The Open Applied Informatics Journal最新文献

{"title":"The Quest for a General and Reliable Fungal DNA Barcode","authors":"V. Robert, S. Szoke, U. Eberhardt, G. Cardinali, W. Meyer, K. Seifert, C. Lévesque, C. Lewis","doi":"10.2174/1874136301105010045","DOIUrl":"https://doi.org/10.2174/1874136301105010045","url":null,"abstract":"DNA sequences are key elements for both identification and classification of living organisms. Mainly for historical reasons, a limited number of genes are currently used for this purpose. From a mathematical point of view, any DNA segment, at any location, even outside of coding regions and even if they do not align, could be used as long as PCR primers could be designed to amplify them. This paper describes two methods to search genomic data for the most efficient DNA segments that can be used for identification and classification.","PeriodicalId":148247,"journal":{"name":"The Open Applied Informatics Journal","volume":"54 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2011-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127293598","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":"Counting of a Degenerate Word in Random Sequences","authors":"Wei Zheng, Ke-Song Liu","doi":"10.2174/1874136301004010010","DOIUrl":"https://doi.org/10.2174/1874136301004010010","url":null,"abstract":"Overlap of words complicates the problem of word counting. The technique of the imbedded Markov chain (IMC) uses an enlarged state space to recover the Markovian property for the word counting problem. A degenerate word represents multiple non-degenerate words. An efficient way to decompose a degenerate word according to its overlapping pattern for implementing IMC is proposed.","PeriodicalId":148247,"journal":{"name":"The Open Applied Informatics Journal","volume":"76 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2010-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"121495291","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":"Classification of Trends in Dose-Response Microarray Experiments Using Information Theory Selection Methods~!2009-02-24~!2009-07-09~!2009-12-23~!","authors":"Dan Lin, Z. Shkedy, T. Burzykowski, M. Aerts, Hinrich W. H. Göhlmann, A. Bondt, Tim Perera, T. Geerts, I. V. D. Wyngaert, L. Bijnens","doi":"10.2174/1874136300903010034","DOIUrl":"https://doi.org/10.2174/1874136300903010034","url":null,"abstract":"Dose-response microarray experiments consist of monitoring expression levels of thousands of genes with respect to increasing dose of the treatment under investigation. The primary goal of such an experiment is to establish a dose-response relationship, while the secondary goals are to determine the minimum effective dose level and to identify the shape of the dose-response curve. Recently, Lin et al. (1) discussed several testing procedures to test for monotone trend based on isotonic regression of the observed means (2,3). Once a monotone relationship between the gene expression and dose is established, there is a set of R possible monotone models that can be fitted to the data. A selection of the best model from this set allows us to identify both the shape of dose-response curve and the minimum effective dose level. In this paper we focus on classification of dose-response curve shapes using the information theory model selection. In particular, the Order Restricted Information Criterion (ORIC) is discussed for the inference under order restriction. The posterior probability of the model is calculated using information criteria that take into account both the goodness-of-fit and the complexity of the models. The method is applied to a dose-response microarray experiment with 12 arrays (for three samples at each of the four dose levels) with 16,998 genes.","PeriodicalId":148247,"journal":{"name":"The Open Applied Informatics Journal","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2009-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"126007337","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":"Solvation Parameters. Part 4: What is the Impact of Recent Chromatographic Data Update?","authors":"P. Laffort, Pierre Héricourt","doi":"10.2174/1874136300903010012","DOIUrl":"https://doi.org/10.2174/1874136300903010012","url":null,"abstract":"Accurate solvation parameters have been established using solely gas/liquid partition data by gas/chromatography from the Kováts group (Laffort et al. J. Chromatog. A, 2005, 1100, 90-107). Because these chromatographic data have been recently updated (Kováts and Kresz, J. Chromatog. A, 2006, 1113, 206-219), the solvation parameters of the involved solutes and stationary phases have been entirely computed on again. It appears from this enquiry that the solute paramers values (127 compounds) are almost identical, whereas solvent parameters (11 stationary phases) have been slightly improved. A simple method of stationary phases classification is derived from these results, as well as a method for further determination of solute parameters. INTRODUCTION The conceptual definition of solvation parameters or descriptors can be expressed as follows: if a matrix of a given solubility property can be expressed as a product of matrices A*B, then A and B are respectively matrices of solute and solvent solvation parameters. Because infinite number of matrices A and B can provide such product, some rules and procedures have been developed in order, among others, to get parameters mutually as independent as possible (i.e. faintly correlated), and clearly reflecting understandable physicochemical properties [1-3]. In addition to these rules and procedures, the second tool needed to rightly characterize the solvation parameters of solutes is a reliable experimental database of solubility properties. Recently, Laffort et al. [1] used an accurate matrix of retention indices in gas-liquid chromatography (GLC) for 133 solutes and 10 stationary phases. Eight of these phases, of polar nature, were established by Kováts and co-authors [4-7], and the other two non polar phases were published by Laffort et al. [1]. However, one year later, Kováts and Kresz [8] published updated values of most of the GLC retention indices previously published in the references [4-7]. This update has raised two questions, the first one should be firstly solved before getting an answer to the second one: • Have the remaining GLC values published by Laffort et al. [1], and principally those on apolar phases, to be similarly updated? • Have these updated results on polar and apolar phases, an impact on the definitions of solvation parameters of solutes and solvents? The aim of the present study is to answer these two points and, if needed, specify some consequences. *Address correspondence to this author at the CNRS, Centre des Sciences du Goût UMR 5170, 15 rue Hugues Picardet, F.21000 Dijon, France; E-mail: laffort@cesg.cnrs.fr CHECKING THE REMAINING GLC VALUES The Original Database According to [1] This experimental data matrix of GLC retention indices RI (133 solutes x 10 stationary phases) is reported in Supplementary Information (Table SI-1), exactly as it was published in [1]. It includes RI values on two families of branched stationary phases, with respectively four and six branches, as","PeriodicalId":148247,"journal":{"name":"The Open Applied Informatics Journal","volume":"9 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2009-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128197810","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":"Estimation of Subcellular Proteomes in Bacterial Species","authors":"Brian R. King, L. Latham, C. Guda","doi":"10.2174/1874136300903010001","DOIUrl":"https://doi.org/10.2174/1874136300903010001","url":null,"abstract":"Computational methods for predicting the subcellular localization of bacterial proteins play a crucial role in the ongoing efforts to annotate the function of these proteins and to suggest potential drug targets. These methods, used in combination with other experimental and computational methods, can play an important role in biomedical research by annotating the proteomes of a wide variety of bacterial species. We use the ngLOC method, a Bayesian classifier that pre- dicts the subcellular localization of a protein based on the distribution of n-grams in a curated dataset of experimentally- determined proteins. Subcellular localization was predicted with an overall accuracy of 89.7% and 89.3% for Gram- negative and Gram-positive bacteria protein sequences, respectively. Through the use of a confidence score threshold, we improve the precision to 96.6% while covering 84.4% of Gram-negative bacterial data, and 96.0% while covering 87.9% of Gram-positive data. We use this method to estimate the subcellular proteomes of ten Gram-negative species and five Gram-positive species, covering an average of 74.7% and 80.6% of the proteome for Gram-negative and Gram-positive sequences, respectively. The current method is useful for large-scale analysis and annotation of the subcellular proteomes of bacterial species. We demonstrate that our method has excellent predictive performance while achieving superior pro- teome coverage compared to other popular methods such as PSORTb and PLoc.","PeriodicalId":148247,"journal":{"name":"The Open Applied Informatics Journal","volume":"34 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2009-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"121215100","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":"Is the Ontological Approach for the Grade Concept a Necessity for Successful Product Profitability Calculation in a Paper Mill","authors":"J. Mattila, T. Tiihonen, Virpi Hotti, M. Juhola","doi":"10.2174/1874136300802010032","DOIUrl":"https://doi.org/10.2174/1874136300802010032","url":null,"abstract":"This article creates a generic grade concept that is a synthesis of wide range of terminologies linked with dif- ferent paper types produced in paper mills. Nearly all paper mills and their system providers define the type and concepts of paper in different ways. The starting point in the grade concept is that it supports the diversified and reliable product profitability calculation as much as possible. Due to the complex nature of grade concept in the paper mills, ontology is used to achieve formal and explicit format for its definition. The formality is understood as an exact description of the concept, which in this article means a mathematical model for the product profitability calculation. The explicit approach means that the concept can be run in a computer by using the third normal mode entity relationship charts (ER). The func- tionality of the equations is demonstrated by a numerical example.","PeriodicalId":148247,"journal":{"name":"The Open Applied Informatics Journal","volume":"47 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2008-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114308094","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":"Solvation Parameters of Solutes: An Attempt of Improvements in Characterization and Determination","authors":"P. Laffort, Pierre Héricourt","doi":"10.2174/1874136300802010022","DOIUrl":"https://doi.org/10.2174/1874136300802010022","url":null,"abstract":"We are presenting here an updated version of our predictive model of solvation parameters of solutes, based on a simplified molecular topology (J. Chem. Inf. Model, 2006, 46, 1723-1734). The learning experimental database of this model is presently larger than in our first version and includes more compounds with more than one functional group of the same type. This experimental database is also surer, in the sense that it only includes compounds in liquid state at room temperature, when the polarizability of a compound in solution is established via its refractive index in gas or crys- talline state. Indeed, we demonstrate in this paper, a bias in this case.","PeriodicalId":148247,"journal":{"name":"The Open Applied Informatics Journal","volume":"118 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2008-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"116281623","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":"Internet in Drug Design and Discovery","authors":"I. Tetko","doi":"10.2174/1874136300802010018","DOIUrl":"https://doi.org/10.2174/1874136300802010018","url":null,"abstract":"The development of Internet technologies and the WWW has dramatically influenced all aspects of modern life. Is their development also beneficial for drug discovery? This article reviews advantages of web technologies and their influence on the drug discovery process. INTRANET TOOLS IN PHARMA COMPANIES Currently, major large pharma companies use Web tech- nology for the Intranet data analysis of small molecules (1- 5). There are at least several clear advantages why compa- nies are investing in the development of web technologies.  Available everywhere. The Web tools are accessible on different platforms thus allowing the users to work in the environment they prefer. This eliminates need to spend resources for training of end-users to work with program installed on specialized systems such as Linux, Unix, etc.  Decreased support costs. The web technologies dramatically decrease costs for installation, support and upgrade of the software. The most recent versions of the software tools become immediately and simul- taneously available for all users within the corporate Intranets following the upgrade of the software at the central server.  Decreased license costs. The licensing of the soft- ware for web use within corporate Intranet can be much cheaper compared to multiple licenses required to install stand-alone versions at multiple computers.","PeriodicalId":148247,"journal":{"name":"The Open Applied Informatics Journal","volume":"36 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2008-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"133213763","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":"JSTRING: A Novel Java Tandem Repeats Searcher in Genomic Sequences with an Interactive Graphic Output","authors":"V. Fonzo, F. Aluffi-Pentini, V. Parisi","doi":"10.2174/1874136300802010014","DOIUrl":"https://doi.org/10.2174/1874136300802010014","url":null,"abstract":"The search of Tandem Repeats in a genomic sequence is of growing interest but unfortunately the existing tools have the drawback of producing cumbersome results that require a painstaking interpretation. In order to help users interpret the results at first glance, we implemented JSTRING that shows the results also in a very clear graphic format, thus allowing their immediate survey. The software is freely available at: http://bioinf.dms.med.uniroma1.it/JSTRING/.","PeriodicalId":148247,"journal":{"name":"The Open Applied Informatics Journal","volume":"322 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2008-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"115867588","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":"MMS: A “R” Package for Metabolomic Markers Search in Stress Response Studies","authors":"G. Cardinali, Paolo Rellini, Cristina Pelliccia, Livio Antonielli, F. Fatichenti","doi":"10.2174/1874136300802010001","DOIUrl":"https://doi.org/10.2174/1874136300802010001","url":null,"abstract":"In stress response studies, metabolomics tries to individuate spectral areas or metabolites whose response to a specific stress is particularly significant. This evaluation is normally carried out with a series of tedious and time consum- ing comparisons of spectral areas obtained from cells subject to different stress intensities. MMS is a package written in \"R\" language able to individuate which part of metabolomic spectra have a statistically significant response giving as out- put the diagrams of the R 2 and of the slope calculated from regression analysis between a vector describing the intensity of the stress and a matrix containing all spectra from differently challenged cells.","PeriodicalId":148247,"journal":{"name":"The Open Applied Informatics Journal","volume":"82 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2008-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"126282961","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}