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

description: A dataset containing 29660 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Brassica oleracea L.)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 29660 records from 467 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0107635-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.h6vnkh
title: Occurrence Download

description: A dataset containing 38 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Germany",
 "GadmGid is DEU.16_1",
 "TaxonKey is Heracleum mantegazzianum Sommier & Levier",
 "Year 2019-2024"
 ]
}

 The dataset includes 38 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0107636-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.13472208
title: research data for the article Elenius et al, 'Where can rewetting of forested peatland reduce extreme flows?'

description: This dataset includes data of changes in hydrology when rewetting of drained forested peatland is performed. Details are explained in the companion article, Elenius et al, 'Where can rewetting of forested peatland reduce extreme flows?'

Data worksheets and columns are described on the readme worksheet in the file.
DOI: 10.15468/dl.3fdk3u
title: Occurrence Download

description: A dataset containing 67024 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Brassica rapa L.)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 67024 records from 714 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0107638-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.y5857s
title: Occurrence Download

description: A dataset containing 5641 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Brassica repanda (Willd.) DC.)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 5641 records from 122 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0107639-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ev2xfr
title: Occurrence Download

description: A dataset containing 1731 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Brazil",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Nasua nasua (Linnaeus, 1766)"
 ]
}

 The dataset includes 1731 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0107640-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gby4q7
title: Occurrence Download

description: A dataset containing 956346 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Watervogels - Wintering waterbirds in Flanders, Belgium"
 ]
}

 The dataset includes 956346 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0107633-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.13475636
title: Aberrant promoter methylation, expression and function of RASSF1A gene in a series of Italian parathyroid tumors

description: Aberrant epigenetic features occurring in parathyroid tumors are key events involved in parathyroid tumorigenesis. They include DNA methylation, histone methylation, and non-coding RNAs. Ras Association Domain Family Protein1 Isoform A (RASSF1A) and Adenomatous Polyposis of Colon (APC) are frequently downregulated in human cancers and they have an emerging role in parathyroid neoplasms. Here, investigating the methylation of RASSF1A and APC promoters in a series of parathyroid adenomas from Italian patients with primary hyperparathyroidism (PAds, n=80), we reported that RASSF1A and APC promoter methylation occurred in about 90% of samples. Parathyroid carcinomas (PCas, n=9) displayed RASSF1A promoter methylation, while APC promoter was methylated only in 2 samples. Of note, RASSF1A promoter methylation negatively correlated with PAds tumor size. However, RASSF1A transcript and protein levels were reduced in PAds and PCas compared with parathyroid normal glands. Investigating the potential mechanism involved in RASSF1A promoter methylation, we found that DNA methyltransferases (DNMTs) activity was variable in PAds and inversely correlated with RASSF1A protein levels. In addition, the RASSF1A promoter methylation negatively correlated with long-non-coding Antisense Intronic Noncoding RASSF1A (ANRASSF1A) mRNA levels, excluding the involvement of ANRASSF1 in RASSF1A regulation. In HEK293A cells transfected with the calcium sensing receptor (CASR), loss of RASSF1A increased basal phosphorylated Extracellular signal-regulated kinase (pERK/ERK) levels blunting the CASR-induced increases. In conclusion, RASSF1A and APC promoter methylation is a hallmark of parathyroid tumors; deregulation of DNMTs activity contributes to modulation of RASSF1A expression. Loss of RASSF1A may be involved in the tuning of ERK pathway in parathyroid tumors
DOI: 10.5281/zenodo.13475637
title: Aberrant promoter methylation, expression and function of RASSF1A gene in a series of Italian parathyroid tumors

description: Aberrant epigenetic features occurring in parathyroid tumors are key events involved in parathyroid tumorigenesis. They include DNA methylation, histone methylation, and non-coding RNAs. Ras Association Domain Family Protein1 Isoform A (RASSF1A) and Adenomatous Polyposis of Colon (APC) are frequently downregulated in human cancers and they have an emerging role in parathyroid neoplasms. Here, investigating the methylation of RASSF1A and APC promoters in a series of parathyroid adenomas from Italian patients with primary hyperparathyroidism (PAds, n=80), we reported that RASSF1A and APC promoter methylation occurred in about 90% of samples. Parathyroid carcinomas (PCas, n=9) displayed RASSF1A promoter methylation, while APC promoter was methylated only in 2 samples. Of note, RASSF1A promoter methylation negatively correlated with PAds tumor size. However, RASSF1A transcript and protein levels were reduced in PAds and PCas compared with parathyroid normal glands. Investigating the potential mechanism involved in RASSF1A promoter methylation, we found that DNA methyltransferases (DNMTs) activity was variable in PAds and inversely correlated with RASSF1A protein levels. In addition, the RASSF1A promoter methylation negatively correlated with long-non-coding Antisense Intronic Noncoding RASSF1A (ANRASSF1A) mRNA levels, excluding the involvement of ANRASSF1 in RASSF1A regulation. In HEK293A cells transfected with the calcium sensing receptor (CASR), loss of RASSF1A increased basal phosphorylated Extracellular signal-regulated kinase (pERK/ERK) levels blunting the CASR-induced increases. In conclusion, RASSF1A and APC promoter methylation is a hallmark of parathyroid tumors; deregulation of DNMTs activity contributes to modulation of RASSF1A expression. Loss of RASSF1A may be involved in the tuning of ERK pathway in parathyroid tumors
DOI: 10.15468/dl.kywnka
title: Occurrence Download

description: A dataset containing 22403 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Brassica tournefortii Gouan)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 22403 records from 212 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0107641-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.12805819
title: Dataset for journal article "Understanding the timeliness of automated data feeds is important for determining their usability for large-scale surveillance of healthcare-associated infections"

description: This dataset was used for the journal article "Understanding the timeliness of automated data feeds is important for determining their usability for large-scale surveillance of healthcare-associated infections".

For a selection of "activity dates", it contains the number of records available centrally at UKHSA on each day after the specified activity date, from a selection of data feeds that could potentially be used for national surveillance of healthcare-associated infections in England.

The associated R code is available from https://github.com/oxfordmmm/ukhsa-datafeeds-timeliness-anon
description: This study was funded by the National Institute for Health Research (NIHR) Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at Oxford University in partnership with the UK Health Security Agency (UKHSA) (NIHR200915), and supported by the NIHR Biomedical Research Centre, Oxford.
DOI: 10.5281/zenodo.12805820
title: Dataset for journal article "Understanding the timeliness of automated data feeds is important for determining their usability for large-scale surveillance of healthcare-associated infections"

description: This dataset was used for the journal article "Understanding the timeliness of automated data feeds is important for determining their usability for large-scale surveillance of healthcare-associated infections".

For a selection of "activity dates", it contains the number of records available centrally at UKHSA on each day after the specified activity date, from a selection of data feeds that could potentially be used for national surveillance of healthcare-associated infections in England.

The associated R code is available from https://github.com/oxfordmmm/ukhsa-datafeeds-timeliness-anon
description: This study was funded by the National Institute for Health Research (NIHR) Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at Oxford University in partnership with the UK Health Security Agency (UKHSA) (NIHR200915), and supported by the NIHR Biomedical Research Centre, Oxford.
DOI: 10.15468/dl.k594c9
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Hieracium pilosella L.)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1900",
 "BasisOfRecord is one of (Specimen)",
 "Country is one of (Australia)",
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than or equal to 20000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0107642-240626123714530/datasets/export for details.
DOI: 10.15468/dl.6cpp3y
title: Occurrence Download

description: A dataset containing 342 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Bretschneidera sinensis Hemsl.)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 342 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0107643-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.uq36gf
title: Occurrence Download

description: A dataset listing the 6 species recorded in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-101.19496 21.65672,57.19696 21.65672,57.19696 84.98636,-101.19496 84.98636,-101.19496 21.65672))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Succisella inflexa (Kluk) G.Beck",
 "Year 1830-2024"
 ]
}

 The dataset's 6 records were derived from 50 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0107637-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.5018433
title: Project files provided as supporting information to the manuscript "How Communication Pathways Bridge Local and Global Conformations in an IgG4 Antibody: a Molecular Dynamics Study"

description: June 23, 2021 Thomas Tarenzi, Marta Rigoli and Raffaello Potestio ================================== The dataset contains the following folders: - contact_area_binding_site: files with the computed surface area, used for the calculation of the contact area between PD-1 and the antibody Fab (Fig. S41). - hbonds_ab-pd1: number of hydrogen bonds between the antigen and the antibody, for each holo cluster (Fig. S41). - mutual_information: matrices with the computed mutual information, for each pair of residues (Fig. S34, S35, S46). The folder contains also the generalized correlation coefficients (Fig. S43) and the correlation scores (Fig. 4, S44, S45), computed from the mutual informations. - networks: communities - for each cluster, each residue is assigned to a community within the interaction network (Fig. S32, S33). betweenness - the values of edge betweenness for each cluster (S30, S31). - output_clustering: each frame of the apo and holo simulations is assigned a cluster index, on the basis of the structural similarity (Fig. S4). - PAD: per-residue values of PAD parameter, for apo and holo systems (Fig. 3, S39). - PCA: principal component analysis for each conformational cluster (Section S2.1). - representative_structures: representative structures for each conformational cluster (Fig. 2). - r_gyr_antibody: radii of gyration of the antibody, for each cluster (Fig. 2). - r_gyr_hinge: radii of gyration of the sole hinge segment, for each cluster (Fig. S36). - RMSD_antibody: distributions of the root-mean-square deviation of the antibody, for each cluster (Fig. S5). - RMSD_antigen: root-mean-square deviation of the antigen PD-1, for each cluster (Fig. S42). - RMSD_binding_site: distributions of the root-mean-square deviation of the residues belonging to the paratope, for each cluster (Fig. S40, S47). - RMSD_matrix: root-mean-square deviation between structures belonging to different pairs of clusters (Fig. S9). - rmsf_antigen: root-mean-square fluctuation of the antigen PD-1, for each cluster (Fig. S42). - rmsf_hinge: difference between the total root-mean-square fluctuations of the two hinge segments, for each cluster (Fig. S38). - salt_bridge: distribution of distances between residues R979 and D1377 (Fig. 4). - sasa_domains: contact area between Fab and Fc antibody domains, for each cluster (Fig. S8). - sasa_hinge: solvent accessible surface area of each hinge segment, for each cluster (Fig. S37).
DOI: 10.5281/zenodo.5018432
title: Project files provided as supporting information to the manuscript "How Communication Pathways Bridge Local and Global Conformations in an IgG4 Antibody: a Molecular Dynamics Study"

description: June 23, 2021 Thomas Tarenzi, Marta Rigoli and Raffaello Potestio ================================== The dataset contains the following folders: - contact_area_binding_site: files with the computed surface area, used for the calculation of the contact area between PD-1 and the antibody Fab (Fig. S41). - hbonds_ab-pd1: number of hydrogen bonds between the antigen and the antibody, for each holo cluster (Fig. S41). - mutual_information: matrices with the computed mutual information, for each pair of residues (Fig. S34, S35, S46). The folder contains also the generalized correlation coefficients (Fig. S43) and the correlation scores (Fig. 4, S44, S45), computed from the mutual informations. - networks: communities - for each cluster, each residue is assigned to a community within the interaction network (Fig. S32, S33). betweenness - the values of edge betweenness for each cluster (S30, S31). - output_clustering: each frame of the apo and holo simulations is assigned a cluster index, on the basis of the structural similarity (Fig. S4). - PAD: per-residue values of PAD parameter, for apo and holo systems (Fig. 3, S39). - PCA: principal component analysis for each conformational cluster (Section S2.1). - representative_structures: representative structures for each conformational cluster (Fig. 2). - r_gyr_antibody: radii of gyration of the antibody, for each cluster (Fig. 2). - r_gyr_hinge: radii of gyration of the sole hinge segment, for each cluster (Fig. S36). - RMSD_antibody: distributions of the root-mean-square deviation of the antibody, for each cluster (Fig. S5). - RMSD_antigen: root-mean-square deviation of the antigen PD-1, for each cluster (Fig. S42). - RMSD_binding_site: distributions of the root-mean-square deviation of the residues belonging to the paratope, for each cluster (Fig. S40, S47). - RMSD_matrix: root-mean-square deviation between structures belonging to different pairs of clusters (Fig. S9). - rmsf_antigen: root-mean-square fluctuation of the antigen PD-1, for each cluster (Fig. S42). - rmsf_hinge: difference between the total root-mean-square fluctuations of the two hinge segments, for each cluster (Fig. S38). - salt_bridge: distribution of distances between residues R979 and D1377 (Fig. 4). - sasa_domains: contact area between Fab and Fc antibody domains, for each cluster (Fig. S8). - sasa_hinge: solvent accessible surface area of each hinge segment, for each cluster (Fig. S37).
DOI: 10.5281/zenodo.5018467
title: Antarctic Radiative and Temperature responses to a doubling of CO2

description: This is the data and python notebooks for the paper, "Antarctic Radiative and Temperature responses to a doubling of CO2". The notebook, dataset_creation, makes the datasets that are found in this repository. To recreate these datasets, you will need the original profiles from Schmithusen et al. 2015 (https://doi.org/10.1002/2015GL066749). The subsequent notebooks create the figures for the paper as well as additional figures for analysis. All of this can also be found in the github repository: https://github.com/lfreese/antarctic-rad.
DOI: 10.5281/zenodo.5018466
title: Antarctic Radiative and Temperature responses to a doubling of CO2

description: This is the data and python notebooks for the paper, "Antarctic Radiative and Temperature responses to a doubling of CO2". The notebook, dataset_creation, makes the datasets that are found in this repository. To recreate these datasets, you will need the original profiles from Schmithusen et al. 2015 (https://doi.org/10.1002/2015GL066749). The subsequent notebooks create the figures for the paper as well as additional figures for analysis. All of this can also be found in the github repository: https://github.com/lfreese/antarctic-rad.
DOI: 10.25934/00002499.0
title: Available IPD datapackage for study 'A Randomized, Double-Blind, Placebo-Controlled, Polysomnography Plus Outpatient Study to Determine the Safety and Efficacy of 4 mg Ramelteon in Adults With Chronic Insomnia'

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: 10.25934/00002499.1
title: IPD datapackage for study 'A Randomized, Double-Blind, Placebo-Controlled, Polysomnography Plus Outpatient Study to Determine the Safety and Efficacy of 4 mg Ramelteon in Adults With Chronic Insomnia' and research request: 'Inferential reproducibility of therapeutic research: a registered report for a cross-sectional study of RCTs available on major data-sharing platforms'

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: 10.25345/c5m52k
title: MassIVE MSV000087687 - HP1 isoform BioID (Heath et al 2021)
title: Heath et al (2021) performed proximity based labeling to probe for protein-protein interactions of the HP1 isoforms (alpha, beta, gamma) with and with-out genotoxic stress.
DOI: 10.6084/m9.figshare.14812770.v1
title: Data for LiuTanWu_JC_2021.rar

description: Modified CP scheme files and input namelist of WRF model, matlab analysis code, and sample data for analysis are included. For complete data of simulations conducted in LiuTanWu_JC_2021, please contact the author (yliu90@nju.edu.cn).
DOI: 10.5281/zenodo.4812964
title: A High-Performance Data Processing Workflow to Incorporate Effect-Directed Analysis in Suspect and Nontarget Screening [Feature Tables]

description: This repository is supplementary to the manuscript "A High-Performance Data Processing Workflow to Incorporate Effect-Directed Analysis in Suspect and Nontarget Screening" (DOI: <em>To be announced</em>) and includes an overview of all measured chemical features and annotations in a waste water treatment plant (WWTP) effluent, dust standard reference material (SRM) 2585 and fetal calf serum (FCS) sample. Samples were measured using liquid chromatography - high resolution mass spectrometry (LC-HRMS) and fractionated into 80 micro-fractions encompassing a couple of seconds from the chromatographic run. The fractions were tested for their bioactivity in the antibiotics and the TTR-binding assay. The samples were processed separately using one, two, and three technical replicates in positive and negative ion mode. The first excel sheet includes all measured chemical features, suspect screening annotation, and corresponding bioassay responses. The second sheet includes all possible isomer annotations from the CECscreen database (DOI: 10.5281/zenodo.3956586) for the annotated features.
description: The work of TJ is part of the research program RoutinEDA with project number 15747, which is (partly) financed by the Dutch Research Council (NWO). The work of JM is part of the HBM4EU project funded by the European Union's Horizon 2020 research and innovation programme under grant agreement No 733032.