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Sample records for approach matching gene

  1. Approaches for Stereo Matching

    Directory of Open Access Journals (Sweden)

    Takouhi Ozanian

    1995-04-01

    Full Text Available This review focuses on the last decade's development of the computational stereopsis for recovering three-dimensional information. The main components of the stereo analysis are exposed: image acquisition and camera modeling, feature selection, feature matching and disparity interpretation. A brief survey is given of the well known feature selection approaches and the estimation parameters for this selection are mentioned. The difficulties in identifying correspondent locations in the two images are explained. Methods as to how effectively to constrain the search for correct solution of the correspondence problem are discussed, as are strategies for the whole matching process. Reasons for the occurrence of matching errors are considered. Some recently proposed approaches, employing new ideas in the modeling of stereo matching in terms of energy minimization, are described. Acknowledging the importance of computation time for real-time applications, special attention is paid to parallelism as a way to achieve the required level of performance. The development of trinocular stereo analysis as an alternative to the conventional binocular one, is described. Finally a classification based on the test images for verification of the stereo matching algorithms, is supplied.

  2. Functional Associations by Response Overlap (FARO), a functional genomics approach matching gene expression phenotypes

    DEFF Research Database (Denmark)

    Nielsen, Henrik Bjørn; Mundy, J.; Willenbrock, Hanni

    2007-01-01

    The systematic comparison of transcriptional responses of organisms is a powerful tool in functional genomics. For example, mutants may be characterized by comparing their transcript profiles to those obtained in other experiments querying the effects on gene expression of many experimental factors...... for deriving 'Functional Association(s) by Response Overlap' (FARO) between microarray gene expression studies. The transcriptional response is defined by the set of differentially expressed genes independent from the magnitude or direction of the change. This approach overcomes the limited comparability...... to confirm and further delineate the functions of Arabidopsis MAP kinase 4 in disease and stress responses. Furthermore, we find that a large, well-defined set of genes responds in opposing directions to different stress conditions and predict the effects of different stress combinations. This demonstrates...

  3. Personalized Medicine: Matching Treatments to Your Genes

    Science.gov (United States)

    ... disclaimer . Subscribe Personalized Medicine Matching Treatments to Your Genes You’re one of a kind. It’s not ... personalized medicine begins with the unique set of genes you inherited from your parents. Genes are stretches ...

  4. Review og pattern matching approaches

    DEFF Research Database (Denmark)

    Manfaat, D.; Duffy, Alex; Lee, B. S.

    1996-01-01

    This paper presents a review of pattern matching techniques. The application areas for pattern matching are extensive, ranging from CAD systems to chemical analysis and from manufacturing to image processing. Published techniques and methods are classified and assessed within the context of three...

  5. A New Approach for Semantic Web Matching

    Science.gov (United States)

    Zamanifar, Kamran; Heidary, Golsa; Nematbakhsh, Naser; Mardukhi, Farhad

    In this work we propose a new approach for semantic web matching to improve the performance of Web Service replacement. Because in automatic systems we should ensure the self-healing, self-configuration, self-optimization and self-management, all services should be always available and if one of them crashes, it should be replaced with the most similar one. Candidate services are advertised in Universal Description, Discovery and Integration (UDDI) all in Web Ontology Language (OWL). By the help of bipartite graph, we did the matching between the crashed service and a Candidate one. Then we chose the best service, which had the maximum rate of matching. In fact we compare two services' functionalities and capabilities to see how much they match. We found that the best way for matching two web services, is comparing the functionalities of them.

  6. Matched filter based iterative adaptive approach

    Science.gov (United States)

    Nepal, Ramesh; Zhang, Yan Rockee; Li, Zhengzheng; Blake, William

    2016-05-01

    Matched Filter sidelobes from diversified LPI waveform design and sensor resolution are two important considerations in radars and active sensors in general. Matched Filter sidelobes can potentially mask weaker targets, and low sensor resolution not only causes a high margin of error but also limits sensing in target-rich environment/ sector. The improvement in those factors, in part, concern with the transmitted waveform and consequently pulse compression techniques. An adaptive pulse compression algorithm is hence desired that can mitigate the aforementioned limitations. A new Matched Filter based Iterative Adaptive Approach, MF-IAA, as an extension to traditional Iterative Adaptive Approach, IAA, has been developed. MF-IAA takes its input as the Matched Filter output. The motivation here is to facilitate implementation of Iterative Adaptive Approach without disrupting the processing chain of traditional Matched Filter. Similar to IAA, MF-IAA is a user parameter free, iterative, weighted least square based spectral identification algorithm. This work focuses on the implementation of MF-IAA. The feasibility of MF-IAA is studied using a realistic airborne radar simulator as well as actual measured airborne radar data. The performance of MF-IAA is measured with different test waveforms, and different Signal-to-Noise (SNR) levels. In addition, Range-Doppler super-resolution using MF-IAA is investigated. Sidelobe reduction as well as super-resolution enhancement is validated. The robustness of MF-IAA with respect to different LPI waveforms and SNR levels is also demonstrated.

  7. Improved Approach for Exact Pattern Matching (Bidirectional Exact Pattern Matching)

    OpenAIRE

    Hussain, Iftikhar; Kausar, Samina; Hussain, Liaqat; Asif Khan, Muhammad

    2013-01-01

    In this research we present Bidirectional exact pattern matching algorithm [20] in detail. Bidirectional (BD) exact pattern matching (EPM) introduced a new idea to compare pattern with Selected Text Window (STW) of text string by using two pointers (right and left) simultaneously in searching phase. In preprocessing phase Bidirectional EPM algorithm improved the shift decision by comparing rightmost and mismatched character of Partial Text Window (PTW) to the left of pattern at sa...

  8. Local Search Approaches in Stable Matching Problems

    Directory of Open Access Journals (Sweden)

    Toby Walsh

    2013-10-01

    Full Text Available The stable marriage (SM problem has a wide variety of practical applications, ranging from matching resident doctors to hospitals, to matching students to schools or, more generally, to any two-sided market. In the classical formulation, n men and n women express their preferences (via a strict total order over the members of the other sex. Solving an SM problem means finding a stable marriage where stability is an envy-free notion: no man and woman who are not married to each other would both prefer each other to their partners or to being single. We consider both the classical stable marriage problem and one of its useful variations (denoted SMTI (Stable Marriage with Ties and Incomplete lists where the men and women express their preferences in the form of an incomplete preference list with ties over a subset of the members of the other sex. Matchings are permitted only with people who appear in these preference lists, and we try to find a stable matching that marries as many people as possible. Whilst the SM problem is polynomial to solve, the SMTI problem is NP-hard. We propose to tackle both problems via a local search approach, which exploits properties of the problems to reduce the size of the neighborhood and to make local moves efficiently. We empirically evaluate our algorithm for SM problems by measuring its runtime behavior and its ability to sample the lattice of all possible stable marriages. We evaluate our algorithm for SMTI problems in terms of both its runtime behavior and its ability to find a maximum cardinality stable marriage. Experimental results suggest that for SM problems, the number of steps of our algorithm grows only as O(n log(n, and that it samples very well the set of all stable marriages. It is thus a fair and efficient approach to generate stable marriages. Furthermore, our approach for SMTI problems is able to solve large problems, quickly returning stable matchings of large and often optimal size, despite the

  9. Matching Alternative Addresses: a Semantic Web Approach

    Science.gov (United States)

    Ariannamazi, S.; Karimipour, F.; Hakimpour, F.

    2015-12-01

    Rapid development of crowd-sourcing or volunteered geographic information (VGI) provides opportunities for authoritatives that deal with geospatial information. Heterogeneity of multiple data sources and inconsistency of data types is a key characteristics of VGI datasets. The expansion of cities resulted in the growing number of POIs in the OpenStreetMap, a well-known VGI source, which causes the datasets to outdate in short periods of time. These changes made to spatial and aspatial attributes of features such as names and addresses might cause confusion or ambiguity in the processes that require feature's literal information like addressing and geocoding. VGI sources neither will conform specific vocabularies nor will remain in a specific schema for a long period of time. As a result, the integration of VGI sources is crucial and inevitable in order to avoid duplication and the waste of resources. Information integration can be used to match features and qualify different annotation alternatives for disambiguation. This study enhances the search capabilities of geospatial tools with applications able to understand user terminology to pursuit an efficient way for finding desired results. Semantic web is a capable tool for developing technologies that deal with lexical and numerical calculations and estimations. There are a vast amount of literal-spatial data representing the capability of linguistic information in knowledge modeling, but these resources need to be harmonized based on Semantic Web standards. The process of making addresses homogenous generates a helpful tool based on spatial data integration and lexical annotation matching and disambiguating.

  10. Iris Matching Based On a Stack Like Structure Graph Approach

    Directory of Open Access Journals (Sweden)

    Roushdi Mohamed FAROUK

    2012-12-01

    Full Text Available In this paper, we present the elastic bunch graph matching as a new approach for iris recognition. The task is difficult because of iris variation in terms of position, size, and partial occlusion. We have used the circular Hough transform to determine the iris boundaries. Individual segmented irises are represented as labeled graphs. We have combined a representative set of individual model graphs into a stack like structure called an iris bunch graph (IBG. Finally, a bunch graph similarity function is proposed to compare a test graph with the IBG. Recognition results are given for galleries of irises from CASIA version and UBIRIS databases. The numerical results show that, the elastic bunch graph matching is an effective technique for iris matching. We also compare our results with previous results and find that, the elastic bunch graph matching is an effective matching performance.

  11. Saliency detection and edge feature matching approach for crater extraction

    Institute of Scientific and Technical Information of China (English)

    An Liu; Donghua Zhou; Lixin Chen; Maoyin Chen

    2015-01-01

    Craters are salient terrain features on planetary sur-faces, and provide useful information about the relative dating of geological unit of planets. In addition, they are ideal landmarks for spacecraft navigation. Due to low contrast and uneven il u-mination, automatic extraction of craters remains a chal enging task. This paper presents a saliency detection method for crater edges and a feature matching algorithm based on edges informa-tion. The craters are extracted through saliency edges detection, edge extraction and selection, feature matching of the same crater edges and robust el ipse fitting. In the edges matching algorithm, a crater feature model is proposed by analyzing the relationship between highlight region edges and shadow region ones. Then, crater edges are paired through the effective matching algorithm. Experiments of real planetary images show that the proposed approach is robust to different lights and topographies, and the detection rate is larger than 90%.

  12. Matching Genes and Vitamins: A Personalized Plan May Be in Your Future

    Science.gov (United States)

    ... 401 kb) Arm Yourself for Good Health Matching Genes and Vitamins Matching Genes and Vitamins A Personalized Plan May Be in ... in the DNA sequences that make up our genes . These changes can occur naturally. Since our DNA ...

  13. A Moment Matching Approach for Generating Synthetic Data.

    Science.gov (United States)

    Bogle, Brittany Megan; Mehrotra, Sanjay

    2016-09-01

    Synthetic data are becoming increasingly important mechanisms for sharing data among collaborators and with the public. Multiple methods for the generation of synthetic data have been proposed, but many have short comings with respect to maintaining the statistical properties of the original data. We propose a new method for fully synthetic data generation that leverages linear and integer mathematical programming models in order to match the moments of the original data in the synthetic data. This method has no inherent disclosure risk and does not require parametric or distributional assumptions. We demonstrate this methodology using the Framingham Heart Study. Existing synthetic data methods that use chained equations were compared with our approach. We fit Cox proportional hazards, logistic regression, and nonparametric models to synthetic data and compared with models fitted to the original data. True coverage, the proportion of synthetic data parameter confidence intervals that include the original data's parameter estimate, was 100% for parametric models when up to four moments were matched, and consistently outperformed the chained equations approach. The area under the curve and accuracy of the nonparametric models trained on synthetic data marginally differed when tested on the full original data. Models were also trained on synthetic data and a partition of original data and were tested on a held-out portion of original data. Fourth-order moment matched synthetic data outperformed others with respect to fitted parametric models but did not always outperform other methods with fitted nonparametric models. No single synthetic data method consistently outperformed others when assessing the performance of nonparametric models. The performance of fourth-order moment matched synthetic data in fitting parametric models suggests its use in these cases. Our empirical results also suggest that the performance of synthetic data generation techniques, including the

  14. Matched field noise suppression:A generalized spatial filtering approach

    Institute of Scientific and Technical Information of China (English)

    YAN Shefeng; MA Yuanliang

    2004-01-01

    An approach to improving the performance of matched field localization by introducing a generalized spatial filter to suppress interference noise and pass the signal of interest with minimal distortion is presented. The spatial filter is designed by minimizing the maximum distortion of the filtered replica vectors within "passband" while guaran-teeing the norm of the filter response within the "stopband" to be lower than some given threshold values. We show that the design problem can be formulated as the second-order cone programming (SOCP) which can be solved efficiently via the well-established interior point method. A modified matched field processor is given to ultimately eliminate the effect of the distortion in the spatially filtered replica vectors. Computer simulation results confirm the effectiveness of the proposed approach by localizing a weak source in the presence of a strong interferer and noise.

  15. Uniform smooth filtering approach for fast template matching

    Science.gov (United States)

    Li, Bing C.

    2016-05-01

    Sum of square difference (SSD) and normalized cross correlation (NCC) are two different template matching techniques and their fast implementations have been investigated independently. The SSD approach is known to be simple and fast, however it is variant to image intensity change that lead to low performance. On the other hand, the NCC method is invariant to intensity change and has high performance, but its computational cost is high. In this paper, we derive an equation that connects NCC and SSD. From this equation, we propose SSD based partial elimination for the fast implementation of NCC template matching. This new technique takes the advantages of both NCC's high performance and SSD's low computational cost. It is fast and has high performance. Then we propose a uniform smoothing approach that further reduces computational cost for NCC. Experiments show that the proposed method is significantly faster than the techniques reported in literature.

  16. Matching of array CGH and gene expression microarray features for the purpose of integrative genomic analyses

    Directory of Open Access Journals (Sweden)

    van Wieringen Wessel N

    2012-05-01

    Full Text Available Abstract Background An increasing number of genomic studies interrogating more than one molecular level is published. Bioinformatics follows biological practice, and recent years have seen a surge in methodology for the integrative analysis of genomic data. Often such analyses require knowledge of which elements of one platform link to those of another. Although important, many integrative analyses do not or insufficiently detail the matching of the platforms. Results We describe, illustrate and discuss six matching procedures. They are implemented in the R-package sigaR (available from Bioconductor. The principles underlying the presented matching procedures are generic, and can be combined to form new matching approaches or be applied to the matching of other platforms. Illustration of the matching procedures on a variety of data sets reveals how the procedures differ in the use of the available data, and may even lead to different results for individual genes. Conclusions Matching of data from multiple genomics platforms is an important preprocessing step for many integrative bioinformatic analysis, for which we present six generic procedures, both old and new. They have been implemented in the R-package sigaR, available from Bioconductor.

  17. Efficient wave-function matching approach for quantum transport calculations

    DEFF Research Database (Denmark)

    Sørensen, Hans Henrik Brandenborg; Hansen, Per Christian; Petersen, Dan Erik;

    2009-01-01

    the propagating and evanescent bulk modes of the left and right electrodes in order to obtain the correct coupling between device and electrode regions. In this paper we will describe a modified WFM approach that allows for the exclusion of the vast majority of the evanescent modes in all parts of the calculation......The wave-function matching (WFM) technique has recently been developed for the calculation of electronic transport in quantum two-probe systems. In terms of efficiency it is comparable to the widely used Green's function approach. The WFM formalism presented so far requires the evaluation of all....... This approach makes it feasible to apply iterative techniques to efficiently determine the few required bulk modes, which allows for a significant reduction of the computational expense of the WFM method. We illustrate the efficiency of the method on a carbon nanotube field-effect-transistor device displaying...

  18. Privacy–Preserving Friend Matching Protocol approach for Pre-match in Social Networks

    DEFF Research Database (Denmark)

    Ople, Shubhangi S.; Deshmukh, Aaradhana A.; Mihovska, Albena Dimitrova;

    2016-01-01

    for use in social networks due to its data sharing problems and information leakage. In this paper, we propose a novel framework for privacy–preserving profile matching. We implement both the client and server portion of the secure match and evaluate its performance network dataset. The results show...... that a secure match can achieve at least one order of accuracy and better computational performance than the techniques that use homomorphic encryption.It can handle and tackle new characteristics and an environment for a particular application in a mobile social network....

  19. Pattern classification approaches to matching building polygons at multiple scales

    NARCIS (Netherlands)

    Zhang, X; Zhao, X.; Molenaar, M.; Stoter, J.; Kraak M-J.; Ai, T.

    2012-01-01

    Matching of building polygons with different levels of detail is crucial in the maintenance and quality assessment of multi-representation databases. Two general problems need to be addressed in the matching process: (1) Which criteria are suitable? (2) How to effectively combine different criteria

  20. An Aerial-Image Dense Matching Approach Based on Optical Flow Field

    Science.gov (United States)

    Yuan, Wei; Chen, Shiyu; Zhang, Yong; Gong, Jianya; Shibasaki, Ryosuke

    2016-06-01

    Dense matching plays an important role in many fields, such as DEM (digital evaluation model) producing, robot navigation and 3D environment reconstruction. Traditional approaches may meet the demand of accuracy. But the calculation time and out puts density is hardly be accepted. Focus on the matching efficiency and complex terrain surface matching feasibility an aerial image dense matching method based on optical flow field is proposed in this paper. First, some high accurate and uniformed control points are extracted by using the feature based matching method. Then the optical flow is calculated by using these control points, so as to determine the similar region between two images. Second, the optical flow field is interpolated by using the multi-level B-spline interpolation in the similar region and accomplished the pixel by pixel coarse matching. Final, the results related to the coarse matching refinement based on the combined constraint, which recognizes the same points between images. The experimental results have shown that our method can achieve per-pixel dense matching points, the matching accuracy achieves sub-pixel level, and fully meet the three-dimensional reconstruction and automatic generation of DSM-intensive matching's requirements. The comparison experiments demonstrated that our approach's matching efficiency is higher than semi-global matching (SGM) and Patch-based multi-view stereo matching (PMVS) which verifies the feasibility and effectiveness of the algorithm.

  1. Active network alignment: a matching-based approach

    CERN Document Server

    Malmi, Eric; Gionis, Aristides

    2016-01-01

    Network alignment is the problem of matching the nodes of two graphs, maximizing the similarity of the matched nodes and the edges between them. This problem is encountered in a wide array of applications - from biological networks to social networks to ontologies - where multiple networked data sources need to be integrated. Due to the difficulty of the task, an accurate alignment can rarely be found without human assistance. Thus, it is of great practical importance to develop network alignment algorithms that can optimally leverage experts who are able to provide the correct alignment for a small number of nodes. Yet, only a handful of existing works address this active network alignment setting. The majority of the existing active methods focus on absolute queries ("are nodes $a$ and $b$ the same or not?"), whereas we argue that it is generally easier for a human expert to answer relative queries ("which node in the set $\\{b_1, \\ldots, b_n\\}$ is the most similar to node $a$?"). This paper introduces a nov...

  2. AN AERIAL-IMAGE DENSE MATCHING APPROACH BASED ON OPTICAL FLOW FIELD

    Directory of Open Access Journals (Sweden)

    W. Yuan

    2016-06-01

    Full Text Available Dense matching plays an important role in many fields, such as DEM (digital evaluation model producing, robot navigation and 3D environment reconstruction. Traditional approaches may meet the demand of accuracy. But the calculation time and out puts density is hardly be accepted. Focus on the matching efficiency and complex terrain surface matching feasibility an aerial image dense matching method based on optical flow field is proposed in this paper. First, some high accurate and uniformed control points are extracted by using the feature based matching method. Then the optical flow is calculated by using these control points, so as to determine the similar region between two images. Second, the optical flow field is interpolated by using the multi-level B-spline interpolation in the similar region and accomplished the pixel by pixel coarse matching. Final, the results related to the coarse matching refinement based on the combined constraint, which recognizes the same points between images. The experimental results have shown that our method can achieve per-pixel dense matching points, the matching accuracy achieves sub-pixel level, and fully meet the three-dimensional reconstruction and automatic generation of DSM-intensive matching’s requirements. The comparison experiments demonstrated that our approach’s matching efficiency is higher than semi-global matching (SGM and Patch-based multi-view stereo matching (PMVS which verifies the feasibility and effectiveness of the algorithm.

  3. Pattern matching approach to pseudosymmetry problems in electron backscatter diffraction.

    Science.gov (United States)

    Nolze, Gert; Winkelmann, Aimo; Boyle, Alan P

    2016-01-01

    We demonstrate an approach to overcome Kikuchi pattern misindexing problems caused by crystallographic pseudosymmetry in electron backscatter diffraction (EBSD) measurements. Based on the quantitative comparison of experimentally measured Kikuchi patterns with dynamical electron diffraction simulations, the algorithm identifies the best-fit orientation from a set of pseudosymmetric candidates. Using measurements on framboidal pyrite (FeS2) as an example, we also show the improvement of the orientation precision using this approach.

  4. Overcoming the matched-sample bottleneck: an orthogonal approach to integrate omic data.

    Science.gov (United States)

    Nguyen, Tin; Diaz, Diana; Tagett, Rebecca; Draghici, Sorin

    2016-01-01

    MicroRNAs (miRNAs) are small non-coding RNA molecules whose primary function is to regulate the expression of gene products via hybridization to mRNA transcripts, resulting in suppression of translation or mRNA degradation. Although miRNAs have been implicated in complex diseases, including cancer, their impact on distinct biological pathways and phenotypes is largely unknown. Current integration approaches require sample-matched miRNA/mRNA datasets, resulting in limited applicability in practice. Since these approaches cannot integrate heterogeneous information available across independent experiments, they neither account for bias inherent in individual studies, nor do they benefit from increased sample size. Here we present a novel framework able to integrate miRNA and mRNA data (vertical data integration) available in independent studies (horizontal meta-analysis) allowing for a comprehensive analysis of the given phenotypes. To demonstrate the utility of our method, we conducted a meta-analysis of pancreatic and colorectal cancer, using 1,471 samples from 15 mRNA and 14 miRNA expression datasets. Our two-dimensional data integration approach greatly increases the power of statistical analysis and correctly identifies pathways known to be implicated in the phenotypes. The proposed framework is sufficiently general to integrate other types of data obtained from high-throughput assays. PMID:27403564

  5. A computationally efficient approach for template matching-based image registration

    Indian Academy of Sciences (India)

    Vilas H Gaidhane; Yogesh V Hote; Vijander Singh

    2014-04-01

    Image registration using template matching is an important step in image processing. In this paper, a simple, robust and computationally efficient approach is presented. The proposed approach is based on the properties of a normalized covariance matrix. The main advantage of the proposed approach is that the image matching can be achieved without calculating eigenvalues and eigenvectors of a covariance matrix, hence reduces the computational complexity. The experimental results show that the proposed approach performs better in the presence of various noises and rigid geometric transformations.

  6. Complementing computationally predicted regulatory sites in Tractor_DB using a pattern matching approach.

    Science.gov (United States)

    Guía, Marylens Hernández; Pérez, Abel González; Angarica, Vladimir Espinosa; Vasconcelos, Ana T; Collado-Vides, Julio

    2005-01-01

    Prokaryotic genomes annotation has focused on genes location and function. The lack of regulatory information has limited the knowledge on cellular transcriptional regulatory networks. However, as more phylogenetically close genomes are sequenced and annotated, the implementation of phylogenetic footprinting strategies for the recognition of regulators and their regulons becomes more important. In this paper we describe a comparative genomics approach to the prediction of new gamma-proteobacterial regulon members. We take advantage of the phylogenetic proximity of Escherichia coli and other 16 organisms of this subdivision and the intensive search of the space sequence provided by a pattern-matching strategy. Using this approach we complement predictions of regulatory sites made using statistical models currently stored in Tractor_DB, and increase the number of transcriptional regulators with predicted binding sites up to 86. All these computational predictions may be reached at Tractor_DB (www.bioinfo.cu/Tractor_DB, www.tractor.lncc.br, www.ccg.unam.mx/Computational_Genomics/tractorDB/). We also take a first step in this paper towards the assessment of the conservation of the architecture of the regulatory network in the gamma-proteobacteria through evaluating the conservation of the overall connectivity of the network. PMID:15972018

  7. Matching theory

    CERN Document Server

    Plummer, MD

    1986-01-01

    This study of matching theory deals with bipartite matching, network flows, and presents fundamental results for the non-bipartite case. It goes on to study elementary bipartite graphs and elementary graphs in general. Further discussed are 2-matchings, general matching problems as linear programs, the Edmonds Matching Algorithm (and other algorithmic approaches), f-factors and vertex packing.

  8. A constructive approach to gene expression dynamics

    International Nuclear Information System (INIS)

    Recently, experiments on mRNA abundance (gene expression) have revealed that gene expression shows a stationary organization described by a scale-free distribution. Here we propose a constructive approach to gene expression dynamics which restores the scale-free exponent and describes the intermediate state dynamics. This approach requires only one assumption: Markov property

  9. FARO server: Meta-analysis of gene expression by matching gene expression signatures to a compendium of public gene expression data

    DEFF Research Database (Denmark)

    Manijak, Mieszko P.; Nielsen, Henrik Bjørn

    2011-01-01

    circumvented by instead matching gene expression signatures to signatures of other experiments. FINDINGS: To facilitate this we present the Functional Association Response by Overlap (FARO) server, that match input signatures to a compendium of 242 gene expression signatures, extracted from more than 1700......BACKGROUND: Although, systematic analysis of gene annotation is a powerful tool for interpreting gene expression data, it sometimes is blurred by incomplete gene annotation, missing expression response of key genes and secondary gene expression responses. These shortcomings may be partially...... Arabidopsis microarray experiments. CONCLUSIONS: Hereby we present a publicly available tool for robust characterization of Arabidopsis gene expression experiments which can point to similar experimental factors in other experiments. The server is available at http://www.cbs.dtu.dk/services/faro/....

  10. Edge-to-edge matching - a new approach to the morphology and crystallography of precipitates

    International Nuclear Information System (INIS)

    An entirely new approach is taken to understanding the morphology and crystallography of partially coherent precipitates formed by diffusional processes 'edge-to-edge matching'. This approach is based on the simple, well founded result put forward by Shiflet and Van der Merwe [Metallurgical and Materials Transactions A. 25A (1994) 1895] - namely that minimisation of interfacial energy results when rows of atoms match across the interface. The geometric conditions necessary to achieve this atom row matching are shown to be possible for a variety of lattice parameters in the fcc/bcc system provided there is edge-to-edge matching of planes containing these rows in each of the two phases. This new model does not rely on physical assumptions of dubious validity, such as the existence of a long-range correspondence. It also differs from the existing models in that it does not need to include the particular orientation relationship as part of the input data. Instead it is capable of predicting the orientation relationship from first principles. The development of the concepts behind edge-to-edge matching are described for the fcc/bcc system, predictions of orientation relationships and habit planes are made for a variety of different precipitates and shown to be in extremely good agreement with reported experimental results

  11. Analytical Structure Matching and Very Precise Approach to the Coulombic Quantum Three-Body Problem

    Institute of Scientific and Technical Information of China (English)

    TAN Shi-Na

    2001-01-01

    A powerful approach to solve the Coulombic quantum three-body problem is proposed. The approach is exponentially convergent and more efficient than the hypcrsphcrical coordinate method and the correlation-function hyperspherical harmonic method. This approach is numerically competitive with the variational methods, such as that using the Hylleraas-type basis functions. Numerical comparisons are made to demonstrate the efficiency of this approach, by calculating the nonrelativistic and infinite-nuclear-mass limit of the ground state energy of the helium atom. The exponential convergency of this approach is due to the full matching between the analytical structure of the basis functions that are used in this paper and the true wavefunction. This full matching was not reached by most other methods. For example, the variational method using the Hylleraas-type basis does not reflects the logarithmic singularity of the true wavefunction at the origin as predicted by Bartlett and Fock. Two important approaches are proposed in this work to reach this full matching: the coordinate transformation method and the asymptotic series method. Besides these, this work makes use of the lcast square method to substitute complicated numerical integrations in solving the Schrodinger equation without much loss of accuracy, which is routinely used by people to fit a theoretical curve with discrete experimental data, but here is used to simplify thc computation.``

  12. Tailoring science outreach through E-matching using a community-based participatory approach.

    Directory of Open Access Journals (Sweden)

    Bernice B Rumala

    2011-03-01

    Full Text Available In an effort to increase science exposure for pre-college (K-12 students and as part of the science education reform agenda, many biomedical research institutions have established university-community partnerships. Typically, these science outreach programs consist of pre-structured, generic exposure for students, with little community engagement. However, the use of a medium that is accessible to both teachers and scientists, electronic web-based matchmaking (E-matching provides an opportunity for tailored outreach utilizing a community-based participatory approach (CBPA, which involves all stakeholders in the planning and implementation of the science outreach based on the interests of teachers/students and scientists. E-matching is a timely and urgent endeavor that provides a rapid connection for science engagement between teachers/students and experts in an effort to fill the science outreach gap. National Lab Network (formerly National Lab Day, an ongoing initiative to increase science equity and literacy, provides a model for engaging the public in science via an E-matching and hands-on learning approach. We argue that science outreach should be a dynamic endeavor that changes according to the needs of a target school. We will describe a case study of a tailored science outreach activity in which a public school that serves mostly under-represented minority students from disadvantaged backgrounds were E-matched with a university, and subsequently became equal partners in the development of the science outreach plan. In addition, we will show how global science outreach endeavors may utilize a CBPA, like E-matching, to support a pipeline to science among under-represented minority students and students from disadvantaged backgrounds. By merging the CBPA concept with a practical case example, we hope to inform science outreach practices via the lens of a tailored E-matching approach.

  13. Sample matching by inferred agonal stress in gene expression analyses of the brain

    Directory of Open Access Journals (Sweden)

    Bunney William E

    2007-09-01

    Full Text Available Abstract Background Gene expression patterns in the brain are strongly influenced by the severity and duration of physiological stress at the time of death. This agonal effect, if not well controlled, can lead to spurious findings and diminished statistical power in case-control comparisons. While some recent studies match samples by tissue pH and clinically recorded agonal conditions, we found that these indicators were sometimes at odds with observed stress-related gene expression patterns, and that matching by these criteria still sometimes results in identifying case-control differences that are primarily driven by residual agonal effects. This problem is analogous to the one encountered in genetic association studies, where self-reported race and ethnicity are often imprecise proxies for an individual's actual genetic ancestry. Results We developed an Agonal Stress Rating (ASR system that evaluates each sample's degree of stress based on gene expression data, and used ASRs in post hoc sample matching or covariate analysis. While gene expression patterns are generally correlated across different brain regions, we found strong region-region differences in empirical ASRs in many subjects that likely reflect inter-individual variabilities in local structure or function, resulting in region-specific vulnerability to agonal stress. Conclusion Variation of agonal stress across different brain regions differs between individuals, revealing a new level of complexity for gene expression studies of brain tissues. The Agonal Stress Ratings quantitatively assess each sample's extent of regulatory response to agonal stress, and allow a strong control of this important confounder.

  14. GeneMatcher: a matching tool for connecting investigators with an interest in the same gene.

    Science.gov (United States)

    Sobreira, Nara; Schiettecatte, François; Valle, David; Hamosh, Ada

    2015-10-01

    Here, we describe an overview and update on GeneMatcher (http://www.genematcher.org), a freely accessible Web-based tool developed as part of the Baylor-Hopkins Center for Mendelian Genomics. We created GeneMatcher with the goal of identifying additional individuals with rare phenotypes who had variants in the same candidate disease gene. We also wanted to facilitate connections to basic scientists working on orthologous genes in model systems with the goal of connecting their work to human Mendelian phenotypes. Meeting these goals will enhance the identification of novel Mendelian genes. Launched in September, 2013, GeneMatcher now has 2,178 candidate genes from 486 submitters spread across 38 countries entered in the database (June 1, 2015). GeneMatcher is also part of the Matchmaker Exchange (http://matchmakerexchange.org/) with an Application Programing Interface enabling submitters to query other databases of genetic variants and phenotypes without having to create accounts and data entries in multiple systems. PMID:26220891

  15. A Bayesian approach to matched field processing in uncertain ocean environments

    Institute of Scientific and Technical Information of China (English)

    LI Jianlong; PAN Xiang

    2008-01-01

    An approach of Bayesian Matched Field Processing(MFP)was discussed in the uncertain ocean environment.In this approach,uncertainty knowledge is modeled and spatial and temporal data Received by the array are fully used.Therefore,a mechanism for MFP is found.which well combines model-based and data-driven methods of uncertain field processing.By theoretical derivation,simulation analysis and the validation of the experimental array data at sea,we find that(1)the basic components of Bayesian matched field processors are the corresponding sets of Bartlett matched field processor,MVDR(minimum variance distortionless response)matched field processor,etc.;(2)Bayesian MVDR/Bartlett MFP are the weighted sum of the MVDR/Bartlett MFP,where the weighted coefficients are the values of the a posteriori probability;(3)with the uncertain ocean environment,Bayesian MFP can more correctly locate the source than MVDR MFP or Bartlett MFP;(4)Bayesian MFP call better suppress sidelobes of the ambiguity surfaces.

  16. HANDBOOK OF SOCCER MATCH ANALYSIS: A SYSTEMATIC APPROACH TO IMPROVING PERFORMANCE

    Directory of Open Access Journals (Sweden)

    Christopher Carling

    2006-03-01

    Analysis Tells Us about Successful Strategy and Tactics in Soccer, 8. From Technical and Tactical Performance Analysis to Training Drills, 9. The Future of Soccer Match Analysis. ASSESSMENT The authors have assembled an essential reading for all who are interested in understanding and doing better coaching and improving the performance in soccer. To this purpose, there is a strong practical approach in the book by giving plenty of examples along with a satisfactory scientific analysis of the subject area. It is concise and well organized in its presentation, creating an effective textbook. I believe, therefore, the book will serve as a first-rate teaching tool and reference for coaches, athletes and professionals in the human performance sciences.

  17. Statistical Approach to Gene Evolution

    CERN Document Server

    Chattopadhyay, S; Chakrabarti, J; Chattopadhyay, Sujay; Kanner, William A.; Chakrabarti, Jayprokas

    2001-01-01

    The evolution in coding DNA sequences brings new flexibility and freedom to the codon words, even as the underlying nucleotides get significantly ordered. These curious contra-rules of gene organisation are observed from the distribution of words and the second moments of the nucleotide letters. These statistical data give us the physics behind the classification of bacteria.

  18. Maximal sequence length of exact match between members from a gene family during early evolution

    Institute of Scientific and Technical Information of China (English)

    WEN Xiao; GUO Xing-yi; FAN Long-jiang

    2005-01-01

    Mutation (substitution, deletion, insertion, etc.) in nucleotide acid causes the maximal sequence lengths of exact match (MALE) between paralogous members from a duplicate event to become shorter during evolution. In this work, MALE changes between members of 26 gene families from four representative species (Arabidopsis thaliana, Oryza sativa, Mus musculus and Homo sapiens) were investigated. Comparative study ofparalogous' MALE and amino acid substitution rate (dA<0.5)indicated that a close relationship existed between them. The results suggested that MALE could be a sound evolutionary scale for the divergent time for paralogous genes during their early evolution. A reference table between MALE and divergent time for the four species was set up, which would be useful widely, for large-scale genome alignment and comparison. As an example, detection of large-scale duplication events of rice genome based on the table was illustrated.

  19. Bioagent Sample Matching using Elemental Composition Data: an Approach to Validation

    Energy Technology Data Exchange (ETDEWEB)

    Velsko, S P

    2006-04-21

    Sample matching is a fundamental capability that can have high probative value in a forensic context if proper validation studies are performed. In this report we discuss the potential utility of using the elemental composition of two bioagent samples to decide if they were produced in the same batch, or by the same process. Using guidance from the recent NRC study of bullet lead analysis and other sources, we develop a basic likelihood ratio framework for evaluating the evidentiary weight of elemental analysis data for sample matching. We define an objective metric for comparing two samples, and propose a method for constructing an unbiased population of test samples. We illustrate the basic methodology with some existing data on dry Bacillus thuringiensis preparations, and outline a comprehensive plan for experimental validation of this approach.

  20. Face recognition using elastic grid matching through photoshop: A new approach

    Directory of Open Access Journals (Sweden)

    Manavpreet Kaur

    2015-12-01

    Full Text Available Computing grids propose to be a very efficacious, economic and ascendable way of image identification. In this paper, we propose a grid based face recognition overture employing a general template matching method to solve the timeconsuming face recognition problem. A new approach has been employed in which the grid was prepared for a specific individual over his photograph using Adobe Photoshop CS5 software. The background was later removed and the grid prepared by merging layers was used as a template for image matching or comparison. This overture is computationally efficient, has high recognition rates and is able to identify a person with minimal efforts and in short time even from photographs taken at different magnifications and from different distances.

  1. TwigINLAB: A Decomposition-Matching-Merging Approach To Improving XML Query Processing

    Directory of Open Access Journals (Sweden)

    Su-Cheng Haw

    2008-01-01

    Full Text Available The emergence of the Web has increased significant interests in querying XML data. Current methods for XML query processing still suffers from producing large intermediate results and are not efficient in supporting query with mixed types of relationships. We propose the TwigINLAB algorithm to process and optimize the query evaluation. Our TwigINLAB adopts the decomposition-matching-merging approach and focuses on optimizing all three sub-processes; introducing a novel compact labeling scheme, optimizing the matching phase and reducing the number of inspection required in the merging phase. Experimental results indicate that TwigINLAB can process both path queries and twig queries better than the TwigStack algorithm on an average of 21.7% and 18.7% respectively in terms of execution time using the SwissProt dataset.

  2. Sherlock: detecting gene-disease associations by matching patterns of expression QTL and GWAS.

    Science.gov (United States)

    He, Xin; Fuller, Chris K; Song, Yi; Meng, Qingying; Zhang, Bin; Yang, Xia; Li, Hao

    2013-05-01

    Genetic mapping of complex diseases to date depends on variations inside or close to the genes that perturb their activities. A strong body of evidence suggests that changes in gene expression play a key role in complex diseases and that numerous loci perturb gene expression in trans. The information in trans variants, however, has largely been ignored in the current analysis paradigm. Here we present a statistical framework for genetic mapping by utilizing collective information in both cis and trans variants. We reason that for a disease-associated gene, any genetic variation that perturbs its expression is also likely to influence the disease risk. Thus, the expression quantitative trait loci (eQTL) of the gene, which constitute a unique "genetic signature," should overlap significantly with the set of loci associated with the disease. We translate this idea into a computational algorithm (named Sherlock) to search for gene-disease associations from GWASs, taking advantage of independent eQTL data. Application of this strategy to Crohn disease and type 2 diabetes predicts a number of genes with possible disease roles, including several predictions supported by solid experimental evidence. Importantly, predicted genes are often implicated by multiple trans eQTL with moderate associations. These genes are far from any GWAS association signals and thus cannot be identified from the GWAS alone. Our approach allows analysis of association data from a new perspective and is applicable to any complex phenotype. It is readily generalizable to molecular traits other than gene expression, such as metabolites, noncoding RNAs, and epigenetic modifications.

  3. Based on Regular Expression Matching of Evaluation of the Task Performance in WSN: A Queue Theory Approach

    OpenAIRE

    2014-01-01

    Due to the limited resources of wireless sensor network, low efficiency of real-time communication scheduling, poor safety defects, and so forth, a queuing performance evaluation approach based on regular expression match is proposed, which is a method that consists of matching preprocessing phase, validation phase, and queuing model of performance evaluation phase. Firstly, the subset of related sequence is generated in preprocessing phase, guiding the validation phase distributed matching...

  4. Differences in Human Cortical Gene Expression Match the Temporal Properties of Large-Scale Functional Networks

    Science.gov (United States)

    Cioli, Claudia; Abdi, Hervé; Beaton, Derek; Burnod, Yves; Mesmoudi, Salma

    2014-01-01

    We explore the relationships between the cortex functional organization and genetic expression (as provided by the Allen Human Brain Atlas). Previous work suggests that functional cortical networks (resting state and task based) are organized as two large networks (differentiated by their preferred information processing mode) shaped like two rings. The first ring–Visual-Sensorimotor-Auditory (VSA)–comprises visual, auditory, somatosensory, and motor cortices that process real time world interactions. The second ring–Parieto-Temporo-Frontal (PTF)–comprises parietal, temporal, and frontal regions with networks dedicated to cognitive functions, emotions, biological needs, and internally driven rhythms. We found–with correspondence analysis–that the patterns of expression of the 938 genes most differentially expressed across the cortex organized the cortex into two sets of regions that match the two rings. We confirmed this result using discriminant correspondence analysis by showing that the genetic profiles of cortical regions can reliably predict to what ring these regions belong. We found that several of the proteins–coded by genes that most differentiate the rings–were involved in neuronal information processing such as ionic channels and neurotransmitter release. The systematic study of families of genes revealed specific proteins within families preferentially expressed in each ring. The results showed strong congruence between the preferential expression of subsets of genes, temporal properties of the proteins they code, and the preferred processing modes of the rings. Ionic channels and release-related proteins more expressed in the VSA ring favor temporal precision of fast evoked neural transmission (Sodium channels SCNA1, SCNB1 potassium channel KCNA1, calcium channel CACNA2D2, Synaptotagmin SYT2, Complexin CPLX1, Synaptobrevin VAMP1). Conversely, genes expressed in the PTF ring favor slower, sustained, or rhythmic activation (Sodium

  5. Differences in human cortical gene expression match the temporal properties of large-scale functional networks.

    Directory of Open Access Journals (Sweden)

    Claudia Cioli

    Full Text Available We explore the relationships between the cortex functional organization and genetic expression (as provided by the Allen Human Brain Atlas. Previous work suggests that functional cortical networks (resting state and task based are organized as two large networks (differentiated by their preferred information processing mode shaped like two rings. The first ring--Visual-Sensorimotor-Auditory (VSA--comprises visual, auditory, somatosensory, and motor cortices that process real time world interactions. The second ring--Parieto-Temporo-Frontal (PTF--comprises parietal, temporal, and frontal regions with networks dedicated to cognitive functions, emotions, biological needs, and internally driven rhythms. We found--with correspondence analysis--that the patterns of expression of the 938 genes most differentially expressed across the cortex organized the cortex into two sets of regions that match the two rings. We confirmed this result using discriminant correspondence analysis by showing that the genetic profiles of cortical regions can reliably predict to what ring these regions belong. We found that several of the proteins--coded by genes that most differentiate the rings--were involved in neuronal information processing such as ionic channels and neurotransmitter release. The systematic study of families of genes revealed specific proteins within families preferentially expressed in each ring. The results showed strong congruence between the preferential expression of subsets of genes, temporal properties of the proteins they code, and the preferred processing modes of the rings. Ionic channels and release-related proteins more expressed in the VSA ring favor temporal precision of fast evoked neural transmission (Sodium channels SCNA1, SCNB1 potassium channel KCNA1, calcium channel CACNA2D2, Synaptotagmin SYT2, Complexin CPLX1, Synaptobrevin VAMP1. Conversely, genes expressed in the PTF ring favor slower, sustained, or rhythmic activation (Sodium

  6. A genetic ensemble approach for gene-gene interaction identification

    Directory of Open Access Journals (Sweden)

    Ho Joshua WK

    2010-10-01

    Full Text Available Abstract Background It has now become clear that gene-gene interactions and gene-environment interactions are ubiquitous and fundamental mechanisms for the development of complex diseases. Though a considerable effort has been put into developing statistical models and algorithmic strategies for identifying such interactions, the accurate identification of those genetic interactions has been proven to be very challenging. Methods In this paper, we propose a new approach for identifying such gene-gene and gene-environment interactions underlying complex diseases. This is a hybrid algorithm and it combines genetic algorithm (GA and an ensemble of classifiers (called genetic ensemble. Using this approach, the original problem of SNP interaction identification is converted into a data mining problem of combinatorial feature selection. By collecting various single nucleotide polymorphisms (SNP subsets as well as environmental factors generated in multiple GA runs, patterns of gene-gene and gene-environment interactions can be extracted using a simple combinatorial ranking method. Also considered in this study is the idea of combining identification results obtained from multiple algorithms. A novel formula based on pairwise double fault is designed to quantify the degree of complementarity. Conclusions Our simulation study demonstrates that the proposed genetic ensemble algorithm has comparable identification power to Multifactor Dimensionality Reduction (MDR and is slightly better than Polymorphism Interaction Analysis (PIA, which are the two most popular methods for gene-gene interaction identification. More importantly, the identification results generated by using our genetic ensemble algorithm are highly complementary to those obtained by PIA and MDR. Experimental results from our simulation studies and real world data application also confirm the effectiveness of the proposed genetic ensemble algorithm, as well as the potential benefits of

  7. Histogram Bins Matching Approach for CBIR Based on Linear grouping for Dimensionality Reduction

    Directory of Open Access Journals (Sweden)

    H. B. Kekre

    2013-11-01

    Full Text Available This paper describes the histogram bins matching approach for CBIR. Histogram bins are reduced from 256 to 32 and 16 by linear grouping and effect of this dimensionality reduction is analyzed, compared, and evaluated. Work presented in this paper contributes in all three main phases of CBIR that are feature extraction, similarity matching and performance evaluation. Feature extraction explores the idea of histogram bins matching for three colors R, G and B. Histogram bin contents are used to represent the feature vector in three forms. First form of feature is count of pixels, and then other forms are obtained by computing the total and mean of intensities for the pixels falling in each of the histogram bins. Initially the size of the feature vector is 256 components as histogram with the all 256 bins. Further the size of the feature vector is reduced to 32 bins and then 16 bins by simple linear grouping of the bins. Feature extraction processes for each size and type of the feature vector is executed over the database of 2000 BMP images having 20 different classes. It prepares the feature vector databases as preprocessing part of this work. Similarity matching between query and database image feature vectors is carried out by means of first five orders of Minkowski distance and also with the cosine correlation distance. Same set of 200 query images are executed for all types of feature vector and for all similarity measures. Performance of all aspects addressed in this paper are evaluated using three parameters PRCP (Precision Recall Cross over Point, LS (longest string, LSRR (Length of String to Retrieve all Relevant images.

  8. a Local Adaptive Approach for Dense Stereo Matching in Architectural Scene Reconstruction

    Science.gov (United States)

    Stentoumis, C.; Grammatikopoulos, L.; Kalisperakis, I.; Petsa, E.; Karras, G.

    2013-02-01

    In recent years, a demand for 3D models of various scales and precisions has been growing for a wide range of applications; among them, cultural heritage recording is a particularly important and challenging field. We outline an automatic 3D reconstruction pipeline, mainly focusing on dense stereo-matching which relies on a hierarchical, local optimization scheme. Our matching framework consists of a combination of robust cost measures, extracted via an intuitive cost aggregation support area and set within a coarse-tofine strategy. The cost function is formulated by combining three individual costs: a cost computed on an extended census transformation of the images; the absolute difference cost, taking into account information from colour channels; and a cost based on the principal image derivatives. An efficient adaptive method of aggregating matching cost for each pixel is then applied, relying on linearly expanded cross skeleton support regions. Aggregated cost is smoothed via a 3D Gaussian function. Finally, a simple "winnertakes- all" approach extracts the disparity value with minimum cost. This keeps algorithmic complexity and system computational requirements acceptably low for high resolution images (or real-time applications), when compared to complex matching functions of global formulations. The stereo algorithm adopts a hierarchical scheme to accommodate high-resolution images and complex scenes. In a last step, a robust post-processing work-flow is applied to enhance the disparity map and, consequently, the geometric quality of the reconstructed scene. Successful results from our implementation, which combines pre-existing algorithms and novel considerations, are presented and evaluated on the Middlebury platform.

  9. Refining gene signatures: a Bayesian approach

    Directory of Open Access Journals (Sweden)

    Labbe Aurélie

    2009-12-01

    Full Text Available Abstract Background In high density arrays, the identification of relevant genes for disease classification is complicated by not only the curse of dimensionality but also the highly correlated nature of the array data. In this paper, we are interested in the question of how many and which genes should be selected for a disease class prediction. Our work consists of a Bayesian supervised statistical learning approach to refine gene signatures with a regularization which penalizes for the correlation between the variables selected. Results Our simulation results show that we can most often recover the correct subset of genes that predict the class as compared to other methods, even when accuracy and subset size remain the same. On real microarray datasets, we show that our approach can refine gene signatures to obtain either the same or better predictive performance than other existing methods with a smaller number of genes. Conclusions Our novel Bayesian approach includes a prior which penalizes highly correlated features in model selection and is able to extract key genes in the highly correlated context of microarray data. The methodology in the paper is described in the context of microarray data, but can be applied to any array data (such as micro RNA, for example as a first step towards predictive modeling of cancer pathways. A user-friendly software implementation of the method is available.

  10. The benefits of a laparoscopic approach in ileal pouch anal anastomosis formation: a single institutional retrospective case-matched experience.

    LENUS (Irish Health Repository)

    Kelly, J

    2010-06-01

    A laparoscopic approach to ileoanal pouch formation is novel. By using prospectively gathered data, laparoscopic and open restorative proctocolectomy procedures in mucosal ulcerative colitis (UC) and familial adenomatous polyposis (FAP) patients were compared using a case-matched design.

  11. Demons deformable registration of CT and cone-beam CT using an iterative intensity matching approach

    Energy Technology Data Exchange (ETDEWEB)

    Nithiananthan, Sajendra; Schafer, Sebastian; Uneri, Ali [Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21205 (United States); and others

    2011-04-15

    Purpose: A method of intensity-based deformable registration of CT and cone-beam CT (CBCT) images is described, in which intensity correction occurs simultaneously within the iterative registration process. The method preserves the speed and simplicity of the popular Demons algorithm while providing robustness and accuracy in the presence of large mismatch between CT and CBCT voxel values (''intensity''). Methods: A variant of the Demons algorithm was developed in which an estimate of the relationship between CT and CBCT intensity values for specific materials in the image is computed at each iteration based on the set of currently overlapping voxels. This tissue-specific intensity correction is then used to estimate the registration output for that iteration and the process is repeated. The robustness of the method was tested in CBCT images of a cadaveric head exhibiting a broad range of simulated intensity variations associated with x-ray scatter, object truncation, and/or errors in the reconstruction algorithm. The accuracy of CT-CBCT registration was also measured in six real cases, exhibiting deformations ranging from simple to complex during surgery or radiotherapy guided by a CBCT-capable C-arm or linear accelerator, respectively. Results: The iterative intensity matching approach was robust against all levels of intensity variation examined, including spatially varying errors in voxel value of a factor of 2 or more, as can be encountered in cases of high x-ray scatter. Registration accuracy without intensity matching degraded severely with increasing magnitude of intensity error and introduced image distortion. A single histogram match performed prior to registration alleviated some of these effects but was also prone to image distortion and was quantifiably less robust and accurate than the iterative approach. Within the six case registration accuracy study, iterative intensity matching Demons reduced mean TRE to (2.5{+-}2.8) mm

  12. Current approaches to gene regulatory network modelling

    Directory of Open Access Journals (Sweden)

    Brazma Alvis

    2007-09-01

    Full Text Available Abstract Many different approaches have been developed to model and simulate gene regulatory networks. We proposed the following categories for gene regulatory network models: network parts lists, network topology models, network control logic models, and dynamic models. Here we will describe some examples for each of these categories. We will study the topology of gene regulatory networks in yeast in more detail, comparing a direct network derived from transcription factor binding data and an indirect network derived from genome-wide expression data in mutants. Regarding the network dynamics we briefly describe discrete and continuous approaches to network modelling, then describe a hybrid model called Finite State Linear Model and demonstrate that some simple network dynamics can be simulated in this model.

  13. The impact of the Indonesian health card program: a matching estimator approach.

    Science.gov (United States)

    Johar, Meliyanni

    2009-01-01

    This study evaluates the effectiveness of a pro-poor nation-wide health card program, which provides free basic health care at public health facilities in Indonesia. To quantify the effect of the program, it departs from the traditional regression-based approach in the literature. It employs propensity score matching to reduce the selection bias due to non-random health card distribution. The setting of the program and the richness of the data set support this strategy in providing accurate estimates of the program's effect on its recipients. The results indicate that, in general, the health card program only has limited impact on the consumption of primary health care by its recipients. This finding suggests the presence of other factors counteracting the generous demand incentive.

  14. IMC-PID design based on model matching approach and closed-loop shaping.

    Science.gov (United States)

    Jin, Qi B; Liu, Q

    2014-03-01

    Motivated by the limitations of the conventional internal model control (IMC), this communication addresses the design of IMC-based PID in terms of the robust performance of the control system. The IMC controller form is obtained by solving an H-infinity problem based on the model matching approach, and the parameters are determined by closed-loop shaping. The shaping of the closed-loop transfer function is considered both for the set-point tracking and for the load disturbance rejection. The design procedure is formulated as a multi-objective optimization problem which is solved by a specific optimization algorithm. A nice feature of this design method is that it permits a clear tradeoff between robustness and performance. Simulation examples show that the proposed method is effective and has a wide applicability.

  15. IMC-PID design based on model matching approach and closed-loop shaping.

    Science.gov (United States)

    Jin, Qi B; Liu, Q

    2014-03-01

    Motivated by the limitations of the conventional internal model control (IMC), this communication addresses the design of IMC-based PID in terms of the robust performance of the control system. The IMC controller form is obtained by solving an H-infinity problem based on the model matching approach, and the parameters are determined by closed-loop shaping. The shaping of the closed-loop transfer function is considered both for the set-point tracking and for the load disturbance rejection. The design procedure is formulated as a multi-objective optimization problem which is solved by a specific optimization algorithm. A nice feature of this design method is that it permits a clear tradeoff between robustness and performance. Simulation examples show that the proposed method is effective and has a wide applicability. PMID:24280534

  16. A Vocabulary Approach to Partial Streamline Matching and Exploratory Flow Visualization.

    Science.gov (United States)

    Tao, Jun; Wang, Chaoli; Shene, Ching-Kuang; Shaw, Raymond A

    2016-05-01

    Measuring the similarity of integral curves is fundamental to many important flow data analysis and visualization tasks such as feature detection, pattern querying, streamline clustering, and hierarchical exploration. In this paper, we introduce FlowString, a novel vocabulary approach that extracts shape invariant features from streamlines and utilizes a string-based method for exploratory streamline analysis and visualization. Our solution first resamples streamlines by considering their local feature scales. We then classify resampled points along streamlines based on the shape similarity around their local neighborhoods. We encode each streamline into a string of well-selected shape characters, from which we construct meaningful words for querying and retrieval. A unique feature of our approach is that it captures intrinsic streamline similarity that is invariant under translation, rotation and scaling. We design an intuitive interface and user interactions to support flexible querying, allowing exact and approximate searches for partial streamline matching. Users can perform queries at either the character level or the word level, and define their own characters or words conveniently for customized search. We demonstrate the effectiveness of FlowString with several flow field data sets of different sizes and characteristics. We also extend FlowString to handle multiple data sets and perform an empirical expert evaluation to confirm the usefulness of this approach. PMID:27045908

  17. Generalized Coupled Dictionary Learning Approach With Applications to Cross-Modal Matching.

    Science.gov (United States)

    Mandal, Devraj; Biswas, Soma

    2016-08-01

    Coupled dictionary learning (CDL) has recently emerged as a powerful technique with wide variety of applications ranging from image synthesis to classification tasks. In this paper, we extend the existing CDL approaches in two aspects to make them more suitable for the task of cross-modal matching. Data coming from different modalities may or may not be paired. For example, for image-text retrieval problem, 100 images of a class are available as opposed to only 50 samples of text data for training. Current CDL approaches are not designed to handle such scenarios, where classes of data points in one modality correspond to classes of data points in the other modality. Given the data from the two modalities, first two dictionaries are learnt for the respective modalities, so that the data have a sparse representation with respect to their own dictionaries. Then, the sparse coefficients from the two modalities are transformed in such a manner that data from the same class are maximally correlated, while that from different classes have very less correlation. This way of modeling the coupling between the sparse representations of the two modalities makes this approach work seamlessly for paired as well as unpaired data. The discriminative coupling term also makes the approach better suited for classification tasks. Experiments on different publicly available cross-modal data sets, namely, CUHK photosketch face data set, HFB visible and near-infrared facial images data set, IXMAS multiview action recognition data set, wiki image and text data set and Multiple Features data set, show that this generalized CDL approach performs better than the state-of-the-art for both paired as well as unpaired data. PMID:27295672

  18. Gene expression in archived newborn blood spots distinguishes infants who will later develop cerebral palsy from matched controls

    OpenAIRE

    Ho, Nhan Thi; Furge, Kyle; Fu, Wenjiang; Busik, Julia; Khoo, Sok Kean; Lu, Qing; Lenski, Madeleine; Wirth, Julia; Hurvitz, Edward; Dodge, Nancy; Resau, James; PANETH, Nigel

    2012-01-01

    Background Gene expression in archived newborn blood spots remaining from newborn screening may reflect pathophysiological disturbances useful in understanding the etiology of cerebral palsy (CP). Methods We quantified the expression of gene sets representing four physiological pathways hypothesized to contribute to CP in archived unfrozen residual newborn blood spot specimens from 53 children with CP and 53 age, gender, and gestational-age–matched controls. We selected four empirical and thr...

  19. Gene expression profiles from formalin fixed paraffin embedded breast cancer tissue are largely comparable to fresh frozen matched tissue.

    Directory of Open Access Journals (Sweden)

    Lorenza Mittempergher

    Full Text Available BACKGROUND AND METHODS: Formalin Fixed Paraffin Embedded (FFPE samples represent a valuable resource for cancer research. However, the discovery and development of new cancer biomarkers often requires fresh frozen (FF samples. Recently, the Whole Genome (WG DASL (cDNA-mediated Annealing, Selection, extension and Ligation assay was specifically developed to profile FFPE tissue. However, a thorough comparison of data generated from FFPE RNA and Fresh Frozen (FF RNA using this platform is lacking. To this end we profiled, in duplicate, 20 FFPE tissues and 20 matched FF tissues and evaluated the concordance of the DASL results from FFPE and matched FF material. METHODOLOGY AND PRINCIPAL FINDINGS: We show that after proper normalization, all FFPE and FF pairs exhibit a high level of similarity (Pearson correlation >0.7, significantly larger than the similarity between non-paired samples. Interestingly, the probes showing the highest correlation had a higher percentage G/C content and were enriched for cell cycle genes. Predictions of gene expression signatures developed on frozen material (Intrinsic subtype, Genomic Grade Index, 70 gene signature showed a high level of concordance between FFPE and FF matched pairs. Interestingly, predictions based on a 60 gene DASL list (best match with the 70 gene signature showed very high concordance with the MammaPrint® results. CONCLUSIONS AND SIGNIFICANCE: We demonstrate that data generated from FFPE material with the DASL assay, if properly processed, are comparable to data extracted from the FF counterpart. Specifically, gene expression profiles for a known set of prognostic genes for a specific disease are highly comparable between two conditions. This opens up the possibility of using both FFPE and FF material in gene expressions analyses, leading to a vast increase in the potential resources available for cancer research.

  20. Gene therapy in glaucoma-3: Therapeutic approaches

    Directory of Open Access Journals (Sweden)

    Mohamed Abdel-Monem Soliman Mahdy

    2010-01-01

    Recently, several promising genetic therapeutic approaches had been investigated. Some are either used to stop apoptosis and halt further glaucomatous damage, wound healing modulating effect or long lasting intraocular pressure lowering effects than the conventional commercially available antiglaucoma medications. Method of Literature Search The literature was searched on the Medline database using the PubMed interface. The key words for search were glaucoma, gene therapy, and genetic diagnosis of glaucoma.

  1. Log-Spiral Keypoint: A Robust Approach toward Image Patch Matching

    OpenAIRE

    Kangho Paek; Min Yao; Zhongwei Liu; Hun Kim

    2015-01-01

    Matching of keypoints across image patches forms the basis of computer vision applications, such as object detection, recognition, and tracking in real-world images. Most of keypoint methods are mainly used to match the high-resolution images, which always utilize an image pyramid for multiscale keypoint detection. In this paper, we propose a novel keypoint method to improve the matching performance of image patches with the low-resolution and small size. The location, scale, and orientation ...

  2. Assessing the hydrologic alteration of the Yangtze River using the histogram matching approach

    Science.gov (United States)

    Huang, F.; Zhang, N.; Guo, L. D.; Xia, Z. Q.

    2016-08-01

    Hydrologic changes of the Yangtze River, an important river with abundant water resources in China, were investigated using the Histogram Matching Approach. Daily streamflow data spanning the time interval from 1955 to 2013 was collected from Yichang and Datong stations, which monitor the hydrologic processes of the upper and lower reach of the Yangtze River, respectively. The Gezhouba Dam, the first dam constructed at the main stream of the Yangtze River, started operations in 1981. 1981 was used to differentiate the pre-dam (1955-1980) and post-dam (1981-2013) hydrologic regimes. The hydrologic regime was quantified by the Indicators of Hydrologic Alteration. The overall alteration degree of the upper Yangtze River was 31% and the alteration degree of every hydrologic indicator ranged from 10% to 81%. Only 1, 5 and 26 hydrologic indicators were altered at high, moderate and low degrees, respectively. The overall alteration degree of the lower Yangtze River was 30%, and the alteration degree of every hydrologic indicator ranged from 8% to 49%. No high alteration degree was detected at the Datong station. Ten hydrologic indicators were altered at moderate degrees and 22 hydrologic indicators were altered at low degrees. Significant increases could be observed for the low-flow relevant indicators, including the monthly flow from January-March, the annual minimum 1, 3, 7, 30 and 90-day flows, and the base flow index.

  3. Based on Regular Expression Matching of Evaluation of the Task Performance in WSN: A Queue Theory Approach

    Directory of Open Access Journals (Sweden)

    Jie Wang

    2014-01-01

    Full Text Available Due to the limited resources of wireless sensor network, low efficiency of real-time communication scheduling, poor safety defects, and so forth, a queuing performance evaluation approach based on regular expression match is proposed, which is a method that consists of matching preprocessing phase, validation phase, and queuing model of performance evaluation phase. Firstly, the subset of related sequence is generated in preprocessing phase, guiding the validation phase distributed matching. Secondly, in the validation phase, the subset of features clustering, the compressed matching table is more convenient for distributed parallel matching. Finally, based on the queuing model, the sensor networks of task scheduling dynamic performance are evaluated. Experiments show that our approach ensures accurate matching and computational efficiency of more than 70%; it not only effectively detects data packets and access control, but also uses queuing method to determine the parameters of task scheduling in wireless sensor networks. The method for medium scale or large scale distributed wireless node has a good applicability.

  4. New algorithmic approaches to protein spot detection and pattern matching in two-dimensional electrophoresis gel databases.

    Science.gov (United States)

    Pleissner, K P; Hoffmann, F; Kriegel, K; Wenk, C; Wegner, S; Sahlström, A; Oswald, H; Alt, H; Fleck, E

    1999-01-01

    Protein spot identification in two-dimensional electrophoresis gels can be supported by the comparison of gel images accessible in different World Wide Web two-dimensional electrophoresis (2-DE) gel protein databases. The comparison may be performed either by visual cross-matching between gel images or by automatic recognition of similar protein spot patterns. A prerequisite for the automatic point pattern matching approach is the detection of protein spots yielding the x(s),y(s) coordinates and integrated spot intensities i(s). For this purpose an algorithm is developed based on a combination of hierarchical watershed transformation and feature extraction methods. This approach reduces the strong over-segmentation of spot regions normally produced by watershed transformation. Measures for the ellipticity and curvature are determined as features of spot regions. The resulting spot lists containing x(s),y(s),i(s)-triplets are calculated for a source as well as for a target gel image accessible in 2-DE gel protein databases. After spot detection a matching procedure is applied. Both the matching of a local pattern vs. a full 2-DE gel image and the global matching between full images are discussed. Preset slope and length tolerances of pattern edges serve as matching criteria. The local matching algorithm relies on a data structure derived from the incremental Delaunay triangulation of a point set and a two-step hashing technique. For the incremental construction of triangles the spot intensities are considered in decreasing order. The algorithm needs neither landmarks nor an a priori image alignment. A graphical user interface for spot detection and gel matching is written in the Java programming language for the Internet. The software package called CAROL (http://gelmatching.inf.fu-berlin.de) is realized in a client-server architecture.

  5. Log-Spiral Keypoint: A Robust Approach toward Image Patch Matching

    Science.gov (United States)

    Paek, Kangho; Liu, Zhongwei; Kim, Hun

    2015-01-01

    Matching of keypoints across image patches forms the basis of computer vision applications, such as object detection, recognition, and tracking in real-world images. Most of keypoint methods are mainly used to match the high-resolution images, which always utilize an image pyramid for multiscale keypoint detection. In this paper, we propose a novel keypoint method to improve the matching performance of image patches with the low-resolution and small size. The location, scale, and orientation of keypoints are directly estimated from an original image patch using a Log-Spiral sampling pattern for keypoint detection without consideration of image pyramid. A Log-Spiral sampling pattern for keypoint description and two bit-generated functions are designed for generating a binary descriptor. Extensive experiments show that the proposed method is more effective and robust than existing binary-based methods for image patch matching. PMID:26074952

  6. Log-Spiral Keypoint: A Robust Approach toward Image Patch Matching

    Directory of Open Access Journals (Sweden)

    Kangho Paek

    2015-01-01

    Full Text Available Matching of keypoints across image patches forms the basis of computer vision applications, such as object detection, recognition, and tracking in real-world images. Most of keypoint methods are mainly used to match the high-resolution images, which always utilize an image pyramid for multiscale keypoint detection. In this paper, we propose a novel keypoint method to improve the matching performance of image patches with the low-resolution and small size. The location, scale, and orientation of keypoints are directly estimated from an original image patch using a Log-Spiral sampling pattern for keypoint detection without consideration of image pyramid. A Log-Spiral sampling pattern for keypoint description and two bit-generated functions are designed for generating a binary descriptor. Extensive experiments show that the proposed method is more effective and robust than existing binary-based methods for image patch matching.

  7. REVERSE DESIGN APPROACH FOR MECHANISM TRAJECTORY BASED ON CODE-CHAINS MATCHING

    Institute of Scientific and Technical Information of China (English)

    ZHANG Shuyou; YI Guodong; XU Xiaofeng

    2007-01-01

    Aiming at the problem of reverse-design of mechanism, a method based on the matching of trajectory code-chains is presented. The motion trajectory of mechanism is described with code-chain,which is normalized to simplify the operation of geometric transformation. The geometric transformation formulas of scale, mirror and rotation for trajectory code-chain are defined, and the reverse design for mechanism trajectory is realized through the analysis and solution of similarity matching between the desired trajectory and the predefined trajectory. The algorithm program and prototype system of reverse design for mechanism trajectory are developed. Application samples show that the method can break the restriction of trajectory patterns in matching, meet the demand of partial matching, and overcome the influence of geometric transformation of trajectory on the reverse design for mechanism.

  8. Tratamiento de imágenes, extracción de características y "matching" en plataformas Android

    OpenAIRE

    Ortega Olivas, Rocío

    2013-01-01

    En este proyecto se estudiará cómo de eficientes son los dispositivos móviles Android para el procesamiento de imágenes, así como una nueva técnica para llevar a cabo el matching entre imágenes (utilizando Teoría de Grafos). Se tratarán conceptos básicos de tratamiento de imágenes, repasando qué es un descriptor de imagen, cuáles son los más utilizados y cómo trabajar con ellos en proyectos de desarrollo, junto con otras funciones típicas del tratamiento de imágenes. Por otro lado, se estudia...

  9. Handbook of Soccer Match Analysis: A Systematic Approach to Improving Performance

    OpenAIRE

    Christopher Carling; Mark Williams, A; Thomas Reilly

    2006-01-01

    DESCRIPTION This book addresses and appropriately explains the soccer match analysis, looks at the very latest in match analysis research, and at the innovative technologies used by professional clubs. This handbook is also bridging the gap between research, theory and practice. The methods in it can be used by coaches, sport scientists and fitness coaches to improve: styles of play, technical ability and physical fitness; objective feedback to players; the development of specific training ro...

  10. A gene sets approach for identifying prognostic gene signatures for outcome prediction

    OpenAIRE

    Kim Yong Sung; Kim Seon-Young

    2008-01-01

    Abstract Background Gene expression profiling is a promising approach to better estimate patient prognosis; however, there are still unresolved problems, including little overlap among similarly developed gene sets and poor performance of a developed gene set in other datasets. Results We applied a gene sets approach to develop a prognostic gene set from multiple gene expression datasets. By analyzing 12 independent breast cancer gene expression datasets comprising 1,756 tissues with 2,411 pr...

  11. A scientific approach to building training with particular reference to basketball – match analysis

    Directory of Open Access Journals (Sweden)

    Riccardo Izzo

    2010-12-01

    Full Text Available Modern sports rely more and more on match analysis for a better understanding of the atheletes interactions as different systems – as individuals, or teams. Not long ago, the data registration was accomplished manualy, empiricaly, through direct observation of the game; today, the possibility of filming the game and through a software to analyse step by step – evend during the action, provides a lot of extra information usefull both the coach and the athletes. The present study tries to present these positive aspects of modern game (match analysi; it must be seen as a useful support for the coach, able to help him to develop his work more rapidly and with greater professional precision. In our opinion, match analysis should be considered more as a philosophy contained in a method that, while certainly comprising several elements, should nevertheless be analysed on a deeper and more professional level.

  12. Combining Generalized Phase Contrast with matched filtering into a versatile beam shaping approach

    DEFF Research Database (Denmark)

    Glückstad, Jesper; Palima, Darwin

    2010-01-01

    We adapt concepts from matched filtering to propose a method for generating reconfigurable multiple beams. Combined with the Generalized Phase Contrast (GPC) technique, the proposed method coined mGPC can yield dynamically reconfigurable optical beam arrays with high light efficiency for optical ...... manipulation, high-speed sorting and other parallel spatial light applications [1].......We adapt concepts from matched filtering to propose a method for generating reconfigurable multiple beams. Combined with the Generalized Phase Contrast (GPC) technique, the proposed method coined mGPC can yield dynamically reconfigurable optical beam arrays with high light efficiency for optical...

  13. Identifying the greatest team and captain - A complex network approach to cricket matches

    OpenAIRE

    Mukherjee, Satyam

    2012-01-01

    We consider all Test matches played between 1877 and 2010 and One Day International (ODI) matches played between 1971 and 2010. We form directed and weighted networks of teams and also of their captains. The success of a team (or captain) is determined by the 'quality' of wins and not on the number of wins alone. We apply the diffusion based PageRank algorithm on the networks to access the importance of wins and rank the teams and captains respectively. Our analysis identifies {\\it Australia}...

  14. Translational Approaches towards Cancer Gene Therapy: Hurdles and Hopes

    OpenAIRE

    Yadollah Omidi; Jaleh Barar

    2012-01-01

    Introduction: Of the cancer gene therapy approaches, gene silencing, suicide/apoptosis inducing gene therapy, immunogene therapy and targeted gene therapy are deemed to sub­stantially control the biological consequences of genomic changes in cancerous cells. Thus, a large number of clinical trials have been conducted against various malignancies. In this review, we will discuss recent translational progresses of gene and cell therapy of cancer. Methods: Essential information on gene therapy o...

  15. Labor Tax Reform and Equilibrium Unemployment : A Search and Matching Approach

    NARCIS (Netherlands)

    Heijdra, B.J.; Ligthart, J.E.

    2004-01-01

    The paper studies simple strategies of labor tax reform in a search and matching model of the labor market featuring endogenous labor supply.Changing the composition of the tax wedge|that is, reducing a payroll tax and increasing a progressive wage tax such that the marginal tax wedge remains unaffe

  16. Perfecting the Frankenstein Approach: Improved asymptotically matched initial data for non-spinning black hole binaries

    Science.gov (United States)

    Yunes, Nicolas; Tichy, Wolfgang

    2006-04-01

    The accuracy of gravitational wave templates produced by numerical simulations is partially determined by the initial data chosen. A promising method to construct accurate data employs asymptotic matching to construct an approximate global 4-metric. In this talk, we will apply this method to a binary system of non-spinning black holes and discuss improvements. A global metric can be constructed by asymptotically matching two tidally perturbed Schwarzschild metrics in isotropic coordinates valid near each hole to an ADMTT post-Newtonian metric valid far from them. As a result, adjacent metrics agree in the matching region up to uncontrolled remainders in the approximations. We build a smooth global 4-metric with transition functions, carefully constructed to avoid introducing errors larger than those in the approximations. The main improvement arises by using metrics in similar coordinates before performing the matching. This similarity leads to adjacent metrics that are similar even near the horizons, thus allowing for a smoother transition and constraint violations. We also construct a map that takes this metric to Kerr-Schild coordinates near each hole.

  17. Pigeons ("Columba Livia") Approach Nash Equilibrium in Experimental Matching Pennies Competitions

    Science.gov (United States)

    Sanabria, Federico; Thrailkill, Eric

    2009-01-01

    The game of Matching Pennies (MP), a simplified version of the more popular Rock, Papers, Scissors, schematically represents competitions between organisms with incentives to predict each other's behavior. Optimal performance in iterated MP competitions involves the production of random choice patterns and the detection of nonrandomness in the…

  18. Labor tax reform and equilibrium unemployment : a search and matching approach

    NARCIS (Netherlands)

    Heijdra, Ben J.; Ligthart, Jenny E.

    2004-01-01

    The paper studies simple strategies of labor tax reform in a search and matching model of the labor market featuring endogenous labor supply. Changing the composition of the tax wedge---that is, reducing a payroll tax and increasing a progressive wage tax such that the marginal tax wedge remains una

  19. Bayesian peak tracking: A novel probabilistic approach to match GCxGC chromatograms.

    Science.gov (United States)

    Barcaru, Andrei; Derks, Eduard; Vivó-Truyols, Gabriel

    2016-10-12

    A novel peak tracking method based on Bayesian statistics is proposed. The method consists of assigning (i.e. tracking) peaks from two GCxGC-FID data sets of the same sample taken in different conditions. Opposed to traditional (i.e. deterministic) peak tracking algorithms, in which the assignment problem is solved with a unique solution, the proposed algorithm is probabilistic. In other words, we quantify the uncertainty of matching two peaks without excluding other possible candidates, ranking the possible peak assignments regarding their posterior probability. This represents a significant advantage over existing deterministic methods. Two algorithms are presented: the blind peak tracking algorithm (BPTA) and peak table matching algorithm (PTMA). PTMA method was able to assign correctly 78% of a selection of peaks in a GCxGC-FID chromatogram of a diesel sample and proved to be extremely fast. PMID:27662758

  20. Offering a New Approach for Approximate Pattern Matching in Example-Based Machine Translation

    Directory of Open Access Journals (Sweden)

    Reza Akbari

    2015-01-01

    Full Text Available In this article, a new model is proposed in order to measure the degree of similarity between two sentences in machine translation based on example. The proposed model has applied genetic algorithm beside a new fitness function which is based on semantic load matching between the two sentences. Here, verbs are considered as the heart of a sentence because they are the main part of a sentence and carry the major part of the semantic load in the sentence; therefore more attention is paid to the verbs in the fitness function. It is noteworthy that the proposed model is largely dependent on the verbal part and the extracted synonyms from WordNet as well as the arrangement of words. The results are promising by precision and recall, indicating that the proposed method improves the quality of the retrieved matched sentences.

  1. Tailoring Science Outreach through E-Matching Using a Community-Based Participatory Approach

    OpenAIRE

    Rumala, Bernice B.; Jack Hidary; Linda Ewool; Christopher Emdin; Ted Scovell

    2011-01-01

    In an effort to increase science exposure for pre-college (K-12) students and as part of the science education reform agenda, many biomedical research institutions have established university-community partnerships. Typically, these science outreach programs consist of pre-structured, generic exposure for students, with little community engagement. However, the use of a medium that is accessible to both teachers and scientists, electronic web-based matchmaking (E-matching) provides an opportu...

  2. Matching Matters!

    CERN Document Server

    Freitas, Ayres; Plehn, Tilman

    2016-01-01

    Effective Lagrangians are a useful tool for a data-driven approach to physics beyond the Standard Model at the LHC. However, for the new physics scales accessible at the LHC, the effective operator expansion is only relatively slowly converging at best. For tree-level processes, it has been found that the agreement between the effective Lagrangian and a range of UV-complete models depends sensitively on the appropriate definition of the matching. We extend this analysis to the one-loop level, which is relevant for electroweak precision data and Higgs decay to photons. We show that near the scale of electroweak symmetry breaking the validity of the effective theory description can be systematically improved through an appropriate matching procedure. In particular, we find a significant increase in accuracy when including suitable terms suppressed by the Higgs vacuum expectation value in the matching.

  3. Gene-based Association Approach Identify Genes Across Stress Traits in Fruit Flies

    DEFF Research Database (Denmark)

    Rohde, Palle Duun; Edwards, Stefan McKinnon; Sarup, Pernille Merete;

    approach grouping variants accordingly to gene position, thus lowering the number of statistical tests performed and increasing the probability of identifying genes with small to moderate effects. Using this approach we identify numerous genes associated with different types of stresses in Drosophila...

  4. Meeting Your Match: How Attractiveness Similarity Affects Approach Behavior in Mixed-Sex Dyads

    NARCIS (Netherlands)

    Straaten, I. van; Engels, R.C.M.E.; Finkenauer, C.; Holland, R.W.

    2009-01-01

    This experimental study investigated approach behavior toward opposite-sex others of similar versus dissimilar physical attractiveness. Furthermore, it tested the moderating effects of sex. Single participants interacted with confederates of high and low attractiveness. Observers rated their behavio

  5. Contemporary Approaches for Identifying Rare Bone Disease Causing Genes

    OpenAIRE

    Farber, Charles R; Clemens, Thomas L.

    2013-01-01

    Recent improvements in the speed and accuracy of DNA sequencing, together with increasingly sophisticated mathematical approaches for annotating gene networks, have revolutionized the field of human genetics and made these once time consuming approaches assessable to most investigators. In the field of bone research, a particularly active area of gene discovery has occurred in patients with rare bone disorders such as osteogenesis imperfecta (OI) that are caused by mutations in single genes. ...

  6. A Template Matching Approach to Classification of QAM Modulation using Genetic Algorithm

    Directory of Open Access Journals (Sweden)

    Negar ahmadi

    2009-11-01

    Full Text Available The automatic recognition of the modulation format of a detected signal, the intermediate step between signal detection and demodulation, is a major task of an intelligent receiver, with various civilian and military applications. Obviously, with no knowledge of the transmitted data and many unknown parameters at the receiver, such as the signal power, carrier frequency and phase offsets, timing information, etc., blind identification of the modulation is a difficult task. This becomes even more challenging in real-world. In this paper modulation classification for QAM is performed by Genetic Algorithm followed by Template matching, considering the constellation of the received signal. In addition this classification finds the decision boundary of the signal which is critical information for bit detection. I have proposed and implemented a technique that casts modulation recognition into shape recognition. Constellation diagram is a traditional and powerful tool for design and evaluation of digital modulations. The simulation results show the capability of this method for modulation classification with high accuracy and appropriate convergence in the presence of noise.

  7. Gene therapy approaches for spinal cord injury

    Science.gov (United States)

    Bright, Corinne

    As the biomedical engineering field expands, combination technologies are demonstrating enormous potential for treating human disease. In particular, intersections between the rapidly developing fields of gene therapy and tissue engineering hold promise to achieve tissue regeneration. Nonviral gene therapy uses plasmid DNA to deliver therapeutic proteins in vivo for extended periods of time. Tissue engineering employs biomedical materials, such as polymers, to support the regrowth of injured tissue. In this thesis, a combination strategy to deliver genes and drugs in a polymeric scaffold was applied to a spinal cord injury model. In order to develop a platform technology to treat spinal cord injury, several nonviral gene delivery systems and polymeric scaffolds were evaluated in vitro and in vivo. Nonviral vector trafficking was evaluated in primary neuronal culture to develop an understanding of the barriers to gene transfer in neurons and their supporting glia. Although the most efficient gene carrier in vitro differed from the optimal gene carrier in vivo, confocal and electron microscopy of these nonviral vectors provided insights into the interaction of these vectors with the nucleus. A novel pathway for delivering nanoparticles into the nuclei of neurons and Schwann cells via vesicle trafficking was observed in this study. Reporter gene expression levels were evaluated after direct and remote delivery to the spinal cord, and the optimal nonviral vector, dose, and delivery strategy were applied to deliver the gene encoding the basic fibroblast growth factor (bFGF) to the spinal cord. An injectable and biocompatible gel, composed of the amphiphillic polymer poly(ethylene glycol)-poly(epsilon-caprolactone)-poly(ethylene glycol) (PEG-PCL-PEG) was evaluated as a drug and gene delivery system in vitro, and combined with the optimized nonviral gene delivery system to treat spinal cord injury. Plasmid DNA encoding the bFGF gene and the therapeutic NEP1--40 peptide

  8. Match filtering approach for signal acquisition in radio-pulsar navigation

    NARCIS (Netherlands)

    Heusdens, R.; Engelen, S.; Buist, P.J.; Noroozi, A.; Sundaramoorthy, P.P.; Verhoeven, C.J.M.; Bentum, M.; Gill, E.K.A.

    2012-01-01

    Pulsars with their periodic pulses and known positions are ideal beacons for navigation. The challenge, however, is the detection of the very weak pulsar signals that are submerged in noise. Radio based approaches allow the use of advanced techniques and methods for the detection and acquisition of

  9. AnyExpress: Integrated toolkit for analysis of cross-platform gene expression data using a fast interval matching algorithm

    Directory of Open Access Journals (Sweden)

    Jung Hyunchul

    2011-03-01

    Full Text Available Abstract Background Cross-platform analysis of gene express data requires multiple, intricate processes at different layers with various platforms. However, existing tools handle only a single platform and are not flexible enough to support custom changes, which arise from the new statistical methods, updated versions of reference data, and better platforms released every month or year. Current tools are so tightly coupled with reference information, such as reference genome, transcriptome database, and SNP, which are often erroneous or outdated, that the output results are incorrect and misleading. Results We developed AnyExpress, a software package that combines cross-platform gene expression data using a fast interval-matching algorithm. Supported platforms include next-generation-sequencing technology, microarray, SAGE, MPSS, and more. Users can define custom target transcriptome database references for probe/read mapping in any species, as well as criteria to remove undesirable probes/reads. AnyExpress offers scalable processing features such as binding, normalization, and summarization that are not present in existing software tools. As a case study, we applied AnyExpress to published Affymetrix microarray and Illumina NGS RNA-Seq data from human kidney and liver. The mean of within-platform correlation coefficient was 0.98 for within-platform samples in kidney and liver, respectively. The mean of cross-platform correlation coefficients was 0.73. These results confirmed those of the original and secondary studies. Applying filtering produced higher agreement between microarray and NGS, according to an agreement index calculated from differentially expressed genes. Conclusion AnyExpress can combine cross-platform gene expression data, process data from both open- and closed-platforms, select a custom target reference, filter out undesirable probes or reads based on custom-defined biological features, and perform quantile-normalization with

  10. GeneYenta: a phenotype-based rare disease case matching tool based on online dating algorithms for the acceleration of exome interpretation.

    Science.gov (United States)

    Gottlieb, Michael M; Arenillas, David J; Maithripala, Savanie; Maurer, Zachary D; Tarailo Graovac, Maja; Armstrong, Linlea; Patel, Millan; van Karnebeek, Clara; Wasserman, Wyeth W

    2015-04-01

    Advances in next-generation sequencing (NGS) technologies have helped reveal causal variants for genetic diseases. In order to establish causality, it is often necessary to compare genomes of unrelated individuals with similar disease phenotypes to identify common disrupted genes. When working with cases of rare genetic disorders, finding similar individuals can be extremely difficult. We introduce a web tool, GeneYenta, which facilitates the matchmaking process, allowing clinicians to coordinate detailed comparisons for phenotypically similar cases. Importantly, the system is focused on phenotype annotation, with explicit limitations on highly confidential data that create barriers to participation. The procedure for matching of patient phenotypes, inspired by online dating services, uses an ontology-based semantic case matching algorithm with attribute weighting. We evaluate the capacity of the system using a curated reference data set and 19 clinician entered cases comparing four matching algorithms. We find that the inclusion of clinician weights can augment phenotype matching. PMID:25703386

  11. GeneYenta: a phenotype-based rare disease case matching tool based on online dating algorithms for the acceleration of exome interpretation.

    Science.gov (United States)

    Gottlieb, Michael M; Arenillas, David J; Maithripala, Savanie; Maurer, Zachary D; Tarailo Graovac, Maja; Armstrong, Linlea; Patel, Millan; van Karnebeek, Clara; Wasserman, Wyeth W

    2015-04-01

    Advances in next-generation sequencing (NGS) technologies have helped reveal causal variants for genetic diseases. In order to establish causality, it is often necessary to compare genomes of unrelated individuals with similar disease phenotypes to identify common disrupted genes. When working with cases of rare genetic disorders, finding similar individuals can be extremely difficult. We introduce a web tool, GeneYenta, which facilitates the matchmaking process, allowing clinicians to coordinate detailed comparisons for phenotypically similar cases. Importantly, the system is focused on phenotype annotation, with explicit limitations on highly confidential data that create barriers to participation. The procedure for matching of patient phenotypes, inspired by online dating services, uses an ontology-based semantic case matching algorithm with attribute weighting. We evaluate the capacity of the system using a curated reference data set and 19 clinician entered cases comparing four matching algorithms. We find that the inclusion of clinician weights can augment phenotype matching.

  12. A stochastic approach to multi-gene expression dynamics

    International Nuclear Information System (INIS)

    In the last years, tens of thousands gene expression profiles for cells of several organisms have been monitored. Gene expression is a complex transcriptional process where mRNA molecules are translated into proteins, which control most of the cell functions. In this process, the correlation among genes is crucial to determine the specific functions of genes. Here, we propose a novel multi-dimensional stochastic approach to deal with the gene correlation phenomena. Interestingly, our stochastic framework suggests that the study of the gene correlation requires only one theoretical assumption-Markov property-and the experimental transition probability, which characterizes the gene correlation system. Finally, a gene expression experiment is proposed for future applications of the model

  13. Meeting your match: how attractiveness similarity affects approach behavior in mixed-sex dyads.

    Science.gov (United States)

    van Straaten, Ischa; Engels, Rutger C M E; Finkenauer, Catrin; Holland, Rob W

    2009-06-01

    This experimental study investigated approach behavior toward opposite-sex others of similar versus dissimilar physical attractiveness. Furthermore, it tested the moderating effects of sex. Single participants interacted with confederates of high and low attractiveness. Observers rated their behavior in terms of relational investment (i.e., behavioral efforts related to the improvement of interaction fluency, communication of positive interpersonal affect, and positive self-presentation). As expected, men displayed more relational investment behavior if their own physical attractiveness was similar to that of the confederate. For women, no effects of attractiveness similarity on relational investment behavior were found. Results are discussed in the light of positive assortative mating, preferences for physically attractive mates, and sex differences in attraction-related interpersonal behaviors. PMID:19336540

  14. Producer-decomposer matching in a simple model ecosystem: A network coevolutionary approach to ecosystem organization

    International Nuclear Information System (INIS)

    The present not is concerned with how the ecosystem maintains its energy and matter processes, and how those processes change throughout ecological and geological time, or how the constituent biota of an ecosystem maintain their life, and how ecological (species) succession and biological evolution proceed within an ecosystem. To advance further Tansky's (1976) approach to ecosystem organization, which investigated the characteristic properties of the developmental process of a model ecosystem, by applying Margalef's (1968) maximum maturity principle to derive its long term change, we seek a course for deriving the macroscopic trends along the organization process of an ecosystem as a consequence of the interactions among its biotic components and their modification of ecological traits. Using a simple ecosystem model consisting of four aggregated components (open-quotes compartmentsclose quotes) connected by nutrient flows, we investigate how a change in the value of a parameter alters the network pattern of flows and stocks, even causing a change in the value of another parameter, which in turn brings about further change in the network pattern and values of some (possible original) parameters. The continuation of this chain reaction involving feedbacks constitutes a possible mechanism for the open-quotes coevolutionclose quotes or open-quotes matchingclose quotes among flows, stocks, and parameters

  15. A detection of the integrated Sachs-Wolfe imprint of cosmic superstructures using a matched-filter approach

    CERN Document Server

    Nadathur, Seshadri

    2016-01-01

    We present a new method for detection of the integrated Sachs-Wolfe (ISW) imprints of cosmic superstructures on the cosmic microwave background, based on a matched filtering approach. The expected signal-to-noise ratio for this method is comparable to that obtained from the full cross-correlation, and unlike other stacked filtering techniques it is not subject to an a posteriori bias. We apply this method to Planck CMB data using voids and superclusters identified in the CMASS galaxy data from the Sloan Digital Sky Survey Data Release 12, and measure the ISW amplitude to be $A_\\mathrm{ISW}=1.64\\pm0.53$ relative to the $\\Lambda$CDM expectation, corresponding to a $3.1\\sigma$ detection. In contrast to some previous measurements of the ISW effect of superstructures, our result is in agreement with the $\\Lambda$CDM model.

  16. A Detection of the Integrated Sachs–Wolfe Imprint of Cosmic Superstructures Using a Matched-filter Approach

    Science.gov (United States)

    Nadathur, Seshadri; Crittenden, Robert

    2016-10-01

    We present a new method for detection of the integrated Sachs–Wolfe (ISW) imprints of cosmic superstructures on the cosmic microwave background (CMB), based on a matched-filtering approach. The expected signal-to-noise ratio for this method is comparable to that obtained from the full cross-correlation, and unlike other stacked filtering techniques it is not subject to an a posteriori bias. We apply this method to Planck CMB data using voids and superclusters identified in the CMASS galaxy data from the Sloan Digital Sky Survey Data Release 12, and measure the ISW amplitude to be {A}{ISW}=1.64+/- 0.53 relative to the ΛCDM expectation, corresponding to a 3.1σ detection. In contrast to some previous measurements of the ISW effect of superstructures, our result is in agreement with the ΛCDM model.

  17. Multiobjective Optimization Methodology A Jumping Gene Approach

    CERN Document Server

    Tang, KS

    2012-01-01

    Complex design problems are often governed by a number of performance merits. These markers gauge how good the design is going to be, but can conflict with the performance requirements that must be met. The challenge is reconciling these two requirements. This book introduces a newly developed jumping gene algorithm, designed to address the multi-functional objectives problem and supplies a viably adequate solution in speed. The text presents various multi-objective optimization techniques and provides the technical know-how for obtaining trade-off solutions between solution spread and converg

  18. Gene gun delivery systems for cancer vaccine approaches.

    Science.gov (United States)

    Aravindaram, Kandan; Yang, Ning Sun

    2009-01-01

    Gene-based immunization with transgenic DNA vectors expressing tumor-associated antigens (TAA), cytokines, or chemokines, alone or in combination, provides an attractive approach to increase the cytotoxic T cell immunity against various cancer diseases. With this consideration, particle-mediated or gene gun technology has been developed as a nonviral method for gene transfer into various mammalian tissues. It has been shown to induce both humoral and cell-mediated immune responses in both small and large experimental animals. A broad range of somatic cell types, including primary cultures and established cell lines, has been successfully transfected ex vivo or in vitro by gene gun technology, either as suspension or adherent cultures. Here, we show that protocols and techniques for use in gene gun-mediated transgene delivery system for skin vaccination against melanoma using tumor-associated antigen (TAA) human gpl00 and reporter gene assays as experimental systems.

  19. Metagenomic gene annotation by a homology-independent approach

    Energy Technology Data Exchange (ETDEWEB)

    Froula, Jeff; Zhang, Tao; Salmeen, Annette; Hess, Matthias; Kerfeld, Cheryl A.; Wang, Zhong; Du, Changbin

    2011-06-02

    Fully understanding the genetic potential of a microbial community requires functional annotation of all the genes it encodes. The recently developed deep metagenome sequencing approach has enabled rapid identification of millions of genes from a complex microbial community without cultivation. Current homology-based gene annotation fails to detect distantly-related or structural homologs. Furthermore, homology searches with millions of genes are very computational intensive. To overcome these limitations, we developed rhModeller, a homology-independent software pipeline to efficiently annotate genes from metagenomic sequencing projects. Using cellulases and carbonic anhydrases as two independent test cases, we demonstrated that rhModeller is much faster than HMMER but with comparable accuracy, at 94.5percent and 99.9percent accuracy, respectively. More importantly, rhModeller has the ability to detect novel proteins that do not share significant homology to any known protein families. As {approx}50percent of the 2 million genes derived from the cow rumen metagenome failed to be annotated based on sequence homology, we tested whether rhModeller could be used to annotate these genes. Preliminary results suggest that rhModeller is robust in the presence of missense and frameshift mutations, two common errors in metagenomic genes. Applying the pipeline to the cow rumen genes identified 4,990 novel cellulases candidates and 8,196 novel carbonic anhydrase candidates.In summary, we expect rhModeller to dramatically increase the speed and quality of metagnomic gene annotation.

  20. Differential gene expression in liver and small intestine from lactating rats compared to age-matched virgin controls detects increased mRNA of cholesterol biosynthetic genes

    Directory of Open Access Journals (Sweden)

    Jungsuwadee Paiboon

    2011-02-01

    Full Text Available Abstract Background Lactation increases energy demands four- to five-fold, leading to a two- to three-fold increase in food consumption, requiring a proportional adjustment in the ability of the lactating dam to absorb nutrients and to synthesize critical biomolecules, such as cholesterol, to meet the dietary needs of both the offspring and the dam. The size and hydrophobicity of the bile acid pool increases during lactation, implying an increased absorption and disposition of lipids, sterols, nutrients, and xenobiotics. In order to investigate changes at the transcriptomics level, we utilized an exon array and calculated expression levels to investigate changes in gene expression in the liver, duodenum, jejunum, and ileum of lactating dams when compared against age-matched virgin controls. Results A two-way mixed models ANOVA was applied to detect differentially expressed genes. Significance calls were defined as a p Cyp7a1, which catalyzes the rate limiting step in the bile acid biosynthetic pathway, was also significantly increased in liver. In addition, decreased levels of mRNA associated with T-cell signaling were found in the jejunum and ileum. Several members of the Solute Carrier (SLC and Adenosine Triphosphate Binding Cassette (ABC superfamilies of membrane transporters were found to be differentially expressed; these genes may play a role in differences in nutrient and xenobiotic absorption and disposition. mRNA expression of SLC39a4_predicted, a zinc transporter, was increased in all tissues, suggesting that it is involved in increased zinc uptake during lactation. Microarray data are available through GEO under GSE19175. Conclusions We detected differential expression of mRNA from several pathways in lactating dams, including upregulation of the cholesterol biosynthetic pathway in liver and intestine, consistent with Srebp activation. Differential T-Cell signaling in the two most distal regions of the small intestine (ileum and

  1. Contemporary Approaches for Identifying Rare Bone Disease Causing Genes

    Institute of Scientific and Technical Information of China (English)

    Charles R.Farber; Thomas L.Clemens

    2013-01-01

    Recent improvements in the speed and accuracy of DNA sequencing, together with increasingly sophisti-cated mathematical approaches for annotating gene networks, have revolutionized the field of human genetics and made these once time consuming approaches assessable to most investigators. In the field of bone research, a particularly active area of gene discovery has occurred in patients with rare bone disorders such as osteogenesis imperfecta (OI) that are caused by mutations in single genes. In this perspective, we highlight some of these technological advances and describe how they have been used to identify the genetic determinants underlying two previously unexplained cases of OI. The widespread availability of advanced methods for DNA sequencing and bioinformatics analysis can be expected to greatly facilitate identification of novel gene networks that normally function to control bone formation and maintenance.

  2. Combinatorial Approaches to Accurate Identification of Orthologous Genes

    OpenAIRE

    Shi, Guanqun

    2011-01-01

    The accurate identification of orthologous genes across different species is a critical and challenging problem in comparative genomics and has a wide spectrum of biological applications including gene function inference, evolutionary studies and systems biology. During the past several years, many methods have been proposed for ortholog assignment based on sequence similarity, phylogenetic approaches, synteny information, and genome rearrangement. Although these methods share many commonly a...

  3. A Fast Hybrid Algorithm Approach for the Exact String Matching Problem Via Berry Ravindran and Alpha Skip Search Algorithms

    Directory of Open Access Journals (Sweden)

    A. A. Almazroi

    2011-01-01

    Full Text Available Problem statement: String matching algorithm had been an essential means for searching biological sequence database. With the constant expansion in scientific data such as DNA and Protein; the development of enhanced algorithms have even become more critical as the major concern had always been how to raise the performances of these search algorithms to meet challenges of scientific information. Approach: Therefore a new hybrid algorithm comprising Berry Ravindran (BR and Alpha Skip Search (ASS is presented. The concept is based on BR shift function and combines with ASS to ensure improved performance. Results: The results obtained in percentages from the proposed hybrid algorithm displayed superior results in terms of number of attempts and number of character comparisons than the original algorithms when various types of data namely DNA, Protein and English text are applied to appraise the hybrid performances. The enhancement of the proposed hybrid algorithm performs better at 71%, 60% and 63% when compared to Berry-Ravindran in DNA, Protein and English text correspondingly. Moreover the rate of enhancement over Alpha Skip Search algorithm in DNA, Protein and English text are 48%, 28% and 36% respectively. Conclusion: The new proposed hybrid algorithm is relevant for searching biological science sequence database and also other string search systems.

  4. The Role of Serotype Interactions and Seasonality in Dengue Model Selection and Control: Insights from a Pattern Matching Approach.

    Science.gov (United States)

    Ten Bosch, Quirine A; Singh, Brajendra K; Hassan, Muhammad R A; Chadee, Dave D; Michael, Edwin

    2016-05-01

    The epidemiology of dengue fever is characterized by highly seasonal, multi-annual fluctuations, and the irregular circulation of its four serotypes. It is believed that this behaviour arises from the interplay between environmental drivers and serotype interactions. The exact mechanism, however, is uncertain. Constraining mathematical models to patterns characteristic to dengue epidemiology offers a means for detecting such mechanisms. Here, we used a pattern-oriented modelling (POM) strategy to fit and assess a range of dengue models, driven by combinations of temporary cross protective-immunity, cross-enhancement, and seasonal forcing, on their ability to capture the main characteristics of dengue dynamics. We show that all proposed models reproduce the observed dengue patterns across some part of the parameter space. Which model best supports the dengue dynamics is determined by the level of seasonal forcing. Further, when tertiary and quaternary infections are allowed, the inclusion of temporary cross-immunity alone is strongly supported, but the addition of cross-enhancement markedly reduces the parameter range at which dengue dynamics are produced, irrespective of the strength of seasonal forcing. The implication of these structural uncertainties on predicted vulnerability to control is also discussed. With ever expanding spread of dengue, greater understanding of dengue dynamics and control efforts (e.g. a near-future vaccine introduction) has become critically important. This study highlights the capacity of multi-level pattern-matching modelling approaches to offer an analytic tool for deeper insights into dengue epidemiology and control. PMID:27159023

  5. Translational Approaches towards Cancer Gene Therapy: Hurdles and Hopes

    Directory of Open Access Journals (Sweden)

    Yadollah Omidi

    2012-09-01

    Full Text Available Introduction: Of the cancer gene therapy approaches, gene silencing, suicide/apoptosis inducing gene therapy, immunogene therapy and targeted gene therapy are deemed to sub­stantially control the biological consequences of genomic changes in cancerous cells. Thus, a large number of clinical trials have been conducted against various malignancies. In this review, we will discuss recent translational progresses of gene and cell therapy of cancer. Methods: Essential information on gene therapy of cancer were reviewed and discussed towards their clinical translations. Results: Gene transfer has been rigorously studied in vitro and in vivo, in which some of these gene therapy endeavours have been carried on towards translational investigations and clinical applications. About 65% of gene therapy trials are related to cancer therapy. Some of these trials have been combined with cell therapy to produce personalized medicines such as Sipuleucel-T (Provenge®, marketed by Dendreon, USA for the treatment of asymptomatic/minimally symptomatic metastatic hormone-refractory prostate cancer. Conclusion: Translational approach links two diverse boundaries of basic and clinical researches. For successful translation of geno­medicines into clinical applications, it is essential 1 to have the guidelines and standard operating procedures for development and application of the genomedicines specific to clinically relevant biomarker(s; 2 to conduct necessary animal experimental studies to show the “proof of concept” for the proposed genomedicines; 3 to perform an initial clinical investigation; and 4 to initiate extensive clinical trials to address all necessary requirements. In short, translational researches need to be refined to accelerate the geno­medicine development and clinical applications.

  6. A sequence-based approach to identify reference genes for gene expression analysis

    Directory of Open Access Journals (Sweden)

    Chari Raj

    2010-08-01

    Full Text Available Abstract Background An important consideration when analyzing both microarray and quantitative PCR expression data is the selection of appropriate genes as endogenous controls or reference genes. This step is especially critical when identifying genes differentially expressed between datasets. Moreover, reference genes suitable in one context (e.g. lung cancer may not be suitable in another (e.g. breast cancer. Currently, the main approach to identify reference genes involves the mining of expression microarray data for highly expressed and relatively constant transcripts across a sample set. A caveat here is the requirement for transcript normalization prior to analysis, and measurements obtained are relative, not absolute. Alternatively, as sequencing-based technologies provide digital quantitative output, absolute quantification ensues, and reference gene identification becomes more accurate. Methods Serial analysis of gene expression (SAGE profiles of non-malignant and malignant lung samples were compared using a permutation test to identify the most stably expressed genes across all samples. Subsequently, the specificity of the reference genes was evaluated across multiple tissue types, their constancy of expression was assessed using quantitative RT-PCR (qPCR, and their impact on differential expression analysis of microarray data was evaluated. Results We show that (i conventional references genes such as ACTB and GAPDH are highly variable between cancerous and non-cancerous samples, (ii reference genes identified for lung cancer do not perform well for other cancer types (breast and brain, (iii reference genes identified through SAGE show low variability using qPCR in a different cohort of samples, and (iv normalization of a lung cancer gene expression microarray dataset with or without our reference genes, yields different results for differential gene expression and subsequent analyses. Specifically, key established pathways in lung

  7. Gene-gene and gene-environmental interactions of childhood asthma: a multifactor dimension reduction approach.

    Directory of Open Access Journals (Sweden)

    Ming-Wei Su

    Full Text Available BACKGROUND: The importance of gene-gene and gene-environment interactions on asthma is well documented in literature, but a systematic analysis on the interaction between various genetic and environmental factors is still lacking. METHODOLOGY/PRINCIPAL FINDINGS: We conducted a population-based, case-control study comprised of seventh-grade children from 14 Taiwanese communities. A total of 235 asthmatic cases and 1,310 non-asthmatic controls were selected for DNA collection and genotyping. We examined the gene-gene and gene-environment interactions between 17 single-nucleotide polymorphisms in antioxidative, inflammatory and obesity-related genes, and childhood asthma. Environmental exposures and disease status were obtained from parental questionnaires. The model-free and non-parametrical multifactor dimensionality reduction (MDR method was used for the analysis. A three-way gene-gene interaction was elucidated between the gene coding glutathione S-transferase P (GSTP1, the gene coding interleukin-4 receptor alpha chain (IL4Ra and the gene coding insulin induced gene 2 (INSIG2 on the risk of lifetime asthma. The testing-balanced accuracy on asthma was 57.83% with a cross-validation consistency of 10 out of 10. The interaction of preterm birth and indoor dampness had the highest training-balanced accuracy at 59.09%. Indoor dampness also interacted with many genes, including IL13, beta-2 adrenergic receptor (ADRB2, signal transducer and activator of transcription 6 (STAT6. We also used likelihood ratio tests for interaction and chi-square tests to validate our results and all tests showed statistical significance. CONCLUSIONS/SIGNIFICANCE: The results of this study suggest that GSTP1, INSIG2 and IL4Ra may influence the lifetime asthma susceptibility through gene-gene interactions in schoolchildren. Home dampness combined with each one of the genes STAT6, IL13 and ADRB2 could raise the asthma risk.

  8. [MATCHE: Management Approach to Teaching Consumer and Homemaking Education.] Consumer Approach Strand: Textiles and Clothing. Module I-D-1: Consumer Approach to Textiles and Clothing.

    Science.gov (United States)

    California State Univ., Fresno. Dept. of Home Economics.

    This competency-based preservice home economics teacher education module on consumer approach to textiles and clothing is the first in a set of four modules on consumer education related to textiles and clothing. (This set is part of a larger series of sixty-seven modules on the Management Approach to Teaching Consumer and Homemaking Education…

  9. Safety evaluation of continuous green T intersections: A propensity scores-genetic matching-potential outcomes approach.

    Science.gov (United States)

    Wood, Jonathan; Donnell, Eric T

    2016-08-01

    The continuous green T intersection is characterized by a channelized left-turn movement from the minor street approach onto the major street, along with a continuous through movement on the major street. The continuous flow through movement is not controlled by the three-phase traffic signal that is used to separate all other movements at the intersection. Rather, the continuous through movement typically has a green through arrow indicator to inform drivers that they do not have to stop. Past research has consistently shown that there are operational and environmental benefits to implementing this intersection form at three-leg locations, when compared to a conventional signalized intersection. These benefits include reduced delay, fuel consumption, and emissions. The safety effects of the conventional green T intersection are less clear. Past research has been limited to small sample sizes, or utilized only statistical comparisons reported crashes to evaluate the safety performance relative to similar intersection types. The present study overcomes past safety research evaluations by using a propensity scores-potential outcomes framework, with genetic matching, to compare the safety performance of the continuous green T to conventional signalized intersections, using treatment and comparison site data from Florida and South Carolina. The results show that the expected total, fatal and injury, and target crash (rear-end, angle, and sideswipe) frequencies are lower at the continuous green T intersection relative to the conventional signalized intersection (CMFs of 0.958 [95% CI=0.772-1.189], 0.846 [95% CI=0.651-1.099], and 0.920 [95% CI=0.714-1.185], respectively). PMID:27129112

  10. A chain reaction approach to modelling gene pathways.

    Science.gov (United States)

    Cheng, Gary C; Chen, Dung-Tsa; Chen, James J; Soong, Seng-Jaw; Lamartiniere, Coral; Barnes, Stephen

    2012-08-01

    BACKGROUND: Of great interest in cancer prevention is how nutrient components affect gene pathways associated with the physiological events of puberty. Nutrient-gene interactions may cause changes in breast or prostate cells and, therefore, may result in cancer risk later in life. Analysis of gene pathways can lead to insights about nutrient-gene interactions and the development of more effective prevention approaches to reduce cancer risk. To date, researchers have relied heavily upon experimental assays (such as microarray analysis, etc.) to identify genes and their associated pathways that are affected by nutrient and diets. However, the vast number of genes and combinations of gene pathways, coupled with the expense of the experimental analyses, has delayed the progress of gene-pathway research. The development of an analytical approach based on available test data could greatly benefit the evaluation of gene pathways, and thus advance the study of nutrient-gene interactions in cancer prevention. In the present study, we have proposed a chain reaction model to simulate gene pathways, in which the gene expression changes through the pathway are represented by the species undergoing a set of chemical reactions. We have also developed a numerical tool to solve for the species changes due to the chain reactions over time. Through this approach we can examine the impact of nutrient-containing diets on the gene pathway; moreover, transformation of genes over time with a nutrient treatment can be observed numerically, which is very difficult to achieve experimentally. We apply this approach to microarray analysis data from an experiment which involved the effects of three polyphenols (nutrient treatments), epigallo-catechin-3-O-gallate (EGCG), genistein, and resveratrol, in a study of nutrient-gene interaction in the estrogen synthesis pathway during puberty. RESULTS: In this preliminary study, the estrogen synthesis pathway was simulated by a chain reaction model. By

  11. Gene prioritization for imaging genetics studies using Gene Ontology and a stratified False Discovery Rate approach

    Directory of Open Access Journals (Sweden)

    Sejal ePatel

    2016-04-01

    Full Text Available Imaging genetics is an emerging field in which the association between genes and neuroimaging-based quantitative phenotypes are used to explore the functional role of genes in neuroanatomy and neurophysiology in the context of healthy function and neuropsychiatric disorders. The main obstacle for researchers in the field is the high dimensionality of the data in both the imaging phenotypes and the genetic variants commonly typed. In this article, we develop a novel method that utilizes Gene Ontology, an online database, to select and prioritize certain genes, employing a stratified false discovery rate (sFDR approach to investigate their associations with imaging phenotypes. sFDR has the potential to increase power in genome wide association studies (GWAS, and is quickly gaining traction as a method for multiple testing correction. Our novel approach addresses both the pressing need in genetic research to move beyond candidate gene studies, while not being overburdened with a loss of power due to multiple testing. As an example of our methodology, we perform a GWAS of hippocampal volume using both the Enhancing NeuroImaging Genetics through Meta-Analysis (ENIGMA2 and the Alzheimer’s Disease Neuroimaging Initiative datasets. The analysis of ENIGMA2 data yielded a set of SNPs with sFDR values between 10 to 20%. Our approach demonstrates a potential method to prioritize genes based on biological systems impaired in a disease.

  12. Informational matching

    OpenAIRE

    Rend??n, Silvio

    2002-01-01

    This paper analyzes the problem of matching heterogeneous agents in a Bayesian learning model. One agent gives a noisy signal to another agent, who is responsible for learning. If production has a strong informational component, a phase of cross-matching occurs, so that agents of low knowledge catch up with those of higher one. It is shown that: (i) a greater informational component in production makes cross-matching more likely; (ii) as the new technology is mastered, pr...

  13. Matching two independent cohorts validates DPH1 as a gene responsible for autosomal recessive intellectual disability with short stature, craniofacial, and ectodermal anomalies.

    Science.gov (United States)

    Loucks, Catrina M; Parboosingh, Jillian S; Shaheen, Ranad; Bernier, Francois P; McLeod, D Ross; Seidahmed, Mohammed Z; Puffenberger, Erik G; Ober, Carole; Hegele, Robert A; Boycott, Kym M; Alkuraya, Fowzan S; Innes, A Micheil

    2015-10-01

    Recently, Alazami et al. (2015) identified 33 putative candidate disease genes for neurogenetic disorders. One such gene was DPH1, in which a homozygous missense mutation was associated with a 3C syndrome-like phenotype in four patients from a single extended family. Here, we report a second homozygous missense variant in DPH1, seen in four members of a founder population, and associated with a phenotype initially reminiscent of Sensenbrenner syndrome. This postpublication "match" validates DPH1 as a gene underlying syndromic intellectual disability with short stature and craniofacial and ectodermal anomalies, reminiscent of, but distinct from, 3C and Sensenbrenner syndromes. This validation took several years after the independent discoveries due to the absence of effective methods for sharing both candidate phenotype and genotype data between investigators. Sharing of data via Web-based anonymous data exchange servers will play an increasingly important role toward more efficient identification of the molecular basis for rare Mendelian disorders. PMID:26220823

  14. Genome classification by gene distribution: An overlapping subspace clustering approach

    Directory of Open Access Journals (Sweden)

    Halgamuge Saman K

    2008-04-01

    Full Text Available Abstract Background Genomes of lower organisms have been observed with a large amount of horizontal gene transfers, which cause difficulties in their evolutionary study. Bacteriophage genomes are a typical example. One recent approach that addresses this problem is the unsupervised clustering of genomes based on gene order and genome position, which helps to reveal species relationships that may not be apparent from traditional phylogenetic methods. Results We propose the use of an overlapping subspace clustering algorithm for such genome classification problems. The advantage of subspace clustering over traditional clustering is that it can associate clusters with gene arrangement patterns, preserving genomic information in the clusters produced. Additionally, overlapping capability is desirable for the discovery of multiple conserved patterns within a single genome, such as those acquired from different species via horizontal gene transfers. The proposed method involves a novel strategy to vectorize genomes based on their gene distribution. A number of existing subspace clustering and biclustering algorithms were evaluated to identify the best framework upon which to develop our algorithm; we extended a generic subspace clustering algorithm called HARP to incorporate overlapping capability. The proposed algorithm was assessed and applied on bacteriophage genomes. The phage grouping results are consistent overall with the Phage Proteomic Tree and showed common genomic characteristics among the TP901-like, Sfi21-like and sk1-like phage groups. Among 441 phage genomes, we identified four significantly conserved distribution patterns structured by the terminase, portal, integrase, holin and lysin genes. We also observed a subgroup of Sfi21-like phages comprising a distinctive divergent genome organization and identified nine new phage members to the Sfi21-like genus: Staphylococcus 71, phiPVL108, Listeria A118, 2389, Lactobacillus phi AT3, A2

  15. A memetic fingerprint matching algorithm

    OpenAIRE

    Sheng, Weiguo; Howells, Gareth; Fairhurst, Michael; Deravi, Farzin

    2007-01-01

    Minutiae point pattern matching is the most common approach for fingerprint verification. Although many minutiae point pattern matching algorithms have been proposed, reliable automatic fingerprint verification remains as a challenging problem, both with respect to recovering the optimal alignment and the construction of an adequate matching function. In this paper, we develop a memetic fingerprint matching algorithm (MFMA) which aims to identify the optimal or near optimal global matching, b...

  16. Joint signal extraction from galaxy clusters in X-ray and SZ surveys: A matched-filter approach

    CERN Document Server

    Tarrío, Paula; Arnaud, Monique; Pratt, Gabriel W

    2016-01-01

    The hot ionized gas of the intra-cluster medium emits thermal radiation in the X-ray band and also distorts the cosmic microwave radiation through the Sunyaev-Zel'dovich (SZ) effect. Combining these two complementary sources of information through innovative techniques can therefore potentially improve the cluster detection rate when compared to using only one of the probes. Our aim is to build such a joint X-ray-SZ analysis tool, which will allow us to detect fainter or more distant clusters while maintaining high catalogue purity. We present a method based on matched multifrequency filters (MMF) for extracting cluster catalogues from SZ and X-ray surveys. We first designed an X-ray matched-filter method, analogous to the classical MMF developed for SZ observations. Then, we built our joint X-ray-SZ algorithm by combining our X-ray matched filter with the classical SZ-MMF, for which we used the physical relation between SZ and X-ray observations. We show that the proposed X-ray matched filter provides correc...

  17. Functionality Pattern Matching as an Efficient Complementary Structure/Reaction Search Tool: an Open-Source Approach

    Directory of Open Access Journals (Sweden)

    Norbert Haider

    2010-07-01

    Full Text Available An open-source software package for creating and operating web-based structure and/or reaction databases is presented. Besides standard search capabilities (text, structure/substructure/similarity, the system offers a fast additional search option, entirely based on binary pattern matching, which uses automatically assigned functional group descriptors.

  18. Gene therapeutic approaches to inhibit hepatitis B virusreplication

    Institute of Scientific and Technical Information of China (English)

    Maren Gebbing; Thorsten Bergmann; Eric Schulz; Anja Ehrhardt

    2015-01-01

    Acute and chronic hepatitis B virus (HBV) infectionsremain to present a major global health problem. Theinfection can be associated with acute symptomaticor asymptomatic hepatitis which can cause chronicinflammation of the liver and over years this can leadto cirrhosis and the development of hepatocellularcarcinomas. Currently available therapeutics forchronically infected individuals aim at reducing viralreplication and to slow down or stop the progressionof the disease. Therefore, novel treatment options areneeded to efficiently combat and eradicate this disease.Here we provide a state of the art overview of genetherapeutic approaches to inhibit HBV replication. Wediscuss non-viral and viral approaches which wereexplored to deliver therapeutic nucleic acids aiming atreducing HBV replication. Types of delivered therapeuticnucleic acids which were studied since many yearsinclude antisense oligodeoxynucleotides and antisenseRNA, ribozymes and DNAzymes, RNA interference,and external guide sequences. More recently designernucleases gained increased attention and wereexploited to destroy the HBV genome. In addition wemention other strategies to reduce HBV replicationbased on delivery of DNA encoding dominant negativemutants and DNA vaccination. In combination withavailable cell culture and animal models for HBVinfection, in vitro and in vivo studies can be performedto test efficacy of gene therapeutic approaches. Recentprogress but also challenges will be specified andfuture perspectives will be discussed. This is an excitingtime to explore such approaches because recentsuccesses of gene therapeutic strategies in the clinicto treat genetic diseases raise hope to find alternativetreatment options for patients chronically infected withHBV.

  19. Joint signal extraction from galaxy clusters in X-ray and SZ surveys: A matched-filter approach

    Science.gov (United States)

    Tarrío, P.; Melin, J.-B.; Arnaud, M.; Pratt, G. W.

    2016-06-01

    The hot ionized gas of the intra-cluster medium emits thermal radiation in the X-ray band and also distorts the cosmic microwave radiation through the Sunyaev-Zel'dovich (SZ) effect. Combining these two complementary sources of information through innovative techniques can therefore potentially improve the cluster detection rate when compared to using only one of the probes. Our aim is to build such a joint X-ray-SZ analysis tool, which will allow us to detect fainter or more distant clusters while maintaining high catalogue purity. We present a method based on matched multifrequency filters (MMF) for extracting cluster catalogues from SZ and X-ray surveys. We first designed an X-ray matched-filter method, analogous to the classical MMF developed for SZ observations. Then, we built our joint X-ray-SZ algorithm by combining our X-ray matched filter with the classical SZ-MMF, for which we used the physical relation between SZ and X-ray observations. We show that the proposed X-ray matched filter provides correct photometry results, and that the joint matched filter also provides correct photometry when the FX/Y500 relation of the clusters is known. Moreover, the proposed joint algorithm provides a better signal-to-noise ratio than single-map extractions, which improves the detection rate even if we do not exactly know the FX/Y500 relation. The proposed methods were tested using data from the ROSAT all-sky survey and from the Planck survey.

  20. A New Approach for Design of Model Matching Controllers for Time Delay Systems by Using GA Technique

    Directory of Open Access Journals (Sweden)

    K. K. D Priyanka

    2015-01-01

    Full Text Available Modeling of physical systems usually results in complex high order dynamic representation. The simulation and design of controller for higher order system is a difficult problem. Normally the cost and complexity of the controller increases with the system order. Hence it is desirable to approximate these models to reduced order model such that these lower order models preserves all salient features of higher order model. Lower order models simplify the understanding of the original higher order system. Modern controller design methods such as Model Matching Technique, LQG produce controllers of order at least equal to that of the plant, usually higher order. These control laws are may be too complex with regards to practical implementation and simpler designs are then sought. For this purpose, one can either reduce the order the plant model prior to controller design, or reduce the controller in the final stage, or both. In the present work, a controller is designed such that the closed loop system which includes a delay response(s matches with those of the chosen model with same time delay as close as possible. Based on desired model, a controller(of higher order is designed using model matching method and is approximated to a lower order one using Approximate Generalized Time Moments (AGTM / Approximate Generalized Markov Moments (AGMM matching technique and Optimal Pade Approximation technique. Genetic Algorithm (GA optimization technique is used to obtain the expansion points one which yields similar response as that of model, minimizing the error between the response of the model and that of designed closed loop system.

  1. A new navigation approach of terrain contour matching based on 3-D terrain reconstruction from onboard image sequence

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    This article presents a passive navigation method of terrain contour matching by reconstructing the 3-D terrain from the image sequence(acquired by the onboard camera).To achieve automation and simultaneity of the image sequence processing for navigation,a correspondence registration method based on control points tracking is proposed which tracks the sparse control points through the whole image sequence and uses them as correspondence in the relation geometry solution.Besides,a key frame selection method based on the images overlapping ratio and intersecting angles is explored,thereafter the requirement for the camera system configuration is provided.The proposed method also includes an optimal local homography estimating algorithm according to the control points,which helps correctly predict points to be matched and their speed corresponding.Consequently,the real-time 3-D terrain of the trajectory thus reconstructed is matched with the referenced terrain map,and the result of which provides navigating information.The digital simulation experiment and the real image based experiment have verified the proposed method.

  2. Novel metal resistance genes from microorganisms: a functional metagenomic approach.

    Science.gov (United States)

    González-Pastor, José E; Mirete, Salvador

    2010-01-01

    Most of the known metal resistance mechanisms are based on studies of cultured microorganisms, and the abundant uncultured fraction could be an important source of genes responsible for uncharacterized resistance mechanisms. A functional metagenomic approach was selected to recover metal resistance genes from the rhizosphere microbial community of an acid-mine drainage (AMD)-adapted plant, Erica andevalensis, from Rio Tinto, Spain. A total of 13 nickel resistant clones were isolated and analyzed, encoding hypothetical or conserved hypothetical proteins of uncertain functions, or well-characterized proteins, but not previously reported to be related to nickel resistance. The resistance clones were classified into two groups according to their nickel accumulation properties: those preventing or those favoring metal accumulation. Two clones encoding putative ABC transporter components and a serine O-acetyltransferase were found as representatives of each group, respectively. PMID:20830571

  3. A phylogenetic approach to the identification of phosphoglucomutase genes.

    Science.gov (United States)

    Whitehouse, D B; Tomkins, J; Lovegrove, J U; Hopkinson, D A; McMillan, W O

    1998-04-01

    The expanding molecular database provides unparalleled opportunities for characterizing genes and for studying groups of related genes. We use sequences drawn from the database to construct an evolutionary framework for examining the important glycolytic enzyme phosphoglucomutase (PGM). Phosphoglucomutase plays a pivotal role in the synthesis and utilization of glycogen and is present in all organisms. In humans, there are three well-described isozymes, PGMI, PGM2, and PGM3. PGM1 was cloned 5 years ago; however, repeated attempts using both immunological approaches and molecular probes designed from PGM1 have failed to isolate either PGM2 or PGM3. Using a phylogenetic strategy, we first identified 47 highly divergent prokaryotic and eukaryotic PGM-like sequences from the database. Although overall amino acid identity often fell below 20%, the relative order, position, and sequence of three structural motifs, the active site and the magnesium--and sugar-binding sites, were conserved in all 47 sequences. The phylogenetic history of these sequences was complex and marked by duplications and translocations; two instances of transkingdom horizontal gene transfer were identified. Nonetheless, the sequences fell within six well-defined evolutionary lineages, three of which contained only prokaryotes. Of the two prokaryotic/eukaryotic lineages, one contained bacterial, yeast, slimemold, invertebrate, and vertebrate homologs to human PGM1 and the second contained likely homologs to human PGM2. Indeed, an amino acid sequence, derived from a partial human cDNA, that fell within the second cross-kingdom lineage bears several characteristics expected for PGM2. A third lineage may contain homologs to human PGM3. On a general level, our phylogenetic-based approach shows promise for the further utilization of the extensive molecular database. PMID:9549096

  4. The Preference for Anterior Approach Major Hepatectomy: Experience Over 3 Decades and a Propensity Score-Matching Analysis in Right Hepatectomy for Hepatocellular Carcinoma.

    Science.gov (United States)

    Chan, Kun-Ming; Wang, Yu-Chao; Wu, Tsung-Han; Lee, Chen-Fang; Wu, Ting-Jung; Chou, Hong-Shiue; Yu, Ming-Chin; Lee, Wei-Chen

    2015-08-01

    Surgical treatment for primary hepatocellular carcinoma (HCC) has progressed enormously over time. The aim of this study was to analyze the evolution of surgical techniques and outcomes of patients undergoing major right hepatectomy (RH) over the last few decades.A retrospective review of 557 consecutive patients who had undergone RH for HCC between January 1982 and December 2011 was performed. Patients were categorized into subgroups and analyzed according to period and surgical approach to hepatectomy. Based on a propensity score-matching model, the surgical approach in patients in the second period was also analyzed in terms of anterior approach (AA) and conventional approach (CA)-RH.Tumor factors remained the most important prognostic factors related to postoperative HCC recurrence throughout the 2 periods examined in this study. Comparison of patients selected by a propensity score-matching model showed that AA-RH led to significantly better outcomes including recurrence-free survival (RFS) (P = 0.011) and overall survival (OS) (P = 0.012) in patients with HCC as compared with CA-RH. The 5-year RFS and OS were 33.4% and 52.2% after AA-RH, and 21.0% and 36.5% after CA-RH.Major hepatectomy has evolved into a safe procedure that can be performed with confidence. RH by an AA has shown several advantages over CA-RH, and can thus be recommended as the standard procedure for liver resection in patients who require right hepatectomy.

  5. Effective Approach to Label Extraction and Matching%一种有效的标签抽取和匹配方法

    Institute of Scientific and Technical Information of China (English)

    邹显春; 吴春明; 李盛瑜

    2012-01-01

    Label extraction and matching are an important part of the query interface understanding. A vision-based label extraction and matching approach was proposed in this paper. First, the factors which affect label matching were deeply analyzed,and then,a method of reconstructing query interface by analyzing its html code was given correspondingly which can restore the visual layout of form effectively. Finally, the element-label matching was realized which comprehensively considers label tag,text semanteme and position feature. Experiments on 277 query interfaces in 8 domains demonstrate the feasibility of our proposed approach.%标签抽取和匹配是查询接口理解的重要组成部分.提出了一种基于视觉的标签抽取和匹配方法,深入分析了相关匹配因子,给出了一种对查询接口表单进行重构的方法,它能依据接口HTML源代码自动还原出该表单的视觉布局特征.在最终的匹配算法中,综合考虑了基于label标记的匹配、基于文本语义的匹配以及基于位置特征的匹配.在8个领域共计277个查询接口上的实验证明了所提方法能取得较高的匹配精度.

  6. Comparison of endoscopic endonasal and bifrontal craniotomy approaches for olfactory groove meningiomas: A matched pair analysis of outcomes and frontal lobe changes on MRI.

    Science.gov (United States)

    de Almeida, John R; Carvalho, Felipe; Vaz Guimaraes Filho, Francisco; Kiehl, Tim-Rasmus; Koutourousiou, Maria; Su, Shirley; Vescan, Allan D; Witterick, Ian J; Zadeh, Gelareh; Wang, Eric W; Fernandez-Miranda, Juan C; Gardner, Paul A; Gentili, Fred; Snyderman, Carl H

    2015-11-01

    We compare the outcomes and postoperative MRI changes of endoscopic endonasal (EEA) and bifrontal craniotomy (BFC) approaches for olfactory groove meningiomas (OGM). All patients who underwent either BFC or EEA for OGM were eligible. Matched pairs were created by matching tumor volumes of an EEA patient with a BFC patient, and matching the timing of the postoperative scans. The tumor dimensions, peritumoral edema, resectability issues, and frontal lobe changes were recorded based on preoperative and postoperative MRI. Postoperative fluid-attenuated inversion recovery (FLAIR) hyperintensity and residual cystic cavity (porencephalic cave) volume were compared using univariable and multivariable analyses. From a total of 70 patients (46 EEA, 24 BFC), 10 matched pairs (20 patients) were created. Three patients (30%) in the EEA group and two (20%) in the BFC had postoperative cerebrospinal fluid leaks (p=0.61). Gross total resections were achieved in seven (70%) of the EEA group and nine (90%) of the BFC group (p=0.26), and one patient from each group developed a recurrence. On postoperative MRI, there was no significant difference in FLAIR signal volumes between EEA and BFC approaches (6.9 versus 13.3 cm(3); p=0.17) or in porencephalic cave volumes (1.7 versus 5.0 cm(3); p=0.11) in univariable analysis. However, in a multivariable analysis, EEA was associated with less postoperative FLAIR change (p=0.02) after adjusting for the volume of preoperative edema. This study provides preliminary evidence that EEA is associated with quantifiable improvements in postoperative frontal lobe imaging.

  7. Towards 3D Face Recognition in the Real: A Registration-Free Approach Using Fine-Grained Matching of 3D Keypoint Descriptors

    KAUST Repository

    Li, Huibin

    2014-11-12

    Registration algorithms performed on point clouds or range images of face scans have been successfully used for automatic 3D face recognition under expression variations, but have rarely been investigated to solve pose changes and occlusions mainly since that the basic landmarks to initialize coarse alignment are not always available. Recently, local feature-based SIFT-like matching proves competent to handle all such variations without registration. In this paper, towards 3D face recognition for real-life biometric applications, we significantly extend the SIFT-like matching framework to mesh data and propose a novel approach using fine-grained matching of 3D keypoint descriptors. First, two principal curvature-based 3D keypoint detectors are provided, which can repeatedly identify complementary locations on a face scan where local curvatures are high. Then, a robust 3D local coordinate system is built at each keypoint, which allows extraction of pose-invariant features. Three keypoint descriptors, corresponding to three surface differential quantities, are designed, and their feature-level fusion is employed to comprehensively describe local shapes of detected keypoints. Finally, we propose a multi-task sparse representation based fine-grained matching algorithm, which accounts for the average reconstruction error of probe face descriptors sparsely represented by a large dictionary of gallery descriptors in identification. Our approach is evaluated on the Bosphorus database and achieves rank-one recognition rates of 96.56, 98.82, 91.14, and 99.21 % on the entire database, and the expression, pose, and occlusion subsets, respectively. To the best of our knowledge, these are the best results reported so far on this database. Additionally, good generalization ability is also exhibited by the experiments on the FRGC v2.0 database.

  8. The direction of causality between exports and firm performance: microeconomic evidence from Croatia using the matching approach

    Directory of Open Access Journals (Sweden)

    Miljana Valdec

    2015-03-01

    Full Text Available This paper contributes to the literature by using propensity score matching to test for causal effects of starting to export on firm performance in Croatian manufacturing firm-level data. The results confirm that exporters have characteristics superior to those of non-exporters. In the main sample specification there is pervasive evidence of self-selection into export markets, meaning that firms are successful years before they become exporters. Using multiple firm performance indicators, panel and cross section data models together with various sample specifications there is scant evidence on learning-by-exporting which holds true only in a few cases. On the other hand, higher sales growth is found to be a more conclusive distinguishing characteristic of new exporters. As in similar studies, we find that a part of the results depends on the number of export starters in the estimation sample.

  9. Data mining approach to predict BRCA1 gene mutation

    Directory of Open Access Journals (Sweden)

    Olegas Niakšu

    2013-09-01

    Full Text Available Breast cancer is the most frequent women cancer form and one of the leading mortality causes among women around the world. Patients with pathological mutation of a BRCA gene have 65% lifelong breast cancer probability. It is known that such patients have different cause of illness. In this study, we have proposed a new approach for the prediction of BRCA mutation carriers by methodically applying knowledge discovery steps and utilizing data mining methods. An alternative BRCA risk assessment model has been created utilizing decision tree classifier model. The biggest challenge was a very small size and imbalanced nature of the initial dataset, which have been collected by clinicians during 4 years of clinical trial. Iterative optimization of initial dataset, optimal algorithms selection and their parameterization have resulted in higher classifier model performance, with acceptable prediction accuracy for the clinical usage. In this study, three data mining problems have been analyzed using eleven data mining algorithms.

  10. Regulation of gene expression by hypoxia: a molecular approach.

    Science.gov (United States)

    Beitner-Johnson, D; Shull, G E; Dedman, J R; Millhorn, D E

    1997-11-01

    Oxygen is a strict requirement for cell function. The cellular mechanisms by which organisms detect and respond to changes in oxygen tension remain a major unanswered question in pulmonary physiology. Part of the difficulty in addressing this question is due to the limited scope of experiments that can be performed in vivo. In the past few years, several laboratories have begun to make progress in this area, using a variety of cell culture model systems and sophisticated genetic manipulations. Here, we review the current state of knowledge of regulation of gene expression by hypoxia, and describe novel experimental approaches that promise to broaden our understanding of how cells and whole organisms respond to alterations in O2 tension. PMID:9407603

  11. Mining a database of single amplified genomes from Red Sea brine pool extremophiles – Improving reliability of gene function prediction using a profile and pattern matching algorithm (PPMA

    Directory of Open Access Journals (Sweden)

    Stefan Wolfgang Grötzinger

    2014-04-01

    Full Text Available Reliable functional annotation of genomic data is the key-step in the discovery of novel enzymes. Intrinsic sequencing data quality problems of single amplified genomes (SAGs and poor homology of novel extremophile’s genomes pose significant challenges for the attribution of functions to the coding sequences identified. The anoxic deep-sea brine pools of the Red Sea are a promising source of novel enzymes with unique evolutionary adaptation. Sequencing data from Red Sea brine pool cultures and SAGs are annotated and stored in the INDIGO data warehouse. Low sequence homology of annotated genes (no similarity for 35% of these genes may translate into false positives when searching for specific functions. The Profile & Pattern Matching (PPM strategy described here was developed to eliminate false positive annotations of enzyme function before progressing to labor-intensive hyper-saline gene expression and characterization. It utilizes InterPro-derived Gene Ontology (GO-terms (which represent enzyme function profiles and annotated relevant PROSITE IDs (which are linked to an amino acid consensus pattern. The PPM algorithm was tested on 15 protein families, which were selected based on scientific and commercial potential. An initial list of 2,577 E.C. numbers was translated into 171 GO-terms and 49 consensus patterns. A subset of INDIGO-sequences consisting of 58 SAGs from six different taxons of bacteria and archaea were selected from 6 different brine pool environments. Those SAGs code for 74,516 genes, which were independently scanned for the GO-terms (profile filter and PROSITE IDs (pattern filter. Following stringent reliability filtering, the non-redundant hits (106 profile hits and 147 pattern hits are classified as reliable, if at least two relevant descriptors (GO-terms and/or consensus patterns are present. Scripts for annotation, as well as for the PPM algorithm, are available through the INDIGO website.

  12. Mining a database of single amplified genomes from Red Sea brine pool extremophiles-improving reliability of gene function prediction using a profile and pattern matching algorithm (PPMA).

    KAUST Repository

    Grötzinger, Stefan W

    2014-04-07

    Reliable functional annotation of genomic data is the key-step in the discovery of novel enzymes. Intrinsic sequencing data quality problems of single amplified genomes (SAGs) and poor homology of novel extremophile\\'s genomes pose significant challenges for the attribution of functions to the coding sequences identified. The anoxic deep-sea brine pools of the Red Sea are a promising source of novel enzymes with unique evolutionary adaptation. Sequencing data from Red Sea brine pool cultures and SAGs are annotated and stored in the Integrated Data Warehouse of Microbial Genomes (INDIGO) data warehouse. Low sequence homology of annotated genes (no similarity for 35% of these genes) may translate into false positives when searching for specific functions. The Profile and Pattern Matching (PPM) strategy described here was developed to eliminate false positive annotations of enzyme function before progressing to labor-intensive hyper-saline gene expression and characterization. It utilizes InterPro-derived Gene Ontology (GO)-terms (which represent enzyme function profiles) and annotated relevant PROSITE IDs (which are linked to an amino acid consensus pattern). The PPM algorithm was tested on 15 protein families, which were selected based on scientific and commercial potential. An initial list of 2577 enzyme commission (E.C.) numbers was translated into 171 GO-terms and 49 consensus patterns. A subset of INDIGO-sequences consisting of 58 SAGs from six different taxons of bacteria and archaea were selected from six different brine pool environments. Those SAGs code for 74,516 genes, which were independently scanned for the GO-terms (profile filter) and PROSITE IDs (pattern filter). Following stringent reliability filtering, the non-redundant hits (106 profile hits and 147 pattern hits) are classified as reliable, if at least two relevant descriptors (GO-terms and/or consensus patterns) are present. Scripts for annotation, as well as for the PPM algorithm, are available

  13. Effect of Prophylactic Antifungal Protocols on the Prognosis of Liver Transplantation: A Propensity Score Matching and Multistate Model Approach

    Science.gov (United States)

    Chen, Yi-Chan; Wang, Yu-Chao; Lee, Chen-Fang; Wu, Ting-Jun; Chou, Hong-Shiue; Chan, Kun-Ming; Lee, Wei-Chen

    2016-01-01

    Background. Whether routine antifungal prophylaxis decreases posttransplantation fungal infections in patients receiving orthotopic liver transplantation (OLT) remains unclear. This study aimed to determine the effectiveness of antifungal prophylaxis for patients receiving OLT. Patients and Methods. This is a retrospective analysis of a database at Chang Gung Memorial Hospital. We have been administering routine antibiotic and prophylactic antifungal regimens to recipients with high model for end-stage liver disease scores (>20) since 2009. After propensity score matching, 402 patients were enrolled. We conducted a multistate model to analyze the cumulative hazards, probability of fungal infections, and risk factors. Results. The cumulative hazards and transition probability of “transplantation to fungal infection” were lower in the prophylaxis group. The incidence rate of fungal infection after OLT decreased from 18.9% to 11.4% (p = 0.052); overall mortality improved from 40.8% to 23.4% (p < 0.001). In the “transplantation to fungal infection” transition, prophylaxis was significantly associated with reduced hazards for fungal infection (hazard ratio: 0.57, 95% confidence interval: 0.34–0.96, p = 0.033). Massive ascites, cadaver transplantation, and older age were significantly associated with higher risks for mortality. Conclusion. Prophylactic antifungal regimens in high-risk recipients might decrease the incidence of posttransplant fungal infections.

  14. Anatomy Ontology Matching Using Markov Logic Networks

    Directory of Open Access Journals (Sweden)

    Chunhua Li

    2016-01-01

    Full Text Available The anatomy of model species is described in ontologies, which are used to standardize the annotations of experimental data, such as gene expression patterns. To compare such data between species, we need to establish relationships between ontologies describing different species. Ontology matching is a kind of solutions to find semantic correspondences between entities of different ontologies. Markov logic networks which unify probabilistic graphical model and first-order logic provide an excellent framework for ontology matching. We combine several different matching strategies through first-order logic formulas according to the structure of anatomy ontologies. Experiments on the adult mouse anatomy and the human anatomy have demonstrated the effectiveness of proposed approach in terms of the quality of result alignment.

  15. High-throughput approaches to understanding gene function and mapping network architecture in bacteria.

    Science.gov (United States)

    Brochado, Ana Rita; Typas, Athanasios

    2013-04-01

    Advances in sequencing technology have provided an unprecedented view of bacterial diversity, along with a daunting number of novel genes. Within this new reality lies the challenge of developing large-scale approaches to assign function to the new genes and place them in pathways. Here, we highlight recent advances on this front, focusing on how high-throughput gene-gene, gene-drug and drug-drug interactions can yield functional and mechanistic inferences in bacteria. PMID:23403119

  16. Biclustering using Parallel Fuzzy Approach for Analysis of Microarray Gene Expression Data

    OpenAIRE

    Dwitiya Tyagi-Tiwari; Sujoy Das; Manoj Jha; Namita Srivastava

    2015-01-01

    Biclusters are required to analyzing gene expression patterns of genes comparing rows in expression profiles and analyzing expression profiles of samples by comparing columns in gene expression matrix. In the process of biclustering we need to cluster genes and samples. The algorithm presented in this paper is based upon the two-way clustering approach in which the genes and samples are clustered using parallel fuzzy C-means clustering using message passing interface, we call it MFCM. MFCM ap...

  17. REVIEW OF PHASE BASED IMAGE MATCHING

    OpenAIRE

    Jaydeep Kale*

    2016-01-01

    This paper review the phase based image matching method. A major approach for image matching is to extract feature vectors corresponding to given images and perform image matching based on some distance metrics. One of the difficult problem with this feature based image matching is that matching performance depends upon many parameters in feature extraction process. So this paper reviews the phase based image matching methods in which 2D DFTs of given images are used to determine resemblance ...

  18. Core set approach to reduce uncertainty of gene trees

    Directory of Open Access Journals (Sweden)

    Okuhara Yoshiyasu

    2006-05-01

    Full Text Available Abstract Background A genealogy based on gene sequences within a species plays an essential role in the estimation of the character, structure, and evolutionary history of that species. Because intraspecific sequences are more closely related than interspecific ones, detailed information on the evolutionary process may be available by determining all the node sequences of trees and provide insight into functional constraints and adaptations. However, strong evolutionary correlations on a few lineages make this determination difficult as a whole, and the maximum parsimony (MP method frequently allows a number of topologies with a same total branching length. Results Kitazoe et al. developed multidimensional vector-space representation of phylogeny. It converts additivity of evolutionary distances to orthogonality among the vectors expressing branches, and provides a unified index to measure deviations from the orthogoality. In this paper, this index is used to detect and exclude sequences with large deviations from orthogonality, and then selects a maximum subset ("core set" of sequences for which MP generates a single solution. Once the core set tree is formed whose all the node sequences are given, the excluded sequences are found to have basically two phylogenetic positions on this tree, respectively. Fortunately, since multiple substitutions are rare in intra-species sequences, the variance of nucleotide transitions is confined to a small range. By applying the core set approach to 38 partial env sequences of HIV-1 in a single patient and also 198 mitochondrial COI and COII DNA sequences of Anopheles dirus, we demonstrate how consistently this approach constructs the tree. Conclusion In the HIV dataset, we confirmed that the obtained core set tree is the unique maximum set for which MP proposes a single tree. In the mosquito data set, the fluctuation of nucleotide transitions caused by the sequences excluded from the core set was very small

  19. Association between Genetic Polymorphisms of DNA Repair Genes and Chromosomal Damage for 1,3-Butadiene-Exposed Workers in a Matched Study in China

    Directory of Open Access Journals (Sweden)

    Menglong Xiang

    2015-01-01

    Full Text Available The aim of the study was to examine the association between polymorphisms of DNA repair genes and chromosomal damage of 1,3-butadiene- (BD- exposed workers. The study was conducted in 45 pairs of occupationally exposed workers in a BD product workshop and matched control workers in an administrative office and a circulatory water workshop in China. Newly developed biomarkers (micronuclei, MNi; nucleoplasmic bridges, NPBs; nuclear buds, NBUDs in the cytokinesis-blocked micronucleus (CBMN cytome assay were adopted to detect chromosomal damage. PCR and PCR-restriction fragment length polymorphism (RFLP are adopted to analyze polymorphisms of DNA repair genes, such as X-ray repair cross-complementing Group 1 (XRCC1, O6-methylguanine-DNA methyltransferase (MGMT, poly (adenosine diphosphate-ribose polymerases (ADPRT, and apurinic/apyrimidinic endonucleases (APE1. The BD-exposed workers exhibited increased frequencies of MNi and NPBs when compared to subjects in the control group. The results also show that the BD-exposed workers carrying XRCC1 diplotypes TCGA-CCGG (4.25±2.06‰ (FR=2.10, 95% CI: 1.03–4.28 and TCGG-TCGA (5.80±3.56‰ (FR=2.75, 95% CI: 0.76–2.65 had statistically higher NBUD frequencies than those who carried diplotype TCGG-TCGG (1.89±1.27‰. Our study suggests that polymorphisms of XRCC1 gene may influence chromosomal damage in BD-exposed workers.

  20. Properties of Submillimeter Galaxies in a Semi-analytic Model using the "Count Matching" Approach: Application to the ECDF-S

    CERN Document Server

    Arancibia, Alejandra M Muñoz; Padilla, Nelson D; Cora, Sofía A; Gawiser, Eric; Kurczynski, Peter L; Ruiz, Andrés N

    2014-01-01

    We present a new technique for modeling submillimeter galaxies (SMGs): the "Count Matching" approach. Using lightcones drawn from a semi-analytic model of galaxy formation, we choose physical galaxy properties given by the model as proxies for their submillimeter luminosities, assuming a monotonic relationship. As recent interferometric observations of the Extended Chandra Deep Field South show that the brightest sources detected by single-dish telescopes are comprised by emission from multiple fainter sources, we assign the submillimeter fluxes so that the combined LABOCA plus bright-end ALMA observed number counts for this field are reproduced. After turning the model catalogs given by the proxies into submillimeter maps, we perform a source extraction to include the effects of the observational process on the recovered counts and galaxy properties. We find that for all proxies, there are lines of sight giving counts consistent with those derived from LABOCA observations, even for input sources with randomi...

  1. Multisided matching games with complementarities

    OpenAIRE

    Katerina Sherstyuk

    1999-01-01

    The paper considers multisided matching games with transfereable utility using the approach of cooperative game theory. Stable matchings are shown to exist when characteristic functions are supermodular, i.e., agents' abilities to contribute to the value of a coalition are complementary across types. We analyze the structure of the core of supermodular matching games and suggest an algorithm for constructing its extreme payoff vectors.

  2. An Improved Systematic Approach to Predicting Transcription Factor Target Genes Using Support Vector Machine

    OpenAIRE

    Song Cui; Eunseog Youn; Joohyun Lee; Maas, Stephan J.

    2014-01-01

    Biological prediction of transcription factor binding sites and their corresponding transcription factor target genes (TFTGs) makes great contribution to understanding the gene regulatory networks. However, these approaches are based on laborious and time-consuming biological experiments. Numerous computational approaches have shown great potential to circumvent laborious biological methods. However, the majority of these algorithms provide limited performances and fail to consider the struct...

  3. Unifying candidate gene and GWAS Approaches in Asthma.

    Directory of Open Access Journals (Sweden)

    Sven Michel

    Full Text Available The first genome wide association study (GWAS for childhood asthma identified a novel major susceptibility locus on chromosome 17q21 harboring the ORMDL3 gene, but the role of previous asthma candidate genes was not specifically analyzed in this GWAS. We systematically identified 89 SNPs in 14 candidate genes previously associated with asthma in >3 independent study populations. We re-genotyped 39 SNPs in these genes not covered by GWAS performed in 703 asthmatics and 658 reference children. Genotyping data were compared to imputation data derived from Illumina HumanHap300 chip genotyping. Results were combined to analyze 566 SNPs covering all 14 candidate gene loci. Genotyped polymorphisms in ADAM33, GSTP1 and VDR showed effects with p-values <0.0035 (corrected for multiple testing. Combining genotyping and imputation, polymorphisms in DPP10, EDN1, IL12B, IL13, IL4, IL4R and TNF showed associations at a significance level between p = 0.05 and p = 0.0035. These data indicate that (a GWAS coverage is insufficient for many asthma candidate genes, (b imputation based on these data is reliable but incomplete, and (c SNPs in three previously identified asthma candidate genes replicate in our GWAS population with significance after correction for multiple testing in 14 genes.

  4. Determinants of reactions to gene technology: a generic approach

    NARCIS (Netherlands)

    Pin, Renske R.; Gutteling, Jan M.; Kuttschreuter, Margot

    2009-01-01

    This paper examines the reactions to gene technology (the intention to buy gene-tech food, worry about abuse, and the public's desire that different actors be able to influence decisions) in a sample of the Dutch population (n = 1010) and studies the relationship between these reactions and percepti

  5. A Novel Approach to Signal Detection of Sensor Array Units Using 5-3-1 Rule Based Matched Filter Algorithm with Intelligent Identifiers

    Directory of Open Access Journals (Sweden)

    Mahmoud Z. Iskandarani

    2010-01-01

    Full Text Available A novel approach to signal detection and identification was developed and tested. The new algorithm was based on provision of tagging a Matched Filter (MF with identifiers to recognize the source signal with and without noise, so that classification can be carried out. The algorithm was applied successfully to chemical Sensor Array Units (SAU. Problem statement: Signals obtained from chemical sensors were sometimes contaminated with noise. Detection of known signals from noisy surroundings was critical in the field of sensors and their applications. Approach: Six chemical sensor array units were tested at different gas concentrations. The testing was carried out under normal conditions and with the presence of noise. The developed algorithm was then applied to detect, identify and classify the results. Results: The 5-3-1 algorithm produced symmetrical arrays with the source signal identifiers at the corners. The symmetry allowed the use of one-third of the produced data for identification, saving processing time and memory storage. Conclusion: The obtained data also proved that gap separation between conducting electrodes to inversely affect device conductance, with different gap widths affected similarly with temperature change per constant deposited film thickness. Also, each device conductance increased in response to increase in applied gas concentration.

  6. A graphical model approach for inferring large-scale networks integrating gene expression and genetic polymorphism

    Directory of Open Access Journals (Sweden)

    Carey Vincent J

    2009-05-01

    Full Text Available Abstract Background Graphical models (e.g., Bayesian networks have been used frequently to describe complex interaction patterns and dependent structures among genes and other phenotypes. Estimation of such networks has been a challenging problem when the genes considered greatly outnumber the samples, and the situation is exacerbated when one wishes to consider the impact of polymorphisms (SNPs in genes. Results Here we describe a multistep approach to infer a gene-SNP network from gene expression and genotyped SNP data. Our approach is based on 1 construction of a graphical Gaussian model (GGM based on small sample estimation of partial correlation and false-discovery rate multiple testing; 2 extraction of a subnetwork of genes directly linked to a target candidate gene of interest; 3 identification of cis-acting regulatory variants for the genes composing the subnetwork; and 4 evaluating the identified cis-acting variants for trans-acting regulatory effects of the target candidate gene. This approach identifies significant gene-gene and gene-SNP associations not solely on the basis of gene co-expression but rather through whole-network modeling. We demonstrate the method by building two complex gene-SNP networks around Interferon Receptor 12B2 (IL12RB2 and Interleukin 1B (IL1B, two biologic candidates in asthma pathogenesis, using 534,290 genotyped variants and gene expression data on 22,177 genes from total RNA derived from peripheral blood CD4+ lymphocytes from 154 asthmatics. Conclusion Our results suggest that graphical models based on integrative genomic data are computationally efficient, work well with small samples, and can describe complex interactions among genes and polymorphisms that could not be identified by pair-wise association testing.

  7. Approaches to diagnose DNA mismatch repair gene defects in cancer

    DEFF Research Database (Denmark)

    Peña-Diaz, Javier; Rasmussen, Lene Juel

    2016-01-01

    already been well defined and their pathogenicity assessed. Despite this substantial wealth of knowledge, the effects of a large number of alterations remain uncharacterized (variants of uncertain significance, VUSs). The advent of personalized genomics is likely to increase the list of VUSs found in MMR...... genes and anticipates the need of diagnostic tools for rapid assessment of their pathogenicity. This review describes current tools and future strategies for addressing the relevance of MMR gene alterations in human disease....... genes also renders cells resistant to some chemotherapeutic agents. Therefore, diagnosis of MMR deficiency has important implications for the management of the patients, the surveillance of their relatives in the case of LS and for the choice of treatment. Some of the alterations found in MMR genes have...

  8. Biclustering using Parallel Fuzzy Approach for Analysis of Microarray Gene Expression Data

    Directory of Open Access Journals (Sweden)

    Dwitiya Tyagi-Tiwari

    2015-09-01

    Full Text Available Biclusters are required to analyzing gene expression patterns of genes comparing rows in expression profiles and analyzing expression profiles of samples by comparing columns in gene expression matrix. In the process of biclustering we need to cluster genes and samples. The algorithm presented in this paper is based upon the two-way clustering approach in which the genes and samples are clustered using parallel fuzzy C-means clustering using message passing interface, we call it MFCM. MFCM applied for clustering on genes and samples which maximize membership function values of the data set. It is a parallelized rework of a parallel fuzzy two-way clustering algorithm for microarray gene expression data [9], to study the efficiency and parallelization improvement of the algorithm. The algorithm uses gene entropy measure to filter the clustered data to find biclusters. The method is able to get highly correlated biclusters of the gene expression dataset.

  9. Randomized Algorithmic Approach for Biclustering of Gene Expression Data

    OpenAIRE

    Sradhanjali Nayak; Debahuti Mishra; Satyabrata Das; Amiya Kumar Rath

    2011-01-01

    Microarray data processing revolves around the pivotal issue of locating genes altering their expression in response to pathogens, other organisms or other multiple environmental conditions resulted out of a comparison between infected and uninfected cells or tissues. To have a comprehensive analysis of the corollaries of certain treatments, deseases and developmental stages embodied as a data matrix on gene expression data is possible through simultaneous observation and monitoring of the ex...

  10. Finding Clocks in Genes: A Bayesian Approach to Estimate Periodicity

    Directory of Open Access Journals (Sweden)

    Yan Ren

    2016-01-01

    Full Text Available Identification of rhythmic gene expression from metabolic cycles to circadian rhythms is crucial for understanding the gene regulatory networks and functions of these biological processes. Recently, two algorithms, JTK_CYCLE and ARSER, have been developed to estimate periodicity of rhythmic gene expression. JTK_CYCLE performs well for long or less noisy time series, while ARSER performs well for detecting a single rhythmic category. However, observing gene expression at high temporal resolution is not always feasible, and many scientists are interested in exploring both ultradian and circadian rhythmic categories simultaneously. In this paper, a new algorithm, named autoregressive Bayesian spectral regression (ABSR, is proposed. It estimates the period of time-course experimental data and classifies gene expression profiles into multiple rhythmic categories simultaneously. Through the simulation studies, it is shown that ABSR substantially improves the accuracy of periodicity estimation and clustering of rhythmic categories as compared to JTK_CYCLE and ARSER for the data with low temporal resolution. Moreover, ABSR is insensitive to rhythmic patterns. This new scheme is applied to existing time-course mouse liver data to estimate period of rhythms and classify the genes into ultradian, circadian, and arrhythmic categories. It is observed that 49.2% of the circadian profiles detected by JTK_CYCLE with 1-hour resolution are also detected by ABSR with only 4-hour resolution.

  11. Data Partitioning for Parallel Entity Matching

    CERN Document Server

    Kirsten, Toralf; Hartung, Michael; Groß, Anika; Köpcke, Hanna; Rahm, Erhard

    2010-01-01

    Entity matching is an important and difficult step for integrating web data. To reduce the typically high execution time for matching we investigate how we can perform entity matching in parallel on a distributed infrastructure. We propose different strategies to partition the input data and generate multiple match tasks that can be independently executed. One of our strategies supports both, blocking to reduce the search space for matching and parallel matching to improve efficiency. Special attention is given to the number and size of data partitions as they impact the overall communication overhead and memory requirements of individual match tasks. We have developed a service-based distributed infrastructure for the parallel execution of match workflows. We evaluate our approach in detail for different match strategies for matching real-world product data of different web shops. We also consider caching of in-put entities and affinity-based scheduling of match tasks.

  12. An approach for the identification of targets specific to bone metastasis using cancer genes interactome and gene ontology analysis.

    Directory of Open Access Journals (Sweden)

    Shikha Vashisht

    Full Text Available Metastasis is one of the most enigmatic aspects of cancer pathogenesis and is a major cause of cancer-associated mortality. Secondary bone cancer (SBC is a complex disease caused by metastasis of tumor cells from their primary site and is characterized by intricate interplay of molecular interactions. Identification of targets for multifactorial diseases such as SBC, the most frequent complication of breast and prostate cancers, is a challenge. Towards achieving our aim of identification of targets specific to SBC, we constructed a 'Cancer Genes Network', a representative protein interactome of cancer genes. Using graph theoretical methods, we obtained a set of key genes that are relevant for generic mechanisms of cancers and have a role in biological essentiality. We also compiled a curated dataset of 391 SBC genes from published literature which serves as a basis of ontological correlates of secondary bone cancer. Building on these results, we implement a strategy based on generic cancer genes, SBC genes and gene ontology enrichment method, to obtain a set of targets that are specific to bone metastasis. Through this study, we present an approach for probing one of the major complications in cancers, namely, metastasis. The results on genes that play generic roles in cancer phenotype, obtained by network analysis of 'Cancer Genes Network', have broader implications in understanding the role of molecular regulators in mechanisms of cancers. Specifically, our study provides a set of potential targets that are of ontological and regulatory relevance to secondary bone cancer.

  13. Matching Two-dimensional Gel Electrophoresis' Spots

    DEFF Research Database (Denmark)

    Dos Anjos, António; AL-Tam, Faroq; Shahbazkia, Hamid Reza;

    2012-01-01

    This paper describes an approach for matching Two-Dimensional Electrophoresis (2-DE) gels' spots, involving the use of image registration. The number of false positive matches produced by the proposed approach is small, when compared to academic and commercial state-of-the-art approaches. This ar......This paper describes an approach for matching Two-Dimensional Electrophoresis (2-DE) gels' spots, involving the use of image registration. The number of false positive matches produced by the proposed approach is small, when compared to academic and commercial state-of-the-art approaches...

  14. Approaches to diagnose DNA mismatch repair gene defects in cancer.

    Science.gov (United States)

    Peña-Diaz, Javier; Rasmussen, Lene Juel

    2016-02-01

    The DNA repair pathway mismatch repair (MMR) is responsible for the recognition and correction of DNA biosynthetic errors caused by inaccurate nucleotide incorporation during replication. Faulty MMR leads to failure to address the mispairs or insertion deletion loops (IDLs) left behind by the replicative polymerases and results in increased mutation load at the genome. The realization that defective MMR leads to a hypermutation phenotype and increased risk of tumorigenesis highlights the relevance of this pathway for human disease. The association of MMR defects with increased risk of cancer development was first observed in colorectal cancer patients that carried inactivating germline mutations in MMR genes and the disease was named as hereditary non-polyposis colorectal cancer (HNPCC). Currently, a growing list of cancers is found to be MMR defective and HNPCC has been renamed Lynch syndrome (LS) partly to include the associated risk of developing extra-colonic cancers. In addition, a number of non-hereditary, mostly epigenetic, alterations of MMR genes have been described in sporadic tumors. Besides conferring a strong cancer predisposition, genetic or epigenetic inactivation of MMR genes also renders cells resistant to some chemotherapeutic agents. Therefore, diagnosis of MMR deficiency has important implications for the management of the patients, the surveillance of their relatives in the case of LS and for the choice of treatment. Some of the alterations found in MMR genes have already been well defined and their pathogenicity assessed. Despite this substantial wealth of knowledge, the effects of a large number of alterations remain uncharacterized (variants of uncertain significance, VUSs). The advent of personalized genomics is likely to increase the list of VUSs found in MMR genes and anticipates the need of diagnostic tools for rapid assessment of their pathogenicity. This review describes current tools and future strategies for addressing the relevance

  15. Editing CCR5: a novel approach to HIV gene therapy.

    Science.gov (United States)

    Cornu, Tatjana I; Mussolino, Claudio; Bloom, Kristie; Cathomen, Toni

    2015-01-01

    Acquired immunodeficiency syndrome (AIDS) is a life-threatening disorder caused by infection of individuals with the human immunodeficiency virus (HIV). Entry of HIV-1 into target cells depends on the presence of two surface proteins on the cell membrane: CD4, which serves as the main receptor, and either CCR5 or CXCR4 as a co-receptor. A limited number of people harbor a genomic 32-bp deletion in the CCR5 gene (CCR5∆32), leading to expression of a truncated gene product that provides resistance to HIV-1 infection in individuals homozygous for this mutation. Moreover, allogeneic hematopoietic stem cell (HSC) transplantation with CCR5∆32 donor cells seems to confer HIV-1 resistance to the recipient as well. However, since Δ32 donors are scarce and allogeneic HSC transplantation is not exempt from risks, the development of gene editing tools to knockout CCR5 in the genome of autologous cells is highly warranted. Targeted gene editing can be accomplished with designer nucleases, which essentially are engineered restriction enzymes that can be designed to cleave DNA at specific sites. During repair of these breaks, the cellular repair pathway often introduces small mutations at the break site, which makes it possible to disrupt the ability of the targeted locus to express a functional protein, in this case CCR5. Here, we review the current promise and limitations of CCR5 gene editing with engineered nucleases, including factors affecting the efficiency of gene disruption and potential off-target effects. PMID:25757618

  16. A Novel Approach to Functional Analysis of the Ribulose Bisphosphate Carboxylase Small Subunit Gene by Agrobacterium-Mediated Gene Silencing

    Institute of Scientific and Technical Information of China (English)

    Xiao-Fu Zhou; Peng-Da Ma; Ren-Hou Wang; Bo Liu; Xing-Zhi Wang

    2006-01-01

    A novel approach to virus-induced post-transcriptional gene silencing for studying the function of the ribulose bisphosphate carboxylase small subunlt (rbcS) gene was established and optimized using potato virus X vector and Nicotiana benthamiana as experimental material. The analysis of silencing phenomena,transcriptional level, protein expression, and pigment measurement showed that the expression of the rbcS endogenous gene was inactivated by the expression of a 500-bp homologous cDNA fragment carried in the virus vector.

  17. The power of phylogenetic approaches to detect horizontally transferred genes

    Directory of Open Access Journals (Sweden)

    Gogarten J Peter

    2007-03-01

    Full Text Available Abstract Background Horizontal gene transfer plays an important role in evolution because it sometimes allows recipient lineages to adapt to new ecological niches. High genes transfer frequencies were inferred for prokaryotic and early eukaryotic evolution. Does horizontal gene transfer also impact phylogenetic reconstruction of the evolutionary history of genomes and organisms? The answer to this question depends at least in part on the actual gene transfer frequencies and on the ability to weed out transferred genes from further analyses. Are the detected transfers mainly false positives, or are they the tip of an iceberg of many transfer events most of which go undetected by current methods? Results Phylogenetic detection methods appear to be the method of choice to infer gene transfers, especially for ancient transfers and those followed by orthologous replacement. Here we explore how well some of these methods perform using in silico transfers between the terminal branches of a gamma proteobacterial, genome based phylogeny. For the experiments performed here on average the AU test at a 5% significance level detects 90.3% of the transfers and 91% of the exchanges as significant. Using the Robinson-Foulds distance only 57.7% of the exchanges and 60% of the donations were identified as significant. Analyses using bipartition spectra appeared most successful in our test case. The power of detection was on average 97% using a 70% cut-off and 94.2% with 90% cut-off for identifying conflicting bipartitions, while the rate of false positives was below 4.2% and 2.1% for the two cut-offs, respectively. For all methods the detection rates improved when more intervening branches separated donor and recipient. Conclusion Rates of detected transfers should not be mistaken for the actual transfer rates; most analyses of gene transfers remain anecdotal. The method and significance level to identify potential gene transfer events represent a trade

  18. Gene discovery in the hamster: a comparative genomics approach for gene annotation by sequencing of hamster testis cDNAs

    Directory of Open Access Journals (Sweden)

    Khan Shafiq A

    2003-06-01

    Full Text Available Abstract Background Complete genome annotation will likely be achieved through a combination of computer-based analysis of available genome sequences combined with direct experimental characterization of expressed regions of individual genomes. We have utilized a comparative genomics approach involving the sequencing of randomly selected hamster testis cDNAs to begin to identify genes not previously annotated on the human, mouse, rat and Fugu (pufferfish genomes. Results 735 distinct sequences were analyzed for their relatedness to known sequences in public databases. Eight of these sequences were derived from previously unidentified genes and expression of these genes in testis was confirmed by Northern blotting. The genomic locations of each sequence were mapped in human, mouse, rat and pufferfish, where applicable, and the structure of their cognate genes was derived using computer-based predictions, genomic comparisons and analysis of uncharacterized cDNA sequences from human and macaque. Conclusion The use of a comparative genomics approach resulted in the identification of eight cDNAs that correspond to previously uncharacterized genes in the human genome. The proteins encoded by these genes included a new member of the kinesin superfamily, a SET/MYND-domain protein, and six proteins for which no specific function could be predicted. Each gene was expressed primarily in testis, suggesting that they may play roles in the development and/or function of testicular cells.

  19. Clustering based gene expression feature selection method: A computational approach to enrich the classifier efficiency of differentially expressed genes

    KAUST Repository

    Abusamra, Heba

    2016-07-20

    The native nature of high dimension low sample size of gene expression data make the classification task more challenging. Therefore, feature (gene) selection become an apparent need. Selecting a meaningful and relevant genes for classifier not only decrease the computational time and cost, but also improve the classification performance. Among different approaches of feature selection methods, however most of them suffer from several problems such as lack of robustness, validation issues etc. Here, we present a new feature selection technique that takes advantage of clustering both samples and genes. Materials and methods We used leukemia gene expression dataset [1]. The effectiveness of the selected features were evaluated by four different classification methods; support vector machines, k-nearest neighbor, random forest, and linear discriminate analysis. The method evaluate the importance and relevance of each gene cluster by summing the expression level for each gene belongs to this cluster. The gene cluster consider important, if it satisfies conditions depend on thresholds and percentage otherwise eliminated. Results Initial analysis identified 7120 differentially expressed genes of leukemia (Fig. 15a), after applying our feature selection methodology we end up with specific 1117 genes discriminating two classes of leukemia (Fig. 15b). Further applying the same method with more stringent higher positive and lower negative threshold condition, number reduced to 58 genes have be tested to evaluate the effectiveness of the method (Fig. 15c). The results of the four classification methods are summarized in Table 11. Conclusions The feature selection method gave good results with minimum classification error. Our heat-map result shows distinct pattern of refines genes discriminating between two classes of leukemia.

  20. Gene Variants Associated with Antisocial Behaviour: A Latent Variable Approach

    Science.gov (United States)

    Bentley, Mary Jane; Lin, Haiqun; Fernandez, Thomas V.; Lee, Maria; Yrigollen, Carolyn M.; Pakstis, Andrew J.; Katsovich, Liliya; Olds, David L.; Grigorenko, Elena L.; Leckman, James F.

    2013-01-01

    Objective: The aim of this study was to determine if a latent variable approach might be useful in identifying shared variance across genetic risk alleles that is associated with antisocial behaviour at age 15 years. Methods: Using a conventional latent variable approach, we derived an antisocial phenotype in 328 adolescents utilizing data from a…

  1. Candidate gene prioritization by network analysis of differential expression using machine learning approaches

    Directory of Open Access Journals (Sweden)

    Nitsch Daniela

    2010-09-01

    Full Text Available Abstract Background Discovering novel disease genes is still challenging for diseases for which no prior knowledge - such as known disease genes or disease-related pathways - is available. Performing genetic studies frequently results in large lists of candidate genes of which only few can be followed up for further investigation. We have recently developed a computational method for constitutional genetic disorders that identifies the most promising candidate genes by replacing prior knowledge by experimental data of differential gene expression between affected and healthy individuals. To improve the performance of our prioritization strategy, we have extended our previous work by applying different machine learning approaches that identify promising candidate genes by determining whether a gene is surrounded by highly differentially expressed genes in a functional association or protein-protein interaction network. Results We have proposed three strategies scoring disease candidate genes relying on network-based machine learning approaches, such as kernel ridge regression, heat kernel, and Arnoldi kernel approximation. For comparison purposes, a local measure based on the expression of the direct neighbors is also computed. We have benchmarked these strategies on 40 publicly available knockout experiments in mice, and performance was assessed against results obtained using a standard procedure in genetics that ranks candidate genes based solely on their differential expression levels (Simple Expression Ranking. Our results showed that our four strategies could outperform this standard procedure and that the best results were obtained using the Heat Kernel Diffusion Ranking leading to an average ranking position of 8 out of 100 genes, an AUC value of 92.3% and an error reduction of 52.8% relative to the standard procedure approach which ranked the knockout gene on average at position 17 with an AUC value of 83.7%. Conclusion In this study we

  2. A LEXICAL DECISION TREE SCHEME FOR SUPPORTING SCHEMA MATCHING

    OpenAIRE

    BEEN-CHIAN CHIEN; SHIANG-YI HE

    2011-01-01

    To manipulate semantic web and integrate different data sources efficiently, automatic schema matching plays a key role. A generic schema matching method generally includes two phases: the linguistic similarity matching phase and the structural similarity matching phase. Since linguistic matching is an essential step for effective schema matching, developing a high accurate linguistic similarity matching scheme is required. In this paper, a schema matching approach called Similarity Yield Mat...

  3. A Gene Selection Approach based on Clustering for Classification Tasks in Colon Cancer

    Directory of Open Access Journals (Sweden)

    José Antonio CASTELLANOS GARZÓN

    2016-06-01

    Full Text Available Gene selection (GS is an important research area in the analysis of DNA-microarray data, since it involves gene discovery meaningful for a particular target annotation or able to discriminate expression profiles of samples coming from different populations. In this context, a wide number of filter methods have been proposed in the literature to identify subsets of relevant genes in accordance with prefixed targets. Despite the fact that there is a wide number of proposals, the complexity imposed by this problem (GS remains a challenge. Hence, this paper proposes a novel approach for gene selection by using cluster techniques and filter methods on the found groupings to achieve informative gene subsets. As a result of applying our methodology to Colon cancer data, we have identified the best informative gene subset between several one subsets. According to the above, the reached results have proven the reliability of the approach given in this paper.

  4. Clinical development of gene therapy needs a tailored approach: a regulatory perspective from the European Union.

    Science.gov (United States)

    Narayanan, Gopalan; Cossu, Giulio; Galli, Maria Cristina; Flory, Egbert; Ovelgonne, Hans; Salmikangas, Paula; Schneider, Christian K; Trouvin, Jean-Hugues

    2014-03-01

    Gene therapy is a rapidly evolving field that needs an integrated approach, as acknowledged in the concept article on the revision of the guideline on gene transfer medicinal products. The first gene therapy application for marketing authorization was approved in the International Conference on Harmonisation (ICH) region in 2012, the product being Alipogene tiparvovec. The regulatory process for this product has been commented on extensively, highlighting the challenges posed by such a novel technology. Here, as current or previous members of the Committee for Advanced Therapies, we share our perspectives and views on gene therapy as a treatment modality based on current common understanding and regulatory experience of gene therapy products in the European Union to date. It is our view that a tailored approach is needed for a given gene therapy product in order to achieve successful marketing authorization. PMID:24649836

  5. Clinical development of gene therapy needs a tailored approach: a regulatory perspective from the European Union.

    Science.gov (United States)

    Narayanan, Gopalan; Cossu, Giulio; Galli, Maria Cristina; Flory, Egbert; Ovelgonne, Hans; Salmikangas, Paula; Schneider, Christian K; Trouvin, Jean-Hugues

    2014-03-01

    Gene therapy is a rapidly evolving field that needs an integrated approach, as acknowledged in the concept article on the revision of the guideline on gene transfer medicinal products. The first gene therapy application for marketing authorization was approved in the International Conference on Harmonisation (ICH) region in 2012, the product being Alipogene tiparvovec. The regulatory process for this product has been commented on extensively, highlighting the challenges posed by such a novel technology. Here, as current or previous members of the Committee for Advanced Therapies, we share our perspectives and views on gene therapy as a treatment modality based on current common understanding and regulatory experience of gene therapy products in the European Union to date. It is our view that a tailored approach is needed for a given gene therapy product in order to achieve successful marketing authorization.

  6. Clinical development of gene therapy needs a tailored approach: a regulatory perspective from the European Union.

    OpenAIRE

    Narayanan, Gopalan; Cossu, Giulio; Galli, Maria Cristina; Flory, Egbert; Ovelgonne, Hans; Salmikangas, Paula; Schneider, Christian K; Trouvin, Jean-Hugues

    2014-01-01

    Gene therapy is a rapidly evolving field that needs an integrated approach, as acknowledged in the concept article on the revision of the guideline on gene transfer medicinal products. The first gene therapy application for marketing authorization was approved in the International Conference on Harmonisation (ICH) region in 2012, the product being Alipogene tiparvovec. The regulatory process for this product has been commented on extensively, highlighting the challenges posed by such a novel ...

  7. Cloning approaches for identifying aging and longevity-related genes in mammals

    OpenAIRE

    Simoes, Davina C.; Gonos, Efstathios S.

    2008-01-01

    Aging is a phenomenon that affects nearly all animal species. Several studies using different systems have identified a number of processes thought to contribute to the aging phenotype. Many differentially expressed genes have been implicated, but the mechanisms governing mammalian aging (and longevity) are not yet fully understood, and the list of concerned genes is still incomplete and fragmented. Different approaches have been used to clone aging and longevity-related genes. In this articl...

  8. Genetics of intracerebral hemorrhage: Insights from candidate gene approaches

    OpenAIRE

    Baoqiong Liu; Le Zhang; Qidong Yang

    2012-01-01

    Intracerebral hemorrhage (ICH) is a heterogeneous disease with genetic factors playing an important role. Association studies on a wide range of candidate pathways suggest a weak but significant effect for several alleles with ICH risk. Among the most widely investigated genes are those involved in the renin-angiotensin-aldosterone system (e.g., angiotensin-converting enzyme), coagulation pathway (e.g., Factor XIII, Factor VII, platelet-activating factor acetylhydrolase, Factor V Leiden, and ...

  9. Gene Therapy: A Potential Approach for Cancer Pain

    OpenAIRE

    Nicholas Boulis; Christina Krudy; Handy, Chalonda R.

    2011-01-01

    Chronic pain is experienced by as many as 9 0 % of cancer patients at some point during the disease. This pain can be directly cancer related or arise from a sensory neuropathy related to chemotherapy. Major pharmacological agents used to treat cancer pain often lack anatomical specificity and can have off-target effects that create new sources of suffering. These concerns establish a need for improved cancer pain management. Gene therapy is emerging as an exciting prospect. This paper discus...

  10. Analysis of diabetic retinopathy biomarker VEGF gene by computational approaches

    OpenAIRE

    Jayashree Sadasivam; Ramesh, N; Vijayalakshmi, K.; Vinni Viridi; Shiva prasad

    2012-01-01

    Diabetic retinopathy, the most common diabetic eye disease, is caused by changes in the blood vessels of the retina which remains the major cause. It is characterized by vascular permeability and increased tissue ischemia and angiogenesis. One of the biomarker for Diabetic retinopathy has been identified as Vascular Endothelial Growth Factor ( VEGF )gene by computational analysis. VEGF is a sub-family of growth factors, the platelet-derived growth factor family of cystine-knot growth factors...

  11. Candidate gene linkage approach to identify DNA variants that predispose to preterm birth

    DEFF Research Database (Denmark)

    Bream, Elise N A; Leppellere, Cara R; Cooper, Margaret E;

    2013-01-01

    Background:The aim of this study was to identify genetic variants contributing to preterm birth (PTB) using a linkage candidate gene approach.Methods:We studied 99 single-nucleotide polymorphisms (SNPs) for 33 genes in 257 families with PTBs segregating. Nonparametric and parametric analyses were...

  12. A novel model-free approach for reconstruction of time-delayed gene regulatory networks

    Institute of Scientific and Technical Information of China (English)

    JIANG; Wei; LI; Xia; GUO; Zheng; LI; Chuanxing; WANG; Lihong

    2006-01-01

    Reconstruction of genetic networks is one of the key scientific challenges in functional genomics. This paper describes a novel approach for addressing the regulatory dependencies between genes whose activities can be delayed by multiple units of time. The aim of the proposed approach termed TdGRN (time-delayed gene regulatory networking) is to reversely engineer the dynamic mechanisms of gene regulations, which is realized by identifying the time-delayed gene regulations through supervised decision-tree analysis of the newly designed time-delayed gene expression matrix, derived from the original time-series microarray data. A permutation technique is used to determine the statistical classification threshold of a tree, from which a gene regulatory rule(s) is extracted. The proposed TdGRN is a model-free approach that attempts to learn the underlying regulatory rules without relying on any model assumptions. Compared with model-based approaches, it has several significant advantages: it requires neither any arbitrary threshold for discretization of gene transcriptional values nor the definition of the number of regulators (k). We have applied this novel method to the publicly available data for budding yeast cell cycling. The numerical results demonstrate that most of the identified time-delayed gene regulations have current biological knowledge supports.

  13. A computational approach to identifying gene-microRNA modules in cancer.

    Science.gov (United States)

    Jin, Daeyong; Lee, Hyunju

    2015-01-01

    MicroRNAs (miRNAs) play key roles in the initiation and progression of various cancers by regulating genes. Regulatory interactions between genes and miRNAs are complex, as multiple miRNAs can regulate multiple genes. In addtion, these interactions vary from patient to patient and even among patients with the same cancer type, as cancer development is a heterogeneous process. These relationships are more complicated because transcription factors and other regulatory molecules can also regulate miRNAs and genes. Hence, it is important to identify the complex relationships between genes and miRNAs in cancer. In this study, we propose a computational approach to constructing modules that represent these relationships by integrating the expression data of genes and miRNAs with gene-gene interaction data. First, we used a biclustering algorithm to construct modules consisting of a subset of genes and a subset of samples to incorporate the heterogeneity of cancer cells. Second, we combined gene-gene interactions to include genes that play important roles in cancer-related pathways. Then, we selected miRNAs that are closely associated with genes in the modules based on a Gaussian Bayesian network and Bayesian Information Criteria. When we applied our approach to ovarian cancer and glioblastoma (GBM) data sets, 33 and 54 modules were constructed, respectively. In these modules, 91% and 94% of ovarian cancer and GBM modules, respectively, were explained either by direct regulation between genes and miRNAs or by indirect relationships via transcription factors. In addition, 48.4% and 74.0% of modules from ovarian cancer and GBM, respectively, were enriched with cancer-related pathways, and 51.7% and 71.7% of miRNAs in modules were ovarian cancer-related miRNAs and GBM-related miRNAs, respectively. Finally, we extensively analyzed significant modules and showed that most genes in these modules were related to ovarian cancer and GBM. PMID:25611546

  14. A computational approach to identifying gene-microRNA modules in cancer.

    Directory of Open Access Journals (Sweden)

    Daeyong Jin

    2015-01-01

    Full Text Available MicroRNAs (miRNAs play key roles in the initiation and progression of various cancers by regulating genes. Regulatory interactions between genes and miRNAs are complex, as multiple miRNAs can regulate multiple genes. In addtion, these interactions vary from patient to patient and even among patients with the same cancer type, as cancer development is a heterogeneous process. These relationships are more complicated because transcription factors and other regulatory molecules can also regulate miRNAs and genes. Hence, it is important to identify the complex relationships between genes and miRNAs in cancer. In this study, we propose a computational approach to constructing modules that represent these relationships by integrating the expression data of genes and miRNAs with gene-gene interaction data. First, we used a biclustering algorithm to construct modules consisting of a subset of genes and a subset of samples to incorporate the heterogeneity of cancer cells. Second, we combined gene-gene interactions to include genes that play important roles in cancer-related pathways. Then, we selected miRNAs that are closely associated with genes in the modules based on a Gaussian Bayesian network and Bayesian Information Criteria. When we applied our approach to ovarian cancer and glioblastoma (GBM data sets, 33 and 54 modules were constructed, respectively. In these modules, 91% and 94% of ovarian cancer and GBM modules, respectively, were explained either by direct regulation between genes and miRNAs or by indirect relationships via transcription factors. In addition, 48.4% and 74.0% of modules from ovarian cancer and GBM, respectively, were enriched with cancer-related pathways, and 51.7% and 71.7% of miRNAs in modules were ovarian cancer-related miRNAs and GBM-related miRNAs, respectively. Finally, we extensively analyzed significant modules and showed that most genes in these modules were related to ovarian cancer and GBM.

  15. A cross-species bi-clustering approach to identifying conserved co-regulated genes

    Science.gov (United States)

    Sun, Jiangwen; Jiang, Zongliang; Tian, Xiuchun; Bi, Jinbo

    2016-01-01

    Motivation: A growing number of studies have explored the process of pre-implantation embryonic development of multiple mammalian species. However, the conservation and variation among different species in their developmental programming are poorly defined due to the lack of effective computational methods for detecting co-regularized genes that are conserved across species. The most sophisticated method to date for identifying conserved co-regulated genes is a two-step approach. This approach first identifies gene clusters for each species by a cluster analysis of gene expression data, and subsequently computes the overlaps of clusters identified from different species to reveal common subgroups. This approach is ineffective to deal with the noise in the expression data introduced by the complicated procedures in quantifying gene expression. Furthermore, due to the sequential nature of the approach, the gene clusters identified in the first step may have little overlap among different species in the second step, thus difficult to detect conserved co-regulated genes. Results: We propose a cross-species bi-clustering approach which first denoises the gene expression data of each species into a data matrix. The rows of the data matrices of different species represent the same set of genes that are characterized by their expression patterns over the developmental stages of each species as columns. A novel bi-clustering method is then developed to cluster genes into subgroups by a joint sparse rank-one factorization of all the data matrices. This method decomposes a data matrix into a product of a column vector and a row vector where the column vector is a consistent indicator across the matrices (species) to identify the same gene cluster and the row vector specifies for each species the developmental stages that the clustered genes co-regulate. Efficient optimization algorithm has been developed with convergence analysis. This approach was first validated on

  16. Pattern recognition and string matching

    CERN Document Server

    Cheng, Xiuzhen

    2002-01-01

    The research and development of pattern recognition have proven to be of importance in science, technology, and human activity. Many useful concepts and tools from different disciplines have been employed in pattern recognition. Among them is string matching, which receives much theoretical and practical attention. String matching is also an important topic in combinatorial optimization. This book is devoted to recent advances in pattern recognition and string matching. It consists of twenty eight chapters written by different authors, addressing a broad range of topics such as those from classifica­ tion, matching, mining, feature selection, and applications. Each chapter is self-contained, and presents either novel methodological approaches or applications of existing theories and techniques. The aim, intent, and motivation for publishing this book is to pro­ vide a reference tool for the increasing number of readers who depend upon pattern recognition or string matching in some way. This includes student...

  17. Analysis of gene translation using a communications theory approach.

    Science.gov (United States)

    Al Bataineh, Mohammad; Huang, Lun; Alonso, Maria; Menhart, Nick; Atkin, Guillermo E

    2010-01-01

    Rapid advances in both genomic data acquisition and computational technology have encouraged the development and use of advanced engineering methods in the field of bioinformatics and computational genomics. Processes in molecular biology can be modeled through the use of these methods. Such processes include identification and annotation of all the functional elements in the genome, including genes and regulatory sequences, which are a fundamental challenge in genomics and computational biology. Since regulatory elements are often short and variable, their identification and discovery using computational algorithms is difficult. However, significant advances have been made in the computational methods for modeling and detection of DNA regulatory elements. This paper proposes a novel use of techniques and principles from communications engineering, coding, and information theory for modeling, identification, and analysis of genomic regulatory elements and biological sequences. The methods proposed are not only able to identify regulatory elements (REs) at their exact locations, but can also "interestingly" distinguish coding from non-coding regions. Therefore, the proposed methods can be utilized to identify genes in the mRNA sequence.

  18. A flexible and economical barcoding approach for highly multiplexed amplicon sequencing of diverse target genes

    Directory of Open Access Journals (Sweden)

    Craig W. Herbold

    2015-07-01

    Full Text Available High throughput sequencing of phylogenetic and functional gene amplicons provides tremendous insight into the structure and functional potential of complex microbial communities. Here, we introduce a highly adaptable and economical PCR approach to barcoding and pooling libraries of numerous target genes. In this approach, we replace gene- and sequencing platform-specific fusion primers with general, interchangeable barcoding primers, enabling nearly limitless customized barcode-primer combinations. Compared to barcoding with long fusion primers, our multiple-target gene approach is more economical because it overall requires lower number of primers and is based on short primers with generally lower synthesis and purification costs. To highlight our approach, we pooled over 900 different small-subunit rRNA and functional gene amplicon libraries obtained from various environmental or host-associated microbial community samples into a single, paired-end Illumina MiSeq run. Although the amplicon regions ranged in size from approximately 290 to 720 bp, we found no significant systematic sequencing bias related to amplicon length or gene target. Our results indicate that this flexible multiplexing approach produces large, diverse and high quality sets of amplicon sequence data for modern studies in microbial ecology.

  19. Automatic Tuning Matching Cycler (ATMC) in situ NMR spectroscopy as a novel approach for real-time investigations of Li- and Na-ion batteries

    Science.gov (United States)

    Pecher, Oliver; Bayley, Paul M.; Liu, Hao; Liu, Zigeng; Trease, Nicole M.; Grey, Clare P.

    2016-04-01

    We have developed and explored the use of a new Automatic Tuning Matching Cycler (ATMC) in situ NMR probe system to track the formation of intermediate phases and investigate electrolyte decomposition during electrochemical cycling of Li- and Na-ion batteries (LIBs and NIBs). The new approach addresses many of the issues arising during in situ NMR, e.g., significantly different shifts of the multi-component samples, changing sample conditions (such as the magnetic susceptibility and conductivity) during cycling, signal broadening due to paramagnetism as well as interferences between the NMR and external cycler circuit that might impair the experiments. We provide practical insight into how to conduct ATMC in situ NMR experiments and discuss applications of the methodology to LiFePO4 (LFP) and Na3V2(PO4)2F3 cathodes as well as Na metal anodes. Automatic frequency sweep 7Li in situ NMR reveals significant changes of the strongly paramagnetic broadened LFP line shape in agreement with the structural changes due to delithiation. Additionally, 31P in situ NMR shows a full separation of the electrolyte and cathode NMR signals and is a key feature for a deeper understanding of the processes occurring during charge/discharge on the local atomic scale of NMR. 31P in situ NMR with "on-the-fly" re-calibrated, varying carrier frequencies on Na3V2(PO4)2F3 as a cathode in a NIB enabled the detection of different P signals within a huge frequency range of 4000 ppm. The experiments show a significant shift and changes in the number as well as intensities of 31P signals during desodiation/sodiation of the cathode. The in situ experiments reveal changes of local P environments that in part have not been seen in ex situ NMR investigations. Furthermore, we applied ATMC 23Na in situ NMR on symmetrical Na-Na cells during galvanostatic plating. An automatic adjustment of the NMR carrier frequency during the in situ experiment ensured on-resonance conditions for the Na metal and

  20. Predicting sensation seeking from dopamine genes: A candidate system approach

    OpenAIRE

    Derringer, Jaime; Robert F Krueger; Dick, Danielle M; Saccone, Scott; Grucza, Richard A.; Agrawal, Arpana; Lin, Peng; Almasy, Laura; Edenberg, Howard J.; Foroud, Tatiana; Nurnberger, John I.; Hesselbrock, Victor M.; Kramer, John R.; Kuperman, Samuel; Porjesz, Bernice

    2010-01-01

    Sensation seeking is a heritable personality trait that has been reliably linked to behavior disorders. The dopamine system has been hypothesized to contribute to individual differences in sensation seeking, and both experimental and observational studies in humans and non-human animals provide evidence for this relationship. We present here a candidate-system approach to genetic association analysis of sensation seeking, in which single nucleotide polymorphisms (SNPs) from a number of dopami...

  1. Discovering potential cancer driver genes by an integrated network-based approach.

    Science.gov (United States)

    Shi, Kai; Gao, Lin; Wang, Bingbo

    2016-08-16

    Although a lot of methods have been proposed to identify driver genes, how to separate the driver mutations from the passenger mutations is still a challenging problem in cancer genomics. The detection of driver genes with rare mutation and low accuracy is unsolved better. In this study, we present an integrated network-based approach to locate potential driver genes in a cohort of patients. The approach is composed of two steps including a network diffusion step and an aggregated ranking step, which fuses the correlation between the gene mutations and gene expression, the relationship between the mutated genes and the heterogeneous characteristic of the patient mutation. We analyze three cancer datasets including Glioblastoma multiforme, Ovarian cancer and Breast cancer. Our method has not only identified the known driver genes with high-frequency mutations, but also discovered the potential driver genes with a rare mutation. At the same time, validation by literature search and functional enrichment analysis reveal that the predicted genes are obviously related to these three kinds of cancers. PMID:27426053

  2. Using the candidate gene approach for detecting genes underlying seed oil concentration and yield in soybean.

    Science.gov (United States)

    Eskandari, Mehrzad; Cober, Elroy R; Rajcan, Istvan

    2013-07-01

    Increasing the oil concentration in soybean seeds has been given more attention in recent years because of demand for both edible oil and biodiesel production. Oil concentration in soybean is a complex quantitative trait regulated by many genes as well as environmental conditions. To identify genes governing seed oil concentration in soybean, 16 putative candidate genes of three important gene families (GPAT: acyl-CoA:sn-glycerol-3-phosphate acyltransferase, DGAT: acyl-CoA:diacylglycerol acyltransferase, and PDAT: phospholipid:diacylglycerol acyltransferase) involved in triacylglycerol (TAG) biosynthesis pathways were selected and their sequences retrieved from the soybean database ( http://www.phytozome.net/soybean ). Three sequence mutations were discovered in either coding or noncoding regions of three DGAT soybean isoforms when comparing the parents of a 203 recombinant inbreed line (RIL) population; OAC Wallace and OAC Glencoe. The RIL population was used to study the effects of these mutations on seed oil concentration and other important agronomic and seed composition traits, including seed yield and protein concentration across three field locations in Ontario, Canada, in 2009 and 2010. An insertion/deletion (indel) mutation in the GmDGAT2B gene in OAC Wallace was significantly associated with reduced seed oil concentration across three environments and reduced seed yield at Woodstock in 2010. A mutation in the 3' untranslated (3'UTR) region of GmDGAT2C was associated with seed yield at Woodstock in 2009. A mutation in the intronic region of GmDGAR1B was associated with seed yield and protein concentration at Ottawa in 2010. The genes identified in this study had minor effects on either seed yield or oil concentration, which was in agreement with the quantitative nature of the traits. However, the novel gene-specific markers designed in the present study can be used in soybean breeding for marker-assisted selection aimed at increasing seed yield and oil

  3. Using the candidate gene approach for detecting genes underlying seed oil concentration and yield in soybean.

    Science.gov (United States)

    Eskandari, Mehrzad; Cober, Elroy R; Rajcan, Istvan

    2013-07-01

    Increasing the oil concentration in soybean seeds has been given more attention in recent years because of demand for both edible oil and biodiesel production. Oil concentration in soybean is a complex quantitative trait regulated by many genes as well as environmental conditions. To identify genes governing seed oil concentration in soybean, 16 putative candidate genes of three important gene families (GPAT: acyl-CoA:sn-glycerol-3-phosphate acyltransferase, DGAT: acyl-CoA:diacylglycerol acyltransferase, and PDAT: phospholipid:diacylglycerol acyltransferase) involved in triacylglycerol (TAG) biosynthesis pathways were selected and their sequences retrieved from the soybean database ( http://www.phytozome.net/soybean ). Three sequence mutations were discovered in either coding or noncoding regions of three DGAT soybean isoforms when comparing the parents of a 203 recombinant inbreed line (RIL) population; OAC Wallace and OAC Glencoe. The RIL population was used to study the effects of these mutations on seed oil concentration and other important agronomic and seed composition traits, including seed yield and protein concentration across three field locations in Ontario, Canada, in 2009 and 2010. An insertion/deletion (indel) mutation in the GmDGAT2B gene in OAC Wallace was significantly associated with reduced seed oil concentration across three environments and reduced seed yield at Woodstock in 2010. A mutation in the 3' untranslated (3'UTR) region of GmDGAT2C was associated with seed yield at Woodstock in 2009. A mutation in the intronic region of GmDGAR1B was associated with seed yield and protein concentration at Ottawa in 2010. The genes identified in this study had minor effects on either seed yield or oil concentration, which was in agreement with the quantitative nature of the traits. However, the novel gene-specific markers designed in the present study can be used in soybean breeding for marker-assisted selection aimed at increasing seed yield and oil

  4. Rule-based Construction of Matching Processes

    CERN Document Server

    Peukert, Eric; Rahm, Erhard

    2011-01-01

    Mapping complex metadata structures is crucial in a number of domains such as data integration, ontology alignment or model management. To speed up that process automatic matching systems were developed to compute mapping suggestions that can be corrected by a user. However, constructing and tuning match strategies still requires a high manual effort by matching experts as well as correct mappings to evaluate generated mappings. We therefore propose a self-configuring schema matching system that is able to automatically adapt to the given mapping problem at hand. Our approach is based on analyzing the input schemas as well as intermediate matching results. A variety of matching rules use the analysis results to automatically construct and adapt an underlying matching process for a given match task. We comprehensively evaluate our approach on different mapping problems from the schema, ontology and model management domains. The evaluation shows that our system is able to robustly return good quality mappings a...

  5. Genetics of intracerebral hemorrhage: Insights from candidate gene approaches

    Directory of Open Access Journals (Sweden)

    Baoqiong Liu

    2012-01-01

    Full Text Available Intracerebral hemorrhage (ICH is a heterogeneous disease with genetic factors playing an important role. Association studies on a wide range of candidate pathways suggest a weak but significant effect for several alleles with ICH risk. Among the most widely investigated genes are those involved in the renin-angiotensin-aldosterone system (e.g., angiotensin-converting enzyme, coagulation pathway (e.g., Factor XIII, Factor VII, platelet-activating factor acetylhydrolase, Factor V Leiden, and beta1-tubulin, lipid metabolism (e.g., apolipoproteins (ApoE, Apo(a, ApoH, homocysteine metabolism (e.g., methylenetetrahydrofolate reductase, inflammation (e.g., interleukin-6 and tumor necrosis-alpha and other candidate pathways. To identify the robustness of the above associations with ICH, a search of Pubmed (1988 through December 2011 was performed, with searches limited to English-language studies conducted among adult human subjects. This article presents a review of the examined literature on the genetics of ICH.

  6. A combinatorial bidirectional and bicistronic approach for coordinated multi-gene expression in corn.

    Science.gov (United States)

    Kumar, Sandeep; AlAbed, Diaa; Whitteck, John T; Chen, Wei; Bennett, Sara; Asberry, Andrew; Wang, Xiujuan; DeSloover, Daniel; Rangasamy, Murugesan; Wright, Terry R; Gupta, Manju

    2015-03-01

    Transgene stacking in trait development process through genetic engineering is becoming complex with increased number of desired traits and multiple modes of action for each trait. We demonstrate here a novel gene stacking strategy by combining bidirectional promoter (BDP) and bicistronic approaches to drive coordinated expression of multi-genes in corn. A unidirectional promoter, Ubiquitin-1 (ZMUbi1), from Zea mays was first converted into a synthetic BDP, such that a single promoter can direct the expression of two genes from each end of the promoter. The BDP system was then combined with a bicistronic organization of genes at both ends of the promoter by using a Thosea asigna virus 2A auto-cleaving domain. With this gene stacking configuration, we have successfully obtained expression in transgenic corn of four transgenes; three transgenes conferring insect (cry34Ab1 and cry35Ab1) and herbicide (aad1) resistance, and a phiyfp reporter gene using a single ZMUbi1 bidirectional promoter. Gene expression analyses of transgenic corn plants confirmed better coordinated expression of the four genes compared to constructs driving each gene by independent unidirectional ZmUbi1 promoter. To our knowledge, this is the first report that demonstrates application of a single promoter for co-regulation of multiple genes in a crop plant. This stacking technology would be useful for engineering metabolic pathways both for basic and applied research. PMID:25657118

  7. A network-based gene-weighting approach for pathway analysis

    Institute of Scientific and Technical Information of China (English)

    Zhaoyuan Fang; Weidong Tian; Hongbin Ji

    2012-01-01

    Classical algorithms aiming at identifying biological pathways significantly related to studying conditions frequently reduced pathways to gene sets,with an obvious ignorance of the constitutive non-equivalence of various genes within a defined pathway.We here designed a network-based method to determine such non-equivalence in terms of gene weights.The gene weights determined are biologically consistent and robust to network perturbations.By integrating the gene weights into the classical gene set analysis,with a subsequent correction for the “over-counting”bias associated with multi-subunit proteins,we have developed a novel gene-weighed pathway analysis approach,as implemented in an R package called “Gene Associaqtion Network-based Pathway Analysis”(GANPA).Through analysis of several microarray datasets,including the p53 dataset,asthma dataset and three breast cancer datasets,we demonstrated that our approach is biologically reliable and reproducible,and therefore helpful for microarray data interpretation and hypothesis generation.

  8. A virus-induced gene silencing approach to understanding alkaloid metabolism in Catharanthus roseus

    Science.gov (United States)

    Liscombe, David K.; O’Connor, Sarah E.

    2011-01-01

    The anticancer agents vinblastine and vincristine are bisindole alkaloids derived from coupling vindoline and catharanthine, monoterpenoid indole alkaloids produced exclusively by Madagascar periwinkle (Catharanthus roseus) plants. Industrial production of vinblastine and vincristine currently relies on isolation from C. roseus leaves, a process that affords these compounds in 0.0003–0.01% yields. Metabolic engineering efforts to improve alkaloid content or provide alternative sources of the bisindole alkaloids ultimately rely on the isolation and characterization of the genes involved. Several vindoline biosynthetic genes have been isolated, and the cellular and subcellular organization of the corresponding enzymes has been well studied. However, due to the leaf-specific localization of vindoline biosynthesis, and the lack of production of this precursor in cell suspension and hairy root cultures of C. roseus, further elucidation of this pathway demands the development of reverse genetics approaches to assay gene function in planta. The bipartite pTRV vector system is a Tobacco Rattle Virus-based virus-induced gene silencing (VIGS) platform that has provided efficient and effective means to assay gene function in diverse plant systems. We have developed a VIGS method to investigate gene function in C. roseus plants using the pTRV vector system. The utility of this approach in understanding gene function in C. roseus leaves is demonstrated by silencing known vindoline biosynthetic genes previously characterized in vitro. PMID:21802100

  9. Using intron splicing trick for preferential gene expression in transduced cells: an approach for suicide gene therapy.

    Science.gov (United States)

    Pourzadegan, F; Shariati, L; Taghizadeh, R; Khanahmad, H; Mohammadi, Z; Tabatabaiefar, M A

    2016-01-01

    Suicide gene therapy is one of the most innovative approaches in which a potential toxic gene is delivered to the targeted cancer cell by different target delivery methods. We constructed a transfer vector to express green fluorescent protein (GFP) in transduced cells but not in packaging cells. We placed gfp under the control of the cytomegalovirus (CMV) promoter, which is positioned between the two long-terminal repeats in reverse direction. The intron-2 sequence of the human beta globin gene with two poly-A signals and several stop codons on the antisense strand was placed on the leading strand between the CMV promoter and gfp. For lentiviral production, the HEK293T and line were co-transfected with the PMD2G, psPAX2 and pLentiGFP-Ins2 plasmids. The HEK293T and line were transduced with this virus. PCR was performed for evaluation of intron splicing in transduced cells. The GFP expression was seen in 65% of the cells transduced. The PCR amplification of the genomic DNA of transduced cells confirmed the splicing of intron 2. The strategy is significant to accomplish our goal for preserving the packaging cells from the toxic gene expression during viral assembly and the resultant reduction in viral titration. Also it serves to address several other issues in the gene therapy.

  10. A cross-species bi-clustering approach to identifying conserved co-regulated genes

    OpenAIRE

    Sun, Jiangwen; Jiang, Zongliang; Tian, Xiuchun; Bi, Jinbo

    2016-01-01

    Motivation: A growing number of studies have explored the process of pre-implantation embryonic development of multiple mammalian species. However, the conservation and variation among different species in their developmental programming are poorly defined due to the lack of effective computational methods for detecting co-regularized genes that are conserved across species. The most sophisticated method to date for identifying conserved co-regulated genes is a two-step approach. This approac...

  11. An efficient approach of attractor calculation for large-scale Boolean gene regulatory networks.

    Science.gov (United States)

    He, Qinbin; Xia, Zhile; Lin, Bin

    2016-11-01

    Boolean network models provide an efficient way for studying gene regulatory networks. The main dynamics of a Boolean network is determined by its attractors. Attractor calculation plays a key role for analyzing Boolean gene regulatory networks. An approach of attractor calculation was proposed in this study, which improved the predecessor-based approach. Furthermore, the proposed approach combined with the identification of constant nodes and simplified Boolean networks to accelerate attractor calculation. The proposed algorithm is effective to calculate all attractors for large-scale Boolean gene regulatory networks. If the average degree of the network is not too large, the algorithm can get all attractors of a Boolean network with dozens or even hundreds of nodes.

  12. Multiple Pattern Matching Algorithm using Pair-count

    Directory of Open Access Journals (Sweden)

    Raju Bhukya

    2011-07-01

    Full Text Available Pattern matching occurs in various applications, ranging from simple text searching in word processors to identification of common motifs in DNA sequences in computational biology. The problem of exact pattern matching has been well studied and a number of efficient algorithms already exist. However these exact pattern matching algorithms are of little help when they are applied to finding patterns in DNA sequences. Pattern matching in a DNA sequence or pattern searching from a large data base is a major research area in computational biology. To extract pattern from a large sequence it takes more time, in order to reduce searching time we have proposed an approach that reduces the search time with accurate retrieval of the matched pattern from the given sequence of any size of a file. Executing patterns from a large DNA or protein data is a computationally intensive task. As performance plays a major role in extracting patterns from a given DNA sequence or from a large database independent of the size of the sequence. More efficient approaches related to multiple pattern matching techniques are becoming more important for finding the functional as well as the structural properties of the proteins and genes. One of the major problems in genomic field is to perform pattern comparison on DNA and protein sequences. In the current approach we explore a new technique which avoids unnecessary comparisons in the DNA sequence and gives the accurate retrieval of the pattern called a multiple pattern matching algorithm using pair count. The proposed technique gives very good performance related to DNA sequence analysis for querying of publicly available genome sequence data. By using this method the number of comparisons gradually decreases and comparison per character ratio of the proposed algorithm reduces accordingly when compared to the some of the existing popular methods. The experimental results show that there is considerable amount of performance

  13. Gene Technology in Winemaking: New Approaches to an Ancient Art

    Directory of Open Access Journals (Sweden)

    Isak S. Pretorius

    2001-03-01

    Full Text Available For the last century, the availability of pure culture yeast has improved reproducibility in wine fermentations and product quality. However, there is not a single wine yeast strain that possesses an ideal combination of oenological characteristics that are optimised for the task set by today´s leading winemakers. With new developments in modern winemaking there has arisen an urgent need to modify wine yeast strains in order to take full advantage of technology and to satisfy the demands of the sophisticated wine consumers. The combined use of mutagenesis, hybridisation and recombinant DNA methods have significantly increased the genetic diversity that can be introduced into Saccharomyces cerevisiae strains. The overall aim of the strain development programmes extends far beyond the primary role of wine yeast to catalyse the rapid and complete conversion of grape sugars into alcohol and carbon dioxide without distorting the flavour of the final product. Starter cultures of S. cerevisiae must now possess a range of other properties that differ with the type and style of wine to be made and the technical requirements of the winery. Our strain development programme focuses on a number of targets that are amenable to a genetic approach, including strain security and quality control, the increase of fermentation and processing efficiencies, and the enhancement of the sensorial quality and health properties of wine and other grape-based beverages. However, successful commercialisation of transgenic wine yeasts will depend on a multitude of scientific, technical, economic, marketing, safety, regulatory, legal and ethical issues. Therefore, it would be foolish to entertain unrealistic expectations over rapid commercialisation and short-term benefits. However, it will be equally unwise to deny the potential advantages of genetically improved wine yeasts to both the winemaker and consumer in the third millennium.

  14. A multiprong approach to cancer gene therapy by coencapsulated cells.

    Science.gov (United States)

    Cirone, Pasquale; Shen, Feng; Chang, Patricia L

    2005-04-01

    Immune-isolation of nonautologous cells with microencapsulation protects these cells from graft rejection, thus allowing the same recombinant therapeutic cell line to be implanted in different recipients. This approach was successful in treating HER2/neu-expressing tumors in mice by delivering an interleukin-2 fusion protein (sFvIL-2), or angiostatin. However, treatment with interleukin-2 led to profuse inflammation, while angiostatin delivery did not result in long-term tumor suppression, in part due to endothelial cell-independent neovascularization (vascular mimicry). We hypothesize that coencapsulating the two producer cells in the same microcapsules may enhance the efficacy and ameliorate the above side effects. Hence, B16-F0/neu tumor-bearing mice were implanted with sFvIL-2- and angiostatin-secreting cells coencapsulated in the same alginate-poly-L-lysine-alginate microcapsules. However, this protocol only produced an incremental but not synergistic improvement, as measured with greater tumor suppression and improved survival. Compared to the single sFvIL-2 treatment, the coencapsulation protocol showed improved efficacy associated with: mobilization of sFvIL-2 from the spleen; a higher level of cytokine delivery systemically and to the tumors; increased tumor and tumor-associated endothelial cell apoptosis; and a reduced host inflammatory response. However, compared to the single angiostatin treatment, the efficacy was reduced, primarily due to a "bystander" effect in which the angiostatin-secreting cells suffered similar transgene silencing as the coencapsulated cytokine-secreting cells. Nevertheless, the level of "vascular mimicry" of the single angiostatin treatment was significantly reduced. Hence, while there was no synergy in efficacy, an incremental improvement and some reduction in undesirable side effects of inflammation and vascular mimicry were achieved over the single treatments. PMID:15692610

  15. Linking Genes and Brain Development of Honeybee Workers: A Whole-Transcriptome Approach

    Science.gov (United States)

    Vleurinck, Christina; Raub, Stephan; Sturgill, David; Oliver, Brian; Beye, Martin

    2016-01-01

    Honeybees live in complex societies whose capabilities far exceed those of the sum of their single members. This social synergism is achieved mainly by the worker bees, which form a female caste. The worker bees display diverse collaborative behaviors and engage in different behavioral tasks, which are controlled by the central nervous system (CNS). The development of the worker brain is determined by the female sex and the worker caste determination signal. Here, we report on genes that are controlled by sex or by caste during differentiation of the worker’s pupal brain. We sequenced and compared transcriptomes from the pupal brains of honeybee workers, queens and drones. We detected 333 genes that are differently expressed and 519 genes that are differentially spliced between the sexes, and 1760 genes that are differentially expressed and 692 genes that are differentially spliced between castes. We further found that 403 genes are differentially regulated by both the sex and caste signals, providing evidence of the integration of both signals through differential gene regulation. In this gene set, we found that the molecular processes of restructuring the cell shape and cell-to-cell signaling are overrepresented. Our approach identified candidate genes that may be involved in brain differentiation that ensures the various social worker behaviors. PMID:27490820

  16. Linking Genes and Brain Development of Honeybee Workers: A Whole-Transcriptome Approach.

    Science.gov (United States)

    Vleurinck, Christina; Raub, Stephan; Sturgill, David; Oliver, Brian; Beye, Martin

    2016-01-01

    Honeybees live in complex societies whose capabilities far exceed those of the sum of their single members. This social synergism is achieved mainly by the worker bees, which form a female caste. The worker bees display diverse collaborative behaviors and engage in different behavioral tasks, which are controlled by the central nervous system (CNS). The development of the worker brain is determined by the female sex and the worker caste determination signal. Here, we report on genes that are controlled by sex or by caste during differentiation of the worker's pupal brain. We sequenced and compared transcriptomes from the pupal brains of honeybee workers, queens and drones. We detected 333 genes that are differently expressed and 519 genes that are differentially spliced between the sexes, and 1760 genes that are differentially expressed and 692 genes that are differentially spliced between castes. We further found that 403 genes are differentially regulated by both the sex and caste signals, providing evidence of the integration of both signals through differential gene regulation. In this gene set, we found that the molecular processes of restructuring the cell shape and cell-to-cell signaling are overrepresented. Our approach identified candidate genes that may be involved in brain differentiation that ensures the various social worker behaviors. PMID:27490820

  17. An IF-FISH Approach for Covisualization of Gene Loci and Nuclear Architecture in Fission Yeast.

    Science.gov (United States)

    Kim, K-D; Iwasaki, O; Noma, K

    2016-01-01

    Recent genomic studies have revealed that chromosomal structures are formed by a hierarchy of organizing processes ranging from gene associations, including interactions among enhancers and promoters, to topologically associating domain formations. Gene associations identified by these studies can be characterized by microscopic analyses. Fission yeast is a model organism, in which gene associations have been broadly mapped across the genome, although many of those associations have not been further examined by cell biological approaches. To address the technically challenging process of the visualization of associating gene loci in the fission yeast nuclei, we provide, in detail, an IF-FISH procedure that allows for covisualizing both gene loci and nuclear structural markers such as the nuclear membrane and nucleolus. PMID:27423862

  18. Genetic treatment of a molecular disorder: gene therapy approaches to sickle cell disease.

    Science.gov (United States)

    Hoban, Megan D; Orkin, Stuart H; Bauer, Daniel E

    2016-02-18

    Effective medical management for sickle cell disease (SCD) remains elusive. As a prevalent and severe monogenic disorder, SCD has been long considered a logical candidate for gene therapy. Significant progress has been made in moving toward this goal. These efforts have provided substantial insight into the natural regulation of the globin genes and illuminated challenges for genetic manipulation of the hematopoietic system. The initial γ-retroviral vectors, next-generation lentiviral vectors, and novel genome engineering and gene regulation approaches each share the goal of preventing erythrocyte sickling. After years of preclinical studies, several clinical trials for SCD gene therapies are now open. This review focuses on progress made toward achieving gene therapy, the current state of the field, consideration of factors that may determine clinical success, and prospects for future development.

  19. Improved bounds for stochastic matching

    CERN Document Server

    Li, Jian

    2010-01-01

    In this paper we study stochastic matching problems that are motivated by applications in online dating and kidney exchange programs. We consider two probing models: edge probing and matching probing. Our main result is an algorithm that finds a matching-probing strategy attaining a small constant approximation ratio. An interesting aspect of our approach is that we compare the cost our solution to the best edge-probing strategy. Thus, we indirectly show that the best matching-probing strategy is only a constant factor away from the best edge-probing strategy. Even though our algorithm has a slightly worse approximation ratio than a greedy algorithm for edge-probing strategies, we show that the two algorithms can be combined to get improved approximations.

  20. Biclustering of gene expression data: hybridization of GRASP with other heuristic/metaheuristic approaches

    OpenAIRE

    Musacchia, Francesco

    2013-01-01

    Researchers who work on large amount of data have to face vari- ous problems such as data mining and information retrieval: this is the case of gene expression. The general scope of these experiments is to find co-regulated genes, in order to understand the biologic pathways underlying a particular phenomenon. A clustering con- cept can be used to find out if co-regulated genes can be active only over some conditions. Recently, some biclustering approaches have been used to find groups of co-...

  1. 一种基于证据理论和任务分配的Deep Web查询接口匹配方法%A Deep Web Query Interface Matching Approach Based on Evidence Theory and Task Assignment

    Institute of Scientific and Technical Information of China (English)

    董永权; 李庆忠; 丁艳辉; 张永新

    2011-01-01

    针对已有查询接口匹配方法匹配器权重设置困难、匹配决策缺乏有效处理的局限性,提出一种基于证据理论和任务分配的Deep Web查询接口匹配方法.该方法通过引人改进的D-S证据理论自动融合多个匹配器结果,避免手工设定匹配器权重,有效减少人工干预.通过对任务分配问题进行扩展,将查询接口的一对一匹配决策问题转化为扩展的任务分配问题,为源查询接口中的每一个属性选择合适的匹配,并在此基础上,采用树结构启发式规则进行一对多匹配决策.实验结果表明ETTA-IM方法具有较高的查准率和查全率.%To solve the limitations of existing query interface matching which have the difficulties of weight setting of the matcher and the absence of the efficient processing of matching decision, a deep web query interface matching approach based on evidence theory and task assignment is proposed called evidence theory and task assignment based query interface matching approach (ETTA-IM).Firstly, an improved D-S evidence theory is used to automatically combine multiple matchers.Thus, the weight of each matcher is not required to be set by hand and human involvement is reduced.Then, a method is used to select a proper attribute correspondence of each source attribute from target query interface, which converts one-to-one matching decision to the extended task assignment problem.Finally, based on one-to-one matching results, some heuristic rules of tree structure are used to perform one-to-many matching decision.Experimental results show that ETTA-IM approach has high precision and recall measure.

  2. Approximating Graphic TSP by Matchings

    CERN Document Server

    Mömke, Tobias

    2011-01-01

    We present a framework for approximating the metric TSP based on a novel use of matchings. Traditionally, matchings have been used to add edges in order to make a given graph Eulerian, whereas our approach also allows for the removal of certain edges leading to a decreased cost. For the TSP on graphic metrics (graph-TSP), the approach yields a 1.461-approximation algorithm with respect to the Held-Karp lower bound. For graph-TSP restricted to a class of graphs that contains degree three bounded and claw-free graphs, we show that the integrality gap of the Held-Karp relaxation matches the conjectured ratio 4/3. The framework allows for generalizations in a natural way and also leads to a 1.586-approximation algorithm for the traveling salesman path problem on graphic metrics where the start and end vertices are prespecified.

  3. A bracket approach to improve the stability and gas sorption performance of a metal-organic framework via in situ incorporating the size-matching molecular building blocks.

    Science.gov (United States)

    Chen, Di-Ming; Tian, Jia-Yue; Liu, Chun-Sen; Du, Miao

    2016-06-28

    Incorporating the in situ formed size-matching molecular building blocks (MBBs) into the open channels will remarkably improve the robustness and gas sorption performance of an evacuated metal-organic framework. As a result, such MBBs can transfer the open metal sites from the framework walls to the channel centers and separate the large channels into multiple smaller voids, leading to a molecular sieving effect and high-performance gas-separation of the modified material. PMID:27301546

  4. A novel parametric approach to mine gene regulatory relationship from microarray datasets

    Directory of Open Access Journals (Sweden)

    Zhu Yunping

    2010-12-01

    Full Text Available Abstract Background Microarray has been widely used to measure the gene expression level on the genome scale in the current decade. Many algorithms have been developed to reconstruct gene regulatory networks based on microarray data. Unfortunately, most of these models and algorithms focus on global properties of the expression of genes in regulatory networks. And few of them are able to offer intuitive parameters. We wonder whether some simple but basic characteristics of microarray datasets can be found to identify the potential gene regulatory relationship. Results Based on expression correlation, expression level variation and vectors derived from microarray expression levels, we first introduced several novel parameters to measure the characters of regulating gene pairs. Subsequently, we used the naïve Bayesian network to integrate these features as well as the functional co-annotation between transcription factors and their target genes. Then, based on the character of time-delay from the expression profile, we were able to predict the existence and direction of the regulatory relationship respectively. Conclusions Several novel parameters have been proposed and integrated to identify the regulatory relationship. This new model is proved to be of higher efficacy than that of individual features. It is believed that our parametric approach can serve as a fast approach for regulatory relationship mining.

  5. PREFACE: Physics approaches to protein interactions and gene regulation Physics approaches to protein interactions and gene regulation

    Science.gov (United States)

    Nussinov, Ruth; Panchenko, Anna R.; Przytycka, Teresa

    2011-06-01

    Physics approaches focus on uncovering, modeling and quantitating the general principles governing the micro and macro universe. This has always been an important component of biological research, however recent advances in experimental techniques and the accumulation of unprecedented genome-scale experimental data produced by these novel technologies now allow for addressing fundamental questions on a large scale. These relate to molecular interactions, principles of bimolecular recognition, and mechanisms of signal propagation. The functioning of a cell requires a variety of intermolecular interactions including protein-protein, protein-DNA, protein-RNA, hormones, peptides, small molecules, lipids and more. Biomolecules work together to provide specific functions and perturbations in intermolecular communication channels often lead to cellular malfunction and disease. A full understanding of the interactome requires an in-depth grasp of the biophysical principles underlying individual interactions as well as their organization in cellular networks. Phenomena can be described at different levels of abstraction. Computational and systems biology strive to model cellular processes by integrating and analyzing complex data from multiple experimental sources using interdisciplinary tools. As a result, both the causal relationships between the variables and the general features of the system can be discovered, which even without knowing the details of the underlying mechanisms allow for putting forth hypotheses and predicting the behavior of the systems in response to perturbation. And here lies the strength of in silico models which provide control and predictive power. At the same time, the complexity of individual elements and molecules can be addressed by the fields of molecular biophysics, physical biology and structural biology, which focus on the underlying physico-chemical principles and may explain the molecular mechanisms of cellular function. In this issue

  6. Determination of the Ultimate Limit States of Shallow Foundations using Gene Expression Programming (GEP) Approach

    DEFF Research Database (Denmark)

    Tahmasebi poor, A; Barari, Amin; Behnia, M;

    2015-01-01

    In this study, a gene expression programming (GEP) approach was employed to develop modified expressions for predicting the bearing capacity of shallow foundations founded on granular material. The model was validate against the results of load tests on full-scale and model footings obtained from...

  7. Characterization of denitrification gene clusters of soil bacteria via a metagenomic approach

    OpenAIRE

    Demanèche, Sandrine; Philippot, Laurent; David, Maude M.; Navarro, Elisabeth; Vogel, Timothy,; Simonet, Pascal

    2009-01-01

    We characterized operons encoding enzymes involved in denitrification, a nitrogen-cycling process involved in nitrogen losses and greenhouse gas emission, using a metagenomic approach which combines molecular screening and pyrosequencing. Screening of 77,000 clones from a soil metagenomic library led to the identification and the subsequent characterization of nine denitrification gene clusters.

  8. Next-generation sequencing approach for connecting secondary metabolites to biosynthetic gene clusters in fungi

    Directory of Open Access Journals (Sweden)

    Ralph A Cacho

    2015-01-01

    Full Text Available Genomics has revolutionized the research on fungal secondary metabolite biosynthesis. To elucidate the molecular and enzymatic mechanisms underlying the biosynthesis of a specific secondary metabolite compound, the important first step is often to find the genes that responsible for its synthesis. The accessibility to fungal genome sequences allows the bypass of the cumbersome traditional library construction and screening approach. The advance in next-generation sequencing (NGS technologies have further improved the speed and reduced the cost of microbial genome sequencing in the past few years, which has accelerated the research in this field. Here, we will present an example work flow for identifying the gene cluster encoding the biosynthesis of secondary metabolites of interest using an NGS approach. We will also review the different strategies that can be employed to pinpoint the targeted gene clusters rapidly by giving several examples stemming from our work.

  9. 一种用于辅助导航的快速图像匹配方法%A Rapid Image Matching Approach for Auxiliary Navigation

    Institute of Scientific and Technical Information of China (English)

    吴政; 冯燕; 陈武

    2009-01-01

    为了提高辅助导航中多传感器图像匹配的精确性和实时性,首先提取图像的边缘特征,并用3-4距离变换(3-4DT)方法对边缘二值图像进行变换,以变换后的边缘距离图像为匹配特征;针对传统Hausdorff距离的局限性提出了一种融合点集重合数的Hausdorff距离,并以之为相似性度量;搜索策略根据人眼视觉系统的机制采用一种由远到近的分层匹配方法,同时使用一种改进的实数编码遗传算法来加快底层图像匹配的速度.实验结果为平均匹配时间为1283ms,平均误差值为1.036,表明匹配方法能满足导航要求.%To improve the velocity and accuracy of multi - sensor image matching in auxiliary navigation, after the edge feature of image is extracted, a 3 -4DT method is applied to transform the edge binary image ,then the transformed edge distance image is taken as the matching feature. A Hausdorff distance integrating points set coincidence numbers (I -HD) is proposed to overcome the limitation of traditional Hauedorff distance, and I -HD can be used as the similarity measure. On the basis of the human visual system, a far - near stratification search strategy is adopt-ed. Meanwhile a genetic algorithm using real - coding is applied to accelerate the speed of matching at the bottom of image matching. Experimental results show that average matching time is 1283ms and average error value is 1.036 , which shows that the method can meet the navigation requirement.

  10. A set-covering approach to specific search for literature about human genes.

    Science.gov (United States)

    Jenssen, T K; Vinterbo, S

    2000-01-01

    With the advent of the cDNA microarray and oligonucleotide array technologies it has become possible to study a large number of genes in a single experiment. While experiments with thousands of genes are routinely performed, searching for literature about several genes by traditional methods is time consuming and error-prone. In addition to the inherent limitations of free text search, use of the conventional Boolean operators often result in either none (when AND'ing terms) or far too many (when OR'ing terms) hits. We have created a two-step procedure as an approach to meeting the challenge of multi-gene queries. Our results so far shows that the returned sets of articles scores high on relevance. PMID:11079910

  11. Structural Weights in Ontology Matching

    Directory of Open Access Journals (Sweden)

    Mohammad Mehdi Keikha

    2013-10-01

    Full Text Available Ontology matching finds correspondences between similar entities of different ontologies. Two ontologies may be similar in some aspects such as structure, semantic etc. Most ontology matching systems integrate multiple matchers to extract all the similarities that two ontologies may have. Thus, we face a major problem to aggregate different similarities.Some matching systems use experimental weights for aggregation of similarities among different matchers while others use machine learning approaches and optimization algorithms to find optimal weights to assign to different matchers. However, both approaches have their own deficiencies.In this paper, we will point out the problems and shortcomings of current similarity aggregation strategies. Then, we propose a new strategy, which enables us to utilize the structural information of ontologies to get weights of matchers, for the similarity aggregation task. For achieving this goal, we create a new Ontology Matching system which it uses three available matchers, namely GMO, ISub and VDoc.We have tested our similarity aggregation strategy on the OAEI 2012 data set. Experimental results show significant improvements in accuracies of several cases, especially in matching the classes of ontologies. We will compare the performance of our similarity aggregation strategy with other well-known strategies.

  12. Statistics of polarisation matching

    NARCIS (Netherlands)

    Naus, H.W.L.; Zwamborn, A.P.M.

    2014-01-01

    The reception of electromagnetic signals depends on the polarisation matching of the transmitting and receiving antenna. The practical matching differs from the theoretical one because of the noise deterioration of the transmitted and eventually received electromagnetic field. In other applications,

  13. A Novel Approach to Revealing Positive and Negative Co-Regulated Genes

    Institute of Scientific and Technical Information of China (English)

    Yu-Hai Zhao; Guo-Ren Wang; Ying Yin; Guang-Yu Xu

    2007-01-01

    As explored by biologists, there is a real and emerging need to identify co-regulated gene clusters, which includeboth positive and negative regulated gene clusters. However, the existing pattern-based and tendency-based clusteringapproaches are only designed for finding positive regulated gene clusters. In this paper, a new subspace clustering modelcalled g-Cluster is proposed for gene expression data. The proposed model has the following advantages: 1) find both positiveand negative co-regulated genes in a shot, 2) get away from the restriction of magnitude transformation relationship amongco-regulated genes, and 3) guarantee quality of clusters and significance of regulations using a novel similarity measurementgCode and a user-specified regulation threshold 5, respectively. No previous work measures up to the task which has been set.Moreover, MDL technique is introduced to avoid insignificant g-Clusters generated. A tree structure, namely GS-tree, is alsodesigned, and two algorithms combined with efficient pruning and optimization strategies to identify all qualified g-Clusters.Extensive experiments are conducted on real and synthetic datasets. The experimental results show that 1) the algorithmis able to find an amount of co-regulated gene clusters missed by previous models, which are potentially of high biologicalsignificance, and 2) the algorithms are effective and efficient, and outperform the existing approaches.

  14. Discovering and understanding oncogenic gene fusions through data intensive computational approaches.

    Science.gov (United States)

    Latysheva, Natasha S; Babu, M Madan

    2016-06-01

    Although gene fusions have been recognized as important drivers of cancer for decades, our understanding of the prevalence and function of gene fusions has been revolutionized by the rise of next-generation sequencing, advances in bioinformatics theory and an increasing capacity for large-scale computational biology. The computational work on gene fusions has been vastly diverse, and the present state of the literature is fragmented. It will be fruitful to merge three camps of gene fusion bioinformatics that appear to rarely cross over: (i) data-intensive computational work characterizing the molecular biology of gene fusions; (ii) development research on fusion detection tools, candidate fusion prioritization algorithms and dedicated fusion databases and (iii) clinical research that seeks to either therapeutically target fusion transcripts and proteins or leverages advances in detection tools to perform large-scale surveys of gene fusion landscapes in specific cancer types. In this review, we unify these different-yet highly complementary and symbiotic-approaches with the view that increased synergy will catalyze advancements in gene fusion identification, characterization and significance evaluation. PMID:27105842

  15. A general co-expression network-based approach to gene expression analysis: comparison and applications

    Directory of Open Access Journals (Sweden)

    Zhang Weixiong

    2010-02-01

    Full Text Available Abstract Background Co-expression network-based approaches have become popular in analyzing microarray data, such as for detecting functional gene modules. However, co-expression networks are often constructed by ad hoc methods, and network-based analyses have not been shown to outperform the conventional cluster analyses, partially due to the lack of an unbiased evaluation metric. Results Here, we develop a general co-expression network-based approach for analyzing both genes and samples in microarray data. Our approach consists of a simple but robust rank-based network construction method, a parameter-free module discovery algorithm and a novel reference network-based metric for module evaluation. We report some interesting topological properties of rank-based co-expression networks that are very different from that of value-based networks in the literature. Using a large set of synthetic and real microarray data, we demonstrate the superior performance of our approach over several popular existing algorithms. Applications of our approach to yeast, Arabidopsis and human cancer microarray data reveal many interesting modules, including a fatal subtype of lymphoma and a gene module regulating yeast telomere integrity, which were missed by the existing methods. Conclusions We demonstrated that our novel approach is very effective in discovering the modular structures in microarray data, both for genes and for samples. As the method is essentially parameter-free, it may be applied to large data sets where the number of clusters is difficult to estimate. The method is also very general and can be applied to other types of data. A MATLAB implementation of our algorithm can be downloaded from http://cs.utsa.edu/~jruan/Software.html.

  16. A Boyer-Moore Approach to Degenerate Pattern Matching%基于BM方法的退化模式匹配算法

    Institute of Scientific and Technical Information of China (English)

    林劼; 林舒晔

    2012-01-01

    退化模式匹配问题在生物信息学中具有重要应用意义,但由于该问题的计算复杂度高,现有的算法均难以在实际中应用.在分析退化模式的特点以及经典的Boyer-Moore (BM)算法的基础上,提出基于BM算法框架解决退化模式匹配问题的方法.在计算偏移数组的预处理过程中,定义兼容规则并计算偏移数组,并将其应用在查找阶段,提高退化模式的匹配速度.在平均情况下,该算法提供了线性的模式匹配速度,在实际应用中得到良好的效果.%Degenerated pattern matching problem has important applications in biology sequences, however, due to the computational complexity of the problem, no existing algorithms can be used in practice. After analyzing the characteristics of degenerated pattern matching problem and classical Boyer-Moore (BM) algorithm, it proposes a practical BM based algorithm to tackle the problem. In the pre-process of computing shift arrays, the algorithm defines comparable rules and arrays, and uses them in the searching phase to improve the matching speed. In average case, the algorithm provides a linear time complexity which can be efficiently used in practice.

  17. Vaccine-induced modulation of gene expression in turbot peritoneal cells. A microarray approach.

    Science.gov (United States)

    Fontenla, Francisco; Blanco-Abad, Verónica; Pardo, Belén G; Folgueira, Iria; Noia, Manuel; Gómez-Tato, Antonio; Martínez, Paulino; Leiro, José M; Lamas, Jesús

    2016-07-01

    We used a microarray approach to examine changes in gene expression in turbot peritoneal cells after injection of the fish with vaccines containing the ciliate parasite Philasterides dicentrarchi as antigen and one of the following adjuvants: chitosan-PVMMA microspheres, Freund́s complete adjuvant, aluminium hydroxide gel or Matrix-Q (Isconova, Sweden). We identified 374 genes that were differentially expressed in all groups of fish. Forty-two genes related to tight junctions and focal adhesions and/or actin cytoskeleton were differentially expressed in free peritoneal cells. The profound changes in gene expression related to cell adherence and cytoskeleton may be associated with cell migration and also with the formation of cell-vaccine masses and their attachment to the peritoneal wall. Thirty-five genes related to apoptosis were differentially expressed. Although most of the proteins coded by these genes have a proapoptotic effect, others are antiapoptotic, indicating that both types of signals occur in peritoneal leukocytes of vaccinated fish. Interestingly, many of the genes related to lymphocytes and lymphocyte activity were downregulated in the groups injected with vaccine. We also observed decreased expression of genes related to antigen presentation, suggesting that macrophages (which were abundant in the peritoneal cavity after vaccination) did not express these during the early inflammatory response in the peritoneal cavity. Finally, several genes that participate in the inflammatory response were differentially expressed, and most participated in resolution of inflammation, indicating that an M2 macrophage response is generated in the peritoneal cavity of fish one day post vaccination. PMID:27318565

  18. Gene prediction in metagenomic fragments: A large scale machine learning approach

    Directory of Open Access Journals (Sweden)

    Morgenstern Burkhard

    2008-04-01

    Full Text Available Abstract Background Metagenomics is an approach to the characterization of microbial genomes via the direct isolation of genomic sequences from the environment without prior cultivation. The amount of metagenomic sequence data is growing fast while computational methods for metagenome analysis are still in their infancy. In contrast to genomic sequences of single species, which can usually be assembled and analyzed by many available methods, a large proportion of metagenome data remains as unassembled anonymous sequencing reads. One of the aims of all metagenomic sequencing projects is the identification of novel genes. Short length, for example, Sanger sequencing yields on average 700 bp fragments, and unknown phylogenetic origin of most fragments require approaches to gene prediction that are different from the currently available methods for genomes of single species. In particular, the large size of metagenomic samples requires fast and accurate methods with small numbers of false positive predictions. Results We introduce a novel gene prediction algorithm for metagenomic fragments based on a two-stage machine learning approach. In the first stage, we use linear discriminants for monocodon usage, dicodon usage and translation initiation sites to extract features from DNA sequences. In the second stage, an artificial neural network combines these features with open reading frame length and fragment GC-content to compute the probability that this open reading frame encodes a protein. This probability is used for the classification and scoring of gene candidates. With large scale training, our method provides fast single fragment predictions with good sensitivity and specificity on artificially fragmented genomic DNA. Additionally, this method is able to predict translation initiation sites accurately and distinguishes complete from incomplete genes with high reliability. Conclusion Large scale machine learning methods are well-suited for gene

  19. Hierarchical model of matching

    Science.gov (United States)

    Pedrycz, Witold; Roventa, Eugene

    1992-01-01

    The issue of matching two fuzzy sets becomes an essential design aspect of many algorithms including fuzzy controllers, pattern classifiers, knowledge-based systems, etc. This paper introduces a new model of matching. Its principal features involve the following: (1) matching carried out with respect to the grades of membership of fuzzy sets as well as some functionals defined on them (like energy, entropy,transom); (2) concepts of hierarchies in the matching model leading to a straightforward distinction between 'local' and 'global' levels of matching; and (3) a distributed character of the model realized as a logic-based neural network.

  20. Multivariate dimensionality reduction approaches to identify gene-gene and gene-environment interactions underlying multiple complex traits.

    Directory of Open Access Journals (Sweden)

    Hai-Ming Xu

    Full Text Available The elusive but ubiquitous multifactor interactions represent a stumbling block that urgently needs to be removed in searching for determinants involved in human complex diseases. The dimensionality reduction approaches are a promising tool for this task. Many complex diseases exhibit composite syndromes required to be measured in a cluster of clinical traits with varying correlations and/or are inherently longitudinal in nature (changing over time and measured dynamically at multiple time points. A multivariate approach for detecting interactions is thus greatly needed on the purposes of handling a multifaceted phenotype and longitudinal data, as well as improving statistical power for multiple significance testing via a two-stage testing procedure that involves a multivariate analysis for grouped phenotypes followed by univariate analysis for the phenotypes in the significant group(s. In this article, we propose a multivariate extension of generalized multifactor dimensionality reduction (GMDR based on multivariate generalized linear, multivariate quasi-likelihood and generalized estimating equations models. Simulations and real data analysis for the cohort from the Study of Addiction: Genetics and Environment are performed to investigate the properties and performance of the proposed method, as compared with the univariate method. The results suggest that the proposed multivariate GMDR substantially boosts statistical power.

  1. Identifying the genetic variation of gene expression using gene sets: application of novel gene Set eQTL approach to PharmGKB and KEGG.

    Directory of Open Access Journals (Sweden)

    Ryan Abo

    Full Text Available Genetic variation underlying the regulation of mRNA gene expression in humans may provide key insights into the molecular mechanisms of human traits and complex diseases. Current statistical methods to map genetic variation associated with mRNA gene expression have typically applied standard linkage and/or association methods; however, when genome-wide SNP and mRNA expression data are available performing all pair wise comparisons is computationally burdensome and may not provide optimal power to detect associations. Consideration of different approaches to account for the high dimensionality and multiple testing issues may provide increased efficiency and statistical power. Here we present a novel approach to model and test the association between genetic variation and mRNA gene expression levels in the context of gene sets (GSs and pathways, referred to as gene set - expression quantitative trait loci analysis (GS-eQTL. The method uses GSs to initially group SNPs and mRNA expression, followed by the application of principal components analysis (PCA to collapse the variation and reduce the dimensionality within the GSs. We applied GS-eQTL to assess the association between SNP and mRNA expression level data collected from a cell-based model system using PharmGKB and KEGG defined GSs. We observed a large number of significant GS-eQTL associations, in which the most significant associations arose between genetic variation and mRNA expression from the same GS. However, a number of associations involving genetic variation and mRNA expression from different GSs were also identified. Our proposed GS-eQTL method effectively addresses the multiple testing limitations in eQTL studies and provides biological context for SNP-expression associations.

  2. The Association between the Availability of Sugar-Sweetened Beverage in School Vending Machines and Its Consumption among Adolescents in California: A Propensity Score Matching Approach

    Directory of Open Access Journals (Sweden)

    Lu Shi

    2010-01-01

    Full Text Available There is controversy over to what degree banning sugar-sweetened beverage (SSB sales at schools could decrease the SSB intake. This paper uses the adolescent sample of 2005 California Health Interview Survey to estimate the association between the availability of SSB from school vending machines and the amount of SSB consumption. Propensity score stratification and kernel-based propensity score matching are used to address the selection bias issue in cross-sectional data. Propensity score stratification shows that adolescents who had access to SSB through their school vending machines consumed 0.170 more drinks of SSB than those who did not (<.05. Kernel-based propensity score matching shows the SSB consumption difference to be 0.158 on the prior day (<.05. This paper strengthens the evidence for the association between SSB availability via school vending machines and the actual SSB consumption, while future studies are needed to explore changes in other beverages after SSB becomes less available.

  3. Test of critical steps towards a combined cell and gene therapy approach for the treatment of Duchenne muscular dystrophy

    DEFF Research Database (Denmark)

    Kajhøj, Tine Qvistgaard; Duch, Mogens R.; Pedersen, Finn Skou;

    2015-01-01

    Background: Therapies for muscular dystrophies remain a major challenge in spite of advanced strategies using either cell or gene therapy. We here propose a combined approach of cell and gene therapy. As gene delivery vehicles with specific homing potential we have chosen mesoangioblasts which...

  4. An improved systematic approach to predicting transcription factor target genes using support vector machine.

    Directory of Open Access Journals (Sweden)

    Song Cui

    Full Text Available Biological prediction of transcription factor binding sites and their corresponding transcription factor target genes (TFTGs makes great contribution to understanding the gene regulatory networks. However, these approaches are based on laborious and time-consuming biological experiments. Numerous computational approaches have shown great potential to circumvent laborious biological methods. However, the majority of these algorithms provide limited performances and fail to consider the structural property of the datasets. We proposed a refined systematic computational approach for predicting TFTGs. Based on previous work done on identifying auxin response factor target genes from Arabidopsis thaliana co-expression data, we adopted a novel reverse-complementary distance-sensitive n-gram profile algorithm. This algorithm converts each upstream sub-sequence into a high-dimensional vector data point and transforms the prediction task into a classification problem using support vector machine-based classifier. Our approach showed significant improvement compared to other computational methods based on the area under curve value of the receiver operating characteristic curve using 10-fold cross validation. In addition, in the light of the highly skewed structure of the dataset, we also evaluated other metrics and their associated curves, such as precision-recall curves and cost curves, which provided highly satisfactory results.

  5. Pollen Sterility—A Promising Approach to Gene Confinement and Breeding for Genetically Modified Bioenergy Crops

    Directory of Open Access Journals (Sweden)

    Albert P. Kausch

    2012-10-01

    Full Text Available Advanced genetic and biotechnology tools will be required to realize the full potential of food and bioenergy crops. Given current regulatory concerns, many transgenic traits might never be deregulated for commercial release without a robust gene confinement strategy in place. The potential for transgene flow from genetically modified (GM crops is widely known. Pollen-mediated transfer is a major component of gene flow in flowering plants and therefore a potential avenue for the escape of transgenes from GM crops. One approach for preventing and/or mitigating transgene flow is the production of trait linked pollen sterility. To evaluate the feasibility of generating pollen sterility lines for gene confinement and breeding purposes we tested the utility of a promoter (Zm13Pro from a maize pollen-specific gene (Zm13 for driving expression of the reporter gene GUS and the cytotoxic gene barnase in transgenic rice (Oryza sativa ssp. Japonica cv. Nipponbare as a monocot proxy for bioenergy grasses. This study demonstrates that the Zm13 promoter can drive pollen-specific expression in stably transformed rice and may be useful for gametophytic transgene confinement and breeding strategies by pollen sterility in food and bioenergy crops.

  6. A systematic approach to mapping recessive disease genes in individuals from outbred populations.

    Directory of Open Access Journals (Sweden)

    Friedhelm Hildebrandt

    2009-01-01

    Full Text Available The identification of recessive disease-causing genes by homozygosity mapping is often restricted by lack of suitable consanguineous families. To overcome these limitations, we apply homozygosity mapping to single affected individuals from outbred populations. In 72 individuals of 54 kindred ascertained worldwide with known homozygous mutations in 13 different recessive disease genes, we performed total genome homozygosity mapping using 250,000 SNP arrays. Likelihood ratio Z-scores (ZLR were plotted across the genome to detect ZLR peaks that reflect segments of homozygosity by descent, which may harbor the mutated gene. In 93% of cases, the causative gene was positioned within a consistent ZLR peak of homozygosity. The number of peaks reflected the degree of inbreeding. We demonstrate that disease-causing homozygous mutations can be detected in single cases from outbred populations within a single ZLR peak of homozygosity as short as 2 Mb, containing an average of only 16 candidate genes. As many specialty clinics have access to cohorts of individuals from outbred populations, and as our approach will result in smaller genetic candidate regions, the new strategy of homozygosity mapping in single outbred individuals will strongly accelerate the discovery of novel recessive disease genes.

  7. A transgenic approach to controlling wheat seed dormancy level by using Triticeae DOG1-like genes.

    Science.gov (United States)

    Ashikawa, Ikuo; Mori, Masahiko; Nakamura, Shingo; Abe, Fumitaka

    2014-08-01

    Seed dormancy is an important agronomic trait: low levels can cause premature germination, while too much can inhibit uniform germination. As an approach to controlling the seed dormancy level in crops, we used Triticeae DOG1-like genes as transgenes. DOG1 is an Arabidopsis gene that underlies natural variation in seed dormancy. We previously showed that although their sequence similarities to DOG1 were low, some cereal DOG1-like genes enhanced seed dormancy in Arabidopsis. Here, we introduced two DOG1-like genes, TaDOG1L4 from wheat and HvDOG1L1 from barley, individually into the wheat cultivar Fielder. Their overexpression under the control of a maize ubiquitin promoter enhanced the seed dormancy level while leaving other traits unchanged. TaDOG1L4 was more effective than HvDOG1L1, which accords with the previously revealed difference in the effectiveness of these two genes in Arabidopsis seed dormancy. Knockdown of endogenous TaDOG1L4 in Fielder using double-strand RNA interference decreased the seed dormancy level by several tens of percent. This result indicates that some degree of seed dormancy inherent in wheat is imparted by DOG1-like genes. PMID:24752830

  8. Fingerprint matching algorithm for poor quality images

    OpenAIRE

    Vedpal Singh; Irraivan Elamvazuthi

    2015-01-01

    The main aim of this study is to establish an efficient platform for fingerprint matching for low-quality images. Generally, fingerprint matching approaches use the minutiae points for authentication. However, it is not such a reliable authentication method for low-quality images. To overcome this problem, the current study proposes a fingerprint matching methodology based on normalised cross-correlation, which would improve the performance and reduce the miscalculations during authentication...

  9. Investigating the Role of Child Sexual Abuse in Intimate Partner Violence Victimization and Perpetration in Young Adulthood From a Propensity Score Matching Approach.

    Science.gov (United States)

    Jennings, Wesley G; Richards, Tara N; Tomsich, Elizabeth; Gover, Angela R

    2015-01-01

    The link between child sexual abuse and adult intimate partner violence surfaces throughout prior research. Nonetheless, methodologies investigating this cycle of violence predominantly involve descriptive, correlational, or traditional regression-based analyses that preclude more definitive statements about the empirical relationship between child sexual abuse and adult partner violence. In recognition of these limitations, the current study presents a quasi-experimental investigation into the relationship between sexual abuse in childhood and physical partner violence victimization and/or perpetration in young adulthood. Propensity score matching analysis of a national data set sampling over 4,000 young adults suggests that experiencing child sexual abuse influences adult intimate partner violence victimization and perpetration. Study implications and directions for future research are discussed. PMID:26340073

  10. 基于曲率特征的自主车辆地图匹配定位方法%A Novel Localization Approach for Autonomous Vehicles Based on Map Matching with Curvature Features

    Institute of Scientific and Technical Information of China (English)

    苏奎峰; 邓志东; 黄振

    2012-01-01

    提出了一种新的基于曲率特征的自主车辆地图匹配定位方法,该方法通过计算自主车辆行驶轨迹和参考轨迹的尺度不变曲率积分特征及其相关性进行匹配,可以有效地消除因航迹推算(DR)传感器标定参数偏差和航向角估计偏差而引起的错误匹配问题.文中首先采用扩展卡尔曼滤波器融合惯性测量单元输出、方向盘转角和4个ABS(防抱死刹车系统)传感器测量的轮速,估计自主车辆的位姿状态,并据此从数字地图中选择匹配的候选路段.然后利用本文提出的曲率空间特征地图匹配算法实现路段匹配,并根据曲率和航向角变化确定匹配点,最后将其作为无迹卡尔曼滤波器的观测值更新滤波器,从而实现高精度的位姿估计.现场道路实验结果表明,该法能够有效地实现地图匹配,降低自主车辆DR产生的累积误差,从而能够在GPS(全球定位系统)信号失效情况下实现长距离精确定位.%Using the curvature features, a novel map-matching based localization approach for autonomous vehicles is proposed. By computing the scale-invariant curvature integral and its correlation of autonomous vehicle's historical and reference trajectories for matching, the proposed approach can effectively eliminate the mismatch problem caused by odometer calibration parameters bias and azimuth estimation errors in dead-reckoning (DR). Firstly, we integrate the inertial measurement unit output, steering angles, and wheel speed measurements from four ABS (anti-lock braking system) sensors by using the extended Kalman filter in order to estimate the autonomous vehicle's position and orientation, which are then used to select the candidate matching segments from digital maps. Then, a map matching algorithm based on spatial curvature features is proposed to accomplish segment matching, and matching points are determined according to the changes in curvature and yaw. Finally, these matching points

  11. Systematic Approach to Computational Design of Gene Regulatory Networks with Information Processing Capabilities.

    Science.gov (United States)

    Moskon, Miha; Mraz, Miha

    2014-01-01

    We present several measures that can be used in de novo computational design of biological systems with information processing capabilities. Their main purpose is to objectively evaluate the behavior and identify the biological information processing structures with the best dynamical properties. They can be used to define constraints that allow one to simplify the design of more complex biological systems. These measures can be applied to existent computational design approaches in synthetic biology, i.e., rational and automatic design approaches. We demonstrate their use on a) the computational models of several basic information processing structures implemented with gene regulatory networks and b) on a modular design of a synchronous toggle switch.

  12. PETModule: a motif module based approach for enhancer target gene prediction.

    Science.gov (United States)

    Zhao, Changyong; Li, Xiaoman; Hu, Haiyan

    2016-01-01

    The identification of enhancer-target gene (ETG) pairs is vital for the understanding of gene transcriptional regulation. Experimental approaches such as Hi-C have generated valuable resources of ETG pairs. Several computational methods have also been developed to successfully predict ETG interactions. Despite these progresses, high-throughput experimental approaches are still costly and existing computational approaches are still suboptimal and not easy to apply. Here we developed a motif module based approach called PETModule that predicts ETG pairs. Tested on eight human cell types and two mouse cell types, we showed that a large number of our predictions were supported by Hi-C and/or ChIA-PET experiments. Compared with two recently developed approaches for ETG pair prediction, we shown that PETModule had a much better recall, a similar or better F1 score, and a larger area under the receiver operating characteristic curve. The PETModule tool is freely available at http://hulab.ucf.edu/research/projects/PETModule/. PMID:27436110

  13. Testing a 'genes-to-ecosystems' approach to understanding aquatic-terrestrial linkages.

    Science.gov (United States)

    Crutsinger, Gregory M; Rudman, Seth M; Rodriguez-Cabal, Mariano A; McKown, Athena D; Sato, Takuya; MacDonald, Andrew M; Heavyside, Julian; Geraldes, Armando; Hart, Edmund M; LeRoy, Carri J; El-Sabaawi, Rana W

    2014-12-01

    A 'genes-to-ecosystems' approach has been proposed as a novel avenue for integrating the consequences of intraspecific genetic variation with the underlying genetic architecture of a species to shed light on the relationships among hierarchies of ecological organization (genes → individuals → communities → ecosystems). However, attempts to identify genes with major effect on the structure of communities and/or ecosystem processes have been limited and a comprehensive test of this approach has yet to emerge. Here, we present an interdisciplinary field study that integrated a common garden containing different genotypes of a dominant, riparian tree, Populus trichocarpa, and aquatic mesocosms to determine how intraspecific variation in leaf litter alters both terrestrial and aquatic communities and ecosystem functioning. Moreover, we incorporate data from extensive trait screening and genome-wide association studies estimating the heritability and genes associated with litter characteristics. We found that tree genotypes varied considerably in the quality and production of leaf litter, which contributed to variation in phytoplankton abundances, as well as nutrient dynamics and light availability in aquatic mesocosms. These 'after-life' effects of litter from different genotypes were comparable to the responses of terrestrial communities associated with the living foliage. We found that multiple litter traits corresponding with aquatic community and ecosystem responses differed in their heritability. Moreover, the underlying genetic architecture of these traits was complex, and many genes contributed only a small proportion to phenotypic variation. Our results provide further evidence that genetic variation is a key component of aquatic-terrestrial linkages, but challenge the ability to predict community or ecosystem responses based on the actions of one or a few genes.

  14. An Approach for Treating the Hepatobiliary Disease of Cystic Fibrosis by Somatic Gene Transfer

    Science.gov (United States)

    Yang, Yiping; Raper, Steven E.; Cohn, Jonathan A.; Engelhardt, John F.; Wilson, James M.

    1993-05-01

    Cystic fibrosis (CF) is an inherited disease of epithelial cell ion transport that is associated with pathology in multiple organ systems, including lung, pancreas, and liver. As treatment of the pulmonary manifestations of CF has improved, management of CF liver disease has become increasingly important in adult patients. This report describes an approach for treating CF liver disease by somatic gene transfer. In situ hybridization and immunocytochemistry analysis of rat liver sections indicated that the endogenous CFTR (cystic fibrosis transmembrane conductance regulator) gene is primarily expressed in the intrahepatic biliary epithelial cells. To specifically target recombinant genes to the biliary epithelium in vivo, recombinant adenoviruses expressing lacZ or human CFTR were infused retrograde into the biliary tract through the common bile duct. Conditions were established for achieving recombinant gene expression in virtually all cells of the intrahepatic bile ducts in vivo. Expression persisted in the smaller bile ducts for the duration of the experiment, which was 21 days. These studies suggest that it may be feasible to prevent CF liver disease by genetically reconstituting CFTR expression in the biliary tract, using an approach that is clinically feasible.

  15. An Integrated Approach to Gene Discovery and Marker Development in Atlantic Cod (Gadus morhua)

    OpenAIRE

    Bowman, Sharen; Hubert, Sophie; Higgins, Brent; Stone, Cynthia; Kimball, Jennifer; Borza, Tudor; Bussey, Jillian Tarrant; Simpson, Gary; Kozera, Catherine; Curtis, Bruce A.; Hall, Jennifer R.; Hori, Tiago S.; Feng, Charles Y.; Rise, Marlies; Booman, Marije

    2010-01-01

    Atlantic cod is a species that has been overexploited by the capture fishery. Programs to domesticate this species are underway in several countries, including Canada, to provide an alternative route for production. Selective breeding programs have been successfully applied in the domestication of other species, with genomics-based approaches used to augment conventional methods of animal production in recent years. Genomics tools, such as gene sequences and sets of variable markers, also hav...

  16. Development of a recA Gene-Based Identification Approach for the Entire Burkholderia Genus

    OpenAIRE

    Payne, George W.; Vandamme, Peter; Morgan, Sara H.; LiPuma, John J.; Coenye, Tom; Weightman, Andrew J.; Jones, T. Hefin; Mahenthiralingam, Eshwar

    2005-01-01

    Burkholderia is an important bacterial genus containing species of ecological, biotechnological, and pathogenic interest. With their taxonomy undergoing constant revision and the phenotypic similarity of several species, correct identification of Burkholderia is difficult. A genetic scheme based on the recA gene has greatly enhanced the identification of Burkholderia cepacia complex species. However, the PCR developed for the latter approach was limited by its specificity for the complex. By ...

  17. Next-generation sequencing approach for connecting secondary metabolites to biosynthetic gene clusters in fungi

    OpenAIRE

    Cacho, Ralph A.; Yi eTang; Yit-Heng eChooi

    2015-01-01

    Genomics has revolutionized the research on fungal secondary metabolite biosynthesis. To elucidate the molecular and enzymatic mechanisms underlying the biosynthesis of a specific secondary metabolite compound, the important first step is often to find the genes that responsible for its synthesis. The accessibility to fungal genome sequences allows the bypass of the cumbersome traditional library construction and screening approach. The advance in next-generation sequencing (NGS) technologies...

  18. Next-generation sequencing approach for connecting secondary metabolites to biosynthetic gene clusters in fungi

    OpenAIRE

    Cacho, Ralph A.; Tang, Yi; Chooi, Yit-Heng

    2015-01-01

    Genomics has revolutionized the research on fungal secondary metabolite (SM) biosynthesis. To elucidate the molecular and enzymatic mechanisms underlying the biosynthesis of a specific SM compound, the important first step is often to find the genes that responsible for its synthesis. The accessibility to fungal genome sequences allows the bypass of the cumbersome traditional library construction and screening approach. The advance in next-generation sequencing (NGS) technologies have further...

  19. Efficacious and safe tissue-selective controlled gene therapy approaches for the cornea.

    Science.gov (United States)

    Mohan, Rajiv R; Sinha, Sunilima; Tandon, Ashish; Gupta, Rangan; Tovey, Jonathan C K; Sharma, Ajay

    2011-04-12

    Untargeted and uncontrolled gene delivery is a major cause of gene therapy failure. This study aimed to define efficient and safe tissue-selective targeted gene therapy approaches for delivering genes into keratocytes of the cornea in vivo using a normal or diseased rabbit model. New Zealand White rabbits, adeno-associated virus serotype 5 (AAV5), and a minimally invasive hair-dryer based vector-delivery technique were used. Fifty microliters of AAV5 titer (6.5×10(12) vg/ml) expressing green fluorescent protein gene (GFP) was topically applied onto normal or diseased (fibrotic or neovascularized) rabbit corneas for 2-minutes with a custom vector-delivery technique. Corneal fibrosis and neovascularization in rabbit eyes were induced with photorefractive keratectomy using excimer laser and VEGF (630 ng) using micropocket assay, respectively. Slit-lamp biomicroscopy and immunocytochemistry were used to confirm fibrosis and neovascularization in rabbit corneas. The levels, location and duration of delivered-GFP gene expression in the rabbit stroma were measured with immunocytochemistry and/or western blotting. Slot-blot measured delivered-GFP gene copy number. Confocal microscopy performed in whole-mounts of cornea and thick corneal sections determined geometric and spatial localization of delivered-GFP in three-dimensional arrangement. AAV5 toxicity and safety were evaluated with clinical eye exam, stereomicroscopy, slit-lamp biomicroscopy, and H&E staining. A single 2-minute AAV5 topical application via custom delivery-technique efficiently and selectively transduced keratocytes in the anterior stroma of normal and diseased rabbit corneas as evident from immunocytochemistry and confocal microscopy. Transgene expression was first detected at day 3, peaked at day 7, and was maintained up to 16 weeks (longest tested time point). Clinical and slit-lamp eye examination in live rabbits and H&E staining did not reveal any significant changes between AAV5-treated and

  20. Efficacious and safe tissue-selective controlled gene therapy approaches for the cornea.

    Directory of Open Access Journals (Sweden)

    Rajiv R Mohan

    Full Text Available Untargeted and uncontrolled gene delivery is a major cause of gene therapy failure. This study aimed to define efficient and safe tissue-selective targeted gene therapy approaches for delivering genes into keratocytes of the cornea in vivo using a normal or diseased rabbit model. New Zealand White rabbits, adeno-associated virus serotype 5 (AAV5, and a minimally invasive hair-dryer based vector-delivery technique were used. Fifty microliters of AAV5 titer (6.5×10(12 vg/ml expressing green fluorescent protein gene (GFP was topically applied onto normal or diseased (fibrotic or neovascularized rabbit corneas for 2-minutes with a custom vector-delivery technique. Corneal fibrosis and neovascularization in rabbit eyes were induced with photorefractive keratectomy using excimer laser and VEGF (630 ng using micropocket assay, respectively. Slit-lamp biomicroscopy and immunocytochemistry were used to confirm fibrosis and neovascularization in rabbit corneas. The levels, location and duration of delivered-GFP gene expression in the rabbit stroma were measured with immunocytochemistry and/or western blotting. Slot-blot measured delivered-GFP gene copy number. Confocal microscopy performed in whole-mounts of cornea and thick corneal sections determined geometric and spatial localization of delivered-GFP in three-dimensional arrangement. AAV5 toxicity and safety were evaluated with clinical eye exam, stereomicroscopy, slit-lamp biomicroscopy, and H&E staining. A single 2-minute AAV5 topical application via custom delivery-technique efficiently and selectively transduced keratocytes in the anterior stroma of normal and diseased rabbit corneas as evident from immunocytochemistry and confocal microscopy. Transgene expression was first detected at day 3, peaked at day 7, and was maintained up to 16 weeks (longest tested time point. Clinical and slit-lamp eye examination in live rabbits and H&E staining did not reveal any significant changes between AAV5

  1. Uncertain Schema Matching

    CERN Document Server

    Gal, Avigdor

    2011-01-01

    Schema matching is the task of providing correspondences between concepts describing the meaning of data in various heterogeneous, distributed data sources. Schema matching is one of the basic operations required by the process of data and schema integration, and thus has a great effect on its outcomes, whether these involve targeted content delivery, view integration, database integration, query rewriting over heterogeneous sources, duplicate data elimination, or automatic streamlining of workflow activities that involve heterogeneous data sources. Although schema matching research has been o

  2. Tissue-engineering strategies to repair joint tissue in osteoarthritis: nonviral gene-transfer approaches.

    Science.gov (United States)

    Madry, Henning; Cucchiarini, Magali

    2014-10-01

    Loss of articular cartilage is a common clinical consequence of osteoarthritis (OA). In the past decade, substantial progress in tissue engineering, nonviral gene transfer, and cell transplantation have provided the scientific foundation for generating cartilaginous constructs from genetically modified cells. Combining tissue engineering with overexpression of therapeutic genes enables immediate filling of a cartilage defect with an engineered construct that actively supports chondrogenesis. Several pioneering studies have proved that spatially defined nonviral overexpression of growth-factor genes in constructs of solid biomaterials or hydrogels is advantageous compared with gene transfer or scaffold alone, both in vitro and in vivo. Notably, these investigations were performed in models of focal cartilage defects, because advanced cartilage-repair strategies based on the principles of tissue engineering have not advanced sufficiently to enable resurfacing of extensively degraded cartilage as therapy for OA. These studies serve as prototypes for future technological developments, because they raise the possibility that cartilage constructs engineered from genetically modified chondrocytes providing autocrine and paracrine stimuli could similarly compensate for the loss of articular cartilage in OA. Because cartilage-tissue-engineering strategies are already used in the clinic, combining tissue engineering and nonviral gene transfer could prove a powerful approach to treat OA.

  3. A combined approach exploring gene function based on Worm-Human Orthology

    Directory of Open Access Journals (Sweden)

    Johnsen Robert

    2005-05-01

    Full Text Available Abstract Background Many aspects of the nematode Caenorhabditis elegans biology are conserved between invertebrates and vertebrates establishing this particular organism as an excellent genetic model. Because of its small size, large populations and self-fertilization of the hermaphrodite, functional predictions carried out by genetic modifications as well as RNAi screens, can be rapidly tested. Results In order to explore the function of a set of C. elegans genes of unknown function, as well as their potential functional roles in the human genome, we performed a phylogenetic analysis to select the most probable worm orthologs. A total of 13 C. elegans genes were subjected to down- regulation via RNAi and characterization of expression profiles using GFP strains. Previously unknown distinct expression patterns were observed for four of the analyzed genes, as well as four visible RNAi phenotypes. In addition, subcellular protein over-expression profiles of the human orthologs for seven out of the thirteen genes using human cells were also analyzed. Conclusion By combining a whole-organism approach using C. elegans with complementary experimental work done on human cell lines, this analysis extends currently available information on the selected set of genes.

  4. An Approach for Predicting Essential Genes Using Multiple Homology Mapping and Machine Learning Algorithms

    Science.gov (United States)

    Hua, Hong-Li; Zhang, Fa-Zhan; Labena, Abraham Alemayehu; Dong, Chuan; Jin, Yan-Ting

    2016-01-01

    Investigation of essential genes is significant to comprehend the minimal gene sets of cell and discover potential drug targets. In this study, a novel approach based on multiple homology mapping and machine learning method was introduced to predict essential genes. We focused on 25 bacteria which have characterized essential genes. The predictions yielded the highest area under receiver operating characteristic (ROC) curve (AUC) of 0.9716 through tenfold cross-validation test. Proper features were utilized to construct models to make predictions in distantly related bacteria. The accuracy of predictions was evaluated via the consistency of predictions and known essential genes of target species. The highest AUC of 0.9552 and average AUC of 0.8314 were achieved when making predictions across organisms. An independent dataset from Synechococcus elongatus, which was released recently, was obtained for further assessment of the performance of our model. The AUC score of predictions is 0.7855, which is higher than other methods. This research presents that features obtained by homology mapping uniquely can achieve quite great or even better results than those integrated features. Meanwhile, the work indicates that machine learning-based method can assign more efficient weight coefficients than using empirical formula based on biological knowledge.

  5. Gene networks associated with conditional fear in mice identified using a systems genetics approach

    Directory of Open Access Journals (Sweden)

    Eskin Eleazar

    2011-03-01

    Full Text Available Abstract Background Our understanding of the genetic basis of learning and memory remains shrouded in mystery. To explore the genetic networks governing the biology of conditional fear, we used a systems genetics approach to analyze a hybrid mouse diversity panel (HMDP with high mapping resolution. Results A total of 27 behavioral quantitative trait loci were mapped with a false discovery rate of 5%. By integrating fear phenotypes, transcript profiling data from hippocampus and striatum and also genotype information, two gene co-expression networks correlated with context-dependent immobility were identified. We prioritized the key markers and genes in these pathways using intramodular connectivity measures and structural equation modeling. Highly connected genes in the context fear modules included Psmd6, Ube2a and Usp33, suggesting an important role for ubiquitination in learning and memory. In addition, we surveyed the architecture of brain transcript regulation and demonstrated preservation of gene co-expression modules in hippocampus and striatum, while also highlighting important differences. Rps15a, Kif3a, Stard7, 6330503K22RIK, and Plvap were among the individual genes whose transcript abundance were strongly associated with fear phenotypes. Conclusion Application of our multi-faceted mapping strategy permits an increasingly detailed characterization of the genetic networks underlying behavior.

  6. Identification of Differentially Expressed Genes in RNA-seq Data of Arabidopsis thaliana: A Compound Distribution Approach

    Science.gov (United States)

    Anjum, Arfa; Jaggi, Seema; Lall, Shwetank; Bhowmik, Arpan; Rai, Anil

    2016-01-01

    Abstract Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product, which may be proteins. A gene is declared differentially expressed if an observed difference or change in read counts or expression levels between two experimental conditions is statistically significant. To identify differentially expressed genes between two conditions, it is important to find statistical distributional property of the data to approximate the nature of differential genes. In the present study, the focus is mainly to investigate the differential gene expression analysis for sequence data based on compound distribution model. This approach was applied in RNA-seq count data of Arabidopsis thaliana and it has been found that compound Poisson distribution is more appropriate to capture the variability as compared with Poisson distribution. Thus, fitting of appropriate distribution to gene expression data provides statistically sound cutoff values for identifying differentially expressed genes. PMID:26949988

  7. A hybrid gene selection approach for microarray data classification using cellular learning automata and ant colony optimization.

    Science.gov (United States)

    Vafaee Sharbaf, Fatemeh; Mosafer, Sara; Moattar, Mohammad Hossein

    2016-06-01

    This paper proposes an approach for gene selection in microarray data. The proposed approach consists of a primary filter approach using Fisher criterion which reduces the initial genes and hence the search space and time complexity. Then, a wrapper approach which is based on cellular learning automata (CLA) optimized with ant colony method (ACO) is used to find the set of features which improve the classification accuracy. CLA is applied due to its capability to learn and model complicated relationships. The selected features from the last phase are evaluated using ROC curve and the most effective while smallest feature subset is determined. The classifiers which are evaluated in the proposed framework are K-nearest neighbor; support vector machine and naïve Bayes. The proposed approach is evaluated on 4 microarray datasets. The evaluations confirm that the proposed approach can find the smallest subset of genes while approaching the maximum accuracy. PMID:27154739

  8. The ethics of germ-line gene therapy: challenges to mainstream approaches by a feminist critique.

    Science.gov (United States)

    Perlman, D

    1993-01-01

    Many mainstream bioethicists visualize the ethical debate surrounding germ-line gene therapy (GLGT) as a conflict of rights and duties between a woman and her fetus and as representative of the larger tension between the principles of autonomy and beneficence and its corollary duty to nonmaleficence. Many feminist ethicists attempt to circumnavigate the purported inadequacies of mainstream ethical approaches and take a much broader, context-oriented approach to reproductive freedom. The first section will describe many of the mainstream conflicts surrounding GLGT and offer a feminist critique of the inadequacies of mainstream approaches. Instead of merely achieving a stalemate in ethical dialogue from the mainstream viewpoint, the application of a feminist view of the fetus and reproductive freedom provides a more equitable and ethically inclusive adjudication of the central issue surrounding the ethics of GLGT, as the second section will show. PMID:8118148

  9. [MATCHE: Management Approach to Teaching Consumer and Homemaking Education.] Occupational Strand: Management. Module II-F-2: Occupational Preparation for Jobs Utilizing Housekeeping Skills.

    Science.gov (United States)

    Karikka, Katherine

    This competency-based preservice home economics teacher education module on occupational preparation for jobs utilizing housekeeping skills is the second in a set of two modules on occupational programs related to home management. (This set is part of a larger set of sixty-seven modules on the Management Approach to Teaching Consumer and…

  10. An Integrated Data Driven Approach to Drug Repositioning Using Gene-Disease Associations.

    Science.gov (United States)

    Mullen, Joseph; Cockell, Simon J; Woollard, Peter; Wipat, Anil

    2016-01-01

    Drug development is both increasing in cost whilst decreasing in productivity. There is a general acceptance that the current paradigm of R&D needs to change. One alternative approach is drug repositioning. With target-based approaches utilised heavily in the field of drug discovery, it becomes increasingly necessary to have a systematic method to rank gene-disease associations. Although methods already exist to collect, integrate and score these associations, they are often not a reliable reflection of expert knowledge. Furthermore, the amount of data available in all areas covered by bioinformatics is increasing dramatically year on year. It thus makes sense to move away from more generalised hypothesis driven approaches to research to one that allows data to generate their own hypothesis. We introduce an integrated, data driven approach to drug repositioning. We first apply a Bayesian statistics approach to rank 309,885 gene-disease associations using existing knowledge. Ranked associations are then integrated with other biological data to produce a semantically-rich drug discovery network. Using this network, we show how our approach identifies diseases of the central nervous system (CNS) to be an area of interest. CNS disorders are identified due to the low numbers of such disorders that currently have marketed treatments, in comparison to other therapeutic areas. We then systematically mine our network for semantic subgraphs that allow us to infer drug-disease relations that are not captured in the network. We identify and rank 275,934 drug-disease has_indication associations after filtering those that are more likely to be side effects, whilst commenting on the top ranked associations in more detail. The dataset has been created in Neo4j and is available for download at https://bitbucket.org/ncl-intbio/genediseaserepositioning along with a Java implementation of the searching algorithm. PMID:27196054

  11. Screening currency notes for microbial pathogens and antibiotic resistance genes using a shotgun metagenomic approach.

    Directory of Open Access Journals (Sweden)

    Saakshi Jalali

    Full Text Available Fomites are a well-known source of microbial infections and previous studies have provided insights into the sojourning microbiome of fomites from various sources. Paper currency notes are one of the most commonly exchanged objects and its potential to transmit pathogenic organisms has been well recognized. Approaches to identify the microbiome associated with paper currency notes have been largely limited to culture dependent approaches. Subsequent studies portrayed the use of 16S ribosomal RNA based approaches which provided insights into the taxonomical distribution of the microbiome. However, recent techniques including shotgun sequencing provides resolution at gene level and enable estimation of their copy numbers in the metagenome. We investigated the microbiome of Indian paper currency notes using a shotgun metagenome sequencing approach. Metagenomic DNA isolated from samples of frequently circulated denominations of Indian currency notes were sequenced using Illumina Hiseq sequencer. Analysis of the data revealed presence of species belonging to both eukaryotic and prokaryotic genera. The taxonomic distribution at kingdom level revealed contigs mapping to eukaryota (70%, bacteria (9%, viruses and archae (~1%. We identified 78 pathogens including Staphylococcus aureus, Corynebacterium glutamicum, Enterococcus faecalis, and 75 cellulose degrading organisms including Acidothermus cellulolyticus, Cellulomonas flavigena and Ruminococcus albus. Additionally, 78 antibiotic resistance genes were identified and 18 of these were found in all the samples. Furthermore, six out of 78 pathogens harbored at least one of the 18 common antibiotic resistance genes. To the best of our knowledge, this is the first report of shotgun metagenome sequence dataset of paper currency notes, which can be useful for future applications including as bio-surveillance of exchangeable fomites for infectious agents.

  12. Screening currency notes for microbial pathogens and antibiotic resistance genes using a shotgun metagenomic approach.

    Science.gov (United States)

    Jalali, Saakshi; Kohli, Samantha; Latka, Chitra; Bhatia, Sugandha; Vellarikal, Shamsudheen Karuthedath; Sivasubbu, Sridhar; Scaria, Vinod; Ramachandran, Srinivasan

    2015-01-01

    Fomites are a well-known source of microbial infections and previous studies have provided insights into the sojourning microbiome of fomites from various sources. Paper currency notes are one of the most commonly exchanged objects and its potential to transmit pathogenic organisms has been well recognized. Approaches to identify the microbiome associated with paper currency notes have been largely limited to culture dependent approaches. Subsequent studies portrayed the use of 16S ribosomal RNA based approaches which provided insights into the taxonomical distribution of the microbiome. However, recent techniques including shotgun sequencing provides resolution at gene level and enable estimation of their copy numbers in the metagenome. We investigated the microbiome of Indian paper currency notes using a shotgun metagenome sequencing approach. Metagenomic DNA isolated from samples of frequently circulated denominations of Indian currency notes were sequenced using Illumina Hiseq sequencer. Analysis of the data revealed presence of species belonging to both eukaryotic and prokaryotic genera. The taxonomic distribution at kingdom level revealed contigs mapping to eukaryota (70%), bacteria (9%), viruses and archae (~1%). We identified 78 pathogens including Staphylococcus aureus, Corynebacterium glutamicum, Enterococcus faecalis, and 75 cellulose degrading organisms including Acidothermus cellulolyticus, Cellulomonas flavigena and Ruminococcus albus. Additionally, 78 antibiotic resistance genes were identified and 18 of these were found in all the samples. Furthermore, six out of 78 pathogens harbored at least one of the 18 common antibiotic resistance genes. To the best of our knowledge, this is the first report of shotgun metagenome sequence dataset of paper currency notes, which can be useful for future applications including as bio-surveillance of exchangeable fomites for infectious agents.

  13. A Genome-Wide Methylation Approach Identifies a New Hypermethylated Gene Panel in Ulcerative Colitis

    Science.gov (United States)

    Kang, Keunsoo; Bae, Jin-Han; Han, Kyudong; Kim, Eun Soo; Kim, Tae-Oh; Yi, Joo Mi

    2016-01-01

    The cause of inflammatory bowel disease (IBD) is still unknown, but there is growing evidence that environmental factors such as epigenetic changes can contribute to the disease etiology. The aim of this study was to identify newly hypermethylated genes in ulcerative colitis (UC) using a genome-wide DNA methylation approach. Using an Infinium HumanMethylation450 BeadChip array, we screened the DNA methylation changes in three normal colon controls and eight UC patients. Using these methylation profiles, 48 probes associated with CpG promoter methylation showed differential hypermethylation between UC patients and normal controls. Technical validations for methylation analyses in a larger series of UC patients (n = 79) were performed by methylation-specific PCR (MSP) and bisulfite sequencing analysis. We finally found that three genes (FAM217B, KIAA1614 and RIBC2) that were significantly elevating the promoter methylation levels in UC compared to normal controls. Interestingly, we confirmed that three genes were transcriptionally silenced in UC patient samples by qRT-PCR, suggesting that their silencing is correlated with the promoter hypermethylation. Pathway analyses were performed using GO and KEGG databases with differentially hypermethylated genes in UC. Our results highlight that aberrant hypermethylation was identified in UC patients which can be a potential biomarker for detecting UC. Moreover, pathway-enriched hypermethylated genes are possibly implicating important cellular function in the pathogenesis of UC. Overall, this study describes a newly hypermethylated gene panel in UC patients and provides new clinical information that can be used for the diagnosis and therapeutic treatment of IBD. PMID:27517910

  14. Gene network homology in prokaryotes using a similarity search approach: queries of quorum sensing signal transduction.

    Directory of Open Access Journals (Sweden)

    David N Quan

    Full Text Available Bacterial cell-cell communication is mediated by small signaling molecules known as autoinducers. Importantly, autoinducer-2 (AI-2 is synthesized via the enzyme LuxS in over 80 species, some of which mediate their pathogenicity by recognizing and transducing this signal in a cell density dependent manner. AI-2 mediated phenotypes are not well understood however, as the means for signal transduction appears varied among species, while AI-2 synthesis processes appear conserved. Approaches to reveal the recognition pathways of AI-2 will shed light on pathogenicity as we believe recognition of the signal is likely as important, if not more, than the signal synthesis. LMNAST (Local Modular Network Alignment Similarity Tool uses a local similarity search heuristic to study gene order, generating homology hits for the genomic arrangement of a query gene sequence. We develop and apply this tool for the E. coli lac and LuxS regulated (Lsr systems. Lsr is of great interest as it mediates AI-2 uptake and processing. Both test searches generated results that were subsequently analyzed through a number of different lenses, each with its own level of granularity, from a binary phylogenetic representation down to trackback plots that preserve genomic organizational information. Through a survey of these results, we demonstrate the identification of orthologs, paralogs, hitchhiking genes, gene loss, gene rearrangement within an operon context, and also horizontal gene transfer (HGT. We found a variety of operon structures that are consistent with our hypothesis that the signal can be perceived and transduced by homologous protein complexes, while their regulation may be key to defining subsequent phenotypic behavior.

  15. Towards the perfect prediction of soccer matches

    OpenAIRE

    Heuer, Andreas; Rubner, Oliver

    2012-01-01

    We present a systematic approach to the prediction of soccer matches. First, we show that the information about chances for goals is by far more informative than about the actual results. Second, we present a multivariate regression approach and show how the prediction quality increases with increasing information content. This prediction quality can be explicitly expressed in terms of just two parameters. Third, by disentangling the systematic and random components of soccer matches we can i...

  16. Snapshot of the eukaryotic gene expression in muskoxen rumen--a metatranscriptomic approach.

    Directory of Open Access Journals (Sweden)

    Meng Qi

    Full Text Available BACKGROUND: Herbivores rely on digestive tract lignocellulolytic microorganisms, including bacteria, fungi and protozoa, to derive energy and carbon from plant cell wall polysaccharides. Culture independent metagenomic studies have been used to reveal the genetic content of the bacterial species within gut microbiomes. However, the nature of the genes encoded by eukaryotic protozoa and fungi within these environments has not been explored using metagenomic or metatranscriptomic approaches. METHODOLOGY/PRINCIPAL FINDINGS: In this study, a metatranscriptomic approach was used to investigate the functional diversity of the eukaryotic microorganisms within the rumen of muskoxen (Ovibos moschatus, with a focus on plant cell wall degrading enzymes. Polyadenylated RNA (mRNA was sequenced on the Illumina Genome Analyzer II system and 2.8 gigabases of sequences were obtained and 59129 contigs assembled. Plant cell wall degrading enzyme modules including glycoside hydrolases, carbohydrate esterases and polysaccharide lyases were identified from over 2500 contigs. These included a number of glycoside hydrolase family 6 (GH6, GH48 and swollenin modules, which have rarely been described in previous gut metagenomic studies. CONCLUSIONS/SIGNIFICANCE: The muskoxen rumen metatranscriptome demonstrates a much higher percentage of cellulase enzyme discovery and an 8.7x higher rate of total carbohydrate active enzyme discovery per gigabase of sequence than previous rumen metagenomes. This study provides a snapshot of eukaryotic gene expression in the muskoxen rumen, and identifies a number of candidate genes coding for potentially valuable lignocellulolytic enzymes.

  17. From System-Wide Differential Gene Expression to Perturbed Regulatory Factors: A Combinatorial Approach.

    Directory of Open Access Journals (Sweden)

    Gaurang Mahajan

    Full Text Available High-throughput experiments such as microarrays and deep sequencing provide large scale information on the pattern of gene expression, which undergoes extensive remodeling as the cell dynamically responds to varying environmental cues or has its function disrupted under pathological conditions. An important initial step in the systematic analysis and interpretation of genome-scale expression alteration involves identification of a set of perturbed transcriptional regulators whose differential activity can provide a proximate hypothesis to account for these transcriptomic changes. In the present work, we propose an unbiased and logically natural approach to transcription factor enrichment. It involves overlaying a list of experimentally determined differentially expressed genes on a background regulatory network coming from e.g. literature curation or computational motif scanning, and identifying that subset of regulators whose aggregated target set best discriminates between the altered and the unaffected genes. In other words, our methodology entails testing of all possible regulatory subnetworks, rather than just the target sets of individual regulators as is followed in most standard approaches. We have proposed an iterative search method to efficiently find such a combination, and benchmarked it on E. coli microarray and regulatory network data available in the public domain. Comparative analysis carried out on artificially generated differential expression profiles, as well as empirical factor overexpression data for M. tuberculosis, shows that our methodology provides marked improvement in accuracy of regulatory inference relative to the standard method that involves evaluating factor enrichment in an individual manner.

  18. From System-Wide Differential Gene Expression to Perturbed Regulatory Factors: A Combinatorial Approach.

    Science.gov (United States)

    Mahajan, Gaurang; Mande, Shekhar C

    2015-01-01

    High-throughput experiments such as microarrays and deep sequencing provide large scale information on the pattern of gene expression, which undergoes extensive remodeling as the cell dynamically responds to varying environmental cues or has its function disrupted under pathological conditions. An important initial step in the systematic analysis and interpretation of genome-scale expression alteration involves identification of a set of perturbed transcriptional regulators whose differential activity can provide a proximate hypothesis to account for these transcriptomic changes. In the present work, we propose an unbiased and logically natural approach to transcription factor enrichment. It involves overlaying a list of experimentally determined differentially expressed genes on a background regulatory network coming from e.g. literature curation or computational motif scanning, and identifying that subset of regulators whose aggregated target set best discriminates between the altered and the unaffected genes. In other words, our methodology entails testing of all possible regulatory subnetworks, rather than just the target sets of individual regulators as is followed in most standard approaches. We have proposed an iterative search method to efficiently find such a combination, and benchmarked it on E. coli microarray and regulatory network data available in the public domain. Comparative analysis carried out on artificially generated differential expression profiles, as well as empirical factor overexpression data for M. tuberculosis, shows that our methodology provides marked improvement in accuracy of regulatory inference relative to the standard method that involves evaluating factor enrichment in an individual manner.

  19. From System-Wide Differential Gene Expression to Perturbed Regulatory Factors: A Combinatorial Approach.

    Science.gov (United States)

    Mahajan, Gaurang; Mande, Shekhar C

    2015-01-01

    High-throughput experiments such as microarrays and deep sequencing provide large scale information on the pattern of gene expression, which undergoes extensive remodeling as the cell dynamically responds to varying environmental cues or has its function disrupted under pathological conditions. An important initial step in the systematic analysis and interpretation of genome-scale expression alteration involves identification of a set of perturbed transcriptional regulators whose differential activity can provide a proximate hypothesis to account for these transcriptomic changes. In the present work, we propose an unbiased and logically natural approach to transcription factor enrichment. It involves overlaying a list of experimentally determined differentially expressed genes on a background regulatory network coming from e.g. literature curation or computational motif scanning, and identifying that subset of regulators whose aggregated target set best discriminates between the altered and the unaffected genes. In other words, our methodology entails testing of all possible regulatory subnetworks, rather than just the target sets of individual regulators as is followed in most standard approaches. We have proposed an iterative search method to efficiently find such a combination, and benchmarked it on E. coli microarray and regulatory network data available in the public domain. Comparative analysis carried out on artificially generated differential expression profiles, as well as empirical factor overexpression data for M. tuberculosis, shows that our methodology provides marked improvement in accuracy of regulatory inference relative to the standard method that involves evaluating factor enrichment in an individual manner. PMID:26562430

  20. Hitchhiking Effect Mapping: A New Approach for Discovering Agronomic Important Genes

    Institute of Scientific and Technical Information of China (English)

    ZHANG Xue-yong; TONG Yi-ping; YOU Guang-xia; HAO Chen-yang; GE Hong-mei; WANG Lan-fen; LI Bin; DONG Yu-shen; LI Zhen-sheng

    2007-01-01

    Besides the natural selection, the crops cultivated today have experienced two episodes of strong artificial selection,domestic and modern breeding. Domestication led to giant genetic structure differentiation between cultivars and their wild species, while modern breeding made further genetic structure differentiation between the modern varieties and the landraces. In a population, diversity of the loci under strong selection is significantly lower than that of other loci. At the same time, diversity in the genomic regions flanking these selected loci also declines in the process of selection. This phenomenon is called hitchhiking effects or selection sweep in genetics. Genomic regions with selection sweep (haplotype block) could be detected after draft genome scanning (genome typing) with molecular markers in a number of released varieties or natural populations. Marker/trait association analysis in these regions would detect the loci (or QTLs) even the favored alleles (genes) in breeding or natural adaptation. Fine scanning of these genomic regions would help to determine the sizes of haplotype blocks and to discover the key genes, thereby providing very valuable information for isolation of the key genes and molecular design of new varieties. Establishment of high density genetic linkage maps in the major crops and availability of high throughput genotyping platform make it possible to discover agronomic important genes through marker/trait association analysis. On the basis of available publications, we give a brief introduction of the hitchhiking effect mapping approach in this paper using plant height, 1 000-grain weight, and phosphorus-deficiency tolerance as examples in wheat.

  1. Experimental approaches for the study of oxytocin and vasopressin gene expression in the central nervous system

    Science.gov (United States)

    Scordalakes, Elka M.; Yue, Chunmei; Gainer, Harold

    2016-01-01

    Intron-specific probes measure heteronuclear RNA (hnRNA) levels and thus approximate the transcription rates of genes, in part because of the rapid turnover of this intermediate form of RNA in the cell nucleus. Previously, we used oxytocin (Oxt)- and vasopressin (Avp)- intron-specific riboprobes to measure changes in Oxt and Avp hnRNA levels in the supraoptic nucleus (SON) by quantitative in situ hybridization (ISH) after various classical physiological perturbations, including acute and chronic salt loading, and lactation. In the present experiments, we used a novel experimental model to study the neurotransmitter regulation of Oxt and Avp gene expression in the rat SON in vivo. Bilateral cannulae connected via tubing to Alzet osmotic mini-pumps were positioned over the SON. In every experiment, one SON was infused with PBS and served as the control SON in each animal, and the contralateral SON received infusions of various neurotransmitter agonists and antagonists. Using this approach, we found that Avp but not Oxt gene expression increased after acute (2–5 h) combined excitatory amino acid agonist and GABA antagonist treatment, similar to what we found after an acute hyperosmotic stimulus. Since both OXT and AVP are known to be comparably and robustly secreted in response to acute osmotic stimuli in vivo and glutamate agonists in vitro, our results indicate a dissociation between OXT secretion and Oxt gene transcription in vivo. PMID:18655870

  2. A Systems’ Biology Approach to Study MicroRNA-Mediated Gene Regulatory Networks

    Directory of Open Access Journals (Sweden)

    Xin Lai

    2013-01-01

    Full Text Available MicroRNAs (miRNAs are potent effectors in gene regulatory networks where aberrant miRNA expression can contribute to human diseases such as cancer. For a better understanding of the regulatory role of miRNAs in coordinating gene expression, we here present a systems biology approach combining data-driven modeling and model-driven experiments. Such an approach is characterized by an iterative process, including biological data acquisition and integration, network construction, mathematical modeling and experimental validation. To demonstrate the application of this approach, we adopt it to investigate mechanisms of collective repression on p21 by multiple miRNAs. We first construct a p21 regulatory network based on data from the literature and further expand it using algorithms that predict molecular interactions. Based on the network structure, a detailed mechanistic model is established and its parameter values are determined using data. Finally, the calibrated model is used to study the effect of different miRNA expression profiles and cooperative target regulation on p21 expression levels in different biological contexts.

  3. Rational design of modular circuits for gene transcription: A test of the bottom-up approach

    Directory of Open Access Journals (Sweden)

    Giordano Emanuele

    2010-11-01

    Full Text Available Abstract Background Most of synthetic circuits developed so far have been designed by an ad hoc approach, using a small number of components (i.e. LacI, TetR and a trial and error strategy. We are at the point where an increasing number of modular, inter-changeable and well-characterized components is needed to expand the construction of synthetic devices and to allow a rational approach to the design. Results We used interchangeable modular biological parts to create a set of novel synthetic devices for controlling gene transcription, and we developed a mathematical model of the modular circuits. Model parameters were identified by experimental measurements from a subset of modular combinations. The model revealed an unexpected feature of the lactose repressor system, i.e. a residual binding affinity for the operator site by induced lactose repressor molecules. Once this residual affinity was taken into account, the model properly reproduced the experimental data from the training set. The parameters identified in the training set allowed the prediction of the behavior of networks not included in the identification procedure. Conclusions This study provides new quantitative evidences that the use of independent and well-characterized biological parts and mathematical modeling, what is called a bottom-up approach to the construction of gene networks, can allow the design of new and different devices re-using the same modular parts.

  4. Identifying Liver Cancer and Its Relations with Diseases, Drugs, and Genes: A Literature-Based Approach

    Science.gov (United States)

    Song, Min

    2016-01-01

    In biomedicine, scientific literature is a valuable source for knowledge discovery. Mining knowledge from textual data has become an ever important task as the volume of scientific literature is growing unprecedentedly. In this paper, we propose a framework for examining a certain disease based on existing information provided by scientific literature. Disease-related entities that include diseases, drugs, and genes are systematically extracted and analyzed using a three-level network-based approach. A paper-entity network and an entity co-occurrence network (macro-level) are explored and used to construct six entity specific networks (meso-level). Important diseases, drugs, and genes as well as salient entity relations (micro-level) are identified from these networks. Results obtained from the literature-based literature mining can serve to assist clinical applications. PMID:27195695

  5. Use of metagenomic approaches to isolate lipolytic genes from activated sludge.

    Science.gov (United States)

    Liaw, Ren-Bao; Cheng, Mei-Ping; Wu, Ming-Che; Lee, Chia-Yin

    2010-11-01

    The aims of this study were to access the bacterial diversity and isolate lipolytic genes using the metagenomic approach in activated sludge of a swine wastewater treatment facility. On the basis of BLASTN analysis of 16S rRNA gene clones, most of these communities (90%) were of uncultivated bacteria. The metagenomic library was constructed using a plasmid vector and DNA extracted directly from activated sludge samples. The average insert size was approximately 5.1 kb. A total of 12 unique and lipolytic clones were obtained using the tributyrin plate assay. The rate of discovering a lipolytic clone in this study was as high as 0.31%. Molecular analysis revealed that most of the 16 putative lipolytic enzymes showed 28-55% identity with non-redundant protein sequences in the database. Briefly, this study demonstrates that activated sludge is an ideal bioresource for isolating new lipolytic enzymes. PMID:20639117

  6. A non-surgical approach for male germ cell mediated gene transmission through transgenesis.

    Science.gov (United States)

    Usmani, Abul; Ganguli, Nirmalya; Sarkar, Hironmoy; Dhup, Suveera; Batta, Suryaprakash R; Vimal, Manoj; Ganguli, Nilanjana; Basu, Sayon; Nagarajan, P; Majumdar, Subeer S

    2013-01-01

    Microinjection of foreign DNA in male pronucleus by in-vitro embryo manipulation is difficult but remains the method of choice for generating transgenic animals. Other procedures, including retroviral and embryonic stem cell mediated transgenesis are equally complicated and have limitations. Although our previously reported technique of testicular transgenesis circumvented several limitations, it involved many steps, including surgery and hemicastration, which carried risk of infection and impotency. We improved this technique further, into a two step non-surgical electroporation procedure, for making transgenic mice. In this approach, transgene was delivered inside both testes by injection and modified parameters of electroporation were used for in-vivo gene integration in germ cells. Using variety of constructs, germ cell integration of the gene and its transmission in progeny was confirmed by PCR, slot blot and immunohistochemical analysis. This improved technique is efficient, requires substantially less time and can be easily adopted by various biomedical researchers.

  7. Gene Pollution and its Therapeutical Approach (Communication Letter/Perspective View

    Directory of Open Access Journals (Sweden)

    M. Srinivasan

    2011-07-01

    Full Text Available Nature plays a role to retain healthy animals by the mechanism called struggle existence. Whereas, in human there are medicines to support even genetic ailment cases to live. As the result of many such events, our genome become like a bin to accumulate defective genes that replace normal genes. This process is just like rusting of iron. In future, the evolution of higher animals from the human origin may be affected or the survival of human being to the natural environment will not be easy as other animals living. Hence, new strategies in therapeutic approach to be considered. This letter discusses the sum of such factors and remedies to avoid the congenital diseases.

  8. Optimal Packed String Matching

    DEFF Research Database (Denmark)

    Ben-Kiki, Oren; Bille, Philip; Breslauer, Dany;

    2011-01-01

    In the packed string matching problem, each machine word accommodates – characters, thus an n-character text occupies n/– memory words. We extend the Crochemore-Perrin constantspace O(n)-time string matching algorithm to run in optimal O(n/–) time and even in real-time, achieving a factor – speedup...... over traditional algorithms that examine each character individually. Our solution can be efficiently implemented, unlike prior theoretical packed string matching work. We adapt the standard RAM model and only use its AC0 instructions (i.e., no multiplication) plus two specialized AC0 packed string...

  9. Identification of Lung-Cancer-Related Genes with the Shortest Path Approach in a Protein-Protein Interaction Network

    Directory of Open Access Journals (Sweden)

    Bi-Qing Li

    2013-01-01

    Full Text Available Lung cancer is one of the leading causes of cancer mortality worldwide. The main types of lung cancer are small cell lung cancer (SCLC and nonsmall cell lung cancer (NSCLC. In this work, a computational method was proposed for identifying lung-cancer-related genes with a shortest path approach in a protein-protein interaction (PPI network. Based on the PPI data from STRING, a weighted PPI network was constructed. 54 NSCLC- and 84 SCLC-related genes were retrieved from associated KEGG pathways. Then the shortest paths between each pair of these 54 NSCLC genes and 84 SCLC genes were obtained with Dijkstra’s algorithm. Finally, all the genes on the shortest paths were extracted, and 25 and 38 shortest genes with a permutation P value less than 0.05 for NSCLC and SCLC were selected for further analysis. Some of the shortest path genes have been reported to be related to lung cancer. Intriguingly, the candidate genes we identified from the PPI network contained more cancer genes than those identified from the gene expression profiles. Furthermore, these genes possessed more functional similarity with the known cancer genes than those identified from the gene expression profiles. This study proved the efficiency of the proposed method and showed promising results.

  10. A novel approach to simulate gene-environment interactions in complex diseases

    Directory of Open Access Journals (Sweden)

    Nicodemi Mario

    2010-01-01

    Full Text Available Abstract Background Complex diseases are multifactorial traits caused by both genetic and environmental factors. They represent the major part of human diseases and include those with largest prevalence and mortality (cancer, heart disease, obesity, etc.. Despite a large amount of information that has been collected about both genetic and environmental risk factors, there are few examples of studies on their interactions in epidemiological literature. One reason can be the incomplete knowledge of the power of statistical methods designed to search for risk factors and their interactions in these data sets. An improvement in this direction would lead to a better understanding and description of gene-environment interactions. To this aim, a possible strategy is to challenge the different statistical methods against data sets where the underlying phenomenon is completely known and fully controllable, for example simulated ones. Results We present a mathematical approach that models gene-environment interactions. By this method it is possible to generate simulated populations having gene-environment interactions of any form, involving any number of genetic and environmental factors and also allowing non-linear interactions as epistasis. In particular, we implemented a simple version of this model in a Gene-Environment iNteraction Simulator (GENS, a tool designed to simulate case-control data sets where a one gene-one environment interaction influences the disease risk. The main aim has been to allow the input of population characteristics by using standard epidemiological measures and to implement constraints to make the simulator behaviour biologically meaningful. Conclusions By the multi-logistic model implemented in GENS it is possible to simulate case-control samples of complex disease where gene-environment interactions influence the disease risk. The user has full control of the main characteristics of the simulated population and a Monte

  11. Splicing-correcting therapeutic approaches for retinal dystrophies: where endogenous gene regulation and specificity matter.

    Science.gov (United States)

    Bacchi, Niccolò; Casarosa, Simona; Denti, Michela A

    2014-05-27

    Splicing is an important and highly regulated step in gene expression. The ability to modulate it can offer a therapeutic option for many genetic disorders. Antisense-mediated splicing-correction approaches have recently been successfully exploited for some genetic diseases, and are currently demonstrating safety and efficacy in different clinical trials. Their application for the treatment of retinal dystrophies could potentially solve a vast panel of cases, as illustrated by the abundance of mutations that could be targeted and the versatility of the technique. In this review, we will give an insight of the different therapeutic strategies, focusing on the current status of their application for retinal dystrophies.

  12. Gene-splitting technology: a novel approach for the containment of transgene flow in Nicotiana tabacum.

    Directory of Open Access Journals (Sweden)

    Xu-Jing Wang

    Full Text Available The potential impact of transgene escape on the environment and food safety is a major concern to the scientists and public. This work aimed to assess the effect of intein-mediated gene splitting on containment of transgene flow. Two fusion genes, EPSPSn-In and Ic-EPSPSc, were constructed and integrated into N. tabacum, using Agrobacterium tumefaciens-mediated transformation. EPSPSn-In encodes the first 295 aa of the herbicide resistance gene 5-enolpyruvyl shikimate-3-phosphate synthase (EPSPS fused with the first 123 aa of the Ssp DnaE intein (In, whereas Ic-EPSPSc encodes the 36 C-terminal aa of the Ssp DnaE intein (Ic fused to the rest of EPSPS C terminus peptide sequences. Both EPSPSn-In and Ic-EPSPSc constructs were introduced into the same N. tabacum genome by genetic crossing. Hybrids displayed resistance to the herbicide N-(phosphonomethyl-glycine (glyphosate. Western blot analysis of protein extracts from hybrid plants identified full-length EPSPS. Furthermore, all hybrid seeds germinated and grew normally on glyphosate selective medium. The 6-8 leaf hybrid plants showed tolerance of 2000 ppm glyphosate in field spraying. These results indicated that functional EPSPS protein was reassembled in vivo by intein-mediated trans-splicing in 100% of plants. In order to evaluate the effect of the gene splitting technique for containment of transgene flow, backcrossing experiments were carried out between hybrids, in which the foreign genes EPSPSn-In and Ic-EPSPSc were inserted into different chromosomes, and non-transgenic plants NC89. Among the 2812 backcrossing progeny, about 25% (664 plantlets displayed glyphosate resistance. These data indicated that transgene flow could be reduced by 75%. Overall, our findings provide a new and highly effective approach for biological containment of transgene flow.

  13. Data Matching Imputation System

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The DMIS dataset is a flat file record of the matching of several data set collections. Primarily it consists of VTRs, dealer records, Observer data in conjunction...

  14. Learning Graphs to Match

    OpenAIRE

    Cho, Minsu; Alahari, Karteek; Ponce, Jean

    2013-01-01

    International audience Many tasks in computer vision are formulated as graph matching problems. Despite the NP-hard nature of the problem, fast and accurate approximations have led to significant progress in a wide range of applications. Learning graph models from observed data, however, still remains a challenging issue. This paper presents an effective scheme to parameterize a graph model, and learn its structural attributes for visual object matching. For this, we propose a graph repres...

  15. Matching with Contracts

    OpenAIRE

    John William Hatfield; Milgrom, Paul R.

    2005-01-01

    We develop a model of matching with contracts which incorporates, as special cases, the college admissions problem, the Kelso-Crawford labor market matching model, and ascending package auctions. We introduce a new "law of aggregate demand" for the case of discrete heterogeneous workers and show that, when workers are substitutes, this law is satisfied by profit-maximizing firms. When workers are substitutes and the law is satisfied, truthful reporting is a dominant strategy for workers in a ...

  16. Functional characterization of Drought-responsive Modules and Genes in Oryza sativa: A Network-based Approach

    Directory of Open Access Journals (Sweden)

    Sanchari eSircar

    2015-07-01

    Full Text Available Drought is one of the major environmental stress conditions affecting the yield of rice across the globe. Unraveling the functional roles of the drought-responsive genes and their underlying molecular mechanisms will provide important leads to improve the yield of rice. Co-expression relationships derived from condition-dependent gene expression data is an effective way to identify the functional associations between genes that are part of the same biological process and may be under similar transcriptional control. For this purpose, vast amount of freely available transcriptomic data can be used for functional annotation. In this study we consider gene expression data for different tissues and developmental stages in response to drought stress. We analyze the network of co-expressed genes to identify drought-responsive genes modules in a tissue and stage-specific manner based on differential expression and gene enrichment analysis. Taking cues from the systems-level behavior of these modules, we propose two approaches to identify clusters of tightly co-expressed/co-regulated genes. Using graph-centrality measures and differential gene expression, we identify biologically informative genes that lack any functional annotation. We show that using orthologous information from other plant species, the conserved co-expression patterns of the uncharacterized genes can be identified. Presence of a conserved neighborhood enables us to extrapolate functional annotation. Alternatively, we show that ‘guide-gene’ approach can help in understanding the tissue-specific transcriptional regulation of uncharacterized genes. Finally, we confirm the predicted roles of uncharacterized genes by the analysis of conserved cis-elements and explain the possible roles of these genes towards drought tolerance

  17. Molecular Approaches to Studying Microbial Communities: Targeting the 16S Ribosomal RNA Gene.

    Science.gov (United States)

    Fukuda, Kazumasa; Ogawa, Midori; Taniguchi, Hatsumi; Saito, Mitsumasa

    2016-09-01

    Culture-independent methods to detect microorganisms have been developed in parallel with traditional culture-based methods ever since the classification of bacteria based on 16S rRNA gene sequences was advocated in the 1970s. The development and the prevalence of culture-independent molecular technologies have provided revolutionary progress in microbial studies. The development of these technologies contributes significantly to the research of microorganisms that cannot be detected by traditional methods such as culture-dependent methods.Many molecular methods targeting the 16S rRNA gene, such as fluorescence in situ hybridization (FISH), quantitative PCR, terminal restriction fragment length polymorphism (T-RFLP), denaturing-gradient gel electrophoresis (DGGE), clone library analysis, and next-generation DNA sequencing (NGS) technologies, have been applied to various microbial studies. Notably, the advent of NGS technologies enabled a large-scale research of the bacterial community. Many recent studies using the NGS technologies have revealed that a larger number of bacteria and taxa than previously thought inhabit various parts of the human body and various places on the earth. The principles and characteristics of each molecular method are different, and each method possesses individual advantages; for example target specificity, comprehensiveness, rapidness, and cost efficiency. Therefore it is important that the methods used in studies are suitable for the objective and materials. Herein, we highlights molecular approaches targeting the 16S rRNA gene in bacterial community analysis, and focuses on the advantages and limitations of each technology. PMID:27627970

  18. Molecular genetic approach to human meningioma: loss of genes on chromosome 22

    Energy Technology Data Exchange (ETDEWEB)

    Seizinger, B.R.; De La Monte, S.; Atkins, L.; Gusella, J.F.; Martuza, R.L.

    1987-08-01

    A molecular genetic approach employing polymorphic DNA markers has been used to investigate the role of chromosomal aberrations in meningioma, one of the most common tumors of the human nervous system. Comparison of the alleles detected by DNA markers in tumor DNA versus DNA from normal tissue revealed chromosomal alterations present in primary surgical specimens. In agreement with cytogenetic studies of cultured meningiomas, the most frequent alteration detected was loss of heterozygosity on chromosome 22. Forty of 51 patients were constitutionally heterozygous for at least one chromosome 22 DNA marker. Seventeen of the 40 constitutionally heterozygotic patients (43%) displayed hemizygosity for the corresponding marker in their meningioma tumor tissues. Loss of heterozygosity was also detected at a significantly lower frequency for markers on several other autosomes. In view of the striking association between acoustic neuroma and meningioma in bilateral acoustic neurofibromatosis and the discovery that acoustic neuromas display specific loss of genes on chromosome 22, the authors propose that a common mechanism involving chromosome 22 is operative in the development of both tumor types. Fine-structure mapping to reveal partial deletions in meningiomas may provide the means to clone and characterize a gene (or genes) of importance for tumorigenesis in this and possibly other clinically associated tumors of the human nervous system.

  19. A suicide gene therapy approach to treat epidermolysis bullosa-associated skin cancer

    International Nuclear Information System (INIS)

    Recessive dystrophic epidermolysis bullosa (RDEB) is an inherited disease causing extensive blister formation within the basal membrane zone (BMZ) of the skin and mucous membranes. It is caused by premature STOP mutations in the COL7A1 gene, which is indispensable for proper skin assembling. RDEB is associated with the development of a highly malignant skin cancer (squamous cell carcinoma, SCC) in early adulthood that displays a life threatening complication within this patient group. To date, neither chemo- nor radiotherapies showed successful results and due to the high metastatic potential of RDEB SCC wide surgical excision is still favoured. In this study we could reveal a new promising cancer treatment using spliceosome mediated RNA trans-splicing (SMaRT) using a suicide gene therapy approach. First we identified the tumour marker gene MMP-9 expressed by RDEB SCC cells in cell culture which was used to generate various pre-mRNA trans-splicing molecules (PTM). PTMs are able to facilitate trans-splicing between a tumour target gene and a cell death inducing peptide/toxin, encoded by the PTM. As a consequence the toxin is expressed in cancer cells leading to the induction of cell death. This technique offers high specificity in cancer cell targeting compared to other conventional cDNA expression studies. Various trans-splicing molecules were pre-evaluated in a fluorescence screening model for their best trans-splicing efficiency with the target molecule. Herein we identified two potent PTMs (PTM BD0 and PTM BD6), that were further adapted for endogenous suicide studies by inserting the toxin streptolysin O. In two independent in vitro cell culture assays we were able to confirm that the trans-splicing molecules are able to induce expression of the toxin resulting in cell membrane permeabilization and increased cell death induction. The results indicate that SMaRT technology offers a new platform for a suicide gene therapy approach to treat malignant squamous cell

  20. Outsourced pattern matching

    DEFF Research Database (Denmark)

    Faust, Sebastian; Hazay, Carmit; Venturi, Daniele

    2013-01-01

    In secure delegatable computation, computationally weak devices (or clients) wish to outsource their computation and data to an untrusted server in the cloud. While most earlier work considers the general question of how to securely outsource any computation to the cloud server, we focus...... on concrete and important functionalities and give the first protocol for the pattern matching problem in the cloud. Loosely speaking, this problem considers a text T that is outsourced to the cloud S by a client C T . In a query phase, clients C 1, …, C l run an efficient protocol with the server S...... and the client C T in order to learn the positions at which a pattern of length m matches the text (and nothing beyond that). This is called the outsourced pattern matching problem and is highly motivated in the context of delegatable computing since it offers storage alternatives for massive databases...

  1. Schema matching and mapping

    CERN Document Server

    Bellahsene, Zohra; Rahm, Erhard

    2011-01-01

    Requiring heterogeneous information systems to cooperate and communicate has now become crucial, especially in application areas like e-business, Web-based mash-ups and the life sciences. Such cooperating systems have to automatically and efficiently match, exchange, transform and integrate large data sets from different sources and of different structure in order to enable seamless data exchange and transformation. The book edited by Bellahsene, Bonifati and Rahm provides an overview of the ways in which the schema and ontology matching and mapping tools have addressed the above requirements

  2. Partial fingerprint matching based on SIFT Features

    Directory of Open Access Journals (Sweden)

    Ms. S.Malathi,

    2010-07-01

    Full Text Available Fingerprints are being extensively used for person identification in a number of commercial, civil, and forensic applications. The current Fingerprint matching technology is quite mature for matching full prints, matching partial fingerprints still needs lots of improvement. Most of the current fingerprint identification systems utilize features that are based on minutiae points and ridge patterns. The major challenges faced in partial fingerprint matching are the absence of sufficient minutiae features and other structures such as core and delta. However, this technology suffers from the problem of handling incomplete prints and often discards any partial fingerprints obtained. Recent research has begun to delve into the problems of latent or partial fingerprints. In this paper we present a novel approach for partial fingerprint matching scheme based on SIFT(Scale Invariant Feature Transform features and matching is achieved using a modified point matching process. Using Neurotechnology database, we demonstrate that the proposed method exhibits an improved performance when matching full print against partial print.

  3. Improved Stereo Matching With Boosting Method

    OpenAIRE

    Shiny B; Dr. Deepa J.

    2015-01-01

    Abstract This paper presents an approach based on classification for improving the accuracy of stereo matching methods. We propose this method for occlusion handling. This work employs classification of pixels for finding the erroneous disparity values. Due to the wide applications of disparity map in 3D television medical imaging etc the accuracy of disparity map has high significance. An initial disparity map is obtained using local or global stereo matching methods from the input stereo i...

  4. Theory of fractional order elements based impedance matching networks

    KAUST Repository

    Radwan, Ahmed

    2011-03-01

    Fractional order circuit elements (inductors and capacitors) based impedance matching networks are introduced for the first time. In comparison to the conventional integer based L-type matching networks, fractional matching networks are much simpler and versatile. Any complex load can be matched utilizing a single series fractional element, which generally requires two elements for matching in the conventional approach. It is shown that all the Smith chart circles (resistance and reactance) are actually pairs of completely identical circles. They appear to be single for the conventional integer order case, where the identical circles completely overlap each other. The concept is supported by design equations and impedance matching examples. © 2010 IEEE.

  5. Deciphering ascorbic acid regulatory pathways in ripening tomato fruit using a weighted gene correlation network analysis approach.

    Science.gov (United States)

    Gao, Chao; Ju, Zheng; Li, Shan; Zuo, Jinhua; Fu, Daqi; Tian, Huiqin; Luo, Yunbo; Zhu, Benzhong

    2013-11-01

    Genotype is generally determined by the co-expression of diverse genes and multiple regulatory pathways in plants. Gene co-expression analysis combining with physiological trait data provides very important information about the gene function and regulatory mechanism. L-Ascorbic acid (AsA), which is an essential nutrient component for human health and plant metabolism, plays key roles in diverse biological processes such as cell cycle, cell expansion, stress resistance, hormone synthesis, and signaling. Here, we applied a weighted gene correlation network analysis approach based on gene expression values and AsA content data in ripening tomato (Solanum lycopersicum L.) fruit with different AsA content levels, which leads to identification of AsA relevant modules and vital genes in AsA regulatory pathways. Twenty-four modules were compartmentalized according to gene expression profiling. Among these modules, one negatively related module containing genes involved in redox processes and one positively related module enriched with genes involved in AsA biosynthetic and recycling pathways were further analyzed. The present work herein indicates that redox pathways as well as hormone-signal pathways are closely correlated with AsA accumulation in ripening tomato fruit, and allowed us to prioritize candidate genes for follow-up studies to dissect this interplay at the biochemical and molecular level.

  6. Deciphering Ascorbic Acid Regulatory Pathways in Ripening Tomato Fruit Using a Weighted Gene Correlation Network Analysis Approach

    Institute of Scientific and Technical Information of China (English)

    Chao Gao; Zheng Ju; Shan Li; Jinhua Zuo; Daqi Fu; Huiqin Tian; Yunbo Luo; Benzhong Zhu

    2013-01-01

    Genotype is generally determined by the co-expression of diverse genes and multiple regulatory pathways in plants. Gene co-expression analysis combining with physiological trait data provides very important information about the gene function and regulatory mechanism. L-Ascorbic acid (AsA), which is an essential nutrient component for human health and plant metabolism, plays key roles in diverse biological processes such as cell cycle, cell expansion, stress resistance, hormone synthesis, and signaling. Here, we applied a weighted gene correlation network analysis approach based on gene expression values and AsA content data in ripening tomato (Solanum lycopersicum L.) fruit with different AsA content levels, which leads to identification of AsA relevant modules and vital genes in AsA regulatory pathways. Twenty-four modules were compartmentalized according to gene expression profiling. Among these modules, one negatively related module containing genes involved in redox processes and one positively related module enriched with genes involved in AsA biosynthetic and recycling pathways were further analyzed. The present work herein indicates that redox pathways as well as hormone-signal pathways are closely correlated with AsA accumulation in ripening tomato fruit, and allowed us to prioritize candidate genes for follow-up studies to dissect this interplay at the biochemical and molecular level.

  7. MATCH PLAY, SOAP HOPE.

    Science.gov (United States)

    Rigby, Perry G; Gururaja, Ramnarayan Paragi; Hilton, Charles

    2015-01-01

    The Medical Education Commission (MEC) has published Graduate Medical Education (GME) data since 1997, including the National Residency Matching Program (NRMP) and the Supplemental Offer and Acceptance Program (SOAP), and totals all GME in Louisiana for annual publication. The NRMP provides the quotas and filled positions by institution. Following the NRMP, SOAP attempts to place unmatched candidates with slots that are unfilled. The NRMP Fellowship match also comes close to filling quotas and has a significant SOAP. Thus, an accurate number of total filled positions is best obtained in July of the same match year. All GME programs in Louisiana are represented for 2014, and the number trend 2005 to 2014 shows that the only dip was post-Katrina in 2005-2006. The March match after SOAP 2014 is at the peak for both senior medical students and post graduate year one (PGY-1) residents. A significant and similar number stay in Louisiana GME institutions after graduation. Also noteworthy is that a lower percentage are staying in state, due to increased enrollment in all Louisiana medical schools. PMID:27159458

  8. Derivatives of Matching.

    Science.gov (United States)

    Herrnstein, R. J.

    1979-01-01

    The matching law for reinforced behavior solves a differential equation relating infinitesimal changes in behavior to infinitesimal changes in reinforcement. The equation expresses plausible conceptions of behavior and reinforcement, yields a simple nonlinear operator model for acquisition, and suggests a alternative to the economic law of…

  9. A Football Match

    Institute of Scientific and Technical Information of China (English)

    彭硕

    2002-01-01

    It was a Saturday morning, our school football team was going to have a match with the No. 28 Middle Schooh They were really a strong team. But we weren't afraid of them. We had many mare good players on our team, so we were stronger than ever before.

  10. Scanner matching optimization

    Science.gov (United States)

    Kupers, Michiel; Klingbeil, Patrick; Tschischgale, Joerg; Buhl, Stefan; Hempel, Fritjof

    2009-03-01

    Cost of ownership of scanners for the manufacturing of front end layers is becoming increasingly expensive. The ability to quickly switch the production of a layer to another scanner in case it is down is important. This paper presents a method to match the scanner grids in the most optimal manner so that use of front end scanners in effect becomes interchangeable. A breakdown of the various components of overlay is given and we discuss methods to optimize the matching strategy in the fab. A concern here is how to separate the scanner and process induced effects. We look at the relative contributions of intrafield and interfield errors caused by the scanner and the process. Experimental results of a method to control the scanner grid are presented and discussed. We compare the overlay results before and after optimizing the scanner grids and show that the matching penalty is reduced by 20%. We conclude with some thoughts on the need to correct the remaining matching errors.

  11. Bayesian grid matching

    DEFF Research Database (Denmark)

    Hartelius, Karsten; Carstensen, Jens Michael

    2003-01-01

    A method for locating distorted grid structures in images is presented. The method is based on the theories of template matching and Bayesian image restoration. The grid is modeled as a deformable template. Prior knowledge of the grid is described through a Markov random field (MRF) model which...

  12. n! matchings, n! posets

    CERN Document Server

    Claesson, Anders

    2010-01-01

    We show that there are n! matchings on 2n points without, so called, left (neighbor) nestings. We also define a set of naturally labeled (2+2)-free posets, and show that there are n! such posets on n elements. Our work was inspired by Bousquet-M\\'elou, Claesson, Dukes and Kitaev [arXiv:0806.0666]. They gave bijections between four classes of combinatorial objects: matchings with no neighbor nestings (due to Stoimenow), unlabeled (2+2)-free posets, permutations avoiding a specific pattern, and so called ascent sequences. We believe that certain statistics on our matchings and posets could generalize the work of Bousquet-M\\'elou et al.\\ and we make a conjecture to that effect. We also identify natural subsets of matchings and posets that are equinumerous to the class of unlabeled (2+2)-free posets. We give bijections that show the equivalence of (neighbor) restrictions on nesting arcs with (neighbor) restrictions on crossing arcs. These bijections are thought to be of independent interest. One of the bijections...

  13. A multistep bioinformatic approach detects putative regulatory elements in gene promoters

    Directory of Open Access Journals (Sweden)

    Pizzi Cinzia

    2005-05-01

    Full Text Available Abstract Background Searching for approximate patterns in large promoter sequences frequently produces an exceedingly high numbers of results. Our aim was to exploit biological knowledge for definition of a sheltered search space and of appropriate search parameters, in order to develop a method for identification of a tractable number of sequence motifs. Results Novel software (COOP was developed for extraction of sequence motifs, based on clustering of exact or approximate patterns according to the frequency of their overlapping occurrences. Genomic sequences of 1 Kb upstream of 91 genes differentially expressed and/or encoding proteins with relevant function in adult human retina were analyzed. Methodology and results were tested by analysing 1,000 groups of putatively unrelated sequences, randomly selected among 17,156 human gene promoters. When applied to a sample of human promoters, the method identified 279 putative motifs frequently occurring in retina promoters sequences. Most of them are localized in the proximal portion of promoters, less variable in central region than in lateral regions and similar to known regulatory sequences. COOP software and reference manual are freely available upon request to the Authors. Conclusion The approach described in this paper seems effective for identifying a tractable number of sequence motifs with putative regulatory role.

  14. Comparison of two approaches for the classification of 16S rRNA gene sequences.

    Science.gov (United States)

    Chatellier, Sonia; Mugnier, Nathalie; Allard, Françoise; Bonnaud, Bertrand; Collin, Valérie; van Belkum, Alex; Veyrieras, Jean-Baptiste; Emler, Stefan

    2014-10-01

    The use of 16S rRNA gene sequences for microbial identification in clinical microbiology is accepted widely, and requires databases and algorithms. We compared a new research database containing curated 16S rRNA gene sequences in combination with the lca (lowest common ancestor) algorithm (RDB-LCA) to a commercially available 16S rDNA Centroid approach. We used 1025 bacterial isolates characterized by biochemistry, matrix-assisted laser desorption/ionization time-of-flight MS and 16S rDNA sequencing. Nearly 80 % of isolates were identified unambiguously at the species level by both classification platforms used. The remaining isolates were mostly identified correctly at the genus level due to the limited resolution of 16S rDNA sequencing. Discrepancies between both 16S rDNA platforms were due to differences in database content and the algorithm used, and could amount to up to 10.5 %. Up to 1.4 % of the analyses were found to be inconclusive. It is important to realize that despite the overall good performance of the pipelines for analysis, some inconclusive results remain that require additional in-depth analysis performed using supplementary methods.

  15. A multistep bioinformatic approach detects putative regulatory elements in gene promoters

    Science.gov (United States)

    Bortoluzzi, Stefania; Coppe, Alessandro; Bisognin, Andrea; Pizzi, Cinzia; Danieli, Gian Antonio

    2005-01-01

    Background Searching for approximate patterns in large promoter sequences frequently produces an exceedingly high numbers of results. Our aim was to exploit biological knowledge for definition of a sheltered search space and of appropriate search parameters, in order to develop a method for identification of a tractable number of sequence motifs. Results Novel software (COOP) was developed for extraction of sequence motifs, based on clustering of exact or approximate patterns according to the frequency of their overlapping occurrences. Genomic sequences of 1 Kb upstream of 91 genes differentially expressed and/or encoding proteins with relevant function in adult human retina were analyzed. Methodology and results were tested by analysing 1,000 groups of putatively unrelated sequences, randomly selected among 17,156 human gene promoters. When applied to a sample of human promoters, the method identified 279 putative motifs frequently occurring in retina promoters sequences. Most of them are localized in the proximal portion of promoters, less variable in central region than in lateral regions and similar to known regulatory sequences. COOP software and reference manual are freely available upon request to the Authors. Conclusion The approach described in this paper seems effective for identifying a tractable number of sequence motifs with putative regulatory role. PMID:15904489

  16. Activation of pluripotency genes in human fibroblast cells by a novel mRNA based approach.

    Directory of Open Access Journals (Sweden)

    Jordan R Plews

    Full Text Available BACKGROUND: Several methods have been used to induce somatic cells to re-enter the pluripotent state. Viral transduction of reprogramming genes yields higher efficiency but involves random insertions of viral sequences into the human genome. Although induced pluripotent stem (iPS cells can be obtained with the removable PiggyBac transposon system or an episomal system, both approaches still use DNA constructs so that resulting cell lines need to be thoroughly analyzed to confirm they are free of harmful genetic modification. Thus a method to change cell fate without using DNA will be very useful in regenerative medicine. METHODOLOGY/PRINCIPAL FINDINGS: In this study, we synthesized mRNAs encoding OCT4, SOX2, cMYC, KLF4 and SV40 large T (LT and electroporated them into human fibroblast cells. Upon transfection, fibroblasts expressed these factors at levels comparable to, or higher than those in human embryonic stem (ES cells. Ectopically expressed OCT4 localized to the cell nucleus within 4 hours after mRNA introduction. Transfecting fibroblasts with a mixture of mRNAs encoding all five factors significantly increased the expression of endogenous OCT4, NANOG, DNMT3β, REX1 and SALL4. When such transfected fibroblasts were also exposed to several small molecules (valproic acid, BIX01294 and 5'-aza-2'-deoxycytidine and cultured in human embryonic stem cell (ES medium they formed small aggregates positive for alkaline phosphatase activity and OCT4 protein within 30 days. CONCLUSION/SIGNIFICANCE: Our results demonstrate that mRNA transfection can be a useful approach to precisely control the protein expression level and short-term expression of reprogramming factors is sufficient to activate pluripotency genes in differentiated cells.

  17. Impedance matching through a single passive fractional element

    KAUST Repository

    Radwan, Ahmed Gomaa

    2012-07-01

    For the first time, a generalized admittance Smith chart theory is introduced to represent fractional order circuit elements. The principles of fractional order matching circuits are described. We show that for fractional order α < 1, a single parallel fractional element can match a wider range of load impedances as compared to its series counterpart. Several matching examples demonstrate the versatility of fractional order series and parallel element matching as compared to the conventional approach. © 2012 IEEE.

  18. Growing a Graph Matching from a Handful of Seeds

    OpenAIRE

    Kazemi, Ehsan; Hassani, S. Hamed; Grossglauser, Matthias

    2015-01-01

    In many graph–mining problems, two networks from different domains have to be matched. In the absence of reliable node attributes, graph matching has to rely on only the link structures of the two networks, which amounts to a generalization of the classic graph isomorphism problem. Graph matching has applications in social–network reconciliation and de-anonymization, protein–network alignment in biology, and computer vision. The most scalable graph–matching approaches use ideas from percolat...

  19. Bayesian refinement of protein functional site matching

    Directory of Open Access Journals (Sweden)

    Gold Nicola D

    2007-07-01

    Full Text Available Abstract Background Matching functional sites is a key problem for the understanding of protein function and evolution. The commonly used graph theoretic approach, and other related approaches, require adjustment of a matching distance threshold a priori according to the noise in atomic positions. This is difficult to pre-determine when matching sites related by varying evolutionary distances and crystallographic precision. Furthermore, sometimes the graph method is unable to identify alternative but important solutions in the neighbourhood of the distance based solution because of strict distance constraints. We consider the Bayesian approach to improve graph based solutions. In principle this approach applies to other methods with strict distance matching constraints. The Bayesian method can flexibly incorporate all types of prior information on specific binding sites (e.g. amino acid types in contrast to combinatorial formulations. Results We present a new meta-algorithm for matching protein functional sites (active sites and ligand binding sites based on an initial graph matching followed by refinement using a Markov chain Monte Carlo (MCMC procedure. This procedure is an innovative extension to our recent work. The method accounts for the 3-dimensional structure of the site as well as the physico-chemical properties of the constituent amino acids. The MCMC procedure can lead to a significant increase in the number of significant matches compared to the graph method as measured independently by rigorously derived p-values. Conclusion MCMC refinement step is able to significantly improve graph based matches. We apply the method to matching NAD(P(H binding sites within single Rossmann fold families, between different families in the same superfamily, and in different folds. Within families sites are often well conserved, but there are examples where significant shape based matches do not retain similar amino acid chemistry, indicating that

  20. Comparative genomics and association mapping approaches for blast resistant genes in finger millet using SSRs.

    Directory of Open Access Journals (Sweden)

    B Kalyana Babu

    Full Text Available The major limiting factor for production and productivity of finger millet crop is blast disease caused by Magnaporthe grisea. Since, the genome sequence information available in finger millet crop is scarce, comparative genomics plays a very important role in identification of genes/QTLs linked to the blast resistance genes using SSR markers. In the present study, a total of 58 genic SSRs were developed for use in genetic analysis of a global collection of 190 finger millet genotypes. The 58 SSRs yielded ninety five scorable alleles and the polymorphism information content varied from 0.186 to 0.677 at an average of 0.385. The gene diversity was in the range of 0.208 to 0.726 with an average of 0.487. Association mapping for blast resistance was done using 104 SSR markers which identified four QTLs for finger blast and one QTL for neck blast resistance. The genomic marker RM262 and genic marker FMBLEST32 were linked to finger blast disease at a P value of 0.007 and explained phenotypic variance (R² of 10% and 8% respectively. The genomic marker UGEP81 was associated to finger blast at a P value of 0.009 and explained 7.5% of R². The QTLs for neck blast was associated with the genomic SSR marker UGEP18 at a P value of 0.01, which explained 11% of R². Three QTLs for blast resistance were found common by using both GLM and MLM approaches. The resistant alleles were found to be present mostly in the exotic genotypes. Among the genotypes of NW Himalayan region of India, VHC3997, VHC3996 and VHC3930 were found highly resistant, which may be effectively used as parents for developing blast resistant cultivars in the NW Himalayan region of India. The markers linked to the QTLs for blast resistance in the present study can be further used for cloning of the full length gene, fine mapping and their further use in the marker assisted breeding programmes for introgression of blast resistant alleles into locally adapted cultivars.

  1. Reverse PCA, a systematic approach for identifying genes important for the physical interaction between protein pairs.

    Directory of Open Access Journals (Sweden)

    Ifat Lev

    Full Text Available Protein-protein interactions (PPIs are of central importance for many areas of biological research. Several complementary high-throughput technologies have been developed to study PPIs. The wealth of information that emerged from these technologies led to the first maps of the protein interactomes of several model organisms. Many changes can occur in protein complexes as a result of genetic and biochemical perturbations. In the absence of a suitable assay, such changes are difficult to identify, and thus have been poorly characterized. In this study, we present a novel genetic approach (termed "reverse PCA" that allows the identification of genes whose products are required for the physical interaction between two given proteins. Our assay starts with a yeast strain in which the interaction between two proteins of interest can be detected by resistance to the drug, methotrexate, in the context of the protein-fragment complementation assay (PCA. Using synthetic genetic array (SGA technology, we can systematically screen mutant libraries of the yeast Saccharomyces cerevisiae to identify those mutations that disrupt the physical interaction of interest. We were able to successfully validate this novel approach by identifying mutants that dissociate the conserved interaction between Cia2 and Mms19, two proteins involved in Iron-Sulfur protein biogenesis and genome stability. This method will facilitate the study of protein structure-function relationships, and may help in elucidating the mechanisms that regulate PPIs.

  2. A PiggyBac-mediated approach for muscle gene transfer or cell therapy.

    Science.gov (United States)

    Ley, Déborah; Van Zwieten, Ruthger; Puttini, Stefania; Iyer, Pavithra; Cochard, Alessia; Mermod, Nicolas

    2014-11-01

    An emerging therapeutic approach for Duchenne muscular dystrophy is the transplantation of autologous myogenic progenitor cells genetically modified to express dystrophin. The use of this approach is challenged by the difficulty in maintaining these cells ex vivo while keeping their myogenic potential, and ensuring sufficient transgene expression following their transplantation and myogenic differentiation in vivo. We investigated the use of the piggyBac transposon system to achieve stable gene expression when transferred to cultured mesoangioblasts and into murine muscles. Without selection, up to 8% of the mesoangioblasts expressed the transgene from 1 to 2 genomic copies of the piggyBac vector. Integration occurred mostly in intergenic genomic DNA and transgene expression was stable in vitro. Intramuscular transplantation of mouse Tibialis anterior muscles with mesoangioblasts containing the transposon led to sustained myofiber GFP expression in vivo. In contrast, the direct electroporation of the transposon-donor plasmids in the mouse Tibialis muscles in vivo did not lead to sustained transgene expression despite molecular evidence of piggyBac transposition in vivo. Together these findings provide a proof-of-principle that piggyBac transposon may be considered for mesoangioblast cell-based therapies of muscular dystrophies. PMID:25310255

  3. Statistical Approaches to Analyse Gene Bank Data Using a Lentil Germplasm Collection as a Case Study

    Directory of Open Access Journals (Sweden)

    Gabriella Sonnante

    2008-09-01

    Full Text Available Normally in a plant gene bank a large number of accessions per each crop and/ or taxon is stored. During their characterization and preliminary evaluation, several quantitative and qualitative data are recorded and, usually, a wide intra accession variation is observed. Th e management of all this information becomes very difficult without effective statistical methods combining these different types of data. At the Institute of Plant Genetics, CNR, in Bari (Italy this problem has been tackled by testing many statistical approaches. The present contribution describes one of these approaches, which to date has proven to be highly adequate; a case study describing a lentil germplasm collection has been used for demonstration. A valuable application of this method is the determination of core subsets important to increase the utilization and accessibility of plant genetic resources. In the presented case study a subset of the lentil germplasm collection was chosen to perform molecular analysis based on ISSR markers. The samples were selected on the basis of both morpho-agronomic evaluation and geographical origin. These markers proved to be useful for distinguishing among closely related genotypes and for possibly substantiating the genetic peculiarity of some interesting material.

  4. A PiggyBac-mediated approach for muscle gene transfer or cell therapy

    Directory of Open Access Journals (Sweden)

    Déborah Ley

    2014-11-01

    Full Text Available An emerging therapeutic approach for Duchenne muscular dystrophy is the transplantation of autologous myogenic progenitor cells genetically modified to express dystrophin. The use of this approach is challenged by the difficulty in maintaining these cells ex vivo while keeping their myogenic potential, and ensuring sufficient transgene expression following their transplantation and myogenic differentiation in vivo. We investigated the use of the piggyBac transposon system to achieve stable gene expression when transferred to cultured mesoangioblasts and into murine muscles. Without selection, up to 8% of the mesoangioblasts expressed the transgene from 1 to 2 genomic copies of the piggyBac vector. Integration occurred mostly in intergenic genomic DNA and transgene expression was stable in vitro. Intramuscular transplantation of mouse Tibialis anterior muscles with mesoangioblasts containing the transposon led to sustained myofiber GFP expression in vivo. In contrast, the direct electroporation of the transposon-donor plasmids in the mouse Tibialis muscles in vivo did not lead to sustained transgene expression despite molecular evidence of piggyBac transposition in vivo. Together these findings provide a proof-of-principle that piggyBac transposon may be considered for mesoangioblast cell-based therapies of muscular dystrophies.

  5. A Novel Approach for Discovering Condition-Specific Correlations of Gene Expressions within Biological Pathways by Using Cloud Computing Technology

    Directory of Open Access Journals (Sweden)

    Tzu-Hao Chang

    2014-01-01

    Full Text Available Microarrays are widely used to assess gene expressions. Most microarray studies focus primarily on identifying differential gene expressions between conditions (e.g., cancer versus normal cells, for discovering the major factors that cause diseases. Because previous studies have not identified the correlations of differential gene expression between conditions, crucial but abnormal regulations that cause diseases might have been disregarded. This paper proposes an approach for discovering the condition-specific correlations of gene expressions within biological pathways. Because analyzing gene expression correlations is time consuming, an Apache Hadoop cloud computing platform was implemented. Three microarray data sets of breast cancer were collected from the Gene Expression Omnibus, and pathway information from the Kyoto Encyclopedia of Genes and Genomes was applied for discovering meaningful biological correlations. The results showed that adopting the Hadoop platform considerably decreased the computation time. Several correlations of differential gene expressions were discovered between the relapse and nonrelapse breast cancer samples, and most of them were involved in cancer regulation and cancer-related pathways. The results showed that breast cancer recurrence might be highly associated with the abnormal regulations of these gene pairs, rather than with their individual expression levels. The proposed method was computationally efficient and reliable, and stable results were obtained when different data sets were used. The proposed method is effective in identifying meaningful biological regulation patterns between conditions.

  6. A novel approach for discovering condition-specific correlations of gene expressions within biological pathways by using cloud computing technology.

    Science.gov (United States)

    Chang, Tzu-Hao; Wu, Shih-Lin; Wang, Wei-Jen; Horng, Jorng-Tzong; Chang, Cheng-Wei

    2014-01-01

    Microarrays are widely used to assess gene expressions. Most microarray studies focus primarily on identifying differential gene expressions between conditions (e.g., cancer versus normal cells), for discovering the major factors that cause diseases. Because previous studies have not identified the correlations of differential gene expression between conditions, crucial but abnormal regulations that cause diseases might have been disregarded. This paper proposes an approach for discovering the condition-specific correlations of gene expressions within biological pathways. Because analyzing gene expression correlations is time consuming, an Apache Hadoop cloud computing platform was implemented. Three microarray data sets of breast cancer were collected from the Gene Expression Omnibus, and pathway information from the Kyoto Encyclopedia of Genes and Genomes was applied for discovering meaningful biological correlations. The results showed that adopting the Hadoop platform considerably decreased the computation time. Several correlations of differential gene expressions were discovered between the relapse and nonrelapse breast cancer samples, and most of them were involved in cancer regulation and cancer-related pathways. The results showed that breast cancer recurrence might be highly associated with the abnormal regulations of these gene pairs, rather than with their individual expression levels. The proposed method was computationally efficient and reliable, and stable results were obtained when different data sets were used. The proposed method is effective in identifying meaningful biological regulation patterns between conditions. PMID:24579087

  7. History Matching in Parallel Computational Environments

    Energy Technology Data Exchange (ETDEWEB)

    Steven Bryant; Sanjay Srinivasan; Alvaro Barrera; Sharad Yadav

    2004-08-31

    In the probabilistic approach for history matching, the information from the dynamic data is merged with the prior geologic information in order to generate permeability models consistent with the observed dynamic data as well as the prior geology. The relationship between dynamic response data and reservoir attributes may vary in different regions of the reservoir due to spatial variations in reservoir attributes, fluid properties, well configuration, flow constrains on wells etc. This implies probabilistic approach should then update different regions of the reservoir in different ways. This necessitates delineation of multiple reservoir domains in order to increase the accuracy of the approach. The research focuses on a probabilistic approach to integrate dynamic data that ensures consistency between reservoir models developed from one stage to the next. The algorithm relies on efficient parameterization of the dynamic data integration problem and permits rapid assessment of the updated reservoir model at each stage. The report also outlines various domain decomposition schemes from the perspective of increasing the accuracy of probabilistic approach of history matching. Research progress in three important areas of the project are discussed: {lg_bullet}Validation and testing the probabilistic approach to incorporating production data in reservoir models. {lg_bullet}Development of a robust scheme for identifying reservoir regions that will result in a more robust parameterization of the history matching process. {lg_bullet}Testing commercial simulators for parallel capability and development of a parallel algorithm for history matching.

  8. Matchings on infinite graphs

    CERN Document Server

    Bordenave, Charles; Salez, Justin

    2011-01-01

    We prove that the local weak convergence of a sequence of graphs is enough to guarantee the convergence of their normalized matching numbers. The limiting quantity is described by a local recursion defined on the weak limit of the graph sequence. However, this recursion may admit several solutions, implying non-trivial long-range dependencies between the edges of a largest matching. We overcome this lack of correlation decay by introducing a perturbative parameter called the temperature, which we let progressively go to zero. When the local weak limit is a unimodular Galton-Watson tree, the recursion simplifies into a distributional equation, resulting into an explicit formula that considerably extends the well-known one by Karp and Sipser for Erd\\"os-R\\'enyi random graphs.

  9. Resurgence Matches Quantization

    CERN Document Server

    Couso-Santamaría, Ricardo; Schiappa, Ricardo

    2016-01-01

    The quest to find a nonperturbative formulation of topological string theory has recently seen two unrelated developments. On the one hand, via quantization of the mirror curve associated to a toric Calabi-Yau background, it has been possible to give a nonperturbative definition of the topological-string partition function. On the other hand, using techniques of resurgence and transseries, it has been possible to extend the string (asymptotic) perturbative expansion into a transseries involving nonperturbative instanton sectors. Within the specific example of the local P2 toric Calabi-Yau threefold, the present work shows how the Borel-Pade-Ecalle resummation of this resurgent transseries, alongside occurrence of Stokes phenomenon, matches the string-theoretic partition function obtained via quantization of the mirror curve. This match is highly non-trivial, given the unrelated nature of both nonperturbative frameworks, signaling at the existence of a consistent underlying structure.

  10. Designing Talent Matching Services

    OpenAIRE

    Kupari, Tiina

    2016-01-01

    There is a disruption going on in recruiting due to digitalization and the competition for the best tal¬ents. Due to these changes, recruiters are forced to re-evaluate their value proposals. Therefore, the case company, a consulting company in recruitment, found the need to update their talent matching services to bring added value to their customers. The aim was to reach the customers and talent understanding, and based on that, design service concepts. The literature review recapitula...

  11. Multithreaded Implementation of Hybrid String Matching Algorithm

    Directory of Open Access Journals (Sweden)

    Akhtar Rasool

    2012-03-01

    Full Text Available Reading and taking reference from many books and articles, and then analyzing the Navies algorithm, Boyer Moore algorithm and Knuth Morris Pratt (KMP algorithm and a variety of improved algorithms, summarizes various advantages and disadvantages of the pattern matching algorithms. And on this basis, a new algorithm – Multithreaded Hybrid algorithm is introduced. The algorithm refers to Boyer Moore algorithm, KMP algorithm and the thinking of improved algorithms. Utilize the last character of the string, the next character and the method to compare from side to side, and then advance a new hybrid pattern matching algorithm. And it adjusted the comparison direction and the order of the comparison to make the maximum moving distance of each time to reduce the pattern matching time. The algorithm reduces the comparison number and greatlyreduces the moving number of the pattern and improves the matching efficiency. Multithreaded implementation of hybrid, pattern matching algorithm performs the parallel string searching on different text data by executing a number of threads simultaneously. This approach is advantageous from all other string-pattern matching algorithm in terms of time complexity. This again improves the overall string matching efficiency.

  12. Towards the perfect prediction of soccer matches

    CERN Document Server

    Heuer, Andreas

    2012-01-01

    We present a systematic approach to the prediction of soccer matches. First, we show that the information about chances for goals is by far more informative than about the actual results. Second, we present a multivariate regression approach and show how the prediction quality increases with increasing information content. This prediction quality can be explicitly expressed in terms of just two parameters. Third, by disentangling the systematic and random components of soccer matches we can identify the optimum level of predictability. These concepts are exemplified for the German Bundesliga.

  13. Gene expression analysis approach to establish possible links between Parkinson's disease, cancer and cardiovascular diseases.

    Science.gov (United States)

    Karim, Sajjad; Mirza, Zeenat; Kamal, Mohammad A; Abuzenadah, Adel M; Al-Qahtani, Mohammed H

    2014-01-01

    Non-communicable chronic diseases have been apparently established as threat to human health, and are currently the world's main killer. Cardiovascular diseases (CVD), cancer, diabetes and neurodegenerative diseases are collectively amounting to more than 60% of non-communicable disease burden across world. Tremendous advancements in healthcare enabled us to fight several health problems primarily infectious diseases. However, this increased longevity where in many cases an individual suffers from several such chronic diseases simultaneously, making treatment complex. Finding whether diseases can coexist in an individual by chance or there exists a possible association between them is vital. Our goal is to establish possible existing link among CVD, cancer and Parkinson's disease (PD) for better understanding of the associated molecular network. In this study, we integrated multiple dataset retrieved from the National Centre for Biotechnology Information's Gene Expression Omnibus database, and took a systems-biology approach to compare and distinguish the molecular network associated with PD, cancer and CVD. We identified 230, 308 and 1619 differentially expressed genes for CVD, cancer and PD dataset respectively using cut off p value2. We integrated these data with known pathways using Ingenuity Pathway Analysis tool and found following common pathways associated with all three diseases to be most affected; epithelial adherens junction signaling, remodelling of epithelial adherens junctions, role of BRCA1 in DNA damage response, sphingomyelin metabolism, 3- phosphoinositide biosynthesis, acute myeloid leukemia signaling, type I diabetes mellitus signaling, agrin interactions at neuromuscular junction, role of IL-17A in arthritis, and antigen presentation pathways. In conclusion, CVD, cancer and PD appear tightly associated at molecular level.

  14. An unbiased approach to identify genes involved in development in a turtle with temperature-dependent sex determination

    Directory of Open Access Journals (Sweden)

    Chojnowski Jena L

    2012-07-01

    Full Text Available Abstract Background Many reptiles exhibit temperature-dependent sex determination (TSD. The initial cue in TSD is incubation temperature, unlike genotypic sex determination (GSD where it is determined by the presence of specific alleles (or genetic loci. We used patterns of gene expression to identify candidates for genes with a role in TSD and other developmental processes without making a priori assumptions about the identity of these genes (ortholog-based approach. We identified genes with sexually dimorphic mRNA accumulation during the temperature sensitive period of development in the Red-eared slider turtle (Trachemys scripta, a turtle with TSD. Genes with differential mRNA accumulation in response to estrogen (estradiol-17β; E2 exposure and developmental stages were also identified. Results Sequencing 767 clones from three suppression-subtractive hybridization libraries yielded a total of 581 unique sequences. Screening a macroarray with a subset of those sequences revealed a total of 26 genes that exhibited differential mRNA accumulation: 16 female biased and 10 male biased. Additional analyses revealed that C16ORF62 (an unknown gene and MALAT1 (a long noncoding RNA exhibited increased mRNA accumulation at the male producing temperature relative to the female producing temperature during embryonic sexual development. Finally, we identified four genes (C16ORF62, CCT3, MMP2, and NFIB that exhibited a stage effect and five genes (C16ORF62, CCT3, MMP2, NFIB and NOTCH2 showed a response to E2 exposure. Conclusions Here we report a survey of genes identified using patterns of mRNA accumulation during embryonic development in a turtle with TSD. Many previous studies have focused on examining the turtle orthologs of genes involved in mammalian development. Although valuable, the limitations of this approach are exemplified by our identification of two genes (MALAT1 and C16ORF62 that are sexually dimorphic during embryonic development. MALAT1 is

  15. Candidate gene approach for parasite resistance in sheep--variation in immune pathway genes and association with fecal egg count.

    Directory of Open Access Journals (Sweden)

    Kathiravan Periasamy

    Full Text Available Sheep chromosome 3 (Oar3 has the largest number of QTLs reported to be significantly associated with resistance to gastro-intestinal nematodes. This study aimed to identify single nucleotide polymorphisms (SNPs within candidate genes located in sheep chromosome 3 as well as genes involved in major immune pathways. A total of 41 SNPs were identified across 38 candidate genes in a panel of unrelated sheep and genotyped in 713 animals belonging to 22 breeds across Asia, Europe and South America. The variations and evolution of immune pathway genes were assessed in sheep populations across these macro-environmental regions that significantly differ in the diversity and load of pathogens. The mean minor allele frequency (MAF did not vary between Asian and European sheep reflecting the absence of ascertainment bias. Phylogenetic analysis revealed two major clusters with most of South Asian, South East Asian and South West Asian breeds clustering together while European and South American sheep breeds clustered together distinctly. Analysis of molecular variance revealed strong phylogeographic structure at loci located in immune pathway genes, unlike microsatellite and genome wide SNP markers. To understand the influence of natural selection processes, SNP loci located in chromosome 3 were utilized to reconstruct haplotypes, the diversity of which showed significant deviations from selective neutrality. Reduced Median network of reconstructed haplotypes showed balancing selection in force at these loci. Preliminary association of SNP genotypes with phenotypes recorded 42 days post challenge revealed significant differences (P<0.05 in fecal egg count, body weight change and packed cell volume at two, four and six SNP loci respectively. In conclusion, the present study reports strong phylogeographic structure and balancing selection operating at SNP loci located within immune pathway genes. Further, SNP loci identified in the study were found to have

  16. Candidate Gene Approach for Parasite Resistance in Sheep – Variation in Immune Pathway Genes and Association with Fecal Egg Count

    Science.gov (United States)

    Periasamy, Kathiravan; Pichler, Rudolf; Poli, Mario; Cristel, Silvina; Cetrá, Bibiana; Medus, Daniel; Basar, Muladno; A. K., Thiruvenkadan; Ramasamy, Saravanan; Ellahi, Masroor Babbar; Mohammed, Faruque; Teneva, Atanaska; Shamsuddin, Mohammed; Podesta, Mario Garcia; Diallo, Adama

    2014-01-01

    Sheep chromosome 3 (Oar3) has the largest number of QTLs reported to be significantly associated with resistance to gastro-intestinal nematodes. This study aimed to identify single nucleotide polymorphisms (SNPs) within candidate genes located in sheep chromosome 3 as well as genes involved in major immune pathways. A total of 41 SNPs were identified across 38 candidate genes in a panel of unrelated sheep and genotyped in 713 animals belonging to 22 breeds across Asia, Europe and South America. The variations and evolution of immune pathway genes were assessed in sheep populations across these macro-environmental regions that significantly differ in the diversity and load of pathogens. The mean minor allele frequency (MAF) did not vary between Asian and European sheep reflecting the absence of ascertainment bias. Phylogenetic analysis revealed two major clusters with most of South Asian, South East Asian and South West Asian breeds clustering together while European and South American sheep breeds clustered together distinctly. Analysis of molecular variance revealed strong phylogeographic structure at loci located in immune pathway genes, unlike microsatellite and genome wide SNP markers. To understand the influence of natural selection processes, SNP loci located in chromosome 3 were utilized to reconstruct haplotypes, the diversity of which showed significant deviations from selective neutrality. Reduced Median network of reconstructed haplotypes showed balancing selection in force at these loci. Preliminary association of SNP genotypes with phenotypes recorded 42 days post challenge revealed significant differences (P<0.05) in fecal egg count, body weight change and packed cell volume at two, four and six SNP loci respectively. In conclusion, the present study reports strong phylogeographic structure and balancing selection operating at SNP loci located within immune pathway genes. Further, SNP loci identified in the study were found to have potential for

  17. A systems genetics approach identifies CXCL14, ITGAX, and LPCAT2 as novel aggressive prostate cancer susceptibility genes.

    Directory of Open Access Journals (Sweden)

    Kendra A Williams

    2014-11-01

    Full Text Available Although prostate cancer typically runs an indolent course, a subset of men develop aggressive, fatal forms of this disease. We hypothesize that germline variation modulates susceptibility to aggressive prostate cancer. The goal of this work is to identify susceptibility genes using the C57BL/6-Tg(TRAMP8247Ng/J (TRAMP mouse model of neuroendocrine prostate cancer. Quantitative trait locus (QTL mapping was performed in transgene-positive (TRAMPxNOD/ShiLtJ F2 intercross males (n = 228, which facilitated identification of 11 loci associated with aggressive disease development. Microarray data derived from 126 (TRAMPxNOD/ShiLtJ F2 primary tumors were used to prioritize candidate genes within QTLs, with candidate genes deemed as being high priority when possessing both high levels of expression-trait correlation and a proximal expression QTL. This process enabled the identification of 35 aggressive prostate tumorigenesis candidate genes. The role of these genes in aggressive forms of human prostate cancer was investigated using two concurrent approaches. First, logistic regression analysis in two human prostate gene expression datasets revealed that expression levels of five genes (CXCL14, ITGAX, LPCAT2, RNASEH2A, and ZNF322 were positively correlated with aggressive prostate cancer and two genes (CCL19 and HIST1H1A were protective for aggressive prostate cancer. Higher than average levels of expression of the five genes that were positively correlated with aggressive disease were consistently associated with patient outcome in both human prostate cancer tumor gene expression datasets. Second, three of these five genes (CXCL14, ITGAX, and LPCAT2 harbored polymorphisms associated with aggressive disease development in a human GWAS cohort consisting of 1,172 prostate cancer patients. This study is the first example of using a systems genetics approach to successfully identify novel susceptibility genes for aggressive prostate cancer. Such

  18. A transcriptomic approach to identify regulatory genes involved in fruit set of wild-type and parthenocarpic tomato genotypes.

    Science.gov (United States)

    Ruiu, Fabrizio; Picarella, Maurizio Enea; Imanishi, Shunsuke; Mazzucato, Andrea

    2015-10-01

    The tomato parthenocarpic fruit (pat) mutation associates a strong competence for parthenocarpy with homeotic transformation of anthers and aberrancy of ovules. To dissect this complex floral phenotype, genes involved in the pollination-independent fruit set of the pat mutant were investigated by microarray analysis using wild-type and mutant ovaries. Normalized expression data were subjected to one-way ANOVA and 2499 differentially expressed genes (DEGs) displaying a >1.5 log-fold change in at least one of the pairwise comparisons analyzed were detected. DEGs were categorized into 20 clusters and clusters classified into five groups representing transcripts with similar expression dynamics. The "regulatory function" group (685 DEGs) contained putative negative or positive fruit set regulators, "pollination-dependent" (411 DEGs) included genes activated by pollination, "fruit growth-related" (815 DEGs) genes activated at early fruit growth. The last groups listed genes with different or similar expression pattern at all stages in the two genotypes. qRT-PCR validation of 20 DEGs plus other four selected genes assessed the high reliability of microarray expression data; the average correlation coefficient for the 20 DEGs was 0.90. In all the groups were evidenced relevant transcription factors encoding proteins regulating meristem differentiation and floral organ development, genes involved in metabolism, transport and response of hormones, genes involved in cell division and in primary and secondary metabolism. Among pathways related to secondary metabolites emerged genes related to the synthesis of flavonoids, supporting the recent evidence that these compounds are important at the fruit set phase. Selected genes showing a de-regulated expression pattern in pat were studied in other four parthenocarpic genotypes either genetically anonymous or carrying lesions in known gene sequences. This comparative approach offered novel insights for improving the present

  19. A Computational Protein Phenotype Prediction Approach to Analyze the Deleterious Mutations of Human MED12 Gene.

    Science.gov (United States)

    Banaganapalli, Babajan; Mohammed, Kaleemuddin; Khan, Imran Ali; Al-Aama, Jumana Y; Elango, Ramu; Shaik, Noor Ahmad

    2016-09-01

    Genetic mutations in MED12, a subunit of Mediator complex are seen in a broad spectrum of human diseases. However, the underlying basis of how these pathogenic mutations elicit protein phenotype changes in terms of 3D structure, stability and protein binding sites remains unknown. Therefore, we aimed to investigate the structural and functional impacts of MED12 mutations, using computational methods as an alternate to traditional in vivo and in vitro approaches. The MED12 gene mutations details and their corresponding clinical associations were collected from different databases and by text-mining. Initially, diverse computational approaches were applied to categorize the different classes of mutations based on their deleterious impact to MED12. Then, protein structures for wild and mutant types built by integrative modeling were analyzed for structural divergence, solvent accessibility, stability, and functional interaction deformities. Finally, this study was able to identify that genetic mutations mapped to exon-2 region, highly conserved LCEWAV and Catenin domains induce biochemically severe amino acid changes which alters the protein phenotype as well as the stability of MED12-CYCC interactions. To better understand the deleterious nature of FS-IDs and Indels, this study asserts the utility of computational screening based on their propensity towards non-sense mediated decay. Current study findings may help to narrow down the number of MED12 mutations to be screened for mediator complex dysfunction associated genetic diseases. This study supports computational methods as a primary filter to verify the plausible impact of pathogenic mutations based on the perspective of evolution, expression and phenotype of proteins. J. Cell. Biochem. 117: 2023-2035, 2016. © 2016 Wiley Periodicals, Inc. PMID:26813965

  20. Linking gene regulation and the exo-metabolome: A comparative transcriptomics approach to identify genes that impact on the production of volatile aroma compounds in yeast

    Directory of Open Access Journals (Sweden)

    Bauer Florian F

    2008-11-01

    Full Text Available Abstract Background 'Omics' tools provide novel opportunities for system-wide analysis of complex cellular functions. Secondary metabolism is an example of a complex network of biochemical pathways, which, although well mapped from a biochemical point of view, is not well understood with regards to its physiological roles and genetic and biochemical regulation. Many of the metabolites produced by this network such as higher alcohols and esters are significant aroma impact compounds in fermentation products, and different yeast strains are known to produce highly divergent aroma profiles. Here, we investigated whether we can predict the impact of specific genes of known or unknown function on this metabolic network by combining whole transcriptome and partial exo-metabolome analysis. Results For this purpose, the gene expression levels of five different industrial wine yeast strains that produce divergent aroma profiles were established at three different time points of alcoholic fermentation in synthetic wine must. A matrix of gene expression data was generated and integrated with the concentrations of volatile aroma compounds measured at the same time points. This relatively unbiased approach to the study of volatile aroma compounds enabled us to identify candidate genes for aroma profile modification. Five of these genes, namely YMR210W, BAT1, AAD10, AAD14 and ACS1 were selected for overexpression in commercial wine yeast, VIN13. Analysis of the data show a statistically significant correlation between the changes in the exo-metabome of the overexpressing strains and the changes that were predicted based on the unbiased alignment of transcriptomic and exo-metabolomic data. Conclusion The data suggest that a comparative transcriptomics and metabolomics approach can be used to identify the metabolic impacts of the expression of individual genes in complex systems, and the amenability of transcriptomic data to direct applications of

  1. PATTERN MATCHING IN MODELS

    Directory of Open Access Journals (Sweden)

    Cristian GEORGESCU

    2005-01-01

    Full Text Available The goal of this paper is to investigate how such a pattern matching could be performed on models,including the definition of the input language as well as the elaboration of efficient matchingalgorithms. Design patterns can be considered reusable micro-architectures that contribute to anoverall system architecture. Frameworks are also closely related to design patterns. Componentsoffer the possibility to radically change the behaviors and services offered by an application bysubstitution or addition of new components, even a long time after deployment. Software testing isanother aspect of reliable development. Testing activities mainly consist in ensuring that a systemimplementation conforms to its specifications.

  2. Apfel's excellent match

    Science.gov (United States)

    1997-01-01

    Apfel's excellent match: This series of photos shows a water drop containing a surfactant (Triton-100) as it experiences a complete cycle of superoscillation on U.S. Microgravity Lab-2 (USML-2; October 1995). The time in seconds appears under the photos. The figures above the photos are the oscillation shapes predicted by a numerical model. The time shown with the predictions is nondimensional. Robert Apfel (Yale University) used the Drop Physics Module on USML-2 to explore the effect of surfactants on liquid drops. Apfel's research of surfactants may contribute to improvements in a variety of industrial processes, including oil recovery and environmental cleanup.

  3. A Combinatory Approach for Selecting Prognostic Genes in Microarray Studies of Tumour Survivals

    Directory of Open Access Journals (Sweden)

    Qihua Tan

    2009-01-01

    Full Text Available Different from significant gene expression analysis which looks for genes that are differentially regulated, feature selection in the microarray-based prognostic gene expression analysis aims at finding a subset of marker genes that are not only differentially expressed but also informative for prediction. Unfortunately feature selection in literature of microarray study is predominated by the simple heuristic univariate gene filter paradigm that selects differentially expressed genes according to their statistical significances. We introduce a combinatory feature selection strategy that integrates differential gene expression analysis with the Gram-Schmidt process to identify prognostic genes that are both statistically significant and highly informative for predicting tumour survival outcomes. Empirical application to leukemia and ovarian cancer survival data through-within- and cross-study validations shows that the feature space can be largely reduced while achieving improved testing performances.

  4. Two approaches for induction and isolation of starch mutants in potato (Solanum tuberosum L.) : random versus gene targeted mutagenesis

    NARCIS (Netherlands)

    Hoogkamp, T.J.H.

    2001-01-01

    In this thesis two approaches were used to induce structural mutations in potato starch biosynthesis genes in potato. First production of new monoploid amf genotypes through parthenogenesis made it possible to initiate mutation breeding for amfae double mutants. Two amf monoploids were selected whic

  5. A bi-ordering approach to linking gene expression with clinical annotations in gastric cancer

    OpenAIRE

    Leckie Christopher; Shi Fan; MacIntyre Geoff; Haviv Izhak; Boussioutas Alex; Kowalczyk Adam

    2010-01-01

    Abstract Background In the study of cancer genomics, gene expression microarrays, which measure thousands of genes in a single assay, provide abundant information for the investigation of interesting genes or biological pathways. However, in order to analyze the large number of noisy measurements in microarrays, effective and efficient bioinformatics techniques are needed to identify the associations between genes and relevant phenotypes. Moreover, systematic tests are needed to validate the ...

  6. Transgenic approach to express the channelrhodopsin 2 gene in arginine vasopressin neurons of rats.

    Science.gov (United States)

    Ishii, Masahiro; Hashimoto, Hirofumi; Ohkubo, Jun-Ichi; Ohbuchi, Toyoaki; Saito, Takeshi; Maruyama, Takashi; Yoshimura, Mitsuhiro; Yamamoto, Yukiyo; Kusuhara, Koichi; Ueta, Yoichi

    2016-09-01

    Optogenetics provides a powerful tool to regulate neuronal activity by light-sensitive ion channels such as channelrhodopsin 2 (ChR2). Arginine vasopressin (AVP; also known as the anti-diuretic hormone) is a multifunctional hormone which is synthesized in the magnocellular neurosecretory cells (MNCs) of the hypothalamus. Here, we have generated a transgenic rat that expresses an AVP-ChR2-enhanced green fluorescent protein (eGFP) fusion gene in the MNCs of the hypothalamus. The eGFP fluorescence that indicates the expression of ChR2-eGFP was observed in the supraoptic nucleus (SON) and in the magnocellular division of the paraventricular nucleus (PVN) that is known to contain AVP-secreting neurons. The eGFP fluorescence intensities in those nuclei and posterior pituitary were markedly increased after chronic salt loading (2% NaCl in drinking water for 5days). ChR2-eGFP was localized mainly in the membrane of AVP-positive MNCs. Whole-cell patch-clamp recordings were performed from single MNCs isolated from the SON of the transgenic rats, and blue light evoked repetitive action potentials. Our work provides for the first time an optogenetic approach to selectively activate AVP neurons in the rat. PMID:27493075

  7. A novel approach for a foreign gene expression by Newcastle disease virus

    Science.gov (United States)

    Newcastle disease virus (NDV) has been developed as vectors using reverse genetics technology to express foreign genes for vaccine, anticancer and gene therapy purposes. The foreign genes are usually inserted into the intergenic region of the NDV genome as an additional transcription unit. Based on ...

  8. Match probabilities in racially admixed populations.

    Science.gov (United States)

    Lange, K

    1993-02-01

    The calculation of match probabilities is the most contentious issue dividing prosecution and defense experts in the forensic applications of DNA fingerprinting. In particular, defense experts question the applicability of the population genetic laws of Hardy-Weinberg and linkage equilibrium to racially admixed American populations. Linkage equilibrium justifies the product rule for computing match probabilities across loci. The present paper suggests a method of bounding match probabilities that depends on modeling gene descent from ancestral populations to contemporary populations under the assumptions of Hardy-Weinberg and linkage equilibrium only in the ancestral populations. Although these bounds are conservative from the defendant's perspective, they should be small enough in practice to satisfy prosecutors.

  9. Matching conditions on capillary ripples

    Energy Technology Data Exchange (ETDEWEB)

    Rodriguez, Aresky H.; Marin Antuna, J.; Rodriguez Coppola, H. [Universidad de La Habana, La Habana (Cuba)

    2001-12-01

    The physics of the oscillatory motion in the interface between two immiscible viscous fluids is presented based on a detailed analysis of the matching conditions. These conditions are almost completely derived from the dynamical equations of the system. This unusual approach in graduated courses in hydrodynamics, is proposed as an alternative. The role of viscosity in the modes of oscillation of the interface is also clearly shown. [Spanish] Se explica la fisica de las oscilaciones de la interfase de dos fluidos viscosos no miscibles a partir del analisis detallado de las condiciones de empalme que se derivan casi completamente del sistema de ecuaciones dinamicas que lo rigen. Ese enfoque, no habitual en los cursos de doctorado de esta materia, se propone como alternativa para estos cursos. Se explica tambien de forma clara el posible papel de la viscosidad en los modos de oscilacion de la interfase.

  10. Robust matching for voice recognition

    Science.gov (United States)

    Higgins, Alan; Bahler, L.; Porter, J.; Blais, P.

    1994-10-01

    This paper describes an automated method of comparing a voice sample of an unknown individual with samples from known speakers in order to establish or verify the individual's identity. The method is based on a statistical pattern matching approach that employs a simple training procedure, requires no human intervention (transcription, work or phonetic marketing, etc.), and makes no assumptions regarding the expected form of the statistical distributions of the observations. The content of the speech material (vocabulary, grammar, etc.) is not assumed to be constrained in any way. An algorithm is described which incorporates frame pruning and channel equalization processes designed to achieve robust performance with reasonable computational resources. An experimental implementation demonstrating the feasibility of the concept is described.

  11. A systems genetics approach identifies genes and pathways for type 2 diabetes in human islets

    DEFF Research Database (Denmark)

    Taneera, Jalal; Lang, Stefan; Sharma, Amitabh;

    2012-01-01

    Close to 50 genetic loci have been associated with type 2 diabetes (T2D), but they explain only 15% of the heritability. In an attempt to identify additional T2D genes, we analyzed global gene expression in human islets from 63 donors. Using 48 genes located near T2D risk variants, we identified......, whereas GPR120 affected apoptosis in islets. Expression variation of the top 20 genes explained 24% of the variance in HbA(1c) with no claim of the direction. The data present a global map of genes associated with islet dysfunction and demonstrate the value of systems genetics for the identification...

  12. Sidescan Sonar Image Matching Using Cross Correlation

    DEFF Research Database (Denmark)

    Thisen, Erik; Sørensen, Helge Bjarup Dissing; Stage, Bjarne

    2003-01-01

    viewpoints. This paper presents a novel approach for matching two sidescan sonar images. The method first registers the two images to ground, then uses the cross correlation of the object positions on the seabed to find the correct displacement between the two images. In order to correct any minor...

  13. Revisiting the Concept of "Style Match"

    Science.gov (United States)

    Zhang, Li-fang; Sternberg, Robert J.; Fan, Jieqiong

    2013-01-01

    Background: Intellectual style, an encompassing term for such constructs as learning style, teaching style, teaching approach, and thinking style, refers to one's preferred way of processing information. For the past several decades, whether or not there is a need for a match between teachers' teaching styles and students' learning styles has been…

  14. Quantity precommitment and price matching

    DEFF Research Database (Denmark)

    Tumennasan, Norovsambuu

    We revisit the question of whether price matching is anti-competitive in a capacity constrained duopoly setting. We show that the effect of price matching depends on capacity. Specifically, price matching has no effect when capacity is relatively low, but it benefits the firms when capacity is...... relatively high. Interestingly, when capacity is in an intermediate range, price matching benefits only the small firm but does not affect the large firm in any way. Therefore, one has to consider capacity seriously when evaluating if price matching is anti-competitive. If the firms choose their capacities...... simultaneously before pricing decisions, then the effect of price matching is either pro-competitive or ambiguous. We show that if the cost of capacity is high, then price matching can only (weakly) decrease the market price. On the other hand, if the cost of capacity is low, then the effect of price matching on...

  15. Active Learning for Matching Problems

    OpenAIRE

    Charlin, Laurent; Zemel, Rich; Boutilier, Craig

    2012-01-01

    Effective learning of user preferences is critical to easing user burden in various types of matching problems. Equally important is active query selection to further reduce the amount of preference information users must provide. We address the problem of active learning of user preferences for matching problems, introducing a novel method for determining probabilistic matchings, and developing several new active learning strategies that are sensitive to the specific matching objective. Expe...

  16. Adeno-Associated Virus-Mediated Gene Transfer to Renal Tubule Cells via a Retrograde Ureteral Approach

    Directory of Open Access Journals (Sweden)

    Daniel C. Chung

    2011-11-01

    Full Text Available Background/Aims: Gene therapy involves delivery of exogenous DNA to provide a therapeutic protein. Ideally, a gene therapy vector should be non-toxic, non-immunogenic, easy to produce, and efficient in protecting and delivering DNA into target cells. Methods: Adeno-associated virus (AAV offers these advantages and few, if any, disadvantages, and over 100 isolates exist. We previously showed that AAV-mediated gene therapy can be used to restore vision to patients with Leber’s congenital amaurosis, a disease of childhood blindness. Results: Here we show that novel recombinant AAV2/8 and AAV2/9 transduce kidney tubule cells with high efficiency both in vitroin cell culture and in vivoin mice. In addition, we adapted and modified a retrograde approach to allow for optimal transgene delivery to renal tubular cells that further minimizes the risk of an immunogenic reaction. Conclusions: We believe that recombinant AAV2, especially AAV2/8, gene delivery to renal tubule cells via a retrograde approach represents a viable method for gene therapy for a multitude of renal disorders ranging from autosomal dominant polycystic kidney disease to acute kidney injury.

  17. Spatial competition with intermediated matching

    NARCIS (Netherlands)

    van Raalte, C.L.J.P.; Webers, H.M.

    1995-01-01

    This paper analyzes the spatial competition in commission fees between two match makers. These match makers serve as middlemen between buyers and sellers who are located uniformly on a circle. The profits of the match makers are determined by their respective market sizes. A limited willingness to p

  18. From essential to persistent genes: a functional approach to constructing synthetic life

    Science.gov (United States)

    Acevedo-Rocha, Carlos G.; Fang, Gang; Schmidt, Markus; Ussery, David W.; Danchin, Antoine

    2013-01-01

    A central undertaking in synthetic biology (SB) is the quest for the ‘minimal genome’. However, ‘minimal sets’ of essential genes are strongly context-dependent and, in all prokaryotic genomes sequenced to date, not a single protein-coding gene is entirely conserved. Furthermore, a lack of consensus in the field as to what attributes make a gene truly essential adds another aspect of variation. Thus, a universal minimal genome remains elusive. Here, as an alternative to defining a minimal genome, we propose that the concept of gene persistence can be used to classify genes needed for robust long-term survival. Persistent genes, although not ubiquitous, are conserved in a majority of genomes, tend to be expressed at high levels, and are frequently located on the leading DNA strand. These criteria impose constraints on genome organization, and these are important considerations for engineering cells and for creating cellular life-like forms in SB. PMID:23219343

  19. A New Two-Step Approach for Hands-On Teaching of Gene Technology: Effects on Students' Activities During Experimentation in an Outreach Gene Technology Lab

    Science.gov (United States)

    Scharfenberg, Franz-Josef; Bogner, Franz X.

    2011-08-01

    Emphasis on improving higher level biology education continues. A new two-step approach to the experimental phases within an outreach gene technology lab, derived from cognitive load theory, is presented. We compared our approach using a quasi-experimental design with the conventional one-step mode. The difference consisted of additional focused discussions combined with students writing down their ideas (step one) prior to starting any experimental procedure (step two). We monitored students' activities during the experimental phases by continuously videotaping 20 work groups within each approach ( N = 131). Subsequent classification of students' activities yielded 10 categories (with well-fitting intra- and inter-observer scores with respect to reliability). Based on the students' individual time budgets, we evaluated students' roles during experimentation from their prevalent activities (by independently using two cluster analysis methods). Independently of the approach, two common clusters emerged, which we labeled as `all-rounders' and as `passive students', and two clusters specific to each approach: `observers' as well as `high-experimenters' were identified only within the one-step approach whereas under the two-step conditions `managers' and `scribes' were identified. Potential changes in group-leadership style during experimentation are discussed, and conclusions for optimizing science teaching are drawn.

  20. Normal ECG Recognition for Express-Diagnostics Based on Scale-Space Representation and Dynamic Matching

    OpenAIRE

    Bilous, Nataliya; Bondarenko, Michael; Kobzar, Gleb; Krasov, Alexey; Rogozyanov, Artyom

    2008-01-01

    A novel approach of normal ECG recognition based on scale-space signal representation is proposed. The approach utilizes curvature scale-space signal representation used to match visual objects shapes previously and dynamic programming algorithm for matching CSS representations of ECG signals. Extraction and matching processes are fast and experimental results show that the approach is quite robust for preliminary normal ECG recognition.

  1. From essential to persistent genes: a functional approach to constructing synthetic life

    DEFF Research Database (Denmark)

    Acevedo-Rocha, Carlos G.; Fang, Gang; Schmidt, Markus;

    2013-01-01

    of consensus in the field as to what attributes make a gene truly essential adds another aspect of variation. Thus, a universal minimal genome remains elusive. Here, as an alternative to defining a minimal genome, we propose that the concept of gene persistence can be used to classify genes needed for robust...... for engineering cells and for creating cellular life-like forms in SB....

  2. Exploring potential new floral organ morphogenesis genes of Arabidopsis thaliana using systems biology approach

    OpenAIRE

    Xie, Wenchuan; Huang, Junfeng; Liu, Yang; Rao, Jianan; Luo, Da; He, Miao

    2015-01-01

    Flowering is one of the important defining features of angiosperms. The initiation of flower development and the formation of different floral organs are the results of the interplays among numerous genes. But until now, just fewer genes have been found linked with flower development. And the functions of lots of genes of Arabidopsis thaliana are still unknown. Although, the quartet model successfully simplified the ABCDE model to elaborate the molecular mechanism by introducing protein-prote...

  3. A multi-gene transcriptional profiling approach to the discovery of cell signature markers

    OpenAIRE

    Wada, Youichiro; Li, Dan; Merley, Anne; Zukauskas, Andrew; Aird, William C.; Dvorak, Harold F.; Shih, Shou-Ching

    2010-01-01

    A profile of transcript abundances from multiple genes constitutes a molecular signature if the expression pattern is unique to one cell type. Here we measure mRNA copy numbers per cell by normalizing per million copies of 18S rRNA and identify 6 genes (TIE1, KDR, CDH5, TIE2, EFNA1 and MYO5C) out of 79 genes tested as excellent molecular signature markers for endothelial cells (ECs) in vitro. The selected genes are uniformly expressed in ECs of 4 different origins but weakly or not expressed ...

  4. Line matching for automatic change detection algorithm

    Science.gov (United States)

    Dhollande, Jérôme; Monnin, David; Gond, Laetitia; Cudel, Christophe; Kohler, Sophie; Dieterlen, Alain

    2012-06-01

    During foreign operations, Improvised Explosive Devices (IEDs) are one of major threats that soldiers may unfortunately encounter along itineraries. Based on a vehicle-mounted camera, we propose an original approach by image comparison to detect signicant changes on these roads. The classic 2D-image registration techniques do not take into account parallax phenomena. The consequence is that the misregistration errors could be detected as changes. According to stereovision principles, our automatic method compares intensity proles along corresponding epipolar lines by extrema matching. An adaptive space warping compensates scale dierence in 3D-scene. When the signals are matched, the signal dierence highlights changes which are marked in current video.

  5. a New Paradigm for Matching - and Aerial Images

    Science.gov (United States)

    Koch, T.; Zhuo, X.; Reinartz, P.; Fraundorfer, F.

    2016-06-01

    This paper investigates the performance of SIFT-based image matching regarding large differences in image scaling and rotation, as this is usually the case when trying to match images captured from UAVs and airplanes. This task represents an essential step for image registration and 3d-reconstruction applications. Various real world examples presented in this paper show that SIFT, as well as A-SIFT perform poorly or even fail in this matching scenario. Even if the scale difference in the images is known and eliminated beforehand, the matching performance suffers from too few feature point detections, ambiguous feature point orientations and rejection of many correct matches when applying the ratio-test afterwards. Therefore, a new feature matching method is provided that overcomes these problems and offers thousands of matches by a novel feature point detection strategy, applying a one-to-many matching scheme and substitute the ratio-test by adding geometric constraints to achieve geometric correct matches at repetitive image regions. This method is designed for matching almost nadir-directed images with low scene depth, as this is typical in UAV and aerial image matching scenarios. We tested the proposed method on different real world image pairs. While standard SIFT failed for most of the datasets, plenty of geometrical correct matches could be found using our approach. Comparing the estimated fundamental matrices and homographies with ground-truth solutions, mean errors of few pixels can be achieved.

  6. A bi-ordering approach to linking gene expression with clinical annotations in gastric cancer

    Directory of Open Access Journals (Sweden)

    Leckie Christopher

    2010-09-01

    Full Text Available Abstract Background In the study of cancer genomics, gene expression microarrays, which measure thousands of genes in a single assay, provide abundant information for the investigation of interesting genes or biological pathways. However, in order to analyze the large number of noisy measurements in microarrays, effective and efficient bioinformatics techniques are needed to identify the associations between genes and relevant phenotypes. Moreover, systematic tests are needed to validate the statistical and biological significance of those discoveries. Results In this paper, we develop a robust and efficient method for exploratory analysis of microarray data, which produces a number of different orderings (rankings of both genes and samples (reflecting correlation among those genes and samples. The core algorithm is closely related to biclustering, and so we first compare its performance with several existing biclustering algorithms on two real datasets - gastric cancer and lymphoma datasets. We then show on the gastric cancer data that the sample orderings generated by our method are highly statistically significant with respect to the histological classification of samples by using the Jonckheere trend test, while the gene modules are biologically significant with respect to biological processes (from the Gene Ontology. In particular, some of the gene modules associated with biclusters are closely linked to gastric cancer tumorigenesis reported in previous literature, while others are potentially novel discoveries. Conclusion In conclusion, we have developed an effective and efficient method, Bi-Ordering Analysis, to detect informative patterns in gene expression microarrays by ranking genes and samples. In addition, a number of evaluation metrics were applied to assess both the statistical and biological significance of the resulting bi-orderings. The methodology was validated on gastric cancer and lymphoma datasets.

  7. An efficient approach to finding Siraitia grosvenorii triterpene biosynthetic genes by RNA-seq and digital gene expression analysis

    Directory of Open Access Journals (Sweden)

    Song Cai

    2011-07-01

    Full Text Available Abstract Background Siraitia grosvenorii (Luohanguo is an herbaceous perennial plant native to southern China and most prevalent in Guilin city. Its fruit contains a sweet, fleshy, edible pulp that is widely used in traditional Chinese medicine. The major bioactive constituents in the fruit extract are the cucurbitane-type triterpene saponins known as mogrosides. Among them, mogroside V is nearly 300 times sweeter than sucrose. However, little is known about mogrosides biosynthesis in S. grosvenorii, especially the late steps of the pathway. Results In this study, a cDNA library generated from of equal amount of RNA taken from S. grosvenorii fruit at 50 days after flowering (DAF and 70 DAF were sequenced using Illumina/Solexa platform. More than 48,755,516 high-quality reads from a cDNA library were generated that was assembled into 43,891 unigenes. De novo assembly and gap-filling generated 43,891 unigenes with an average sequence length of 668 base pairs. A total of 26,308 (59.9% unique sequences were annotated and 11,476 of the unique sequences were assigned to specific metabolic pathways by the Kyoto Encyclopedia of Genes and Genomes. cDNA sequences for all of the known enzymes involved in mogrosides backbone synthesis were identified from our library. Additionally, a total of eighty-five cytochrome P450 (CYP450 and ninety UDP-glucosyltransferase (UDPG unigenes were identified, some of which appear to encode enzymes responsible for the conversion of the mogroside backbone into the various mogrosides. Digital gene expression profile (DGE analysis using Solexa sequencing was performed on three important stages of fruit development, and based on their expression pattern, seven CYP450s and five UDPGs were selected as the candidates most likely to be involved in mogrosides biosynthesis. Conclusion A combination of RNA-seq and DGE analysis based on the next generation sequencing technology was shown to be a powerful method for identifying

  8. Angiogenesis related gene expression profiles of EA.hy926 cells induced by irbesartan: a possible novel therapeutic approach

    Institute of Scientific and Technical Information of China (English)

    MA Cong; LU Xue-chun; LUO Yun; CAO Jian; YANG Bo; GAO Yan; LIU Xian-feng; FAN Li

    2012-01-01

    Background Angiogenesis occurs commonly in various physiological and pathological processes.Improving blood supply through promoting angiogenesis is a novel approach for treating ischemic diseases.Angiotensin Ⅱ type 1 receptor blockers (ARBs) dominate the management of hypertension,but evidence of their role in angiogenesis is contradictory.Here we explored the angiogenic effects of ARBs through characterizing gene expression of the human umbilical vein endothelial cell line EA.hy926 exposed to irbesartan.Methods The human umbilical vein endothelial cell line EA.hy926 was grown for 72 hours after treatment with different concentrations of irbesartan.The cell proliferative capacity was assessed by CCK8 assay at 24,48 and 72 hours.Gene expression levels in EA.hy926 cells responding to irbesartan were measured under optimal proliferation conditions by microarray analysis using Affymetrix U133 plus 2.0.The differential expression of genes involved in angiogenesis was identified through cluster analysis of the resulting microarray data.Quantitative RT-PCR and Western blotting analyses were used to validate differential gene expression related to the angiogenesis process.Results In the 10-4,10-5,10-6 mol/L treatment groups,cell proliferation studies revealed significantly increased proliferation in EA.hy926 cells after 24 hours of irbesartan treatment.However,after 48 and 72 hours of treatment with different concentrations of irbesartan,there was no significant difference in cell proliferation observed in any treatment group.We selected the group stimulated with irbersartan at a concentration of 10-6 mol/L for microarray experiments.Statistical analysis of the microarray data resulted in the identification of 56 gene transcripts whose expression patterns were significantly correlated,negatively or positively,with irbesartan treatment.Cluster analysis showed that these genes were involved in angiogenesis,extracellular stimulus,binding reactions and skeletal system

  9. A combinatory approach for selecting prognostic genes in microarray studies of tumour survivals

    DEFF Research Database (Denmark)

    Tan, Qihua; Thomassen, Mads; Jochumsen, Kirsten M;

    2009-01-01

    differential gene expression analysis with the Gram-Schmidt process to identify prognostic genes that are both statistically significant and highly informative for predicting tumour survival outcomes. Empirical application to leukemia and ovarian cancer survival data through-within- and cross-study validations...

  10. Gene-Environment Interactions in Genome-Wide Association Studies: Current Approaches and New Directions

    Science.gov (United States)

    Winham, Stacey J.; Biernacka, Joanna M.

    2013-01-01

    Background: Complex psychiatric traits have long been thought to be the result of a combination of genetic and environmental factors, and gene-environment interactions are thought to play a crucial role in behavioral phenotypes and the susceptibility and progression of psychiatric disorders. Candidate gene studies to investigate hypothesized…

  11. A Systems Genetics Approach Identifies Gene Regulatory Networks Associated with Fatty Acid Composition in Brassica rapa Seed.

    Science.gov (United States)

    Basnet, Ram Kumar; Del Carpio, Dunia Pino; Xiao, Dong; Bucher, Johan; Jin, Mina; Boyle, Kerry; Fobert, Pierre; Visser, Richard G F; Maliepaard, Chris; Bonnema, Guusje

    2016-01-01

    Fatty acids in seeds affect seed germination and seedling vigor, and fatty acid composition determines the quality of seed oil. In this study, quantitative trait locus (QTL) mapping of fatty acid and transcript abundance was integrated with gene network analysis to unravel the genetic regulation of seed fatty acid composition in a Brassica rapa doubled haploid population from a cross between a yellow sarson oil type and a black-seeded pak choi. The distribution of major QTLs for fatty acids showed a relationship with the fatty acid types: linkage group A03 for monounsaturated fatty acids, A04 for saturated fatty acids, and A05 for polyunsaturated fatty acids. Using a genetical genomics approach, expression quantitative trait locus (eQTL) hotspots were found at major fatty acid QTLs on linkage groups A03, A04, A05, and A09. An eQTL-guided gene coexpression network of lipid metabolism-related genes showed major hubs at the genes BrPLA2-ALPHA, BrWD-40, a number of seed storage protein genes, and the transcription factor BrMD-2, suggesting essential roles for these genes in lipid metabolism. Three subnetworks were extracted for the economically important and most abundant fatty acids erucic, oleic, linoleic, and linolenic acids. Network analysis, combined with comparison of the genome positions of cis- or trans-eQTLs with fatty acid QTLs, allowed the identification of candidate genes for genetic regulation of these fatty acids. The generated insights in the genetic architecture of fatty acid composition and the underlying complex gene regulatory networks in B. rapa seeds are discussed. PMID:26518343

  12. A system biology approach highlights a hormonal enhancer effect on regulation of genes in a nitrate responsive "biomodule"

    Directory of Open Access Journals (Sweden)

    Nero Damion

    2009-06-01

    Full Text Available Abstract Background Nitrate-induced reprogramming of the transcriptome has recently been shown to be highly context dependent. Herein, a systems biology approach was developed to identify the components and role of cross-talk between nitrate and hormone signals, likely to be involved in the conditional response of NO3- signaling. Results Biclustering was used to identify a set of genes that are N-responsive across a range of Nitrogen (N-treatment backgrounds (i.e. nitrogen treatments under different growth conditions using a meta-dataset of 76 Affymetrix ATH1 chips from 5 different laboratories. Twenty-one biclusters were found to be N-responsive across subsets of this meta-dataset. N-bicluster 9 (126 genes was selected for further analysis, as it was shown to be reproducibly responsive to NO3- as a signal, across a wide-variety of background conditions and datasets. N-bicluster 9 genes were then used as "seed" to identify putative cross-talk mechanisms between nitrate and hormone signaling. For this, the 126 nitrate-regulated genes in N-bicluster 9 were biclustered over a meta-dataset of 278 ATH1 chips spanning a variety of hormone treatments. This analysis divided the bicluster 9 genes into two classes: i genes controlled by NO3- only vs. ii genes controlled by both NO3- and hormones. The genes in the latter group showed a NO3- response that is significantly enhanced, compared to the former. In silico analysis identified two Cis-Regulatory Elements candidates (CRE (E2F, HSE potentially involved the interplay between NO3- and hormonal signals. Conclusion This systems analysis enabled us to derive a hypothesis in which hormone signals are proposed to enhance the nitrate response, providing a potential mechanistic explanation for the link between nitrate signaling and the control of plant development.

  13. Exploring potential new floral organ morphogenesis genes of Arabidopsis thaliana using systems biology approach.

    Science.gov (United States)

    Xie, Wenchuan; Huang, Junfeng; Liu, Yang; Rao, Jianan; Luo, Da; He, Miao

    2015-01-01

    Flowering is one of the important defining features of angiosperms. The initiation of flower development and the formation of different floral organs are the results of the interplays among numerous genes. But until now, just fewer genes have been found linked with flower development. And the functions of lots of genes of Arabidopsis thaliana are still unknown. Although, the quartet model successfully simplified the ABCDE model to elaborate the molecular mechanism by introducing protein-protein interactions (PPIs). We still don't know much about several important aspects of flower development. So we need to discriminate even more genes involving in the flower development. In this study, we identified seven differentially modules through integrating the weighted gene co-expression network analysis (WGCNA) and Support Vector Machine (SVM) method to analyze co-expression network and PPIs using the public floral and non-floral expression profiles data of Arabidopsis thaliana. Gene set enrichment analysis was used for the functional annotation of the related genes, and some of the hub genes were identified in each module. The potential floral organ morphogenesis genes of two significant modules were integrated with PPI information in order to detail the inherent regulation mechanisms. Finally, the functions of the floral patterning genes were elucidated by combining the PPI and evolutionary information. It was indicated that the sub-networks or complexes, rather than the genes, were the regulation unit of flower development. We found that the most possible potential new genes underlining the floral pattern formation in A. thaliana were FY, CBL2, ZFN3, and AT1G77370; among them, FY, CBL2 acted as an upstream regulator of AP2; ZFN3 activated the flower primordial determining gene AP1 and AP2 by HY5/HYH gene via photo induction possibly. And AT1G77370 exhibited similar function in floral morphogenesis, same as ELF3. It possibly formed a complex between RFC3 and RPS15 in

  14. Exploring potential new floral organ morphogenesis genes of Arabidopsis thaliana using systems biology approach

    Directory of Open Access Journals (Sweden)

    Wenchuan eXie

    2015-10-01

    Full Text Available Flowering is one of the important defining features of angiosperms. The initiation of flower development and the formation of different floral organs are the results of the interplays among numerous genes. But until now, just fewer genes have been found linked with flower development. And the functions of lots of genes of Arabidopsis thaliana are still unknown. Although, the quartet model successfully simplified the ABCDE model to elaborate the molecular mechanism by introducing protein-protein interactions (PPIs. We still don't know much about several important aspects of flower development. So we need to discriminate even more genes involving in the flower development. In this study, we identified seven differentially modules through integrating the weighted gene co-expression network analysis (WGCNA and Support Vector Machine (SVM method to analyze co-expression network and PPIs using the public floral and non-floral expression profiles data of Arabidopsis thaliana. Gene set enrichment analysis was used for the functional annotation of the related genes, and some of the hub genes were identified in each module. The potential floral organ morphogenesis genes of two significant modules were integrated with PPI information in order to detail the inherent regulation mechanisms. Finally, the functions of the floral patterning genes were elucidated by combining the PPI and evolutionary information. It was indicated that the sub-networks or complexes, rather than the genes, were the regulation unit of flower development. We found that the most possible potential new genes underlining the floral pattern formation in A. thaliana were FY, CBL2, ZFN3 and AT1G77370; among them, FY, CBL2 acted as an upstream regulator of AP2; ZFN3 activated the flower primordial determining gene AP1 and AP2 by HY5/HYH gene via photo induction possibly. And AT1G77370 exhibited similar function in floral morphogenesis, same as ELF3. It possibly formed a complex between RFC3

  15. Correlating overrepresented upstream motifs to gene expression a computational approach to regulatory element discovery in eukaryotes

    CERN Document Server

    Caselle, M; Provero, P

    2002-01-01

    Gene regulation in eukaryotes is mainly effected through transcription factors binding to rather short recognition motifs generally located upstream of the coding region. We present a novel computational method to identify regulatory elements in the upstream region of eukaryotic genes. The genes are grouped in sets sharing an overrepresented short motif in their upstream sequence. For each set, the average expression level from a microarray experiment is determined: If this level is significantly higher or lower than the average taken over the whole genome, then the overerpresented motif shared by the genes in the set is likely to play a role in their regulation. The method was tested by applying it to the genome of Saccharomyces cerevisiae, using the publicly available results of a DNA microarray experiment, in which expression levels for virtually all the genes were measured during the diauxic shift from fermentation to respiration. Several known motifs were correctly identified, and a new candidate regulat...

  16. Transverse Matching Techniques for the SNS Linac

    CERN Document Server

    Jeon Dong Oh; Danilov, Viatcheslav V

    2005-01-01

    It is crucial to minimize beam loss and machine activation by obtaining optimal transverse matching for a high-intensity linear accelerator such as the Spallation Neutron Source linac. For matching the Drift Tube Linac (DTL) to Coupled Cavity Linac (CCL), there are four wire-scanners installed in series in CCL module 1 as proposed by the author.* A series of measurements was conducted to minimize envelope breathing and the results are presented here. As an independent approach, Chu et al is developing an application based on another technique by estimating rms emittance using the wire scanner profile data.** For matching the Medium Energy Beam Transport Line to the DTL, a technique of minimizing rms emittance was used and emittance data show that tail is minimized as well.

  17. Improved Stereo Matching With Boosting Method

    Directory of Open Access Journals (Sweden)

    Shiny B

    2015-06-01

    Full Text Available Abstract This paper presents an approach based on classification for improving the accuracy of stereo matching methods. We propose this method for occlusion handling. This work employs classification of pixels for finding the erroneous disparity values. Due to the wide applications of disparity map in 3D television medical imaging etc the accuracy of disparity map has high significance. An initial disparity map is obtained using local or global stereo matching methods from the input stereo image pair. The various features for classification are computed from the input stereo image pair and the obtained disparity map. Then the computed feature vector is used for classification of pixels by using GentleBoost as the classification method. The erroneous disparity values in the disparity map found by classification are corrected through a completion stage or filling stage. A performance evaluation of stereo matching using AdaBoostM1 RUSBoost Neural networks and GentleBoost is performed.

  18. Covariant diagrams for one-loop matching

    CERN Document Server

    Zhang, Zhengkang

    2016-01-01

    We present a diagrammatic formulation of recently-revived covariant functional approaches to one-loop matching from an ultraviolet (UV) theory to a low-energy effective field theory. Various terms following from a covariant derivative expansion (CDE) are represented by diagrams which, unlike conventional Feynman diagrams, involve gauge-covariant quantities and are thus dubbed "covariant diagrams." The use of covariant diagrams helps organize and simplify one-loop matching calculations, which we illustrate with examples. Of particular interest is the derivation of UV model-independent universal results, which reduce matching calculations of specific UV models to applications of master formulas. We show how such derivation can be done in a more concise manner than the previous literature, and discuss how additional structures that are not directly captured by existing universal results, including mixed heavy-light loops, open covariant derivatives, and mixed statistics, can be easily accounted for.

  19. Gene

    Data.gov (United States)

    U.S. Department of Health & Human Services — Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes,...

  20. Quantum image matching

    Science.gov (United States)

    Jiang, Nan; Dang, Yijie; Wang, Jian

    2016-09-01

    Quantum image processing (QIP) means the quantum-based methods to speed up image processing algorithms. Many quantum image processing schemes claim that their efficiency is theoretically higher than their corresponding classical schemes. However, most of them do not consider the problem of measurement. As we all know, measurement will lead to collapse. That is to say, executing the algorithm once, users can only measure the final state one time. Therefore, if users want to regain the results (the processed images), they must execute the algorithms many times and then measure the final state many times to get all the pixels' values. If the measurement process is taken into account, whether or not the algorithms are really efficient needs to be reconsidered. In this paper, we try to solve the problem of measurement and give a quantum image matching algorithm. Unlike most of the QIP algorithms, our scheme interests only one pixel (the target pixel) instead of the whole image. It modifies the probability of pixels based on Grover's algorithm to make the target pixel to be measured with higher probability, and the measurement step is executed only once. An example is given to explain the algorithm more vividly. Complexity analysis indicates that the quantum scheme's complexity is O(2n) in contradistinction to the classical scheme's complexity O(2^{2n+2m}), where m and n are integers related to the size of images.

  1. A new experimental approach for studying bacterial genomic island evolution identifies island genes with bacterial host-specific expression patterns

    Directory of Open Access Journals (Sweden)

    Nickerson Cheryl A

    2006-01-01

    Full Text Available Abstract Background Genomic islands are regions of bacterial genomes that have been acquired by horizontal transfer and often contain blocks of genes that function together for specific processes. Recently, it has become clear that the impact of genomic islands on the evolution of different bacterial species is significant and represents a major force in establishing bacterial genomic variation. However, the study of genomic island evolution has been mostly performed at the sequence level using computer software or hybridization analysis to compare different bacterial genomic sequences. We describe here a novel experimental approach to study the evolution of species-specific bacterial genomic islands that identifies island genes that have evolved in such a way that they are differentially-expressed depending on the bacterial host background into which they are transferred. Results We demonstrate this approach by using a "test" genomic island that we have cloned from the Salmonella typhimurium genome (island 4305 and transferred to a range of Gram negative bacterial hosts of differing evolutionary relationships to S. typhimurium. Systematic analysis of the expression of the island genes in the different hosts compared to proper controls allowed identification of genes with genera-specific expression patterns. The data from the analysis can be arranged in a matrix to give an expression "array" of the island genes in the different bacterial backgrounds. A conserved 19-bp DNA site was found upstream of at least two of the differentially-expressed island genes. To our knowledge, this is the first systematic analysis of horizontally-transferred genomic island gene expression in a broad range of Gram negative hosts. We also present evidence in this study that the IS200 element found in island 4305 in S. typhimurium strain LT2 was inserted after the island had already been acquired by the S. typhimurium lineage and that this element is likely not

  2. A multi-gene transcriptional profiling approach to the discovery of cell signature markers.

    Science.gov (United States)

    Wada, Youichiro; Li, Dan; Merley, Anne; Zukauskas, Andrew; Aird, William C; Dvorak, Harold F; Shih, Shou-Ching

    2011-01-01

    A profile of transcript abundances from multiple genes constitutes a molecular signature if the expression pattern is unique to one cell type. Here we measure mRNA copy numbers per cell by normalizing per million copies of 18S rRNA and identify 6 genes (TIE1, KDR, CDH5, TIE2, EFNA1 and MYO5C) out of 79 genes tested as excellent molecular signature markers for endothelial cells (ECs) in vitro. The selected genes are uniformly expressed in ECs of 4 different origins but weakly or not expressed in 4 non-EC cell lines. A multi-gene transcriptional profile of these 6 genes clearly distinguishes ECs from non-ECs in vitro. We conclude that (i) a profile of mRNA copy numbers per cell from a well-chosen multi-gene panel can act as a sensitive and accurate cell type signature marker, and (ii) the method described here can be applied to in vivo cell fingerprinting and molecular diagnosis. PMID:20972619

  3. Direct Detection and Differentiation of Pathogenic Leptospira Species Using a Multi-Gene Targeted Real Time PCR Approach

    OpenAIRE

    Ana Sofia Ferreira; Pedro Costa; Teresa Rocha; Ana Amaro; Maria Luísa Vieira; Ahmed Ahmed; Gertrude Thompson; Hartskeerl, Rudy A.; João Inácio

    2014-01-01

    Leptospirosis is a growing public and veterinary health concern caused by pathogenic species of Leptospira. Rapid and reliable laboratory tests for the direct detection of leptospiral infections in animals are in high demand not only to improve diagnosis but also for understanding the epidemiology of the disease. In this work we describe a novel and simple TaqMan-based multi-gene targeted real-time PCR approach able to detect and differentiate Leptospira interrogans, L. kirschneri, L. borgpet...

  4. Classification of Micro Array Gene Expression Data using Factor Analysis Approach with Naïve Bayesian Classifier

    OpenAIRE

    Tamilselvi Madeswaran; G.M.Kadhar Nawaz

    2013-01-01

    Microarray data studies produce large number of data and in order to analyze such large micro array data lies on Data mining or Statistical Analysis. Our objective is to classify the micro arraygene expression data. Usually before going for the classification the dimensionality reduction will be performed on the micro array gene expression dataset. A statistical approach for the extraction of thegene has been proposed. The drawback in the statistical analysis is that, it doesn’t identify the ...

  5. Point pattern matching based on kernel partial least squares

    Institute of Scientific and Technical Information of China (English)

    Weidong Yan; Zheng Tian; Lulu Pan; Jinhuan Wen

    2011-01-01

    @@ Point pattern matching is an essential step in many image processing applications. This letter investigates the spectral approaches of point pattern matching, and presents a spectral feature matching algorithm based on kernel partial least squares (KPLS). Given the feature points of two images, we define position similarity matrices for the reference and sensed images, and extract the pattern vectors from the matrices using KPLS, which indicate the geometric distribution and the inner relationships of the feature points.Feature points matching are done using the bipartite graph matching method. Experiments conducted on both synthetic and real-world data demonstrate the robustness and invariance of the algorithm.%Point pattern matching is an essential step in many image processing applications. This letter investigates the spectral approaches of point pattern matching, and presents a spectral feature matching algorithm based on kernel partial least squares (KPLS). Given the feature points of two images, we define position similarity matrices for the reference and sensed images, and extract the pattern vectors from the matrices using KPLS, which indicate the geometric distribution and the inner relationships of the feature points.Feature points matching are done using the bipartite graph matching method. Experiments conducted on both synthetic and real-world data demonstrate the robustness and invariance of the algorithm.

  6. Approach of combined cancer gene therapy and radiation: response of promoters to ionizing radiation

    International Nuclear Information System (INIS)

    Gene therapy is an emerging cancer treatment modality. We are interested in developing a radiation-inducible gene therapy system to sensitize the tumor vasculature to the effects of ionizing radiation (IR) treatment. An expression system based on irradiation-inducible promoters will drive the expression of anti-tumor genes in the tumor vasculature. Solid tumors are dependent on angio genesis, a process in which new blood vessels are formed from the pre-existing vasculature. Vascular endothelial cells are un transformed and genetically stable, thus avoiding the problem of resistance to the treatments. Vascular endothelial cells may therefore represent a suitable target for this therapeutic gene therapy strategy.The identification of IR-inducible promoters native to endothelial cells was performed by gene expression profiling using cDNA micro array technology. We describe the genes modified by clinically relevant doses of IR. The extension to high doses aimed at studying the effects of total radiation delivery to the tumor. The radio-inductiveness of the genes selected for promoter study was confirmed by RT-PCR. Analysis of the activity of promoters in response to IR was also assessed in a reporter plasmid. We found that authentic promoters cloned onto a plasmid are not suitable for cancer gene therapy due to their low induction after IR. In contrast, synthetic promoters containing repeated sequence-specific binding sites for IR-activated transcription factors such as NF-κB are potential candidates for gene therapy. The activity of five tandemly repeated TGGGGACTTTCCGC elements for NF-κB binding in a luciferase reporter was increased in a dose-dependent manner. Interestingly, the response to fractionated low doses was improved in comparison to the total single dose. Thus, we put present evidence that a synthetic promoter for NF-κB specific binding may have application in the radio-therapeutic treatment of cancer. (author)

  7. Exploration of structural stability in deleterious nsSNPs of the XPA gene: A molecular dynamics approach

    Directory of Open Access Journals (Sweden)

    N NagaSundaram

    2011-01-01

    Full Text Available Background: Distinguishing the deleterious from the massive number of non-functional nsSNPs that occur within a single genome is a considerable challenge in mutation research. In this approach, we have used the existing in silico methods to explore the mutation-structure-function relationship in the XPA gene. Materials and Methods: We used the Sorting Intolerant From Tolerant (SIFT, Polymorphism Phenotyping (PolyPhen, I-Mutant 2.0, and the Protein Analysis THrough Evolutionary Relationships methods to predict the effects of deleterious nsSNPs on protein function and evaluated the impact of mutation on protein stability by Molecular Dynamics simulations. Results: By comparing the scores of all the four in silico methods, nsSNP with an ID rs104894131 at position C108F was predicted to be highly deleterious. We extended our Molecular dynamics approach to gain insight into the impact of this non-synonymous polymorphism on structural changes that may affect the activity of the XPA gene. Conclusion: Based on the in silico methods score, potential energy, root-mean-square deviation, and root-mean-square fluctuation, we predict that deleterious nsSNP at position C108F would play a significant role in causing disease by the XPA gene. Our approach would present the application of in silico tools in understanding the functional variation from the perspective of structure, evolution, and phenotype.

  8. DOE Matching Grant Program

    International Nuclear Information System (INIS)

    Funding used to support a portion of the Nuclear Engineering Educational Activities. Upgrade of teaching labs, student support to attend professional conferences, salary support for graduate students. The US Department of Energy (DOE) has funded Purdue University School of Nuclear Engineering during the period of five academic years covered in this report starting in the academic year 1996-97 and ending in the academic year 2000-2001. The total amount of funding for the grant received from DOE is $416K. In the 1990's, Nuclear Engineering Education in the US experienced a significant slow down. Student enrollment, research support, number of degrees at all levels (BS, MS, and PhD), number of accredited programs, University Research and Training Reactors, all went through a decline to alarmingly low levels. Several departments closed down, while some were amalgamated with other academic units (Mechanical Engineering, Chemical Engineering, etc). The School of Nuclear Engineering at Purdue University faced a major challenge when in the mid 90's our total undergraduate enrollment for the Sophomore, Junior and Senior Years dropped in the low 30's. The DOE Matching Grant program greatly strengthened Purdue's commitment to the Nuclear Engineering discipline and has helped to dramatically improve our undergraduate and graduate enrollment, attract new faculty and raise the School of Nuclear Engineering status within the University and in the National scene (our undergraduate enrollment has actually tripled and stands at an all time high of over 90 students; total enrollment currently exceeds 110 students). In this final technical report we outline and summarize how the grant was expended at Purdue University

  9. DOE Matching Grant Program

    Energy Technology Data Exchange (ETDEWEB)

    Tsoukalas, L.

    2002-12-31

    Funding used to support a portion of the Nuclear Engineering Educational Activities. Upgrade of teaching labs, student support to attend professional conferences, salary support for graduate students. The US Department of Energy (DOE) has funded Purdue University School of Nuclear Engineering during the period of five academic years covered in this report starting in the academic year 1996-97 and ending in the academic year 2000-2001. The total amount of funding for the grant received from DOE is $416K. In the 1990's, Nuclear Engineering Education in the US experienced a significant slow down. Student enrollment, research support, number of degrees at all levels (BS, MS, and PhD), number of accredited programs, University Research and Training Reactors, all went through a decline to alarmingly low levels. Several departments closed down, while some were amalgamated with other academic units (Mechanical Engineering, Chemical Engineering, etc). The School of Nuclear Engineering at Purdue University faced a major challenge when in the mid 90's our total undergraduate enrollment for the Sophomore, Junior and Senior Years dropped in the low 30's. The DOE Matching Grant program greatly strengthened Purdue's commitment to the Nuclear Engineering discipline and has helped to dramatically improve our undergraduate and graduate enrollment, attract new faculty and raise the School of Nuclear Engineering status within the University and in the National scene (our undergraduate enrollment has actually tripled and stands at an all time high of over 90 students; total enrollment currently exceeds 110 students). In this final technical report we outline and summarize how the grant was expended at Purdue University.

  10. Matching for Human Leukocyte Antigens (HLA) in corneal transplantation - to do or not to do.

    Science.gov (United States)

    van Essen, T H; Roelen, D L; Williams, K A; Jager, M J

    2015-05-01

    As many patients with severe corneal disease are not even considered as candidates for a human graft due to their high risk of rejection, it is essential to find ways to reduce the chance of rejection. One of the options is proper matching of the cornea donor and recipient for the Human Leukocyte Antigens (HLA), a subject of much debate. Currently, patients receiving their first corneal allograft are hardly ever matched for HLA and even patients undergoing a regraft usually do not receive an HLA-matched graft. While anterior and posterior lamellar grafts are not immune to rejection, they are usually performed in low risk, non-vascularized cases. These are the cases in which the immune privilege due to the avascular status and active immune inhibition is still intact. Once broken due to infection, sensitization or trauma, rejection will occur. There is enough data to show that when proper DNA-based typing techniques are being used, even low risk perforating corneal transplantations benefit from matching for HLA Class I, and high risk cases from HLA Class I and probably Class II matching. Combining HLA class I and class II matching, or using the HLAMatchmaker could further improve the effect of HLA matching. However, new techniques could be applied to reduce the chance of rejection. Options are the local or systemic use of biologics, or gene therapy, aiming at preventing or suppressing immune responses. The goal of all these approaches should be to prevent a first rejection, as secondary grafts are usually at higher risk of complications including rejections than first grafts. PMID:25601193

  11. Isolation and manipulation of quantitative trait loci for disease resistance in rice using a candidate gene approach.

    Science.gov (United States)

    Hu, Ke-Ming; Qiu, De-Yun; Shen, Xiang-Ling; Li, Xiang-Hua; Wang, Shi-Ping

    2008-09-01

    Bacterial blight caused by Xanthomonas oryzae pv. oryzae and fungal blast caused by Magnaporthe grisea result in heavy production losses in rice, a main staple food for approximately 50% of the world's population. Application of host resistance to these pathogens is the most economical and environment-friendly approach to solve this problem. Quantitative trait loci (QTLs) controlling quantitative resistance are valuable sources for broad-spectrum and durable disease resistance. Although large numbers of QTLs for bacterial blight and blast resistance have been identified, these sources have not been used effectively in rice improvement because of the complex genetic control of quantitative resistance and because the genes underlying resistance QTLs are unknown. To isolate disease resistance QTLs, we established a candidate gene strategy that integrates linkage map, expression profile, and functional complementation analyses. This strategy has proven to be applicable for identifying the genes underlying minor resistance QTLs in rice-Xoo and rice-M. grisea systems and it may also help to shed light on disease resistance QTLs of other cereals. Our results also suggest that a single minor QTL can be used in rice improvement by modulating the expression of the gene underlying the QTL. Pyramiding two or three minor QTL genes, whose expression can be managed and that function in different defense signal transduction pathways, may allow the breeding of rice cultivars that are highly resistant to bacterial blight and blast.

  12. Isolation of Novel CreERT2-Driver Lines in Zebrafish Using an Unbiased Gene Trap Approach.

    Directory of Open Access Journals (Sweden)

    Peggy Jungke

    Full Text Available Gene manipulation using the Cre/loxP-recombinase system has been successfully employed in zebrafish to study gene functions and lineage relationships. Recently, gene trapping approaches have been applied to produce large collections of transgenic fish expressing conditional alleles in various tissues. However, the limited number of available cell- and tissue-specific Cre/CreERT2-driver lines still constrains widespread application in this model organism. To enlarge the pool of existing CreERT2-driver lines, we performed a genome-wide gene trap screen using a Tol2-based mCherry-T2a-CreERT2 (mCT2aC gene trap vector. This cassette consists of a splice acceptor and a mCherry-tagged variant of CreERT2 which enables simultaneous labeling of the trapping event, as well as CreERT2 expression from the endogenous promoter. Using this strategy, we generated 27 novel functional CreERT2-driver lines expressing in a cell- and tissue-specific manner during development and adulthood. This study summarizes the analysis of the generated CreERT2-driver lines with respect to functionality, expression, integration, as well as associated phenotypes. Our results significantly enlarge the existing pool of CreERT2-driver lines in zebrafish and combined with Cre-dependent effector lines, the new CreERT2-driver lines will be important tools to manipulate the zebrafish genome.

  13. Isolation of Novel CreERT2-Driver Lines in Zebrafish Using an Unbiased Gene Trap Approach.

    Science.gov (United States)

    Jungke, Peggy; Hammer, Juliane; Hans, Stefan; Brand, Michael

    2015-01-01

    Gene manipulation using the Cre/loxP-recombinase system has been successfully employed in zebrafish to study gene functions and lineage relationships. Recently, gene trapping approaches have been applied to produce large collections of transgenic fish expressing conditional alleles in various tissues. However, the limited number of available cell- and tissue-specific Cre/CreERT2-driver lines still constrains widespread application in this model organism. To enlarge the pool of existing CreERT2-driver lines, we performed a genome-wide gene trap screen using a Tol2-based mCherry-T2a-CreERT2 (mCT2aC) gene trap vector. This cassette consists of a splice acceptor and a mCherry-tagged variant of CreERT2 which enables simultaneous labeling of the trapping event, as well as CreERT2 expression from the endogenous promoter. Using this strategy, we generated 27 novel functional CreERT2-driver lines expressing in a cell- and tissue-specific manner during development and adulthood. This study summarizes the analysis of the generated CreERT2-driver lines with respect to functionality, expression, integration, as well as associated phenotypes. Our results significantly enlarge the existing pool of CreERT2-driver lines in zebrafish and combined with Cre-dependent effector lines, the new CreERT2-driver lines will be important tools to manipulate the zebrafish genome. PMID:26083735

  14. Combined subtractive cDNA cloning and array CGH: an efficient approach for identification of overexpressed genes in DNA amplicons

    Directory of Open Access Journals (Sweden)

    De Paepe Anne

    2004-02-01

    Full Text Available Abstract Background Activation of proto-oncogenes by DNA amplification is an important mechanism in the development and maintenance of cancer cells. Until recently, identification of the targeted genes relied on labour intensive and time consuming positional cloning methods. In this study, we outline a straightforward and efficient strategy for fast and comprehensive cloning of amplified and overexpressed genes. Results As a proof of principle, we analyzed neuroblastoma cell line IMR-32, with at least two amplification sites along the short arm of chromosome 2. In a first step, overexpressed cDNA clones were isolated using a PCR based subtractive cloning method. Subsequent deposition of these clones on a custom microarray and hybridization with IMR-32 DNA, resulted in the identification of clones that were overexpressed due to gene amplification. Using this approach, amplification of all previously reported amplified genes in this cell line was detected. Furthermore, four additional clones were found to be amplified, including the TEM8 gene on 2p13.3, two anonymous transcripts, and a fusion transcript, resulting from 2p13.3 and 2p24.3 fused sequences. Conclusions The combinatorial strategy of subtractive cDNA cloning and array CGH analysis allows comprehensive amplicon dissection, which opens perspectives for improved identification of hitherto unknown targeted oncogenes in cancer cells.

  15. Sequence Matching Analysis for Curriculum Development

    Directory of Open Access Journals (Sweden)

    Liem Yenny Bendatu

    2015-01-01

    Full Text Available Many organizations apply information technologies to support their business processes. Using the information technologies, the actual events are recorded and utilized to conform with predefined model. Conformance checking is an approach to measure the fitness and appropriateness between process model and actual events. However, when there are multiple events with the same timestamp, the traditional approach unfit to result such measures. This study attempts to develop a sequence matching analysis. Considering conformance checking as the basis of this approach, this proposed approach utilizes the current control flow technique in process mining domain. A case study in the field of educational process has been conducted. This study also proposes a curriculum analysis framework to test the proposed approach. By considering the learning sequence of students, it results some measurements for curriculum development. Finally, the result of the proposed approach has been verified by relevant instructors for further development.

  16. A Hybrid SOM-SVM Approach for the Zebrafish Gene Expression Analysis

    Institute of Scientific and Technical Information of China (English)

    Wei Wu; Xin Liu; Min Xu; Jin-Rong Peng; Rudy Setiono

    2005-01-01

    Microarray technology can be employed to quantitatively measure the expression of thousands of genes in a single experiment. It has become one of the main tools for global gene expression analysis in molecular biology research in recent years. The large amount of expression data generated by this technology makes the study of certain complex biological problems possible, and machine learning methods are expected to play a crucial role in the analysis process. In this paper,we present our results from integrating the self-organizing map (SOM) and the support vector machine (SVM) for the analysis of the various functions of zebrafish genes based on their expression. The most distinctive characteristic of our zebrafish gene expression is that the number of samples of different classes is imbalanced. We discuss how SOM can be used as a data-filtering tool to improve the classification performance of the SVM on this data set.

  17. Swarm Intelligence Approach Based on Adaptive ELM Classifier with ICGA Selection for Microarray Gene Expression and Cancer Classification

    Directory of Open Access Journals (Sweden)

    T. Karthikeyan

    2014-05-01

    Full Text Available The aim of this research study is based on efficient gene selection and classification of microarray data analysis using hybrid machine learning algorithms. The beginning of microarray technology has enabled the researchers to quickly measure the position of thousands of genes expressed in an organic/biological tissue samples in a solitary experiment. One of the important applications of this microarray technology is to classify the tissue samples using their gene expression representation, identify numerous type of cancer. Cancer is a group of diseases in which a set of cells shows uncontrolled growth, instance that interrupts upon and destroys nearby tissues and spreading to other locations in the body via lymph or blood. Cancer has becomes a one of the major important disease in current scenario. DNA microarrays turn out to be an effectual tool utilized in molecular biology and cancer diagnosis. Microarrays can be measured to establish the relative quantity of mRNAs in two or additional organic/biological tissue samples for thousands/several thousands of genes at the same time. As the superiority of this technique become exactly analysis/identifying the suitable assessment of microarray data in various open issues. In the field of medical sciences multi-category cancer classification play a major important role to classify the cancer types according to the gene expression. The need of the cancer classification has been become indispensible, because the numbers of cancer victims are increasing steadily identified by recent years. To perform this proposed a combination of Integer-Coded Genetic Algorithm (ICGA and Artificial Bee Colony algorithm (ABC, coupled with an Adaptive Extreme Learning Machine (AELM, is used for gene selection and cancer classification. ICGA is used with ABC based AELM classifier to chose an optimal set of genes which results in an efficient hybrid algorithm that can handle sparse data and sample imbalance. The

  18. Identification of conserved drought-adaptive genes using a cross-species meta-analysis approach

    OpenAIRE

    Shaar-Moshe, Lidor; Hübner, Sariel; Peleg, Zvi

    2015-01-01

    Background Drought is the major environmental stress threatening crop-plant productivity worldwide. Identification of new genes and metabolic pathways involved in plant adaptation to progressive drought stress at the reproductive stage is of great interest for agricultural research. Results We developed a novel Cross-Species meta-Analysis of progressive Drought stress at the reproductive stage (CSA:Drought) to identify key drought adaptive genes and mechanisms and to test their evolutionary c...

  19. Pollen Sterility—A Promising Approach to Gene Confinement and Breeding for Genetically Modified Bioenergy Crops

    OpenAIRE

    Joel P. Hague; Dellaporta, Stephen L.; Moreno, Maria A.; Chip Longo; Kimberly Nelson; Albert P. Kausch

    2012-01-01

    Advanced genetic and biotechnology tools will be required to realize the full potential of food and bioenergy crops. Given current regulatory concerns, many transgenic traits might never be deregulated for commercial release without a robust gene confinement strategy in place. The potential for transgene flow from genetically modified (GM) crops is widely known. Pollen-mediated transfer is a major component of gene flow in flowering plants and therefore a potential avenue for the escape of tr...

  20. Establishing RNA interference as a reverse-genetic approach for gene functional analysis in protoplasts.

    Science.gov (United States)

    Zhai, Zhiyang; Sooksa-nguan, Thanwalee; Vatamaniuk, Olena K

    2009-02-01

    Double-stranded (ds)RNA interference (RNAi) is widely used for functional analysis of plant genes and is achieved via generating stable transformants expressing dsRNA in planta. This study demonstrated that RNAi can also be utilized to examine gene functions in protoplasts. Because protoplasts are nongrowing cells, effective RNAi-triggered gene silencing depends not only on a depletion of gene transcripts but also on turnover rates of corresponding polypeptides. Herein, we tested if transient RNAi in protoplasts would result in the depletion of a targeted polypeptide and, because protoplasts have a limited life span, if functional assays of RNAi knockout genes would be feasible in protoplasts. We showed that protoplasts transfection with an in vitro-synthesized dsRNA against Arabidopsis (Arabidopsis thaliana) beta-glutamylcysteine synthase (ECS1), a key enzyme in the synthesis of glutathione, resulted in a 95% depletion of ECS1 transcript, a 72% decrease of ECS1 polypeptide, and a 60% drop in glutathione content. These results were comparable with those obtained upon analysis of Arabidopsis seedlings bearing the cad2-1 mutant allele of ECS1. We also improved the procedure for RNAi inactivation of several genes simultaneously. Finally, because we isolated protoplasts from tissues of 14-d-old seedlings instead of 1-month-old mature plants, the described procedure is rapid (as it only takes 20 d from seed planting to functional studies), suitable for analyzing multiple genes in parallel, and independent of cloning dsRNAs into plant expression vectors. Therefore, RNAi in protoplasts complements existing genetic tools, as it allows rapid, cost- and space-efficient initial screening and selection of genes for subsequent in planta studies.

  1. A Novel Approach of Low-frequency Ultrasonic Naked Plasmid Gene Delivery and Its Assessment

    Institute of Scientific and Technical Information of China (English)

    WEI WANG; ZHENG-ZHONG BIAN; YONG-JIE WU; YA-LIN MIAO

    2005-01-01

    Objective To deliver the naked genes into cells through the bioeffects of cell membrane porous produced by low-frequency ultrasound (US) and to investigate the safety by determining the threshold of cell damage and membrane permeability. Methods The suspension of red cells from chickens, rabbits, rats, and S180 cells was exposed to calibrated US field with different parameters in still and flowing state. Laser scanning confocal microscopy, fluorescent microscopy, scanning electron microscopy, flow cytometry and spectrophotometry were used to examine cell morphology, membrane permeability, enzymes, free radicals, naked gene expression efficiency, threshold of cell damage and cell viability. Results The plasmid of green fluorescent protein (GFP) as a reporter gene was delivered into S180 cells under optimal conditions without cell damage and cytotoxicity. The transfection rate was (35.83±2.53)% (n=6) in viable cells, and the cell viability was (90.17±1.47)% (n=6). Also, malondialdehyde, hydroxyl free radical, alkaline phosphatase, and acid phosphatase showed a S-shaped growth model (r=0.98±0.01) in response to the permeability change and alteration of cell morphology. The constant E of energy accumulation in US delivery at 90% cell viability was an optimal control factor, and at 80% cell viability was the damage threshold. Conclusion US under optimal conditions is a versatile gene therapy tool. The intensity of GFP expression in US group has a higher fluorescent peak than that in AVV-GFP group and control group (P<0.001). The optimal gene uptakes, expression of gene and safety depend on E, which can be applied to control gene delivery efficiency in combination with other parameters. The results are helpful for development of a novel clinical naked gene therapeutic system and non-hyperthermia cancer therapeutic system.

  2. A novel biclustering approach with iterative optimization to analyze gene expression data

    Directory of Open Access Journals (Sweden)

    Ohta H

    2012-09-01

    Full Text Available Sawannee Sutheeworapong,1,2 Motonori Ota,4 Hiroyuki Ohta,1 Kengo Kinoshita2,31Department of Biological Sciences, Graduate School of Biosciences and Biotechnology, Tokyo Institute of Technology, Tokyo, Japan; 2Graduate School of Information Sciences, 3Institute of Development, Aging and Cancer, Tohoku University, Miyagi, Japan; 4Graduate School of Information Sciences, Nagoya University, Nagoya, JapanObjective: With the dramatic increase in microarray data, biclustering has become a promising tool for gene expression analysis. Biclustering has been proven to be superior over clustering in identifying multifunctional genes and searching for co-expressed genes under a few specific conditions; that is, a subgroup of all conditions. Biclustering based on a genetic algorithm (GA has shown better performance than greedy algorithms, but the overlap state for biclusters must be treated more systematically.Results: We developed a new biclustering algorithm (binary-iterative genetic algorithm [BIGA], based on an iterative GA, by introducing a novel, ternary-digit chromosome encoding function. BIGA searches for a set of biclusters by iterative binary divisions that allow the overlap state to be explicitly considered. In addition, the average of the Pearson’s correlation coefficient was employed to measure the relationship of genes within a bicluster, instead of the mean square residual, the popular classical index. As compared to the six existing algorithms, BIGA found highly correlated biclusters, with large gene coverage and reasonable gene overlap. The gene ontology (GO enrichment showed that most of the biclusters are significant, with at least one GO term over represented.Conclusion: BIGA is a powerful tool to analyze large amounts of gene expression data, and will facilitate the elucidation of the underlying functional mechanisms in living organisms.Keywords: biclustering, microarray data, genetic algorithm, Pearson’s correlation coefficient

  3. The genetic basis of quality of life in healthy Swedish women: a candidate gene approach.

    Directory of Open Access Journals (Sweden)

    Dounya Schoormans

    Full Text Available Quality of life (QoL is an increasingly important parameter in clinical practice as it predicts mortality and poor health outcomes. It is hypothesized that one may have a genetic predisposition for QoL. We therefore related 139 candidate genes, selected through a literature search, to QoL in healthy females.In 5,142 healthy females, background characteristics (i.e. demographic, clinical, lifestyle, and psychological factors were assessed. QoL was measured by the EORTC QLQ-C30, which consists of 15 domains. For all women genotype information was available. For each candidate gene, single nucleotide polymorphisms (SNPs were identified based on their functional (n = 2,663 and physical annotation (n = 10,649. SNPs were related to each QoL-domain, while controlling for background characteristics and population stratification. Finally, gene-based analyses were performed relating the combined effect of 10,649 SNPs (selected based on physical annotation for each gene, to QoL using the statistical software package VEGAS.Overall, we found no relation between genetic variations (SNPs and genes and 14 out of 15 QoL-domains. The strongest association was found between cognitive functioning and the top SNP rs1468951 (p = 1.21E-05 in the GSTZ1 gene. Furthermore, results of the gene-based test showed that the combined effect of 11 SNPs within the GSTZ1 gene is significantly associated with cognitive functioning (p = 2.60E-05.If validated, the involvement of GSTZ1 in cognitive functioning underscores its heritability which is likely the result of differences in the dopamine pathway, as GSTZ1 contributes to the equilibrium between dopamine and its neurotoxic metabolites via the glutathione redox cycle.

  4. Bridging the Gap between Genes and Language Deficits in Schizophrenia: An Oscillopathic Approach

    Science.gov (United States)

    Murphy, Elliot; Benítez-Burraco, Antonio

    2016-01-01

    Schizophrenia is characterized by marked language deficits, but it is not clear how these deficits arise from the alteration of genes related to the disease. The goal of this paper is to aid the bridging of the gap between genes and schizophrenia and, ultimately, give support to the view that the abnormal presentation of language in this condition is heavily rooted in the evolutionary processes that brought about modern language. To that end we will focus on how the schizophrenic brain processes language and, particularly, on its distinctive oscillatory profile during language processing. Additionally, we will show that candidate genes for schizophrenia are overrepresented among the set of genes that are believed to be important for the evolution of the human faculty of language. These genes crucially include (and are related to) genes involved in brain rhythmicity. We will claim that this translational effort and the links we uncover may help develop an understanding of language evolution, along with the etiology of schizophrenia, its clinical/linguistic profile, and its high prevalence among modern populations.

  5. Bridging the Gap between Genes and Language Deficits in Schizophrenia: An Oscillopathic Approach.

    Science.gov (United States)

    Murphy, Elliot; Benítez-Burraco, Antonio

    2016-01-01

    Schizophrenia is characterized by marked language deficits, but it is not clear how these deficits arise from the alteration of genes related to the disease. The goal of this paper is to aid the bridging of the gap between genes and schizophrenia and, ultimately, give support to the view that the abnormal presentation of language in this condition is heavily rooted in the evolutionary processes that brought about modern language. To that end we will focus on how the schizophrenic brain processes language and, particularly, on its distinctive oscillatory profile during language processing. Additionally, we will show that candidate genes for schizophrenia are overrepresented among the set of genes that are believed to be important for the evolution of the human faculty of language. These genes crucially include (and are related to) genes involved in brain rhythmicity. We will claim that this translational effort and the links we uncover may help develop an understanding of language evolution, along with the etiology of schizophrenia, its clinical/linguistic profile, and its high prevalence among modern populations. PMID:27601987

  6. Combining phylogenomic and supermatrix approaches, and a time-calibrated phylogeny for squamate reptiles (lizards and snakes) based on 52 genes and 4162 species.

    Science.gov (United States)

    Zheng, Yuchi; Wiens, John J

    2016-01-01

    Two common approaches for estimating phylogenies in species-rich groups are to: (i) sample many loci for few species (e.g. phylogenomic approach), or (ii) sample many species for fewer loci (e.g. supermatrix approach). In theory, these approaches can be combined to simultaneously resolve both higher-level relationships (with many genes) and species-level relationships (with many taxa). However, fundamental questions remain unanswered about this combined approach. First, will higher-level relationships more closely resemble those estimated from many genes or those from many taxa? Second, will branch support increase for higher-level relationships (relative to the estimate from many taxa)? Here, we address these questions in squamate reptiles. We combined two recently published datasets, one based on 44 genes for 161 species, and one based on 12 genes for 4161 species. The likelihood-based tree from the combined matrix (52 genes, 4162 species) shared more higher-level clades with the 44-gene tree (90% vs. 77% shared). Branch support for higher level-relationships was marginally higher than in the 12-gene tree, but lower than in the 44-gene tree. Relationships were apparently not obscured by the abundant missing data (92% overall). We provide a time-calibrated phylogeny based on extensive sampling of genes and taxa as a resource for comparative studies.

  7. Statistical methods for history matching

    DEFF Research Database (Denmark)

    Johansen, Kent

    Denne afhandling beskriver statistiske metoder til history matching af olieproduktion. History matching er en vigtig del af driften af et oliefelt og er ofte forbundet med problemer relateret til kompleksiteten af reservoiret og selve størrelsen af reservoirsimuleringsmodellen. Begrebet history m...... history matching metode. Den foreslåede metode forsøger at forbedre konvergensen af traditionel probability perturbation ved at inkludere kvalitativ gradient information....

  8. Improved Bidirectional Exact Pattern Matching

    OpenAIRE

    Hussain, Iftikhar; Hassan Kazmi, Syed Zaki; Ali Khan, Israr; Mehmood, Rashid

    2013-01-01

    In this research, we present an improved version of Bidirectional (BD) exact pattern matching (EPM) algorithm to solve the problem of exact pattern matching. Improved-Bidirectional (IBD) exact pattern matching algorithm introduced a new idea of scanning partial text window (PTW) as well with the pattern to take decision of moving pattern to the right of partial text window. IBD algorithm compares the characters of pattern to selected text window (STW) from both sides simultaneously as BD....

  9. Maximum matching on random graphs

    OpenAIRE

    Zhou, Haijun; Ou-Yang, Zhong-Can

    2003-01-01

    The maximum matching problem on random graphs is studied analytically by the cavity method of statistical physics. When the average vertex degree \\mth{c} is larger than \\mth{2.7183}, groups of max-matching patterns which differ greatly from each other {\\em gradually} emerge. An analytical expression for the max-matching size is also obtained, which agrees well with computer simulations. Discussion is made on this {\\em continuous} glassy phase transition and the absence of such a glassy phase ...

  10. Ridge-based fingerprint matching

    OpenAIRE

    Pohar, Jaka

    2013-01-01

    The diploma thesis presents an upgrade of the FingerIdent fingerprint verification system. The current version of the system uses a minutia matching procedure for comparison of two fingerprints. In order to improve the security of the system we have implemented an additional matching procedure which is based on the use of fingerprint ridges. Algorithm inputs are lists of ridge points of two fingerprints. At the beginning the algorithm searches the initial base ridge pair and matches it. Th...

  11. Teaching medical terminology using word-matching games.

    Science.gov (United States)

    Nuetzman, Amy L; Abdullaev, Yalchin

    2012-07-01

    The use of word-matching games for classroom teaching of medical terminology to nursing and other health sciences students is described. Students work in small groups and match cards containing medical terms to cards containing their English translation. This approach encourages student-centered active learning and employs multiple modes of learning, including visual, auditory, kinesthetic, and text-based styles.

  12. Robust and accurate multi-view reconstruction by prioritized matching

    DEFF Research Database (Denmark)

    Ylimaki, M.; Kannala, J.; Holappa, J.;

    2012-01-01

    prioritized matching method which expands the most promising seeds first. The output of the method is a three-dimensional point cloud. Unlike previous correspondence growing approaches our method allows to use the best-first matching principle in the generic multi-view stereo setting with arbitrary number of...

  13. Matching Games with Additive Externalities

    DEFF Research Database (Denmark)

    Branzei, Simina; Michalak, Tomasz; Rahwan, Talal;

    2012-01-01

    Two-sided matchings are an important theoretical tool used to model markets and social interactions. In many real life problems the utility of an agent is influenced not only by their own choices, but also by the choices that other agents make. Such an influence is called an externality. Whereas...... fully expressive representations of externalities in matchings require exponential space, in this paper we propose a compact model of externalities, in which the influence of a match on each agent is computed additively. In this framework, we analyze many-to-many and one-to-one matchings under neutral...

  14. An evolutionary genomic approach to identify genes involved in human birth timing.

    Directory of Open Access Journals (Sweden)

    Jevon Plunkett

    2011-04-01

    Full Text Available Coordination of fetal maturation with birth timing is essential for mammalian reproduction. In humans, preterm birth is a disorder of profound global health significance. The signals initiating parturition in humans have remained elusive, due to divergence in physiological mechanisms between humans and model organisms typically studied. Because of relatively large human head size and narrow birth canal cross-sectional area compared to other primates, we hypothesized that genes involved in parturition would display accelerated evolution along the human and/or higher primate phylogenetic lineages to decrease the length of gestation and promote delivery of a smaller fetus that transits the birth canal more readily. Further, we tested whether current variation in such accelerated genes contributes to preterm birth risk. Evidence from allometric scaling of gestational age suggests human gestation has been shortened relative to other primates. Consistent with our hypothesis, many genes involved in reproduction show human acceleration in their coding or adjacent noncoding regions. We screened >8,400 SNPs in 150 human accelerated genes in 165 Finnish preterm and 163 control mothers for association with preterm birth. In this cohort, the most significant association was in FSHR, and 8 of the 10 most significant SNPs were in this gene. Further evidence for association of a linkage disequilibrium block of SNPs in FSHR, rs11686474, rs11680730, rs12473870, and rs1247381 was found in African Americans. By considering human acceleration, we identified a novel gene that may be associated with preterm birth, FSHR. We anticipate other human accelerated genes will similarly be associated with preterm birth risk and elucidate essential pathways for human parturition.

  15. Effect of Thyrotropin Releasing Hormone (TRH on Gene Expressions in Rat Pancreas: Approach by Microarray Hybridization

    Directory of Open Access Journals (Sweden)

    Luo LG

    2004-07-01

    Full Text Available CONTEXT: Thyrotropin releasing hormone (TRH, originally identified as a hypothalamic hormone, expresses in the pancreas. The effects of TRH such as, inhibiting amylase secretion in rats through a direct effect on acinar cells, enhancing basal glucagon secretion from isolated perfused rat pancreas, and potentiating glucose-stimulated insulin secretion in perfused rat islets and insulin-secreting clonal beta-cell lines, suggest that TRH may play a role in pancreas. TRH also enlarged pancreas and increased pancreatic DNA content but deletion of TRH gene expression caused hyperglycemia in mice, suggesting that TRH may play a critical role in pancreatic development; however, the biological mechanisms of TRH in the adult pancreas remains unclear. OBJECTIVES: This study explored the effect of TRH on rat pancreas. SUBJECTS: Four male-Sprague-Dawley-rats (200-250 g were given 10 microg/kg BW of TRH intraperitoneally on 1st and 3rd day and sacrificed on 7th day. Four same-strain rats without TRH injection served as controls. MAIN OUTCOME MEASURES: Wet pancreatic weights were measured. Pancreatic tissues were homogenized and extracted. The insulin levels of the extracts were measured by ELISA. Total RNA from the pancreases were fluorescently labeled and hybridized to microarray with 1,081 spot genes. RESULTS: TRH increased pancreatic wet weight and insulin contents. About 75% of the 1,081 genes were detected in the pancreas. TRH regulated up 99 genes and down 76 genes. The administration of TRH induced various types of gene expressions, such as G-protein coupled receptors (GPCR and signal transduction related genes (GPCR kinase 4, transducin beta subunit 5, arrestin beta1MAPK3, MAPK5, c-Src kinase, PKCs, PI3 kinase, growth factors (PDGF-B, IGF-2, IL-18, IGF-1, IL-2, IL-6, endothelin-1 and apoptotic factors (Bcl2, BAD, Bax. CONCLUSION: Reprogramming of transcriptome may be a way for TRH-regulation of pancreatic cellular functions.

  16. A Systems Approach Identifies Networks and Genes Linking Sleep and Stress: Implications for Neuropsychiatric Disorders

    Directory of Open Access Journals (Sweden)

    Peng Jiang

    2015-05-01

    Full Text Available Sleep dysfunction and stress susceptibility are comorbid complex traits that often precede and predispose patients to a variety of neuropsychiatric diseases. Here, we demonstrate multilevel organizations of genetic landscape, candidate genes, and molecular networks associated with 328 stress and sleep traits in a chronically stressed population of 338 (C57BL/6J × A/J F2 mice. We constructed striatal gene co-expression networks, revealing functionally and cell-type-specific gene co-regulations important for stress and sleep. Using a composite ranking system, we identified network modules most relevant for 15 independent phenotypic categories, highlighting a mitochondria/synaptic module that links sleep and stress. The key network regulators of this module are overrepresented with genes implicated in neuropsychiatric diseases. Our work suggests that the interplay among sleep, stress, and neuropathology emerges from genetic influences on gene expression and their collective organization through complex molecular networks, providing a framework for interrogating the mechanisms underlying sleep, stress susceptibility, and related neuropsychiatric disorders.

  17. Matching ERP System Functionality to Customer Requirements

    OpenAIRE

    Rolland, Colette; Prakash, Naveen

    2001-01-01

    International audience Although procuring Enterprise Resource Planning systems from commercial suppliers is becoming increasingly popular in our industry, fitting those systems to customer requirements remains problematic. In this paper, we propose an approach for matching ERP system functionality to customer requirements. The assumption made is that the ERP system postulates a set of requirements that are worth eliciting from the ERP documentation as abstractions of the ERP system functio...

  18. Impedance Matched Absorptive Thermal Blocking Filters

    CERN Document Server

    Wollack, E J; Rostem, K; U-Yen, K

    2014-01-01

    We have designed, fabricated and characterized absorptive thermal blocking filters for cryogenic microwave applications. The transmission line filter's input characteristic impedance is designed to match $50\\,\\Omega$ and its response has been validated from 0-to-50\\,GHz. The observed return loss in the 0-to-20\\,GHz design band is greater than $20\\,$dB and shows graceful degradation with frequency. Design considerations and equations are provided that enable this approach to be scaled and modified for use in other applications.

  19. Evolutionary approaches for the reverse-engineering of gene regulatory networks: A study on a biologically realistic dataset

    Directory of Open Access Journals (Sweden)

    Gidrol Xavier

    2008-02-01

    Full Text Available Abstract Background Inferring gene regulatory networks from data requires the development of algorithms devoted to structure extraction. When only static data are available, gene interactions may be modelled by a Bayesian Network (BN that represents the presence of direct interactions from regulators to regulees by conditional probability distributions. We used enhanced evolutionary algorithms to stochastically evolve a set of candidate BN structures and found the model that best fits data without prior knowledge. Results We proposed various evolutionary strategies suitable for the task and tested our choices using simulated data drawn from a given bio-realistic network of 35 nodes, the so-called insulin network, which has been used in the literature for benchmarking. We assessed the inferred models against this reference to obtain statistical performance results. We then compared performances of evolutionary algorithms using two kinds of recombination operators that operate at different scales in the graphs. We introduced a niching strategy that reinforces diversity through the population and avoided trapping of the algorithm in one local minimum in the early steps of learning. We show the limited effect of the mutation operator when niching is applied. Finally, we compared our best evolutionary approach with various well known learning algorithms (MCMC, K2, greedy search, TPDA, MMHC devoted to BN structure learning. Conclusion We studied the behaviour of an evolutionary approach enhanced by niching for the learning of gene regulatory networks with BN. We show that this approach outperforms classical structure learning methods in elucidating the original model. These results were obtained for the learning of a bio-realistic network and, more importantly, on various small datasets. This is a suitable approach for learning transcriptional regulatory networks from real datasets without prior knowledge.

  20. General approach for in vivo recovery of cell type-specific effector gene sets.

    Science.gov (United States)

    Barsi, Julius C; Tu, Qiang; Davidson, Eric H

    2014-05-01

    Differentially expressed, cell type-specific effector gene sets hold the key to multiple important problems in biology, from theoretical aspects of developmental gene regulatory networks (GRNs) to various practical applications. Although individual cell types of interest have been recovered by various methods and analyzed, systematic recovery of multiple cell type-specific gene sets from whole developing organisms has remained problematic. Here we describe a general methodology using the sea urchin embryo, a material of choice because of the large-scale GRNs already solved for this model system. This method utilizes the regulatory states expressed by given cells of the embryo to define cell type and includes a fluorescence activated cell sorting (FACS) procedure that results in no perturbation of transcript representation. We have extensively validated the method by spatial and qualitative analyses of the transcriptome expressed in isolated embryonic skeletogenic cells and as a consequence, generated a prototypical cell type-specific transcriptome database.

  1. An integrative systems genetics approach reveals potential causal genes and pathways related to obesity

    DEFF Research Database (Denmark)

    Kogelman, Lisette; Zhernakova, Daria V.; Westra, Harm-Jan;

    2015-01-01

    expression analysis was performed using the Obesity Index as a continuous variable in a linear model. eQTL mapping was then performed to integrate 60 K porcine SNP chip data with the RNA sequencing data. Results were restricted based on genome-wide significant single nucleotide polymorphisms, detected...... polymorphisms to detect obesity-related genes and pathways. Building a co-expression network using eQTLs resulted in the detection of a module strongly associated with lipid pathways. Furthermore, we detected several obesity candidate genes, for example, ENPP1, CTSL, and ABHD12B. CONCLUSIONS: To our knowledge......BACKGROUND: Obesity is a multi-factorial health problem in which genetic factors play an important role. Limited results have been obtained in single-gene studies using either genomic or transcriptomic data. RNA sequencing technology has shown its potential in gaining accurate knowledge about...

  2. Evaluation of microbial population and functional genes during the bioremediation of petroleum-contaminated soil as an effective monitoring approach.

    Science.gov (United States)

    Shahi, Aiyoub; Aydin, Sevcan; Ince, Bahar; Ince, Orhan

    2016-03-01

    This study investigated the abundance and diversity of soil n-alkane and polycyclic aromatic hydrocarbon (PAH)-degrading bacterial communities. It also investigated the quantity of the functional genes, the occurrence of horizontal gene transfer (HGT) in the identified bacterial communities and the effect that such HGT can have on biostimulation process. Illumina sequencing was used to detect the microbial diversity of petroleum-polluted soil prior to the biostimulation process, and quantitative real-time PCR was used to determine changes in the bacterial community and functional genes (alkB, phnAc and nah) expressions throughout the biostimulation of petroleum-contaminated soil. The illumine results revealed that γ-proteobacteria, Chloroflexi, Firmicutes, and δ-proteobacteria were the most dominant bacterial phyla in the contaminated site, and that most of the strains were Gram-negative. The results of the gene expression results revealed that gram-negative bacteria and alkB are critical to successful bioremediation. Failure to maintain the stability of hydrocarbon-degrading bacteria and functional gene will reduce the extend to which alkanes and PAHs are degraded. According to the results of the study, the application of a C:N:P ratio of was 100:15:1 in the biodegradation experiment resulted in the highest rate at which petroleum hydrocarbons were biodegraded. The diversity of pollutant-degrading bacteria and the effective transfer of degrading genes among resident microorganisms are essential factors for the successful biostimulation of petroleum hydrocarbons. As such, screening these factors throughout the biostimulation process represents an effective monitoring approach by which the success of the biostimulation can be assessed. PMID:26685788

  3. Evaluation of microbial population and functional genes during the bioremediation of petroleum-contaminated soil as an effective monitoring approach.

    Science.gov (United States)

    Shahi, Aiyoub; Aydin, Sevcan; Ince, Bahar; Ince, Orhan

    2016-03-01

    This study investigated the abundance and diversity of soil n-alkane and polycyclic aromatic hydrocarbon (PAH)-degrading bacterial communities. It also investigated the quantity of the functional genes, the occurrence of horizontal gene transfer (HGT) in the identified bacterial communities and the effect that such HGT can have on biostimulation process. Illumina sequencing was used to detect the microbial diversity of petroleum-polluted soil prior to the biostimulation process, and quantitative real-time PCR was used to determine changes in the bacterial community and functional genes (alkB, phnAc and nah) expressions throughout the biostimulation of petroleum-contaminated soil. The illumine results revealed that γ-proteobacteria, Chloroflexi, Firmicutes, and δ-proteobacteria were the most dominant bacterial phyla in the contaminated site, and that most of the strains were Gram-negative. The results of the gene expression results revealed that gram-negative bacteria and alkB are critical to successful bioremediation. Failure to maintain the stability of hydrocarbon-degrading bacteria and functional gene will reduce the extend to which alkanes and PAHs are degraded. According to the results of the study, the application of a C:N:P ratio of was 100:15:1 in the biodegradation experiment resulted in the highest rate at which petroleum hydrocarbons were biodegraded. The diversity of pollutant-degrading bacteria and the effective transfer of degrading genes among resident microorganisms are essential factors for the successful biostimulation of petroleum hydrocarbons. As such, screening these factors throughout the biostimulation process represents an effective monitoring approach by which the success of the biostimulation can be assessed.

  4. Transformation of GbSGT1 gene into banana by an Agrobacterium-mediated approach

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    SGT1 is a homologue of the yeast ubiquitin ligase-associated protein. It controls some protein degradation and activates defense pathway in plants. Cotton GbSGT1 gene (Gossypium barbadense) has been isolated and characterized in previous work. In this study, the plant expression vector pBSGT1 with bar gene as a selection agent was constructed and transgenic banana was obtained via Agrobacterium-mediated transformation with the assistance of particle bombardment and screened with PCR and Basta spreading on banana plant leaves. Estimating of transgenic banana plants for resistance to Panama wilt is in progress.

  5. A novel approach to quantitative ultrasonic naked gene delivery and its non-invasive assessment.

    Science.gov (United States)

    Wei, Wang; Zhengzhong, Bian; Yongjie, Wu; Lafeng, Yan; Yalin, Miao

    2004-12-01

    The purpose of this study was to investigate practical, safe, easy-to-use, non-cytotoxic, and reliable parameters to apply to an ultrasound (US) naked gene therapy system. The ultrasound pressure at the point of cell exposure was measured using a calibrated hydrophone and the intensity calculated. An acoustic power meter calibrated using a hydrophone was used to measure the power of the transducer. Four cell types were exposed to US with different exposure times and intensities. Fluorescent microscopy, spectrophotometry, scanning electron microscope, laser scanning confocal microscopy, flow cytometry and histogram analysis were used to evaluate the results of the study. The plasmid of green fluorescent protein (GFP) served as the reporter gene. The energy accumulation E in US gene delivery for 90% cell survival was defined as the optimal parameters (E=3.56+/-0.06), and at 80% cell survival was defined as the damage threshold (E=59.67+/-3.54). US safely delivered GFP into S180 cells (35.1 kHz) at these optimal parameters without obvious damage or cytotoxity in vitro. Exposed cell function was proved normal in vivo. The transfection rate was 35.83+/-2.53% (n=6) in viable cells, corresponding to 90.17+/-1.47% (n=6) cell viability. The intensity of GFP expression showed a higher fluorescent peak in the group of adeno-associated virus GFP vector (AVV-GFP) than in the control group (P<0.001). The effect of US gene delivery and cell viability correlated as a fifth order polynomial with US intensity and exposure time. With optimal parameters, US can safely deliver naked a gene into a cell without damage to cell function. Both optimal uptake and expression of gene depend on the energy E at 90% cell survival. E can be applied as a control factor for bioeffects when combined with other parameters. Stable caviation results in optimal parameters for gene delivery and the transient caviation may cause cell damage, which will bring about a sharp rise of permeabilization. The

  6. Intact School Matching in Education: Exploring the Relative Importance of Focal and Local Matching

    Science.gov (United States)

    Wong, Vivian C.; Hallberg, Kelly; Cook, Thomas D.

    2013-01-01

    The nested data structure inherent in education (i.e. students nested in schools nested in districts) makes intact school matching an appealing approach in observational studies of educational interventions and policies for both theoretical and practical purposes. This paper provides guidance to applied education researchers who are employing…

  7. Optical tracking of organically modified silica nanoparticles as DNA carriers: A nonviral, nanomedicine approach for gene delivery

    Science.gov (United States)

    Roy, Indrajit; Ohulchanskyy, Tymish Y.; Bharali, Dhruba J.; Pudavar, Haridas E.; Mistretta, Ruth A.; Kaur, Navjot; Prasad, Paras N.

    2005-01-01

    This article reports a multidisciplinary approach to produce fluorescently labeled organically modified silica nanoparticles as a nonviral vector for gene delivery and biophotonics methods to optically monitor intracellular trafficking and gene transfection. Highly monodispersed, stable aqueous suspensions of organically modified silica nanoparticles, encapsulating fluorescent dyes and surface functionalized by cationic-amino groups, are produced by micellar nanochemistry. Gel-electrophoresis studies reveal that the particles efficiently complex with DNA and protect it from enzymatic digestion of DNase 1. The electrostatic binding of DNA onto the surface of the nanoparticles, due to positively charged amino groups, is also shown by intercalating an appropriate dye into the DNA and observing the Förster (fluorescence) resonance energy transfer between the dye (energy donor) intercalated in DNA on the surface of nanoparticles and a second dye (energy acceptor) inside the nanoparticles. Imaging by fluorescence confocal microscopy shows that cells efficiently take up the nanoparticles in vitro in the cytoplasm, and the nanoparticles deliver DNA to the nucleus. The use of plasmid encoding enhanced GFP allowed us to demonstrate the process of gene transfection in cultured cells. Our work shows that the nanomedicine approach, with nanoparticles acting as a drug-delivery platform combining multiple optical and other types of probes, provides a promising direction for targeted therapy with enhanced efficacy as well as for real-time monitoring of drug action. nonviral vector | ORMOSIL nanoparticles | confocal microscopy

  8. Seeking signatures of reinforcement at the genetic level: a hitchhiking mapping and candidate gene approach in the house mouse

    Science.gov (United States)

    Caminade, Pierre; Thoma, Marios; Latour, Yasmin; Roux, Camille; Thoss, Michaela; Penn, Dustin J.; Ganem, Guila; Boursot, Pierre

    2016-01-01

    Reinforcement is the process by which prezygotic isolation is strengthened as a response to selection against hybridisation. Most empirical support for reinforcement comes from the observation of its possible phenotypic signature: an accentuated degree of prezygotic isolation in the hybrid zone as compared to allopatry. Here, we implemented a novel approach to this question by seeking for the signature of reinforcement at the genetic level. In the house mouse, selection against hybrids and enhanced olfactory-based assortative mate preferences are observed in a hybrid zone between the two European subspecies Mus musculus musculus and M. m. domesticus, suggesting a possible recent reinforcement event. To test for the genetic signature of reinforcing selection and identify genes involved in sexual isolation, we adopted a hitchhiking mapping approach targeting genomic regions containing candidate genes for assortative mating in mice. We densely scanned these genomic regions in hybrid zone and allopatric samples using a large number of fast evolving microsatellite loci that allow the detection of recent selection events. We found a handful of loci showing the expected pattern of significant reduction of variability in populations close to the hybrid zone and showing assortative odour preference in mate choice experiments as compared to populations further away and displaying no such preference. These loci lie close to genes that we pinpoint as testable candidates for further investigation. PMID:26132782

  9. Loss of dsRNA-based gene silencing in Entamoeba histolytica: implications for approaches to genetic analysis.

    Science.gov (United States)

    MacFarlane, Ryan C; Singh, Upinder

    2008-06-01

    The ability to regulate gene expression in the protozoan parasite Entamoeba histolytica is critical in determining gene function. We previously published that expression of dsRNA specific to E. histolytica serine threonine isoleucine rich protein (EhSTIRP) resulted in reduction of gene expression [MacFarlane, R.C., Singh, U., 2007. Identification of an Entamoeba histolytica serine, threonine, isoleucine, rich protein with roles in adhesion and cytotoxicity. Eukaryotic Cell 6, 2139-2146]. However, after approximately one year of continuous drug selection, the expression of EhSTIRP reverted to wild-type levels. We confirmed that the parasites (i) contained the appropriate dsRNA plasmid, (ii) were not contaminated with other plasmids, (iii) the drug selectable marker was functional, and (iv) sequenced the dsRNA portion of the construct. This work suggests that in E. histolytica long term cultivation of parasites expressing dsRNA can lead to the loss of dsRNA based silencing through the selection of "RNAi" negative parasites. Thus, users of the dsRNA silencing approach should proceed with caution and regularly confirm gene down regulation. The development and use of constructs for inducible expression of dsRNA may help alleviate this potential problem. PMID:18346737

  10. Ecotoxicological diagnosis of striped dolphin (Stenella coeruleoalba) from the Mediterranean basin by skin biopsy and gene expression approach.

    Science.gov (United States)

    Panti, Cristina; Spinsanti, Giacomo; Marsili, Letizia; Casini, Silvia; Frati, Francesco; Fossi, Maria Cristina

    2011-11-01

    Mediterranean cetacean odontocetes are exposed to environmental stress, in particular to persistent organic pollutants, polycyclic aromatic hydrocarbons and trace elements. In the present study, the response of "gene-expression biomarkers" was evaluated in Mediterranean striped dolphin (Stenella coeruleoalba) skin biopsies collected in three sampling areas: Pelagos sanctuary (Ligurian sea), Ionian sea, and Strait of Gibraltar. The mRNA levels of five putative biomarker genes (aryl hydrocarbon receptor, E2F-1 transcription factor, cytochrome P450 1A, estrogen receptor 1, and heat shock protein 70) were measured for the first time by quantitative real-time PCR in cetacean skin biopsies. The different responses of most of the genes reflected contamination levels in the three sampling areas. Pelagos sanctuary dolphins appeared to be the most exposed to toxicological stress, having the highest up-regulation of CYP1A and AHR. Moreover, a cluster analysis distinguished the populations on the basis of the gene expression biomarker used in our study, showing different pattern between Mediterranean sea and Strait of Gibraltar. Our results suggest that this molecular approach applied to non-destructive biopsy material is a powerful diagnostic tool for evaluating ecotoxicological impact on cetacean populations. PMID:21695511

  11. Ecotoxicological diagnosis of striped dolphin (Stenella coeruleoalba) from the Mediterranean basin by skin biopsy and gene expression approach.

    Science.gov (United States)

    Panti, Cristina; Spinsanti, Giacomo; Marsili, Letizia; Casini, Silvia; Frati, Francesco; Fossi, Maria Cristina

    2011-11-01

    Mediterranean cetacean odontocetes are exposed to environmental stress, in particular to persistent organic pollutants, polycyclic aromatic hydrocarbons and trace elements. In the present study, the response of "gene-expression biomarkers" was evaluated in Mediterranean striped dolphin (Stenella coeruleoalba) skin biopsies collected in three sampling areas: Pelagos sanctuary (Ligurian sea), Ionian sea, and Strait of Gibraltar. The mRNA levels of five putative biomarker genes (aryl hydrocarbon receptor, E2F-1 transcription factor, cytochrome P450 1A, estrogen receptor 1, and heat shock protein 70) were measured for the first time by quantitative real-time PCR in cetacean skin biopsies. The different responses of most of the genes reflected contamination levels in the three sampling areas. Pelagos sanctuary dolphins appeared to be the most exposed to toxicological stress, having the highest up-regulation of CYP1A and AHR. Moreover, a cluster analysis distinguished the populations on the basis of the gene expression biomarker used in our study, showing different pattern between Mediterranean sea and Strait of Gibraltar. Our results suggest that this molecular approach applied to non-destructive biopsy material is a powerful diagnostic tool for evaluating ecotoxicological impact on cetacean populations.

  12. A population genetic approach to mapping neurological disorder genes using deep resequencing.

    Directory of Open Access Journals (Sweden)

    Rachel A Myers

    2011-02-01

    Full Text Available Deep resequencing of functional regions in human genomes is key to identifying potentially causal rare variants for complex disorders. Here, we present the results from a large-sample resequencing (n  =  285 patients study of candidate genes coupled with population genetics and statistical methods to identify rare variants associated with Autism Spectrum Disorder and Schizophrenia. Three genes, MAP1A, GRIN2B, and CACNA1F, were consistently identified by different methods as having significant excess of rare missense mutations in either one or both disease cohorts. In a broader context, we also found that the overall site frequency spectrum of variation in these cases is best explained by population models of both selection and complex demography rather than neutral models or models accounting for complex demography alone. Mutations in the three disease-associated genes explained much of the difference in the overall site frequency spectrum among the cases versus controls. This study demonstrates that genes associated with complex disorders can be mapped using resequencing and analytical methods with sample sizes far smaller than those required by genome-wide association studies. Additionally, our findings support the hypothesis that rare mutations account for a proportion of the phenotypic variance of these complex disorders.

  13. A Complementary Bioinformatics Approach to Identify Potential Plant Cell Wall Glycosyltransferase-Encoding Genes

    DEFF Research Database (Denmark)

    Egelund, Jack; Skjøt, Michael; Geshi, Naomi;

    2004-01-01

    . Although much is known with regard to composition and fine structures of the plant CW, only a handful of CW biosynthetic GT genes-all classified in the CAZy system-have been characterized. In an effort to identify CW GTs that have not yet been classified in the CAZy database, a simple bioinformatics...

  14. Identification of a strawberry flavor gene candidate using an integrated genetic-genomic-analytical chemistry approach

    Science.gov (United States)

    Background: There is interest in improving the flavor of commercial strawberry (Fragaria × ananassa) varieties. Fruit flavor is shaped by combinations of sugars, acids and volatile compounds. Many efforts seek to use genomics-based strategies to identify genes controlling flavor, and then designing ...

  15. An integrative systems genetics approach reveals potential causal genes and pathways related to obesity

    NARCIS (Netherlands)

    Kogelman, Lisette J. A.; Zhernakova, Daria V.; Westra, Harm-Jan; Cirera, Susanna; Fredholm, Merete; Franke, Lude; Kadarmideen, Haja N.

    2015-01-01

    Background: Obesity is a multi-factorial health problem in which genetic factors play an important role. Limited results have been obtained in single-gene studies using either genomic or transcriptomic data. RNA sequencing technology has shown its potential in gaining accurate knowledge about the tr

  16. A NEW APPROACH TO GENE DIAGNOSIS OF DUCHENNE/BECKER MUSCULAR DYSTROPHY AMPLIFIED FRAGMENT LENGTH POLYMORPHISMS

    Institute of Scientific and Technical Information of China (English)

    许顺斌; 黄尚志; 罗会元

    1994-01-01

    Four (CA), repeats, located in introns,44,45,49 and 50 of the dystrophin gene,were evaluated in Chinese.These loci are highly polymorphic,with polymorphism information contents of 0.872,0.772,0.870 and 0.718,respectively.All four loci can be easily amplified and labelled using two duplex PCR reactions with α-32P-dCTP and can be detected by denaturing polyacrylamide gel electrophoresis.Using these four loci and the two polymorphic(CA)n repeats located at the 5′ and 3′ ends of the dystrophin gene,we have developed a new PCR-based procedure-Amp-FLP( amplified fragment length polymorphism)linkage analysis for the gene diagnosis of DMD/BMD.This method can detect intragenic recombination rapidly and efficiently and greatly improves the success rate of carrier deterction and prenatal diagnosis in non-deletion DMD/BMD families.All of the loci used in this procedure are intragenic.In addition ,the loci in introns 44,45,49 and 50 are located in the deletion-prone region of the dystrophin gene,making them valuable and usefui in the identification of deletion mutations.Here we report one case of deletion detection using these four loci.

  17. A simple but highly effective approach to evaluate the prognostic performance of gene expression signatures.

    Directory of Open Access Journals (Sweden)

    Maud H W Starmans

    Full Text Available BACKGROUND: Highly parallel analysis of gene expression has recently been used to identify gene sets or 'signatures' to improve patient diagnosis and risk stratification. Once a signature is generated, traditional statistical testing is used to evaluate its prognostic performance. However, due to the dimensionality of microarrays, this can lead to false interpretation of these signatures. PRINCIPAL FINDINGS: A method was developed to test batches of a user-specified number of randomly chosen signatures in patient microarray datasets. The percentage of random generated signatures yielding prognostic value was assessed using ROC analysis by calculating the area under the curve (AUC in six public available cancer patient microarray datasets. We found that a signature consisting of randomly selected genes has an average 10% chance of reaching significance when assessed in a single dataset, but can range from 1% to ∼40% depending on the dataset in question. Increasing the number of validation datasets markedly reduces this number. CONCLUSIONS: We have shown that the use of an arbitrary cut-off value for evaluation of signature significance is not suitable for this type of research, but should be defined for each dataset separately. Our method can be used to establish and evaluate signature performance of any derived gene signature in a dataset by comparing its performance to thousands of randomly generated signatures. It will be of most interest for cases where few data are available and testing in multiple datasets is limited.

  18. Genetic Susceptibility to Vitiligo: GWAS Approaches for Identifying Vitiligo Susceptibility Genes and Loci.

    Science.gov (United States)

    Shen, Changbing; Gao, Jing; Sheng, Yujun; Dou, Jinfa; Zhou, Fusheng; Zheng, Xiaodong; Ko, Randy; Tang, Xianfa; Zhu, Caihong; Yin, Xianyong; Sun, Liangdan; Cui, Yong; Zhang, Xuejun

    2016-01-01

    Vitiligo is an autoimmune disease with a strong genetic component, characterized by areas of depigmented skin resulting from loss of epidermal melanocytes. Genetic factors are known to play key roles in vitiligo through discoveries in association studies and family studies. Previously, vitiligo susceptibility genes were mainly revealed through linkage analysis and candidate gene studies. Recently, our understanding of the genetic basis of vitiligo has been rapidly advancing through genome-wide association study (GWAS). More than 40 robust susceptible loci have been identified and confirmed to be associated with vitiligo by using GWAS. Most of these associated genes participate in important pathways involved in the pathogenesis of vitiligo. Many susceptible loci with unknown functions in the pathogenesis of vitiligo have also been identified, indicating that additional molecular mechanisms may contribute to the risk of developing vitiligo. In this review, we summarize the key loci that are of genome-wide significance, which have been shown to influence vitiligo risk. These genetic loci may help build the foundation for genetic diagnosis and personalize treatment for patients with vitiligo in the future. However, substantial additional studies, including gene-targeted and functional studies, are required to confirm the causality of the genetic variants and their biological relevance in the development of vitiligo.

  19. Detection of antibiotic resistance genes in wastewater treatment plant – molecular and classical approach

    Directory of Open Access Journals (Sweden)

    Ziembińska-Buczyńska Aleksandra

    2015-12-01

    Full Text Available Antibiotics are a group of substances potentially harmful to the environment. They can play a role in bacterial resistance transfer among pathogenic and non-pathogenic bacteria. In this experiment three representatives of medically important chemotherapeutics, confirmed to be present in high concentrations in wastewater treatment plants with HPLC analysis were used: erythromycin, sulfamethoxazole and trimethoprim. Erythromycin concentration in activated sludge was not higher than 20 ng L−1. N-acetylo-sulfamethoxazole concentration was 3349 ± 719 in winter and 2933 ± 429 ng L−1 in summer. Trimethoprim was present in wastewater at concentrations 400 ± 22 and 364 ± 60 ng L−1, respectively in winter and summer. Due to a wide variety of PCR-detectable resistance mechanisms towards these substances, the most common found in literature was chosen. For erythromycin: erm and mef genes, for sulfamethoxazole: sul1, sul2, sul3 genes, in the case of trimethoprim resistance dhfrA1 and dhfr14 were used in this study. The presence of resistance genes were analyzed in pure strains isolated from activated sludge and in the activated sludge sample itself. The research revealed that the value of minimal inhibitory concentration (MIC did not correspond with the expected presence of more than one resistance mechanisms. Most of the isolates possessed only one of the genes responsible for a particular chemotherapeutic resistance. It was confirmed that it is possible to monitor the presence of resistance genes directly in activated sludge using PCR. Due to the limited isolates number used in the experiment these results should be regarded as preliminary.

  20. A new physical mapping approach refines the sex-determining gene positions on the Silene latifolia Y-chromosome

    Science.gov (United States)

    Kazama, Yusuke; Ishii, Kotaro; Aonuma, Wataru; Ikeda, Tokihiro; Kawamoto, Hiroki; Koizumi, Ayako; Filatov, Dmitry A.; Chibalina, Margarita; Bergero, Roberta; Charlesworth, Deborah; Abe, Tomoko; Kawano, Shigeyuki

    2016-01-01

    Sex chromosomes are particularly interesting regions of the genome for both molecular genetics and evolutionary studies; yet, for most species, we lack basic information, such as the gene order along the chromosome. Because they lack recombination, Y-linked genes cannot be mapped genetically, leaving physical mapping as the only option for establishing the extent of synteny and homology with the X chromosome. Here, we developed a novel and general method for deletion mapping of non-recombining regions by solving “the travelling salesman problem”, and evaluate its accuracy using simulated datasets. Unlike the existing radiation hybrid approach, this method allows us to combine deletion mutants from different experiments and sources. We applied our method to a set of newly generated deletion mutants in the dioecious plant Silene latifolia and refined the locations of the sex-determining loci on its Y chromosome map.

  1. Classification of Micro Array Gene Expression Data using Factor Analysis Approach with Naïve Bayesian Classifier

    Directory of Open Access Journals (Sweden)

    Tamilselvi Madeswaran

    2013-10-01

    Full Text Available Microarray data studies produce large number of data and in order to analyze such large micro array data lies on Data mining or Statistical Analysis. Our objective is to classify the micro arraygene expression data. Usually before going for the classification the dimensionality reduction will be performed on the micro array gene expression dataset. A statistical approach for the extraction of thegene has been proposed. The drawback in the statistical analysis is that, it doesn’t identify the important genes. Here for the classification process we use k-nearest neighbor and SVM and Naïve Bayesian classifiers. From the experimental result our proposed classifiers show increase in the efficiency and accuracy.

  2. Identification of bacteria associated with underground parts of Crocus sativus by 16S rRNA gene targeted metagenomic approach.

    Science.gov (United States)

    Ambardar, Sheetal; Sangwan, Naseer; Manjula, A; Rajendhran, J; Gunasekaran, P; Lal, Rup; Vakhlu, Jyoti

    2014-10-01

    Saffron (Crocus sativus L), an autumn-flowering perennial sterile plant, reproduces vegetatively by underground corms. Saffron has biannual corm-root cycle that makes it an interesting candidate to study microbial dynamics in its rhizosphere and cormosphere (area under influence of corm). Culture independent 16S rRNA gene metagenomic study of rhizosphere and cormosphere of Saffron during flowering stage revealed presence of 22 genera but none of the genus was common in all the three samples. Bulk soil bacterial community was represented by 13 genera with Acidobacteria being dominant. In rhizosphere, out of eight different genera identified, Pseudomonas was the most dominant genus. Cormosphere bacteria comprised of six different genera, dominated by the genus Pantoea. This study revealed that the bacterial composition of all the three samples is significantly different (P rhizosphere, cormosphere and bulk soil of Saffron, using cultivation independent 16S rRNA gene targeted metagenomic approach. PMID:24989343

  3. Novel approach to abuse the hyperactive K-Ras pathway for adenoviral gene therapy of colorectal cancer

    Energy Technology Data Exchange (ETDEWEB)

    Naumov, Inna [Integrated Cancer Prevention Center, Tel Aviv (Israel); Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv (Israel); Kazanov, Dina [Integrated Cancer Prevention Center, Tel Aviv (Israel); Lisiansky, Victoria [Integrated Cancer Prevention Center, Tel Aviv (Israel); Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv (Israel); Starr, Alex [Lung and Allergy Institute, Tel Aviv Sourasky Medical Center, Tel Aviv (Israel); Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv (Israel); Aroch, Ilan; Shapira, Shiran; Kraus, Sarah [Integrated Cancer Prevention Center, Tel Aviv (Israel); Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv (Israel); Arber, Nadir, E-mail: narber@post.tau.ac.il [Integrated Cancer Prevention Center, Tel Aviv (Israel); Department of Gastroenterology, Tel Aviv Sourasky Medical Center, Tel Aviv (Israel); Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv (Israel)

    2012-01-15

    Background: Functional activation of oncogenic K-Ras signaling pathway plays an important role in the early events of colorectal carcinogenesis (CRC). K-Ras proto-oncogene is involved in 35-40% of CRC cases. Mutations in the Ras gene trigger the transduction of proliferative and anti-apoptotic signals, even in the absence of extra cellular stimuli. The objective of the current study was to use a gene-targeting approach to kill human CRC cells selectively harboring mutated K-Ras. Results: A recombinant adenovirus that carries a lethal gene, PUMA, under the control of a Ras responsive promoter (Ad-Py4-SV40-PUMA) was used selectively to target CRC cells (HCT116, SW480, DLD1 and RIE-Ras) that possess a hyperactive Ras pathway while using HT29 and RIE cells as a control that harbors wild type Ras and exhibit very low Ras activity. Control vector, without the Ras responsive promoter elements was used to assess the specificity of our 'gene therapy' approach. Both adenoviral vectors were assed in vitro and in xenograft model in vivo. Ad-Py4-SV40-PUMA showed high potency to induce {approx} 50% apoptosis in vitro, to abolish completely tumor formation by infecting cells with the Ad-Py4-SV40-PUMA prior xenografting them in nude mice and high ability to suppress by {approx} 35% tumor progression in vivo in already established tumors. Conclusions: Selective targeting of CRC cells with the activated Ras pathway may be a novel and effective therapy in CRC. The high potency of this adenoviral vector may help to overcome an undetectable micro metastasis that is the major hurdle in challenging with CRC.

  4. Novel approach to abuse the hyperactive K-Ras pathway for adenoviral gene therapy of colorectal cancer

    International Nuclear Information System (INIS)

    Background: Functional activation of oncogenic K-Ras signaling pathway plays an important role in the early events of colorectal carcinogenesis (CRC). K-Ras proto-oncogene is involved in 35–40% of CRC cases. Mutations in the Ras gene trigger the transduction of proliferative and anti-apoptotic signals, even in the absence of extra cellular stimuli. The objective of the current study was to use a gene-targeting approach to kill human CRC cells selectively harboring mutated K-Ras. Results: A recombinant adenovirus that carries a lethal gene, PUMA, under the control of a Ras responsive promoter (Ad-Py4-SV40-PUMA) was used selectively to target CRC cells (HCT116, SW480, DLD1 and RIE-Ras) that possess a hyperactive Ras pathway while using HT29 and RIE cells as a control that harbors wild type Ras and exhibit very low Ras activity. Control vector, without the Ras responsive promoter elements was used to assess the specificity of our “gene therapy” approach. Both adenoviral vectors were assed in vitro and in xenograft model in vivo. Ad-Py4-SV40-PUMA showed high potency to induce ∼ 50% apoptosis in vitro, to abolish completely tumor formation by infecting cells with the Ad-Py4-SV40-PUMA prior xenografting them in nude mice and high ability to suppress by ∼ 35% tumor progression in vivo in already established tumors. Conclusions: Selective targeting of CRC cells with the activated Ras pathway may be a novel and effective therapy in CRC. The high potency of this adenoviral vector may help to overcome an undetectable micro metastasis that is the major hurdle in challenging with CRC.

  5. A Novel Algorithm for Macromolecular Epitope Matching

    Directory of Open Access Journals (Sweden)

    Stanislav Jakuschev

    2009-03-01

    Full Text Available Many macromolecules, namely proteins, show functional substructures or epitopes defined by characteristic spatial arrangements of groups of specific atoms or residues. The identification of such substructures in a set of macromolecular 3D-structures solves an important problem in molecular biology as it allows the assignment of functions to molecular moieties and thus opens the possibility of a mechanistic understanding of molecular function. We have devised an algorithm that models a functional epitope formed by a group of atoms or residues as set of points in cartesian space with associated functional properties. The algorithm searches for similar epitopes in a database of structures by an efficient multistage comparison of distance sets in the epitope and in the structures from the database. The search results in a list of optimal matches and corresponding optimal superpositions of query epitope and matching epitopes from the database. The algorithm is discussed against the background of related approaches, and it is successfully tested in three application scenarios: global match of two homologous proteins, search for an epitope on a homologous protein, and finding matching epitopes in a protein database.

  6. Case-control association studies with matching and genomic controlling.

    Science.gov (United States)

    Lee, Wen-Chung

    2004-07-01

    Family-based association studies have gained in popularity for mapping disease-susceptibility gene(s) of complex diseases. However, recruiting family controls is often more difficult than recruiting unrelated controls. The author proposes a case-control study, where the possible biases due to population stratification are controlled by matching in the design stage and by genomic controlling in the data-analytic stage. The matching is based on a set of "stratum-delineating variables," such as, race, ethnicity, nationality, ancestry, and birthplace; and the genomic controlling is based on typing a number of null markers across the genome and applying the principle of multiplicative scaling of chi-square distribution. It pays to match carefully to have a higher proportion of correctly matched sets, as computer simulation showed that this would increase the power of the study. If matching is crude, one loses power but still has the correct type I error rate after genomic controlling. Power studies showed that the numbers of affected subjects required for the pair-matched study are comparable to those required by the case-parents design, if the study was conducted in a homogeneous population. As the (control-to-case) matching ratio increases, the number of affected subjects required decreases. With matching ratio tending toward infinity, the number required shrinks roughly by half. The case-control study with matching and genomic controlling frees us from family bondage, and the genetic problem as complicated as mapping genes can now be studied using simple epidemiologic methods. PMID:15185398

  7. Optimizing matching and analysis combinations for estimating causal effects

    Science.gov (United States)

    Colson, K. Ellicott; Rudolph, Kara E.; Zimmerman, Scott C.; Goin, Dana E.; Stuart, Elizabeth A.; Laan, Mark Van Der; Ahern, Jennifer

    2016-03-01

    Matching methods are common in studies across many disciplines. However, there is limited evidence on how to optimally combine matching with subsequent analysis approaches to minimize bias and maximize efficiency for the quantity of interest. We conducted simulations to compare the performance of a wide variety of matching methods and analysis approaches in terms of bias, variance, and mean squared error (MSE). We then compared these approaches in an applied example of an employment training program. The results indicate that combining full matching with double robust analysis performed best in both the simulations and the applied example, particularly when combined with machine learning estimation methods. To reduce bias, current guidelines advise researchers to select the technique with the best post-matching covariate balance, but this work finds that such an approach does not always minimize mean squared error (MSE). These findings have important implications for future research utilizing matching. To minimize MSE, investigators should consider additional diagnostics, and use of simulations tailored to the study of interest to identify the optimal matching and analysis combination.

  8. History Matching in Parallel Computational Environments

    Energy Technology Data Exchange (ETDEWEB)

    Steven Bryant; Sanjay Srinivasan; Alvaro Barrera; Yonghwee Kim; Sharad Yadav

    2006-08-31

    A novel methodology for delineating multiple reservoir domains for the purpose of history matching in a distributed computing environment has been proposed. A fully probabilistic approach to perturb permeability within the delineated zones is implemented. The combination of robust schemes for identifying reservoir zones and distributed computing significantly increase the accuracy and efficiency of the probabilistic approach. The information pertaining to the permeability variations in the reservoir that is contained in dynamic data is calibrated in terms of a deformation parameter rD. This information is merged with the prior geologic information in order to generate permeability models consistent with the observed dynamic data as well as the prior geology. The relationship between dynamic response data and reservoir attributes may vary in different regions of the reservoir due to spatial variations in reservoir attributes, well configuration, flow constrains etc. The probabilistic approach then has to account for multiple r{sub D} values in different regions of the reservoir. In order to delineate reservoir domains that can be characterized with different r{sub D} parameters, principal component analysis (PCA) of the Hessian matrix has been done. The Hessian matrix summarizes the sensitivity of the objective function at a given step of the history matching to model parameters. It also measures the interaction of the parameters in affecting the objective function. The basic premise of PC analysis is to isolate the most sensitive and least correlated regions. The eigenvectors obtained during the PCA are suitably scaled and appropriate grid block volume cut-offs are defined such that the resultant domains are neither too large (which increases interactions between domains) nor too small (implying ineffective history matching). The delineation of domains requires calculation of Hessian, which could be computationally costly and as well as restricts the current

  9. History Matching in Parallel Computational Environments

    Energy Technology Data Exchange (ETDEWEB)

    Steven Bryant; Sanjay Srinivasan; Alvaro Barrera; Sharad Yadav

    2005-10-01

    A novel methodology for delineating multiple reservoir domains for the purpose of history matching in a distributed computing environment has been proposed. A fully probabilistic approach to perturb permeability within the delineated zones is implemented. The combination of robust schemes for identifying reservoir zones and distributed computing significantly increase the accuracy and efficiency of the probabilistic approach. The information pertaining to the permeability variations in the reservoir that is contained in dynamic data is calibrated in terms of a deformation parameter rD. This information is merged with the prior geologic information in order to generate permeability models consistent with the observed dynamic data as well as the prior geology. The relationship between dynamic response data and reservoir attributes may vary in different regions of the reservoir due to spatial variations in reservoir attributes, well configuration, flow constrains etc. The probabilistic approach then has to account for multiple r{sub D} values in different regions of the reservoir. In order to delineate reservoir domains that can be characterized with different rD parameters, principal component analysis (PCA) of the Hessian matrix has been done. The Hessian matrix summarizes the sensitivity of the objective function at a given step of the history matching to model parameters. It also measures the interaction of the parameters in affecting the objective function. The basic premise of PC analysis is to isolate the most sensitive and least correlated regions. The eigenvectors obtained during the PCA are suitably scaled and appropriate grid block volume cut-offs are defined such that the resultant domains are neither too large (which increases interactions between domains) nor too small (implying ineffective history matching). The delineation of domains requires calculation of Hessian, which could be computationally costly and as well as restricts the current approach to

  10. A PiggyBac-mediated approach for muscle gene transfer or cell therapy

    OpenAIRE

    Déborah Ley; Ruthger Van Zwieten; Stefania Puttini; Pavithra Iyer; Alessia Cochard; Nicolas Mermod

    2014-01-01

    An emerging therapeutic approach for Duchenne muscular dystrophy is the transplantation of autologous myogenic progenitor cells genetically modified to express dystrophin. The use of this approach is challenged by the difficulty in maintaining these cells ex vivo while keeping their myogenic potential, and ensuring sufficient transgene expression following their transplantation and myogenic differentiation in vivo. We investigated the use of the piggyBac transposon system to achieve stable ge...

  11. Advances in combining gene therapy with cell and tissue engineering-based approaches to enhance healing of the meniscus.

    Science.gov (United States)

    Cucchiarini, M; McNulty, A L; Mauck, R L; Setton, L A; Guilak, F; Madry, H

    2016-08-01

    Meniscal lesions are common problems in orthopaedic surgery and sports medicine, and injury or loss of the meniscus accelerates the onset of knee osteoarthritis (OA). Despite a variety of therapeutic options in the clinics, there is a critical need for improved treatments to enhance meniscal repair. In this regard, combining gene-, cell-, and tissue engineering-based approaches is an attractive strategy to generate novel, effective therapies to treat meniscal lesions. In the present work, we provide an overview of the tools currently available to improve meniscal repair and discuss the progress and remaining challenges for potential future translation in patients. PMID:27063441

  12. Isolation and Manipulation of Quantitative Tra it Loci for DIsease Resistance in Rice Using a Candid ate Gene Approach

    Institute of Scientific and Technical Information of China (English)

    Ke-Ming Hu; De-Yun Qiu; Xiang-Ling Shen; Xiang-Hua Li; Shi-Ping Wang

    2008-01-01

    Bacterial blight caused by Xanthomonas oryzae pv.oryzae and fungal blast caused by Magnaporthe grisea result in heavy production losses in rice,a main staple food for approximately 50%of the world's population.Application of host resistance to these pathogens iS the most economical and environment-friendly approach to solve this problem.Quantitative trait loci(QTLs)controlling quantitative resistance are valuable sources for broad.spectrum and durable disease resistance.Although large numbers of QTLs for bacteriaI blight and blast resistance have been identified.these sources have not been used effectively in rice improvement because of the complex genetic controI of quantitative resistance and because the genes underlying resistance QTLs are unknown.To isolate disease resistance QTLs,we established a candidate gene strategy that integrates linkage map,expression profile,and functionaI complementation analyses.This strategy has proven to be applicable for identifying the genes underlying minor resistance QTLs in rice-Xoo and rice-M grisea systems and it may also help to shed light on disease resistance QTLs of other cereals.Our results also suggest that a single minor QTL can be used in rice improvement by modulating the expression of the gene underlying the QTL.Pyramiding two or three minor QTL genes,whose expression can be managed and that function in different defense signaI transduction pathways,may allow the breeding of rice cultivars that are highly resistant to bacteriaI blight and blast.

  13. Dietary approaches to stop hypertension influence on insulin receptor substrate-1gene expression: A randomized controlled clinical trial

    Directory of Open Access Journals (Sweden)

    Marzieh Kafeshani

    2015-01-01

    Full Text Available Background: Insulin receptor substrate (IRS Type 1 is a main substrate for the insulin receptor, controls insulin signaling in skeletal muscle, adipose tissue, and the vascular, so it is an important candidate gene for insulin resistance (IR. We aimed to compare the effects of the Dietary Approaches to Stop Hypertension (DASH and Usual Dietary Advices (UDA on IRS1 gene expression in women at risk for cardiovascular disease. Materials and Methods: A randomized controlled clinical trial was performed in 44 women at risk for cardiovascular disease. Participants were randomly assigned to a UDA diet or the DASH diet. The DASH diet was rich in fruits, vegetables, whole grains, and low-fat dairy products and low in saturated fat, total fat, cholesterol, refined grains, and sweets, with a total of 2400 mg/day sodium. The UDA diet was a regular diet with healthy dietary advice. Gene expression was assessed by the real-time polymerase chain reaction at the first of study and after 12 weeks. Independent sample t-test and paired-samples t-test were used to compare means of all variables within and between two groups respectively. Results: IRS1 gene expression was increased in DASH group compared with UDA diet (P = 0.00. Weight and waist circumference decreased in DASH group significantly compared to the UDA group (P < 0.05 but the results between the two groups showed no significant difference. Conclusion: DASH diet increased IRS1 gene expression and probably has beneficial effects on IR risks.

  14. Genomics-based Approach and Prognostic Stratification Significance of Gene Mutations in Intermediate-risk Acute Myeloid Leukemia

    Institute of Scientific and Technical Information of China (English)

    Bian-Hong Wang; Yong-Hui Li; Li Yu

    2015-01-01

    Objective:Intermediate-risk acute myeloid leukemia (IR-AML),which accounts for a substantial number of AML cases,is highly heterogeneous.We systematically summarize the latest research progress on the significance ofgene mutations for prognostic stratification of IR-AML.Data Sources:We conducted a systemic search from the PubMed database up to October,2014 using various search terms and their combinations including IR-AML,gene mutations,mutational analysis,prognosis,risk stratification,next generation sequencing (NGS).Study Selection:Clinical or basic research articles on NGS and the prognosis of gene mutations in IR-AML were included.Results:The advent of the era of whole-genome sequencing has led to the discovery of an increasing number of molecular genetics aberrations that involved in leukemogenesis,and some of them have been used for prognostic risk stratification.Several studies have consistently identified that some gene mutations have prognostic relevance,however,there are still many controversies for some genes because of lacking sufficient evidence.In addition,tumor cells harbor hundreds of mutated genes and multiple mutations often coexist,therefore,single mutational analysis is not sufficient to make accurate prognostic predictions.The comprehensive analysis of multiple mutations based on sophisticated genomic technologies has raised increasing interest in recent years.Conclusions:NGS represents a pioneering and helpful approach to prognostic risk stratification of IR-AML patients.Further large-scale studies for comprehensive molecular analysis are needed to provide guidance and a theoretical basis for IR-AML prognostic stratification and clinical management.

  15. Use of linkage disequilibrium approaches to map genes for bipolar disorder in the Costa Rican population

    Energy Technology Data Exchange (ETDEWEB)

    Escamilla, M.A.; Reus, V.I.; Smith, L.B.; Freimer, N.B. [Univ. of California, San Francisco, CA (United States)] [and others

    1996-05-31

    Linkage disequilibrium (LD) analysis provides a powerful means for screening the genome to map the location of disease genes, such as those for bipolar disorder (BP). As described in this paper, the population of the Central Valley of Costa Rica, which is descended from a small number of founders, should be suitable for LD mapping; this assertion is supported by reconstruction of extended haplotypes shared by distantly related individuals in this population suffering low-frequency hearing loss (LFHL1), which has previously been mapped by linkage analysis. A sampling strategy is described for applying LD methods to map genes for BP, and clinical and demographic characteristics of an initially collected sample are discussed. This sample will provide a complement to a previously collected set of Costa Rican BP families which is under investigation using standard linkage analysis. 42 refs., 4 figs., 2 tabs.

  16. Characterization of broad-spectrum antibiotic resistance genes in wastewater treatment reactors through metagenomic approaches

    OpenAIRE

    Yang, Ying; 楊穎

    2014-01-01

    The spread of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) have attracted great concerns worldwide. Wastewater treatment plants (WWTPs) are reservoirs of ARGs while wastewater/sludge treatment processes are considered as important means to control these emerging biological pollutants. However, the full profiles of ARGs in WWTPs or the removal efficiency of ARGs by wastewater/sludge treatment process was not well characterized yet. Thus, the major tasks in this st...

  17. Chemoprevention gene therapy (CGT): novel combinatorial approach for preventing and treating pancreatic cancer.

    Science.gov (United States)

    Sarkar, S; Azab, B M; Das, S K; Quinn, B A; Shen, X; Dash, R; Emdad, L; Thomas, S; Dasgupta, S; Su, Z-Z; Wang, X-Y; Sarkar, D; Fisher, P B

    2013-08-01

    Pancreatic cancer remains one of the deadliest of all cancers despite aggressive surgical treatment combined with adjuvant radiotherapy and chemotherapy. Chemoresistance and radioresistance are the principal causes of failure of pancreatic cancer patients to respond to therapy. Conditionally replication competent adenovirus (CRCA)-based cancer gene therapy is an innovative strategy for treating cancers displaying inherent resistance to treatment. Limitations of current adenovirus (Ad)-based gene therapies for malignant tumors include lack of cancer-specificity, and effective and targeted delivery. To remedy this situation, CRCAs have been designed that express E1A, necessary for Ad replication, under the control of a cancer-specific progression elevated gene-3 promoter (PEG-Prom) with concomitant expression of an immunomodulatory cytokine, such as mda-7/IL-24 or interferon-γ (IFN-γ), under the control of a ubiquitous and strong cytomegalovirus promoter (CMV-Prom) from the E3 region. These bipartite CRCAs, when armed with a transgene, are called cancer terminator viruses (CTVs), i.e., Ad.PEG-E1A-CMV-mda-7 (CTV-M7) and Ad.PEG-E1A-CMV-IFN-γ (CTV-γ), because of their universal effectiveness in cancer treatment irrespective of p53/pRb/p16 or other genetic alterations in tumor cells. In addition to their selective oncolytic effects in tumor cells, the potent 'bystander antitumor' properties of MDA-7/IL-24 and IFN-γ embody the CTVs with expanded treatment properties for both primary and distant cancers. Pancreatic cancer cells display a "translational block" of mda-7/IL-24 mRNA, limiting production of MDA-7/IL-24 protein and cancer-specific apoptosis. Specific chemopreventive agents abrogate this "translational block" resulting in pancreatic cancer-specific killing. This novel chemoprevention gene therapy (CGT) strategy holds promise for both prevention and treatment of pancreatic cancers where all other strategies have proven ineffective.

  18. An ex vivo Gene Therapy Approach to Treat Muscular Dystrophy Using inducible Pluripotent Stem Cells

    OpenAIRE

    Filareto, Antonio; Parker, Sarah; Darabi, Radbod; Borges, Luciene; Iacovino, Michelina; Schaaf, Tory; Mayerhofer, Timothy; Jeffrey S. Chamberlain; Ervasti, James M.; McIvor, R. Scott; Kyba, Michael; Perlingeiro, Rita C. R.

    2013-01-01

    Duchenne muscular dystrophy is a progressive and incurable neuromuscular disease caused by genetic and biochemical defects of the dystrophin-glycoprotein complex. Here we show the regenerative potential of myogenic progenitors derived from corrected dystrophic induced pluripotent stem (iPS) cells generated from fibroblasts of mice lacking both dystrophin and utrophin. We correct the phenotype of dystrophic iPS cells using a Sleeping Beauty transposon carrying the micro-utrophin (μUTRN) gene, ...

  19. An Evolutionary Genomic Approach to Identify Genes Involved in Human Birth Timing

    OpenAIRE

    Jevon Plunkett; Scott Doniger; Guilherme Orabona; Thomas Morgan; Ritva Haataja; Mikko Hallman; Hilkka Puttonen; Ramkumar Menon; Edward Kuczynski; Errol Norwitz; Victoria Snegovskikh; Aarno Palotie; Leena Peltonen; Vineta Fellman; DeFranco, Emily A

    2010-01-01

    Coordination of fetal maturation with birth timing is essential for mammalian reproduction. In humans, preterm birth is a disorder of profound global health significance. The signals initiating parturition in humans have remained elusive, due to divergence in physiological mechanisms between humans and model organisms typically studied. Because of relatively large human head size and narrow birth canal cross-sectional area compared to other primates, we hypothesized that genes involved in par...

  20. Metagenomic approach reveals variation of microbes with arsenic and antimony metabolism genes from highly contaminated soil.

    Directory of Open Access Journals (Sweden)

    Jinming Luo

    Full Text Available Microbes have great potential for arsenic (As and antimony (Sb bioremediation in heavily contaminated soil because they have the ability to biotransform As and Sb to species that have less toxicity or are more easily removed. In this study, we integrated a metagenomic method with physicochemical characterization to elucidate the composition of microbial community and functional genes (related to As and Sb in a high As (range from 34.11 to 821.23 mg kg-1 and Sb (range from 226.67 to 3923.07 mg kg-1 contaminated mine field. Metagenomic analysis revealed that microbes from 18 phyla were present in the 5 samples of soil contaminated with high As and Sb. Moreover, redundancy analysis (RDA of the relationship between the 18 phyla and the concentration of As and Sb demonstrated that 5 phyla of microbes, i.e. Actinobacteria, Firmicutes, Nitrospirae, Tenericutes and Gemmatimonadetes were positively correlated with As and Sb concentration. The distribution, diversity and abundance of functional genes (including arsC, arrA, aioA, arsB and ACR3 were much higher for the samples containing higher As and Sb concentrations. Based on correlation analysis, the results showed a positive relationship between arsC-like (R2 = 0.871 and aioA-like (R2 = 0.675 gene abundance and As concentration, and indicated that intracellular As(V reduction and As(III oxidation could be the dominant As detoxification mechanism enabling the microbes to survive in the environment. This study provides a direct and reliable reference on the diversity of microbial community and functional genes in an extremely high concentration As- and Sb-contaminated environment.

  1. COMPUTATIONAL APPROACH FOR DESIGNING AND DEVELOPMENT OF POTENT DRUG INHIBITOR FOR APP GENE IN ALZHEIMER'S DISEASE

    Directory of Open Access Journals (Sweden)

    Santosh Kumar Behera*, Ritesh Kumar Behera and Manas Ranjan Barik

    2013-03-01

    Full Text Available ABSTRACT: Alzheimer’s disease (AD is an irreversible, progressive brain disease that slowly destroys memory and thinking skills, reasoning, planning, language, and perception, and eventually even the ability to carry out the simplest tasks. Many scientists believe that Alzheimer's disease results from an increase in the production or accumulation of a specific protein (beta-amyloid protein in the brain that leads to nerve cell death. The brains of people with AD have an abundance of two abnormal structures amyloid plaques and neurofibrillary tangles that are made of misfolded proteins. This is especially true in certain regions of the brain that are important in memory. In people with Alzheimer's disease, deposits called amyloid plaques build up in the brain. These are composed, in part, of a protein called beta-amyloid, which is a fragment of the amyloid precursor protein (APP. A mutation in the gene that makes APP is believed to be responsible for 5 to 20 percent of all early onset familial Alzheimer's disease. People with a mutation in the APP gene tend to develop Alzheimer's disease at around age 50. The present work deals with the designing a suitable drug by molecular docking which acts on the APP gene to regulate the amyloid plagues formation in the brain.

  2. Automated spectral classification using template matching

    Institute of Scientific and Technical Information of China (English)

    Fu-Qing Duan; Rong Liu; Ping Guo; Ming-Quan Zhou; Fu-Chao Wu

    2009-01-01

    An automated spectral classification technique for large sky surveys is pro-posed. We firstly perform spectral line matching to determine redshift candidates for an observed spectrum, and then estimate the spectral class by measuring the similarity be-tween the observed spectrum and the shifted templates for each redshift candidate. As a byproduct of this approach, the spectral redshift can also be obtained with high accuracy. Compared with some approaches based on computerized learning methods in the liter-ature, the proposed approach needs no training, which is time-consuming and sensitive to selection of the training set. Both simulated data and observed spectra are used to test the approach; the results show that the proposed method is efficient, and it can achieve a correct classification rate as high as 92.9%, 97.9% and 98.8% for stars, galaxies and quasars, respectively.

  3. Unintended Changes in Genetically Modified Rice Expressing the Lysine-Rich Fusion Protein Gene Revealed by a Proteomics Approach

    Institute of Scientific and Technical Information of China (English)

    ZHAO Xiang-xiang; TANG Tang; LIU Fu-xia; LU Chang-li; HU Xiao-lan; JI Li-lian; LIU Qiao-quan

    2013-01-01

    Development of new technologies for evaluating genetically modiifed (GM) crops has revealed that there are unintended insertions and expression changes in GM crops. Proifling techniques are non-targeted approaches and are capable of detecting more unintended changes in GM crops. Here, we report the application of a comparative proteomic approach to investigate the protein proifle differences between a GM rice line, which has a lysine-rich protein gene, and its non-transgenic parental line. Proteome analysis by two-dimensional gel electrophoresis (2-DE) and mass spectrum analysis of the seeds identiifed 22 differentially expressed protein spots. Apart from a number of glutelins that were detected as targeted proteins in the GM line, the majority of the other changed proteins were involved in carbohydrate metabolism, protein synthesis and stress responses. These results indicated that the altered proteins were not associated with plant allergens or toxicity.

  4. Hip arthroplasty by matching cups.

    Science.gov (United States)

    Gerard, Y

    1978-01-01

    A total hip surface arthroplasty consisting of matching cups and uncemented prosthetic components is a noteworthy operation. The femoral cup obtains cylindrical support from the femoral head which is reamed in the shape of a cylinder. The acetabular cup is metallic with a polyethylene liner. It is mobile over the bone but its position is constrained by contact with the femoral cup and therefore "self-centering." On the femoral side, the cup must be placed strictly in the axis of the femoral neck. The main consideration in femoral head surface replacement is the vitality of the underlying bone. Necrosis was observed in the earliest clinical trials but there have been no cases of necrosis in the past 3 1/2 years. This is attributed to a more limited surgical approach in which only the anterior part of the gluteus medius is divided and all the posterior elements of the hip are preserved. The acetabulum is sufficiently reamed to receive the cup, which protrudes beyond the external margins of the acetabulum in all positions. Errors have been committed while perfecting the prosthetic material, but the results as determined by a 6 1/2 year follow-up on purely metallic cups are encouraging. Metal-polyethylene cups presently under investigation have almost a 2 year follow-up. The reaction of the acetabulum to an uncemented cup is not yet known. However, the existence of 2 sliding surfaces and the fact that the acetabular cup moves only during the extremes of hip movement, is reason to assume that if the acetabulum is not reamed to expose cancellous bone, the risks of protrusion are minimal or delayed. Total surface arthroplasty by concentric cups has been performed in 335 hips to date. The operation is especially recommended when osteotomy is no longer possible and disabling coxarthrosis is present in relatively young patients. PMID:729253

  5. A microarray approach to identify genes involved in seed-pericarp cross-talk and development in peach

    Directory of Open Access Journals (Sweden)

    Zaffalon Valerio

    2011-06-01

    Full Text Available Abstract Background Field observations and a few physiological studies have demonstrated that peach embryogenesis and fruit development are tightly coupled. In fact, attempts to stimulate parthenocarpic fruit development by means of external tools have failed. Moreover, physiological disturbances during early embryo development lead to seed abortion and fruitlet abscission. Later in embryo development, the interactions between seed and fruit development become less strict. As there is limited genetic and molecular information about seed-pericarp cross-talk and development in peach, a massive gene approach based on the use of the μPEACH 1.0 array platform and quantitative real time RT-PCR (qRT-PCR was used to study this process. Results A comparative analysis of the transcription profiles conducted in seed and mesocarp (cv Fantasia throughout different developmental stages (S1, S2, S3 and S4 evidenced that 455 genes are differentially expressed in seed and fruit. Among differentially expressed genes some were validated as markers in two subsequent years and in three different genotypes. Seed markers were a LTP1 (lipid transfer protein, a PR (pathogenesis-related protein, a prunin and LEA (Late Embryogenesis Abundant protein, for S1, S2, S3 and S4, respectively. Mesocarp markers were a RD22-like protein, a serin-carboxypeptidase, a senescence related protein and an Aux/IAA, for S1, S2, S3 and S4, respectively. The microarray data, analyzed by using the HORMONOMETER platform, allowed the identification of hormone-responsive genes, some of them putatively involved in seed-pericarp crosstalk. Results indicated that auxin, cytokinins, and gibberellins are good candidates, acting either directly (auxin or indirectly as signals during early development, when the cross-talk is more active and vital for fruit set, whereas abscisic acid and ethylene may be involved later on. Conclusions In this research, genes were identified marking different phases of

  6. No difference in the frequency of locus-specific methylation in the peripheral blood DNA of women diagnosed with breast cancer and age-matched controls

    DEFF Research Database (Denmark)

    Wojdacz, Tomasz K; Thestrup, Britta Boserup; Cold, Søren;

    2011-01-01

    might predispose for cancer development. Here, we have used the methlyation-sensitive high-resolution melting approach to examine the methylation status of the BRCA1, BRCA2, APC, RASSF1A and RARβ2 genes in PBLs of a group of women diagnosed with breast cancer, and an age-matched control group with no...... signs of breast cancer. No significant differences in the frequency of methylation of the above genes were found between cases and controls in our study. Hence, testing for the presence of methylation of cancer-related genes in PBL DNA from women diagnosed with sporadic breast cancer and classified for...

  7. Systems Biology as a Comparative Approach to Understand Complex Gene Expression in Neurological Diseases

    Directory of Open Access Journals (Sweden)

    Francisco J. Esteban

    2013-05-01

    Full Text Available Systems biology interdisciplinary approaches have become an essential analytical tool that may yield novel and powerful insights about the nature of human health and disease. Complex disorders are known to be caused by the combination of genetic, environmental, immunological or neurological factors. Thus, to understand such disorders, it becomes necessary to address the study of this complexity from a novel perspective. Here, we present a review of integrative approaches that help to understand the underlying biological processes involved in the etiopathogenesis of neurological diseases, for example, those related to autism and autism spectrum disorders (ASD endophenotypes. Furthermore, we highlight the role of systems biology in the discovery of new biomarkers or therapeutic targets in complex disorders, a key step in the development of personalized medicine, and we demonstrate the role of systems approaches in the design of classifiers that can shorten the time for behavioral diagnosis of autism.

  8. Approximate Matching of Hierarchial Data

    DEFF Research Database (Denmark)

    Augsten, Nikolaus

    formally proof that the pq-gram index can be incrementally updated based on the log of edit operations without reconstructing intermediate tree versions. The incremental update is independent of the data size and scales to a large number of changes in the data. We introduce windowed pq-grams for the......-gram based distance between streets, introduces a global greedy matching that guarantees stable pairs, and links addresses that are stored with different granularity. The connector has been successfully tested with public administration databases. Our extensive experiments on both synthetic and real world......The goal of this thesis is to design, develop, and evaluate new methods for the approximate matching of hierarchical data represented as labeled trees. In approximate matching scenarios two items should be matched if they are similar. Computing the similarity between labeled trees is hard as in...

  9. Matched Spectral Filter Imager Project

    Data.gov (United States)

    National Aeronautics and Space Administration — OPTRA proposes the development of an imaging spectrometer for greenhouse gas and volcanic gas imaging based on matched spectral filtering and compressive imaging....

  10. Designing self-matching linacs

    International Nuclear Information System (INIS)

    The present trend in ion-linac design is to begin with a radio-frequency quadrupole (RFQ) linac followed by one or more drift-tube linac (DTL) tanks in which permanent-magnet quadrupoles are used for transverse focusing. The lack of adjustable elements (knobs) strongly suggests that one should seek linac designs with intertank matching solutions that are insensitive to beam currents and emittances, which can be accomplished if there are no sharp discontinuities in the focusing properties along the entire linac. Guidelines are presented for linac design and describe techniques for longitudinal as well as transverse matching between tanks. For a wide range of beam currents and emittances, a beam matched at the entrance to the RFQ should remain well matched throughout the entire linac

  11. 基于GPS与IC卡数据的公交站点匹配方法%An Approach on Station ID and Trade Record Match Based on GPS and IC Card Data

    Institute of Scientific and Technical Information of China (English)

    陈绍辉; 陈艳艳; 赖见辉

    2012-01-01

    一票制(单次刷卡)公交线路IC卡数据中缺少乘客上车站点信息,为获得乘客上车站点信息,需要将IC卡交易数据与公交站点进行匹配.首先根据公交车辆GPS数据和公交IC卡数据分别推算站点间运行时间,建立匹配约束规则完成首次站点匹配,并求得公交车辆GPS系统与公交IC卡收费系统的时间平均偏差值,再将时间平均偏差嵌入数据匹配模型,利用禁忌搜索算法对其他未匹配的交易记录进行二次匹配.为作比较,数据试验还包括仅根据站点间运行时间对GPS和IC卡数据进行匹配,从而找到IC卡交易记录与公交站点对应关系.数据试验表明:在GPS数据较完整的条件下,该方法能够精确实现IC卡交易记录与上车站点的匹配,而对比试验方法的匹配精度为80%,低于本文所研究方法.%It is difficult for public traffic IC card data mining and analysis for lacking of boarding station ID information in the IC database of flat fare public traffic routes. To solve the problem, the IC card trade record should be matched with station ID. First, according to the GPS and IC data respectively, the travel time between stations was calculated, the matching restriction rule has been settled up to assist the first travel time matching to obtain the average time deviation between GPS and IC systems. Then, the time deviation was used in the data matching model. After that, the tabu search method was used for matching the other trade records. In contrast, the GPS and IC card data was matched according to the travel time between stations to find out the relationship between trade record and boarding station ID. The data experiment shows that the result is quite accurate and all the trade records and boarding station IDs has been successfully matched with complete GPS data, while the accuracy rate of comparison experiment is 80% which is lower than the presented method.

  12. Rational design of modular circuits for gene transcription: A test of the bottom-up approach

    OpenAIRE

    Giordano Emanuele; Furini Simone; Ceroni Francesca; Cavalcanti Silvio

    2010-01-01

    Abstract Background Most of synthetic circuits developed so far have been designed by an ad hoc approach, using a small number of components (i.e. LacI, TetR) and a trial and error strategy. We are at the point where an increasing number of modular, inter-changeable and well-characterized components is needed to expand the construction of synthetic devices and to allow a rational approach to the design. Results We used interchangeable modular biological parts to create a set of novel syntheti...

  13. Optimal affine-invariant matching: performance characterization

    Science.gov (United States)

    Costa, Mauro S.; Haralick, Robert M.; Shapiro, Linda G.

    1992-04-01

    The geometric hashing scheme proposed by Lamdan and Wolfson can be very efficient in a model-based matching system, not only in terms of the computational complexity involved, but also in terms of the simplicity of the method. In a recent paper, we discussed errors that can occur with this method due to quantization, stability, symmetry, and noise problems. These errors make the original geometric hashing technique unsuitable for use on the factory floor. Beginning with an explicit noise model, which the original Lamdan and Wolfson technique lacks, we derived an optimal approach that overcomes these problems. We showed that the results obtained with the new algorithm are clearly better than the results from the original method. This paper addresses the performance characterization of the geometric hashing technique, more specifically the affine-invariant point matching, applied to the problem of recognizing and determining the pose of sheet metal parts. The experiments indicate that with a model having 10 to 14 points, with 2 points of the model undetected and 10 extraneous points detected, and with the model points perturbed by Gaussian noise of standard deviation 3 (0.58 of range), the average amount of computation required to obtain an answer is equivalent to trying 11 of the possible three-point bases. The misdetection rate, measured by the percentage of correct bases matches that fail to verify, is 0.9. The percentage of incorrect bases that successfully produced a match that did verify (false alarm rate) is 13. And, finally, 2 of the experiments failed to find a correct match and verify it. Results for experiments with real images are also presented.

  14. An Incentive Theory of Matching

    OpenAIRE

    Dennis Snower; Christian Merkl; Alessio J. G. Brown

    2010-01-01

    We construct a theoretical model explaining two-sided selection through microeconomic incentives. Firms face adjustment costs in responding to heterogeneous variations in the characteristics of workers and jobs. Matches and separations are described through firms' job offer and firing decisions and workers' job acceptance and quit decisions. Our calibrated model for the U.S. can account for important empirical regularities that the conventional matching model cannot.

  15. An Efficient Pattern Matching Algorithm

    Science.gov (United States)

    Sleit, Azzam; Almobaideen, Wesam; Baarah, Aladdin H.; Abusitta, Adel H.

    In this study, we present an efficient algorithm for pattern matching based on the combination of hashing and search trees. The proposed solution is classified as an offline algorithm. Although, this study demonstrates the merits of the technique for text matching, it can be utilized for various forms of digital data including images, audio and video. The performance superiority of the proposed solution is validated analytically and experimentally.

  16. Minimalist surface-colour matching

    OpenAIRE

    Amano, Kinjiro; Foster, David H.; Nascimento, Sérgio M. C.

    2005-01-01

    Some theories of surface-colour perception assume that observers estimate the illuminant on a scene so that its effects can be discounted. A critical test of this interpretation of colour constancy is whether surface-colour matching is worse when the number of surfaces in a scene is so small that any illuminant estimate is unreliable. In the experiment reported here, observers made asymmetric colour matches between pairs of simultaneously presented Mondrian-like patterns under different dayli...

  17. Matching games with partial information

    OpenAIRE

    Paolo Laureti Yi-Cheng Zhang

    2003-01-01

    We analyze different ways of pairing agents in a bipartite matching problem, with regard to its scaling properties and to the distribution of individual ``satisfactions''. Then we explore the role of partial information and bounded rationality in a generalized {\\it Marriage Problem}, comparing the benefits obtained by self-searching and by a matchmaker. Finally we propose a modified matching game intended to mimic the way consumers' information makes firms to enhance the quality of their prod...

  18. Procedurally fair and stable matching

    OpenAIRE

    Klaus, Bettina; Klijn, Flip

    2006-01-01

    We motivate procedural fairness for matching mechanisms and study two procedurally fair and stable mechanisms: employment by lotto (Aldershof et al., 1999) and the random order mechanism (Roth and Vande Vate, 1990, Ma, 1996). For both mechanisms we give various examples of probability distributions on the set of stable matchings and discuss properties that differentiate employment by lotto and the random order mechanism. Finally, we consider an adjustment of the random order mechanism, the eq...

  19. From the Cover: A polymer library approach to suicide gene therapy for cancer

    Science.gov (United States)

    Anderson, Daniel G.; Peng, Weidan; Akinc, Akin; Hossain, Naushad; Kohn, Anat; Padera, Robert; Langer, Robert; Sawicki, Janet A.

    2004-11-01

    Optimal gene therapy for cancer must (i) deliver DNA to tumor cells with high efficiency, (ii) induce minimal toxicity, and (iii) avoid gene expression in healthy tissues. To this end, we generated a library of >500 degradable, poly(-amino esters) for potential use as nonviral DNA vectors. Using high-throughput methods, we screened this library in vitro for transfection efficiency and cytotoxicity. We tested the best performing polymer, C32, in mice for toxicity and DNA delivery after intratumor and i.m. injection. C32 delivered DNA intratumorally 4-fold better than one of the best commercially available reagents, jetPEI (polyethyleneimine), and 26-fold better than naked DNA. Conversely, the highest transfection levels after i.m. administration were achieved with naked DNA, followed by polyethyleneimine; transfection was rarely observed with C32. Additionally, polyethyleneimine induced significant local toxicity after i.m. injection, whereas C32 demonstrated no toxicity. Finally, we used C32 to deliver a DNA construct encoding the A chain of diphtheria toxin (DT-A) to xenografts derived from LNCaP human prostate cancer cells. This construct regulates toxin expression both at the transcriptional level by the use of a chimeric-modified enhancer/promoter sequence of the human prostate-specific antigen gene and by DNA recombination mediated by Flp recombinase. C32 delivery of the A chain of diphtheria toxin DNA to LNCaP xenografts suppressed tumor growth and even caused 40% of tumors to regress in size. Because C32 transfects tumors locally at high levels, transfects healthy muscle poorly, and displays no toxicity, it may provide a vehicle for the local treatment of cancer. prostate | cationic polymers

  20. A multi-gene approach reveals a complex evolutionary history in the Cyanistes species group.

    Science.gov (United States)

    Illera, Juan Carlos; Koivula, Kari; Broggi, Juli; Päckert, Martin; Martens, Jochen; Kvist, Laura

    2011-10-01

    Quaternary climatic oscillations have been considered decisive in shaping much of the phylogeographic structure around the Mediterranean Basin. Within this paradigm, peripheral islands are usually considered as the endpoints of the colonization processes. Here, we use nuclear and mitochondrial markers to investigate the phylogeography of the blue tit complex (blue tit Cyanistes caeruleus, Canary blue tit C. teneriffae and azure tit C. cyanus), and assess the role of the Canary Islands for the geographic structuring of genetic variation. The Canary blue tit exhibits strong genetic differentiation within the Canary Islands and, in combination with other related continental species, provides an ideal model in which to examine recent differentiation within a closely related group of continental and oceanic island avian species. We analysed DNA sequences from 51 breeding populations and more than 400 individuals in the blue tit complex. Discrepancies in the nuclear and mitochondrial gene trees provided evidence of a complex evolutionary process around the Mediterranean Basin. Coalescent analyses revealed gene flow between C. caeruleus and C. teneriffae suggesting a dynamic process with multiple phases of colonization and geographic overlapping ranges. Microsatellite data indicated strong genetic differentiation among the Canary Islands and between the Canary archipelago and the close continental areas, indicating limited contemporary gene flow. Diversification of the blue tit complex is estimated to have started during the early Pliocene (≈ 5 Ma), coincident with the end of Messinian salinity crisis. Phylogenetic analyses indicated that the North African blue tit is derived from the Canary blue tits, a pattern is avian 'back colonization' that contrasts with more traditionally held views of islands being sinks rather than sources. PMID:21880092

  1. Direct detection and differentiation of pathogenic Leptospira species using a multi-gene targeted real time PCR approach.

    Science.gov (United States)

    Ferreira, Ana Sofia; Costa, Pedro; Rocha, Teresa; Amaro, Ana; Vieira, Maria Luísa; Ahmed, Ahmed; Thompson, Gertrude; Hartskeerl, Rudy A; Inácio, João

    2014-01-01

    Leptospirosis is a growing public and veterinary health concern caused by pathogenic species of Leptospira. Rapid and reliable laboratory tests for the direct detection of leptospiral infections in animals are in high demand not only to improve diagnosis but also for understanding the epidemiology of the disease. In this work we describe a novel and simple TaqMan-based multi-gene targeted real-time PCR approach able to detect and differentiate Leptospira interrogans, L. kirschneri, L. borgpeteresenii and L. noguchii, which constitute the veterinary most relevant pathogenic species of Leptospira. The method uses sets of species-specific probes, and respective flanking primers, designed from ompL1 and secY gene sequences. To monitor the presence of inhibitors, a duplex amplification assay targeting both the mammal β-actin and the leptospiral lipL32 genes was implemented. The analytical sensitivity of all primer and probe sets was estimated to be Dolichotis patagonum and Sus domesticus). Two samples were infected with L. borgpetersenii, two with L. interrogans and one with L. kirschneri. The possibility to detect and identify these pathogenic agents to the species level in domestic and wildlife animals reinforces the diagnostic information and will enhance our understanding of the epidemiology of leptopirosis. PMID:25398140

  2. Stress-sensitive neurosignalling in depression: an integrated network biology approach to candidate gene selection for genetic association analysis

    Directory of Open Access Journals (Sweden)

    J. Anke M. van Eekelen

    2012-07-01

    Full Text Available Genetic risk for depressive disorders is poorly understood despite consistent suggestions of a high heritable component. Most genetic studies have focused on risk associated with single variants, a strategy which has so far only yielded small (often non-replicable risks for depressive disorders. In this paper we argue that more substantial risks are likely to emerge from genetic variants acting in synergy within and across larger neurobiological systems (polygenic risk factors. We show how knowledge of major integrated neurobiological systems provides a robust basis for defining and testing theoretically defensible polygenic risk factors. We do this by describing the architecture of the overall stress response. Maladaptation via impaired stress responsiveness is central to the aetiology of depression and anxiety and provides a framework for a systems biology approach to candidate gene selection. We propose principles for identifying genes and gene networks within the neurosystems involved in the stress response and for defining polygenic risk factors based on the neurobiology of stress-related behaviour. We conclude that knowledge of the neurobiology of the stress response system is likely to play a central role in future efforts to improve genetic prediction of depression and related disorders.

  3. PR gene families of citrus: their organ specific-biotic and abiotic inducible expression profiles based on ESTs approach

    Directory of Open Access Journals (Sweden)

    Magnólia A. Campos

    2007-01-01

    Full Text Available In silico expression profiles, of the discovered 3,103 citrus ESTs putatively encoding for PR protein families (PR-1 to PR-17, were evaluated using the Brazil citrus genome EST CitEST/database. Hierarchical clustering was displayed to identify similarities in expression patterns among citrus PR-like gene families (PRlgf in 33 selected cDNA libraries. In this way, PRlgf preferentially expressed by organ and citrus species, and library conditions were highlighted. Changes in expression profiles of clusters for each of the 17 PRlgf expressed in organs infected by pathogens or drought-stressed citrus species were displayed for relative suppression or induction gene expression in relation to the counterpart control. Overall, few PRlgf showed expression 2-fold higher in pathogen-infected than in uninfected organs, even though the differential expression profiles displayed have been quite diverse among studied species and organs. Furthermore, an insight into some contigs from four PRlgf pointed out putative members of multigene families. They appear to be evolutionarily conserved within citrus species and/or organ- or stress-specifically expressed. Our results represent a starting point regarding the extent of expression pattern differences underlying PRlgf expression and reveal genes that may prove to be useful in studies regarding biotechnological approaches or citrus resistance markers.

  4. The Genetic Basis of Quality of Life in Healthy Swedish Women: A Candidate Gene Approach

    OpenAIRE

    Dounya Schoormans; Jingmei Li; Hatef Darabi; Yvonne Brandberg; Sprangers, Mirjam A. G.; Mikael Eriksson; Zwinderman, Koos H.; Per Hall

    2015-01-01

    Background Quality of life (QoL) is an increasingly important parameter in clinical practice as it predicts mortality and poor health outcomes. It is hypothesized that one may have a genetic predisposition for QoL. We therefore related 139 candidate genes, selected through a literature search, to QoL in healthy females. Methods In 5,142 healthy females, background characteristics (i.e. demographic, clinical, lifestyle, and psychological factors) were assessed. QoL was measured by the EORTC QL...

  5. A Bayesian approach for decision making on the identification of genes with different expression levels: an application to Escherichia coli bacterium data.

    Science.gov (United States)

    Saraiva, Erlandson F; Louzada, Francisco; Milan, Luís A; Meira, Silvana; Cobre, Juliana

    2012-01-01

    A common interest in gene expression data analysis is to identify from a large pool of candidate genes the genes that present significant changes in expression levels between a treatment and a control biological condition. Usually, it is done using a statistic value and a cutoff value that are used to separate the genes differentially and nondifferentially expressed. In this paper, we propose a Bayesian approach to identify genes differentially expressed calculating sequentially credibility intervals from predictive densities which are constructed using the sampled mean treatment effect from all genes in study excluding the treatment effect of genes previously identified with statistical evidence for difference. We compare our Bayesian approach with the standard ones based on the use of the t-test and modified t-tests via a simulation study, using small sample sizes which are common in gene expression data analysis. Results obtained report evidence that the proposed approach performs better than standard ones, especially for cases with mean differences and increases in treatment variance in relation to control variance. We also apply the methodologies to a well-known publicly available data set on Escherichia coli bacterium.

  6. Self-organizing Approach for Automated Gene Identification in Whole Genomes

    OpenAIRE

    Gorban, Alexander N; Zinovyev, Andrey Yu.; Popova, Tatyana G.

    2001-01-01

    An approach based on using the idea of distinguished coding phase in explicit form for identification of protein-coding regions (exons) in whole genome has been proposed. For several genomes an optimal window length for averaging GC-content function and calculating codon frequencies has been found. Self-training procedure based on clustering in multidimensional space of triplet frequencies is proposed. For visualization of data in the space of triplet requiencies method of elastic maps was ap...

  7. An ex vivo gene therapy approach to treat muscular dystrophy using inducible pluripotent stem cells.

    Science.gov (United States)

    Filareto, Antonio; Parker, Sarah; Darabi, Radbod; Borges, Luciene; Iacovino, Michelina; Schaaf, Tory; Mayerhofer, Timothy; Chamberlain, Jeffrey S; Ervasti, James M; McIvor, R Scott; Kyba, Michael; Perlingeiro, Rita C R

    2013-01-01

    Duchenne muscular dystrophy is a progressive and incurable neuromuscular disease caused by genetic and biochemical defects of the dystrophin-glycoprotein complex. Here we show the regenerative potential of myogenic progenitors derived from corrected dystrophic induced pluripotent stem cells generated from fibroblasts of mice lacking both dystrophin and utrophin. We correct the phenotype of dystrophic induced pluripotent stem cells using a Sleeping Beauty transposon system carrying the micro-utrophin gene, differentiate these cells into skeletal muscle progenitors and transplant them back into dystrophic mice. Engrafted muscles displayed large numbers of micro-utrophin-positive myofibers, with biochemically restored dystrophin-glycoprotein complex and improved contractile strength. The transplanted cells seed the satellite cell compartment, responded properly to injury and exhibit neuromuscular synapses. We also detect muscle engraftment after systemic delivery of these corrected progenitors. These results represent an important advance towards the future treatment of muscular dystrophies using genetically corrected autologous induced pluripotent stem cells. PMID:23462992

  8. Systems-Level Nutrition Approaches to Define Phenotypes Resulting from Complex Gene-Environment Interactions.

    Science.gov (United States)

    Kaput, Jim

    2016-01-01

    High-throughput metabolomic, proteomic, and genomic technologies have delivered 21st-century data showing that humans cannot be randomized into groups: individuals are genetically and biochemically distinct. Gene-environment interactions caused by unique dietary and lifestyle factors contribute to the heterogeneity in physiologies observed in human studies. The risk factors determined for populations (i.e. the population-attributable risk) cannot be applied to the individual. Developing individual risk/benefit factors in light of the genetic diversity of human populations, the complexity of foods, culture and lifestyle, and the variety in metabolic processes that lead to health or disease are significant challenges for personalizing dietary advice for healthy or diseased individuals. PMID:26764468

  9. Fingerprint Matching and Non-Matching Analysis for Different Tolerance Rotation Degrees in Commercial Matching Algorithms

    Directory of Open Access Journals (Sweden)

    A. J. Perez-Diaz

    2010-08-01

    Full Text Available Fingerprint verification is the most important step in the fingerprint-based biometric systems. The matching score islinked to the chance of identifying a person. Nowadays, two fingerprint matching methods are the most popular: thecorrelation-based method and the minutiae-based method. In this work, three biometric systems were evaluated:Neurotechnology Verifinger 6.0 Extended, Innovatrics IDKit SDK and Griaule Fingerprint SDK 2007. The evaluationwas performed according to the experiments of the Fingerprint Verification Competition (FVC. The influence of thefingerprint rotation degrees on false match rate (FMR and false non-match rate (FNMR was evaluated. The resultsshowed that the FMR values increase as rotation degrees increase too, meanwhile, the FNMR values decrease.Experimental results demonstrate that Verifinger SDK shows good performance on false non-match testing, with anFNMR mean of 7%, followed by IDKit SDK (6.71% ~ 13.66% and Fingerprint SDK (50%. However, Fingerprint SDKdemonstrates a better performance on false match testing, with an FMR mean of ~0%, followed by Verifinger SDK(7.62% - 9% and IDKit SDK (above 28%. As result of the experiments, Verifinger SDK had, in general, the bestperformance. Subsequently, we calculated the regression functions to predict the behavior of FNMR and FMR fordifferent threshold values with different rotation degrees.

  10. Is gene activity in plant cells affected by UMTS-irradiation? A whole genome approach

    Directory of Open Access Journals (Sweden)

    Julia C Engelmann

    2008-10-01

    Full Text Available Julia C Engelmann3,* Rosalia Deeken1,* Tobias Müller3, Günter Nimtz2, M Rob G Roelfsema1, Rainer Hedrich11Molecular Plant Physiology and Biophysics, Julius-von-Sachs Institute for Biosciences; 2Institute of Physics II, University of Cologne, Cologne, Germany; 3Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany; *These authors contributed equally to this workAbstract: Mobile phone technology makes use of radio frequency (RF electromagnetic fields transmitted through a dense network of base stations in Europe. Possible harmful effects of RF fields on humans and animals are discussed, but their effect on plants has received little attention. In search for physiological processes of plant cells sensitive to RF fields, cell suspension cultures of Arabidopsis thaliana were exposed for 24 h to a RF field protocol representing typical microwave exposition in an urban environment. mRNA of exposed cultures and controls was used to hybridize Affymetrix-ATH1 whole genome microarrays. Differential expression analysis revealed significant changes in transcription of 10 genes, but they did not exceed a fold change of 2.5. Besides that 3 of them are dark-inducible, their functions do not point to any known responses of plants to environmental stimuli. The changes in transcription of these genes were compared with published microarray datasets and revealed a weak similarity of the microwave to light treatment experiments. Considering the large changes described in published experiments, it is questionable if the small alterations caused by a 24 h continuous microwave exposure would have any impact on the growth and reproduction of whole plants.Keywords: suspension cultured plant cells, radio frequency electromagnetic fields, microarrays, Arabidopsis thaliana

  11. Efficient gene targeting in Penicillium chrysogenum using novel Agrobacterium-mediated transformation approaches.

    Science.gov (United States)

    de Boer, Paulo; Bronkhof, Jurian; Dukiќ, Karolina; Kerkman, Richard; Touw, Hesselien; van den Berg, Marco; Offringa, Remko

    2013-12-01

    The industrial production of β-lactam antibiotics by Penicillium chrysogenum has increased tremendously over the last decades, however, further optimization via classical strain and process improvement has reached its limits. The availability of the genome sequence provides new opportunities for directed strain improvement, but this requires the establishment of an efficient gene targeting (GT) system. Recently, mutations affecting the non-homologous end joining (NHEJ) pathway were shown to increase GT efficiencies following PEG-mediated DNA transfer in P. chrysogenum from 1% to 50%. Apart from direct DNA transfer many fungi can efficiently be transformed using the T-DNA transfer system of the soil bacterium Agrobacterium tumefaciens, however, for P. chrysogenum no robust system for Agrobacterium-mediated transformation was available. We obtained efficient AMT of P. chrysogenum spores with the nourseothricin acetyltransferase gene as selection marker, and using this system we investigated if AMT in a NHEJ mutant background could further enhance GT efficiencies. In general, AMT resulted in higher GT efficiencies than direct DNA transfer, although the final frequencies depended on the Agrobacterium strain and plasmid backbone used. Providing overlapping and complementing fragments on two different plasmid backbones via the same Agrobacterium host was shown to be most effective. This so-called split-marker or bi-partite method resulted in highly efficient GT (>97%) almost exclusively without additional ectopic T-DNA insertions. As this method provides for an efficient GT method independent of protoplasts, it can be applied to other fungi for which no protoplasts can be generated or for which protoplast transformation leads to varying results.

  12. Time Series Analysis Using Geometric Template Matching.

    Science.gov (United States)

    Frank, Jordan; Mannor, Shie; Pineau, Joelle; Precup, Doina

    2013-03-01

    We present a novel framework for analyzing univariate time series data. At the heart of the approach is a versatile algorithm for measuring the similarity of two segments of time series called geometric template matching (GeTeM). First, we use GeTeM to compute a similarity measure for clustering and nearest-neighbor classification. Next, we present a semi-supervised learning algorithm that uses the similarity measure with hierarchical clustering in order to improve classification performance when unlabeled training data are available. Finally, we present a boosting framework called TDEBOOST, which uses an ensemble of GeTeM classifiers. TDEBOOST augments the traditional boosting approach with an additional step in which the features used as inputs to the classifier are adapted at each step to improve the training error. We empirically evaluate the proposed approaches on several datasets, such as accelerometer data collected from wearable sensors and ECG data. PMID:22641699

  13. Block Matching for Object Tracking

    Energy Technology Data Exchange (ETDEWEB)

    Gyaourova, A; Kamath, C; Cheung, S

    2003-10-13

    Models which describe road traffic patterns can be helpful in detection and/or prevention of uncommon and dangerous situations. Such models can be built by the use of motion detection algorithms applied to video data. Block matching is a standard technique for encoding motion in video compression algorithms. We explored the capabilities of the block matching algorithm when applied for object tracking. The goal of our experiments is two-fold: (1) to explore the abilities of the block matching algorithm on low resolution and low frame rate video and (2) to improve the motion detection performance by the use of different search techniques during the process of block matching. Our experiments showed that the block matching algorithm yields good object tracking results and can be used with high success on low resolution and low frame rate video data. We observed that different searching methods have small effect on the final results. In addition, we proposed a technique based on frame history, which successfully overcame false motion caused by small camera movements.

  14. Association study of inflammatory genes with rheumatic heart disease in North Indian population: A multi-analytical approach.

    Science.gov (United States)

    Gupta, Usha; Mir, Snober S; Garg, Naveen; Agarwal, Surendra K; Pande, Shantanu; Mittal, Balraj

    2016-06-01

    Rheumatic heart disease (RHD) is an inflammatory, autoimmune disease; occurring as a consequence of group A streptococcal infection complicated by rheumatic fever (RF). An inappropriate immune response is the central signature tune to the complex pathogenesis of RHD. However, some of those infected develop RHD, and genetic host susceptibility factors are thought to play a key role in diseasedevelopment. Therefore, the present study was designed to explore the role of genetic variants in inflammatory genes in conferring risk of RHD. The study recruited total of 700 subjects, including 400 RHD patients and 300 healthy controls. We examined the associations of 8 selected polymorphisms in seven inflammatory genes: IL-6 [rs1800795G/C], IL-10 [rs1800896G/A], TNF-A [rs1800629G/A], IL-1β [rs2853550C/T], IL-1VNTR [rs2234663], TGF-β1 [rs1800469C/T]; [rs1982073T/C], and CTLA-4 [rs5742909C/T] with RHD risk. Genotyping for all the polymorphisms was done using PCR-ARMS/PCR/RFLP methods. Multifactor dimensionality reduction and classification and regression tree approaches were combined with logistic regression to discover high-order gene-gene interactions in studiedgenes involved in RHD susceptibility.In univariate logistic regression analysis, we found significant association of variant-containing genotypes (CT&TT) of TGF-β1 869T/C [rs1982073]; [p=0.0.004 & 0.001, OR (95% CI)=1.65 (1.2-2.3) & 2.25 (1.4-3.6) respectively], variant genotype (CC) of IL-1β -511C/T [rs2853550]; [p=0.001, OR (95% CI)=2.33 (1.4-3.8)] and IL-1 VNTR [rs2234663]; [p=0.03, OR (95% CI)=5.25 (1.2-23.4)] SNPs with RHD risk. CART analysis revealed that individuals with the combined genotypes of TGF-β1T/C_ rs1982073 (CT/TT) and IL-1 β_ rs2853550 (CC) had significantly higher susceptibility for RHD [p=0.0005, OR (95% CI)=5.91 (2.9-12.5)]. In MDR analysis, TGF-β1 869T>C yielded the highest testing accuracy of 0.562. In conclusion, using multi-analytical approaches, our study revealed important role of TGF

  15. Typed and unambiguous pattern matching on strings using regular expressions

    DEFF Research Database (Denmark)

    Brabrand, Claus; Thomsen, Jakob G.

    2010-01-01

    pinpointing all ambiguities in terms of the structure of the regular expression and report shortest ambiguous strings. We also show how pattern matching can be integrated into statically typed programming languages for deconstructing strings and reproducing typed and structured values. We validate our...... approach by giving a full implementation of the approach presented in this paper. The resulting tool, reg-exp-rec, adds typed and unambiguous pattern matching to Java in a stand-alone and non-intrusive manner. We evaluate the approach using several realistic examples....

  16. Typed and Unambiguous Pattern Matching on Strings using Regular Expressions

    DEFF Research Database (Denmark)

    Brabrand, Claus; Thomsen, Jakob Grauenkjær

    2010-01-01

    pinpointing all ambiguities in terms of the structure of the regular expression and report shortest ambiguous strings. We also show how pattern matching can be integrated into statically typed programming languages for deconstructing strings and reproducing typed and structured values. We validate our...... approach by giving a full implementation of the approach presented in this paper.  The resulting tool, reg-exp-rec, adds typed and unambiguous pattern matching to Java in a stand-alone and non-intrusive manner.  We evaluate the approach using several realistic examples....

  17. Coarse-to-fine region selection and matching

    KAUST Repository

    Yang, Yanchao

    2015-10-15

    We present a new approach to wide baseline matching. We propose to use a hierarchical decomposition of the image domain and coarse-to-fine selection of regions to match. In contrast to interest point matching methods, which sample salient regions to reduce the cost of comparing all regions in two images, our method eliminates regions systematically to achieve efficiency. One advantage of our approach is that it is not restricted to covariant salient regions, which is too restrictive under large viewpoint and leads to few corresponding regions. Affine invariant matching of regions in the hierarchy is achieved efficiently by a coarse-to-fine search of the affine space. Experiments on two benchmark datasets shows that our method finds more correct correspondence of the image (with fewer false alarms) than other wide baseline methods on large viewpoint change. © 2015 IEEE.

  18. One-loop effective lagrangians after matching

    Energy Technology Data Exchange (ETDEWEB)

    Aguila, F. del; Santiago, J. [Universidad de Granada, Departamento de Fisica Teorica y del Cosmos and CAFPE, Granada (Spain); Kunszt, Z. [ETH Zuerich, Institute for Theoretical Physics, Zuerich (Switzerland)

    2016-05-15

    We discuss the limitations of the covariant derivative expansion prescription advocated to compute the one-loop Standard Model (SM) effective lagrangian when the heavy fields couple linearly to the SM. In particular, one-loop contributions resulting from the exchange of both heavy and light fields must be explicitly taken into account through matching because the proposed functional approach alone does not account for them. We review a simple case with a heavy scalar singlet of charge -1 to illustrate the argument. As two other examples where this matching is needed and this functional method gives a vanishing result, up to renormalization of the heavy sector parameters, we re-evaluate the one-loop corrections to the T-parameter due to a heavy scalar triplet with vanishing hypercharge coupling to the Brout-Englert-Higgs boson and to a heavy vector-like quark singlet of charged 2/3 mixing with the top quark, respectively. In all cases we make use of a new code for matching fundamental and effective theories in models with arbitrary heavy field additions. (orig.)

  19. Fingerprint matching algorithm for poor quality images

    Directory of Open Access Journals (Sweden)

    Vedpal Singh

    2015-04-01

    Full Text Available The main aim of this study is to establish an efficient platform for fingerprint matching for low-quality images. Generally, fingerprint matching approaches use the minutiae points for authentication. However, it is not such a reliable authentication method for low-quality images. To overcome this problem, the current study proposes a fingerprint matching methodology based on normalised cross-correlation, which would improve the performance and reduce the miscalculations during authentication. It would decrease the computational complexities. The error rate of the proposed method is 5.4%, which is less than the two-dimensional (2D dynamic programming (DP error rate of 5.6%, while Lee's method produces 5.9% and the combined method has 6.1% error rate. Genuine accept rate at 1% false accept rate is 89.3% but at 0.1% value it is 96.7%, which is higher. The outcome of this study suggests that the proposed methodology has a low error rate with minimum computational effort as compared with existing methods such as Lee's method and 2D DP and the combined method.

  20. Effective anisotropy through traveltime and amplitude matching

    KAUST Repository

    Wang, Hui

    2014-08-05

    Introducing anisotropy to seismic wave propagation reveals more realistic physics of our Earth\\'s subsurface as compared to the isotropic assumption. However wavefield modeling, the engine of seismic inverse problems, in anisotropic media still suffers from computational burdens, in particular with complex anisotropy such as transversely isotropic (TI) and Orthorhombic anisotropy. We develop effective isotropic velocity and density models to package the effects of anisotropy such that the wave propagation behavior using these effective models approximate those of the original anisotropic model. We build these effective models through the high frequency asymptotic approximation based on the eikonal and transport equations. We match the geometrical behavior of the wave-fields, given by traveltimes, from the anisotropic and isotropic eikonal equations. This matching yields the effective isotropic velocity that approximates the kinematics of the anisotropic wavefield. Equivalently, we calculate the effective densities by equating the anisotropic and isotropic transport equations. The effective velocities and densities are then fed into the isotropic acoustic variable density wave equation to obtain cheaper anisotropic wavefields. We justify our approach by testing it on an elliptical anisotropic model. The numerical results demonstrate a good matching of both traveltime and amplitude between anisotropic and effective isotropic wavefields.

  1. Computing the Matched Filter in Linear Time

    CERN Document Server

    Fish, Alexander; Hadani, Ronny; Sayeed, Akbar; Schwartz, Oded

    2011-01-01

    A fundamental problem in wireless communication is the time-frequency shift (TFS) problem: Find the time-frequency shift of a signal in a noisy environment. The shift is the result of time asynchronization of a sender with a receiver, and of non-zero speed of a sender with respect to a receiver. A classical solution of a discrete analog of the TFS problem is called the matched filter algorithm. It uses a pseudo-random waveform S(t) of the length p, and its arithmetic complexity is O(p^{2} \\cdot log (p)), using fast Fourier transform. In these notes we introduce a novel approach of designing new waveforms that allow faster matched filter algorithm. We use techniques from group representation theory to design waveforms S(t), which enable us to introduce two fast matched filter (FMF) algorithms, called the flag algorithm, and the cross algorithm. These methods solve the TFS problem in O(p\\cdot log (p)) operations. We discuss applications of the algorithms to mobile communication, GPS, and radar.

  2. Matched molecular pair analysis in drug discovery.

    Science.gov (United States)

    Dossetter, Alexander G; Griffen, Edward J; Leach, Andrew G

    2013-08-01

    Multiple parameter optimisation in drug discovery is difficult, but Matched Molecular Pair Analysis (MMPA) can help. Computer algorithms can process data in an unbiased way to yield design rules and suggest better molecules, cutting the number of design cycles. The approach often makes more suggestions than can be processed manually and methods to deal with this are proposed. However, there is a paucity of contextually specific design rules, which would truly make the technique powerful. By combining extracted information from multiple sources there is an opportunity to solve this problem and advance medicinal chemistry in a matter of months rather than years. PMID:23557664

  3. Controlling HIV-1: Non-coding RNA gene therapy approaches to a functional cure

    Directory of Open Access Journals (Sweden)

    Chantelle L Ahlenstiel

    2015-09-01

    Full Text Available The current treatment strategy for HIV-1 involves prolonged and intensive combined antiretroviral therapy (cART, which successfully suppresses plasma viremia. It has transformed HIV-1 infection into a chronic disease. However, despite the success of cART, a latent form of HIV-1 infection persists as integrated provirus in resting memory CD4+ T cells. Virus can reactivate from this reservoir upon cessation of treatment and hence HIV requires lifelong therapy. The reservoir represents a major barrier to eradication. Understanding molecular mechanisms regulating HIV-1 transcription and latency are crucial to developing alternate treatment strategies which impact upon the reservoir and provide a path towards a functional cure in which there is no detectable viremia in the absence of cART. Numerous reports have suggested ncRNAs are involved in regulating viral transcription and latency. This review will discuss the latest developments in ncRNAs, specifically short interfering (siRNA and short hairpin (shRNA, targeting molecular mechanisms of HIV-1 transcription, which may represent potential future therapeutics. It will also briefly address animal models available for testing potential therapeutics and current gene therapy clinical trials.

  4. Bayesian computational approaches for gene regulation studies of bioethanol and biohydrogen production

    Energy Technology Data Exchange (ETDEWEB)

    Lawrence, Charles E [Brown Univ., Providence, RI (United States); Newberg, Lee [Wadsworth Center; McCue, LeeAnn [Pacific Northwest Labs; Thomspon, Williams [Brown University

    2012-03-01

    It has recently become clear that regulatory RNAs play a major role in regulation of gene expression in bacteria. RNA secondary structures play a major role in the function of many regulatory RNAs, and structural features are often key to their interaction with other cellular components. Thus, there has been considerable interest in the prediction of the secondary structures for RNA families. A paper describing our new algorithm, RNAG, to predict consensus secondary structures for unaligned sequences using the blocked Gibbs sampler has been published[1]. This sampling algorithm iteratively samples from the conditional probability distributions: P(Structure | Alignment) and P(Alignment | Structure). Subsequent to publication of the RNAG paper we have employed the technology from RNAG in the development of an RNA motif finding algorithm. To develop and RNA motif finding algorithm, RGibbs, we capitalized on our long experience in DNA motif finding and RNA secondary structure prediction. We applied RGibbs to three data sets from the literature and compared it to existing methods: one for training and two others for tests sets. In both test sets we found RGibbs out performed existing procedures.

  5. Ice Hockey Match Prediction Using Data Mining Model

    OpenAIRE

    Matuš, Martin

    2014-01-01

    This thesis focuses on creation and comparison of ice hockey matches prediction models with the view on ice hockey world championship matches. The first part is dedicated to collecting theoretical knowledge needed for solving this problem and the second to applying this set of knowledge. The model creation approach is intertwined with the CRISP-DM data mining methodology, which also defines several chapters of this work. As input data for the models I used performance statistics of individual...

  6. New avenues for phase matching in nonlinear hyperbolic metamaterials

    OpenAIRE

    Duncan, C; L. Perret; Palomba, S; Lapine, M.; Kuhlmey, B. T.; Martijn de Sterke, C.

    2015-01-01

    Nonlinear optical processes, which are of paramount importance in science and technology, involve the generation of new frequencies. This requires phase matching to avoid that light generated at different positions interferes destructively. Of the two original approaches to achieve this, one relies on birefringence in optical crystals, and is therefore limited by the dispersion of naturally occurring materials, whereas the other, quasi-phase-matching, requires direct modulation of material pr...

  7. Light bullets by synthetic diffraction-dispersion matching

    OpenAIRE

    Lobanov, Valery E.; Kartashov, Yaroslav; Torner Sabata, Lluís

    2010-01-01

    We put forward a new approach to generate stable, fully three-dimensional light bullets, which is based on the matching of the intrinsic material dispersion with a suitable effective diffraction. The matching is achieved in adequate waveguide arrays whose refractive index is periodically modulated along the direction of light propagation. We show that by using non-conventional, out-of-phase longitudinal modulation of the refractive index of neighboring channels, it is possible to tune the eff...

  8. Brood parasites lay eggs matching the appearance of host clutches

    OpenAIRE

    Honza, Marcel; Šulc, Michal; Jelínek, Václav; Požgayová, Milica; Procházka, Petr

    2014-01-01

    Interspecific brood parasitism represents a prime example of the coevolutionary arms race where each party has evolved strategies in response to the other. Here, we investigated whether common cuckoos (Cuculus canorus) actively select nests within a host population to match the egg appearance of a particular host clutch. To achieve this goal, we quantified the degree of egg matching using the avian vision modelling approach. Randomization tests revealed that cuckoo eggs in naturally parasitiz...

  9. Production of transgenic mice carrying green fluorescence protein gene by a lentiviral vector-mediated approach

    Institute of Scientific and Technical Information of China (English)

    ZHANG Jingzhi; GUO Xinbing; XIE Shuyang; ZHU Yiwen; HUANG Ying; WANG Shu; REN Zhaorui

    2006-01-01

    A pseudo-lentivirus, which carries green fluorescence protein (GFP) expressing cassette, was injected into the perivitelline space of murine fertilized oocytes before transplanting into the oviducts of the foster mothers. The GFP transgenic pups were then obtained. By PCR amplification, fluorescent microscopy and flow assisted cytometry sorting analysis, we found that the integration rate of the transgene was estimated at above 40%. Real-time PCR analysis indicated that the copy number of the integrated GFP cassette was around 40. Fluorescent in situ hybridization analysis demonstrated that the integration pattern was random but inheritable. The transgenic mice with multi-integration sites and various expression levels possessed a great value in practice as well as research. The approach reported herein provides an efficient way to generate and screen the transgenic mouse strains.

  10. Establish keypoint matches on multispectral images utilizing descriptor and global information over entire image

    Science.gov (United States)

    Li, Yong; Zou, Junwei; Jing, Jing; Jin, Hongbin; Yu, Hang

    2016-05-01

    This paper proposes an approach to registering multispectral images by establishing keypoint matches. The matching ability of descriptors is characterized by the repeatability and distinctiveness that typically decrease on multispectral images. The decrease of matching ability often yields a set of keypoint matches containing a high rate of incorrect matches, and in this case the outlier matches are very difficult to be removed. To establish reliable keypoint matches, this paper proposes an approach of two stages. Firstly, keypoint matches of smaller descriptor distance are obtained as an initial set. Secondly, complementary information to the local window for computing descriptors is employed to evaluate keypoint matches and find good matches. A smaller descriptor distance for a keypoint match implies a greater probability of being correct and hence the initial set contains a higher rate of correct matches. The global information can be viewed as a means of enhancing the matching ability of descriptors, compensating the decrease of common information between multispectral images. Experimental results show that the proposed method can effectively establish keypoint matches on multispectral images of large spectral difference.

  11. Approaches to systems biology. Four methods to study single-cell gene expression, cell motility, antibody reactivity, and respiratory metabolism

    DEFF Research Database (Denmark)

    Hagedorn, Peter

    To understand how complex systems, such as cells, function, comprehensive Measurements of their constituent parts must be made. This can be achieved by combining methods that are each optimized to measure specific parts of the system. Four such methods,each covering a different area, are presented......: Transcript profiling of one cell type extracted from a complex tissue containing several cell types; observation and recording of cell motility; measurement of antibody reactivities using microarrays; and invivo measurement of free and bound NADH in mitochondria. Detailed statistical analysis of the data...... from such measurements allows models of the system to be developed and tested. For each of the methods, such analysis and modelling approaches have beenapplied and are presented: Differentially regulated genes are identified and classified according to function; cell-specfic motility models...

  12. An Approach for Building Extraction Based on Dense-matching Points Cloud of Visible Image%一种可见光影像稠密匹配点云的单栋建筑物提取方法

    Institute of Scientific and Technical Information of China (English)

    杨振发; 万刚; 曹雪峰; 李锋

    2016-01-01

    建筑物点云提取是城市快速三维建模的基础。针对城区中建筑物和树木空间距离较近导致建筑物点云误提取的问题,提出一种颜色约束的欧式聚类算法。该方法利用低空拍摄可见光影像进行三维重建、获取点云数据,在建立点云K邻域索引和表面估计的基础上,以曲率最小的点作为欧式聚类的种子点,将点云的RGB值转换成Lab颜色模型,对建筑物点云的聚类提取进行约束。实验表明,该方法可以有效地解决可见光影像匹配点云中建筑物提取时将树木误提取的问题。%Abstratc:Building extraction of point cloud is the basis of the rapid urban modeling.A problem of mistaken extraction will be arisen when the spatial distance of buildings and trees are too close in city.To solve this problem, a method of European clustering algorithm based on color constrain was proposed.This method regarded minimum curvature points as the European clustering seeds on the basis of establishing point cloud KNN and estimation surface, and constrained the clustering extraction of trees point cloud by converting the RGB values of point cloud to Lab color space, utilizing the point cloud of images matching.The experiments showed that this method could effectively solve the problem of building mistaken extraction based on the visible image matching point cloud.

  13. Direct detection and differentiation of pathogenic Leptospira species using a multi-gene targeted real time PCR approach.

    Directory of Open Access Journals (Sweden)

    Ana Sofia Ferreira

    Full Text Available Leptospirosis is a growing public and veterinary health concern caused by pathogenic species of Leptospira. Rapid and reliable laboratory tests for the direct detection of leptospiral infections in animals are in high demand not only to improve diagnosis but also for understanding the epidemiology of the disease. In this work we describe a novel and simple TaqMan-based multi-gene targeted real-time PCR approach able to detect and differentiate Leptospira interrogans, L. kirschneri, L. borgpeteresenii and L. noguchii, which constitute the veterinary most relevant pathogenic species of Leptospira. The method uses sets of species-specific probes, and respective flanking primers, designed from ompL1 and secY gene sequences. To monitor the presence of inhibitors, a duplex amplification assay targeting both the mammal β-actin and the leptospiral lipL32 genes was implemented. The analytical sensitivity of all primer and probe sets was estimated to be <10 genome equivalents (GE in the reaction mixture. Application of the amplification reactions on genomic DNA from a variety of pathogenic and non-pathogenic Leptospira strains and other non-related bacteria revealed a 100% analytical specificity. Additionally, pathogenic leptospires were successfully detected in five out of 29 tissue samples from animals (Mus spp., Rattus spp., Dolichotis patagonum and Sus domesticus. Two samples were infected with L. borgpetersenii, two with L. interrogans and one with L. kirschneri. The possibility to detect and identify these pathogenic agents to the species level in domestic and wildlife animals reinforces the diagnostic information and will enhance our understanding of the epidemiology of leptopirosis.

  14. A gene to organism approach--assessing the impact of environmental pollution in eelpout (Zoarces viviparus) females and larvae.

    Science.gov (United States)

    Asker, Noomi; Carney Almroth, Bethanie; Albertsson, Eva; Coltellaro, Mariateresa; Bignell, John Paul; Hanson, Niklas; Scarcelli, Vittoria; Fagerholm, Björn; Parkkonen, Jari; Wijkmark, Emma; Frenzilli, Giada; Förlin, Lars; Sturve, Joachim

    2015-07-01

    A broad biomarker approach was applied to study the effects of marine pollution along the Swedish west coast using the teleost eelpout (Zoarces viviparus) as the sentinel species. Measurements were performed on different biological levels, from the molecular to the organismal, including measurements of messenger RNA (mRNA), proteins, cellular and tissue changes, and reproductive success. Results revealed that eelpout captured in Stenungsund had significantly higher hepatic ethoxyresorufin O-deethylase activity, high levels of both cytochrome P4501A and diablo homolog mRNA, and high prevalence of dead larvae and nuclear damage in erythrocytes. Eelpout collected in Göteborg harbor displayed extensive macrovesicular steatosis, whereby the majority of hepatocytes were affected throughout the liver, which could indicate an effect on lipid metabolism. Results also indicate that eelpouts collected at polluted sites might have an affected immune system, with lower mRNA expression of genes involved in the innate immune system and a higher number of lymphocytes. Biomarker assessment also was performed on livers dissected from unborn eelpout larvae collected from the ovary of the females. No significant differences were noted, which might indicate that the larvae to some extent are protected from effects of environmental pollutants. In conclusion, usage of the selected set of biological markers, covering responses from gene to organism, has demonstrated site-specific biomarker patterns that provided a broad and comprehensive picture of the impact of environmental stressors.

  15. Algorithmic approach for methyl-CpG binding protein 2 (MECP2) gene testing in patients with neurodevelopmental disabilities.

    Science.gov (United States)

    Sanmann, Jennifer N; Schaefer, G Bradley; Buehler, Bruce A; Sanger, Warren G

    2012-03-01

    Methyl-CpG binding protein 2 gene (MECP2) testing is indicated for patients with numerous clinical presentations, including Rett syndrome (classic and atypical), unexplained neonatal encephalopathy, Angelman syndrome, nonspecific mental retardation, autism (females), and an X-linked family history of developmental delay. Because of this complexity, a gender-specific approach for comprehensive MECP2 gene testing is described. Briefly, sequencing of exons 1 to 4 of MECP2 is recommended for patients with a Rett syndrome phenotype, unexplained neonatal encephalopathy, an Angelman syndrome phenotype (with negative 15q11-13 analysis), nonspecific mental retardation, or autism (females). Additional testing for large-scale MECP2 deletions is recommended for patients with Rett syndrome or Angelman syndrome phenotypes (with negative 15q11-13 analysis) following negative sequencing. Alternatively, testing for large-scale MECP2 duplications is recommended for males presenting with mental retardation, an X-linked family history of developmental delay, and a significant proportion of previously described clinical features (particularly a history of recurrent respiratory infections).

  16. The promoter competition assay (PCA): a new approach to identify motifs involved in the transcriptional activity of reporter genes.

    Science.gov (United States)

    Hube, Florent; Myal, Yvonne; Leygue, Etienne

    2006-05-01

    Identifying particular motifs responsible for promoter activity is a crucial step toward the development of new gene-based preventive and therapeutic strategies. However, to date, experimental methods to study promoter activity remain limited. We present in this report a promoter competition assay designed to identify, within a given promoter region, motifs critical for its activity. This assay consists in co-transfecting the promoter to be analyzed and double-stranded oligonucleotides which will compete for the binding of transcription factors. Using the recently characterized SBEM promoter as model, we first delineated the feasibility of the method and optimized the experimental conditions. We then identified, within an 87-bp region responsible for a strong expression of the reporter gene, an octamer-binding site essential for its transcriptional regulation. The importance of this motif has been confirmed by site-directed mutagenesis. The promoter competition assay appears to be a fast and efficient approach to identify, within a given promoter sequence, sites critical for its activity.

  17. Transcriptional Reactivation of the FMR1 Gene. A Possible Approach to the Treatment of the Fragile X Syndrome.

    Science.gov (United States)

    Tabolacci, Elisabetta; Palumbo, Federica; Nobile, Veronica; Neri, Giovanni

    2016-01-01

    Fragile X syndrome (FXS) is the most common cause of inherited intellectual disability, caused by CGG expansion over 200 repeats (full mutation, FM) at the 5' untranslated region (UTR) of the fragile X mental retardation 1 (FMR1) gene and subsequent DNA methylation of the promoter region, accompanied by additional epigenetic histone modifications that result in a block of transcription and absence of the fragile X mental retardation protein (FMRP). The lack of FMRP, involved in multiple aspects of mRNA metabolism in the brain, is thought to be the direct cause of the FXS phenotype. Restoration of FMR1 transcription and FMRP production can be obtained in vitro by treating FXS lymphoblastoid cell lines with the demethylating agent 5-azadeoxycytidine, demonstrating that DNA methylation is key to FMR1 inactivation. This concept is strengthened by the existence of rare male carriers of a FM, who are unable to methylate the FMR1 promoter. These individuals produce limited amounts of FMRP and are of normal intelligence. Their inability to methylate the FMR1 promoter, whose cause is not yet fully elucidated, rescues them from manifesting the FXS. These observations demonstrate that a therapeutic approach to FXS based on the pharmacological reactivation of the FMR1 gene is conceptually tenable and worthy of being further pursued. PMID:27548224

  18. Identification of bacteria associated with underground parts of Crocus sativus by 16S rRNA gene targeted metagenomic approach.

    Science.gov (United States)

    Ambardar, Sheetal; Sangwan, Naseer; Manjula, A; Rajendhran, J; Gunasekaran, P; Lal, Rup; Vakhlu, Jyoti

    2014-10-01

    Saffron (Crocus sativus L), an autumn-flowering perennial sterile plant, reproduces vegetatively by underground corms. Saffron has biannual corm-root cycle that makes it an interesting candidate to study microbial dynamics in its rhizosphere and cormosphere (area under influence of corm). Culture independent 16S rRNA gene metagenomic study of rhizosphere and cormosphere of Saffron during flowering stage revealed presence of 22 genera but none of the genus was common in all the three samples. Bulk soil bacterial community was represented by 13 genera with Acidobacteria being dominant. In rhizosphere, out of eight different genera identified, Pseudomonas was the most dominant genus. Cormosphere bacteria comprised of six different genera, dominated by the genus Pantoea. This study revealed that the bacterial composition of all the three samples is significantly different (P < 0.05) from each other. This is the first report on the identification of bacteria associated with rhizosphere, cormosphere and bulk soil of Saffron, using cultivation independent 16S rRNA gene targeted metagenomic approach.

  19. Expression profiling of 519 kinase genes in matched malignant peripheral nerve sheath tumor/plexiform neurofibroma samples is discriminatory and identifies mitotic regulators BUB1B, PBK and NEK2 as overexpressed with transformation.

    Science.gov (United States)

    Stricker, Thomas P; Henriksen, Kammi J; Tonsgard, James H; Montag, Anthony G; Krausz, Thomas N; Pytel, Peter

    2013-07-01

    About 50% of all malignant peripheral nerve sheath tumors (MPNSTs) arise as neurofibromatosis type 1 associated lesions. In those patients malignant peripheral nerve sheath tumors are thought to arise through malignant transformation of a preexisting plexiform neurofibroma. The molecular changes associated with this transformation are still poorly understood. We sought to test the hypothesis that dysregulation of expression of kinases contributes to this malignant transformation. We analyzed expression of all 519 kinase genes in the human genome using the nanostring nCounter system. Twelve cases of malignant peripheral nerve sheath tumor arising in a background of preexisting plexiform neurofibroma were included. Both components were separately sampled. Statistical analysis compared global changes in expression levels as well as changes observed in the pairwise comparison of samples taken from the same surgical specimen. Immunohistochemical studies were performed on tissue array slides to confirm expression of selected proteins. The expression pattern of kinase genes can separate malignant peripheral nerve sheath tumors and preexisting plexiform neurofibromas. The majority of kinase genes is downregulated rather than overexpressed with malignant transformation. The patterns of expression changes are complex without simple recurring alteration. Pathway analysis demonstrates that differentially expressed kinases are enriched for kinases involved in the direct regulation of mitosis, and several of these show increased expression in malignant peripheral nerve sheath tumors. Immunohistochemical studies for the mitotic regulators BUB1B, PBK and NEK2 confirm higher expression levels at the protein level. These results suggest that the malignant transformation of plexiform neurofibroma is associated with distinct changes in the expression of kinase genes. The patterns of these changes are complex and heterogeneous. There is no single unifying alteration. Kinases involved

  20. Acceptable Ungrammaticality in Sentence Matching

    Science.gov (United States)

    Duffield, Nigel; Matsuo, Ayumi; Roberts, Leah

    2007-01-01

    This article presents a new set of experiments using the "sentence-matching paradigm" (Forster, 1979; Freedman and Forster, 1985; see also Bley-Vroman and Masterson, 1989), investigating native speakers' and second language (L2) learners' knowledge of constraints on clitic placement in French. Our purpose is three-fold: (1) to shed more light on…