cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.26030/bkh4-tq49
title: Deficits in Sustained Attention and Changes in Dopaminergic Protein Levels following Exposure to Proton Radiation Are Related to Basal Dopaminergic Function (Rodent Psychomotor Vigilance Test)

description: The current report assessed the effects of low-level proton irradiation in inbred adult male Fischer 344 and Lewis rats performing an analog of the human Psychomotor Vigilance Test (PVT), commonly utilized as an object risk assessment tool to quantify fatigue and sustained attention in laboratory, clinical, and operational settings. These strains were used to determine if genetic differences in dopaminergic function would impact radiation-induced deficits in sustained attention. Exposure to head-only proton irradiation (25 or 100 cGy) disrupted rPVT performance in a strain-specific manner, with 25 cGy-exposed Fischer 344 rats displaying the most severe deficits in sustained attention (i.e., decreased accuracy and increased premature responding); Lewis rats did not display behavioral deficits following radiation. Fischer 344 rats displayed greater tyrosine hydroxylase and dopamine transporter levels in the frontal cortex compared to the Lewis rats, even though radiation exposure increased both of these proteins in the Lewis rats only. Tyrosine hydroxylase was decreased in the parietal cortex of both rat strains following radiation exposure, regardless of proton dose. Strain-specific cytokine changes were also found in the frontal cortex, with the Lewis rats displaying increased levels of putative neurotrophic cytokines (e.g., CNTF). These data support the hypothesis that basal dopaminergic function impacts the severity of radiation-induced deficits in sustained attention. This study derives results from the Rodent Psychomotor Vigilance Test (rPVT) assay. Results from the Western Blot assays can be found in OSD-896 (frontal cortex) and OSD-897 (parietal cortex).
DOI: 10.15468/dl.3ysm3e
title: Occurrence Download

description: A dataset containing 248 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Scomber scombrus",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1950",
 "Year is less than or equal to 1959"
 ]
}

 The dataset includes 248 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006642-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17705167
title: Anterior–posterior patterning in the chaetognath Spadella cephaloptera: insights into the evolution of the bilaterian nervous system and postanal tail

description: Supplementary code for “Anterior–posterior patterning in the chaetognath Spadella cephaloptera: insights into the evolution of the bilaterian nervous system and postanal tail”*

Scripts used to download, assemble, and annotate transcriptomes for Hox gene mining in public SRA datasets. 

---

## Hox gene mining pipeline from public transcriptomes

This repository contains example scripts and a minimal walkthrough of the pipeline used to identify Hox genes from publicly available transcriptomes.

The workflow has four main steps:

1. **Download RNA-seq reads from SRA**     Script: `01_dowload_RNAseqData.sh`

2. **Trim and quality-filter reads, then assemble transcriptomes**     Script: `02_qc_and_assemble.sh`

3. **Annotate assembled transcripts with DIAMOND against a custom Spiralian Hox database**     Scripts: `03.1_03.1_makeHoxDB.sh` and `03.2_annot_diamonBlast.sh`

4. **Manually inspect and confirm candidate Hox genes by NCBI BLAST**   - Filter DIAMOND hits for strong matches (e.g. e-value ≤ 1e-25) to identify candidate Hox transcripts.   - Extract the corresponding transcript IDs from the assembly FASTA.   - BLAST these candidates against NCBI (nt/nr) to confirm their identity and assign orthology.   - Retain only well-supported Hox sequences for downstream phylogenetic analyses.

The scripts are written for a SLURM-based HPC cluster using `module load`, but can be adapted to other environments.

---

## Requirements

- Linux environment- SLURM (or adjust the `#SBATCH` lines)- Installed software:  - [SRA Toolkit](https://github.com/ncbi/sra-tools) (tested with ≥ 3.2.0)  - [Trimmomatic](http://www.usadellab.org/cms/?page=trimmomatic) (≥ 0.39)  - [SPAdes](https://cab.spbu.ru/software/spades/) with RNA mode (`spades.py --rna`)  - [DIAMOND](https://github.com/bbuchfink/diamond) (≥ 2.1.x)- Adapter FASTA for Trimmomatic (e.g. `TruSeq3-PE.fa`)- A FASTA file containing Spiralian Hox protein sequences to build the custom DIAMOND database
DOI: 10.5281/zenodo.17705168
title: Anterior–posterior patterning in the chaetognath Spadella cephaloptera: insights into the evolution of the bilaterian nervous system and postanal tail

description: Supplementary code for “Anterior–posterior patterning in the chaetognath Spadella cephaloptera: insights into the evolution of the bilaterian nervous system and postanal tail”*

Scripts used to download, assemble, and annotate transcriptomes for Hox gene mining in public SRA datasets. 

---

## Hox gene mining pipeline from public transcriptomes

This repository contains example scripts and a minimal walkthrough of the pipeline used to identify Hox genes from publicly available transcriptomes.

The workflow has four main steps:

1. **Download RNA-seq reads from SRA**     Script: `01_dowload_RNAseqData.sh`

2. **Trim and quality-filter reads, then assemble transcriptomes**     Script: `02_qc_and_assemble.sh`

3. **Annotate assembled transcripts with DIAMOND against a custom Spiralian Hox database**     Scripts: `03.1_03.1_makeHoxDB.sh` and `03.2_annot_diamonBlast.sh`

4. **Manually inspect and confirm candidate Hox genes by NCBI BLAST**   - Filter DIAMOND hits for strong matches (e.g. e-value ≤ 1e-25) to identify candidate Hox transcripts.   - Extract the corresponding transcript IDs from the assembly FASTA.   - BLAST these candidates against NCBI (nt/nr) to confirm their identity and assign orthology.   - Retain only well-supported Hox sequences for downstream phylogenetic analyses.

The scripts are written for a SLURM-based HPC cluster using `module load`, but can be adapted to other environments.

---

## Requirements

- Linux environment- SLURM (or adjust the `#SBATCH` lines)- Installed software:  - [SRA Toolkit](https://github.com/ncbi/sra-tools) (tested with ≥ 3.2.0)  - [Trimmomatic](http://www.usadellab.org/cms/?page=trimmomatic) (≥ 0.39)  - [SPAdes](https://cab.spbu.ru/software/spades/) with RNA mode (`spades.py --rna`)  - [DIAMOND](https://github.com/bbuchfink/diamond) (≥ 2.1.x)- Adapter FASTA for Trimmomatic (e.g. `TruSeq3-PE.fa`)- A FASTA file containing Spiralian Hox protein sequences to build the custom DIAMOND database
DOI: 10.6084/m9.figshare.28998833
title: Stimulus representations in visual cortex shaped by spatial attention and microsaccades

description: Authored by: Karthik Srinivasan, Eric Lowet, Bruno Gomes, Robert DesimoneDataset for the paper "Stimulus representations in visual cortex shaped by spatial attention and microsaccades".Dataset saved as (.mat) files.Details on data collection can be found in the Materials and Methods, and SI Appendix sections of the paper.Dataset includes spike times and eye movement signals for 2 monkeys across 3 brain areas and in 2 types of stimulus conditions.
DOI: 10.6084/m9.figshare.28998833.v2
title: Stimulus representations in visual cortex shaped by spatial attention and microsaccades

description: Authored by: Karthik Srinivasan, Eric Lowet, Bruno Gomes, Robert DesimoneDataset for the paper "Stimulus representations in visual cortex shaped by spatial attention and microsaccades".Dataset saved as (.mat) files.Details on data collection can be found in the Materials and Methods, and SI Appendix sections of the paper.Dataset includes spike times and eye movement signals for 2 monkeys across 3 brain areas and in 2 types of stimulus conditions.
DOI: 10.6084/m9.figshare.28998833.v1
title: Stimulus representations in visual cortex shaped by spatial attention and microsaccades

description: Authored by: Karthik Srinivasan, Eric Lowet, Bruno Gomes, Robert DesimoneDataset for the paper "Stimulus representations in visual cortex shaped by spatial attention and microsaccades".Dataset saved as (.mat) files.Details on data collection can be found in the Materials and Methods, and SI Appendix sections of the paper.Dataset includes spike times and eye movement signals for 2 monkeys across 3 brain areas and in 2 types of stimulus conditions.
DOI: 10.15468/dl.rum36w
title: Occurrence Download

description: A dataset containing 2033 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Scomber scombrus",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1960",
 "Year is less than or equal to 1969"
 ]
}

 The dataset includes 2033 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006643-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.30119989
title: V1-V4_NativeSpecies

description: This dataset accompanies the following research article:Evans T and Cuthbert RN. 2025.<b> </b>Management of alien bird impacts does not reflect their severity. <i>J Environ Manage</i>, 396, 128053. https://doi.org/10.1016/j.jenvman.2025.128053It provides evidence to demonstrate that the impact reports and management reports selected for the study focussed on the biodiversity impacts of alien birds. It also includes data on the native species selected to produce four predictor variables (V1 - V4) used in the analysis.
DOI: 10.6084/m9.figshare.30119989.v2
title: V1-V4_NativeSpecies

description: This dataset accompanies the following research article:Evans T and Cuthbert RN. 2025.<b> </b>Management of alien bird impacts does not reflect their severity. <i>J Environ Manage</i>, 396, 128053. https://doi.org/10.1016/j.jenvman.2025.128053It provides evidence to demonstrate that the impact reports and management reports selected for the study focussed on the biodiversity impacts of alien birds. It also includes data on the native species selected to produce four predictor variables (V1 - V4) used in the analysis.
DOI: 10.6084/m9.figshare.30119989.v1
title: V1-V4_NativeSpecies

description: This dataset is associated with a study that identifies factors that influence management actions to protect native animals from the impacts of alien birds. It provides evidence to demonstrate that the impact reports and management reports selected for that study were focussed on the biodiversity impacts of alien birds. It also includes data on the native species selected to produce four predictor variables used in the analysis for the study (V1 - V4).
DOI: 10.5281/zenodo.17705020
title: GRNITE: Gene Regulatory Network Inference with Text Embeddings.
DOI: 10.5281/zenodo.17705019
title: GRNITE: Gene Regulatory Network Inference with Text Embeddings.
DOI: 10.5281/zenodo.17704756
title: Extinction data from: The potential of Stratospheric Aerosol Injection to reduce the climatic risks of explosive volcanic eruptions

description: Data from Quaglia et al. (2024): The potential of Stratospheric Aerosol Injection to reduce the climatic risks of explosive volcanic eruptions, https://doi.org/10.1029/2023GL107702

Files name are organized as b.e21.BWSSP245.f09_g17.release-cesm2.1.3.WACCM-MA-1deg.<EXPERIMENT_NAME>.<ENSEMBLE_MEMBERS>.cam.h0.<VARIABLE_NAME>.<SIMULATED_YEARS>.nc



VARIABLE_NAME are: EXTINCTdn, EXTINCTNIRdn, EXTINCTUVdn

EXPERIMENT_NAME are:


2055_Pina_10Tg  (in the paper is Volc10Tg): medium (10 Tg-SO2) volcanic eruption simulated under SSP2-4.5

2055_Pina_50Tg  (in the paper is Volc50Tg): large (50 Tg-SO2) volcanic eruption simulated under SSP2-4.5

2055_PinaSAI_10Tg (in the paper is Volc10Tg + SAI_nhoff): medium (10 Tg-SO2) volcanic eruption simulated under SAI. SAI is immediately stopped everywhere when the eruption occurs.

2055_PinaSAIr_10Tg (in the paper is Volc10Tg + SAI_nhoff): medium (10 Tg-SO2) volcanic eruption simulated under SAI. It follows the 2055_PinaSAI_10Tg simulation after the end of 2026, with SAI restarted in the Northern Hemisphere.

2055_PinaSAISP_10Tg (in the paper is Volc10Tg + SAI_off): medium (10 Tg-SO2) volcanic eruption simulated under SAI. SAI is immediately stopped everywhere when the eruption occurs.

2055_PinaSAI_50Tg (in the paper is Volc50Tg + SAI_off): large (50 Tg-SO2) volcanic eruption simulated under SAI. SAI is immediately stopped everywhere when the eruption occurs.

 



There are 3 ENSEMBLE_MEMBERS for each experiment: 001, 002, 003

SIMULATED_YEARS depends on the EXPERIMENT_NAME
DOI: 10.5281/zenodo.17704757
title: Extinction data from: The potential of Stratospheric Aerosol Injection to reduce the climatic risks of explosive volcanic eruptions

description: Data from Quaglia et al. (2024): The potential of Stratospheric Aerosol Injection to reduce the climatic risks of explosive volcanic eruptions, https://doi.org/10.1029/2023GL107702

Files name are organized as b.e21.BWSSP245.f09_g17.release-cesm2.1.3.WACCM-MA-1deg.<EXPERIMENT_NAME>.<ENSEMBLE_MEMBERS>.cam.h0.<VARIABLE_NAME>.<SIMULATED_YEARS>.nc



VARIABLE_NAME are: EXTINCTdn, EXTINCTNIRdn, EXTINCTUVdn

EXPERIMENT_NAME are:


2055_Pina_10Tg  (in the paper is Volc10Tg): medium (10 Tg-SO2) volcanic eruption simulated under SSP2-4.5

2055_Pina_50Tg  (in the paper is Volc50Tg): large (50 Tg-SO2) volcanic eruption simulated under SSP2-4.5

2055_PinaSAI_10Tg (in the paper is Volc10Tg + SAI_nhoff): medium (10 Tg-SO2) volcanic eruption simulated under SAI. SAI is immediately stopped everywhere when the eruption occurs.

2055_PinaSAIr_10Tg (in the paper is Volc10Tg + SAI_nhoff): medium (10 Tg-SO2) volcanic eruption simulated under SAI. It follows the 2055_PinaSAI_10Tg simulation after the end of 2026, with SAI restarted in the Northern Hemisphere.

2055_PinaSAISP_10Tg (in the paper is Volc10Tg + SAI_off): medium (10 Tg-SO2) volcanic eruption simulated under SAI. SAI is immediately stopped everywhere when the eruption occurs.

2055_PinaSAI_50Tg (in the paper is Volc50Tg + SAI_off): large (50 Tg-SO2) volcanic eruption simulated under SAI. SAI is immediately stopped everywhere when the eruption occurs.

 



There are 3 ENSEMBLE_MEMBERS for each experiment: 001, 002, 003

SIMULATED_YEARS depends on the EXPERIMENT_NAME
DOI: 10.15468/dl.ckc2we
title: Occurrence Download

description: A dataset containing 5521 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Scomber scombrus",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1970",
 "Year is less than or equal to 1979"
 ]
}

 The dataset includes 5521 records from 46 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006645-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2tb9bd
title: Occurrence Download

description: A dataset containing 17350 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "OccurrenceStatus is Present",
 "TaxonKey is Senecio"
 ]
}

 The dataset includes 17350 records from 200 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006646-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.57967/hf/7081
title: Reasoning_as_Fluid
DOI: 10.15468/dl.6e4bds
title: Occurrence Download

description: A dataset containing 1511 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Specimen, Material sample)",
 "Geometry POLYGON((-100.26461 14.23568,-73.23695 -21.01226,-53.53882 -22.71277,-35.06228 -4.54541,-42.08642 1.55756,-64.07503 20.21233,-66.9763 21.0697,-69.11409 17.17526,-82.39887 12.15447,-88.96491 17.75788,-97.66874 18.0485,-100.26461 14.23568))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Caiman crocodilus crocodilus, Caiman crocodilus)"
 ]
}

 The dataset includes 1511 records from 64 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006647-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.72vcs6
title: Occurrence Download

description: A dataset containing 9445 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Scomber scombrus",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1980",
 "Year is less than or equal to 1989"
 ]
}

 The dataset includes 9445 records from 45 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006648-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.h7uvgm
title: Occurrence Download

description: A dataset containing 4930 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Stephanoxis lalandi"
 ]
}

 The dataset includes 4930 records from 23 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006649-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5519/qd.8yzw86id
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (6818 records)
DOI: 10.15468/dl.qbvh35
title: Occurrence Download

description: A dataset containing 48096 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Scomber scombrus",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1990",
 "Year is less than or equal to 1999"
 ]
}

 The dataset includes 48096 records from 57 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006650-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zkb72k
title: Occurrence Download

description: A dataset containing 43174 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is South America",
 "Country is Brazil",
 "GadmGid is one of (BRA.24_1, BRA.21_1)",
 "OccurrenceStatus is Present",
 "TaxonKey is Asteraceae"
 ]
}

 The dataset includes 43174 records from 156 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006651-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9fnrr5
title: Occurrence Download

description: A dataset containing 3394 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Hexanchus griseus",
 "Year 1874-2025"
 ]
}

 The dataset includes 3394 records from 90 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006652-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15131/shef.data.25673379
title: Cognitive-Behavioural Therapy (CBT) for Outpatients with Anorexia Nervosa: A Systematic Review and Meta-Analysis of Clinical Effectiveness (Datafiles and Guidelines)

description: The data files presented relate to a pre-registered systematic review and meta-analysis of outpatient CBT for anorexia nervosa. It was conducted to assess the effectiveness of outpatient CBT for anorexia nervosa and explore potential moderators in order to inform clinical practice. Preregistration: PROSPERO (CRD42023484924)The following documents are intended for reading alongside the published paper: http://dx.doi.org/10.1080/16506073.2025.2465745 (published March 2025).The provided documents are: An Excel file containing a workbook with the dataset used in this review, named "main datafile". The front tab serves as a contents page, and further details on how the data were obtained are provided in PROSPERO and the accompanying Word document.*A zip file with CSV versions of each sheet in the above Excel workbook.A Word document titled <i>Reviewer Guidelines for Full Paper Screening, Data Extraction, and Quality Assessment</i>. This document contains the instructions the reviewers used for screening, data extraction, and quality assessment. A .txt version of this file is also provided. An Excel file containing the risk of bias assessments conducted for the included studies. The first tab provides overall guidance for each of the three risk-of-bias assessments conducted. Each set of assessments has another tab with guidance followed by the reviewer for each set of assessments.A zip file with CSV versions of each sheet in the above Excel worksheet.A Word document titled <i>Holm-Bonferroni Corrections for Results Tables. </i>A .txt version of this file. Populated Meta-Essentials workbooks for each of the included meta-analyses (.csv versions of these workbooks are not provided as Meta-Essentials only works in Excel). There are workbooks for each of the following variables: weight, eating disorder symptoms, depression, anxiety, and quality of life. <i> </i><i>Note. </i>If you download any of the Meta-Essentials workbooks, please keep the following in mind:Workbooks must be opened in Microsoft Excel only, as other spreadsheet programs (e.g., Google Sheets, Numbers) will not run the calculations correctly.When you open a workbook, Excel may display a security warning. Please click “Enable Editing” and, if prompted, “Enable Content” so that all formulas and functions work properly.All formulas, references, and embedded calculations should work exactly as in the original file. The online preview in ORDA may not display calculations correctly but they should work in the downloaded files. If the files do not work for you, or if you wish to run analyses with the data file themselves, we have provided the dataset and you can download the Meta-Essentials workbooks at: https://www.eur.nl/en/erim/research-support/meta-essentials/download*Note. Rossi et al. (2023) was corrected to Rossi et al. (2024) in the published paper.