Although members of the Mycobacterium tuberculosis complex (MTBC) exhibit high similarity, they are characterized by differences with respect to virulence, immune response, and transmissibility. To understand the virulence of these bacteria and identify potential novel therapeutic targets, we systemically investigated the total cell protein contents of virulent H37Rv, attenuated H37Ra, and avirulent M. bovis BCG vaccine strains at the log and stationary phases, based on tandem mass tag (TMT) quantitative proteomics. Data analysis revealed that...

Buffalo holds an excellent potential for beef production, and circRNA plays an important role in regulating myogenesis. However, the regulatory mechanism of circRNAs during buffalo skeletal muscle development has not been fully explored. In this study, circRNA expression profiles during the proliferation and differentiation stages of buffalo myoblasts were analysed by RNA-seq. Here, a total of 3,142 circRNAs candidates were identified, and 110 of them were found to be differentially expressed in the proliferation and...

Additional file 4: Targets information of DM.

The HCC spectral library generated in this work

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...

In Saccharomyces cerevisiae, Atg9 is an important autophagy-related (Atg) protein, and interacts with hundreds of other proteins. How many Atg9-interacting proteins are involved in macroautophagy/autophagy is unclear. Here, we conducted a multi-omic profiling of Atg9-dependent molecular landscapes during nitrogen starvation-induced autophagy, and identified 290 and 256 genes to be markedly regulated by ATG9 in transcriptional and translational levels, respectively. Unexpectedly, we found most of known Atg proteins and autophagy regulators that interact with Atg9 were...

Motivated by a product warranty claims data set, we propose clustered coefficient regression models in a non-homogeneous Poisson process for recurrent event data. The proposed method, referred as CLUPP, can estimate the group structure and parameters simultaneously. In our proposed method, a penalized regression approach is used to identify the group structure. Numerical studies show that the proposed approach can identify the group structure well, and outperforms traditional methods such as hierarchical clustering and K-means....

Subfornical organ (SFO) is vital in chronic kidney disease (CKD) progression caused by high salt levels. The current study investigated the effects of high salt on phosphoproteomic changes in SFO in CKD rats. 5/6 nephrectomized rats were fed a normal-salt diet (0.4%) (NC group) or a high-salt diet (4%) (HC group) for three weeks, while sham-operated rats were fed a normal-salt diet (0.4%) (NS group). For phosphoproteomic analysis of SFO in different groups, TiO2 enrichment,...

To explore the association of KISS1, LIN28B, vitamin D receptor (VDR), and estrogen receptor α (ERα) gene polymorphisms and the risk of early with fast puberty (EFP) risk, and with hormone levels in EFP cases, in Chinese girls. The analysis was based on the data of 141 girls with EFP and 152 girls without EFP. Clinical features were documented, and all SNP genotyping was conducted using SNaPshot method. Statistical analysis was performed to assess the...

Chimeric RNAs are gaining more and more attention as they have broad implications in both cancer and normal physiology. To date, over 40 chimeric RNA prediction methods have been developed to facilitate their identification from RNA sequencing data. However, a limited number of studies have been conducted to compare the performance of these tools; additionally, previous studies have become outdated as more software tools have been developed within the last three years. In this study,...

Interactions between multiple anthropogenic environmental changes can drive non-additive effects in ecological systems, and the non-additive effects can in turn be amplified or dampened by spatial covariation among environmental changes. We investigated the combined effects of night-time warming and light pollution on pea aphids and two predatory ladybeetle species. As expected, neither night-time warming nor light pollution changed the suppression of aphids by the ladybeetle species that forages effectively in darkness. However, for the more-visual...

Y RNAs (84–112 nt) are non-coding RNAs transcribed by RNA polymerase III and are characterized by a distinctive secondary structure. Human Y RNAs interact with the autoimmune proteins SSB and RO60 that together form a ribonucleoprotein (RNP) complex termed RoRNP and Y RNAs also perform regulatory roles in DNA and RNA replication and stability, which has major implications for diseases including cancer. During cellular stress and apoptosis, Y RNAs are cleaved into 3’ and 5’...

Supplemental Material for MiR-362-5p inhibits cartilage repair in osteoarthritis via targeting plexin B1 by Qian Li, Ping Xu, Chi Zhang and Yang Gao in Journal of Orthopaedic Surgery

Supplemental material, sj-xlsx-2-onc-10.1177_11795549221116834 for Concordance of Genomic Profiles in Matched Tissue and Plasma Samples From Chinese Patients With Lung Cancer by Yueming He, Weifeng Guo, Meng Xu, Junling Huang, Xiange Zhang, Huanzhang Su, Dongxia Hong and Qun Liu in Clinical Medicine Insights: Oncology

Additional file 1: Table S1. Baseline characteristics on death and MACE risks. Table S2. Baseline characteristics on LVEF and LVMI. Table S3. Relationship between metabolites and death risk. Table S4. Relationship between metabolites and MACE risk. Table S5. Multivariate Cox proportional hazards model for clinical outcomes. Table S6. Spearman correlation analysis between clinical factors and those metabolites associated with death risk. Table S7. Spearman correlation analysis between clinical factors and those metabolites associated with death...

Distributional data analysis, concerned with the statistical analysis of data objects consisting of random probability distributions in the framework of functional data analysis (FDA), has received considerable interest in recent years and is increasingly applied in various fields including engineering. Outlier detection and robustness are of great practical interest; however, these aspects remain unexplored for distributional data. To this end, this study focuses on density-valued outlier detection and its application in robust distributional regression. Specifically,...

Rheumatoid arthritis (RA) is a most common chronic joint disease belonging to inflammatory autoimmune disease. The aim of this study was to determine the role and mechanism of bone marrow mesenchymal stem cells (BMSCs)-derived exosomes and fibrinogen-like protein 1 (FGL1) overexpression exosomes shuttled by BMSCs (FGL1-Exos) on RA. All of the exosomes were visualized by transmission electron microscope (TEM) and the characteristic proteins were detected by western blot. To investigate the therapeutic effect of FGL1-Exos,...

Rheumatoid arthritis (RA) is a most common chronic joint disease belonging to inflammatory autoimmune disease. The aim of this study was to determine the role and mechanism of bone marrow mesenchymal stem cells (BMSCs)-derived exosomes and fibrinogen-like protein 1 (FGL1) overexpression exosomes shuttled by BMSCs (FGL1-Exos) on RA. All of the exosomes were visualized by transmission electron microscope (TEM) and the characteristic proteins were detected by western blot. To investigate the therapeutic effect of FGL1-Exos,...

Additional file 1: Table S1.Clinical data of each patients.

Abstract Background Subarachnoid hemorrhage (SAH) is an uncommon and serious subtype of stroke, which leads to the loss of the patient’s ability to produce and live for many years. Objective To investigate the clinical effect of nimodipine in the treatment of SAH. Methods Electronic databases including China National Knowledge Infrastructure (CNKI), VIP, SinoMed, China Master’s Theses Full-text Database (CMFD), China Doctoral Dissertations Full-text Database (CDFD), Cochrane Library, PubMed and Embase were searched from 2010 and...

Abstract Background Subarachnoid hemorrhage (SAH) is an uncommon and serious subtype of stroke, which leads to the loss of the patient’s ability to produce and live for many years. Objective To investigate the clinical effect of nimodipine in the treatment of SAH. Methods Electronic databases including China National Knowledge Infrastructure (CNKI), VIP, SinoMed, China Master’s Theses Full-text Database (CMFD), China Doctoral Dissertations Full-text Database (CDFD), Cochrane Library, PubMed and Embase were searched from 2010 and...

The HCC spectral library generated in this work

Additional file 3: Table S3. Results of GO enrichment on differentially expressed genes from RNA-seq data.

Additional file 5: Table S5. Results of KEGG enrichment on differentially expressed genes from GSE159676 datasets.

Additional file 7: Table S7. Differentially expressed genes that appeared in both RNA-seq data and the GSE159676 datasets