cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/yzxtxn4nmd.2
title: RNA Sequencing-Based Single Sample Predictors of Molecular Subtype and Risk of Recurrence for Clinical Assessment of Early-Stage Breast Cancer

description: Gene expression data and associated supplementary files from RNAseq of breast cancer samples from Staaf et al. npj Breast Cancer 2022 (source reference below). Library preparation for mRNA-sequencing was done by a stranded dUTP mRNA protocol or by Illumina stranded TruSeq mRNA protocol. Expression data (Fragments Per Kilobase per Million reads, FPKM) was generated by an analysis pipeline utilizing Hisat/StringTie with GRCh38 human genome primary assembly and GENCODE Release 27 transcripts/genes. Gene expression data is summarized on GENCODE gene identifier. Gene and transcript definitions and gene annotations are from GENCODE Release 27.

Detailed description including material and methods for RNAseq, Hisat/StringTie analysis pipeline, and the development of the Single Sample Predictor (SSP) models for Breast Cancer is available in Staaf et al. npj Breast Cancer 2022 (source reference below).

The developed SSP models are available as an R package available at GitHub (reference below).
DOI: 10.17632/yzxtxn4nmd.3
title: RNA Sequencing-Based Single Sample Predictors of Molecular Subtype and Risk of Recurrence for Clinical Assessment of Early-Stage Breast Cancer

description: Gene expression data and associated supplementary files from RNAseq of breast cancer samples from Staaf et al. npj Breast Cancer 2022 (source reference below). Library preparation for mRNA-sequencing was done by a stranded dUTP mRNA protocol or by Illumina stranded TruSeq mRNA protocol. Expression data (Fragments Per Kilobase per Million reads, FPKM) was generated by an analysis pipeline utilizing Hisat/StringTie with GRCh38 human genome primary assembly and GENCODE Release 27 transcripts/genes. Gene expression data is summarized on GENCODE gene identifier. Gene and transcript definitions and gene annotations are from GENCODE Release 27.

Detailed description including material and methods for RNAseq, Hisat/StringTie analysis pipeline, and the development of the Single Sample Predictor (SSP) models for Breast Cancer is available in Staaf et al. npj Breast Cancer 2022 (source reference below).

The developed SSP models are available as an R package available at GitHub (reference below).
DOI: 10.17632/yzxtxn4nmd.1
title: RNA Sequencing-Based Single Sample Predictors of Molecular Subtype and Risk of Recurrence for Clinical Assessment of Early-Stage Breast Cancer

description: Gene expression data and associated supplementary files from RNAseq of breast cancer samples from Staaf et al. (source reference below). Library preparation for mRNA-sequencing was done by a stranded dUTP mRNA protocol or by Illumina stranded TruSeq mRNA protocol. Expression data (Fragments Per Kilobase per Million reads, FPKM) was generated by an analysis pipeline utilizing Hisat/StringTie with GRCh38 human genome primary assembly and GENCODE Release 27 transcripts/genes. Gene expression data is summarized on GENCODE gene identifier. Gene and transcript definitions and gene annotations are from GENCODE Release 27.

Detailed description including material and methods for RNAseq, Hisat/StringTie analysis pipeline, and the development of the Single Sample Predictor (SSP) models for Breast Cancer is available in Staaf et al. (source reference below).

The developed SSP models are available as an R package available at GitHub (reference below).
DOI: 10.17632/yzxtxn4nmd.4
title: RNA Sequencing-Based Single Sample Predictors of Molecular Subtype and Risk of Recurrence for Clinical Assessment of Early-Stage Breast Cancer

description: Gene expression data and associated supplementary files from RNAseq of breast cancer samples from Staaf et al. npj Breast Cancer 2022 (source reference below). Library preparation for mRNA-sequencing was done by a stranded dUTP mRNA protocol or by Illumina stranded TruSeq mRNA protocol. Expression data (Fragments Per Kilobase per Million reads, FPKM) was generated by an analysis pipeline utilizing Hisat/StringTie with GRCh38 human genome primary assembly and GENCODE Release 27 transcripts/genes. Gene expression data is summarized on GENCODE gene identifier. Gene and transcript definitions and gene annotations are from GENCODE Release 27.

Detailed description including material and methods for RNAseq, Hisat/StringTie analysis pipeline, and the development of the Single Sample Predictor (SSP) models for Breast Cancer is available in Staaf et al. npj Breast Cancer 2022 (source reference below).

The developed SSP models are available as an R package available at GitHub (reference below).
DOI: 10.15468/dl.s98pt9
title: Occurrence Download

description: A dataset containing 213 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is EOD – eBird Observation Dataset",
 "GadmGid is CHN.23.12_1",
 "TaxonKey is Passeriformes",
 "Year 1994-2025"
 ]
}

 The dataset includes 213 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0063852-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mj679a
title: Occurrence Download

description: A dataset containing 10234 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ahnfeltia plicata (Huds.) Fr."
 ]
}

 The dataset includes 10234 records from 202 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0063853-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17632/96z6whg4c5.1
title: Equilibrium-Traffic-Networks

description: This repository contains three DGL datasets generated for the study "A hybrid deep-learning-metaheuristic framework for bi-level network design problems" by Bahman Madadi and Gonçalo H. de Almeida Correia, published in Expert Systems with Applications. The datasets are generated and used to train and evaluate models for solving the User Equilibrium (UE) problem on three transportation networks (Sioux-Falls, Eastern-Massachusetts, and Anaheim) from the well-known "transport networks for research" repository.
Detailed information can be found in the "Metadata.md" file.

Note: This dataset is maintained at Figshare (https://doi.org/10.6084/m9.figshare.27889251).

References
Article: A hybrid deep-learning-metaheuristic framework for bi-level network design problems (https://doi.org/10.1016/j.eswa.2023.122814)
GitHub Repository: HDLMF_GIN-GA (https://github.com/bahmanmdd/HDLMF_GIN-GA)
Primary Figshare data repository: https://doi.org/10.6084/m9.figshare.27889251
DOI: 10.17632/96z6whg4c5.2
title: Equilibrium-Traffic-Networks

description: This repository contains three DGL datasets generated for the study "A hybrid deep-learning-metaheuristic framework for bi-level network design problems" by Bahman Madadi and Gonçalo H. de Almeida Correia, published in Expert Systems with Applications. The datasets are generated and used to train and evaluate models for solving the User Equilibrium (UE) problem on three transportation networks (Sioux-Falls, Eastern-Massachusetts, and Anaheim) from the well-known "transport networks for research" repository.
Detailed information can be found in the "Metadata.md" file.

Note: This dataset is maintained at Figshare (https://doi.org/10.6084/m9.figshare.27889251).

References
Article: A hybrid deep-learning-metaheuristic framework for bi-level network design problems (https://doi.org/10.1016/j.eswa.2023.122814)
GitHub Repository: HDLMF_GIN-GA (https://github.com/bahmanmdd/HDLMF_GIN-GA)
Primary Figshare data repository: https://doi.org/10.6084/m9.figshare.27889251
DOI: 10.17632/fhc566gp7w.1
title: Balkan Peace Index

description: This dataset is a result of development of the Balkan Peace Index, a model tailored for evaluating levels of peacefulness in the Balkans. Leaning on the local turn principle in International Relations, the dataset addresses the necessity of a region-specific model. Unlike conventional ranking systems, the Balkan Peace Index focuses on a peace classification method, aiming to explain the decision to policy-makers with an explanation of a country's position on the peace continuum. The objective extends beyond a snapshot of the current state, emphasizing actionable insights for improvement and pre-emptive measures against potential deterioration. As a method we choose a qualitative method for classification -- Decision EXpert. This method allows transparency in the score design, consistency of the scores, and it is convenient through its easy to understand nature and the possibility to perform sensitivity analysis. An integral aspect of this research is the sharing of methodology, data, and results with the wider research community, which can serve as a valuable resource for decision and policy-makers.
DOI: 10.17632/fhc566gp7w.2
title: Balkan Peace Index

description: This dataset is a result of development of the Balkan Peace Index, a model tailored for evaluating levels of peacefulness in the Balkans. Leaning on the local turn principle in International Relations, the dataset addresses the necessity of a region-specific model. Unlike conventional ranking systems, the Balkan Peace Index focuses on a peace classification method, aiming to explain the decision to policy-makers with an explanation of a country's position on the peace continuum. The objective extends beyond a snapshot of the current state, emphasizing actionable insights for improvement and pre-emptive measures against potential deterioration. As a method we choose a qualitative method for classification -- Decision EXpert. This method allows transparency in the score design, consistency of the scores, and it is convenient through its easy to understand nature and the possibility to perform sensitivity analysis. An integral aspect of this research is the sharing of methodology, data, and results with the wider research community, which can serve as a valuable resource for decision and policy-makers.
DOI: 10.17632/gpjm65pz63.1
title: HE staining images

description: To observe the effects of CIP on rat hippocampal tissues, we performed HE staining on samples from each group. In the sham group, the cytoplasm and nuclei of the neuronal cells in the CA1 region of the hippocampus of the SD rats exhibited uniform staining, and the cells were neatly arranged without any evident pathological alterations. In the I/R group, the neuronal cells in the CA1 region of the hippocampus of the SD rats were disorganized with a decreased number of neuronal cells, the microstructure was loose, with obvious edema, and ghost cells were visible. In the CIP group, the arrangement of neuronal cells in the CA1 area of the hippocampus was significantly more ordered and compact than that in the I/R group; the degree of cell damage was improved, but local edema was still present, and the number of ghost cells was significantly reduced. Thus, the results suggest that CIP can ameliorate MCAO-induced neuronal cell damage in rats.
DOI: 10.17632/743zn3sxwz.1
title: LDHU3_20.2120

description: Amidohydrolase; Leishmania donovani (HU3 strain)
DOI: 10.17632/tvpv2g6x2d.1
title: LDHU3_20.2130

description: Amidohydrolase; Leishmania donovani (HU3 strain)
DOI: 10.5281/zenodo.12609117
title: Associated code and data for "A Practical Guideline for MicroRNA Sequencing Data Analysis in Chronic Lymphocytic Leukemia".

description: This deposit contains the data, code, and analysis to recreate the results in the manuscript - Tuulikki Suomela, Liang Zhang, Julio Vera, Heiko Bruns, Xin Lai. A Practical Guideline for MicroRNA Sequencing Data Analysis in Chronic Lymphocytic Leukemia. Methods Mol Biol, Humana Press, 2883, 403-426 (2024). https://doi.org/10.1007/978-1-0716-4290-0_18.

If you have used the code for your research, please cite the original publication. Thank you very much.
DOI: 10.17632/8frktxtw72.1
title: LDHU3_20.2140

description: mt-SAF2 | KRIPP2; Leishmania donovani (HU3 strain)
DOI: 10.17632/54t7jy9z4b.1
title: LDHU3_20.2160

description: Protein with WD-40 repeats; Leishmania donovani (HU3 strain)
DOI: 10.15468/dl.hway3w
title: Occurrence Download

description: A dataset containing 62 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Aedes circumluteolus (Theobald, 1908)"
 ]
}

 The dataset includes 62 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0063854-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17632/k3tzv2vp4v.1
title: LDHU3_20.2170

description: Hypothetical protein - conserved; Leishmania donovani (HU3 strain)
DOI: 10.17632/3b3k3vrvpt.1
title: Data & Resources: Evaluating the Ability of Spatial Indicators to Classify Fish Stock Status

description: This repository contains all data and code to reproduce results, tables, and figures. The repository can also be cloned from https://github.com/peterjosephkidd/spatind_paper1. 

Abstract
A positive relationship between fish abundance and spatial distribution suggests that indicators of spatial distribution could be used as proxies of abundance and stock status. This study evaluated the ability of 10 spatial indicators to classify the health status of 25 data-rich stocks, identifying the best performing indicators and the conditions that influence their performance using a combination of machine learning techniques. Spatial indicators were able to detect health status better than a random classifier for the majority of stocks studied. The occupancy and aggregation indicators showed the best overall performance, suggesting that years of healthy stock status were often associated with presence in more survey hauls or more evenly distributed fish density. However, indicator performance depended on the source of survey data used and varied stock-by-stock. Explanations of these findings are provided and future research is suggested to further explore the impact of survey design and environmental variables. Our findings highlight the potential for spatial indicators to improve the assessment of category 5 and 6 data-limited stocks managed by the International Council for the Exploration of the Seas (ICES).

Data
The data used to calculate spatial indicators is downloaded from ICES Database of Trawl Surveys (DATRAS). This repository contains the DATRAS data downloaded and used within this study. Redownloading data from DATRAS may result in changes in outputs due to retrospective corrections/additions to the data. It is therefore advised that users intending to replicate this papers findings use the DATRAS data provide in this repository. 

Software
Reference to software used to complete this work is recorded in the PckgBibReport.html file
DOI: 10.17632/zwwx2gmk6f.1
title: LDHU3_20.2180

description: Cysteine and histidine-rich domain-containing protein | CHORD; Leishmania donovani (HU3 strain)
DOI: 10.15468/dl.j7tbu6
title: Occurrence Download

description: A dataset containing 2552 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Rhododendron minus Michx."
 ]
}

 The dataset includes 2552 records from 131 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0063855-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17632/9ytr89jmx3.1
title: Fixed Bed Combustion of Rice Husk Briquettes Enriched with Croton Megalocarpus Oil

description: The data presented is for experimental analysis of fixed bed combustion of rice husk briquettes enriched with croton megalocarpus. The briquettes were combusted in fixed bed reactor. Investigation was conducted for different air mass flux and oil absorption percentages.
DOI: 10.17632/wr8xrcghmh.1
title: Trends in Non-squamous cervical cancer prevalence, histological type, stage, age, and human papillomavirus type in southwest China from 2009 to 2023: A Large Retrospective Study

description: To describe the trends in non-squamous cervical cancer (Non-SCC) prevalence, histological type, stage, age, and human papillomavirus type in southwest China from 2009 to 2023.
DOI: 10.17632/wr8xrcghmh.2
title: Trends in Non-squamous cervical cancer prevalence, histological type, stage, age, and human papillomavirus type in southwest China from 2009 to 2023: A Large Retrospective Study

description: To describe the trends in non-squamous cervical cancer (Non-SCC) prevalence, histological type, stage, age, and human papillomavirus type in southwest China from 2009 to 2024.
DOI: 10.17632/z2fp5kbgbh.1
title: Tracking Plant Growth Using Image Sequence Analysis- Datasets

description: This dataset consists of five subsets with annotated images in COCO format, designed for object detection and tracking plant growth:
1. Cucumber_Train Dataset (for Faster R-CNN)
- Includes training, validation, and test images of cucumbers from different angles.
- Annotations: Bounding boxes in COCO format for object detection tasks.

2. Tomato Dataset
- Contains images of tomato plants for 24 hours at hourly intervals from a fixed angle.
- Annotations: Bounding boxes in COCO format.

3. Pepper Dataset
- Contains images of pepper plants for 24 hours at hourly intervals from a fixed angle.
- Annotations: Bounding boxes in COCO format.

4. Cannabis Dataset
- Contains images of cannabis plants for 24 hours at hourly intervals from a fixed angle.
- Annotations: Bounding boxes in COCO format.

5. Cucumber Dataset
- Contains images of cucumber plants for 24 hours at hourly intervals from a fixed angle.
- Annotations: Bounding boxes in COCO format.

This dataset supports training and evaluation of object detection models across diverse crops.
DOI: 10.5281/zenodo.14628250
title: Correlative bioimaging of structural biochemistry in plant and food quality research within an interoperable data acquisition platform

description: Made available are matrices of distributions of aluminum (Al), silicon (Si), phoshporus (P), sulfur (S), chlorine (Cl), potassium (K), calcium (Ca), manganese (Mn), iron (Fe) and zinc (Zn) as obtained by using either laser ablation-inductively coupled plasma-mass spectrometry (LAICPMS) or micro-particle induced X-ray emission (PIXE), distributions of molecules with peaks at m/z values (39, 303, 339, 398, 522, 578, 603, 785, 786 and 825) as obtained by MeV-secondary ion mass spectrometry (SIMS) and scanning electron microscopy (SEM) image of a single sample, Tartary buckwheat (Fagopyrum tataricum) grain cross section. These matrices can be used in ImageJ to generate overlays of elemental or molecular distribution over morphological image.
DOI: 10.5281/zenodo.14628251
title: Correlative bioimaging of structural biochemistry in plant and food quality research within an interoperable data acquisition platform

description: Made available are matrices of distributions of aluminum (Al), silicon (Si), phoshporus (P), sulfur (S), chlorine (Cl), potassium (K), calcium (Ca), manganese (Mn), iron (Fe) and zinc (Zn) as obtained by using either laser ablation-inductively coupled plasma-mass spectrometry (LAICPMS) or micro-particle induced X-ray emission (PIXE), distributions of molecules with peaks at m/z values (39, 303, 339, 398, 522, 578, 603, 785, 786 and 825) as obtained by MeV-secondary ion mass spectrometry (SIMS) and scanning electron microscopy (SEM) image of a single sample, Tartary buckwheat (Fagopyrum tataricum) grain cross section. These matrices can be used in ImageJ to generate overlays of elemental or molecular distribution over morphological image.
DOI: 10.15468/dl.jfdw53
title: Occurrence Download

description: A dataset containing 4817 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Wahlenbergiella mucosa (Wahlenb. ex Ach.) Gueidan & Thüs"
 ]
}

 The dataset includes 4817 records from 118 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0063857-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.uwbrh8
title: Occurrence Download

description: A dataset containing 7959 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Aedes communis (De Geer, 1776)"
 ]
}

 The dataset includes 7959 records from 62 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0063858-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.par6uq
title: Occurrence Download

description: A dataset containing 11874 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Martes martes (Linnaeus, 1758)",
 "HasCoordinate is true",
 "Year is greater than or equal to 2013",
 "Year is less than or equal to 2018",
 "CoordinateUncertaintyInMeters is less than or equal to 1000"
 ]
}

 The dataset includes 11874 records from 165 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0063859-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.myfz8j
title: Occurrence Download

description: A dataset containing 7477 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Bonnemaisonia hamifera Hariot"
 ]
}

 The dataset includes 7477 records from 148 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0063860-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14628312
title: Code and data accompanying the paper "Specific types of male infertility are correlated with T cell exhaustion or senescence signatures"
DOI: 10.5281/zenodo.14628313
title: Code and data accompanying the paper "Specific types of male infertility are correlated with T cell exhaustion or senescence signatures"
DOI: 10.5281/zenodo.14628680
title: Code and data accompanying the paper "Specific types of male infertility are correlated with T cell exhaustion or senescence signatures"
DOI: 10.15468/dl.h65ng7
title: Occurrence Download

description: A dataset containing 2042 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ovis aries musimon (Pallas, 1811)",
 "HasCoordinate is true",
 "Year is greater than or equal to 2013",
 "Year is less than or equal to 2018",
 "CoordinateUncertaintyInMeters is less than or equal to 1000"
 ]
}

 The dataset includes 2042 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0063862-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qtvatm
title: Occurrence Download

description: A dataset containing 39490987 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Europe",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Aves",
 "Year 2022-2022"
 ]
}

 The dataset includes 39490987 records from 2539 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0063844-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.