cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.j37ysu
title: Occurrence Download

description: A dataset containing 8454 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "PublishingCountry is Colombia",
 {
 "and" : [
 "Country is Colombia",
 {
 "not" : {
 "Issue" : [
 "is Country coordinate mismatch"
 ]
 }
 }
 ]
 }
 ]
 },
 "Geometry POLYGON((-73.00416 4.67483,-73.00416 4.52498,-72.85583 4.52195,-72.85583 4.67332,-73.00416 4.67483))"
 ]
}

 The dataset includes 8454 records from 40 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0037987-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.c.3641384_d2.v1
title: MOESM1 of Within leaf variation is the largest source of variation in agroinfiltration of Nicotiana benthamiana

description: Additional file 1: Table S1. Measurements of luciferase activity from the first experiment and calculation of variance components. Table S2. Measurements of luciferase activity from the second experiment and calculation of variance components.
DOI: 10.6084/m9.figshare.c.3641435_d1.v1
title: Additional file 5: Figure S4. of The impact of “early” versus “late” initiation of renal replacement therapy in critical care patients with acute kidney injury: a systematic review and evidence synthesis

description: a Mortality forest plot of subgroup analysis of high-quality studies based on the definition of “early” according to time criteria (hours or days) (n = 4). b Mortality forest plot of subgroup analysis of high-quality studies based on the definition of “early” according to biochemical parameters (i.e., rising creatinine, uremia, oliguria) (n = 5). (ZIP 121 kb)
DOI: 10.6084/m9.figshare.c.3641435_d2.v1
title: Additional file 4: Figure S3. of The impact of “early” versus “late” initiation of renal replacement therapy in critical care patients with acute kidney injury: a systematic review and evidence synthesis

description: a Mortality forest plot of subgroup analysis of high-quality studies according to post-surgical ICU admission type (n = 3). b Mortality forest plot of subgroup analysis of high-quality studies according to medical ICU admission type (n = 6). (ZIP 120 kb)
DOI: 10.6084/m9.figshare.c.3641462_d7.v1
title: MOESM14 of Revealing new candidate genes for reproductive traits in pigs: combining Bayesian GWAS and functional pathways

description: Additional file 14: Table S6. Transcription factors (TF) identified for genes associated with NT, location in base pairs (bp) of the window sequence that carries binding sites, and p-value of the window confidence that was obtained from the TFM-explorer tool.
DOI: 10.6084/m9.figshare.c.3641462_d6.v1
title: MOESM12 of Revealing new candidate genes for reproductive traits in pigs: combining Bayesian GWAS and functional pathways

description: Additional file 12: Table S4. Pathway and Gene Ontology terms (GO) of genes associated with significant SNPs identified for NT.
DOI: 10.7266/7kwq7s3z
title: Surface water quality data of the Mississippi Sound sampled from 2022-09-12 to 2022-09-16
DOI: 10.15468/dl.7njjnw
title: Occurrence Download

description: A dataset containing 17118 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Siproeta stelenes Linnaeus, 1758"
 ]
}

 The dataset includes 17118 records from 141 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0037986-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.c.3641501_d1.v1
title: Additional file 4: of Repeated measures of inflammation, blood pressure, and heart rate variability associated with traffic exposures in healthy adults

description: Slopes (95 % Confidence Intervals) generated from mixed effect models between percent changes in pollutant concentrations and health effects for the subjects, adjusting for apparent temperature, location, and random subject effects. Analysis was completed removing 2 subject that presented with BMI &gt; 39. Percent change were calculated between the pre-exposure measurement and each subsequent measurement (i.e. post or 24 h post).
DOI: 10.6084/m9.figshare.c.3641501_d3.v1
title: Additional file 1: of Repeated measures of inflammation, blood pressure, and heart rate variability associated with traffic exposures in healthy adults

description: Additionally measured exposure metrics at each location. Values represent means ± SD. Traffic volume data for the GSP were obtained for the Essex Toll Plaza using the New Jersey Turnpike Authority’s Open Public Records Act. Traffic volume data at the GWB were obtained for the GWB upper level and Palisades Interstate Parkway toll records from the PANYNJ. No traffic was observed at SF, as verified by study staff during exposures. SF = Sterling Forest; GSP = Garden State Parkway; GWB = George Washington Bridge. N/A = not applicable. aUnpaired t-test. bOnly a single measurement of noise was made at SF. Noise levels at SF without sampler on were below detection limit for instrument (dB
DOI: 10.6084/m9.figshare.c.3641501_d4.v1
title: Additional file 3: of Repeated measures of inflammation, blood pressure, and heart rate variability associated with traffic exposures in healthy adults

description: Slopes (95Â % Confidence Intervals) generated from mixed effect models between percent changes in pollutant concentrations and health effects for the subjects, adjusting for apparent temperature, location, and random subject effects. Percent change were calculated between the pre-exposure measurement and each subsequent measurement (i.e. post or 24Â h post).
DOI: 10.6084/m9.figshare.c.3641513_d2.v1
title: Additional file 2: Table S2. of Gastric bypass surgery reveals independency of obesity and diabetes melitus type 2

description: Maximal changes in glucose-related variables. Values and summary statistics for glucose-related variables and diabetes for both gender combined. An excerpt of the table of the central variables related to diabetes is presented in TableÂ 2. (XLS 48 kb)
DOI: 10.6084/m9.figshare.c.3641513_d3.v1
title: Additional file 6: Table S6. of Gastric bypass surgery reveals independency of obesity and diabetes melitus type 2

description: Clustering summary using the scikit k-means procedure. The three subpopulations non-diabetics, diabetics turned non-diabetics and diabetics staying diabetics after gastric bypass were partitioned into subpopulations using the k-mean procedure for changes in body mass index (BMI) during time. In all, at least 11 subpopulations were identified. (XLS 21 kb)
DOI: 10.6084/m9.figshare.c.3641513_d1.v1
title: Additional file 4: Table S4. of Gastric bypass surgery reveals independency of obesity and diabetes melitus type 2

description: Komogorov-Smirnoff test for equality of distributions of traits. Traits are pair-wise tested for distributional similarity of the time-evolving changes in trait values (trajectories), that is to which extent the traits may be correlated. The comparisons of distributions are done for all subpopulations and gender separately. (XLS 22 kb)
DOI: 10.6084/m9.figshare.c.3641513_d4.v1
title: Additional file 1: Table S1. of Gastric bypass surgery reveals independency of obesity and diabetes melitus type 2

description: Maximal changes in variables and the day after RYGB. Values and summary statistics of all variables analysed before and after gastric bypass for the subpopulations non-diabetics, diabetics turned non-diabetics post-surgery and diabetics that stayed diabetics post-surgery. Values and statistics are given for female and males, respectively. (XLS 226 kb)
DOI: 10.6084/m9.figshare.c.3641513_d6.v1
title: Additional file 5: Table S5. of Gastric bypass surgery reveals independency of obesity and diabetes melitus type 2

description: Komogorov-Smirnoff test for equality of distributions of traits between NDM and DMT2-NDM. Traits are tested for distributional similarity between the non-diabetic subpopulation and the diabetic turned non-diabetic subpopulation. (XLS 22 kb)
DOI: 10.6084/m9.figshare.c.3641513_d5.v1
title: Additional file 3: Table S3. of Gastric bypass surgery reveals independency of obesity and diabetes melitus type 2

description: Relative changes in variables after RYGB. The changes in all traits are calculated as fraction relative to pre-surgery values for non-diabetics and diabetics turned non-diabetics, respectively. The changes and significance are calculated for female and males separately. (XLS 28 kb)
DOI: 10.6084/m9.figshare.c.3641561_d2.v1
title: Additional file 2: Table S2. of Conditional deletion of caspase-8 in macrophages alters macrophage activation in a RIPK-dependent manner

description: ANOVA comparison data from Affymetrix QuantiGene 2.0 custom panel 21522 for analysis of macrophage polarization. (XLS 68 kb)
DOI: 10.6084/m9.figshare.c.3641567_d1.v1
title: Additional file 1: Table S1. of Haplotype analysis of the HFE gene among populations of Northern Eurasia, in patients with metabolic disorders or stomach cancer, and in long-lived people

description: Pearson’s correlation matrix between HFE genotype frequency profiles. Values in bold are different from 0 with a significance level alpha = 0.05. MS + AH: metabolic syndrome associated with arterial hypertension, T2DM: type 2 diabetes mellitus, FLD: fatty liver disease, St. cancer: stomach cancer, LL: long lived. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.c.3641573_d1.v1
title: Additional file 7: of Identification and characterization of abundant repetitive sequences in Eragrostis tef cv. Enatite genome

description: Nucleotide sequences from paralogs in Clade 1 (Additional file 6 : Figure S6). (FAS 10 kb)
DOI: 10.6084/m9.figshare.c.3641573_d2.v1
title: Additional file 4: of Identification and characterization of abundant repetitive sequences in Eragrostis tef cv. Enatite genome

description: Multiple alignment of Ty3-gypsy RT paralog sequences identified in teff, Rice and Maize. (MSF 135 kb)
DOI: 10.6084/m9.figshare.c.3641573_d3.v1
title: Additional file 15: of Identification and characterization of abundant repetitive sequences in Eragrostis tef cv. Enatite genome

description: 1,000 sequences of the satellite monomer. (FAS 185 kb)
DOI: 10.6084/m9.figshare.c.3641573_d7.v1
title: Additional file 3: of Identification and characterization of abundant repetitive sequences in Eragrostis tef cv. Enatite genome

description: Multiple alignment of Ty1-copia RT paralog sequences identified in teff, Rice and Maize. (MSF 110 kb)
DOI: 10.6084/m9.figshare.c.3641573_d6.v1
title: Additional file 11: of Identification and characterization of abundant repetitive sequences in Eragrostis tef cv. Enatite genome

description: Multiple alignment of MuDr transposase paralog sequences identified in teff, Rice and Maize. (MSF 7 kb)
DOI: 10.6084/m9.figshare.c.3641573_d5.v1
title: Additional file 17: of Identification and characterization of abundant repetitive sequences in Eragrostis tef cv. Enatite genome

description: Tracts of TE coding domains used as queries in similarity searches to retrieve copies of TE paralogs. (FAS 663 bytes)
DOI: 10.6084/m9.figshare.c.3641573_d8.v1
title: Additional file 8: of Identification and characterization of abundant repetitive sequences in Eragrostis tef cv. Enatite genome

description: Nucleotide sequences from paralogs in Clade 2 (Additional file 6 : Figure S6). (FAS 6 kb)
DOI: 10.6084/m9.figshare.c.3641573_d9.v1
title: Additional file 14: of Identification and characterization of abundant repetitive sequences in Eragrostis tef cv. Enatite genome

description: Multiple alignment of non-LTR RT paralog sequences identified in teff cv Enantite and Tsedey. (MSF 45 kb)
DOI: 10.6084/m9.figshare.c.3641573_d12.v1
title: Additional file 9: of Identification and characterization of abundant repetitive sequences in Eragrostis tef cv. Enatite genome

description: Multiple alignment of CACTA transposase paralog sequences identified in teff, Rice and Maize. (MSF 12 kb)
DOI: 10.6084/m9.figshare.c.3641621_d2.v1
title: Additional file 2: of Origin and evolution of the enhancer of split complex

description: Alignments used for phylogenetic analyses. (TXT 111 kb)
DOI: 10.6084/m9.figshare.c.3641621_d1.v1
title: Additional file 1: of Origin and evolution of the enhancer of split complex

description: Table of bHLH Orange domain genes used in this analysis. (XLSX 35 kb)
DOI: 10.7266/r03c55bt
title: Water quality data from three depths of the Mississippi Sound obtained from 2022-04-01 to 2022-09-16
DOI: 10.6084/m9.figshare.c.3641717_d3.v1
title: MOESM5 of Time-scale dynamics of proteome and transcriptome of the white-rot fungus Phlebia radiata: growth on spruce wood and decay effect on lignocellulose

description: Additional file 5: Table S2. Summary of lignocellulose acting proteins identified in the spruce wood cultivation proteomes of P. radiata by peptide LC–MS/MS analysis.
DOI: 10.6084/m9.figshare.c.3641753_d5.v1
title: Additional file 6: Table S3 of The transcriptional and splicing landscape of intestinal organoids undergoing nutrient starvation or endoplasmic reticulum stress

description: Alternative splicing events in murine enteroids upon either ER stress or nutrient starvation. (XLSX 933Â kb)
DOI: 10.6084/m9.figshare.c.3641753_d6.v1
title: Additional file 2: Table S2 of The transcriptional and splicing landscape of intestinal organoids undergoing nutrient starvation or endoplasmic reticulum stress

description: Analysis of expression patterns of various genes upregulated or downregulated during metabolic stress, including those associated with metabolism and innate immunity. (XLS 60Â kb)
DOI: 10.6084/m9.figshare.c.3641753_d9.v1
title: Additional file 1: Table S1 of The transcriptional and splicing landscape of intestinal organoids undergoing nutrient starvation or endoplasmic reticulum stress

description: cFPKM values for the global analysis of gene expression in murine enteroids upon either ER stress or nutrient starvation. (XLSX 5705Â kb)
DOI: 10.6084/m9.figshare.c.3641765_d3.v1
title: Additional file 3: Table S2. of Abdominal fat depots associated with insulin resistance and metabolic syndrome risk factors in black African young adults

description: Pearsonâ  s correlation coefficients (P-values) between body fat parameters and individual metabolic traits in women. (XLS 11Â kb)
DOI: 10.6084/m9.figshare.c.3641765_d2.v1
title: Additional file 2: Table S1. of Abdominal fat depots associated with insulin resistance and metabolic syndrome risk factors in black African young adults

description: Pearsonâ  s correlation coefficients (P-values) between body fat parameters and individual metabolic traits in men. (XLS 11Â kb)
DOI: 10.6084/m9.figshare.c.3641789_d1.v1
title: Additional file 1: Table S2. of The Perchlorate Reduction Genomic Island: Mechanisms and Pathways of Evolution by Horizontal Gene Transfer

description: List of locus tags for all of the genes mentioned explicitly or present in figures in this manuscript. (XLSX 53 kb)
DOI: 10.6084/m9.figshare.c.3641789_d2.v1
title: Additional file 2: Table S1. of The Perchlorate Reduction Genomic Island: Mechanisms and Pathways of Evolution by Horizontal Gene Transfer

description: Information on all 13 genomes used in this manuscript. (XLSX 42 kb)
DOI: 10.34943/13e5ff05-ec77-4124-bdf3-c13c8bc5580f
title: ODP 1027C Hydrophone Deployed 2020-10-01

description: The Ocean Sonics icListen HF Hydrophone 6021 was deployed on 2020-10-01 at ODP 1027C. ODP 1027C is a borehole site used to pinpoint an area within Cascadia Basin. This device is a Hydrophone. Hydrophones are devices containing transducers that convert underwater sound waves into electrical signals. They are acoustic instruments that can process data while they are being collected to produce calibrated waveform data. Hydrophones are typically used to study vocalizations of marine mammals, ship traffic and ambient noise. It was deployed on a fixed platform. Data from this deployment were archived and made available through Ocean Networks Canada's Oceans 3.0 digital infrastructure, with quality assurance and derived data products following established practices.
DOI: 10.6084/m9.figshare.c.3641816_d2.v1
title: Additional file 2: of ABO allele-level frequency estimation based on population-scale genotyping by next generation sequencing

description: JAGS model specification file (ABO_model.bug). (BUG 38 kb)
DOI: 10.6084/m9.figshare.c.3641816_d3.v1
title: Additional file 1: Table S1. of ABO allele-level frequency estimation based on population-scale genotyping by next generation sequencing

description: Primer sequences for ABO assay 1 and 2. Table S2. Alleles excluded from the reference allele set downloaded from NCBI dbRBC. Table S3. Alleles included in our final reference allele set and definition of allele groups as used in this study. Prevalence information of alleles are based on “The Blood Group Antigen FactsBook” [17], and the estimated frequencies are based on 113,367 German samples. Table S4. Alleles identified with so far undescribed nucleotide substitutions and structural variations. We provide numbers of observations per allele and positions of nucleotide changes relative to the cDNA of the reference alleles (ABO*A1.01.01.1 for antigens A and O, ABO*B1.01.01.1 for antigen B). A putative antigen designation was derived from sequence similarities to the exons harboring the nucleotide changes. (XLSX 38 kb)
DOI: 10.6084/m9.figshare.c.3641816_d4.v1
title: Additional file 3: of ABO allele-level frequency estimation based on population-scale genotyping by next generation sequencing

description: EAG group frequency counts (ABO_count.data) as input for the JAGS model specified in “ABO_model.bug”. (DATA 879 bytes)
DOI: 10.6084/m9.figshare.c.3641837_d2.v1
title: Additional file 6 of GenAp: a distributed SQL interface for genomic data

description: This is sample code that uses Spark SQL to perform an interval based join to the contents of sampleReads.adam with the contents of Additional File 5. (SCALA 1 kb)
DOI: 10.5519/qd.zvcfjxdh
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (10 records)
DOI: 10.6084/m9.figshare.c.3641837_d4.v1
title: Additional file 1 of GenAp: a distributed SQL interface for genomic data

description: This file contains instructions on how to clone and build our modification of Apache spark and run it in local mode on a userâ  s computer. (TXT 1 kb)
DOI: 10.6084/m9.figshare.c.3641837_d5.v1
title: Additional file 3 of GenAp: a distributed SQL interface for genomic data

description: This tarball contains a sample file of aligned reads in ADAM format. Note that this is a binary format and we provide a user the oportunity to explore this file by attaching the equivalent SAM file of the same alignments. (TAR 21 kb)
DOI: 10.6084/m9.figshare.c.3641837_d6.v1
title: Additional file 5 of GenAp: a distributed SQL interface for genomic data

description: This is a sample vcf file similar to the one we used in the results section. (VCF 9 kb)
DOI: 10.6084/m9.figshare.c.3641837_d7.v1
title: Additional file 7 of GenAp: a distributed SQL interface for genomic data

description: This tarball contains the custom C++ software that we wrote to implement the last query of the results section. For reference, it also contains the respective Spark SQL implementation. (TAR 9 kb)
DOI: 10.6084/m9.figshare.c.3641870_d1.v1
title: MOESM6 of Whole exome sequencing and single nucleotide polymorphism array analyses to identify germline alterations in genes associated with testosterone metabolism in a patient with androgen insensitivity syndrome and early-onset colorectal cancer

description: Additional file 6: Table S6. Chromosomal rearrangements of cancer function-related genes detected in the proband through single nucleotide polymorphism.
DOI: 10.6084/m9.figshare.c.3641870_d3.v1
title: MOESM4 of Whole exome sequencing and single nucleotide polymorphism array analyses to identify germline alterations in genes associated with testosterone metabolism in a patient with androgen insensitivity syndrome and early-onset colorectal cancer

description: Additional file 4: Table S4. List of disorder of sex development (DSD) genes used to filter exome sequencing variants.
DOI: 10.6084/m9.figshare.c.3641870_d6.v1
title: MOESM1 of Whole exome sequencing and single nucleotide polymorphism array analyses to identify germline alterations in genes associated with testosterone metabolism in a patient with androgen insensitivity syndrome and early-onset colorectal cancer

description: Additional file 1: Table S1. Variants of tumor genes detected by Sanger sequencing in the proband.
DOI: 10.6084/m9.figshare.c.3641870_d5.v1
title: MOESM8 of Whole exome sequencing and single nucleotide polymorphism array analyses to identify germline alterations in genes associated with testosterone metabolism in a patient with androgen insensitivity syndrome and early-onset colorectal cancer

description: Additional file 8: Table S8. List of truncating mutations identified in the proband and his relatives.
DOI: 10.6084/m9.figshare.c.3641870_d4.v1
title: MOESM7 of Whole exome sequencing and single nucleotide polymorphism array analyses to identify germline alterations in genes associated with testosterone metabolism in a patient with androgen insensitivity syndrome and early-onset colorectal cancer

description: Additional file 7: Table S7. List of variants identified in whole-genome sequencing (WES) data of the proband (blood sample and normal colon tissue) through the candidate gene approach.
DOI: 10.6084/m9.figshare.c.3641870_d7.v1
title: MOESM5 of Whole exome sequencing and single nucleotide polymorphism array analyses to identify germline alterations in genes associated with testosterone metabolism in a patient with androgen insensitivity syndrome and early-onset colorectal cancer

description: Additional file 5: Table S5. List of single nucleotide variants (SNVs) and small insertions and deletions (INDELs) detected in WES data of III.2 and III.3 subjects.
DOI: 10.6084/m9.figshare.c.3641870_d8.v1
title: MOESM3 of Whole exome sequencing and single nucleotide polymorphism array analyses to identify germline alterations in genes associated with testosterone metabolism in a patient with androgen insensitivity syndrome and early-onset colorectal cancer

description: Additional file 3: Table S3. List of genes significantly mutated in 233 colorectal tumors (TCGA project).
DOI: 10.7266/xeg6jgcj
title: Remote sensing data and imagery collected in Mississippi Sound by UAS, from 2021-07-26 to 2021-07-29
DOI: 10.6084/m9.figshare.c.3641879_d2.v1
title: Additional file 14: Table S5. of Phenotypic convergence in bacterial adaptive evolution to ethanol stress

description: (CSV 3Â kb)List of primers used in this study.
DOI: 10.6084/m9.figshare.c.3641879_d5.v1
title: Additional file 1: Table S1. of Phenotypic convergence in bacterial adaptive evolution to ethanol stress

description: (CSV 876Â kb)Time series expression analysis. The expression levels of 6 independent culture series (0, 384, 744, 1224, 1824, and 2496 hours after starting the culture) are presented.
DOI: 10.6084/m9.figshare.c.3641879_d7.v1
title: Additional file 13: Table S4. of Phenotypic convergence in bacterial adaptive evolution to ethanol stress

description: (CSV 3Â kb)Â Point mutations and indels found in the parent strains in comparison with W3110 reference genome.
DOI: 10.6084/m9.figshare.c.3641879_d9.v1
title: Additional file 9: Table S3. of Phenotypic convergence in bacterial adaptive evolution to ethanol stress

description: (CSV 11Â kb)Identified mutations in the tolerant strain A.
DOI: 10.6084/m9.figshare.c.3641912_d3.v1
title: MOESM2 of Presenilin 1 transgene addition to amyloid precursor protein overexpressing transgenic rats increases amyloid beta 42 levels and results in loss of memory retention

description: Additional file 2: Table 2. contains dataset for serum Aβ42, Aβ40 and Aβ42/Aβ40 ratio of F1 and F2 generation transgenic rats (see Fig. 3).