cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.30187966.v1
title: CS——raw date.xlsx

description: This dataset underpins the findings of the cross-sectional study titled "The mediating role of dyslipidemia and muscle mass in the visceral adiposity-metabolic syndrome link." The study investigates the association between visceral adiposity, lipid metabolism, body composition, and Circadian Syndrome (CircS) in a Chinese middle-aged and elderly population, with a focus on identifying mediating pathways and threshold effects.The data is a subset derived from the China Health and Retirement Longitudinal Study (CHARLS), a nationally representative survey. The analytical sample comprises 2,074 participants, including 835 individuals with CircS and 1,239 without CircS.<b>The dataset contains the following key variables:</b><b>Outcome:</b> Circadian Syndrome (CircS) status (binary).<b>Primary Exposures:</b> Lipid metabolism indices, including Visceral Adiposity Index (VAI), Atherogenic Index of Plasma (AIP), Non-HDL Cholesterol (NHDL), Residual Cholesterol (RC), and Castelli Risk Indices (I & II).<b>Mediators and Body Composition Indicators:</b> Appendicular Skeletal Muscle Mass (ASM), Frailty Index, Frailty Status (binary), and Hypertension status.<b>Comprehensive Covariates:</b> Demographic factors (age, gender, residence, marital status, education), lifestyle factors (smoking, drinking), and social factors (social isolation).<b>Data Reuse Potential:</b><br>This curated dataset is valuable for researchers interested in metabolic disorders, geriatric health, epidemiology, and statistical mediation analysis. It provides a practical example for replicating advanced statistical methods, including multiple logistic regression, stratified analysis, threshold effect analysis using piecewise linear regression, and causal mediation analysis within a counterfactual framework. The data can also be used for educational purposes in teaching epidemiological methods and for secondary analysis exploring other research questions related to aging and health in the Chinese population.<b>File(s) included:</b><code>CHARLS_Subset_CircS_Analysis.csv</code> (Primary dataset in CSV format)<b>Usage Notes:</b><br>To ensure accurate replication of the study's results, please refer to the formulas and diagnostic criteria provided in the associated manuscript for calculating derived indices (e.g., VAI, AIP, ASM, Frailty Index).<br>
DOI: 10.15468/dl.3svykk
title: Occurrence Download

description: A dataset containing 43 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cerinthe major",
 "Country is Netherlands",
 "HasCoordinate is true"
 ]
}

 The dataset includes 43 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008814-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/q9ltse
title: Marine photic zone, New Caledonia Lagoon raw sequence reads, nitrogenase amplicons

description: The VAHINE mesocosm experiment, conducted in the low-nutrient low-chlorophyll waters of the Noumea Lagoon (coastal New Caledonia) was designed to trace the incorporation of nitrogen (N) fixed by diazotrophs into the food web, using large volume (50 m3) mesocosms. This experiment provided a unique opportunity to study the succession of N2-fixing microorganisms (diazotrophs) and calculate in situ net growth and mortality rates in response to fertilization with dissolved inorganic phosphate (DIP) over a 23-day period, using both polymerase chain reaction (PCR) amplification of nitrogenase genes (nifH) and quantitative PCR (qPCR) assays targeting known marine diazotroph lineages.
DOI: 10.15468/dl.w3ndmc
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cerinthe major",
 "Country is Switzerland",
 "HasCoordinate is true"
 ]
}

 The dataset includes 8 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008815-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/hhsz9w
title: Annual Dynamics of Bacterial & Archaeal Communities in Fram Strait (2017-2018)

description: 16S rRNA amplicon sequences derived from moored autonomous samplers. Moorings: F4-S-2, HG-IV-S-2, Fevi-36, EGC-4.
DOI: 10.15468/eob0r2
title: Marine subseafloor sediment Targeted Locus (Loci)

description: We propose to apply 454-based tag pyrosequencing to investigate how microbial communities change with depth, lithology, and porewater geochemistry in the sediment that underlies one of the highest productivity regions in the world ocean. To accomplish this goal, we propose to analyze extracted DNA from 16 samples taken in high resolution in conjunction with detailed porewater geochemistry. This dataset will provide an unprecedented insight into the microbial ecology of a highly productive open ocean site (35 cm/k.y) to a sediment depth of 750 m and an age of 2.1 Ma. We anticipate that through this use of next-generation sequencing technology in combination with biogeochemical and cell count data sets collected during IODP expedition 323, we will obtain significant insight into this previously uncharted ecosystem.
DOI: 10.21227/gb51-qv46
title: "MELD"

description: "\u4eceMELD\u4e2d\u63d0\u53d6\u7684\u4eba\u8138\u5e8f\u5217"
DOI: 10.15468/k2fb0s
title: Surface samples of the NW Pacific Ocean Targeted Locus (Loci)

description: Diversity of DMS-producing dddP genes in the NW Pacific Ocean
DOI: 10.15468/6e5eqv
title: Groundwater microbiome
DOI: 10.5281/zenodo.17184449
title: Dissecting Oxidative Stress and Organismic Response to a Temperature Gradient in the midge Chironomus riparius

description: Oxidative stress, caused by reactive oxygen species (ROS), poses a major challenge for organisms facing temperature fluctuations. This study provides the first direct in vivo measurements of ROS production together with transcriptome analysis of oxidative stress genes across a broad range of ecologically relevant temperatures in insect larvae of the dipteran midge Chironomus riparius. We observed a U-shaped pattern of oxidative stress, with minimal ROS levels within an optimal thermal window (12-18°C) and significantly elevated stress at both cold and warm extremes. Crucially, our findings reveal distinct underlying molecular mechanisms for ROS generation at these extremes: at low temperatures, predominantly ROS produced is of the superoxide group, linked to hypoxia-induced hemoglobin autoxidation. Conversely, at high temperatures, the hydrogen peroxide group dominates, associated with increased metabolic rate and heat stress signaling pathways. Transcriptomic analysis shows that C. riparius's antioxidant defense system adapts accordingly, selectively upregulating mechanisms to counteract the specific dominant ROS type at different temperatures. This mechanistically differentiated oxidative stress at different temperatures and the modulated organismic response reflects the ecological niche and evolution of C. riparius.
DOI: 10.5281/zenodo.17184450
title: Dissecting Oxidative Stress and Organismic Response to a Temperature Gradient in the midge Chironomus riparius

description: Oxidative stress, caused by reactive oxygen species (ROS), poses a major challenge for organisms facing temperature fluctuations. This study provides the first direct in vivo measurements of ROS production together with transcriptome analysis of oxidative stress genes across a broad range of ecologically relevant temperatures in insect larvae of the dipteran midge Chironomus riparius. We observed a U-shaped pattern of oxidative stress, with minimal ROS levels within an optimal thermal window (12-18°C) and significantly elevated stress at both cold and warm extremes. Crucially, our findings reveal distinct underlying molecular mechanisms for ROS generation at these extremes: at low temperatures, predominantly ROS produced is of the superoxide group, linked to hypoxia-induced hemoglobin autoxidation. Conversely, at high temperatures, the hydrogen peroxide group dominates, associated with increased metabolic rate and heat stress signaling pathways. Transcriptomic analysis shows that C. riparius's antioxidant defense system adapts accordingly, selectively upregulating mechanisms to counteract the specific dominant ROS type at different temperatures. This mechanistically differentiated oxidative stress at different temperatures and the modulated organismic response reflects the ecological niche and evolution of C. riparius.
DOI: 10.15468/9k8caf
title: Global Ocean Sampling Expedition

description: Collection of metagenomes obtained during the Global Ocean Sampling Expedition
DOI: 10.15468/fo3bny
title: suspended particulate matter Raw sequence reads

description: Analysis of microbial diversity in the Black Sea water column
DOI: 10.15468/ntcm3h
title: Regional and vertical patterns in microbial communities across Fram Strait (2015-2019)

description: This study portrays bacterial and archaeal community composition over five summers in the Arctic Fram Strait (80°N). The dataset includes 16S rRNA gene amplicons derived from annual samplings along a longitudinal transect (6°W–12°E) from the surface to the lower photic zone, covering Arctic- / Atlantic-influenced waters in western / eastern Fram Strait.
DOI: 10.34740/kaggle/dsv/13147426
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.15468/nyfjcn
title: Amplicon sequencing of Tara Oceans Polar Circle DNA samples corresponding to size fractions for protists.

description: Analysis of 18S DNA in Tara Oceans Polar Circle Protists size fractions through amplicon sequencing: Seawater was filtered from different depths to retain small and large cell sizes. The DNA was extracted and amplified by PCR.
DOI: 10.15468/jtp2dl
title: Structure and function of picoplankton and virus communities along zonal gradients in the South Pacific Ocean

description: Picoplankton (0.2-2.7 µm fraction) and virus (&lt;0.22 µm fraction) samples were obtained on the BiG-RAPA (Biogeochemical Gradients Role in Arranging Planktonic Assemblages) expedition in the late austral spring of 2010. Additional samples obtained during this expedition include whole community biomass (&gt;0.22 µm fraction) samples that profile a deep (150 m) subsurface chlorophyll maximum in the South Pacific Gyre. High throughput, short read, shotgun sequencing was used to produce metagenomic data from the extracted DNA of these samples. These data enable the assessment of how picoplankton and viral populations are structured along strong physical and chemical gradients on a zonal transect from the upwelling along the western coast of South America to the oligotrophic gyre in the South Pacific.
DOI: 10.15468/dl.mwmgk4
title: Occurrence Download

description: A dataset containing 554 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Human Observation, Specimen, Occurrence evidence)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Conus omaria"
 ]
}

 The dataset includes 554 records from 41 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008819-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/imcjlx
title: Marine Water Column Samples Targeted loci environmental

description: Surface water samples collected from locations within Mobile Bay out into the northern Gulf of Mexico shelf region off the coast of Alabama for examination of microbial eukaryotes. 20-24 L water samples were collected bi-monthly from July 2009- Dec 2011, prefiltered through a 150um mesh and eukaryotic fraction was collected on a 0.7um glass fiber filter. This data was used to explore spatial and temporal variation as well as impact of the Deepwater Horizon Oil Spill on this community.
DOI: 10.15468/8mrybg
title: Mount Hope Bay bacteria Targeted Locus (Loci)

description: Coastal marine environments have been impacted by human activity for several centuries, including shoreline alteration, nutrient introduction, sedimentation, toxic compound release, and thermal modification. Mt. Hope Bay, Massachusetts is an ideal site to base a study of human pathogen presence and distribution because it has several important sources of human impact, including sewage disposal sites and the thermal outfall of a power plant within a mile of each other. The Bay has undergone limited monitoring for several different parameters, including fish populations, river runoff, meteorological forcing, tidal cycles and water chemistry as part of the Mt. Hope Bay Natural Laboratory (MHBNL) program, a 5-year interdisciplinary project at the University of Massachusetts Dartmouth School of Marine Science and Technology (SMAST). While phytoplankton and zooplankton communities in the water column have been fairly well monitored, although not at a molecular level, microbial communities remain relatively uncharacterized. This project presents comprehensive (eukaryal, bacterial, archaeal) data from small-subunit ribosomal RNA gene clone libraries and next-generation Illumina amplicon sequencing for samples collected near the thermal plume and underlying sediments of the Brayton Point Power Plant. Not surprising, our findings reveal a highly diverse consortium of the three domains including relatives of sludge bacteria, polyaromatic hydrocarbon-degrading bacteria, and representatives related to the genera Staphylococcus, Streptococcus, and Clostridium. It is clear that even limited knowledge about the overall microbial community composition can lead to important observations about the ecosystem as a whole. Furthermore, understanding whether free-living pathogens participate in relationships with other members of the microbial community will be important in understanding their distributions and persistence.
DOI: 10.15468/dl.6xhxfx
title: Occurrence Download

description: A dataset containing 17 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cerinthe minor",
 "Country is Belgium",
 "HasCoordinate is true"
 ]
}

 The dataset includes 17 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008820-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/xvg1ho
title: Pyrosequencing reveals highly diverse and species-specific microbial communities in sponges from the Red Sea

description: Marine sponges are associated with a remarkable array of microorganisms. Using a tag pyrosequencing technology, this study was the first to deeply investigate the microbial communities associated with three Red Sea sponges, Hyrtios erectus, Stylissa carteri, and Xestospongia testudinaria. We revealed highly diverse sponge-associated bacterial communities with up to 1,000 microbial OTUs and an estimate of up to 2,000 species. Altogether 26 bacterial phyla were detected from the Red Sea sponges, 11 of which were absent from the surrounding seawater and 4 of which were recorded in sponges for the first time. Up to 100 OTUs with an estimate of up to 300 archaeal species were revealed from a single sponge species. This is by far the highest diversity ever recorded for sponges. A non-negligible proportion of unclassified reads in sponges may represent the presence of novel species. Our results demonstrated that the sponge-associated microbial communities remained highly consistent in the same sponge species from different locations although they varied to certain degrees among different sponge species. A significant proportion of the tag sequences from the sponges could be assigned into one of the sponge-specific clusters previously defined. In addition, the sponge-associated microbial communities were consistently diverged from those in the surrounding seawater. Our results suggested the Red Sea sponges possess highly sponge-species specific microbial communities which are resistant to environmental influence. Although sponges have been regarded as microbial fermenters with a huge microbial diversity being reported among the animal kingdom, much of their microbial diversity remains to be explored.
DOI: 10.15468/dl.58m3zm
title: Occurrence Download

description: A dataset containing 286 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cerinthe minor",
 "Country is Czechia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 286 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008822-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/hfai2t
title: lake sediment Raw sequence reads

description: methanotrophs diversity in lake sediments
DOI: 10.15468/dl.dx4exf
title: Occurrence Download

description: A dataset containing 24 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cerinthe minor",
 "Country is Bulgaria",
 "HasCoordinate is true"
 ]
}

 The dataset includes 24 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008821-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dg8a2j
title: Microbial communities associated with Eurasian watermilfoil, water and sediment

description: Characterize microbial communities associated with Eurasian watermilfoil, water and sediment in freshwater lakes in Minnesota USA
DOI: 10.5281/zenodo.17184329
title: 241207_4DHSI_Bovine_Heart_LeftAtrium_RFA
title: 2024-12-07 / Heart Radiofrequency Ablation and 4D-Hyperspectral Imaging/ Heart-RFA-4D-HSI

description: Materials and Methods

A fresh heart extracted from a male bovine (age: 1 year and 6-7 months, weight: 130-140 kg, death time: 11:15, heart removal time: 11:52) was delivered on ice to the Orbeli Institute, and dissection started at 13:04. Pieces of tissue were extracted from the left atrium. Three left atria tissue pieces were used for executing several RFA lesions and imaging. RFA machine (EPT-1000 XP, Boston Scientific) was set up at 8 W power and 15 s duration. The data with respect to each sample is shown in the following table.

Ablation description:








Sample 1 



Starting time 13:15



Sample 2



Starting time 14:11



Sample 3



Starting time 15:14







Lesion number



Duration (s)



Lesion number



Duration (s)



Lesion number



Duration (s)





1



15



1



15



1



15





2



15



2



15



2



15





3



15



3



15



3 (due to muscle contraction, catheter tip moved during RFA)



15





4



15



4



15



4



15





5



15



5



15



5



15





6



15



6



15

 
 




7



15

 
 
 
 




8



15

 
 
 
 





Hyperspectral Imaging (HSI)

Images were taken under illumination with a light source constructed by the lab, consisting of a xenon lamp and filter wheel (343, 351, 360, 370, 380 and 390 nm). White light image was taken under illumination with white LED light. While imaging, the samples were immersed in cold PBS together with ice.

Hyperspectral images were taken with a Nuance FX Imaging System (model: N-MSI-FX, CRi, Woburn, MA, USA). For each sample, several cubes were acquired under illumination with each of the wavelengths above mentioned, as described in the respective metadata files for each sample. 





Metadata_Sample1.csv




Metadata_Sample2.csv




Metadata_Sample3.csv



Pixel Calibration

Pixel size can be calculated based on the scale images acquired at approximately the same distance from the camera. These are available as:





Scale_Sample1.tif




Scale_Sample2.tif




Scale_Sample3.tif



In this dataset scale images are copies of the same for all samples, in order to facilitate programmatic access via parametrization.

TTC

After HSI acquisition, the ablation on the samples were revealed with 2,3,5-Triphenyltetrazolium chloride (TTC) staining. TTC solution was prepared the same day at 1% concentration. Two slices (denoted as “a” and “b”) were cut from the center of each lesion, and immersed in TTC solution. After at least 20 minutes of incubation, slices were photographed together with scale, for estimating lesion size.

Respective data are available in the following folders:





TTC_Sample1




TTC_Sample2




TTC_Sample3



Data Management

This dataset has been organized and structured according to the following guidelines: https://doi.org/10.5281/zenodo.17176953
DOI: 10.5281/zenodo.17184330
title: 241207_4DHSI_Bovine_Heart_LeftAtrium_RFA
title: 2024-12-07 / Heart Radiofrequency Ablation and 4D-Hyperspectral Imaging/ Heart-RFA-4D-HSI

description: Materials and Methods

A fresh heart extracted from a male bovine (age: 1 year and 6-7 months, weight: 130-140 kg, death time: 11:15, heart removal time: 11:52) was delivered on ice to the Orbeli Institute, and dissection started at 13:04. Pieces of tissue were extracted from the left atrium. Three left atria tissue pieces were used for executing several RFA lesions and imaging. RFA machine (EPT-1000 XP, Boston Scientific) was set up at 8 W power and 15 s duration. The data with respect to each sample is shown in the following table.

Ablation description:








Sample 1 



Starting time 13:15



Sample 2



Starting time 14:11



Sample 3



Starting time 15:14







Lesion number



Duration (s)



Lesion number



Duration (s)



Lesion number



Duration (s)





1



15



1



15



1



15





2



15



2



15



2



15





3



15



3



15



3 (due to muscle contraction, catheter tip moved during RFA)



15





4



15



4



15



4



15





5



15



5



15



5



15





6



15



6



15

 
 




7



15

 
 
 
 




8



15

 
 
 
 





Hyperspectral Imaging (HSI)

Images were taken under illumination with a light source constructed by the lab, consisting of a xenon lamp and filter wheel (343, 351, 360, 370, 380 and 390 nm). White light image was taken under illumination with white LED light. While imaging, the samples were immersed in cold PBS together with ice.

Hyperspectral images were taken with a Nuance FX Imaging System (model: N-MSI-FX, CRi, Woburn, MA, USA). For each sample, several cubes were acquired under illumination with each of the wavelengths above mentioned, as described in the respective metadata files for each sample. 





Metadata_Sample1.csv




Metadata_Sample2.csv




Metadata_Sample3.csv



Pixel Calibration

Pixel size can be calculated based on the scale images acquired at approximately the same distance from the camera. These are available as:





Scale_Sample1.tif




Scale_Sample2.tif




Scale_Sample3.tif



In this dataset scale images are copies of the same for all samples, in order to facilitate programmatic access via parametrization.

TTC

After HSI acquisition, the ablation on the samples were revealed with 2,3,5-Triphenyltetrazolium chloride (TTC) staining. TTC solution was prepared the same day at 1% concentration. Two slices (denoted as “a” and “b”) were cut from the center of each lesion, and immersed in TTC solution. After at least 20 minutes of incubation, slices were photographed together with scale, for estimating lesion size.

Respective data are available in the following folders:





TTC_Sample1




TTC_Sample2




TTC_Sample3



Data Management

This dataset has been organized and structured according to the following guidelines: https://doi.org/10.5281/zenodo.17176953