cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.n9vegg
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{"type":"and","predicates":[{"type":"within","geometry":"POLYGON ((103.219 -3.180831, 103.148629 -3.186396, 103.079988 -3.202952, 103.014766 -3.230093, 102.954567 -3.267151, 102.900871 -3.313214, 102.855001 -3.367151, 102.818086 -3.427633, 102.791036 -3.493172, 102.774519 -3.562156, 102.768944 -3.632887, 102.77445 -3.703624, 102.790905 -3.772624, 102.817905 -3.838188, 102.854788 -3.898701, 102.900647 -3.952671, 102.954354 -3.998769, 103.014585 -4.035857, 103.079857 -4.063023, 103.14856 -4.079594, 103.219 -4.085164, 103.28944 -4.079594, 103.358143 -4.063023, 103.423415 -4.035857, 103.483646 -3.998769, 103.537353 -3.952671, 103.583212 -3.898701, 103.620095 -3.838188, 103.647095 -3.772624, 103.66355 -3.703624, 103.669056 -3.632887, 103.663481 -3.562156, 103.646964 -3.493172, 103.619914 -3.427633, 103.582999 -3.367151, 103.537129 -3.313214, 103.483433 -3.267151, 103.423234 -3.230093, 103.358012 -3.202952, 103.289371 -3.186396, 103.219 -3.180831))"},{"type":"equals","key":"CLASS_KEY","value":"212","matchCase":false},{"type":"greaterThanOrEquals","key":"YEAR","value":"2015","matchCase":false},{"type":"not","predicate":{"type":"in","key":"BASIS_OF_RECORD","values":["MATERIAL_CITATION","MATERIAL_SAMPLE","PRESERVED_SPECIMEN"],"matchCase":false}},{"type":"lessThanOrEquals","key":"COORDINATE_UNCERTAINTY_IN_METERS","value":"10000","matchCase":false},{"type":"equals","key":"LICENSE","value":"CC BY 4.0","matchCase":false}]}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045256-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17605/osf.io/d8jgr
title: Monocytes and Leishmania aethiopica

description: Raw dataset used for analyses in "Different isolates of Leishmania aethiopica elicit distinct effector functions in primary human monocytes"
DOI: 10.15468/dl.dbc8ge
title: Occurrence Download

description: A dataset containing 41 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is North America",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Culicoides mohave",
 "Year 1950-2025"
 ]
}

 The dataset includes 41 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045258-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.s55g4z
title: Occurrence Download

description: A dataset containing 11 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Oreocharis hirsuta"
 ]
}

 The dataset includes 11 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045261-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.33xnxq
title: Occurrence Download

description: A dataset containing 1769 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Euclymene lombricoides",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 1769 records from 70 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045259-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fux9jp
title: Occurrence Download

description: A dataset containing 365 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Rucervus duvaucelii",
 "HasCoordinate is TRUE"
 ]
}

 The dataset includes 365 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045262-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5tcdpr
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{"type":"and","predicates":[{"type":"within","geometry":"POLYGON ((104.87 -3.174831, 104.799629 -3.180396, 104.730989 -3.196952, 104.665767 -3.224093, 104.605568 -3.261151, 104.551873 -3.307214, 104.506003 -3.361151, 104.469089 -3.421633, 104.442039 -3.487172, 104.425522 -3.556157, 104.419947 -3.626888, 104.425453 -3.697624, 104.441908 -3.766624, 104.468908 -3.832188, 104.50579 -3.892701, 104.551649 -3.946671, 104.605355 -3.992769, 104.665586 -4.029857, 104.730858 -4.057023, 104.79956 -4.073594, 104.87 -4.079164, 104.94044 -4.073594, 105.009142 -4.057023, 105.074414 -4.029857, 105.134645 -3.992769, 105.188351 -3.946671, 105.23421 -3.892701, 105.271092 -3.832188, 105.298092 -3.766624, 105.314547 -3.697624, 105.320053 -3.626888, 105.314478 -3.556157, 105.297961 -3.487172, 105.270911 -3.421633, 105.233997 -3.361151, 105.188127 -3.307214, 105.134432 -3.261151, 105.074233 -3.224093, 105.009011 -3.196952, 104.940371 -3.180396, 104.87 -3.174831))"},{"type":"equals","key":"CLASS_KEY","value":"212","matchCase":false},{"type":"greaterThanOrEquals","key":"YEAR","value":"2015","matchCase":false},{"type":"not","predicate":{"type":"in","key":"BASIS_OF_RECORD","values":["MATERIAL_CITATION","MATERIAL_SAMPLE","PRESERVED_SPECIMEN"],"matchCase":false}},{"type":"lessThanOrEquals","key":"COORDINATE_UNCERTAINTY_IN_METERS","value":"10000","matchCase":false},{"type":"equals","key":"LICENSE","value":"CC BY 4.0","matchCase":false}]}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045263-251120083545085/datasets/export for details.
DOI: 10.6084/m9.figshare.30752232
title: Streamlining single-cell spatial transcriptomics for human kidney tissue

description: Single-cell spatial technologies have emerged in recent years, enabling characterization of tissue architecture and organization at unprecedented resolution. However, computational analysis of spatial transcriptomics data remains a bottleneck for scientific discoveries in the absence of dedicated bioinformatics expertise. Here, we describe a novel cell area normalization method and workflow to annotate 15 kidney cell types from a dataset generated using NanoString’s CosMx single-cell-resolution spatial transcriptomic platform. This approach enabled a comparison between two healthy kidney biopsies and two diseased samples. We validated our pipeline’s accuracy using gene expression analysis, demonstrating increased sensitivity compared with other normalization methods and consistency with pathological changes observed in biopsy-proven diabetic kidney disease (DKD). Using precise cell type annotation, we observed significant changes in the proportions of podocytes and immune cells in DKD, with regional enrichment of immune cells and differential gene expression. Injured proximal tubules showed the expected upregulation of <i>HAVCR1</i> and <i>VCAM1,</i> as well as other genes associated with diabetes, including <i>IL18</i>, <i>ITGA3</i>, and <i>ITGB1</i>. The workflow, now fully integrated into the BioTuring SpatialX (Lens V2.0), is available as a platform designed for users with no formal bioinformatics training, providing accessible web-based tools for spatial data analysis. Kidney biopsy samples from two healthy patients and two diabetic kidney disease patients were analyzed using CosMx single-cell spatial transcriptomics. We developed a cell annotation and analysis pipeline using a novel cell area based normalization technique. Our workflow is fully integrated into the BioTuring SpatialX (Lens V2.0) platform, offering web-based analysis tools that provide a low barrier to entry for spatial data analysis. Developed a cell area normalization for CosMx single-cell spatial transcriptomics integrated in a web-based platform.Achieved higher sensitivity in gene expression analysis compared with existing normalization approaches.Annotation of 15 kidney cell types using NanoString’s 1000-plex CosMx platform combined with a custom panel of 29 kidney-specific genes.Comparative spatial analysis between healthy and diabetic kidney disease tissues identifies DKD-associated gene changes and regional immune enrichment at single-cell resolution. Developed a cell area normalization for CosMx single-cell spatial transcriptomics integrated in a web-based platform. Achieved higher sensitivity in gene expression analysis compared with existing normalization approaches. Annotation of 15 kidney cell types using NanoString’s 1000-plex CosMx platform combined with a custom panel of 29 kidney-specific genes. Comparative spatial analysis between healthy and diabetic kidney disease tissues identifies DKD-associated gene changes and regional immune enrichment at single-cell resolution.
DOI: 10.6084/m9.figshare.30752232.v1
title: Streamlining single-cell spatial transcriptomics for human kidney tissue

description: Single-cell spatial technologies have emerged in recent years, enabling characterization of tissue architecture and organization at unprecedented resolution. However, computational analysis of spatial transcriptomics data remains a bottleneck for scientific discoveries in the absence of dedicated bioinformatics expertise. Here, we describe a novel cell area normalization method and workflow to annotate 15 kidney cell types from a dataset generated using NanoString’s CosMx single-cell-resolution spatial transcriptomic platform. This approach enabled a comparison between two healthy kidney biopsies and two diseased samples. We validated our pipeline’s accuracy using gene expression analysis, demonstrating increased sensitivity compared with other normalization methods and consistency with pathological changes observed in biopsy-proven diabetic kidney disease (DKD). Using precise cell type annotation, we observed significant changes in the proportions of podocytes and immune cells in DKD, with regional enrichment of immune cells and differential gene expression. Injured proximal tubules showed the expected upregulation of <i>HAVCR1</i> and <i>VCAM1,</i> as well as other genes associated with diabetes, including <i>IL18</i>, <i>ITGA3</i>, and <i>ITGB1</i>. The workflow, now fully integrated into the BioTuring SpatialX (Lens V2.0), is available as a platform designed for users with no formal bioinformatics training, providing accessible web-based tools for spatial data analysis. Kidney biopsy samples from two healthy patients and two diabetic kidney disease patients were analyzed using CosMx single-cell spatial transcriptomics. We developed a cell annotation and analysis pipeline using a novel cell area based normalization technique. Our workflow is fully integrated into the BioTuring SpatialX (Lens V2.0) platform, offering web-based analysis tools that provide a low barrier to entry for spatial data analysis. Developed a cell area normalization for CosMx single-cell spatial transcriptomics integrated in a web-based platform.Achieved higher sensitivity in gene expression analysis compared with existing normalization approaches.Annotation of 15 kidney cell types using NanoString’s 1000-plex CosMx platform combined with a custom panel of 29 kidney-specific genes.Comparative spatial analysis between healthy and diabetic kidney disease tissues identifies DKD-associated gene changes and regional immune enrichment at single-cell resolution. Developed a cell area normalization for CosMx single-cell spatial transcriptomics integrated in a web-based platform. Achieved higher sensitivity in gene expression analysis compared with existing normalization approaches. Annotation of 15 kidney cell types using NanoString’s 1000-plex CosMx platform combined with a custom panel of 29 kidney-specific genes. Comparative spatial analysis between healthy and diabetic kidney disease tissues identifies DKD-associated gene changes and regional immune enrichment at single-cell resolution.
DOI: 10.25810/3hvn-ef66.62
title: Danish Newspaper Coverage of Climate Change or Global Warming, 2004-2025 - November 2025

description: The Media and Climate Change Observatory Data monitors 126 sources (across newspapers, radio and TV) in 58 countries in seven different regions around the world. Data is assembled by accessing archives through the Lexis Nexis, Proquest and Factiva databases via the University of Colorado libraries. More information may be found at: http://mecco.colorado.edu.
DOI: 10.6084/m9.figshare.28950793
title: Long-Term Outcomes of Pediatric Vogt–Koyanagi–Harada Disease

description: To study the clinical presentation, outcomes, and factors affecting the final visual outcome of Vogt-Koyanagi-Harada (VKH) disease in the pediatric age group. Pediatric patients who were diagnosed with VKH at King Khaled Eye Specialist Hospital (KKESH) between 2007 and 2024. Demographic and clinical data were collected and analyzed for an association with the final visual outcome. Sixty-nine children (138 eyes) with an age range upon presentation from 2 years old to 18 years old and a mean age of 12.2 ± 4.0 years were included. The mean duration of follow-up was 6.5 ± 3.1 years. There were 35 (50.7%) males and 34 (49.3%) females. Sixty children (86.9%) had initial-onset acute VKH, while 9 children had chronic recurrent VKH. At initial presentation, the mean LogMAR BCVA was 0.6 (Snellen = 20/70) ± 0.6. Children with chronic recurrent VKH presented at an earlier age (<i>p</i> = 0.003), had more severe corneal involvement (<i>p</i> &lt; 0.001) and more severe AC reaction (<i>p</i> &lt; 0.001). Cataract developed in 33 (23.9%) eyes, 54 eyes (39.1%) developed glaucoma, and 36 eyes (26.1%) developed choroidal neovascular membranes (CNVM). Children with chronic recurrent VKH disease had higher rates of pre-existing or developing cataract, glaucoma, and CNVM. On the last visit, the BCVA improved from an average of 20/70 to 20/50. The visual improvement was statistically significant (<i>p</i> = 0.005). Good visual outcomes can be achieved in the majority of pediatric patients with VKH disease. Children with chronic recurrent VKH disease present with more aggressive anterior segment inflammation, have higher risk of developing ocular complications, and less favorable visual outcomes.
DOI: 10.6084/m9.figshare.28950793.v1
title: Long-Term Outcomes of Pediatric Vogt–Koyanagi–Harada Disease

description: To study the clinical presentation, outcomes, and factors affecting the final visual outcome of Vogt-Koyanagi-Harada (VKH) disease in the pediatric age group. Pediatric patients who were diagnosed with VKH at King Khaled Eye Specialist Hospital (KKESH) between 2007 and 2024. Demographic and clinical data were collected and analyzed for an association with the final visual outcome. Sixty-nine children (138 eyes) with an age range upon presentation from 2 years old to 18 years old and a mean age of 12.2 ± 4.0 years were included. The mean duration of follow-up was 6.5 ± 3.1 years. There were 35 (50.7%) males and 34 (49.3%) females. Sixty children (86.9%) had initial-onset acute VKH, while 9 children had chronic recurrent VKH. At initial presentation, the mean LogMAR BCVA was 0.6 (Snellen = 20/70) ± 0.6. Children with chronic recurrent VKH presented at an earlier age (<i>p</i> = 0.003), had more severe corneal involvement (<i>p</i> &lt; 0.001) and more severe AC reaction (<i>p</i> &lt; 0.001). Cataract developed in 33 (23.9%) eyes, 54 eyes (39.1%) developed glaucoma, and 36 eyes (26.1%) developed choroidal neovascular membranes (CNVM). Children with chronic recurrent VKH disease had higher rates of pre-existing or developing cataract, glaucoma, and CNVM. On the last visit, the BCVA improved from an average of 20/70 to 20/50. The visual improvement was statistically significant (<i>p</i> = 0.005). Good visual outcomes can be achieved in the majority of pediatric patients with VKH disease. Children with chronic recurrent VKH disease present with more aggressive anterior segment inflammation, have higher risk of developing ocular complications, and less favorable visual outcomes.
DOI: 10.6084/m9.figshare.30611135
title: Complexities in the Terminology Used for Describing, Diagnosing, and Classifying Retinal Vasculitis: A Scoping Review from the International Uveitis Study Group (IUSG) Retinal Vasculitis Study (ReViSe)–Report 6

description: Retinal vasculitis (RV) is a complex inflammatory condition that affects the retinal vessels, often presenting as perivascular sheathing, vascular leakage, and occlusion. Despite its well-documented clinical and angiographic features, the definition and classification of RV remain inconsistent across clinical and research settings. This lack of uniformity has led to challenges in diagnosis, management, and understanding of research findings. Thus, this scoping review aims to objectively identify any ambiguity in the terminology of RV and discuss possible reasons for it, laying the groundwork for a subsequent panel of experts to provide consensus definitions for RV through a Delphi process. This review included 97 studies. The authors extracted and summarised data on the definitions and diagnostic criteria used for RV, the definitions used for subtypes of RV (e.g. isolated, idiopathic, undifferentiated, primary RV), the imaging modalities used for RV diagnosis, and any references to existing guidelines. The results confirmed a significant degree of ambiguity in RV terminology. Among the 17 papers that explicitly defined RV in their methodology, four distinct definitions emerged. We also found that the terms’ idiopathic,’ ‘primary,’ and ‘undifferentiated’ RV were often used interchangeably, despite reflecting distinct aspects of the disease. Notably, all 52 studies that noted the diagnostic modalities used included fluorescein angiography, although the usage of other modalities was contentious. There are significant inconsistencies and ambiguities in defining and classifying RV, highlighting the need for a standardized, consensus-based framework to improve clarity and consistency in both research and clinical practice.
DOI: 10.6084/m9.figshare.30611135.v1
title: Complexities in the Terminology Used for Describing, Diagnosing, and Classifying Retinal Vasculitis: A Scoping Review from the International Uveitis Study Group (IUSG) Retinal Vasculitis Study (ReViSe)–Report 6

description: Retinal vasculitis (RV) is a complex inflammatory condition that affects the retinal vessels, often presenting as perivascular sheathing, vascular leakage, and occlusion. Despite its well-documented clinical and angiographic features, the definition and classification of RV remain inconsistent across clinical and research settings. This lack of uniformity has led to challenges in diagnosis, management, and understanding of research findings. Thus, this scoping review aims to objectively identify any ambiguity in the terminology of RV and discuss possible reasons for it, laying the groundwork for a subsequent panel of experts to provide consensus definitions for RV through a Delphi process. This review included 97 studies. The authors extracted and summarised data on the definitions and diagnostic criteria used for RV, the definitions used for subtypes of RV (e.g. isolated, idiopathic, undifferentiated, primary RV), the imaging modalities used for RV diagnosis, and any references to existing guidelines. The results confirmed a significant degree of ambiguity in RV terminology. Among the 17 papers that explicitly defined RV in their methodology, four distinct definitions emerged. We also found that the terms’ idiopathic,’ ‘primary,’ and ‘undifferentiated’ RV were often used interchangeably, despite reflecting distinct aspects of the disease. Notably, all 52 studies that noted the diagnostic modalities used included fluorescein angiography, although the usage of other modalities was contentious. There are significant inconsistencies and ambiguities in defining and classifying RV, highlighting the need for a standardized, consensus-based framework to improve clarity and consistency in both research and clinical practice.
DOI: 10.6084/m9.figshare.28950790
title: Long-Term Effects of Adalimumab in Juvenile Idiopathic Arthritis-Associated Uveitis: 3- and 6-Year Results of the ADJUVITE Trial

description: To evaluate the long-term efficacy of and tolerance to adalimumab in patients with juvenile idiopathic arthritis-associated uveitis (JIA-U). This retrospective study included patients with JIA-U who completed the ADJUVITE trial with at least 2 years and up to 5 years of follow-up after the end of the trial (<i>i.e</i>. at least 3 years and up to 6 years of follow-up after randomization). Data, including treatment course, visual and anatomical outcomes, uveitis activity evaluated by laser flare photometry, and safety were collected from medical records. Forty-one eyes of 25 participants with a mean age of 10.5 ± 4.0 years at the end of the trial were enrolled. Twenty-one patients (84%) responded to adalimumab during a mean follow-up period of 68.0 ± 21.6 months (range 26–109 months, post-trial), and among the responders, one patient could discontinue adalimumab without further uveitis relapse. Five years after the end of the trial, the mean BCVA improved to 0.07 ± 0.39 logMAR (vs. 0.14 ± 0.20 logMAR, <i>p</i> = 0.048) and the mean anterior chamber flare decreased to 29.9 ± 19.1 ph/ms (vs. 37.2 ± 35.0 ph/ms, <i>p</i> = 0.170). The mean dose of methotrexate decreased significantly from 11.3 ± 4.4 mg/week at the end of the trial to 5.2 ± 6.2 mg/week at the last follow-up (<i>p</i> = 0.002). Four patients did not respond to adalimumab and required other biologics. Adalimumab was well-tolerated in all patients. Adalimumab was effective in maintaining long-term uveitis control in patients with JIA-U, with a good safety profile. However, complete discontinuation was not possible in most cases, confirming the suspending effect of adalimumab.
DOI: 10.6084/m9.figshare.28950790.v1
title: Long-Term Effects of Adalimumab in Juvenile Idiopathic Arthritis-Associated Uveitis: 3- and 6-Year Results of the ADJUVITE Trial

description: To evaluate the long-term efficacy of and tolerance to adalimumab in patients with juvenile idiopathic arthritis-associated uveitis (JIA-U). This retrospective study included patients with JIA-U who completed the ADJUVITE trial with at least 2 years and up to 5 years of follow-up after the end of the trial (<i>i.e</i>. at least 3 years and up to 6 years of follow-up after randomization). Data, including treatment course, visual and anatomical outcomes, uveitis activity evaluated by laser flare photometry, and safety were collected from medical records. Forty-one eyes of 25 participants with a mean age of 10.5 ± 4.0 years at the end of the trial were enrolled. Twenty-one patients (84%) responded to adalimumab during a mean follow-up period of 68.0 ± 21.6 months (range 26–109 months, post-trial), and among the responders, one patient could discontinue adalimumab without further uveitis relapse. Five years after the end of the trial, the mean BCVA improved to 0.07 ± 0.39 logMAR (vs. 0.14 ± 0.20 logMAR, <i>p</i> = 0.048) and the mean anterior chamber flare decreased to 29.9 ± 19.1 ph/ms (vs. 37.2 ± 35.0 ph/ms, <i>p</i> = 0.170). The mean dose of methotrexate decreased significantly from 11.3 ± 4.4 mg/week at the end of the trial to 5.2 ± 6.2 mg/week at the last follow-up (<i>p</i> = 0.002). Four patients did not respond to adalimumab and required other biologics. Adalimumab was well-tolerated in all patients. Adalimumab was effective in maintaining long-term uveitis control in patients with JIA-U, with a good safety profile. However, complete discontinuation was not possible in most cases, confirming the suspending effect of adalimumab.