cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15156/bio/sh2757451.08fu
title: SH2757451.08FU

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/sh490465.07fu
title: SH490465.07FU

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/sh490466.07fu
title: SH490466.07FU

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/sh490467.07fu
title: SH490467.07FU

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/sh2757452.08fu
title: SH2757452.08FU

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/sh2757453.08fu
title: SH2757453.08FU

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: 10.6084/m9.figshare.17131299.v1
title: Quantitative evaluation of drug efficacy in the treatment of myasthenia gravis

description: This study aimed to quantitatively evaluate placebo effect and drug efficacy characteristics and identify associated factors that affect quantitative myasthenia gravis (MG) score (QMGs) and MG activities of daily living score (MG-ADLs) in patients with MG. Randomized placebo-controlled clinical trials were comprehensively searched in public databases (PubMed, EMBASE, and Cochrane Library databases). A model-based meta-analysis was developed to describe time-course about drug efficacy and placebo effect. Twelve articles including 13 trials (673 participants) that were eligible for this study evaluated four immunosuppressants (tacrolimus, cyclosporine, prednisone, and mycophenolate mofetil) and five targeted therapy drugs (eculizumab, belimumab, zilucoplan, efgartigimod, and iscalimab). The pharmacodynamic model showed that eculizumab had the highest efficacy in reducing QMGs scores (3.66 points), and efgartigimod had the highest efficacy in reducing MG-ADLs scores (1.97 points). The placebo effect of QMGs and MG-ADLs increased apparently with time and reached 52% and 90% of their maximum effect in 12 weeks, respectively. In addition, this study found that the activities of daily living ability increased with the increase of the proportion of patients undergoing thymectomy. This study analyzed the efficacy characteristics of nine drugs. The present findings provide necessary quantitative information for drug development of MG.
DOI: 10.6084/m9.figshare.16606935.v1
title: Additional file 5 of Eicosapentaenoic and docosahexaenoic acids attenuate hyperglycemia through the microbiome-gut-organs axis in db/db mice

description: Additional file 4. Fecal metabolome
DOI: 10.6084/m9.figshare.9791273
title: SQSTM1-dependent autophagic degradation of PKM2 inhibits the production of mature IL1B/IL-1β and contributes to LIPUS-mediated anti-inflammatory effect

description: Synovitis is implicated in the pathology of osteoarthritis (OA) and significantly contributes to the development of OA. As a noninvasive physical therapy, low-intensity pulsed ultrasound (LIPUS) has been reported to possess anti-inflammatory effect in recent years. However, the role of LIPUS on synovitis of OA and the underlying mechanisms are little known. The present study showed that LIPUS ameliorated synovial inflammation in destabilization of the medial meniscus (DMM) mouse model and air pouch model, and alleviated pain gait patterns of DMM mouse. LIPUS dramatically inhibited the production of mature IL1B/IL-1β (interleukin 1 beta) <i>in vitro</i> and <i>in vivo</i>. In addition, LIPUS upregulated the macroautophagy/autophagy level as well as accelerated the formation of an SQSTM1 (sequestosome1)-PKM (pyruvate kinase, muscle) complex in the lipopolysaccharide (LPS)-adenosine triphosphate (ATP)-treated macrophages. Besides, LIPUS downregulated the level of PKM2 in LPS-ATP-treated macrophages, which could be reversed by SQSTM1 knockdown. In brief, the present study for the first time demonstrates that LIPUS inhibits the production of mature IL1B partially via SQSTM1-dependent autophagic degradation of PKM2 in LPS-ATP-treated macrophages, which may further ameliorate the synovial inflammation and gait patterns in animal models. Our data provide new clues for the treatments of synovitis and other inflammatory diseases using LIPUS. 3-MA: 3-methyladenene; ATG7: autophagy-related 7; ATP: adenosine triphosphate; BafA1: bafilomycin A<sub>1</sub>; BMDMs: bone marrow derived macrophages; CHX: cycloheximide; DMM: destabilization of the medial meniscus; ELISA: enzyme-linked immunosorbent assay; GFP: green fluorescent protein; IL1B/IL-1β: interleukin 1 beta; LIPUS: low-intensity pulsed ultrasound; LIR: LC3-interacting region; LPS: lipopolysaccharide; MAP1LC3B/LC3B: microtubule associated protein 1 light chain 3 beta; MDP: muramyl dipeptide; NFKB/NF-κB: nuclear factor kappa B; NLRP3: NLR family, pyrin domain containing 3; OA: osteoarthritis; PKM/PKM2: pyruvate kinase M1/2; PMA: phorbol-12-myristate-13-acetate; PYCARD/ASC; PYD and CARD domain containing; RFP: red fluorescent protein; siRNAs: small interfering RNAs; SQSTM1: sequestosome 1; TEM: transmission electron microscopy
DOI: 10.6084/m9.figshare.9791273.v1
title: SQSTM1-dependent autophagic degradation of PKM2 inhibits the production of mature IL1B/IL-1β and contributes to LIPUS-mediated anti-inflammatory effect

description: Synovitis is implicated in the pathology of osteoarthritis (OA) and significantly contributes to the development of OA. As a noninvasive physical therapy, low-intensity pulsed ultrasound (LIPUS) has been reported to possess anti-inflammatory effect in recent years. However, the role of LIPUS on synovitis of OA and the underlying mechanisms are little known. The present study showed that LIPUS ameliorated synovial inflammation in destabilization of the medial meniscus (DMM) mouse model and air pouch model, and alleviated pain gait patterns of DMM mouse. LIPUS dramatically inhibited the production of mature IL1B/IL-1β (interleukin 1 beta) <i>in vitro</i> and <i>in vivo</i>. In addition, LIPUS upregulated the macroautophagy/autophagy level as well as accelerated the formation of an SQSTM1 (sequestosome1)-PKM (pyruvate kinase, muscle) complex in the lipopolysaccharide (LPS)-adenosine triphosphate (ATP)-treated macrophages. Besides, LIPUS downregulated the level of PKM2 in LPS-ATP-treated macrophages, which could be reversed by SQSTM1 knockdown. In brief, the present study for the first time demonstrates that LIPUS inhibits the production of mature IL1B partially via SQSTM1-dependent autophagic degradation of PKM2 in LPS-ATP-treated macrophages, which may further ameliorate the synovial inflammation and gait patterns in animal models. Our data provide new clues for the treatments of synovitis and other inflammatory diseases using LIPUS.
DOI: 10.6084/m9.figshare.9791273.v2
title: SQSTM1-dependent autophagic degradation of PKM2 inhibits the production of mature IL1B/IL-1β and contributes to LIPUS-mediated anti-inflammatory effect

description: Synovitis is implicated in the pathology of osteoarthritis (OA) and significantly contributes to the development of OA. As a noninvasive physical therapy, low-intensity pulsed ultrasound (LIPUS) has been reported to possess anti-inflammatory effect in recent years. However, the role of LIPUS on synovitis of OA and the underlying mechanisms are little known. The present study showed that LIPUS ameliorated synovial inflammation in destabilization of the medial meniscus (DMM) mouse model and air pouch model, and alleviated pain gait patterns of DMM mouse. LIPUS dramatically inhibited the production of mature IL1B/IL-1β (interleukin 1 beta) <i>in vitro</i> and <i>in vivo</i>. In addition, LIPUS upregulated the macroautophagy/autophagy level as well as accelerated the formation of an SQSTM1 (sequestosome1)-PKM (pyruvate kinase, muscle) complex in the lipopolysaccharide (LPS)-adenosine triphosphate (ATP)-treated macrophages. Besides, LIPUS downregulated the level of PKM2 in LPS-ATP-treated macrophages, which could be reversed by SQSTM1 knockdown. In brief, the present study for the first time demonstrates that LIPUS inhibits the production of mature IL1B partially via SQSTM1-dependent autophagic degradation of PKM2 in LPS-ATP-treated macrophages, which may further ameliorate the synovial inflammation and gait patterns in animal models. Our data provide new clues for the treatments of synovitis and other inflammatory diseases using LIPUS. 3-MA: 3-methyladenene; ATG7: autophagy-related 7; ATP: adenosine triphosphate; BafA1: bafilomycin A<sub>1</sub>; BMDMs: bone marrow derived macrophages; CHX: cycloheximide; DMM: destabilization of the medial meniscus; ELISA: enzyme-linked immunosorbent assay; GFP: green fluorescent protein; IL1B/IL-1β: interleukin 1 beta; LIPUS: low-intensity pulsed ultrasound; LIR: LC3-interacting region; LPS: lipopolysaccharide; MAP1LC3B/LC3B: microtubule associated protein 1 light chain 3 beta; MDP: muramyl dipeptide; NFKB/NF-κB: nuclear factor kappa B; NLRP3: NLR family, pyrin domain containing 3; OA: osteoarthritis; PKM/PKM2: pyruvate kinase M1/2; PMA: phorbol-12-myristate-13-acetate; PYCARD/ASC; PYD and CARD domain containing; RFP: red fluorescent protein; siRNAs: small interfering RNAs; SQSTM1: sequestosome 1; TEM: transmission electron microscopy
DOI: 10.5281/zenodo.10672824
title: IODP Expedition 393 Laser height profile (section half)

description: Height profile data were measured on the Section Half Multisensor Logger (SHMSL) by a rangefinding laser and recorded in uncorrected height units in millimeters in CSV files.
DOI: 10.5281/zenodo.10672825
title: IODP Expedition 393 Laser height profile (section half)

description: Height profile data were measured on the Section Half Multisensor Logger (SHMSL) by a rangefinding laser and recorded in uncorrected height units in millimeters in CSV files.
DOI: 10.6084/m9.figshare.11888436
title: Additional file 3 of Metabolic alterations provide insights into Stylosanthes roots responding to phosphorus deficiency

description: Additional file 3: Table S2 General information of identified metabolites from metabolomic analysis in stylo roots.
DOI: 10.6084/m9.figshare.11888436.v1
title: Additional file 3 of Metabolic alterations provide insights into Stylosanthes roots responding to phosphorus deficiency

description: Additional file 3: Table S2 General information of identified metabolites from metabolomic analysis in stylo roots.
DOI: 10.6084/m9.figshare.11888445
title: Additional file 4 of Metabolic alterations provide insights into Stylosanthes roots responding to phosphorus deficiency

description: Additional file 4: Table S3 General information about differentially accumulated metabolites (DAMs) from metabolomic analysis in stylo roots.
DOI: 10.6084/m9.figshare.11888445.v1
title: Additional file 4 of Metabolic alterations provide insights into Stylosanthes roots responding to phosphorus deficiency

description: Additional file 4: Table S3 General information about differentially accumulated metabolites (DAMs) from metabolomic analysis in stylo roots.
DOI: 10.6084/m9.figshare.16606968.v1
title: Additional file 4 of A near complete genome for goat genetic and genomic research

description: Additional file 4: Table S12. Gene annotation of identified structural variations between Saanen_v1 and ARS1. The structural variations between Saanen_v1 and ARS1 were annotated using ANNOVAR.
DOI: 10.6084/m9.figshare.16606968
title: Additional file 4 of A near complete genome for goat genetic and genomic research

description: Additional file 4: Table S12. Gene annotation of identified structural variations between Saanen_v1 and ARS1. The structural variations between Saanen_v1 and ARS1 were annotated using ANNOVAR.
DOI: 10.6084/m9.figshare.16606971
title: Additional file 5 of A near complete genome for goat genetic and genomic research

description: Additional file 5: Table S14. List of probes showing SNP positional discrepancy. The data listed the probes that showed SNP positional discrepancy in Saanen_v1 as compared with ARS1.
DOI: 10.6084/m9.figshare.16606977
title: Additional file 6 of A near complete genome for goat genetic and genomic research

description: Additional file 6: Table S16. Y chromosome-linked scaffolds in ARS1 that we suggest to be replaced by our Y chromosome scaffold from Saanen_v1. The Y chromosome-linked scaffolds in ARS1 were listed which could be replaced by our new Y chromosome scaffold from Saanen_v1 to facilitate downstream analysis.
DOI: 10.6084/m9.figshare.16606971.v1
title: Additional file 5 of A near complete genome for goat genetic and genomic research

description: Additional file 5: Table S14. List of probes showing SNP positional discrepancy. The data listed the probes that showed SNP positional discrepancy in Saanen_v1 as compared with ARS1.
DOI: 10.6084/m9.figshare.16606977.v1
title: Additional file 6 of A near complete genome for goat genetic and genomic research

description: Additional file 6: Table S16. Y chromosome-linked scaffolds in ARS1 that we suggest to be replaced by our Y chromosome scaffold from Saanen_v1. The Y chromosome-linked scaffolds in ARS1 were listed which could be replaced by our new Y chromosome scaffold from Saanen_v1 to facilitate downstream analysis.
DOI: 10.13020/ksry-8x96
title: Data supporting "Single-cell detection of copy number changes reveals dynamic mechanisms of adaptation to antifungals in vitro and in vivo"

description: Genomic copy number changes are associated with antifungal drug resistance and virulence across diverse fungal pathogens. Despite the high prevalence of both gain and loss events, the rate and dynamics of these genomic changes in the presence of antifungal drugs is not known for any organism. We optimized a dual-fluorescent reporter system in the diploid pathogen Candida albicans to quantify copy number variation (CNV) and loss of heterozygosity (LOH) at the single cell level with flow cytometry. We followed the rate and dynamics of CNV and LOH at two distinct genomic locations during parallel evolution experiments in the presence and absence of antifungal drugs in vitro and in a murine model of infection. Copy number changes were rapid and dynamic during adaptation to three different concentrations of the azole drug fluconazole. The fluorescent reporters revealed competing sub-populations with distinct genotypes in the drug-evolved lineages. Extensive whole genome sequencing identified recurrent genotypes that cause increased competitive fitness in the presence of antifungal drug. Specifically, at low concentrations of drug, chromosome 3 (Chr3) LOH frequently arose and led to significantly increased competitive fitness. In contrast, at high drug concentrations, Chr3 and Chr6 aneuploidy arose together, and these concurrent aneuploidies conferred multi-azole tolerance. In the murine model, copy number changes were only detected in isolates recovered from mice treated with fluconazole, and included whole-genome duplication events resulting in polyploidy. This study provides the first quantitative evidence for the incredible speed at which diverse genotypes arise and undergo dynamic population-level fluctuations during adaptation to antifungal drugs in vitro and in vivo. â€ƒ
description: Most of data are flow cytometry data with file format .fcs and supplemented with a readme file (.pdf) providing the sample name and layout. There are also some yeast growth curve data with file format .xlsx
DOI: 10.6084/m9.figshare.11888460
title: Additional file 1 of Cell-free DNA analysis reveals POLR1D-mediated resistance to bevacizumab in colorectal cancer

description: Additional file 1. Age spectrum and sex distribution of the CRC cohort used in this study.
DOI: 10.6084/m9.figshare.11888460.v1
title: Additional file 1 of Cell-free DNA analysis reveals POLR1D-mediated resistance to bevacizumab in colorectal cancer

description: Additional file 1. Age spectrum and sex distribution of the CRC cohort used in this study.
DOI: 10.5281/zenodo.10672823
title: IODP Expedition 393 Piece log

description: Dataset includes length data for every whole-round piece: bin length, whole-round piece length (measured by curation staff), and both the archive- and working-half piece lengths (optionally measured by scientists).
DOI: 10.6084/m9.figshare.16607049
title: Additional file 1 of Predictive value of qSOFA score for death in emergency department resuscitation room among adult trauma patients:a retrospective study

description: Additional file 1.
DOI: 10.6084/m9.figshare.16607049.v1
title: Additional file 1 of Predictive value of qSOFA score for death in emergency department resuscitation room among adult trauma patients:a retrospective study

description: Additional file 1.