cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.25170701
title: Evaluating Riboglow-FLIM probes for RNA sensing

description: The files were posted as .zip files - in order to access the files please download them to see them clearly. We recently developed Riboglow-FLIM, where we genetically tag and track RNA molecules in live cells through measuring the fluorescence lifetime of a small molecule probe that binds the RNA tag. Here, we systematically and quantitatively evaluated key elements of Riboglow-FLIM that may serve as the foundation for Riboglow-FLIM applications and further tool development efforts. Our investigation focused on measuring changes in fluorescence lifetime of representative Riboglow-FLIM probes with different linkers and fluorophores in different environments. <i>In vitro</i> measurements revealed distinct lifetime differences among the probe variants as a result of different linker designs and fluorophore selections. To expand on the platform's versatility, probes in a wide variety of mammalian cell types were examined using fluorescence lifetime imaging microscopy (FLIM), and possible effects on cell physiology were evaluated by metabolomics. The results demonstrated that variations in lifetime were dependent on both probe and cell type. Interestingly, distinct differences in lifetime values were observed between cell lines, while no overall change in cell health was measured. These findings underscore the importance of probe selection and cellular environment when employing Riboglow-FLIM for RNA detection, serving as a foundation for future tool development and applications across diverse fields and biological systems.
DOI: 10.6084/m9.figshare.14746821
title: Additional file 2 of Mitochondrial genome copy number measured by DNA sequencing in human blood is strongly associated with metabolic traits via cell-type composition differences

description: Additional file 2:. Excel format (.xlsx). Large Supplementary Tables. Contains Tables S1, S5-S8, and S10.
DOI: 10.6084/m9.figshare.22611248
title: Additional file 2 of A novel 1.38-kb deletion combined with a single nucleotide variant in KIAA0586 as a cause of Joubert syndrome

description: Additional file 2.  Table S2. Results of qPCR for the 1.38kb deletion.
DOI: 10.6084/m9.figshare.22611245.v1
title: Additional file 1 of A novel 1.38-kb deletion combined with a single nucleotide variant in KIAA0586 as a cause of Joubert syndrome

description: Additional file 1.  Table S1. Primers for verification of candidate variants.
DOI: 10.6084/m9.figshare.22611284.v1
title: Additional file 1 of The impact of intrahepatic cholestasis on pregnancy outcomes: a retrospective cohort study

description: Additional file 1: Raw data of the 39,244 pregnant women participating in this study.
DOI: 10.6084/m9.figshare.22606462.v1
title: Additional file 5 of Comparison of structural variants detected by PacBio-CLR and ONT sequencing in pear

description: Additional file 5. The number of SVs detected by Sniffles_v2, CuteSV, and Nanovar and merged by SURVIVOR.
DOI: 10.6084/m9.figshare.8979968
title: Comparative efficacy and safety of immunosuppressive therapies for systemic sclerosis related interstitial lung disease: A Bayesian network analysis

description: <b>Objectives:</b> Immunosuppressive therapies for the treatment of patients with systemic sclerosis (SSc) and SSc related interstitial lung diseases (SSc-ILD) include cyclophosphamide (CYC), mycophenolate mofetil (MMF), azathioprine (AZA) and methotrexate (MTX). The objectives were to compare and rank these therapies in term of forced vital capacity (FVC) % predicted, diffusing capacity of the lung for carbon monoxide (DLco) % predicted and adverse events (AEs). <b>Methods:</b> We present pooled estimates of mean difference (MD) and odds rates (ORs) with 95% confidence intervals (CIs) among different therapies. We also ranked these agents with surface under the cumulative ranking probability (SUCRA). <b>Results:</b> CYC plus AZA had the highest SUCRA probability (70%) on reducing risk of the deterioration of FVC compared with CYC, observation (OBS), MMF and AZA. While for the prevention of the deterioration of DLco, MMF showed the highest SUCRA probability (76%) compared with others. Moreover, AZA showed the lowest probability (32%) for AEs among active interventions. <b>Conclusions:</b> CYC plus AZA was the preferred immunosuppressive strategies compared to others on preventing the deterioration of FVC. MMF resulted with the highest probability as the best in preventing the deterioration of DLco. Monotherapy of AZA was less pulmonary function benefit but related less AEs.
DOI: 10.6084/m9.figshare.22611314.v1
title: Additional file 2 of Genetic association of circulating C-reactive protein levels with idiopathic pulmonary fibrosis: a two-sample Mendelian randomization study

description: Additional file 2. The 56 SNPs in IPF GWAS.
DOI: 10.6084/m9.figshare.22611317.v1
title: Additional file 3 of Genetic association of circulating C-reactive protein levels with idiopathic pulmonary fibrosis: a two-sample Mendelian randomization study

description: Additional file 3. IVs for circulating CRP levels.
DOI: 10.6084/m9.figshare.22611311.v1
title: Additional file 1 of Genetic association of circulating C-reactive protein levels with idiopathic pulmonary fibrosis: a two-sample Mendelian randomization study

description: Additional file 1. The 57 SNPs related to circulating CRP levels at a genome-wide significant level.
DOI: 10.6084/m9.figshare.24103086
title: <b>Establishing Riboglow-FLIM to visualize non-coding RNAs inside live Zebrafish embryos</b><b>.</b>

description: Raw and processed data files associated to https://doi.org/10.1016/j.bpr.2023.100132
DOI: 10.6084/m9.figshare.24103086.v1
title: <b>Establishing Riboglow-FLIM to visualize non-coding RNAs inside live Zebrafish embryos</b><b>.</b>

description: Raw and processed data files associated to https://doi.org/10.1016/j.bpr.2023.100132
DOI: 10.6084/m9.figshare.14222794
title: Cell-free DNA methylome profiling by MBD-seq with ultra-low input

description: Methylation signatures in cell-free DNA (cfDNA) have shown great sensitivity and specificity in the characterization of tumour status and classification of tumour types, as well as the response to therapy and recurrence. Currently, most cfDNA methylation studies are based on bisulphite conversion, especially targeted bisulphite sequencing, while enrichment-based methods such as cfMeDIP-seq are beginning to show potential. Here, we report an enrichment-based ultra-low input cfDNA methylation profiling method using methyl-CpG binding proteins capture, termed cfMBD-seq. We optimized the conditions for cfMBD capture by adjusting the amount of MethylCap protein along with using methylated filler DNA. Our data show high correlation between low input cfMBD-seq and standard MBD-seq (&gt;1000 ng input). When compared to cfMEDIP-seq, cfMBD-seq demonstrates higher sequencing data quality with more sequenced reads passed filter and less duplicate rate. cfMBD-seq also outperforms cfMeDIP-seq in the enrichment of CpG islands. This new bisulphite-free ultra-low input methylation profiling technology has great potential in non-invasive and cost-effective cancer detection and classification.
DOI: 10.6084/m9.figshare.22606447.v1
title: Additional file 1 of Comparison of structural variants detected by PacBio-CLR and ONT sequencing in pear

description: Additional file 1. SVs detected by Sniffles_v2, CuteSV, and Nanovar after mapping with Minimap2, NGMLR, LRA and Winnowmap2.
DOI: 10.6084/m9.figshare.14222794.v1
title: Cell-free DNA methylome profiling by MBD-seq with ultra-low input

description: Methylation signatures in cell-free DNA (cfDNA) have shown great sensitivity and specificity in the characterization of tumour status and classification of tumour types, as well as the response to therapy and recurrence. Currently, most cfDNA methylation studies are based on bisulphite conversion, especially targeted bisulphite sequencing, while enrichment-based methods such as cfMeDIP-seq are beginning to show potential. Here, we report an enrichment-based ultra-low input cfDNA methylation profiling method using methyl-CpG binding proteins capture, termed cfMBD-seq. We optimized the conditions for cfMBD capture by adjusting the amount of MethylCap protein along with using methylated filler DNA. Our data show high correlation between low input cfMBD-seq and standard MBD-seq (&gt;1000 ng input). When compared to cfMEDIP-seq, cfMBD-seq demonstrates higher sequencing data quality with more sequenced reads passed filter and less duplicate rate. cfMBD-seq also outperforms cfMeDIP-seq in the enrichment of CpG islands. This new bisulphite-free ultra-low input methylation profiling technology has great potential in non-invasive and cost-effective cancer detection and classification.
DOI: 10.6084/m9.figshare.22611404
title: Additional file 1 of A WeChat-based competency and performance checklist in basic surgical skills course for military medical academy undergraduates

description: Additional file 1. Dataset.
DOI: 10.6084/m9.figshare.22611404.v1
title: Additional file 1 of A WeChat-based competency and performance checklist in basic surgical skills course for military medical academy undergraduates

description: Additional file 1. Dataset.
DOI: 10.6084/m9.figshare.8979968.v1
title: Comparative efficacy and safety of immunosuppressive therapies for systemic sclerosis related interstitial lung disease: A Bayesian network analysis

description: <b>Objectives:</b> Immunosuppressive therapies for the treatment of patients with systemic sclerosis (SSc) and SSc related interstitial lung diseases (SSc-ILD) include cyclophosphamide (CYC), mycophenolate mofetil (MMF), azathioprine (AZA) and methotrexate (MTX). The objectives were to compare and rank these therapies in term of forced vital capacity (FVC) % predicted, diffusing capacity of the lung for carbon monoxide (DLco) % predicted and adverse events (AEs). <b>Methods:</b> We present pooled estimates of mean difference (MD) and odds rates (ORs) with 95% confidence intervals (CIs) among different therapies. We also ranked these agents with surface under the cumulative ranking probability (SUCRA). <b>Results:</b> CYC plus AZA had the highest SUCRA probability (70%) on reducing risk of the deterioration of FVC compared with CYC, observation (OBS), MMF and AZA. While for the prevention of the deterioration of DLco, MMF showed the highest SUCRA probability (76%) compared with others. Moreover, AZA showed the lowest probability (32%) for AEs among active interventions. <b>Conclusions:</b> CYC plus AZA was the preferred immunosuppressive strategies compared to others on preventing the deterioration of FVC. MMF resulted with the highest probability as the best in preventing the deterioration of DLco. Monotherapy of AZA was less pulmonary function benefit but related less AEs.
DOI: 10.6084/m9.figshare.22611455.v1
title: Additional file 2 of The prognostic value and immune correlation of IL18 expression and promoter methylation in renal cell carcinoma

description: Additional file 2. The supplementary tables in this study.
DOI: 10.6084/m9.figshare.22606529.v1
title: Additional file 6 of Non-CpG sites preference in G:C &gt; A:T transition of TP53 in gastric cancer of Eastern Europe (Poland, Romania and Hungary) compared to East Asian countries (China and Japan)

description: Additional file 6: Table S1. Primers for PCR amplification of TP53 gene. Table S2. Histological type and TP53 mutation status. Table S3. Mutation distribution in TP53 (exon 4–8). Table S4. Mutation functions of TP53 (exon 4-8) in Eastern Europe, China and Japan. Table S5. Mutation spectrum of TP53 (exon 4–8) in Eastern Europe, China and Japan. Table S6. Hotspot mutation in Eastern Europe, China and Japan.
DOI: 10.6084/m9.figshare.22606559
title: Additional file 1 of Risk factors for early neurologic deterioration in single small subcortical infarction without carrier artery stenosis: predictors at the early stage

description: Additional file 1.
DOI: 10.6084/m9.figshare.22611502
title: Additional file 5 of Trends and influence factors in the prevalence, intervention, and control of metabolic syndrome among US adults, 1999–2018

description: Additional file 5. sTable 4 Trend in prevalence of reduced HDL among US adults from 1999 to 2018.
DOI: 10.6084/m9.figshare.22611520
title: Additional file 11 of Trends and influence factors in the prevalence, intervention, and control of metabolic syndrome among US adults, 1999–2018

description: Additional file 11. sTable 10 Change in distribution of characteristics among elevated blood glucose from 1999 to 2018.
DOI: 10.6084/m9.figshare.22611547
title: Additional file 20 of Trends and influence factors in the prevalence, intervention, and control of metabolic syndrome among US adults, 1999–2018

description: Additional file 20. sTable 19 Trend in control rate of HbA1camong metabolic syndrome from 1999 to 2018.
DOI: 10.15156/bio/sh164049.07fu
title: SH164049.07FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh164050.07fu
title: SH164050.07FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh164051.07fu
title: SH164051.07FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh164052.07fu
title: SH164052.07FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh164053.07fu
title: SH164053.07FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh164054.07fu
title: SH164054.07FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh164055.07fu
title: SH164055.07FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh164056.07fu
title: SH164056.07FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh164057.07fu
title: SH164057.07FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.