cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.19311257
title: Additional file 8 of Host-microbiome protein-protein interactions capture disease-relevant pathways

description: Additional file 8: Table S7. Cocrystal structures representing interactions in our dataset. All pairs of detected bacterial proteins and human proteins in the nine metagenomic datasets that have BLASTp matches to two different chains within the same PDB cocrystal structure (totaling 8 bacterial protein clusters and 10 human proteins). This list includes structures with at least one chain exclusive to each bacterial and human proteins.
DOI: 10.6084/m9.figshare.19311257.v1
title: Additional file 8 of Host-microbiome protein-protein interactions capture disease-relevant pathways

description: Additional file 8: Table S7. Cocrystal structures representing interactions in our dataset. All pairs of detected bacterial proteins and human proteins in the nine metagenomic datasets that have BLASTp matches to two different chains within the same PDB cocrystal structure (totaling 8 bacterial protein clusters and 10 human proteins). This list includes structures with at least one chain exclusive to each bacterial and human proteins.
DOI: 10.6084/m9.figshare.19311260
title: Additional file 9 of Host-microbiome protein-protein interactions capture disease-relevant pathways

description: Additional file 9: Table S8. Experimental protein-protein interactions that were used for mapping to microbiomes.
DOI: 10.6084/m9.figshare.12219119
title: Additional file 5 of Milk exosome-derived miRNAs from water buffalo are implicated in immune response and metabolism process

description: Additional file 5. Predicted targets of significantly down-regulated miRNAs in buffalo milk exosome
DOI: 10.6084/m9.figshare.12219122
title: Additional file 6 of Milk exosome-derived miRNAs from water buffalo are implicated in immune response and metabolism process

description: Additional file 6. The KEGG analysis of the up-regulated miRNAs’ targets
DOI: 10.6084/m9.figshare.16943679
title: Additional file 3 of ciRS-7 is a prognostic biomarker and potential gene therapy target for renal cell carcinoma

description: Additional file 3: Excel S2. circBank, miRanda, circAtlas and RNAhybrid databases predict the possible miRNAs bound by ciRS-7.
DOI: 10.6084/m9.figshare.16943685.v1
title: Additional file 5 of ciRS-7 is a prognostic biomarker and potential gene therapy target for renal cell carcinoma

description: Additional file 5: Excel S4. Lab-free quantitative results.
DOI: 10.6084/m9.figshare.19311254
title: Additional file 7 of Host-microbiome protein-protein interactions capture disease-relevant pathways

description: Additional file 7: Table S6. Extended information for bacterial proteins targeting known drug targets in Fig. 4. Bacterial clusters depicted in Fig. 4 are listed with their UniRef number and detected taxa, according to HUMANN3.
DOI: 10.6084/m9.figshare.16943682
title: Additional file 4 of ciRS-7 is a prognostic biomarker and potential gene therapy target for renal cell carcinoma

description: Additional file 4: Excel S3. RNA sequencing results.
DOI: 10.6084/m9.figshare.19311254.v1
title: Additional file 7 of Host-microbiome protein-protein interactions capture disease-relevant pathways

description: Additional file 7: Table S6. Extended information for bacterial proteins targeting known drug targets in Fig. 4. Bacterial clusters depicted in Fig. 4 are listed with their UniRef number and detected taxa, according to HUMANN3.
DOI: 10.6084/m9.figshare.12750030.v1
title: Additional file 7 of Contribution of anthocyanin pathways to fruit flesh coloration in pitayas

description: Additional file 7: Table S2. Differentially expressed genes encoding transcription factors detected between three Hylocereus spp. cultivars. DH, FR, and BR represent the red, pink and white colored flesh samples, respectively.
DOI: 10.6084/m9.figshare.12219086.v1
title: Additional file 1 of Milk exosome-derived miRNAs from water buffalo are implicated in immune response and metabolism process

description: Additional file 1. Exosomal miRNA expression between buffalo and non-buffalo milks. Buffalo_9, buffalo_10, buffalo_11 and buffalo_12 represented for 4 buffalo milk samples; cow_13, cow_14, cow_15 and cow_16 represented for 4 cow milk samples; pig_0_rep1, pig_0_rep2, pig_0_rep3, pig_3d, pig_7d, pig_14d, pig_21d and pig_28d represented for 8 pig milk samples; human_rep1, human_rep2, human_rep3 and human_rep4 represented for 4 human milk samples; panda_0d, panda_3d_rep1, panda_3d_rep2, panda_3d_rep3, panda_7d, panda_15d and panda_30d represented for 7 panda milk samples; logFC, log fold change; logCPM, log counts per million; FDR, false discovery rate.
DOI: 10.6084/m9.figshare.12219101.v1
title: Additional file 3 of Milk exosome-derived miRNAs from water buffalo are implicated in immune response and metabolism process

description: Additional file 3. The KEGG analysis of top 10 expressed miRNAs’ targets
DOI: 10.6084/m9.figshare.19311260.v1
title: Additional file 9 of Host-microbiome protein-protein interactions capture disease-relevant pathways

description: Additional file 9: Table S8. Experimental protein-protein interactions that were used for mapping to microbiomes.
DOI: 10.6084/m9.figshare.8031347
title: Hydrogen sulfide protects H9c2 cardiomyoblasts against H2O2-induced apoptosis

description: Reactive oxygen species (ROS) are highly reactive chemical species that may cause irreversible tissue damage, and play a critical role in cardiovascular diseases. Hydrogen sulfide (H2S) is a gasotransmitter that acts as a ROS scavenger with cardio-protective effects. In this study, we investigated the cytoprotective effect of H2S against H2O2-induced apoptosis in cardiomyocytes. H9c2 rat cardiomyoblasts were treated with H2S (100 μM) 24 h before challenging with H2O2 (100 μM). Apoptosis was then assessed by annexin V and PI, and mitochondrial membrane potential was measured using a fluorescent probe, JC-1. Our results revealed that H2S improved cell viability, reduced the apoptotic rate, and preserved mitochondrial membrane potential. An increased Bcl-2 to Bax ratio was also seen in myocytes treated with H2S after H2O2-induced stress. Our findings indicated a therapeutic potential for H2S in preventing myocyte death following ischemia/reperfusion.
DOI: 10.25545/ngmohk/nrhyye
title: Supplementary+Date+Table+S4.xls

description: :unav
DOI: 10.6084/m9.figshare.12750095
title: Additional file 1 of Physiological and transcriptome analysis of Poa pratensis var. anceps cv. Qinghai in response to cold stress

description: Additional file 1: Table S1. Overview of the RNA sequencing data.
DOI: 10.6084/m9.figshare.22187221.v2
title: Follow-up outcomes of asymptomatic brucellosis: a systematic review and meta-analysis

description: Balancing the potentially serious outcomes of asymptomatic brucellosis and “waiting” for treatment in clinical practice is an urgent issue. Therefore, we assessed the follow-up outcomes and epidemiological characteristics of asymptomatic brucellosis in the absence of treatment to provide evidence-based clinical clues. We searched eight databases in which 3610 studies from 1990 to 2021 were related to the follow-up outcomes of asymptomatic brucellosis. Thirteen studies, involving 107 cases, were finally included. Regarding the follow-up outcomes, we examined the presence or absence of symptoms and decreased serum agglutination test (SAT) titre. During the 0.5–18 months follow-up period, the pooled prevalence of appearing symptomatic was 15.4% (95% CI 2.1%–34.3%), cases that remained asymptomatic were 40.3% (95% CI 16.6%–65.8%), and decreased SAT titre was observed in 36.5% (95% CI 11.6%–66.1%). Subgroup analysis indicated that the pooled prevalence of appearing symptomatic with follow-up times of less than 6 months, 6–12 months, and 12–18 months was 11.5%, 26.4%, and 47.6%, respectively. The student subgroup had a higher prevalence of symptoms (46.6%) than the occupational and family populations. In conclusion, asymptomatic brucellosis has a high likelihood of appearing symptomatic and its severity may be underestimated. Active screening of occupational and family populations should be enhanced, and special attention should be paid to high-titre students for early intervention, if necessary. Additionally, future prospective, long-term, and large-sample follow-up studies are essential.
DOI: 10.6084/m9.figshare.12218891.v1
title: Additional file 4 of Wheat chromatin architecture is organized in genome territories and transcription factories

description: Additional file 4:Table S3. With a summary of Hi-C and HiChIP libraries statistics.
DOI: 10.5281/zenodo.10357277
title: TrueVG
DOI: 10.5281/zenodo.10357278
title: TrueVG
DOI: 10.6084/m9.figshare.16943816.v1
title: Interleukin-8 concentrations in obstructive sleep apnea syndrome: A systematic review and meta-analysis

description: Interleukin (IL)-8 has been shown to play an important role in obstructive sleep apnea syndrome (OSAS). However, its role in OSAS development is still controversial. This meta-analysis was to explore the correlation between interleukin (IL)-8concentration and OSAS. Database (from the inception to July 2021) searches on PubMed, Web of Science, Medline, EMBASE, and Cochrane Library were conducted for studies analyzing the correlation between IL-8 concentration and OSAS, regardless of the language of publication. Standardized mean difference (SMD) and 95% confidence intervals (CI) were used to analyze any prospective association between IL-8 concentration and OSAS.A total of 25 eligible studies, including 2301 participants and 1123 controls, were included in this meta-analysis. The included studies evaluating the association between serum IL-8 concentration and OSAS indicated that adults and children with OSAS had elevated serum concentrations of IL-8 compared with controls (SMD = 0.997, 95% CI = 0.437-1.517, P&lt;0.001; SMD = 0.431, 95% CI = 0.104-0.759, P = 0.01). Categorization of the study population into subgroups according to body mass index, apnea-hypopnea index (AHI), ethnicity, and sample size also showed that individuals with OSAS had elevated serum concentrations of IL-8 compared with controls. Additionally, the results demonstrated that higher the AHI, higher was the IL-8 concentration. Similar results were observed in the literature on the association between plasma IL-8 concentration and OSAS. This meta-analysis verified that compared with controls, children and adults with OSAS have significantly elevated IL-8 concentrations.
DOI: 10.6084/m9.figshare.8030921.v1
title: Altered peripheral lymphocyte subsets in untreated systemic lupus erythematosus patients with infections

description: The leading cause of death in systemic lupus erythematosus (SLE) patients is infection. The objective of this study was to evaluate the distribution of lymphocyte subsets in untreated SLE patients with infections. This was a cross-sectional study. Data from January 2017 to May 2018 were collected. Flow cytometry was used to measure the peripheral lymphocyte subsets including CD3+T cells, CD4+T cells, CD8+T cells, CD19+B cells, CD3-CD16+CD56NK cells, and CD3+CD16+CD56NKT cells in 25 healthy controls and 52 treatment-naive SLE patients, among whom 13 were complicated with infections. Association between the lymphocyte subsets and infections was further analyzed. SLE patients with infections (n=13) showed a significantly higher incidence rate of fever (84.6 vs 28.2%) and serositis (84.6 vs 23.1%), increased level of erythrocyte sedimentation rate (60.5±30.1 vs 37.4±27.1 mm/h), serum C-reactive protein (CRP) (102.7±94.9 vs 9.4±14.9 mg/L), procalcitonin (PCT) (1.07±0.08 vs 0.16±0.13 μg/L), and lower blood hemoglobin (Hb) (93.0±20.5 vs 110.4±16.0 g/L) level compared with non-infection patients (n=39) (all P&lt;0.05). In comparison with non-infectious SLE patients (387.9±261.6/μL), CD4+T cells count decreased significantly in infectious SLE patients (217.8±150.4/μL) (P&lt;0.05), and it was negatively correlated with infection-related indicators including PCT (r=−0.573, P=0.041) and CRP (r=−0.596, P=0.032) levels. Our findings suggested that abnormalities of peripheral lymphocyte subsets were related to the immune disorder of lupus itself, regardless of immunosuppressive treatment. Monitoring lymphocyte subsets, especially CD4+T cells, may be helpful for identifying the presence of infection in SLE patients.
DOI: 10.6084/m9.figshare.12218840.v1
title: Additional file 2 of Comparison of microbiomes in ulcerative and normal mucosa of recurrent aphthous stomatitis (RAS)-affected patients

description: Additional file 2. Significantly differentially represented taxa in oral mucosa microbiomes and aphthous ulcer microbiomes (by t-test).
DOI: 10.6084/m9.figshare.12750033
title: Additional file 8 of Contribution of anthocyanin pathways to fruit flesh coloration in pitayas

description: Additional file 8: Table S3. The primer sequences of genes used for quantitative real time PCR.
DOI: 10.6084/m9.figshare.12750033.v1
title: Additional file 8 of Contribution of anthocyanin pathways to fruit flesh coloration in pitayas

description: Additional file 8: Table S3. The primer sequences of genes used for quantitative real time PCR.
DOI: 10.6084/m9.figshare.22187221
title: Follow-up outcomes of asymptomatic brucellosis: a systematic review and meta-analysis

description: Balancing the potentially serious outcomes of asymptomatic brucellosis and “waiting” for treatment in clinical practice is an urgent issue. Therefore, we assessed the follow-up outcomes and epidemiological characteristics of asymptomatic brucellosis in the absence of treatment to provide evidence-based clinical clues. We searched eight databases in which 3610 studies from 1990 to 2021 were related to the follow-up outcomes of asymptomatic brucellosis. Thirteen studies, involving 107 cases, were finally included. Regarding the follow-up outcomes, we examined the presence or absence of symptoms and decreased serum agglutination test (SAT) titre. During the 0.5–18 months follow-up period, the pooled prevalence of appearing symptomatic was 15.4% (95% CI 2.1%–34.3%), cases that remained asymptomatic were 40.3% (95% CI 16.6%–65.8%), and decreased SAT titre was observed in 36.5% (95% CI 11.6%–66.1%). Subgroup analysis indicated that the pooled prevalence of appearing symptomatic with follow-up times of less than 6 months, 6–12 months, and 12–18 months was 11.5%, 26.4%, and 47.6%, respectively. The student subgroup had a higher prevalence of symptoms (46.6%) than the occupational and family populations. In conclusion, asymptomatic brucellosis has a high likelihood of appearing symptomatic and its severity may be underestimated. Active screening of occupational and family populations should be enhanced, and special attention should be paid to high-titre students for early intervention, if necessary. Additionally, future prospective, long-term, and large-sample follow-up studies are essential.
DOI: 10.6084/m9.figshare.12750026.v1
title: Additional file 3 of Genome-wide DNA methylation profiling identifies epigenetic signatures of gastric cardiac intestinal metaplasia

description: Additional file 3: Table S2. List of IM-related differentially methylated CpGs comparing gastric cardiac IM and normal tissue.
DOI: 10.6084/m9.figshare.12218840
title: Additional file 2 of Comparison of microbiomes in ulcerative and normal mucosa of recurrent aphthous stomatitis (RAS)-affected patients

description: Additional file 2. Significantly differentially represented taxa in oral mucosa microbiomes and aphthous ulcer microbiomes (by t-test).
DOI: 10.6084/m9.figshare.12750032
title: Additional file 4 of Genome-wide DNA methylation profiling identifies epigenetic signatures of gastric cardiac intestinal metaplasia

description: Additional file 4: Table S3. Genomic distribution of the probes in different groups.
DOI: 10.6084/m9.figshare.12750095.v1
title: Additional file 1 of Physiological and transcriptome analysis of Poa pratensis var. anceps cv. Qinghai in response to cold stress

description: Additional file 1: Table S1. Overview of the RNA sequencing data.
DOI: 10.6084/m9.figshare.12750032.v1
title: Additional file 4 of Genome-wide DNA methylation profiling identifies epigenetic signatures of gastric cardiac intestinal metaplasia

description: Additional file 4: Table S3. Genomic distribution of the probes in different groups.
DOI: 10.6084/m9.figshare.12750035.v1
title: Additional file 5 of Genome-wide DNA methylation profiling identifies epigenetic signatures of gastric cardiac intestinal metaplasia

description: Additional file 5: Table S4. List of 6784 DMPs located in promoter-associated CpG islands.
DOI: 10.6084/m9.figshare.12219122.v1
title: Additional file 6 of Milk exosome-derived miRNAs from water buffalo are implicated in immune response and metabolism process

description: Additional file 6. The KEGG analysis of the up-regulated miRNAs’ targets
DOI: 10.6084/m9.figshare.12218885.v1
title: Additional file 3 of Wheat chromatin architecture is organized in genome territories and transcription factories

description: Additional file 3:Table S2. With odds ratios (OR) and effect size (Cramer’s V) for all combinations of features of interacting genes pairs.
DOI: 10.6084/m9.figshare.8031170.v1
title: Optimal Simulation of the Land-Use Structure Based on the Local Ecological Environment: the Case of Huanghua City in Hebei Province, China

description: ABSTRACT The overuse of land has resulted in a sharp decline in ecological functions, affecting the environment as it relates to the existence and sustainable development of the whole biosphere. This work aims to evaluate the ecological and economic efficiencies of the land-use structure. A simulation model, CLUE-S (Conversion of Land-Use and its Effects at Small Region Extent), and an integrated model based on the MOP (Multi-Objective Program) and CLUE-S were applied to assess the suitability of unutilized lands in Huanghua City, China. This was to simulate the optimal structure of land-use in the research zone to avoid loss of the land ecological service functions and the decreasing values with rapid changes in the land-use structure. By the year 2020, the simulation of the single model shows that the economic efficiency is expected to increase, but the ecological efficiency will decline. Depending on the evaluation of the suitability of unutilized land and the optimization results of the integrated MOP- and CLUE-S-based models, the ecological and economic efficiencies are expected to increase by 1.17 and 2.23 %, respectively, compared with those in 2012. In addition, the sum of the two land functions will increase for the integrated MOP- and CLUE-S-based model by the year 2020 compared with the single model. Consequently, the ecological efficiency will significantly increase. However, the optimization solution based on the integrated MOP and CLUE-S model is better than the one based on the CLUE-S model.
DOI: 10.6084/m9.figshare.12750071
title: Additional file 3 of Novel bioinformatic classification system for genetic signatures identification in diffuse large B-cell lymphoma

description: Additional file 3: Table S7. Top 50 frequent variants included in the in-house curated blacklist.
DOI: 10.6084/m9.figshare.12750083
title: Additional file 7 of Novel bioinformatic classification system for genetic signatures identification in diffuse large B-cell lymphoma

description: Additional file 7: Table S4. Binary matrix of the status of one-hot encoded genetic alterations, initial defined genetic signatures, and final convergent genetic signatures
DOI: 10.6084/m9.figshare.12219125.v1
title: Additional file 7 of Milk exosome-derived miRNAs from water buffalo are implicated in immune response and metabolism process

description: Additional file 7. The KEGG analysis of the down-regulated miRNAs’ targets
DOI: 10.6084/m9.figshare.12750086.v1
title: Additional file 8 of Novel bioinformatic classification system for genetic signatures identification in diffuse large B-cell lymphoma

description: Additional file 8: Table S5. Multivariate analysis including our set of four signatures and IPI score using enter method in cox proportional hazard regression model
DOI: 10.6084/m9.figshare.12750089
title: Additional file 9 of Novel bioinformatic classification system for genetic signatures identification in diffuse large B-cell lymphoma

description: Additional file 9 Table S6. Genetic alterations had been revealed to be of importance but not included in this study.
DOI: 10.6084/m9.figshare.12750030
title: Additional file 7 of Contribution of anthocyanin pathways to fruit flesh coloration in pitayas

description: Additional file 7: Table S2. Differentially expressed genes encoding transcription factors detected between three Hylocereus spp. cultivars. DH, FR, and BR represent the red, pink and white colored flesh samples, respectively.
DOI: 10.6084/m9.figshare.12750089.v1
title: Additional file 9 of Novel bioinformatic classification system for genetic signatures identification in diffuse large B-cell lymphoma

description: Additional file 9 Table S6. Genetic alterations had been revealed to be of importance but not included in this study.
DOI: 10.6084/m9.figshare.12750098
title: Additional file 2 of Physiological and transcriptome analysis of Poa pratensis var. anceps cv. Qinghai in response to cold stress

description: Additional file 2: Table S2. Summary statistics of the common vetch transcriptome assemblies.
DOI: 10.6084/m9.figshare.16944549
title: Additional file 5 of Genome-wide analysis of Dof transcription factors and their response to cold stress in rice (Oryza sativa L.)

description: Additional file 5
DOI: 10.6084/m9.figshare.12750023
title: Additional file 2 of Genome-wide DNA methylation profiling identifies epigenetic signatures of gastric cardiac intestinal metaplasia

description: Additional file 2: Table S1. General characteristics of the study subjects.
DOI: 10.6084/m9.figshare.12750027.v1
title: Additional file 6 of Contribution of anthocyanin pathways to fruit flesh coloration in pitayas

description: Additional file 6: Table S1. Ion intensity of the 444 metabolites detected in the three Hylocereus spp. cultivars. Data represent average values from six biological replicates. DH, FR, and BR represent the red, pink and white colored flesh samples, respectively.
DOI: 10.6084/m9.figshare.16944549.v1
title: Additional file 5 of Genome-wide analysis of Dof transcription factors and their response to cold stress in rice (Oryza sativa L.)

description: Additional file 5
DOI: 10.6084/m9.figshare.12750035
title: Additional file 5 of Genome-wide DNA methylation profiling identifies epigenetic signatures of gastric cardiac intestinal metaplasia

description: Additional file 5: Table S4. List of 6784 DMPs located in promoter-associated CpG islands.
DOI: 10.6084/m9.figshare.12750023.v1
title: Additional file 2 of Genome-wide DNA methylation profiling identifies epigenetic signatures of gastric cardiac intestinal metaplasia

description: Additional file 2: Table S1. General characteristics of the study subjects.
DOI: 10.6084/m9.figshare.12750065.v1
title: Additional file 1 of Novel bioinformatic classification system for genetic signatures identification in diffuse large B-cell lymphoma

description: Additional file 1: Table S1. Patient characteristics and genetic variants information.
DOI: 10.6084/m9.figshare.16944552
title: Additional file 6 of Genome-wide analysis of Dof transcription factors and their response to cold stress in rice (Oryza sativa L.)

description: Additional file 6
DOI: 10.6084/m9.figshare.16944558
title: Additional file 8 of Genome-wide analysis of Dof transcription factors and their response to cold stress in rice (Oryza sativa L.)

description: Additional file 8
DOI: 10.6084/m9.figshare.12750077
title: Additional file 5 of Novel bioinformatic classification system for genetic signatures identification in diffuse large B-cell lymphoma

description: Additional file 5: Table S3. Variant list