Open Bioinformatics Journal最新文献

{"title":"Epigenetics, Maternal Diet and Metabolic Programming","authors":"K. Ramírez-Alarcón, Ángela Sánchez-Agurto, L. Lamperti, M. Martorell","doi":"10.2174/1874196701907010045","DOIUrl":"https://doi.org/10.2174/1874196701907010045","url":null,"abstract":"Department of Nutrition and Dietetics, Faculty of Pharmacy, University of Concepcion, Concepcion, Chile Master Program in Human Nutrition, Faculty of Pharmacy, University of Concepcion, Concepcion, Chile School of Nutrition and Dietetics, Faculty of Health, University of Talca, Talca, Chile Department of Clinical Biochemistry and Immunology, Faculty of Pharmacy, University of Concepción, Concepción, Chile","PeriodicalId":38956,"journal":{"name":"Open Bioinformatics Journal","volume":"7 1","pages":"45-51"},"PeriodicalIF":0.0,"publicationDate":"2019-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68053007","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"maGUI: A Graphical User Interface for Analysis and Annotation of DNA Microarray Data","authors":"Dhammapal Bharne, P. Kant, V. Vindal","doi":"10.2174/1875036201912010040","DOIUrl":"https://doi.org/10.2174/1875036201912010040","url":null,"abstract":"\u0000 \u0000 maGUI is a graphical user interface designed to analyze microarray data produced from experiments performed on various platforms such as Affymetrix, Agilent, Illumina, and Nimblegen and so on, automatically. It follows an integrated workflow for pre-processing and analysis of the microarray data. The user may proceed from loading of microarray data to normalization, quality check, filtering, differential gene expression, principal component analysis, clustering and classification. It also provides miscellaneous applications such as gene set test and enrichment analysis for identifying gene symbols using Bioconductor packages. Further, the user can build a co-expression network for differentially expressed genes. Tables and figures generated during the analysis can be viewed and exported to local disks. The graphical user interface is very friendly especially for the biologists to perform the most microarray data analyses and annotations without much need of learning R command line programming.\u0000 \u0000 \u0000 \u0000 maGUI is an R package which can be downloaded freely from Comprehensive R Archive Network resource. It can be installed in any R environment with version 3.0.2 or above.\u0000","PeriodicalId":38956,"journal":{"name":"Open Bioinformatics Journal","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47752883","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Simple Genetic Algorithm for Optimizing Multiple Sequence Alignment on the Spread of the SARS Epidemic","authors":"S. Amiroch, M. S. Pradana, M. I. Irawan, I. Mukhlash","doi":"10.2174/1875036201912010030","DOIUrl":"https://doi.org/10.2174/1875036201912010030","url":null,"abstract":"Multiple sequence alignment is a method of getting genomic relationships between 3 sequences or more. In multiple alignments, there are 3 mutation network analyses, namely topological network system, mutation region network and network system of mutation mode. In general, the three analyses show stable and unstable regions that map mutation regions. This area of ​​mutation is described further in a phylogenetic tree which simultaneously illustrates the path of the spread of an epidemic, the Severe Acute Respiratory Syndrome (SARS) epidemic. The process of spreading the SARS viruses, in this case, is described as the process of phylogenetic tree formation, and as a novelty of this research, multiple alignments in the process are analyzed in detail and then optimized with genetic algorithms.The data used to form the phylogenetic tree for the spread of the SARS epidemic are 14 DNA sequences which are then optimized by using genetic algorithms. The phylogenetic tree is constructed by using the neighbor-joining algorithm with a distance matrix that the intended distance is the genetic distance obtained from sequence alignment by using the Needleman Wunsch Algorithm.The results of the analysis obtained 3649 stable areas and 19 unstable areas. The results of phylogenetic tree from the network system analysis indicated that the spread of the SARS epidemic extended from Guangzhou 16/12/02 to Zhongshan 27/12/02, then spread simultaneously to Guangzhou 18/02/03 and Guangzhou hospital. After that, the virus reached Metropole, Zhongshan, Hongkong, Singapore, Taiwan, Hong kong, and Hanoi which then continued to Guangzhou 01/01/03 and Toronto at once. The results of the mutation region network system demonstrate decomposition of orthogonal mutations in the 1st order arc.","PeriodicalId":38956,"journal":{"name":"Open Bioinformatics Journal","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42882748","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Polyp Shape Recovery from Single Endoscope Image using Medical Suture","authors":"Hiroyasu Usami, Y. Iwahori, Aili Wang, M. Bhuyan, N. Ogasawara, K. Kasugai","doi":"10.2174/1875036201912010001","DOIUrl":"https://doi.org/10.2174/1875036201912010001","url":null,"abstract":"Polyp shapes play an important role in colorectal diagnosis. However, endoscopy images are usually composed of nonrigid objects such as a polyp. Hence, it is challenging for polyp shape recovery. It is demanded to establish a support system of the colorectal diagnosis system based on polyp shape.Shape from Shading (SFS) is one valuable approach based on photoclinometry for polyp shape recovery. SFS and endoscope image are compatible on the first sight, but there are constraints for applying SFS to endoscope image. Those approaches need some parameters like a depth from the endoscope lens to the surface, and surface reflectance factor . Furthermore, those approaches assume the whole surface which has the same value of for the Lambertian surface.This paper contributes to mitigating constraint for applying SFS to the endoscope image based on a cue from the medical structure. An extracted medical suture is used to estimate parameters, and a method of polyp shape recovery method is proposed using both geometric and photometric constraint equations. Notably, the proposed method realizes polyp shape recovery from a single endoscope image.From experiments it was confirmed that the approximate polyp model shape was recovered and the proposed method recovered absolute size and shape of polyp using medical suture information and obtained parameters from a single endoscope image.This paper proposed a polyp shape recovery method which mitigated the constraint for applying SFS to the endoscope image using the medical suture. Notably, the proposed method realized polyp shape recovery from a single endoscope image without generating uniform Lambertian reflectance.","PeriodicalId":38956,"journal":{"name":"Open Bioinformatics Journal","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46432985","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification and “in silico” Structural Analysis of the Glutamine-rich Protein Qrp (YheA) in Staphylococcus Aureus","authors":"J. Escobar-Pérez, Katterine Ospina-Garcia, Zayda Lorena Corredor Rozo, R. A. Márquez-Ortiz, J. Castellanos, N. Gómez","doi":"10.2174/1875036201912010018","DOIUrl":"https://doi.org/10.2174/1875036201912010018","url":null,"abstract":"\u0000 \u0000 YlbF and YmcA are two essential proteins for the formation of biofilm, sporulation, and competence in Bacillus subtilis. In these two proteins, a new protein domain called com_ylbF was recently discovered, but its role and protein function has not yet been established.\u0000 \u0000 \u0000 \u0000 In this study, we identified and performed an “in silico” structural analysis of the YheA protein, another com_ylbF-containing protein, in the opportunistic pathogen Staphylococcus aureus.\u0000 \u0000 \u0000 \u0000 The search of the yheA gene was performed using BLAST-P and tBLASn algorithms. The three-dimensional (3D) models of YheA, as well as YlbF and YmcA proteins, were built using the I-TASSER and Quark programs. The identification of the native YheA in Staphylococcus aureus was carried out through chromatography using the FPLC system.\u0000 \u0000 \u0000 \u0000 We found that YheA protein is more widely distributed in Gram-positive bacteria than YlbF and YmcA. Two new and important characteristics for YheA and other com_ylbF-containing proteins were found: a highly conserved 3D structure and the presence of a putative conserved motif located in the central region of the domain, which could be involved in its function. Additionally, we established that Staphylococcus aureus expresses YheA protein in both planktonic growth and biofilm. Finally, we suggest renaming YheA as glutamine-rich protein (Qrp) in S. aureus.\u0000 \u0000 \u0000 \u0000 The Grp (YheA), YlbF, and YmcA proteins adopt a highly conserved three-dimensional structure, harboring a protein-specific putative motif within the com_ylbF domain, which possibly favors the interaction with their substrates. Finally, Staphylococcus aureus expresses the Grp (YheA) protein in both planktonic and biofilm growth.\u0000","PeriodicalId":38956,"journal":{"name":"Open Bioinformatics Journal","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41339230","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Numerical Investigation of Anatomic Anterior Cruciate Ligament Reconstruction","authors":"B. K. Bhat, Raviraj Adhikari, Kiran Acharya","doi":"10.2174/1875036201811080259","DOIUrl":"https://doi.org/10.2174/1875036201811080259","url":null,"abstract":"\u0000 \u0000 Anterior Cruciate Ligament (ACL) reconstruction by anatomic method is the most popular method of reconstruction. This method of ACL reconstruction utilizes Anteromedial Portal (AMP) techniques.\u0000 \u0000 \u0000 \u0000 In this study, five human subjects with healthy knee joints were considered on which Lachman test was simulated. Traditional Transtibial (TT) and AMP techniques were simulated in this study. The mean value of Von – Mises stress on the ACL was calculated. ACL reconstruction using hamstring tendon graft was simulated in a finite element analysis on four healthy human knee joints. Magnetic Resonance Images (MRI) of knee joints of four healthy human subjects were analyzed in this study for statistical significance of the results. Both techniques were simulated in each of the subjects. The hamstring tendon graft used had a diameter of 9 mm. The tibial foot print was 44.6 ± 2.5% from the anterior margin and 48 ± 3% from the medial margin. The femoral foot print was calculated based on Mochizuki’s method at 38.7 ± 2.7% from the deep subchondral margin.\u0000 \u0000 \u0000 \u0000 The obliquity of reconstructed – ACL (R – ACL) to the tibial plateau for AM technique was in the range of 51 to 58 degrees in the sagittal plane and 69 to 76 degrees in the coronal plane. In the case of TT technique, it was in the range of 59 to 69 degrees in the coronal plane and 72 to 78 degrees in the coronal plane in the femur. Similarly, the sagittal obliquity of R – ACL in the tibia was 55 degrees. The mean Von–Mises stress in the R – ACL for AMP technique was 17.74 ± 3.01 MPa. The stresses in the R – ACL for AMP technique is consistently near to the mean stress in the intact ACL. Whereas, stresses in the R – ACL used in TT technique are not consistently near to the stresses in the intact ACL of a healthy human knee joint.\u0000 \u0000 \u0000 \u0000 Hence, AMP technique is the better technique between AMP and TT techniques of ACL reconstruction.\u0000","PeriodicalId":38956,"journal":{"name":"Open Bioinformatics Journal","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-11-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47820163","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Common Ancestor of Deinococcus Species was Rod-Shaped","authors":"Y. Morita, H. Nishida","doi":"10.2174/1875036201811010252","DOIUrl":"https://doi.org/10.2174/1875036201811010252","url":null,"abstract":"The genusDeinococcusconsists of species in rod-shape (Bacilli) and spherical shape (Cocci).In this study, we aimed to determine whether the common ancestor ofDeinococcusspecies was rod-shaped or spherical.We compared the homologs of the proteins related to the rod-shape in bacteria (MreB, MreC, MreD, MrdA, RodA, and RodZ) in variousDeinococcusspecies andThermus thermophilus.The phylogenetic trees based on each protein and the homologs reflected the evolutionary relationships of the species, indicating that the Horizontal transfer of the genes did not occur during theDeinococcusevolution.The ancestor of the genusDeinococcuswas rod-shaped, and the spherical forms appeared when the rod-shaped formation system was lost during evolution and diversification within the genus.","PeriodicalId":38956,"journal":{"name":"Open Bioinformatics Journal","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43578587","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Protein Network Analysis to Prioritize Key Genes and Pathway for Stress-Mediated Neurodegeneration","authors":"N. Srivastava, B. Mishra, P. Srivastava","doi":"10.2174/1875036201811010240","DOIUrl":"https://doi.org/10.2174/1875036201811010240","url":null,"abstract":"Oxidative Stress (OS) has been implicated in the pathophysiology of many neurodegenerative diseases. OS can cause cellular damage that results in cell death due to overproduction of reactive oxygen species (ROS) that may play the crucial role in the disease progression. An impaired mechanism in correlation with reduced expression of antioxidant proteins is the very common feature among most of the age-related disorders. Variousin-vitroandin-vivostudies suggest the major contribution of oxidative stress in neurodegeneration. Role of Nrf2 gene is well established as a neuroprotective gene especially in concern with stress-mediated neurodegeneration. Nrf2 is a bZIP transcription factor that forms the heterodimer with small Maf protein and transcription factor AP1 that regulates transcription by binding to ARE which coordinates the transcription of genes involved in phase II detoxification and an antioxidant defense that is used to protect the cell from oxidative stress.The currentinsilicostudy was attempted to prioritize key genes and pathway in stress-mediated neurodegeneration through network-based analysis.Protein-protein interaction network was constructed and analyzed using 63 Nrf2 regulating candidate genes obtained from NCBI database based on literature studies usingSTRING 10.0database andCytoscape v 3.6.0software plug-inNetwork Analyzer.Further, the functional enrichment analysis of identified gene was done usingPANTHER GENE ONTOLOGYsoftware and DAVID tool.Based on network topological parameter, TP53, JUN, MYC, NFE2L2, AKT1, PIK3CA & UBC were identified as the key gene in the network. Among them, TP53 gene was obtained as a super hub gene with the highest Betweenness Centrality (BC) and node degree. The functional enrichment analysis was done usingPANTHER GENE ONTOLOGYsoftware and DAVID tool reveals their significant role in neurotrophin signaling pathway, MAPK signaling pathway, cellular response to stress & in the regulation of stress.The network analysis will help in prioritizing genes in the pathway that helps in understanding the underlying mechanism of disease. Thus, further study on these genes and their biological mechanism and pathway may, therefore, provide a potential target for the treatment of stress-mediated neurodegeneration.","PeriodicalId":38956,"journal":{"name":"Open Bioinformatics Journal","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42322169","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Challenge of Genome Sequence Assembly","authors":"A. Collins","doi":"10.2174/1875036201811010231","DOIUrl":"https://doi.org/10.2174/1875036201811010231","url":null,"abstract":"\u0000 \u0000 Although whole genome sequencing is enabling numerous advances in many fields achieving complete chromosome-level sequence assemblies for diverse species presents difficulties. The problems in part reflect the limitations of current sequencing technologies. Chromosome assembly from ‘short read’ sequence data is confounded by the presence of repetitive genome regions with numerous similar sequence tracts which cannot be accurately positioned in the assembled sequence. Longer sequence reads often have higher error rates and may still be too short to span the larger gaps between contigs.\u0000 \u0000 \u0000 \u0000 Given the emergence of exciting new applications using sequencing technology, such as the Earth BioGenome Project, it is necessary to further develop and apply a range of strategies to achieve robust chromosome-level sequence assembly. Reviewed here are a range of methods to enhance assembly which include the use of cross-species synteny to understand relationships between sequence contigs, the development of independent genetic and/or physical scaffold maps as frameworks for assembly (for example, radiation hybrid, optical motif and chromatin interaction maps) and the use of patterns of linkage disequilibrium to help position, orient and locate contigs.\u0000 \u0000 \u0000 \u0000 A range of methods exist which might be further developed to facilitate cost-effective large-scale sequence assembly for diverse species. A combination of strategies is required to best assemble sequence data into chromosome-level assemblies. There are a number of routes towards the development of maps which span chromosomes (including physical, genetic and linkage disequilibrium maps) and construction of these whole chromosome maps greatly facilitates the ordering and orientation of sequence contigs.\u0000","PeriodicalId":38956,"journal":{"name":"Open Bioinformatics Journal","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46590029","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Electrocardiogram Fiducial Points Detection and Estimation Methodology for Automatic Diagnose","authors":"René Yáñez de la Rivera, M. Soto-Bajo, A. Fraguela-Collar","doi":"10.2174/1875036201811010208","DOIUrl":"https://doi.org/10.2174/1875036201811010208","url":null,"abstract":"The estimation of fiducial points is specially important in the analysis and automatic diagnose of Electrocardiographic (ECG) signals.A new algorithm which could be easily implemented is presented to accomplish this task.Its methodology is rather simple, and starts from some ideas available in the literature combined with new approachs provided by the authors. First, aQRScomplex detection algorithm is presented based on the computation of energy maxima in ECG signals which allow the measurement of cardiac frequency (in beats per minute) and the estimation of R peaks temporal positions (in number of samples). From these ones, an estimation of fiducial points Q, S, J, P and T waves onset and offset points are worked out, supported in a simple modified slope method with constraints.The location process of fiducial points is assisted with the help of the so called curvature filters, which allow to improve the accuracy in this task.The procedure is simulated in Matlab and GNU Octave by using test signals from the MIT medical database, Cardiosim II equipment patterns and synthetic signals developed by the authors.One of the novelties of this work is the global strategy. Also, another significant innovation is the introduction of the curvature filters. We think this concept will prove to be a useful tool in signal processing, not only in ECG analysis.","PeriodicalId":38956,"journal":{"name":"Open Bioinformatics Journal","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44362517","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}