cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.9706601.v1
title: Supplementary Material for: Tumor Necrosis Factor Receptor-Associated Factor 5 Promotes Arterial Neointima Formation through Smooth Muscle Cell Proliferation

description: Tumor necrosis factor (TNF) receptor-associated factors (TRAFs) are cytoplasmic adaptor proteins of the TNF/interleukin (IL)-1/Toll-like receptor superfamily. Ligands of this family such as TNFα, CD40L, and IL-1β promote chronic inflammatory processes such as atherosclerosis and restenosis, the latter being a common adverse reaction after vascular interventions. We previously reported overexpression of TRAF5 in murine and human atheromata and TRAF5-dependent proinflammatory functions in vitro. However, the role of TRAF5 in restenosis remains unsettled. To evaluate whether TRAF5 affects neointima formation, TRAF5<sup>–/–</sup>LDLR<sup>–/–</sup> and TRAF5<sup>+/+</sup>LDLR<sup>–/–</sup> mice consuming a high cholesterol diet (HCD) received wire-induced injury of the carotid artery. After 28 days, TRAF5-deficient mice showed a 45% decrease in neointimal area formation compared with TRAF5-compentent mice. Furthermore, neointimal vascular smooth muscle cells (vSMC) and macrophages decreased whereas collagen increased in TRAF5-deficient mice. Mechanistically, the latter expressed lower transcript levels of the matrix metalloproteinases 2 and 9, both instrumental in extracellular matrix degradation and vSMC mobilization. Additionally, TRAF5-specific siRNA interference rendered murine vSMC less proliferative upon CD40L stimulation. In accordance with these findings, fewer vSMC isolated from TRAF5-deficient aortas were in a proliferative state as assessed by Ki67 and cyclin B1 expression. In conclusion, TRAF5 deficiency mitigates neointima formation in mice, likely through a TRAF5-dependent decrease in vSMC proliferation.
DOI: 10.6084/m9.figshare.9705788
title: Evasive Flight Behavior Raw Observations

description: Evasive flight behavior for tiger moth species examined in the associated article. TRUE = moth performed evasive maneuver. FALSE = moth did not perform evasive maneuver. Data for Bertholdia trigona come from Corcoran and Conner, 2012 (10.1242/jeb.076943)
DOI: 10.6084/m9.figshare.9705788.v1
title: Evasive Flight Behavior Raw Observations

description: Evasive flight behavior for tiger moth species examined in the associated article. TRUE = moth performed evasive maneuver. FALSE = moth did not perform evasive maneuver. Data for Bertholdia trigona come from Corcoran and Conner, 2012 (10.1242/jeb.076943)
DOI: 10.6084/m9.figshare.9706187.v2
title: Palatability Raw Dataset

description: palatability_data.csv: Contains hand-feeding and free-flight palatability data for tiger moth species examined in the associated article. TRUE = moth was completely accepted and/or captured and not dropped by bat predators. FALSE = moth was completely rejected and/or dropped by bat predators. Data for Bertholdia trigona come from Corcoran and Conner, 2012 (10.1242/jeb.076943)<br>control_palatability_data.csv: Contains hand-feeding palatability data for control Noctuidae species examined in the associated article. TRUE = moth was completely accepted by bat predators. FALSE = moth was completely rejected by bat predators.<br>
DOI: 10.6084/m9.figshare.9705227
title: data.rar

description: The data supporting this meta-analysis are from previously reported studies and datasets, which have been cited. The processed data are available
DOI: 10.6084/m9.figshare.9706187.v1
title: Palatability Raw Dataset

description: Contains palatability data for select tiger moth species. TRUE = moth was completely accepted and/or captured and not dropped by bat predators. FALSE = moth was completely reject and/or dropped by bat predators.
DOI: 10.6084/m9.figshare.9705227.v1
title: data.rar

description: The data supporting this meta-analysis are from previously reported studies and datasets, which have been cited. The processed data are available
DOI: 10.6084/m9.figshare.9705263
title: Data from: Impacts of microplastics on growth and health of hermatypic corals are species-specific

description: 3D models and data from "Impacts of microplastics on growth and health of hermatypic corals are species-specific"
DOI: 10.6084/m9.figshare.9704930
title: Supplementary Material for: Possible Involvement of Nitric Oxide in the Antipruritic Effect of Metformin on Chloroquine-Induced Scratching in Mice

description: <b><i>Background:</i></b> Metformin ameliorates non-histamine-mediated itch. We have recently reported that the nitric oxide (NO) pathway is involved in chloroquine (CQ)-induced scratching behavior. Here we investigated the involvement of the NO pathway in the antipruritic effect of metformin on CQ-induced itch. <b><i>Methods:</i></b> Metformin (5–200 mg/kg, given intraperitoneally [i.p.]) was injected 4 h before CQ (400 µg/site, given intradermally [i.d.]) or compound 48/80 (100 µg/site, i.d.). A nonspecific nitric oxide synthase (NOS) inhibitor, NG-nitro-L-arginine methyl ester (L-NAME; 1 and 10 mg/kg, i.p.), or an NO precursor, L-arginine (10 and 100 mg/kg, i.p.) was administered 30 min before injection of CQ. A neural NOS (nNOS) inhibitor, 7-nitroindazole (7-NI; 1 and 10 nmol/site, i.d.) was concurrently administered with CQ. The scratching behavior was recorded for 30 min following the injection of CQ. We studied the changes in skin and spinal nitrite levels after treatments. <b><i>Results:</i></b> Our results showed that metformin (100 and 200 mg/kg) significantly reduced the CQ-induced scratching behavior but not the compound 48/80-induced scratching behavior. L-Arginine inhibited the antipruritic effect of metformin, while L-NAME and 7-NI significantly potentiated the inhibitory effects of a subeffective dose of metformin on the CQ-induced scratching behavior. The skin but not the spinal nitrite level was significantly increased after CQ administration. The elevated cutaneous nitrite level was reversed by effective doses of either metformin or 7-NI, but not by the subeffective doses of metformin + 7-NI. <b><i>Conclusion:</i></b> Acute injection of metformin significantly inhibits CQ-induced scratching behavior. This effect is mediated through inhibition of the NO pathway, especially by inhibiting the dermal nNOS enzyme.
DOI: 10.6084/m9.figshare.9704732
title: Data from: Investigation of the structural competing and atomic ordering in Heusler compounds Fe2NiSi and Ni2FeSi under strain condition

description: All datasets reported in this work
DOI: 10.6084/m9.figshare.9704732.v1
title: Data from: Investigation of the structural competing and atomic ordering in Heusler compounds Fe2NiSi and Ni2FeSi under strain condition

description: All datasets reported in this work
DOI: 10.6084/m9.figshare.9703940
title: Supplementary Material for: Rethinking the Effects of Body Size on the Study of Brain Size Evolution

description: Body size correlates with most structural and functional components of an organism’s phenotype – brain size being a prime example of allometric scaling with animal size. Therefore, comparative studies of brain evolution in vertebrates rely on controlling for the scaling effects of body size variation on brain size variation by calculating brain weight/body weight ratios. Differences in the brain size-body size relationship between taxa are usually interpreted as differences in selection acting on the brain or its components, while selection pressures acting on body size, which are among the most prevalent in nature, are rarely acknowledged, leading to conflicting and confusing conclusions. We address these problems by comparing brain-body relationships from across &gt;1,000 species of birds and non-avian reptiles. Relative brain size in birds is often assumed to be 10 times larger than in reptiles of similar body size. We examine how differences in the specific gravity of body tissues and in body design (e.g., presence/absence of a tail or a dense shell) between these two groups can affect estimates of relative brain size. Using phylogenetic comparative analyses, we show that the gap in relative brain size between birds and reptiles has been grossly exaggerated. Our results highlight the need to take into account differences between taxa arising from selection pressures affecting body size and design, and call into question the widespread misconception that reptile brains are small and incapable of supporting sophisticated behavior and cognition.
DOI: 10.6084/m9.figshare.9703244
title: Grazing and short-term precipitation affect ecosystem functioning; C, N, and P contents; and CNP stoichiometry in the desert steppe of the Mongolia Plateau.xlsx

description: Field data were obtained from July 20 to August 10, which represented the highest annual plant growth peaks in 2016, 2017 and 2018. In each treatment, five 1 × 1 m quadrats were established randomly to observe the plant community coverage and species number, and then the aboveground biomass and litter biomass were clipped at the ground level. <br><br>Soil samples were obtained from five 5 cm diameter soil cores at depths of 0 to 10, 10 to 20, 20 to 30 and 30 to 40 cm. The five cores from each quadrat were mixed in situ as one composite sample and rocks and visible plant materials were removed by hand. The soil was air-dried and ground to pass a 1 mm sieve for C, N and P analysis.
DOI: 10.6084/m9.figshare.9702986
title: Model predicted management area boundaries

description: Shapefile showing management areas for the Scottish west coast region, as recommended by the analysis of connectivity estimates generated using a hydrodynamic model. The methods used to generate the layout are described by Adams et al. (2016); a threshold connection probability of 0.01 (weak: in either direction) between individual farm sites contained within each area was applied.<br>
DOI: 10.6084/m9.figshare.9702947
title: JCEM-jc-2019-01933-FROMMER-SUPPLEMENTAL_MATERIAL

description: <br><b>Context</b>: The structure of the human leucocyte antigen (HLA) peptide-binding clefts strongly contributes to monoglandular and polyglandular autoimmunity (AP). <br><b>Objective</b>: To investigate the impact of amino acid polymorphisms on the peptide binding interactions within HLA class II and its association with AP <br><b>Design: </b>immunogenetic study <br><b>Setting</b>: Tertiary referral center for autoimmune endocrine diseases <br><b>Subjects</b>: 587 subjects with AP, autoimmune thyroid disease (AITD), type 1 diabetes (T1D) and healthy unrelated controls were typed for HLA class II. <br><b>Methods: </b>Amino acids within the peptide binding cleft that are encoded by HLA class II exon 2 were listed for all codon positions in all subjects. Overall comparisons between disease and control groups with respect to allele distribution at a given locus were performed by assembling rare alleles applying an exact Freeman Halton contingency table test with Monte-Carlo p values based on 150,000 samples. <br><b>Results</b>: The Montecarlo Exact Fisher Test demonstrated marked differences in all three Loci, <i>DQA1</i>, <i>DQB1</i>, <i>DRB1</i> (p&lt;0.0001) between AP versus both AITD and controls, as well as between AP type II (Addison’s disease as major endocrine component) and AP type III (T1D + AITD). Differences were also noted between AP and T1D pertaining to the <i>DRB1</i> allele (p&lt;0.041). The following seven amino acid positions DRB1-13, DRB1-26, DRB1-71, DRB1-74, DQA1-47, DQA1-56, and DQB1-57 significantly contributed to AP. Five positions in <i>DQA1</i> (11, 47, 50, 56, and 69) completely correlated (p&lt;0.0001). <br><b>Conclusion</b>: Amino acid polymorphisms within HLA class II exon 2 mediate the AP risk and differentiate between thyroid and polyglandular autoimmunity. <br>
DOI: 10.6084/m9.figshare.9702986.v1
title: Model predicted management area boundaries

description: Shapefile showing management areas for the Scottish west coast region, as recommended by the analysis of connectivity estimates generated using a hydrodynamic model. The methods used to generate the layout are described by Adams et al. (2016); a threshold connection probability of 0.01 (weak: in either direction) between individual farm sites contained within each area was applied.<br>
DOI: 10.6084/m9.figshare.9703244.v1
title: Grazing and short-term precipitation affect ecosystem functioning; C, N, and P contents; and CNP stoichiometry in the desert steppe of the Mongolia Plateau.xlsx

description: Field data were obtained from July 20 to August 10, which represented the highest annual plant growth peaks in 2016, 2017 and 2018. In each treatment, five 1 × 1 m quadrats were established randomly to observe the plant community coverage and species number, and then the aboveground biomass and litter biomass were clipped at the ground level. <br><br>Soil samples were obtained from five 5 cm diameter soil cores at depths of 0 to 10, 10 to 20, 20 to 30 and 30 to 40 cm. The five cores from each quadrat were mixed in situ as one composite sample and rocks and visible plant materials were removed by hand. The soil was air-dried and ground to pass a 1 mm sieve for C, N and P analysis.
DOI: 10.6084/m9.figshare.9702926
title: the level of P-tau(ser202) in 28d by western blot.xlsx

description: The level of P-tau(ser202) in 28d by western blot in a pentamethazol epilepsy model.
DOI: 10.6084/m9.figshare.9702926.v1
title: the level of P-tau(ser202) in 28d by western blot.xlsx

description: The level of P-tau(ser202) in 28d by western blot in a pentamethazol epilepsy model.
DOI: 10.6084/m9.figshare.9702947.v1
title: JCEM-AMINO ACID POLYMORPHISMS IN HLA CLASS II DIFFERENTIATE BETWEEN THYROID AND POLYGLANDULAR AUTOIMMUNITY

description: <b>Context</b>: The structure of the human leucocyte antigen (HLA) peptide-binding clefts within the major histocompatibility complex strongly contributes to monoglandular and polyglandular autoimmunity (AP). <b>Objective</b>: To investigate the impact of amino acid polymorphisms on the peptide binding interactions within HLA class II and its association with AP <b>Design: </b>immunogenetic study <b>Setting</b>: Tertiary referral center for autoimmune endocrine diseases <b>Subjects</b>: 587 subjects with AP, autoimmune thyroid disease (AITD), type 1 diabetes (T1D) and healthy controls were typed for HLA class II. <b>Methods: </b>Positions within HLA class II exon 2 where codons translate into different amino acids were detected in all subjects. Amino acids were listed for all codon positions and overall comparisons between disease and control groups with respect to allele distribution at a given locus were performed by assembling rare alleles applying an exact Freeman Halton contingency table test with Monte-Carlo p values based on 150000 samples. <b>Results</b>: The Montecarlo Exact Fisher Test demonstrated marked differences in all three Loci, DQA1, DQB1, DRB1 (p&lt;0.0001) between AP versus both AITD and controls as well as between AP type II (Addison’s disease as major component) and type III (T1D+AITD). Differences were also noted between AP and T1D pertaining to the DRB1 allele (p&lt;0.041). The following seven positions DRB1-13, DRB1-26, DRB1-71, DRB1-74, DQA1-47, DQA1-56, and DQB1-57 significantly contributed to AP <b>Conclusion</b>: Amino acid polymorphisms in codon positions within HLA class II exon 2 confer risk to AP and differentiate between thyroid and polyglandular autoimmunity.
DOI: 10.6084/m9.figshare.9702845
title: Epidemiology of Viral Hepatitis B and C in Punjab, Pakistan: A Multicenter Cross-sectional Study, 2017-18

description: This data is from prevention and control program under the umbrella of Pakistan Kidney and Liver Institute and Research Center, Lahore Pakistan. The data is submitted here as a requirement for F1000 Journal Publication Process. The data is based on Screening through ELISA from Punjab Province. The research article submitted based on this data for the purpose of publication is solely based on this data file.
DOI: 10.6084/m9.figshare.9702851
title: Data and do-files from "Anatomy of a demand shock: Quantitative analysis of crowding in hospital emergency departments in Victoria, Australia during the 2009 influenza pandemic"

description: These files are the Stata do file and two datasets needed to replicate the graphs and regression results in the paper "Anatomy of a demand shock: Quantitative analysis of crowding in hospital emergency departments in Victoria, Australia during the 2009 influenza pandemic"
DOI: 10.6084/m9.figshare.9702845.v1
title: Epidemiology of Viral Hepatitis B and C in Punjab, Pakistan: A Multicenter Cross-sectional Study, 2017-18

description: This data is from prevention and control program under the umbrella of Pakistan Kidney and Liver Institute and Research Center, Lahore Pakistan. The data is submitted here as a requirement for F1000 Journal Publication Process. The data is based on Screening through ELISA from Punjab Province. The research article submitted based on this data for the purpose of publication is solely based on this data file.
DOI: 10.6084/m9.figshare.9702947.v2
title: Supplemental Material- JCEM-AMINO ACID POLYMORPHISMS IN HLA CLASS II DIFFERENTIATE BETWEEN THYROID AND POLYGLANDULAR AUTOIMMUNITY

description: <b>Context</b>: The structure of the human leucocyte antigen (HLA) peptide-binding clefts within the major histocompatibility complex strongly contributes to monoglandular and polyglandular autoimmunity (AP). <b>Objective</b>: To investigate the impact of amino acid polymorphisms on the peptide binding interactions within HLA class II and its association with AP <b>Design: </b>immunogenetic study <b>Setting</b>: Tertiary referral center for autoimmune endocrine diseases <b>Subjects</b>: 587 subjects with AP, autoimmune thyroid disease (AITD), type 1 diabetes (T1D) and healthy controls were typed for HLA class II. <b>Methods: </b>Positions within HLA class II exon 2 where codons translate into different amino acids were detected in all subjects. Amino acids were listed for all codon positions and overall comparisons between disease and control groups with respect to allele distribution at a given locus were performed by assembling rare alleles applying an exact Freeman Halton contingency table test with Monte-Carlo p values based on 150000 samples. <b>Results</b>: The Montecarlo Exact Fisher Test demonstrated marked differences in all three Loci, DQA1, DQB1, DRB1 (p&lt;0.0001) between AP versus both AITD and controls as well as between AP type II (Addison’s disease as major component) and type III (T1D+AITD). Differences were also noted between AP and T1D pertaining to the DRB1 allele (p&lt;0.041). The following seven positions DRB1-13, DRB1-26, DRB1-71, DRB1-74, DQA1-47, DQA1-56, and DQB1-57 significantly contributed to AP <b>Conclusion</b>: Amino acid polymorphisms in codon positions within HLA class II exon 2 confer risk to AP and differentiate between thyroid and polyglandular autoimmunity.
DOI: 10.6084/m9.figshare.9702608
title: MOESM1 of A global consistent positive effect of urban green area size on bird richness

description: Additional file 1: Table S1. List of studies analysed with their environmental and bird trait information and fit and slope values of each study.
DOI: 10.6084/m9.figshare.9702947.v5
title: JCEM-jc-2019-01933-FROMMER-SUPPLEMENTAL_MATERIAL

description: <br><b>Context</b>: The structure of the human leucocyte antigen (HLA) peptide-binding clefts strongly contributes to monoglandular and polyglandular autoimmunity (AP). <br><b>Objective</b>: To investigate the impact of amino acid polymorphisms on the peptide binding interactions within HLA class II and its association with AP <br><b>Design: </b>immunogenetic study <br><b>Setting</b>: Tertiary referral center for autoimmune endocrine diseases <br><b>Subjects</b>: 587 subjects with AP, autoimmune thyroid disease (AITD), type 1 diabetes (T1D) and healthy unrelated controls were typed for HLA class II. <br><b>Methods: </b>Amino acids within the peptide binding cleft that are encoded by HLA class II exon 2 were listed for all codon positions in all subjects. Overall comparisons between disease and control groups with respect to allele distribution at a given locus were performed by assembling rare alleles applying an exact Freeman Halton contingency table test with Monte-Carlo p values based on 150,000 samples. <br><b>Results</b>: The Montecarlo Exact Fisher Test demonstrated marked differences in all three Loci, <i>DQA1</i>, <i>DQB1</i>, <i>DRB1</i> (p&lt;0.0001) between AP versus both AITD and controls, as well as between AP type II (Addison’s disease as major endocrine component) and AP type III (T1D + AITD). Differences were also noted between AP and T1D pertaining to the <i>DRB1</i> allele (p&lt;0.041). The following seven amino acid positions DRB1-13, DRB1-26, DRB1-71, DRB1-74, DQA1-47, DQA1-56, and DQB1-57 significantly contributed to AP. Five positions in <i>DQA1</i> (11, 47, 50, 56, and 69) completely correlated (p&lt;0.0001). <br><b>Conclusion</b>: Amino acid polymorphisms within HLA class II exon 2 mediate the AP risk and differentiate between thyroid and polyglandular autoimmunity. <br>
DOI: 10.6084/m9.figshare.9702947.v4
title: Supplemental Material- JCEM-AMINO ACID POLYMORPHISMS IN HLA CLASS II DIFFERENTIATE BETWEEN THYROID AND POLYGLANDULAR AUTOIMMUNITY

description: <b>Context</b>: The structure of the human leucocyte antigen (HLA) peptide-binding clefts within the major histocompatibility complex strongly contributes to monoglandular and polyglandular autoimmunity (AP). <b>Objective</b>: To investigate the impact of amino acid polymorphisms on the peptide binding interactions within HLA class II and its association with AP <b>Design: </b>immunogenetic study <b>Setting</b>: Tertiary referral center for autoimmune endocrine diseases <b>Subjects</b>: 587 subjects with AP, autoimmune thyroid disease (AITD), type 1 diabetes (T1D) and healthy controls were typed for HLA class II. <b>Methods: </b>Positions within HLA class II exon 2 where codons translate into different amino acids were detected in all subjects. Amino acids were listed for all codon positions and overall comparisons between disease and control groups with respect to allele distribution at a given locus were performed by assembling rare alleles applying an exact Freeman Halton contingency table test with Monte-Carlo p values based on 150000 samples. <b>Results</b>: The Montecarlo Exact Fisher Test demonstrated marked differences in all three Loci, DQA1, DQB1, DRB1 (p&lt;0.0001) between AP versus both AITD and controls as well as between AP type II (Addison’s disease as major component) and type III (T1D+AITD). Differences were also noted between AP and T1D pertaining to the DRB1 allele (p&lt;0.041). The following seven positions DRB1-13, DRB1-26, DRB1-71, DRB1-74, DQA1-47, DQA1-56, and DQB1-57 significantly contributed to AP <b>Conclusion</b>: Amino acid polymorphisms in codon positions within HLA class II exon 2 confer risk to AP and differentiate between thyroid and polyglandular autoimmunity.
DOI: 10.6084/m9.figshare.9702608.v1
title: MOESM1 of A global consistent positive effect of urban green area size on bird richness

description: Additional file 1: Table S1. List of studies analysed with their environmental and bird trait information and fit and slope values of each study.
DOI: 10.6084/m9.figshare.9702584
title: MOESM3 of The DNA repair protein SHPRH is a nucleosome-stimulated ATPase and a nucleosome-E3 ubiquitin ligase

description: Additional file 3. Sites of SHPRH self-ubiquitination which were identified by mass spectrometry analyses of ubiquitination reactions using SHPRH and UBE2D1, in the presence of nucleosomes.
DOI: 10.6084/m9.figshare.9702584.v1
title: MOESM3 of The DNA repair protein SHPRH is a nucleosome-stimulated ATPase and a nucleosome-E3 ubiquitin ligase

description: Additional file 3. Sites of SHPRH self-ubiquitination which were identified by mass spectrometry analyses of ubiquitination reactions using SHPRH and UBE2D1, in the presence of nucleosomes.