cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14791347.v2
title: In vitro activities of the tetrazole VT-1161 compared with itraconazole and fluconazole against <i>Cryptococcus</i> and non-<i>albicans Candida</i> species

description: Recently, <i>Cryptococcus</i> and non-<i>albicans Candida</i> (NAC) have emerged as health-threatening pathogens for clinical fungal infections. Due to their increased resistance to existing antifungal drugs, novel antifungals are urgently needed. In this study, we evaluated the antifungal effect of VT-1161 and its comparators itraconazole and fluconazole against common fluconazole-sensitive or -resistant <i>Cryptococcus</i> and NAC strains. The tested strains were obtained from Chinese patients by the Invasive Fungal Infection Group within the past 2 years. The minimum inhibitory concentrations (MICs) of VT-1161 and other triazoles were measured according to the Clinical and Laboratory Standards Institute (CLSI) M27-Ed4 guidelines. We found that VT-1161 exhibited strong in vitro activity against <i>Cryptococcus</i> spp.. VT-1161 (geometric mean MIC = 0.024 μg/mL) was 21.7-fold and 104.5-fold more potent than itraconazole and fluconazole, respectively. Against the seven <i>Cryptococcus neoformans</i> isolates with higher fluconazole MICs (≥8 μg/mL based on the MIC<sub>90</sub> value of this azole), VT-1161 maintained potent activities, with MICs ranging between 0.031 and 0.5 μg/mL. For NAC spp., VT-1161 (geometric mean MIC = 0.099 μg/mL) was 6.0-fold and 11.4-fold more effective than itraconazole and fluconazole, respectively. There is a positive correlation of the MICs between VT-1161 and itraconazole/fluconazole. The MIC values of VT-1161 against <i>Candida glabrata</i> and <i>Candida tropicalis</i> were significantly lower than those of fluconazole, whereas for <i>Candida parapsilosis</i> the differences in the MIC values between VT-1161 and fluconazole were not statistically significant. The results showed that tetrazole VT-1161 might be a promising candidate for treating <i>Cryptococcus</i> and NAC infections.
DOI: 10.6084/m9.figshare.22655408
title: Additional file 5 of Identification of genetic variants that impact gene co-expression relationships using large-scale single-cell data

description: Additional file 5: Table S6. The significant co-eQTLs for the major cell types with the filtering strategy
DOI: 10.6084/m9.figshare.22655396.v1
title: Additional file 1 of Identification of genetic variants that impact gene co-expression relationships using large-scale single-cell data

description: Additional file 1: Supplementary Tables. Collection of small supplementary tables (S1-2,4-5,7-8,11-12) plus all table captions; large supplementary tables are saved as separate csv files in the following.
DOI: 10.6084/m9.figshare.22655414
title: Additional file 6 of Identification of genetic variants that impact gene co-expression relationships using large-scale single-cell data

description: Additional file 6: Table S9. BIOS replication for filtered co-eQTLs for major cell types.
DOI: 10.6084/m9.figshare.22655420
title: Additional file 8 of Identification of genetic variants that impact gene co-expression relationships using large-scale single-cell data

description: Additional file 8: Table S13. BIOS replication for unfiltered co-eQTLs for major cell types
DOI: 10.6084/m9.figshare.22655420.v1
title: Additional file 8 of Identification of genetic variants that impact gene co-expression relationships using large-scale single-cell data

description: Additional file 8: Table S13. BIOS replication for unfiltered co-eQTLs for major cell types
DOI: 10.6084/m9.figshare.22655426
title: Additional file 10 of Identification of genetic variants that impact gene co-expression relationships using large-scale single-cell data

description: Additional file 10: Table S15. TF enrichment of co-eGenes co-eGenes associated with the same eQTL, for all eQTLs with at least 5 co-eGenes, using the Remap 2022 ChIP-seq data
DOI: 10.6084/m9.figshare.22655426.v1
title: Additional file 10 of Identification of genetic variants that impact gene co-expression relationships using large-scale single-cell data

description: Additional file 10: Table S15. TF enrichment of co-eGenes co-eGenes associated with the same eQTL, for all eQTLs with at least 5 co-eGenes, using the Remap 2022 ChIP-seq data
DOI: 10.6084/m9.figshare.16888450.v1
title: Targeting USP11 may alleviate radiation-induced pulmonary fibrosis by regulating endothelium tight junction

description: Radiation-induced pulmonary fibrosis (RIPF) is a major side effect after radiotherapy for thoracic malignancies. However, rare anti-RIPF therapeutics show definitive effects for treating this disease. Ubiquitin-specific peptidase 11 (USP11) has been reported to promote transforming growth factor β (TGFβ) signaling which plays an essential role underlying RIPF. Herein, we explored the role of USP11 on RIPF. In the present study, USP11-knockout (<i>Usp11<sup>-/-</sup></i>) mice were used to explore the effects of USP11 on RIPF. The lung tissue was obtained after receiving 30 Gy X-ray irradiation. The expression of USP11, TGF-β1, and a-SMA was determined by immunohistochemical and Western Blot, respectively. γ-H<sub>2</sub>AX foci and TUNEL positive cells were detected by fluorescent technique to assess DNA damage and apoptosis. High-throughput proteomic analysis was applied to further explore the related mechanisms. The transwell co-culture method was used to investigate bystander effects in HELF cells induced by irradiated HMEC-1 cells <i>in vitro</i>. Here we found that radiation activated USP11 <i>in vivo</i> and <i>in vitro</i>. Our results showed that USP11 deficiency effectively decreased serum TGF-β1 level, suppressed α-SMA expression, and mitigated pulmonary fibrosis. In addition, fewer γ-H<sub>2</sub>AX foci and decreased apoptotic cells were identified after irradiation in the primary cells isolated from the lungs of <i>Usp11<sup>-/-</sup></i> mice. High-throughput proteomics analysis results showed that 22-upregulated and 158-downregulated proteins were identified in the lung tissues of <i>Usp11<sup>-/-</sup></i> mice after irradiation. Furthermore, gene set enrichment analysis (GSEA) revealed that USP11 deficiency affects the tight junction signaling pathway. We verified that USP11 deficiency remarkably reinforced tight junction in the endothelial cells and alleviated TGF-β1 to inhibit fibrosis of fibroblast cells. The present study preliminarily showed that USP11-knockout mitigated RIPF via reinforcement endothelial barrier function.
DOI: 10.6084/m9.figshare.22655441
title: Additional file 15 of Identification of genetic variants that impact gene co-expression relationships using large-scale single-cell data

description: Additional file 15: Table S20. GO enrichment for co-eGenes associated with the same eQTL, variation of Supplementary Table 14 with a stricter background
DOI: 10.6084/m9.figshare.22655435
title: Additional file 13 of Identification of genetic variants that impact gene co-expression relationships using large-scale single-cell data

description: Additional file 13: Table S18. Colocalization results for eQTL signal with GWAS signal
DOI: 10.6084/m9.figshare.22655435.v1
title: Additional file 13 of Identification of genetic variants that impact gene co-expression relationships using large-scale single-cell data

description: Additional file 13: Table S18. Colocalization results for eQTL signal with GWAS signal
DOI: 10.6084/m9.figshare.12170097.v1
title: SNP discovery of <i>Camellia oleifera</i> based on RNA-seq and its application for identification of genetic relationships and locus for oil content among different cultivars

description: Tea oil camellia (<i>Camellia oleifera</i>) is a perennial evergreen shrub or small tree. Enhancing oil content is an important breeding objective in this species. In this study, we (i) used the high-throughput RNA-seq to discovery SNP sites located in target genes involved in lipid biosynthesis, (ii) determined genetic relationship among 102 accessions based on SNP-seq data, and (iii) identify SNP loci associated with oil content. Results showed that 20 SNP markers of targeted genes were discovered based on RNA-seq data. The SNP-seq of 20 pairs of SNP primers across 102 accessions generated 644 SNPs. The phylogenetic tree was constructed based on these SNPs, which clearly presented genetic relationship among 102 accessions. The <i>C. chekiangoleosa</i> belonging to different sect. with other accessions is far from other accessions. Phylogenetic analysis showed the clustering of accessions into groups which was in good agreement with their taxonomic classification, and revealed the presence of different accessions with the same name and identical accessions but with a different name. Moreover, seven SNP locus associated with oil content were identified (<i>p</i> &lt; 0.01). Our data discovered SNP sites of target genes involved in lipid biosynthesis, and provide scientific basic for germplasm collection and identification of tea oil camellia.
DOI: 10.6084/m9.figshare.23700710.v1
title: Additional file 3 of Ancestry-driven metabolite variation provides insights into disease states in admixed populations

description: Additional file 3: Extended Data Table S1. Significant independent local ancestry regions from admixture mapping. Extended Data Table S2. Genetic variants that do not explain association between local ancestry regions and metabolites. Extended Data Table S3. Replication of significant independent local ancestry regions from admixture mapping for 64 metabolites avaialble in the replication dataset.
DOI: 10.6084/m9.figshare.23700731
title: Additional file 1 of Whole-genome sequencing and functional annotation of pathogenic Paraconiothyrium brasiliense causing human cellulitis

description: Additional file 1: Table S1. KEGG functional annotation of P. brasiliense GGX 413
DOI: 10.6084/m9.figshare.16888728.v1
title: Theoretical study on mechanism of decomposition reaction of 1,2,4-triazole derivatives

description: The internal connection between the electronic structure and decomposition mechanism for ANTA and AHNTA is investigated by DFT method. The molecular electrostatic potential shows that hydrogen atoms of the amino group are easily transferred to the nitro group. The excitation process of <i>S</i><sub>0</sub>→<i>T</i><sub>1</sub> can be regarded as the local π→π∗ excitation. For the substituent dissociation, amino group is easily separated from the ring. For the ring cleavage, the C–N bond will be weakened by substituents on the C and N atoms. Especially at the excited state, the C–N bond with a nitro group on the C atom is the easiest to break. The charged state is beneficial to CONO isomerisation, and the H transfer is promoted at the excited state. For ANTA, the reaction rate of CONO isomerisation is faster than ring cleavage at the ground or the positively charged state. At the negatively charged state, the reaction rate of H transfer is the fastest. For AHNTA, at the ground state or the charged state, the reaction rate of CONO isomerisation is the fastest, compared to ones of the H transfer and ring cleavage reactions. At the excited state, the order is <i>k</i><sub>(H transfer)</sub>&gt;<i>k</i><sub>(ring cleavage</sub><sub>) </sub>for ANTA and AHNTA.
DOI: 10.6084/m9.figshare.23700681
title: Additional file 2 of Association of immune cell composition with the risk factors and incidence of acute coronary syndrome

description: Additional file 2. Table S3. Association between immune cell composition and risk factors of ACS.
DOI: 10.6084/m9.figshare.23700734.v1
title: Additional file 2 of Whole-genome sequencing and functional annotation of pathogenic Paraconiothyrium brasiliense causing human cellulitis

description: Additional file 2: Table S2. The secretome of P. brasiliense GGX 413
DOI: 10.6084/m9.figshare.7975427.v1
title: MOESM2 of Mutation of 4-coumarate: coenzyme A ligase 1 gene affects lignin biosynthesis and increases the cell wall digestibility in maize brown midrib5 mutants

description: Additional file 2: Table S2. SNPs with SNP-index 1 within the candidate genomic region detected on chromosome 5.
DOI: 10.6084/m9.figshare.18461831.v1
title: Additional file 1 of Differential proteomic analysis demonstrates follicle fluid participate immune reaction and protein translation in yak

description: Additional file 1. All identified proteins.
DOI: 10.6084/m9.figshare.12170097
title: SNP discovery of <i>Camellia oleifera</i> based on RNA-seq and its application for identification of genetic relationships and locus for oil content among different cultivars

description: Tea oil camellia (<i>Camellia oleifera</i>) is a perennial evergreen shrub or small tree. Enhancing oil content is an important breeding objective in this species. In this study, we (i) used the high-throughput RNA-seq to discovery SNP sites located in target genes involved in lipid biosynthesis, (ii) determined genetic relationship among 102 accessions based on SNP-seq data, and (iii) identify SNP loci associated with oil content. Results showed that 20 SNP markers of targeted genes were discovered based on RNA-seq data. The SNP-seq of 20 pairs of SNP primers across 102 accessions generated 644 SNPs. The phylogenetic tree was constructed based on these SNPs, which clearly presented genetic relationship among 102 accessions. The <i>C. chekiangoleosa</i> belonging to different sect. with other accessions is far from other accessions. Phylogenetic analysis showed the clustering of accessions into groups which was in good agreement with their taxonomic classification, and revealed the presence of different accessions with the same name and identical accessions but with a different name. Moreover, seven SNP locus associated with oil content were identified (<i>p</i> &lt; 0.01). Our data discovered SNP sites of target genes involved in lipid biosynthesis, and provide scientific basic for germplasm collection and identification of tea oil camellia.
DOI: 10.6084/m9.figshare.23700681.v1
title: Additional file 2 of Association of immune cell composition with the risk factors and incidence of acute coronary syndrome

description: Additional file 2. Table S3. Association between immune cell composition and risk factors of ACS.
DOI: 10.6084/m9.figshare.18461837.v1
title: Additional file 3 of Differential proteomic analysis demonstrates follicle fluid participate immune reaction and protein translation in yak

description: Additional file 3. Upregulated DEPs in immature FF.
DOI: 10.6084/m9.figshare.18461846.v1
title: Additional file 6 of Differential proteomic analysis demonstrates follicle fluid participate immune reaction and protein translation in yak

description: Additional file 6. KEGG of upregulated DEPs in mature FF.
DOI: 10.6084/m9.figshare.22655471.v1
title: Additional file 2 of Diacerein versus non-steroidal anti-inflammatory drugs in the treatment of knee osteoarthritis: a meta-analysis

description: Additional file 2: Results of fixed effects model.
DOI: 10.25549/usctheses-c89-452792
title: Life in action: novel techniques for imaging dynamic biological systems [PDF]
DOI: 10.6084/m9.figshare.16888728
title: Theoretical study on mechanism of decomposition reaction of 1,2,4-triazole derivatives

description: The internal connection between the electronic structure and decomposition mechanism for ANTA and AHNTA is investigated by DFT method. The molecular electrostatic potential shows that hydrogen atoms of the amino group are easily transferred to the nitro group. The excitation process of <i>S</i><sub>0</sub>→<i>T</i><sub>1</sub> can be regarded as the local π→π∗ excitation. For the substituent dissociation, amino group is easily separated from the ring. For the ring cleavage, the C–N bond will be weakened by substituents on the C and N atoms. Especially at the excited state, the C–N bond with a nitro group on the C atom is the easiest to break. The charged state is beneficial to CONO isomerisation, and the H transfer is promoted at the excited state. For ANTA, the reaction rate of CONO isomerisation is faster than ring cleavage at the ground or the positively charged state. At the negatively charged state, the reaction rate of H transfer is the fastest. For AHNTA, at the ground state or the charged state, the reaction rate of CONO isomerisation is the fastest, compared to ones of the H transfer and ring cleavage reactions. At the excited state, the order is <i>k</i><sub>(H transfer)</sub>&gt;<i>k</i><sub>(ring cleavage</sub><sub>) </sub>for ANTA and AHNTA.
DOI: 10.6084/m9.figshare.18461840
title: Additional file 4 of Differential proteomic analysis demonstrates follicle fluid participate immune reaction and protein translation in yak

description: Additional file 4. GO of upregulated DEPs in mature FF.
DOI: 10.6084/m9.figshare.18461834.v1
title: Additional file 2 of Differential proteomic analysis demonstrates follicle fluid participate immune reaction and protein translation in yak

description: Additional file 2. Upregulated DEPs in mature FF.
DOI: 10.6084/m9.figshare.18461846
title: Additional file 6 of Differential proteomic analysis demonstrates follicle fluid participate immune reaction and protein translation in yak

description: Additional file 6. KEGG of upregulated DEPs in mature FF.
DOI: 10.6084/m9.figshare.18461849
title: Additional file 7 of Differential proteomic analysis demonstrates follicle fluid participate immune reaction and protein translation in yak

description: Additional file 7. KEGG of upregulated DEPs in immature FF.
DOI: 10.6084/m9.figshare.18461834
title: Additional file 2 of Differential proteomic analysis demonstrates follicle fluid participate immune reaction and protein translation in yak

description: Additional file 2. Upregulated DEPs in mature FF.
DOI: 10.6084/m9.figshare.22655471
title: Additional file 2 of Diacerein versus non-steroidal anti-inflammatory drugs in the treatment of knee osteoarthritis: a meta-analysis

description: Additional file 2: Results of fixed effects model.
DOI: 10.6084/m9.figshare.18461840.v1
title: Additional file 4 of Differential proteomic analysis demonstrates follicle fluid participate immune reaction and protein translation in yak

description: Additional file 4. GO of upregulated DEPs in mature FF.
DOI: 10.6084/m9.figshare.18461849.v1
title: Additional file 7 of Differential proteomic analysis demonstrates follicle fluid participate immune reaction and protein translation in yak

description: Additional file 7. KEGG of upregulated DEPs in immature FF.
DOI: 10.6084/m9.figshare.18461843.v1
title: Additional file 5 of Differential proteomic analysis demonstrates follicle fluid participate immune reaction and protein translation in yak

description: Additional file 5. GO of upregulated DEPs in immature FF.
DOI: 10.6084/m9.figshare.18461906.v1
title: Additional file 1 of EWSR1-induced circNEIL3 promotes glioma progression and exosome-mediated macrophage immunosuppressive polarization via stabilizing IGF2BP3

description: Additional file 1: Table S1. Genes positively correlated with circNEIL3. Table S2. Interacting proteins identified by circNEIL3 pulldown assays. Table S3. Interacting proteins identified by IGF2BP3 Co-IP assays. Table S4. Genes differentially expressed in circNEIL3 high group. Compared with low group. Table S5. Enriched terms across upregulated genes in circNEIL3 high group. Table S6. Genes differentially expressed in IGF2BP3 high group. Compared with low group in TCGA glioma cohort. Table S7. Enriched terms across upregulated genes in IGF2BP3 high group. Table S8. The detailed clinicopathological characteristics of glioma patients in our local cohort. Table S9. The detailed qRT-PCR primers used in this study. Table S10. The detailed siRNA sequences used in this study. Table S11. The detailed antibody information used in this study.
DOI: 10.6084/m9.figshare.18462000.v1
title: Additional file 1 of A prognostic model based on immune-related long noncoding RNAs for patients with epithelial ovarian cancer

description: Additional file 1. Supplementary Table S1: A list of 2483 immune-related genes from ImmPort.
DOI: 10.6084/m9.figshare.24233280
title: Identification of ferroptotic genes and phenotypes in idiopathic nonobstructive azoospermia

description: Effective treatments for nonobstructive azoospermia (NOA), which affects 1% of all men globally, are limited by undefined pathogenic mechanisms, especially in idiopathic NOA (iNOA). Here, we tried to identify the functional ferroptosis-related genes and phenotypes involved in iNOA. Differentially expressed ferroptotic genes were identified from iNOA mRNA microarray datasets by bioinformatic analyses, and these ferroptotic genes were subsequently filtered by various algorithms. Then, receiver operating characteristic (ROC) curves were generated to evaluate the diagnostic ability of the abovementioned genes for iNOA. Generally, 11 differentially expressed ferroptotic genes were downregulated, and five genes were upregulated in iNOA samples. Four genes, including DUSP1, GPX4, HSD17B11, and SLC2A8, were technically selected and determined to be potential biomarkers for iNOA. Subsequently, similar expression levels were validated at both the RNA and protein levels in the iNOA specimens. Finally, morphologic and biochemical assays were applied to define the ferroptotic phenotypes in testes. The ferroptotic features, like shrunken mitochondria with electron-dense membranes and a reduction in cristae were observed across various cell types within iNOA patients, accompanied by the overload of ferrous ions and increased lipid peroxidation production. Our findings demonstrated that these ferroptosis genes could be involved in the underlying pathogenesis mechanisms of iNOA by regulating ferroptosis and serve as potential diagnostic biomarkers. Also, the ferroptotic phenotypes were identified in iNOA patients.
DOI: 10.6084/m9.figshare.24233280.v1
title: Identification of ferroptotic genes and phenotypes in idiopathic nonobstructive azoospermia

description: Effective treatments for nonobstructive azoospermia (NOA), which affects 1% of all men globally, are limited by undefined pathogenic mechanisms, especially in idiopathic NOA (iNOA). Here, we tried to identify the functional ferroptosis-related genes and phenotypes involved in iNOA. Differentially expressed ferroptotic genes were identified from iNOA mRNA microarray datasets by bioinformatic analyses, and these ferroptotic genes were subsequently filtered by various algorithms. Then, receiver operating characteristic (ROC) curves were generated to evaluate the diagnostic ability of the abovementioned genes for iNOA. Generally, 11 differentially expressed ferroptotic genes were downregulated, and five genes were upregulated in iNOA samples. Four genes, including DUSP1, GPX4, HSD17B11, and SLC2A8, were technically selected and determined to be potential biomarkers for iNOA. Subsequently, similar expression levels were validated at both the RNA and protein levels in the iNOA specimens. Finally, morphologic and biochemical assays were applied to define the ferroptotic phenotypes in testes. The ferroptotic features, like shrunken mitochondria with electron-dense membranes and a reduction in cristae were observed across various cell types within iNOA patients, accompanied by the overload of ferrous ions and increased lipid peroxidation production. Our findings demonstrated that these ferroptosis genes could be involved in the underlying pathogenesis mechanisms of iNOA by regulating ferroptosis and serve as potential diagnostic biomarkers. Also, the ferroptotic phenotypes were identified in iNOA patients.
DOI: 10.6084/m9.figshare.25195703
title: Gold exploration using groundwater in Western Australia

description: Supplementary Table 1.
DOI: 10.6084/m9.figshare.25195703.v1
title: Gold exploration using groundwater in Western Australia

description: Supplementary Table 1.
DOI: 10.6084/m9.figshare.7980665.v1
title: Additional file 15: of RNA-Seq and iTRAQ reveal multiple pathways involved in storage root formation and development in sweet potato (Ipomoea batatas L.)

description: Table S8. Primer pairs used in real-time quantitative RT-PCR. (XLS 35 kb)