cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.12725745
title: Reprocessing of the dataset "Plasma Proteome Profiling Reveals the Effects of Weight Loss on the Apolipoprotein Family and Systemic Inflammation Status"

description: Reprocessing of the MassIVE repository MSV000080596, originally generated to investigate the dynamic changes in the plasma proteomes of a cohort of individuals with obesity following weight loss and maintenance. The reprocessing included all samples from 52 individuals taken right after the weight-loss process and during the weight maintenance phase of the study (Weeks 0, 4, 13, 26, 39, and 52).

We used the sequence database generated by ProHap (https://github.com/ProGenNo/ProHap) representing all populations from the 1000 Genomes Project (doi.org/10.5281/zenodo.10149277). For the search, SearchGUI version 4.3.1 and PeptideShaker version 3.0.0 were used with the X!Tandem and Tide search engines. The modification settings specified were carbamidomethylation of C as fixed and oxidation of M, deamidation of N and Q, Pyrrolidone of E and Q, and acetylation of protein N-terminus as variable modifications. The maximum peptide length was set to 40 amino acids and the precursor and fragment ion tolerances were set to 7 and 20 ppm, respectively. Resulting PSMs were processed as described in (doi.org/10.1021/acs.jproteome.3c00243) using Percolator version 3.5 provided with features based on peptide retention time (DeepLC version 1.1.2) and fragmentation predictors (MS2PIP version 3.9.0), and filtered at a 1% estimated FDR.

The attached file contains all the peptide-spectrum matches identified at 1% FDR. The peptides have been annotated with transcripts, genes, and alleles using the ProHap Peptide Annotator v1.1 (https://github.com/ProGenNo/ProHap_PeptideAnnotator).
DOI: 10.5281/zenodo.12725746
title: Reprocessing of the dataset "Plasma Proteome Profiling Reveals the Effects of Weight Loss on the Apolipoprotein Family and Systemic Inflammation Status"

description: Reprocessing of the MassIVE repository MSV000080596, originally generated to investigate the dynamic changes in the plasma proteomes of a cohort of individuals with obesity following weight loss and maintenance. The reprocessing included all samples from 52 individuals taken right after the weight-loss process and during the weight maintenance phase of the study (Weeks 0, 4, 13, 26, 39, and 52).

We used the sequence database generated by ProHap (https://github.com/ProGenNo/ProHap) representing all populations from the 1000 Genomes Project (doi.org/10.5281/zenodo.10149277). For the search, SearchGUI version 4.3.1 and PeptideShaker version 3.0.0 were used with the X!Tandem and Tide search engines. The modification settings specified were carbamidomethylation of C as fixed and oxidation of M, deamidation of N and Q, Pyrrolidone of E and Q, and acetylation of protein N-terminus as variable modifications. The maximum peptide length was set to 40 amino acids and the precursor and fragment ion tolerances were set to 7 and 20 ppm, respectively. Resulting PSMs were processed as described in (doi.org/10.1021/acs.jproteome.3c00243) using Percolator version 3.5 provided with features based on peptide retention time (DeepLC version 1.1.2) and fragmentation predictors (MS2PIP version 3.9.0), and filtered at a 1% estimated FDR.

The attached file contains all the peptide-spectrum matches identified at 1% FDR. The peptides have been annotated with transcripts, genes, and alleles using the ProHap Peptide Annotator v1.1 (https://github.com/ProGenNo/ProHap_PeptideAnnotator).
DOI: 10.7266/n7th8jn6
title: WB 1305 CTD, R/V Weatherbird, Florida to DeSoto Canyon, 2012-09-22 - 2012-09-29
DOI: 10.6084/m9.figshare.19553203
title: DOS calculation of StructOpt a-TiO2

description: Density of States for Structopt amorphous TiO2 model by DFT using VASP
DOI: 10.6084/m9.figshare.19553203.v1
title: DOS calculation of StructOpt a-TiO2

description: Density of States for Structopt amorphous TiO2 model by DFT using VASP
DOI: 10.25574/00550
title: Chandra X-ray Observatory ObsId 00550

description: DETERMINATION OF H0/Q0
DOI: 10.25345/c5280594x
title: MassIVE MSV000095303 - Unraveling Cecal Alterations in Clostridioides difficile Colonized Mice through a Comprehensive Metabolic Profile of 289 Compound
title: Unraveling Cecal Alterations in Clostridioides difficile Colonized Mice through a Comprehensive Metabolic Profile of 289 Compound
DOI: 10.6084/m9.figshare.25533367.v1
title: coastalNet, global estimates of coastal oceanographic connectivity

description: The coastalNet R package offers a suite of tools for the analysis of oceanographic connectivity and its implications for marine biodiversity. Developed to address the complex dynamics of how ocean currents influence the distribution, evolution, and conservation of marine species, coastalNet leverages high-resolution ocean current data, biophysical modeling, and graph theory to offer a comprehensive toolkit for marine ecology research.The integration of biophysical modeling with graph theory stands at the core of coastalNet's approach. By simulating the dispersal routes of marine species and applying graph theory, coastalNet identifies critical connectivity hubs and pathways, offering realistic estimates of population connectivity. This methodological innovation allows for a nuanced understanding of marine biodiversity dynamics, challenging simplistic predictive models and unveiling the complex relationships between ocean currents and genetic structuring across marine species distributions.
DOI: 10.6084/m9.figshare.19552729
title: Experiment V(k)

description: Experimental V(k) data for amorphous TiO2 thin film
DOI: 10.6084/m9.figshare.19552729.v1
title: Experiment V(k)

description: Experimental V(k) data for amorphous TiO2 thin film
DOI: 10.6084/m9.figshare.19552717
title: Experimental G(r)

description: Experimental G(r) data for amorphous TiO2
DOI: 10.6084/m9.figshare.19552717.v1
title: experimental G(r)

description: Experimental G(r) data for amorphous TiO2
DOI: 10.6084/m9.figshare.19552717.v2
title: Experimental G(r)

description: Experimental G(r) data for amorphous TiO2
DOI: 10.6084/m9.figshare.19552807
title: Atomic structure of a-TiO2

description: atomic structure of a-TiO2
DOI: 10.6084/m9.figshare.19552807.v1
title: atomic structure of a-TiO2

description: atomic structure of a-TiO2
DOI: 10.5066/p1hyvyfz
title: Deep SEARCH eDNA metabarcoding data

description: The Deep SEARCH Project (Deep sea exploration to advance research on cold corals/canyon/cold seep habitats) included a cruise in April 2019 aboard the NOAA ship Ron Brown to various sites along the Mid-Atlantic North American coast. An ROV was used to collect samples of bottom water at these sites, which were then subjected to eDNA extraction and analyses. This data release describes what samples were collected for eDNA analyses, and how eDNA was extracted, sequenced, and bioinformatically analyzed.
DOI: 10.25345/c5xg9fp0g
title: MassIVE MSV000095304 - RAP proteins regulate apicoplast noncoding RNA processing in Plasmodium falciparum (IP-MS_RAP03_RAP08 dataset)
title: Mass spectrometry analysis of IP-MS samples used for identifying RAP03 and RAP08 associated proteins.
DOI: 10.5281/zenodo.12725981
title: CheXphoto WhatsApp Dataset
DOI: 10.5281/zenodo.12725982
title: CheXphoto WhatsApp Dataset
DOI: 10.5281/zenodo.12582058
title: Pelagomonas calceolata gene expression levels in different nitrogen conditions and differential expression analysis.

description: These files contains the expression levels and DESeq2 results of Pelagomonas calceolata genes cultivated with different nitrate conditions. Two strains of P. calceolata (RCC100 and RCC697)  were cultivated and their RNAs reads were aligned on the predicted genes of P. calceolata RCC100 genome: https://www.ncbi.nlm.nih.gov/Traces/wgs/CAKKNE01?display=download

The following culture conditions were analysed :

882 µM of Nitrate (RCC100 and RCC697) 

441 µM of Nitrate (RCC100)

220 µM of Nitrate (RCC100 and RCC697)

50 µM of Nitrate (RCC697)

882 µM Cyanate (RCC100)

882 µM Ammonia (RCC100)

441 µM Urea (RCC100)

20230427_RCC100-Nitrate_transcriptomes_rawcounts.tsv : the file contains the raw read counts of RCC100 in 6 culture conditions in triplicate + the gene names = 19 columns.

20230427_RCC100-Nitrate_transcriptomes_TPM.tsv : same data normalized in transcript per kb per million mapped reads (TPM).

20230427_RCC697-Nitrate_transcriptomes_rawcounts.tsv : the file contains the raw read counts of RCC697 of 3 culture conditions in triplicate + the gene names = 10 columns.

20230427_RCC697-Nitrate_transcriptomes_TPM.tsv : same data normalized in transcript per kb per million mapped reads (TPM).

Differential expression analysis (DESeq2) was performed by pairwise comparisons between the standard condition (882 µM nitrate) and low-nitrate conditions (50, 220 or 441 µM nitrate) or changing nitrogen sources (882 µM ammonium, 882 µM cyanate and 441 µM urea). Each DESeq-results_RCCxxx_xxx.tsv file contains 6 columns : P.calceolata gene name, base Mean, log2 Fold Change, standard error value (lfcSE), pvalue and adjusted pvalue (padj).
DOI: 10.5281/zenodo.12582059
title: Pelagomonas calceolata gene expression levels in different nitrogen conditions

description: These files contains the expression levels of Pelagomonas calceolata genes cultivated with different nitrate conditions. Two strains of P. calceolata (RCC100 and RCC697)  were cultivated and their RNAs reads were aligned on the predicted genes of P. calceolata RCC100 genome: https://www.ncbi.nlm.nih.gov/Traces/wgs/CAKKNE01?display=download

The following culture conditions were analysed :

882 µM of Nitrate (RCC100 and RCC697) 

441 µM of Nitrate (RCC100)

220 µM of Nitrate (RCC100 and RCC697)

50 µM of Nitrate (RCC697)

882 µM Cyanate (RCC100)

882 µM Ammonia (RCC100)

441 µM Urea (RCC100)

20230427_RCC100-Nitrate_transcriptomes_rawcounts.tsv : the file contains the raw read counts of RCC100 in 6 culture conditions in triplicate + the gene names = 19 columns.

20230427_RCC100-Nitrate_transcriptomes_TPM.tsv : same data normalized in transcript per kb per million mapped reads (TPM).

20230427_RCC697-Nitrate_transcriptomes_rawcounts.tsv : the file contains the raw read counts of RCC697 of 3 culture conditions in triplicate + the gene names = 10 columns.

20230427_RCC697-Nitrate_transcriptomes_TPM.tsv : same data normalized in transcript per kb per million mapped reads (TPM).
DOI: 10.5281/zenodo.12725931
title: Pelagomonas calceolata gene expression levels in different nitrogen conditions and differential expression analysis.

description: These files contains the expression levels and DESeq2 results of Pelagomonas calceolata genes cultivated with different nitrate conditions. Two strains of P. calceolata (RCC100 and RCC697)  were cultivated and their RNAs reads were aligned on the predicted genes of P. calceolata RCC100 genome: https://www.ncbi.nlm.nih.gov/Traces/wgs/CAKKNE01?display=download

The following culture conditions were analysed :

882 µM of Nitrate (RCC100 and RCC697) 

441 µM of Nitrate (RCC100)

220 µM of Nitrate (RCC100 and RCC697)

50 µM of Nitrate (RCC697)

882 µM Cyanate (RCC100)

882 µM Ammonia (RCC100)

441 µM Urea (RCC100)

20230427_RCC100-Nitrate_transcriptomes_rawcounts.tsv : the file contains the raw read counts of RCC100 in 6 culture conditions in triplicate + the gene names = 19 columns.

20230427_RCC100-Nitrate_transcriptomes_TPM.tsv : same data normalized in transcript per kb per million mapped reads (TPM).

20230427_RCC697-Nitrate_transcriptomes_rawcounts.tsv : the file contains the raw read counts of RCC697 of 3 culture conditions in triplicate + the gene names = 10 columns.

20230427_RCC697-Nitrate_transcriptomes_TPM.tsv : same data normalized in transcript per kb per million mapped reads (TPM).

Differential expression analysis (DESeq2) was performed by pairwise comparisons between the standard condition (882 µM nitrate) and low-nitrate conditions (50, 220 or 441 µM nitrate) or changing nitrogen sources (882 µM ammonium, 882 µM cyanate and 441 µM urea). Each DESeq-results_RCCxxx_xxx.tsv file contains 6 columns : P.calceolata gene name, base Mean, log2 Fold Change, standard error value (lfcSE), pvalue and adjusted pvalue (padj).
DOI: 10.5281/zenodo.12726053
title: Pelagomonas calceolata gene expression levels in different nitrogen conditions and differential expression analysis.

description: These files contains the expression levels and DESeq2 results of Pelagomonas calceolata genes cultivated with different nitrate conditions. Two strains of P. calceolata (RCC100 and RCC697)  were cultivated and their RNAs reads were aligned on the predicted genes of P. calceolata RCC100 genome: https://www.ncbi.nlm.nih.gov/Traces/wgs/CAKKNE01?display=download

The following culture conditions were analysed :

882 µM of Nitrate (RCC100 and RCC697) 

441 µM of Nitrate (RCC100)

220 µM of Nitrate (RCC100 and RCC697)

50 µM of Nitrate (RCC697)

882 µM Cyanate (RCC100)

882 µM Ammonia (RCC100)

441 µM Urea (RCC100)

20230427_RCC100-Nitrate_transcriptomes_rawcounts.tsv : the file contains the raw read counts of RCC100 in 6 culture conditions in triplicate + the gene names = 19 columns.

20230427_RCC100-Nitrate_transcriptomes_TPM.tsv : same data normalized in transcript per kb per million mapped reads (TPM).

20230427_RCC697-Nitrate_transcriptomes_rawcounts.tsv : the file contains the raw read counts of RCC697 of 3 culture conditions in triplicate + the gene names = 10 columns.

20230427_RCC697-Nitrate_transcriptomes_TPM.tsv : same data normalized in transcript per kb per million mapped reads (TPM).

Differential expression analysis (DESeq2) was performed by pairwise comparisons between the standard condition (882 µM nitrate) and low-nitrate conditions (50, 220 or 441 µM nitrate) or changing nitrogen sources (882 µM ammonium, 882 µM cyanate and 441 µM urea). Each DESeq-results_RCCxxx_xxx.tsv file contains 6 columns : P.calceolata gene name, base Mean, log2 Fold Change, standard error value (lfcSE), pvalue and adjusted pvalue (padj).
DOI: 10.5519/qd.i5rq6zhv
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (46 records)
DOI: 10.6084/m9.figshare.25533367.v2
title: coastalNet, global estimates of coastal oceanographic connectivity

description: The coastalNet R package offers a suite of tools for the analysis of oceanographic connectivity and its implications for marine biodiversity. Developed to address the complex dynamics of how ocean currents influence the distribution, evolution, and conservation of marine species, coastalNet leverages high-resolution ocean current data, biophysical modeling, and graph theory to offer a comprehensive toolkit for marine ecology research.The integration of biophysical modeling with graph theory stands at the core of coastalNet's approach. By simulating the dispersal routes of marine species and applying graph theory, coastalNet identifies critical connectivity hubs and pathways, offering realistic estimates of population connectivity. This methodological innovation allows for a nuanced understanding of marine biodiversity dynamics, challenging simplistic predictive models and unveiling the complex relationships between ocean currents and genetic structuring across marine species distributions.
DOI: 10.6084/m9.figshare.26240264
title: Data and R code to run the analysis for “Soil legacies of tree species composition in mature forest affect tree seedlings’ performance”

description: This dataset contains data of a plant-soil feedback experiment performed using soil collected in FunDivEUROPE plots in Białowieża Forest. The plots differ in species composition. The dataset comprises of chemical soil characteristics, and measured and derived emergence and growth measures of tree seedlings (hornbeam, birch, oak, and pine).Seeds were sown in pots and seedlings were grown for one growing season. The emergence was monitored for 80 days, after which all seedlings were measured in a non-destructive way, and when more than one seedling was present in the soil, the seedlings where thinned to one seedling per pot. After 225 days, the seedlings were harvested and destructive measurements were taken of the leaves, shoot, and roots. For a subset of the oak seedlings, the mycorrhizal root tip colonisations was measured.The R markdown code to obtain the tables and figures in “Dhiedt E., Baeten L., De Smedt P., Jaroszewicz B., Verheyen K. (2024). Soil legacies of tree species composition in mature forest affect tree seedlings’ performance. Ecosystems.” is also provided, as well as a html version of the code.A more detailed description of the data is provided in the supporting information (supporting_information.docx).
DOI: 10.5281/zenodo.12724716
title: MODES DATA - Hough functions and frequencies - 1 v2
DOI: 10.5281/zenodo.12724717
title: MODES DATA - Hough functions and frequencies - 1 v2
DOI: 10.25934/pr00004910.0
title: Available IPD datapackage for study 'Efficacy and safety of a flexible dose of risperidone versus placebo in the treatment of psychosis of Alzheimer’s disease. A double-blind, placebo-controlled, parallel-group study.'

description: Vivli is an independent, non-profit organization that has developed a global data-sharing and analytics platform to serve all elements of the international research community. Our mission is to promote, coordinate, and facilitate scientific sharing and reuse of clinical research data through the creation and implementation of a sustainable global data-sharing enterprise. The Vivli platform includes an independent data repository, in-depth search engine and a cloud-based, secure analytics platform.
DOI: 10.25574/00580
title: Chandra X-ray Observatory ObsId 00580

description: DEEP ACIS OBSERVATION OF THE HUBBLE DEEP FIELD
DOI: 10.25345/c5st7f80j
title: MassIVE MSV000095305 - RAP proteins regulate apicoplast noncoding RNA processing in Plasmodium falciparum (HyPR_Mito dataset)
title: Mass spectrometry analysis of HyPR_Mito samples used for identifying mitochondrial rRNA-associated proteins.
DOI: 10.5281/zenodo.12725085
title: MODES DATA - Hough functions and frequencies - 2 v2
DOI: 10.5281/zenodo.12725086
title: MODES DATA - Hough functions and frequencies - 2 v2
DOI: 10.15468/dl.3gjmjz
title: Occurrence Download

description: A dataset containing 32 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is (Table 1) Proportion of Toxoplasma gondii seropositive arctic foxes (Alopex lagopus) by age group and geographic area"
 ]
}

 The dataset includes 32 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032605-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.txdgn6
title: Occurrence Download

description: A dataset containing 32 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is (Table 1) Proportion of Toxoplasma gondii seropositive arctic foxes (Alopex lagopus) by age group and geographic area"
 ]
}

 The dataset includes 32 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032601-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.skrshn
title: Occurrence Download

description: A dataset containing 954 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Peru",
 "Geometry POLYGON((-92.18112 -19.56934,-56.81888 -19.56934,-56.81888 -5.43066,-92.18112 -5.43066,-92.18112 -19.56934))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Geositta crassirostris P.L.Sclater, 1866"
 ]
}

 The dataset includes 954 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020796-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zhqm9a
title: Occurrence Download

description: A dataset containing 537861 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Spain",
 "Year 1000-1980",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 537861 records from 465 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022615-191105090559680/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yehrfg
title: Occurrence Download

description: A dataset containing 15 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Telmatobius pefauri Veloso & Trueb, 1976"
 ]
}

 The dataset includes 15 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020798-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.veksgn
title: Occurrence Download

description: A dataset containing 15843 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is Panama",
 "OccurrenceStatus is Present",
 "TaxonKey is Hemiptera"
 ]
}

 The dataset includes 15843 records from 63 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020799-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yjjtnv
title: Occurrence Download

description: A dataset containing 45197 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is United States of America",
 "OccurrenceStatus is Present",
 "TaxonKey is Juniperus virginiana L."
 ]
}

 The dataset includes 45197 records from 255 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020797-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ka7p2x
title: Occurrence Download

description: A dataset containing 282 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is Grallaricula peruviana Chapman, 1923"
 ]
}

 The dataset includes 282 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006027-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3ub2cs
title: Occurrence Download

description: A dataset containing 367 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is CHN.30_1",
 "TaxonKey is Pyrus pashia Buch.-Ham. ex D.Don"
 ]
}

 The dataset includes 367 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0234618-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.s3cj98
title: Occurrence Download

description: A dataset containing 16 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Calathea jondule H.Kenn. & Hammel"
 ]
}

 The dataset includes 16 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0149479-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.