AndreaBozzo/ceres-open-data-index huggingface dataset:
The Structure and Composition of Puerto Rico's Urban Mangroves MetaData

Mangrove forests face heightened pressure from human development, which may directly replace these ecosystems or indirectly influence their structure and composition through a variety of anthropogenic activities. As a result, surrounding human communities receive lower overall ecosystem services from the remaining forests, which have been valued among the highest in the world and include fisheries habitat support, shoreline protection and stabilization from natural disasters, and water filtration. Although urban mangrove forests have been characterized as distinct in composition and structure in comparison with their non-urban counterparts, previous studies lack quantified representations of urbanness as well as any inclusion of hydrology or water chemistry, which are important influences on mangrove forest structure, composition, and function. This study uses ground-based and LiDAR measurements of mangroves across urban gradients in Puerto Rico to characterize forest composition and structure. It then tests for the relative importance of urbanization alongside flooding metrics and surface water chemistry in explaining observed variability in forest structure and composition. This data set includes all data and R scripts used in the analysis of Puerto Rico's urban mangroves. Data sets include individual tree species identification and diameter measurements as well as biomass. It also includes summary statistics from LiDAR (Light Detection and Ranging) measurements flown by NASA's GLiHT program. Finally, data sets include descriptive metrics for study sites such as land cover and land use, hydrology, and water chemistry. 

This dataset is associated with the following publication:
branoff, b., and S. Martinuzzi. The Structure and Composition of Puerto Rico’s Urban Mangroves.   Forests. MDPI AG, Basel,  SWITZERLAND, 11(10): 1119, (2020).

Tags: social-ecological-systems, urban-forestry, urban-mangroves
Organization: U.S. Environmental Protection Agency
formalin effects data

RNA sequencing data from paired: (1) fresh-frozen, (2) direct-fixed in formalin for 18 hours, (3) frozen then formalin-fixed, or (4) frozen then ethanol-fixed and paraffin-embedded (n=6/group/condition) tissue samples from the livers of mice exposed to 600 ppm phenobarbital vs. vehicle control for 7 days in drinking water. RNA sequencing data from paired fresh frozen and 18 hr. formalin-fixed paraffin-embedded liver tissue from mice administered 1500, 3000, and 6000 ppm DEHP or vehicle control for 7 days by dietary ingestion; or RNA sequencing data from paired fresh frozen, 18 hr. formalin fixed paraffin embedded, or 3 wk. formalin fixed paraffin embedded liver tissue from mice administered 8 mg/kg/d Furan or vehicle control for 3 weeks by gavage. 

This dataset is associated with the following publication:
Wehmas, L., S. Hester, and C.E. Wood. Direct Formalin Fixation Induces Widespread Transcriptomic Effects in Archival Tissue Samples.   Scientific Reports. Nature Publishing Group, London,  UK, 10: 14497, (2020).

Tags: dehp, formalin-fixed-paraffin-embedded-samples, furan, gene-expression-profiles, mode-of-action-moa, molecular-pathway-analysis, phenobarbital, rna-sequencing
Organization: U.S. Environmental Protection Agency
TullyJennifer_A-sj4n_SDMP_20200303

Calculations and the underlying data used to characterize and describe the calcium-lead phosphate minerals identified in lead service line pipe scales. 

This dataset is associated with the following publication:
DeSantis, M., M. Schock, J. Tully, and C. Bennett-Stamper. Orthophosphate Interactions with Destabilized PbO2 Scales.   ENVIRONMENTAL SCIENCE & TECHNOLOGY. American Chemical Society, Washington, DC, USA, 54(22): 14302–14311, (2020).

Tags: corrosion-control, lead, pbiv, phosphate, pipe-scale
Organization: U.S. Environmental Protection Agency
TZurlinden_pluripotent human (H9) embryonic stem cell

The data presented here support the application of the Stemina devTOXqP platform for predictive toxicology and further demonstrate its value in ToxCast as a novel resource that can generate testable hypotheses aimed at characterizing potential pathways for teratogenicity and HTS prioritization of environmental chemicals for an exposure-based assessment of developmental hazard.

The dataset from the Stemina (STM) assay is annotated in the ToxCast portfolio as STM. Major findings from the analysis of ToxCast_STM dataset include (1) 19% of 1065 chemicals yielded a prediction of developmental toxicity, (2) assay performance reached 79%-82% accuracy with high specificity (> 84%) but modest sensitivity (< 67%) when compared with in vivo animal models of human prenatal developmental toxicity, (3) sensitivity improved as more stringent weights of evidence requirements were applied to the animal studies, and (4) statistical analysis of the most potent chemical hits on specific biochemical targets in ToxCast revealed positive and negative associations with the STM response, providing insights into the mechanistic underpinnings of the targeted endpoint and its biological domain. The results of this study will be useful to improving our ability to predict in vivo developmental toxicants based on in vitro data and in silico models. 

This dataset is associated with the following publication:
Zurlinden, T., K. Saili, N. Rush, P. Kothiya, R. Judson, K. Houck, E. Hunter, N. Baker, J. Palmer, R. Thomas, and T. Knudsen. Profiling the ToxCast Library With a Pluripotent Human (H9) Stem Cell Line-Based Biomarker Assay for Developmental Toxicity.   TOXICOLOGICAL SCIENCES. Society of Toxicology, RESTON, VA,  174(2): 189-209, (2020).

Tags: developmental-toxicology, embryonic-stem-cells, predictive-toxicology, tipping-points, vembryo, virtual-embryo, virtual-tissues
Organization: U.S. Environmental Protection Agency
KPF_Examining the Utility of In Vitro Bioactivity as a Protective Point of Departure: A Case Study_APCRA

The files and .R scripts here are provided to aid in understanding and reproduction of the analyses in the submitted paper, "Examining the Utility of In Vitro Bioactivity as a Protective Point of Departure: A Case Study."
The scripts in the .R folder reference source files in the other folders. 

This dataset is associated with the following publication:
Friedman, K., M. Gagne, L. Loo, P. Karamertzanis, T. Netzeva, T. Sobanski, J. Franzosa, A. Richard, R. Lougee, A. Gissi, J.J. Lee, M. Angrish, J. Dorne, S. Foster, K. Raffaele, T. Bahadori, M. Gwinn, J. Lambert, M. Whelan, M. Rasenberg, T. Barton-Maclaren, and R. Thomas. Utility of In Vitro Bioactivity as a Lower Bound Estimate of In Vivo Adverse Effect Levels and in Risk-Based Prioritization.   TOXICOLOGICAL SCIENCES. Society of Toxicology, RESTON, VA,  173(1): 202-225, (2020).

Tags: actor, high-throughput-screening, high-throughput-toxicokinetics, new-approach-methodologies, point-of-departure-pod, threshold-of-toxicological-concern-ttc
Organization: U.S. Environmental Protection Agency
Gulf of Mexico Nutrient, carbon, CTD data

Gulf of Mexico cruise, nearshore and CTD data collected by the USEPA during 2002 - 2008. 

This dataset is associated with the following publication:
Pauer, J., W. Melendez, T. Feist, J. Lehrter, B. Rashleigh, L. Lowe, and R. Greene. The impact of alternative nutrient kinetics and computational grid size on model predicted primary production and hypoxic area in the northern Gulf of Mexico.   ENVIRONMENTAL MODELLING AND SOFTWARE. Elsevier Science Ltd, New York, NY, USA, 26: 1-13, (2020).

Tags: gulf-of-mexico, hypoxia, mathematical-model, model-uncertainty
Organization: U.S. Environmental Protection Agency
Transitioning the generalised read-across approach (GenRA) to quantitative predictions: A case study using acute oral toxicity data

This repository contains code, input and output files associated with the GenRA acute toxicity case study that was published by Helman et al (2019) in Computational Toxicology. 

This dataset is associated with the following publication:
Helman, G., I. Shah, and G. Patlewicz. Transitioning the Generalised Read-Across approach (GenRA) to quantitative predictions: A case study using acute oral toxicity data.   Computational Toxicology. Elsevier B.V., Amsterdam,  NETHERLANDS, 12(November 2019): 100097, (2019).

Tags: dsstox
Organization: U.S. Environmental Protection Agency
National Epidemiologic Survey on Alcohol and Related Conditions (NESARC) - III

The National Epidemiologic Survey on Alcohol and Related Conditions - III (NESARC-III) is a nationally representative survey of 46,500 adult Americans that collected data on alcohol use disorders and their associated disabilities in addition to collecting saliva samples for the purpose of understanding the prevalence, risk factors, health disparities, economic costs and gene-environment interactions related to alcohol use disorders and their associated disabilities. 

Results from the study are not yet available. The data collection is also associated with clinical trial number: NCT01273220. 

Tags: adult, alcohol, anxiety, disability, disparities, mental-health, mood-disorder, sexual-assault, substance-use
Organization: U.S. Department of Health & Human Services
National Sexual Violence Resource Center (NSVRC)

The National Sexual Violence Resource Center (NSVRC) is a national information and resource hub relating to all aspects of sexual violence. 

NSVRC staff collect and disseminate a wide range of resources on sexual violence including statistics, research, position statements, statutes, training curricula, prevention initiatives and program information. With these resources, NSVRC assists coalitions, advocates and others interested in understanding and eliminating sexual violence. NSVRC has an active and diverse Advisory Council that assists and advises staff and ensures a broad national perspective. NSVRC also enjoys a strong partnership with state, territory and tribal anti-sexual assault coalitions and allied organizations.

NSVRC is funded through a cooperative agreement from the Centers for Disease Control and Prevention (CDC) Division of Violence Prevention.

Tags: abuse, curricula, prevention, publications, resource-center, sexual-assault, violence, women
Organization: U.S. Department of Health & Human Services
HCUP Nationwide Emergency Department Database (NEDS)

The Nationwide Emergency Department Sample (NEDS) was created to enable analyses of emergency department (ED) utilization patterns and support public health professionals, administrators, policymakers, and clinicians in their decision-making regarding this critical source of care. The NEDS can be weighted to produce national estimates.

The NEDS is the largest all-payer ED database in the United States.  It was constructed using records from both the HCUP State Emergency Department Databases (SEDD) and the State Inpatient Databases (SID), both also described in healthdata.gov. The SEDD capture information on ED visits that do not result in an admission (i.e., treat-and-release visits and transfers to another hospital). The SID contain information on patients initially seen in the emergency room and then admitted to the same hospital. 

The NEDS contains 25-30 million (unweighted) records for ED visits for over 950 hospitals and approximates a 20-percent stratified sample of U.S. hospital-based EDs. 

The NEDS contains information about geographic characteristics, hospital characteristics, patient characteristics, and the nature of visits (e.g., common reasons for ED visits, including injuries).   The NEDS contains clinical and resource use information included in a typical discharge abstract, with safeguards to protect the privacy of individual patients, physicians, and hospitals (as required by data sources). It includes ED charge information for over 75% of patients, regardless of payer, including patients covered by Medicaid, private insurance, and the uninsured. The NEDS excludes data elements that could directly or indirectly identify individuals, hospitals, or states.


Tags: claims, diagnoses, emergency-department, hcup, health-care, health-statistics, hospital, inpatient, procedures, sexual-assault, utilization
Organization: U.S. Department of Health & Human Services
HCUP State Emergency Department Databases (SEDD)

The State Emergency Department Databases (SEDD) contain the universe of emergency department visits in participating States. The data are translated into a uniform format to facilitate multi-State comparisons and analyses. The SEDD consist of data from hospital-based emergency departments and include all patients, regardless of payer, e.g., persons covered by Medicare, Medicaid, private insurance, and the uninsured. 

The SEDD contain clinical and resource use information included in a typical discharge abstract, with safeguards to protect the privacy of individual patients, physicians, and facilities (as required by data sources). Data elements include but are not limited to: diagnoses, procedures, admission and discharge status, patient demographics (e.g., gender, age), total charges, length of stay, and expected payment source (e.g., Medicare, Medicaid, private insurance, self-pay; for some States, additional discrete payer categories, such as managed care). In addition to the core set of uniform data elements common to all SEDD, some include State-specific data elements, such as the patient's race.  The SEDD exclude data elements that could directly or indirectly identify individuals.  For some States, hospital and county identifiers are included that permit linkage to the American Hospital Association Annual Survey File and the Area Resource File. 

Tags: claims, community-health, diagnoses, emergency-department, hcup, health-care, health-statistics, hospital, procedures, sexual-assault, utilization
Organization: U.S. Department of Health & Human Services
Mental Health Treatement Facilities Locator

An online resource for locating mental health treatment facilities and programs supported by the Substance Abuse and Mental Health Services Administration (SAMHSA). The Mental Health Treatment Locator section of the Behavioral Health Treatment Services Locator lists facilities providing mental health services to persons with mental illness. It includes:
Public mental health facilities that are funded by their State mental health agency (SMHA) or other State agency or department
Mental health treatment facilities administered by the Department of Veterans Affairs, Private for-profit and non-profit mental health facilities that are licensed by the State or accredited by a national accreditation organization.

NOTE: The Mental Health Treatment Locator does not include facilities whose primary or only focus is the provision of services to persons with Mental Retardation (MR), Developmental Disability (DD), and Traumatic Brain Injuries (TBI). Facilities that provide treatment exclusively to persons with mental illness who are incarcerated. Mental health professionals in private practice (individual) or in a small group practice not licensed or certified as a mental health clinic or (community) mental health center.

SAMHSA endeavors to keep the Locator current. All information in the Locator is updated annually based on facility responses to SAMHSA's National Mental Health Services Survey (N-MHSS). The most recent complete update includes data collected as of April 30, 2010 in the N-MHSS. New facilities are added monthly. Updates to facility names, addresses, telephone numbers and services are made weekly, if facilities inform SAMHSA of changes.

For additional advice, you may call the Referral Helpline operated by SAMHSA's Center for Substance Abuse Treatment:

    1-800-662-HELP (English & Español)

    1-800-487-4889 (TTY)

Tags: help, locator, mental-health-treatment-facilities, provider, psychatrist, psychologist, sexual-assault, substance-abuse-buprenorphine, suicide-prevention, therapy
Organization: U.S. Department of Health & Human Services
Service Locator - Comprehensive Healthcare

This location-based tool allows you to search near your current location for community health clinics that offer primary care including: wellness, check ups, vaccines, testing, sexual health, family planning, dental, mental health, substance abuse treatment, and HIV/AIDS care. It is available as an API, widget and website.

Created originally by the AIDS.gov team, the tool can be used by anyone looking for health and support services. The tool combines results for federally qualified health centers (FQHCs), FQHC look alikes, and Ryan White HIV/AIDS treatment centers from datawarehouse.hrsa.gov;for mental health and substance abuse from findtreatment.samhsa.gov; and for family planning from hhs.gov/opa/title-x-family-planning/.

Tags: aids, community-health, family-planning, health-services, hiv, locator, primary-care, providers, sexual-assault, testing, treatment, wellness
Organization: U.S. Department of Health & Human Services
Find a Health Center

The Find Health Center tool is a locator tool designed to make data and information concerning Federally-Funded Health Centers more readily available to our users. It is intended to help people in greatest need for health care locate where they could obtain care in their particular location. The user is able to search for health centers nearest to a specific complete address, city and state, state and county, or ZIP code. The search results (health centers) are returned in groups of ten (numbered from one to ten) and are sorted by increasing distance away from the center of the search area (address or county). For each health center entry in the list the user is provided the health center name, address, approximate distance from the center point of the search, telephone number, website address (where available), and a link for driving directions. The user has the option of viewing the search results either on a map or as text (default) and both views provide links to get more detailed information for each returned opportunity.

Tags: checkups, child-health-care, children, dental-care, federally-funded-health-center, find-health-center, fqhc, health-center, health-services, high-need, immunization, low-income, medical, mental-health, pregnant, prescription-drugs, preventive-care, primary-care, service, sexual-assault, testing, treatment
Organization: U.S. Department of Health & Human Services
TIGER/Line Shapefile, 2012, Series Information File for the Current Area Landmark Shapefiles

The TIGER/Line shapefiles and related database files (.dbf) are an extract of selected geographic and cartographic information from the
               U.S. Census Bureau's Master Address File / Topologically Integrated Geographic Encoding and Referencing (MAF/TIGER) Database (MTDB). The MTDB represents
               a seamless national file with no overlaps or gaps between parts, however, each TIGER/Line shapefile is designed to stand alone as an independent data
               set, or they can be combined to cover the entire nation. The Census Bureau includes landmarks in the MTDB for locating special features and to help
               enumerators during field operations. Some of the more common landmark types include area landmarks such as airports, cemeteries, parks, schools, and
               churches and other religious institutions. The Census Bureau added landmark features to MTDB on an as-needed basis and made no attempt to ensure that all
               instances of a particular feature were included. The presence or absence of a landmark such as a hospital or prison does not mean that the living
               quarters associated with that landmark were geocoded to that census tabulation block or excluded from the census enumeration. The Area Landmark Shapefile
               does not include military installations or water bodies because they each appear in their own separate shapefiles, MIL.shp and AREAWATER.shp
               respectively.

Tags: area landmark, polygon, state or equivalent entity, u.s.
Organization: U.S. Census Bureau, Department of Commerce
TIGER/Line Shapefile, 2012, Series Information File for the Current County Subdivision State-based Shapefile

The TIGER/Line shapefiles and related database files (.dbf) are an extract of selected geographic and cartographic information from the
               U.S. Census Bureau's Master Address File / Topologically Integrated Geographic Encoding and Referencing (MAF/TIGER) Database (MTDB). The MTDB represents
               a seamless national file with no overlaps or gaps between parts, however, each TIGER/Line shapefile is designed to stand alone as an independent data
               set, or they can be combined to cover the entire nation. County subdivisions are the primary divisions of counties and their equivalent entities for the
               reporting of Census Bureau data, and they include legally minor civil divisions (MCDs) and statistical census county divisions (CCDs), and unorganized
               territories. For the 2010 Census, the legal MCDs are the primary governmental and/or administrative divisions of counties in 29 States and Puerto Rico;
               Tennessee changed from having CCDs for Census 2000 to having MCDs for the 2010 Census. In MCD States where no MCD exists or is not defined, the Census
               Bureau creates statistical unorganized territories to complete coverage. The entire area of the United States, Puerto Rico, and the Island Areas is
               covered by county subdivisions. The boundaries of all 2010 Census legal MCDs are as of January 1, 2010 as reported through the Census Bureau's Boundary
               and Annexation Survey (BAS). For the 2010 Census, CCDs or their equivalents are delineated in 21 States. The boundaries of all 2010 Census statistical
               CCDs were delineated as part of the Census Bureau's Participant Statistical Areas Program (PSAP).

Tags: barrio, ccd, census county division, county subdivision, mcd, minor civil division, polygon, state or equivalent entity, subdivision, town, township, u.s., unorganized territory, ut
Organization: U.S. Census Bureau, Department of Commerce
TIGER/Line Shapefile, 2012, Series Information File for the Current Topological Faces-Area Landmark Relationship Files

The TIGER/Line shapefiles and related database files (.dbf) are an extract of selected geographic and cartographic information from the
               U.S. Census Bureau's Master Address File / Topologically Integrated Geographic Encoding and Referencing (MAF/TIGER) Database (MTDB). The MTDB represents
               a seamless national file with no overlaps or gaps between parts, however, each TIGER/Line shapefile is designed to stand alone as an independent data
               set, or they can be combined to cover the entire nation. The Topological Faces / Area Landmark Relationship File (FACESAL.dbf) contains a record for each
               face / area landmark relationship. Face refers to the areal (polygon) topological primitives that make up MTDB. A face is bounded by one or more edges;
               its boundary includes only the edges that separate it from other faces, not any interior edges contained within the area of the face. The face to which a
               record in the Topological Faces / Area Landmark Relationship File (FACESAL.dbf) applies can be determined by linking to the Topological Faces Shapefile
               (FACES.shp) on the permanent topological face identifier (TFID) attribute. The area landmark to which a record in the Topological Faces / Area Landmark
               Relationship File (FACESAL.dbf) applies can be determined by linking to the Area Landmark Shapefile (AREALM.shp) on the area landmark identifier (AREAID)
               attribute. A face may be part of multiple area landmarks. An area landmark may consist of multiple faces.

Tags: area landmark identifier, county ansi code, county fips code, landmark, permanent face id, state ansi code, state fips code, state or equivalent entity, table, topological faces, u.s.
Organization: U.S. Census Bureau, Department of Commerce