Mathematical Analysis of a PDE System for Biological Network Formation

Motivated by recent physics papers describing rules for natural network formation, we study an elliptic-parabolic system of partial differential equations proposed by Hu and Cai [13 Hu , D. (2013). Optimization, Adaptation, and Initialization of Biological Transport Networks. Workshop on multiscale problems from physics, biology and material sciences. May 28–31st, 2014, Shanghai. Available at: http://math.sjtu.edu.cn/conference/multiscale2014/ (accessed 6 January 2015). [Google Scholar], 15 Hu , D. , Cai , D. ( 2013 ). Adaptation and optimization of biological transport networks . Phys. Rev. Lett. 111 : 138701 .[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]]. The model describes the pressure field thanks to Darcy's type equation and the dynamics of the conductance network under pressure force effects with a diffusion rate D ≥ 0 representing randomness in the material structure. We prove the existence of global weak solutions and of local mild solutions and study their long term behavior. It turns out that, by energy dissipation, steady states play a central role to understand the network formation capacity of the system. We show that for a large diffusion coefficient D, the zero steady state is stable, while network formation occurs for small values of D due to the instability of the zero steady state, and the borderline case D = 0 exhibits a large class of dynamically stable (in the linearized sense) steady states.     

Swelling and Network Parameters of 1-Hexadecene-Co-Trimethylolpropane Distearate Monoacrylate Sorbers

Linear and crosslinked copolymers with different compositions of 1-hexadecene and trimethylolpropane distearate monoacrylate monomers were synthesized and evaluated for oil-absorbency application. Different concentrations of ethylene glycol diacrylate (EGDA) and ethylene glycol dimethacrylate (EGDMA) crosslinkers were used. The concentration of both crosslinkers was varied from 0.5% to 2%. Copolymer compositions were determined from ¹H NMR spectroscopy. Monomer reactivity ratios were calculated using Fineman-Ross and Kelen-Tudos techniques at low conversions. The oil absorbency and swelling rate constant were measured and influenced mainly by the degree of crosslinking and the hydrophobicity of copolymer units. The final equilibrium oil content, volume fraction of polymer and swelling capacity were determined at 298 K. The effective crosslinking density V_e, theoretical crosslink density V_t, the average molecular weight between the crosslinks M_c and the polymer-toluene interaction parameter χ were determined from swelling measurements. The efficiencies of EGDA and EGDMA crosslinking agents toward copolymers were determined.     

Polymer networks by molecular dynamics simulation: Formation, thermal, structural and mechanical properties

A molecular dynamics simulation method is presented and used in the study of the formation of polymer networks. We study the formation of networks representing the methylene repeating units as united atoms. The network formation is accomplished by cross-linking polymer chains with dedicated functional end groups. The simulations reveal that during the cross-linking process, initially branched molecules are formed before the gel point; approaching the gel point, larger branched entities are formed through integration of smaller branched molecules, and at the gel point a network spanning the simulation box is obtained; beyond the gel point the network continues to grow through the addition of the remaining molecules of the sol phase onto the gel (the network); the final completion of the reaction occurs by intra-network connection of dangling ends onto unsaturated cross-linkers. The conformational properties of the strands in the undeformed network are found to be very similar with the conformational properties of the chains before cross-linking. The uniaxial deformation of the formed networks is investigated and the modulus determined from the stress-strain curves shows reciprocal scaling with the precursor chain length for networks formed from sufficiently large precursor chains (N ≥ 20).     

政府补贴、国企国有化系数与中国企业的产能过剩

近年来中国产能过剩日益严重,化解该矛盾已成为十八大后中国推进经济体制改革、调整产业结构的重中之重.考虑中国国情,从微观层面出发,构建混合寡占竞争模型,能有效解决产能过剩.分析表明:1政府调整对国有企业的补贴以及国有企业国有化系数可以有效解决民营企业的产能过剩问题;2在中国的现状下,国有企业确实存在产能过剩,并且减少政府对国有企业的补贴以及调整国有企业国有化系数可以有效减少国有企业的产能过剩量.     

基于层次分析法的企业网络舆情危机应对评价研究

网络舆情危机应对评价是企业在新的舆论背景下研究危机应对的重点.采用定量和定性分析有机结合的层次分析法确定指标体系及权重,给出了企业网络舆情危机应对评价的步骤,并进行了评价验证.该评价体系为相关单位网络舆情危机应对评价提供一定的参考和指导.     

基于布谷鸟算法与BP神经网络的煤灰变形温度预测

以120种煤样为数据基础,采用布谷鸟算法(CS)优化BP(Back Propagation)神经网络,建立了CSBP模型对单煤、煤掺添加剂和配煤等3类样本的煤灰变形温度(DT)样本进行预测。模型以煤灰化学成分及其组合参数等13个变量作为输入量,以变形温度(DT)作为输出量。CSBP模型预测结果与BP神经网络模型预测结果进行对比发现,无论是单煤、煤掺添加剂还是配煤,CSBP模型较BP模型对煤灰变形温度(DT)的预测都更加精准,平均相对误差分别达到了3.11%、4.08%和4.22%。另外,对比3类样本预测结果发现,无论是CSBP模型还是BP模型,相比单煤预测而言,煤掺添加剂及配煤的预测误差都有明显的增加。     

Exploring the mechanism of Cremastra Appendiculata (SUANPANQI) against breast cancer by network pharmacology and molecular docking

BackgroundSUANPANQI, the pseudo phosphorous stem of Cremastra appendiculata, is one of the most well-known traditional Chinese medicine, which has been shown to inhibit tumorigenesis in various human cancers. However, the underlying mechanism of SUANPANQI treatment against breast cancer (BRCA) remains unclear. In this study. we aim to investigate the bioactive compounds and mechanisms of SUANPANQI in the treatment of BRCA based on network pharmacology and molecular docking.MethodsThe compounds were collected from previous research. SwissADME was used to screen bioactive compounds. The targets corresponding to SUANPANQI and BRCA were obtained using MalaCards and SwissTargetPrediction. SUANPANQI-related and BRCA-related targets were found and then overlapped to get intersections, which represented potential anti-BRCA targets of SUANPANQI. The Cytoscape software was used to construct bioactive compounds targeting the BRCA network. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of the targets was extracted from the metascape database, then conducted using the Cluster Profiler package in R software. Protein-Protein interaction (PPI) network was constructed using the STRING online database and analyzed using Cytoscape software. Pivotal genes were screened using the topological analysis, survival analysis, and pathological stage analysis. Molecular docking analysis was used to verify whether the bioactive compounds had a definite affinity with the pivotal targets.ResultsSixty-five bioactive compounds of SUANPANQI were involved with 225 predicted BRCA targets. Then, a compound-target network and a PPI network were constructed. The GO analysis and KEGG enrichment analysis suggested that SUANPANQI worked against BRCA via PI3K-Akt, Ras, FoxO, Rap1, and ErbB signaling pathways, etc. After topological analysis, survival analysis, and pathological stage analysis of the SUANPANQI potential targets against BRCA, 6 pivotal target genes (AR, HSP90AA1, MMP9, PGR, PTGS2, TNF) that were highly responsible for the therapeutic effects of SUANPANQI against BRCA were obtained. Molecular docking results showed that 6 bioactive compounds of SUANPANQI had strong binding efficiency with the 6 pivotal genes.ConclusionsThe present study clarifies the mechanism of SUANPANQI against BRCA through multiple targets and pathways, and provides evidence to support its clinical use.     

Exploration of the mechanism of Zisheng Shenqi decoction against gout arthritis using network pharmacology

BackgroundIn this study, the network pharmacological methods were used to predict the target of effective components of compounds in Zisheng Shenqi Decoction (ZSD, or Nourishing Kidney Qi Decoction) in the treatment of gouty arthritis (GA).MethodThe main effective components and corresponding key targets of herbs in the ZSD were discerned through the Traditional Chinese Medicine Systems Pharmacology Database and Analysis (TCMSP), Bioinformatics Analysis Tool for Molecular mechanism of Traditional Chinese Medicine (BATMAN-TCM) database. UniProt database and Swiss Target Prediction (STP) database was used to rectify and unify the target names and supply the target information. The targets related to GA were obtained by using GeneCards database. After we discovered the potential common targets between ZSD and GA, the interaction network diagram of “ZSD-component-GA-target” was constructed by Cytoscape software (Version 3.7.1). Subsequently, the Protein-protein interaction (PPI) network of ZSD effective components-targets and GA-related targets was constructed by Search Tool for the Retrieval of Interacting Genes Database (STRING). Bioconductor package “org.Hs.eg.db” and “cluster profiler” package were installed in R software (Version 3.6.0) which used for Gene Ontology analysis and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichment analysis.Results146 components and 613 targets of 11 herbal medicines in the ZSD were got from TCMSP database and BATMAN-TCM database. 987 targets of GA were obtained from GeneCards database. After intersected and removed duplications, 132 common targets between ZSD and GA were screened out by Cytoscape software (Version 3.7.1). These common targets derived from 81 effective components of 146 components, such as quercetin, stigmasterol and kaempferol. They were closely related to anti-inflammatory, analgesic and anti oxidative stress and the principal targets comprised of Purinergic receptor P2X, ligand-gated ion channel 7 (P2x7R), Nod-like receptor protein 3 (NLRP3) and IL-1β. GO enrichment analysis and KEGG pathway enrichment analysis by R software (Version 3.6.0) showed that the key target genes had close relationship with oxidative stress, reactive oxygen species (ROS) metabolic process and leukocyte migration in aspects of biological process, cell components and molecular function. It also indicated that ZSD could decrease inflammatory reaction, alleviate ROS accumulation and attenuate pain by regulating P2 × 7R and NOD like receptor signaling pathway of inflammatory reaction.ConclusionA total of 81 effective components and 132 common target genes between ZSD and GA were screened by network pharmacology. The PPI network, GO enrichment analysis and KEGG pathway enrichment analysis suggested that ZSD can exerte anti-inflammatory and analgesic effects on the treatment of GA by reducing decreasing inflammatory reaction, alleviating ROS accumulation, and attenuating pain. The possible molecular mechanism of it mainly involved multiple components, multiple targets and multiple signaling pathways, which provided a comprehensive understanding for further study. In general, the network pharmacological method applied in this study provides an alternative strategy for the mechanism of ZSD in the treatment of GA.     

Analysis of aging-related protein interactome and cross-network module comparisons across tissues provide new insights into aging

Delaying the human aging process and thus eliminating the risk factors for age-related diseases is one of the prime objectives. While various aging-associated genes and proteins have been characterized, which provide a significant understanding of the human aging process, a significant success in regulating aging is not achieved yet. Understanding how aging proteins interact with each other and also with other proteins could provide important insights into the underlying mechanisms governing the aging process. Therefore, in this work, information of gene expression was included to the static aging-related protein interactome to understand the network-based relationships among aging-related essential (AE) proteins, aging-related non-essential (ANE) proteins, and housekeeping-proteins that could regulate or influence aging. Comprehensive analyses provided various systems-level insights into the regulatory characteristics of aging; for example, (i) network-based correlation analysis predicted functional relationships among AE proteins and ANE proteins; (ii) network variability analysis predicted aging to affect different tissues in strikingly different ways by differentially regulating various regulatory interactions; (iii) cross-network comparisons identified two aging-related modules to be significantly conserved across most of the tissues. Overall, the findings obtained during this study could be helpful for researchers to delay, prevent, or even reverse various aspects of the aging.