cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25934/pr00009834
title:  Clinical and molecular profiles of Hepatocellular Carcinoma (HCC)

description: Liver cancer ranks as the sixth most common cancer and the third leading cause of cancer-related deaths globally. Hepatocellular carcinoma (HCC), accounting for over 80% of liver cancer cases, is the primary cause of cancer deaths worldwide. As clinical trials for HCC progress rapidly, numerous studies are focused on novel therapeutic agents that have the potential to improve patient outcomes. However, there is still a lack of evaluation regarding the effectiveness of various treatment options.

The aim of this study is to assess the impact of various clinical and molecular factors on the efficacy of current treatment methods, thereby promoting the development of personalized treatment strategies for HCC. To achieve this, we plan to conduct an analysis using the data from clinical trials that have already been conducted to investigate the prognostic value (how well they can predict disease progress) of HCC's clinical features (such as tumor size, whether it has spread to other places) and molecular markers (such as the presence of particular genes) and their correlation with clinical outcomes.

Participants in each trial will be categorized into different subgroups based on key clinical and molecular characteristics that may be associated with treatment response.  A meta-analysis will be performed, this is where the results of several studies will be combined and analyzed together, to compare the effectiveness of each subgroup for each characteristic or endpoint.

The analysis will compare overall survival (OS) (the percentage of people who are alive five years after diagnosis or start of treatment) and disease-free survival (DFS) (the time between cancer treatment and signs that it has come back) between subgroups. It will also look at pathologic complete response (pCR) (the absence of any active cancer cells after treatment) in patients who received neoadjuvant therapy (treatment given before the main treatment to increase that treatment's chances of success). These analyses will provide insights into patients’ responses to different treatment approaches.

By considering the impact of clinical and molecular factors, this study aims to personalize treatment approaches and ultimately improve patient outcomes. The findings of this study are expected to inform clinical decision-making, enabling more tailored and effective treatment strategies for patients with HCC.
DOI: 10.15468/dl.rtwtty
title: Occurrence Download

description: A dataset containing 312 species occurrences available in GBIF matching the query:
{
 "RecordedBy" : [
 "is Richard Petersson, Anna Asp"
 ]
}

 The dataset includes 312 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016813-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gqfjxs
title: Occurrence Download

description: A dataset containing 155 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is North America",
 "Country is Mexico",
 "TaxonKey is Casuarina equisetifolia L.",
 "Year 2000-2023"
 ]
}

 The dataset includes 155 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016814-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.f72r2t
title: Occurrence Download

description: A dataset containing 155 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is North America",
 "Country is Mexico",
 "TaxonKey is Casuarina equisetifolia L.",
 "Year 2000-2023"
 ]
}

 The dataset includes 155 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016815-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.shh53e
title: Occurrence Download

description: A dataset containing 126 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "OccurrenceStatus is Present",
 "TaxonKey is Psilocybe zapotecorum R.Heim"
 ]
}

 The dataset includes 126 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016817-241107131044228/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.27764853
title: Multifactorial data for IOP, CCT, CMT for males

description: The study's primary aim was to investigate the associations between ocular parameters (intraocular pressure [IOP], central corneal [CCT] and macular [CMT] thickness) and systemic, metabolic, and hormone parameters in a small sample of young healthy men. IOP, CCT, and CMT were measured in nine healthy male volunteers. These measures along with blood glucose, blood pressure, and sex steroid hormones (testosterone, estrogen, and progesterone) were measured twice for each subject and regressed (along with self-reported age, height, and weight) onto IOP, CCT, and CMT.
DOI: 10.5281/zenodo.13137231
title: Genomic profiling of NSCLC tumors with the TruSight Oncology 500 assay provides broad coverage of clinically actionable genomic alterations and detection of known and novel associations between genomic alterations, TMB, and PD-L1

description: Wallen ZD, Ko H, Nesline MK, Tierno M, Roos A, Schnettler E, Husain H, Sathyan P, Caveney B, Eisenberg M, Severson EA, Ramkissoon SH. Genomic profiling of NSCLC tumors with the TruSight Oncology 500 assay provides broad coverage of clinically actionable genomic alterations and detection of known and novel associations between genomic. Front Oncol. 2024 Nov 5;14:1473327. doi: 10.3389/fonc.2024.1473327.

ABSTRACT

Introduction: Matching patients to an effective targeted therapy or immunotherapy is a challenge for advanced and metastatic non-small cell lung cancer (NSCLC), especially when relying on assays that test one marker at a time. Unlike traditional single marker tests, comprehensive genomic profiling (CGP) can simultaneously assess NSCLC tumors for hundreds of genomic biomarkers and markers for immunotherapy response, leading to quicker and more precise matches to therapeutics. Methods: In this study, we performed CGP on 7,606 patients with advanced or metastatic NSCLC using the Illumina TruSight Oncology 500 (TSO 500) CGP assay to show its coverage and utility in detecting known and novel features of NSCLC. Results: Testing revealed distinct genomic profiles of lung adenocarcinoma and squamous cell carcinomas and detected variants with a current targeted therapy or clinical trial in >72% of patient tumors. Known associations between genomic alterations and immunotherapy markers were observed including significantly lower TMB levels in tumors with therapy-associated alterations and significantly higher PD-L1 levels in tumors with ALK, MET, BRAF, or ROS1 driver mutations. Co-occurrence analysis followed by network analysis with gene module detection revealed known and novel co-occurrences between genomic alterations. Further, certain modules of genes with co-occurring genomic alterations had dose-dependent relationships with histology and increasing or decreasing levels of PD-L1 and TMB, suggesting a complex relationship between PD-L1, TMB, and genomic alterations in these gene modules. Discussion: This study is the largest clinical study to date utilizing the TSO 500. It provides an opportunity to further characterize the landscape of NSCLC using this newer technology and show its clinical utility in detecting known and novel facets of NSCLC to inform treatment decision-making.

DATA AVAILABILITY

The data and code presented in the study are deposited in this Zenodo repository, accession number 13137232 (https://zenodo.org/record/13137232). Raw sequencing data were derived from routine clinical testing of real-world patients and cannot be shared publicly. Further data inquiries can be directed to the corresponding author.
DOI: 10.5281/zenodo.13137232
title: Genomic profiling of NSCLC tumors with the TruSight Oncology 500 assay provides broad coverage of clinically actionable genomic alterations and detection of known and novel associations between genomic alterations, TMB, and PD-L1

description: Wallen ZD, Ko H, Nesline MK, Tierno M, Roos A, Schnettler E, Husain H, Sathyan P, Caveney B, Eisenberg M, Severson EA, Ramkissoon SH. Genomic profiling of NSCLC tumors with the TruSight Oncology 500 assay provides broad coverage of clinically actionable genomic alterations and detection of known and novel associations between genomic. Front Oncol. 2024 Nov 5;14:1473327. doi: 10.3389/fonc.2024.1473327.

ABSTRACT

Introduction: Matching patients to an effective targeted therapy or immunotherapy is a challenge for advanced and metastatic non-small cell lung cancer (NSCLC), especially when relying on assays that test one marker at a time. Unlike traditional single marker tests, comprehensive genomic profiling (CGP) can simultaneously assess NSCLC tumors for hundreds of genomic biomarkers and markers for immunotherapy response, leading to quicker and more precise matches to therapeutics. Methods: In this study, we performed CGP on 7,606 patients with advanced or metastatic NSCLC using the Illumina TruSight Oncology 500 (TSO 500) CGP assay to show its coverage and utility in detecting known and novel features of NSCLC. Results: Testing revealed distinct genomic profiles of lung adenocarcinoma and squamous cell carcinomas and detected variants with a current targeted therapy or clinical trial in >72% of patient tumors. Known associations between genomic alterations and immunotherapy markers were observed including significantly lower TMB levels in tumors with therapy-associated alterations and significantly higher PD-L1 levels in tumors with ALK, MET, BRAF, or ROS1 driver mutations. Co-occurrence analysis followed by network analysis with gene module detection revealed known and novel co-occurrences between genomic alterations. Further, certain modules of genes with co-occurring genomic alterations had dose-dependent relationships with histology and increasing or decreasing levels of PD-L1 and TMB, suggesting a complex relationship between PD-L1, TMB, and genomic alterations in these gene modules. Discussion: This study is the largest clinical study to date utilizing the TSO 500. It provides an opportunity to further characterize the landscape of NSCLC using this newer technology and show its clinical utility in detecting known and novel facets of NSCLC to inform treatment decision-making.

DATA AVAILABILITY

The data and code presented in the study are deposited in this Zenodo repository, accession number 13137232 (https://zenodo.org/record/13137232). Raw sequencing data were derived from routine clinical testing of real-world patients and cannot be shared publicly. Further data inquiries can be directed to the corresponding author.
DOI: 10.15468/dl.nvxdkz
title: Occurrence Download

description: A dataset containing 239 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "Geometry POLYGON((-818.22647 19.34469,-818.23713 19.33976,-818.27027 19.32601,-818.27174 19.29492,-818.26438 19.28068,-818.25739 19.27348,-818.25113 19.26618,-818.24009 19.26618,-818.22721 19.26618,-818.21764 19.2707,-818.21837 19.28008,-818.21948 19.28946,-818.21617 19.29815,-818.21543 19.30996,-818.2088 19.32073,-818.20439 19.32976,-818.20328 19.3433,-818.22647 19.34469))",
 "HasGeospatialIssue is false",
 "StateProvince is Tlaxcala",
 "TaxonKey is Lepidoptera"
 ]
}

 The dataset includes 239 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016819-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vvgaw2
title: Occurrence Download

description: A dataset containing 18498 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Pomatoschistus microps (Krøyer, 1838)"
 ]
}

 The dataset includes 18498 records from 160 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016820-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.57745/6oufyf
title: 05-CONSORTIUM_PROPAGATION.7z

description: Metabarcoding analysis of propagated bacterial consortium: raw data, abundance table and R scripts.
DOI: 10.57745/ddiwgo
title: 03-KINETICS.7z

description: Growth kinetics of bacteria by enumeration and R scripts.
DOI: 10.57745/hdvyfn
title: 04-COMPETITION.7z

description: Bacterial enumerations in competition experiments and R scripts.
DOI: 10.57745/yibiwz
title: 01-PARTICLE_SIZE_DISTRIBUTIONS.7z

description: Raw data from granulomorphometric analysis of invert emulsions and R scripts.
DOI: 10.57745/ymyheq
title: 02-INOCULUM_LEVELS.7z

description: Bacterial enumerations to investigate the effect of inoculum levels on bacterial growth and competition, and R scripts
DOI: 10.57745/wmyaen
title: README.pptx

description: Description of files and folder tree.
DOI: 10.15468/dl.h2me78
title: Occurrence Download

description: A dataset listing the 63 species recorded in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is Colombia",
 "Geometry POLYGON((-74.22318 3.34248,-74.35327 3.13901,-74.2065 2.83547,-73.89629 2.7354,-73.56607 2.90552,-73.58942 3.11566,-73.71617 3.40252,-73.80956 3.55596,-74.07975 3.49926,-74.22318 3.34248))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Squamata"
 ]
}

 The dataset's 63 records were derived from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016812-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25387/g3.25893463
title: Supplemental Material for Ragasa et al., 2024

description: Copper has been widely used as a main component in fungicides due to its versatility and effectiveness. However, overuse of copper-based fungicides may alter local biodiversity and force the selection of organisms that are tolerant to copper toxicity. These copper-tolerant fungi may proliferate and cause damage to economically important crops. Since the mechanisms of copper tolerance in fungal pathogens remain unclear, there is a need to investigate survival mechanisms of these fungi in high copper. Here, we aim to determine genes related to the high copper tolerance of a <em>Fusarium oxysporum</em> strain isolated from a <em>Solanum nigrum</em> plant growing in a high copper environment. The existence of a copper-tolerant Fusarium species variant raises concerns regarding the ability of Fusarium species to develop an adaptive mechanism to tolerate copper-based fungicides and cause damage to agricultural crops.
DOI: 10.25387/g3.25893463.v1
title: Supplemental Material for Ragasa et al., 2024

description: Copper has been widely used as a main component in fungicides due to its versatility and effectiveness. However, overuse of copper-based fungicides may alter local biodiversity and force the selection of organisms that are tolerant to copper toxicity. These copper-tolerant fungi may proliferate and cause damage to economically important crops. Since the mechanisms of copper tolerance in fungal pathogens remain unclear, there is a need to investigate survival mechanisms of these fungi in high copper. Here, we aim to determine genes related to the high copper tolerance of a <em>Fusarium oxysporum</em> strain isolated from a <em>Solanum nigrum</em> plant growing in a high copper environment. The existence of a copper-tolerant Fusarium species variant raises concerns regarding the ability of Fusarium species to develop an adaptive mechanism to tolerate copper-based fungicides and cause damage to agricultural crops.
DOI: 10.15468/dl.gffwdu
title: Occurrence Download

description: A dataset containing 1606 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (Chile, Argentina)",
 "TaxonKey is Araucaria araucana (Molina) K.Koch"
 ]
}

 The dataset includes 1606 records from 48 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016822-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.57745/jq21vr
title: AccuracyBirdPred_assess_Rproj_V.14.11.zip

description: R project of all codes and associated datasets
DOI: 10.15468/dl.b48edu
title: Occurrence Download

description: A dataset listing the 1 species recorded in GBIF matching the query:
{
 "and" : [
 "Continent is North America",
 "Country is Mexico",
 "TaxonKey is Casuarina equisetifolia L.",
 "Year 2000-2023"
 ]
}

 The dataset's 1 records were derived from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016816-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9n35zt
title: Occurrence Download

description: A dataset containing 407914 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Megaptera novaeangliae (Borowski, 1781)"
 ]
}

 The dataset includes 407914 records from 590 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016801-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.12685123
title: Classical Tibetan Verbal Paradigms

description: This is a collection of verb paradigms in Classical Tibetan (Written Tibetan), conforming to the Paralex (https://www.paralex-standard.org) standard. The metadata conforms to the Frictionless (https://frictionlessdata.io/) standard. Datafiles are encoded as csv files.
DOI: 10.15468/dl.6rfqv6
title: Occurrence Download

description: A dataset containing 467 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "TaxonKey is Fraxinus uhdei (Wenz.) Lingelsh.",
 "Year 2000-2023"
 ]
}

 The dataset includes 467 records from 29 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016823-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.12685122
title: Classical Tibetan Verbal Paradigms

description: This is a collection of verb paradigms in Classical Tibetan (Written Tibetan), conforming to the Paralex (https://www.paralex-standard.org) standard. The metadata conforms to the Frictionless (https://frictionlessdata.io/) standard. Datafiles are encoded as csv files.
DOI: 10.5281/zenodo.14170906
title: Classical Tibetan Verbal Paradigms

description: This is a collection of verb paradigms in Classical Tibetan (Written Tibetan), conforming to the Paralex (https://www.paralex-standard.org) standard. The metadata conforms to the Frictionless (https://frictionlessdata.io/) standard. Datafiles are encoded as csv files.
DOI: 10.15468/dl.tckxxm
title: Occurrence Download

description: A dataset containing 110713 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Balaenoptera physalus (Linnaeus, 1758)"
 ]
}

 The dataset includes 110713 records from 420 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016804-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tx2tph
title: Occurrence Download

description: A dataset containing 65 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is Ameerega petersi (Silverstone, 1976)"
 ]
}

 The dataset includes 65 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0046343-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.brfry8
title: Occurrence Download

description: A dataset containing 9 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Eleocharis trilateralis Tang & F.T.Wang"
 ]
}

 The dataset includes 9 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035418-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qkk2wm
title: Occurrence Download

description: A dataset containing 177411 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "Country is Dominican Republic",
 "Country is Haiti"
 ]
 },
 "TaxonKey is Plantae"
 ]
}

 The dataset includes 177411 records from 204 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009542-190918142434337/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.33wk22
title: Occurrence Download

description: A dataset containing 48 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Begonia horticola Irmsch."
 ]
}

 The dataset includes 48 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0053797-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ccr8n3
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Dryopteris pseudoparasitica Alderw."
 ]
}

 The dataset includes 6 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035484-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.lfxvnz
title: Occurrence Download

description: A dataset containing 26052 species occurrences available in GBIF matching the query:
{
 "or" : [
 "TaxonKey is Metachirus nudicaudatus (É.Geoffroy Saint-Hilaire, 1803)",
 "TaxonKey is Tayassu pecari (Link, 1795)",
 "TaxonKey is Eira barbara (Linnaeus, 1758)",
 "TaxonKey is Leopardus pardalis (Linnaeus, 1758)",
 "TaxonKey is Herpailurus yagouaroundi (É.Geoffroy Saint-Hilaire, 1803)",
 "TaxonKey is Panthera onca (Linnaeus, 1758)",
 "TaxonKey is Ateles geoffroyi Kuhl, 1820",
 "TaxonKey is Nasua narica (Linnaeus, 1766)",
 "TaxonKey is Tamandua mexicana (Saussure, 1860)"
 ]
}

 The dataset includes 26052 records from 283 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009554-190918142434337/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.