cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.23645/epacomptox.6328037.v3
title: ToxCast and Tox21 High-throughput Screening Assay Descriptions

description: ToxCast and Tox21 High-throughput Screening Assay Descriptions.
DOI: 10.23645/epacomptox.6328037.v5
title: ToxCast and Tox21 High-throughput Screening Assay Description Documentation

description: ToxCast and Tox21 High-throughput Screening Assay Descriptions.
DOI: 10.23645/epacomptox.6328037.v6
title: ToxCast and Tox21 High-throughput Screening Assay Description Documentation

description: ToxCast and Tox21 High-throughput Screening Assay Descriptions.
DOI: 10.6084/m9.figshare.6327815
title: Hilfield Pk Reservoir 04052018 TQ 15673 96366 pt 2

description: Hilfield Pk Reservoir 04052018 TQ 15673 96366 pt 2
DOI: 10.6084/m9.figshare.6327815.v1
title: Hilfield Pk Reservoir 04052018 TQ 15673 96366 pt 2

description: Hilfield Pk Reservoir 04052018 TQ 15673 96366 pt 2
DOI: 10.6084/m9.figshare.6327401
title: Supplementary data file: generic presence/absence matrix. The Weeks Formation Konservat–Lagerstätte and the evolutionary transition of Cambrian marine life

description: Generic presence/absence data matrix used for the similarity analyses of the Cambrian exceptionally-preserved faunas of Utah.
DOI: 10.6084/m9.figshare.6327344
title: Supplementary Material for: A Central Role for Heme Oxygenase-1 in the Control of Intestinal Epithelial Chemokine Expression

description: In mucosal inflammatory disorders, the protective influence of heme oxygenase-1 (HO-1) and its metabolic byproducts, carbon monoxide (CO) and biliverdin, is a topic of significant interest. Mechanisms under investigation include the regulation of macrophage function and mucosal cytokine expression. While there is an increasing recognition of the importance of epithelial-derived factors in the maintenance of intestinal mucosal homeostasis, the contribution of intestinal epithelial cell (IEC) HO-1 on inflammatory responses has not previously been investigated. We examined the influence of modulating HO-1 expression on the inflammatory response of human IECs. Engineered deficiency of HO-1 in Caco-2 and T84 IECs led to increased proinflammatory chemokine expression in response to pathogenic bacteria and inflammatory cytokine stimulation. Crosstalk with activated leukocytes also led to increased chemokine expression in HO-1-deficient cells in an IL-1β dependent manner. Treatment of Caco-2 cells with a pharmacological inducer of HO-1 led to the inhibition of chemokine expression. Mechanistic studies suggest that HO-1 and HO-1-related transcription factors, but not HO-1 metabolic products, are partly responsible for the influence of HO-1 on chemokine expression. In conclusion, our data identify HO-1 as a central regulator of IEC chemokine expression that may contribute to homeo­stasis in the intestinal mucosa.
DOI: 10.6084/m9.figshare.6327035
title: Change maps

description: In study created change maps for all study area.
DOI: 10.6084/m9.figshare.6327035.v1
title: Change maps

description: In study created change maps for all study area.
DOI: 10.6084/m9.figshare.6326957
title: Mitochondrial genomes of the headstanders <i>Megaleporinus muyscorum</i> (Steindachner 1900) and <i>Megaleporinus obtusidens</i> (Valenciennes 1837), (Characiformes, Anostomidae)

description: We report two mitochondrial genomes of headstanders, derived from target capture and Illumina sequencing (HiSeq 2500 PE100). One trans-Andean species <i>Megaleporinus muyscorum</i> (mitochondrial consensus genome of 25 individuals) from Colombia and one cis-Andean species <i>M. obtusidens</i> from Argentina. Regarding <i>M. muyscorum</i>, mitochondrial genome has 13 protein-coding genes, 1 D-loop, 2 ribosomal RNAs, 21 transfer RNAs, and is 14,434 bp in length, for <i>M. obtusidens</i> mitochondrial genome has 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and is 15,546 bp in length.
DOI: 10.6084/m9.figshare.6326957.v2
title: Mitochondrial genomes of the headstanders <i>Megaleporinus muyscorum</i> (Steindachner 1900) and <i>Megaleporinus obtusidens</i> (Valenciennes 1837), (Characiformes, Anostomidae)

description: We report two mitochondrial genomes of headstanders, derived from target capture and Illumina sequencing (HiSeq 2500 PE100). One trans-Andean species <i>Megaleporinus muyscorum</i> (mitochondrial consensus genome of 25 individuals) from Colombia and one cis-Andean species <i>M. obtusidens</i> from Argentina. Regarding <i>M. muyscorum</i>, mitochondrial genome has 13 protein-coding genes, 1 D-loop, 2 ribosomal RNAs, 21 transfer RNAs, and is 14,434 bp in length, for <i>M. obtusidens</i> mitochondrial genome has 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and is 15,546 bp in length.
DOI: 10.6084/m9.figshare.6326723
title: Pre-implementation survey

description: Attitudes of village malaria workers to their role and smartphone use, prior to the introduction of smartphones with a novel software application for data collection
DOI: 10.6084/m9.figshare.6326723.v1
title: Pre-implementation survey

description: Attitudes of village malaria workers to their role and smartphone use, prior to the introduction of smartphones with a novel software application for data collection
DOI: 10.6084/m9.figshare.6326057
title: Bis coumarinyl bis triazolothiadiazinyl ethane derivatives: Synthesis, antiviral activity evaluation, and molecular docking studies

description: A series of novel 3,3′-(3,3′-(dihydroxy/hydroxyethane-1,2-diyl)bis(7<i>H</i>-[1,2,4]triazolo[3,4-<i>b</i>][1,3,4]thiadiazine-6,3-diyl))bis(2<i>H</i>-chromen-2-ones) were prepared by the condensation of thiocarbohydrazide with tartaric acid or malic acid followed by various 3-(2-bromoacetyl)-2<i>H</i>-chromen-2-ones in two steps with good yields. All the synthesized compounds were characterized by analytical and spectral (IR, <sup>1</sup>H NMR, <sup>13</sup>C NMR, and mass) data. These synthesized bis(triazolothiadiazinyl coumarin) compounds were evaluated for broad spectrum of antiviral activity. Among all the tested compounds, compound <b>5f</b> exhibited antiviral activity against H1N1 virus. The molecular docking studies of these compounds against H1N1 neuraminidase enzyme were performed. The binding affinity and binding values were compared with standard drugs.
DOI: 10.6084/m9.figshare.6326057.v1
title: Bis coumarinyl bis triazolothiadiazinyl ethane derivatives: Synthesis, antiviral activity evaluation, and molecular docking studies

description: A series of novel 3,3′-(3,3′-(dihydroxy/hydroxyethane-1,2-diyl)bis(7<i>H</i>-[1,2,4]triazolo[3,4-<i>b</i>][1,3,4]thiadiazine-6,3-diyl))bis(2<i>H</i>-chromen-2-ones) were prepared by the condensation of thiocarbohydrazide with tartaric acid or malic acid followed by various 3-(2-bromoacetyl)-2<i>H</i>-chromen-2-ones in two steps with good yields. All the synthesized compounds were characterized by analytical and spectral (IR, <sup>1</sup>H NMR, <sup>13</sup>C NMR, and mass) data. These synthesized bis(triazolothiadiazinyl coumarin) compounds were evaluated for broad spectrum of antiviral activity. Among all the tested compounds, compound <b>5f</b> exhibited antiviral activity against H1N1 virus. The molecular docking studies of these compounds against H1N1 neuraminidase enzyme were performed. The binding affinity and binding values were compared with standard drugs.
DOI: 10.6084/m9.figshare.6326054
title: Limited dispersal and geographic barriers cause population differentiation and structuring in <i>Begonia maxwelliana</i> at both large and small scales

description: <b><i>Background</i></b>: Genetic divergence is one of the key processes in speciation. In the Begoniaceae, genetic divergence caused by limited gene flow may explain its high species diversity and endemicity. This hypothesis has been supported by past genetic work but there is a lack of empirical studies on the causes of limited gene flow. <b><i>Aim</i></b>: To identify the causes of limited gene flow in <i>Begonia</i>. <b><i>Methods</i></b>: We examined the genetic structure among the populations of <i>Begonia maxwelliana</i> at the macro- and micro-spatial scales using microsatellites, measured seed dispersal range and observed flowering phenology. <b><i>Results</i></b>: Population differentiation and structuring were detected at both the macro- and micro-scales. Dispersal range was short, and all populations showed similar reproductive behaviour. <b><i>Conclusions</i></b>: The strong population differentiation and structuring among the populations studied imply that they are evolutionarily significant units and possible candidates for speciation. Geographical barriers and limited seed dispersal restrict gene flow in the populations, and these factors may be responsible for the rapid speciation and large diversity in the family.
DOI: 10.6084/m9.figshare.6326054.v1
title: Limited dispersal and geographic barriers cause population differentiation and structuring in <i>Begonia maxwelliana</i> at both large and small scales

description: <b><i>Background</i></b>: Genetic divergence is one of the key processes in speciation. In the Begoniaceae, genetic divergence caused by limited gene flow may explain its high species diversity and endemicity. This hypothesis has been supported by past genetic work but there is a lack of empirical studies on the causes of limited gene flow. <b><i>Aim</i></b>: To identify the causes of limited gene flow in <i>Begonia</i>. <b><i>Methods</i></b>: We examined the genetic structure among the populations of <i>Begonia maxwelliana</i> at the macro- and micro-spatial scales using microsatellites, measured seed dispersal range and observed flowering phenology. <b><i>Results</i></b>: Population differentiation and structuring were detected at both the macro- and micro-scales. Dispersal range was short, and all populations showed similar reproductive behaviour. <b><i>Conclusions</i></b>: The strong population differentiation and structuring among the populations studied imply that they are evolutionarily significant units and possible candidates for speciation. Geographical barriers and limited seed dispersal restrict gene flow in the populations, and these factors may be responsible for the rapid speciation and large diversity in the family.
DOI: 10.6084/m9.figshare.6325985
title: The Tail Wagging the Dog? Supplementary Material

description: The paper investigates the link between the sub-national variation of political regimes in a (at the federal level) non-democratic country and the appointments of federal officials in the sub-national provinces. In particular, we look at the appointment of the chief federal inspectors to the regions in the Putin's Russia in 2000-2012. Our main research question is whether appointment patterns can be explained by top-down concerns of the central government willing to keep control over the most unruly regions or by bottom-up self-selection of bureaucrats belonging to influential groups into more attractive positions more suitable for rent-seeking. The advantage of our case is that data we have at hand allow us to distinguish these two logics. Our results indicate that for the Russian chief federal inspectors in 2000-2012 the bottom-up self-selection appears to be the more plausible explanation of the link between sub-national political regimes and appointment patterns.<br>
DOI: 10.6084/m9.figshare.6325985.v1
title: The Tail Wagging the Dog? Supplementary Material

description: The paper investigates the link between the sub-national variation of political regimes in a (at the federal level) non-democratic country and the appointments of federal officials in the sub-national provinces. In particular, we look at the appointment of the chief federal inspectors to the regions in the Putin's Russia in 2000-2012. Our main research question is whether appointment patterns can be explained by top-down concerns of the central government willing to keep control over the most unruly regions or by bottom-up self-selection of bureaucrats belonging to influential groups into more attractive positions more suitable for rent-seeking. The advantage of our case is that data we have at hand allow us to distinguish these two logics. Our results indicate that for the Russian chief federal inspectors in 2000-2012 the bottom-up self-selection appears to be the more plausible explanation of the link between sub-national political regimes and appointment patterns.<br>
DOI: 10.6084/m9.figshare.6325847
title: Hilfield Pk Res 11052018 TQ 15886 95516 pt 1

description: Hilfield Pk Res 11052018 TQ 15886 95516 pt 1
DOI: 10.6084/m9.figshare.6325847.v1
title: Hilfield Pk Res 11052018 TQ 15886 95516 pt 1

description: Hilfield Pk Res 11052018 TQ 15886 95516 pt 1
DOI: 10.6084/m9.figshare.6325712
title: Hilfield Pk Res 10052018 TQ 15886 95516 pt 3

description: Hilfield Pk Res 10052018 TQ 15886 95516 pt 3
DOI: 10.6084/m9.figshare.6325712.v1
title: Hilfield Pk Res 10052018 TQ 15886 95516 pt 3

description: Hilfield Pk Res 10052018 TQ 15886 95516 pt 3
DOI: 10.6084/m9.figshare.6325667
title: Geometries (PDB files) of stationary points of mechanism of glycerol dehydration catalysed by B12-dependent and B12-independent glycerol dehydratase (GDH) calculated using QM/MM method

description: We provide PDBs with Cartesian coordinates of reactant, transition states, intermediates and product of glycerol dehydration, catalysed by two different enzymes: B12-dependent and B12-independent GDH.<br><br>All stationary points were calculated using QM/MM method.<br><br>All folders and corresponding PDB files are titled in a way that enables simple connection between geometries (coordinates) enclosed here and figures shown in SI associated with the corresponding manuscript.<br>
DOI: 10.6084/m9.figshare.6325667.v1
title: Geometries (PDB files) of the model systems atomic Cartesian coordinates associated with all steps in catalytic mechanism of B12-dependent and independent glycerol dehydratase (GDH) calculated using QM/MM method

description: We provide PDBs with Cartesian coordinates of all steps including enzyme geometries of reactants, transition states, intermediates and products calculated with QM/MM using model systems of B12-dependent and independent GDH.<br>All folders and PDB files within are titled in a way that one can easily associate geometries with figures from SI that follows the corresponding manuscript.<br>
DOI: 10.6084/m9.figshare.6325667.v2
title: Geometries (PDB files) of the model systems atomic Cartesian coordinates associated with all steps in catalytic mechanism of B12-dependent and independent glycerol dehydratase (GDH) calculated using QM/MM method

description: We provide PDBs with Cartesian coordinates of all steps including enzyme geometries of reactants, transition states, intermediates and products calculated with QM/MM using model systems of B12-dependent and independent GDH.<br>All folders and PDB files within are titled in a way that one can easily associate geometries with figures from SI that follows the corresponding manuscript.<br>
DOI: 10.6084/m9.figshare.6325667.v4
title: Geometries (PDB files) of stationary points of mechanism of glycerol dehydration catalysed by B12-dependent and B12-independent glycerol dehydratase (GDH) calculated using QM/MM method

description: We provide PDBs with Cartesian coordinates of reactant, transition states, intermediates and product of glycerol dehydration, catalysed by two different enzymes: B12-dependent and B12-independent GDH.<br><br>All stationary points were calculated using QM/MM method.<br><br>All folders and corresponding PDB files are titled in a way that enables simple connection between geometries (coordinates) enclosed here and figures shown in SI associated with the corresponding manuscript.<br>
DOI: 10.6084/m9.figshare.6325667.v3
title: Geometries (PDB files) of the model systems atomic Cartesian coordinates associated with all steps in catalytic mechanism of B12-dependent and independent glycerol dehydratase (GDH) calculated using QM/MM method

description: We provide PDBs with Cartesian coordinates of all steps including enzyme geometries of reactants, transition states, intermediates and products calculated with QM/MM using model systems of B12-dependent and independent GDH.<br>All folders and PDB files within are titled in a way that one can easily associate geometries with figures from SI that follows the corresponding manuscript.<br>
DOI: 10.6084/m9.figshare.6325457
title: L. anisa cgMLST 3140 targets ref-seqs.fasta

description: cgMLST scheme was constructed using the genomes of three <i>L. anisa </i>strains downloaded from NCBI (RefSeq: NZ_CANP00000000.1; RefSeq: NZ_NBTX00000000.1; RefSeq: NZ_LNXS00000000.1), using Ridom SeqSphere+ cgMLST Target Definer with the following parameters: a minimum length filter that removes all genes smaller than 50 bp; a start codon filter that discards all genes that contain no start codon at the beginning of the gene; a stop codon filter that discards all genes that contain no stop codon or more than one stop codon or that do not have the stop codon at the end of the gene; a homologous gene filter that discards all genes with fragments that occur in multiple copies within a genome (with identity of 90% and &gt;100 bp overlap); and a gene overlap filter that discards the shorter gene from the cgMLST scheme if the two genes affected overlap &gt;4 bp. The remaining genes were then used in a pairwise comparison using BLAST version 2.2.12 (parameters used were word size 11, mismatch penalty −1, match reward 1, gap open costs 5, and gap extension costs 2). All genes of the reference genome that were common in all query genomes with a sequence identity of ≥90% and 100% overlap and, with the default parameter stop codon percentage filter turned on, formed the final cgMLST scheme
DOI: 10.6084/m9.figshare.6325457.v1
title: L. anisa cgMLST 3140 targets ref-seqs.fasta

description: cgMLST scheme was constructed using the genomes of three <i>L. anisa </i>strains downloaded from NCBI (RefSeq: NZ_CANP00000000.1; RefSeq: NZ_NBTX00000000.1; RefSeq: NZ_LNXS00000000.1), using Ridom SeqSphere+ cgMLST Target Definer with the following parameters: a minimum length filter that removes all genes smaller than 50 bp; a start codon filter that discards all genes that contain no start codon at the beginning of the gene; a stop codon filter that discards all genes that contain no stop codon or more than one stop codon or that do not have the stop codon at the end of the gene; a homologous gene filter that discards all genes with fragments that occur in multiple copies within a genome (with identity of 90% and &gt;100 bp overlap); and a gene overlap filter that discards the shorter gene from the cgMLST scheme if the two genes affected overlap &gt;4 bp. The remaining genes were then used in a pairwise comparison using BLAST version 2.2.12 (parameters used were word size 11, mismatch penalty −1, match reward 1, gap open costs 5, and gap extension costs 2). All genes of the reference genome that were common in all query genomes with a sequence identity of ≥90% and 100% overlap and, with the default parameter stop codon percentage filter turned on, formed the final cgMLST scheme
DOI: 10.6084/m9.figshare.6325406.v2
title: Phenomenal Shrinkage in Global Biodiversity

description: World is losing 100 species of plants and animals a day.
DOI: 10.6084/m9.figshare.6325193
title: Supplementary Material for: Disparities in Chronic Kidney Disease Prevalence among Males and Females in 195 Countries: Analysis of the Global Burden of Disease 2016 Study

description: <b><i>Background:</i></b> Chronic kidney disease (CKD) imposes a substantial burden on health care systems. There are some especially vulnerable groups with a high CKD burden, one of which is women. We performed an analysis of gender disparities in the prevalence of all CKD stages and renal replacement therapy (defined as impaired kidney function [IKF]) in 195 countries. <b><i>Methods:</i></b> We used estimates produced by the Global Burden of Disease (GBD) Study 2016 revision using a Bayesian-regression analytic tool, DisMoD-MR 2.1. Data on gross domestic product based on purchasing power parity per capita (GDP PPP) was obtained via the World Bank International Comparison Program database. To estimate gender disparities, we calculated the male:female all-age prevalence rate ratio for each IKF condition. <b><i>Results:</i></b> In 2016, the global number of individuals with IKF reached 752.7 million, including 417.0 million females and 335.7 million males. The most prevalent form of IKF in both groups was albuminuria with preserved glomerular filtration rate. Geospatial analysis shows a very heterogeneous distribution of the male:female ratio for all IKF conditions, with the most prominent contrast found in kidney transplant patients. The median male:female ratio varies substantially according to GDP PPP quintiles; however, countries with different economic states could have similar male:female ratios. A strong correlation of GDP PPP with dialysis-to-transplant ratio was found. <b><i>Conclusions:</i></b> The GBD study highlights the prominent gender disparities in CKD prevalence among 195 countries. The nature of these disparities, however, is complex and must be interpreted cautiously taking into account all possible circumstances.
DOI: 10.6084/m9.figshare.6324815
title: Supplementary Material for: A de novo <b><i>KCNA1</i></b> Mutation in a Patient with Tetany and Hypomagnesemia

description: Mutations in the <i>KCNA1</i> gene encoding the voltage-gated potassium (K<sup>+</sup>) channel Kv1.1 have been linked to rare neurological syndromes, episodic ataxia type 1 (EA1) and myokymia. In 2009, a <i>KCNA1</i> mutation was identified in a large family with autosomal dominant hypomagnesemia. Despite efforts in establishing a genotype-phenotype correlation for the wide variety of symptoms in EA1, little is known on the serum magnesium (Mg<sup>2+</sup>) levels in these patients. In the present study, we describe a new de novo <i>KCNA1</i> mutation in a Polish patient with tetany and hypomagnesemia. Electrophysiological and biochemical analyses were performed to determine the pathogenicity of the mutation. A female patient presented with low serum Mg<sup>2+</sup> levels, renal Mg<sup>2+</sup> wasting, muscle cramps, and tetanic episodes. Whole exome sequencing identified a p.Leu328Val mutation in <i>KCNA1</i> encoding the Kv1.1 K<sup>+</sup> channel. Electrophysiological examinations demonstrated that the p.Leu328Val mutation caused a dominant-negative loss of function of the encoded Kv1.1 channel. Cell surface biotinylation showed normal plasma membrane expression. Taken together, this is the second report linking <i>KCNA1</i> with hypomagnesemia, thereby emphasizing the need for further evaluation of the clinical phenotypes observed in patients carrying <i>KCNA1</i> mutations.