cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.7931445
title: CREMP: Conformer-Rotamer Ensembles of Macrocyclic Peptides for Machine Learning

description: CREMP: A resource generated for the rapid development and evaluation of machine learning models for macrocyclic peptides. CREMP contains 36,198 unique macrocyclic peptides and their high-quality structural ensembles generated using the Conformer-Rotamer Ensemble Sampling Tool (CREST). Altogether, this dataset contains nearly 31.3 million unique macrocycle geometries, each annotated with energies derived from semi-empirical tight-binding DFT calculations. We anticipate that this dataset will enable the development of machine learning models that can improve peptide design and optimization for novel therapeutics. We provide the data in two available formats, either as Python pickle files, which provide quick read access with RDKit version 2022.09.5 or later, and as text-based SDF files with associated metadata in JSON format. Each file is named based on its amino acid sequence, with residues separated by periods, using standard one-letter codes with lowercase letters representing D-amino acids and "Me" prefixes representing <em>N</em>-methylated amino acids. The sequences are in no particular order, e.g., "C.R.E.M.P" and "R.E.M.P.C" correspond to the same peptide macrocycle. The filename extensions are ".pickle", ".sdf", and ".json". Each file in the “pickle” folder contains a Python dictionary with amino acid sequence, SMILES, CREST metadata, and a single RDKit molecule object containing all conformers. All files in the folder were compressed into a single “pickle.tar.gz” archive. In the “sdf_and_json” folder, each individual SDF file contains all conformers, each associated with its own JSON file that contains CREST metadata. Similarly, all are compressed into another single archive, “sdf_and_json.tar.bz2”. A single summary CSV file is also provided containing ”sequence”, “smiles”, “num_monomers”, “num_atoms”, “num_heavy_atoms”, along with the CREST metadata “totalconfs”, “uniqueconfs”, “lowestenergy”, “poplowestpct”, “temperature”, “ensembleenergy”, “ensembleentropy”, and “ensemblefreeenergy”. The number of unique conformers with different 3D structures is given by “uniqueconfs”, while “totalconfs” includes the number of rotamers in addition. The unzipped sizes of the archives are approximately 32 GB for "pickle.tar.gz" and 210 GB for "sdf_and_json.tar.bz2".
DOI: 10.5281/zenodo.8010582
title: CREMP: Conformer-rotamer ensembles of macrocyclic peptides for machine learning

description: CREMP: A resource generated for the rapid development and evaluation of machine learning models for macrocyclic peptides. CREMP contains 36,198 unique macrocyclic peptides and their high-quality structural ensembles generated using the Conformer-Rotamer Ensemble Sampling Tool (CREST). Altogether, this dataset contains nearly 31.3 million unique macrocycle geometries, each annotated with energies derived from semi-empirical tight-binding DFT calculations. We anticipate that this dataset will enable the development of machine learning models that can improve peptide design and optimization for novel therapeutics.

We provide the data in two available formats, either as Python pickle files, which provide quick read access with RDKit version 2022.09.5 or later, and as text-based SDF files with associated metadata in JSON format. Each file is named based on its amino acid sequence, with residues separated by periods, using standard one-letter codes with lowercase letters representing D-amino acids and "Me" prefixes representing N-methylated amino acids. The sequences are in no particular order, e.g., "C.R.E.M.P" and "R.E.M.P.C" correspond to the same peptide macrocycle. The filename extensions are ".pickle", ".sdf", and ".json".

Each file in the “pickle” folder contains a Python dictionary with amino acid sequence, SMILES, CREST metadata, and a single RDKit molecule object containing all conformers. All files in the folder were compressed into a single “pickle.tar.gz” archive. In the “sdf_and_json” folder, each individual SDF file contains all conformers, each associated with its own JSON file that contains CREST metadata. Similarly, all are compressed into another single archive, “sdf_and_json.tar.bz2”. A single summary CSV file is also provided containing ”sequence”, “smiles”, “num_monomers”, “num_atoms”, “num_heavy_atoms”, along with the CREST metadata “totalconfs”, “uniqueconfs”, “lowestenergy”, “poplowestpct”, “temperature”, “ensembleenergy”, “ensembleentropy”, and “ensemblefreeenergy”. The number of unique conformers with different 3D structures is given by “uniqueconfs”, while “totalconfs” includes the number of rotamers in addition.

The unzipped sizes of the archives are approximately 32 GB for "pickle.tar.gz" and 210 GB for "sdf_and_json.tar.bz2". If you encounter errors when trying to load the pickle files, please make sure your RDKit version is at least 2022.09.5. If that doesn't work, try other Python versions.
description: This version fixes the corrupted pickle.tar.gz file.
DOI: 10.6084/m9.figshare.26599879
title: Additional file 1 of Identification of TIMP1 as an inflammatory biomarker associated with temporal lobe epilepsy based on integrated bioinformatics and experimental analyses

description: Additional file 1: Table S1. Differentially expressed genes in the IRGcluster A group and IRGcluster B group.
DOI: 10.6084/m9.figshare.26568163.v1
title: Additional file 3 of Comparative analysis of pathogen distribution in patients with fracture-related infection and periprosthetic joint infection: a retrospective study

description: Additional file 3: Supplemental table 3. Analysis of drug resistance rates and sensitivity rates of Gram-positive cocci in PJI.
DOI: 10.25934/pr00009911
title: Prognosis of inoperable patients after preoperative atezolizumab administration: A post hoc analysis of Lung Cancer Mutation Consortium (LCMC) 3

description: 
Every year, about 2.2 million people find out they have lung cancer all over the world. It's the number one cancer that causes people to die, affecting both men and women. There are two main types of lung cancer, but the one most people get is called non-small cell lung cancer (NSCLC). Sadly, when many people find out they have NSCLC, it's already at a tough stage to treat, and their chances of getting better aren't great. There's a special medicine called immune checkpoint inhibitor (ICI), which has helped some people a lot before they have surgery to remove the cancer. But, there's a chance it might make it so they can't have their surgery as planned.

There was a study called Lung Cancer Mutation Consortium (LCMC) 3 that looked at how safe and effective a specific ICI, atezolizumab, is for people who can have surgery to remove their lung cancer. The study found that this medicine was safe and did a good job according to the main goal they were looking at, which is how much it could shrink the cancer before surgery. But, we don't know much about what happens to people who can't have surgery after taking the medicine or how other medicines they might be taking affect how well atezolizumab works.

The main goals of this study are to find out what happens to people who can't have surgery after getting atezolizumab and how other medicines they take might make atezolizumab work better or worse.

To do this, we're going to look back at the data from the LCMC3 study. We'll compare two groups of people: those who had surgery and those who didn't. We're especially interested in how long people lived without their cancer getting worse and their overall survival. We'll also look into why some people couldn't have surgery, whether their cancer spread far or stayed close, and where it spread. We're also curious about how taking other medicines might have played a role in how well the atezolizumab worked.

This study is important because it might help doctors figure out the best way to treat lung cancer that's in a tough stage to treat, using medicines like atezolizumab before surgery.
DOI: 10.6084/m9.figshare.26599879.v1
title: Additional file 1 of Identification of TIMP1 as an inflammatory biomarker associated with temporal lobe epilepsy based on integrated bioinformatics and experimental analyses

description: Additional file 1: Table S1. Differentially expressed genes in the IRGcluster A group and IRGcluster B group.
DOI: 10.6084/m9.figshare.26568169.v1
title: Additional file 5 of Comparative analysis of pathogen distribution in patients with fracture-related infection and periprosthetic joint infection: a retrospective study

description: Additional file 5: Supplemental table 5. Analysis of drug resistance rates and sensitivity rates of Gram-positive cocci in FRI.
DOI: 10.15468/dl.frnuql
title: Occurrence Download

description: A dataset containing 198358 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lythrum salicaria L."
 ]
}

 The dataset includes 198358 records from 485 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005121-160118175350007/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dcakk3
title: Occurrence Download

description: A dataset containing 1101 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Monitoreo y seguimiento de fauna terrestre para el AID y AII de la Central Hidroeléctrica de Calima. 2017-B."
 ]
}

 The dataset includes 1101 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0042716-231002084531237/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.uepj4q
title: Occurrence Download

description: A dataset containing 1115 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Gelidium spinosum (S.G.Gmelin) P.C.Silva",
 "Geometry POLYGON((-24.368297 72.843754,-24.368297 8.883842,44.731251 8.883842,44.731251 72.843754,-24.368297 72.843754))",
 "EventDate is greater than or equal to 1980-01-01"
 ]
}

 The dataset includes 1115 records from 29 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005121-160311141623029/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nmqsvv
title: Occurrence Download

description: A dataset containing 1453 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Composición florística y estructura de una parcela permanente en bosques secos tropicales de afloramiento rocoso del Parque Nacional Natural El Tuparro"
 ]
}

 The dataset includes 1453 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0042714-231002084531237/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.blutt1
title: Occurrence Download

description: A dataset containing 244 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Parthenium argentatum A.Gray",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 244 records from 28 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005121-170627171947987/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vzp35f
title: Occurrence Download

description: A dataset containing 21090 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Fauna y flora asociada al proyecto piloto de investigación integral - PPII Platero, departamento de Santander"
 ]
}

 The dataset includes 21090 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0042720-231002084531237/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pv7tew
title: Occurrence Download

description: A dataset containing 844 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Amblyrhynchus cristatus Bell, 1825"
 ]
}

 The dataset includes 844 records from 41 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005121-170826194755519/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.snfnrn
title: Occurrence Download

description: A dataset containing 472 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Hibiscus arnottianus A.Gray"
 ]
}

 The dataset includes 472 records from 41 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0055786-231002084531237/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dq9fnl
title: Occurrence Download

description: A dataset containing 1304 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ficus deltoidea Jack"
 ]
}

 The dataset includes 1304 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005121-171025204727650/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gj3s8j
title: Occurrence Download

description: A dataset containing 11344 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Colección de Plantas Vasculares del Herbario Forestal UDBC \"Gilberto Emilio Mahecha Vega\""
 ]
}

 The dataset includes 11344 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0042730-231002084531237/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zbrcis
title: Occurrence Download

description: A dataset containing 7790 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Orconectes limosus (Rafinesque, 1817)"
 ]
}

 The dataset includes 7790 records from 69 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005121-171219132708484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fwp2p4
title: Occurrence Download

description: A dataset containing 2118 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Avifauna de la Reserva de la Biosfera La Sepultura, Chiapas"
 ]
}

 The dataset includes 2118 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0160609-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.w0hp8x
title: Occurrence Download

description: A dataset containing 7823 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Laminaria digitata (Huds.) J.V.Lamour.",
 "Geometry POLYGON((-24.368297 72.843754,-24.368297 8.883842,44.731251 8.883842,44.731251 72.843754,-24.368297 72.843754))",
 "EventDate is greater than or equal to 1980-01-01"
 ]
}

 The dataset includes 7823 records from 55 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005122-160311141623029/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.td4yfc
title: Occurrence Download

description: A dataset containing 6147 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Aratinga auricapillus (Kuhl, 1820))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
}

 The dataset includes 6147 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0160625-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.lnwv3v
title: Occurrence Download

description: A dataset containing 5959 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pennisetum clandestinum Hochst. ex Chiov."
 ]
}

 The dataset includes 5959 records from 102 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005122-160509122628363/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4kpnex
title: Occurrence Download

description: A dataset containing 54 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cyrtandra tahuatensis Fosberg & Sachet"
 ]
}

 The dataset includes 54 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0160614-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vezq7r
title: Occurrence Download

description: A dataset containing 3459 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Rhizophora mangle L."
 ]
}

 The dataset includes 3459 records from 173 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005122-160623103540712/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.t3mxt9
title: Occurrence Download

description: A dataset containing 23682 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Setophaga chrysoparia (P.L.Sclater & Salvin, 1860)",
 "HasCoordinate is True",
 "Year is greater than or equal to 2000",
 "Year is less than or equal to 2021",
 "Month is greater than or equal to January",
 "Month is less than or equal to December",
 "HasGeospatialIssue is False"
 ]
}

 The dataset includes 23682 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0160638-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fg8spo
title: Occurrence Download

description: A dataset containing 135 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Total foraminifera counts of multinet M21/3_MSN688"
 ]
}

 The dataset includes 135 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005122-160822134323880/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bxuq7e
title: Occurrence Download

description: A dataset containing 396 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Interacciones entre Corales y Céspedes algales en el atolón Albuquerque durante la Expedición Seaflower 2018 - Proyecto Colombia BIO"
 ]
}

 The dataset includes 396 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0042721-231002084531237/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5517/ccdc.csd.cc2bn54b
title: CCDC 2164331: Experimental Crystal Structure Determination

description: Related Article: Maria Loizou, Petri Papaphilippou, Manolis Vlasiou, Maria Spilia, Dimitrios Peschos, Yannis V. Simos, Anastasios D. Keramidas, Chryssoula Drouza|2022|J.Inorg.Biochem.|235|111911|doi:10.1016/j.jinorgbio.2022.111911
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.15468/dl.vymjt6
title: Occurrence Download

description: A dataset containing 16 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Dypsis cabadae (H.E.Moore) Beentje & J.Dransf."
 ]
}

 The dataset includes 16 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005122-170627171947987/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nf6c94
title: Occurrence Download

description: A dataset containing 994 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Artibeus phaeotis (Miller, 1902)",
 "Country is Mexico",
 "HasGeospatialIssue is false",
 "HasCoordinate is true"
 ]
}

 The dataset includes 994 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005123-150528172251762/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cj39f5
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cyrtandra toreniiflora B.L.Burtt"
 ]
}

 The dataset includes 4 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0160649-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qksfkf
title: Occurrence Download

description: A dataset containing 17 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ajania pacifica (Nakai) K.Bremer & Humphries"
 ]
}

 The dataset includes 17 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005123-150922153815467/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wkmnzd
title: Occurrence Download

description: A dataset containing 40 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is United States of America",
 "GadmGid is USA.38_1",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "PublishingOrg is one of (ac5e8480-3714-11da-bc2e-b8a03c50a862, 1e26a630-7203-11dc-a0d8-b8a03c50a862)",
 "TaxonKey is Diadasia diminuta (Cresson, 1879)"
 ]
}

 The dataset includes 40 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0160659-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.z9h2um
title: Occurrence Download

description: A dataset containing 40 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-0.56221 44.84914,-0.55571 44.84549,-0.55167 44.84806,-0.55709 44.85205,-0.56221 44.84914))",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 40 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0160619-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.p33rhk
title: Occurrence Download

description: A dataset containing 128 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Feresa attenuata Gray, 1874"
 ]
}

 The dataset includes 128 records from 23 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005123-160118175350007/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.