cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8099480
title: Additional file 3: of Widespread gene duplication and adaptive evolution in the RNA interference pathways of the Drosophila obscura group

description: Table S2. MK test of duplicated RNAi genes in D. pseudoobscura-D. miranda. Ds is synonymous divergence, Dn is non-synonymous divergence, Pn is the non-synonymous polymorphisms, Ps is the synonymous polymorphisms, α represents proportion of substitutions that are adaptive, a is the absolute number of adaptive substitutions. Ln is the number of non-synonymous sites, Ls is the number of synonymous sites. Ka is the number of non-synonymous mutations per non-synonymous sites and Ks the number of synonymous mutations per synonymous sites from single randomly chosen strain for each species (Li, 1993 [92] calculated using R package seqinr). Parameter ωa is identical to Ka/Ks ratio except that the numerator only takes adaptive divergence (α * Dn)/Ln)/(Ds/Ls). (XLSX 10 kb)
DOI: 10.6084/m9.figshare.8099501.v1
title: Additional file 1: of Mobile genetic elements explain size variation in the mitochondrial genomes of four closely-related Armillaria species

description: Table S1. Tandem repeats detected in four Armillaria mitogenomes using Tandem Repeats Finder. (XLSX 14â kb)
DOI: 10.6084/m9.figshare.8099483
title: Additional file 4: of Widespread gene duplication and adaptive evolution in the RNA interference pathways of the Drosophila obscura group

description: Table S3. Additional MK test analysis. Table the results of additional MK test analysis where minor allele frequency is removed, repetition with larger dataset and results in D. melanogaster. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.8099483.v1
title: Additional file 4: of Widespread gene duplication and adaptive evolution in the RNA interference pathways of the Drosophila obscura group

description: Table S3. Additional MK test analysis. Table the results of additional MK test analysis where minor allele frequency is removed, repetition with larger dataset and results in D. melanogaster. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.8099480.v1
title: Additional file 3: of Widespread gene duplication and adaptive evolution in the RNA interference pathways of the Drosophila obscura group

description: Table S2. MK test of duplicated RNAi genes in D. pseudoobscura-D. miranda. Ds is synonymous divergence, Dn is non-synonymous divergence, Pn is the non-synonymous polymorphisms, Ps is the synonymous polymorphisms, α represents proportion of substitutions that are adaptive, a is the absolute number of adaptive substitutions. Ln is the number of non-synonymous sites, Ls is the number of synonymous sites. Ka is the number of non-synonymous mutations per non-synonymous sites and Ks the number of synonymous mutations per synonymous sites from single randomly chosen strain for each species (Li, 1993 [92] calculated using R package seqinr). Parameter ωa is identical to Ka/Ks ratio except that the numerator only takes adaptive divergence (α * Dn)/Ln)/(Ds/Ls). (XLSX 10 kb)
DOI: 10.6084/m9.figshare.8099465
title: Additional file 1: of Widespread gene duplication and adaptive evolution in the RNA interference pathways of the Drosophila obscura group

description: Table S1. The detailed RNAi genes and its duplicate in D. pseudoobscura. The genomic position is based on the D. pseudoobscura assembly 3.0. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.8099465.v1
title: Additional file 1: of Widespread gene duplication and adaptive evolution in the RNA interference pathways of the Drosophila obscura group

description: Table S1. The detailed RNAi genes and its duplicate in D. pseudoobscura. The genomic position is based on the D. pseudoobscura assembly 3.0. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.8099453
title: Additional file 4: of Over-ground walking or robot-assisted gait training in people with multiple sclerosis: does the effect depend on baseline walking speed and disease related disabilities? A systematic review and meta-regression

description: Data set RAGT CGT, the data set used for the analyses (CSV 2 kb)
DOI: 10.6084/m9.figshare.8099453.v2
title: Additional file 4: of Over-ground walking or robot-assisted gait training in people with multiple sclerosis: does the effect depend on baseline walking speed and disease related disabilities? A systematic review and meta-regression

description: Data set RAGT CGT, the data set used for the analyses (CSV 2 kb)
DOI: 10.6084/m9.figshare.8099453.v1
title: Additional file 4: of Over-ground walking or robot-assisted gait training in people with .multiple sclerosis: does the effect depend on baseline walking speed and disease related disabilities? A systematic review and meta-regression

description: Data set RAGT CGT, the data set used for the analyses (CSV 2 kb)
DOI: 10.6084/m9.figshare.8099417
title: Additional file 5: of Weighted gene co-expression network analysis to explain the relationship between plasma total carotenoids and lipid profile

description: Table S5. Significant p values of regressions between expression levels of hub genes and plasma lipid concentrations. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.8099417.v1
title: Additional file 5: of Weighted gene co-expression network analysis to explain the relationship between plasma total carotenoids and lipid profile

description: Table S5. Significant p values of regressions between expression levels of hub genes and plasma lipid concentrations. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.8099411
title: Additional file 1: of Baicalin ameliorates neuroinflammation-induced depressive-like behavior through inhibition of toll-like receptor 4 expression via the PI3K/AKT/FoxO1 pathway

description: The details of primary mouse microglial cell culture. Figure S1. Iba-1 immunostaining images and morphology pictures of primary microglias isolated using mild trypsinization. Scale bar = 50 μm (TIF 7.29 mb). Figure S2. Iba-1 immunostaining images and morphology pictures of primary microglia isolated using shaking. The scale bar = 50 μm and arrows refer to the enlarged round cell body. (ZIP 24043 kb)
DOI: 10.6084/m9.figshare.8099408
title: Additional file 4: of Weighted gene co-expression network analysis to explain the relationship between plasma total carotenoids and lipid profile

description: Table S4. Functional enrichment analysis in blue module using Gene Ontology and Reactome databases. (XLSX 28 kb)
DOI: 10.6084/m9.figshare.8099402
title: Additional file 3: of Weighted gene co-expression network analysis to explain the relationship between plasma total carotenoids and lipid profile

description: Table S3. Functional enrichment analysis in the brown module using GO and Reactome databases (XLSX 15 kb)
DOI: 10.6084/m9.figshare.8099411.v1
title: Additional file 1: of Baicalin ameliorates neuroinflammation-induced depressive-like behavior through inhibition of toll-like receptor 4 expression via the PI3K/AKT/FoxO1 pathway

description: The details of primary mouse microglial cell culture. Figure S1. Iba-1 immunostaining images and morphology pictures of primary microglias isolated using mild trypsinization. Scale bar = 50 μm (TIF 7.29 mb). Figure S2. Iba-1 immunostaining images and morphology pictures of primary microglia isolated using shaking. The scale bar = 50 μm and arrows refer to the enlarged round cell body. (ZIP 24043 kb)
DOI: 10.6084/m9.figshare.8099402.v1
title: Additional file 3: of Weighted gene co-expression network analysis to explain the relationship between plasma total carotenoids and lipid profile

description: Table S3. Functional enrichment analysis in the brown module using GO and Reactome databases (XLSX 15 kb)
DOI: 10.6084/m9.figshare.8099408.v1
title: Additional file 4: of Weighted gene co-expression network analysis to explain the relationship between plasma total carotenoids and lipid profile

description: Table S4. Functional enrichment analysis in blue module using Gene Ontology and Reactome databases. (XLSX 28 kb)
DOI: 10.6084/m9.figshare.8099396
title: Additional file 2: of Weighted gene co-expression network analysis to explain the relationship between plasma total carotenoids and lipid profile

description: Table S2. Probes showing significant association with plasma total carotenoids (n = 533) (XLSX 42 kb)
DOI: 10.6084/m9.figshare.8099387
title: Additional file 1: of Weighted gene co-expression network analysis to explain the relationship between plasma total carotenoids and lipid profile

description: Table S1. Concentrations of plasma carotenoids (micromoles per liter of plasma). (XLSX 15 kb)
DOI: 10.6084/m9.figshare.8099396.v1
title: Additional file 2: of Weighted gene co-expression network analysis to explain the relationship between plasma total carotenoids and lipid profile

description: Table S2. Probes showing significant association with plasma total carotenoids (n = 533) (XLSX 42 kb)
DOI: 10.6084/m9.figshare.8099387.v1
title: Additional file 1: of Weighted gene co-expression network analysis to explain the relationship between plasma total carotenoids and lipid profile

description: Table S1. Concentrations of plasma carotenoids (micromoles per liter of plasma). (XLSX 15 kb)
DOI: 10.6084/m9.figshare.8099243
title: Additional file 9: of Histone H3 lysine 4 methyltransferase is required for facultative heterochromatin at specific loci

description: Differences and location of H3K9me3 and H3K4me3 peak intensities in WT relative to the contrasting deletion strain in the dark and light. (XLS 684 kb)
DOI: 10.6084/m9.figshare.8099243.v1
title: Additional file 9: of Histone H3 lysine 4 methyltransferase is required for facultative heterochromatin at specific loci

description: Differences and location of H3K9me3 and H3K4me3 peak intensities in WT relative to the contrasting deletion strain in the dark and light. (XLS 684 kb)
DOI: 10.6084/m9.figshare.8099225
title: Additional file 5: of Histone H3 lysine 4 methyltransferase is required for facultative heterochromatin at specific loci

description: Table of genes showing a transcriptional deficit in ∆kmt2/∆set-1 and ∆kmt1/∆dim-5 relative to WT under dark and light conditions. (XLS 768 kb)
DOI: 10.6084/m9.figshare.8099225.v1
title: Additional file 5: of Histone H3 lysine 4 methyltransferase is required for facultative heterochromatin at specific loci

description: Table of genes showing a transcriptional deficit in ∆kmt2/∆set-1 and ∆kmt1/∆dim-5 relative to WT under dark and light conditions. (XLS 768 kb)
DOI: 10.6084/m9.figshare.8099216
title: Additional file 3: of Histone H3 lysine 4 methyltransferase is required for facultative heterochromatin at specific loci

description: Table of Light-responsive genes in WT, ∆kmt2/∆set-1 and ∆kmt1/∆dim-5. (XLS 285 kb)
DOI: 10.6084/m9.figshare.8099216.v1
title: Additional file 3: of Histone H3 lysine 4 methyltransferase is required for facultative heterochromatin at specific loci

description: Table of Light-responsive genes in WT, ∆kmt2/∆set-1 and ∆kmt1/∆dim-5. (XLS 285 kb)
DOI: 10.6084/m9.figshare.8099180
title: Additional file 14: of Histone H3 lysine 4 methyltransferase is required for facultative heterochromatin at specific loci

description: Genome location of H3K9me3 peaks that have a change in intensity in response to light. (XLSX 27 kb)
DOI: 10.6084/m9.figshare.8099162
title: Additional file 12: of Histone H3 lysine 4 methyltransferase is required for facultative heterochromatin at specific loci

description: Location of presumptive bivalent domains containing both H3K9me3 and H3K4me3. (XLS 55 kb)
DOI: 10.6084/m9.figshare.8099180.v1
title: Additional file 14: of Histone H3 lysine 4 methyltransferase is required for facultative heterochromatin at specific loci

description: Genome location of H3K9me3 peaks that have a change in intensity in response to light. (XLSX 27 kb)
DOI: 10.6084/m9.figshare.8099162.v1
title: Additional file 12: of Histone H3 lysine 4 methyltransferase is required for facultative heterochromatin at specific loci

description: Location of presumptive bivalent domains containing both H3K9me3 and H3K4me3. (XLS 55 kb)
DOI: 10.6084/m9.figshare.8098250
title: N-acetylcysteine reduces glutamate-induced cytotoxicity to fibroblasts of rat supraspinatus tendons

description: <b>Purpose</b>: Neuronal theory regarding rotator cuff degeneration has developed from the findings that glutamate, an amino acid and an excitatory neurotransmitter, is present in increased concentrations in tendon tissues with tendinopathy and that glutamate induces cell death in fibroblasts of origin in rat supraspinatus tendon. The purpose of the current study was to determine whether N-acetylcysteine (NAC) has cytoprotective effects against glutamate-induced fibroblast death. <b>Materials and Methods</b>: Primary cultured fibroblasts were obtained from rat supraspinatus tendons. Varying concentrations of glutamate (0.5, 1, 5, and 10 mM) and of NAC (0.5, 1, 2, and 5 mM) were used for evaluation of cytotoxicity. Cell viability, cell cycles, types of cell death, intracellular ROS production, expressions of caspase-3/7, and Ca<sup>2+</sup> influx were evaluated. <b>Results</b>: Glutamate significantly induced cell death, apoptosis, and Ca<sup>2+</sup> influx and significantly increased caspase-3/7 activity and intracellular ROS production (<i>p </i>2+ influx, caspase-3/7 activity, and intracellular ROS production (<i>p </i> <b>Conclusions</b>: The glutamate-induced cytotoxic effects can be reduced by NAC, an antioxidant, through the reduction of intracellular oxidative stress and/or Ca<sup>2+</sup> influx.
DOI: 10.6084/m9.figshare.8098250.v1
title: N-acetylcysteine reduces glutamate-induced cytotoxicity to fibroblasts of rat supraspinatus tendons

description: <b>Purpose</b>: Neuronal theory regarding rotator cuff degeneration has developed from the findings that glutamate, an amino acid and an excitatory neurotransmitter, is present in increased concentrations in tendon tissues with tendinopathy and that glutamate induces cell death in fibroblasts of origin in rat supraspinatus tendon. The purpose of the current study was to determine whether N-acetylcysteine (NAC) has cytoprotective effects against glutamate-induced fibroblast death. <b>Materials and Methods</b>: Primary cultured fibroblasts were obtained from rat supraspinatus tendons. Varying concentrations of glutamate (0.5, 1, 5, and 10 mM) and of NAC (0.5, 1, 2, and 5 mM) were used for evaluation of cytotoxicity. Cell viability, cell cycles, types of cell death, intracellular ROS production, expressions of caspase-3/7, and Ca<sup>2+</sup> influx were evaluated. <b>Results</b>: Glutamate significantly induced cell death, apoptosis, and Ca<sup>2+</sup> influx and significantly increased caspase-3/7 activity and intracellular ROS production (<i>p </i>2+ influx, caspase-3/7 activity, and intracellular ROS production (<i>p </i> <b>Conclusions</b>: The glutamate-induced cytotoxic effects can be reduced by NAC, an antioxidant, through the reduction of intracellular oxidative stress and/or Ca<sup>2+</sup> influx.
DOI: 10.6084/m9.figshare.8098022
title: Raw data for water parameters

description: This dataset includes water quality- related parameters that were used for calculating the different indexes used in the study such as: <br> Potential Hydrogen pH Conductivity Temperature Dissolved oxygen Turbidity Total dissolved solids Phosphates (PO4) Nitrates -N (NO3) Total hardness Alkalinity DBO5 DQO Total coliforms Fecal Coliforms <br>
DOI: 10.6084/m9.figshare.8097992
title: Graphs of Materials Project 20190401

description: The `mp.2019.04.01.json.zip` data set contains 133420 graph-target pairs for structures materials project used to train the latest megnet formation energy models. <br>The whole data is a list with each item being a dictionary. The keys for the dictionary are - "material_id": the material id in materials project- "graph": the graph dictionary computed with megnet, cutoff radius is 5 A- "formation_energy_per_atom": the formation energy per atom (eV/atom)- "structure": cif string of the structure<br>The `mp_elastic.2019.04.01.json.zip` contains a list of length 12179, where each item is a dictionary with the following keys- "material_id"- "graph"- "K": bulk modulus- "G": shear modulus <br>
DOI: 10.6084/m9.figshare.8097998
title: Persistence of Burkholderia thailandensis E264 in Lung Tissue After a Single Binge Alcohol Episode

description: The following data sets describes the major findings in "Persistence of Burkholderia thailandensis E264 in Lung Tissue After a Single Binge Alcohol Episode"
DOI: 10.6084/m9.figshare.8097941
title: data info for ADMA paper.xlsx

description: This data set includes information from a questionnaire collected from cases of essential hypertension and control people without hypertension. In addition this data set include the lab results from the volunteers. The questionnaire had questions about basic demographic features, information about duration of hypertension if present and associated other diseases. The end of the data set also include the lab results of basic clinical chemistry in addition to ADMA, arginine and SDMA levels.
DOI: 10.6084/m9.figshare.8097941.v1
title: data info for ADMA paper.xlsx

description: This data set includes information from a questionnaire collected from cases of essential hypertension and control people without hypertension. In addition this data set include the lab results from the volunteers. The questionnaire had questions about basic demographic features, information about duration of hypertension if present and associated other diseases. The end of the data set also include the lab results of basic clinical chemistry in addition to ADMA, arginine and SDMA levels.
DOI: 10.6084/m9.figshare.8097806
title: side_collision.zip

description: contains radial velocity plots of offsets 0.0, 0.2, 0.4, 0.6, 0.8<br>
DOI: 10.6084/m9.figshare.8097809
title: Saccharomycotina genome annotations filtered for mitochondrial data

description: This dataset contains two folders. The main folder contains Saccharomycotina genome annotations that have been filtered for putatively mitochondrial sequences and filtered for input to stAI calc. These filters include removing CDSs without a start codon, removing ambiguous codons, and removing short CDSs. <br>Within the mito_CDS_removed folder there is a file for the putatively mitochondrial CDS sequences removed from each genome
DOI: 10.6084/m9.figshare.8097797
title: Saccharomycotina genomic contigs removed for analysis

description: For each saccharomycotina genome analyzed there is a file of the putatively mitochondrial contigs subsequently removed from the analysis
DOI: 10.6084/m9.figshare.8097809.v1
title: Saccharomycotina genome annotations filtered for mitochondrial data

description: This dataset contains two folders. The main folder contains Saccharomycotina genome annotations that have been filtered for putatively mitochondrial sequences and filtered for input to stAI calc. These filters include removing CDSs without a start codon, removing ambiguous codons, and removing short CDSs. <br>Within the mito_CDS_removed folder there is a file for the putatively mitochondrial CDS sequences removed from each genome
DOI: 10.6084/m9.figshare.8097797.v1
title: Saccharomycotina genomic contigs removed for analysis

description: For each saccharomycotina genome analyzed there is a file of the putatively mitochondrial contigs subsequently removed from the analysis
DOI: 10.6084/m9.figshare.8097620
title: Data for Margolskee et al. (2019) "Ventilation pathways for the North Pacific Oxygen Deficient Zone".

description: ROMS model output for Margolskee et al. (2019), "Ventilation Pathways for the North Pacific Oxygen Deficient Zone", Global Biogeochemical Cycles. 1 year of monthly averaged O2, u, and v model fields are available from year 23 of the model simulation) used for secondary oxygen maximum analysis and creation of velocity maps in the figures. Oxygen is in units of mmol/m3 and u and v are in units of m/s. Also uploaded is the ROMS grid file that has the necessary lon/lat coordinates for the model u/v/rho grids. Please contact me at amargol@uw.edu for any other model output.
DOI: 10.6084/m9.figshare.8097503
title: Input_data_figure-code.zip

description: Additional material (Input proxy and instrumental data and code to generate the figures)<br>
DOI: 10.6084/m9.figshare.8097539
title: edge2vec vector.zip

description: The calculated vectors used in our edge2vc paper
DOI: 10.6084/m9.figshare.8097500
title: Saccharomycotina_CDS_Codon_Optimization.gz

description: For each Saccharomycotina genome analyzed there are 4 datafiles. <br><i>genome</i>.gc3 - GC component of the 3rd codon position in each CDS for the genome<br><i>genome</i>.nc.txt - Effective Number of Codons (ENC) for each CDS in the genome<br><i>genome</i>.stest.txt - Input file for the S-test<br><i>genome.</i>stest.txt - tRNA Adaptation Index (tAI) for each CDS in the genome
DOI: 10.6084/m9.figshare.8097620.v2
title: Data for Margolskee et al. (2019) "Ventilation pathways for the North Pacific Oxygen Deficient Zone".

description: ROMS model output for Margolskee et al. (2019), "Ventilation Pathways for the North Pacific Oxygen Deficient Zone", Global Biogeochemical Cycles. 1 year of monthly averaged O2, u, and v model fields are available from year 23 of the model simulation) used for secondary oxygen maximum analysis and creation of velocity maps in the figures. Oxygen is in units of mmol/m3 and u and v are in units of m/s. Also uploaded is the ROMS grid file that has the necessary lon/lat coordinates for the model u/v/rho grids. Please contact me at amargol@uw.edu for any other model output.
DOI: 10.6084/m9.figshare.8097620.v1
title: Data for Margolskee et al. (2019) "Ventilation pathways for the North Pacific Oxygen Deficient Zone".

description: ROMS model output for Margolskee et al. (2019), "Ventilation pathways for the North Pacific Oxygen Deficient Zone", Global Biogeochemical Cycles. 1 year of monthly averaged O2, u, and v model fields are available from year 23 of the model simulation) used for secondary oxygen maximum analysis and creation of velocity maps in the figures. Oxygen is in units of mmol/m3 and u and v are in units of m/s. Also uploaded is the ROMS grid file that has the necessary lon/lat coordinates for the model u/v/rho grids. Please contact me at amargol@uw.edu for any other model output.
DOI: 10.6084/m9.figshare.8097500.v1
title: Saccharomycotina_CDS_Codon_Optimization.gz

description: For each Saccharomycotina genome analyzed there are 4 datafiles. <br><i>genome</i>.gc3 - GC component of the 3rd codon position in each CDS for the genome<br><i>genome</i>.nc.txt - Effective Number of Codons (ENC) for each CDS in the genome<br><i>genome</i>.stest.txt - Input file for the S-test<br><i>genome.</i>stest.txt - tRNA Adaptation Index (tAI) for each CDS in the genome
DOI: 10.6084/m9.figshare.8097488
title: Life history stage explains social behavior

description: This file contains the data and R markdown file to complete the analysis and re-create the figures in the PeerJ manuscript "Life history stage explains behavior in a social network before and during the early breeding season in a cooperatively breeding bird."<br>The data file contains group-by-individual matrices for the 2017 and 2018 pre and early breeding season of Florida scrub-jays at Archbold Biological Station. Individual attributes, including sex and life history stage for each individual are included as well as resident territory and the territory on which each observation was recorded.<br>Individual identities of the birds have been obscured and the identity of a bird in this data set does not relate to the identification number of the same bird in any other published data set on this population. If you wish to use longitudinal data from this population please contact the Avian Ecology Program at Archbold Biological Station.<br>