cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.30000481
title: Supplementary Material for: Visual Recovery in LHON Plus: A Case Report and Literature Insight

description: We describe an 18-year-old male cricket player who presented with a six-month history of gradually worsening, painless visual loss in both eyes. His best-corrected visual acuity (BCVA) was 6/60 in the right eye and 3/60 in the left. Color vision was reduced in the left eye, but improved when tested with a red filter, raising suspicion of optic nerve pathology. Fundus examination revealed hyperemic optic discs, and visual field testing identified central and paracentral scotomas. MRI of the orbits showed bilateral T2 hyperintensities in the intraorbital portions of the optic nerves. Genetic testing confirmed a homoplasmic MT:14484C&gt;T mutation in the MT-ND6 gene. The patient also reported systemic symptoms including palpitations and excessive sweating. Cardiac evaluation revealed mitral valve prolapse, sinus tachycardia, and elevated blood pressure. These findings led to a diagnosis of Leber’s Hereditary Optic Neuropathy Plus (LHON Plus). He was started on Coenzyme Q10, oral nutritional supplements, and a short course of topical corticosteroids. Remarkably, over the course of a year, he regained full visual acuity with only residual optic disc pallor. This case underscores the importance of considering LHON Plus in young patients with bilateral optic neuropathy and systemic features, particularly when the MT:14484C&gt;T mutation is present, as early mitochondrial support can lead to favorable outcomes.
DOI: 10.6084/m9.figshare.30000481.v1
title: Supplementary Material for: Visual Recovery in LHON Plus: A Case Report and Literature Insight

description: We describe an 18-year-old male cricket player who presented with a six-month history of gradually worsening, painless visual loss in both eyes. His best-corrected visual acuity (BCVA) was 6/60 in the right eye and 3/60 in the left. Color vision was reduced in the left eye, but improved when tested with a red filter, raising suspicion of optic nerve pathology. Fundus examination revealed hyperemic optic discs, and visual field testing identified central and paracentral scotomas. MRI of the orbits showed bilateral T2 hyperintensities in the intraorbital portions of the optic nerves. Genetic testing confirmed a homoplasmic MT:14484C&gt;T mutation in the MT-ND6 gene. The patient also reported systemic symptoms including palpitations and excessive sweating. Cardiac evaluation revealed mitral valve prolapse, sinus tachycardia, and elevated blood pressure. These findings led to a diagnosis of Leber’s Hereditary Optic Neuropathy Plus (LHON Plus). He was started on Coenzyme Q10, oral nutritional supplements, and a short course of topical corticosteroids. Remarkably, over the course of a year, he regained full visual acuity with only residual optic disc pallor. This case underscores the importance of considering LHON Plus in young patients with bilateral optic neuropathy and systemic features, particularly when the MT:14484C&gt;T mutation is present, as early mitochondrial support can lead to favorable outcomes.
DOI: 10.6084/m9.figshare.30000484
title: Supplementary Material for: SOX9 gene variants in 27 French Bulldogs with disorder of sex development (XX, SRY-negative): identification of first case of skeletal abnormalities associated with SOX9 triplication

description: Introduction: The SOX9 gene encodes a transcription factor that acts downstream of the Y-linked SRY gene and plays a pivotal role in fetal testis development. Duplication of SOX9 or its regulatory sequences is a known cause of testicular or ovotesticular disorder of sex development (DSD) in chromosomal females (XX DSD). Numerous reports have described canine XX DSD, characterized by virilization (e.g., enlarged clitoris) and the presence of testes or ovotestes. This study aimed to identify SOX9 variants in a cohort of French Bulldogs with XX (SRY-negative) DSD. 
Methods: In total, 27 DSD dogs were studied, including 19 with abdominal, spermatogenetically inactive testes; four with inactive testis and ovotestis; one with inactive testis and ovary; one with ovotestes; and in two dogs, histological analysis could not be performed. Moreover, 24 control females of the same breed, all with normal external female genitalia, were included. 
Results: Three known DNA variants were identified in SOX9: a 3 bp insertion/deletion (CCT/---, rs852828782), a T&gt;C SNP (rs22704771) in the 5’ UTR, and an intronic T&gt;G SNP (rs9183825). These variants were rare, and their distribution was similar in both cohorts. Additionally, the number of SOX9 gene copies was assessed using ddPCR. A single XX DSD case with additional skeletal malformations carried three copies of SOX9, while all other cases and control females had two copies. 
Conclusion. We conclude that SOX9 duplication is a rare cause of XX DSD in French Bulldogs, and that the identified sequence variants in this gene are not associated with the disorder.
DOI: 10.6084/m9.figshare.30000484.v1
title: Supplementary Material for: SOX9 gene variants in 27 French Bulldogs with disorder of sex development (XX, SRY-negative): identification of first case of skeletal abnormalities associated with SOX9 triplication

description: Introduction: The SOX9 gene encodes a transcription factor that acts downstream of the Y-linked SRY gene and plays a pivotal role in fetal testis development. Duplication of SOX9 or its regulatory sequences is a known cause of testicular or ovotesticular disorder of sex development (DSD) in chromosomal females (XX DSD). Numerous reports have described canine XX DSD, characterized by virilization (e.g., enlarged clitoris) and the presence of testes or ovotestes. This study aimed to identify SOX9 variants in a cohort of French Bulldogs with XX (SRY-negative) DSD. 
Methods: In total, 27 DSD dogs were studied, including 19 with abdominal, spermatogenetically inactive testes; four with inactive testis and ovotestis; one with inactive testis and ovary; one with ovotestes; and in two dogs, histological analysis could not be performed. Moreover, 24 control females of the same breed, all with normal external female genitalia, were included. 
Results: Three known DNA variants were identified in SOX9: a 3 bp insertion/deletion (CCT/---, rs852828782), a T&gt;C SNP (rs22704771) in the 5’ UTR, and an intronic T&gt;G SNP (rs9183825). These variants were rare, and their distribution was similar in both cohorts. Additionally, the number of SOX9 gene copies was assessed using ddPCR. A single XX DSD case with additional skeletal malformations carried three copies of SOX9, while all other cases and control females had two copies. 
Conclusion. We conclude that SOX9 duplication is a rare cause of XX DSD in French Bulldogs, and that the identified sequence variants in this gene are not associated with the disorder.
DOI: 10.6084/m9.figshare.30000487
title: Supplementary Material for: Predictive performance of HAS-BLED score in patients with atrial fibrillation and cancer: A meta-analysis

description: Introduction:
Patients with atrial fibrillation (AF) and a history of cancer face unique bleeding risks, complicating the applicability of standard bleeding risk scores like HAS-BLED. This meta-analysis aimed to evaluate the performance of HAS-BLED in predicting bleeding events in this high-risk population.

Methods:
The MEDLINE, PubMed and EMBASE databases were searched from 1st of January 2010 to 30th of November 2024 for relevant studies using keywords, such as “AF” “cancer” “bleeding” and “HAS-BLED”. Data on C-statistics were extracted to assess the predictive performance of HAS-BLED score.

Results:
Our analysis included seven retrospective cohort studies, recruiting a total of 436,102 patients. The quality of the included studies was deemed acceptable for analysis. The reported C-statistics for HAS-BLED score varied widely across studies, ranging from 0.45 to 0.77. Subgroup analyses demonstrated moderate discrimination in patients with breast cancer (0.56–0.80), prostate cancer (0.58–0.72), and lung cancer (0.59–0.80), while poorer performance was observed in hematological malignancies (0.45–0.70) and in anticoagulated patients (pooled C-statistic = 0.55; 95% CI: 0.54–0.56). Significant heterogeneity was observed in the overall analysis and most subgroups (I² &gt; 90%), except for the anticoagulated subgroup. A sensitivity analysis excluding the largest study reduced heterogeneity and improved funnel plot symmetry, indicating that study size contributed to variability in HAS-BLED performance.
Conclusion:
The HAS-BLED score has shown variable predictive abilities in AF patients with cancer ranging from poor to good, with notable heterogeneity across studies secondary to various contributing factors. This emphasizes the need for individualized risk assessment tailored to the unique characteristics of cancer patients to effectively guide clinical decision-making.
DOI: 10.6084/m9.figshare.30000487.v1
title: Supplementary Material for: Predictive performance of HAS-BLED score in patients with atrial fibrillation and cancer: A meta-analysis

description: Introduction:
Patients with atrial fibrillation (AF) and a history of cancer face unique bleeding risks, complicating the applicability of standard bleeding risk scores like HAS-BLED. This meta-analysis aimed to evaluate the performance of HAS-BLED in predicting bleeding events in this high-risk population.

Methods:
The MEDLINE, PubMed and EMBASE databases were searched from 1st of January 2010 to 30th of November 2024 for relevant studies using keywords, such as “AF” “cancer” “bleeding” and “HAS-BLED”. Data on C-statistics were extracted to assess the predictive performance of HAS-BLED score.

Results:
Our analysis included seven retrospective cohort studies, recruiting a total of 436,102 patients. The quality of the included studies was deemed acceptable for analysis. The reported C-statistics for HAS-BLED score varied widely across studies, ranging from 0.45 to 0.77. Subgroup analyses demonstrated moderate discrimination in patients with breast cancer (0.56–0.80), prostate cancer (0.58–0.72), and lung cancer (0.59–0.80), while poorer performance was observed in hematological malignancies (0.45–0.70) and in anticoagulated patients (pooled C-statistic = 0.55; 95% CI: 0.54–0.56). Significant heterogeneity was observed in the overall analysis and most subgroups (I² &gt; 90%), except for the anticoagulated subgroup. A sensitivity analysis excluding the largest study reduced heterogeneity and improved funnel plot symmetry, indicating that study size contributed to variability in HAS-BLED performance.
Conclusion:
The HAS-BLED score has shown variable predictive abilities in AF patients with cancer ranging from poor to good, with notable heterogeneity across studies secondary to various contributing factors. This emphasizes the need for individualized risk assessment tailored to the unique characteristics of cancer patients to effectively guide clinical decision-making.
DOI: 10.15468/dl.g85det
title: Occurrence Download

description: A dataset containing 74 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Halimeda incrassata",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Geometry POLYGON ((-6.6 29.26705, -6.6 50.94, 40.81373 50.94, 40.81373 29.26705, -6.6 29.26705))",
 "BasisOfRecord is one of (Human Observation, Machine Observation, Observation, Material sample)"
 ]
}

 The dataset includes 74 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003105-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.57707/fmi-b2share.60ed65a7cbb04147ae3efce572dd8fd0
title: Model outputs and measurement data to support "The effects of peat thickness and water table depth on CO2 and N2O emissions from agricultural peatlands - a process-based modelling approach" by Kajasilta et al.

description: The LDNDC model ouputs for peatland simulations at Ruukki site (blocks 1-6). The output data have been used to calculate and plot the results in the paper. Link for parameter and model descriptions can be found from "Supplementary information" under FMI Metadata section.
Measurement data of continuous fluxes (NEE, GPP, TER, evapotranspiration and N2O) from the site. References for calculating and filtering processes for data are explained more in detail in the paper.
DOI: 10.5281/zenodo.16633311
title: Monthly data on caesarean practice using the Ten Group Classification System (2020-2025)

description: This dataset present summary statistics (numbers of vaginal deliveries and number of caesarean sections according to the Ten groups) that were collected daily from January 2020 to June 2025 in the 32 hospitals participating in the Quali-Dec project. The data were extracted from the hospitals’ birth registers and medical records by a trained health care provider and controlled quarterly by the country data manager. Monthly summary statistics were collected and managed by using REDCap electronic data capture tools hosted at the Karolinska Institute and controlled at a monthly frequency by the principal data manager for pending data and duplicated records. The dataset is composed with 1984 monthly records that have been uploaded to Redcap: 400 from Argentina, 392 from Burkina Faso, 404 from Thailand and 401 from Vietnam. The data collected covered 728,586 deliveries: 392,194 vaginal births and 336,392 caesarean sections.
DOI: 10.5281/zenodo.12657387
title: Monthly data on caesarean practice using the Ten Group Classification System (2020-2025)

description: This dataset present summary statistics (numbers of vaginal deliveries and number of caesarean sections according to the Ten groups) that were collected daily from January 2020 to June 2025 in the 32 hospitals participating in the Quali-Dec project. The data were extracted from the hospitals’ birth registers and medical records by a trained health care provider and controlled quarterly by the country data manager. Monthly summary statistics were collected and managed by using REDCap electronic data capture tools hosted at the Karolinska Institute and controlled at a monthly frequency by the principal data manager for pending data and duplicated records. The dataset is composed with 1984 monthly records that have been uploaded to Redcap: 400 from Argentina, 392 from Burkina Faso, 404 from Thailand and 401 from Vietnam. The data collected covered 728,586 deliveries: 392,194 vaginal births and 336,392 caesarean sections.
DOI: 10.15468/dl.hmt5vu
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ipomoea tricolor",
 "Country is Madagascar",
 "HasCoordinate is true"
 ]
}

 The dataset includes 6 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003108-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4bunxz
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ipomoea tricolor",
 "Country is Italy",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003107-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8v8p6f
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ipomoea tricolor",
 "Country is India",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003106-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.e9xtds
title: Occurrence Download

description: A dataset containing 625 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Lindera fragrans"
 ]
}

 The dataset includes 625 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003109-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8makxh
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Hemileiocassis panjang)",
 "BasisOfRecord is one of (Specimen, Literature Occurrence, Human Observation, Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1991",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003110-250827131500795/datasets/export for details.
DOI: 10.15468/dl.6zhwba
title: Occurrence Download

description: A dataset containing 550 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Continent is Asia",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Carex duvaliana"
 ]
}

 The dataset includes 550 records from 28 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003111-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.z9ncuj
title: Occurrence Download

description: A dataset containing 217307 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Manscape",
 "Country is Belgium"
 ]
}

 The dataset includes 217307 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003095-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6pugtt
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ipomoea tricolor",
 "Country is Romania",
 "HasCoordinate is true"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003115-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gaqp5w
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ipomoea tricolor",
 "Country is Rwanda",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003116-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nfyuks
title: Occurrence Download

description: A dataset containing 161 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Bursatella leachii",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Geometry POLYGON ((-6.6 29.26705, -6.6 50.94, 40.81373 50.94, 40.81373 29.26705, -6.6 29.26705))",
 "BasisOfRecord is one of (Human Observation, Machine Observation, Observation, Material sample)"
 ]
}

 The dataset includes 161 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003113-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.q6vsar
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ipomoea tricolor",
 "Country is Mozambique",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003114-250827131500795/datasets/export for details.
DOI: 10.15468/dl.fd3q92
title: Occurrence Download

description: A dataset containing 1149 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Dalbergia mimosoides"
 ]
}

 The dataset includes 1149 records from 33 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003118-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xmk59n
title: Occurrence Download

description: A dataset containing 206 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Asia",
 "Country is India",
 "OccurrenceStatus is Present",
 "TaxonKey is Panthera pardus",
 "Year 2023-2025"
 ]
}

 The dataset includes 206 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003119-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14748957
title: The Genome Resolved Open Watersheds database (GROWdb V2)

description: This repository contains data for version 2 of the Genome Resolved Open Watersheds database (GROWdb), along with data for the manuscript describing functional response of river sediment microbiomes to environmental stressors and key MAG metabolic functions. This includes data on both, the gene database and the MAG database.

"Conserved adaptation to environmental factors by stream microbiomes in the hyporheic zone across North America"

Tom L. Stach, Jörn Starke , Feriel Bouderka, Till L. V. Bornemann, André R. Soares, Michael J. Wilkins, Amy. E. Goldman, James C. Stegen,  Mikayla A. Borton  and Alexander J. Probst 

GROWdb Global MAG files



GROWdbv2_MAG_dereplicated_MAGs.tar.gz- Fasta files of MAGs.

GROWdbv2_MAG_dRep_DRAMv2_annotation.tsv- Functional annotation of GROWdb v2 MAGs using DRAMv2 (beta)

GROWdbv2_MAG_dRep_gtdbtk_tax.summary.tsv- Taxonomic annotation of GROWdb v2 MAGs using GTDB-TK (v2.4.0) based on database r220.


GROWdb Global Gene files



GROWdbv2_Gene_DB_95AAI_no_singeltons.genes.faa.gz- FAA file of genes which make the gene DB.

GROWdbv2_Gene_DB_95AAI_no_singeltons_annotation_FunTaxDB1.4.b6_cut_annotation.tsv- Functional annotation of GROWdb v2 Gene DB (95% AAI) using FunTaxDB (v1.4 | https://zenodo.org/records/7180192#.Y6Mjn-LMLtN) 

GROWdbv2_Gene_DB_95AAI_no_singeltons_annotation_DRAM_extract_KEGG_id.annotation.tsv- Functional annotation of GROWdb v2 Gene DB (95% AAI) using DRAMv2 (beta). Only KEGG hits are extracted.