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Interdisciplinary Sciences, Computational Life Sciences

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https://www.readbyqxmd.com/read/29882026/a-fast-projection-based-algorithm-for-clustering-big-data
#1
Yun Wu, Zhiquan He, Hao Lin, Yufei Zheng, Jingfen Zhang, Dong Xu
With the fast development of various techniques, more and more data have been accumulated with the unique properties of large size (tall) and high dimension (wide). The era of big data is coming. How to understand and discover new knowledge from these data has attracted more and more scholars' attention and has become the most important task in data mining. As one of the most important techniques in data mining, clustering analysis, a kind of unsupervised learning, could group a set data into objectives(clusters) that are meaningful, useful, or both...
June 7, 2018: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/29728983/study-on-feature-selection-methods-for-depression-detection-using-three-electrode-eeg-data
#2
Hanshu Cai, Yunfei Chen, Jiashuo Han, Xiangzi Zhang, Bin Hu
The early diagnosis of depression is important to the treatment of this condition, whereas a timely diagnosis can reduce the incidence of mortality caused in patients with depression. In the present study, we collected the EEG signals of Fp2, Fpz and Fp1, compared with 128 channels EEG, a simpler test (3 channels EEG) can make diagnosis more accessible and widespread, researchers can perform more tests on more patients given the same amount of time and money. The difference between the depressed and the non-depressed patients was explored by the linear and non-linear characteristics of these EEG signals...
May 4, 2018: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/29721784/subtractive-genomics-molecular-docking-and-molecular-dynamics-simulation-revealed-lpxc-as-a-potential-drug-target-against-multi-drug-resistant-klebsiella-pneumoniae
#3
Sajjad Ahmad, Afifa Navid, Amina Saleem Akhtar, Syed Sikander Azam, Abdul Wadood, Horacio Pérez-Sánchez
The emergence and dissemination of pan drug resistant clones of Klebsiella pneumoniae are great threat to public health. In this regard new therapeutic targets must be highlighted to pave the path for novel drug discovery and development. Subtractive proteomic pipeline brought forth UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase (LpxC), a Zn+2 dependent cytoplasmic metalloprotein and catalyze the rate limiting deacetylation step of lipid A biosynthesis pathway. Primary sequence analysis followed by 3-dimensional (3-D) structure elucidation of the protein led to the detection of K...
May 2, 2018: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/29691712/gc-formula-see-text-nmf-a-novel-matrix-factorization-framework-for-gene-phenotype-association-prediction
#4
Yaogong Zhang, Jiahui Liu, Xiaohu Liu, Yuxiang Hong, Xin Fan, Yalou Huang, Yuan Wang, Maoqiang Xie
Gene-phenotype association prediction can be applied to reveal the inherited basis of human diseases and facilitate drug development. Gene-phenotype associations are related to complex biological processes and influenced by various factors, such as relationship between phenotypes and that among genes. While due to sparseness of curated gene-phenotype associations and lack of integrated analysis of the joint effect of multiple factors, existing applications are limited to prediction accuracy and potential gene-phenotype association detection...
April 24, 2018: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/29644494/review-of-crispr-cas9-sgrna-design-tools
#5
REVIEW
Yingbo Cui, Jiaming Xu, Minxia Cheng, Xiangke Liao, Shaoliang Peng
The adaptive immunity system in bacteria and archaea, Clustered Regularly Interspaced Short Palindromic Repeats, CRISPR-associate (CRISPR/Cas), has been adapted as a powerful gene editing tool and got a broad application in genome research field due to its ease of use and cost-effectiveness. The performance of CRISPR/Cas relies on well-designed single-guide RNA (sgRNA), so a lot of bioinformatic tools have been developed to assist the design of highly active and specific sgRNA. These tools vary in design specifications, parameters, genomes and so on...
June 2018: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/29500549/study-on-the-mechanisms-of-active-compounds-in-traditional-chinese-medicine-for-the-treatment-of-influenza-virus-by-virtual-screening
#6
Haixin Ai, Xuewei Wu, Mengyuan Qi, Li Zhang, Huan Hu, Qi Zhao, Jian Zhao, Hongsheng Liu
In recent years, new strains of influenza virus such as H7N9, H10N8, H5N6 and H5N8 had continued to emerge. There was an urgent need for discovery of new anti-influenza virus drugs as well as accurate and efficient large-scale inhibitor screening methods. In this study, we focused on six influenza virus proteins that could be anti-influenza drug targets, including neuraminidase (NA), hemagglutinin (HA), matrix protein 1 (M1), M2 proton channel (M2), nucleoprotein (NP) and non-structural protein 1 (NS1). Structure-based molecular docking was utilized to identify potential inhibitors for these drug targets from 13144 compounds in the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform...
June 2018: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/29383565/an-across-target-study-on-visual-attentions-in-facial-expression-recognition
#7
Baomin Li, Fenglei Yang
As a simulation of human expression recognition, the studies on automatic expression recognition expect to draw useful enlightenment through close, accurate observation on human expression processing via advanced devices. Eye-trackers are mostly used devices that are technically designed to obtain eye-movement data. However, due to the discrepancy between target faces, across-target analysis is limited in these studies, and this much reduces the chance of finding the latent eye-behavior patterns. Through the utilization of correspondences between targets, this study achieves an across-target analysis to explore the attention pattern in expression recognition...
June 2018: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/29282626/detoxification-of-aflatoxins-on-prospective-approach-effect-on-structural-mechanical-and-optical-properties-under-pressures
#8
Yong-Kai Wei, Xiao-Miao Zhao, Meng-Meng Li, Jing-Xin Yu, Selvaraj Gurudeeban, Yan-Fei Hu, Guang-Fu Ji, Dong-Qing Wei
Aflatoxins are sequential of derivatives of coumarin and dihydrofuran with similar chemical structures and well-known carcinogenic agent. Many studies performed to detoxify aflatoxins, but the result is not ideal. Therefore, we studied structural, infrared spectrum, mechanical, and optical properties of these compounds in the aim of perspective physics. Mulliken charge distributions and infrared spectral analysis performed to understand the structural difference between the basic types of aflatoxins. In addition, the effect of pressure, different polarized, and incident directions on their structural changes was determined...
June 2018: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/29260504/modeling-and-control-of-a-delayed-hepatitis-b-virus-model-with-incubation-period-and-combination-treatment
#9
Deshun Sun, Fei Liu
In this paper, a hepatitis B virus (HBV) model with an incubation period and delayed state and control variables is firstly proposed. Furthermore, the combination treatment is adopted to have a longer-lasting effect than mono-therapy. The equilibrium points and basic reproduction number are calculated, and then the local stability is analyzed on this model. We then present optimal control strategies based on the Pontryagin's minimum principle with an objective function not only to reduce the levels of exposed cells, infected cells and free viruses nearly to zero at the end of therapy, but also to minimize the drug side-effect and the cost of treatment...
June 2018: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28631174/studies-of-the-interaction-of-influenza-virus-rna-polymerase-pa-n-with-endonuclease-inhibitors
#10
Li-Hua Dong, Xiao-Rong Cao
Influenza virus is a major causative agent of respiratory viral infections, and RNA polymerase catalyzes its replication and transcription activities in infected cell nuclei. Since it is highly conserved in all virus strains, RNA polymerase becomes a key target of anti-influenza virus agents. Although experimental studies have revealed the good inhibitory activity of endonuclease inhibitors to RNA polymerase, the mechanism is still unclear. In this study, the docking and molecular dynamics simulations have been performed to explore the interaction of three kinds of endonuclease inhibitors with the subunit (PAN ) of RNA polymerase...
June 2018: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28560699/identification-of-strategic-residues-at-the-interface-of-antigen-antibody-interactions-by-in-silico-mutagenesis
#11
Lu Xin, Hai Yu, Qiyang Hong, Xingjian Bi, Xiao Zhang, Zhiqing Zhang, Zhibo Kong, Qingbing Zheng, Ying Gu, Qinjian Zhao, Jun Zhang, Shaowei Li, Ningshao Xia
Structural information pertaining to antigen-antibody interactions is fundamental in immunology, and benefits structure-based vaccine design. Modeling of antigen-antibody immune complexes from co-crystal structures or molecular docking simulations provides an extensive profile of the epitope at the interface; however, the key amino acids involved in the interaction must be further clarified, often through the use of experimental mutagenesis and subsequent binding assays. Here, we describe an in silico mutagenesis method to identify key sites at antigen-antibody interfaces, using significant increase in pH-dependency energy among saturated point mutations...
June 2018: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28527150/development-of-in-silico-protocols-to-predict-structural-insights-into-the-metabolic-activation-pathways-of-xenobiotics
#12
M Kalim A Khan, Salman Akhtar, Jamal M Arif
To establish in silico model to predict the structural insight into the metabolic bioactivation pathway of xenobiotics, we considered two specific and one non-specific mammary procarcinogen [e.g., dibenzo[a,l]pyrene (DBP), 7,12-dimethylbenz[a]anthracene (DMBA), and benzo[a]pyrene (BP)]. The CYP1A1, 1B1, 2C9, 1A2 and 2B6 reported in wet-lab studies to actively metabolize DBP also showed strong binding energies (kcal/mol) of -11.50, -10.67, -10.37, -9.76 and -9.72, respectively, with inhibition constants ranging between 0...
June 2018: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28271460/structural-evaluation-and-binding-mode-analysis-of-ccl19-and-ccr7-proteins-identification-of-novel-leads-for-rheumatic-and-autoimmune-diseases-an-insilico-study
#13
Santhi Prada Vellanki, Ramasree Dulapalli, Bhargavi Kondagari, Navaneetha Nambigari, Rajender Vadija, Vishwanath Ramatenki, Rama Krishna Dumpati, Uma Vuruputuri
The Human Chemokine (C-C motif) ligand 19 (CCL19) protein plays a major role in rheumatic and autoimmune diseases. The 3D models of the CCL19 and its receptor CCR7 are generated using homology modeling and are validated using standard computational protocols. Disulfide bridges identified in 3D model of CCL19 protein give extra stability to the overall protein structure. The active site region of protein CCL19, containing N-terminal amino acid residues (Gly22 to Leu31), is predicted using in silico techniques...
June 2018: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/27896664/molecular-interactions-structural-transitions-and-alterations-in-soxb-protein-due-to-soxyz-interaction-from-two-distinct-%C3%AE-proteobacteria-an-in-silico-approach-towards-the-thiosulfate-oxidation-and-recycling-of-soxy-protein
#14
Sujay Ray, Semanti Ghosh, Angshuman Bagchi
Microbial oxidation-reduction reactions utilizing the environmental thiosulfate ions and mediated mainly by the sox operon are very much essential to maintain the sulfur balance in the environment. Majority of the previously documented wet laboratory studies show genetics behind the functionality of Sox proteins encoded by the sox operon. However, the molecular details of the involvements of the essential SoxB, SoxY and SoxZ proteins in the beta-proteobacteria have not yet been elucidated. In this work, an attempt was made to analyze the interaction profiles of the aforementioned SoxB, SoxY and SoxZ proteins to predict their roles in biological sulfur oxidation process...
June 2018: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/27878455/structural-insight-into-binding-mode-of-9-hydroxy-aristolochic-acid-diclofenac-and-indomethacin-to-pla-2
#15
Mohsen Ebrahimi, Omidreza Firuzi, Ramin Miri, Nima Razzaghi-Asl, Ahmad Ebadi
Phospholipase A2 (PLA2 ) catalyzes the hydrolysis of phospholipids into arachidonic acid and lysophospholipids. Arachidonic acid is modified by cyclooxygenases into active compounds called eicosanoids that act as signaling molecules in a number of physiological processes. Excessive production of eicosanoids leads to several pathological conditions such as inflammation. In order to block the inflammatory effect of these compounds, upstream enzymes such as PLA2 are valid targets. In the present contribution, molecular dynamic analysis was performed to evaluate the binding of diclofenac, 9-hydroxy aristolochic acid (9-HAA) and indomethacin to PLA2 ...
June 2018: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/27837427/microwave-assisted-zrsio-2-catalysed-synthesis-characterization-and-computational-study-of-novel-spiro-indole-thiazolidines-derivatives-as-anti-tubercular-agents
#16
Mayuri A Borad, Manoj N Bhoi, Sanjay K Rathwa, Mahesh S Vasava, Hitesh D Patel, Chirag N Patel, Himanshu A Pandya, Edwin A Pithawala, John J Georrge
In the current investigation, we prepared a series of novel spiro[indole-thiazolidines] derivatives (5a-5h) from 5-substituted isatin derivatives and thioglycolic acid (TGA) with ZrSiO2 as an efficient catalyst under microwave irradiation. The significant merits of this protocol have some significant merits such as simplicity in operation, simple, efficient workup, good practical yields of product and the employment of recyclable catalyst. All the new synthesized scaffold has been well characterized by various spectroscopic methods and elemental analysis...
June 2018: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/27778232/a-computational-systems-biology-approach-for-identifying-candidate-drugs-for-repositioning-for-cardiovascular-disease
#17
Alvin Z Yu, Stephen A Ramsey
We report an in silico method to screen for receptors or pathways that could be targeted to elicit beneficial transcriptional changes in a cellular model of a disease of interest. In our method, we integrate: (1) a dataset of transcriptome responses of a cell line to a panel of drugs; (2) two sets of genes for the disease; and (3) mappings between drugs and the receptors or pathways that they target. We carried out a gene set enrichment analysis (GSEA) test for each of the two gene sets against a list of genes ordered by fold-change in response to a drug in a relevant cell line (HL60), with the overall score for a drug being the difference of the two enrichment scores...
June 2018: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/27757767/a-new-seyhan-s-approach-in-case-of-heterogeneity-of-regression-slopes-in-ancova
#18
Handan Ankarali, Sengul Cangur, Seyit Ankarali
In this study, when the assumptions of linearity and homogeneity of regression slopes of conventional ANCOVA are not met, a new approach named as SEYHAN has been suggested to use conventional ANCOVA instead of robust or nonlinear ANCOVA. The proposed SEYHAN's approach involves transformation of continuous covariate into categorical structure when the relationship between covariate and dependent variable is nonlinear and the regression slopes are not homogenous. A simulated data set was used to explain SEYHAN's approach...
June 2018: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/27718149/the-topology-prediction-of-membrane-proteins-a-web-based-tutorial
#19
Cagin Kandemir-Cavas, Levent Cavas, Hakan Alyuruk
There is a great need for development of educational materials on the transfer of current bioinformatics knowledge to undergraduate students in bioscience departments. In this study, it is aimed to prepare an example in silico laboratory tutorial on the topology prediction of membrane proteins by bioinformatics tools. This laboratory tutorial is prepared for biochemistry lessons at bioscience departments (biology, chemistry, biochemistry, molecular biology and genetics, and faculty of medicine). The tutorial is intended for students who have not taken a bioinformatics course yet or already have taken a course as an introduction to bioinformatics...
June 2018: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/27709544/evaluation-and-elucidation-studies-of-natural-aglycones-for-anticancer-potential-using-apoptosis-related-markers-an-in-silico-study
#20
Salman Akhtar, M Kalim A Khan, Jamal M Arif
Exposure to exogenous and endogenous chemicals and subsequent cellular and molecular changes has been linked to enhanced cell proliferation and restricted apoptosis phenomenon. Though in the past decades numerous anticancer drugs inducing programmed cell death in cancer cells by targeting specific apoptotic markers have reached the market, they have been allied with unwanted side effects, ranging from mild to severe toxicity. With further understanding on the functional mechanism of p53 and MDM2 in apoptosis and in our continuous search for new and potent multi-target anticancer lead compounds, we have carried out molecular docking and inhibition studies of the selected aglycones along with selected anticancer leads, against the specific apoptotic and cell cycle markers using AutoDock Tools 4...
June 2018: Interdisciplinary Sciences, Computational Life Sciences
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