cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.22600231.v1
title: Additional file 2 of Single-gene FISH maps and major chromosomal rearrangements in Elymus sibiricus and E. nutans

description: Additional file 2: Table S1. The information of single-gene probes. Table S2. Localization of single-gene probes by FISH on chromosomes of H. bogdanii. Table S3. Localization of single-gene probes by FISH on chromosomes in material DY of E. sibiricus. Table S4. Localization of single probes by FISH on chromosomes in material PJC of E. nutans.
DOI: 10.6084/m9.figshare.22602572.v1
title: Additional file 6 of Comparative genomic analysis of Citrobacter sp. XT1-2-2 reveals insights into the molecular mechanism of microbial immobilization of heavy metals

description: Additional file 6: Supplementary Table S6. all the genes on the genomic islands of Citrobacter sp. XT1-2-2.
DOI: 10.6084/m9.figshare.22602578.v1
title: Additional file 8 of Comparative genomic analysis of Citrobacter sp. XT1-2-2 reveals insights into the molecular mechanism of microbial immobilization of heavy metals

description: Additional file 8: Supplementary Table S8. The core genes in gene category of Citrobacter sp. XT1-2-2.
DOI: 10.6084/m9.figshare.22602587.v1
title: Additional file 10 of Comparative genomic analysis of Citrobacter sp. XT1-2-2 reveals insights into the molecular mechanism of microbial immobilization of heavy metals

description: Additional file 10: Supplementary Table S10. The accessory genes in gene category of Citrobacter sp. XT1-2-2.
DOI: 10.6084/m9.figshare.22600277.v1
title: Additional file 5 of Integrated transcriptome and proteome revealed that the declined expression of cell cycle-related genes associated with follicular atresia in geese

description: Additional file 5: Table S2. Summary of Transcripts and Unigene.
DOI: 10.6084/m9.figshare.22600277
title: Additional file 5 of Integrated transcriptome and proteome revealed that the declined expression of cell cycle-related genes associated with follicular atresia in geese

description: Additional file 5: Table S2. Summary of Transcripts and Unigene.
DOI: 10.6084/m9.figshare.22602530
title: Additional file 2 of Combining a machine-learning derived 4-lncRNA signature with AFP and TNM stages in predicting early recurrence of hepatocellular carcinoma

description: Additional file 2. Table S1. Clinical characteristic of 314 TCGA-LIHC patients. Table S2. Differentially expressed lncRNAs associated with DFS. Table S3. Primers used in RT qPCR. Table S4. Drugs respond differently in the low- and high-risk group HCC patients. Table S5. Clinical characteristic of 24 HCC patients from Jinling cohort.
DOI: 10.6084/m9.figshare.5829639
title: PLEMT: A Novel Pseudolikelihood-Based EM Test for Homogeneity in Generalized Exponential Tilt Mixture Models

description: Motivated by analyses of DNA methylation data, we propose a semiparametric mixture model, namely, the generalized exponential tilt mixture model, to account for heterogeneity between differentially methylated and nondifferentially methylated subjects in the cancer group, and capture the differences in higher order moments (e.g., mean and variance) between subjects in cancer and normal groups. A pairwise pseudolikelihood is constructed to eliminate the unknown nuisance function. To circumvent boundary and nonidentifiability problems as in parametric mixture models, we modify the pseudolikelihood by adding a penalty function. In addition, the test with simple asymptotic distribution has computational advantages compared with permutation-based test for high-dimensional genetic or epigenetic data. We propose a pseudolikelihood-based expectation–maximization test, and show the proposed test follows a simple chi-squared limiting distribution. Simulation studies show that the proposed test controls Type I errors well and has better power compared to several current tests. In particular, the proposed test outperforms the commonly used tests under all simulation settings considered, especially when there are variance differences between two groups. The proposed test is applied to a real dataset to identify differentially methylated sites between ovarian cancer subjects and normal subjects. Supplementary materials for this article are available online.
DOI: 10.4121/f2aa4e23-3779-4b80-9fb5-c97a82f73633.v2
title: Analysis output from: Potential of boreholes combined with deep-rooted cover crops to ameliorate subsoil compaction

description: Due to climate change longer periods of drought and high precipitation in short periods of time will become more common. Subsoil compaction causes cropland to be less resilient to such changes due to worse root growth, water infiltration and less capillary rise of water. There is a lack of measures to ameliorate subsoil compaction. Two experiments were performed where the potential of different types of boreholes were compared to deep subsoiling and an untreated reference. Effects on soil structure and crop productivity were analyzed. Data and scripts are not provided, only HTML output files.
DOI: 10.6084/m9.figshare.22606915
title: Oxygen isotope data of Changjiang Estuary sediment oxygen consumption

description: This dataset are oxygen isotope compositions and the fractionation factors associated with sediment oxygen consumption. We carried out dark incubations using sediments from the Changjiang Estuary and measured the oxygen isotope variations during the course of respiration. The dataset includes: (1) Table 1, isotopic and O2 concentration data during incubations; (2) Table 2, total organic carbon content, respiration rate and oxygen isotopic fractionation factor during sediment oxygen consumption. (3) Model data based on a two-layer model proposed in Brandes and Devol (1997).
DOI: 10.6084/m9.figshare.22602688
title: Additional file 3 of Clinical and radiographic outcomes of stand-alone oblique lateral interbody fusion in the treatment of adult degenerative scoliosis: a retrospective observational study

description: Additional file 3.
DOI: 10.6084/m9.figshare.22602793.v1
title: Additional file 1 of Gallbladder disease is associated with the risk of cardiovascular disease among Uyghurs in Xinjiang: a prospective cohort study

description: Additional file 1: Supplementary Table S1. Overall baseline characteristics of the studypopulation for the GBD subgroup. Supplementary Table S1.  should appear in the 4.1 Baseline characteristics section of thearticle. Supplementary Figure S1. Forest plot of the results of the multi-factor Cox regression analysis for CVD. Supplementary Figure S2. Kaplan–Meier estimates for cumulative CVDincidence based on the presence of GBD, hypertension, T2DM, dyslipidaemia, overweight, abdominal obesity.
DOI: 10.6084/m9.figshare.14738351
title: Additional file 2 of 2-kupl: mapping-free variant detection from DNA-seq data of matched samples

description: Additional file 2: Table S1. This supplementary table includes recurrent SNVs, SVs and mutated genes identified by 2-kupl.
DOI: 10.6084/m9.figshare.14738363
title: Additional file 6 of 2-kupl: mapping-free variant detection from DNA-seq data of matched samples

description: Additional file 6: Table S5. 2-kupl detected structural variants that are missed by Delly.
DOI: 10.5517/ccdc.csd.cc2fy8b0
title: CCDC 2262452: Experimental Crystal Structure Determination

description: Related Article: Jatinder Singh, Richard Staples, Jean'ne Shreeve|2023|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.6084/m9.figshare.14738354.v1
title: Additional file 3 of 2-kupl: mapping-free variant detection from DNA-seq data of matched samples

description: Additional file 3: Table S2. Comparison with the Fraser et al's recurrent PRAD mutations.
DOI: 10.6084/m9.figshare.14738354
title: Additional file 3 of 2-kupl: mapping-free variant detection from DNA-seq data of matched samples

description: Additional file 3: Table S2. Comparison with the Fraser et al's recurrent PRAD mutations.
DOI: 10.6084/m9.figshare.14738357.v1
title: Additional file 4 of 2-kupl: mapping-free variant detection from DNA-seq data of matched samples

description: Additional file 4: Table S3. Prostate cancer related genes collected from various resources.
DOI: 10.6084/m9.figshare.14738363.v1
title: Additional file 6 of 2-kupl: mapping-free variant detection from DNA-seq data of matched samples

description: Additional file 6: Table S5. 2-kupl detected structural variants that are missed by Delly.
DOI: 10.6084/m9.figshare.14738357
title: Additional file 4 of 2-kupl: mapping-free variant detection from DNA-seq data of matched samples

description: Additional file 4: Table S3. Prostate cancer related genes collected from various resources.
DOI: 10.6084/m9.figshare.6874130
title: MOESM3 of Engineered global regulator H-NS improves the acid tolerance of E. coli

description: Additional file 3: Table S2. Genes differently expressed at transcriptional level between strain 3-36 and wild type strain MG.
DOI: 10.6084/m9.figshare.22602688.v1
title: Additional file 3 of Clinical and radiographic outcomes of stand-alone oblique lateral interbody fusion in the treatment of adult degenerative scoliosis: a retrospective observational study

description: Additional file 3.
DOI: 10.6084/m9.figshare.14738351.v1
title: Additional file 2 of 2-kupl: mapping-free variant detection from DNA-seq data of matched samples

description: Additional file 2: Table S1. This supplementary table includes recurrent SNVs, SVs and mutated genes identified by 2-kupl.
DOI: 10.6084/m9.figshare.14738360
title: Additional file 5 of 2-kupl: mapping-free variant detection from DNA-seq data of matched samples

description: Additional file 5: Table S4. True positive variants in the bacterial WGS data.
DOI: 10.6084/m9.figshare.22600261.v1
title: Additional file 1 of Clinical characteristics and outcomes of gastrointestinal stromal tumor patients receiving surgery with or without TKI therapy: a retrospective real-world study

description: Additional file file 1: Supplement file 1.
DOI: 10.6084/m9.figshare.6874145
title: Additional file 2: of Transcriptomic analysis identifies the key genes involved in stamen petaloid in lotus (Nelumbo nucifera)

description: 3900 DEGs. (XLSX 749 kb)
DOI: 10.6084/m9.figshare.14738360.v1
title: Additional file 5 of 2-kupl: mapping-free variant detection from DNA-seq data of matched samples

description: Additional file 5: Table S4. True positive variants in the bacterial WGS data.
DOI: 10.6084/m9.figshare.6874160
title: Additional file 3: of Transcriptomic analysis identifies the key genes involved in stamen petaloid in lotus (Nelumbo nucifera)

description: Hormone related genes. (XLSX 65 kb)
DOI: 10.6084/m9.figshare.6874187.v1
title: Additional file 5: of Transcriptomic analysis identifies the key genes involved in stamen petaloid in lotus (Nelumbo nucifera)

description: 225 TFs. (XLSX 77 kb)
DOI: 10.6084/m9.figshare.6874169.v1
title: Additional file 4: of Transcriptomic analysis identifies the key genes involved in stamen petaloid in lotus (Nelumbo nucifera)

description: Floral organ homeotic genes. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.6874160.v1
title: Additional file 3: of Transcriptomic analysis identifies the key genes involved in stamen petaloid in lotus (Nelumbo nucifera)

description: Hormone related genes. (XLSX 65 kb)
DOI: 10.6084/m9.figshare.6874187
title: Additional file 5: of Transcriptomic analysis identifies the key genes involved in stamen petaloid in lotus (Nelumbo nucifera)

description: 225 TFs. (XLSX 77 kb)
DOI: 10.6084/m9.figshare.22602793
title: Additional file 1 of Gallbladder disease is associated with the risk of cardiovascular disease among Uyghurs in Xinjiang: a prospective cohort study

description: Additional file 1: Supplementary Table S1. Overall baseline characteristics of the studypopulation for the GBD subgroup. Supplementary Table S1.  should appear in the 4.1 Baseline characteristics section of thearticle. Supplementary Figure S1. Forest plot of the results of the multi-factor Cox regression analysis for CVD. Supplementary Figure S2. Kaplan–Meier estimates for cumulative CVDincidence based on the presence of GBD, hypertension, T2DM, dyslipidaemia, overweight, abdominal obesity.
DOI: 10.6084/m9.figshare.6874130.v1
title: MOESM3 of Engineered global regulator H-NS improves the acid tolerance of E. coli

description: Additional file 3: Table S2. Genes differently expressed at transcriptional level between strain 3-36 and wild type strain MG.
DOI: 10.6084/m9.figshare.6874169
title: Additional file 4: of Transcriptomic analysis identifies the key genes involved in stamen petaloid in lotus (Nelumbo nucifera)

description: Floral organ homeotic genes. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.22602670
title: Additional file 5 of Nontargeted metabolomics reveals the potential mechanism underlying the association between birthweight and metabolic disturbances

description: Additional file 5: Table S4. Metabolites and pathway information.
DOI: 10.6084/m9.figshare.22600283
title: Additional file 7 of Integrated transcriptome and proteome revealed that the declined expression of cell cycle-related genes associated with follicular atresia in geese

description: Additional file 7: Table S4. The FPKM value of all genes in the goose follicles.
DOI: 10.25625/7ftdh7/gg3sll
title: Daten_hochladen.png

description: :unav
DOI: 10.6084/m9.figshare.14211672
title: Additional file 2 of Unveiling the long non-coding RNA profile of porcine reproductive and respiratory syndrome virus-infected porcine alveolar macrophages

description: Additional file 2.
DOI: 10.6084/m9.figshare.25163639
title: Supplementary Material for: Severe Colitis in 2 Patients with Melanoma Treated with BRAF/MEK Inhibitors: Case Report and Literature Review

description: <b><i>Introduction:</i></b> Encorafenib and binimetinib, a combination of BRAF and MEK inhibitors, is a standard of care for patients with advanced BRAFV600-mutant melanoma. This combination is known to have gastrointestinal side effects, most of which are mild and managed symptomatically. However, very few studies have reported severe colitis. <b><i>Case Presentation:</i></b> We report here 2 patients with advanced melanoma who developed severe ulcerated right colitis manifested by diarrhea and hematochezia while being treated with encorafenib and binimetinib after immune checkpoint therapy. <b><i>Conclusion:</i></b> This rare but serious adverse event was not described in early phase 3 trials but has emerged in recent years, particularly with the sequential use of immune checkpoint inhibitors followed by BRAF/MEK inhibitors. In a comprehensive review of the existing literature, we identified 20 cases of severe colitis due to BRAF/MEK inhibitors. Clinical, endoscopic, and histological features are described to provide insight into the current understanding of this poorly understood clinical entity.
DOI: 10.6084/m9.figshare.25163639.v1
title: Supplementary Material for: Severe Colitis in 2 Patients with Melanoma Treated with BRAF/MEK Inhibitors: Case Report and Literature Review

description: <b><i>Introduction:</i></b> Encorafenib and binimetinib, a combination of BRAF and MEK inhibitors, is a standard of care for patients with advanced BRAFV600-mutant melanoma. This combination is known to have gastrointestinal side effects, most of which are mild and managed symptomatically. However, very few studies have reported severe colitis. <b><i>Case Presentation:</i></b> We report here 2 patients with advanced melanoma who developed severe ulcerated right colitis manifested by diarrhea and hematochezia while being treated with encorafenib and binimetinib after immune checkpoint therapy. <b><i>Conclusion:</i></b> This rare but serious adverse event was not described in early phase 3 trials but has emerged in recent years, particularly with the sequential use of immune checkpoint inhibitors followed by BRAF/MEK inhibitors. In a comprehensive review of the existing literature, we identified 20 cases of severe colitis due to BRAF/MEK inhibitors. Clinical, endoscopic, and histological features are described to provide insight into the current understanding of this poorly understood clinical entity.
DOI: 10.6084/m9.figshare.22602719
title: Additional file 3 of Clustering pattern and evolution characteristic of microRNAs in grass carp (Ctenopharyngodon idella)

description: Additional file 3: Table S1. miRNA location in the grass carp genome. Table S2. The miRNA family of twelve species analyzed. Table S3. miRNA clusters in the grass carp genome. Table S4. Expression correlation between miRNA duplication of grass crap. Table S5. MiRNA evolution rate. Table S6. The colinearity blocks of protein between grass carp and zebrafish. Table S7. The colinearity blocks of miRNA between grass carp and zebrafish. Table S8. Tissue-specific miRNAs in the grass carp. Table S9. Expression correlation between neighbouring miRNAs of grass carp. Table S10. Expression level of grass carp miRNAs with different genomic context. Table S11. The predicted common miRNA/target pairs.
DOI: 10.6084/m9.figshare.25163627.v1
title: Raw LCMJ20 Force-Time Data

description: Raw Force-time data for Loaded counter-movement jumps
DOI: 10.6084/m9.figshare.25163627
title: Raw LCMJ20 Force-Time Data

description: Raw Force-time data for Loaded counter-movement jumps
DOI: 10.6084/m9.figshare.22600280
title: Additional file 6 of Integrated transcriptome and proteome revealed that the declined expression of cell cycle-related genes associated with follicular atresia in geese

description: Additional file 6: Table S3. Summary of the functional annotation of assembled unigenes.
DOI: 10.6084/m9.figshare.14738544
title: Additional file 1 of Prevalence of self-medication with antibiotics and its related factors among Chinese residents: a cross-sectional study

description: Additional file 1: Appendix S1 for the statistical analysis process.
DOI: 10.6084/m9.figshare.14738544.v1
title: Additional file 1 of Prevalence of self-medication with antibiotics and its related factors among Chinese residents: a cross-sectional study

description: Additional file 1: Appendix S1 for the statistical analysis process.
DOI: 10.6084/m9.figshare.22600274
title: Additional file 4 of Integrated transcriptome and proteome revealed that the declined expression of cell cycle-related genes associated with follicular atresia in geese

description: Additional file 4: Table S1. Summary of transcriptome sequencing quality.
DOI: 10.6084/m9.figshare.22602853
title: Additional file 1 of Identification of candidate genes and pathways associated with juvenile idiopathic arthritis by integrative transcriptome-wide association studies and mRNA expression profiles

description: Additional file 1:. TWAS results.
DOI: 10.6084/m9.figshare.22602856.v1
title: Additional file 2 of Identification of candidate genes and pathways associated with juvenile idiopathic arthritis by integrative transcriptome-wide association studies and mRNA expression profiles

description: Additional file 2:. mRNA results.
DOI: 10.6084/m9.figshare.22602859.v1
title: Additional file 3 of Identification of candidate genes and pathways associated with juvenile idiopathic arthritis by integrative transcriptome-wide association studies and mRNA expression profiles

description: Additional file 3:. CGSEA results.
DOI: 10.15156/bio/sh143282.07fu
title: SH143282.07FU

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/sh143283.07fu
title: SH143283.07FU

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/sh143284.07fu
title: SH143284.07FU

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/sh143285.07fu
title: SH143285.07FU

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.