AndreaBozzo/ceres-open-data-index huggingface dataset:
Data From: Effects of species and sex on the gut microbiome of four laboratory-reared fruit fly lines (Diptera: Tephritidae) using full-length 16S rRNA PacBio Kinnex sequencing

<p dir="ltr">Species- and sex-related differences of four laboratory tephritid fruit fly (Diptera: Tephritidae) gut microbiomes evaluated with full-length 16S rRNA PacBio Kinnex sequencing. Insect gut microbiomes are shaped by multiple endogenous and environmental factors. Our study evaluated the impacts of how host sex and species influence the microbiome in laboratory-reared tephritids fruit flies when controlled for location, time, and adult diet. We evaluated the gut microbiome of four lines of pest tephritid fruit fly adults (<i>Bactrocera dorsalis, Bactrocera latifrons, Ceratitis capitata, Zeugodacus cucurbitae</i>) using near full-length 16S rRNA sequencing with a PacBio Kinnex concatenation-based approach. We analyzed groups of males and females from each species at the same set of time, across four timepoints in a core insectary. Results demonstrate a clear impact of fruit fly species on the gut microbiome composition of the different fruit flies. Furthermore, for <i>B. dorsalis, B. latifrons, </i>and <i>C. capitata</i>, we saw an influence of sex on amplicon sequence variant (ASV) composition. However, while there was a separation of samples between the sexes for each timepoint, there was no characteristic male or female microbiome in all cases.</p><p dir="ltr">Dataset includes ASV count, taxonomy, fasta files, metadata, and R scripts. Raw sequence data has been deposited to the National Center for Biotechnology Information Sequence Read Archive (NCBI SRA) under the accession number PRJNA1196954.</p>

Tags: 16s, bacteria, fruit-fly, host, mediteranean-fruit-fly, melon-fly, microbiome, oriental-fruit-fly, ribosomal-rna, source-code
Organization: Department of Agriculture
2012 State Profile - Michigan

This is a National Survey of Substance Abuse Treatment Services (N-SSATS) annual report showing the state profile for Michigan in 2012. N-SSATS is designed to collect data on the location, characteristics, and use of alcohol and drug abuse treatment facilities and services throughout the 50 States, the District of Columbia, and other U.S. jurisdictions.

Tags: michigan, n-ssats, samhsa, substance-abuse-treatment, treatment-facilities
Organization: U.S. Department of Health & Human Services
Nutritional Status Influence on Acaricide Tolerance in Varroa destructor: A Multi-Level Analysis of Physiological and Proteomic Mechanisms

<p dir="ltr"><i>Varroa destructor</i> are harmful ectoparasitic mites of <i>Apis mellifera</i> honey bees. Recently, high colony losses have been reported by U.S. beekeepers. The effects of mites, spurned on by the resistance of mites to conventional pesticides used by many U.S. beekeepers, is likely a key factor driving high colony losses. While molecular mechanisms granting resistance have been described, another, less studied factor is tolerance of <i>Varroa</i> mites to pesticide exposure depending on the mites’ 'feed state', or the nutritional status, which may depend on the host developmental stage (adult, pupa) the mite has fed upon at the time of pesticide exposure. Here we conducted over 500 laboratory bioassays exposing over 2,000 mites to three different conventional pesticides used for their control and fed prior to exposure on honey bee adult or pupal hosts. We analyzed the mites for their protein levels (proteomic analysis) and also the activity levels of key detoxification enzymes. Protein analyses showed mites surviving exposure to pesticides had over 10-fold higher level of host proteins and more active detoxification enzymes. The results highlight the importance of having knowledge of mites' nutritional 'feed state' when conducting pesticide laboratory research with <i>Varroa</i> mites.</p>

Tags: acaricide-tolerance, feed-state, nutritional-status, proteomics, varroa-destructor
Organization: Department of Agriculture
Data from: Fruit Cuticle Thickness and Anatomical Changes in Pedicel Xylem Vessels Influence Fruit Transpiration and Calcium Accumulation in Cranberry Fruit

<p dir="ltr">Calcium is a key nutrient for fruit quality due to its role in bonding with pectin in the cell wall, providing strength through cell-to-cell adhesion, thus increasing fruit firmness and extending post-harvest life. However, Ca accumulation is mostly limited to the initial stages of fruit development due to anatomical and physiological changes that occur as fruits develop. The objective of this study was to evaluate fruit transpiration, cuticle thickness, and pedicel vessel changes during cranberry fruit development and the effect these parameters might have on Ca translocation. ‘Stevens’ cranberry fruits were collected weekly, starting seven days after full bloom (DAFB) until 70 DAFB. For each collection date, fruit transpiration was evaluated in the field, and samples were taken to analyze total fruit Ca content, stomata density, cuticle thickness, pedicel anatomical changes, and xylem functionality. Ca accumulation in the fruit exhibited a sigmoidal curve, beginning at 0.04 mg per berry at 7 DAFB, increasing to a maximum of 0.1 mg per berry at 28 DAFB, and remaining constant until harvest (70 DAFB). Fruit Ca accumulation was mostly explained by fruit transpiration, which exhibited a similar sigmoidal pattern. The rapid decline in fruit transpiration was largely modulated by increases in cuticle thickness, as well as anatomical changes in the pedicel xylem, thereby reducing the capacity to transport water and nutrients into the fruit. Thus, this research could help cranberry growers maximize fruit Ca content by prioritizing fertilization during the early stages of fruit development.</p>

Tags: cranberry, cuticle, pedicel-vessels, transpiration
Organization: Department of Agriculture
Data from: An updated molecular toolkit for genomics-assisted breeding of waxy sorghum [Sorghum bicolor (L.) Moench

<p dir="ltr">Specific types of sorghum germplasm contain genes that result in lower than normal levels of amylose, a specific type of starch found in the grain. These types of sorghum are referred to as "waxy." Waxy starch has unique properties which would provide novel functionality for food, feed, and biofuel markets. To help facilitate breeding efforts to develop improved waxy sorghum varieties, this project developed new genetic markers for the waxy trait and provides new molecular tools to help sorghum breeders and geneticists develop new waxy sorghum with improved agronomic properties. This data set contains near infrared spectroscopy predictions of amylose content in sorghum grain generated by co-author Scott Bean.</p>

Tags: amylose, sorghum, starch, waxy-grain
Organization: Department of Agriculture
Data from: Adult dietary experience influences mortality of the pest melon fly<i>, Zeugodacus cucurbitae</i> (Diptera: Tephritidae), to an ingested toxin

<p dir="ltr">In this study, we investigated how protein deprivation following adult emergence influences lethal and sublethal effects of boric acid on the pest tephritid melon fly, <i>Zeugodacus cucurbitae</i>. We performed a series of experiments to address the impact of prior diet on mortality, diet consumption, enzymes involved in detoxification and antioxidation, and fly activity. Newly emerged melon fly adults were provided either diet containing 3:1 sucrose:yeast hyrdrolysate or just sucrose for three days prior to bioassays. The raw data from the bioassays and  R scripts for the analyses are provided. </p>

Tags: boric-acid, foraging, nutrition, oxidative-stress, sucrose, yeast-hydrolysate
Organization: Department of Agriculture
Colletotrichum shisoi FDWSRU 21-072 nuclear and mitochondrial genome annotations

<p dir="ltr"><i>Colletotrichum shisoi</i> is a fungal plant pathogen of <i>Perilla frutescens</i>, a mint species cultivated in some Asian countries but considered invasive in the United States. This dataset contains a new, highly contiguous genome sequence generated from the North American <i>C. shisoi</i> isolate FDWSRU 21-072, which has been proposed for use as a biological control agent of invasive <i>P. frutescens</i>. Long-read PacBio sequencing produced a nuclear genome assembly of 48 contigs and 86.9 Mb. Structural and functional gene annotations were generated with the FunAnnotate v1.8.16 pipeline. Repetitive contents were annotated using RepeatMasker v4.1.5. A complete mitochondrial genome was assembled using MitoHifi and Flye, and mitochondrial annotations were predicted using MFannot.</p>

Tags: colletotrichum-shisoi, fungus, genome, invasive, perilla-fruescens, perilla-mint, plant-pathogen, weed
Organization: Department of Agriculture
Data from: Microbial source tracking for antibiotic resistance genes in southwest Wisconsin private wells

<p dir="ltr">Groundwater was collected by dead-end ultrafiltration and small-volume grab sampling from 138 wells in southwest Wisconsin across Grant, Iowa, and Lafayette Counties. Samples were collected to assess occurrence of antibiotic resistance genes in private wells and investigate their association with microbial source tracking markers. For ultrafiltration samples, microbes were backflushed, desiccated beef extract was added to the eluate, and samples were concentrated by polyethylene glycol precipitation; concentrate was frozen at -80 degrees Celcius (C). Small-volume grab samples were concentrated on 0.45-micron mixed cellulose ester filters, filters were eluted, and eluate was frozen at -80 degrees C following addition of beef extract. Nucleic acids were extracted from both sample types using a QIAcube and QIAamp DNA mini kit with viral lysis buffer (AVL) and carrier RNA (Qiagen). Nucleic acids were extracted from 280 microliter (µL) of sample concentrate and eluted into 140 µL AE Buffer (Qiagen). Nucleic acids were analyzed in duplicate using quantitative polymerase chain reaction (qPCR) on a Roche LightCycler 480 II using hydrolysis probes. Inhibition was assessed for every sample using Sketa DNA as inhibition control and mitigated by dilution with AE buffer as necessary. No-template negative controls were performed for all analysis steps: secondary concentration, nucleic acid extraction, and qPCR. For each assay with amplification in negative controls, the cycle of quantification (Cq) in unknown samples must be below the censoring threshold to be accepted as positive. Censoring thresholds were calculated as the mean Cq of negative controls - 3 standard deviations; censoring thresholds for each assay and sample type are reported in a separate file (Censoring thresholds.csv). Positive controls (bovine herpes virus vaccine) for extraction were included with each analysis batch and evaluated qualitatively. Positive controls were run in duplicate reactions for all targets and had to be within 0.5 cycles of the expected Cq. Data are expressed as genomic copies per liter of groundwater sampled. Dataset consists of 1 spreadsheet file (qPCR data results.csv). Variables in this file are described in the included data dictionary.</p>

Tags: antibiotic-resistance-genes, dead-end-ultrafiltration, groundwater, microbial-source-tracking, private-wells, small-volume-grab-sampling
Organization: Department of Agriculture
JALFHCC - Patient Registration Service

<p>The Captain James A. Lovell Federal Health Care Center (JALFHCC) Patient Registration Service supports the operation of the first VA/Navy Federal Health Care Center and involves leveraging of the Veterans Health Information Systems and Technology Architecture (VistA) for VA and the Department of Defenses (DoDs) Health Information System.The integration of JALFHCC and eMI was accomplished in multiple phases. JALFHCC Phase 1 consisted of the integration of the Orders Portability service with eMI to allow for VA and DoD communications for Orders Portability through eMI. JALFHCC Phase 1 went live in production in May 2015 and supported an average of 10,000 messages per day. JALFHCC Phase 2 and 3 involved the integration of five additional services or message flows with eMI and the full sunset of the Vitria Businessware Service, JALFHCC Oracle Service Bus (OSB), and Oracle Service Registry (OSR) at VA JALFHCC. JALFHCC Phase 2 and 3 went live in August 2015.</p>

Tags: jalfhcc, patient
Organization: Department of Veterans Affairs
2016 Uniform Reporting System (URS) Table for New Jersey

This is the 2016 Uniform Reporting System (URS) Output Tables for New Jersey. The URS state reporting system is collected annually to support the Community Mental Health Services Block Grant program. State Mental Health Authorities report on National Outcome Measures (NOMS), evidence based practices, and utilization measures providing an overview of state mental health delivery systems.

Tags: evidence-based-practices, mental-health-services, national-outcome-measures, samhsa, utilization-measures
Organization: U.S. Department of Health & Human Services
Geographic Distribution of VA Expenditures FY1998

<p>This report details VA expenditures at the state, county, and Congressional District level. It includes categories such as Compensation and Pension, Construction, Insurance, and Medical Care. Veteran population estimates and the number of unique patients who used VA health care services are also available.</p>

Tags: 2012, compensation-and-pension, congressional-district, construction, county, distribution, education, expenditures, general-operating-expenses, insurance, medical-care
Organization: Department of Veterans Affairs
National Health Care Practitioner Database (NHCPD)

<p>This database is part of the National Medical Information System (NMIS). The National Health Care Practitioner Database (NHCPD) supports Veterans Health Administration Privacy Act requirements by segregating personal information about health care practitioners such as name and social security number from patient information recorded in the National Patient Care Database for Ambulatory Care Reporting and Primary Care Management Module.</p>

Tags: ambulatory, clinical, encounter, health, outpatient, practitioner, va, veteran
Organization: Department of Veterans Affairs
Pools

<span style='color:rgb(68, 68, 68); font-family:&quot;Avenir Next W01&quot;, &quot;Avenir Next W00&quot;, &quot;Avenir Next&quot;, Avenir, &quot;Helvetica Neue&quot;, sans-serif; font-size:medium;'>The planimetric data was compiled by The Sanborn Map Company, Inc for the Metropolitan District and is based on an aerial flight performed in April 2015. In addition, the City's GIS staff has been updating limited planimetric features based on information on file in various City departments. The planimetric data has also been updated in 2016 and yearly to current based on spring aerial flights by EagleView.</span>

Tags: gis-data, hartford-ct, planimetric, pool
Organization: City of Hartford
Profile of Adolescent Discharges from Substance Abuse Treatment

This report uses the 2011 Treatment Episode Data Set–Discharges (TEDS-D), a national data system of annual discharges from substance abuse treatment facilities, to create a profile of adolescents who enter treatment for substance abuse.  Specifically, the report examines demographic characteristics of discharges from treatment, treatment setting, health insurance, primary substance of abuse, criminal justice referral, and treatment disposition.

Tags: adolescent-substance-abuse, samhsa, substance-abuse-treatment, teds-d, treatment-discharges
Organization: U.S. Department of Health & Human Services
Treeline

<span style='color:rgb(68, 68, 68); font-family:&quot;Avenir Next W01&quot;, &quot;Avenir Next W00&quot;, &quot;Avenir Next&quot;, Avenir, &quot;Helvetica Neue&quot;, sans-serif; font-size:medium;'>The planimetric data was compiled by The Sanborn Map Company, Inc for the Metropolitan District and is based on an aerial flight performed in April 2015. In addition, the City's GIS staff has been updating limited planimetric features based on information on file in various City departments. The planimetric data has also been updated in 2016 and yearly to current based on spring aerial flights by EagleView.</span>

Tags: gis-data, hartford-ct, planimetric, treeline, vegetation
Organization: City of Hartford
Water Bodies

<span style='color:rgb(68, 68, 68); font-family:&quot;Avenir Next W01&quot;, &quot;Avenir Next W00&quot;, &quot;Avenir Next&quot;, Avenir, &quot;Helvetica Neue&quot;, sans-serif; font-size:medium;'>The planimetric data was compiled by The Sanborn Map Company, Inc for the Metropolitan District and is based on an aerial flight performed in April 2015. In addition, the City's GIS staff has been updating limited planimetric features based on information on file in various City departments. The planimetric data has also been updated in 2016 and yearly to current based on spring aerial flights by EagleView.</span>

Tags: gis-data, hartford-ct, hydrography, lake, pond, river, swamp, water, water-body
Organization: City of Hartford
H13525: NOS Hydrographic Survey , 2021-08-22

The National Oceanic and Atmospheric Administration (NOAA) has the statutory mandate to collect hydrographic data in support of nautical chart compilation for safe navigation and to provide background data for engineers, scientific, and other commercial and industrial activities. Hydrographic survey data primarily consist of water depths, but may also include features (e.g. rocks, wrecks), navigation aids, shoreline identification, and bottom type information.
							NOAA is responsible for archiving and distributing the source data as described in this metadata record.

Tags: acoustic sounders, bathymetry, bathymetry/seafloor topography, continent, doc/noaa/nesdis/ncei, doc/noaa/nesdis/ngdc, earth remote sensing instruments, earth science, global positioning system/inertial measurement unit, gps, gps receivers, gps/imu, hydrographic surveys for selected locations within the united states (hydro_bathy_2006), in situ ocean-based platforms, in situ/laboratory instruments, little lake to crisp point, marine sediments, mbes, michigan, msbs, multibeam mapping system, multibeam swath bathymetry system, national centers for environmental information, national geophysical data center, nesdis, noaa, north america, ocean, oceans, passive remote sensing, positioning/navigation, profilers/sounders, seafloor topography, sediment composition, ships, sonar, sound navigation and ranging, u.s. department of commerce, united states of america, vicinity of whitefish point, water depth
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
H12617: NOS Hydrographic Survey , Approaches to LA Long Beach, CA, 2013-11-03

The National Oceanic and Atmospheric Administration (NOAA) has the statutory mandate to collect hydrographic data in support of nautical chart compilation for safe navigation and to provide background data for engineers, scientific, and other commercial and industrial activities. Hydrographic survey data primarily consist of water depths, but may also include features (e.g. rocks, wrecks), navigation aids, shoreline identification, and bottom type information.
							NOAA is responsible for archiving and distributing the source data as described in this metadata record.

Tags: acoustic sounders, bathymetry, bathymetry/seafloor topography, ca, california, continent, doc/noaa/nesdis/ncei, doc/noaa/nesdis/ngdc, earth remote sensing instruments, earth science, global positioning system/inertial measurement unit, gps, gps receivers, gps/imu, hydrographic surveys for selected locations within the united states (hydro_bathy_2006), in situ ocean-based platforms, in situ/laboratory instruments, long beach, marine sediments, mbes, msbs, multibeam mapping system, multibeam swath bathymetry system, national centers for environmental information, national geophysical data center, nesdis, noaa, north america, ocean, oceans, passive remote sensing, positioning/navigation, profilers/sounders, san pedro and vicinity, seafloor topography, sediment composition, ships, sonar, sound navigation and ranging, u.s. department of commerce, united states of america, water depth
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
H12047: NOS Hydrographic Survey , Honolulu Harbor, Hawaii, 2009-05-03

The National Oceanic and Atmospheric Administration (NOAA) has the statutory mandate to collect hydrographic data in support of nautical chart compilation for safe navigation and to provide background data for engineers, scientific, and other commercial and industrial activities. Hydrographic survey data primarily consist of water depths, but may also include features (e.g. rocks, wrecks), navigation aids, shoreline identification, and bottom type information.
							NOAA is responsible for archiving and distributing the source data as described in this metadata record.

Tags: acoustic sounders, approaches to honolulu, bathymetry, bathymetry/seafloor topography, continent, doc/noaa/nesdis/ncei, doc/noaa/nesdis/ngdc, earth remote sensing instruments, earth science, global positioning system/inertial measurement unit, gps, gps receivers, gps/imu, hawaii, hydrographic surveys for selected locations within the united states (hydro_bathy_2006), in situ ocean-based platforms, in situ/laboratory instruments, marine sediments, mbes, msbs, multibeam mapping system, multibeam swath bathymetry system, national centers for environmental information, national geophysical data center, nesdis, noaa, north america, north pacific ocean, ocean, oceans, passive remote sensing, positioning/navigation, profilers/sounders, seafloor topography, sediment composition, ships, sonar, sound navigation and ranging, u.s. department of commerce, united states of america, water depth
Organization: National Oceanic and Atmospheric Administration, Department of Commerce
H12312: NOS Hydrographic Survey , Southern Puget Sound, Washington, 2011-11-10

The National Oceanic and Atmospheric Administration (NOAA) has the statutory mandate to collect hydrographic data in support of nautical chart compilation for safe navigation and to provide background data for engineers, scientific, and other commercial and industrial activities. Hydrographic survey data primarily consist of water depths, but may also include features (e.g. rocks, wrecks), navigation aids, shoreline identification, and bottom type information.
							NOAA is responsible for archiving and distributing the source data as described in this metadata record.

Tags: acoustic sounders, bathymetry, bathymetry/seafloor topography, continent, doc/noaa/nesdis/ncei, doc/noaa/nesdis/ngdc, earth remote sensing instruments, earth science, global positioning system/inertial measurement unit, gps, gps receivers, gps/imu, hydrographic surveys for selected locations within the united states (hydro_bathy_2006), in situ ocean-based platforms, in situ/laboratory instruments, marine sediments, mbes, msbs, multibeam mapping system, multibeam swath bathymetry system, national centers for environmental information, national geophysical data center, nesdis, noaa, north america, northern carr inlet, ocean, oceans, passive remote sensing, positioning/navigation, profilers/sounders, seafloor topography, sediment composition, ships, sonar, sound navigation and ranging, southern puget sound, u.s. department of commerce, united states of america, washington, water depth
Organization: National Oceanic and Atmospheric Administration, Department of Commerce