cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11925213.v1
title: Additional file 5 of Genome-wide identification of CNGC genes in Chinese jujube (Ziziphus jujuba Mill.) and ZjCNGC2 mediated signalling cascades in response to cold stress

description: Additional file S5. The number of introns and exons of ZjCNGCs.
DOI: 10.6084/m9.figshare.20307490
title: Additional file 13 of A functional reference map of the RNF8 interactome in cancer

description: Additional file 13. Supplementary information_3: Proteomics data.
DOI: 10.6084/m9.figshare.5633737
title: Mitochondrial genome mutations in 13 subunits of respiratory chain complexes in Chinese Han and Mongolian hypertensive individuals

description: Mitochondrial DNA (mtDNA) mutations are associated with cardiovascular disease, including hypertension (HTN). Here we performed a genetic and molecular analysis of 13 mtDNA-encoded subunits of respiratory chain complexes in 100 Chinese Han and 80 Mongolian HTN cases, and 100 Han and 42 Mongolian normotension subjects. The total cholesterol of the Mongolian normotensive subjects was higher than that of the Han normotensive group (<i>p</i> &lt; .05). Sequence analysis identified 636 point mutations in the 13 mtDNA-encoded subunits in the Han and Mongolian hypertensive individuals, including 66 in NADH dehydrogenase subunit 1(ND1), 62 in ND2, 71 in COI, 29 in COII, 17 in ATP8, one in ATP6/8, 49 in ATP6, 27 in COIII, 27 in ND3, 14 in ND4L, 74 in ND4, 97 in ND5, 24 in ND6, and 78 in CYTB. Eight of these point mutations were present at significantly different frequencies in Han and Mongolian hypertensive individuals. Thirty-one point mutations were present only in Mongolian hypertensive individuals, while 73 were present only in Han hypertensive individuals. The relation between point mutations in 13 mtDNA-encoded subunits of respiratory chain complexes and HTN is worth to further research in future; however, the functional effects of these mutations require elucidation.
DOI: 10.6084/m9.figshare.12449264
title: Understanding human and nature interaction outcomes for sustaining tourist destinations: An example of Jiuzhaigou Nature Reserve, China

description: Studying interactions of coupled human-natural system components provides better understanding of their influences on ecosystem health and improves effectiveness of managing such systems. To understand how human-nature interactions determine the sustainability of tourist destinations, using Jiuzhaigou Nature Reserve as an example, we analyzed how human-nature interactions influenced the reserve’s ecological services extraction, environmental conditions, and corresponding management actions through a historical lens. We first developed a model that represented the components and their interactions under coupled human and natural systems framework. We then summarized such interactions and their resulted environmental conditions in a time sequence. Human activities have changed Jiuzhaigou system from largely human-nature balanced to partially degraded, and then to recovered and intensively managed system during the past six decades. Such changes resulted from human-nature interactions predominantly driven by overuse of natural resources, responded to by natural components in loss of ecosystem functions, and then responded by management actions to restore the functions. The increased nutrient and sediment, modified benthic communities, and decreased travertine (crystal substrate formed by the precipitation of carbonate minerals) indicate that tourism pressure in Jiuzhaigou under the current intensive management strategy has exceeded its carrying capacity. Much more aggressive environmental friendly tourism policies are needed to sustain this valuable tourist destination. Our findings based on coupled human-natural system framework analysis have important implications for sustaining natural resources and ecological services, and the governance of both for the management of nature reserves.
DOI: 10.6084/m9.figshare.12449264.v1
title: Understanding human and nature interaction outcomes for sustaining tourist destinations: An example of Jiuzhaigou Nature Reserve, China

description: Studying interactions of coupled human-natural system components provides better understanding of their influences on ecosystem health and improves effectiveness of managing such systems. To understand how human-nature interactions determine the sustainability of tourist destinations, using Jiuzhaigou Nature Reserve as an example, we analyzed how human-nature interactions influenced the reserve’s ecological services extraction, environmental conditions, and corresponding management actions through a historical lens. We first developed a model that represented the components and their interactions under coupled human and natural systems framework. We then summarized such interactions and their resulted environmental conditions in a time sequence. Human activities have changed Jiuzhaigou system from largely human-nature balanced to partially degraded, and then to recovered and intensively managed system during the past six decades. Such changes resulted from human-nature interactions predominantly driven by overuse of natural resources, responded to by natural components in loss of ecosystem functions, and then responded by management actions to restore the functions. The increased nutrient and sediment, modified benthic communities, and decreased travertine (crystal substrate formed by the precipitation of carbonate minerals) indicate that tourism pressure in Jiuzhaigou under the current intensive management strategy has exceeded its carrying capacity. Much more aggressive environmental friendly tourism policies are needed to sustain this valuable tourist destination. Our findings based on coupled human-natural system framework analysis have important implications for sustaining natural resources and ecological services, and the governance of both for the management of nature reserves.
DOI: 10.6084/m9.figshare.11924952
title: Additional file 24 of Comparative functional genomics analysis of cytochrome P450 gene superfamily in wheat and maize

description: Additional file 24: Table S7. The TPM and log2FoldChange values of 119 TaCYP450s under drought stress.
DOI: 10.6084/m9.figshare.6682367
title: Peritumoral monocytes induce cancer cell autophagy to facilitate the progression of human hepatocellular carcinoma

description: Macroautophagy/autophagy is an important catabolic process mediating cellular homeostasis and plays critical roles in cancer development. Whereas autophagy has been widely studied in various pathological models, little is known about the distribution, clinical significance and regulatory mechanism of this process in human hepatocellular carcinoma (HCC). In the present study, we found that tumor tissues exhibited significantly increased levels of autophagy compared with non-tumor tissues, and cancer cells with higher levels of autophagy were predominantly enriched in the invading edge regions of human HCC. Increased MAP1LC3B/LC3B expression in the invading edge regions was significantly correlated with a higher density of closely located monocytes, and TNF and IL1B derived from tumor-activated monocytes synergistically induced cancer cell autophagy in the invading edge regions of HCC. Monocyte-elicited autophagy induced the epithelial-mesenchymal transition (EMT) of cancer cells and promoted tumor metastasis by activating the NFKB-SNAI1 signaling pathway. Moreover, the increase of LC3B<sup>+</sup> cancer cells in the invading edge areas was associated with high mortality and reduced survival of patients with HCC. These findings indicated that cancer cell autophagy is regulated by a collaborative interaction between tumor and immune cell components in distinct HCC microenvironments, thus allowing the inflammatory monocytes to be rerouted in a tumor-promoting direction.
DOI: 10.6084/m9.figshare.11924943
title: Additional file 22 of Comparative functional genomics analysis of cytochrome P450 gene superfamily in wheat and maize

description: Additional file 22: Table S6. List of TPM values of 101 ZmCYP450s in six organs.
DOI: 10.6084/m9.figshare.13498051.v1
title: Additional file 2 of Integrative analysis of histopathological images and chromatin accessibility data for estrogen receptor-positive breast cancer

description: Additional file 2: Supplemental Table 1. The epithelial tissue proportion data of 54 TCGA ER-positive BRCA cases. Supplemental Table 2. The ATAC-seq peak signal data of 54 TCGA ER-positive BRCA cases. Supplemental Table 3. Significant epithelial tissue proportion-associated peaks and their target genes. Supplemental Table 4. Promoter and distal enhancer peak-to-gene links and their target genes. Supplemental Table 5. Expression data of the identified genes and clinical information for 663 TCGA ER-positive BRCA cases. Supplemental Table 6. Results of the univariate survival analysis.
DOI: 10.6084/m9.figshare.17161649.v1
title: Additional file 2 of Exploration of the value of progesterone and progesterone/estradiol ratio on the hCG trigger day in predicting pregnancy outcomes of PCOS patients undergoing IVF/ICSI: a retrospective cohort study

description: Additional file 2.
DOI: 10.6084/m9.figshare.17161633.v1
title: Additional file 2 of Microbial co-occurrence complicates associations of gut microbiome with US immigration, dietary intake and obesity

description: Additional file 2: Table S2. Associations of 84 gut bacterial genera with obesity and US exposure.
DOI: 10.6084/m9.figshare.5633755
title: Involvement of programmed cell death in suppression of the number of root nodules formed in soybean induced by <i>Bradyrhizobium</i> infection

description: Legumes establish symbiosis with nitrogen-fixing rhizobia through root nodules to acquire nitrogen. Legumes control nodule number through systemic (autoregulation of nodulation) as well as local regulation. Moreover, plants defend themselves against bacteria and other pathogens through the induction of localized (localized acquired resistance) and systemic (SAR, systemic acquired resistance; ISR, induced systemic resistance) responses. Herein, we show that the number of root nodules is suppressed by programmed cell death (PCD), and is simultaneously controlled by SAR and ISR in soybean (<i>Glycine max</i> [L.] Merr.). The wild-type soybean cultivar Williams 82 showed markedly fewer root nodule primordia and PCD symptoms, including accelerated DNA degradation, enhanced generation of reactive oxygen species (visualized by 3,3′-diaminobenzidine staining), and excessive cell death (detected on staining with trypan blue) compared to the hypernodulation mutant NOD1-3. These results suggest that PCD suppresses the formation of root nodules in wild-type soybean. In addition, microarray and gene ontology analyses showed that essential components of hypersensitive response (HR) or disease resistance, such as resistance (R) genes, mitogen-activated protein kinase cascade, SAR, salicylic acid, jasmonic acid, ethylene, etc., were activated in wild-type plants. These analyses corroborate the above findings, demonstrating that the suppression of root nodule formation by PCD is accompanied by HR, and is simultaneously controlled by SAR and ISR in soybean. These findings provide new insight into the control of nodulation to balance nutritional requirements and energy status in legumes.
DOI: 10.6084/m9.figshare.11924958.v1
title: Additional file 25 of Comparative functional genomics analysis of cytochrome P450 gene superfamily in wheat and maize

description: Additional file 25: Table S8. The TPM and log2FoldChange values of 86 ZmCYP450s under drought stress.
DOI: 10.6084/m9.figshare.20307481.v1
title: Additional file 1 of Transcriptomic analysis reveals the key role of histone deacetylation via mediating different phytohormone signalings in fiber initiation of cotton

description: Additional file 1: Table S1. The gene ID list of 4,209 DEGs identified between mock and TSA-treated ovules.
DOI: 10.6084/m9.figshare.11924964.v1
title: Additional file 2 of Sirt2-associated transcriptome modifications in cisplatin-induced neuronal injury

description: Additional File 2 Potential targets of deferential expressed genes with fold change &gt; 10 and FDR &lt; 0.1 in comparisons of Sirt2-expressing cells vs Sirt2-deficient cells; Sirt2-expression (cisplatin treated vs untreated) cells and Sirt2-deficient (cisplatin treated vs untreated) cells.
DOI: 10.6084/m9.figshare.11924982
title: Additional file 29 of Comparative functional genomics analysis of cytochrome P450 gene superfamily in wheat and maize

description: Additional file 29: Table S11. Significantly enriched KEGG pathways in 22 modules.
DOI: 10.6084/m9.figshare.11924982.v1
title: Additional file 29 of Comparative functional genomics analysis of cytochrome P450 gene superfamily in wheat and maize

description: Additional file 29: Table S11. Significantly enriched KEGG pathways in 22 modules.
DOI: 10.6084/m9.figshare.11924994
title: Additional file 31 of Comparative functional genomics analysis of cytochrome P450 gene superfamily in wheat and maize

description: Additional file 31: Table S13. List of identified wheat JA biosynthesis-related genes.
DOI: 10.6084/m9.figshare.17161651
title: Additional file 8 of Microbial co-occurrence complicates associations of gut microbiome with US immigration, dietary intake and obesity

description: Additional file 8: Table S9. Associations of gut bacterial genera with US exposure, stratified by birth place, among the first generation immigrants.
DOI: 10.6084/m9.figshare.17161648.v1
title: Additional file 7 of Microbial co-occurrence complicates associations of gut microbiome with US immigration, dietary intake and obesity

description: Additional file 7: Table S8. Associations of gut bacterial genera with obesity (BMI), stratified by birth place, among the first generation immigrants.
DOI: 10.6084/m9.figshare.13498361
title: Analysis of Collagen type X alpha 1 (COL10A1) expression and prognostic significance in gastric cancer based on bioinformatics

description: Collagen type X alpha 1 (COL10A1) is a member of the collagen family and the main matrix component. However, COL10A1 expression and prognosis relationship remains unclear in gastric cancer (GC). Through the analysis of database of Oncomine, the Cancer Genome Atlas (TCGA) as well as the Gene Expression Omnibus (GEO), in contrast to the tissue of normal gastric, COL10A1 in gastric cancer, had been upregulated. The high expression of COL10A1 was obviously related to T stage (<i>P</i> = 0.025) and lymph node metastasis (<i>P</i> = 0.025). It has been illustrated by the analysis of logistic regression that COL10A1’s heightened expression in gastric cancer had been essentially linked with pathological stage, tumor differentiation, and T classification. The Kaplan–Meier curve in the Kaplan-Meier plotter database (<i>P</i> = 0.0371) and GSE84437 (<i>P</i> = 0.002) indicate that patients with high COL10A1 expression possess poor prognosis, specifically GC patients with lymph node metastasis have it. TCGA’s Multivariate analysis (<i>P</i> = 0.025) and GSE84437 dataset (<i>P</i> = 0.034) show that high expression COL10A1 is a key independent predictor of poor overall survival. Searching KEGG pathway enrichment by GSEA, the results suggested that 29 pathways were enriched. qRT-PCR technique was used for verification of the COL10A1’s high expression in gastric cancer in contrast to the normal gastric tissues. In conclusion, COL10A1 is of great importance in predicting the survival rate of GC patients.
DOI: 10.6084/m9.figshare.11924976.v1
title: Additional file 28 of Comparative functional genomics analysis of cytochrome P450 gene superfamily in wheat and maize

description: Additional file 28: Table S10. List of 477 TaCYP450s in 22 modules.
DOI: 10.6084/m9.figshare.20307481
title: Additional file 1 of Transcriptomic analysis reveals the key role of histone deacetylation via mediating different phytohormone signalings in fiber initiation of cotton

description: Additional file 1: Table S1. The gene ID list of 4,209 DEGs identified between mock and TSA-treated ovules.
DOI: 10.6084/m9.figshare.11925213
title: Additional file 5 of Genome-wide identification of CNGC genes in Chinese jujube (Ziziphus jujuba Mill.) and ZjCNGC2 mediated signalling cascades in response to cold stress

description: Additional file S5. The number of introns and exons of ZjCNGCs.
DOI: 10.6084/m9.figshare.20307493.v1
title: Additional file 3 of Transcriptomic analysis reveals the key role of histone deacetylation via mediating different phytohormone signalings in fiber initiation of cotton

description: Additional file 3: Table S3. The FPKM values of each gene in classifications a, b, c, and d.
DOI: 10.6084/m9.figshare.11925216
title: Additional file 6 of Genome-wide identification of CNGC genes in Chinese jujube (Ziziphus jujuba Mill.) and ZjCNGC2 mediated signalling cascades in response to cold stress

description: Additional file S6. The primer sequences for amplification of the ZjCNGC genes for qPCR.
DOI: 10.6084/m9.figshare.17161633
title: Additional file 2 of Microbial co-occurrence complicates associations of gut microbiome with US immigration, dietary intake and obesity

description: Additional file 2: Table S2. Associations of 84 gut bacterial genera with obesity and US exposure.
DOI: 10.6084/m9.figshare.17161636
title: Additional file 3 of Microbial co-occurrence complicates associations of gut microbiome with US immigration, dietary intake and obesity

description: Additional file 3: Table S4. Associations of 84 gut bacterial genera with obesity and US exposure after further adjusted for Hispanic background.
DOI: 10.6084/m9.figshare.20307493
title: Additional file 3 of Transcriptomic analysis reveals the key role of histone deacetylation via mediating different phytohormone signalings in fiber initiation of cotton

description: Additional file 3: Table S3. The FPKM values of each gene in classifications a, b, c, and d.
DOI: 10.34740/kaggle/dsv/7329748
title: Global Temperature Records (1743-2013)
DOI: 10.6084/m9.figshare.11925216.v1
title: Additional file 6 of Genome-wide identification of CNGC genes in Chinese jujube (Ziziphus jujuba Mill.) and ZjCNGC2 mediated signalling cascades in response to cold stress

description: Additional file S6. The primer sequences for amplification of the ZjCNGC genes for qPCR.
DOI: 10.6084/m9.figshare.17161642.v1
title: Additional file 5 of Microbial co-occurrence complicates associations of gut microbiome with US immigration, dietary intake and obesity

description: Additional file 5: Table S6. Associations of gut bacterial genera with obesity (BMI), stratified by Hispanic background groups.
DOI: 10.6084/m9.figshare.25253971
title: genomes.txt

description: this is the genome.txt file for a UCSC hub
DOI: 10.6084/m9.figshare.25253971.v1
title: genomes.txt

description: this is the genome.txt file for a UCSC hub
DOI: 10.26207/73fv-ft48
title: Data and code for "Complementary feedback control enables effective gaze stabilization in animals"
DOI: 10.6084/m9.figshare.13498051
title: Additional file 2 of Integrative analysis of histopathological images and chromatin accessibility data for estrogen receptor-positive breast cancer

description: Additional file 2: Supplemental Table 1. The epithelial tissue proportion data of 54 TCGA ER-positive BRCA cases. Supplemental Table 2. The ATAC-seq peak signal data of 54 TCGA ER-positive BRCA cases. Supplemental Table 3. Significant epithelial tissue proportion-associated peaks and their target genes. Supplemental Table 4. Promoter and distal enhancer peak-to-gene links and their target genes. Supplemental Table 5. Expression data of the identified genes and clinical information for 663 TCGA ER-positive BRCA cases. Supplemental Table 6. Results of the univariate survival analysis.
DOI: 10.6084/m9.figshare.20307688.v1
title: Additional file 4 of Genome-wide identification and expression analysis of the ftsH protein family and its response to abiotic stress in Nicotiana tabacum L

description: Additional file 4: Table S2. List of the tandem repeat gene pairs of ftsH in tobacco.
DOI: 10.6084/m9.figshare.7731314.v1
title: Autophagy-dependent release of zinc ions is critical for acute lung injury triggered by zinc oxide nanoparticles

description: Pulmonary exposure to zinc oxide nanoparticles (ZnONPs) could cause acute lung injury (ALI), but the underlying molecular mechanism remains unclear. Herein, we established a ZnONPs-induced ALI mouse model, characterized by the histopathological changes (edema and infiltration of inflammatory cells in lung tissues), and the elevation of total protein and cytokine interleukin-6 in bronchoalveolar lavage fluid in time- and dose-dependent manners. This model also exhibited features like the disturbance of redox-state (reduced of glutathione to glutathione disulfide ratio, elevation of heme oxygenase-1 and superoxide dismutase 2), the decrease of adenosine triphosphate synthesis and the release of zinc ions in the lung tissues. Interestingly, we found that ZnONPs exposure caused the accumulation of autophagic vacuoles and the elevation of microtubule-associated proteins 1A/1B light chain (LC)3B-II and p62, indicating the impairment of autophagic flux. Our data indicated that the above process might be regulated by the activation of AMP-activated protein kinase but not the mammalian target of rapamycin pathway. The association between ZnONPs-induced ALI and autophagy was further verified by a classical autophagy inhibitor, 3-methyladenine (3-MA). 3-MA administration reduced the accumulation of autophagic vacuoles, the expression of LC3B-II and p62, followed by a significant attenuation of histopathological changes, inflammation, and oxidative stress. More importantly, 3-MA could directly decrease the release of zinc ions in lung tissues. Taken together, our study provides the evidence that ZnONPs-induced pulmonary toxicity is autophagy-dependent, suggests that limiting the release of zinc ions by inhibiting autophagy could be a feasible strategy for the prevention of ZnONPs-associated pulmonary toxicity.
DOI: 10.6084/m9.figshare.6682367.v2
title: Peritumoral monocytes induce cancer cell autophagy to facilitate the progression of human hepatocellular carcinoma

description: Macroautophagy/autophagy is an important catabolic process mediating cellular homeostasis and plays critical roles in cancer development. Whereas autophagy has been widely studied in various pathological models, little is known about the distribution, clinical significance and regulatory mechanism of this process in human hepatocellular carcinoma (HCC). In the present study, we found that tumor tissues exhibited significantly increased levels of autophagy compared with non-tumor tissues, and cancer cells with higher levels of autophagy were predominantly enriched in the invading edge regions of human HCC. Increased MAP1LC3B/LC3B expression in the invading edge regions was significantly correlated with a higher density of closely located monocytes, and TNF and IL1B derived from tumor-activated monocytes synergistically induced cancer cell autophagy in the invading edge regions of HCC. Monocyte-elicited autophagy induced the epithelial-mesenchymal transition (EMT) of cancer cells and promoted tumor metastasis by activating the NFKB-SNAI1 signaling pathway. Moreover, the increase of LC3B<sup>+</sup> cancer cells in the invading edge areas was associated with high mortality and reduced survival of patients with HCC. These findings indicated that cancer cell autophagy is regulated by a collaborative interaction between tumor and immune cell components in distinct HCC microenvironments, thus allowing the inflammatory monocytes to be rerouted in a tumor-promoting direction.
DOI: 10.6084/m9.figshare.25254016
title: hub.txt

description: this is the hub file for a UCSC hub
DOI: 10.6084/m9.figshare.25254016.v1
title: hub.txt

description: this is the hub file for a UCSC hub
DOI: 10.34740/kaggle/dsv/7666087
title: Full TMDB Movies Dataset 2024 (985K Movies)