cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11968533.v1
title: Supplementary Material for: In vitro Conversion into CD4<sup>+</sup>CD25<sup>+</sup>Foxp3<sup>+</sup> Induced Regulatory T Cells Is Reduced in Atopic Dermatitis Patients

description: <b><i>Background:</i></b> Atopic dermatitis (AD) is one of the most common inflammatory skin diseases, with an increasing incidence in clinical practice. AD models have demonstrated that TGF-β signaling is compromised in regulatory T cells (Tregs). <b><i>Objectives:</i></b> This study aimed to investigate the TGF-β-dependent in vitro conversion of CD4<sup>+</sup>CD25<sup>–</sup> T cells derived from AD-patients into CD4<sup>+</sup>CD25<sup>+</sup>Foxp3<sup>+</sup> induced Tregs (iTregs) in comparison to healthy controls. <b><i>Methods:</i></b> To analyze in vitro iTreg conversion, human CD4<sup>+</sup>CD25<sup>–</sup> T cells were cultured on anti-CD3-coated plates in the presence of TGF-β and IL-2 for up to 3 days. Consequently, the underlying mechanism of impaired CD4<sup>+</sup>CD25<sup>+</sup>Foxp3<sup>+</sup> iTreg generation was explored by focusing on TGF-β signaling. Finally, the functionality of iTregs was investigated. <b><i>Results:</i></b> Conversion of CD4<sup>+</sup>CD25<sup>–</sup>Foxp3<sup>–</sup> into CD4<sup>+</sup>CD25<sup>+</sup>Foxp3<sup>+</sup> iTregs was diminished in AD individuals. Impaired iTreg generation was accompanied by a reduced surface expression of GARP (glycoprotein A repetitions predominant), a marker for activated Tregs. A reduced expression of Smad3 mRNA was revealed in CD4<sup>+</sup>CD25<sup>–</sup> T cells. Interestingly, the suppressive quality of iTregs was found to be equal in cells derived from AD and healthy donors. <b><i>Conclusion:</i></b> The signaling effect of TGF-β receptors on the suppressor quality of iTreg conversion is conserved. Impaired iTreg generation might be a reason for the lack of immune suppression in AD patients and contributes to the chronicity of the disease.
DOI: 10.6084/m9.figshare.11968521.v1
title: A Computationally More Efficient Bayesian Approach for Estimating Continuous-Time Models

description: Continuous-time modeling is gaining in popularity as more and more intensive longitudinal data need to be analyzed. Current Bayesian software implementations of continuous-time models suffer from rather high, inadequate run times. Therefore, we apply a model reformulation approach to reduce run time. In a simulation study, we investigate the estimation quality and run time gain. We then illustrate our optimized Bayesian continuous-time model estimation and compare it to established continuous-time modeling software using an empirical example. Parameter estimates and inference statistics were very comparable, while run times were very different. Our approach reduces the run times for Bayesian estimations of continuous-time models from hours to minutes.
DOI: 10.6084/m9.figshare.11968521.v2
title: A Computationally More Efficient Bayesian Approach for Estimating Continuous-Time Models

description: Continuous-time modeling is gaining in popularity as more and more intensive longitudinal data need to be analyzed. Current Bayesian software implementations of continuous-time models suffer from rather high, inadequate run times. Therefore, we apply a model reformulation approach to reduce run time. In a simulation study, we investigate the estimation quality and run time gain. We then illustrate our optimized Bayesian continuous-time model estimation and compare it to established continuous-time modeling software using an empirical example. Parameter estimates and inference statistics were very comparable, while run times were very different. Our approach reduces the run times for Bayesian estimations of continuous-time models from hours to minutes.
DOI: 10.6084/m9.figshare.11968503
title: Nord, Hegemann & Folkow Seasonal variation in innate immune function in Svalbard ptarmigan data

description: Data for the paper "Reduced immune responsiveness contributes to energy conservation in an Arctic bird" by Nord, A., Hegemann, A., Folkow, L. P., J. Exp. Biol.
DOI: 10.6084/m9.figshare.11968503.v1
title: Nord, Hegemann & Folkow Seasonal variation in innate immune function in Svalbard ptarmigan data

description: Data for the paper "Reduced immune responsiveness contributes to energy conservation in an Arctic bird" by Nord, A., Hegemann, A., Folkow, L. P., J. Exp. Biol.
DOI: 10.6084/m9.figshare.11968485
title: Kreisnamen und Konkordanzen

description: Im Rahmen von Deutschland in Daten wurden 21 interaktive Choroplethenkarten auf Kreisebene erstellt. Insgesamt wurden zu acht Themengebieten (Bevölkerungsdichte, Geburten, Mindestsicherungsquote, Wahlbeteiligung, Gefährliche Körperverletzung, Erwerbstätige im produzierenden Gewerbe, Arbeitslose und Konfessionen), zu denen für die Bundesrepublik Statistiken auf Kreisebene vorhanden sind, für das Kaiserreich sieben und für die Weimarer Republik fünf Vergleiche erstellt. Für die Darstellungen wurden vorhandene Kartengeometrien des Max-Planck-Instituts für demografische Forschung sowie von Daniel Ziblatt und Jeffrey C. Blossom mit Datensätzen verknüpft, die in den 1980er und 1990er Jahren erstellt wurden und auf umfangreichem Veröffentlichungsmaterial der amtlichen Statistik basieren. Die XLSX-Datei enthält das Mapping der Datensätze zu den Kartengeometrien sowie die vollständigen Kreisnamen und zugehörigen übergeordneten Verwaltungseinheiten.<br><b>Dokumentation:</b><br>Rahlf, Thomas, Dokumentation zu Choroplethenkarten für Deutschland, 1882-2017, Version 01 (= Historical Social Research Transition 33v01), Köln 2020. DOI:10.12759/hsr.trans.33.v01.2020<br>
DOI: 10.6084/m9.figshare.11968443
title: Metadata record for: Rapid flood and damage mapping using synthetic aperture radar in response to Typhoon Hagibis, Japan

description: This dataset contains key characteristics about the data described in the Data Descriptor Rapid flood and damage mapping using synthetic aperture radar in response to Typhoon Hagibis, Japan. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format
DOI: 10.6084/m9.figshare.11968443.v1
title: Metadata record for: Rapid flood and damage mapping using synthetic aperture radar in response to Typhoon Hagibis, Japan

description: This dataset contains key characteristics about the data described in the Data Descriptor Rapid flood and damage mapping using synthetic aperture radar in response to Typhoon Hagibis, Japan. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format
DOI: 10.6084/m9.figshare.11968314
title: Wetland cover and species richness data table

description: These data represent the proportional wetland coverage (ha / 100km^2) of the conterminous United States spatially joined to the species richness of amphibians, birds, mammals, reptiles and cumulative endemic species. Data is provided as both a csv file and as a georeferenced shapefile.<br>Any use of this data should include citation to both: <br>Dertien et al. 2020. The relationship between biodiversity and proportional wetland cover varies across regions of the conterminous United States. Plos One &Jenkins et al. 2015. U.S. protected lands mismatch biodiversity priorities. PNAS. 112: 5091-5086 doi:10.1073/pnas.1418034112
DOI: 10.6084/m9.figshare.11968305
title: Dataset 2 from Structural variation in <i>Drosophila melanogaster</i> spermathecal ducts and its association with sperm competition dynamics

description: Data on SDP presence/absence in young and old virgin Dahomey females.
DOI: 10.6084/m9.figshare.11968314.v1
title: Wetland cover and species richness data table

description: These data represent the proportional wetland coverage (ha / 100km^2) of the conterminous United States spatially joined to the species richness of amphibians, birds, mammals, reptiles and cumulative endemic species. Data is provided as both a csv file and as a georeferenced shapefile.<br>Any use of this data should include citation to both: <br>Dertien et al. 2020. The relationship between biodiversity and proportional wetland cover varies across regions of the conterminous United States. Plos One &Jenkins et al. 2015. U.S. protected lands mismatch biodiversity priorities. PNAS. 112: 5091-5086 doi:10.1073/pnas.1418034112
DOI: 10.6084/m9.figshare.11968302
title: Matrix file of analysis 1 in TNT format from <i>Colobops</i>: a juvenile rhynchocephalian reptile (Lepidosauromorpha), not a diminutive archosauromorph with an unusually strong bite

description: Matrix file used for the phylogenetic analysis 1.
DOI: 10.6084/m9.figshare.11968299
title: Dataset 1 from Structural variation in <i>Drosophila melanogaster</i> spermathecal ducts and its association with sperm competition dynamics

description: Data on SDP presence/absence, offspring counts, and sperm counts across the range of ages, genotypes, and mating treatments tested.
DOI: 10.6084/m9.figshare.11968305.v1
title: Dataset 2 from Structural variation in <i>Drosophila melanogaster</i> spermathecal ducts and its association with sperm competition dynamics

description: Data on SDP presence/absence in young and old virgin Dahomey females.
DOI: 10.6084/m9.figshare.11968299.v1
title: Dataset 1 from Structural variation in <i>Drosophila melanogaster</i> spermathecal ducts and its association with sperm competition dynamics

description: Data on SDP presence/absence, offspring counts, and sperm counts across the range of ages, genotypes, and mating treatments tested.
DOI: 10.6084/m9.figshare.11968302.v1
title: Matrix file of analysis 1 in TNT format from <i>Colobops</i>: a juvenile rhynchocephalian reptile (Lepidosauromorpha), not a diminutive archosauromorph with an unusually strong bite

description: Matrix file used for the phylogenetic analysis 1.
DOI: 10.6084/m9.figshare.11968293
title: 3D model of skull in Polygon File Format (PLY files in zipped folder) from <i>Colobops</i>: a juvenile rhynchocephalian reptile (Lepidosauromorpha), not a diminutive archosauromorph with an unusually strong bite

description: The rendered 3D model provided as individual .ply files and additional Meshlab project (“Colobops combined”) file, which can be opened with a variety of freely available viewers (e.g., Meshlab: sourceforge.net/projects/meshlab/).
DOI: 10.6084/m9.figshare.11968293.v1
title: 3D model of skull in Polygon File Format (PLY files in zipped folder) from <i>Colobops</i>: a juvenile rhynchocephalian reptile (Lepidosauromorpha), not a diminutive archosauromorph with an unusually strong bite

description: The rendered 3D model provided as individual .ply files and additional Meshlab project (“Colobops combined”) file, which can be opened with a variety of freely available viewers (e.g., Meshlab: sourceforge.net/projects/meshlab/).
DOI: 10.6084/m9.figshare.11968284
title: Matrix file of analysis 2 in TNT format from <i>Colobops</i>: a juvenile rhynchocephalian reptile (Lepidosauromorpha), not a diminutive archosauromorph with an unusually strong bite

description: Matrix file used for the phylogenetic analysis 2.
DOI: 10.6084/m9.figshare.11968272
title: Study3_Data.csv from The interaction between map complexity and crowd movement on navigation decisions in virtual reality

description: Experiment data from Study 3
DOI: 10.6084/m9.figshare.11968284.v1
title: Matrix file of analysis 2 in TNT format from <i>Colobops</i>: a juvenile rhynchocephalian reptile (Lepidosauromorpha), not a diminutive archosauromorph with an unusually strong bite

description: Matrix file used for the phylogenetic analysis 2.
DOI: 10.6084/m9.figshare.11968272.v1
title: Study3_Data.csv from The interaction between map complexity and crowd movement on navigation decisions in virtual reality

description: Experiment data from Study 3
DOI: 10.6084/m9.figshare.11968254
title: Study1_Data.csv from The interaction between map complexity and crowd movement on navigation decisions in virtual reality

description: Experiment data from Study 1
DOI: 10.6084/m9.figshare.11968257
title: Study2_Data.csv from The interaction between map complexity and crowd movement on navigation decisions in virtual reality

description: Experiment data from Study 2
DOI: 10.6084/m9.figshare.11968254.v1
title: Study1_Data.csv from The interaction between map complexity and crowd movement on navigation decisions in virtual reality

description: Experiment data from Study 1
DOI: 10.6084/m9.figshare.11968257.v1
title: Study2_Data.csv from The interaction between map complexity and crowd movement on navigation decisions in virtual reality

description: Experiment data from Study 2
DOI: 10.6084/m9.figshare.11968230
title: Metadata record for: Generation of a murine SWATH-MS spectral library to quantify more than 11,000 proteins

description: This dataset contains key characteristics about the data described in the Data Descriptor Generation of a murine SWATH-MS spectral library to quantify more than 11,000 proteins. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format
DOI: 10.6084/m9.figshare.11968230.v1
title: Metadata record for: Generation of a murine SWATH-MS spectral library to quantify more than 11,000 proteins

description: This dataset contains key characteristics about the data described in the Data Descriptor Generation of a murine SWATH-MS spectral library to quantify more than 11,000 proteins. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format
DOI: 10.6084/m9.figshare.11968224
title: Supplementary Material for: Association between Genetic and Immunological Background of Hepatocellular Carcinoma and Expression of Programmed Cell Death-1

description: <b><i>Background and Aim:</i></b> Immune checkpoint inhibitors are promising agents for the treatment of hepatocellular carcinomas (HCC) refractory to conventional therapies. To enhance the efficacy of this treatment, immunological and molecular characteristics of HCC with programmed cell death ligand 1 (PD-L1) should be explored. <b><i>Methods:</i></b> Clinical backgrounds, PD-L1 expression, and the amount of CD8+ tumor-infiltrating mononuclear cells (TIMCs) were analyzed in 154 HCCs. The expression of 3 stem cell markers and co-inhibitory receptors on tumor cells and TIMCs, respectively, were examined by immunohistochemical analysis. Somatic mutations in the 409 cancer-associated genes and TERT promoter were determined; HCCs were classified based on the presence of gene alterations affecting the 8 oncogenic pathways. The results were validated using the dataset from the Cancer Genome Atlas. <b><i>Results:</i></b> The expression of PD-L1 in the HCCs was positively correlated with progressive tumor features, the presence of cytokeratin 19 (CK19), Sal-like protein 4 (SALL4), and the mutations of genes involving the phosphatidyl inositol 3-kinase (PI3K)-Akt pathway. Although CD8+ cells were densely infiltrated in PD-L1-positive tumors, these TIMCs frequently expressed multiple co-inhibitory receptors. However, a subset of PD-L1-positive tumors characterized by activating mutations of the PI3K-Akt pathway showed a low degree of TIMCs. Conversely, PD-L1-negative HCCs were associated with mutations in the β-catenin pathway and a small number of TIMCs, although the expression of co-inhibitory receptors was rare. <b><i>Conclusions:</i></b> PD-L1-positive HCCs frequently showed an inflamed phenotype with stem cell features; a subset of PD-L1-positive HCCs with mutations in the PI3K-Akt pathway showed a non-inflamed phenotype. In HCCs with dense infiltration of TIMCs, CD8+ cells expressed multiple co-inhibitory receptors, suggesting T cell exhaustion. On the other hand, PD-L1-negative HCCs showed mutations leading to β-catenin activation and exhibited a non-inflamed background. These characteristics should be taken into consideration for developing novel combination therapies using immune checkpoint inhibitors.
DOI: 10.6084/m9.figshare.11968224.v1
title: Supplementary Material for: Association between Genetic and Immunological Background of Hepatocellular Carcinoma and Expression of Programmed Cell Death-1

description: <b><i>Background and Aim:</i></b> Immune checkpoint inhibitors are promising agents for the treatment of hepatocellular carcinomas (HCC) refractory to conventional therapies. To enhance the efficacy of this treatment, immunological and molecular characteristics of HCC with programmed cell death ligand 1 (PD-L1) should be explored. <b><i>Methods:</i></b> Clinical backgrounds, PD-L1 expression, and the amount of CD8+ tumor-infiltrating mononuclear cells (TIMCs) were analyzed in 154 HCCs. The expression of 3 stem cell markers and co-inhibitory receptors on tumor cells and TIMCs, respectively, were examined by immunohistochemical analysis. Somatic mutations in the 409 cancer-associated genes and TERT promoter were determined; HCCs were classified based on the presence of gene alterations affecting the 8 oncogenic pathways. The results were validated using the dataset from the Cancer Genome Atlas. <b><i>Results:</i></b> The expression of PD-L1 in the HCCs was positively correlated with progressive tumor features, the presence of cytokeratin 19 (CK19), Sal-like protein 4 (SALL4), and the mutations of genes involving the phosphatidyl inositol 3-kinase (PI3K)-Akt pathway. Although CD8+ cells were densely infiltrated in PD-L1-positive tumors, these TIMCs frequently expressed multiple co-inhibitory receptors. However, a subset of PD-L1-positive tumors characterized by activating mutations of the PI3K-Akt pathway showed a low degree of TIMCs. Conversely, PD-L1-negative HCCs were associated with mutations in the β-catenin pathway and a small number of TIMCs, although the expression of co-inhibitory receptors was rare. <b><i>Conclusions:</i></b> PD-L1-positive HCCs frequently showed an inflamed phenotype with stem cell features; a subset of PD-L1-positive HCCs with mutations in the PI3K-Akt pathway showed a non-inflamed phenotype. In HCCs with dense infiltration of TIMCs, CD8+ cells expressed multiple co-inhibitory receptors, suggesting T cell exhaustion. On the other hand, PD-L1-negative HCCs showed mutations leading to β-catenin activation and exhibited a non-inflamed background. These characteristics should be taken into consideration for developing novel combination therapies using immune checkpoint inhibitors.
DOI: 10.6084/m9.figshare.11968071
title: Integrative taxonomic consideration of the Holarctic <i>Euconulus fulvus</i> group of land snails (Gastropoda, Stylommatophora)

description: While among the most common Holarctic land snails, species of the <i>Euconulus fulvus</i> group have been subject to considerable recent taxonomic controversy. Based on 76 <i>Euconulus</i> populations collected across Eurasia and North America, we empirically evaluated these competing taxonomic hypotheses through an integration of nDNA and mtDNA phylogenetics, shell morphometrics and various qualitative traits. Our results support the existence of five taxa: <i>Euconulus alderi</i> (Atlantic Europe to western North America), <i>E. fresti</i> sp. nov. (North America), <i>E. fulvus fulvus</i> (Europe), <i>E. fulvus egenus</i> (central Asia to Atlantic North America), and <i>E. polygyratus</i> (north-eastern North America). Each species-level entity possessed a unique suite of observable shell features allowing for accurate identification without need of DNA sequence information. Our data did not support the recent erection of <i>E. callopisticus</i>, <i>E. praticola</i>, and <i>E. trochiformis</i> to species-level status. This work also helps illustrate the importance of using consensus across DNA and shell/soft body features in assessing species-level taxonomy and in determining those features which allow for accurate identification. It furthermore documents the importance of basing taxonomic work on samples drawn from across the entire geographic and ecological range of the study group. http://zoobank.org/urn:lsid:zoobank.org:pub:97985479-EDF8-4B94-A825-AC42BF31F597
DOI: 10.6084/m9.figshare.11968059
title: None

description: Kill you 3 days.
DOI: 10.6084/m9.figshare.11968068
title: Supplementary Material for: Clinical Benefit Derived from Decitabine Therapy for Advanced Phases of Myeloproliferative Neoplasms

description: Treatment options are limited for patients with advanced forms of myeloproliferative neoplasms (MPN) including blast-phase disease (MPN-BP). Decitabine has frequently been deployed but its efficacy and safety profile are not well described in this population. We retrospectively reviewed 42 patients treated with decitabine either alone or in combination with ruxolitinib at our institution: 16 with MPN-BP, 14 with MPN accelerated-phase (MPN-AP), and 12 with myelofibrosis with high-risk features (MF-HR). The median overall survival (OS) for the MPN-BP patients was 2.6 months, and for those who received ≥2 cycles of decitabine therapy, it was 6.7 months (3.8–29.8). MPN-BP patients with a poor performance status and who required hospitalization at the time of the initiation of decitabine had a dismal prognosis. After a median follow-up of 12.4 months for MPN-AP patients, and 38.7 months for MF-HR patients, the median OS was not reached for either cohort, with 1 and 2 patients alive at 60 months, respectively. The probability of spleen length reduction and transfusion independence within 12 months of initiating decitabine was 28.6 and 23.5%, respectively. The combination of decitabine and ruxolitinib appeared to improve overall survival versus single-agent decitabine (21 and 12.9 months, respectively). Decitabine, alone or in combination with ruxolitinib, appears to have clinical benefit for patients with advanced phases of MPN when initiated early in the disease course prior to the development of MPN-BP.
DOI: 10.6084/m9.figshare.11968071.v1
title: Integrative taxonomic consideration of the Holarctic <i>Euconulus fulvus</i> group of land snails (Gastropoda, Stylommatophora)

description: While among the most common Holarctic land snails, species of the <i>Euconulus fulvus</i> group have been subject to considerable recent taxonomic controversy. Based on 76 <i>Euconulus</i> populations collected across Eurasia and North America, we empirically evaluated these competing taxonomic hypotheses through an integration of nDNA and mtDNA phylogenetics, shell morphometrics and various qualitative traits. Our results support the existence of five taxa: <i>Euconulus alderi</i> (Atlantic Europe to western North America), <i>E. fresti</i> sp. nov. (North America), <i>E. fulvus fulvus</i> (Europe), <i>E. fulvus egenus</i> (central Asia to Atlantic North America), and <i>E. polygyratus</i> (north-eastern North America). Each species-level entity possessed a unique suite of observable shell features allowing for accurate identification without need of DNA sequence information. Our data did not support the recent erection of <i>E. callopisticus</i>, <i>E. praticola</i>, and <i>E. trochiformis</i> to species-level status. This work also helps illustrate the importance of using consensus across DNA and shell/soft body features in assessing species-level taxonomy and in determining those features which allow for accurate identification. It furthermore documents the importance of basing taxonomic work on samples drawn from across the entire geographic and ecological range of the study group. http://zoobank.org/urn:lsid:zoobank.org:pub:97985479-EDF8-4B94-A825-AC42BF31F597