cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.3334/cdiac/otg.clivar_aaiw05
title: Partial pressure (or fugacity) of carbon dioxide, dissolved inorganic carbon, pH, alkalinity, temperature, salinity and other variables collected from discrete sample and profile observations using Alkalinity titrator, CTD and other instruments from the KNORR in the South Pacific Ocean from 2005-08-21 to 2005-10-06 (NCEI Accession 0108071)

description: This dataset includes chemical, discrete sample, physical and profile data collected from KNORR in the South Pacific Ocean from 2005-08-21 to 2005-10-06 and retrieved during cruise CLIVAR_AAIW05. These data include ALKALINITY, CHLOROFLUOROCARBON-11 (CFC-11), CHLOROFLUOROCARBON-113 (CFC-113), CHLOROFLUOROCARBON-12 (CFC-12), Carbon tetrachloride (CCL4), DISSOLVED INORGANIC CARBON, DISSOLVED OXYGEN, HYDROSTATIC PRESSURE, NITRATE, NITRITE, PHOSPHATE, Partial pressure (or fugacity) of carbon dioxide, SALINITY, SILICATE, WATER TEMPERATURE and pH. The instruments used to collect these data include Alkalinity titrator, CTD, Coulometer for DIC measurement and bottle. These data were collected by Andrew G. Dickson and James H. Swift of Scripps Institution of Oceanography (SIO) and Lynne D. Talley of University of Rhode Island; Graduate School of Oceanography (GSO) as part of the CLIVAR_AAIW05 dataset.

The International CLIVAR Global Ocean Carbon and Repeat Hydrography Program carries out a systematic and global re-occupation of select WOCE/JGOFS hydrographic sections to quantify changes in storage and transport of heat, fresh water, carbon dioxide (CO2), and related parameters.
DOI: 10.15468/dl.dawf39
title: Occurrence Download

description: A dataset containing 24208 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Germany",
 "OccurrenceStatus is Present",
 "TaxonKey is Senecio inaequidens DC."
 ]
}

 The dataset includes 24208 records from 88 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015876-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ujdzq2
title: Occurrence Download

description: A dataset containing 17159 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((71 33,98 33,98 51,71 51,71 33))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Caryophyllaceae"
 ]
}

 The dataset includes 17159 records from 86 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015877-250426092105405/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.28918622
title: Supplementary Data Table 1 - Sex differences in resting skeletal muscle and the acute and long-term response to endurance exercise in individuals with overweight and obesity

description: Endurance exercise reduces the risk of metabolic diseases by improving skeletal muscle metabolism, particularly in individuals with overweight and obesity. As biological sex impacts glucose and fatty acid handling in skeletal muscle, we hypothesized sex differences at the transcriptomic and proteomic level in the acute response to exercise and after an 8-week exercise intervention.We analyzed skeletal muscle biopsies from 25 sedentary subjects (16f/9m) with overweight and obesity using transcriptomics and proteomics at baseline, after acute exercise, and following an 8-week endurance training program. Regulation of sex-specific differences was studied in primary myotubes from the donors.At baseline, differentially methylated CpG-sites potentially explain up to 59% of transcriptomic and 67% of proteomic sex differences. Differences were dominated by higher abundance of fast-twitch fiber type proteins, and transcripts and proteins regulating glycogen degradation and glycolysis in males. Females showed higher abundance of proteins regulating fatty acid uptake and storage. Acute exercise induced stress-responsive transcripts and serum myoglobin predominantly in males. Both sexes adapted to 8-week endurance training by upregulating mitochondrial proteins involved in TCA cycle, oxidative phosphorylation, and β-oxidation. Training equalized fast-twitch fiber type protein levels, mainly by reducing them in males. In vivo sex differences in autosomal genes were poorly retained in myotubes but partially restored by sex hormone treatment.In conclusion, our findings highlight sex-specific molecular signatures that reflect known differences in glucose and lipid metabolism between female and male skeletal muscle. After just 8 weeks of endurance training, these sex differences were attenuated, suggesting a convergence towards a shared beneficial adaptation at the molecular level.
DOI: 10.6084/m9.figshare.28918622.v1
title: Supplementary Data Table 1 - Sex differences in resting skeletal muscle and the acute and long-term response to endurance exercise in individuals with overweight and obesity

description: Endurance exercise reduces the risk of metabolic diseases by improving skeletal muscle metabolism, particularly in individuals with overweight and obesity. As biological sex impacts glucose and fatty acid handling in skeletal muscle, we hypothesized sex differences at the transcriptomic and proteomic level in the acute response to exercise and after an 8-week exercise intervention.We analyzed skeletal muscle biopsies from 25 sedentary subjects (16f/9m) with overweight and obesity using transcriptomics and proteomics at baseline, after acute exercise, and following an 8-week endurance training program. Regulation of sex-specific differences was studied in primary myotubes from the donors.At baseline, differentially methylated CpG-sites potentially explain up to 59% of transcriptomic and 67% of proteomic sex differences. Differences were dominated by higher abundance of fast-twitch fiber type proteins, and transcripts and proteins regulating glycogen degradation and glycolysis in males. Females showed higher abundance of proteins regulating fatty acid uptake and storage. Acute exercise induced stress-responsive transcripts and serum myoglobin predominantly in males. Both sexes adapted to 8-week endurance training by upregulating mitochondrial proteins involved in TCA cycle, oxidative phosphorylation, and β-oxidation. Training equalized fast-twitch fiber type protein levels, mainly by reducing them in males. In vivo sex differences in autosomal genes were poorly retained in myotubes but partially restored by sex hormone treatment.In conclusion, our findings highlight sex-specific molecular signatures that reflect known differences in glucose and lipid metabolism between female and male skeletal muscle. After just 8 weeks of endurance training, these sex differences were attenuated, suggesting a convergence towards a shared beneficial adaptation at the molecular level.
DOI: 10.15468/dl.k8brkp
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Actinomyces qiguomingii sp. nov., isolated from the Pantholops hodgsonii"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015878-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.7289/v5rn35s0
title: Surface and Oceanographic profile temperature, salinity and other measurements using CTD and thermosalinograph, taken from the PUERTO DESEADO in the Coastal South Atlantic, South Atlantic and other locations from 2005 to 2006 (NCEI Accession 0110317)

description: These data were collected as part of the scientific agenda of the United Nations Development Program (UNDP) and sponsored by the Secretary of Environment and Sustainable Development of Argentina (http://www.ambiente.gov.ar). The project Coastal Pollution Prevention and Marine Biodiversity Management (Project 28385-AR-UNDP-ARG/02/018l) also referred to as GEF Patagonia was partially funded by the Global Environment Facility (GEF), with additional funding from the Inter-American Institute for Global Change Research (CRN061 and 2076). The project goal was to determine the seasonal variability of physical-chemical properties of highly productive regions of the southwest South Atlantic continental shelf.

The GEF Patagonia field experiments consisted of three oceanographic cruises carried out on board R/V ARA PUERTO DESEADO, in October 2005 (PD GEFPAT_1), and March (PD GEFPAT_2) and September 2006 (PD GEFPAT_3). In each cruise, hydrographic stations were occupied along cross-shelf sections spanning the shelf and extending to the onshore edge of the western boundary currents between 38° and 55°S. This submission reports the CTD and thermosalinograph data collected during the three GEF Patagonia cruises.
DOI: 10.7910/dvn/putxl9
title: Replication Data for: Metabolic modelling links gut microbiota to metabolic perturbations in Parkinson's disease

description: *** DESCRIPTION ***

Input data for replication of paper titled: "Metabolic modelling links gut microbiota to metabolic perturbations in Parkinson's disease". 

*** CONTENT ***

- ApolloAgora2panSpecies: Folder with AGORA2 + APOLLO pan species gut microbe reconstructions.
- luo_2024_replicated_PD_mets.xlsx: List of metabolites for which a replicated association with Parkinson's disease (PD) diagnosis was found by Luo et al. (2024, https://doi.org/10.1038/s41531-024-00732-z)
- metaboliteChemicalAnnotation.xlsx: Chemical annotations of PD-associated metabolites that mapped onto the blood compartment of WBM version 1.04c. Chemical annotations were taken from Luo et al. (2024, https://doi.org/10.1038/s41531-024-00732-z).
- metadata.xlsx: File with sample and patient metadata information. This file was taken and adapted from Wallen et al. (2022, https://doi.org/10.1038/s41467-022-34667-x)
- mWBM_SET1-mWBM_SET5: Folder with microbiome personalised WBMs (version 1.04c). 
- PD_associatedTaxa_subsetPresentSpeciesMARS.xlsx: List of microbial species for which an association with PD diagnosis was found by Wallen et al. (2022, https://doi.org/10.1038/s41467-022-34667-x).
- resultFlux: Folder with FBA flux solutions from the generated microbiome personalised WBMs. 
- resultMARS: Folder with gut microbiome mapping results after metagenomic mapping on the AGORA2+APOLLO pan species resource.
description: Is Supplement To: Metabolic modelling links gut microbiota to metabolic perturbations in Parkinson's disease, Tim Hensen, Ines Thiele.


*** INSTRUCTIONS FOR REPLICATION OF ANALYSIS ***

To replicate the analysis performed by Hensen et al. (2025), please first perform the following steps:

1. Unzip the downloaded files
2. Create a project folder for replication
3. Within the project folder (e.g, "project"), create a folder named "inputs"
4. Move all files to the "project/inputs"
5. Create the following folder structure and populate the "project/inputs" folder as follows:

- project
 - inputs
 - resultFlux
 - luo_2024_replicated_PD_mets.xlsx
 - metadata.xlsx
 - PD_associatedTaxa_subsetPresentSpeciesMARS.csv
 - metaboliteChemicalAnnotation.xlsx
 - models
 - ApolloAgora2panSpecies
 - HMmodels

The "HMmodels" folder should contain all .mat from mWBM_SET1 to mWBM_SET5 as follows: 

- HMmodels
 - muWBM_DC001_male.mat
 - muWBM_DC003_female.mat
 - etcetera

6. After setting up the input data, please obtain the scripts from "https://github.com/ThieleLab/CodeBase" and deposit the associated helper functions in "project/functions".

 7. At this point, the computational analysis can be replicated.
DOI: 10.15468/dl.gk46qz
title: Occurrence Download

description: A dataset containing 5629 species occurrences available in GBIF matching the query:
{
 "and" : [
 "SpeciesKey is one of (Arabidopsis arenosa (L.) Lawalrée)",
 "Year is greater than or equal to 1981",
 "Year is less than or equal to 2025",
 "Continent is Europe",
 "CoordinateUncertaintyInMeters is 100",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 5629 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015879-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.94d7b3
title: Occurrence Download

description: A dataset containing 2082 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Himantoglossum robertianum (Loisel.) P.Delforge",
 "DatasetKey is iNaturalist Research-grade Observations",
 "Country is France",
 "Year is greater than or equal to 2014",
 "Year is less than or equal to 2024"
 ]
}

 The dataset includes 2082 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015880-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.smm26q
title: Occurrence Download

description: A dataset containing 13274 species occurrences available in GBIF matching the query:
{
 "and" : [
 "SpeciesKey is one of (Arabidopsis arenosa (L.) Lawalrée)",
 "HasCoordinate is true",
 "Year is greater than or equal to 1981",
 "Year is less than or equal to 2025",
 "Continent is Europe",
 "CoordinateUncertaintyInMeters is less than or equal to 100",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 13274 records from 73 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015881-250426092105405/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.26928178
title: pyGOT package data

description: This is the data source of dataset API of pyGOT package
DOI: 10.15468/dd.nvmcvn
title: Distribution records of Electrona antarctica

description: These records of Electrona antarctica were downloaded from GBIF on 2019-09-11.
DOI: 10.7289/v5mk69t9
title: Dissolved inorganic carbon, total alkalinity, dissolved oxygen, and pH monitored from benthic Free Ocean Carbon Enrichment (FOCE) -type study in Heron Island reef flat (NCEI Accession 0113856)

description: Ocean acidification poses multiple challenges for coral reefs on molecular to ecological scales, yet previous experimental studies of the impact of projected CO2 concentrations have mostly been done in aquarium systems with corals removed from their natural ecosystem and placed under artificial light and seawater conditions. The Coral-Proto Free Ocean Carbon Enrichment System (CP-FOCE) uses a network of sensors to monitor conditions within each flume and maintain experimental pH as an offset from environmental pH using feedback control on the injection of low pH seawater. Carbonate chemistry conditions maintained in the -0.06 and -0.22 pH offset treatments were significantly different than environmental conditions. The results from this short-term experiment suggest that the CP-FOCE is an important new experimental system to study in situ impacts of ocean acidification on coral reef ecosystems.
DOI: 10.3334/cdiac/otg.carina_18sn19970924
title: Dissolved inorganic carbon, alkalinity, temperature, salinity and other variables collected from discrete sample and profile observations using CTD, bottle and other instruments from the LOUIS S. ST. LAURENT in the Arctic Ocean and Beaufort Sea from 1997-09-24 to 1997-10-15 (NCEI Accession 0113984)

description: This dataset includes chemical, discrete sample, physical and profile data collected from LOUIS S. ST. LAURENT in the Arctic Ocean and Beaufort Sea from 1997-09-24 to 1997-10-15 and retrieved during cruise CARINA/18SN19970924, JOIS 97 and Leg 4. These data include ALKALINITY, CHLOROFLUOROCARBON-11 (CFC-11), CHLOROFLUOROCARBON-113 (CFC-113), CHLOROFLUOROCARBON-12 (CFC-12), Carbon tetrachloride (CCL4), DISSOLVED INORGANIC CARBON, DISSOLVED OXYGEN, HYDROSTATIC PRESSURE, NITRATE, NITRITE, PHOSPHATE, Potential temperature (theta), SALINITY, SILICATE and WATER TEMPERATURE. The instruments used to collect these data include CTD and bottle. These data were collected by E. Peter Jones and Kumiko Azetsu-Scott of Bedford Institute of Oceanography (BIO) and James H. Swift of Scripps Institution of Oceanography (SIO) as part of the CARINA/18SN19970924 dataset.

The CARINA (CARbon dioxide IN the Atlantic Ocean) data synthesis project is an international collaborative effort of the EU IP CARBOOCEAN, and U.S. partners. It has produced a merged internally consistent dataset of open ocean subsurface measurements for biogeochemical investigations, in particular, studies involving the carbon system. The original focus area was the North Atlantic Ocean, but over time the geographic extent expanded and CARINA now includes data from the entire Atlantic, the Arctic Ocean, and the Southern Ocean.
DOI: 10.15468/dl.f8464w
title: Occurrence Download

description: A dataset containing 3034 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Qatar",
 "TaxonKey is Acridotheres tristis (Linnaeus, 1766)"
 ]
}

 The dataset includes 3034 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015882-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3334/cdiac/otg.ndp065
title: Partial pressure (or fugacity) of carbon dioxide, dissolved inorganic carbon, temperature, salinity and other variables collected from discrete sample and profile observations using CTD, bottle and other instruments from the KNORR in the North Pacific Ocean and South Pacific Ocean from 1992-10-06 to 1993-04-13 (NCEI Accession 0115156)

description: This dataset includes chemical, discrete sample, physical and profile data collected from KNORR in the North Pacific Ocean and South Pacific Ocean from 1992-10-06 to 1993-04-13 and retrieved during cruise WOCE_P16AP17A, WOCE_P17EP19S and WOCE_P19C. These data include CHLOROFLUOROCARBON-11 (CFC-11), CHLOROFLUOROCARBON-12 (CFC-12), DELTA CARBON-13, DELTA CARBON-14, DELTA HELIUM-3, DISSOLVED INORGANIC CARBON, DISSOLVED OXYGEN, HELIUM, HYDROSTATIC PRESSURE, NEON, NITRATE, NITRITE, PHOSPHATE, Partial pressure (or fugacity) of carbon dioxide, Potential temperature (theta), SALINITY, SILICATE, Tritium (Hydrogen isotope) and WATER TEMPERATURE. The instruments used to collect these data include CTD and bottle. These data were collected by David W. Chipman and Taro Takahashi of Lamont-Doherty Earth Observatory (LDEO) as part of the WOCE_P16AP17A, WOCE_P17EP19S and WOCE_P19C dataset.

The World Ocean Circulation Experiment (WOCE) was a major component of the World Climate Research Program with the overall goal of better understanding the ocean's role in climate and climatic changes resulting from both natural and anthropogenic causes. The CO2 survey took advantage of the sampling opportunities provided by the WOCE Hydrographic Program (WHP) cruises during this period between 1990 and 1998. The final collection covers approximately 23,000 stations from 94 WOCE cruises.
DOI: 10.15468/dd.d2qs84
title: Distribution records of Gymnoscopelus opisthopterus

description: These records of Gymnoscopelus opisthopterus were downloaded from GBIF on 2019-09-11.
DOI: 10.15468/dl.dpahfu
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is BRA.10.17_2",
 "TaxonKey is Aves"
 ]
}

 The dataset includes 7 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015883-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dd.6fgkse
title: Distribution records of Gymnoscopelus braueri

description: These records of Gymnoscopelus braueri were downloaded from GBIF on 2019-09-11.
DOI: 10.3334/cdiac/otg.eq92_spring
title: Partial pressure (or fugacity) of carbon dioxide, dissolved inorganic carbon, pH, alkalinity, temperature, salinity and other variables collected from discrete sample and profile observations using Alkalinity titrator, CTD and other instruments from NOAA Ship MALCOLM BALDRIGE in the North Pacific Ocean and South Pacific Ocean from 1992-02-24 to 1992-05-19 (NCEI Accession 0117498)

description: This dataset includes biological, chemical, discrete sample, physical and profile data collected from NOAA Ship MALCOLM BALDRIGE in the North Pacific Ocean and South Pacific Ocean from 1992-02-24 to 1992-05-19. These data include CHLOROPHYLL A, DELTA CARBON-13, DELTA CARBON-14, DISSOLVED INORGANIC CARBON (DIC), DISSOLVED OXYGEN, Delta Oxygen-18, HYDROSTATIC PRESSURE, NITRATE, NITRITE, PHAEOPHYTIN, Partial pressure (or fugacity) of carbon dioxide - water, Potential temperature (theta), SALINITY, TOTAL ALKALINITY (TA), WATER TEMPERATURE, pH, phosphate and silicate. The instruments used to collect these data include Alkalinity titrator, CTD, Coulometer for DIC measurement, Flask with closed headspace for discrete carbon dioxide (CO2) measurement, bottle and spectrophotometer.

These data were collected by Rik Wanninkhof of NOAA Atlantic Oceanographic and Meteorological Laboratory (AOML) and Richard A. Feely of NOAA Pacific Marine Environmental Laboratory (PMEL) as part of the EQ92_SPRING dataset. CDIAC associated the following cruise ID(s) with this dataset: EQ92_SPRING
DOI: 10.15468/dd.vuusyj
title: Distribution records of Gymnoscopelus nicholsi

description: These records of Gymnoscopelus nicholsi were downloaded from GBIF on 2019-09-11.
DOI: 10.7289/v55m63mf
title: Dissolved inorganic carbon, total alkalinity, nitrate, phosphate, temperature and other variables collected from time series observations at Heron Island Reef Flat from 2010-06-01 to 2010-12-13 (NCEI Accession 0127256)

description: This dataset contains carbonate chemistry and environmental parameters data that were collected from a 200-day time series monitoring on the Heron Island reef flat near the Great Barrier Reef. Understanding the temporal dynamics of present thermal and pH exposure on coral reefs is crucial for elucidating reef response to future global change. Diel ranges in temperature and carbonate chemistry parameters coupled with seasonal changes in the mean conditions define periods during the year when a reef habitat is exposed to anomalous thermal and/or pH exposure. In this study we define anomalous conditions as pH and temperature values that exceed a threshold that we have operationally defined for each variable. We present a 200-day time series from June through December 2010 of carbonate chemistry and environmental parameters measured on the Heron Island reef flat. These data reveal that aragonite saturation state, pH, and pCO2 were primarily modulated by biologically-driven, changes in dissolved organic carbon (DIC) and total alkalinity (TA), rather than salinity and temperature. The largest diel temperature ranges occurred in austral spring, in October (1.5 - 6.6 degrees Celsius) and lowest diel ranges (0.9 - 3.2 degrees Celsius) were observed in July, at the peak of winter. We observed large diel total pH variability, with a maximum range of 7.7 - 8.5 total pH units, with minimum diel average pH values occurring during spring and maximum during fall. As with many other reefs, the nighttime pH minima on the reef flat were far lower than pH values predicted for the open ocean by 2100. DIC and TA both increased from June (end of Fall) to December (end of Spring). Using this high-resolution dataset, we developed exposure metrics of pH and temperature individually for intensity, duration, and severity of low pH and high temperature events, as well as a combined metric. Periods of anomalous temperature and pH exposure were asynchronous on the Heron Island reef flat, which underlines the importance of understanding the dynamics of co-occurrence of multiple stressors on coastal ecosystems.
DOI: 10.6084/m9.figshare.28930571
title: 女性視角下敘事場域轉換——“愛情閑話”締造海派電影《愛情神話》

description: 女性視角下敘事場域轉換——“愛情閑話”締造海派電影《愛情神話》