cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12768812.v1
title: Additional file 5 of Transcriptomic profiling revealed key signaling pathways for cold tolerance and acclimation of two carp species

description: Additional file 5. Differentially expressed genes in each group obtained through Venn’s diagrams.
DOI: 10.6084/m9.figshare.12768818
title: Additional file 7 of Transcriptomic profiling revealed key signaling pathways for cold tolerance and acclimation of two carp species

description: Additional file 7. Representative GO terms for biological processes in each group.
DOI: 10.6084/m9.figshare.8050229.v1
title: Additional file 2: of Alterations in the gut microbiome and metabolism with coronary artery disease severity

description: Table S1. The extrinsic host factor profile included diet, lifestyle, and stool consistency in CAD and controlÂ individuals. Table S2. Description of metabolite clusters of serum metabolites under polar ionic mode and their associations with Gensini score, no. of stenosed vessels and cTnI in 201 individuals. Table S3. Description of metabolite clusters of serum metabolites under lipid mode and their associations with Gensini score, no. of stenosed vessels and cTnI in 201 individuals. Table S4. Composition of the 29 fasting serum metabolite clusters comprising the CAD-positive- and CAD-negative metabotypes in 201 subjects. Table S5. Adonis results based on unweighted UniFrac distances. Table S6. Multi-omic analysis of the gut microbiome, metabolites and CAD phenotype. Table S7. Baseline characteristics of validation-phase subjects. (XLSX 53 kb)
DOI: 10.6084/m9.figshare.12768809
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.12768818.v1
title: Additional file 7 of Transcriptomic profiling revealed key signaling pathways for cold tolerance and acclimation of two carp species

description: Additional file 7. Representative GO terms for biological processes in each group.
DOI: 10.6084/m9.figshare.8051000.v1
title: Additional file 5: of Identification of cucumber circular RNAs responsive to salt stress

description: Table S5. circRNAs derived from orthologous genes of cucumber and seven other species. (XLSX 235 kb)
DOI: 10.6084/m9.figshare.22730406
title: Analysis and optimization of impact energy absorption performance of mine refuge chamber filled with concave triangular negative poisson's ratio material

description: Abstract In this paper, negative poisson's ratio material is used to fill the interlayer of mine refuge chamber, and its characteristics such as light weight, thermal insulation, vibration isolation and impact resistance are used to improve the impact resistance and thermal insulation ability of mine refuge chamber. The equivalent density, elastic modulus and yield strength of negative poisson's ratio structure of material Q345 were obtained by simulation analysis. The negative poisson's ratio material was filled into the mine refuge chamber, and the impact energy absorption and explosion transient thermal analysis were carried out. The results show that compared with the prototype, the maximum inner skin temperature of the negative poisson's ratio refuge chamber is reduced by 44.86%, the transverse and longitudinal stiffeners temperature is reduced by nearly 46.77%, and the impact deformation is reduced by 35mm, which has better safety performance. The response surface optimization method was used to optimize the whole refuge chamber filled with negative poisson's ratio material, which was more secure than before.
DOI: 10.6084/m9.figshare.8050922.v1
title: Additional file 10: of Identification of cucumber circular RNAs responsive to salt stress

description: Table S9. miRNAs sponged by circRNAs. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.20103954.v1
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.
DOI: 10.6084/m9.figshare.8051033
title: Additional file 9: of Identification of cucumber circular RNAs responsive to salt stress

description: Table S8. Significantly differentially expressed circRNAs in leaf. (XLSX 19 kb)
DOI: 10.6084/m9.figshare.14866335.v1
title: Dolutegravir-based regimens in treatment-naive and treatment-experienced aging populations: analyses of 6 phase III clinical trials

description: <b>Background:</b> Older adults living with HIV (OALWH) are a growing population facing unique challenges to successful antiretroviral therapy. <b>Objective:</b> To assess efficacy and safety profiles of antiretroviral regimens, including those containing dolutegravir, in OALWH. <b>Methods:</b> Combined data from 6 phase III/IIIb trials in treatment-naive (ARIA, FLAMINGO, SINGLE, SPRING-2; <i>N</i> = 2634) and treatment-experienced (DAWNING, SAILING; <i>N</i> = 1339) participants receiving dolutegravir- or non–dolutegravir-based regimens were analyzed by age (&lt;50, ≥50 to &lt;65, and ≥65 years). Baseline data included comorbidities and numbers of concomitant medications. Week 48 efficacy outcomes included virologic response (HIV-1 RNA &lt;50 copies/mL) and CD4+ cell count change from baseline. Safety outcomes included incidence of adverse events (AEs), serious AEs, and AE-related withdrawals. <b>Results:</b> Use of ≥5 concomitant medications was more frequently reported among treatment-naive and treatment-experienced participants aged ≥50 to &lt;65 (30% [90/296] and 25% [57/227], respectively) and ≥65 years (43% [10/23] and 29% [4/14]) than among those aged &lt;50 years (13% [310/2315] and 11% [118/1098]). Comorbidities were more prevalent in the older age groups. For dolutegravir-based regimens, Week 48 rates of virologic response and change in CD4+ cell count were similar across age groups (treatment naive, 80–87% and 234–251 cells/mm<sup>3</sup>; treatment experienced, 70–100% and 105–156 cells/mm<sup>3</sup>, respectively). There were no major differences in safety outcomes in each age group. <b>Conclusions:</b> In these analyses of combined phase III/IIIb trial data, efficacy and safety of dolutegravir-based regimens were generally similar across age groups in treatment-naive or treatment-experienced participants. Polypharmacy and comorbidities were more common among OALWH than those aged &lt;50 years.
DOI: 10.6084/m9.figshare.23254799
title: Supplementary Material for: Dynamic profiling of the immune tumor microenvironment in locally advanced gastric cancer treated with perioperative chemotherapy

description: Introduction: In locally advanced gastric cancer (GC), FLOT represents the standard perioperative regimen and combination with immunotherapy is under investigation. However, the role of immune tumor microenvironment (TME) is poorly recognized in this setting. We aimed to study TME characteristics and dynamics during FLOT. 
Methods: Paired biopsy (PRE) and surgical (POST) samples of 25 patients treated with FLOT were prospectively analyzed. After collection of clinic-pathological data, NanoString analyses were performed. The primary objective of the study was to assess the changes induced by chemotherapy in POST compared to PRE samples. 
Results: The unsupervised hierarchical method analysis clearly distinguished PRE and POST samples, even though some cases showed high immune gene expression at baseline. When POST samples were compared with PRE, a differential expression in hyper-expressed gene sets related to cytotoxicity, T-cell functions, complement system, tumor necrosis factor-superfamily, cell cycle and regulation was recognized. Downstaging of the primary tumor (T-regression, measured by pathologic compared to clinical T stage) was the covariate most frequently associated with these changes. Using the immune cell profiling, cases with T-regression reported a significant increase of T, CD8+ T and B-cells and a decrease in mast cells, while non-responders demonstrated an increase of T, B, cytotoxic and mast cells. 
Conclusion: Our analysis shows that FLOT significantly influences immune TME of GC. While relevant modifications preferentially occur in tumors showing primary tumor regression, response to treatment seems to be associated with a specific immune profile.
DOI: 10.6084/m9.figshare.19579951
title: Additional file 3 of Influence of the geometric and material properties of lumbar endplate on lumbar interbody fusion failure: a systematic review

description: Additional file 3. Results of quality assessment on each included study.
DOI: 10.6084/m9.figshare.8050748.v1
title: MOESM1 of Omics-based analyses revealed metabolic responses of Clostridium acetobutylicum to lignocellulose-derived inhibitors furfural, formic acid and phenol stress for butanol fermentation

description: Additional file 1. Metabolomic data.
DOI: 10.6084/m9.figshare.20109069
title: Recombinant expression of hen egg white lysozyme with the assistance of xylanase fusion partner in <i>Pichia pastoris</i>

description: Due to its bacteriolytic activity, hen egg white lysozyme (HEWL) is widely used in the feed, food, and pharmaceutical industries. However, its application is hindered by low protein expression levels in microbial expression systems. In this work, a novel fusion protein expression strategy was proposed for increasing the expression level of HEWL. First, HEWL, fused with a highly expressed fusion protein partner xylanase XynCDBFV, is expressed in <i>Pichia pastoris</i>. Secondly, a linker including endogenous protease cleavage sites was introduced between two fusion proteins in order to separate them directly during the secretion process. Finally, the results show that the supernatant of XynCDBFV-HEWL has a higher HEWL expression level and activity compared with HEWL only. It should be noted that the expression of HEWL reaches to about 3.5 g/L, and the activity of HEWL against <i>Micrococcus lysodeikticus</i> reaches to 1.50 × 10<sup>5</sup> U/mL in a fed-batch fermentation, which is currently the highest level of recombinant expression of an egg white-derived lysozyme. Taken together, we acquired bioactive HEWL for large-scale recombinant production in <i>Pichia pastor</i>is using a novel fusion protein expression strategy, which could then be used for a variety of applications.
DOI: 10.6084/m9.figshare.20109069.v1
title: Recombinant expression of hen egg white lysozyme with the assistance of xylanase fusion partner in <i>Pichia pastoris</i>

description: Due to its bacteriolytic activity, hen egg white lysozyme (HEWL) is widely used in the feed, food, and pharmaceutical industries. However, its application is hindered by low protein expression levels in microbial expression systems. In this work, a novel fusion protein expression strategy was proposed for increasing the expression level of HEWL. First, HEWL, fused with a highly expressed fusion protein partner xylanase XynCDBFV, is expressed in <i>Pichia pastoris</i>. Secondly, a linker including endogenous protease cleavage sites was introduced between two fusion proteins in order to separate them directly during the secretion process. Finally, the results show that the supernatant of XynCDBFV-HEWL has a higher HEWL expression level and activity compared with HEWL only. It should be noted that the expression of HEWL reaches to about 3.5 g/L, and the activity of HEWL against <i>Micrococcus lysodeikticus</i> reaches to 1.50 × 10<sup>5</sup> U/mL in a fed-batch fermentation, which is currently the highest level of recombinant expression of an egg white-derived lysozyme. Taken together, we acquired bioactive HEWL for large-scale recombinant production in <i>Pichia pastor</i>is using a novel fusion protein expression strategy, which could then be used for a variety of applications.
DOI: 10.6084/m9.figshare.23254799.v1
title: Supplementary Material for: Dynamic profiling of the immune tumor microenvironment in locally advanced gastric cancer treated with perioperative chemotherapy

description: Introduction: In locally advanced gastric cancer (GC), FLOT represents the standard perioperative regimen and combination with immunotherapy is under investigation. However, the role of immune tumor microenvironment (TME) is poorly recognized in this setting. We aimed to study TME characteristics and dynamics during FLOT. 
Methods: Paired biopsy (PRE) and surgical (POST) samples of 25 patients treated with FLOT were prospectively analyzed. After collection of clinic-pathological data, NanoString analyses were performed. The primary objective of the study was to assess the changes induced by chemotherapy in POST compared to PRE samples. 
Results: The unsupervised hierarchical method analysis clearly distinguished PRE and POST samples, even though some cases showed high immune gene expression at baseline. When POST samples were compared with PRE, a differential expression in hyper-expressed gene sets related to cytotoxicity, T-cell functions, complement system, tumor necrosis factor-superfamily, cell cycle and regulation was recognized. Downstaging of the primary tumor (T-regression, measured by pathologic compared to clinical T stage) was the covariate most frequently associated with these changes. Using the immune cell profiling, cases with T-regression reported a significant increase of T, CD8+ T and B-cells and a decrease in mast cells, while non-responders demonstrated an increase of T, B, cytotoxic and mast cells. 
Conclusion: Our analysis shows that FLOT significantly influences immune TME of GC. While relevant modifications preferentially occur in tumors showing primary tumor regression, response to treatment seems to be associated with a specific immune profile.
DOI: 10.6084/m9.figshare.25211756
title: Data Feminisme.numbers

description: Just data of sexual behaviour in Indonesia
DOI: 10.6084/m9.figshare.25211756.v1
title: Data Feminisme.numbers

description: Just data of sexual behaviour in Indonesia
DOI: 10.6084/m9.figshare.8050934
title: Additional file 11: of Identification of cucumber circular RNAs responsive to salt stress

description: Table S11. miRNAs sponged by significantly differentially expressed circRNAs and their mRNA targets in root. (XLSX 90 kb)
DOI: 10.6084/m9.figshare.8050946
title: Additional file 12: of Identification of cucumber circular RNAs responsive to salt stress

description: Table S12. miRNAs sponged by significantly differentially expressed circRNAs and their mRNA targets in leaf. (XLSX 39 kb)
DOI: 10.6084/m9.figshare.8050946.v1
title: Additional file 12: of Identification of cucumber circular RNAs responsive to salt stress

description: Table S12. miRNAs sponged by significantly differentially expressed circRNAs and their mRNA targets in leaf. (XLSX 39 kb)
DOI: 10.6084/m9.figshare.8050982
title: Additional file 2: of Identification of cucumber circular RNAs responsive to salt stress

description: Table S2. The mature sequences of reported cucumber miRNAs. (XLSX 87 kb)
DOI: 10.6084/m9.figshare.8050754.v1
title: MOESM2 of Omics-based analyses revealed metabolic responses of Clostridium acetobutylicum to lignocellulose-derived inhibitors furfural, formic acid and phenol stress for butanol fermentation

description: Additional file 2. Proteomic data.
DOI: 10.6084/m9.figshare.8051000
title: Additional file 5: of Identification of cucumber circular RNAs responsive to salt stress

description: Table S5. circRNAs derived from orthologous genes of cucumber and seven other species. (XLSX 235 kb)
DOI: 10.6084/m9.figshare.8051024.v1
title: Additional file 8: of Identification of cucumber circular RNAs responsive to salt stress

description: Table S7. Significantly differentially expressed circRNAs in root. (XLSX 474 kb)
DOI: 10.6084/m9.figshare.8051033.v1
title: Additional file 9: of Identification of cucumber circular RNAs responsive to salt stress

description: Table S8. Significantly differentially expressed circRNAs in leaf. (XLSX 19 kb)
DOI: 10.6084/m9.figshare.8050922
title: Additional file 10: of Identification of cucumber circular RNAs responsive to salt stress

description: Table S9. miRNAs sponged by circRNAs. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.20103939.v1
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.8050934.v1
title: Additional file 11: of Identification of cucumber circular RNAs responsive to salt stress

description: Table S11. miRNAs sponged by significantly differentially expressed circRNAs and their mRNA targets in root. (XLSX 90 kb)
DOI: 10.6084/m9.figshare.14866689
title: Silencing of the chemokine CXC receptor 4 (CXCR4) hampers cancer progression and increases cisplatin (DDP)-sensitivity in clear cell renal cell carcinoma (ccRCC)

description: Aberrant expression of the chemokine CXC receptor 4 (CXCR4) is closely associated with cancer progression and drug-resistance in multiple cancers, and we first investigated the role of CXCR4 in regulating cancer pathogenesis and cisplatin (DDP)-resistance in clear cell renal cell carcinoma (ccRCC) in the present study. Here, we identified that CXCR4 acted as an oncogene to promote cancer progression and genetically silencing of CXCR4 increased cisplatin (DDP)-sensitivity in ccRCC <i>in vitro</i> and <i>in vivo</i>. Functionally, analysis from the clinical and cellular data indicated that CXCR4 was significantly upregulated in ccRCC tissues and cells, compared to their normal counterparts. Next, the loss-of-function experiments validated that knock-down of CXCR4 suppressed cell proliferation, invasion, migration and epithelial-mesenchymal transition (EMT) in ccRCC cells, while CXCR4 overexpression had opposite effects on the above cellular functions. Consistently, the xenograft tumor-bearing mice models were established, and the results supported that knock-down of CXCR4 inhibited tumor growth and the expression levels of Ki67 protein <i>in vivo</i>. In addition, the ccRCC cells were exposed to DDP treatment, and we surprisingly found that upregulation of CXCR4 increased DDP-resistance in ccRCC cells, and conversely, CXCR4 ablation sensitized ccRCC cells to DDP stimulation. Taken together, we concluded that CXCR4 ablation hindered cancer progression and enhanced DDP-sensitivity in ccRCC, and the present study identified a novel therapeutic biomarker for ccRCC.
DOI: 10.6084/m9.figshare.8051186
title: Additional file 2: of Gene domain-specific DNA methylation episignatures highlight distinct molecular entities of ADNP syndrome

description: Table S1. CpG sites differentially methylated between ADNP-1 and controls. Table S2. CpG sites differentially methylated between ADNP-2 and controls. Table S3. Differentially methylated regions in ADNP-1. Table S4. Differentially methylated regions in ADNP-2. Table S5. Gene ontology (GO) terms in ADNP-1 (green: FDRâ &lt;â 0.01). Table S6. Gene ontology (GO) terms in ADNP-2. Table S7. Gene ontology (GO) terms in ADNP-1 and ADNP-2. Table S8. Pathways enriched in ADNP-1 episignature. Table S9. Pathways enriched in ADNP-1 and ADNP-2 episignatures. Table S10. EpiMods of DNA methylation protein-protein interactions in ADNP-1. Table S11. EpiMods of DNA methylation protein-protein interactions in ADNP-2. Table S12. Details of the SVM classifier. Table S13 Scores generated for various blood cells. (XLSX 910 kb)
DOI: 10.6084/m9.figshare.8051015.v1
title: Additional file 7: of Identification of cucumber circular RNAs responsive to salt stress

description: Table S6. circRNAs with complementary or MITE flanking sequences. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.8051024
title: Additional file 8: of Identification of cucumber circular RNAs responsive to salt stress

description: Table S7. Significantly differentially expressed circRNAs in root. (XLSX 474 kb)
DOI: 10.6084/m9.figshare.8051186.v1
title: Additional file 2: of Gene domain-specific DNA methylation episignatures highlight distinct molecular entities of ADNP syndrome

description: Table S1. CpG sites differentially methylated between ADNP-1 and controls. Table S2. CpG sites differentially methylated between ADNP-2 and controls. Table S3. Differentially methylated regions in ADNP-1. Table S4. Differentially methylated regions in ADNP-2. Table S5. Gene ontology (GO) terms in ADNP-1 (green: FDRâ &lt;â 0.01). Table S6. Gene ontology (GO) terms in ADNP-2. Table S7. Gene ontology (GO) terms in ADNP-1 and ADNP-2. Table S8. Pathways enriched in ADNP-1 episignature. Table S9. Pathways enriched in ADNP-1 and ADNP-2 episignatures. Table S10. EpiMods of DNA methylation protein-protein interactions in ADNP-1. Table S11. EpiMods of DNA methylation protein-protein interactions in ADNP-2. Table S12. Details of the SVM classifier. Table S13 Scores generated for various blood cells. (XLSX 910 kb)
DOI: 10.6084/m9.figshare.14866689.v1
title: Silencing of the chemokine CXC receptor 4 (CXCR4) hampers cancer progression and increases cisplatin (DDP)-sensitivity in clear cell renal cell carcinoma (ccRCC)

description: Aberrant expression of the chemokine CXC receptor 4 (CXCR4) is closely associated with cancer progression and drug-resistance in multiple cancers, and we first investigated the role of CXCR4 in regulating cancer pathogenesis and cisplatin (DDP)-resistance in clear cell renal cell carcinoma (ccRCC) in the present study. Here, we identified that CXCR4 acted as an oncogene to promote cancer progression and genetically silencing of CXCR4 increased cisplatin (DDP)-sensitivity in ccRCC <i>in vitro</i> and <i>in vivo</i>. Functionally, analysis from the clinical and cellular data indicated that CXCR4 was significantly upregulated in ccRCC tissues and cells, compared to their normal counterparts. Next, the loss-of-function experiments validated that knock-down of CXCR4 suppressed cell proliferation, invasion, migration and epithelial-mesenchymal transition (EMT) in ccRCC cells, while CXCR4 overexpression had opposite effects on the above cellular functions. Consistently, the xenograft tumor-bearing mice models were established, and the results supported that knock-down of CXCR4 inhibited tumor growth and the expression levels of Ki67 protein <i>in vivo</i>. In addition, the ccRCC cells were exposed to DDP treatment, and we surprisingly found that upregulation of CXCR4 increased DDP-resistance in ccRCC cells, and conversely, CXCR4 ablation sensitized ccRCC cells to DDP stimulation. Taken together, we concluded that CXCR4 ablation hindered cancer progression and enhanced DDP-sensitivity in ccRCC, and the present study identified a novel therapeutic biomarker for ccRCC.
DOI: 10.6084/m9.figshare.8050958.v1
title: Additional file 13: of Identification of cucumber circular RNAs responsive to salt stress

description: Table S10. Evolutionary conserved miRNAs sponged by circRNAs. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.8050958
title: Additional file 13: of Identification of cucumber circular RNAs responsive to salt stress

description: Table S10. Evolutionary conserved miRNAs sponged by circRNAs. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.8050982.v1
title: Additional file 2: of Identification of cucumber circular RNAs responsive to salt stress

description: Table S2. The mature sequences of reported cucumber miRNAs. (XLSX 87 kb)
DOI: 10.6084/m9.figshare.8050985
title: Additional file 3: of Identification of cucumber circular RNAs responsive to salt stress

description: Table S3. Primers used for circRNAs sequences validation. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.8050991
title: Additional file 4: of Identification of cucumber circular RNAs responsive to salt stress

description: Table S4. Detailed information of identified circRNAs. (XLSX 726 kb)
DOI: 10.6084/m9.figshare.8050991.v1
title: Additional file 4: of Identification of cucumber circular RNAs responsive to salt stress

description: Table S4. Detailed information of identified circRNAs. (XLSX 726 kb)
DOI: 10.6084/m9.figshare.8051015
title: Additional file 7: of Identification of cucumber circular RNAs responsive to salt stress

description: Table S6. circRNAs with complementary or MITE flanking sequences. (XLSX 18 kb)