Network-based support vector machine for classification of microarray samples

Background: The importance of network-based approach to identifying biological markers for diagnostic classification and prognostic assessment in the context of microarray data has been increasingly recognized. To our knowledge, there have been few, if any, statistical tools that explicitly incorporate the prior information of gene networks into classifier building. The main idea of this paper is to take full advantage of the biological observation that neighboring genes in a network tend to function together in biological processes and to embed this information into a formal statistical framework. Results: We propose a network-based support vecto

2-(4-Bromo­phen­yl)-3,4-dihydro­isoquinolin-2-ium thio­cyanate hemihydrate

In the title hemihydrated salt, C15H13BrN+·NCS−·0.5H2O, the two benzene rings are aligned at a dihedral angle of 46.9 (1)°. The six-membered heterocycle of the dihydro­isoquinoline unit adopts a half-chair conformation. The water mol­ecule and thio­cyanate ion are linked by O—H⋯N hydrogen bonds, generating a four-membered ring motif. In addition, C—H⋯O and C—H⋯S inter­actions link the components into a chain along the c axis. π–π inter­actions [centroid–centroid distance = 3.974 (2) Å] link the chains into sheets and further π—π [centroid–centroid distance = 3.746 (2) Å] and C—H⋯π inter­actions give rise to a three-dimensional nework

Increased Air Pollution Causing Cancers and Its Rapid Online Monitoring

Pollution of indoor and outdoor air has considerably been taken attention abroad as an important environmental problem, and there is sufficient evidence that exposure to outdoor air pollution causes lung cancer and other cancers. Therefore, the current situation of air pollution will be deeply discussed, and a portable environmental gas monitor integrated by a variety of highly sensitive sensors will be developed for rapidly monitoring air pollution, which is able to provide scientific data for environmental pollution control. By this way, human beings are able to be far away from cancer caused by environmental pollution and its suffering

Phage family classification under Caudoviricetes: A review of current tools using the latest ICTV classification framework

Bacteriophages, which are viruses infecting bacteria, are the most ubiquitous and diverse entities in the biosphere. There is accumulating evidence revealing their important roles in shaping the structure of various microbiomes. Thanks to (viral) metagenomic sequencing, a large number of new bacteriophages have been discovered. However, lacking a standard and automatic virus classification pipeline, the taxonomic characterization of new viruses seriously lag behind the sequencing efforts. In particular, according to the latest version of ICTV, several large phage families in the previous classification system are removed. Therefore, a comprehensive review and comparison of taxonomic classification tools under the new standard are needed to establish the state-of-the-art. In this work, we retrained and tested four recently published tools on newly labeled databases. We demonstrated their utilities and tested them on multiple datasets, including the RefSeq, short contigs, simulated metagenomic datasets, and low-similarity datasets. This study provides a comprehensive review of phage family classification in different scenarios and a practical guidance for choosing appropriate taxonomic classification pipelines. To our best knowledge, this is the first review conducted under the new ICTV classification framework. The results show that the new family classification framework overall leads to better conserved groups and thus makes family-level classification more feasible

Association between Nine Types of TCM Constitution and Five Chronic Diseases: A Correspondence Analysis Based on a Sample of 2,660 Participants

Objective. The purpose of this study was to explore the association of nine types of Traditional Chinese Medicine (TCM) constitution with the five chronic diseases: hypertension, hyperlipidemia, diabetes mellitus, heart disease, and obesity. Methods. Chi-squared test was performed to investigate the distribution characteristics of TCM constitutions in the participants with the five chronic diseases in questionnaire. Correspondence analysis was used to explore the correlation between them. Results. A total of 2,660 participants (1,400 males; 1,260 females) were included in this study. The mean age was 52.54 ± 13.92. Of them, 600 were of gentleness type accounting for 22.56%. Proportions of gentleness type in the chronic diseases (16.00%~23.70%) were less than that in general population (32.14%). The gentleness type and yin-deficiency type were significantly correlated with hypertension and diabetes mellitus, qi-deficiency type was correlated with heart disease, phlegm-dampness type was associated with obesity, and dampness-heat type was correlated with hyperlipidemia. Conclusions. The correlations between TCM constitution types and the five chronic diseases were different. This may have a significant implication for TCM practice, and even the people with gentleness type should not be ignored in health management

Fusobacterium nucleatum upregulates MMP7 to promote metastasis-related characteristics of colorectal cancer cell via activating MAPK(JNK)-AP1 axis

Abstract Background Colorectal cancer (CRC) is the third most common malignant tumor. Fusobacterium nucleatum (F. nucleatum) is overabundant in CRC and associated with metastasis, but the role of F. nucleatum in CRC cell migration and metastasis has not been fully elucidated. Methods Differential gene analysis, protein−protein interaction, robust rank aggregation analysis, functional enrichment analysis, and gene set variation analysis were used to figure out the potential vital genes and biological functions affected by F. nucleatum infection. The 16S rDNA sequencing and q-PCR were used to detect the abundance of F. nucleatum in tissues and stools. Then, we assessed the effect of F. nucleatum on CRC cell migration by wound healing and transwell assays, and confirmed the role of Matrix metalloproteinase 7 (MMP7) induced by F. nucleatum in cell migration. Furthermore, we dissected the mechanisms involved in F. nucleatum induced MMP7 expression. We also investigated the MMP7 expression in clinical samples and its correlation with prognosis in CRC patients. Finally, we screened out potential small molecular drugs that targeted MMP7 using the HERB database and molecular docking. Results F. nucleatum infection altered the gene expression profile and affected immune response, inflammation, biosynthesis, metabolism, adhesion and motility related biological functions in CRC. F. nucleatum was enriched in CRC and promoted the migration of CRC cell by upregulating MMP7 in vitro. MMP7 expression induced by F. nucleatum infection was mediated by the MAPK(JNK)-AP1 axis. MMP7 was highly expressed in CRC and correlated with CMS4 and poor clinical prognosis. Small molecular drugs such as δ-tocotrienol, 3,4-benzopyrene, tea polyphenols, and gallic catechin served as potential targeted therapeutic drugs for F. nucleatum induced MMP7 in CRC. Conclusions Our study showed that F. nucleatum promoted metastasis-related characteristics of CRC cell by upregulating MMP7 via MAPK(JNK)-AP1 axis. F. nucleatum and MMP7 may serve as potential therapeutic targets for repressing CRC advance and metastasis

Prostaglandin E2 Promotes Endothelial Differentiation from Bone Marrow-Derived Cells through AMPK Activation

Prostaglandin E2 (PGE2) has been reported to modulate angiogenesis, the process of new blood vessel formation, by promoting proliferation, migration and tube formation of endothelial cells. Endothelial progenitor cells are known as a subset of circulating bone marrow mononuclear cells that have the capacity to differentiate into endothelial cells. However, the mechanism underlying the stimulatory effects of PGE2 and its specific receptors on bone marrow-derived cells (BMCs) in angiogenesis has not been fully characterized. Treatment with PGE2 significantly increased the differentiation and migration of BMCs. Also, the markers of differentiation to endothelial cells, CD31 and von Willebrand factor, and the genes associated with migration, matrix metalloproteinases 2 and 9, were significantly upregulated. This upregulation was abolished by dominant-negative AMP-activated protein kinase (AMPK) and AMPK inhibitor but not protein kinase, a inhibitor. As a functional consequence of differentiation and migration, the tube formation of BMCs was reinforced. Along with altered BMCs functions, phosphorylation and activation of AMPK and endothelial nitric oxide synthase, the target of activated AMPK, were both increased which could be blocked by EP4 blocking peptide and simulated by the agonist of EP4 but not EP1, EP2 or EP3. The pro-angiogenic role of PGE2 could be repressed by EP4 blocking peptide and retarded in EP4+/− mice. Therefore, by promoting the differentiation and migration of BMCs, PGE2 reinforced their neovascularization by binding to the receptor of EP4 in an AMPK-dependent manner. PGE2 may have clinical value in ischemic heart disease