cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12530621
title: Additional file 3 of Analysis of structural variants in four African cichlids highlights an association with developmental and immune related genes

description: Additional file 3: Supplementary file 2.Results of MW test to compare SV size distribution across different conservation categories. For each comparison, the p-value is indicated. In the case of a significant difference, the directionality of the change is indicated. For example, “1
DOI: 10.6084/m9.figshare.12530624
title: Additional file 4 of Analysis of structural variants in four African cichlids highlights an association with developmental and immune related genes

description: Additional file 4: Supplementary file 3. Names and corresponding GO annotation for different subsets of genes inside duplicated and inverted regions
DOI: 10.6084/m9.figshare.12530627.v1
title: Additional file 5 of Analysis of structural variants in four African cichlids highlights an association with developmental and immune related genes

description: Additional file 5: Supplementary file 4. Genes found inside PCR validated inversions. Each row corresponds to one gene. Genomic coordinates of the associated inversion, and the number of species carrying the inversion are indicated, along with the gene name and ncbi id.
DOI: 10.6084/m9.figshare.12530618
title: Additional file 2 of Analysis of structural variants in four African cichlids highlights an association with developmental and immune related genes

description: Additional file 2: Supplementary file 1. Genomic coordinates and annotation across species for all SV classes.
DOI: 10.6084/m9.figshare.12530624.v1
title: Additional file 4 of Analysis of structural variants in four African cichlids highlights an association with developmental and immune related genes

description: Additional file 4: Supplementary file 3. Names and corresponding GO annotation for different subsets of genes inside duplicated and inverted regions
DOI: 10.6084/m9.figshare.12530618.v1
title: Additional file 2 of Analysis of structural variants in four African cichlids highlights an association with developmental and immune related genes

description: Additional file 2: Supplementary file 1. Genomic coordinates and annotation across species for all SV classes.
DOI: 10.6084/m9.figshare.12530621.v1
title: Additional file 3 of Analysis of structural variants in four African cichlids highlights an association with developmental and immune related genes

description: Additional file 3: Supplementary file 2.Results of MW test to compare SV size distribution across different conservation categories. For each comparison, the p-value is indicated. In the case of a significant difference, the directionality of the change is indicated. For example, “1
DOI: 10.6084/m9.figshare.12530597
title: Additional file 1 of Therapeutic potential of mesenchymal stem cells and their exosomes in severe novel coronavirus disease 2019 (COVID-19) cases

description: Additional file 1: Table S1. Clinical trials using mesenchymal stem cells (MSCs) and exosomes and registered on ClinicalTrials.gov.
DOI: 10.6084/m9.figshare.12530588
title: Additional file 1 of Development of the WHO Antenatal Care Recommendations Adaptation Toolkit: a standardised approach for countries

description: Additional file 1. Baseline Assessment Tool (BAT).
DOI: 10.6084/m9.figshare.12530597.v1
title: Additional file 1 of Therapeutic potential of mesenchymal stem cells and their exosomes in severe novel coronavirus disease 2019 (COVID-19) cases

description: Additional file 1: Table S1. Clinical trials using mesenchymal stem cells (MSCs) and exosomes and registered on ClinicalTrials.gov.
DOI: 10.6084/m9.figshare.12530534
title: code_dataset

description: This file contains raw data and R.code associated with all the figures of the article entitled <i>Vegetation drives the structure of active microbial communities on an acidogenic mine tailings deposit</i>. The files for Fig.2, 4, and 5 contain the raw data for the 30 most abundant 16S or ITS taxa, as well as the physico-chemical characteristics of the soils and mine tailings. The files for Fig.3, Fig. 6, Fig. 7, Fig. 8, and Fig. 9 contain the R.code associated with the raw data of the 16S and ITS taxa, as well as that for the physico-chemical characteristics of the soils and mine tailings. The file for Fig.10 contains the R.code and raw data related to 16S and ITS chaos results. The file for Table S1 contains the raw data associated with this table. Finally, the files for Tables S5 and S6 contain raw data consisting of soil and mine tailings' physico-chemical characteristics, in addition to the R code associated with these tables. The raw data listed are for the Venn's Tables.
DOI: 10.6084/m9.figshare.12530588.v1
title: Additional file 1 of Development of the WHO Antenatal Care Recommendations Adaptation Toolkit: a standardised approach for countries

description: Additional file 1. Baseline Assessment Tool (BAT).
DOI: 10.6084/m9.figshare.12530315
title: Supplementary Material for: Mepolizumab in Severe Eosinophilic Asthma: A 2-Year Follow-Up in Specialized Asthma Clinics in Greece: An Interim Analysis

description: <b><i>Introduction:</i></b> Mepolizumab is a monoclonal antibody against IL-5 for the treatment of severe eosinophilic asthma. The aim of the current study was to present a predesigned interim analysis of the data of patients who have completed 1 year of therapy with mepolizumab. <b><i>Methods:</i></b> This study is a prospective multicenter, noninterventional 2-year observational study and aims to describe the clinical benefit and safety profile of mepolizumab in patients with severe eosinophilic asthma. <b><i>Results:</i></b> Compared to the year preceding the initiation of treatment, the annual rate of exacerbations decreased significantly, from 4.3 ± 2.3 to 1.3 ± 1.8; <i>p</i> &lt; 0.0001. Forty-two patients received maintenance dose of oral corticosteroids (OCS) at baseline. From these patients at the end of 1 year of therapy with mepolizumab, 17 patients (40%) had achieved OCS discontinuation. A reduction in the median dose of OCS was also achieved. After 1 year of treatment with mepolizumab, the asthma control test score significantly increased from 16.3 ± 3.7 to 21.2 ± 3.8 (<i>p</i> &lt; 0.0001). This marked clinical improvement was paralleled by a significant reduction of blood eosinophil count. All patients showed a considerable improvement of airflow limitation. In respect to adverse events of treatment with mepolizumab, 19 patients (27%) were recorded to have at least one such occurrence during their 1-year treatment. <b><i>Conclusions:</i></b> We have shown that in patients with severe eosinophilic asthma, 1 year of treatment with mepolizumab was safe, resulted in significant reduction of the annual exacerbation rate, reduction (or even discontinuation) of the needed dose of OCS, and improvements of asthma control and lung function.
DOI: 10.6084/m9.figshare.12530525
title: Clean data of 3v3 circRNA seq (PBMCs of IgAN patients) part 1.

description: The clean data of peripheral blood mononuclear cells' circRNA seq of 3 IgA nephropathy patients vs. 3 healthy controls.Part 1 of 3 part.
DOI: 10.6084/m9.figshare.12530534.v1
title: code_dataset

description: This file contains raw data and R.code associated with Fig.2, 4 and 5. Raw data contains the 30 most abundant 16S or ITS taxa. Raw data contains edaphic parameters. This file contains R.code associated with Fig.3, Fig. 6 and 8, and Fig. 7 and 9 and the raw data associated with Figs 3, 6, 7, 8 and 9. Raw data contains all 16S or ITS taxa. Raw data contains edaphic parameters. Fig.10 contains R.code and raw data related to 16S and ITS chaos results. The file also contains raw data associated with Table S1. Raw data consists of edaphic parameters and contains R code associated with Table_S5 and Table_S6. Raw data are lists necessary to made Venn's Table.
DOI: 10.6084/m9.figshare.12530042
title: Dataset for 'A typology of scientific breakthroughs'

description: Dataset of scientific breakthroughs as identified by Science Magazine's Breakthrough of the Year 1999 - 2012. Number of authors is retrieved from Web of Science, using the DOI of each article. The variables <i>question, new, anomalies, applied </i>and<i> basic</i> are coded by means of the article's full text, as described in the paper. This data was collected in April-May 2018. WoS queries ran on April 24 and 25 2018.
DOI: 10.6084/m9.figshare.12530315.v1
title: Supplementary Material for: Mepolizumab in Severe Eosinophilic Asthma: A 2-Year Follow-Up in Specialized Asthma Clinics in Greece: An Interim Analysis

description: <b><i>Introduction:</i></b> Mepolizumab is a monoclonal antibody against IL-5 for the treatment of severe eosinophilic asthma. The aim of the current study was to present a predesigned interim analysis of the data of patients who have completed 1 year of therapy with mepolizumab. <b><i>Methods:</i></b> This study is a prospective multicenter, noninterventional 2-year observational study and aims to describe the clinical benefit and safety profile of mepolizumab in patients with severe eosinophilic asthma. <b><i>Results:</i></b> Compared to the year preceding the initiation of treatment, the annual rate of exacerbations decreased significantly, from 4.3 ± 2.3 to 1.3 ± 1.8; <i>p</i> &lt; 0.0001. Forty-two patients received maintenance dose of oral corticosteroids (OCS) at baseline. From these patients at the end of 1 year of therapy with mepolizumab, 17 patients (40%) had achieved OCS discontinuation. A reduction in the median dose of OCS was also achieved. After 1 year of treatment with mepolizumab, the asthma control test score significantly increased from 16.3 ± 3.7 to 21.2 ± 3.8 (<i>p</i> &lt; 0.0001). This marked clinical improvement was paralleled by a significant reduction of blood eosinophil count. All patients showed a considerable improvement of airflow limitation. In respect to adverse events of treatment with mepolizumab, 19 patients (27%) were recorded to have at least one such occurrence during their 1-year treatment. <b><i>Conclusions:</i></b> We have shown that in patients with severe eosinophilic asthma, 1 year of treatment with mepolizumab was safe, resulted in significant reduction of the annual exacerbation rate, reduction (or even discontinuation) of the needed dose of OCS, and improvements of asthma control and lung function.
DOI: 10.6084/m9.figshare.12530525.v1
title: Clean data of 3v3 circRNA seq (PBMCs of IgAN patients) part 1.

description: The clean data of peripheral blood mononuclear cells' circRNA seq of 3 IgA nephropathy patients vs. 3 healthy controls.Part 1 of 3 part.
DOI: 10.6084/m9.figshare.12529655
title: HT–LP crustal syntectonic anatexis as a source of the Permian magmatism in the Eastern Southern Alps: evidence from xenoliths in the Euganean trachytes (NE Italy).

description: EMP data
DOI: 10.6084/m9.figshare.12529655.v1
title: HT–LP crustal syntectonic anatexis as a source of the Permian magmatism in the Eastern Southern Alps: evidence from xenoliths in the Euganean trachytes (NE Italy).

description: EMP data
DOI: 10.6084/m9.figshare.12529523
title: Cryptocarpus_Sea analyses

description: Dataset and scripts used in the paper "In the realm between landscape and seascape genetics: oceanic currents favour active colonization of a coastal plant (<i>Cryptocarpus pyriformis</i>) across the Galápagos Islands"<br>Dataset (.vcf):<i> Cryptocarpus pyriformis </i>SNPs obtained by ddRADseq and processed with ipyrad with clustering threshold 0.93 and minimum depth of 10. Postrior filtering removing all loci with &gt;70% missing data was performed using vcftools. The file "one-snpxlocus.vcf" is a subset of "Cp_CONT-GAL_ipyradc93d10-filt30.vcf" only with Galápagos samples and with one SNP per locus.<br><br>Scripts: <br>"sea_currents_analysis.R": reciprocal causal modelling and redundancy analysis."functions_sea.R": functions used in the previous script.<br><br>
DOI: 10.6084/m9.figshare.12529523.v1
title: Cryptocarpus_Sea analyses

description: Dataset and scripts used in the paper "In the realm between landscape and seascape genetics: oceanic currents favour active colonization of a coastal plant (<i>Cryptocarpus pyriformis</i>) across the Galápagos Islands"<br>Dataset (.vcf):<i> Cryptocarpus pyriformis </i>SNPs obtained by ddRADseq and processed with ipyrad with clustering threshold 0.93 and minimum depth of 10. Postrior filtering removing all loci with &gt;70% missing data was performed using vcftools. The file "one-snpxlocus.vcf" is a subset of "Cp_CONT-GAL_ipyradc93d10-filt30.vcf" only with Galápagos samples and with one SNP per locus.<br><br>Scripts: <br>"sea_currents_analysis.R": reciprocal causal modelling and redundancy analysis."functions_sea.R": functions used in the previous script.<br><br>
DOI: 10.6084/m9.figshare.12529316
title: Supplementary Material for: Attention Deficit/Hyperactivity Disorder and Global Severity Profiles in Treatment-Seeking Patients with Substance Use Disorders

description: <b><i>Introduction:</i></b> Comorbid attention deficit/hyperactivity disorder (ADHD) is present in 15–25% of all patients seeking treatment for substance use disorders (SUDs). Some studies suggest that comorbid ADHD increases clinical severity related to SUDs, other psychiatric comorbidities, and social impairment, but could not disentangle their respective influences. <b><i>Objectives:</i></b> To investigate whether comorbid adult ADHD in treatment-seeking SUD patients is associated with more severe clinical profiles in these domains assessed altogether. <b><i>Methods:</i></b> Treatment-seeking SUD patients from 8 countries (<i>N =</i> 1,294: 26% females, mean age 40 years [SD = 11 years]) were assessed for their history of DSM-IV ADHD, SUDs, and other psychiatric conditions and sociodemographic data. SUD patients with and without comorbid ADHD were compared on indicators of severity across 3 domains: addiction (number of SUD criteria and diagnoses), psychopathological complexity (mood disorders, borderline personality disorder, lifetime suicidal thoughts, or behavior), and social status (education level, occupational and marital status, and living arrangements). Regression models were built to account for confounders for each severity indicator. <b><i>Results:</i></b> Adult ADHD was present in 19% of the SUD patients. It was significantly associated with higher SUD severity, more frequent comorbid mood or borderline personality disorder, and less frequent “married” or “divorced” status, as compared with the absence of comorbid ADHD. ADHD comorbidity was independently associated with a higher number of dependence diagnoses (OR = 1.97) and more psychopathology (OR = 1.5), but not marital status. <b><i>Conclusions:</i></b> In treatment-seeking SUD patients, comorbid ADHD is associated with polysubstance dependence, psychopathological complexity, and social risks, which substantiates the clinical relevance of screening, diagnosing, and treating ADHD in patients with SUDs.
DOI: 10.6084/m9.figshare.12529484
title: Metadata record for: TAASRAD19, a high-resolution weather radar reflectivity dataset for precipitation nowcasting

description: This dataset contains key characteristics about the data described in the Data Descriptor TAASRAD19, a high-resolution weather radar reflectivity dataset for precipitation nowcasting. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format <br> <br> <br>
DOI: 10.6084/m9.figshare.12528308
title: sanger sequencing

description: Sanger sequencing data to find the enriched SNV
DOI: 10.6084/m9.figshare.12528416
title: sanger sequencing.rar

description: sanger sequencing to find enriched SNV
DOI: 10.6084/m9.figshare.12529484.v1
title: Metadata record for: TAASRAD19, a high-resolution weather radar reflectivity dataset for precipitation nowcasting

description: This dataset contains key characteristics about the data described in the Data Descriptor TAASRAD19, a high-resolution weather radar reflectivity dataset for precipitation nowcasting. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format <br> <br> <br>
DOI: 10.6084/m9.figshare.12528308.v1
title: sanger sequencing

description: Sanger sequencing data to find the enriched SNV
DOI: 10.6084/m9.figshare.12527984
title: Mosses modify effects of warmer and wetter conditions on tree seedlings at the alpine treeline

description: Data, meta data and R-scripts for results in 'Mosses modify effects of warmer and wetter conditions on tree seedlings at the alpine treeline'. 3 years of tree seedling survival data and final growth data from warming experiment with sites along a precipitation gradient. Sites are at/above treeline. Seedlings were transplanted into 3 different moss species. Growing season soil moisture and temperature data. See publication for further details on methods (Lett et all 2020 Global Change Biology, doc: 10.1111/gcb.15256). <br><br>
DOI: 10.6084/m9.figshare.12528296
title: Supplementary Material for: Vascular Endothelial Growth Factor Blockade Induces Dermal Endothelial Cell Apoptosis in a Clinically Relevant Skin Organ Culture Model

description: <b><i>Background/Aims:</i></b> Vascular endothelial growth factor (VEGF), a key mediator of angiogenesis, plays a key role in physiological processes and is a major contributor to several diseases including cancer and psoriasis. Anti-VEGF therapies are widely used as cancer and ophthalmological treatments. There is some evidence that VEGF blockade may have utility in the management of psoriasis, although their potential has been largely unexplored. We hypothesized that a human skin organ culture could provide a stable ex vivo model in which the cutaneous microvascular network could be studied and experimentally manipulated. <b><i>Methods:</i></b> Punch biopsies (3 mm) of skin, donated by healthy individuals (39–72 years old, <i>n</i> = 5), were incubated with monoclonal antibody (mAb) to human VEGF (bevacizumab) at doses based on data from animal and clinical studies. After 3-day culture, cell death and proliferation as well as vascular endothelial cell changes were assessed using quantitative immunohistomorphometry. <b><i>Results:</i></b> Anti-VEGF mAb at 0.8 mg/mL induced a significant increase in cleaved caspase-3 expression in CD31<sup>+</sup> cells (<i>p</i> &lt; 0.05). None of the doses tested increased TUNEL or decreased Ki-67 expression in the basal layer of the epidermis, confirming the model’s viability. In addition, the lactate dehydrogenase (LDH) assay showed no increase in LDH activity in treated samples compared to untreated control. The highest anti-VEGF mAb dose (0.8 mg/mL) induced an increase in TUNEL expression in the upper epidermis, which did not correlate with caspase-3 immunoreactivity. Further investigation revealed that anti-VEGF mAb did not change the expression of markers of terminal differentiation such as keratin 10, filaggrin, and involucrin, suggesting that VEGF depletion does not affect keratinocyte terminal differentiation. In contrast to the control group, levels of VEGF protein were undetectable in the culture supernatant of samples treated with 0.8 mg/mL of anti-VEGF mAb, suggesting sufficient dose. <b><i>Conclusion:</i></b> Our pilot study provides the first evidence that anti-VEGF therapy promotes endothelial cell apoptosis in human skin ex vivo. Our pragmatic human skin organ culture assay offers a valuable tool for future preclinical endothelial cell and translational microvascular network/anti-angiogenesis research in human skin.
DOI: 10.6084/m9.figshare.12527921
title: WATNEEDS CODE

description: WATNEEDS code
DOI: 10.6084/m9.figshare.12528215
title: Supplementary Material for: CASC9 Facilitates Cell Proliferation in Bladder Cancer by Regulating CBX2 Expression

description: <b><i>Background:</i></b> As the seventh most common urologic carcinoma worldwide, approximately 430,000 patients are diagnosed with bladder cancer (BC) every year. Increasing evidence indicates that long noncoding RNAs (lncRNAs) play crucial roles in the progression of BC. <b><i>Objectives:</i></b> This study is aimed to explore the function and mechanism of CASC9 in BC. <b><i>Methods:</i></b> Bioinformatics analysis and experiments including RT-qPCR, luciferase reporter, Cell Counting Kit-8 assay, Western blot, RNA immunoprecipitation assay, and TUNEL staining were applied to explore the function and mechanism of CASC9 in BC tissues and cell lines. <b><i>Results:</i></b> Our study demonstrated that CASC9 was upregulated in BC tissues and cell lines. Moreover, we found that CASC9 knockdown notably decreased proliferation while increased apoptotic rate in BC cells. Mechanistically, bioinformatics prediction and following experiments indicated that CASC9 worked as a competing endogenous RNA (ceRNA) of CBX2 through sponging miR-497-5p. Meanwhile, we recognized that CASC9 and miR-497-5p negatively regulated each other in a mutual way. Furthermore, we found that miR-497-5p shared binding site with CBX2. In addition, miR-497-5p could negatively regulated CBX2, while CASC9 could positively regulated CBX2. Rescue assays reveled that CBX2 overexpression could reversed the reduction of cell proliferation or the enhancement of cell apoptosis induced by CASC9 suppression. <b><i>Conclusions:</i></b> Our study manifests the first evidence that CASC9 serves as an oncogene in BC and accelerates cell proliferation by modulating miR-497-5p/CBX2 axis. The present study may provide a cogitable target for BC therapy.
DOI: 10.6084/m9.figshare.12528215.v1
title: Supplementary Material for: CASC9 Facilitates Cell Proliferation in Bladder Cancer by Regulating CBX2 Expression

description: <b><i>Background:</i></b> As the seventh most common urologic carcinoma worldwide, approximately 430,000 patients are diagnosed with bladder cancer (BC) every year. Increasing evidence indicates that long noncoding RNAs (lncRNAs) play crucial roles in the progression of BC. <b><i>Objectives:</i></b> This study is aimed to explore the function and mechanism of CASC9 in BC. <b><i>Methods:</i></b> Bioinformatics analysis and experiments including RT-qPCR, luciferase reporter, Cell Counting Kit-8 assay, Western blot, RNA immunoprecipitation assay, and TUNEL staining were applied to explore the function and mechanism of CASC9 in BC tissues and cell lines. <b><i>Results:</i></b> Our study demonstrated that CASC9 was upregulated in BC tissues and cell lines. Moreover, we found that CASC9 knockdown notably decreased proliferation while increased apoptotic rate in BC cells. Mechanistically, bioinformatics prediction and following experiments indicated that CASC9 worked as a competing endogenous RNA (ceRNA) of CBX2 through sponging miR-497-5p. Meanwhile, we recognized that CASC9 and miR-497-5p negatively regulated each other in a mutual way. Furthermore, we found that miR-497-5p shared binding site with CBX2. In addition, miR-497-5p could negatively regulated CBX2, while CASC9 could positively regulated CBX2. Rescue assays reveled that CBX2 overexpression could reversed the reduction of cell proliferation or the enhancement of cell apoptosis induced by CASC9 suppression. <b><i>Conclusions:</i></b> Our study manifests the first evidence that CASC9 serves as an oncogene in BC and accelerates cell proliferation by modulating miR-497-5p/CBX2 axis. The present study may provide a cogitable target for BC therapy.
DOI: 10.6084/m9.figshare.12527828
title: Read me

description: Read me file
DOI: 10.6084/m9.figshare.12527984.v1
title: Mosses modify effects of warmer and wetter conditions on tree seedlings at the alpine treeline

description: Data, meta data and R-scripts for results in 'Mosses modify effects of warmer and wetter conditions on tree seedlings at the alpine treeline'. 3 years of tree seedling survival data and final growth data from warming experiment with sites along a precipitation gradient. Sites are at/above treeline. Seedlings were transplanted into 3 different moss species. Growing season soil moisture and temperature data. See publication for further details on methods (Lett et all 2020 Global Change Biology, doc: 10.1111/gcb.15256). <br><br>