cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11880840
title: The cryptic unstable transcripts are associated with developmentally regulated gene expression in blood-stage <i>Plasmodium falciparum</i>

description: The tight gene expression regulation controls the development and pathogenesis of human malaria parasite <i>Plasmodium falciparum</i> throughout the complex life cycle. Recent studies have revealed the pervasive nascent transcripts in the genome of <i>P. falciparum</i>, suggesting the existence of a hidden transcriptome involved in the dynamic gene expression. However, the landscape and related biological functions of nascent non-coding RNAs (ns-ncRNAs) are still poorly explored. Here we profiled the transcription dynamics of nascent RNAs by rRNA-depleted and stranded RNA sequencing over the course of 48-h intraerythrocytic developmental cycle (IDC). We identified the genome-wide sources of a total of 2252 ns-ncRNAs, mostly originating from intergenic and untranslated regions of annotated genes. By integrating the nascent RNA abundances with ATAC-seq and ChIP-seq analysis, we uncovered the euchromatic microenvironment surrounding the ns-ncRNA loci, and revealed a positive correlation between ns-ncRNAs and corresponding mRNA abundances. Finally, by gene knock-down strategy, we showed that the cooperation of RNA exosome catalytic subunit PfDis3 and PfMtr4 cofactor played a major role in ns-ncRNAs degradation. Collectively, this study contributes to understanding of the potential roles of short-lived nascent ncRNAs in regulating gene expression in malaria parasites.
DOI: 10.6084/m9.figshare.7686302.v1
title: MOESM3 of ZEB1-AS1 initiates a miRNA-mediated ceRNA network to facilitate gastric cancer progression

description: Additional file 4. The down-regulated miRNAs were obtained by screening the TCGA database.
DOI: 10.6084/m9.figshare.7686326.v1
title: MOESM6 of ZEB1-AS1 initiates a miRNA-mediated ceRNA network to facilitate gastric cancer progression

description: Additional file 7. 576 consensus genes targeted by miR-610, miR-149 and miR-204.
DOI: 10.6084/m9.figshare.9783695
title: Phylogenetic tree

description: Phylogenetic tree of C. crocuta and seven other species constructed by the maximum likelihood method based on 6,601 single-copy orthologues.
DOI: 10.6084/m9.figshare.9783704
title: Gene structure annotation

description: Gene structure annotation
DOI: 10.6084/m9.figshare.9783704.v1
title: Gene structure annotation

description: Gene structure annotation
DOI: 10.6084/m9.figshare.9783716
title: Single-copy orthologues alignmens

description: single-copy orthologues alignmens for phylogenetic analysis
DOI: 10.6084/m9.figshare.7686362
title: MOESM2 of Peripheral T cell receptor beta immune repertoire is promptly reconstituted after acute myocardial infarction

description: Additional file 2: Table S1. The analysis of TCRÎ˛ immune repertoire sequencing data.
DOI: 10.6084/m9.figshare.7686380.v1
title: MOESM4 of Peripheral T cell receptor beta immune repertoire is promptly reconstituted after acute myocardial infarction

description: Additional file 4: Table S3. The distribution of V-J combinations in each sample.
DOI: 10.6084/m9.figshare.7686560
title: MOESM3 of Quantitative proteomic characterization of lung tissue in idiopathic pulmonary fibrosis

description: Additional file 3. Identified matrisomal proteins in lung tissue from IPF.
DOI: 10.6084/m9.figshare.7686578
title: MOESM5 of Quantitative proteomic characterization of lung tissue in idiopathic pulmonary fibrosis

description: Additional file 5. KEGG pathway enrichment analysis of differentially expressed proteins.
DOI: 10.6084/m9.figshare.7686596
title: Additional file 2: of Global transcriptome analysis of H5N1 influenza virus-infected human cells

description: Table S2. The differential unique genes in the A/QH group relative to biological process. (XLSX 46 kb)
DOI: 10.6084/m9.figshare.12365144
title: Additional file 1 of Genomic characterization of a newly established esophageal squamous cell carcinoma cell line from China and published esophageal squamous cell carcinoma cell lines

description: Additional file 1: Table S1. ESCC cell line information from Cellosaurus and literatures.
DOI: 10.6084/m9.figshare.7686326
title: MOESM6 of ZEB1-AS1 initiates a miRNA-mediated ceRNA network to facilitate gastric cancer progression

description: Additional file 7. 576 consensus genes targeted by miR-610, miR-149 and miR-204.
DOI: 10.6084/m9.figshare.7686554.v1
title: MOESM1 of Quantitative proteomic characterization of lung tissue in idiopathic pulmonary fibrosis

description: Additional file 1. The distribution of peptide length.
DOI: 10.6084/m9.figshare.7686557
title: MOESM2 of Quantitative proteomic characterization of lung tissue in idiopathic pulmonary fibrosis

description: Additional file 2. Differentially expressed proteins.
DOI: 10.6084/m9.figshare.10308125
title: Annal values of ensemble mean for 50 Sub-regions of Ontario

description: In this directory, there are 90 csv files, 52 files for the 4 basic variables (mean, minimum and maximum temperature, and precipitation; 12 monthly averages and 1 annual average) and 48 files for climate extremes indices.<br>In each file, there are 121 columns (RCPs,Region Name, and Data_1[year of 1981], Data_2[year of 1982],...,Data_119[2099]), and 201 rows (row 1: head, 50 rows for RCP2.6 + 50 rows for RCP4.5 + 50 rows for RCP 6.0 +50 rows for RCP8.5). Each row represents one region indicated by regName.
DOI: 10.6084/m9.figshare.7686467
title: Additional file 2: of Analysing the rice young panicle transcriptome reveals the gene regulatory network controlled by TRIANGULAR HULL1

description: Table S2. All genes expression profile. (XLSX 3158 kb)
DOI: 10.6084/m9.figshare.7686590
title: Additional file 1: of Global transcriptome analysis of H5N1 influenza virus-infected human cells

description: Table S1. Differentially expressed genes of A549 and 293T cells. (XLS 26 kb)
DOI: 10.6084/m9.figshare.11880894
title: Preparation of monodisperse SiO<sub>2</sub> nanorods with hollow structure and parameters affecting the length-diameter ratio

description: Monodisperse SiO<sub>2</sub> nanorods with hollow structure were prepared using FeOOH as a template. Powder X-ray diffraction, scanning electron microscopy, transmission electron microscopy, and nitrogen adsorption-desorption isotherms were utilized to characterize the products. With a FeCl<sub>3</sub> concentration of 0.1 M, the average length and width of the prepared hollow SiO<sub>2</sub> nanorods were 397 nm and 116 nm, respectively, and the average length-diameter ratio was calculated as 3.4. The average size of the nanopores of the amorphous SiO<sub>2</sub> shell were measured as 2.5 nm. Furthermore, increasing the concentration of Cl<sup>−</sup> ions improved length-diameter ratios of the FeOOH nanorod template and hollow SiO<sub>2</sub> nanorods.
DOI: 10.6084/m9.figshare.7686338.v1
title: MOESM7 of ZEB1-AS1 initiates a miRNA-mediated ceRNA network to facilitate gastric cancer progression

description: Additional file 8. The gene enrichment analysis of the 576 target genes.
DOI: 10.6084/m9.figshare.7686473.v1
title: Additional file 3: of Analysing the rice young panicle transcriptome reveals the gene regulatory network controlled by TRIANGULAR HULL1

description: Table S3. Differentially expressed genes. (XLSX 111 kb)
DOI: 10.6084/m9.figshare.11880897
title: Introduction of two predators to control <i>Dendrothrips minowai</i> (Thysanoptera: Thripidae) in tea (<i>Camellia sinensis)</i> plantations in China

description: <i>Dendrothrips minowai</i> Priesner (Thysanoptera: Thripidae) is the main pest thrips in tea (<i>Camellia sinensis</i>) plantations in Guizhou Province, damaging tea shoots and leaves. In this study, we tested the control of the predatory mite <i>Amblyseius cucumeris</i> Oudermans and the ladybeetle <i>Harmonia axyridis</i> Pallas against <i>D. minowai</i> in the laboratory and tea plantations in Guizhou, China. The results showed that <i>D. minowai</i> suppression by <i>A. cucumeris</i> was 29.0% at the predator to prey ratio of 1:10 and 45.3% at 1:5, and by <i>H. axyridis</i> it was 45.0% at the 1:10 ratio and 67.2% at 1:5 in the laboratory. After the introduction of these two predators in tea plantations, during the period of highest density of <i>D. minowai</i> (between May and August), the release of <i>A. cucumeris</i> and <i>H. axyridis</i> reduced <i>D. minowai</i> by 26.3 and 56.7% in 2015 and by 40.3 and 54.5% in 2016, respectively. Densities of <i>A. cucumeris</i> and <i>H. axyridis</i> per 100 tea leaves ranged from 50.3 to 137.5 for the mite and from 18.0 to 65.0 for the ladybird beetle. Thus, <i>A. cucumeris</i> and <i>H. axyridis</i> can be used as effective predators in controlling <i>D. minowai</i> in Chinese tea plantations.
DOI: 10.6084/m9.figshare.19221046
title: Additional file 7 of Asprosin induces vascular endothelial-to-mesenchymal transition in diabetic lower extremity peripheral artery disease

description: Additional file 7: Table S7. Downregulated expressed genes in the aorta tissues from db/db mice compared to db/m mice.
DOI: 10.6084/m9.figshare.25244593
title: clean_seurat.rds

description: processed snRNA-seq dataset of mice gonadal white adipose tissue (GWAT) from 4 conditions : WT NCD, TM4SF19 KO NCD, WT HFD, TM4SF19 KO HFD. Each condition has two replicates.Related code is available at https://github.com/CB-postech/snRNA-seq_adipose_TM4SF19
DOI: 10.6084/m9.figshare.25244593.v1
title: clean_seurat.rds

description: processed snRNA-seq dataset of mice gonadal white adipose tissue (GWAT) from 4 conditions : WT NCD, TM4SF19 KO NCD, WT HFD, TM4SF19 KO HFD. Each condition has two replicates.Related code is available at https://github.com/CB-postech/snRNA-seq_adipose_TM4SF19
DOI: 10.6084/m9.figshare.19745056
title: Additional file 1 of N6-methyladenosine-modified TRAF1 promotes sunitinib resistance by regulating apoptosis and angiogenesis in a METTL14-dependent manner in renal cell carcinoma

description: Additional file 1: Table S2. Sequences of shRNA&siRNA against specific target in this study. Fig. S1 A Colony formation assay of sunitinib-resistant cell lines and control cell lines with DMSO in 12-well dish for 3 weeks (n = 3). Fig. S2 A TRAF1 pathways in KEGG. B Proteins involed in angiogenesis signaling were mediated by TRAF1 in OS-RC-2 cells. Fig. S3 A and B ChIP assays were used to assess the degree of H3K4me3 within the regions 1-3 of the TRAF1 promoter in 78S and 78R cells.
DOI: 10.6084/m9.figshare.7686386
title: MOESM5 of Peripheral T cell receptor beta immune repertoire is promptly reconstituted after acute myocardial infarction

description: Additional file 5: Table S4. The distribution of V-D-J combinations in each sample.
DOI: 10.6084/m9.figshare.7686554
title: MOESM1 of Quantitative proteomic characterization of lung tissue in idiopathic pulmonary fibrosis

description: Additional file 1. The distribution of peptide length.
DOI: 10.6084/m9.figshare.7686398
title: MOESM6 of Peripheral T cell receptor beta immune repertoire is promptly reconstituted after acute myocardial infarction

description: Additional file 6: Table S5. The distribution of CDR3 AA clonotypes in each sample.
DOI: 10.6084/m9.figshare.7686404.v1
title: MOESM7 of Peripheral T cell receptor beta immune repertoire is promptly reconstituted after acute myocardial infarction

description: Additional file 7: Table S6. The distribution of AA usage in CDR3.
DOI: 10.6084/m9.figshare.19221046.v1
title: Additional file 7 of Asprosin induces vascular endothelial-to-mesenchymal transition in diabetic lower extremity peripheral artery disease

description: Additional file 7: Table S7. Downregulated expressed genes in the aorta tissues from db/db mice compared to db/m mice.
DOI: 10.6084/m9.figshare.19220998.v1
title: Additional file 1 of Exosomes derived from M2 type tumor-associated macrophages promote osimertinib resistance in non-small cell lung cancer through MSTRG.292666.16-miR-6836-5p-MAPK8IP3 axis

description: Additional file 1: Table S1. All differentially expressed miRNAs between the exosomes isolated from the sensitive and resistant plasma with the thresholds of |log2Fold change (FC)|&gt; 1 and false discovery rate (FDR) &lt; 0.05.
DOI: 10.6084/m9.figshare.7686467.v1
title: Additional file 2: of Analysing the rice young panicle transcriptome reveals the gene regulatory network controlled by TRIANGULAR HULL1

description: Table S2. All genes expression profile. (XLSX 3158 kb)
DOI: 10.6084/m9.figshare.19221037
title: Additional file 4 of Asprosin induces vascular endothelial-to-mesenchymal transition in diabetic lower extremity peripheral artery disease

description: Additional file 4: Table S4. The 4 differentially expressed metabolites that exist simultaneously when comparing DM + PAD group to DM group and comparing DM group to NC group.
DOI: 10.6084/m9.figshare.19221040
title: Additional file 5 of Asprosin induces vascular endothelial-to-mesenchymal transition in diabetic lower extremity peripheral artery disease

description: Additional file 5: Table S5. All differentially expressed genes in the aorta tissues from db/db mice compared to db/m mice.
DOI: 10.6084/m9.figshare.15026667.v1
title: Additional file 3 of Identification of novel antioxidant gene signature to predict the prognosis of patients with gastric cancer

description: Additional file 3: Supplementary Data 1. Original data of clinical information.
DOI: 10.6084/m9.figshare.7686596.v1
title: Additional file 2: of Global transcriptome analysis of H5N1 influenza virus-infected human cells

description: Table S2. The differential unique genes in the A/QH group relative to biological process. (XLSX 46 kb)
DOI: 10.6084/m9.figshare.7686719
title: Additional file 1: of Comparison of D2 and D2 plus radical surgery for advanced distal gastric cancer: a randomized controlled study

description: D2 plus radical surgery for advanced distal gastric cancer. (RMVB 73272Â kb)
DOI: 10.6084/m9.figshare.7686719.v1
title: Additional file 1: of Comparison of D2 and D2 plus radical surgery for advanced distal gastric cancer: a randomized controlled study

description: D2 plus radical surgery for advanced distal gastric cancer. (RMVB 73272Â kb)
DOI: 10.6084/m9.figshare.15026608.v1
title: Additional file 1 of Ferroptosis-related gene signature predicts the prognosis in Oral squamous cell carcinoma patients

description: Additional file 1.
DOI: 10.6084/m9.figshare.7686770.v1
title: Additional file 3: of Genome-wide analysis of the NAC transcription factor family in Tartary buckwheat (Fagopyrum tataricum)

description: Table S3. One-to-one orthologous relationships between Tartary buckwheat and other plants. (XLS 88 kb)
DOI: 10.6084/m9.figshare.7686755
title: Additional file 1: of Genome-wide analysis of the NAC transcription factor family in Tartary buckwheat (Fagopyrum tataricum)

description: Table S1. List of the 80 FtNAC genes identified in this study. (XLS 184 kb)
DOI: 10.6084/m9.figshare.19220998
title: Additional file 1 of Exosomes derived from M2 type tumor-associated macrophages promote osimertinib resistance in non-small cell lung cancer through MSTRG.292666.16-miR-6836-5p-MAPK8IP3 axis

description: Additional file 1: Table S1. All differentially expressed miRNAs between the exosomes isolated from the sensitive and resistant plasma with the thresholds of |log2Fold change (FC)|&gt; 1 and false discovery rate (FDR) &lt; 0.05.
DOI: 10.6084/m9.figshare.19221031.v1
title: Additional file 2 of Asprosin induces vascular endothelial-to-mesenchymal transition in diabetic lower extremity peripheral artery disease

description: Additional file 2: Table S2. The differentially expressed metabolites in serums from participants using One-way ANOVA.
DOI: 10.6084/m9.figshare.19221034
title: Additional file 3 of Asprosin induces vascular endothelial-to-mesenchymal transition in diabetic lower extremity peripheral artery disease

description: Additional file 3: Table S3. The 59 differentially expressed metabolites that exist simultaneously in DM + PAD group compared to both DM and NC group.
DOI: 10.6084/m9.figshare.15026535
title: Additional file 1 of Repetitive brief ischemia accelerates tibial shaft fracture healing: a 5-years prospective preliminary clinical trial (PCT)

description: Additional file 1.
DOI: 10.6084/m9.figshare.19221109
title: Additional file 5 of Comparative transcriptome analysis identifies crucial candidate genes and pathways in the hypothalamic-pituitary-gonadal axis during external genitalia development of male geese

description: Additional file 5: Table S4. Top 30 KEGG pathways enriched by the DEGs in different tissues and related information.
DOI: 10.6084/m9.figshare.19221034.v1
title: Additional file 3 of Asprosin induces vascular endothelial-to-mesenchymal transition in diabetic lower extremity peripheral artery disease

description: Additional file 3: Table S3. The 59 differentially expressed metabolites that exist simultaneously in DM + PAD group compared to both DM and NC group.
DOI: 10.6084/m9.figshare.11881074.v3
title: An infectious clone of enterovirus 71(EV71) that is capable of infecting neonatal immune competent mice without adaptive mutations

description: Enterovirus 71 (EV71) is a major pathogen that causes hand, foot and mouth disease (HFMD), which is a life threatening disease in certain children. The pathogenesis of EV71-caused HFMD is poorly defined due to the lack of simple and robust animal models with severe phenotypes that recapitulate symptoms observed in humans. Here, we generated the infectious clone of a clinical isolate from a severe HFMD patient. Virus rescued from the cDNA clone was infectious in cell lines. When administrated intraperitoneally to neonatal ICR, BALB/c and C57 immune competent mice at a dosage of1.4 × 10<sup>4</sup> pfu per mouse, the virus caused weight loss, paralysis and death in the infected mice after 4–5 days of infection. In the infected mice, detectable viral replication was detected in various tissues such as heart, liver, brain, lung, kidney, small intestine, leg skeletal muscle and medulla oblongata. The histology of the infected mice included massive myolysis, glomerular atrophy, villous blunting in small intestine, widened alveolar septum, diminished alveolar spaces and lymphocytes infiltration into the lung. By using the UV-inactivated virus as a control, we elucidated that the virus first amplified in the leg skeletal muscle tissue and the muscle tissue served as a primary viral replication site. In summary, we generated a stable EV71 infectious clone that is capable of infecting neonatal immune competent mice without adaptive mutations and provide a simple, valuable animal model for the studies of EV71pathogenesis and therapy.
DOI: 10.6084/m9.figshare.15026535.v1
title: Additional file 1 of Repetitive brief ischemia accelerates tibial shaft fracture healing: a 5-years prospective preliminary clinical trial (PCT)

description: Additional file 1.
DOI: 10.6084/m9.figshare.14502255.v1
title: Keys to Unlock the Enigma of Ocular Toxocariasis: A Systematic Review and Meta-analysis

description: Ocular toxocariasis (OT) is a zoonotic infection caused by larval stages of <i>Toxocara canis</i> and <i>T. cati</i>. The current review and meta-analysis aimed to evaluate the global prevalence of OT. Five English (PubMed, Scopus, Science Direct, Web of Science, and Google Scholar) databases were explored and 101 articles met the inclusion criteria. The pooled prevalence (95% confidence interval) of OT was higher in immunological studies (9%. 6–12%) than in studies that applied ophthalmic examination (1%. 1–2%). The lower middle-income level countries had the highest prevalence (6%. 2–12%) as well as the African region (10%. 7–13%). The highest infection rate (4%. 2–7%) was detected in the 1–25 mean age group. Regular anthelminthic treatment of cats and dogs, and removal of animal feces from public places must be considered.
DOI: 10.6084/m9.figshare.19221115.v1
title: Additional file 7 of Comparative transcriptome analysis identifies crucial candidate genes and pathways in the hypothalamic-pituitary-gonadal axis during external genitalia development of male geese

description: Additional file 7: Table S6. Sample quality control.
DOI: 10.6084/m9.figshare.19221043
title: Additional file 6 of Asprosin induces vascular endothelial-to-mesenchymal transition in diabetic lower extremity peripheral artery disease

description: Additional file 6: Table S6. Upregulated expressed genes in the aorta tissues from db/db mice compared to db/m mice.
DOI: 10.6084/m9.figshare.9783707
title: Gene family construction

description: Gene family construction result using orthoMCL
DOI: 10.6084/m9.figshare.19221043.v1
title: Additional file 6 of Asprosin induces vascular endothelial-to-mesenchymal transition in diabetic lower extremity peripheral artery disease

description: Additional file 6: Table S6. Upregulated expressed genes in the aorta tissues from db/db mice compared to db/m mice.
DOI: 10.6084/m9.figshare.7686755.v1
title: Additional file 1: of Genome-wide analysis of the NAC transcription factor family in Tartary buckwheat (Fagopyrum tataricum)

description: Table S1. List of the 80 FtNAC genes identified in this study. (XLS 184 kb)
DOI: 10.6084/m9.figshare.7686560.v1
title: MOESM3 of Quantitative proteomic characterization of lung tissue in idiopathic pulmonary fibrosis

description: Additional file 3. Identified matrisomal proteins in lung tissue from IPF.
DOI: 10.6084/m9.figshare.7686761
title: Additional file 2: of Genome-wide analysis of the NAC transcription factor family in Tartary buckwheat (Fagopyrum tataricum)

description: Table S2. Analysis and distribution of conserved motifs in Tartary buckwheat NAC proteins. (XLS 31 kb)
DOI: 10.6084/m9.figshare.10308260
title: Changes of basic variables for maps for 2050s and 2080s

description: Data in this directory is for generating spatial distribution maps of the four bisic variables (Tm, Tx, Tn and Pr). For each variable, there are 17 files representing 12 months, 4 seasons and annual averages. <br>In each table, there are 43 colums include id, Longitude, Latitude, 5 percentiles [5%,25%,50%,75% and 95%] for each of the 4 RCPs for 2 periods [2050s and 2080]<br>In each table, there are 8965 rows (head and 8964 grids).<br><br><br>
DOI: 10.6084/m9.figshare.7686473
title: Additional file 3: of Analysing the rice young panicle transcriptome reveals the gene regulatory network controlled by TRIANGULAR HULL1

description: Table S3. Differentially expressed genes. (XLSX 111 kb)
DOI: 10.6084/m9.figshare.11881074.v1
title: An infectious clone of enterovirus 71(EV71) that is capable of infecting neonatal immune competent mice without adaptive mutations

description: Enterovirus 71 (EV71) is a major pathogen that causes hand, foot and mouth disease (HFMD), which is a life threatening disease in certain children. The pathogenesis of EV71-caused HFMD is poorly defined due to the lack of simple and robust animal models with severe phenotypes that recapitulate symptoms observed in humans. Here, we generated the infectious clone of a clinical isolate from a severe HFMD patient. Virus rescued from the cDNA clone was infectious in cell lines. When administrated intraperitoneally to neonatal ICR, BALB/c and C57 immune competent mice at a dosage of1.4 × 10<sup>4</sup> pfu per mouse, the virus caused weight loss, paralysis and death in the infected mice after 4–5 days of infection. In the infected mice, detectable viral replication was detected in various tissues such as heart, liver, brain, lung, kidney, small intestine, leg skeletal muscle and medulla oblongata. The histology of the infected mice included massive myolysis, glomerular atrophy, villous blunting in small intestine, widened alveolar septum, diminished alveolar spaces and lymphocytes infiltration into the lung. By using the UV-inactivated virus as a control, we elucidated that the virus first amplified in the leg skeletal muscle tissue and the muscle tissue served as a primary viral replication site. In summary, we generated a stable EV71 infectious clone that is capable of infecting neonatal immune competent mice without adaptive mutations and provide a simple, valuable animal model for the studies of EV71pathogenesis and therapy.