Weighted edge based clustering to identify protein complexes in protein–protein interaction networks incorporating gene expression profile

Protein complex detection from protein–protein interaction (PPI) network has received a lot of focus in recent years. A number of methods identify protein complexes as dense sub-graphs using network information while several other methods detect protein complexes based on topological information. While the methods based on identifying dense sub-graphs are more effective in identifying protein complexes, not all protein complexes have high density. Moreover, existing methods focus more on static PPI networks and usually overlook the dynamic nature of protein complexes. Here, we propose a new method, Weighted Edge based Clustering (WEC), to identify protein complexes based on the weight of the edge between two interacting proteins, where the weight is defined by the edge clustering coefficient and the gene expression correlation between the interacting proteins. Our WEC method is capable of detecting highly inter-connected and co-expressed protein complexes. The experimental results of WEC on three real life data shows that our method can detect protein complexes effectively in comparison with other highly cited existing methods.Availability: The WEC tool is available at http://agnigarh.tezu.ernet.in/~rosy8/shared.html.     

Validation of a headspace trap gas chromatography and mass spectrometry method for the quantitative analysis of volatile compounds from degraded rapeseed oil

Due to lipid oxidation, off‐flavors, characterized by a fishy odor, are emitted during the heating of rapeseed oil in a fryer and affect the flavor of rapeseed oil even at low concentrations. Thus, there is a need for analytical methods to identify and quantify these products. To study the headspace composition of degraded rapeseed oil, and more specifically the compounds responsible for the fishy odor, a headspace trap gas chromatography with mass spectrometry method was developed and validated. Six volatile compounds formed during the degradation of rapeseed oil were quantified: 1‐penten‐3‐one, (Z)‐4‐heptenal, hexanal, nonanal, (E,E)‐heptadienal, and (E)‐2‐heptenal. Validation using accuracy profiles allowed us to determine the valid ranges of concentrations for each compound, with acceptance limits of 40% and tolerance limits of 80%. This method was then successfully applied to real samples of degraded oils.     

Role of the flavonoid-rich fraction in the antioxidant and cytotoxic activities of Bauhinia forficata Link. (Fabaceae) leaves extract

Bauhinia forficata Link. is utilised as an antidiabetic in Brazilian folk-medicine; furthermore, its antioxidant properties suggest a potential usefulness in the prevention of diabetes complications associated with oxidative stress. The contribution of a flavonoid-rich fraction (FRF), HPLC-PDA-ESI-MS characterised, to the antioxidant and cytotoxic properties of B. forficata hydro-alcoholic leaves extract was evaluated for the first time. Both extract and FRF showed radical-scavenging activity and reducing power with a strong relationship with the flavonoid content found; hence, flavonoids are mainly responsible for the primary antioxidant activity of B. forficata extract. The extract significantly decreased FO-1 cell viability at the higher concentrations. FRF did not exert any effect; thus, flavonoids do not appear to be responsible for the cytotoxicity of the extract. The extract resulted virtually non-toxic against both Artemia salina and normal human lymphocytes, demonstrating potential selectivity in inhibiting cancer cell growth. Finally, no antimicrobial activity was observed against the bacteria and yeasts tested.     

基于基因表达谱数据筛选差异表达基因新方法

提出一种基于基因表达谱数据筛选差异表达基因的新方法;介绍了筛选差异表达基因常见方法-错误发现率方法(False Discovery Rate,FDR,),分析了多重假设检验p值性质,并根据p值性质提出了一种筛选差异表达基因新方法-单位γ度量法(Unit Measure-γ,UM-γ),建立了计算机模拟基因表达谱数据模型,制定了假阴性率、假阳性率、灵敏度、特异度以及总体错误率等作为考核指标,并使用基因表达谱模拟数据进行计算、比较;单位γ度量法估计非差异表达基因个数具有较高的稳定性和准确性;单位γ度量法既能够同时控制假阳性、假阴性以及总体错事件的发生,又能在一定程度上提高筛选结果的灵敏度和变异度;新提出的方法能有效、准确且稳定的对模拟数据差异表达基因进行筛选.     

On a reaction diffusion equation with nonlinear time‐nonlocal source term

In this article, we prove the local existence of a unique solution to a nonlocal in time and space evolution equation with a time nonlocal nonlinearity of exponential growth. Moreover, under some suitable conditions on the initial data, it is shown that local solutions experience blow‐up. The time profile of the blowing‐up solutions is also presented. Copyright © 2015 John Wiley & Sons, Ltd.     

Annealing of thin B/Nb<Subscript>2</Subscript>N bilayers,B/Nb bilayers and Nb/B/Nb trilayers via rapid thermal processing (RTP)

B/Nb and B/Nb₂N bilayers and Nb/B/Nb trilayers of about 550 nm total thickness have been deposited on Si(100) wafers with 100 nm thermally grown oxide. Nb and B layers were deposited by magnetron sputtering. Nb₂N layers were prepared by nitridation of Nb films via rapid thermal processing (RTP). The samples were annealed subsequently at temperatures between 600 and 1,200 °C in an RTP system under Ar or NH₃ gas flow to study interdiffusion and reactivity of niobium, boron and nitrogen. Formation of phases was investigated by X-ray diffraction (XRD); surface morphology and roughness were studied via scanning electron microscopy (SEM) and atomic force microscopy (AFM), respectively. Elemental depth profiles of selected samples were recorded by secondary ion mass spectrometry (SIMS). Annealing of the B/Nb bilayers and Nb/B/Nb trilayers under Ar leads to the formation of Nb₃B₂ at 1,200 °C at the B/Nb interface. At lower temperatures the high oxygen content in the boron layer is supposed to hinder the formation of borides due to formation of glass-like boron oxides. In NH₃ several niobium nitrides are formed but no boride phases. Here again the reactivity of boron with niobium is suppressed by the high oxygen content and boron oxide formation. During annealing of the B/Nb₂N bilayers no borides were formed indicating that well-formed Nb₂N is an effective diffusion barrier for B.     

Asymptotic behavior of solutions for the damped wave equation with slowly decaying data

We consider the Cauchy problem for the damped wave equation

     

Existence theory of abstract approximate deconvolution models of turbulence

This report studies an abstract approach to modeling the motion of large eddies in a turbulent flow. If the Navier-Stokes equations (NSE) are averaged with a local, spatial convolution type filter, , the resulting system is not closed due to the filtered nonlinear term . An approximate deconvolution operator D is a bounded linear operator which is an approximate filter inverse

Chemical profiling and mechanistic studies of Zhi-Shang-Feng granules against influenza virus by high-performance liquid chromatography coupled with Q exactive focus hybrid quadrupole orbitrap high-resolution mass spectrometry in combination with network pharmacology analysis

Zhi-Shang-Feng Granules are used in the clinical treatment of influenza to relieve headaches, chills and fever, bronchitis, nasal congestion, neuralgia and other symptoms. To decipher the components responsible for therapeutic effects of Zhi-Shang-Feng g ranules against influenza virus, an analytical method based on high-performance liquid chromatography coupled with Q exactive focus hybrid quadrupole orbitrap high resolution mass spectrometry was developed and the chemical profile of Zhi-Shang-Feng granules was characterized. Then, the identified components were used to conduct network pharmacological analysis and determine the potential mechanism of Zhi-Shang-Feng Granules. As a result, 177 compounds were putatively identified through comprehensive analysis by liquid chromatography coupled with high-resolution mass spectrometry, of which 23 compounds were unambiguously confirmed with reference standards. Components in Zhi-Shang-Feng Granules were found to specifically act on different enzymes, G-protein-coupled receptors, ion channels and transporters in the immune, endocrine, nervous, and circulatory systems. The potential mechanism was related to several biological processes, including cell growth and death, pattern recognition receptor signalling, signalling by interleukins, and lipid metabolism. The combination of chemical profile characterization and network construction provided useful insight into the overall chemical composition of Zhi-Shang-Feng granules and revealed their potential anti-infection, anti-inflammatory and immunoregulatory mechanisms against influenza virus infected disease.     

圆柱形纳米孔道内受限溶液I2/Ar的分子动力学模拟研究

利用分子动力学模拟方法, 考察了受限于圆柱形纳米孔道内I2/Ar溶液的振动传能及扩散动力学. 计算得到了溶质振动弛豫时间T1、溶剂轴向扩散系数Dz随孔道半径变化的规律. 结果表明: T1随着孔道半径的增大而减小; 而Dz随着孔道半径的增大而增大; 与预期的一致, 随着孔道半径的增大, 孔道的限制作用逐渐减小, T1与Dz趋近于相应的非受限溶液体相值. 此外, 通过考察溶质、溶剂与孔道的相互作用, 在原子、分子层次上揭示了限制作用对传能与传质影响的机制.