cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13220221.v2
title: ESRRA (estrogen related receptor alpha) is a critical regulator of intestinal homeostasis through activation of autophagic flux via gut microbiota

description: The orphan nuclear receptor ESRRA (estrogen related receptor alpha) is critical in mitochondrial biogenesis and macroautophagy/autophagy function; however, the roles of ESRRA in intestinal function remain uncharacterized. Herein we identified that ESRRA acts as a key regulator of intestinal homeostasis by amelioration of colonic inflammation through activation of autophagic flux and control of host gut microbiota. <i>Esrra</i>-deficient mice presented with increased susceptibility to dextran sodium sulfate (DSS)-induced colitis with upregulation of intestinal inflammation. In addition, <i>esrra</i>-null mice had depressed AMP-activated protein kinase phosphorylation (AMPK), lower levels of TFEB (transcription factor EB), and accumulation of SQSTM1/p62 (sequestosome 1) with defective mitochondria in intestinal tissues. <i>Esrra</i>-deficient mice showed distinct gut microbiota composition and significantly higher microbial diversity than wild-type (WT) mice. Cohousing or fecal microbiota transplantation from WT mice to <i>Esrra</i>-deficient mice ameliorated DSS-induced colitis severity. Importantly, patients with ulcerative colitis (UC) had significantly decreased <i>ESRRA</i> expression in intestinal mucosal tissues that correlated with disease activity, suggesting clinical relevance of ESRRA in UC. Taken together, our results show that ESRRA contributes to intestinal homeostasis through autophagy activation and gut microbiota control to protect the host from detrimental inflammation and dysfunctional mitochondria.
DOI: 10.6084/m9.figshare.7453586
title: Additional file 1: of Genetic ancestry, admixture and health determinants in Latin America

description: Table S1. Lists of all SNPs that show significant ancestry-enrichment. For each admixed Latin American population, all ancestry-enriched SNPs (q &lt; 0.05) are given along with their meta-information, observed and expected reference and alternate allele frequencies, and significance values. The allele (reference or alternate) and enriched ancestry (African, European or Native American) are designated for each ancestry-enriched SNP. (XLSX 177 kb)
DOI: 10.6084/m9.figshare.13220224.v3
title: Equine lentivirus counteracts SAMHD1 restriction by Rev-mediated degradation of SAMHD1 via the BECN1-dependent lysosomal pathway

description: The innate immune restriction factor SAMHD1 can inhibit diverse viruses in myeloid cells. Mechanistically, SAMHD1 inhibits lentiviral replication including HIV-1 by depleting the nucleotide pool to interfere with their reverse transcription. Equine infectious anemia virus (EIAV) is an ancient lentivirus that preferentially attacks macrophages. However, the mechanism by which EIAV successfully establishes infection in macrophages with functional SAMHD1 remains unclear. Here, we demonstrate that while equine SAMDH1 can limit EIAV replication in equine macrophages at the reverse transcription stage, the antiviral effect is counteracted by the well-known transcriptional regulator Rev, which downregulates equine SAMHD1 through the lysosomal pathway. Remarkably, Rev hijacks BECN1 (beclin 1) and PIK3C3 to mediate SAMHD1 degradation in a canonical macroautophagy/autophagy-independent pathway. Our study illustrates that equine lentiviral Rev possesses important functions in evading cellular innate immunity in addition to its RNA regulatory function, and may provide new insights into the co-evolutionary arms race between SAMHD1 and lentiviruses. <b>Abbreviations</b>:3-MA: 3-methyladenine; AA: amino acid; ACTB: actin beta; AD: activation domain; ATG: autophagy related; Baf A1: bafilomycin A<sub>1</sub>; BD: binding domain; BECN1: beclin 1; BH3: BCL2-homology-3 domain; BiFC: bimolecular fluorescence complementation; CCD: coiled-coil domain; class III PtdIns3K: class III phosphatidylinositol 3-kinase; CQ: chloroquine; Co-IP: co-immunoprecipitation; dNTPase: dGTP-stimulated deoxynucleoside triphosphate triphosphohydrolase; ECD: evolutionarily conserved domain; EIAV: equine infectious anemia virus; eMDMs: equine monocyte-derived macrophages; GFP: green fluorescent protein; HD: histidine-aspartic; HIV-1: human immunodeficiency virus-1; hpi: hours post infection; hpt: hours post transfection; KO: knockout; LAMP2: lysosomal associated membrane protein 2; LMB: leptomycin B; PMA: phorbol 12-myristate 13-acetate; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; ND: unknown non-essential domain; NES: nuclear export signal; NLS: localization signal; NS: statistically non-significant; PIK3C3: phosphatidylinositol 3-kinase catalytic subunit type 3; RBD: RNA binding domain; RT: reverse transcriptase; siRNAs: small interfering RNAs; SAMHD1: SAM and HD domain containing deoxynucleoside triphosphate triphosphohydrolase 1; SIV: simian immunodeficiency virus; VN: C-terminal residues of Venus 174 to 238; VC: N-terminal residues 2 to 173 of Venus
DOI: 10.6084/m9.figshare.7453586.v1
title: Additional file 1: of Genetic ancestry, admixture and health determinants in Latin America

description: Table S1. Lists of all SNPs that show significant ancestry-enrichment. For each admixed Latin American population, all ancestry-enriched SNPs (q &lt; 0.05) are given along with their meta-information, observed and expected reference and alternate allele frequencies, and significance values. The allele (reference or alternate) and enriched ancestry (African, European or Native American) are designated for each ancestry-enriched SNP. (XLSX 177 kb)
DOI: 10.6084/m9.figshare.7453589.v1
title: Additional file 2: of Genetic ancestry, admixture and health determinants in Latin America

description: Table S2. Lists of pathways that show significant enrichment of genes with mapped ancestry-enriched SNPs for each admixed Latin American population. For each KEGG pathway with significant enrichment of genes with mapped ancestry-enriched SNPs in at least one of the four populations, the overlapping genes and FDR q-values are given. (XLSX 29.6 kb)
DOI: 10.6084/m9.figshare.12172101.v1
title: Additional file 5 of Network Pharmacology Approach to Uncover the Mechanism Governing the Effect of Radix Achyranthis Bidentatae on Osteoarthritis

description: Additional file 5. Supplementary Table 5: Results of ligand-receptor protein molecular docking.
DOI: 10.6084/m9.figshare.12172077.v1
title: Additional file 1 of Network Pharmacology Approach to Uncover the Mechanism Governing the Effect of Radix Achyranthis Bidentatae on Osteoarthritis

description: Additional file 1. Supplementary Table 1: Potential target information of RAB for OA.
DOI: 10.6084/m9.figshare.12172095
title: Additional file 4 of Network Pharmacology Approach to Uncover the Mechanism Governing the Effect of Radix Achyranthis Bidentatae on Osteoarthritis

description: Additional file 4. Supplementary Table 4: Compound-target pair information.
DOI: 10.6084/m9.figshare.12172101
title: Additional file 5 of Network Pharmacology Approach to Uncover the Mechanism Governing the Effect of Radix Achyranthis Bidentatae on Osteoarthritis

description: Additional file 5. Supplementary Table 5: Results of ligand-receptor protein molecular docking.
DOI: 10.6084/m9.figshare.12172089.v1
title: Additional file 3 of Network Pharmacology Approach to Uncover the Mechanism Governing the Effect of Radix Achyranthis Bidentatae on Osteoarthritis

description: Additional file 3. Supplementary Table 3: Common gene of RAB in the treatment of OA.
DOI: 10.6084/m9.figshare.12172095.v1
title: Additional file 4 of Network Pharmacology Approach to Uncover the Mechanism Governing the Effect of Radix Achyranthis Bidentatae on Osteoarthritis

description: Additional file 4. Supplementary Table 4: Compound-target pair information.
DOI: 10.6084/m9.figshare.7453556.v1
title: MOESM2 of Global discovery of small RNAs in the fish pathogen Edwardsiella piscicida: key regulator of adversity and pathogenicity

description: Additional file 2. Differential expression anlysis of sRNAs during three stress condition.
DOI: 10.6084/m9.figshare.7453625.v1
title: Additional file 2: of Differential responses of Lasiopodomys mandarinus and Lasiopodomys brandtii to chronic hypoxia: a cross-species brain transcriptome analysis

description: Table S5. DEGs for L. mandarinus and L. brandtii. (XLSX 48 kb)
DOI: 10.6084/m9.figshare.7453562
title: MOESM4 of Global discovery of small RNAs in the fish pathogen Edwardsiella piscicida: key regulator of adversity and pathogenicity

description: Additional file 4. Predicted DEsRNA target genes.
DOI: 10.6084/m9.figshare.12172077
title: Additional file 1 of Network Pharmacology Approach to Uncover the Mechanism Governing the Effect of Radix Achyranthis Bidentatae on Osteoarthritis

description: Additional file 1. Supplementary Table 1: Potential target information of RAB for OA.
DOI: 10.6084/m9.figshare.12172089
title: Additional file 3 of Network Pharmacology Approach to Uncover the Mechanism Governing the Effect of Radix Achyranthis Bidentatae on Osteoarthritis

description: Additional file 3. Supplementary Table 3: Common gene of RAB in the treatment of OA.
DOI: 10.6084/m9.figshare.7453562.v1
title: MOESM4 of Global discovery of small RNAs in the fish pathogen Edwardsiella piscicida: key regulator of adversity and pathogenicity

description: Additional file 4. Predicted DEsRNA target genes.
DOI: 10.6084/m9.figshare.7453571
title: MOESM5 of Global discovery of small RNAs in the fish pathogen Edwardsiella piscicida: key regulator of adversity and pathogenicity

description: Additional file 5. The expression of Hfq-dependent sRNAs were identified by quantitative real time PCR. Five upregulated sRNAs (left) and 14 downregulated sRNAs (right) identified by RNA-sequencing were checked by qRT-PCR. The experiment was performed three times, and values are shown as mean ± SEM. *P &lt; 0.05, **P &lt; 0.01.
DOI: 10.6084/m9.figshare.7453532
title: Additional file 1: of Impact of parental migration on oral health outcomes of left-behind school-aged children in Luchuan, southern China

description: Table S1. Comparisons of oral health-related variables between various experiences of parental migration (NÂ =â 1085). (XLS 33 kb)
DOI: 10.6084/m9.figshare.13151796.v1
title: Additional file 7 of Ecological genomics of Chinese wheat improvement: implications in breeding for adaptation

description: Additional file 7: Table S3. Genotypic information regarding the 438 wheat accessions used in this study.
DOI: 10.6084/m9.figshare.4308032.v2
title: Detecting signatures of selection within the Tibetan sheep mitochondrial genome

description: Tibetan sheep, a Chinese indigenous breed, are mainly distributed in plateau and mountain-valley areas at a terrestrial elevation between 2260 and 4100 m. The herd is genetically distinct from the other domestic sheep and undergoes acclimatization to adapt to the hypoxic environment. To date, whether the mitochondrial DNA modification of Tibetan sheep shares the same feature as the other domestic breed remains unknown. In this study, we compared the whole mitogenome sequences from 32 Tibetan sheep, 22 domestic sheep and 24 commercial sheep to identify the selection signatures of hypoxic-tolerant in Tibetan sheep. Nucleotide diversity analysis using the sliding window method showed that the highest level of nucleotide diversity was observed in the control region with a peak value of <i>π</i> = 0.05215, while the lowest <i>π</i> value was detected in the <i>tRNAs</i> region. qPCR results showed that the relative mtDNA copy number in Tibetan sheep was significantly lower than that in Suffolk sheep. None of the mutations in <i>12S rRNA</i> were fixed in Tibetan sheep, which indicated that there has been less artificial selection in this herd than the other domestic and commercial breeds. Although one site (1277G) might undergo the purifying selection, it was not identified as the breed-specific allele in Tibetan sheep. We proposed that nature selection was the main drive during the domestication of Tibetan sheep and single mutation (or locus) could not reveal the signature of selection as for the high diversity in the mitogenome of Tibetan sheep.
DOI: 10.6084/m9.figshare.13151796
title: Additional file 7 of Ecological genomics of Chinese wheat improvement: implications in breeding for adaptation

description: Additional file 7: Table S3. Genotypic information regarding the 438 wheat accessions used in this study.
DOI: 10.6084/m9.figshare.4308032.v1
title: Detecting signatures of selection within the Tibetan sheep mitochondrial genome

description: Tibetan sheep, a Chinese indigenous breed, are mainly distributed in plateau and mountain-valley areas at a terrestrial elevation between 2260 and 4100 m. The herd is genetically distinct from the other domestic sheep and undergoes acclimatization to adapt to the hypoxic environment. To date, whether the mitochondrial DNA modification of Tibetan sheep shares the same feature as the other domestic breed remains unknown. In this study, we compared the whole mitogenome sequences from 32 Tibetan sheep, 22 domestic sheep and 24 commercial sheep to identify the selection signatures of hypoxic-tolerant in Tibetan sheep. Nucleotide diversity analysis using the sliding window method showed that the highest level of nucleotide diversity was observed in the control region with a peak value of <i>π</i> = 0.05215, while the lowest <i>π</i> value was detected in the <i>tRNAs</i> region. qPCR results showed that the relative mtDNA copy number in Tibetan sheep was significantly lower than that in Suffolk sheep. None of the mutations in <i>12S rRNA</i> were fixed in Tibetan sheep, which indicated that there has been less artificial selection in this herd than the other domestic and commercial breeds. Although one site (1277G) might undergo the purifying selection, it was not identified as the breed-specific allele in Tibetan sheep. We proposed that nature selection was the main drive during the domestication of Tibetan sheep and single mutation (or locus) could not reveal the signature of selection as for the high diversity in the mitogenome of Tibetan sheep.
DOI: 10.6084/m9.figshare.7453751.v1
title: MOESM1 of A heterogeneous label propagation approach to explore the potential associations between miRNA and disease

description: Additional file 1. All candidate miRNAs were ranked by HLPMDA for all the diseases in HMDD v2.0. Prediction results could be obtained publicly for further research and experimental validation.
DOI: 10.6084/m9.figshare.13151802
title: Additional file 9 of Ecological genomics of Chinese wheat improvement: implications in breeding for adaptation

description: Additional file 9: Table S4. Frequencies of allelic variations of 47 polymorphic genes in Chinese landraces (CL) and modern Chinese cultivars (MCC) in ten wheat agro-ecological zones.
DOI: 10.6084/m9.figshare.7453571.v1
title: MOESM5 of Global discovery of small RNAs in the fish pathogen Edwardsiella piscicida: key regulator of adversity and pathogenicity

description: Additional file 5. The expression of Hfq-dependent sRNAs were identified by quantitative real time PCR. Five upregulated sRNAs (left) and 14 downregulated sRNAs (right) identified by RNA-sequencing were checked by qRT-PCR. The experiment was performed three times, and values are shown as mean ± SEM. *P &lt; 0.05, **P &lt; 0.01.
DOI: 10.6084/m9.figshare.7453823
title: Additional file 1: of SKA1 overexpression is associated with poor prognosis in hepatocellular carcinoma

description: Expression data of SKA1 in matched HCC and non-tumor liver tissues from TCGA database. (XLS 61 kb)
DOI: 10.6084/m9.figshare.13151787
title: Additional file 4 of Ecological genomics of Chinese wheat improvement: implications in breeding for adaptation

description: Additional file 4: Table S2. Genetic diversity and Fst for 47 polymorphic genes between Chinese landraces (CL) and modern Chinese cultivars (MCC) in ten wheat agro-ecological zones.
DOI: 10.6084/m9.figshare.7453751
title: MOESM1 of A heterogeneous label propagation approach to explore the potential associations between miRNA and disease

description: Additional file 1. All candidate miRNAs were ranked by HLPMDA for all the diseases in HMDD v2.0. Prediction results could be obtained publicly for further research and experimental validation.
DOI: 10.6084/m9.figshare.13151802.v1
title: Additional file 9 of Ecological genomics of Chinese wheat improvement: implications in breeding for adaptation

description: Additional file 9: Table S4. Frequencies of allelic variations of 47 polymorphic genes in Chinese landraces (CL) and modern Chinese cultivars (MCC) in ten wheat agro-ecological zones.
DOI: 10.6084/m9.figshare.25195637
title: Supplementary Material for: The Wound Healing of Autologous Regenerative Factor on Recurrent Benign Airway Stenosis: A Canine Experimental and Pilot Study

description: <b><i>Introduction:</i></b> Benign airway stenosis (BAS) is a severe pathologic condition. Complex stenosis has a high recurrence rate and requires repeated bronchoscopic interventions for achieving optimal control, leading to recurrent BAS (RBAS) due to intraluminal granulation. <b><i>Methods:</i></b> This study explored the potential of autologous regenerative factor (ARF) for treating RBAS using a post-intubation tracheal stenosis canine model. Bronchoscopic follow-ups were conducted, and RNA-seq analysis of airway tissue was performed. A clinical study was also initiated involving 17 patients with recurrent airway stenosis. <b><i>Results:</i></b> In the animal model, ARF demonstrated significant effectiveness in preventing further collapse of the injured airway, maintaining airway patency and promoting tissue regeneration. RNA-seq results showed differential gene expression, signifying alterations in cellular components and signaling pathways. The clinical study found that ARF treatment was well-tolerated by patients with no severe adverse events requiring hospitalization. ARF treatment yielded a high response rate, especially for post-intubation tracheal stenosis and idiopathic tracheal stenosis patients. <b><i>Conclusion:</i></b> The study concludes that ARF presents a promising, effective, and less-invasive method for treating RBAS. ARF has shown potential in prolonging the intermittent period and reducing treatment failure in patients with recurrent tracheal stenosis by facilitating tracheal mucosal wound repair and ameliorating tracheal fibrosis. This novel approach could significantly impact future clinical applications.
DOI: 10.6084/m9.figshare.7453823.v1
title: Additional file 1: of SKA1 overexpression is associated with poor prognosis in hepatocellular carcinoma

description: Expression data of SKA1 in matched HCC and non-tumor liver tissues from TCGA database. (XLS 61 kb)
DOI: 10.5281/zenodo.10638698
title: DMLR @ ICLR 2024 Dataset for Atomic Data Groups

description: Use the most recent up-to-date version in the right-hand sidebar of this page.

 

The data contained herein is sufficient and necessary to reproduce the results of the paper "Atomic Data Groups: An issue in train-test splits for thereal world as demonstrated through digital hardware design".
DOI: 10.5281/zenodo.10638699
title: DMLR @ ICLR 2024 Dataset for Atomic Data Groups

description: Use the most recent up-to-date version in the right-hand sidebar of this page.

 

The data contained herein is sufficient and necessary to reproduce the results of the paper "Atomic Data Groups: An issue in train-test splits for thereal world as demonstrated through digital hardware design".
DOI: 10.5281/zenodo.10638650
title: Real-time RT-PCR targeting S2

description: Figure S1: Determination of the limit of detection (LOD) of S2 subunit; 

Table S1: Sequences of SARS-CoV-2 genome submitted from January to October 2022; 

Table S2: Mutations in the binding sites of primers and probe.
DOI: 10.5281/zenodo.10638651
title: Real-time RT-PCR targeting S2

description: Figure S1: Determination of the limit of detection (LOD) of S2 subunit; 

Table S1: Sequences of SARS-CoV-2 genome submitted from January to October 2022; 

Table S2: Mutations in the binding sites of primers and probe.
DOI: 10.6084/m9.figshare.20033217.v1
title: Additional file 7 of Comprehensive identification and characterization of the HERV-K (HML-9) group in the human genome

description: Additional file 7: Table S5. PBS types in HML-9.
DOI: 10.6084/m9.figshare.20033187
title: Additional file 2 of Comprehensive identification and characterization of the HERV-K (HML-9) group in the human genome

description: Additional file 2: Dataset S2. The nucleotide sequence of HML-9 solo LTR elements.
DOI: 10.5281/zenodo.10638629
title: Thematic Analysis Data
DOI: 10.5281/zenodo.10638630
title: Thematic Analysis Data
DOI: 10.6084/m9.figshare.22655253.v1
title: Additional file 2 of Identification of a m6A-related ferroptosis signature as a potential predictive biomarker for lung adenocarcinoma

description: Additional file 2: Supplementary Table 2. 348 ferroptosis genes were downloaded from the FerrDb database.
DOI: 10.6084/m9.figshare.20033151
title: Additional file 2 of Characterization of a prognostic model for lung squamous cell carcinoma based on eight stemness index-related genes

description: Additional file 2: Table S1. The results of differential expression analysis.
DOI: 10.6084/m9.figshare.20033187.v1
title: Additional file 2 of Comprehensive identification and characterization of the HERV-K (HML-9) group in the human genome

description: Additional file 2: Dataset S2. The nucleotide sequence of HML-9 solo LTR elements.
DOI: 10.6084/m9.figshare.7460012
title: Additional file 2: of Detecting the priority areas for health workforce allocation with LISA functions: an empirical analysis for China

description: Table S1. The number of different types of health workforce and population data in urban China in 2016. (XLSX 11â kb)
DOI: 10.6084/m9.figshare.22133961.v2
title: Joint Diagnosis of High-Dimensional Process Mean and Covariance Matrix based on Bayesian Model Selection

description: Apart from the quick detection of abnormal changes in a process, it is also critical to pinpoint faulty variables after an out-of-control signal. The existing diagnostic procedures mainly focus on the diagnosis of changes in the process mean. This article investigates the joint diagnosis of high-dimensional process mean and covariance matrix based on Bayesian model selection with nonlocal priors. The proposed procedure enjoys two promising features. First, in addition to the isolation of shifted components, it can also provide a probability that the identified components are true, which is very useful for elimination of root causes of abnormal changes. Second, it possesses the model consistency property in the sense that the probability of identifying the true components with shifts approaches one as the sample size increases. The performance comparisons favor the proposed procedure. A real example based on the urban waste water treatment process is provided to illustrate the implementation of the proposed method.