cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.23788453.v1
title: Additional file 12 of Early-life prophylactic antibiotic treatment disturbs the stability of the gut microbiota and increases susceptibility to H9N2 AIV in chicks

description: Additional file 12: Supplementary Table 1. Group setting of the study. Supplementary Table 2. Sequencing depth of the 16S rRNA genes for the samples in the long-term treatment trial. Supplementary Table 3. Results of the PERMANOVA test in the LAT trial. Supplementary Table 4. Sequencing depth of the 16S rRNA genes for the samples in the short-term treatment trial. Supplementary Table 5. Information of samples used for metagenomic sequencing. Supplementary Table 6. Relative abundance of ARG types.
DOI: 10.6084/m9.figshare.23264636
title: The effect of guar gum consumption on the lipid profile in type 2 diabetes mellitus: a systematic review and meta-analysis of randomized controlled trials

description: Dyslipidemia is a common encounter in type 2 diabetes mellitus (T2DM) and the current strategies to manage it are still suboptimal. Subsequently, identifying newer molecules with lipid-lowering effects is necessary. A great deal of attention has been given in recent years to fiber supplements, e.g., guar gum. Thus, we screened and evaluated the quality of the evidence regarding the benefits of guar gum supplementation in T2DM and conducted a meta-analysis to assess the effects of this compound on serum lipids in T2DM. We conducted a comprehensive search in PubMed/Medline, Web of Science, Scopus, Google Scholar and Embase, from the inception of these databases until January 2021. In total, 11 papers were included based on the eligible criteria in our meta-analysis. The meta-analysis of the eligible trials demonstrated a significant reduction of total cholesterol (TC) (WMD: −20.32 mg/dL, 95% CI: −27.02, −13.62, P &lt; 0.001) and low-density lipoprotein cholesterol (LDL-C) (WMD: −14.52 mg/dL, 95% CI: −20.69, −8.35, P &lt; 0.001) following guar gum supplementation in T2DM patients. The subgroup analysis based on the dosage (g/day) of this compound revealed that ≥20 g/day of guar gum led to a notable decrease in triglyceride (TG) levels (WMD: −12.55 mg/dL, 95% CI: −23.72, −1.37, P = 0.02) versus &lt; 20 g/day (WMD: −1.84 mg/dL, 95% CI: −32.18, 28.49, P = 0.90). Guar gum supplementation had no effects on high-density lipoprotein cholesterol (HDL-C) (WMD: 0.66 mg/dL, 95% CI: −0.95, 2.28, P = 0.42). Guar gum consumption has lipid-lowering effects when administered to patients with type 2 diabetes mellitus and it is particularly able to reduce TC, LDL-C and TG levels. Further research is however needed to confirm our findings.
DOI: 10.6084/m9.figshare.7011158
title: Electronic supplementary material from Removal of Hg0 from simulated flue gas over silver-loaded rice husk gasification char

description: Mercury released into the atmosphere from coal combustion is harmful to humans and the environment. Rice husk gasification char (RHGC) is an industrial waste of biomass gasification power generation, which is silver-loaded to develop a novel and efficient sorbent for mercury removal from simulated flue gas. The experiment was carried out in a fixed bed experimental system. The Hg<sup>0</sup> adsorption performance of RHGC was improved significantly after loading silver. Hg<sup>0 </sup>adsorption capacity and mercury inlet concentration were found to be nonlinear. The adsorption capacity of RHGC decreased with the increase of reaction temperature. SO<sub>2</sub> inhibited mercury removal, NO and HCl promoted mercury removal; the Hg<sup>0 </sup>adsorption capacity in the simulated flue gas was higher than that in pure N<sub>2</sub>. The silver-loaded rice husk gasification char (SRHGC) could be recycled for about five times without significantly losing its removal efficiency. The SRHGC will not only reduce the cost of mercury removal but also save energy and reduce environmental pollution, at the same time, it provides a new way for the resource utilization of RHGC.
DOI: 10.6084/m9.figshare.6487736
title: Additional file 10: of Diversification and independent domestication of Asian and European pears

description: List of genes in selective sweep regions of P. ussuriensis during domestication from wild to cultivated pears. (XLSX 44 kb)
DOI: 10.6084/m9.figshare.7012037.v1
title: MiR-3606-3p inhibits systemic sclerosis through targeting TGF-β type II receptor

description: Systemic sclerosis (SSc) is a multisystemic fibrotic disease characterized by excessive collagen deposition and extracellular matrix synthesis. Though transforming growth factor-β (TGF-β) plays a fundamental role in the pathogenesis of SSc, the mechanism by which TGF-β signaling acts in SSc remains largely unclear. Here, we showed that TGF-β type II receptor (TGFBR2) was significantly upregulated in both human SSc dermal tissues and primary fibroblasts. In fibroblasts, siRNA-induced knockdown of <i>TGFBR2</i> resulted in a reduction of p-SMAD2/3 levels and reduced production of type I collagen. Additionally, functional experiments revealed that downregulation of <i>TGFBR2</i> yielded an anti-growth effect on fibroblasts through inhibiting cell cycle progression. Further studies showed that miR-3606-3p could directly target the 3′-UTR of <i>TGFBR2</i> and significantly decrease the levels of both TGFBR2 mRNA and protein. Furthermore, SSc dermal tissues and primary fibroblasts contain significantly reduced amounts of miR-3606-3p, and the overexpression of miR-3606-3p in fibroblasts replicates the phenotype of TGFBR2 downregulation. Collectively, our findings demonstrated that increased TGFBR2 could be responsible for the hyperactive TGF-β signaling observed in SSc. Moreover, we identified a pivotal role for miR-3606-3p in SSc, which acts, at least partly, through the attenuation of TGF-β signaling via TGFBR2 repression, suggesting that the regulation of miR-3606-3p/TGFBR2 could be a promising therapeutic target that could improve the treatment strategy for fibrosis.
DOI: 10.6084/m9.figshare.9108935
title: Additional file 4: of Systematic analysis of the intersection of disease mutations with protein modifications

description: Hotspot mutations on PTM sites found in the TCGA dataset. (XLSX 55 kb)
DOI: 10.6084/m9.figshare.9108935.v1
title: Additional file 4: of Systematic analysis of the intersection of disease mutations with protein modifications

description: Hotspot mutations on PTM sites found in the TCGA dataset. (XLSX 55 kb)
DOI: 10.6084/m9.figshare.23788454.v1
title: Additional file 3 of A traditional gynecological medicine inhibits ovarian cancer progression and eliminates cancer stem cells via the LRPPRC–OXPHOS axis

description: Additional file 3. Data 2. Primer sequence.
DOI: 10.6084/m9.figshare.23788451
title: Additional file 2 of A traditional gynecological medicine inhibits ovarian cancer progression and eliminates cancer stem cells via the LRPPRC–OXPHOS axis

description: Additional file 2. Data 1. Inhibition rate of natural compounds on ovarian cancer cells.
DOI: 10.6084/m9.figshare.23788396
title: Additional file 1 of Identification and evaluation of circulating exosomal miRNAs for the diagnosis of postmenopausal osteoporosis

description: Additional file 1. The sequence of primers and probes for candidate exosomal miRNAs.
DOI: 10.6084/m9.figshare.12254672
title: Improvement in the Analysis of Vaccine Adverse Event Reporting System Database

description: As a national public health surveillance resource, Vaccine Adverse Event Reporting System (VAERS) is a key component in ensuring the safety of vaccines. Numerous methods have been used to conduct safety studies with the VAERS database. These efforts focus on the downstream statistical analysis of the vaccine and adverse event associations. In this article, we primarily focus on processing the raw data in VAERS before the analysis step, which is also an important part of the signal detection process. Due to the semiannual update in the Medical Dictionary for Regulatory Activities (MedDRA) coding system, adverse event terms that describe the same symptom might change in VAERS; therefore, we identify these terms and combine them to increase the signal detection power. We also consider the uncertainty of the vaccine and adverse event pairs that arise from reports with multiple vaccines. Finally, we discuss four commonly used statistics in assessing the vaccine and adverse event associations, and propose to use the statistics that are robust to the reporting bias in VAERS and adjust for potential confounders of the vaccine and adverse event association to increase signal detection accuracy.
DOI: 10.6084/m9.figshare.23788396.v1
title: Additional file 1 of Identification and evaluation of circulating exosomal miRNAs for the diagnosis of postmenopausal osteoporosis

description: Additional file 1. The sequence of primers and probes for candidate exosomal miRNAs.
DOI: 10.6084/m9.figshare.23788399
title: Additional file 2 of Identification and evaluation of circulating exosomal miRNAs for the diagnosis of postmenopausal osteoporosis

description: Additional file 2. The number of pregnancies in both cohorts.
DOI: 10.6084/m9.figshare.23788399.v1
title: Additional file 2 of Identification and evaluation of circulating exosomal miRNAs for the diagnosis of postmenopausal osteoporosis

description: Additional file 2. The number of pregnancies in both cohorts.
DOI: 10.6084/m9.figshare.9108947
title: Additional file 6: of Systematic analysis of the intersection of disease mutations with protein modifications

description: Phosphosite-mimicking (A) hotspot mutations and (B) disease SNPs. (C) Disease SNPs on phosphosites mimicking constitutive activation. (XLSX 105 kb)
DOI: 10.6084/m9.figshare.13302971.v2
title: Metabolome and microbiome alterations in tongue coating of gastric precancerous lesion patients

description: <b>Objective</b>: This paper seeks to provide mechanistic insight into the pathological transition through the analysis of metabolites and microorganisms in the tongue coating of gastric precancerous lesions (GPL) patients. <b>Methods</b>: GC-TOF-MS and UHPLC-QE-MS metabolomics, combined with 16S rRNA microbiome techniques, were performed to explore the changes in metabolites and microorganisms in the tongue coating of GPL patients. <b>Results</b>: When compared with 15 controls, 133 metabolites were found to be differentially expressed in 60 GPL cases, of which could be divided into ten categories. Among them, most of the differentially expressed metabolites identified were lipids or lipid-like molecules. These metabolites were implicated in 6 metabolic pathways including glycine, serine and threonine metabolism, arginine and proline metabolism, sphingolipid metabolism, valine, leucine and isoleucine degradation, arachidonic acid metabolism, and tyrosine metabolism. The relative abundances of Alloprevotella, Solobacterium, Rothia, Eikenella, and Aggregatibacter in the GPL group increased significantly relative to the controls and were associated with lipids and lipid-like molecules, organic nitrogen compounds, organic oxygen compounds, phenylpropanoids and polyketides, and organoheterocyclic compounds, respectively. <b>Conclusions</b>: Compared with healthy people, the changes of tongue coating metabolites in GPL patients were mainly characterized by alterations in lipid metabolism and were associated with localized changes in the microbiome.
DOI: 10.6084/m9.figshare.23788411
title: Additional file 6 of Identification and evaluation of circulating exosomal miRNAs for the diagnosis of postmenopausal osteoporosis

description: Additional file 6. The p-value of Delong test between different diagnostic models.
DOI: 10.6084/m9.figshare.9108980.v1
title: Additional file 2: of RaPID: ultra-fast, powerful, and accurate detection of segments identical by descent (IBD) in biobank-scale cohorts

description: Supplementary Tables S1â S4. (XLSX 26 kb)
DOI: 10.6084/m9.figshare.20110607
title: Additional file 2 of Postoperative morbidity and health-related quality of life in children with delayed reconstruction of esophageal atresia: a nationwide Swedish study

description: Additional file 2. Presents descriptives for generic and condition-specific HRQOL scores in children with DREA and PA, complementary to Figs. 3, 4, 5, 6.
DOI: 10.6084/m9.figshare.23788451.v1
title: Additional file 2 of A traditional gynecological medicine inhibits ovarian cancer progression and eliminates cancer stem cells via the LRPPRC–OXPHOS axis

description: Additional file 2. Data 1. Inhibition rate of natural compounds on ovarian cancer cells.
DOI: 10.6084/m9.figshare.9108911
title: Additional file 1: of Systematic analysis of the intersection of disease mutations with protein modifications

description: The hotspot score (delta S) and number of somatic alterations in each protein. (XLSX 2740 kb)
DOI: 10.6084/m9.figshare.6487736.v1
title: Additional file 10: of Diversification and independent domestication of Asian and European pears

description: List of genes in selective sweep regions of P. ussuriensis during domestication from wild to cultivated pears. (XLSX 44 kb)
DOI: 10.6084/m9.figshare.12254963
title: Modeling and Regionalization of China’s PM<sub>2.5</sub> Using Spatial-Functional Mixture Models

description: <b><i>Abstract–</i>Severe air pollution affects billions of people around the world, particularly in developing countries such as China. Effective emission control policies rely primarily on a proper assessment of air pollutants and accurate spatial clustering outcomes. Unfortunately, emission patterns are difficult to observe as they are highly confounded by many meteorological and geographical factors. In this study, we propose a novel approach for modeling and clustering PM</b>2.5<b>concentrations across China. We model observed concentrations from monitoring stations as spatially dependent functional data and assume latent emission processes originate from a functional mixture model with each component as a spatio-temporal process. Cluster memberships of monitoring stations are modeled as a Markov random field, in which confounding effects are controlled through energy functions. The superior performance of our approach is demonstrated using extensive simulation studies. Our method is effective in dividing China and the Beijing-Tianjin-Hebei region into several regions based on PM</b>2.5<b>concentrations, suggesting that separate local emission control policies are needed. Supplementary materials for this article, including a standardized description of the materials available for reproducing the work, are available as an online supplement.</b>
DOI: 10.6084/m9.figshare.9108911.v1
title: Additional file 1: of Systematic analysis of the intersection of disease mutations with protein modifications

description: The hotspot score (delta S) and number of somatic alterations in each protein. (XLSX 2740 kb)
DOI: 10.6084/m9.figshare.9108947.v1
title: Additional file 6: of Systematic analysis of the intersection of disease mutations with protein modifications

description: Phosphosite-mimicking (A) hotspot mutations and (B) disease SNPs. (C) Disease SNPs on phosphosites mimicking constitutive activation. (XLSX 105 kb)
DOI: 10.6084/m9.figshare.9108956
title: Additional file 8: of Systematic analysis of the intersection of disease mutations with protein modifications

description: Delta-Scansite predictions for (A) somatic and (B) germline alterations in flanking regions of PTM sites. (XLSX 105 kb)
DOI: 10.6084/m9.figshare.9108956.v1
title: Additional file 8: of Systematic analysis of the intersection of disease mutations with protein modifications

description: Delta-Scansite predictions for (A) somatic and (B) germline alterations in flanking regions of PTM sites. (XLSX 105 kb)
DOI: 10.6084/m9.figshare.9108980
title: Additional file 2: of RaPID: ultra-fast, powerful, and accurate detection of segments identical by descent (IBD) in biobank-scale cohorts

description: Supplementary Tables S1â S4. (XLSX 26 kb)
DOI: 10.6084/m9.figshare.6487862
title: Additional file 5: of Diversification and independent domestication of Asian and European pears

description: List of genes in selective sweeps in Asian and European groups during domestication from wild to cultivated pears. (XLSX 188Â kb)
DOI: 10.6084/m9.figshare.9108944
title: Additional file 5: of Systematic analysis of the intersection of disease mutations with protein modifications

description: Disease SNPs overlapping with PTM sites. (XLSX 85 kb)
DOI: 10.6084/m9.figshare.9108944.v1
title: Additional file 5: of Systematic analysis of the intersection of disease mutations with protein modifications

description: Disease SNPs overlapping with PTM sites. (XLSX 85 kb)
DOI: 10.6084/m9.figshare.9108821
title: Additional file 1: of Relationship between ALDH2 genotype and in-stent restenosis in Chinese Han patients after percutaneous coronary intervention

description: Table S1. Clinical information of all patients in this study. (XLSX 90 kb)
DOI: 10.6084/m9.figshare.7012052
title: Identification of compound CA-5f as a novel late-stage autophagy inhibitor with potent anti-tumor effect against non-small cell lung cancer

description: Currently, particular focus is placed on the implication of autophagy in a variety of human diseases, including cancer. Discovery of small-molecule modulators of autophagy as well as their potential use as anti-cancer therapeutic agents would be of great significance. To this end, a series of curcumin analogs previously synthesized in our laboratory were screened. Among these compounds, (3E,5E)-3-(3,4-dimethoxybenzylidene)-5-[(1H-indol-3-yl)methylene]-1-methylpiperidin-4-one (CA-5f) was identified as a potent late-stage macroautophagy/autophagy inhibitor via inhibiting autophagosome-lysosome fusion. We found that CA-5f neither impaired the hydrolytic function nor the quantity of lysosomes. Use of an isobaric tag for relative and absolute quantitation (iTRAQ)-based proteomic screen in combination with bioinformatics analysis suggested that treatment of human umbilical vein endothelial cells (HUVECs) with CA-5f for 1 h suppressed the levels of cytoskeletal proteins and membrane traffic proteins. Subsequent studies showed that CA-5f exhibited strong cytotoxicity against A549 non-small cell lung cancer (NSCLC) cells, but low cytotoxicity to normal human umbilical vein endothelial cells (HUVECs), by increasing mitochondrial-derived reactive oxygen species (ROS) production. Moreover, CA-5f effectively suppressed the growth of A549 lung cancer xenograft as a single agent with an excellent tolerance in vivo. Results from western blot, immunofluorescence, and TdT-mediated dUTP nick end labeling (TUNEL) assays showed that CA-5f inhibited autophagic flux, induced apoptosis, and did not affect the level of CTSB (cathepsin B) and CTSD (cathepsin D) in vivo, which were consistent with the in vitro data. Collectively, these results demonstrated that CA-5f is a novel late-stage autophagy inhibitor with potential clinical application for NSCLC therapy. <b>Abbreviations</b>: 3-MA, 3-methyladenine; ANXA5, annexin A5; ATG, autophagy related; CA-5f, (3E,5E)-3-(3,4-dimethoxybenzylidene)-5-[(1H-indol-3-yl)methylene]-1-methylpiperidin-4-one; CQ, chloroquine; CTSB, cathepsin B; CTSD, cathepsin D; DMSO, dimethyl sulfoxide; DNM2, dynamin 2; EBSS, Earle’s balanced salt solution; GFP, green fluorescent protein; HCQ, hydroxyl CQ; HEK293, human embryonic kidney 293; HUVEC, human umbilical vein endothelial cells; LAMP1, lysosomal associated membrane protein 1; LC-MS/MS, liquid chromatography coupled to tandem mass spectrometry; LDH, lactic acid dehydrogenase; LMO7, LIM domain 7; MAP1LC3B/LC3B, microtubule associated protein 1 light chain 3 beta; NAC, N-acetyl cysteine; MYO1E, myosin IE; NSCLC, non-small cell lung cancer; PARP1, poly(ADP-ribose) polymerase 1; PI, propidium iodide; RFP, red fluorescent protein; ROS, reactive oxygen species; SQSTM1, sequestosome 1; TUNEL, terminal deoxynucleotidyl transferase-mediated dUTP nick-end labeling.
DOI: 10.6084/m9.figshare.9109301.v1
title: Additional file 2: of Integrative analysis of loss-of-function variants in clinical and genomic data reveals novel genes associated with cardiovascular traits

description: Tables S1-S9. (XLSX 1175â kb)
DOI: 10.6084/m9.figshare.12254690.v1
title: Identifying and profiling the microRNAs associated with skin colour in the Muchuan black-bone chicken

description: MicroRNAs (miRNAs) are an abundant class of small non-protein-coding RNAs that regulate gene expression in plants and animals. Skin colour is an important economic consideration in chicken production, and chickens with black skin have high market value. Nevertheless, little research has been conducted on miRNA regulation of melanogenesis in chicken skin. In this study, we sampled the dorsal skins of chickens with black (BS) and white (WS) skin to construct six small RNA libraries. High-throughput sequencing technology was then used to identify which miRNAs were expressed differentially between the BS and WS phenotypes. A total of 645 known and 64 novel miRNAs were identified from the six sequencing libraries. Additionally, the expression of 18 miRNAs was significantly different between the two phenotypes, including 9 miRNAs that were up-regulated, and 9 that were down-regulated. We identified 2 miRNAs, i.e. miR-204 and miR-6631-5p, that may be important for melanogenesis in chicken skin. Our data contribute to the understanding of the molecular mechanism, through miRNA regulation, of melanin formation in chicken skin.HighlightsDifferentially expressed miRNAs were identified in black skin (BS) and white skin (WS) of black-bone chickensEighteen DEMs were detected in BS and WS groups.miR-204 and miR-6631-5p were potential candidates influencing skin melanogenesis in chicken.
 Differentially expressed miRNAs were identified in black skin (BS) and white skin (WS) of black-bone chickens Eighteen DEMs were detected in BS and WS groups. miR-204 and miR-6631-5p were potential candidates influencing skin melanogenesis in chicken.
DOI: 10.6084/m9.figshare.13294951
title: Additional file 2 of Speciation and adaptive evolution reshape antioxidant enzymatic system diversity across the phylum Nematoda

description: Additional file 2: Table S3. Assembly and gene annotation information of 59 nematodes.
DOI: 10.6084/m9.figshare.20110656
title: Additional file 2 of Metabolomics and integrated network pharmacology analysis reveal SNKAF decoction suppresses cell proliferation and induced cell apoptisis in hepatocellular carcinoma via PI3K/Akt/P53/FoxO signaling axis

description: Additional file 2: Table S2. 89 differentially metabolized compounds.
DOI: 10.6084/m9.figshare.20110656.v1
title: Additional file 2 of Metabolomics and integrated network pharmacology analysis reveal SNKAF decoction suppresses cell proliferation and induced cell apoptisis in hepatocellular carcinoma via PI3K/Akt/P53/FoxO signaling axis

description: Additional file 2: Table S2. 89 differentially metabolized compounds.