Semi-supervised drug-protein interaction prediction from heterogeneous biological spaces

biological space

An information-flow-based model with dissipation, saturation and direction for active pathway inference

<p>Abstract</p> <p>Background</p> <p>Biological systems process the genetic information and environmental signals through pathways. How to map the pathways systematically and efficiently from high-throughput genomic and proteomic data is a challenging open problem. Previous methods design different heuristics but do not describe explicitly the behaviours of the information flow.</p> <p>Results</p> <p>In this study, we propose new concepts of dissipation, saturation and direction to decipher the information flow behaviours in the pathways and thereby infer the biological pathways from a given source to its target. This model takes into account explicitly the common features of the information transmission and provides a general framework to model the biological pathways. It can incorporate different types of bio-molecular interactions to infer the signal transduction pathways and interpret the expression quantitative trait loci (eQTL) associations. The model is formulated as a linear programming problem and thus is solved efficiently. Experiments on the real data of yeast indicate that the reproduced pathways are highly consistent with the current knowledge.</p> <p>Conclusions</p> <p>Our model explicitly treats the biological pathways as information flows with dissipation, saturation and direction. The effective applications suggest that the three new concepts may be valid to describe the organization rules of biological pathways. The deduced linear programming should be a promising tool to infer the various biological pathways from the high-throughput data.</p

Nature of the X(6900)X(6900) in partial wave decomposition of J/ψJ/ψJ/\psi J/\psi scattering

In this letter, we perform partial wave decomposition on coupled channel scattering amplitudes, $J/\psi J/\psi$-$J/\psi \psi(2S)$-$J/\psi \psi(3770)$, to study the resonance appears in these processes. Effective Lagrangians are used to describe the interactions of four charmed vector mesons, and the scattering amplitudes are calculated up to the next-to-leading order. Partial wave projections are performed, and unitarization is implemented by Pad\'e approximation. Then we fit the amplitudes to the $J/\psi J/\psi$ invariant mass spectra measured by LHCb and determine the unknown couplings. The pole parameters of the $X(6900)$ are extracted as $M=6861.0^{+6.3}_{-8.8}$~MeV and $\Gamma=129.0^{+5.6}_{-3.4}$~MeV. Our analysis implies that its quantum number prefers to be $0^{++}$. The pole counting rule and phase shifts show that it is a normal Breit-Wigner resonance and hence should be a compact tetraquark.Comment: 6 pages, 4 figure

Transcriptome Sequencing Investigated the Tumor-Related Factors Changes After T. gondii Infection

Toxoplasma gondii is an intracellular parasite and causes a global epidemic parasitic disease. T. gondii-infection could inhibit the growth of tumor. In this study, the transcriptomes of samples were detected by deep sequencing analysis. The transcriptome data was compared with reference genome to perform sequence alignment and the further analysis. The analyses of differential expression and the differentially expressed genes were performed in the present study. Genes involved in P53 signaling pathway, COLORECTAL cancer pathway, NON-SMALL CELL LUNG cancer signaling pathway, and BREAST cancer signaling pathway were up-regulated or down-regulated among the samples. The KEGG analysis indicated that the cancer pathways changed after infection of T. gondii. Furthermore, tumor-related mRNAs from different samples had a large difference, which suggested that the difference might provide important information in resisting cancer. The protein results indicated that tumor-related protein changes occurred after infection of T. gondii. In conclusion, the infection changed the cancer pathways, which could possibly inhibit the growth of tumor

Atherosclerosis and Helminths Infection

Atherosclerosis is a chronic disease that causes various cardiovascular complications. Plaque formation in atherosclerosis is considered similar to the pathogenesis of other autoimmune diseases; thus, immunomodulation and immunosuppression may present strategies for the treatment and prevention of these diseases. Interestingly helminth infection was found to inhibit T helper 1-mediated autoimmune diseases and T helper 2-mediated allergy and asthma, indicating significant potential for clinical application. Some study even found that therapeutic efficacy of the viable tapeworm was superior to dexamethasone treatment. Recently, some studies have shown an inverse association between helminth infections and inflammatory diseases, including diabetes mellitus, lipid abnormality, and atherosclerosis. Will the underlying mechanism bring us a new idea on the treatment for these diseases? We tried to find an answer by reviewing recent articles