cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3578382.v1
title: Epigenome-wide differential DNA methylation between HIV-infected and uninfected individuals

description: Epigenetic control of human immunodeficiency virus-1 (HIV-1) genes is critical for viral integration and latency. However, epigenetic changes in the HIV-1-infected host genome have not been well characterized. Here, we report the first large-scale epigenome-wide association study of DNA methylation for HIV-1 infection. We recruited HIV-infected (n = 261) and uninfected (n = 117) patients from the Veteran Aging Cohort Study (VACS) and all samples were profiled for 485,521 CpG sites in DNA extracted from the blood. After adjusting for cell type and clinical confounders, we identified 20 epigenome-wide significant CpGs for HIV-1 infection. Importantly, 2 CpGs in the promoter of the <i>NLR family, CARD domain containing gene 5</i> (<i>NLRC5</i>), a key regulator of major histocompatibility complex class I gene expression, showed significantly lower methylation in HIV-infected subjects than in uninfected subjects (cg07839457: t = −6.03, <i>P</i><sub>nominal</sub> = 4.96 × 10<sup>−9</sup>; cg16411857: t = −7.63, <i>P</i><sub>nominal</sub> = 3.07 × 10<sup>−13</sup>). Hypomethylation of these 2 CpGs was replicated in an independent sample (GSE67705: cg07839457: t = −4.44, <i>P</i><sub>nominal</sub> = 1.61 × 10<sup>−5</sup>; cg16411857: t = −5.90; <i>P</i> = 1.99 × 10<sup>−8</sup>). Methylation of these 2 CpGs in <i>NLRC5</i> was negatively correlated with viral load in the 2 HIV-infected samples (cg07839457: <i>P</i> = 1.8 × 10<sup>−4</sup>; cg16411857: <i>P</i> = 0.03 in the VACS; and cg07839457: <i>P</i> = 0.04; cg164111857: <i>P</i> = 0.01 in GSE53840). Our findings demonstrate that differential DNA methylation is associated with HIV infection and suggest the involvement of a novel host gene, <i>NLRC5</i>, in HIV pathogenesis.
DOI: 10.17632/8fv4ttfvjx.1
title: Minat Mahasiswa Terhadap Bahasa Indonesia

description: Memotret minat mahasiswa Prodi Bahasa dan Sastra Arab terhadap Bahasa Indonesia
DOI: 10.6084/m9.figshare.3578376
title: Hierarchical Phylogeographic Structure of Coho Salmon in California

description: Evaluation of population genetic structure and variation is an important part of planning for the recovery and management of protected species. Data from 18 polymorphic microsatellite DNA markers were used to analyze the phylogeographic structure of protected Coho Salmon <i>Oncorhynchus kisutch</i> from populations throughout California. Fish from 30 locations in two evolutionarily significant units (ESUs) representing most of the extant populations in the state were studied. Multiple analyses indicated a hierarchical pattern of population structure: the greatest divergence was found at the broadest geographic scale (ESU), followed by the divergences between basins and populations within basins. The populations of the large Klamath River basin were consistently identified as a distinct phylogenetic group, nearly as divergent from all other populations as the two ESUs were from each other. All populations in different basins were differentiated from each other and a pattern of isolation by distance was found at a California-wide scale, but not at smaller spatial scales. Similarly, most individuals were accurately assigned to their population of origin, and almost all misassignments were to an adjacent or geographically proximal basin, indicating that there is substantial gene flow within each region but much less between regions. The number of parents contributing to each population was highly variable and reflected larger patterns of genetic variation, which was found to be generally higher in the southerly, low-elevation coastal populations than in the northern, interior, higher-elevation populations. The results strongly support the current boundary between the two ESU regions, and the detailed understanding of phylogeographic structure provided here will help to guide the management and recovery of Coho Salmon at the southern end of their geographic range. Received August 25, 2015; accepted May 4, 2016 Published online August 12, 2016
DOI: 10.6084/m9.figshare.3578376.v1
title: Hierarchical Phylogeographic Structure of Coho Salmon in California

description: Evaluation of population genetic structure and variation is an important part of planning for the recovery and management of protected species. Data from 18 polymorphic microsatellite DNA markers were used to analyze the phylogeographic structure of protected Coho Salmon <i>Oncorhynchus kisutch</i> from populations throughout California. Fish from 30 locations in two evolutionarily significant units (ESUs) representing most of the extant populations in the state were studied. Multiple analyses indicated a hierarchical pattern of population structure: the greatest divergence was found at the broadest geographic scale (ESU), followed by the divergences between basins and populations within basins. The populations of the large Klamath River basin were consistently identified as a distinct phylogenetic group, nearly as divergent from all other populations as the two ESUs were from each other. All populations in different basins were differentiated from each other and a pattern of isolation by distance was found at a California-wide scale, but not at smaller spatial scales. Similarly, most individuals were accurately assigned to their population of origin, and almost all misassignments were to an adjacent or geographically proximal basin, indicating that there is substantial gene flow within each region but much less between regions. The number of parents contributing to each population was highly variable and reflected larger patterns of genetic variation, which was found to be generally higher in the southerly, low-elevation coastal populations than in the northern, interior, higher-elevation populations. The results strongly support the current boundary between the two ESU regions, and the detailed understanding of phylogeographic structure provided here will help to guide the management and recovery of Coho Salmon at the southern end of their geographic range. Received August 25, 2015; accepted May 4, 2016 Published online August 12, 2016
DOI: 10.17632/v8bkp92bw8.1
title: Dataset: Bromatological composition of the herbaceous and shrub-arboreal vegetation of the Caatinga

description: This dataset is correspondent to the investigation of the influence of the vegetal strata and season on the bromatological composition of a seasonally dry tropical forest (Caatinga), during a two-year field trial.
DOI: 10.6084/m9.figshare.3578346
title: Geology of the Classical Karst Region (SW Slovenia–NE Italy)

description: The paper aims to present the geology of the western part of the Classical Karst (NW Dinarides), located at the border between Slovenia and Italy. The work is based on archive, published and new data collected by Slovenian and Italian researchers within several scientific national and Cross Border Cooperation projects. The map, produced at a scale of 1:50,000, summarizes the lithological and structural setting and is supplemented by three geological cross-sections of the study area.
DOI: 10.17632/j7cncgsvr5.3
title: Public Speaking Anxiety

description: Public speaking anxiety VR project raw data
DOI: 10.6084/m9.figshare.3578346.v1
title: Geology of the Classical Karst Region (SW Slovenia–NE Italy)

description: The paper aims to present the geology of the western part of the Classical Karst (NW Dinarides), located at the border between Slovenia and Italy. The work is based on archive, published and new data collected by Slovenian and Italian researchers within several scientific national and Cross Border Cooperation projects. The map, produced at a scale of 1:50,000, summarizes the lithological and structural setting and is supplemented by three geological cross-sections of the study area.
DOI: 10.6084/m9.figshare.3578340
title: New specimens of horned dinosaurs from the Aguja Formation of West Texas, and a revision of <i>Agujaceratops</i>

description: Most horned dinosaur remains recovered from the Aguja Formation in West Texas are referable to the endemic chasmosaurine <i>Agujaceratops mariscalensis</i>. One specimen, however, differs sufficiently to justify its designation as the holotype of a new species, <i>Agujaceratops mavericus</i> sp. nov. This specimen and an isolated postorbital horncore from the same vicinity are stratigraphically the highest found in the Aguja Formation. A well-preserved juvenile specimen exhibits some unique features, and others compatible with <i>A. mavericus</i>, but due to its immature condition cannot be identified with certainty. A parietal referred to <i>A. mariscalensis</i> is the most complete thus far known, and shows that the frill of this taxon is more elaborately ornamented than previously believed, bearing a set of large horn-like spikes at the posterolateral corners. These two species share features of the premaxilla and squamosal, which warrant their inclusion in the same genus. However, characters thought to distinguish the two species vary in a manner similar to that found in other chasmosaurines, where debate persists as to their taxonomic significance. A consensus species concept has yet to be adopted for ceratopsid genera, of which most are monotypic. As a result, the two <i>Agujaceratops</i> species could be interpreted as arbitrary anagenetic stages in a single lineage, end-members in a spectrum of ontogenetic and sex-associated variation in that lineage, or two sympatric lineages that occupied separate niches in the same range. http://zoobank.org/urn:lsid:zoobank.org:pub:1846D524-AC7F-4126-8787-33B26D80CF52
DOI: 10.6084/m9.figshare.3578340.v1
title: New specimens of horned dinosaurs from the Aguja Formation of West Texas, and a revision of <i>Agujaceratops</i>

description: Most horned dinosaur remains recovered from the Aguja Formation in West Texas are referable to the endemic chasmosaurine <i>Agujaceratops mariscalensis</i>. One specimen, however, differs sufficiently to justify its designation as the holotype of a new species, <i>Agujaceratops mavericus</i> sp. nov. This specimen and an isolated postorbital horncore from the same vicinity are stratigraphically the highest found in the Aguja Formation. A well-preserved juvenile specimen exhibits some unique features, and others compatible with <i>A. mavericus</i>, but due to its immature condition cannot be identified with certainty. A parietal referred to <i>A. mariscalensis</i> is the most complete thus far known, and shows that the frill of this taxon is more elaborately ornamented than previously believed, bearing a set of large horn-like spikes at the posterolateral corners. These two species share features of the premaxilla and squamosal, which warrant their inclusion in the same genus. However, characters thought to distinguish the two species vary in a manner similar to that found in other chasmosaurines, where debate persists as to their taxonomic significance. A consensus species concept has yet to be adopted for ceratopsid genera, of which most are monotypic. As a result, the two <i>Agujaceratops</i> species could be interpreted as arbitrary anagenetic stages in a single lineage, end-members in a spectrum of ontogenetic and sex-associated variation in that lineage, or two sympatric lineages that occupied separate niches in the same range. http://zoobank.org/urn:lsid:zoobank.org:pub:1846D524-AC7F-4126-8787-33B26D80CF52
DOI: 10.17632/p6tzwp3zc7.1
title: Dataset of Brand Image Publication (1961-2019)

description: The Brand Image research & publication dataset, which was indexed by Scopus from 1961 to 2019. The dataset contains data authors, authors ID Scopus, title, year, source title, volume, issue, article number in Scopus, DOI, link, affiliation, abstract, index keywords, references, Correspondence Address, editors, publisher, conference name, conference date, conference code, ISSN, language, document type, access type, and EID.
DOI: 10.6084/m9.figshare.3578313
title: Mapping file of InChIStrings, InChIKeys and DTXSIDs for the EPA CompTox Dashboard

description: The foundation of chemical safety testing relies on chemistry information such as high-quality chemical structures and physical chemical properties. This information is used by scientists to predict the potential health risks of chemicals.The iCSS CompTox Dashboard is part of a suite of dashboards developed by EPA to help evaluate the safety of chemicals. The dashboard provides access to a variety of information on over 700,000 chemicals currently in use. Within the dashboard, users can access chemical structures, experimental and predicted physicochemical and toxicity data, and additional links to relevant websites and applications. It maps curated physicochemical property data associated with chemical substances to their corresponding chemical structures.This data are compiled from sources including the EPA’s computational toxicology research databases, and public domain databases such as the National Center for Biotechnology Information’s PubChem database. This dataset is a mapping file between the dashboard chemicals and the associated InChIStrings and InChIKeys. This file is the version produced by an export of the database on July 1st 2016
DOI: 10.17632/vs48zct2xp.1
title: APP Family Regulates Neuronal Excitability and Synaptic Plasticity but Not Neuronal Survival (Lee et al., Neuron 2020)
DOI: 10.6084/m9.figshare.3578307
title: Testing the “Read-across hypothesis” by investigating the effects of ibuprofen on fish.

description: Human pharmaceuticals present in the environment have the potential to cause adverse effects on non-target organisms. The “read-across hypothesis” stipulates that pharmaceuticals will exhibit similar biological effects across species (e.g. human and fish) if the molecular target has been conserved and the effective drug concentrations are reached (C<sub>max</sub>). We tested this hypothesis by evaluating if ibuprofen, a non-selective inhibitor of prostaglandins and the cyclooxygenase (COX) enzyme, can mimic its primary effect in humans, on fish, at comparable plasma concentrations. The endpoints, “prostaglandin E metabolite” (PGEM) levels and the mRNA expression of COX (<i>ptgs</i>) gene, were measured in the gills of control and exposed fathead minnows (<i>Pimephales promelas</i>), using enzyme-immunoassay and quantitative real-time PCR (qPCR). Fish were exposed, for 24-72 h, to measured water concentrations of 9 (n= 12), 370 (n= 40) and 470 µg ibuprofen/L (n= 12). Water and blood plasma concentrations were determined using LC-MS/MS. Results showed that PGEM levels in fish exposed to 370 and 470 µg ibuprofen/L were significantly decreased compared to control fish, when mean plasma ibuprofen concentrations were 1.8 to 5.6-fold below the C<sub>max</sub>. The plasma ibuprofen concentrations and PGEM levels varied greatly between individuals. In fish exposed to 9 µg ibuprofen/L, when the mean plasma ibuprofen concentration was 224-fold below C<sub>max</sub>, no change in PGEM levels was observed. These data provide evidence for the read-across hypothesis, but suggest establishing a direct dose-response between internal plasma and PGEM is difficult, and would require significantly larger numbers of fish to overcome the inter-individual variation.
DOI: 10.6084/m9.figshare.3578307.v1
title: Testing the “Read-across hypothesis” by investigating the effects of ibuprofen on fish.

description: Human pharmaceuticals present in the environment have the potential to cause adverse effects on non-target organisms. The “read-across hypothesis” stipulates that pharmaceuticals will exhibit similar biological effects across species (e.g. human and fish) if the molecular target has been conserved and the effective drug concentrations are reached (C<sub>max</sub>). We tested this hypothesis by evaluating if ibuprofen, a non-selective inhibitor of prostaglandins and the cyclooxygenase (COX) enzyme, can mimic its primary effect in humans, on fish, at comparable plasma concentrations. The endpoints, “prostaglandin E metabolite” (PGEM) levels and the mRNA expression of COX (<i>ptgs</i>) gene, were measured in the gills of control and exposed fathead minnows (<i>Pimephales promelas</i>), using enzyme-immunoassay and quantitative real-time PCR (qPCR). Fish were exposed, for 24-72 h, to measured water concentrations of 9 (n= 12), 370 (n= 40) and 470 µg ibuprofen/L (n= 12). Water and blood plasma concentrations were determined using LC-MS/MS. Results showed that PGEM levels in fish exposed to 370 and 470 µg ibuprofen/L were significantly decreased compared to control fish, when mean plasma ibuprofen concentrations were 1.8 to 5.6-fold below the C<sub>max</sub>. The plasma ibuprofen concentrations and PGEM levels varied greatly between individuals. In fish exposed to 9 µg ibuprofen/L, when the mean plasma ibuprofen concentration was 224-fold below C<sub>max</sub>, no change in PGEM levels was observed. These data provide evidence for the read-across hypothesis, but suggest establishing a direct dose-response between internal plasma and PGEM is difficult, and would require significantly larger numbers of fish to overcome the inter-individual variation.
DOI: 10.6084/m9.figshare.3578268
title: Dispepsia funcional en estudiantes de ocho facultades de medicina peruanas. Influencia de los hábitos

description: La dispepsia funcional genera impacto en la calidad de vida. Debido a su etiología multifactorial, es difícil su caracterización, sobre todo en poblaciones de riesgo como los estudiantes de medicina. Objetivo. Determinar si los hábitos nocivos comportamentales están asociados a la dispepsia funcional en los estudiantes de medicina de ocho universidades del Perú. Métodos. Estudio transversal analítico y multicéntrico. Se realizó utilizando un cuestionario auto-aplicado en estudiantes de ocho facultades de medicina del Perú. La dispepsia funcional se midió por un test validado en nuestro medio; las características de alimentación, el consumir alcohol, tabaco, café o bebidas energizantes fueron considerados hábitos comportamentales, además se midieron otros del ámbito educativo y social. Se halló estadísticas de asociación bivariado y multivariado. Resultados. De los 1.923 encuestados, la mediana de las edades fue 20 años, 55% fueron mujeres y 24% tuvieron dispepsia funcional. Son factores que disminuyen la frecuencia de dispepsia funcional el sexo masculino (RPa:0,75; IC95%:0,64-0,87; p &lt; 0,001), las horas que le dedica al estudio (RPa:0,97; IC95%:0,96-0,99; p &lt; 0,001) y el comer dentro de sus horarios regulares (RPa: 0,80; IC95%:0,67-0,95; p = 0,013); en cambio, el haber desaprobado un curso aumenta la frecuencia de la dispepsia funcional (RPa:1,24; IC95%:1,13-1,37; p &lt; 0,001), ajustado por la edad, los problemas para conciliar el sueño y la depresión. Conclusión. Muchos estudiantes de medicina tienen dispepsia funcional, que se relaciona a ciertas variables comportamentales. Esto debe ser motivo de más estudios e intervenciones por las instituciones educativas, por los problemas que a mediano y largo plazo podrían significar.<br><br><b>AUTOR :</b><b>Vargas, Mariela</b>; <b>Talledo Ulfe, Lincolth</b>; <b>Samaniego, Reimer O.</b>; <b>Heredia, Paula</b>; <b>Rodríguez, Christian A S.</b>; <b>Mogollón, César A.</b>; <b>Enriquez, Walter F.</b>; <b>Mejia, Christian R.</b><br><b>EDITORIAL :</b><b>Sociedad Argentina de Gastroenterología (SAGE)</b><br><b>REVISTA:</b><b>Acta Gastroenterológica Latinoamericana (Acta Gastroenterol Latinoam)</b><br><b>FECHA DE PUBLICACIÓN :</b>Jun-2016<br><b>URL :</b>http://hdl.handle.net/10757/617222<br><b>PDF:</b>Full text / Texto completo
DOI: 10.6084/m9.figshare.3578055
title: Identification, visualization and clonal analysis of intestinal stem cells in fish

description: <b>Movie 1: The rostral part of the medaka intestinal tract. </b> A 3D view of X-ray data starting from the buccal cavity and going through the mid-gut reveals distinct topographical regions along the rostro-­‐caudal axis. <b> </b> <b>Movie 2: The caudal part of the medaka intestinal tract. </b> A 3D view of X-ray data from the hind-gut indicating the narrower passage in the caudal part of the intestine with smaller folds. <b>Movie 3: The Gaudí</b><b><i>RS</i></b><b><i>Gubiquitin</i>:<sup>ERT2</sup>Cre (10dpi) </b> MuVi-Spim 3D visualization of a gut segment at 10days after induction shows already labeling of strings of clonally related groups representing the stem cells and their descendants (green). <b>Movie 4: The Gaudí</b><b><i>RS</i></b><b><i>Gubiquitin</i>:<sup>ERT2</sup>Cre (30dpi) </b> MuVi-Spim 3D visualization of a gut segment at 30 days after induction showing intestinal folds that are either broadly labelled by H2B-­‐ EGFP (green), or not at all (grey) indicating longitudinal expansion of the clones. <b> </b> <b>Movie 5: The Gaudí</b><b><i>RS</i></b><b><i>Gubiquitin</i>:<sup>ERT2</sup>Cre (150dpi)</b> MuVi-Spim 3D visualization of a gut segment at 150 days after induction. Two large clones (in green) established by symmetric division and neutral drift. <b>Movie 6: The Gaudí<i><sup>Lx</sup></i></b><b><i>BB</i></b><b><i>W</i> hsp70:nlsCRE (90dpi)</b> MuVi-Spim 3D visualization of a gut segment 90 days after induction shows that stochastically triggered clonal multi-color labeling results in adjacent clones of different sizes discernible by different fluorescent proteins demonstrated in this movie by yellow, green, blue and purple color.<b></b>
DOI: 10.6084/m9.figshare.3578055.v2
title: Identification, visualization and clonal analysis of intestinal stem cells in fish

description: <b>Movie 1: The rostral part of the medaka intestinal tract. </b> A 3D view of X-ray data starting from the buccal cavity and going through the mid-gut reveals distinct topographical regions along the rostro-­‐caudal axis. <b> </b> <b>Movie 2: The caudal part of the medaka intestinal tract. </b> A 3D view of X-ray data from the hind-gut indicating the narrower passage in the caudal part of the intestine with smaller folds. <b>Movie 3: The Gaudí</b><b><i>RS</i></b><b><i>Gubiquitin</i>:<sup>ERT2</sup>Cre (10dpi) </b> MuVi-Spim 3D visualization of a gut segment at 10days after induction shows already labeling of strings of clonally related groups representing the stem cells and their descendants (green). <b>Movie 4: The Gaudí</b><b><i>RS</i></b><b><i>Gubiquitin</i>:<sup>ERT2</sup>Cre (30dpi) </b> MuVi-Spim 3D visualization of a gut segment at 30 days after induction showing intestinal folds that are either broadly labelled by H2B-­‐ EGFP (green), or not at all (grey) indicating longitudinal expansion of the clones. <b> </b> <b>Movie 5: The Gaudí</b><b><i>RS</i></b><b><i>Gubiquitin</i>:<sup>ERT2</sup>Cre (150dpi)</b> MuVi-Spim 3D visualization of a gut segment at 150 days after induction. Two large clones (in green) established by symmetric division and neutral drift. <b>Movie 6: The Gaudí<i><sup>Lx</sup></i></b><b><i>BB</i></b><b><i>W</i> hsp70:nlsCRE (90dpi)</b> MuVi-Spim 3D visualization of a gut segment 90 days after induction shows that stochastically triggered clonal multi-color labeling results in adjacent clones of different sizes discernible by different fluorescent proteins demonstrated in this movie by yellow, green, blue and purple color.<b></b>