cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.7731192
title: Full results of the t test and/or ANOVA test for Figures.

description: Complete results of t-tests and/or ANOVA tests for all figures, as well as tables with post hoc results where all P values are presented in numerical form.
DOI: 10.5281/zenodo.7731191
title: Full results of the t test and/or ANOVA test for Figures.

description: Complete results of t-tests and/or ANOVA tests for all figures, as well as tables with post hoc results where all P values are presented in numerical form.
DOI: 10.6084/m9.figshare.22267078
title: Urbanization and agriculture influence stream dissolved organic matter quality variability more than decomposition rates and macroinvertebrate diversity across seasonal time scales

description: In the era of the Anthropocene, humans have impacted over half of the Earth’s surface. Urbanized and agricultural land use pressures have easily become some of the dominating forces shaping ecosystems today, revealing similar impacts on freshwater ecosystems. Streams and rivers are among the most heavily impacted due to the influence of catchment land use on stream water quality and ecological condition. Structural and functional indicators collected by biomonitoring programs are underused as tools for targeting stream restoration efforts. In the present study we applied a novel combination of indicators—dissolved organic matter (DOM) composition, cotton strip decomposition, and benthic invertebrate sampling—to determine if streams highly impacted by urbanized and agricultural land use across Windsor-Essex (southwestern Ontario, Canada) were consistent by season, anthropogenic land use or some combination of both. Overall, our results suggest that agricultural and urban streams are indeed degraded at a similar level, with high decomposition rates and low levels of macroinvertebrate diversity. Moreover, DOM quality proved to be the most effective indicator, integrating insights from both decomposition and macroinvertebrate indices while remaining stable seasonally. Microbial humic-like DOM correlated positively with decomposition rates, and negatively with invertebrate species richness. Our findings show that function changes in stream ecological condition can be effectively tracked by structural indicators like DOM composition. We suggest that these measures should be incoporated into monitoring programs to develop functional indicators for targeting stream restoration.
DOI: 10.25451/flinders.20366346
title: DataFiles_Mssplendida_Rainforest_Riverscape.zip

description: #DESCRIBING DATA FOR: "Environmental selection, rather than neutral processes, best explain patterns of diversity in a tropical rainforest fish" <br> #AUTHORS: Katie Gates, Jonathan Sandoval-Castillo, Chris J. Brauer, Peter J. Unmack, Martin Laporte, Louis Bernatchez, Luciano B. Beheregaray <br> #CORRESPONDENCE: Luciano Beheregaray (luciano.beheregaray@flinders.edu.au) <br> <br> ##DATA FILES: <br> #1: "MSSplendida_Sampling_And_Environmental_Data.csv" - Comma-delimited spreadsheet containing location-specific sampling and environmental data for Melanotaenia splendida splendida* - Fields include: Date (sampling date) Location (sampling location) Code (sampling location code used for individual IDs in other data files) Catchment (river drainage of sampling location) Latitude (latitude of sampling location) Longitude (longitude of sampling location) Collected n (sample size of collected individuals) Final n (DNA) (sample size of final SNP dataset) Final n (Morpho) (sample size of final morphometric dataset) Final n (GxPxE) (sample size of overlapping datasets used for genotype x phenotype x environment analysis) STRANNTEMP (average annual mean temperature (decrees celsius)) STRANNRAIN (average annual mean rainfall (mm)) RUNSUMMERMEAN (average summer mean runoff (ML)) RDI (river disturbance index (index: 0-1)) ASPECT (stream segment aspect (degrees)) STRDENSITY (stream density; total length of upstream segments calculated for the segment pour-point (km/km^2)) <br> *NOTE: Additional metadata describing the environmental data can be accessed at http://www.ga.gov.au/scientific-topics/water/national-surface-water-information <br> #2: "MSSplendida_Full_SNP_Dataset.vcf" - VCF file containing the 14,540 SNP genotypes identified for 210 Melanotaenia splendida splendida individuals, used as a basis for all downstream genomic analyses - A description of data fields can be accessed at https://samtools.github.io/hts-specs/VCFv4.2.pdf <br> #3: "MSSplendida_Morphometric_Landmarks_And_Size.csv" - Comma-delimited spreadsheet containing coordinates (x,y) for 18 morphometric landmarks, as well as centroid size, for individuals used in geometric morphometric and GxPxE analyses <br> <br> ##CODE: <br> #1: "RDA_GEA" - Folder containing R code and input files for genotype-environment association (GEA) RDA <br> #2: "RDA_PEA" - Folder containing R code and input files for phenotype-environment association (PEA) RDA <br> #3: "RDA_GxPxE" - Folder containing R code and input files for genotype-phenotype-environment association (GxPxE) RDA <br>
DOI: 10.25451/flinders.20366346.v1
title: DataFiles_Mssplendida_Rainforest_Riverscape.zip

description: #DESCRIBING DATA FOR: "Environmental selection, rather than neutral processes, best explain patterns of diversity in a tropical rainforest fish" <br> #AUTHORS: Katie Gates, Jonathan Sandoval-Castillo, Chris J. Brauer, Peter J. Unmack, Martin Laporte, Louis Bernatchez, Luciano B. Beheregaray <br> #CORRESPONDENCE: Luciano Beheregaray (luciano.beheregaray@flinders.edu.au) <br> <br> ##DATA FILES: <br> #1: "MSSplendida_Sampling_And_Environmental_Data.csv" - Comma-delimited spreadsheet containing location-specific sampling and environmental data for Melanotaenia splendida splendida* - Fields include: Date (sampling date) Location (sampling location) Code (sampling location code used for individual IDs in other data files) Catchment (river drainage of sampling location) Latitude (latitude of sampling location) Longitude (longitude of sampling location) Collected n (sample size of collected individuals) Final n (DNA) (sample size of final SNP dataset) Final n (Morpho) (sample size of final morphometric dataset) Final n (GxPxE) (sample size of overlapping datasets used for genotype x phenotype x environment analysis) STRANNTEMP (average annual mean temperature (decrees celsius)) STRANNRAIN (average annual mean rainfall (mm)) RUNSUMMERMEAN (average summer mean runoff (ML)) RDI (river disturbance index (index: 0-1)) ASPECT (stream segment aspect (degrees)) STRDENSITY (stream density; total length of upstream segments calculated for the segment pour-point (km/km^2)) <br> *NOTE: Additional metadata describing the environmental data can be accessed at http://www.ga.gov.au/scientific-topics/water/national-surface-water-information <br> #2: "MSSplendida_Full_SNP_Dataset.vcf" - VCF file containing the 14,540 SNP genotypes identified for 210 Melanotaenia splendida splendida individuals, used as a basis for all downstream genomic analyses - A description of data fields can be accessed at https://samtools.github.io/hts-specs/VCFv4.2.pdf <br> #3: "MSSplendida_Morphometric_Landmarks_And_Size.csv" - Comma-delimited spreadsheet containing coordinates (x,y) for 18 morphometric landmarks, as well as centroid size, for individuals used in geometric morphometric and GxPxE analyses <br> <br> ##CODE: <br> #1: "RDA_GEA" - Folder containing R code and input files for genotype-environment association (GEA) RDA <br> #2: "RDA_PEA" - Folder containing R code and input files for phenotype-environment association (PEA) RDA <br> #3: "RDA_GxPxE" - Folder containing R code and input files for genotype-phenotype-environment association (GxPxE) RDA <br>
DOI: 10.6084/m9.figshare.14745478
title: Janus kinase inhibitors ruxolitinib and baricitinib impair glycoprotein-VI mediated platelet function

description: Several Janus kinase (JAK) inhibitors (jakinibs) have recently been approved to treat inflammatory, autoimmune and hematological conditions. Despite emerging roles for JAKs and downstream signal transducer and activator of transcription (STAT) proteins in platelets, it remains unknown whether jakinibs affect platelet function. Here, we profile platelet biochemical and physiological responses <i>in vitro</i> in the presence of five different clinically relevant jakinibs, including ruxolitinib, upadacitinib, oclacitinib, baricitinib and tofacitinib. Flow cytometry, microscopy and other assays found that potent JAK1/2 inhibitors baricitinib and ruxolitinib reduced platelet adhesion to collagen, as well as platelet aggregation, secretion and integrin α<sub>IIb</sub>β<sub>3</sub> activation in response to the glycoprotein VI (GPVI) agonist collagen-related peptide (CRP-XL). Western blot analysis demonstrated that jakinibs reduced Akt phosphorylation and activation following GPVI activation, where ruxolitinib and baricitinib prevented DAPP1 phosphorylation. In contrast, jakinibs had no effects on platelet responses to thrombin. Inhibitors of GPVI and JAK signaling also abrogated platelet STAT5 phosphorylation following CRP-XL stimulation. Additional pharmacologic experiments supported roles for STAT5 in platelet secretion, integrin activation and cytoskeletal responses. Together, our results demonstrate that ruxolitinib and baricitinib have inhibitory effects on platelet function <i>in vitro</i> and support roles for JAK/STAT5 pathways in GPVI/ITAM mediated platelet function.
DOI: 10.6084/m9.figshare.14745478.v1
title: Janus kinase inhibitors ruxolitinib and baricitinib impair glycoprotein-VI mediated platelet function

description: Several Janus kinase (JAK) inhibitors (jakinibs) have recently been approved to treat inflammatory, autoimmune and hematological conditions. Despite emerging roles for JAKs and downstream signal transducer and activator of transcription (STAT) proteins in platelets, it remains unknown whether jakinibs affect platelet function. Here, we profile platelet biochemical and physiological responses <i>in vitro</i> in the presence of five different clinically relevant jakinibs, including ruxolitinib, upadacitinib, oclacitinib, baricitinib and tofacitinib. Flow cytometry, microscopy and other assays found that potent JAK1/2 inhibitors baricitinib and ruxolitinib reduced platelet adhesion to collagen, as well as platelet aggregation, secretion and integrin α<sub>IIb</sub>β<sub>3</sub> activation in response to the glycoprotein VI (GPVI) agonist collagen-related peptide (CRP-XL). Western blot analysis demonstrated that jakinibs reduced Akt phosphorylation and activation following GPVI activation, where ruxolitinib and baricitinib prevented DAPP1 phosphorylation. In contrast, jakinibs had no effects on platelet responses to thrombin. Inhibitors of GPVI and JAK signaling also abrogated platelet STAT5 phosphorylation following CRP-XL stimulation. Additional pharmacologic experiments supported roles for STAT5 in platelet secretion, integrin activation and cytoskeletal responses. Together, our results demonstrate that ruxolitinib and baricitinib have inhibitory effects on platelet function <i>in vitro</i> and support roles for JAK/STAT5 pathways in GPVI/ITAM mediated platelet function.
DOI: 10.6084/m9.figshare.15111752
title: The voltage-gated K<sup>+</sup> channel Kv1.3 modulates platelet motility and α<sub>2</sub>β<sub>1</sub> integrin-dependent adhesion to collagen

description: Kv1.3 is a voltage-gated K<sup>+</sup>-selective channel with roles in immunity, insulin-sensitivity, neuronal excitability and olfaction. Despite being one of the largest ionic conductances of the platelet surface membrane, its contribution to platelet function is poorly understood. Here we show that Kv1.3-deficient platelets display enhanced ADP-evoked platelet aggregation and secretion, and an increased surface expression of platelet integrin α<sub>IIb</sub>. In contrast, platelet adhesion and thrombus formation <i>in vitro</i> under arterial shear conditions on surfaces coated with collagen were reduced for samples from Kv1.3<sup>−/-</sup> compared to wild type mice. Use of collagen-mimetic peptides revealed a specific defect in the engagement with α<sub>2</sub>β<sub>1</sub>. Kv1.3<sup>−/-</sup> platelets developed significantly fewer, and shorter, filopodia than wild type platelets during adhesion to collagen fibrils. Kv1.3<sup>−/-</sup> mice displayed no significant difference in thrombus formation within cremaster muscle arterioles using a laser-induced injury model, thus other pro-thrombotic pathways compensate <i>in vivo</i> for the adhesion defect observed <i>in vitro</i>. This may include the increased platelet counts of Kv1.3<sup>−/-</sup> mice, due in part to a prolonged lifespan. The ability of Kv1.3 to modulate integrin-dependent platelet adhesion has important implications for understanding its contribution to normal physiological platelet function in addition to its reported roles in auto-immune diseases and thromboinflammatory models of stroke.
DOI: 10.6084/m9.figshare.15111752.v2
title: The voltage-gated K<sup>+</sup> channel Kv1.3 modulates platelet motility and α<sub>2</sub>β<sub>1</sub> integrin-dependent adhesion to collagen

description: Kv1.3 is a voltage-gated K<sup>+</sup>-selective channel with roles in immunity, insulin-sensitivity, neuronal excitability and olfaction. Despite being one of the largest ionic conductances of the platelet surface membrane, its contribution to platelet function is poorly understood. Here we show that Kv1.3-deficient platelets display enhanced ADP-evoked platelet aggregation and secretion, and an increased surface expression of platelet integrin α<sub>IIb</sub>. In contrast, platelet adhesion and thrombus formation <i>in vitro</i> under arterial shear conditions on surfaces coated with collagen were reduced for samples from Kv1.3<sup>−/-</sup> compared to wild type mice. Use of collagen-mimetic peptides revealed a specific defect in the engagement with α<sub>2</sub>β<sub>1</sub>. Kv1.3<sup>−/-</sup> platelets developed significantly fewer, and shorter, filopodia than wild type platelets during adhesion to collagen fibrils. Kv1.3<sup>−/-</sup> mice displayed no significant difference in thrombus formation within cremaster muscle arterioles using a laser-induced injury model, thus other pro-thrombotic pathways compensate <i>in vivo</i> for the adhesion defect observed <i>in vitro</i>. This may include the increased platelet counts of Kv1.3<sup>−/-</sup> mice, due in part to a prolonged lifespan. The ability of Kv1.3 to modulate integrin-dependent platelet adhesion has important implications for understanding its contribution to normal physiological platelet function in addition to its reported roles in auto-immune diseases and thromboinflammatory models of stroke.
DOI: 10.6084/m9.figshare.15111752.v1
title: The voltage-gated K<sup>+</sup> channel Kv1.3 modulates platelet motility and α<sub>2</sub>β<sub>1</sub> integrin-dependent adhesion to collagen

description: Kv1.3 is a voltage-gated K<sup>+</sup>-selective channel with roles in immunity, insulin-sensitivity, neuronal excitability and olfaction. Despite being one of the largest ionic conductances of the platelet surface membrane, its contribution to platelet function is poorly understood. Here we show that Kv1.3-deficient platelets display enhanced ADP-evoked platelet aggregation and secretion, and an increased surface expression of platelet integrin α<sub>IIb</sub>. In contrast, platelet adhesion and thrombus formation <i>in vitro</i> under arterial shear conditions on surfaces coated with collagen were reduced for samples from Kv1.3<sup>−/-</sup> compared to wild type mice. Use of collagen-mimetic peptides revealed a specific defect in the engagement with α<sub>2</sub>β<sub>1</sub>. Kv1.3<sup>−/-</sup> platelets developed significantly fewer, and shorter, filopodia than wild type platelets during adhesion to collagen fibrils. Kv1.3<sup>−/-</sup> mice displayed no significant difference in thrombus formation within cremaster muscle arterioles using a laser-induced injury model, thus other pro-thrombotic pathways compensate <i>in vivo</i> for the adhesion defect observed <i>in vitro</i>. This may include the increased platelet counts of Kv1.3<sup>−/-</sup> mice, due in part to a prolonged lifespan. The ability of Kv1.3 to modulate integrin-dependent platelet adhesion has important implications for understanding its contribution to normal physiological platelet function in addition to its reported roles in auto-immune diseases and thromboinflammatory models of stroke.
DOI: 10.6084/m9.figshare.22057352
title: Host trees used for co-phylogenetic analysis

description: mtDNA and UCE loci termite trees were used for co-phylogenetic analysis against microbial trees.
DOI: 10.6084/m9.figshare.22057352.v1
title: Host trees used for co-phylogenetic analysis

description: mtDNA and UCE loci termite trees were used for co-phylogenetic analysis against microbial trees.
DOI: 10.6084/m9.figshare.22268290
title: The metabolomic data set for "A multi-omic resource of wheat seed tissues for nutrient deposition and improvement for human health"

description: To capture the dynamic changes in nutritional profiles of different wheat seed regions (<em>i.e.</em>, the embryo, endosperm and outer layers) during developmental stages, the seeds of wheat cultivar L88-31 have been collected at 20, 25, 30 and 35 days after pollination (DAP), dissected into three sections (i.e., embryo, endosperm and outer layers) and subject to metabolomics analysis. The abundance other information regarding the metabolomic data sets (including Q1, RT, molecular weight, CAS No., differential metabolites, etc.) are provided.
DOI: 10.6084/m9.figshare.22268290.v1
title: The metabolomic data set for "A multi-omic resource of wheat seed tissues for nutrient deposition and improvement for human health"

description: To capture the dynamic changes in nutritional profiles of different wheat seed regions (<em>i.e.</em>, the embryo, endosperm and outer layers) during developmental stages, the seeds of wheat cultivar L88-31 have been collected at 20, 25, 30 and 35 days after pollination (DAP), dissected into three sections (i.e., embryo, endosperm and outer layers) and subject to metabolomics analysis. The abundance other information regarding the metabolomic data sets (including Q1, RT, molecular weight, CAS No., differential metabolites, etc.) are provided.
DOI: 10.6084/m9.figshare.22247470
title: Molecular and clinical studies in 84 patients with pseudohypoparathyroidism type 1B

description: We conducted epigenotype-phenotype analysis in 84 patients with methylation defects of the DMRs on the <em>GNAS </em>locus classified into three groups according to the etiologies and methylation defect patterns of the DMRs on the <em>GNAS </em>locus.
DOI: 10.6084/m9.figshare.22247470.v3
title: Molecular and clinical studies in 84 patients with pseudohypoparathyroidism type 1B

description: We conducted epigenotype-phenotype analysis in 84 patients with methylation defects of the DMRs on the <em>GNAS </em>locus classified into three groups according to the etiologies and methylation defect patterns of the DMRs on the <em>GNAS </em>locus.
DOI: 10.6084/m9.figshare.22247470.v2
title: Epigenotype-phenotype analysis in 84 patients with pseudohypoparathyroidism type 1B based on the methylation patterns of four differentially methylated regions on the GNAS locus

description: We conducted epigenotype-phenotype analysis in 84 patients with methylation defects of the DMRs on the <em>GNAS </em>locus classified into three groups according to the etiologies and methylation defect patterns of the DMRs on the <em>GNAS </em>locus.
DOI: 10.5281/zenodo.7731374
title: DATA RESEARCH

description: This data is part of the supplementary file for publication
DOI: 10.5281/zenodo.7731373
title: DATA RESEARCH

description: This data is part of the supplementary file for publication
DOI: 10.7270/q2jq14v2
title: BindingDB Entry 10932: Mu opioid receptor modulators

description: Small molecule binding data for protein Delta-type opioid receptor, Kappa-type opioid receptor, Mu-type opioid receptor, and Mu-type opioid receptor [N127C], Uniprot P35372, P41143, and P41145
DOI: 10.7270/q2dz0d4r
title: BindingDB Entry 10933: Synthesis of (+)-cannabinoids and their therapeutic effects

description: Small molecule binding data for protein Cannabinoid receptor 1 and Cannabinoid receptor 2, Uniprot P21554 and P34972
DOI: 10.7270/q2959nds
title: BindingDB Entry 10934: Deuterated compounds as rock inhibitors

description: Small molecule binding data for protein Rho-associated protein kinase 1 and Rho-associated protein kinase 2, Uniprot O75116 and Q13464
DOI: 10.7270/q25h7m3s
title: BindingDB Entry 10935: Compounds for treatment of PD-L1 diseases

description: Small molecule binding data for protein Programmed cell death 1 ligand 1, Uniprot Q9NZQ7
DOI: 10.7270/q21r6vc2
title: BindingDB Entry 10936: Compounds for inhibiting TNIK and medical uses thereof

description: Small molecule binding data for protein TRAF2 and NCK-interacting protein kinase, Uniprot Q9UKE5
DOI: 10.7270/q2x06bxh
title: BindingDB Entry 10937: N-methyl, n-(6-(methoxy)pyridazin-3-yl) amine derivatives as autotaxin (ATX) modulators

description: Small molecule binding data for protein Ataxin-1, Uniprot P54253
DOI: 10.7270/q2s75m66
title: BindingDB Entry 10938: Compounds and methods useful in the treatment of a PRMT5-mediated disorder

description: Small molecule binding data for protein Methylosome protein 50/Protein arginine N-methyltransferase 5, Uniprot O14744 and Q9BQA1
DOI: 10.7270/q2ng4vhx
title: BindingDB Entry 10939: Substituted pyrazolopyrimidines and substituted purines and their use as ubiquitin-specific-processing protease 1 (USP1) inhibitors

description: Small molecule binding data for protein Ubiquitin carboxyl-terminal hydrolase 1, Uniprot O94782
DOI: 10.7270/q2hq43r4
title: BindingDB Entry 10940: Substituted imidazo[1,2-c]pyrimidines as PRC2 inhibitors

description: Small molecule binding data for protein Histone-binding protein RBBP4/Polycomb protein EED/Polycomb protein SUZ12/Zinc finger protein AEBP2, Uniprot O75530, Q09028, Q15022, and Q6ZN18
DOI: 10.7270/q2cz3c1t
title: BindingDB Entry 10941: Amido spirocyclic amide and sulfonamide derivatives

description: Small molecule binding data for protein Nicotinamide phosphoribosyltransferase, Uniprot P43490
DOI: 10.7270/q28919p8
title: BindingDB Entry 10942: Dopamine D2 receptor ligands

description: Small molecule binding data for protein D(2) dopamine receptor, Uniprot P14416
DOI: 10.7270/q24j0jzj
title: BindingDB Entry 10943: Azaindolylpyridone and diazaindolylpyridone compounds

description: Small molecule binding data for protein Phosphatidylinositol 3-kinase catalytic subunit type 3, Uniprot Q8NEB9
DOI: 10.7270/q20r9t84
title: BindingDB Entry 10944: Tricyclic heterocycles as BET protein inhibitors

description: Small molecule binding data for protein Bromodomain-containing protein 4 [353-454] and Bromodomain-containing protein 4 [58-164], Uniprot O60885
DOI: 10.7270/q2w099s4
title: BindingDB Entry 10945: Pyrimidine-fused cyclic compound, preparation method therefor and application thereof

description: Small molecule binding data for protein Tyrosine-protein phosphatase non-receptor type 11, Uniprot Q06124
DOI: 10.7270/q2r78k2t
title: BindingDB Entry 10946: 1H-pyrazolo[4,3-b]pyridines as PDE1 inhibitors

description: Small molecule binding data for protein Dual specificity calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1A, Dual specificity calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1B, and Dual specificity calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1C, Uniprot P54750, Q01064, and Q14123
DOI: 10.7270/q2mg7tb3
title: BindingDB Entry 10947: Therapeutic methods and combinations

description: Small molecule binding data for protein Metallo-beta-lactamase VIM-2, Uniprot Q3Y6Q3
DOI: 10.7270/q2gq72mr
title: BindingDB Entry 10948: Amide derivatives useful in the treatment of HBV infection or HBV-induced diseases

description: Small molecule binding data for protein Capsid protein, Uniprot Q03732