cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4806970.v1
title: Estrogen signaling, through estrogen receptor β, regulates DNA methylation and its machinery in male germ line in adult rats

description: Estrogen, through its receptors, regulates various aspects of spermatogenesis and male fertility. To understand the roles of estrogen receptors (ERα and ERβ) in male fertility, we have developed <i>in vivo</i> selective ER agonist administration models. Treatment of adult male rats with ERα or ERβ agonist for 60 d decreases fertility and litter size mainly due to increased pre- and post-implantation embryo loss. Since epigenetic mechanisms like DNA methylation play a crucial role in male fertility, we investigated the effects of the ER agonists on DNA methylation in spermatozoa. Treatment with ERβ agonist causes a significant decrease in DNA methylation both at the global level and at the <i>H19</i> differentially methylated region (DMR). This could be due to decrease in DNA methyltransferases in the testis upon ERβ agonist treatment. The hypomethylation observed at the <i>H19</i> DMR corroborates with aberrant expression of <i>Igf2</i> and <i>H19</i> imprinted genes in the resorbed embryos sired by ERβ agonist-treated males. Thus, our study demonstrates that ERβ regulates DNA methylation and methylating enzymes during adult rat spermatogenesis. Activation of estrogen signaling through ERβ could therefore cause DNA methylation defects leading to impaired male fertility. These results define a role for estrogen in epigenetic regulation of male germ line, suggesting that epigenetic insults by exposure to environmental estrogens could potentially affect male fertility.
DOI: 10.6084/m9.figshare.4806985.v1
title: Hypoxia and Hypoglycemia Synergistically Regulate mRNA Stability

description: Ischemic events, common in many diseases, result from decreased blood flow and impaired delivery of oxygen and glucose to tissues of the body. While much is known about the cellular transcriptional response to ischemia, much less is known about the posttranscriptional response to oxygen and glucose deprivation. The goal of this project was to investigate one such posttranscriptional response, the regulation of mRNA stability. To that end, we have identified a number of novel ischemia-related mRNAs that are synergistically stabilized by oxygen and glucose deprivation including VEGF, MYC, MDM2, and CYR61. This increase in mRNA half-life requires the synergistic effects of both low oxygen (1%) as well as low glucose (≤1 g/L) conditions. Oxygen or glucose deprivation alone fails to initiate the response, as exposure to either high glucose (4 g/L) or normoxic conditions inhibits the response. Furthermore, in response to hypoxia/hypoglycemia, the identified mRNAs are released from the RNA binding protein KHSRP which likely contributes to their stabilization.
DOI: 10.15131/shef.data.4806910
title: Database of Cerebral Artery Geometries including Aneurysms at the Middle Cerebral Artery Bifurcation

description: The database consists of 50 patient-specific cerebral artery geometries, each including at least an aneurysm at the middle cerebral artery (MCA) bifurcation. It also includes the corresponding patient age and sex, and the MCA aneurysm rupture status. The geometries were selected from the @neurIST database and obtained from segmentation of 3D Rotational Angiography (3DRA) images, and subsequent manual correction. They are high-quality vascular geometries, including at least 12 vessel diameters upstream the aneurysm and 4 vessel diameters downstream the aneurysm.<br>
DOI: 10.6084/m9.figshare.4806871
title: Violence against Peruvian doctors in social rural service

description: Health professionals performing their social health service (SHS) in rural communities could have be in risk of developing depression. Moreover, those who migrate from farther places to perform their SHS could have an increased risk. The objective was to evaluate the association between place of origin and the presence of depressive symptoms, in health professionals performing rural social health service (SHS) in Ancash, Peru <b>Methods:</b> Cross-sectional study. During April 2015, a survey was applied to health professionals performing SHS in the Peruvian Ministry of Health (MINSA) facilities in Ancash. The main outcome was the presence of depressive symptoms, defined as a score ≥2 points in the Patient Health Questionnaire-2. The main exposure was the place of origin, defined as the place where the subjects have completed their undergraduate professional studies (Ancash, Lima city, or others).
DOI: 10.6084/m9.figshare.4806739
title: Tectono-stratigraphic architecture of the Ionian piedmont between the Arso Stream and Nicà River catchments (Calabria, Southern Italy)

description: Along the northern Ionian margin of Calabria, three Neogene basins comprise wedge-top depozones containing syntectonic deposits which cover the frontal part of the fold-thrust belt. One of the best exposed onshore allochthonous siliciclastic successions is represented by the Cariati Nappe, cropping out in the Cirò Basin. Field geological mapping and aerial interpretations were used to characterize the stratigraphy and tectonics of the area between the Arso Stream and Nicà River catchments (about 170 km<sup>2</sup>), including a Paleozoic metamorphic basement complex unconformably overlain by Upper Oligocene to Quaternary siliciclastic deposits and minor carbonates. This paper presents a 1:25,000 scale map of the Ionian study area, providing lithological and structural data towards reconstructing its tectono-sedimentary evolution.
DOI: 10.6084/m9.figshare.4806739.v1
title: Tectono-stratigraphic architecture of the Ionian piedmont between the Arso Stream and Nicà River catchments (Calabria, Southern Italy)

description: Along the northern Ionian margin of Calabria, three Neogene basins comprise wedge-top depozones containing syntectonic deposits which cover the frontal part of the fold-thrust belt. One of the best exposed onshore allochthonous siliciclastic successions is represented by the Cariati Nappe, cropping out in the Cirò Basin. Field geological mapping and aerial interpretations were used to characterize the stratigraphy and tectonics of the area between the Arso Stream and Nicà River catchments (about 170 km<sup>2</sup>), including a Paleozoic metamorphic basement complex unconformably overlain by Upper Oligocene to Quaternary siliciclastic deposits and minor carbonates. This paper presents a 1:25,000 scale map of the Ionian study area, providing lithological and structural data towards reconstructing its tectono-sedimentary evolution.
DOI: 10.6084/m9.figshare.4806685
title: ORI Organisation and Repository Information 'Discovery' dataset and ontology

description: ORI Organisation and Repository Information. This dataset, frozen as at April 2017, comprises three files:<br><br>* oarj_rdf.xml <br>A data set that links Organisations, Networks, and <br> Repositories.<br>File type : RDF-XML. <br><br>* ori.ttl<br>A data set that links Organisations, Networks, and <br> Repositories.<br>File type : Turtle (N3) see https://www.dajobe.org/2004/01/turtle/2007-09-11/<br><br>* oarj_ontology.rdf<br>Ontology (for ORI RDF) that describes the main classes and properties which the Open Access Repository Junction data set adds to adds to FOAF, <br> DC, SIOC, etc. and some notes on the patterns this data will take.<br><br>Two files containing documentation are also included here:<br><br>* about_the_ORI.html<br>* oriarchit.png<br>
DOI: 10.6084/m9.figshare.4806667
title: Publicationism, satisfaction and the struggle of survival in the science arena

description: This is a questionaire and the raw data of a study performed to assess the effect of science policy on our publication behaviour and well-being. <br><br>The questionnaire was composed as structured online website using the SoSci-Survey online tool (Leiner, 2014). We performed the survey for a total of 119 days (from 8/3/2015 to 11/30/2015).<br><br>A total of 930 completed surveys were returned; 918 of these surveys were provided by participants representing our target group. <br>
DOI: 10.6084/m9.figshare.4806685.v1
title: ORI Organisation and Repository Information 'Discovery' dataset and ontology

description: ORI Organisation and Repository Information. This dataset, frozen as at April 2017, comprises three files:<br><br>* oarj_rdf.xml <br>A data set that links Organisations, Networks, and <br> Repositories.<br>File type : RDF-XML. <br><br>* ori.ttl<br>A data set that links Organisations, Networks, and <br> Repositories.<br>File type : Turtle (N3) see https://www.dajobe.org/2004/01/turtle/2007-09-11/<br><br>* oarj_ontology.rdf<br>Ontology (for ORI RDF) that describes the main classes and properties which the Open Access Repository Junction data set adds to adds to FOAF, <br> DC, SIOC, etc. and some notes on the patterns this data will take.<br><br>Two files containing documentation are also included here:<br><br>* about_the_ORI.html<br>* oriarchit.png<br>
DOI: 10.6084/m9.figshare.4806661
title: Supplementary Material for: In vivo Imaging of the Cerebral Endothelial Glycocalyx in Mice

description: <b><i>Background/Aims:</i></b> Endothelial glycocalyx refers to the proteoglycan or glycoprotein layer of vessel walls and has critical physiological functions. Cerebral glycocalyx may have additional functions considering the blood-brain barrier and other features. However, the assessment of it has only been performed ex vivo, which includes processes presumably damaging the glycocalyx layer. Here we visualize and characterize the cerebral endothelial glycocalyx in vivo. <b><i>Methods:</i></b> We visualized and quantified the cerebral endothelial glycocalyx in vivo under a 2-photon microscope by tagging glycocalyx and vessel lumen with wheat germ agglutinin lectin and dextran, respectively. The radial intensity was analyzed to measure the thickness of the cerebral endothelial glycocalyx in each vessel type. <b><i>Results:</i></b> Cerebral arteries and capillaries have an intact endothelial glycocalyx, but veins and venules do not. The thickness of the glycocalyx layer in pial arteries, penetrating arteries, and capillaries was different; however, it was not correlated with the vessel diameter within each vessel type. <b><i>Conclusion:</i></b> We characterized the distribution of the cerebral endothelial glycocalyx in vivo. Compared to the results from ex vivo studies, the layer is thicker, indicating that the layer may be damaged in ex vivo systems. We also observed an inhomogeneous cerebral endothelial glycocalyx distribution that might reflect the functional heterogeneity of the vessel type.
DOI: 10.6084/m9.figshare.4806667.v1
title: Publicationism, satisfaction and the struggle of survival in the science arena

description: This is a questionaire and the raw data of a study performed to assess the effect of science policy on our publication behaviour and well-being. <br><br>The questionnaire was composed as structured online website using the SoSci-Survey online tool (Leiner, 2014). We performed the survey for a total of 119 days (from 8/3/2015 to 11/30/2015).<br><br>A total of 930 completed surveys were returned; 918 of these surveys were provided by participants representing our target group. <br>
DOI: 10.6084/m9.figshare.4806658
title: Supplementary Material for: Changes in IP3 Receptor Expression and Function in Aortic Smooth Muscle of Atherosclerotic Mice

description: Peroxynitrite is an endothelium-independent vasodilator that induces relaxation via membrane hyperpolarization. The activation of IP3 receptors triggers the opening of potassium channels and hyperpolarization. Previously we found that relaxation to peroxynitrite was maintained during the development of atherosclerosis due to changes in the expression of calcium-regulatory proteins. In this study we investigated: (1) the mechanism of peroxynitrite-induced relaxation in the mouse aorta, (2) the effect of atherosclerosis on relaxation to peroxynitrite and other vasodilators, and (3) the effect of atherosclerosis on the expression and function of the IP3 receptor. Aortic function was studied using wire myography, and atherosclerosis was induced by fat-feeding ApoE<sup>-/-</sup> mice. The expression of IP3 receptors was studied using Western blotting and immunohistochemistry. Relaxation to peroxynitrite was attenuated by the IP3 antagonists 2-APB and xestospongin C and also the K<sub>v</sub> channel blocker 4-aminopyridine (4-AP). Atherosclerosis attenuated vasodilation to cromakalim and the AMPK activator A769662 but not peroxynitrite. Relaxation was attenuated to a greater extent by 2-APB in atherosclerotic aortae despite the reduced expression of IP3 receptors. 4-AP was less effective in ApoE<sup>-/-</sup> mice fat-fed for 4 months. Peroxynitrite relaxation involves an IP3-induced calcium release and K<sub>V</sub> channel activation. This mechanism becomes less important as atherosclerosis develops, and relaxation to peroxynitrite may be maintained by increased calcium extrusion.
DOI: 10.6084/m9.figshare.4806664
title: An integrative approach to species discrimination in the <i>Anagrus atomus</i> group <i>sensu stricto</i> (Hymenoptera: Mymaridae), with a description of a new species

description: Egg parasitoids of the genus <i>Anagrus</i> Haliday (Hymenoptera: Mymaridae) are natural enemies of many pests around the world. We used an integrative approach to characterize some species belonging to the <i>Anagrus atomus</i> group, using specimens reared from leafhoppers infesting some Lamiaceae. Starting from morphological identifications based on available keys, we carried out a multi-locus genetic characterization using phylogenetic and species delimitation analyses, and integrated it with biological and morphometric evidence. This approach revealed the existence of a new species, <i>A. nepetellae</i> sp. nov., here described along with its phenological traits. The approach also allowed us to characterize the expected taxonomic stability of other putative species within the group. We propose two new species groups called the <i>atomus</i> group <i>sensu stricto</i> and the <i>vilis</i> group, with the goal of streamlining the taxonomy of the <i>atomus</i> group. We also present a key for the identification of females of the European species of the <i>atomus</i> group <i>sensu stricto</i>. Some specimens show heterozygosity in 28S-D2 sequences, suggesting hybridization between <i>A. atomus</i> and <i>A. nepetellae</i>, which, if it is common between other species as well, could partly explain the taxonomic problems in the genus <i>Anagrus</i>. DNA sequencing of specimens reared by the same biofactory at different times suggests involuntary contamination leading to the displacement of a laboratory strain of <i>A. atomus</i> by <i>A. nepetellae</i>, which may have resulted from undetected partial reproductive compatibility.http://zoobank.org/urn:lsid:zoobank.org:pub:DFCD7654-5AA5-4E4F-AE48-24377BAACEFE
DOI: 10.6084/m9.figshare.4806664.v2
title: An integrative approach to species discrimination in the <i>Anagrus atomus</i> group <i>sensu stricto</i> (Hymenoptera: Mymaridae), with a description of a new species

description: Egg parasitoids of the genus <i>Anagrus</i> Haliday (Hymenoptera: Mymaridae) are natural enemies of many pests around the world. We used an integrative approach to characterize some species belonging to the <i>Anagrus atomus</i> group, using specimens reared from leafhoppers infesting some Lamiaceae. Starting from morphological identifications based on available keys, we carried out a multi-locus genetic characterization using phylogenetic and species delimitation analyses, and integrated it with biological and morphometric evidence. This approach revealed the existence of a new species, <i>A. nepetellae</i> sp. nov., here described along with its phenological traits. The approach also allowed us to characterize the expected taxonomic stability of other putative species within the group. We propose two new species groups called the <i>atomus</i> group <i>sensu stricto</i> and the <i>vilis</i> group, with the goal of streamlining the taxonomy of the <i>atomus</i> group. We also present a key for the identification of females of the European species of the <i>atomus</i> group <i>sensu stricto</i>. Some specimens show heterozygosity in 28S-D2 sequences, suggesting hybridization between <i>A. atomus</i> and <i>A. nepetellae</i>, which, if it is common between other species as well, could partly explain the taxonomic problems in the genus <i>Anagrus</i>. DNA sequencing of specimens reared by the same biofactory at different times suggests involuntary contamination leading to the displacement of a laboratory strain of <i>A. atomus</i> by <i>A. nepetellae</i>, which may have resulted from undetected partial reproductive compatibility.http://zoobank.org/urn:lsid:zoobank.org:pub:DFCD7654-5AA5-4E4F-AE48-24377BAACEFE
DOI: 10.6084/m9.figshare.4806649
title: Supplementary Material for: Methylation Patterns of SOX3, SOX9, and WNT4 Genes in Gonads of Dogs with XX (SRY-Negative) Disorder of Sexual Development

description: Ovotesticular or testicular disorder of sexual development in dogs with female karyotype and lack of <i>SRY</i> (XX DSD) is a common sexual anomaly diagnosed in numerous breeds. The molecular background, however, remains unclear, and epigenetic mechanisms, including DNA methylation, have not been studied. The aim of our study was comparative methylation analysis of CpG islands in promoters of candidate genes for XX DSD: <i>SOX9</i>, <i>SOX3</i>, and <i>WNT4</i>. Methylation studies were performed on DNA extracted from formalin-fixed/paraffin-embedded or frozen gonads from 2 dogs with ovotesticular and 2 dogs with testicular XX DSD as well as control females (<i>n</i> = 4) and males (<i>n</i> = 2). Bisulfite-converted DNA was used for CpG methylation analysis using quantitative pyrosequencing. Promoter regions of <i>SOX9</i> and <i>WNT4</i> showed similar CpG methylation in each group, ranging from 0 to 5.5% and from 39 to 74%, respectively. The <i>SOX3</i> promoter showed significantly higher methylation in the ovotesticular XX DSD cases and the testicular XX DSD and control males, suggesting that <i>SOX3</i> methylation may play a role in canine XX DSD pathogenesis.
DOI: 10.6084/m9.figshare.4806664.v1
title: An integrative approach to species discrimination in the <i>Anagrus atomus</i> group <i>sensu stricto</i> (Hymenoptera: Mymaridae), with a description of a new species

description: Egg parasitoids of the genus <i>Anagrus</i> Haliday (Hymenoptera: Mymaridae) are natural enemies of many pests around the world. We used an integrative approach to characterize some species belonging to the <i>Anagrus atomus</i> group, using specimens reared from leafhoppers infesting some Lamiaceae. Starting from morphological identifications based on available keys, we carried out a multi-locus genetic characterization using phylogenetic and species delimitation analyses, and integrated it with biological and morphometric evidence. This approach revealed the existence of a new species, <i>A. nepetellae</i> sp. nov., here described along with its phenological traits. The approach also allowed us to characterize the expected taxonomic stability of other putative species within the group. We propose two new species groups called the <i>atomus</i> group <i>sensu stricto</i> and the <i>vilis</i> group, with the goal of streamlining the taxonomy of the <i>atomus</i> group. We also present a key for the identification of females of the European species of the <i>atomus</i> group <i>sensu stricto</i>. Some specimens show heterozygosity in 28S-D2 sequences, suggesting hybridization between <i>A. atomus</i> and <i>A. nepetellae</i>, which, if it is common between other species as well, could partly explain the taxonomic problems in the genus <i>Anagrus</i>. DNA sequencing of specimens reared by the same biofactory at different times suggests involuntary contamination leading to the displacement of a laboratory strain of <i>A. atomus</i> by <i>A. nepetellae</i>, which may have resulted from undetected partial reproductive compatibility.http://zoobank.org/urn:lsid:zoobank.org:pub:DFCD7654-5AA5-4E4F-AE48-24377BAACEFE
DOI: 10.6084/m9.figshare.4806631
title: Dataset 2: Single nucleotide polymorphisms (SNPs) and distance differences between Plasmodium falciparum parasite pairs sampled during a parasitological survey of primary school children in western Kenya.

description: Differences were computed for all parasite pairwise comparisons. Sample_id and sample_id_x are unique sample identifiers; snps represent the number of SNP differences between parasite pairs; distance represents geographical distance, in kilometres, between parasite pairs.
DOI: 10.6084/m9.figshare.4806631.v1
title: Dataset 2: Single nucleotide polymorphisms (SNPs) and distance differences between Plasmodium falciparum parasite pairs sampled during a parasitological survey of primary school children in western Kenya.

description: Differences were computed for all parasite pairwise comparisons. Sample_id and sample_id_x are unique sample identifiers; snps represent the number of SNP differences between parasite pairs; distance represents geographical distance, in kilometres, between parasite pairs.
DOI: 10.6084/m9.figshare.4806616
title: The effect of initial treatment on hearing prognosis in idiopathic sudden sensorineural hearing loss: a nationwide survey in Japan

description: <b>Objective:</b> To investigate the hearing prognosis of idiopathic sudden sensorineural hearing loss (SSNHL) treated with different initial therapies. <b>Methods:</b> Subjects consisted of patients diagnosed with idiopathic SSNHL within 7 days from onset and showing severe hearing loss (≥60 dB), who were registered in a Japanese multicenter database between April 2014 and March 2016. Subjects were divided into four groups according to initial therapy: (1) steroids, (2) steroids + Prostaglandins (PGs), (3) intratympanic steroids (ITS), and (4) no steroids. Hearing outcomes were compared among the groups. <b>Results:</b> In total, 1305 patients were enrolled. The final hearing level and hearing gain of patients treated with steroids + PGs were significantly higher than those of patients treated with steroids alone or no steroids. The ratio of good prognosis (complete recovery or marked improvement) in patients treated with steroids + PGs was higher than that in patients treated with steroids alone or no steroids. There was no difference in the prognosis of patients treated with steroids alone or no steroids. <b>Conclusion:</b> A large number of patients with idiopathic SSNHL were registered in a multicenter database. PG use in combination with steroid administration was associated with a good hearing prognosis in patients with severe hearing loss.
DOI: 10.6084/m9.figshare.4806619
title: Dataset 1: Genotyping results for 111 single nucleotide polymorphisms (SNPs) typed in 2486 Plasmodium falciparum samples collected from primary school children during a parasitological survey in western Kenya in 2009 and 2010.

description: The columns contain the following information: sample_id, unique sample identifier; admin1, provincial location of school; district_name, district location of school; date_visit, date of sample collection; assay_code, name of assay; allele1 and allele2, alternative alleles at a specific SNP position; result, genotype call after processing; allele_ratio1, proportion of allele 1; allele_ratio2, proportion of allele 2; pass_fail, coding of SNP based on availability of valid genotype (pass=1) or lack of a valid genotype (fail=0). Geospatial data for individual school locations is considered sensitive data and therefore cannot be made open access. However, it can be accessed through a request to our data governance committee at dgc@kemri-wellcome.org. The criteria for such access is specified in detail in the data sharing guidelines under which the DGC operates, and relates to a) addressing health research, b)operating within the bounds of informed consent, c)complying with confidentiality procedures, d) mitigating potential harm to participants in research.