cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14865087
title: Structure and dynamics of major histocompatibility class Ib molecule H2-M3 complexed with mitochondrial-derived peptides

description: Presentation of antigenic peptides to T-cell receptors is an essential step in the adaptive immune response. In the mouse the class Ib major histocompatibility complex molecule, H2-M3, presents bacterial- and mitochondrial-derived peptides to T-cell receptors on cytotoxic T cells. Four mitochondrial heptapeptides, differing only at residue 6, form complexes with H2-M3 which can be distinguished by T cells. No structures of relevant receptors are available. To investigate the structural basis for this distinction, crystal structures were determined and molecular dynamics simulations over one microsecond were done for each complex. In the crystal structures of the heptapeptide complexes with H2-M3, presented here, the side chains of the peptide residues at position 6 all point into the H2-M3 binding groove, and are thus inaccessible, so that the very similar structures do not suggest how recognition and initiation of responses by the T cells may occur. However, conformational differences, which could be crucial to T-cell discrimination, appear within one microsecond during molecular dynamics simulations of the four complexes. Specifically, the three C-terminal residues of peptide ligands with alanine or threonine at position 6 partially exit the binding groove; this does not occur in peptide ligands with isoleucine or valine at position 6. Structural changes associated with partial peptide exit from the binding groove, along with relevant peptide binding energetics and immunological results are discussed. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.21152060
title: Additional file 3 of A circular RNA derived from GLIS3 accelerates the proliferation of glioblastoma cells through competitively binding with miR-449c-5p to upregulate CAPG and GLIS3

description: Additional file 3: Table S1. Sequences used for gene knockdown and overexpression.
DOI: 10.6084/m9.figshare.7001348
title: Methods used to assess the performance of biomarkers for the diagnosis of acute kidney injury: a systematic review and meta-analysis

description: <b>Purpose:</b> Methods used to explore biomarkers for acute kidney injury (AKI) might have a major impact on the results and the use of these biomarkers. We evaluated the methods used to investigate biomarkers of AKI. <b>Materials and methods:</b> A systematic review and meta-analysis were performed using a computerized search of the MEDLINE and the EMBASE databases (PROSPERO CRD42017059618). Articles reporting biomarker’s performance to diagnose AKI were included. The outcome included a description of the methods used to assess the performance of biomarkers to diagnose AKI. <b>Results:</b> Among the 295 included studies, assessment of biomarkers was the primary endpoint in 284 with sample size calculation in only 8% of cases. Eighty-five percent of the studies summarized the performance of biomarkers with receiver operating characteristic (ROC) curves; however, 74 studies (25%) did not provide the threshold, sensibility or specificity. A total of 176 studies evaluated more than one biomarker, and only 25% combined biomarkers to increase diagnostic performance. We determined that the definition of AKI and study design impacted the diagnostic performance using uNGAL (urinary neutrophil gelatinase-associated lipocalin) as an example. Major publication bias was identified. <b>Conclusions:</b> Most articles that reported biomarkers of AKI performance present methodological weaknesses. Basic rules should be provided to increase the quality of reporting in this area.
DOI: 10.6084/m9.figshare.13292463.v1
title: Long noncoding RNA HOTAIR regulates myeloid differentiation through the upregulation of p21 via miR-17-5p in acute myeloid leukemia

description: Long non-coding RNA HOTAIR has been reported to play a key role in regulating various biological processes in various cancers. However, the roles and mechanisms of HOTAIR in acute myeloid leukemia (AML) are still unclear and need to be investigated. In this study, we induced differentiation of four AML cell lines by all-trans retinoic acid (ATRA) and found HOTAIR was significantly upregulated in the process. Chromatin immunoprecipitation (ChIP) assays indicated that C/EBPβ upregulated HOTAIR during ATRA induced differentiation in HL-60 cells. By gain- and loss-of-function analysis, we then observed that HOTAIR expression was positively correlated with ATRA-induced differentiation and negatively regulated G1 phase arrest in HL-60 cells. In addition, we found that HOTAIR promoted ATRA-induced differentiation via the regulation of the cell cycle regulator p21 via miR-17-5p. Moreover, we detected the expression of HOTAIR in 84 de novo AML patients, HOTAIR was found significantly downregulated in the AML patients compared to the iron deficiency anemia (IDA) control group, negatively correlated with the platelet level in M2 patients. In all, our data suggest that HOTAIR may be subtype-specific in AML-M2 patients, also HOTAIR regulates AML differentiation by C/EBPBβ/HOTAIR/miR-17-5p/p21 pathway. The findings of the present study provide a novel insight into the mechanism of lncRNA-mediated differentiation and indicate that HOTAIR may be a promising therapeutic target for leukemia, especially for AML with M2 type.
DOI: 10.6084/m9.figshare.22724223
title: Additional file 2 of Polycyclic aromatic hydrocarbon (PAH) biodegradation capacity revealed by a genome-function relationship approach

description: Additional file 2. The summary of protein sequences in the PAH-degrading gene database. Detailed information of 225 strains with complete/near-complete PAH-degrading gene cluster.
DOI: 10.6084/m9.figshare.12854120.v1
title: The nature of Early Palaeozoic Kwangsian orogenic event in the South China Block: constraints from detrital zircons in Cambrian strata

description: The tectonic nature of Early Palaeozoic Kwangsian orogeny in the South China Block (SCB) is still debated, due to controversy whether there was a Cambrian ocean between the Yangtze Block and the Cathaysia Block. Similarly, continental affinities of the SCB with India and Australia in East Gondwana during the Cambrian are also controversial. Herein, we present detrital zircon U-Pb geochronology of Cambrian sandstone samples from the southern SCB. Cambrian samples (including our new samples and published samples) from the Cathaysia Block and the Yangtze Block show similar detrital zircon age spectra with one prominent age cluster of ~1000-900 Ma and several subordinate age groups, as well as similar cumulative proportion curves (CPC). Such signatures, together with other geological records, suggest that a Cambrian ocean did not exist between the Cathaysia Block and the Yangtze Block, and that Early Palaeozoic Kwangsian orogeny resulted from an intra-continental collision. Cambrian samples from the SCB have much more similar detrital zircon age spectra and CPC to those from Himalaya and Qiangtang than those from Australia, but detrital zircons in Cambrian samples from the SCB, Himalaya, Qiangtang and Australia have a similar prominent age group of ~1000-900 Ma. Thus, the SCB were likely located between Australia and India during the Cambrian, receiving sediments both from India and Australia.
DOI: 10.6084/m9.figshare.19583559
title: Oxycodone protects cardiac microvascular endothelial cells against ischemia/reperfusion injury by binding to Sigma-1 Receptor

description: Endothelial dysfunction is an important mechanism involved in myocardial ischemia-reperfusion (I/R) injury. We aimed to explore the effects of Oxycodone on myocardial I/R injury in vivo and in vitro to reveal its mechanisms related to Sigma-1 Receptor (SIGMAR1). A rat model of I/R-induced myocardial injury was developed. The ischemic area and myocardial histopathological changes after oxycodone addition were evaluated by TTC staining and H&E staining. LDH, CK-MB and cTnI levels were used to assess myocardial function. Then, the endothelial integrity was reflected by the expressions of ZO-1, Claudin-1 and Occludin. Afterward, ELISA, RT-qPCR, western blot and immunofluorescence assays were adopted for the detection of inflammation-related genes. SIGMAR1 expression in myocardial tissues induced by I/R and cardiac microvascular endothelial cells (CMECs) under hypoxic/reoxygenation (H/R) was determined using RT-qPCR and western blotting. Subsequently, after SIGMAR1 silencing or BD1047 addition (a SIGMAR1 antagonist), cell apoptosis and endothelial integrity were analyzed in the presence of Oxycodone in H/R-stimulated CMECs. Results indicated that Oxycodone decreased the ischemic area and improved myocardial function in myocardial I/R injury rat. Oxycodone improved myocardial histopathological injury and elevated endothelial integrity, evidenced by upregulated ZO-1, Claudin-1 and Occludin expressions. Moreover, inflammatory response was alleviated after Oxycodone administration. Molecular docking suggested that SIGMAR1 could directly bind to Oxycodone. Oxycodone elevated SIGMAR1 expression and SIGMAR1 deletion or BD1047 addition attenuated the impacts of Oxycodone on apoptosis and endothelial integrity of CMECs induced by H/R. Collectively, Oxycodone alleviates myocardial I/R injury in vivo and in vitro by binding to SIGMAR1.
DOI: 10.6084/m9.figshare.19583559.v1
title: Oxycodone protects cardiac microvascular endothelial cells against ischemia/reperfusion injury by binding to Sigma-1 Receptor

description: Endothelial dysfunction is an important mechanism involved in myocardial ischemia-reperfusion (I/R) injury. We aimed to explore the effects of Oxycodone on myocardial I/R injury in vivo and in vitro to reveal its mechanisms related to Sigma-1 Receptor (SIGMAR1). A rat model of I/R-induced myocardial injury was developed. The ischemic area and myocardial histopathological changes after oxycodone addition were evaluated by TTC staining and H&E staining. LDH, CK-MB and cTnI levels were used to assess myocardial function. Then, the endothelial integrity was reflected by the expressions of ZO-1, Claudin-1 and Occludin. Afterward, ELISA, RT-qPCR, western blot and immunofluorescence assays were adopted for the detection of inflammation-related genes. SIGMAR1 expression in myocardial tissues induced by I/R and cardiac microvascular endothelial cells (CMECs) under hypoxic/reoxygenation (H/R) was determined using RT-qPCR and western blotting. Subsequently, after SIGMAR1 silencing or BD1047 addition (a SIGMAR1 antagonist), cell apoptosis and endothelial integrity were analyzed in the presence of Oxycodone in H/R-stimulated CMECs. Results indicated that Oxycodone decreased the ischemic area and improved myocardial function in myocardial I/R injury rat. Oxycodone improved myocardial histopathological injury and elevated endothelial integrity, evidenced by upregulated ZO-1, Claudin-1 and Occludin expressions. Moreover, inflammatory response was alleviated after Oxycodone administration. Molecular docking suggested that SIGMAR1 could directly bind to Oxycodone. Oxycodone elevated SIGMAR1 expression and SIGMAR1 deletion or BD1047 addition attenuated the impacts of Oxycodone on apoptosis and endothelial integrity of CMECs induced by H/R. Collectively, Oxycodone alleviates myocardial I/R injury in vivo and in vitro by binding to SIGMAR1.
DOI: 10.6084/m9.figshare.8050121.v1
title: Additional file 1: of Translation of the circular RNA circÎ˛-catenin promotes liver cancer cell growth through activation of the Wnt pathway

description: Table S1. A gene list of 143 Wnt pathway-related genes and their corresponding circular RNAs (XLSX 34 kb)
DOI: 10.6084/m9.figshare.12768821
title: Additional file 8 of Transcriptomic profiling revealed key signaling pathways for cold tolerance and acclimation of two carp species

description: Additional file 8. Results of KEGG enrichment analysis in each group.
DOI: 10.6084/m9.figshare.12768800.v1
title: Additional file 1 of Transcriptomic profiling revealed key signaling pathways for cold tolerance and acclimation of two carp species

description: Additional file 1. Survival rates of Songpu mirror carp and Barbless carp under cold stress.
DOI: 10.6084/m9.figshare.12768803
title: Additional file 2 of Transcriptomic profiling revealed key signaling pathways for cold tolerance and acclimation of two carp species

description: Additional file 2. Primers used for qPCR.
DOI: 10.6084/m9.figshare.12768734
title: Additional file 3 of Molecular surveillance for drug resistance markers in Plasmodium vivax isolates from symptomatic and asymptomatic infections at the China–Myanmar border

description: Additional file 3: Table S3. The variables used for each isolate input in the ClustVis online program. Column A indicaes the all variables of each gene. Second row indicates the samples used and Third raw indicates the groups. The reference and alternate allele is shown by 0 and 1, respectively.
DOI: 10.6084/m9.figshare.12768821.v1
title: Additional file 8 of Transcriptomic profiling revealed key signaling pathways for cold tolerance and acclimation of two carp species

description: Additional file 8. Results of KEGG enrichment analysis in each group.
DOI: 10.6084/m9.figshare.7001348.v1
title: Methods used to assess the performance of biomarkers for the diagnosis of acute kidney injury: a systematic review and meta-analysis

description: <b>Purpose:</b> Methods used to explore biomarkers for acute kidney injury (AKI) might have a major impact on the results and the use of these biomarkers. We evaluated the methods used to investigate biomarkers of AKI. <b>Materials and methods:</b> A systematic review and meta-analysis were performed using a computerized search of the MEDLINE and the EMBASE databases (PROSPERO CRD42017059618). Articles reporting biomarker’s performance to diagnose AKI were included. The outcome included a description of the methods used to assess the performance of biomarkers to diagnose AKI. <b>Results:</b> Among the 295 included studies, assessment of biomarkers was the primary endpoint in 284 with sample size calculation in only 8% of cases. Eighty-five percent of the studies summarized the performance of biomarkers with receiver operating characteristic (ROC) curves; however, 74 studies (25%) did not provide the threshold, sensibility or specificity. A total of 176 studies evaluated more than one biomarker, and only 25% combined biomarkers to increase diagnostic performance. We determined that the definition of AKI and study design impacted the diagnostic performance using uNGAL (urinary neutrophil gelatinase-associated lipocalin) as an example. Major publication bias was identified. <b>Conclusions:</b> Most articles that reported biomarkers of AKI performance present methodological weaknesses. Basic rules should be provided to increase the quality of reporting in this area.
DOI: 10.6084/m9.figshare.12768734.v1
title: Additional file 3 of Molecular surveillance for drug resistance markers in Plasmodium vivax isolates from symptomatic and asymptomatic infections at the China–Myanmar border

description: Additional file 3: Table S3. The variables used for each isolate input in the ClustVis online program. Column A indicaes the all variables of each gene. Second row indicates the samples used and Third raw indicates the groups. The reference and alternate allele is shown by 0 and 1, respectively.
DOI: 10.6084/m9.figshare.8050151.v1
title: Additional file 4: of Identification of the defense-related gene VdWRKY53 from the wild grapevine Vitis davidii using RNA sequencing and ectopic expression analysis in Arabidopsis

description: Details of genes classified in subcluster K03. (XLSX 69 kb)
DOI: 10.6084/m9.figshare.12750113
title: Additional file 7 of Physiological and transcriptome analysis of Poa pratensis var. anceps cv. Qinghai in response to cold stress

description: Additional file 7: Table S4. List of primers used for qRT-PCR.
DOI: 10.6084/m9.figshare.19584094.v1
title: MicroRNA-642b-3p functions as an oncomiR in gastric cancer by down-regulating the CUB and sushi multiple domains protein 1/smad axis

description: Aberrant expression of microRNAs (miRNAs or miRs) has been involved in the progression of gastric cancer (GC). Our analysis of GC-related gene expression profiles identified the significantly up-regulated miR-642b-3p expression, which has been reported as a mediator in various cancers but rarely mentioned in researches on GC. Herein, this study intends to investigate the role of miR-642b-3p in GC development. Bioinformatics analysis was conducted to predict the downstream target gene of miR-642b-3p. Expression patterns of miR-642b-3p and CUB and sushi multiple domains protein 1 (CSMD1) in GC tissues and cell lines was then determined. Immunofluorescence, wound healing and Transwell invasion assays were performed to observe the malignant behaviors of GC cells with altered expression of miR-642b-3p and CSMD1. Nude mice with xenograft tumors were developed for <i>in vivo</i> validation. miR-642b-3p expression was increased in GC tissues and cell lines. miR-642b-3p targeted CSMD1 and reduced the expression of CSMD1, thereby inhibiting the activation of Smad signaling pathway. By this mechanism, the epithelial–mesenchymal transition (EMT), invasive and migratory potentials of GC cells were repressed. Meanwhile, <i>in vivo</i> data verified that miR-642b-3p enhanced the tumor growth of GC cells, which was associated with blockade of CSMD1-dependent activation of the Smad signaling pathway. Overall, miR-642b-3p acts as an oncomiR promoting tumor development in GC through suppressing CSMD1 expression and inactivating the Smad signaling pathway, which may enable the development of new therapeutic strategies for treatment of GC.
DOI: 10.6084/m9.figshare.21680616.v1
title: Additional file 7 of Identification and validation of an E2F-related gene signature for predicting recurrence-free survival in human prostate cancer

description: Additional file 7: Table S7. The results of univariate Cox regression analysis in the MSKCC cohort.
DOI: 10.6084/m9.figshare.21680616
title: Additional file 7 of Identification and validation of an E2F-related gene signature for predicting recurrence-free survival in human prostate cancer

description: Additional file 7: Table S7. The results of univariate Cox regression analysis in the MSKCC cohort.
DOI: 10.25387/g3.11719890
title: Supplemental Material for Lu et al., 2020

description: Figure
S1. Estimates of divergence time. File S1.
Codon sequences with evidences of positive selection in FASTA format. File S2.
Protein sequences containing convergent/parallel substitutions in FASTA format. File S3.
Protein sequences containing multiple amino acid substitutions specific to
Shedao pit-viper in FASTA format. File S4.
Codon sequence alignments of all single-copy genes used in this study in FASTA
format. Table S1. Genomic data, assembly version, and data sources used in this study. Table S2. Calibration points used in divergence date estimation. Table S3. List of genes that bear signals of positive selection in the Shedao pit-viper.Table S4. List of genes that possess sites of convergent substitutions. Table S5. List of genes that possess sites of parallel substitutions.
DOI: 10.6084/m9.figshare.21680601
title: Additional file 2 of Identification and validation of an E2F-related gene signature for predicting recurrence-free survival in human prostate cancer

description: Additional file 2: Table S2. The GSVA results of TCGA-PRAD dataset.
DOI: 10.6084/m9.figshare.14865601.v1
title: Two new physalins from <i>Physalis alkekengi</i> L. var. <i>franchetii</i> (Mast.) Makino

description: Two new physalins, 7α-hydroxy-5-deoxy-4-dehydrophysalin IX (<b>1</b>) and 5-deoxy-4-dehydrophysalin IX (<b>2</b>), together with six known compounds, luteolin (<b>3</b>), luteolin-7-<i>O</i>-glucoside (<b>4</b>), neoechinulin A (<b>5</b>), 3-(4-hydroxy-3-methoxyphenyl)-<i>N</i>-(4-methylphenyl)-2-propenamide (<b>6</b>), physalin D (<b>7</b>) and blumenol A (<b>8</b>) were isolated from <i>Physalis alkekengi</i> L. var. <i>franchetii</i> (Mast.) Makino. Their structures were elucidated by NMR spectroscopic analysis, HR-ESI-MS, X-ray crystallographic data analysis and comparison with the known compounds. Among them, compounds <b>5</b> and <b>6</b> were isolated from the genus <i>Physalis</i> for the first time. Compound <b>1</b> exhibited weak NAD(P)H: quinone reductase (QR) inducing activity.
DOI: 10.6084/m9.figshare.12768800
title: Additional file 1 of Transcriptomic profiling revealed key signaling pathways for cold tolerance and acclimation of two carp species

description: Additional file 1. Survival rates of Songpu mirror carp and Barbless carp under cold stress.
DOI: 10.6084/m9.figshare.12768803.v1
title: Additional file 2 of Transcriptomic profiling revealed key signaling pathways for cold tolerance and acclimation of two carp species

description: Additional file 2. Primers used for qPCR.
DOI: 10.6084/m9.figshare.12768809.v1
title: Additional file 4 of Transcriptomic profiling revealed key signaling pathways for cold tolerance and acclimation of two carp species

description: Additional file 4. Differentially expressed genes between two groups.
DOI: 10.6084/m9.figshare.8050142
title: Additional file 3: of Translation of the circular RNA circÎ˛-catenin promotes liver cancer cell growth through activation of the Wnt pathway

description: Table S2. The RNA expression profile for deregulated genes after knockdown of circÎ˛-catenin (XLSX 477 kb)
DOI: 10.6084/m9.figshare.20103933.v1
title: Additional file 3 of Transcriptional changes in the peripheral blood leukocytes from Brangus cattle before and after tick challenge with Rhipicephalus australis

description: Additional file 3.
DOI: 10.6084/m9.figshare.8050121
title: Additional file 1: of Translation of the circular RNA circÎ˛-catenin promotes liver cancer cell growth through activation of the Wnt pathway

description: Table S1. A gene list of 143 Wnt pathway-related genes and their corresponding circular RNAs (XLSX 34 kb)
DOI: 10.6084/m9.figshare.20103924
title: Additional file 10 of Transcriptional changes in the peripheral blood leukocytes from Brangus cattle before and after tick challenge with Rhipicephalus australis

description: Additional file 10.
DOI: 10.6084/m9.figshare.20103939
title: Additional file 5 of Transcriptional changes in the peripheral blood leukocytes from Brangus cattle before and after tick challenge with Rhipicephalus australis

description: Additional file 5.
DOI: 10.6084/m9.figshare.20103942.v1
title: Additional file 6 of Transcriptional changes in the peripheral blood leukocytes from Brangus cattle before and after tick challenge with Rhipicephalus australis

description: Additional file 6.
DOI: 10.6084/m9.figshare.22724223.v1
title: Additional file 2 of Polycyclic aromatic hydrocarbon (PAH) biodegradation capacity revealed by a genome-function relationship approach

description: Additional file 2. The summary of protein sequences in the PAH-degrading gene database. Detailed information of 225 strains with complete/near-complete PAH-degrading gene cluster.
DOI: 10.6084/m9.figshare.8050139
title: Additional file 3: of Identification of the defense-related gene VdWRKY53 from the wild grapevine Vitis davidii using RNA sequencing and ectopic expression analysis in Arabidopsis

description: Details of the KEGG pathways investigated in this study. (XLSX 122 kb)
DOI: 10.6084/m9.figshare.20103924.v1
title: Additional file 10 of Transcriptional changes in the peripheral blood leukocytes from Brangus cattle before and after tick challenge with Rhipicephalus australis

description: Additional file 10.
DOI: 10.6084/m9.figshare.20103933
title: Additional file 3 of Transcriptional changes in the peripheral blood leukocytes from Brangus cattle before and after tick challenge with Rhipicephalus australis

description: Additional file 3.
DOI: 10.6084/m9.figshare.20103954
title: Additional file 9 of Transcriptional changes in the peripheral blood leukocytes from Brangus cattle before and after tick challenge with Rhipicephalus australis

description: Additional file 9.