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

description: A dataset listing the 2341344 species recorded in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset's 2341344 records were derived from 36001 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0357501-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5522/04/25476172
title: Postsubicular head direction cell recordings following dLGN lesions (rats)

description: These files contain the (1) MATLAB code, and (2) raw and processed files pertaining to the publication by Street and Jeffery, " ".(1): The MATLAB code uploaded here is carbon copied in the state it was when these analyses were run on our local analysis machine(s). A list of function descriptions and use can be found in \Code\Function descriptions.txt. Up-to-date and more curated code will be made available on https://github.com/bejamz.(2): Data files are organised as follows:Data from animal is organised into a distinct folder named after the animal (e.g. \R777\). In each animal folder, a metadata xls sheet exists (e.g. R777_MetaData.xlsx) containing filepaths and cell IDs for each recorded single unit, alongside pertinent trial information for that session (e.g. cylinder rotations). Note that filepaths for data files are given as absolute Windows directory paths and will need to be edited to access on other systems. Two summary statistics .mat files exist in the top level directory for each animal: SessionInfo.mat (information about session statistics, movement, etc.) and CellInfo.mat (information about cell statistics, firing rates, DIC, etc.).Subdirectories in each animal folder are as follows:\[Animal name]\Screening: These are screening recordings taken from a distinct room when identifying head direction cells, and before experimental recordings began.\[Animal name]\Experiments\[Date]: These directories contain the raw Axona recording files for experimental sessions (trials 1-8, usually), named for instance as R777_20180404_Tr1.\[Animal name]\Histology: These contain the raw microscopy images captured for each slice through the dLGN, alongside .txt files containing coordinate traces of the dLGN or the lesion for the left or the right hemisphere.\[Animal name]\Analysis\[CellID]: This is the analysis of an individual cell. Importantly, CellData.mat contains pertinent information for that individual cell recorded through all sessions, including its spike timestamps, tuning curve, Rayleigh vector lengths, and other general cell and session statistics.<br>
DOI: 10.5522/04/25476172.v1
title: Postsubicular head direction cell recordings following dLGN lesions (rats)

description: These files contain the (1) MATLAB code, and (2) raw and processed files pertaining to the publication by Street and Jeffery, " ".(1): The MATLAB code uploaded here is carbon copied in the state it was when these analyses were run on our local analysis machine(s). A list of function descriptions and use can be found in \Code\Function descriptions.txt. Up-to-date and more curated code will be made available on https://github.com/bejamz.(2): Data files are organised as follows:Data from animal is organised into a distinct folder named after the animal (e.g. \R777\). In each animal folder, a metadata xls sheet exists (e.g. R777_MetaData.xlsx) containing filepaths and cell IDs for each recorded single unit, alongside pertinent trial information for that session (e.g. cylinder rotations). Note that filepaths for data files are given as absolute Windows directory paths and will need to be edited to access on other systems. Two summary statistics .mat files exist in the top level directory for each animal: SessionInfo.mat (information about session statistics, movement, etc.) and CellInfo.mat (information about cell statistics, firing rates, DIC, etc.).Subdirectories in each animal folder are as follows:\[Animal name]\Screening: These are screening recordings taken from a distinct room when identifying head direction cells, and before experimental recordings began.\[Animal name]\Experiments\[Date]: These directories contain the raw Axona recording files for experimental sessions (trials 1-8, usually), named for instance as R777_20180404_Tr1.\[Animal name]\Histology: These contain the raw microscopy images captured for each slice through the dLGN, alongside .txt files containing coordinate traces of the dLGN or the lesion for the left or the right hemisphere.\[Animal name]\Analysis\[CellID]: This is the analysis of an individual cell. Importantly, CellData.mat contains pertinent information for that individual cell recorded through all sessions, including its spike timestamps, tuning curve, Rayleigh vector lengths, and other general cell and session statistics.<br>
DOI: 10.6084/m9.figshare.26348452
title: Supplementary Table S1-S6

description: <b>Supplementary Table S1-S6</b><b>Table S1. Primers associated with qRT-PCR validation of DEGs compared between</b><b><i> Mycoplasma bovis</i></b><b> NX114 VS PG45</b><b>Table S2. DEGs of </b><b><i>Mycoplasma bovis</i></b><b> NX114 vs PG45</b><b>Table S3. Database annotation of DEGs in</b><b><i> Mycoplasma bovis</i></b><b> NX114 vs PG45</b><b>Table S4. DEGs of</b><b><i> Mycoplasma bovis</i></b><b> NX114 vs PG45</b><b>Table S5. GO annotation of DEPs in </b><b><i>Mycoplasma bovis</i></b><b> NX114 vs PG45</b><b>Table S6. KEGG annotation of DEPs in</b><b><i> Mycoplasma bovis</i></b><b> NX114 vs PG45</b>
DOI: 10.15468/dl.b6mz6u
title: Occurrence Download

description: A dataset containing 500808 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Neptune Deep-Sea Microfossil Occurrence Database"
 ]
}

 The dataset includes 500808 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032516-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.12794908
title: nicator_chloris_decontaminated_FSCR.fasta.gz

description: .
DOI: 10.5281/zenodo.12794909
title: nicator_chloris_decontaminated_FSCR.fasta.gz

description: .
DOI: 10.15468/dl.vy367b
title: Occurrence Download

description: A dataset containing 11 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Thailand",
 "DatasetKey is iNaturalist Research-grade Observations",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Oryzias javanicus (Bleeker, 1854)",
 "Year 2000-2024"
 ]
}

 The dataset includes 11 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032521-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.1594/pangaea.959991
title: Benthic foraminifera census data of sediment core GeoTü SL78

description: The data set contains census counts of deep-sea benthic foraminifera from sediment core GeoTü SL78. Given are counted individuals of benthic foraminiferal taxa versus sediment depth in cm below sea floor. The counts are based on representative splits of the size fraction &gt;125 µm. The original counting was performed in 2010, a taxonomic revision was carried out in 2022. Gravity core GeoTü SL78, also referred to as M40/4-SL78-3, was retrieved during R.V. METEOR cruise M40/4 in 1998 (Hieke et al., 1999) from the upper bathyal Strait of Sicily in the central Mediterranean Sea, at 37°02.2'N, 13°11.4'E, 467 m water depth, core recovery 5.32 m. The sediment core was retrieved for the reconstruction of circulation and productivity changes in the in the eastern and central Mediterranean Sea during the last glacial and Holocene with particular focus on the formation of sapropel S1.
DOI: 10.1594/pangaea.960020
title: Benthic foraminifera census data of the Holocene section of sediment core GeoTü SL99

description: The data set contains census counts of deep-sea benthic foraminifera from the Holocene section of sediment core GeoTü SL99. Given are counted individuals of benthic foraminiferal taxa versus sediment depth in cm below sea floor. The counts are based on representative splits of the size fraction &gt;125 µm. The original counting was performed in 2020, a taxonomic revision was carried out in 2022. Gravity core GeoTü SL99, was retrieved at station no. 564 during R.V. METEOR cruise M51/3 in 2001 (Hemleben et al., 2003) from the southwestern Levantine Basin in the eastern Mediterranean Sea, at 33°00.0'N, 23°37.6'E, 1476 m water depth, core recovery 5.32 m. The sediment core was retrieved for the reconstruction of circulation and productivity changes in the eastern Mediterranean Sea during the late Quaternary with particular focus on sapropel formation.
DOI: 10.1594/pangaea.960021
title: Benthic foraminifera census data of sediment core GeoTü SL99

description: The data set contains census counts of deep-sea benthic foraminifera from the Late Quaternary section of sediment core GeoTü SL99. Given are counted individuals of benthic foraminiferal taxa versus sediment depth in cm below sea floor. The counts are based on representative splits of the size fraction &gt;125 µm. The original counting was performed in 2020, a taxonomic revision was carried out in 2022. Gravity core GeoTü SL99, was retrieved at station no. 564 during R.V. METEOR cruise M51/3 in 2001 (Hemleben et al., 2003) from the southwestern Levantine Basin in the eastern Mediterranean Sea, at 33°00.0'N, 23°37.6'E, 1476 m water depth, core recovery 5.32 m. The sediment core was retrieved for the reconstruction of circulation and productivity changes in the eastern Mediterranean Sea during the late Quaternary with particular focus on sapropel formation.
DOI: 10.1594/pangaea.960060
title: Benthic foraminifera census data of sediment core GeoTü SL167

description: The data set contains census counts of deep-sea benthic foraminifera from the Late Quaternary section of sediment core GeoTü SL167. Given are counted individuals of benthic foraminiferal taxa versus sediment depth in cm below sea floor. The counts are based on representative splits of the size fraction &gt;125 µm. The original counting and taxonomic revision were carried out in 2022. Gravity core GeoTü SL167, was retrieved at station no. 960 during R.V. METEOR cruise M74/1b in 2007 (Bohrmann et al., 2010) from the northwestern Arabian Sea off Oman, at 22°37.2'N, 59°41.5'E, 774 m water depth, core recovery 7.39 m. The sediment core was retrieved for the reconstruction of circulation and productivity changes in the eastern Mediterranean Sea during the late Quaternary with particular focus on changes in the Indian monsoon system.
DOI: 10.1594/pangaea.962113
title: Physical oceanography, anthropogenic tracers and noble gases during Maria S. Merian cruise MSM73

description: The bottle data on cruise MSM73 contain measurements of pressure, temperature, salinity and oxygen (derived from CTD values at the location of closing bottles) and direct measurements of oxygen, CFC-12, SF6 and the noble gases helium and neon. The data were collected with the research vessel Maria S. Merian. Region: subpolar North Atlantic, 11°W-54°W, 44°N-61°N, Ports: Cadiz - St. John's, Date: April 06 - May 22, 2018. The bottle data were collected by an SBE 32 water sampler system in connection with a SBE 911 plus CTD. The CTD was mounted to a metal frame with 22 Niskin bottles of 10 l volume, which was lowered from the sea surface down to 10 m above the seafloor. Pressure, temperature, salinity and oxygen data from the CTD were recorded at the time when closing the bottles. In addition, direct samples of salinity and oxygen from the water bottles have been taken to calibrate the CTD data. The accuracy of the CTD measurements is: 1 dbar for pressure, 0.001 °C for temperature, 0.003 for salinity, 4.0 µmol/kg for oxygen. The oxygen samples from the Niskin bottles have been analysed by Winkler titration with an accuracy of 2.5 µmol/kg. In addition, samples for the analyses of CFC-12 and SF6 have been analysed on board by a capillary-chromatographic system with electron capture detector. This device is an advancement from the one described in: Bulsiewicz, K., H. Rose, O. Klatt, A. Putzka, and W. Roether (1998), A capillary -column chromatographic system for efficient chlorofluorocarbon measurement in ocean waters, J. Geophys, Res., 103, 15959-15970. CFC-12 and SF6 values are reported on the SIO-98 scale. Accuracy is 2.5% for SF6 and 2.0% for CFC-12, detection limt 0.01 fmol/kg for SF6 and 0.002 pmol/kg for CFC-12. The samples for the noble gas measurements were stored in copper tubes. The gas from the tubes was extracted with a ultra high vacuum extraction system and then analysed with respect to helium and neon at the mass spectrometer facility at the University of Bremen (department of oceanography). Analytical precision based on duplicate samples is 0.3% for helium and 0.4% for neon. The Bremen mass spectrometer facility has been described in detail in: Sültenfuß, J., M. Rhein, and W. Roether (2009), The Bremen Mass Spectrometric Facility for the measurement of helium isotopes, neon, and tritium in water. Isotopes in Environmental and Health Studies, 45(2), 1-13, doi:10.1080/10256010902871929.
DOI: 10.1594/pangaea.945966
title: benthic foraminifera of sediment core DA17-NG-ST-08-092G
DOI: 10.15468/dl.xkwdkw
title: Occurrence Download

description: A dataset containing 13 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pristimera biholongii N.Hallé"
 ]
}

 The dataset includes 13 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032523-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ay4wcx
title: Occurrence Download

description: A dataset containing 244 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Dendrobium chrysotoxum Lindl."
 ]
}

 The dataset includes 244 records from 40 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032522-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.1594/pangaea.602492
title: Grain size graphs and photographic images of sediment core GC-90-1/TG-5
DOI: 10.1594/pangaea.602490
title: Grain size graphs and photographic images of sediment core GC-90-1/TG-20
DOI: 10.1594/pangaea.602493
title: Grain size graphs and photographic images of sediment core GC-90-1/TG-6
DOI: 10.1594/pangaea.602486
title: Grain size graphs and photographic images of sediment core GC-90-1/TG-13
DOI: 10.1594/pangaea.602491
title: Grain size graphs and photographic images of sediment core GC-90-1/TG-24
DOI: 10.15468/dl.hdtb2e
title: Occurrence Download

description: A dataset containing 18 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Dendrobium huoshanense Z.Z.Tang & S.J.Cheng"
 ]
}

 The dataset includes 18 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032524-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.1594/pangaea.602495
title: Grain size graphs and photographic images of sediment core GC-90-1/TG-8
DOI: 10.1594/pangaea.602494
title: Grain size graphs and photographic images of sediment core GC-90-1/TG-7
DOI: 10.1594/pangaea.602488
title: Grain size graphs and photographic images of sediment core GC-90-1/TG-15
DOI: 10.1594/pangaea.602485
title: Grain size graphs and photographic images of sediment core GC-90-1/TG-11
DOI: 10.1594/pangaea.906171
title: High resolution in situ temperatures at 24m water depth across coral reef slopes at Iriomote-jima, Japan
DOI: 10.1594/pangaea.88637
title: GeoB X-ray fluorescence (XRF) core scanner archive
DOI: 10.15468/dl.5tupvz
title: Occurrence Download

description: A dataset containing 699 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Dendrobium nobile Lindl."
 ]
}

 The dataset includes 699 records from 98 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032525-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.1594/pangaea.906187
title: High resolution in situ temperatures across coral reef slopes at 10m water depth in the Gulf of Chiriquí, Panama
DOI: 10.1594/pangaea.906185
title: High resolution in situ temperatures at 40m water depth across coral reef slopes at Iriomote-jima, Japan
DOI: 10.5281/zenodo.10992086
title: Data from the paper "The landscape of biomedical research"

description: Data from the paper "The landscape of biomedical research".

The paper used the PubMed 2020 baseline (download date: 26.01.2021, not available anymore) supplemented with additional files from the 2021 baseline (download date: 27.04.2022, not available anymore), both originally obtained from https://www.nlm.nih.gov/databases/download/pubmed_medline.html, courtesy of the U.S. National Library of Medicine. This data can be found in v2 of this repository (https://zenodo.org/records/7849020).

In the latest version of this repository we provide the PubMed 2024 baseline (download date: 06.02.2024) including all papers until the end of 2023, which is not the main data we analyzed in the paper but an updated version including newer articles. The paper contains two supplementary figures (S9 and S10) with the updated embedding.

The latest version provided here includes the following files:

pubmed_landscape_data_2024.zip, which includes:

- from the PubMed database: article title, journal, PMID, and publication year.

- produced by us: t-SNE embedding X and Y coordinates, label, color, whether the paper is retracted or not (combining PubMed and Retraction Watch information), and affiliation country (from the first affiliation of the first author).

 

pubmed_landscape_abstracts_2024.zip, which includes:

- from the PubMed database: PMID, and paper abstracts.

 

PubMedBERT_embeddings_float16_2024.npy, which includes:

- produced by us: PubMedBERT embeddings of the paper abstracts (numpy.ndarray of shape 23,389,083x768).
DOI: 10.5281/zenodo.12794883
title: Data from the paper "The landscape of biomedical research"

description: Data from the paper "The landscape of biomedical research".

The paper used the PubMed 2020 baseline (download date: 26.01.2021, not available anymore) supplemented with additional files from the 2021 baseline (download date: 27.04.2022, not available anymore), both originally obtained from https://www.nlm.nih.gov/databases/download/pubmed_medline.html, courtesy of the U.S. National Library of Medicine. This data can be found in v2 of this repository (https://zenodo.org/records/7849020).

In the latest version of this repository we provide the PubMed 2024 baseline (download date: 06.02.2024) including all papers until the end of 2023, which is not the main data we analyzed in the paper but an updated version including newer articles. The paper contains two supplementary figures (S9 and S10) with the updated embedding.

The latest version provided here includes the following files:

pubmed_landscape_data_2024_v2.zip, which includes:

- from the PubMed database: article title, journal, PMID, and publication year.

- produced by us: t-SNE embedding X and Y coordinates, label, color, whether the paper is retracted or not (combining PubMed and Retraction Watch information), affiliation country ( from the first affiliation of the first author), and inferred gender (of both first and last author).

(Note: pubmed_landscape_data_2024_v2.zip is identical to pubmed_landscape_data_2024.zip from v3 of this repository, but includes inferred genders additionally.)

 

pubmed_landscape_abstracts_2024.zip, which includes:

- from the PubMed database: PMID, and paper abstracts.

 

PubMedBERT_embeddings_float16_2024.npy, which includes:

- produced by us: PubMedBERT embeddings of the paper abstracts (numpy.ndarray of shape 23,389,083x768).
DOI: 10.5281/zenodo.7695389
title: Data from the paper "The landscape of biomedical research"

description: Data from the paper "The landscape of biomedical research".

The paper used the PubMed 2020 baseline (download date: 26.01.2021, not available anymore) supplemented with additional files from the 2021 baseline (download date: 27.04.2022, not available anymore), both originally obtained from https://www.nlm.nih.gov/databases/download/pubmed_medline.html, courtesy of the U.S. National Library of Medicine. This data can be found in v2 of this repository (https://zenodo.org/records/7849020).

In the latest version of this repository we provide the PubMed 2024 baseline (download date: 06.02.2024) including all papers until the end of 2023, which is not the main data we analyzed in the paper but an updated version including newer articles. The paper contains two supplementary figures (S9 and S10) with the updated embedding.

The latest version provided here includes the following files:

pubmed_landscape_data_2024_v2.zip, which includes:

- from the PubMed database: article title, journal, PMID, and publication year.

- produced by us: t-SNE embedding X and Y coordinates, label, color, whether the paper is retracted or not (combining PubMed and Retraction Watch information), affiliation country ( from the first affiliation of the first author), and inferred gender (of both first and last author).

(Note: pubmed_landscape_data_2024_v2.zip is identical to pubmed_landscape_data_2024.zip from v3 of this repository, but includes inferred genders additionally.)

 

pubmed_landscape_abstracts_2024.zip, which includes:

- from the PubMed database: PMID, and paper abstracts.

 

PubMedBERT_embeddings_float16_2024.npy, which includes:

- produced by us: PubMedBERT embeddings of the paper abstracts (numpy.ndarray of shape 23,389,083x768).
DOI: 10.5281/zenodo.7695390
title: Data from the paper "The landscape of biomedical research"

description: Data from the paper "The landscape of biomedical research" (https://www.biorxiv.org/content/10.1101/2023.04.10.536208v1). The paper used the PubMed 2020 baseline (download date: 26.01.2021, not available anymore) supplemented with additional files from the 2021 baseline (download date: 27.04.2022, not available anymore), both originally obtained from https://www.nlm.nih.gov/databases/download/pubmed_medline.html, courtesy of the U.S. National Library of Medicine. The data provided here includes: - from the PubMed database: article title, journal, PMID, and publication year. - produced by us: t-SNE embedding X and Y coordinates, label, and color.
DOI: 10.5281/zenodo.7849020
title: Data from the paper "The landscape of biomedical research"

description: Data from the paper "The landscape of biomedical research" (https://www.biorxiv.org/content/10.1101/2023.04.10.536208v1). The paper used the PubMed 2020 baseline (download date: 26.01.2021, not available anymore) supplemented with additional files from the 2021 baseline (download date: 27.04.2022, not available anymore), both originally obtained from https://www.nlm.nih.gov/databases/download/pubmed_medline.html, courtesy of the U.S. National Library of Medicine. The data provided here includes the following files: pubmed_landscape_data.zip, which includes: - from the PubMed database: article title, journal, PMID, and publication year. - produced by us: t-SNE embedding X and Y coordinates, label, and color. pubmed_landscape_abstracts.zip, which includes: - from the PubMed database: PMID, and paper abstracts. PubMedBERT_embeddings_float16.npy, which includes: - produced by us: PubMedBERT embeddings of the paper abstracts (numpy.ndarray of shape 20,687,150x768).