cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.31281223
title: <b>Multi-omics profiling of fungal balls in chronic pulmonary aspergillosis patients reveals microbiome dynamics and metabolic adaptations</b>

description: Fungal balls (aspergillomas) are a debilitating complication of chronic pulmonary aspergillosis, but their functional biology as multi-kingdom ecosystems is poorly understood. Through integrated multi-omics analysis of 61 patient-derived fungal balls, we reveal their complex ecology. While <i>Aspergillus fumigatus</i> dominates the fungal niche (59% of patients), bacterial co-colonization is ubiquitous, primarily by <i>Pseudomonas aeruginosa</i> and <i>Haemophilus influenzae</i>. Metabolomics and metatranscriptomics unveil a structured division of labour and active warfare, including metabolic cross-feeding, competition for iron, and reciprocal antagonism via secondary metabolites, such as fumagillin and fumigaclavine C produced by <i>A. fumigatus</i>. Host metabolomics and transcriptomics revealed a potent but dysregulated human immune response, characterized by neutrophil activation and failed resolution. Our findings redefine aspergilloma not as a mere fungal aggregate, but as a resilient polymicrobial biofilm across kingdoms, in which synergistic and antagonistic inter-kingdom interactions drive pathogenesis and chronicity, suggesting new therapeutic strategies targeting the pathogenic consortium.
DOI: 10.6084/m9.figshare.31281223.v1
title: <b>Multi-omics profiling of fungal balls in chronic pulmonary aspergillosis patients reveals microbiome dynamics and metabolic adaptations</b>

description: Fungal balls (aspergillomas) are a debilitating complication of chronic pulmonary aspergillosis, but their functional biology as multi-kingdom ecosystems is poorly understood. Through integrated multi-omics analysis of 61 patient-derived fungal balls, we reveal their complex ecology. While <i>Aspergillus fumigatus</i> dominates the fungal niche (59% of patients), bacterial co-colonization is ubiquitous, primarily by <i>Pseudomonas aeruginosa</i> and <i>Haemophilus influenzae</i>. Metabolomics and metatranscriptomics unveil a structured division of labour and active warfare, including metabolic cross-feeding, competition for iron, and reciprocal antagonism via secondary metabolites, such as fumagillin and fumigaclavine C produced by <i>A. fumigatus</i>. Host metabolomics and transcriptomics revealed a potent but dysregulated human immune response, characterized by neutrophil activation and failed resolution. Our findings redefine aspergilloma not as a mere fungal aggregate, but as a resilient polymicrobial biofilm across kingdoms, in which synergistic and antagonistic inter-kingdom interactions drive pathogenesis and chronicity, suggesting new therapeutic strategies targeting the pathogenic consortium.
DOI: 10.60645/bdc-938i-u385
title: Clinical and Genetic Correlates of the Gut Microbiome and Relation to Cardiometabolic Risk

description: 
The human gut harbors trillions of microbes that play dynamic roles in health. While the microbiome contributes to many cardiometabolic traits by modulating host inflammation and metabolism, there is an incomplete understanding regarding the extent and mechanisms by which individual microbes impact risk and development of cardiovascular disease (CVD). The Framingham Heart Study (FHS) is a multi-generational observational study following participants over decades to identify risk factors for CVD by correlating genetic and phenotypic factors with clinical outcomes. As a large-scale population-based cohort with extensive clinical phenotyping, FHS provides a rich landscape to explore the relationships between the gut microbiome and cardiometabolic traits

Available Data sets

Currently we have the following data set available in the 'Authorized Access' area of dbGaP.

1. Cholesterol Metabolism by Uncultured Human Gut Bacteria Influences Host Cholesterol


This data set, consisting of metagenome FASTQ data from 624 FHS participants, was released in conjunction with PMID: [32544460](https://pubmed.ncbi.nlm.nih.gov/32544460/).
DOI: 10.60645/bdc-eu74-ww1h
title: Framingham Heart Study RNA Sequencing in Postmortem Brain Tissue

description: 
The biology of obesity is complex, involving both environmental and genetic factors and affecting metabolic and endocrine mechanisms in tissues of the gut, adipose, and brain. This study was conducted to identify transcripts in postmortem human brain tissue associated with obesity status. We conducted both large and small RNA sequencing of hypothalamus and nucleus accumbens from postmortem brain tissue samples from Framingham Heart Study participants defined as consistently obese, consistently normal weight as controls based on longitudinal BMI measures or selected without respect to BMI and falling within neither case nor control definition.
DOI: 10.60645/bdc-qc2f-i5e9
title: Framingham Heart Study RNA Sequencing in Postmortem Brain Tissue

description: 
The biology of obesity is complex, involving both environmental and genetic factors and affecting metabolic and endocrine mechanisms in tissues of the gut, adipose, and brain. This study was conducted to identify transcripts in postmortem human brain tissue associated with obesity status. We conducted both large and small RNA sequencing of hypothalamus and nucleus accumbens from postmortem brain tissue samples from Framingham Heart Study participants defined as consistently obese, consistently normal weight as controls based on longitudinal BMI measures or selected without respect to BMI and falling within neither case nor control definition.
DOI: 10.60645/bdc-vf49-m104
title: COVID-19 ACTIV-4 ACUTE: A Multicenter, Adaptive, Randomized Controlled Platform Trial of the Safety and Efficacy of Antithrombotic Strategies in Hospitalized Adults with COVID-19 (ACTIV4A)

description: 
This is a randomized, open label, adaptive platform trial to compare the effectiveness of antithrombotic strategies for prevention of adverse outcomes in COVID-19 positive inpatients.
DOI: 10.60645/bdc-4f2q-q821
title: COVID-19 Outpatient Thrombosis Prevention Trial (ACTIV-4B)

description: 
An adaptive randomized double-blind placebo-controlled platform trial to compare the effectiveness of anticoagulation with antiplatelet agents and with placebo to prevent thrombotic events in patients diagnosed with COVID-19 who are not admitted to hospital as COVID-19 related symptoms are currently stable.
DOI: 10.60645/bdc-y577-2cdu
title: National Sleep Research Resource (NSRR): Cleveland Family Study (CFS)

description: 
The [Cleveland Family Study (CFS)](https://sleepdata.org/datasets/cfs) is a family-based study of sleep apnea, consisting of 2,284 individuals (46% African American) from 361 families studied on up to 4 occasions over a period of 16 years. The study began in 1990 with the initial aims of quantifying the familial aggregation of sleep apnea. National Institutes of Health (NIH) renewals provided expansion of the original cohort, including increased minority recruitment, and longitudinal follow-up, with the last exam occurring in February 2006. The [CFS](https://sleepdata.org/datasets/cfs) was designed to provide fundamental epidemiological data on risk factors for sleep disordered breathing (SDB). The sample was selected by identifying affected probands who had laboratory diagnosed obstructive sleep apnea. All first-degree relatives, spouses and available second-degree relatives of affected probands were studied. In addition, during the first 5 study years, neighborhood control families were identified through a neighborhood proband, and his/her spouses and first-degree relatives. Each exam, occurring at approximately 4-year intervals, included new enrollment as well as follow up exams for previously enrolled subjects. For the first three visits, data, including an overnight sleep study, were collected in participants' homes while the last visit occurred in a general clinical research center (GCRC). Phenotypic characterization of the entire cohort included overnight sleep apnea studies, blood pressure, spirometry, anthropometry and questionnaires. Currently, data of 710 individuals are available for use through [BioData Catalyst](https://biodatacatalyst.nhlbi.nih.gov/) (with genotype data available through [dbGaP](https://www.ncbi.nlm.nih.gov/gap/)).

The [National Sleep Research Resource](https://sleepdata.org/) (NSRR) is a NIH-supported sleep data repository that offers free access to large collections of de-identified physiological signals and related clinical data from a large range of cohort studies, clinical trials and other data sources from children and adults, including healthy individuals from the community and individuals with known sleep or other health disorders.  The goals of [NSRR](https://sleepdata.org/) are to facilitate rigorous research that requires access to large or more diverse data sets, including raw physiological signals, to promote a better understanding of risk factors for sleep and circadian disorders and/or the impact of sleep disturbances on health-related outcomes.  Data from over 15 data sources and more than 40,000 individual sleep studies, many linked to dozens if not hundreds of clinical data elements, are available (as of Feb. 2022). Query tools are available to identify variables of interest, and their meta-data and provenance.
DOI: 10.60645/bdc-wpb9-u84d
title: Reasons for Geographic and Racial Differences in Stroke Cardiorenal GWAS

description: 
REGARDS is a national, population-based, longitudinal study of incident stroke and associated risk factors including over 30,000 Black and White adults aged 45 years or older from all 48 contiguous U.S. states and the District of Columbia. The study was designed to investigate reasons underlying the higher rate of stroke mortality among Black participants compared to White participants and among residents of the Southeastern U.S. compared to other U.S. regions. By design, Black adults and residents of the deep south were oversampled. Between 2003 and 2007 (baseline visit) participants completed a computer-assisted telephone interview to collect demographic information and medication adherence, and an in-home visit for blood pressure measurements and collection of blood and urine samples. Following the baseline visit, participants have been contacted by phone at six-month intervals to obtain information on incident stroke or secondary outcomes. Additionally, samples and data were collected on about 50% of the original cohort during a second study visit an average of 10 years after the baseline visit. Genotyping was performed as part of an ancillary study on 10,788 (84% Black) participants using Illumina MEGA arrays.
DOI: 10.60645/bdc-77p4-rj63
title: Clinical Trial of COVID-19 Convalescent Plasma in Outpatients (C3PO)

description: 
The Clinical Trial of COVID-19 Convalescent Plasma in Outpatients (C3PO) is a multicenter, randomized, single blind, two-arm, placebo controlled Phase III trial with blinded outcome assessments to establish the safety and efficacy of single dose of convalescent plasma for preventing the progression from mild to severe COVID-19 illness.
DOI: 10.60645/bdc-2g89-2h3n
title: MUSIC: Long-TerM OUtcomes after the Multisystem Inflammatory Syndrome In Children

description: 
This study is an observational cohort study that will use routinely-collected clinical and cardiac (EKG, echocardiogram, CMR, exercise testing) data to assess the association between MIS-C (multisystem inflammatory syndrome in children) and cardiac outcomes within the first year after hospital discharge. Research funding will be available for EKGs, echocardiograms and MRIs in protocol windows that are not ordered by primary caregivers. Our principal goal is to determine the spectrum and early time course of coronary artery involvement, LV systolic function, and arrhythmias or conduction system abnormalities, and, using these data, to define associated clinical and laboratory factors. We will include all eligible patients, including retrospective cases beginning January 1, 2020, with follow-up (in-person or telehealth) up to one year and annual medical history forms until up to 5 years have elapsed since illness onset. 

Because many patients will have been identified by retrospective review, we will obtain consent at different times in their illness course. For this reason, it may be hard to reach some patients and their families. Waiver of consent will be obtained after three attempts have been made to locate the patient and family without success, as well as for the rare child who dies before informed consent can be obtained. We will include a HIPAA-compliant cryptographic algorithm to create a sharable &#8220;hashed&#8221; identifier from patient information. If blood work for research purposes is added to usual clinically-indicated blood work during follow-up visits, this will be covered by other informed consent forms. Our primary outcomes are the largest proximal Left Anterior Descending Coronary Artery (LAD) or Right Coronary Artery (RCA) z score and lowest Left Ventricular Ejection Fraction (LVEF).
DOI: 10.60645/bdc-8074-821o
title: Nulliparous Pregnancy Outcomes Study: Monitoring Mothers-to-be Heart Health Study (nuMoM2b Heart Health Study)

description: 
Participants from study sites that recruited during the original study funded by NICHD of pregnant people, called nuMoM2b, participated in this study. The nuMoM2b-HHS1 was a prospective observational follow-up study of the [nuMoM2b](https://www.nichd.nih.gov/research/supported/nuMoM2b) cohort consisting of interval contacts via phone or web every 6 months to about a year, and an in-person visit 2 to 7 years after the end of the nuMoM2b pregnancy including: 
- Demographics - Self-administered questionnaires - Clinical measurements - Lab results - An in-home sleep breathing assessment for the subset of participants with at least one valid sleep breathing assessment during nuMoM2b - Abstraction of medical records for pregnancies subsequent to nuMoM2b involving self-reported adverse pregnancy outcomes or multiple births - Abstraction of medical records of selected cardiovascular risk-related events or procedures reported by participants. 
The study capitalized on the rich and unique data prospectively collected during nuMoM2b (biomarkers, uterine artery Doppler studies, fetal growth, psychosocial determinants, sleep, and blood pressure) and rigorous definitions of adverse pregnancy outcomes. These data are stored in the NICHD repository DASH (https://dash.nichd.nih.gov/study/226675). 

A total of 8,838 nuMoM2b participants were targeted for contact during nuMoM2b-HHS and 7,872 participants were reached, of whom 7,003 completed one or more interval contacts. Of these, 5,206 agreed to the visit, and 4,508 attended an in-person visit.
DOI: 10.60645/bdc-84c3-9u04
title: Collaborative Cohort of Cohorts for COVID-19 Research (C4R): Jackson Heart Study (JHS)

description: None
DOI: 10.60645/bdc-m194-69g1
title: Collaborative Cohort of Cohorts for COVID-19 Research (C4R): Jackson Heart Study (JHS)

description: None
DOI: 10.60645/bdc-16u0-oa4c
title: Collaborative Cohort of Cohorts for COVID-19 Research (C4R): Jackson Heart Study (JHS)

description: None
DOI: 10.60645/bdc-b4yt-6qhj
title: Collaborative Cohort of Cohorts for COVID-19 Research (C4R): Jackson Heart Study (JHS)

description: None
DOI: 10.60645/bdc-zhox-5968
title: Collaborative Cohort of Cohorts for COVID-19 Research (C4R): Hispanic Community Health Study/Study of Latinos (HCHS/SOL)

description: None
DOI: 10.60645/bdc-x050-ks1v
title: Collaborative Cohort of Cohorts for COVID-19 Research (C4R): Hispanic Community Health Study/Study of Latinos (HCHS/SOL)

description: None
DOI: 10.60645/bdc-q3hi-3510
title: Collaborative Cohort of Cohorts for COVID-19 Research (C4R): Subpopulations and Intermediate Outcome Measures in COPD Study (SPIROMICS)

description: 
<u>**Cohort Description **</u><br>The Subpopulations and Intermediate Outcome Measures in COPD Study (SPIROMICS) is a multi-center, observational, longitudinal case-control study designed to guide future development of therapies for COPD. SPIROMICS has recruited 2,983 COPD cases and controls, 40-80 years old with 20+ pack-years of smoking at 12 US sites in 2010&#8211;2015.
DOI: 10.60645/bdc-8kqy-142p
title: Collaborative Cohort of Cohorts for COVID-19 Research (C4R): Subpopulations and Intermediate Outcome Measures in COPD Study (SPIROMICS)

description: 
<u>**Cohort Description **</u><br>The Subpopulations and Intermediate Outcome Measures in COPD Study (SPIROMICS) is a multi-center, observational, longitudinal case-control study designed to guide future development of therapies for COPD. SPIROMICS has recruited 2,983 COPD cases and controls, 40-80 years old with 20+ pack-years of smoking at 12 US sites in 2010&#8211;2015.
DOI: 10.60645/bdc-9208-5c18
title: Collaborative Cohort of Cohorts for COVID-19 Research (C4R): Subpopulations and Intermediate Outcome Measures in COPD Study (SPIROMICS)

description: 
<u>**Cohort Description **</u><br>The Subpopulations and Intermediate Outcome Measures in COPD Study (SPIROMICS) is a multi-center, observational, longitudinal case-control study designed to guide future development of therapies for COPD. SPIROMICS has recruited 2,983 COPD cases and controls, 40-80 years old with 20+ pack-years of smoking at 12 US sites in 2010&#8211;2015.
DOI: 10.60645/bdc-ju53-48a2
title: Collaborative Cohort of Cohorts for COVID-19 Research (C4R): Subpopulations and Intermediate Outcome Measures in COPD Study (SPIROMICS)

description: 
<u>**Cohort Description **</u><br>The Subpopulations and Intermediate Outcome Measures in COPD Study (SPIROMICS) is a multi-center, observational, longitudinal case-control study designed to guide future development of therapies for COPD. SPIROMICS has recruited 2,983 COPD cases and controls, 40-80 years old with 20+ pack-years of smoking at 12 US sites in 2010&#8211;2015.
DOI: 10.60645/bdc-859m-35b1
title: Collaborative Cohort of Cohorts for COVID-19 Research (C4R): Subpopulations and Intermediate Outcome Measures in COPD Study (SPIROMICS)

description: 
<u>**Cohort Description **</u><br>The Subpopulations and Intermediate Outcome Measures in COPD Study (SPIROMICS) is a multi-center, observational, longitudinal case-control study designed to guide future development of therapies for COPD. SPIROMICS has recruited 2,983 COPD cases and controls, 40-80 years old with 20+ pack-years of smoking at 12 US sites in 2010&#8211;2015.
DOI: 10.60645/bdc-l5jw-6zo0
title: Collaborative Cohort of Cohorts for COVID-19 Research (C4R): Subpopulations and Intermediate Outcome Measures in COPD Study (SPIROMICS)

description: 
<u>**Cohort Description **</u><br>The Subpopulations and Intermediate Outcome Measures in COPD Study (SPIROMICS) is a multi-center, observational, longitudinal case-control study designed to guide future development of therapies for COPD. SPIROMICS has recruited 2,983 COPD cases and controls, 40-80 years old with 20+ pack-years of smoking at 12 US sites in 2010&#8211;2015.
DOI: 10.60645/bdc-1e0w-k01a
title: Collaborative Cohort of Cohorts for COVID-19 Research (C4R): Subpopulations and Intermediate Outcome Measures in COPD Study (SPIROMICS)

description: 
<u>**Cohort Description **</u><br>The Subpopulations and Intermediate Outcome Measures in COPD Study (SPIROMICS) is a multi-center, observational, longitudinal case-control study designed to guide future development of therapies for COPD. SPIROMICS has recruited 2,983 COPD cases and controls, 40-80 years old with 20+ pack-years of smoking at 12 US sites in 2010&#8211;2015.
DOI: 10.60645/bdc-of0g-626k
title: Collaborative Cohort of Cohorts for COVID-19 Research (C4R): Subpopulations and Intermediate Outcome Measures in COPD Study (SPIROMICS)

description: 
<u>**Cohort Description **</u><br>The Subpopulations and Intermediate Outcome Measures in COPD Study (SPIROMICS) is a multi-center, observational, longitudinal case-control study designed to guide future development of therapies for COPD. SPIROMICS has recruited 2,983 COPD cases and controls, 40-80 years old with 20+ pack-years of smoking at 12 US sites in 2010&#8211;2015.
DOI: 10.15468/dl.wgh6yx
title: Occurrence Download

description: A dataset containing 273 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ptychosperma elegans",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 273 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016314-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60645/bdc-1ihx-2jfd
title: Collaborative Cohort of Cohorts for COVID-19 Research (C4R): Genetic Epidemiology of COPD Study (COPDGene)

description: 
<u>**Cohort Description**</u> <br>The Genetic Epidemiology of COPD (COPDGene) study is a non-interventional, multicenter, longitudinal, case-control study at 21 US sites of smokers with a &#8805;10 pack-year history of smoking, with and without COPD, and healthy never smokers. The initial goal was to characterize disease-related phenotypes and explore associations with susceptibility genes. 

<u>**Data Being Submitted**</u> <br>Wave 1 questionnaire data includes 397 variables for up to 3683 COPDGene participants in C4R. <br>Wave 2 questionnaire data includes 447 variables for up to 2191 COPDGene participants in C4R. <br>Dried Blood Spot/Serosurvey data includes 7 variables for up to 1692 COPDGene participants in C4R. <br>Derived data includes 43 variables for up to 4082 COPDGene participants in C4R. <br>Phenotype data includes 113 variables for up to 4082 COPDGene participants in C4R.
DOI: 10.60645/bdc-y857-80vw
title: Collaborative Cohort of Cohorts for COVID-19 Research (C4R): Genetic Epidemiology of COPD Study (COPDGene)

description: 
<u>**Cohort Description**</u> <br>The Genetic Epidemiology of COPD (COPDGene) study is a non-interventional, multicenter, longitudinal, case-control study at 21 US sites of smokers with a &#8805;10 pack-year history of smoking, with and without COPD, and healthy never smokers. The initial goal was to characterize disease-related phenotypes and explore associations with susceptibility genes. 

<u>**Data Being Submitted**</u> <br>Wave 1 questionnaire data includes 397 variables for up to 3683 COPDGene participants in C4R. <br>Wave 2 questionnaire data includes 447 variables for up to 2191 COPDGene participants in C4R. <br>Dried Blood Spot/Serosurvey data includes 7 variables for up to 1692 COPDGene participants in C4R. <br>Derived data includes 43 variables for up to 4082 COPDGene participants in C4R. <br>Phenotype data includes 113 variables for up to 4082 COPDGene participants in C4R.
DOI: 10.60645/bdc-bce4-hw56
title: Collaborative Cohort of Cohorts for COVID-19 Research (C4R): Framingham Heart Study (FHS)

description: 
<u>**Cohort Description**</u>

**<u>Data Being Submitted</u>**
- Wave 1 questionnaire data includes 3967 variables for up to 3112 FHS participants in C4R.- Wave 2 questionnaire data includes 448 variables for up to 2337 FHS participants in C4R.- Dried Blood Spot/Serosurvey data includes 7 variables for up to 2189 FHS participants in C4R.- Derived data includes 43 variables for up to 3151 FHS participants in C4R.- Phenotype data includes 113 variables for up to 3151 FHS participants in C4R.
DOI: 10.60645/bdc-hhp5-6qx0
title: Collaborative Cohort of Cohorts for COVID-19 Research (C4R): Framingham Heart Study (FHS)

description: 
<u>**Cohort Description**</u>

**<u>Data Being Submitted</u>**
- Wave 1 questionnaire data includes 3967 variables for up to 3112 FHS participants in C4R.- Wave 2 questionnaire data includes 448 variables for up to 2337 FHS participants in C4R.- Dried Blood Spot/Serosurvey data includes 7 variables for up to 2189 FHS participants in C4R.- Derived data includes 43 variables for up to 3151 FHS participants in C4R.- Phenotype data includes 113 variables for up to 3151 FHS participants in C4R.