cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.2138965
title: The effect of hydroxychloroquine on lupus erythematosus-like skin lesions in MRL/lpr mice

description: <i>Objectives</i>: To evaluate the effect and safety of hydroxychloroquine (HCQ) on lupus erythematosus (LE)-like skin lesions in the MRL/lpr mouse, a model for systemic LE (SLE). <i>Methods</i>: We divided the MRL/lpr mice into three groups that were given: (1) drinking water, (2) HCQ at a dose of 4 mg/kg/d, or (3) HCQ at a dose of 40 mg/kg/d. The HCQ was administered to examine the effect and safety of HCQ on skin lesions and the number of infiltrating cells including mast cells in the dermis. <i>Results</i>: Six of 13 mice in the group given drinking water, 3 of 11 mice in the group administered low-dose HCQ (4 mg/kg/d), and 1 of 10 mice in the group administered high-dose HCQ (40 mg/kg/d) presented the skin lesions. The average number of mast cells was 81, 50, and 12 (magnification, ×100), the mortality rate was 24%, 8%, and 9% and the mean body weight gain was 4.6 g, 8.0 g and 5.1 g, respectively. <i>Conclusions</i>: HCQ was demonstrated to decrease the appearance of LE-like lesions and the number of mast cells in the dermis. Furthermore, there were no obvious systemic adverse effects. This study provides evidence that suggests benefits in human patients.
DOI: 10.6084/m9.figshare.2885308.v330
title: UNH-RVAT 3-D SST RANS simulation results

description: Results from simulating the UNH-RVAT cross-flow turbine in three dimensions using the k-omega SST RANS model in OpenFOAM 2.3.x (590d57f32fed). See the link below for case files and download instructions.
DOI: 10.6084/m9.figshare.2138965.v1
title: The effect of hydroxychloroquine on lupus erythematosus-like skin lesions in MRL/lpr mice

description: <i>Objectives</i>: To evaluate the effect and safety of hydroxychloroquine (HCQ) on lupus erythematosus (LE)-like skin lesions in the MRL/lpr mouse, a model for systemic LE (SLE). <i>Methods</i>: We divided the MRL/lpr mice into three groups that were given: (1) drinking water, (2) HCQ at a dose of 4 mg/kg/d, or (3) HCQ at a dose of 40 mg/kg/d. The HCQ was administered to examine the effect and safety of HCQ on skin lesions and the number of infiltrating cells including mast cells in the dermis. <i>Results</i>: Six of 13 mice in the group given drinking water, 3 of 11 mice in the group administered low-dose HCQ (4 mg/kg/d), and 1 of 10 mice in the group administered high-dose HCQ (40 mg/kg/d) presented the skin lesions. The average number of mast cells was 81, 50, and 12 (magnification, ×100), the mortality rate was 24%, 8%, and 9% and the mean body weight gain was 4.6 g, 8.0 g and 5.1 g, respectively. <i>Conclusions</i>: HCQ was demonstrated to decrease the appearance of LE-like lesions and the number of mast cells in the dermis. Furthermore, there were no obvious systemic adverse effects. This study provides evidence that suggests benefits in human patients.
DOI: 10.6084/m9.figshare.2951263.v333
title: UNH-RVAT 3-D Spalart--Allmaras RANS simulation results

description: Results from simulating the UNH-RVAT cross-flow turbine in three dimensions with the Spalart--Allmaras RANS model in OpenFOAM 2.3.x (590d57f32fed). See link below for case files (note: use the `SpalartAllmaras` branch), which include a script for downloading and extracting, as well as scripts for post-processing.
DOI: 10.6084/m9.figshare.2885308.v331
title: UNH-RVAT 3-D SST RANS simulation results

description: Results from simulating the UNH-RVAT cross-flow turbine in three dimensions using the k-omega SST RANS model in OpenFOAM 2.3.x (590d57f32fed). See the link below for case files and download instructions.
DOI: 10.6084/m9.figshare.2137831
title: Insights from the ganglionic acetylcholine receptor autoantibodies in patients with Sjögren’s syndrome

description: <i>Objective</i>: It is not known whether autonomic neuropathy is a feature of Sjögren’s syndrome (SS) or whether it is related to circulating antiganglionic acetylcholine receptor (gAChR) antibodies. The goal of the present study was to investigate the autonomic dysfunction in patients with SS and the associations between autonomic dysfunction, anti-gAChR antibodies, and clinical features of SS. <i>Methods</i>: (1) The first observational study tested for the presence of gAChR antibodies in the serum samples from 39 patients with SS (absent information regarding autonomic symptoms) and healthy volunteers. (2) In the second study, serological and clinical data from 10 Japanese patients diagnosed with SS were reviewed. These patients showed autonomic dysfunction, and luciferase immunoprecipitation systems (LIPS) test was conducted to detect anti-α3 and anti-β4 gAChR antibodies. (3) In the final analysis, we combined the data of seropositive SS patients with autonomic symptom from the first study with all of the patients from the second study, and analyzed the clinical features. <i>Results</i>: (1) The LIPS assay revealed that anti-gAChRα3 and anti-gAChRβ4 antibodies were detected in the sera from patients with SS (23.1%, 9/39). Five of nine SS patients had autonomic symptoms. (2) Anti-α3 and anti-β4 gAChR antibodies were also detected in 80.0% (8/10) of patients with SS with autonomic symptoms. Six of the ten patients were diagnosed as having SS after neurological symptoms developed. These seropositive patients had predominant and severe autonomic symptoms and were diagnosed with autonomic neuropathy. (3) Thirteen of fifteen SS patients with autonomic symptoms (86.7%) were seropositive for anti-gAChR antibodies, and we confirmed sicca complex, orthostatic hypotension, upper and lower gastrointestinal (GI) symptoms, and bladder dysfunction at high rates. <i>Conclusion</i>: The present results suggest the possibility of anti-gAChR antibodies aiding the diagnostics of SS with autonomic dysfunction.
DOI: 10.6084/m9.figshare.2137831.v1
title: Insights from the ganglionic acetylcholine receptor autoantibodies in patients with Sjögren’s syndrome

description: <i>Objective</i>: It is not known whether autonomic neuropathy is a feature of Sjögren’s syndrome (SS) or whether it is related to circulating antiganglionic acetylcholine receptor (gAChR) antibodies. The goal of the present study was to investigate the autonomic dysfunction in patients with SS and the associations between autonomic dysfunction, anti-gAChR antibodies, and clinical features of SS. <i>Methods</i>: (1) The first observational study tested for the presence of gAChR antibodies in the serum samples from 39 patients with SS (absent information regarding autonomic symptoms) and healthy volunteers. (2) In the second study, serological and clinical data from 10 Japanese patients diagnosed with SS were reviewed. These patients showed autonomic dysfunction, and luciferase immunoprecipitation systems (LIPS) test was conducted to detect anti-α3 and anti-β4 gAChR antibodies. (3) In the final analysis, we combined the data of seropositive SS patients with autonomic symptom from the first study with all of the patients from the second study, and analyzed the clinical features. <i>Results</i>: (1) The LIPS assay revealed that anti-gAChRα3 and anti-gAChRβ4 antibodies were detected in the sera from patients with SS (23.1%, 9/39). Five of nine SS patients had autonomic symptoms. (2) Anti-α3 and anti-β4 gAChR antibodies were also detected in 80.0% (8/10) of patients with SS with autonomic symptoms. Six of the ten patients were diagnosed as having SS after neurological symptoms developed. These seropositive patients had predominant and severe autonomic symptoms and were diagnosed with autonomic neuropathy. (3) Thirteen of fifteen SS patients with autonomic symptoms (86.7%) were seropositive for anti-gAChR antibodies, and we confirmed sicca complex, orthostatic hypotension, upper and lower gastrointestinal (GI) symptoms, and bladder dysfunction at high rates. <i>Conclusion</i>: The present results suggest the possibility of anti-gAChR antibodies aiding the diagnostics of SS with autonomic dysfunction.
DOI: 10.6084/m9.figshare.2885308.v332
title: UNH-RVAT 3-D SST RANS simulation results

description: Results from simulating the UNH-RVAT cross-flow turbine in three dimensions using the k-omega SST RANS model in OpenFOAM 2.3.x (590d57f32fed). See the link below for case files and download instructions.
DOI: 10.6084/m9.figshare.2951263.v334
title: UNH-RVAT 3-D Spalart--Allmaras RANS simulation results

description: Results from simulating the UNH-RVAT cross-flow turbine in three dimensions with the Spalart--Allmaras RANS model in OpenFOAM 2.3.x (590d57f32fed). See link below for case files (note: use the `SpalartAllmaras` branch), which include a script for downloading and extracting, as well as scripts for post-processing.
DOI: 10.6084/m9.figshare.2951263.v335
title: UNH-RVAT 3-D Spalart--Allmaras RANS simulation results

description: Results from simulating the UNH-RVAT cross-flow turbine in three dimensions with the Spalart--Allmaras RANS model in OpenFOAM 2.3.x (590d57f32fed). See link below for case files (note: use the `SpalartAllmaras` branch), which include a script for downloading and extracting, as well as scripts for post-processing.
DOI: 10.6084/m9.figshare.2885308.v333
title: UNH-RVAT 3-D SST RANS simulation results

description: Results from simulating the UNH-RVAT cross-flow turbine in three dimensions using the k-omega SST RANS model in OpenFOAM 2.3.x (590d57f32fed). See the link below for case files and download instructions.
DOI: 10.6084/m9.figshare.2885308.v334
title: UNH-RVAT 3-D SST RANS simulation results

description: Results from simulating the UNH-RVAT cross-flow turbine in three dimensions using the k-omega SST RANS model in OpenFOAM 2.3.x (590d57f32fed). See the link below for case files and download instructions.
DOI: 10.6084/m9.figshare.2132731
title: Data associated with "Transhydrogenase and growth substrate influence lipid hydrogen isotope ratios in Desulfovibrio alaskensis G20"

description: Supplemental data associated with Leavitt et al., 2016<br><b>Fig S1</b>: Correlation of total fractionation with % branched fatty acids<b>Fig S2</b>: Fractionation of individual fatty acids relative to water<b>Fig S3</b>: Schematic of correlation coefficients between lipid abundances, growth rate, and total fractionation<b>Table S1</b>: FAME IDs<b>Table S2</b>: Major NADPH-producing reactions<b>Table S3</b>: H-isotope fractionation of individual fatty acids <b>Table S4</b>: Raw uncorrected dD values, corrected dD values, and fractionations for each fatty acid<b>Table S5</b>: Percent abundances of major fatty acids in each culture, along with growth rate and total fractionation<b>Table S6</b>: Pearson correlation coefficients between each pair of fatty acid abundances, growth rate, and total fractionation<b>NfnAB.aa.sequences.fasta</b>: fasta sequences of NfnAB sequences used to generate Figure 7<br><br>
DOI: 10.6084/m9.figshare.2133535
title: Influence of local environmental conditions and bleaching histories on the diversity and distribution of <i>Symbiodinium</i> in reef-building corals in Tanzania

description: Pollution, turbidity and coral bleaching history, as well as coral diversity, vary along the Tanzanian coastline. Prior to this study, it was not known whether exposure to such environmental variation might have influenced the diversity and distribution of <i>Symbiodinium</i> along this coastline. Such information can provide insight into whether Tanzanian reef-building corals develop adaptation to current trends of climate change. Here, 10 reef-building coral samples were collected from different reefs along the Tanzanian coast with different micro-environments and bleaching histories. The ITS-2 region of ribosomal DNA was employed in the characterisation of <i>Symbiodinium</i> harboured by reef-building corals. DGGE fingerprints and DNA sequences showed that most coral species host a single <i>Symbiodinium</i> type, which is maintained throughout the coast regardless of local environmental differences. We present polymorphic symbioses in <i>Acropora</i> spp., <i>Millepora</i> sp. and <i>Galaxea fascicularis</i> in mainly turbid and warm environments as a sign of adaptation to harsh conditions. However, such adaptation may not provide marked resistance to bleaching because <i>Acropora</i> is a bleaching-susceptible genus.
DOI: 10.6084/m9.figshare.2951263.v336
title: UNH-RVAT 3-D Spalart--Allmaras RANS simulation results

description: Results from simulating the UNH-RVAT cross-flow turbine in three dimensions with the Spalart--Allmaras RANS model in OpenFOAM 2.3.x (590d57f32fed). See link below for case files (note: use the `SpalartAllmaras` branch), which include a script for downloading and extracting, as well as scripts for post-processing.
DOI: 10.6084/m9.figshare.2885308.v335
title: UNH-RVAT 3-D SST RANS simulation results

description: Results from simulating the UNH-RVAT cross-flow turbine in three dimensions using the k-omega SST RANS model in OpenFOAM 2.3.x (590d57f32fed). See the link below for case files and download instructions.
DOI: 10.6084/m9.figshare.2132731.v1
title: Data associated with "Transhydrogenase and growth substrate influence lipid hydrogen isotope ratios in Desulfovibrio alaskensis G20"

description: Supplemental data associated with Leavitt et al., 2016<br><b>Fig S1</b>: Correlation of total fractionation with % branched fatty acids<b>Fig S2</b>: Fractionation of individual fatty acids relative to water<b>Fig S3</b>: Schematic of correlation coefficients between lipid abundances, growth rate, and total fractionation<b>Table S1</b>: FAME IDs<b>Table S2</b>: Major NADPH-producing reactions<b>Table S3</b>: H-isotope fractionation of individual fatty acids <b>Table S4</b>: Raw uncorrected dD values, corrected dD values, and fractionations for each fatty acid<b>Table S5</b>: Percent abundances of major fatty acids in each culture, along with growth rate and total fractionation<b>Table S6</b>: Pearson correlation coefficients between each pair of fatty acid abundances, growth rate, and total fractionation<b>NfnAB.aa.sequences.fasta</b>: fasta sequences of NfnAB sequences used to generate Figure 7<br><br>
DOI: 10.6084/m9.figshare.2885308.v336
title: UNH-RVAT 3-D SST RANS simulation results

description: Results from simulating the UNH-RVAT cross-flow turbine in three dimensions using the k-omega SST RANS model in OpenFOAM 2.3.x (590d57f32fed). See the link below for case files and download instructions.
DOI: 10.6084/m9.figshare.2951263.v337
title: UNH-RVAT 3-D Spalart--Allmaras RANS simulation results

description: Results from simulating the UNH-RVAT cross-flow turbine in three dimensions with the Spalart--Allmaras RANS model in OpenFOAM 2.3.x (590d57f32fed). See link below for case files (note: use the `SpalartAllmaras` branch), which include a script for downloading and extracting, as well as scripts for post-processing.
DOI: 10.6084/m9.figshare.2120026
title: Phylogenomic datasets from "Resolving evolutionary relationships in lichen-forming fungi using diverse phylogenomic datasets and analytical approaches"

description: <br><b>100, 1kb data matrix</b> - svdquart+PAUP* (100_1kb_realPHY_v1_svdquart.nex): The ‘100, 1 kb loci’ dataset was comprised of 100, 1 kilobase loci selected from each of the 100 largest contigs in the <i>R. melanophthalma</i> reference genome assembly.<b>303 Core Eukaryotic Genes (CEGs)</b>(303_CEG_rhizoplaca_v1.nex): 303 Core Eukaryotic Genes (CEGs) that passed filtering requirements - from the original 430 core eukaryotic genes and associated introns, each with an average length of ca. 5500 base pairs/CEG.<b>'CEGMA' matrix</b> (FcC_smatrix.nex): The ‘CEGMA’ matrix included 430 core eukaryotic genes and associated introns, each with an average length of ca. 5500 base pairs/CEG<b>'REALPHY' dataset </b>(polymorphisms_move.phy): The ‘RealPhy’ dataset was constructed by mapping reads from all sampled specimens to the <i>R. melanophthalma</i> reference assembly using RealPhy v1.12<b>subset 'A' from the ‘100, 1 kb loci’ dataset </b>(25a_1kb_realPHY_v1_BEAST.nex): 25-locus subsets from the ‘100, 1 kb loci’ dataset: loci 1-25.<b>subset 'B' from the ‘100, 1 kb loci’ dataset </b>(25b_1kb_realPHY_v1_BEAST.nex): subset 'B' from the ‘100, 1 kb loci’ dataset: loci 26-50subset 'C' from the ‘100, 1 kb loci’ dataset (25c_1kb_realPHY_v1_BEAST.nex): subset 'C' from the ‘100, 1 kb loci’ dataset: loci 51-75.<b>subset 'D' from the ‘100, 1 kb loci’ dataset </b>(25d_1kb_realPHY_v1_BEAST.nex): subset 'D' from the ‘100, 1 kb loci’ dataset: loci 76-100<b>subset '1-50' from the ‘100, 1 kb loci’ dataset</b> (50a_1kb_realPHY_v2_BEAST.nex): subset from the ‘100, 1 kb loci’ dataset: loci 1-50<b>subset '51-100' from the ‘100, 1 kb loci’ dataset</b> (50a_1kb_realPHY_v2_BEAST.nex): subset from the ‘100, 1 kb loci’ dataset: loci 51-100
DOI: 10.6084/m9.figshare.2131864
title: phytoplankton NGS raw read data for PeerJ(2016.01)

description: NGS raw read files generated from each sample for the phytoplankton community structure analsysis.MIS: surface water from station I in May 2014 Station I surface water, MIIS: surface water from station II in May 2014, MIID: 50 m water from station 2 in May 2014, JIS: surface water from station I in July 2014, JIIS: surface water from station II in July 2014.
DOI: 10.6084/m9.figshare.2133535.v2
title: Influence of local environmental conditions and bleaching histories on the diversity and distribution of <i>Symbiodinium</i> in reef-building corals in Tanzania

description: Pollution, turbidity and coral bleaching history, as well as coral diversity, vary along the Tanzanian coastline. Prior to this study, it was not known whether exposure to such environmental variation might have influenced the diversity and distribution of <i>Symbiodinium</i> along this coastline. Such information can provide insight into whether Tanzanian reef-building corals develop adaptation to current trends of climate change. Here, 10 reef-building coral samples were collected from different reefs along the Tanzanian coast with different micro-environments and bleaching histories. The ITS-2 region of ribosomal DNA was employed in the characterisation of <i>Symbiodinium</i> harboured by reef-building corals. DGGE fingerprints and DNA sequences showed that most coral species host a single <i>Symbiodinium</i> type, which is maintained throughout the coast regardless of local environmental differences. We present polymorphic symbioses in <i>Acropora</i> spp., <i>Millepora</i> sp. and <i>Galaxea fascicularis</i> in mainly turbid and warm environments as a sign of adaptation to harsh conditions. However, such adaptation may not provide marked resistance to bleaching because <i>Acropora</i> is a bleaching-susceptible genus.
DOI: 10.6084/m9.figshare.2118049
title: C. elegans Embryonic Differentiation Tree (10 division events)

description: Differentiation tree (Gordon, 1999) of <i>Caenorhabditis elegans </i>(Nematode, roundworm) embryo up to 10 division events. Data from lineage trees and fate maps of Sulston and Horvitz (1977) and Hobert (2010). Division event timing approximated from Bhatla (2016). Cell size information approximated from Bao et.al (2006).<br>A division event occurs when a mother cell divides into two daughter cells. In rare instances, a mother cell only produces a single daughter cell. In this case, no size information is available for the daughter cell. According to the differentiation tree convention, smaller cells are placed to the left and larger cells are placed to the right. <br>Each cell is annotated with its standard nomenclature and a decimal value that describes the relative size of each daughter cell (e.g. smaller cell is 0.49, larger cell is 0.51).<br><br>References:Bao, Z.R.; Murray, J.I.; Boyle, T.; Ooi, S.L.; Sandel, M.J.; Waterston, R.H. 2006. Automated cell lineage tracing in Caenorhabditis elegans. Proceedings of the National Academy of Sciences of the United States of America, 103, 2707-2712.<br>Bhatla, N. 2016. <i>C. elegans</i> Cell Lineage. WormWeb, http://wormweb.org/celllineage Accessed on 2/12/2016.Hobert O. 2010. Neurogenesis in the nematode <i>Caenorhabditis </i><i>elegans</i>. WormBook, doi:10.1895/ wormbook.1.12.2.Sulston, J.E. and Horvitz, H.R. 1977. Post-embryonic cell lineages of the nematode <i>Caenorhabditis </i><i>elegans</i>. Developmental Biology, 56, 110-156.
DOI: 10.6084/m9.figshare.2119573
title: Ying etal-TES Paper-Solar Energy-2015.pdf

description: The paper presents experimental measurements and simulation results of a pilot-scale thermal energy storage system with encapsulated sodium nitrates for high temperature applications. <br>
DOI: 10.6084/m9.figshare.2120026.v1
title: Phylogenomic datasets from "Resolving evolutionary relationships in lichen-forming fungi using diverse phylogenomic datasets and analytical approaches"

description: <br><b>100, 1kb data matrix</b> - svdquart+PAUP* (100_1kb_realPHY_v1_svdquart.nex): The ‘100, 1 kb loci’ dataset was comprised of 100, 1 kilobase loci selected from each of the 100 largest contigs in the <i>R. melanophthalma</i> reference genome assembly.<b>303 Core Eukaryotic Genes (CEGs)</b>(303_CEG_rhizoplaca_v1.nex): 303 Core Eukaryotic Genes (CEGs) that passed filtering requirements - from the original 430 core eukaryotic genes and associated introns, each with an average length of ca. 5500 base pairs/CEG.<b>'CEGMA' matrix</b> (FcC_smatrix.nex): The ‘CEGMA’ matrix included 430 core eukaryotic genes and associated introns, each with an average length of ca. 5500 base pairs/CEG<b>'REALPHY' dataset </b>(polymorphisms_move.phy): The ‘RealPhy’ dataset was constructed by mapping reads from all sampled specimens to the <i>R. melanophthalma</i> reference assembly using RealPhy v1.12<b>subset 'A' from the ‘100, 1 kb loci’ dataset </b>(25a_1kb_realPHY_v1_BEAST.nex): 25-locus subsets from the ‘100, 1 kb loci’ dataset: loci 1-25.<b>subset 'B' from the ‘100, 1 kb loci’ dataset </b>(25b_1kb_realPHY_v1_BEAST.nex): subset 'B' from the ‘100, 1 kb loci’ dataset: loci 26-50subset 'C' from the ‘100, 1 kb loci’ dataset (25c_1kb_realPHY_v1_BEAST.nex): subset 'C' from the ‘100, 1 kb loci’ dataset: loci 51-75.<b>subset 'D' from the ‘100, 1 kb loci’ dataset </b>(25d_1kb_realPHY_v1_BEAST.nex): subset 'D' from the ‘100, 1 kb loci’ dataset: loci 76-100<b>subset '1-50' from the ‘100, 1 kb loci’ dataset</b> (50a_1kb_realPHY_v2_BEAST.nex): subset from the ‘100, 1 kb loci’ dataset: loci 1-50<b>subset '51-100' from the ‘100, 1 kb loci’ dataset</b> (50a_1kb_realPHY_v2_BEAST.nex): subset from the ‘100, 1 kb loci’ dataset: loci 51-100
DOI: 10.6084/m9.figshare.2885308.v337
title: UNH-RVAT 3-D SST RANS simulation results

description: Results from simulating the UNH-RVAT cross-flow turbine in three dimensions using the k-omega SST RANS model in OpenFOAM 2.3.x (590d57f32fed). See the link below for case files and download instructions.
DOI: 10.6084/m9.figshare.2119573.v1
title: Ying etal-TES Paper-Solar Energy-2015.pdf

description: The paper presents experimental measurements and simulation results of a pilot-scale thermal energy storage system with encapsulated sodium nitrates for high temperature applications. <br>
DOI: 10.6084/m9.figshare.2951263.v338
title: UNH-RVAT 3-D Spalart--Allmaras RANS simulation results

description: Results from simulating the UNH-RVAT cross-flow turbine in three dimensions with the Spalart--Allmaras RANS model in OpenFOAM 2.3.x (590d57f32fed). See link below for case files (note: use the `SpalartAllmaras` branch), which include a script for downloading and extracting, as well as scripts for post-processing.
DOI: 10.6084/m9.figshare.2885308.v338
title: UNH-RVAT 3-D SST RANS simulation results

description: Results from simulating the UNH-RVAT cross-flow turbine in three dimensions using the k-omega SST RANS model in OpenFOAM 2.3.x (590d57f32fed). See the link below for case files and download instructions.
DOI: 10.6084/m9.figshare.2131864.v1
title: JIID_R1.fastq.gz

description: JIIDR1
DOI: 10.6084/m9.figshare.2117734
title: Assessing Research in Mexico

description: Excel databases Research products SNI Area IV