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In clinical practice at Tibetan area of China, Traditional Tibetan Medicine formula Wuwei-Ganlu-Yaoyu-Keli(WGYK) is widely added in warm water of bath therapy to treat rheumatoid arthritis (RA). However, its action mechanism is not well interpreted yet. In this study, based on gene expression data from microarray experiments, we apply approaches of network pharmacology to further reveal the action...
Many modern big data applications deal with graph structured data, such as databases of molecular compounds represented as graphs of atoms and bonds, or “structured interaction networks” in biological and social networks, where nodes refer to entities (proteins, people, etc.) and edges represent their relationships. Central to high performance graph analytics over such data, is to locate patterns...
Stenotrophomonas maltophilia DHHJ, a new feather-degrading bacterium, was subjected to mutation by ultraviolet light for 90 s. The mutant L2 was selected due to its greater activity in comparison with the wild strain. After incubation at 40 °C for 6 days, the feathers degraded by mutant L2 were 1.3-fold more than S. maltophilia DHHJ, and the keratinase was secreted. After cultivation for 6 days in...
In the context of the prosperous development of Proteomics in life science, protein quantification, especially these based on Mass Spectrometry (short for MS) method, becomes an essential part of research. In our previous work, we developed a new software package called QuantWiz for high performance Liquid Chromatography (short for LC)-MS-based label-free protein quantification. We solved those problems...
In current service composition efforts, the intermediate products such as data and related process fragments are neglected in many cases when the deviation occurs from predefined composition. The lack of adequate provenance support makes it not convenient when building the composition in an exploratory fashion. In this paper, we present ViPen model, and illustrate its operations to enhance the provenance...
Since diseases might be related with each other, systematically assessing their relationships could provide us novel insight into their mechanisms. One of the most important methods to study diseases' relationships is to calculate their phenotype similarity scores based on the text and clinical synopsis parts of their records in the OMIM database. However, as demonstrated in this paper, the similarity...
The functional knowledge of cancer proteins and cancer pathways is currently limited and not detailed enough, remaining as a major hurdle to cancer studies. Particularly, many cancer proteins are only annotated to high-level general GO categories. Here, we apply an efficient algorithm, by constructing function-specific protein-protein interaction sub-networks, to find finer functions of the cancer...
Di-n-butyl phthalate (DBP) was used in the plastic industry and widely distributed in the environment, which might cause adverse effects to living organisms. Previously, it had been shown that DBP produced reproductive, developmental toxicity and liver enlargement in rodents, and the mechanisms behind this could involve oxidative injury. To study the effects of DBP on the acute oxidative damage, the...
Neural stimulation and recording with high spatiotemporal precision is desirable for studying the real time cellular basis of neural circuits, as well as developing possible therapeutic treatments for neurological diseases. Optical stimulation of genetically targeted neurons expressing the light sensitive ion channel protein Channelrhodopsin (ChR2) and Halorhodopsin (NpHR) has recently been reported...
Nowadays proteomics becomes more and more popular in life science. Protein quantification, especially based on mass spectrometry (short for MS) method, is perceived as an essential part of research on proteomics. There have been some algorithms and software for protein quantification based on MS. But they have difficulties on portability, applicability and longtime running. To solve these problems,...
Selecting differentially expressed genes (DEGs) is one of the most important tasks in microarray applications. However, the sample sizes typically used in current cancer studies may only partially reflect the widely altered gene expressions in cancers. By analyzing three large cancer datasets, we show that, in each cancer, a wide range of functional modules are altered and have high disease classification...
In addition to enabling controlled sharing and isolation, the virtualization mechanism can help to provide users a single image, and to realize a more abstract and uniform view from a set of fine-grained, heterogeneous and un-ordered instances. The paper explores ways of business-oriented service abstraction, Web service virtualization, presents a practical approach and discusses the effects thereof...
Cyberworlds could be a platform for both research and e-learning particularly in research intensive disciplines such as biology, physical chemistry, molecular medicine, biophysics, structural biology, bioinformatics, etc. The computer simulation of assembling molecules has been studied intensively in the field of computer-aided rational drug design. The assembly of molecules in a three-dimensional...
We analyzed the generalized Hurst exponents for the amino acid sequences of proteins and secretory signal peptides used the multifractal detrended fluctuation analysis (MF-DFA) method. The numeralization of the amino acid sequences was completed according to the three amino acid indice: EIIP, polarity and accessible surface area. The results show that the proteins sequences have multifractal properties...
We analyzed the Hurst exponent for the amino acid sequences of proteins and secretory signal peptides using the aggregated variance method. Then the diversification entropy of the sequences was calculated. The numeralization of the amino acid sequences are according with the three amino acid indices: EIIP, polarity and accessible surface area. The results show that when an amino acid sequence coding...
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