cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.nabqz7
title: Occurrence Download

description: A dataset containing 2006 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is North America",
 "Country is Canada",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "License is one of (CC0 1.0, CC-BY 4.0, CC-BY-NC 4.0)",
 "PublishingOrg is one of (28eb1a3f-1c15-4a95-931a-4af90ecb574d, da86174a-a605-43a4-a5e8-53d484152cd3)",
 "TaxonKey is Ambrosia artemisiifolia",
 "Year 2023-2025"
 ]
}

 The dataset includes 2006 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005028-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.z6r2k4
title: Occurrence Download

description: A dataset containing 4745 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Guarea glabra",
 "HasCoordinate is true"
 ]
}

 The dataset includes 4745 records from 164 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005027-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8y9zpa
title: Occurrence Download

description: A dataset containing 56291 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is Mexico",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "License is one of (CC0 1.0, CC-BY 4.0, CC-BY-NC 4.0)",
 "TaxonKey is Orchidaceae"
 ]
}

 The dataset includes 56291 records from 204 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005021-251120083545085/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.30690479
title: <b>Supplementary Information</b>

description: U–Pb data for zircon and apatite from Salisbury Plain stream sediment and automated mineralogy results.
DOI: 10.6084/m9.figshare.30690479.v1
title: <b>Supplementary Information</b>

description: U–Pb data for zircon and apatite from Salisbury Plain stream sediment and automated mineralogy results.
DOI: 10.6084/m9.figshare.30690605
title: Supplementary Material for: Changes in salivary matrix metalloproteinase-8 concentrations are not associated with oral health during early adolescence

description: Background 
Salivary matrix metalloproteinase-8 (MMP-8) concentration is considered a biomarker of oral health in adults, but studies in pediatric populations, especially with longitudinal data, are scarce. 

Methods
We examined the associations of caries experience (DFT index) and gingivitis/calculus (CPITN) retrieved from public dental records with repeated salivary MMP-8 concentrations. Salivary MMP-8 were measured from 403 Finnish adolescents (50% girls) at the mean (SD) age of 11.4 (0.4) and 13.8 (0.5) years, using an ELISA kit. Oral health was determined on average 42 (27) days after saliva collection at baseline. The DFT index was categorized into no caries experience (DFT = 0) and having caries experience (DFT &gt; 0), and CPITN into no gingivitis/calculus (CPITN = 0) or having gingivitis/calculus (CPITN &gt; 0). 

Results
Of the participants, 19.1% presented with caries experience, and 69.5% had gingivitis/calculus. The mean MMP-8 increased during follow-up by 0.125 ng/ml (95% CI 0.05; 0.20, p = 0.006). MMP-8 at the two time points correlated weakly in all participants (r = 0.137, p = 0.006), especially in girls (r = 0.204, p = 0.004). The change in MMP-8 was not associated with caries experience or gingivitis/calculus in all participants or in gender-specific analyses (repeated measures ANOVA p &gt; 0.05). Puberty status and medication use were not related to MMP-8 concentration. 

Conclusions
Oral health indices retrieved from public health records were not associated with changes in MMP-8 concentrations in early adolescents over a 2-year follow-up. Salivary MMP-8 may not be a suitable biomarker of oral health in pediatric populations.
DOI: 10.6084/m9.figshare.30690605.v1
title: Supplementary Material for: Changes in salivary matrix metalloproteinase-8 concentrations are not associated with oral health during early adolescence

description: Background 
Salivary matrix metalloproteinase-8 (MMP-8) concentration is considered a biomarker of oral health in adults, but studies in pediatric populations, especially with longitudinal data, are scarce. 

Methods
We examined the associations of caries experience (DFT index) and gingivitis/calculus (CPITN) retrieved from public dental records with repeated salivary MMP-8 concentrations. Salivary MMP-8 were measured from 403 Finnish adolescents (50% girls) at the mean (SD) age of 11.4 (0.4) and 13.8 (0.5) years, using an ELISA kit. Oral health was determined on average 42 (27) days after saliva collection at baseline. The DFT index was categorized into no caries experience (DFT = 0) and having caries experience (DFT &gt; 0), and CPITN into no gingivitis/calculus (CPITN = 0) or having gingivitis/calculus (CPITN &gt; 0). 

Results
Of the participants, 19.1% presented with caries experience, and 69.5% had gingivitis/calculus. The mean MMP-8 increased during follow-up by 0.125 ng/ml (95% CI 0.05; 0.20, p = 0.006). MMP-8 at the two time points correlated weakly in all participants (r = 0.137, p = 0.006), especially in girls (r = 0.204, p = 0.004). The change in MMP-8 was not associated with caries experience or gingivitis/calculus in all participants or in gender-specific analyses (repeated measures ANOVA p &gt; 0.05). Puberty status and medication use were not related to MMP-8 concentration. 

Conclusions
Oral health indices retrieved from public health records were not associated with changes in MMP-8 concentrations in early adolescents over a 2-year follow-up. Salivary MMP-8 may not be a suitable biomarker of oral health in pediatric populations.
DOI: 10.6084/m9.figshare.30690614
title: Supplementary Material for: Long-term outcomes and prognostic factors for Vedolizumab-treated Japanese patients with Ulcerative Colitis

description: Introduction: Vedolizumab (VDZ) has been available for Japanese patients with ulcerative colitis (UC). However, real-world data regarding the long-term efficacy and safety of VDZ in Japanese patients with active ulcerative colitis remain limited. This study aimed to evaluate the long-term outcomes of VDZ and identify prognostic factors in Japanese patients with UC.
Methods: This retrospective multicenter cohort study was conducted at six hospitals and one clinic in Hokkaido, Japan. A total of 172 patients with UC who received VDZ treatment between November 2018 and October 2022 were included. Treatment persistence rates at 52, 104, and 156 weeks were evaluated. The median follow-up duration was 51 weeks (range: 1–156).
Clinical response, clinical remission, and mucosal healing rates were assessed at weeks 6 and 52. Prognostic factors for treatment response were analyzed using univariate and multivariate logistic regression analyses.
Results: The cumulative treatment persistence rates at weeks 52, 104, and 156 were 68.1%, 58.1%, and 50.7%, with 64, 32, and 17 patients remaining on vedolizumab at those respective weeks.Clinical response and remission rates at week 6 were 63.3% and 52.3%, while clinical remission, corticosteroid-free remission, and mucosal healing rates at week 52 were 59.3%, 53.9%, and 52.3%, respectively. Multivariable analysis identified male sex and absence of prior anti-tumor necrosis factor (TNF) exposure as factors associated with clinical response at week 6 (odds ratio [OR] 2.17, p = 0.045; OR 2.26, p = 0.046). Clinical response at week 6 was strongly associated with clinical remission at week 52 (OR 14.5, p &lt; 0.01). Among patients previously treated with anti-TNF agents, those with secondary loss of response had significantly higher remission rates at week 52 than did those with primary non-response (p &lt; 0.01). Adverse events were observed in six patients, with one case leading to treatment discontinuation; no severe adverse events were reported.
Conclusions: VDZ demonstrated favorable long-term treatment persistence, efficacy, and safety in Japanese patients with UC. The efficacy of VDZ may vary depending on prior anti-TNF therapy outcomes, particularly the reasons for discontinuation. These findings provide valuable insights for optimizing treatment strategies in UC patients, although further prospective studies are warranted.
DOI: 10.6084/m9.figshare.30690614.v1
title: Supplementary Material for: Long-term outcomes and prognostic factors for Vedolizumab-treated Japanese patients with Ulcerative Colitis

description: Introduction: Vedolizumab (VDZ) has been available for Japanese patients with ulcerative colitis (UC). However, real-world data regarding the long-term efficacy and safety of VDZ in Japanese patients with active ulcerative colitis remain limited. This study aimed to evaluate the long-term outcomes of VDZ and identify prognostic factors in Japanese patients with UC.
Methods: This retrospective multicenter cohort study was conducted at six hospitals and one clinic in Hokkaido, Japan. A total of 172 patients with UC who received VDZ treatment between November 2018 and October 2022 were included. Treatment persistence rates at 52, 104, and 156 weeks were evaluated. The median follow-up duration was 51 weeks (range: 1–156).
Clinical response, clinical remission, and mucosal healing rates were assessed at weeks 6 and 52. Prognostic factors for treatment response were analyzed using univariate and multivariate logistic regression analyses.
Results: The cumulative treatment persistence rates at weeks 52, 104, and 156 were 68.1%, 58.1%, and 50.7%, with 64, 32, and 17 patients remaining on vedolizumab at those respective weeks.Clinical response and remission rates at week 6 were 63.3% and 52.3%, while clinical remission, corticosteroid-free remission, and mucosal healing rates at week 52 were 59.3%, 53.9%, and 52.3%, respectively. Multivariable analysis identified male sex and absence of prior anti-tumor necrosis factor (TNF) exposure as factors associated with clinical response at week 6 (odds ratio [OR] 2.17, p = 0.045; OR 2.26, p = 0.046). Clinical response at week 6 was strongly associated with clinical remission at week 52 (OR 14.5, p &lt; 0.01). Among patients previously treated with anti-TNF agents, those with secondary loss of response had significantly higher remission rates at week 52 than did those with primary non-response (p &lt; 0.01). Adverse events were observed in six patients, with one case leading to treatment discontinuation; no severe adverse events were reported.
Conclusions: VDZ demonstrated favorable long-term treatment persistence, efficacy, and safety in Japanese patients with UC. The efficacy of VDZ may vary depending on prior anti-TNF therapy outcomes, particularly the reasons for discontinuation. These findings provide valuable insights for optimizing treatment strategies in UC patients, although further prospective studies are warranted.
DOI: 10.6084/m9.figshare.30690617
title: Supplementary Material for: A Novel GUCY2D Frameshift Deletion Identified in a Patient with Leber Congenital Amaurosis 1: A Case Report

description: Introduction: This study aimed to describe the clinical characteristics of a 1-year-old male patient with Leber congenital amaurosis type 1 (LCA1) and investigate the genetic variations underlying his symptoms.
 
Case Presentation: A comprehensive medical history of the patient was obtained with thorough examinations via mydriatic optometry, fundus photography, and flash electroretinography. To identify causative mutations, whole-exome sequencing (WES) was conducted. Potential pathogenic mutations identified with WES were further validated via Sanger sequencing, which was also performed on family members to confirm the origins of the mutations. Based on clinical and laboratory findings, the patient was diagnosed with LCA1. Two heterozygous mutations in the GUCY2D gene, c.835G&gt;A and c.2516_2517del, were detected in the patient with WES. Both mutations were assigned as likely pathogenic according to ACMG guidelines. c.2516_2517del has not been described previously. Sanger sequencing confirmed that the unaffected father and mother carried c.835G&gt;A and c.2516_2517del, respectively.
 
Conclusion: The patient was a typical case of LCA1 with two GUCY2D mutations. To the best of our knowledge, this is the first report of the allele mutation c.2516_2517del in a patient with LCA1.
DOI: 10.6084/m9.figshare.30690617.v1
title: Supplementary Material for: A Novel GUCY2D Frameshift Deletion Identified in a Patient with Leber Congenital Amaurosis 1: A Case Report

description: Introduction: This study aimed to describe the clinical characteristics of a 1-year-old male patient with Leber congenital amaurosis type 1 (LCA1) and investigate the genetic variations underlying his symptoms.
 
Case Presentation: A comprehensive medical history of the patient was obtained with thorough examinations via mydriatic optometry, fundus photography, and flash electroretinography. To identify causative mutations, whole-exome sequencing (WES) was conducted. Potential pathogenic mutations identified with WES were further validated via Sanger sequencing, which was also performed on family members to confirm the origins of the mutations. Based on clinical and laboratory findings, the patient was diagnosed with LCA1. Two heterozygous mutations in the GUCY2D gene, c.835G&gt;A and c.2516_2517del, were detected in the patient with WES. Both mutations were assigned as likely pathogenic according to ACMG guidelines. c.2516_2517del has not been described previously. Sanger sequencing confirmed that the unaffected father and mother carried c.835G&gt;A and c.2516_2517del, respectively.
 
Conclusion: The patient was a typical case of LCA1 with two GUCY2D mutations. To the best of our knowledge, this is the first report of the allele mutation c.2516_2517del in a patient with LCA1.
DOI: 10.6084/m9.figshare.30690620
title: Supplementary Material for: Body Mass Index and Interindividual Variation in Salivary Amylase Gene Copy Number Assessed Using an In-House Validated Method: A Pilot Study from the National Nutrition Survey of a High Rice-Consuming Nation

description: Introduction: The AMY1 gene, which encodes salivary amylase, exhibits copy number variation (CNV) that affects starch metabolism and may influence obesity risk. This study aimed to assess AMY1 CNV among selected participants of the 2018-2019 Expanded National Nutrition Survey (ENNS), using a validated digital PCR (dPCR) method.
Methodology: The method validation was initially performed using certified reference material. Whole blood DNA was isolated from selected nutrition survey respondents who had available daily rice intake data. The daily rice intake of participants was divided into tertiles. chi-square tests was used to compare AMY1 CNV, age, BMI, smoking and alcohol status, and other variables across daily rice intake tertiles.
Results: Data from selected ENNS participants revealed AMY1 CNV ranging from 6–18 copies. Higher rice intake was significantly associated with increased AMY1 CNV (p = 0.035). Lower AMY1 CNV was more prevalent among overweight and obese individuals. 
Conclusion: Findings highlight gene-diet interactions and support the relevance of personalized nutrition approaches in the Philippines.
DOI: 10.6084/m9.figshare.30690620.v1
title: Supplementary Material for: Body Mass Index and Interindividual Variation in Salivary Amylase Gene Copy Number Assessed Using an In-House Validated Method: A Pilot Study from the National Nutrition Survey of a High Rice-Consuming Nation

description: Introduction: The AMY1 gene, which encodes salivary amylase, exhibits copy number variation (CNV) that affects starch metabolism and may influence obesity risk. This study aimed to assess AMY1 CNV among selected participants of the 2018-2019 Expanded National Nutrition Survey (ENNS), using a validated digital PCR (dPCR) method.
Methodology: The method validation was initially performed using certified reference material. Whole blood DNA was isolated from selected nutrition survey respondents who had available daily rice intake data. The daily rice intake of participants was divided into tertiles. chi-square tests was used to compare AMY1 CNV, age, BMI, smoking and alcohol status, and other variables across daily rice intake tertiles.
Results: Data from selected ENNS participants revealed AMY1 CNV ranging from 6–18 copies. Higher rice intake was significantly associated with increased AMY1 CNV (p = 0.035). Lower AMY1 CNV was more prevalent among overweight and obese individuals. 
Conclusion: Findings highlight gene-diet interactions and support the relevance of personalized nutrition approaches in the Philippines.
DOI: 10.6084/m9.figshare.30690623
title: Supplementary Material for: Cytarabine-induced Cerebellar Toxicity in a Young Patient with B-cell ALL: A Case Report

description: Background: Acute cerebellar toxicity following high-dose cytarabine treatment is a well-documented but rare complication. Symptoms can progress if therapy continues even after the initial onset of deficits hence, prompt recognition and termination of treatment is essential. 
Methods: We report a case of a 20-year-old Filipino male with B-cell acute lymphoblastic leukemia (ALL) in relapse, with leptomeningeal spread, presenting with impaired saccades and pursuits, scanning speech, head titubation, limb and truncal ataxia after chemotherapy with high dose cytarabine. The patient was treated with intravenous dexamethasone with resolution of cerebellar deficits.
Results and Conclusion: Certain risk factors are speculated to predispose patients to cerebellar toxicity however, no single factor has been proven to be an absolute determinant. Our case highlights central nervous system disease as a risk factor for cytarabine-induced cerebellar degeneration.
DOI: 10.6084/m9.figshare.30690623.v1
title: Supplementary Material for: Cytarabine-induced Cerebellar Toxicity in a Young Patient with B-cell ALL: A Case Report

description: Background: Acute cerebellar toxicity following high-dose cytarabine treatment is a well-documented but rare complication. Symptoms can progress if therapy continues even after the initial onset of deficits hence, prompt recognition and termination of treatment is essential. 
Methods: We report a case of a 20-year-old Filipino male with B-cell acute lymphoblastic leukemia (ALL) in relapse, with leptomeningeal spread, presenting with impaired saccades and pursuits, scanning speech, head titubation, limb and truncal ataxia after chemotherapy with high dose cytarabine. The patient was treated with intravenous dexamethasone with resolution of cerebellar deficits.
Results and Conclusion: Certain risk factors are speculated to predispose patients to cerebellar toxicity however, no single factor has been proven to be an absolute determinant. Our case highlights central nervous system disease as a risk factor for cytarabine-induced cerebellar degeneration.
DOI: 10.15468/dl.jpa67q
title: Occurrence Download

description: A dataset containing 30456 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Datura wrightii"
 ]
}

 The dataset includes 30456 records from 240 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005032-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6fkhmz
title: Occurrence Download

description: A dataset containing 31498 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "TaxonKey is Sturnus vulgaris"
 ]
}

 The dataset includes 31498 records from 23 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005033-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34740/kaggle/dsv/13845547
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.15468/dl.yyqvuw
title: Occurrence Download

description: A dataset containing 3074 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Heliothrips haemorrhoidalis"
 ]
}

 The dataset includes 3074 records from 59 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005034-251120083545085/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.30690581
title: Comparative analysis of human and mouse ovaries across age, DOI: 10.1126/science.adx0659, Seurat Object of subsetted C57BL/6 Mouse Oocytes from this study (GSE290742) merged with those from Isola <i>et al.</i> 2024 (https://doi.org/10.1038/s43587-023-00552-5, GEO GSE232309)

description: The mouse is a tractable model for human ovarian biology, however its utility is limited by incomplete understanding of how transcription and signaling differ interspecifically and with age. We compared ovaries between species using three-dimensional imaging, single-cell transcriptomics, and functional studies. In mice, we mapped declining follicle numbers and oocyte competence during aging; in human ovaries, we identified cortical follicle pockets and decreases in density. Oocytes had species-specific gene expression patterns during growth that converged toward maturity. Age-related transcriptional changes were greater in oocytes than granulosa cells across species, although mature oocytes change more in humans. We identified ovarian sympathetic nerves and glia; axon density increased in aged ovaries and, when ablated in mice, perturbed folliculogenesis. This comparative atlas defines shared and species-specific hallmarks of ovarian biology.
DOI: 10.6084/m9.figshare.30690581.v1
title: Comparative analysis of human and mouse ovaries across age, DOI: 10.1126/science.adx0659, Seurat Object of subsetted C57BL/6 Mouse Oocytes from this study (GSE290742) merged with those from Isola <i>et al.</i> 2024 (https://doi.org/10.1038/s43587-023-00552-5, GEO GSE232309)

description: The mouse is a tractable model for human ovarian biology, however its utility is limited by incomplete understanding of how transcription and signaling differ interspecifically and with age. We compared ovaries between species using three-dimensional imaging, single-cell transcriptomics, and functional studies. In mice, we mapped declining follicle numbers and oocyte competence during aging; in human ovaries, we identified cortical follicle pockets and decreases in density. Oocytes had species-specific gene expression patterns during growth that converged toward maturity. Age-related transcriptional changes were greater in oocytes than granulosa cells across species, although mature oocytes change more in humans. We identified ovarian sympathetic nerves and glia; axon density increased in aged ovaries and, when ablated in mice, perturbed folliculogenesis. This comparative atlas defines shared and species-specific hallmarks of ovarian biology.
DOI: 10.5281/zenodo.14834929
title: RA IHC dataset accompanying VIMA paper

description: This archive contains both the raw data from the dataset as well as outputs generated by processing the data with the VIMA method.
DOI: 10.5281/zenodo.17694679
title: RA IHC dataset accompanying VIMA paper

description: This archive contains both the raw data from the dataset as well as outputs generated by processing the data with the VIMA method.
DOI: 10.15468/dl.9s63rm
title: Occurrence Download

description: A dataset containing 64619 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Mytilus trossulus"
 ]
}

 The dataset includes 64619 records from 73 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0049351-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.