cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11793762
title: Supplementary Material for: Hidradenitis Suppurativa in Sweden: A Registry-Based Cross-Sectional Study of 13,538 Patients

description: <b><i>Background:</i></b> Hidradenitis suppurativa (HS) is a chronic, inflammatory skin condition with nodules and fistula formation and scarring. It is a debilitating disease with a severe negative impact on quality of life. There is a need for increased knowledge about the social and lifestyle characteristics of patients with HS in general, and pregnant women in particular. <b><i>Objectives:</i></b> The aims of this study were to investigate and describe social characteristics and comorbidity in all HS patients in Sweden as well as to study the prevalence of lifestyle factors associated with negative impact on health and pregnancy in Swedish pregnant women with HS. <b><i>Methods:</i></b> A registry-based cross-sectional study was performed by record linkage between Swedish registers covering the entire population. A cohort of 13,538 HS patients diagnosed with HS in specialised care during the years 2001–2014 and a subgroup of 1,368 HS patients who had undergone pregnancy during 2010–2015 were defined and described. Aggregated public data on the entire Swedish population and all pregnancies in 2014 were described for reference. <b><i>Results:</i></b> The HS population had an average age of 44 years on December 31, 2014. The prevalence of HS was 0.14%. In comparison to the Swedish reference population the HS patients were more often women, unmarried (36 vs. 44% married), and had lower education (68 vs. 82% with an upper-secondary school degree or higher) and lower income (39 vs. 16% made SEK &lt;100,000 a year). Comorbidity was 3% for inflammatory bowel disease and 8% for type 2 diabetes. The subgroup analysis showed high prevalence of overweight, obesity, and smoking in pregnant women with HS. <b><i>Conclusions:</i></b> The results from this comprehensive characterisation of Swedish HS patients may be used to improve preventive measures, information, and care for this vulnerable group.
DOI: 10.6084/m9.figshare.11793801.v1
title: HiD_GenomeBiology2020_RawData

description: Raw microscopy data used throughtout the manuscript.
DOI: 10.6084/m9.figshare.11793816.v1
title: Metadata record for: China CO2 emission accounts 2016-2017

description: This dataset contains key characteristics about the data described in the Data Descriptor China CO2 emission accounts 2016-2017. <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.11793762.v1
title: Supplementary Material for: Hidradenitis Suppurativa in Sweden: A Registry-Based Cross-Sectional Study of 13,538 Patients

description: <b><i>Background:</i></b> Hidradenitis suppurativa (HS) is a chronic, inflammatory skin condition with nodules and fistula formation and scarring. It is a debilitating disease with a severe negative impact on quality of life. There is a need for increased knowledge about the social and lifestyle characteristics of patients with HS in general, and pregnant women in particular. <b><i>Objectives:</i></b> The aims of this study were to investigate and describe social characteristics and comorbidity in all HS patients in Sweden as well as to study the prevalence of lifestyle factors associated with negative impact on health and pregnancy in Swedish pregnant women with HS. <b><i>Methods:</i></b> A registry-based cross-sectional study was performed by record linkage between Swedish registers covering the entire population. A cohort of 13,538 HS patients diagnosed with HS in specialised care during the years 2001–2014 and a subgroup of 1,368 HS patients who had undergone pregnancy during 2010–2015 were defined and described. Aggregated public data on the entire Swedish population and all pregnancies in 2014 were described for reference. <b><i>Results:</i></b> The HS population had an average age of 44 years on December 31, 2014. The prevalence of HS was 0.14%. In comparison to the Swedish reference population the HS patients were more often women, unmarried (36 vs. 44% married), and had lower education (68 vs. 82% with an upper-secondary school degree or higher) and lower income (39 vs. 16% made SEK &lt;100,000 a year). Comorbidity was 3% for inflammatory bowel disease and 8% for type 2 diabetes. The subgroup analysis showed high prevalence of overweight, obesity, and smoking in pregnant women with HS. <b><i>Conclusions:</i></b> The results from this comprehensive characterisation of Swedish HS patients may be used to improve preventive measures, information, and care for this vulnerable group.
DOI: 10.6084/m9.figshare.11793627
title: Generic Feature Format "GFF3" for Brycon orbignyanus

description: Generic Feature Format file containing the genomic annotation for B. orbignyanus, from sequences above 10 kb extracted from a larger genomic assembly (https://doi.org/10.6084/m9.figshare.5661802)
DOI: 10.6084/m9.figshare.11793627.v1
title: Generic Feature Format "GFF3" for Brycon orbignyanus

description: Generic Feature Format file containing the genomic annotation for B. orbignyanus, from sequences above 10 kb extracted from a larger genomic assembly (https://doi.org/10.6084/m9.figshare.5661802)
DOI: 10.6084/m9.figshare.11793624
title: Supplementary Material for: Impact of Intravitreal Ranibizumab Therapy on Vision Outcomes in Diabetic Macular Edema Patients: A Meta-Analysis

description: <b><i>Purpose:</i></b> Evaluation of the impact of the injection frequency of ranibizumab on best-corrected visual acuity (BCVA) outcomes in patients with diabetic macular edema (DME). <b><i>Methods:</i></b> A meta-analysis of randomized controlled trials (RCTs) and real-world studies was performed to quantify the effect of ranibizumab treatment on BCVA and central foveal thickness (CFT) in DME as well as the relationship between the number of injections and the change in BCVA/CFT. <b><i>Results:</i></b> All combined sources (29 RCTs and 11 real-life studies) showed a significant increase in BCVA from baseline following anti-vascular endothelial growth factor (VEGF) treatment (8.2, 9.4, and 10.3 ETDRS letters gained after 12, 24, and 36 months of ranibizumab treatment, respectively). The largest changes in BCVA were observed in RCTs and the smallest in real-life studies at 12 months. A significant relationship was found between the number of injections and change in BCVA at 12 months. <b><i>Conclusions:</i></b> Inferior vision outcomes were observed in clinical practice compared with RCTs and might be partly attributable to administration of fewer anti-VEGF injections. Physicians should be aware that early and appropriate anti-VEGF treatment regimens are necessary to obtain the results reported in RCTs and help prevent irreversible vision loss in DME patients.
DOI: 10.6084/m9.figshare.11791992
title: Supplementary Material for: Ulcerative Colitis: Disease Burden, Impact on Daily Life, and Reluctance to Consult Medical Professionals: Results from a Japanese Internet Survey

description: <b><i>Background and Aim:</i></b> The prevalence of ulcerative colitis has increased in Asian populations in recent years. This Japanese internet survey investigated the symptoms, impact, and treatment of ulcerative colitis, and communication between patients and medical professionals. <b><i>Methods:</i></b> This was a non-interventional analysis of responses from participants with ulcerative colitis who had regularly visited medical providers for their disease in the past year. <b><i>Results:</i></b> In 501 evaluable participants, the mean age was 39.8 years and mean disease duration was 7.6 years. Ulcerative colitis had a “significant impact” on daily life in 43.5% of participants who experienced bowel urgency and 48.6% who experienced bowel incontinence. Although the prevalence of bowel urgency and bowel incontinence was associated with higher stool frequency and rectal bleeding scores (<i>p</i> value for trend &lt;0.0001), they still existed even in patients without frequent stools or rectal bleeding. Around 30% of participants hesitated to discuss symptoms such as bowel incontinence with a medical professional. Approximately three-quarters preferred to use websites for medical information. Most participants (78.0%) had used topical treatments. However, 25.7% were hesitant to use such treatments due to concerns about discomfort (48.1%) and administration difficulty (47.3%). <b><i>Conclusions:</i></b> Ulcerative colitis significantly affects daily life, largely due to symptoms such as bowel urgency and bowel incontinence. Despite desiring to improve bowel incontinence, patients are embarrassed to consult physicians or nurses. Therefore, medical professionals should make an active effort to draw out patients’ individual concerns, including symptoms that patients may not initially feel able to talk about openly.
DOI: 10.6084/m9.figshare.11791992.v1
title: Supplementary Material for: Ulcerative Colitis: Disease Burden, Impact on Daily Life, and Reluctance to Consult Medical Professionals: Results from a Japanese Internet Survey

description: <b><i>Background and Aim:</i></b> The prevalence of ulcerative colitis has increased in Asian populations in recent years. This Japanese internet survey investigated the symptoms, impact, and treatment of ulcerative colitis, and communication between patients and medical professionals. <b><i>Methods:</i></b> This was a non-interventional analysis of responses from participants with ulcerative colitis who had regularly visited medical providers for their disease in the past year. <b><i>Results:</i></b> In 501 evaluable participants, the mean age was 39.8 years and mean disease duration was 7.6 years. Ulcerative colitis had a “significant impact” on daily life in 43.5% of participants who experienced bowel urgency and 48.6% who experienced bowel incontinence. Although the prevalence of bowel urgency and bowel incontinence was associated with higher stool frequency and rectal bleeding scores (<i>p</i> value for trend &lt;0.0001), they still existed even in patients without frequent stools or rectal bleeding. Around 30% of participants hesitated to discuss symptoms such as bowel incontinence with a medical professional. Approximately three-quarters preferred to use websites for medical information. Most participants (78.0%) had used topical treatments. However, 25.7% were hesitant to use such treatments due to concerns about discomfort (48.1%) and administration difficulty (47.3%). <b><i>Conclusions:</i></b> Ulcerative colitis significantly affects daily life, largely due to symptoms such as bowel urgency and bowel incontinence. Despite desiring to improve bowel incontinence, patients are embarrassed to consult physicians or nurses. Therefore, medical professionals should make an active effort to draw out patients’ individual concerns, including symptoms that patients may not initially feel able to talk about openly.
DOI: 10.6084/m9.figshare.11791968
title: Supplementary C: Isotopic data for geo/thermochronology. Structural evolution and medium-temperature thermochronology of central Madagascar: implications for Gondwana amalgamation

description: Supplementary C: Isotopic data for geo/thermochronology.
DOI: 10.6084/m9.figshare.11791968.v1
title: Supplementary C: Isotopic data for geo/thermochronology. Structural evolution and medium-temperature thermochronology of central Madagascar: implications for Gondwana amalgamation

description: Supplementary C: Isotopic data for geo/thermochronology.
DOI: 10.6084/m9.figshare.11791680
title: Regulation of the Ysh1 endonuclease of the mRNA cleavage/polyadenylation complex by ubiquitin-mediated degradation

description: Mutation of the essential yeast protein Ipa1 has previously been demonstrated to cause defects in pre-mRNA 3ʹ end processing and growth, but the mechanism underlying these defects was not clear. In this study, we show that the <i>ipa1-1</i> mutation causes a striking depletion of Ysh1, the evolutionarily conserved endonuclease subunit of the 19-subunit mRNA Cleavage/Polyadenylation (C/P) complex, but does not decrease other C/P subunits. <i>YSH1</i> overexpression rescues both the growth and 3ʹ end processing defects of the <i>ipa1-1</i> mutant. <i>YSH1</i> mRNA level is unchanged in <i>ipa1-1</i> cells, and proteasome inactivation prevents Ysh1 loss and causes accumulation of ubiquitinated Ysh1. Ysh1 ubiquitination is mediated by the Ubc4 ubiquitin-conjugating enzyme and Mpe1, which in addition to its function in C/P, is also a RING ubiquitin ligase. In summary, Ipa1 affects mRNA processing by controlling the availability of the C/P endonuclease and may represent a regulatory mechanism that could be rapidly deployed to facilitate reprogramming of cellular responses.
DOI: 10.6084/m9.figshare.11791698
title: DepMap 20Q1 Public

description: This dataset contains the results of Avana library CRISPR-Cas9 genome-scale knockout (prefixed with Achilles) as well as mutation, copy number and gene expression data (prefixed with CCLE) for cancer cell lines as part of the Broad Institute’s Cancer Dependency Map project. We have repackaged our fileset to include all quarterly-updating datasets produced by DepMap.<br>The Avana CRISPR-Cas9 genome-scale knockout data has expanded to include 739 cell lines, the RNAseq data includes 1270 cell lines, and the copy number data includes 1713 cell lines. Please see the README files for details regarding data processing pipeline procedures updates.<br>As our screening efforts continue, we will be releasing additional cancer dependency data on a quarterly basis for unrestricted use. For the latest datasets available, further analyses, and to subscribe to our mailing list visit https://depmap.org.<br>Descriptions of the experimental methods and the CERES algorithm are published in http://dx.doi.org/10.1038/ng.3984. Some cell lines were process using copy number data based on the Sanger Institute whole exome sequencing data (COSMIC: http://cancer.sanger.ac.uk.cell_lines, EGA accession number: EGAD00001001039) reprocessed using CCLE pipelines. A detailed description of the pipelines and tool versions for CCLE expression can be found here: https://github.com/broadinstitute/gtex-pipeline/blob/v9/TOPMed_RNAseq_pipeline.md.<br>v2 changes: The sample_info.csv file in version 1 was missing lineage information for some cell lines. Version 2 corrects this.<br><br>v3 changes: UACC62_SKIN_CJ1_RESISTANT has been removed from Public 19Q4 Achilles files due to an issue with fingerprinting. Values for this cell line have been NAed in the following files: Achilles_gene_effect.csv, Achilles_gene_effect_unscaled.csv, Achilles_gene_dependency.csv, Achilles_logfold_change.csv, Achilles_raw_readcounts.csv.
DOI: 10.6084/m9.figshare.11791680.v2
title: Regulation of the Ysh1 endonuclease of the mRNA cleavage/polyadenylation complex by ubiquitin-mediated degradation

description: Mutation of the essential yeast protein Ipa1 has previously been demonstrated to cause defects in pre-mRNA 3ʹ end processing and growth, but the mechanism underlying these defects was not clear. In this study, we show that the <i>ipa1-1</i> mutation causes a striking depletion of Ysh1, the evolutionarily conserved endonuclease subunit of the 19-subunit mRNA Cleavage/Polyadenylation (C/P) complex, but does not decrease other C/P subunits. <i>YSH1</i> overexpression rescues both the growth and 3ʹ end processing defects of the <i>ipa1-1</i> mutant. <i>YSH1</i> mRNA level is unchanged in <i>ipa1-1</i> cells, and proteasome inactivation prevents Ysh1 loss and causes accumulation of ubiquitinated Ysh1. Ysh1 ubiquitination is mediated by the Ubc4 ubiquitin-conjugating enzyme and Mpe1, which in addition to its function in C/P, is also a RING ubiquitin ligase. In summary, Ipa1 affects mRNA processing by controlling the availability of the C/P endonuclease and may represent a regulatory mechanism that could be rapidly deployed to facilitate reprogramming of cellular responses.
DOI: 10.6084/m9.figshare.11791680.v1
title: Regulation of the Ysh1 endonuclease of the mRNA cleavage/polyadenylation complex by ubiquitin-mediated degradation

description: Mutation of the essential yeast protein Ipa1 has previously been demonstrated to cause defects in pre-mRNA 3ʹ end processing and growth, but the mechanism underlying these defects was not clear. In this study, we show that the <i>ipa1-1</i> mutation causes a striking depletion of Ysh1, the evolutionarily conserved endonuclease subunit of the 19-subunit mRNA Cleavage/Polyadenylation (C/P) complex, but does not decrease other C/P subunits. <i>YSH1</i> overexpression rescues both the growth and 3ʹ end processing defects of the <i>ipa1-1</i> mutant. <i>YSH1</i> mRNA level is unchanged in <i>ipa1-1</i> cells, and proteasome inactivation prevents Ysh1 loss and causes accumulation of ubiquitinated Ysh1. Ysh1 ubiquitination is mediated by the Ubc4 ubiquitin conjugating enzyme and Mpe1, which in addition to its function in C/P, is also a RING ubiquitin ligase. In summary, Ipa1 affects mRNA processing by controlling availability of the C/P endonuclease, and may represent a regulatory mechanism that could be rapidly deployed to facilitate reprogramming of cellular responses.
DOI: 10.6084/m9.figshare.11791698.v1
title: DepMap 20Q1 Public

description: This dataset contains the results of Avana library CRISPR-Cas9 genome-scale knockout (prefixed with Achilles) as well as mutation, copy number and gene expression data (prefixed with CCLE) for cancer cell lines as part of the Broad Institute’s Cancer Dependency Map project. We have repackaged our fileset to include all quarterly-updating datasets produced by DepMap.<br>The Avana CRISPR-Cas9 genome-scale knockout data has expanded to include 739 cell lines, the RNAseq data includes 1270 cell lines, and the copy number data includes 1713 cell lines. Please see the README files for details regarding data processing pipeline procedures updates.<br>As our screening efforts continue, we will be releasing additional cancer dependency data on a quarterly basis for unrestricted use. For the latest datasets available, further analyses, and to subscribe to our mailing list visit https://depmap.org.<br>Descriptions of the experimental methods and the CERES algorithm are published in http://dx.doi.org/10.1038/ng.3984. Some cell lines were process using copy number data based on the Sanger Institute whole exome sequencing data (COSMIC: http://cancer.sanger.ac.uk.cell_lines, EGA accession number: EGAD00001001039) reprocessed using CCLE pipelines. A detailed description of the pipelines and tool versions for CCLE expression can be found here: https://github.com/broadinstitute/gtex-pipeline/blob/v9/TOPMed_RNAseq_pipeline.md.<br>
DOI: 10.6084/m9.figshare.11791602
title: Sensory Dataset

description: Spike timings (neuromorphic implementation using izhikevich algorithm) based on tactile sensory data for a given texture.<br>These data sets were used in :<br>1) DOI: 10.1109/TNNLS.2015.2472477<br>2) https://doi.org/10.1016/j.neunet.2019.11.020<br>
DOI: 10.6084/m9.figshare.11791497
title: HiD_GenomeBiology2020_RawData_U2OS_SiR_DNA_SingleCell

description: Used in Figure 3 and 5 of the publication.
DOI: 10.6084/m9.figshare.11791494
title: HiD_GenomeBiology2020_RawData_U2OS_SiR_DNA

description: Used in Figure 2 and 4 of the publication.
DOI: 10.6084/m9.figshare.11791494.v1
title: HiD_GenomeBiology2020_RawData_U2OS_SiR_DNA

description: Used in Figure 2 and 4 of the publication.
DOI: 10.6084/m9.figshare.11791497.v1
title: HiD_GenomeBiology2020_RawData_U2OS_SiR_DNA_SingleCell

description: Used in Figure 3 and 5 of the publication.
DOI: 10.6084/m9.figshare.11791398
title: Dispersible chitosan particles showing bacteriostatic effect against <i>Streptococcus mutans</i> and their dental polishing effect

description: Nontoxic and biodegradable chitosan is potentially useful in various applications. We prepared submicron chitosan particles with high dispersibility in aqueous solution utilizing the electrostatic interaction phase separation method described in a previous report, but using citric acid as the polyvalent anionic compound instead of sodium sulfate. The submicron chitosan particles showed significant antibacterial activity and anti-adhesive action against <i>Streptococcus mutans</i>, even at around neutral pH. However, chitosan granules showed no antibacterial activity under the same conditions. The addition of the chitosan particles to dental polishing paste provided stainless steel discs (the same hardness as dental enamel) with a smoother surface than polishing paste without additives. In view of their submicron size and antibacterial activity, chitosan particles could potentially be multifunctional components of oral and dental cleaning materials. Dispersible chitosan particles (DCPs) −1.0; 1.0 equivalents of citric acid carboxy groups relative to chitosan amino groups.
DOI: 10.6084/m9.figshare.11791407
title: Physicochemical Characteristics of Sandstone Media

description: This data set contains the measured values of the physicochemcial rock properties of a deltaic formation in Germany that was sampled in the complete quarry area as well as by two rock cubes (OSB1_c and OSB2_c). Provided is a measurement series on rock plugs extracted from both rock cubes as well as on plugs extracted from the outcrop wall directly. Also, we provide a series of geochemical measurements conducted on all faces of both rock cubes. All samples are referenced in a local coordinate system. The origin of the relative coordinate system is a point in the quarry.
DOI: 10.6084/m9.figshare.11791386
title: Among cradles and museums: seasonally dry forest promotes lineage exchanges between rain forest and savanna

description: <b>Background</b>: Cerrado comprises heterogeneous vegetation types. The flora of the vegetation types has distinct biogeographic origins and thus can be hypothesised to have distinct evolutionary imprints. <b>Aims</b>: We hypothesised that the flora of riparian forest was phylogenetically overdispersed, whereas those of more open habitats were phylogenetically clustered. <b>Methods</b>: We built a species-level phylogeny for 1,663 species of trees, shrubs and palms and analysed the pattern of lineage distribution, alpha and beta phylogenetic diversity among Cerrado vegetation types (riparian forest, rocky savana, savana and seasonally dry forest - SDTF). <b>Results</b>: We found a gradient of high phylogenetic diversity and overdispersion from riparian forests towards phylogenetic clustering in vegetation in more open and drier habitats. Habitat shifts were common along the evolutionary history of all families analysed and most families showed a high frequency of shifts from SDTF to riparian forest and savanna. <b>Conclusions</b>: SDTF seems to be a transitional habitat in evolutionary terms, promoting lineage exchanges between stands of riparian forest and savanna. While riparian forest can be seen as a ‘museum’, that harbours ancient lineages, savanna and rocky savanna are a ‘cradle’ of derived lineages. Habitat shifts are an important underlying drive of high present-day Cerrado flora diversity.