cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.30664193.v1
title: Supplementary Material for: High Dose Upadacitinib Maintenance Therapy for Refractory Crohn's Disease: A Case Series and Review of The Literature

description: Introduction: Crohn’s disease (CD) is a chronic, relapsing-remitting disorder affecting the gastrointestinal tract that falls under the umbrella term of inflammatory bowel disease (IBD). Its etiology is unknown, but it is suggested that there is a strong genetic and environmental interaction leading to its development. The mainstay of treatment for patients with moderate to severe CD is advanced therapy, such as biologics or small molecules. Despite the use of these medications, the disease may be unresponsive to these agents leading to refractory disease. The use of novel therapies expanded the treatment options for patients with refractory CD or those who failed multiple biologics. Upadacitinib (UPA), a small molecule drug, belongs to a class of medications known as Janus kinase (JAK) inhibitors. Upadacitinib is known to be effective against CD with a dosage of either 15 or 30 mg. However, this dose deemed to be ineffective in the cases we reported. A higher maintenance dose of 45 mg was introduced and the patient’s reported resolution of symptoms. It is important to note that larger studies are required to prove the efficacy of this treatment for CD. 
Case presentations: This is a case-series of three patients with a history of refractory CD and prior exposure to at least 1 biologic agent, who achieved clinical remission and endoscopic healing on UPA maintenance therapy 45 mg orally once daily. 
Conclusion: This case series illustrates potential benefit and supports the rationale for larger controlled studies evaluating high-dose UPA maintenance therapy.
DOI: 10.5683/sp3/gsmtr6
title: ODRC data schema: Nursery 1 ventilation data

description: This is a data schema created using &lt;a href="http://agrifooddatacanada.ca"&gt;Agri-food Data Canada's&lt;/a&gt; &lt;a href= "https://semanticengine.org"&gt; Semantic Engine &lt;a/&gt;. Data schemas describe data that are collected on an ongoing basis from research centres, and provide add-on documentation that enhances the value of raw data. This schema is designed for the standardized collection of ventilation data recorded every 15 minutes from sensors spread across Nursery 201. It is applicable to all datasets aimed at monitoring environmental conditions affecting dairy cattle in Nursery 201. Data described in this schema is sample data, to request access to the related data, please visit the &lt;a href="https://odrcdata.uoguelph.ca"&gt; Ontario Dairy Research Centre Data Portal&lt;/a&gt;.
description: Agri-food Data Canada's Semantic Engine
DOI: 10.5683/sp3/nlmlae
title: Data from: Inversions contribute disproportionately to parallel genomic divergence in dune sunflowers

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;&lt;p&gt;The probability of parallel genetic evolution is a function of the strength of selection and constraints imposed by genetic architecture. Inversions capture locally adapted alleles and suppress recombination between them, which limits the range of adaptive responses. Also, the combined phenotypic effect of alleles within inversions is likely to be greater than that of individual alleles, which should further increase the contributions of inversions to parallel evolution. We tested the hypothesis that inversions contribute disproportionately to parallel genetic evolution in independent dune ecotypes of &lt;em&gt;Helianthus petiolaris&lt;/em&gt;. We analyzed habitat data and identified variables underlying parallel habitat shifts. Genotype-environment association analyses of these variables indicated parallel responses of inversions to shared selective pressures. We also confirmed larger seed size across the dunes and performed quantitative trait locus (QTL) mapping with multiple crosses. QTL shared between locations fell into inversions more than expected by chance. We used whole-genome sequencing data to identify selective sweeps in the dune ecotypes and found that the majority of shared swept regions were found within inversions. Phylogenetic analyses of shared regions indicate that within inversions the same allele typically was found in the dune habitat at both sites. These results confirm predictions that inversions drive parallel divergence in the dune ecotypes. &lt;/p&gt;
description: &lt;b&gt;Methods&lt;/b&gt;&lt;br /&gt;&lt;p&gt;This dataset includes: &lt;/p&gt;
&lt;ul&gt;
&lt;li&gt;Habitat data collected from areas where wild &lt;em&gt;H. petiolaris &lt;/em&gt;sunflowers grow&lt;/li&gt;
&lt;li&gt;Seed size data collected from &lt;em&gt;H. petiolaris&lt;/em&gt; growing in the wild and under common garden conditions&lt;/li&gt;
&lt;li&gt;Unfiltered vcfs used for QTL mapping seed size and looking for genotype environement associations&lt;/li&gt;
&lt;li&gt;Genomic locations of previously identified haploblocks (inversions) within &lt;em&gt;H. petiolaris&lt;/em&gt; &lt;/li&gt;
&lt;li&gt;Inversion genotypes for the QTL mapping populations &lt;/li&gt;
&lt;/ul&gt;
&lt;p&gt;Please see the README file and associated publication for more complete descriptions of each dataset.&lt;/p&gt;
description: <b>Dryad version number:</b> 5
<b>Version status:</b> submitted
<b>Dryad curation status:</b> Published
<b>Sharing link:</b> http://datadryad.org/dataset/doi:10.5061/dryad.bcc2fqznn
<b>Storage size:</b> 1059511035
<b>Visibility:</b> public
DOI: 10.5683/sp3/wsgr3l
title: ODRC data schema: Nursery 2 ventilation data

description: This is a data schema created using &lt;a href="http://agrifooddatacanada.ca"&gt;Agri-food Data Canada's&lt;/a&gt; &lt;a href= "https://semanticengine.org"&gt; Semantic Engine &lt;a/&gt;. Data schemas describe data that are collected on an ongoing basis from research centres, and provide add-on documentation that enhances the value of raw data. This schema is designed for the standardized collection of ventilation data recorded every 15 minutes from sensors spread across Nursery 202. It is applicable to all datasets aimed at monitoring environmental conditions affecting dairy cattle in Nursery 202. Data described in this schema is sample data, to request access to the related data, please visit the &lt;a href="https://odrcdata.uoguelph.ca"&gt; Ontario Dairy Research Centre Data Portal&lt;/a&gt;.
description: Agri-food Data Canada's Semantic Engine
DOI: 10.6084/m9.figshare.30664196
title: Supplementary Material for: Using artificial intelligence to automate the analysis of psoriasis severity: A pilot study

description: Introduction: The Psoriasis Area and Severity Index (PASI) score is widely used to assess psoriasis severity; however, manual PASI scoring is susceptible to environmental variability and subjective interpretation. This study leverages artificial intelligence to improve the consistency and objectivity of psoriasis severity classification based on features extracted from 2D clinical images. 
Methods: This study employed the YOLOv8 deep learning model to classify psoriatic lesions according to the severity of erythema, thickness, and scaling— key subcomponents of the PASI scoring system. Severity was assessed as follows: (0), mild (1), moderate (2), severe (3), or very severe (4). Model training and analysis were conducted in a cloud-based environment (Google Colab) using three different datasets. Stratified k-fold cross-validation was employed to ensure robustness by preserving the distribution of PASI scores across folds. Model performance was assessed using a confusion matrix and accuracy metrics. 
Results: In experiments, the YOLOv8 model proved highly effective in classifying psoriasis images based on PASI scores. Stratified k-fold cross-validation was shown to enhance model reliability across diverse datasets. 
Conclusions: This study represents a significant advancement in the application of AI to the automated classification of lesion severity based on erythema, thickness, and scaling—key subcomponents of PASI.
DOI: 10.5683/sp3/7k5wtv
title: Data from: Investigation of heterotrophs reveals new insights in dinoflagellate evolution

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;&lt;p&gt;Dinoflagellates are diverse and ecologically important protists characterized by many morphological and molecular traits that set them apart from other eukaryotes. These features include, but are not limited to, massive genomes organized using bacterially-derived histone-like proteins (HLPs) and dinoflagellate viral nucleoproteins (DVNP) rather than histones, and a complex history of photobiology with many independent losses of photosynthesis, numerous cases of serial secondary and tertiary plastid gains, and the presence of horizontally acquired bacterial rhodopsins and type II RuBisCo. Elucidating how this all evolved depends on knowing the phylogenetic relationships between dinoflagellate lineages. Half of these species are heterotrophic, but existing molecular data is strongly biased toward the photosynthetic dinoflagellates due to their amenability to cultivation and prevalence in culture collections. These biases make it impossible to interpret the evolution of photosynthesis, but may also affect phylogenetic inferences that impact our understanding of character evolution. Here, we address this problem by isolating individual cells from the Salish Sea and using single cell, culture-free transcriptomics to expand molecular data for dinoflagellates to include 27 more heterotrophic taxa, resulting in a roughly balanced representation. Using these data, we performed a comprehensive search for proteins involved in chromatin packaging, plastid function, and photoactivity across all dinoflagellates. These searches reveal that 1) photosynthesis was lost at least 21 times, 2) two known types of HLP were horizontally acquired around the same time rather than sequentially as previously thought; 3) multiple rhodopsins are present across the dinoflagellates, acquired multiple times from different donors; 4) kleptoplastic species have nucleus-encoded genes for proteins targeted to their temporary plastids and they are derived from multiple lineages, and 5) warnowiids are the only heterotrophs that retain a whole photosystem, although some photosynthesis-related electron transport genes are widely retained in heterotrophs, likely as part of the iron-sulfur cluster pathway that persists in non-photosynthetic plastids.&lt;/p&gt;
description: <b>Dryad version number:</b> 7
<b>Version status:</b> submitted
<b>Dryad curation status:</b> Published
<b>Sharing link:</b> http://datadryad.org/stash/dataset/doi:10.5061/dryad.x95x69prq
<b>Storage size:</b> 215031036
<b>Visibility:</b> public
DOI: 10.6084/m9.figshare.30664196.v1
title: Supplementary Material for: Using artificial intelligence to automate the analysis of psoriasis severity: A pilot study

description: Introduction: The Psoriasis Area and Severity Index (PASI) score is widely used to assess psoriasis severity; however, manual PASI scoring is susceptible to environmental variability and subjective interpretation. This study leverages artificial intelligence to improve the consistency and objectivity of psoriasis severity classification based on features extracted from 2D clinical images. 
Methods: This study employed the YOLOv8 deep learning model to classify psoriatic lesions according to the severity of erythema, thickness, and scaling— key subcomponents of the PASI scoring system. Severity was assessed as follows: (0), mild (1), moderate (2), severe (3), or very severe (4). Model training and analysis were conducted in a cloud-based environment (Google Colab) using three different datasets. Stratified k-fold cross-validation was employed to ensure robustness by preserving the distribution of PASI scores across folds. Model performance was assessed using a confusion matrix and accuracy metrics. 
Results: In experiments, the YOLOv8 model proved highly effective in classifying psoriasis images based on PASI scores. Stratified k-fold cross-validation was shown to enhance model reliability across diverse datasets. 
Conclusions: This study represents a significant advancement in the application of AI to the automated classification of lesion severity based on erythema, thickness, and scaling—key subcomponents of PASI.
DOI: 10.5683/sp3/weg6es
title: Data from: Robust phylogenomics settles controversies of classification and reveals evolution of male embolic complex of the Laufeia clade (Araneae, Salticidae, Euophryini)

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;&lt;p&gt;The &lt;em&gt;Laufeia&lt;/em&gt; clade is a peculiar lineage of euophryine jumping spiders showing elevated divergence of male genitalic structures, especially the embolic complex that directly interacts with female genitalia during sperm transfer. With the rapid growth of species discovery in the &lt;em&gt;Laufeia&lt;/em&gt; clade, the controversy in its classification has become a crucial problem. In this study, we applied a phylogenomic approach using ultra-conserved element data to infer the phylogeny of the &lt;em&gt;Laufeia&lt;/em&gt; clade with extensive taxon sampling. A comparative morphological study was also performed to evaluate diagnostic characters and understand the evolution of male embolic complex within the &lt;em&gt;Laufeia &lt;/em&gt;clade. The results provide a strongly supported phylogenetic framework and updated generic concepts for the &lt;em&gt;Laufeia&lt;/em&gt; clade. The updated genera within the &lt;em&gt;Laufeia &lt;/em&gt;clade were all recovered as monophyletic with well-defined synapomorphies identified through character mapping on the phylogeny. Ancestral state reconstruction analyses revealed that the Type I embolic complex was ancestral and gradually evolved into the Type II and III embolic complex, and that some shapes of embolus often evolved multiple times independently in different lineages of the &lt;em&gt;Laufeia&lt;/em&gt; clade. The shift from foliage dwelling to tree trunk dwelling at the common ancestor of the &lt;em&gt;Laufeia &lt;/em&gt;clade may have facilitated the divergent evolution of male embolic complex in the &lt;em&gt;Laufeia &lt;/em&gt;clade. This study provides a solid foundation for future studies of systematics and evolution of this group.&lt;/p&gt;
description: <b>Dryad version number:</b> 2
<b>Version status:</b> submitted
<b>Dryad curation status:</b> Published
<b>Sharing link:</b> http://datadryad.org/stash/dataset/doi:10.5061/dryad.0rxwdbs97
<b>Storage size:</b> 273392477
<b>Visibility:</b> public
DOI: 10.6084/m9.figshare.30664199
title: Supplementary Material for: Enhanced multimodal diagnosis of peripheral lung lesions using Iriscope and radial endobronchial ultrasonography: results from a randomized controlled trial.

description: Introduction. Iriscope, a novel ultra-thin video probe designed to be inserted through the bronchoscope working channel enables direct visualization of peripheral lung lesions. However, its diagnostic value in comparison or in combination with established bronchoscopic guidance techniques remains unclear. This study aims to evaluate the added benefit of combining Iriscope with radial endobronchial ultrasonography (R-EBUS) compared to R-EBUS alone for the diagnosis of peripheral lung lesions sized 20–50 mm.
Methods. 81 patients were randomized into two groups: bronchoscopy guided by R-EBUS or bronchoscopy guided by both Iriscope and R-EBUS. Fluoroscopic guidance and forceps biopsy were used in both groups. In the combined group, the Iriscope was used first, followed by insertion of the ultrasound probe through the working channel for lesion visualization. Biopsies were taken in case of abnormal lesion visualized by R-EBUS. The primary outcome was diagnostic yield. Secondary outcomes included yield stratified by lesion size, presence of bronchus sign, and lesion visualization on fluoroscopy.
Results. The diagnostic yield was higher in the combined group (32/40, 80%) compared to R-EBUS alone (23/41, 55%, p=0.036). The improved yield in the combined approach was consistent regardless of lesion size, bronchus sign presence, or fluoroscopic visualization.
Conclusion. Combining Iriscope with R-EBUS significantly improves diagnostic yield compared to R-EBUS alone in patients with peripheral lung lesions sized 20–50 mm.
DOI: 10.6084/m9.figshare.30664199.v1
title: Supplementary Material for: Enhanced multimodal diagnosis of peripheral lung lesions using Iriscope and radial endobronchial ultrasonography: results from a randomized controlled trial.

description: Introduction. Iriscope, a novel ultra-thin video probe designed to be inserted through the bronchoscope working channel enables direct visualization of peripheral lung lesions. However, its diagnostic value in comparison or in combination with established bronchoscopic guidance techniques remains unclear. This study aims to evaluate the added benefit of combining Iriscope with radial endobronchial ultrasonography (R-EBUS) compared to R-EBUS alone for the diagnosis of peripheral lung lesions sized 20–50 mm.
Methods. 81 patients were randomized into two groups: bronchoscopy guided by R-EBUS or bronchoscopy guided by both Iriscope and R-EBUS. Fluoroscopic guidance and forceps biopsy were used in both groups. In the combined group, the Iriscope was used first, followed by insertion of the ultrasound probe through the working channel for lesion visualization. Biopsies were taken in case of abnormal lesion visualized by R-EBUS. The primary outcome was diagnostic yield. Secondary outcomes included yield stratified by lesion size, presence of bronchus sign, and lesion visualization on fluoroscopy.
Results. The diagnostic yield was higher in the combined group (32/40, 80%) compared to R-EBUS alone (23/41, 55%, p=0.036). The improved yield in the combined approach was consistent regardless of lesion size, bronchus sign presence, or fluoroscopic visualization.
Conclusion. Combining Iriscope with R-EBUS significantly improves diagnostic yield compared to R-EBUS alone in patients with peripheral lung lesions sized 20–50 mm.
DOI: 10.5683/sp3/bqu8zd
title: ODRC data schema: Nursery 3 ventilation data

description: This is a data schema created using &lt;a href="http://agrifooddatacanada.ca"&gt;Agri-food Data Canada's&lt;/a&gt; &lt;a href= "https://semanticengine.org"&gt; Semantic Engine &lt;a/&gt;. Data schemas describe data that are collected on an ongoing basis from research centres, and provide add-on documentation that enhances the value of raw data. This schema is designed for the standardized collection of ventilation data recorded every 15 minutes from sensors spread across Nursery 203. It is applicable to all datasets aimed at monitoring environmental conditions affecting dairy cattle in Nursery 203. Data described in this schema is sample data, to request access to the related data, please visit the &lt;a href="https://odrcdata.uoguelph.ca"&gt; Ontario Dairy Research Centre Data Portal&lt;/a&gt;.
description: Agri-food Data Canada's Semantic Engine
DOI: 10.5683/sp3/b8z0hf
title: ODRC data schema: Nursery 4 ventilation data

description: This is a data schema created using &lt;a href="http://agrifooddatacanada.ca"&gt;Agri-food Data Canada's&lt;/a&gt; &lt;a href= "https://semanticengine.org"&gt; Semantic Engine &lt;a/&gt;. Data schemas describe data that are collected on an ongoing basis from research centres, and provide add-on documentation that enhances the value of raw data. This schema is designed for the standardized collection of ventilation data recorded every 15 minutes from sensors spread across Nursery 204. It is applicable to all datasets aimed at monitoring environmental conditions affecting dairy cattle in Nursery 204. Data described in this schema is sample data, to request access to the related data, please visit the &lt;a href="https://odrcdata.uoguelph.ca"&gt; Ontario Dairy Research Centre Data Portal&lt;/a&gt;.
description: Agri-food Data Canada's Semantic Engine
DOI: 10.6084/m9.figshare.30664202
title: Supplementary Material for: Impact of increased single-inhaler triple therapy use in appropriate patients on COPD exacerbations, mortality, and medical costs: PROMETHEUS Spain.

description: Introduction: COPD is the third cause of death in Spain. The ETHOS (NCT02465567) and IMPACT (NCT02164513) RCTs showed reduced exacerbations and all-cause mortality for single-inhaler triple therapy (SITT), but no studies have evaluated the potential impact on COPD outcomes of higher SITT adoption in Spain.

Methods: We used literature-based data on patient characteristics, incidence, COPD severity changes, treatment distributions/transitions, mortality, exacerbations, and medical costs, to inform a stochastic simulation of the Spanish COPD population for 2025-2034 under two scenarios: “Status Quo” and “Increased SITT”, in which higher SITT use is driven by airflow limitation, exacerbation history (as per 2025 GOLD guidelines) and SITT replacing multiple-inhaler triple therapy (MITT). Additionally, we present results separately for the subset of patients that met the criteria for SITT use, referred to as “flagged population.”

Results: In our 10-year simulation, increased SITT use in the flagged population could lead to 51,000 deaths avoided resulting in a 14.6% reduction in mortality rates and extended patient life by 1.2 years per COPD flagged patient. Additionally, increased SITT use in the flagged population reduced severe and moderate exacerbations by 62,000 (an 11.5% reduction) and 366,000 (an 11.6% reduction), respectively, resulting in total medical savings of €384 million. 

Conclusion: Based on our simulation, increased use of SITT in the Spanish COPD population, consistent with the most recent 2025 GOLD guidelines’ recommendations, could reduce mortality and exacerbations and their corresponding medical costs. Increasing SITT utilization in patients with COPD may constitute a long-term strategy with relevant clinical and economic benefits.
DOI: 10.6084/m9.figshare.30664202.v1
title: Supplementary Material for: Impact of increased single-inhaler triple therapy use in appropriate patients on COPD exacerbations, mortality, and medical costs: PROMETHEUS Spain.

description: Introduction: COPD is the third cause of death in Spain. The ETHOS (NCT02465567) and IMPACT (NCT02164513) RCTs showed reduced exacerbations and all-cause mortality for single-inhaler triple therapy (SITT), but no studies have evaluated the potential impact on COPD outcomes of higher SITT adoption in Spain.

Methods: We used literature-based data on patient characteristics, incidence, COPD severity changes, treatment distributions/transitions, mortality, exacerbations, and medical costs, to inform a stochastic simulation of the Spanish COPD population for 2025-2034 under two scenarios: “Status Quo” and “Increased SITT”, in which higher SITT use is driven by airflow limitation, exacerbation history (as per 2025 GOLD guidelines) and SITT replacing multiple-inhaler triple therapy (MITT). Additionally, we present results separately for the subset of patients that met the criteria for SITT use, referred to as “flagged population.”

Results: In our 10-year simulation, increased SITT use in the flagged population could lead to 51,000 deaths avoided resulting in a 14.6% reduction in mortality rates and extended patient life by 1.2 years per COPD flagged patient. Additionally, increased SITT use in the flagged population reduced severe and moderate exacerbations by 62,000 (an 11.5% reduction) and 366,000 (an 11.6% reduction), respectively, resulting in total medical savings of €384 million. 

Conclusion: Based on our simulation, increased use of SITT in the Spanish COPD population, consistent with the most recent 2025 GOLD guidelines’ recommendations, could reduce mortality and exacerbations and their corresponding medical costs. Increasing SITT utilization in patients with COPD may constitute a long-term strategy with relevant clinical and economic benefits.