cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7040177
title: Discovery of a small molecule targeting autophagy via ATG4B inhibition and cell death of colorectal cancer cells in vitro and in vivo

description: Human Atg4 homologs are cysteine proteases, which play key roles in the macroautophagy/autophagy process by cleaving Atg8 homologs for conjugation to lipid membranes and for deconjugation of Atg8 homologs from membranes. Expression of ATG4B is significantly increased in colorectal cancer cells compared to normal cells, suggesting that ATG4B may be important for cancer biology. Inhibition of ATG4B may reduce the autophagy activity, thereby sensitizing cancer cells to therapeutic agents. Thus, developing specific and potent ATG4B inhibitors for research as well as for potential therapeutic uses is highly needed. In this study, we integrated <i>in silico</i> screening and <i>in vitro</i> assays to discover a potent ATG4B inhibitor, named S130, from a noncommercial library. This chemical binds to ATG4B with strong affinity and specifically suppresses the activity of ATG4B but not other proteases. S130 did not cause the impairment of autophagosome fusion, nor did it result in the dysfunction of lysosomes. Instead, S130 might attenuate the delipidation of LC3-II on the autolysosomes to suppress the recycling of LC3-I, which normally occurs after LC3-II cleavage by ATG4B. Intriguingly, S130 induced cell death, which was accompanied with autophagy stress and could be further exacerbated by nutrient deprivation. Such cytotoxicity could be partially reversed by enhancing ATG4B activity. Finally, we found that S130 was distributed in tumor tissues in vivo and was also effective in arresting the growth of colorectal cancer cells. Thus, this study indicates that ATG4B is a potential anticancer target and S130 might be a novel small-molecule candidate for future cancer therapy.
DOI: 10.6084/m9.figshare.12291245
title: R code for Leaf senescence exhibits stronger climatic responses during warm than during cold autumns

description: A warmer
world could extend growing seasons for plants. Changes in spring phenology have
been studied, yet autumn phenology remains poorly understood. Using &gt;500,000
phenological records of four temperate tree species between 1951 and 2013 in
Europe, we show that leaf senescence in warm autumns exhibits significantly
stronger climate responses, with a higher phenological plasticity, than in cold autumns, indicating a nonlinear response to climate. The
onset of leaf senescence in warm autumns was delayed due to the stronger
climate response, primarily caused by
nighttime warming. However, daytime warming, especially during warm autumns, imposes a drought stress which
advances leaf senescence. This may
counteract the extension of growing season under global warming. These findings provide guidance for more reliable predictions of
plant phenology and biosphere-atmosphere feedbacks in the context of global
warming.
DOI: 10.6084/m9.figshare.7564556
title: Additional file 2: of Plasma acylcarnitines could predict prognosis and evaluate treatment of IgA nephropathy

description: Table S2. Predict models. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.7564154
title: Additional file 6: of Systematic evaluation of C. elegans lincRNAs with CRISPR knockout mutants

description: Table S4. LincRNA-microRNA interactions. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.7564154.v1
title: Additional file 6: of Systematic evaluation of C. elegans lincRNAs with CRISPR knockout mutants

description: Table S4. LincRNA-microRNA interactions. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.7564166
title: Additional file 8: of Systematic evaluation of C. elegans lincRNAs with CRISPR knockout mutants

description: Table S5. Data for the rescue experiments. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.7564166.v1
title: Additional file 8: of Systematic evaluation of C. elegans lincRNAs with CRISPR knockout mutants

description: Table S5. Data for the rescue experiments. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.7564553
title: Additional file 1: of Plasma acylcarnitines could predict prognosis and evaluate treatment of IgA nephropathy

description: Table S1. Characteristics of the Baseline Plasma Acylcarnitines. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.7040177.v1
title: Discovery of a small molecule targeting autophagy via ATG4B inhibition and cell death of colorectal cancer cells in vitro and in vivo

description: Human Atg4 homologs are cysteine proteases, which play key roles in the macroautophagy/autophagy process by cleaving Atg8 homologs for conjugation to lipid membranes and for deconjugation of Atg8 homologs from membranes. Expression of ATG4B is significantly increased in colorectal cancer cells compared to normal cells, suggesting that ATG4B may be important for cancer biology. Inhibition of ATG4B may reduce the autophagy activity, thereby sensitizing cancer cells to therapeutic agents. Thus, developing specific and potent ATG4B inhibitors for research as well as for potential therapeutic uses is highly needed. In this study, we integrated <i>in silico</i> screening and <i>in vitro</i> assays to discover a potent ATG4B inhibitor, named S130, from a noncommercial library. This chemical binds to ATG4B with strong affinity and specifically suppresses the activity of ATG4B but not other proteases. S130 did not cause the impairment of autophagosome fusion, nor did it result in the dysfunction of lysosomes. Instead, S130 might attenuate the delipidation of LC3-II on the autolysosomes to suppress the recycling of LC3-I, which normally occurs after LC3-II cleavage by ATG4B. Intriguingly, S130 induced cell death, which was accompanied with autophagy stress and could be further exacerbated by nutrient deprivation. Such cytotoxicity could be partially reversed by enhancing ATG4B activity. Finally, we found that S130 was distributed in tumor tissues in vivo and was also effective in arresting the growth of colorectal cancer cells. Thus, this study indicates that ATG4B is a potential anticancer target and S130 might be a novel small-molecule candidate for future cancer therapy.
DOI: 10.6084/m9.figshare.20147038.v1
title: Additional file 13 of circEXOC6B interacting with RRAGB, an mTORC1 activator, inhibits the progression of colorectal cancer by antagonizing the HIF1A-RRAGB-mTORC1 positive feedback loop

description: Additional file 13: Supplementary Table S4. Proteins might bind to circEXOC6B were identified by mass spectrometry (MS).
DOI: 10.6084/m9.figshare.11758965.v1
title: Additional file 20 of De novo transcriptome assembly for the five major organs of Zanthoxylum armatum and the identification of genes involved in terpenoid compound and fatty acid metabolism

description: Additional file 20: Table S10. The primers of qRT-PCR used for validation of expression trend in Zanthoxylum armatum.
DOI: 10.6084/m9.figshare.11758971.v1
title: Additional file 2 of De novo transcriptome assembly for the five major organs of Zanthoxylum armatum and the identification of genes involved in terpenoid compound and fatty acid metabolism

description: Additional file 2: Table S2. Overview of the sequencing data of Zanthoxylum armatum transcriptome.
DOI: 10.6084/m9.figshare.11758980
title: Additional file 4 of De novo transcriptome assembly for the five major organs of Zanthoxylum armatum and the identification of genes involved in terpenoid compound and fatty acid metabolism

description: Additional file 4: Table S3. The summary of SSR in the total of unigenes.
DOI: 10.6084/m9.figshare.7564556.v1
title: Additional file 2: of Plasma acylcarnitines could predict prognosis and evaluate treatment of IgA nephropathy

description: Table S2. Predict models. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.11758902
title: Additional file 1 of A comparison of curated gene sets versus transcriptomics-derived gene signatures for detecting pathway activation in immune cells

description: Additional file 1 All Evaluation Results Description: Contains the results for all combinations of signatures, target data sets, and alternative statistical methods. Each sheet represents a statistical method. Each row contains a signature, a target and a series of values that are specific to each of the different approaches.
DOI: 10.6084/m9.figshare.11759001.v1
title: Additional file 8 of De novo transcriptome assembly for the five major organs of Zanthoxylum armatum and the identification of genes involved in terpenoid compound and fatty acid metabolism

description: Additional file 8: Table S4. KEGG annotation of nonredundant unigenes in Zanthoxylum armatum.
DOI: 10.6084/m9.figshare.11758911.v1
title: Additional file 3 of A comparison of curated gene sets versus transcriptomics-derived gene signatures for detecting pathway activation in immune cells

description: Additional file 3 Common Signature Genes and Enrichment Results Description: These are the PANTHER GO analysis results for the set of genes found to be in common among all data-derived signatures.
DOI: 10.6084/m9.figshare.11758908.v1
title: Additional file 13 of De novo transcriptome assembly for the five major organs of Zanthoxylum armatum and the identification of genes involved in terpenoid compound and fatty acid metabolism

description: Additional file 13: Table S5. The significant pathways of KEGG enrichment related to organ-specific unigenes in Zanthoxylum armatum.
DOI: 10.6084/m9.figshare.11759052
title: Additional file 3 of Choice of library size normalization and statistical methods for differential gene expression analysis in balanced two-group comparisons for RNA-seq studies

description: Additional file 3. R code for the analysis.
DOI: 10.6084/m9.figshare.11758944
title: Additional file 18 of De novo transcriptome assembly for the five major organs of Zanthoxylum armatum and the identification of genes involved in terpenoid compound and fatty acid metabolism

description: Additional file 18: Table S9. The RNA-seq data of the DEGs selected for qRT-PCR validation.
DOI: 10.6084/m9.figshare.7564553.v1
title: Additional file 1: of Plasma acylcarnitines could predict prognosis and evaluate treatment of IgA nephropathy

description: Table S1. Characteristics of the Baseline Plasma Acylcarnitines. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.23812662
title: Additional file 4 of Identification of a novel immune-related transcriptional regulatory network in sarcopenia

description: Additional file 4. Results of ORA.
DOI: 10.6084/m9.figshare.23812677
title: Additional file 8 of Identification of a novel immune-related transcriptional regulatory network in sarcopenia

description: Additional file 8. Results of co-analysis.
DOI: 10.34740/kaggle/dsv/7623873
title: Global Genomic Neurofibromatosis Neoplasia
DOI: 10.15161/oar.it/143144
title: Spectral micro-CT of osteochondral samples with iodine cationic contrast agent : Dataset

description: Tomographic data described and analyzed in the article concerning spectral micro-CT of osteochondral samples with iodine cationic contrast agent, submitted to EPJ Plus.

The folder "spectral_microCT" contains the reconstructed tomography slices obtained with the spectral system. Two sets of data are included:

1) the slices reconstructed from the acquisition below the energy threshold set to 33 keV (files marked with "low_")

2) the slices reconstructed from the acquisition above threshold (files marked with "high_") .

 

The folder "conventional_microCT" contains the reconstruction obtained with the commercial scanner with no spectral capabilities. The two datasets are spatially coregistered.
DOI: 10.15161/oar.it/143143
title: Spectral micro-CT of osteochondral samples with iodine cationic contrast agent : Dataset

description: Tomographic data described and analyzed in the article concerning spectral micro-CT of osteochondral samples with iodine cationic contrast agent, submitted to EPJ Plus.

The folder "spectral_microCT" contains the reconstructed tomography slices obtained with the spectral system. Two sets of data are included:

1) the slices reconstructed from the acquisition below the energy threshold set to 33 keV (files marked with "low_")

2) the slices reconstructed from the acquisition above threshold (files marked with "high_") .

 

The folder "conventional_microCT" contains the reconstruction obtained with the commercial scanner with no spectral capabilities. The two datasets are spatially coregistered.
DOI: 10.6084/m9.figshare.23812683
title: Additional file 10 of Identification of a novel immune-related transcriptional regulatory network in sarcopenia

description: Additional file 10. Clinical characterization of patients.
DOI: 10.6084/m9.figshare.19623483.v1
title: Structure and features of the complete chloroplast genome of <i>Salix triandroides</i> (Salicaceae)

description: <i>Salix triandroides</i> W. P. Fang, an indigenous small willow with high potential for heavy-metal soil remediation and levee protection, has been used for wetland ecological restoration for decades. However, studies on the evolution and genetic breeding of <i>S. triandoides</i> have been hindered by the lack of its genetic information. Here, we present the complete chloroplast genome of <i>S. triandroides,</i> which was assembled from Illumina sequencing data. The chloroplast genome of this species is circular, 155,683 bp in length and includes two inverted repeat regions (IRs) (27,490 bp) separated by a large single-copy (LSC) region (84,463 bp) and a small single-copy (SSC) region (16,240 bp). A total of 126 unique genes were identified, including 81 protein-coding genes, 37 tRNA genes and eight rRNA genes. Comparative analysis identified some hypervariable regions, with potential to be used as specific DNA barcodes or candidate markers for phylogenetic studies. Based on the sequences of the protein-coding genes, the phylogenetic analysis assigned 32 <i>Salix</i> species into two major clades and revealed that <i>S. triandoides</i> was a sister taxon to <i>S. triandra</i>. Our results provide a foundation for further molecular breeding of <i>S. triandroides</i> and insights into the evolution of <i>Salix</i>. Supplemental data for this article is available online at https://doi.org/10.1080/13102818.2021.2023326 .
DOI: 10.6084/m9.figshare.13331987.v1
title: Additional file 4 of Comparative analysis of COVID-19 guidelines from six countries: a qualitative study on the US, China, South Korea, the UK, Brazil, and Haiti

description: Additional file 4. Confirmed and Deaths Data.
DOI: 10.6084/m9.figshare.11758902.v1
title: Additional file 1 of A comparison of curated gene sets versus transcriptomics-derived gene signatures for detecting pathway activation in immune cells

description: Additional file 1 All Evaluation Results Description: Contains the results for all combinations of signatures, target data sets, and alternative statistical methods. Each sheet represents a statistical method. Each row contains a signature, a target and a series of values that are specific to each of the different approaches.
DOI: 10.6084/m9.figshare.11758908
title: Additional file 13 of De novo transcriptome assembly for the five major organs of Zanthoxylum armatum and the identification of genes involved in terpenoid compound and fatty acid metabolism

description: Additional file 13: Table S5. The significant pathways of KEGG enrichment related to organ-specific unigenes in Zanthoxylum armatum.
DOI: 10.6084/m9.figshare.11758920.v1
title: Additional file 15 of De novo transcriptome assembly for the five major organs of Zanthoxylum armatum and the identification of genes involved in terpenoid compound and fatty acid metabolism

description: Additional file 15: Table S7. The FPKM of the unigenes detected in the significant KEGG enrichment pathways of only up-regulation in fruit samples of Zanthoxylum armatum.
DOI: 10.5281/zenodo.10656777
title: GOSI9 with local ME GVC in the Nordic OVF region - model geometry ancillary files

description: This dataset includes the ancillary files describing the model geometry of the Met Office GOSI9 configuration at 1/4 of degree of resolution and employing local multi-envelope (ME) general vertical coordinates (GVC) in the Nordic overflows (OVF) region as described in Bruciaferri et al. 2024 (accepted for publication in JAMES, an early pre-print can be found at https://doi.org/10.22541/essoar.168771422.22225431/v1).

This configuration is currently being tested - see e.g.  https://github.com/JMMP-Group/GO_coordination/issues/15
DOI: 10.5281/zenodo.10656778
title: GOSI9 with local ME GVC in the Nordic OVF region - model geometry ancillary files

description: This dataset includes the ancillary files describing the model geometry of the Met Office GOSI9 configuration at 1/4 of degree of resolution and employing local multi-envelope (ME) general vertical coordinates (GVC) in the Nordic overflows (OVF) region as described in Bruciaferri et al. 2024 (accepted for publication in JAMES, an early pre-print can be found at https://doi.org/10.22541/essoar.168771422.22225431/v1).

This configuration is currently being tested - see e.g.  https://github.com/JMMP-Group/GO_coordination/issues/15
DOI: 10.6084/m9.figshare.11758911
title: Additional file 3 of A comparison of curated gene sets versus transcriptomics-derived gene signatures for detecting pathway activation in immune cells

description: Additional file 3 Common Signature Genes and Enrichment Results Description: These are the PANTHER GO analysis results for the set of genes found to be in common among all data-derived signatures.
DOI: 10.6084/m9.figshare.11758929
title: Additional file 16 of De novo transcriptome assembly for the five major organs of Zanthoxylum armatum and the identification of genes involved in terpenoid compound and fatty acid metabolism

description: Additional file 16: Table S8. The TAIR annotation of the DEGs associated with terpenoid compounds and fatty acids biosynthesis and metabolism in fruit samples of Zanthoxylum armatum.
DOI: 10.6084/m9.figshare.13331817
title: Additional file 1 of An optimized base editor with efficient C-to-T base editing in zebrafish

description: Additional file 1: Fig.S1. Whole zebrafish codon-optimized zAncBE4max and its alignment with AncBE4max sequence (nucleotides and amino acids). Fig. S2. Indel frequency (%).
DOI: 10.6084/m9.figshare.11759001
title: Additional file 8 of De novo transcriptome assembly for the five major organs of Zanthoxylum armatum and the identification of genes involved in terpenoid compound and fatty acid metabolism

description: Additional file 8: Table S4. KEGG annotation of nonredundant unigenes in Zanthoxylum armatum.
DOI: 10.6084/m9.figshare.11758914.v1
title: Additional file 14 of De novo transcriptome assembly for the five major organs of Zanthoxylum armatum and the identification of genes involved in terpenoid compound and fatty acid metabolism

description: Additional file 14: Table S6. The significant paythways of KEGG enrichment related to the unigenes only up- or down- regulation in fruit samples of Zanthoxylum armatum.
DOI: 10.6084/m9.figshare.11758944.v1
title: Additional file 18 of De novo transcriptome assembly for the five major organs of Zanthoxylum armatum and the identification of genes involved in terpenoid compound and fatty acid metabolism

description: Additional file 18: Table S9. The RNA-seq data of the DEGs selected for qRT-PCR validation.
DOI: 10.6084/m9.figshare.11759040.v1
title: Additional file 2 of Choice of library size normalization and statistical methods for differential gene expression analysis in balanced two-group comparisons for RNA-seq studies

description: Additional file 2. Contains datasets used for the analysis. This zipped file folder contains MAQC2 and MAQC3 raw read counts, cancer raw data files filtered with zero counts (AdLC, OC and TNBC), and description of these data files named Supplementary Material.docx.
DOI: 10.6084/m9.figshare.13331817.v1
title: Additional file 1 of An optimized base editor with efficient C-to-T base editing in zebrafish

description: Additional file 1: Fig.S1. Whole zebrafish codon-optimized zAncBE4max and its alignment with AncBE4max sequence (nucleotides and amino acids). Fig. S2. Indel frequency (%).
DOI: 10.6084/m9.figshare.13331820.v1
title: Additional file 2 of An optimized base editor with efficient C-to-T base editing in zebrafish

description: Additional file 2: Table S1. Germline transmission rate. Table S2. Sequencing data. Table S3. Original values related to Fig. 3. Table S4. Primer sequences and PCR conditions.
DOI: 10.6084/m9.figshare.23812685
title: Additional file 5 of Genetic impacts on DNA methylation help elucidate regulatory genomic processes

description: Additional file 5: Tables S26–S27. Table S26. List of GWASs summary statistics used for the SMR. Table S27. Summary of co-localisations by phenotypic class.
DOI: 10.6084/m9.figshare.23812676.v1
title: Additional file 3 of Genetic impacts on DNA methylation help elucidate regulatory genomic processes

description: Additional file 3: Tables S5–S25. Table S5. List of all the enrichment analyses, set of CpGs/SNPs of interest, and background set used in each. Tables S6–S17. Enrichment analyses on genomic annotations. Tables S18–S21. Enrichment analyses on specific transcription factor binding sites annotations. Tables S22–S25. Enrichment analyses on gene ontologies.
DOI: 10.6084/m9.figshare.23812673
title: Additional file 2 of Genetic impacts on DNA methylation help elucidate regulatory genomic processes

description: Additional file 2. Summary statistics of meQTL replication results for selected CpG sites using MeDIP-seq. TSV file with the following fields: (1) SNP: meQTL SNP ID in the format of chr:pos_A1_A2. (2) bin: MeDIP-seq bin ID in the format of chr.pos1.pos2. (3) CpG: CpG ID included within the bin. (4) type: type of association, can be cis or trans. (5) beta: association coefficient estimate. (6) t-stat: t-statistic value. (7) p-value: raw P-value of the association. (8) R2: coefficient of determination of the association.
DOI: 10.6084/m9.figshare.11759040
title: Additional file 2 of Choice of library size normalization and statistical methods for differential gene expression analysis in balanced two-group comparisons for RNA-seq studies

description: Additional file 2. Contains datasets used for the analysis. This zipped file folder contains MAQC2 and MAQC3 raw read counts, cancer raw data files filtered with zero counts (AdLC, OC and TNBC), and description of these data files named Supplementary Material.docx.
DOI: 10.6084/m9.figshare.23293327.v1
title: Additional file 1 of Home confinement’s impact on myopia control by using orthokeratology in school-aged children

description: Additional file 1.
DOI: 10.6084/m9.figshare.11759052.v1
title: Additional file 3 of Choice of library size normalization and statistical methods for differential gene expression analysis in balanced two-group comparisons for RNA-seq studies

description: Additional file 3. R code for the analysis.
DOI: 10.6084/m9.figshare.23812685.v1
title: Additional file 5 of Genetic impacts on DNA methylation help elucidate regulatory genomic processes

description: Additional file 5: Tables S26–S27. Table S26. List of GWASs summary statistics used for the SMR. Table S27. Summary of co-localisations by phenotypic class.
DOI: 10.6084/m9.figshare.11758959.v1
title: Additional file 1 of De novo transcriptome assembly for the five major organs of Zanthoxylum armatum and the identification of genes involved in terpenoid compound and fatty acid metabolism

description: Additional file 1: Table S1. The quality of RNA extration.
DOI: 10.6084/m9.figshare.11758980.v1
title: Additional file 4 of De novo transcriptome assembly for the five major organs of Zanthoxylum armatum and the identification of genes involved in terpenoid compound and fatty acid metabolism

description: Additional file 4: Table S3. The summary of SSR in the total of unigenes.