cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.26567827.v1
title: Additional file 1 of Liver saturated fat content associates with hepatic DNA methylation in obese individuals

description: Additional file 1: Table S1. SFA-related DNA methylation in human liver. The table contains the 3169 CpGs found to be associated with total liver saturated fat content.
DOI: 10.6084/m9.figshare.26567845
title: Additional file 6 of Liver saturated fat content associates with hepatic DNA methylation in obese individuals

description: Additional file 6: Table S3. Proportions of significant correlation between the CpGs and the clinical variables. The correlations for all the four groups CpGs were correlated with the clinical variables and were adjusted for multiple testing. The proportions of significant correlations (adjusted p value &lt; 0.1) for each variable and group are tabulated in the file.
DOI: 10.6084/m9.figshare.26567845.v1
title: Additional file 6 of Liver saturated fat content associates with hepatic DNA methylation in obese individuals

description: Additional file 6: Table S3. Proportions of significant correlation between the CpGs and the clinical variables. The correlations for all the four groups CpGs were correlated with the clinical variables and were adjusted for multiple testing. The proportions of significant correlations (adjusted p value &lt; 0.1) for each variable and group are tabulated in the file.
DOI: 10.5281/zenodo.13322718
title: Test Mlinvitrotox model

description: asdf
DOI: 10.6084/m9.figshare.26567887
title: Additional file 12 of Patterns of variation in equine strongyle community structure across age groups and gut compartments

description: Additional file 10. Dataset 1. Strongyle species co-occurrence estimates derived from data collected in Normandy, France or Victoria State, Australia.
DOI: 10.18712/nsd-nsd2325-v2
title: Substituted Furans: A Novel Group of Food Processing Contaminants and Their Influence on Intestinal Cancer Development and Human Health Risk, 2015

description: Colorectal cancer is among the most prevalent types of cancers in Norway and current data show that the risk of developing colorectal cancer is diet associated. Most foods are processed before consumed, and this leads to formation of new compounds some of which can be hazardous to humans. The substituted furans are a novel class of such food processing contaminants; some have already been shown to induce tumours in mice. However, little or no information on the hazard, human intake and occurrence in food are available for most members of this broad group of food processing contaminants. This project gave more relevant characterisation of the hazards from substituted furans. The aim was to evaluate the human health risk of dietary exposure to substituted furans. Humans do more efficiently bioactivate substituted furans than rodents, it is thereby imperative to use appropriate models. In this study in vitro and in vivo models with bioactivating systems more similar to humans were used. Human intake studies along with analyses of substituted furan concentrations in food and their biomarkers in human urine gave together with the hazard characterisation information to an evaluation of the human health risk. The results are useful for scientists, authorities and industry.

Articles and associated data files:
- "Genotoxicity of three food processing contaminants in transgenic mice expressing human sulphotransferases 1A1 and 1A2 as assessed by the in vivo alkaline single cell gel electrophoresis assay". Data set: Rapportering av rådata Comet.
- "Formation of DNA adducts in wild type and transgenic mice expressing human sulphotransferase 1A1 and 1A2 after oral exposure to furfuryl alcohol". Data set: Rapportering av rådata FFA addukter, figure 3 - UPLC-MSMSchromatograms DNA sample of FFA exposed SULT mice.
- "Intestinal Tumour Development in C57BL/6J-ApcMin/+ Mice Expressing Human Sulphotransferases 1A1 and 1A2 After Oral Exposure to 2,5-Dimethylfuran". Data set: Rapportering av rådata DMF og kreftutvikling.
- "DNA adducts induced by food mutagen PhIP in a mouse model expressing human sulfotransferases 1A1 and 1A2". Data set: Rapportering av rådata PhIP addukter, figure 1.
- "An in vitro study on the genotoxic effect of substituted furans in cells transfected with human metabolizing enzymes: 2,5-Dimethylfuran and furfuryl alcohol". Data set: Rapportering av rådata DMF in vitro Komet, rådata furfuryl alcohol in vitro Komet.
DOI: 10.6084/m9.figshare.26567887.v1
title: Additional file 12 of Patterns of variation in equine strongyle community structure across age groups and gut compartments

description: Additional file 10. Dataset 1. Strongyle species co-occurrence estimates derived from data collected in Normandy, France or Victoria State, Australia.
DOI: 10.6084/m9.figshare.26567810.v1
title: Additional file 2 of Parity is associated with long-term differences in DNA methylation at genes related to neural plasticity in multiple sclerosis

description: Additional file 2: Supplementary Tables.
DOI: 10.15468/dl.rtanhy
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Rhododendron coelorum Wernham"
 ]
}

 The dataset includes 5 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0066492-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25497/d73s3f
title: RECOVER MAP 3.2.4.6 Salinity Relationships of Epifaunal Species in Near-Shore Biscayne Bay

description: The pink shrimp (Farfantepenaeus duorarum), supports a multi-million dollar industry in South Florida and provides a critical food resource for higher trophic level species in Biscayne Bay. Florida pink shrimp spawn offshore of the Dry Tortugas and the larvae migrate to critical nursery grounds in Florida and Biscayne Bays. Pink shrimp recruitment studies focusing on Florida Bay have shown a large degree of correlation between water quality/conditions and shrimp abundance. Specifically, salinity and temperature have been shown to have direct effects on the production of the pink shrimp nursery in Florida Bay. Therefore, understanding the physiological state and performance of pink shrimp, at different salinities and temperatures in Biscayne Bay is critical in predicting the effects of changing salinity and temperature on secondary productivity in, and the overall health of, the bay. This study investigated the effects of different salinity and temperature exposure scenarios on pink shrimp (Farfantepenaeus duorarum) collected from Biscayne Bay. The purpose was to determine the optimum salinity and temperature conditions for pink shrimp as defined for performance measures (i.e. survival, development, growth). Preliminary testing showed that at 25 degress Celsius, significant differences (p=0.05) were found in the survival of post-larval pink shrimp at different salinities from the control (30 ppt). The lowest salinity at which there was no significant difference from the control was 10 ppt.
DOI: 10.6084/m9.figshare.26567923.v1
title: Additional file 3 of Low muscle mass in lung cancer is associated with an inflammatory and immunosuppressive tumor microenvironment

description: Additional file 3: Table S1. Human Protein Atlas (HPA) list of 2943 secretory genes predicted using majority decision-based method for secreted proteins (MDSEC). Table S2. Lung cancer cell lines and lung tumor 3D organoids. Table S3. List of differentially expressed genes in low-muscularity patients compared to high-muscularity patients. Table S4. List of cachexia-inducing factors described in the literature. Table S5. List of genes specifically expressed in exhausted tumor CD8+ T cells according to Guo et al., 2018.
DOI: 10.6084/m9.figshare.26598863
title: Additional file 2 of Novel models by machine learning to predict prognosis of breast cancer brain metastases

description: Additional file 2: Table S2. Univariate and multivariate COX analysis of characteristics (stratified by molecular subtype).
DOI: 10.6084/m9.figshare.26598860
title: Additional file 1 of Novel models by machine learning to predict prognosis of breast cancer brain metastases

description: Additional file 1: Table S1. Clinical and prognostic information from patients with BCBM from our hospital.
DOI: 10.15468/dl.rtdr4k
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "POLYGON ((148.564886 -32.44559, 148.564886 -32.450082, 148.560395 -32.450082, 148.560395 -32.452327, 148.558149 -32.452327, 148.558149 -32.454573, 148.564886 -32.454573, 148.564886 -32.452327, 148.567132 -32.452327, 148.567132 -32.44559, 148.564886 -32.44559))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0066493-240626123714530/datasets/export for details.
DOI: 10.6084/m9.figshare.26598863.v1
title: Additional file 2 of Novel models by machine learning to predict prognosis of breast cancer brain metastases

description: Additional file 2: Table S2. Univariate and multivariate COX analysis of characteristics (stratified by molecular subtype).
DOI: 10.6084/m9.figshare.26598860.v1
title: Additional file 1 of Novel models by machine learning to predict prognosis of breast cancer brain metastases

description: Additional file 1: Table S1. Clinical and prognostic information from patients with BCBM from our hospital.
DOI: 10.6084/m9.figshare.26598770
title: Additional file 2 of Progesterone attenuates Th17-cell pathogenicity in autoimmune uveitis via Id2/Pim1 axis

description: Additional file 2: Table S1. Cell clustering strategy in scRNA-seq. Table S2. The differential expression analysis in Treg of Figure 4F-G. Table S3. The differential expression analysis in Th17 and Treg of Figure 5A. Table S4. The expression correlation analysis of downregulated rescue-DEGs of Th17 cells and the genes related to T cell activation, Th17 cell differentiation, IL-17 signaling pathway.
DOI: 10.6084/m9.figshare.26598770.v1
title: Additional file 2 of Progesterone attenuates Th17-cell pathogenicity in autoimmune uveitis via Id2/Pim1 axis

description: Additional file 2: Table S1. Cell clustering strategy in scRNA-seq. Table S2. The differential expression analysis in Treg of Figure 4F-G. Table S3. The differential expression analysis in Th17 and Treg of Figure 5A. Table S4. The expression correlation analysis of downregulated rescue-DEGs of Th17 cells and the genes related to T cell activation, Th17 cell differentiation, IL-17 signaling pathway.
DOI: 10.34740/kaggle/dsv/9173451
title: Public Opinion on Climate Change (Updated Daily)
DOI: 10.15468/dl.hrcvgt
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "MULTIPOLYGON (((144.488761 -36.858585, 144.493253 -36.858585, 144.493253 -36.854094, 144.488761 -36.854094, 144.488761 -36.858585)), ((144.488761 -36.858585, 144.486515 -36.858585, 144.486515 -36.860831, 144.488761 -36.860831, 144.488761 -36.858585)))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0066495-240626123714530/datasets/export for details.
DOI: 10.6084/m9.figshare.26599055
title: Additional file 3 of Using three-dimensional printed models for trainee orbital fracture education

description: Supplementary Material 3
DOI: 10.6084/m9.figshare.26598992.v1
title: Additional file 1 of Epipericardial fat necrosis in chest CT and MRI: a case report of an unusual cause of chest pain associated with the initial diagnosis of undifferentiated connective tissue disease

description: Additional file 1. Contrast-enhanced chest CT axial, sagittaland reformatted sagittal obliqueclip videos demonstrating an ovoid-shaped mediastinal fat lesion with soft tissue stranding, consistent with necrosis of the epicardial fat at the left cardiophrenic angle.
DOI: 10.6084/m9.figshare.26598992
title: Additional file 1 of Epipericardial fat necrosis in chest CT and MRI: a case report of an unusual cause of chest pain associated with the initial diagnosis of undifferentiated connective tissue disease

description: Additional file 1. Contrast-enhanced chest CT axial, sagittaland reformatted sagittal obliqueclip videos demonstrating an ovoid-shaped mediastinal fat lesion with soft tissue stranding, consistent with necrosis of the epicardial fat at the left cardiophrenic angle.
DOI: 10.6084/m9.figshare.26598995
title: Additional file 2 of Epipericardial fat necrosis in chest CT and MRI: a case report of an unusual cause of chest pain associated with the initial diagnosis of undifferentiated connective tissue disease

description: Additional file 2. Chest MRI sagittal (File 4) and sagittal oblique (File 5) fluid sensitive T2 sequence clip videos showing a fatty lesion with increased signal (edema) stranding in the left cardiophrenic angle.
DOI: 10.6084/m9.figshare.26598995.v1
title: Additional file 2 of Epipericardial fat necrosis in chest CT and MRI: a case report of an unusual cause of chest pain associated with the initial diagnosis of undifferentiated connective tissue disease

description: Additional file 2. Chest MRI sagittal (File 4) and sagittal oblique (File 5) fluid sensitive T2 sequence clip videos showing a fatty lesion with increased signal (edema) stranding in the left cardiophrenic angle.
DOI: 10.15468/dl.4wcqpj
title: Occurrence Download

description: A dataset containing 155 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "MULTIPOLYGON (((148.582853 -32.450082, 148.587344 -32.450082, 148.587344 -32.443344, 148.582853 -32.443344, 148.582853 -32.450082)), ((148.582853 -32.450082, 148.573869 -32.450082, 148.573869 -32.452327, 148.582853 -32.452327, 148.582853 -32.450082)))"
 ]
}

 The dataset includes 155 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0066496-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25497/d77g6q
title: RECOVER MAP 3.1.3.6 Landscape Pattern - Ridge, Slough, and Tree Island function: Surfacewater-Groundwater Interaction in WCA3 TIs

description: This project is a component of the GE Wetland module of the CERP Monitoring and Assessment Plan (MAP) and is directly linked to the a) Ridge and Slough Landscape monitoring and research component of CERP, and b) Tree Island Stage Duration and the measurement of water depth on tree islands located in WCA 3A and 3B. It will significantly improve RECOVER and the SFWMD's ability to support Central Everglades Plan Process (CEPP), Everglades Forever Act, Minimum Flows and Levels (MFL), Regulatory Operations and CERP by: 1) developing a way to reverse the significant loss of tree island in WCA-2A (Worth 1988) and WCA-3 (Sklar and van der Valk 2002), 2) conduct environmental assessments for weekly SFWMD operational meetings, and 3) develop criteria to protect the flora and fauna that rely on the existence of Tree Islands.
This research monitoring will take place at four different tree islands located in the Water Conservation Area 3. This Statement of Work (SOW) includes the study objectives, a general description of the scope, a detailed listing of tasks to be undertaken and associated deliverables, and the timeframes citing the methodologies to be used by the contractor to perform assigned work efforts.

This project will compare the characteristics and dynamics of four Everglades tree islands such that hydraulic patterns and hydrogeochemical processes can be characterized. This monitoring project aims to understand how biogeochemical pattern and processes operating at inter-annual temporal and spatial scales can mediate tree island growth and patch maintenance through interaction of biological, geochemical, and climatic factors. It is hypothesized that water movement, mediated by hydraulic processes that are punctuated during the dry season by increased tree island evapotranspiration (ET), influence the lateral flux of nutrients to downstream components of the tree island ecosystem, thus concentrating phosphorus at the intersection between local and regional water pools. The objectives of this project are: 1) monitor and characterize spatial and temporal variability in diurnal ET patterns, 2) monitor and characterize temporal local and regional hydraulic patterns, and 3) characterize spatial and temporal hydro-chemical patterns in ions and nutrients among tree island plant communities and the adjacent deep water slough, and 4) design and implement a field experiment addressing questions linked to environmental conditions for soil development and feasibility of active management as a means to restore the structure and function of degraded tree islands.
DOI: 10.15468/dl.t236rj
title: Occurrence Download

description: A dataset containing 3339 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Parambassis siamensis (Fowler, 1937), Pristolepis fasciata (Bleeker, 1851), Esomus metallicus Ahl, 1923)",
 "Year is not null",
 {
 "not" : {
 "Issue" : [
 "is one of (Recorded date invalid, Taxon match fuzzy, Taxon match higher rank)"
 ]
 }
 }
 ]
}

 The dataset includes 3339 records from 44 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0066499-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.u9jcqh
title: Occurrence Download

description: A dataset containing 121301 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is South Africa",
 "GadmGid is ZAF.5_1",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Plantae"
 ]
}

 The dataset includes 121301 records from 89 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0066420-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15156771
title: Assessing Software Evolution with the Stickiness Score: Evaluating Code Persistence Across Files, Folders, and Developers - Replication Package

description: This package contains data and source code for the Devotion backend, frontend, and hypothesis testing. It is organized into two main folders:



Devotion: Contains the source code for both the frontend and backend of Devotion.

Hypothesis_Testing: Includes the preprocess-input folder, where Devotion’s output files are processed for hypothesis testing. The tokens folder requires a Git token. Other subfolders contain data, source code for hypothesis testing, test results, and plots corresponding to research questions.


Below are the instructions for running the Python scripts.



Instructions






Prerequisites


Before running the backend, install these dependencies using the following command:



pip install -r ./Devotion/requirements.txt

 




Running the Backend


To run the backend of Devotion, navigate to the Devotion folder and use the following command:



cd ./Devotion
python ./runner.py <GitHub_Repo_URL> <Log_File_Name>

 




Running the Web Application


Before starting the web application, ensure all dependencies are installed by running:



npm install

 


To start the web application of Devotion, navigate to the client folder and run:



cd ./Devotion/frontend/client
npm run start

 




Running the Hypothesis Testing Code






Write your GitHub token:



Save your GitHub token in the Hypothesis_Testing/tokens/github-token.txt file to allow the scripts to access the GitHub API.





Place the required files:



Copy authors.json and folder_structure.json from the Devotion/frontend/client/src folder into the Hypothesis_Testing/preprocess-input folder, inside a new folder named after your project.





Execute the hypothesis testing for each research question:



First, run the Python script located in the preprocess folder.

Then, run the Python script in the hypothesis folder.





Output:



Results, including data points, plots, and the outcomes of normality and correlation tests, will be saved in the hypothesis-output folder.
DOI: 10.5281/zenodo.15156772
title: Assessing Software Evolution with the Stickiness Score: Evaluating Code Persistence Across Files, Folders, and Developers - Replication Package

description: This package contains data and source code for the Devotion backend, frontend, and hypothesis testing. It is organized into two main folders:



Devotion: Contains the source code for both the frontend and backend of Devotion.

Hypothesis_Testing: Includes the preprocess-input folder, where Devotion’s output files are processed for hypothesis testing. The tokens folder requires a Git token. Other subfolders contain data, source code for hypothesis testing, test results, and plots corresponding to research questions.


Below are the instructions for running the Python scripts.



Instructions






Prerequisites


Before running the backend, install these dependencies using the following command:



pip install -r ./Devotion/requirements.txt

 




Running the Backend


To run the backend of Devotion, navigate to the Devotion folder and use the following command:



cd ./Devotion
python ./runner.py <GitHub_Repo_URL> <Log_File_Name>

 




Running the Web Application


Before starting the web application, ensure all dependencies are installed by running:



npm install

 


To start the web application of Devotion, navigate to the client folder and run:



cd ./Devotion/frontend/client
npm run start

 




Running the Hypothesis Testing Code






Write your GitHub token:



Save your GitHub token in the Hypothesis_Testing/tokens/github-token.txt file to allow the scripts to access the GitHub API.





Place the required files:



Copy authors.json and folder_structure.json from the Devotion/frontend/client/src folder into the Hypothesis_Testing/preprocess-input folder, inside a new folder named after your project.





Execute the hypothesis testing for each research question:



First, run the Python script located in the preprocess folder.

Then, run the Python script in the hypothesis folder.





Output:



Results, including data points, plots, and the outcomes of normality and correlation tests, will be saved in the hypothesis-output folder.
DOI: 10.15468/dl.4zdfpk
title: Occurrence Download

description: A dataset containing 15467 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-21.44531 31.35364,-38.32031 14.87679,-9.07031 0.98428,4.42969 -9.65709,12.30469 -41.92843,32.55469 -42.75993,57.86719 -32.54681,58.99219 7.15321,33.11719 30.87204,15.67969 38.71294,-21.44531 31.35364))",
 "HasCoordinate is true",
 "TaxonKey is Streptopelia decipiens (Hartlaub & Finsch, 1870)",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 15467 records from 41 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013863-190918142434337/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mctj2c
title: Occurrence Download

description: A dataset containing 2223 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is Phapitreron amethystinus Bonaparte, 1855"
 ]
}

 The dataset includes 2223 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0055477-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.