cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.19996775.v1
title: Dexmedetomidine Leads to the Mitigation of Myocardial Ischemia/Reperfusion-Induced Acute Lung Injury in Diabetic Rats Via Modulation of Hypoxia-Inducible Factor-1α

description: ABSTRACT Introduction: The objective of this study is to investigate the protective mechanism of dexmedetomidine (Dex) in myocardial ischemia/reperfusion (MIR)-induced acute lung injury (ALI) of diabetic rats by inhibiting hypoxia-inducible factor-1α (HIF-1α). Methods: Initially, healthy male Sprague Dawley rats were treated with streptozocin to induce diabetes. Then, three weeks after the induction, Dex or lentiviral vector (LV)-HIF-1α was injected into the rats 30 minutes prior to the MIR modeling. After four weeks, lung tissues were harvested for pathological changes observation and the wet/dry weight (W/D) ratio determination. Afterwards, oxidative stress indicators and pro-inflammatory factors were measured. In addition, HIF-1α expression was assessed by immunohistochemistry and western blot analysis. Results: Dex could suppress inflammatory cell infiltration, improve lung tissue structure, reduce pathological score and the W/D ratio, and block oxidative stress and inflammatory response in MIR-induced ALI of diabetic rats. Besides, Dex could also inhibit HIF-1α expression. Moreover, Dex + LV-HIF-1α reversed the protective role of Dex on diabetic MIR-induced ALI. Conclusion: Our study has made it clear that Dex inhibited the upregulation of HIF-1α in diabetic MIR-induced ALI, and thus protect lung functions by quenching the accumulation of oxygen radical and reducing lung inflammatory response.
DOI: 10.6084/m9.figshare.22618054.v1
title: Additional file 2 of Comprehensive analysis of the laccase gene family in tea plant highlights its roles in development and stress responses

description: Additional file 2: Table S2. Primers developed for six CsLAC genes for qRT‒PCR and CsLAC3 for subcellular localization.
DOI: 10.6084/m9.figshare.22618054
title: Additional file 2 of Comprehensive analysis of the laccase gene family in tea plant highlights its roles in development and stress responses

description: Additional file 2: Table S2. Primers developed for six CsLAC genes for qRT‒PCR and CsLAC3 for subcellular localization.
DOI: 10.6084/m9.figshare.22618178
title: Additional file 5 of Automated quantitative trait locus analysis (AutoQTL)

description: Additional file 5.
DOI: 10.6084/m9.figshare.22618190
title: Additional file 8 of Automated quantitative trait locus analysis (AutoQTL)

description: Additional file 8.
DOI: 10.6084/m9.figshare.22617206
title: Additional file 1 of GelFAP v2.0: an improved platform for Gene functional analysis in Gastrodia elata

description: Additional file 1: Table S1. Summary of RNA-seq datasets collected in G.elata. Table S2. Key enzymes genes of flavonoid biosynthesis in G.elata. Table S3. Co-expression Relationship between key enzymes genes in flavonoid biosynthesis and transcription factor coding genes. Table S4. Co-expression Relationship between key enzymes genes in flavonoid biosynthesis.
DOI: 10.6084/m9.figshare.10036634
title: MOESM9 of Comparative transcriptomics among floral organs of the basal eudicot Eschscholzia californica as reference for floral evolutionary developmental studies

description: Additional file 9: Probe design in the microarray and properties of E. californicaprobe sets designed by MODIT and other methods and primers used for RT-PCR experiments. This additional file contains probe design and orientation of the custom microarray, properties of probe sets and primers for RT-PCR. (XLS 4 MB)
DOI: 10.6084/m9.figshare.10036634.v1
title: MOESM9 of Comparative transcriptomics among floral organs of the basal eudicot Eschscholzia californica as reference for floral evolutionary developmental studies

description: Additional file 9: Probe design in the microarray and properties of E. californicaprobe sets designed by MODIT and other methods and primers used for RT-PCR experiments. This additional file contains probe design and orientation of the custom microarray, properties of probe sets and primers for RT-PCR. (XLS 4 MB)
DOI: 10.6084/m9.figshare.22618142.v1
title: Additional file 1 of Thiram, an inhibitor of 11ß-hydroxysteroid dehydrogenase type 2, enhances the inhibitory effects of hydrocortisone in the treatment of osteosarcoma through Wnt/β-catenin pathway

description: Additional file 1.
DOI: 10.6084/m9.figshare.22618163.v1
title: Additional file 7 of Thiram, an inhibitor of 11ß-hydroxysteroid dehydrogenase type 2, enhances the inhibitory effects of hydrocortisone in the treatment of osteosarcoma through Wnt/β-catenin pathway

description: Additional file 7.
DOI: 10.6084/m9.figshare.19996775
title: Dexmedetomidine Leads to the Mitigation of Myocardial Ischemia/Reperfusion-Induced Acute Lung Injury in Diabetic Rats Via Modulation of Hypoxia-Inducible Factor-1α

description: ABSTRACT Introduction: The objective of this study is to investigate the protective mechanism of dexmedetomidine (Dex) in myocardial ischemia/reperfusion (MIR)-induced acute lung injury (ALI) of diabetic rats by inhibiting hypoxia-inducible factor-1α (HIF-1α). Methods: Initially, healthy male Sprague Dawley rats were treated with streptozocin to induce diabetes. Then, three weeks after the induction, Dex or lentiviral vector (LV)-HIF-1α was injected into the rats 30 minutes prior to the MIR modeling. After four weeks, lung tissues were harvested for pathological changes observation and the wet/dry weight (W/D) ratio determination. Afterwards, oxidative stress indicators and pro-inflammatory factors were measured. In addition, HIF-1α expression was assessed by immunohistochemistry and western blot analysis. Results: Dex could suppress inflammatory cell infiltration, improve lung tissue structure, reduce pathological score and the W/D ratio, and block oxidative stress and inflammatory response in MIR-induced ALI of diabetic rats. Besides, Dex could also inhibit HIF-1α expression. Moreover, Dex + LV-HIF-1α reversed the protective role of Dex on diabetic MIR-induced ALI. Conclusion: Our study has made it clear that Dex inhibited the upregulation of HIF-1α in diabetic MIR-induced ALI, and thus protect lung functions by quenching the accumulation of oxygen radical and reducing lung inflammatory response.
DOI: 10.6084/m9.figshare.22618169.v1
title: Additional file 2 of Automated quantitative trait locus analysis (AutoQTL)

description: Additional file 2.
DOI: 10.6084/m9.figshare.20521071
title: Additional file 2 of Phenotypic, chemical component and molecular assessment of genetic diversity and population structure of Morinda officinalis germplasm

description: Additional file 2.
DOI: 10.6084/m9.figshare.20521068
title: Additional file 1 of Phenotypic, chemical component and molecular assessment of genetic diversity and population structure of Morinda officinalis germplasm

description: Additional file 1.
DOI: 10.6084/m9.figshare.22618196
title: Additional file 10 of Automated quantitative trait locus analysis (AutoQTL)

description: Additional file 10.
DOI: 10.6084/m9.figshare.19996789
title: Expression Level and Significance of Tim-3 in CD4+ T Lymphocytes in Peripheral Blood of Patients with Coronary Heart Disease

description: Abstract Objective: To investigate the expression level and significance of T cell immunoglobulin and mucin-domain containing molecules-3 (Tim-3) and interleukin-7 (IL-7) in CD4+ T lymphocytes in peripheral blood of patients with coronary heart disease (CHD). Methods: 75 patients with CHD treated at our hospital were selected and classified as mild group (25 cases), moderate group (25 cases) and severe group (25 cases), according to the severity of illness. Twenty-five healthy volunteers who underwent a physical examination at our hospital during the same period were selected as the control group. The expression level of Tim-3 in CD4+ T lymphocytes in peripheral blood of patients in four groups was detected by flow cytometry and quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR). The expression level of IL-7 in peripheral blood serum was measured by enzyme-linked immunosorbent assay (ELISA). Correlation analyses of Tim-3 and IL-7, Tim-3 and disease severity and IL-7 and disease severity were performed, respectively. Results: Flow cytometry and qRT-PCR demonstrated that the expression of Tim-3 in CD4+ T lymphocytes in peripheral blood of patients with CHD increased with the aggravation of the disease. ELISA showed that the tendency of IL-7 expression in peripheral blood serum was consistent with the expression of Tim-3, and the expression of Tim-3 had a positive correlation with IL-7. The expression levels of both Tim-3 and IL-7 were positively correlated with the Gensini score. Conclusion: The expression of Tim-3 and IL-7 in peripheral blood of patients with CHD was upregulated and increased with the aggravation of CHD.
DOI: 10.6084/m9.figshare.22618196.v1
title: Additional file 10 of Automated quantitative trait locus analysis (AutoQTL)

description: Additional file 10.
DOI: 10.6084/m9.figshare.8986862
title: Irreversible Pulpitis - A Source of Antibiotic Over-Prescription?

description: Abstract Antibiotic resistance is a growing public health concern. Antibiotics continue to be prescribed by some clinicians to resolve dental pain even though research indicates that antibiotics are not effective for treating conditions such as irreversible pulpitis. The objective of this study was to determine the extent to which current research and evidence around irreversible pulpitis has been translated into dental practice and the gaps in dentists’ knowledge. An on-line clinical vignette format survey questionnaire about treatment of irreversible pulpitis was distributed to the members of the Academy of Operative Dentistry and Academy of General Dentistry (US based international dental bodies). Their responses were recorded and evaluated. A total of 403 dentists participated in the survey. Over a third (39.3%) indicated they would prescribe antibiotics for symptomatic irreversible pulpitis in a permanent tooth occurring without any signs of systemic infection. The rest indicated they would not prescribe antibiotics; most of them would prescribe an analgesic combined with pulpectomy. Those who had undertaken advanced education training achieved a significantly higher mean knowledge score compared to those with just a primary dental degree (p=0.011). Similarly, full or part time academicians had a higher mean knowledge score than the clinicians who work only in private practice (p=0.014). Some dentists continue to prescribe antibiotics inappropriately for alleviating pain due to irreversible pulpitis. Antibiotic prescribing practices of dentists with advanced education or academic engagement were better as compared to the other participants. There is clear evidence of antibiotic over-prescribing for irreversible pulpitis which needs to be addressed urgently.
DOI: 10.25387/g3.10559621
title: Supplemental Material for Chen et al., 2020

description: HPLC chromatography
for determation of anthocyanins and catechins (Figure S1 and Table S1,
Supplemental data 1).The number of ZJ (Purple digital) and YK (Green digital)
isoforms that are enriched in terms of molecular function, cellular component,
and biological process based on GeneOntology (GO) analysis(Figure S2).Gene
annotation of KEGG pathways involved in biosynthesis of ZJ and YK. The isoforms
of ZJ and YK have been gathering in KEGG database，and the numbers have been shown and
compared(Figure S3).The relative expression quantity of genes and their AS
transtrips in ZJ and YK one leaf and two buds to ZJ Mature leaves based on
qRT-PCR studies (Figure S4) and the Primers used in the study have been listed
(Table S2).The number of isoforms in anthocyanidin biosynthesis of YK and ZJ
(Supplemental data 2 and 3).The GeneOntology (GO) annotation of ZJ and YK
PacBio Iso-seq isoforms (Supplemental data 4) and The KEGG annotation of ZJ and
YK PacBio Iso-seq isoforms(Supplemental data 5).The classification of AS evens
happened in ZJ and YK (Supplemental data 6).The number of AS evens happened in
anthocyanidin biosynthesis in YK and ZJ (Supplemental data 7).The relative
expression quantity of genes and their AS transtrips in ZJ and YK one leaf and
two buds to ZJ Mature leaves (Supplemental data 8).The coefficient of
association matrix between chemical composition contents and gene
expressions(Supplemental data 9)
DOI: 10.6084/m9.figshare.22618396
title: Additional file 4 of Controlling taxa abundance improves metatranscriptomics differential analysis

description: Additional file 4: Supplementary Table 1. list of differential features and PubMed literature support. 1st column: name of the feature; 2nd column: name of the gene pathway; 3rd column: keyword of the pathway used to perform literature search; 4th column: term used in Pubmed search; 5th column: Number of PubMed hits searching for both crohn's disease and the keyword in the third column. 6th-8th columns: If the feature is identified as differential in DNA+Taxa, DNA, or Taxa model. 9th column: Pubmed ID of the paper manually validated to be associated with both crohn's disease and the keyword in the third column. 10th column: date search was performed.
DOI: 10.6084/m9.figshare.22618268
title: Additional file 9 of The impact of culture systems on the gut microbiota and gut metabolome of bighead carp (Hypophthalmichthys nobilis)

description: Additional file 9. Table S5. The parameters and evaluation of PCA and OPLS-DA models.
DOI: 10.6084/m9.figshare.22618256.v1
title: Additional file 5 of The impact of culture systems on the gut microbiota and gut metabolome of bighead carp (Hypophthalmichthys nobilis)

description: Additional file 5. Table S1. The abundance and taxonomy of OTUs.
DOI: 10.5281/zenodo.10633552
title: supplement figures, tables and materials
DOI: 10.5281/zenodo.10633553
title: supplement figures, tables and materials
DOI: 10.6084/m9.figshare.19996789.v1
title: Expression Level and Significance of Tim-3 in CD4+ T Lymphocytes in Peripheral Blood of Patients with Coronary Heart Disease

description: Abstract Objective: To investigate the expression level and significance of T cell immunoglobulin and mucin-domain containing molecules-3 (Tim-3) and interleukin-7 (IL-7) in CD4+ T lymphocytes in peripheral blood of patients with coronary heart disease (CHD). Methods: 75 patients with CHD treated at our hospital were selected and classified as mild group (25 cases), moderate group (25 cases) and severe group (25 cases), according to the severity of illness. Twenty-five healthy volunteers who underwent a physical examination at our hospital during the same period were selected as the control group. The expression level of Tim-3 in CD4+ T lymphocytes in peripheral blood of patients in four groups was detected by flow cytometry and quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR). The expression level of IL-7 in peripheral blood serum was measured by enzyme-linked immunosorbent assay (ELISA). Correlation analyses of Tim-3 and IL-7, Tim-3 and disease severity and IL-7 and disease severity were performed, respectively. Results: Flow cytometry and qRT-PCR demonstrated that the expression of Tim-3 in CD4+ T lymphocytes in peripheral blood of patients with CHD increased with the aggravation of the disease. ELISA showed that the tendency of IL-7 expression in peripheral blood serum was consistent with the expression of Tim-3, and the expression of Tim-3 had a positive correlation with IL-7. The expression levels of both Tim-3 and IL-7 were positively correlated with the Gensini score. Conclusion: The expression of Tim-3 and IL-7 in peripheral blood of patients with CHD was upregulated and increased with the aggravation of CHD.
DOI: 10.17028/rd.lboro.12656828
title: Supplementary information files for Extraction of connected river networks from multi-temporal remote sensing imagery using a path tracking technique

description: Supplementary files for Extraction of connected river networks from multi-temporal remote sensing imagery using a path tracking technique. Precise delineation of river networks is important for accurate hydrological and flood modelling. Whilst remote sensing (RS) has showed great potential in monitoring hydrological changes over space and time, the existing RS-based methods extract river networks based on local morphologies and seldom take into account the overall hydrological connectivity of the rivers. The existing methods also commonly neglect the effect of seasonal variation of water surfaces and the existence of temporary water bodies, which deteriorate the precision of positioning river networks. To address these challenges, a new two-stage method is developed to Extract spatiotemporal variation of water surfaces based on Multi-temporal remote sensing Imagery and Delineate connected river networks with improved accuracy (EMID method for short) using a path tracking technique. The EMID method delineates connected river networks using (a) multi-temporal imagery and a Random Forest model to synoptically map the location and extent of water surfaces under different hydrological conditions, and (b) an optimization algorithm to find the best river paths based on water-occurrence frequency. Four drainage basins with various river morphologies are considered to validate EMID. Comparing with alternative methods, the EMID method consistently produces river network results with improved accuracy in terms of stream location, river coverage and network connectivity.<br>
DOI: 10.17028/rd.lboro.12656828.v1
title: Supplementary information files for Extraction of connected river networks from multi-temporal remote sensing imagery using a path tracking technique

description: Supplementary files for Extraction of connected river networks from multi-temporal remote sensing imagery using a path tracking technique. Precise delineation of river networks is important for accurate hydrological and flood modelling. Whilst remote sensing (RS) has showed great potential in monitoring hydrological changes over space and time, the existing RS-based methods extract river networks based on local morphologies and seldom take into account the overall hydrological connectivity of the rivers. The existing methods also commonly neglect the effect of seasonal variation of water surfaces and the existence of temporary water bodies, which deteriorate the precision of positioning river networks. To address these challenges, a new two-stage method is developed to Extract spatiotemporal variation of water surfaces based on Multi-temporal remote sensing Imagery and Delineate connected river networks with improved accuracy (EMID method for short) using a path tracking technique. The EMID method delineates connected river networks using (a) multi-temporal imagery and a Random Forest model to synoptically map the location and extent of water surfaces under different hydrological conditions, and (b) an optimization algorithm to find the best river paths based on water-occurrence frequency. Four drainage basins with various river morphologies are considered to validate EMID. Comparing with alternative methods, the EMID method consistently produces river network results with improved accuracy in terms of stream location, river coverage and network connectivity.<br>
DOI: 10.25387/g3.10559621.v1
title: Supplemental Material for Chen et al., 2020

description: HPLC chromatography
for determation of anthocyanins and catechins (Figure S1 and Table S1,
Supplemental data 1).The number of ZJ (Purple digital) and YK (Green digital)
isoforms that are enriched in terms of molecular function, cellular component,
and biological process based on GeneOntology (GO) analysis(Figure S2).Gene
annotation of KEGG pathways involved in biosynthesis of ZJ and YK. The isoforms
of ZJ and YK have been gathering in KEGG database，and the numbers have been shown and
compared(Figure S3).The relative expression quantity of genes and their AS
transtrips in ZJ and YK one leaf and two buds to ZJ Mature leaves based on
qRT-PCR studies (Figure S4) and the Primers used in the study have been listed
(Table S2).The number of isoforms in anthocyanidin biosynthesis of YK and ZJ
(Supplemental data 2 and 3).The GeneOntology (GO) annotation of ZJ and YK
PacBio Iso-seq isoforms (Supplemental data 4) and The KEGG annotation of ZJ and
YK PacBio Iso-seq isoforms(Supplemental data 5).The classification of AS evens
happened in ZJ and YK (Supplemental data 6).The number of AS evens happened in
anthocyanidin biosynthesis in YK and ZJ (Supplemental data 7).The relative
expression quantity of genes and their AS transtrips in ZJ and YK one leaf and
two buds to ZJ Mature leaves (Supplemental data 8).The coefficient of
association matrix between chemical composition contents and gene
expressions(Supplemental data 9)
DOI: 10.6084/m9.figshare.22618274.v1
title: Additional file 11 of The impact of culture systems on the gut microbiota and gut metabolome of bighead carp (Hypophthalmichthys nobilis)

description: Additional file 11. Table S7. The potential metabolites and microbes at the phylum level.
DOI: 10.6084/m9.figshare.22618259.v1
title: Additional file 6 of The impact of culture systems on the gut microbiota and gut metabolome of bighead carp (Hypophthalmichthys nobilis)

description: Additional file 6. Table S2. The abundance and significance of top 10 microbes at the phylum level.
DOI: 10.6084/m9.figshare.22618277
title: Additional file 12 of The impact of culture systems on the gut microbiota and gut metabolome of bighead carp (Hypophthalmichthys nobilis)

description: Additional file 12. Table S8. The potential metabolites and microbes at the genus level.
DOI: 10.6084/m9.figshare.22618271.v1
title: Additional file 10 of The impact of culture systems on the gut microbiota and gut metabolome of bighead carp (Hypophthalmichthys nobilis)

description: Additional file 10. Table S6. The significance and impact of enriched pathways.
DOI: 10.6084/m9.figshare.22618277.v1
title: Additional file 12 of The impact of culture systems on the gut microbiota and gut metabolome of bighead carp (Hypophthalmichthys nobilis)

description: Additional file 12. Table S8. The potential metabolites and microbes at the genus level.
DOI: 10.6084/m9.figshare.22618265
title: Additional file 8 of The impact of culture systems on the gut microbiota and gut metabolome of bighead carp (Hypophthalmichthys nobilis)

description: Additional file 8. Table S4. The abundance and classification of metabolites.
DOI: 10.6084/m9.figshare.13181217.v1
title: Diagnostic value of circulating lncRNAs as biomarkers of digestive system cancers: A systematic review and meta-analysis

description: This meta-analysis aims to explore the diagnostic value and accuracy of circulating lncRNAs as biomarkers of digestive system tumors. PubMed, Embase, Cochrane Library, and Web of science were searched for relevant articles that were published before April 2019, and a meta-analysis was conducted. 52 studies with 63 lncRNAs were discussed in the meta-analysis. The pooled sensitivity and specificity of diagnosis were 0.80 (95% CI: 0.79–0.81) and 0.76 (95% CI: 0.75–0.77), respectively. The pooled DOR (the diagnostic odds ratio) was 15.63 (95% CI: 12.77–19.12), and the overall AUC (the area under the curve) was 0.87. Besides, subgroup analyzes showed that the DOR and AUC of large sample sizes (&gt;80), multiple lncRNAs, serum-based lncRNAs, and downregulation group were superior to those of small sample sizes (≤80), single lncRNA, plasma-based lncRNAs, and upregulation group, respectively. The current data also highlight that the diagnostic accuracy of circulating lncRNAs in the case of colorectal cancer was higher than gastric cancer, hepatocellular carcinoma, esophageal carcinoma, and pancreatic cancer. And there is no difference in the perspective of geographical regions. The circulating lncRNAs have high diagnostic value and accuracy in digestive system cancers and may serve as potential biomarkers.