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Interdisciplinary Sciences, Computational Life Sciences

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https://www.readbyqxmd.com/read/29728983/study-on-feature-selection-methods-for-depression-detection-using-three-electrode-eeg-data
#1
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
#2
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
#3
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/29675796/construction-of-transcriptional-regulatory-network-of-alzheimer-s-disease-based-on-panda-algorithm
#4
Jieyuan Ding, Wei Kong, Xiaoyang Mou, Shuaiqun Wang
The focus of modern biomedical research concentrates on molecular level regulatory mechanisms and how the normal and abnormal phenotypes of tissue functional are affected by regulatory mechanisms. Most of the research on regulatory mechanism starts from the reconstruction of gene regulation network. At present, a large number of reconstruction methods construct the network using a single data set. These methods of inferring and predicting the relationship between the target gene and the transcription factor (TF) can be used to identify individual interactions between genes, while there is not much research on the interaction of many functional-related genes...
April 19, 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...
April 11, 2018: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/29594726/modified-global-flower-pollination-algorithm-and-its-application-for-optimization-problems
#6
Moh'd Khaled Yousef Shambour, Ahmed A Abusnaina, Ahmed I Alsalibi
Flower Pollination Algorithm (FPA) has increasingly attracted researchers' attention in the computational intelligence field. This is due to its simplicity and efficiency in searching for global optimality of many optimization problems. However, there is a possibility to enhance its search performance further. This paper aspires to develop a new FPA variant that aims to improve the convergence rate and solution quality, which will be called modified global FPA (mgFPA). The mgFPA is designed to better utilize features of existing solutions through extracting its characteristics, and direct the exploration process towards specific search areas...
March 28, 2018: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/29582245/quantum-calculations-on-plant-cell-wall-component-interactions
#7
Hui Yang, Heath D Watts, Virgil Gibilterra, T Blake Weiss, Loukas Petridis, Daniel J Cosgrove, James D Kubicki
Density functional theory calculations were performed to assess the relative interaction energies of plant cell wall components: cellulose, xylan, lignin and pectin. Monomeric and tetramer linear molecules were allowed to interact in four different configurations for each pair of compounds. The M05-2X exchange-correlation functional which implicitly accounts for short- and mid-range dispersion was compared against MP2 and RI-MP2 to assess the reliability of the former for modeling van der Waals forces between these PCW components...
March 26, 2018: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/29549628/iikmta-inter-and-intra-kingdom-mirna-target-analyzer
#8
Chittabrata Mal, Md Aftabuddin, Sudip Kundu
BACKGROUND: Growing evidences suggest that microRNAs (miRNAs) can efficiently regulate gene expression at intracellular and extracellular levels. It has been previously reported that plant/food-derived miRNAs are highly enriched in human serum or serum from phytophagous animals, and they are responsible for regulating mammalian gene expression. Thus, miRNAs could function as active signaling molecules, which carry information across distinct species or even kingdoms. However, the mode of miRNA shuttling among various organisms is still a mystery to unravel...
March 16, 2018: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/29525981/neuropp-a-tool-for-the-prediction-of-neuropeptide-precursors-based-on-optimal-sequence-composition
#9
Juanjuan Kang, Yewei Fang, Pengcheng Yao, Ning Li, Qiang Tang, Jian Huang
Neuropeptides (NPs) are short secreted peptides produced mainly in the nervous system and digestive system. They activate signaling cascades to control a wide range of biological functions, such as metabolism, sensation, and behavior. NPs are typically produced from a larger NP precursor (NPP) which includes a signal peptide sequence, one or more NP sequences, and other sequences. With the drastic growth of unknown protein sequences generated in the post-genomic age, it is highly desired to develop computational methods for identifying NPP rapidly and efficiently...
March 10, 2018: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/29520635/computational-analysis-of-high-risk-snps-in-human-dby-gene-responsible-for-male-infertility-a-functional-and-structural-impact
#10
Mili Nailwal, Jenabhai B Chauhan
BACKGROUND: DEAD-box helicase 3, Y-linked (DBY) is a candidate gene of the AZF region which is involved in spermatogenesis process. Mutations in the DBY gene may disrupt the spermatogenesis and lead to infertility in men. Identification of functionally neutral mutation from the disease-causing mutation is the biggest challenge in human genetic variation analysis. Owing to the importance of DBY in male infertility, functional analysis was carried out to reveal the association between genetic mutation and phenotypic variation through various in silico approaches...
March 8, 2018: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/29492842/genome-wide-pathway-analysis-of-microarray-data-identifies-risk-pathways-related-to-salt-stress-in-arabidopsis-thaliana
#11
Mingming Zhang, Hongbo Mu, Ruijie Zhang, Shenkui Liu, Imshik Lee
Salt stress is a common abiotic stress in agricultural production, which is affected by multiple genes and environmental factors. Although transcriptome analyses have detected some salt-related genes in Arabidopsis thaliana, these genes are often major genes and can not adequately explain the molecular mechanism of salt tolerance. Some genes related to salt stress, but does not reach significant threshold in gene expression analysis (called modest effect genes), are often ignored. Therefore, we took full account of the role of modest effect genes and performed a pathway-based analysis of three gene microarray datasets to identify the pathways related to salt stress...
February 28, 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
#12
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/29460086/systematic-analysis-of-primary-sequence-domain-segments-for-the-discrimination-between-class-c-gpcr-subtypes
#13
Caroline König, René Alquézar, Alfredo Vellido, Jesús Giraldo
G-protein-coupled receptors (GPCRs) are a large and diverse super-family of eukaryotic cell membrane proteins that play an important physiological role as transmitters of extracellular signal. In this paper, we investigate Class C, a member of this super-family that has attracted much attention in pharmacology. The limited knowledge about the complete 3D crystal structure of Class C receptors makes necessary the use of their primary amino acid sequences for analytical purposes. Here, we provide a systematic analysis of distinct receptor sequence segments with regard to their ability to differentiate between seven class C GPCR subtypes according to their topological location in the extracellular, transmembrane, or intracellular domains...
March 2018: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/29405013/region-specific-methylation-profiling-in-acute-myeloid-leukemia
#14
Agnieszka Cecotka, Joanna Polanska
Alteration of DNA methylation level in cancer diseases leads to deregulation of gene expression-silencing of tumor suppressor genes and enhancing of protooncogenes. There are several tools devoted to the problem of identification of CpG sites' demethylation but majority of them focuses on single site level and does not allow for quantification of region methylation changes. The aim was to create an adaptive algorithm supporting detection of differentially methylated CpG sites and genomic regions specific for acute myeloid leukemia...
March 2018: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/29383564/large-scale-analyses-and-visualization-of-adaptive-amino-acid-changes-projects
#15
Noé Vázquez, Cristina P Vieira, Bárbara S R Amorim, André Torres, Hugo López-Fernández, Florentino Fdez-Riverola, José L R Sousa, Miguel Reboiro-Jato, Jorge Vieira
When changes at few amino acid sites are the target of selection, adaptive amino acid changes in protein sequences can be identified using maximum-likelihood methods based on models of codon substitution (such as codeml). Although such methods have been employed numerous times using a variety of different organisms, the time needed to collect the data and prepare the input files means that tens or hundreds of coding regions are usually analyzed. Nevertheless, the recent availability of flexible and easy to use computer applications that collect relevant data (such as BDBM) and infer positively selected amino acid sites (such as ADOPS), means that the entire process is easier and quicker than before...
March 2018: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/29380342/risk-predicting-model-for-incident-of-essential-hypertension-based-on-environmental-and-genetic-factors-with-support-vector-machine
#16
Zhiyong Pei, Jielin Liu, Manjiao Liu, Wenchao Zhou, Pengcheng Yan, Shaojun Wen, Yubao Chen
Essential hypertension (EH) has become a major chronic disease around the world. To build a risk-predicting model for EH can help to interpose people's lifestyle and dietary habit to decrease the risk of getting EH. In this study, we constructed a EH risk-predicting model considering both environmental and genetic factors with support vector machine (SVM). The data were collected through Epidemiological investigation questionnaire from Beijing Chinese Han population. After data cleaning, we finally selected 9 environmental factors and 12 genetic factors to construct the predicting model based on 1200 samples, including 559 essential hypertension patients and 641 controls...
March 2018: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/29313209/an-ensemble-framework-coping-with-instability-in-the-gene-selection-process
#17
José A Castellanos-Garzón, Juan Ramos, Daniel López-Sánchez, Juan F de Paz, Juan M Corchado
This paper proposes an ensemble framework for gene selection, which is aimed at addressing instability problems presented in the gene filtering task. The complex process of gene selection from gene expression data faces different instability problems from the informative gene subsets found by different filter methods. This makes the identification of significant genes by the experts difficult. The instability of results can come from filter methods, gene classifier methods, different datasets of the same disease and multiple valid groups of biomarkers...
March 2018: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/29214497/comparing-reverse-complementary-genomic-words-based-on-their-distance-distributions-and-frequencies
#18
Ana Helena Tavares, Jakob Raymaekers, Peter J Rousseeuw, Raquel M Silva, Carlos A C Bastos, Armando Pinho, Paula Brito, Vera Afreixo
In this work, we study reverse complementary genomic word pairs in the human DNA, by comparing both the distance distribution and the frequency of a word to those of its reverse complement. Several measures of dissimilarity between distance distributions are considered, and it is found that the peak dissimilarity works best in this setting. We report the existence of reverse complementary word pairs with very dissimilar distance distributions, as well as word pairs with very similar distance distributions even when both distributions are irregular and contain strong peaks...
March 2018: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/29204795/inferring-gene-regulatory-networks-based-on-a-hybrid-parallel-genetic-algorithm-and-the-threshold-restriction-method
#19
Ming Zheng, Shugong Zhang, You Zhou, Guixia Liu
Inferring gene regulatory networks (GRNs) is a challenging computational task in system biology. Many inference algorithms have been proposed along with related modifications to various problems. Every algorithm has its own advantages and drawbacks. In particular, the efficiency of each algorithm is not as good as people expect. A novel inference algorithm is proposed in this paper that can be divided into two parts. In the first part, the pre-computational part, two tasks must be accomplished: singular value decomposition for solution space determination and the threshold restriction method for redundant edge deletion...
March 2018: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/29098594/a-comprehensive-computational-analysis-of-mycobacterium-genomes-pinpoints-the-genes-co-occurring-with-ycze-a-membrane-protein-coding-gene-under-the-putative-control-of-a-mocr-and-predicts-its-function
#20
Teresa Milano, Sebastiana Angelaccio, Angela Tramonti, Martino Luigi di Salvo, Isabel Nogues, Roberto Contestabile, Stefano Pascarella
Bacterial proteins belonging to the YczE family are predicted to be membrane proteins of yet unknown function. In many bacterial species, the yczE gene coding for the YczE protein is divergently transcribed with respect to an adjacent transcriptional regulator of the MocR family. According to in silico predictions, proteins named YczR are supposed to regulate the expression of yczE genes. These regulators linked to the yczE genes are predicted to constitute a subfamily within the MocR family. To put forward hypotheses amenable to experimental testing about the possible function of the YczE proteins, a phylogenetic profile strategy was applied...
March 2018: Interdisciplinary Sciences, Computational Life Sciences
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