cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.23639931
title: Additional file 2 of Genome-wide identification of SrbHLH transcription factors highlights its potential role in rebaudioside A (RA) biosynthesis in Stevia rebaudiana

description: Additional file 2: Table S2. The collinear relationships among SrbHLHs.
DOI: 10.6084/m9.figshare.23639928.v1
title: Additional file 1 of Genome-wide identification of SrbHLH transcription factors highlights its potential role in rebaudioside A (RA) biosynthesis in Stevia rebaudiana

description: Additional file 1: Table S1. Primers used in this study.
DOI: 10.6084/m9.figshare.6338465.v1
title: Additional file 1: of Long-term health and germline transmission in transgenic cattle following transposon-mediated gene transfer

description: Raw data of blood analysis from transgenic cattle. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.16821533
title: Additional file 3 of Biogeographic traits of dimethyl sulfide and dimethylsulfoniopropionate cycling in polar oceans

description: Additional file 2: Table S1. Raw abundances of DMS/DMSP related genes in Arctic and Antarctic seawater samples. Table S2. A list of enzymes selected as outgroups for phylogenetic analyses. Table S3. Raw abundances and taxonomic composition of DMS/DMSP related genes in MAGs. Table S4. Raw abundances of DMS/DMSP related genes in Tara Ocean samples. Table S5. Raw abundances of DMS/DMSP related genes in metatranscriptomes. Table S6. The predicted hits with enzymatic activity. Table S7. Biplot scores for constraining variables. Table S8. Taxonomy composition of DMS/DMSP related genes in polar ocean samples. Table S9. Occurrence of DMS/DMSP related genes in genomes from IMG/M database. Table S10. Raw abundances of MTO in metagenomic and metatranscriptomic samples.
DOI: 10.6084/m9.figshare.23639931.v1
title: Additional file 2 of Genome-wide identification of SrbHLH transcription factors highlights its potential role in rebaudioside A (RA) biosynthesis in Stevia rebaudiana

description: Additional file 2: Table S2. The collinear relationships among SrbHLHs.
DOI: 10.6084/m9.figshare.16821524.v1
title: Additional file 3 of Gut bacterial metabolites modulate endoplasmic reticulum stress

description: Additional file 3: Table S2. List of protease inhibitors.
DOI: 10.6084/m9.figshare.22067078.v1
title: Analysis of the Microbiomes on Two Cultural Heritage Sites

description: In the World Cultural Heritage of Leshan Giant Buddha and the West Lake area, the statues and monuments have been affected by the colonizing organisms. In the past three years, we used next-generation sequencing technology to analyze the biofilm of 14 sites in two places. The result showed that microbiomes were different on monuments, especially in terms of microbial composition, diversity, and potential functions. More phototrophic organisms and bacteria involved in the nitrogen-sulfur cycle were found in the West Lake area (WLA), while heterotrophs were discovered in the Leshan Giant Buddha area (LGBA). The biofilms on sandstone in LGBA possessed a higher alpha diversity of bacteria and fungi community than that on limestone in WLA. Biofilms in LGBA showed higher gene expression in metabolisms, such as the metabolism of carbohydrates, lipids, xenobiotics, and terpenoids. While biofilms in WLA exhibited higher levels of genetic information processing genes, which are associated with coping with harsh environments. Combine with XRD and SEM-EDS analysis, petrographic properties were considered the main factors that affect biological colonization. Environmental conditions (temperature, humidity, and precipitation) were similar in the two regions, which are suitable for the growth of organisms. Microbiome dissimilarities (beta diversity) indicated that the microbial compositions of biofilms were associated with the geographic features of the sampling sites. The stones in the two regions have their own petrographic properties that greatly influence microbiome colonization, such as microstructure, porosity, water permeability, and minerals composition.
DOI: 10.6084/m9.figshare.22067078
title: Analysis of the Microbiomes on Two Cultural Heritage Sites

description: In the World Cultural Heritage of Leshan Giant Buddha and the West Lake area, the statues and monuments have been affected by the colonizing organisms. In the past three years, we used next-generation sequencing technology to analyze the biofilm of 14 sites in two places. The result showed that microbiomes were different on monuments, especially in terms of microbial composition, diversity, and potential functions. More phototrophic organisms and bacteria involved in the nitrogen-sulfur cycle were found in the West Lake area (WLA), while heterotrophs were discovered in the Leshan Giant Buddha area (LGBA). The biofilms on sandstone in LGBA possessed a higher alpha diversity of bacteria and fungi community than that on limestone in WLA. Biofilms in LGBA showed higher gene expression in metabolisms, such as the metabolism of carbohydrates, lipids, xenobiotics, and terpenoids. While biofilms in WLA exhibited higher levels of genetic information processing genes, which are associated with coping with harsh environments. Combine with XRD and SEM-EDS analysis, petrographic properties were considered the main factors that affect biological colonization. Environmental conditions (temperature, humidity, and precipitation) were similar in the two regions, which are suitable for the growth of organisms. Microbiome dissimilarities (beta diversity) indicated that the microbial compositions of biofilms were associated with the geographic features of the sampling sites. The stones in the two regions have their own petrographic properties that greatly influence microbiome colonization, such as microstructure, porosity, water permeability, and minerals composition.
DOI: 10.6084/m9.figshare.6338444.v1
title: Additional file 8 of Investigation of the thermophilic mechanism in the genus Porphyrobacter by comparative genomic analysis

description: Summary of sources of Alphaproteobacteria strains applied in investigations of conserved proteins. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.6338405.v1
title: Additional file 6: of Embryonic transcriptome and proteome analyses on hepatic lipid metabolism in chickens divergently selected for abdominal fat content

description: Table S5. DEGs identified in liver of E21 embryos between the fat and lean lines. (XLSX 31Â kb)
DOI: 10.6084/m9.figshare.6338459.v1
title: Additional file 1: of Pulse actinomycin D as first-line treatment of low-risk post-molar non-choriocarcinoma gestational trophoblastic neoplasia

description: Raw data. This file contains data generated or analysed during this study. (XLSX 24Â kb)
DOI: 10.6084/m9.figshare.22067124
title: Codes of Figures 4-13 from Periodic gaits and flip bifurcation of a biped robot walking on level ground with two feasible switching patterns of motion

description: The Codes of Figures 4-13 are in the ESM file Code_of_paper0570
DOI: 10.6084/m9.figshare.23639928
title: Additional file 1 of Genome-wide identification of SrbHLH transcription factors highlights its potential role in rebaudioside A (RA) biosynthesis in Stevia rebaudiana

description: Additional file 1: Table S1. Primers used in this study.
DOI: 10.6084/m9.figshare.22067124.v1
title: Codes of Figures 4-13 from Periodic gaits and flip bifurcation of a biped robot walking on level ground with two feasible switching patterns of motion

description: The Codes of Figures 4-13 are in the ESM file Code_of_paper0570
DOI: 10.6084/m9.figshare.6338465
title: Additional file 1: of Long-term health and germline transmission in transgenic cattle following transposon-mediated gene transfer

description: Raw data of blood analysis from transgenic cattle. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.22067135
title: The Intestinal Microbiota Involves in the Deterioration of Live Sea Cucumber During Storage

description: This study was designed to explore the relationship between the deterioration of sea cucumbers and intestinal flora’s diversity change during preservation using 16S rRNA gene sequencing. We show that the body wall of sea cucumber develops white spots on day 4, and the epidermis dissolves on day 7. The distinctive OTUs remain relatively low during four days of storage but increase on day 7. The potential gut microbiota biomarkers are <i>Psychrobacter-cibarius</i>, <i>Ralstonia-pickettii</i>, and Clostridiales during the deterioration of sea cucumber. The result of mixed storage of fresh and deteriorated sea cucumbers validates the influence of microbiota on healthy sea cucumbers.
DOI: 10.6084/m9.figshare.16821554.v1
title: Additional file 2 of Genome-wide survey of Gγ subunit gene family in eight Rosaceae and expression analysis of PbrGGs in pear (Pyrus bretschneideri)

description: Additional file 2: Table S2. Synteny analysis of Gγ subunit gene regions in Rosaceae
DOI: 10.6084/m9.figshare.19445716.v1
title: Additional file 2 of Bacterial communities in surface and basal ice of a glacier terminus in the headwaters of Yangtze River on the Qinghai–Tibet Plateau

description: Additional file 2. OTU table of the sample sites.
DOI: 10.6084/m9.figshare.19445716
title: Additional file 2 of Bacterial communities in surface and basal ice of a glacier terminus in the headwaters of Yangtze River on the Qinghai–Tibet Plateau

description: Additional file 2. OTU table of the sample sites.
DOI: 10.6084/m9.figshare.23639997
title: Additional file 5 of Genome-wide identification, characterization and transcriptional profile of the SWEET gene family in Dendrobium officinale

description: Supplementary Material 5
DOI: 10.6084/m9.figshare.23640003.v1
title: Additional file 7 of Genome-wide identification, characterization and transcriptional profile of the SWEET gene family in Dendrobium officinale

description: Supplementary Material 7
DOI: 10.6084/m9.figshare.23640006.v2
title: Additional file 8 of Genome-wide identification, characterization and transcriptional profile of the SWEET gene family in Dendrobium officinale

description: Supplementary Material 8
DOI: 10.6084/m9.figshare.23639994
title: Additional file 4 of Genome-wide identification, characterization and transcriptional profile of the SWEET gene family in Dendrobium officinale

description: Supplementary Material 4
DOI: 10.6084/m9.figshare.23640000
title: Additional file 6 of Genome-wide identification, characterization and transcriptional profile of the SWEET gene family in Dendrobium officinale

description: Supplementary Material 6
DOI: 10.6084/m9.figshare.23640000.v2
title: Additional file 6 of Genome-wide identification, characterization and transcriptional profile of the SWEET gene family in Dendrobium officinale

description: Supplementary Material 6
DOI: 10.6084/m9.figshare.23640003
title: Additional file 7 of Genome-wide identification, characterization and transcriptional profile of the SWEET gene family in Dendrobium officinale

description: Supplementary Material 7
DOI: 10.6084/m9.figshare.23639994.v2
title: Additional file 4 of Genome-wide identification, characterization and transcriptional profile of the SWEET gene family in Dendrobium officinale

description: Supplementary Material 4
DOI: 10.6084/m9.figshare.23640006
title: Additional file 8 of Genome-wide identification, characterization and transcriptional profile of the SWEET gene family in Dendrobium officinale

description: Supplementary Material 8
DOI: 10.6084/m9.figshare.16821515
title: Additional file 1 of Gut bacterial metabolites modulate endoplasmic reticulum stress

description: Additional file 1: Table S1. List of MBB molecules.
DOI: 10.5281/zenodo.10053604
title: Data for Weimann et al - Evolution and host-specific pathoadaptation of Pseudomonas aeruginosa

description: Additional data that was generated as part of this work, including clone trees, alignments, variants and accessory genome graph.

Pairwise SNP distances between all patient representative and environmental samples (all_patient_dist_square.txt.gz)
Variants that have occurred since the emergence of individual clone with detailed variant effects with variants due to recombination removed (all_mutations_wo_recomb.txt.gz)
A summary of all single nucleotide variants that lead to amino acid changes with SIFT and FoldX predictions (all_aa_variants_info.txt.gz)
Pseudogenome alignments for 155 individual clones (all_clones_aln.fasta.tar.gz)
Clone trees inferred with Gubbins/RaxML (all_clones.nwk.tar.gz)
BEAST input alignments for 21 epidemic clones (after pruning) (epidemic_clones_alignments_for_beast.fasta.tar.gz)
BEAST input XMLs  for 21 epidemic clones (lognormal/uniform/date randomisation test where applicable) (beast_xmls.tar.gz)
BEAST combined trees for 21 epidemic clones (beast_trees.tar.gz)
BEAST input XMLs  for discrete trait phylogeographic analysis for 3 epidemic clones (beast_phylogeography.xmls.tar.gz)
BEAST combined phylogeographic trees for 3 epidemic clones (phylogeography_trees.tar.gz) 
Cytoscape session file for Panaroo genome graph laid out and subset to ancestral genome representatives (ancestral_representatives_graph_layout.cys)
Panaroo genome graph output based on all patient representative/environmental genomes (final_graph.gml.gz)
Cytoscape session file for pathoadaptive STRING pathoadaptive gene-product network (pathoadaptive_gene_products_string_odds_ratio.cys)
DOI: 10.6084/m9.figshare.21542889
title: Comparative efficacy and safety of antiviral traditional Chinese medicine injections for viral pneumonia: a systematic review and network meta-analysis

description: Viral pneumonia (VP) is becoming a persistent and pervasive burden of disease. Traditional Chinese medicine Injections (TCMIs) have been proved effective in the treatment of patients with VP, which are now widely used in China. The evidence of TCMIs for VP is evolving rapidly. This study aims to assess the comparative efficacy and safety of TCMIs to provide more evidence and sights for the treatment selection of VP. Seven databases were searched from their inception up to 16 March 2022. Only randomized controlled trials (RCTs) are included to compare the efficacy and safety of antiviral TCMIs for the treatment of viral pneumonia. Clinical efficacy and rate of adverse events were considered as primary outcomes. A total of 76 RCTs with eight TCMIs comprising 7925 patients were included in the NMA. According to NMA, Reduning Injection combined with conventional antiviral drugs (CAD) produced superior effects in the effective outcomes and reduced the adverse event incidence rate of VP. This study indicated that TCMIs combined with CAD was more effective and safer than CAD monotherapy and compared different TCMIs therapies, which provided guidance and reference for the selection of clinical treatment medication.
DOI: 10.6084/m9.figshare.21542889.v1
title: Comparative efficacy and safety of antiviral traditional Chinese medicine injections for viral pneumonia: a systematic review and network meta-analysis

description: Viral pneumonia (VP) is becoming a persistent and pervasive burden of disease. Traditional Chinese medicine Injections (TCMIs) have been proved effective in the treatment of patients with VP, which are now widely used in China. The evidence of TCMIs for VP is evolving rapidly. This study aims to assess the comparative efficacy and safety of TCMIs to provide more evidence and sights for the treatment selection of VP. Seven databases were searched from their inception up to 16 March 2022. Only randomized controlled trials (RCTs) are included to compare the efficacy and safety of antiviral TCMIs for the treatment of viral pneumonia. Clinical efficacy and rate of adverse events were considered as primary outcomes. A total of 76 RCTs with eight TCMIs comprising 7925 patients were included in the NMA. According to NMA, Reduning Injection combined with conventional antiviral drugs (CAD) produced superior effects in the effective outcomes and reduced the adverse event incidence rate of VP. This study indicated that TCMIs combined with CAD was more effective and safer than CAD monotherapy and compared different TCMIs therapies, which provided guidance and reference for the selection of clinical treatment medication.
DOI: 10.6084/m9.figshare.19970044
title: Paeoniflorin alleviates the progression of retinal vein occlusion via inhibiting hypoxia inducible factor-1α/vascular endothelial growth factor/STAT3 pathway

description: Retinal vein occlusion (RVO) is a severe retinal vascular disease involving several complications, leading to weakening of vision and even blindness. Globally, over 16 million patients with RVO were found in the middle-aged population. Paeoniflorin (PF), a monomer of Taohong Siwu decoction, was reported to exhibit many pharmacological activities including anti-inflammatory, antioxidant, cardioprotective, and neuroprotective effects. However, the effect of PF on the progression of RVO remains unclear. In the current study, CCK8 assay was performed to investigate the cell viability. In addition, transwell assay and western blot were used to measure cell invasion and protein expression, respectively. Moreover, a mouse model of oxygen-induced dischemic retinopathy (OIR) was established. We found PF was able to inhibit the migration and angiogenesis of human retinal capillary endothelial cells under normoxia. Additionally, PF notably prevented hypoxia-induced angiogenesis of human retinal capillary endothelial cells via inhibiting hypoxia-inducible factor-1α (HIF-1α)/vascular endothelial growth factor (VEGF)/STAT3 pathway. Eventually, PF significantly alleviated the retinal lesions in the mouse with OIR. All in all, PF was able to alleviate the progression of retinal vein occlusion via inhibiting HIF-1α/VEGF/STAT3 pathway. These findings might provide some theoretical knowledge for exploring novel effective treatment for patients with RVO.
DOI: 10.6084/m9.figshare.16821533.v1
title: Additional file 3 of Biogeographic traits of dimethyl sulfide and dimethylsulfoniopropionate cycling in polar oceans

description: Additional file 2: Table S1. Raw abundances of DMS/DMSP related genes in Arctic and Antarctic seawater samples. Table S2. A list of enzymes selected as outgroups for phylogenetic analyses. Table S3. Raw abundances and taxonomic composition of DMS/DMSP related genes in MAGs. Table S4. Raw abundances of DMS/DMSP related genes in Tara Ocean samples. Table S5. Raw abundances of DMS/DMSP related genes in metatranscriptomes. Table S6. The predicted hits with enzymatic activity. Table S7. Biplot scores for constraining variables. Table S8. Taxonomy composition of DMS/DMSP related genes in polar ocean samples. Table S9. Occurrence of DMS/DMSP related genes in genomes from IMG/M database. Table S10. Raw abundances of MTO in metagenomic and metatranscriptomic samples.
DOI: 10.6084/m9.figshare.16821679.v1
title: Additional file 2 of Genome-wide selection signatures detection in Shanghai Holstein cattle population identified genes related to adaption, health and reproduction traits

description: Additional file 2
DOI: 10.6084/m9.figshare.19970047
title: LINC00514 facilitates cell proliferation, migration, invasion, and epithelial-mesenchymal transition in non-small cell lung cancer by acting on the Wnt/β-catenin signaling pathway

description: The long non-coding RNA (lncRNA) LINC00514 was identified to play an essential oncogenic function in different human cancers, but its effects in non-small cell lung cancer (NSCLC) are yet to be elucidated. In this study, we evaluated the function of LINC00514 in NSCLC. LINC00514 expression and prognosis in NSCLC were analyzed using qRT-PCR and online bioinformatic tools. The bioeffects of LINC0514 in NSCLC cells were examined using cell counting kit-8, colony formation, and transwell assays. Western blotting was used to measure the expression of the target proteins. The LINC00514 regulation of the Wnt/β-catenin signaling pathway was assessed using a specific agonist (LiCl) and luciferase reporter assay. We found that LINC00514 expression was elevated in NSCLC cells and clinical samples and that increased LINC00514 expression predicted poorer patient prognosis. Silencing LINC00514 suppresses proliferation, migration, and invasion of NSCLC cells. Downregulation of LINC00514 inhibited Wnt/β-catenin signaling and epithelial-mesenchymal transition (EMT). Moreover, suppression of the biological phenotypes of NSCLC cells induced by LINC00514 gene silencing was restored after LiCl treatment. Finally, we found that silencing LINC00514 attenuated the growth of xenograft tumors in vivo. Altogether, this study provides the latest convincing evidence that LINC00514 facilitates the malignant biological behavior of NSCLC cells through activation of the Wnt/β-catenin pathway, which might offer a beneficial approach for the treatment of NSCLC.
DOI: 10.6084/m9.figshare.19970050
title: Plumbagin relieves rheumatoid arthritis through nuclear factor kappa-B (NF-κB) pathway

description: This study aimed to explore the effects of plumbagin on rheumatoid arthritis (RA) and its mechanism. The RA cell model was simulated following the treatment of interleukin-1β (IL-1β). After the treatment of various concentrations of plumbagin, the impact of plumbagin on the cell viability was examined by 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. The collagen-induced arthritis (CIA) model was established using the solution of bovine type II collagen. Hematoxylin-eosin staining was used to observe the changes of ankle joint tissue, while enzyme-linked immunosorbent assay and western blot were applied to detect the level of inflammatory cytokines. Plumbagin inhibited the viability of human fibroblast-like synoviocytes (HFLS) at the concentration of 1 ~ 3.5 μM. The inhibitory effect of 1 μM plumbagin on cell proliferation was similar to that of methotrexate, the drug used as the positive control. Plumbagin downregulated the levels of inflammatory cytokines and matrix metalloproteinases (MMPs) in IL-1β-treated HFLS, and suppressed the activation of IκB and nuclear factor kappa-B (NF-κB) as well as the entry of p65 into the nucleus. It was also demonstrated in animal experiments that plumbagin inhibited the activation of NF-κB pathway, down-regulated the levels of tumor necrosis factor-α (TNF-α), interleukin-6 (IL-6) and MMPs, and alleviated joint damage in CIA-modeled mice. Collectively speaking, plumbagin might down-regulate the levels of inflammatory cytokines and MMPs through inhibiting the activation of the NF-κB pathway, thereby attenuating RA-induced damage to cells and joints. <b>Abbreviations</b>: CIA: Collagen-induced arthritis; ELISA: Enzyme-linked immuno sorbent assay; HFLS: Human fibroblast-like synoviocytes; IL-6: Interleukin-6; IL-1β: Interleukin-1β; NF-κB: nuclear factor kappa-B; MTT: 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide; MMPs: Matrix metalloproteinase; OD: Optical density; RA: Rheumatoid arthritis; SDS: Sodium dodecyl sulfate; SD: Standard deviation; TNF-α: Tumor necrosis factor-α; PVDF: Polyvinylidene fluoride.