when triploids expressed higher similarity to the parent contributing two genome sets. This dosage effect was symmetric in the germline (oocyte gene expression), interestingly though, we observed an overall bias toward C. taenia in somatic tissues and traits. At the level of individual genes, expression-level dominance vastly prevailed over additivity or transgressivity. Also, trans-regulation of gene expression was less efficient in diploid hybrids than in triploids, where the expression modulation of homoeologs derived from the “haploid” parent was stronger than those derived from the “diploid” parent.Our findings suggest that the apparent intermediacy of hybrid phenotypes results from the combination of individual genes with dominant expression rather than from simple additivity. The efficiency of cross-talk between trans-regulatory elements further appears dosage dependent. Important effects of polyploidization may thus stem from changes in relative concentrations of trans-regulatory elements and their binding sites between hybridizing genomes. Links between gene regulation and asexuality are discussed.
Inclusion of an extended treatment with recovery improves the results for the human peripheral blood lymphocyte micronucleus assay
Authors: Whitwell James , Smith Robert , Chirom Teresa , Watters Gary , Hargreaves Victoria , Lloyd Mel , Phillips Sarah , Clements Julie 
Published: May 2019

AbstractThe in vitro micronucleus (IVMN) test was endorsed for regulatory genotoxicity testing with adoption of the Organisation for Economic Co-operation and Development (OECD) test guideline (TG) 487 in 2010. This included two equally acceptable options for extended treatment in the absence of metabolic activation: a treatment for 1.5–2.0 cell cycles with harvest at the end of treatment (Option A) or treatment for 1.5–2.0 cell cycles followed by recovery for 1.5–2.0 cell cycles prior to harvest (Option B). Although no preferences were discussed, TG 487 cautions that Option B may not be appropriate for stimulated lymphocytes where exponential growth may be declining at 96 h after phytohaemagglutinin (PHA) stimulation. Following revision of TG 487 in 2014 and 2016, emphasis has been placed on using Option A. Given the purpose of the IVMN assay is to determine both clastogenic and aneugenic potential, the authors believe the assay is compromised if an extended treatment with recovery is not included for sensitive detection of certain classes of chemical. In this study, average generation time (via bromodeoxyuridine incorporation) of human peripheral blood lymphocytes (HPBL) was measured up to 144 h after PHA stimulation. In addition, the HPBL micronucleus (MN) assay was performed using Option A and B treatment schedules. Cytotoxicity (replication index) and MN induction were determined following treatment with 14 chemicals. The data demonstrate that lymphocytes actively divide beyond 96 h after PHA stimulation. Furthermore, MN induction was only observed with some aneugenic chemicals and nucleoside analogues in HPBLs following extended treatment with a recovery period. For the majority of chemicals tested the magnitude of MN induction was generally greater and MN induction was observed across a wider concentration range following the Option B treatment schedule. In addition, steep concentration-related toxicity following treatment without recovery is more common, making selection of suitable concentrations (within regulatory toxicity limits) for MN analysis challenging.
The Gene Sculpt Suite: a set of tools for genome editing
Authors: Mann Carla M , Martínez-Gálvez Gabriel , Welker Jordan M , Wierson Wesley A , Ata Hirotaka , Almeida Maira P , Clark Karl J , Essner Jeffrey J , McGrail Maura , Ekker Stephen C , Dobbs Drena 
Published: May 2019

Abstract
The discovery and development of DNA-editing nucleases (Zinc Finger Nucleases, TALENs, CRISPR/Cas systems) has given scientists the ability to precisely engineer or edit genomes as never before. Several different platforms, protocols and vectors for precision genome editing are now available, leading to the development of supporting web-based software. Here we present the Gene Sculpt Suite (GSS), which comprises three tools: (i) GTagHD, which automatically designs and generates oligonucleotides for use with the GeneWeld knock-in protocol; (ii) MEDJED, a machine learning method, which predicts the extent to which a double-stranded DNA break site will utilize the microhomology-mediated repair pathway; and (iii) MENTHU, a tool for identifying genomic locations likely to give rise to a single predominant microhomology-mediated end joining allele (PreMA) repair outcome. All tools in the GSS are freely available for download under the GPL v3.0 license and can be run locally on Windows, Mac and Linux systems capable of running R and/or Docker. The GSS is also freely available online at www.genesculpt.org.
Bundle Theory with Kinds
Authors: Keinänen Markku , Tahko Tuomas E 
Published: May 2019

Abstract
Is it possible to get by with just one ontological category? We evaluate L.A. Paul's attempt to do so: the mereological bundle theory. The upshot is that Paul's attempt to construct a one category ontology may be challenged with some of her own arguments. In the positive part of the paper we outline a two category ontology with property universals and kind universals. We will also examine Paul's arguments against a version of universal bundle theory that takes spatiotemporal co-location instead of compresence or coinstantiation as the feature by which we can identify genuine bundles. We compare this novel theory, bundle theory with kinds, and Paul's mereological bundle theory and apply them to a case study concerning entangled fermions and co-located bosons.
Investment Timing and Incentive Costs*
Authors: Gryglewicz Sebastian , Hartman-Glaser Barney 
Published: May 2019

Abstract
We analyze how the costs of smoothly adjusting capital, such as incentive costs, affect investment timing. In our model, the owner of a firm holds a real option to increase a lumpy form of capital and can also smoothly adjust an incremental form of capital. Increasing the cost of incremental capital can delay or accelerate investment in lumpy capital. Incentive costs due to moral hazard are a natural source of costs for the accumulation of incremental capital. When moral hazard is severe, delaying investment in lumpy capital is costly, and overinvesting relative to the first-best case is optimal.
Received January 24, 2017; editorial decision March 15, 2019 by Editor Itay Goldstein.
Ventromedial and dorsolateral prefrontal interactions underlie will to fight and die for a cause
Authors: Pretus Clara , Hamid Nafees , Sheikh Hammad , Gómez Ángel , Ginges Jeremy , Tobeña Adolf , Davis Richard , Vilarroya Oscar , Atran Scott 
Published: May 2019

AbstractWillingness to fight and die (WFD) has been developed as a measure to capture willingness to incur costly sacrifices for the sake of a greater cause in the context of entrenched conflict. WFD measures have been repeatedly used in field studies, including studies on the battlefield, although their neurofunctional correlates remain unexplored. Our aim was to identify the neural underpinnings of WFD, focusing on neural activity and interconnectivity of brain areas previously associated with value-based decision-making, such as the ventromedial prefrontal cortex (vmPFC) and the dorsolateral prefrontal cortex (dlPFC). A sample of Pakistani participants supporting the Kashmiri cause was selected and invited to participate in an functional magnetic resonance (fMRI) paradigm where they were asked to convey their WFD for a series of values related to Islam and current politics. As predicted, higher compared to lower WFD was associated with increased ventromedial prefrontal activity and decreased dorsolateral activity, as well as lower connectivity between the vmPFC and the dlPFC. Our findings suggest that WFD more prominently relies on brain areas typically associated with subjective value (vmPFC) rather than integration of material costs (dlPFC) during decision-making, supporting the notion that decisions on costly sacrifices may not be mediated by cost-benefit computation.
Cattle stratified on genetic merit segregate on carcass characteristics, but there is scope for improvement1
Authors: Berry Donagh P , Pabiou Thierry , Brennan Denis , Hegarthy Patrick J , Judge Michelle M 
Published: May 2019

AbstractThe study objective was to quantify the ability of genetic merit for a generated carcass index to differentiate animals on primal carcass cut weights using data from 1,446 herds on 9,414 heifers and 22,413 steers with weights for 14 different primal carcass cuts (plus 3 generated groups of cuts). The carcass genetic merit index was compromised of carcass weight (positive weight), conformation (positive weight), and fat score (negative weight), each equally weighted within the index. The association analyses were undertaken using linear mixed models; models were run with or without carcass weight as a covariate. In a further series of analyses, carcass weight and carcass fat score were both included as covariates in the models. Whether the association between primal cut yield and carcass weight differed by genetic merit stratum was also investigated. Genetic merit was associated (P &lt; 0.001) with the weight of all cuts evaluated even when adjusted to a common carcass weight (P &lt; 0.01); when simultaneously adjusted to a common carcass weight and fat score, genetic merit was not associated with the weight of the cuberoll or the group cuts termed minced-meat. The weight of the different primal cuts increased almost linearly within increasing genetic merit, with the exception of the rump and bavette. The difference in mean primal cut weight between the very low and very high genetic merit strata, as a proportion of the overall mean weight of that cut in the entire data set, varied from 0.05 (bavette) to 0.28 (eye of round); the average was 0.17. Following adjustment for differences in carcass weight, there was no difference in cut weight between the very low and very high strata for the rump, chuck tender, and mince cut group; the remaining cuts were heavier in the higher index animals with the exception of the cuberoll and bavette, which were lighter in the very high index animals. The association between carcass weight and the weight of each of the evaluated primal cuts differed (P &lt; 0.05) by genetic merit stratum for all cuts evaluated with the exception of the rump, striploin, and brisket as well as the group cuts of frying and mincing. With the exception of these 5 primal (group) cuts, the regression coefficients of primal cut weight on carcass weight increased consistently for all traits with increasing genetic merit stratum, other than for the fillet, cuberoll, bavette, chuck and neck, and heel and shank.
C. elegans Runx/CBFβ suppresses POP-1(TCF) to convert asymmetric to proliferative division of stem cell-like seam cells
Authors: van der Horst Suzanne E. M. , Cravo Janine , Woollard Alison , Teapal Juliane , van den Heuvel Sander 
Published: May 2019

ABSTRACTA correct balance between proliferative and asymmetric cell divisions underlies normal development, stem cell maintenance and tissue homeostasis. What determines whether cells undergo symmetric or asymmetric cell division is poorly understood. To gain insight in the mechanisms involved, we studied the stem cell-like seam cells in the Caenorhabditis elegans epidermis. Seam cells go through a reproducible pattern of asymmetric divisions, instructed by non-canonical Wnt/β-catenin asymmetry signaling, and symmetric divisions that increase the seam cell number. Using time-lapse fluorescence microscopy, we show that symmetric cell divisions maintain the asymmetric localization of Wnt/β-catenin pathway components. Observations based on lineage-specific knockout and GFP-tagging of endogenous pop-1 support the model that POP-1TCF induces differentiation at a high nuclear level, while low nuclear POP-1 promotes seam cell self-renewal. Before symmetric division, the transcriptional regulator rnt-1Runx and cofactor bro-1CBFβ temporarily bypass Wnt/β-catenin asymmetry by downregulating pop-1 expression. Thereby, RNT-1/BRO-1 appears to render POP-1 below the level required for its repressor function, which converts differentiation into self-renewal. Thus, opposition between the C. elegans Runx/CBFβ and TCF stem-cell regulators controls the switch between asymmetric and symmetric seam cell division.
Microbiota of the alien species Paraleucilla magna (Porifera, Calcarea) from the Southwestern Atlantic, and a comparison with that of other calcareous sponges
Authors: Lopes Maira Ferreira , Mágna Beatriz , Klautau Michelle , Esteves Eduardo Leal , Albano Rodolpho M. 
Published: May 2019

AbstractSponges (Porifera) co-evolved with microorganisms in a well-established symbiotic relationship. Based on this characteristic, sponges can be separated into high microbial abundance (HMA) and low microbial abundance (LMA) species. Paraleucilla magna (Calcarea, Porifera) is an alien species of ecological importance in the Brazilian coastline. Little is known about the composition of its microbiota and that of other calcareous species, especially those inhabiting the Southwest Atlantic. Here, we describe the microbiota of P. magna and compare it to that of other calcareous sponge species for which such data exist. P. magna’s microbiota shows a lower diversity than that of Clathrina clathrus, C. coriacea, Leucosolenia sp., Leuconia sp. and Leucetta antarctica. P. magna microbiota is dominated by two bacterial OTUs of the Alphaproteobacteria class, that could not be classified beyond class (OTU001) and family levels (OTU002; Rhodospirillaceae). The Thaumarcheota was the predominant archaeal phylum in P. magna, with OTUs mainly affiliated to the genus candidatus Nitrosopumilus. The comparison with other calcareous species showed that microbiota composition correlated well with sponge phylogenetic affiliation. Metabolic prediction with PICRUSt software of P. magna bacterial microbiota indicated that membrane transport and carbohydrate, amino acid and energy metabolisms were most abundant while, for the archaeal domain, pathways related to translation, and energy metabolisms were predominant. Predicted metabolic features were compared between the different sponge species and seawater samples, showing that pathways related to cell motility, membrane transport, genetic information processing, xenobiotics metabolism and signal transduction are higher in the former while amino acid and nucleotide metabolism, translation, replication and repair, folding, sorting and degradation and glycan biosynthesis and metabolism are abundant in the latter. This study shows that P. magna’s microbiota is typical of an LMA sponge and that it differs from the microbiota of other calcareous sponges both in its composition and in predicted metabolic pathways.
Genomic basis of European ash tree resistance to ash dieback fungus
Authors: Stocks Jonathan J. , Metheringham Carey L. , Plumb William , Lee Steve J. , Kelly Laura J. , Nichols Richard A. , Buggs Richard J. A. 
Published: May 2019

SummaryPopulations of European ash trees (Fraxinus excelsior) are being devastated by the invasive alien fungusHymenoscyphus fraxineus, which causes ash dieback (ADB). We sequenced whole genomic DNA from 1250 ash trees in 31 DNA pools, each pool containing trees with the same ADB damage status in a screening trial and from the same seed-source zone. A genome-wide association study (GWAS) identified 3,149 single nucleotide polymorphisms (SNPs) associated with low versus high ADB damage. Sixty-one of the 203 most significant SNPs were in, or close to, genes with putative homologs already known to be involved in pathogen responses in other plant species. We also used the pooled sequence data to train a genomic prediction (GP) model, cross-validated using individual whole genome sequence data generated for 75 healthy and 75 damaged trees from a single seed source. Using the top 30% of our genomic estimated breeding values from 200 SNPs, we could predict tree health with over 90% accuracy. We infer that ash dieback resistance inF. excelsioris a polygenic trait that should respond well to both natural selection and breeding, which could be accelerated using GP.
Dissemination and Stakeholder Engagement Practices Among Dissemination & Implementation Scientists: Results from an Online Survey
Authors: Knoepke Christopher E. , Pilar Ingle M. , Matlock Daniel D. , Brownson Ross C. , Glasgow Russell E. 
Published: May 2019

AbstractIntroductionThere has been an increasing focus on disseminating research findings, but less about practices specific to disseminating and engaging non-researchers. The present project sought to describe dissemination practices and engagement of stakeholders among dissemination & implementation (D&I) scientists.MethodsMethods to disseminate to and engage non-research stakeholders were assessed using an online survey sent to a broad, diverse sample of D&I scientists.ResultsSurveys were received from 210 participants. The majority of respondents were from university or research settings in the U.S. (69%) or Canada (13%), representing a mix of clinical (28%) and community settings (34%). 26% had received formal training in D&I. Respondents indicated routinely engaging in a variety of dissemination-related activities, with academic journal publications (88%), conference presentations (86%), and reports to funders (74%) being the most frequent. Journal publication was identified as the most impactful on respondents’ careers (94%), but face-to-face meetings with stakeholders were rated as most impactful on practice or policy (40%). Stakeholder involvement in research was common, with clinical and community-based researchers engaging stakeholder groups in broadly similar ways, but with critical differences noted between researchers with greater seniority, those with more D&I training, those based in the US, and those in community vs, clinical research settings.ConclusionsThere have been increases in stakeholder engagement, but few other practices since the 2012 survey, and some differences across subgroups. Methods to engage different stakeholders deserve more in-depth investigation. D&I researchers report substantial misalignment of incentives and behaviors related to dissemination to non-research audiences.
High Frequency of Enteroparasitoses in the Municipality of Oiapoque, Amapá State, Brazil, on the Border With French Guiana
Authors: Menezes Rubens Alex de Oliveira , Gomes Margarete do Socorro Mendonça , Mendes Anapaula Martins , Nascimento Silvestre Rodrigues do , Couto Álvaro Augusto Ribeiro D’ Almeida , Nacher Mathieu , Enk Martin Johannes , Machado Ricardo Luiz Dantas 
Published: May 2019

AbstractIntroductionEnteroparasites represent a considerable proportion of infectious parasitic diseases worldwide. This study evaluated the frequency of enteroparasites and the correlation of enteroparasites with hemoglobin levels. This study evaluated the frequency of enteroparasites and the correlation of themwith hemoglobin levels.MethodsA cross-sectional study was performed in the municipality of Oiapoque in the state of Amapá in northern Brazil, which is located at the western border of the Amazon region. Fecal samples collected over a one-year period (2014/2015) were analyzed using direct methods and spontaneous sedimentation.ResultsThe study included 446 individuals ranging in age from 7 to 61 years. Among the investigated individuals, 58.6% (261/446) were infected with some type of enteroparasites. Of these infected individuals, 45.2% (118/261) were infected only by helminth, 40.9% (107/261) were infected with protozoa, and 13.8% (36/261) had combined infections. Ascaris lumbricoides (19.9%, 52/261) was the most commonly detected helminth, followed by Entamoeba coli and Endolimax nana that were the most frequent protozoan (17.2%, 45/261). The study showed an inversely proportional correlation between the hemoglobin level and the presence of detected parasites. Conclusions: In Oiapoque, enteroparasitosis diseases may be one of the causes of anemia in the population. The high frequency of enteroparasites is a clear reflection of the lack of sanitation in the studied region, indicating an epidemiological state of concern.