WorldWideScience

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...... including treatments, mutations and pathogen infections. Similarly, drugs may be discovered by the relationship between the transcript profiles effectuated or impacted by a candidate drug and by the target disease. The integration of such data enables systems biology to predict the interplay between...

  3. 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...... key issues: pattern classes, similiarity types and mathing methods. It has been shown that the techniques and approaches are as diverse and varied as the applications....

  4. 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.

  5. 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

  6. 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.

  7. MATCHING ALTERNATIVE ADDRESSES: A SEMANTIC WEB APPROACH

    Directory of Open Access Journals (Sweden)

    S. Ariannamazi

    2015-12-01

    Full Text Available 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.

  8. 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.

  9. 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 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 ...

  10. 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

  11. 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.

  12. Matching sensors to missions using a knowledge-based approach

    Science.gov (United States)

    Preece, Alun; Gomez, Mario; de Mel, Geeth; Vasconcelos, Wamberto; Sleeman, Derek; Colley, Stuart; Pearson, Gavin; Pham, Tien; La Porta, Thomas

    2008-04-01

    Making decisions on how best to utilise limited intelligence, surveillance and reconnaisance (ISR) resources is a key issue in mission planning. This requires judgements about which kinds of available sensors are more or less appropriate for specific ISR tasks in a mission. A methodological approach to addressing this kind of decision problem in the military context is the Missions and Means Framework (MMF), which provides a structured way to analyse a mission in terms of tasks, and assess the effectiveness of various means for accomplishing those tasks. Moreover, the problem can be defined as knowledge-based matchmaking: matching the ISR requirements of tasks to the ISR-providing capabilities of available sensors. In this paper we show how the MMF can be represented formally as an ontology (that is, a specification of a conceptualisation); we also represent knowledge about ISR requirements and sensors, and then use automated reasoning to solve the matchmaking problem. We adopt the Semantic Web approach and the Web Ontology Language (OWL), allowing us to import elements of existing sensor knowledge bases. Our core ontologies use the description logic subset of OWL, providing efficient reasoning. We describe a prototype tool as a proof-of-concept for our approach. We discuss the various kinds of possible sensor-mission matches, both exact and inexact, and how the tool helps mission planners consider alternative choices of sensors.

  13. 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

    Social services make the most use of the user profile matching to help the users to discover friends with similar social attributes (e.g. interests, location, age). However, there are many privacy concerns that prevent to enable this functionality. Privacy preserving encryption is not suitable...... 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....

  14. 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

  15. A bayesian approach to deformed pattern matching of iris images.

    Science.gov (United States)

    Thornton, Jason; Savvides, Marios; Vijaya Kumar, B V K

    2007-04-01

    We describe a general probabilistic framework for matching patterns that experience in-plane nonlinear deformations, such as iris patterns. Given a pair of images, we derive a maximum a posteriori probability (MAP) estimate of the parameters of the relative deformation between them. Our estimation process accomplishes two things simultaneously: It normalizes for pattern warping and it returns a distortion-tolerant similarity metric which can be used for matching two nonlinearly deformed image patterns. The prior probability of the deformation parameters is specific to the pattern-type and, therefore, should result in more accurate matching than an arbitrary general distribution. We show that the proposed method is very well suited for handling iris biometrics, applying it to two databases of iris images which contain real instances of warped patterns. We demonstrate a significant improvement in matching accuracy using the proposed deformed Bayesian matching methodology. We also show that the additional computation required to estimate the deformation is relatively inexpensive, making it suitable for real-time applications.

  16. Synoname: The Getty's New Approach to Pattern Matching for Personal Names.

    Science.gov (United States)

    Siegfried, Susan L.; Bernstein, Julie

    1991-01-01

    Describes "Synoname," the Getty Museum's computer program that matches varying versions of personal names for research purposes. Reports that the program uses an ordered algorithm sequence for pattern matching that includes both character- and word-matching techniques. Concludes that the technique can approach near-total accuracy at the…

  17. 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

    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...... 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...

  18. 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.

  19. A network approach in analysis of the matching hypothesis

    Science.gov (United States)

    Jia, Tao; Spivey, Robert; Korniss, Gyorgy; Szymanski, Boleslaw

    2014-03-01

    The matching hypothesis in social psychology claimed that people are more likely to form a committed relationship with someone who is equally attractive. This phenomenon can be well interpreted by the principle of homophily that people are apt to get in touch with others similar to them. Yet, social experiments indicate that people in general tend to prefer more attractive individuals regardless of their own attractiveness. Here study the stochastic matching process for different underlying networks and different attractiveness distributions. We showed that the correlation of attractiveness within couples could purely due to the limited number of acquaintance each person has and such correlation decreases as the network becomes more sparse. We also analyzed the effect of the degree distribution and the attractiveness on the number of individuals that can not find their partners. This work is supported by ARL NS-CTA, ARO, and ONR.

  20. Mutual Fund Style, Characteristic-Matched Performance Benchmarks and Activity Measures: A New Approach

    OpenAIRE

    Daniel Buncic; Jon E. Eggins; Robert J. Hill

    2010-01-01

    We propose a new approach for measuring mutual fund style and constructing characteristic-matched performance benchmarks that requires only portfolio holdings and two reference portfolios in each style dimension. The characteristic-matched performance benchmark literature typically follows a bottom-up approach by first matching individual stocks with benchmarks and then obtaining a portfolio’s excess return as a weighted average of the excess returns on each of its constituent stocks. Our app...

  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. 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.

  5. 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.

  6. A matching approach to communicate through the plasma sheath surrounding a hypersonic vehicle

    Energy Technology Data Exchange (ETDEWEB)

    Gao, Xiaotian; Jiang, Binhao, E-mail: jiangbh@hit.edu.cn [Harbin Institute of Technology, 92 West Dazhi Street, Nan Gang District, Harbin (China)

    2015-06-21

    In order to overcome the communication blackout problem suffered by hypersonic vehicles, a matching approach has been proposed for the first time in this paper. It utilizes a double-positive (DPS) material layer surrounding a hypersonic vehicle antenna to match with the plasma sheath enclosing the vehicle. Analytical analysis and numerical results indicate a resonance between the matched layer and the plasma sheath will be formed to mitigate the blackout problem in some conditions. The calculated results present a perfect radiated performance of the antenna, when the match is exactly built between these two layers. The effects of the parameters of the plasma sheath have been researched by numerical methods. Based on these results, the proposed approach is easier to realize and more flexible to the varying radiated conditions in hypersonic flight comparing with other methods.

  7. AN INTEGRATED RANSAC AND GRAPH BASED MISMATCH ELIMINATION APPROACH FOR WIDE-BASELINE IMAGE MATCHING

    Directory of Open Access Journals (Sweden)

    M. Hasheminasab

    2015-12-01

    Full Text Available In this paper we propose an integrated approach in order to increase the precision of feature point matching. Many different algorithms have been developed as to optimizing the short-baseline image matching while because of illumination differences and viewpoints changes, wide-baseline image matching is so difficult to handle. Fortunately, the recent developments in the automatic extraction of local invariant features make wide-baseline image matching possible. The matching algorithms which are based on local feature similarity principle, using feature descriptor as to establish correspondence between feature point sets. To date, the most remarkable descriptor is the scale-invariant feature transform (SIFT descriptor , which is invariant to image rotation and scale, and it remains robust across a substantial range of affine distortion, presence of noise, and changes in illumination. The epipolar constraint based on RANSAC (random sample consensus method is a conventional model for mismatch elimination, particularly in computer vision. Because only the distance from the epipolar line is considered, there are a few false matches in the selected matching results based on epipolar geometry and RANSAC. Aguilariu et al. proposed Graph Transformation Matching (GTM algorithm to remove outliers which has some difficulties when the mismatched points surrounded by the same local neighbor structure. In this study to overcome these limitations, which mentioned above, a new three step matching scheme is presented where the SIFT algorithm is used to obtain initial corresponding point sets. In the second step, in order to reduce the outliers, RANSAC algorithm is applied. Finally, to remove the remained mismatches, based on the adjacent K-NN graph, the GTM is implemented. Four different close range image datasets with changes in viewpoint are utilized to evaluate the performance of the proposed method and the experimental results indicate its robustness and

  8. 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.``

  9. 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.

  10. 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.

  11. 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.

  12. Public-Private Wage Gap In Latin America (1999-2007): A Matching Approach

    OpenAIRE

    Alejandra Mizala; Pilar Romaguera; Sebastian Gallegos

    2010-01-01

    Using matching methods, we estimate the public-private wage gap in seven Latin American countries—Argentina, Bolivia, Brazil, Chile, Costa Rica, Paraguay and Uruguay—for the years 1999 and 2007. These methods do not require any estimation of earnings equations and hence no validity-out-of-the-support assumptions; furthermore, this approach allows us to estimate not only the average wage gap but also its distribution. Our main findings indicate that the average public sector worker earns more ...

  13. A polytomous conditional likelihood approach for combining matched and unmatched case-control studies.

    Science.gov (United States)

    Gebregziabher, Mulugeta; Guimaraes, Paulo; Cozen, Wendy; Conti, David V

    2010-04-30

    In genetic association studies it is becoming increasingly imperative to have large sample sizes to identify and replicate genetic effects. To achieve these sample sizes, many research initiatives are encouraging the collaboration and combination of several existing matched and unmatched case-control studies. Thus, it is becoming more common to compare multiple sets of controls with the same case group or multiple case groups to validate or confirm a positive or negative finding. Usually, a naive approach of fitting separate models for each case-control comparison is used to make inference about disease-exposure association. But, this approach does not make use of all the observed data and hence could lead to inconsistent results. The problem is compounded when a common case group is used in each case-control comparison. An alternative to fitting separate models is to use a polytomous logistic model but, this model does not combine matched and unmatched case-control data. Thus, we propose a polytomous logistic regression approach based on a latent group indicator and a conditional likelihood to do a combined analysis of matched and unmatched case-control data. We use simulation studies to evaluate the performance of the proposed method and a case-control study of multiple myeloma and Inter-Leukin-6 as an example. Our results indicate that the proposed method leads to a more efficient homogeneity test and a pooled estimate with smaller standard error.

  14. A robust approach to optimal matched filter design in ultrasonic non-destructive evaluation (NDE)

    Science.gov (United States)

    Li, Minghui; Hayward, Gordon

    2017-02-01

    The matched filter was demonstrated to be a powerful yet efficient technique to enhance defect detection and imaging in ultrasonic non-destructive evaluation (NDE) of coarse grain materials, provided that the filter was properly designed and optimized. In the literature, in order to accurately approximate the defect echoes, the design utilized the real excitation signals, which made it time consuming and less straightforward to implement in practice. In this paper, we present a more robust and flexible approach to optimal matched filter design using the simulated excitation signals, and the control parameters are chosen and optimized based on the real scenario of array transducer, transmitter-receiver system response, and the test sample, as a result, the filter response is optimized and depends on the material characteristics. Experiments on industrial samples are conducted and the results confirm the great benefits of the method.

  15. 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.

  16. 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.

  17. 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.

  18. A pattern matching approach for the estimation of alignment between any two given DNA sequences.

    Science.gov (United States)

    Basu, K; Sriraam, N; Richard, R J A

    2007-08-01

    For a given DNA sequence, it is well known that pair wise alignment schemes are used to determine the similarity with the DNA sequences available in the databanks. The efficiency of the alignment decides the type of amino acids and its corresponding proteins. In order to evaluate the given DNA sequence for its proteomic identity, a pattern matching approach is proposed in this paper. A block based semi-global alignment scheme is introduced to determine the similarity between the DNA sequences (known and given). The two DNA sequences are divided into blocks of equal length and alignment is performed which minimizes the computational complexity. The efficiency of the alignment scheme is evaluated using the parameter, percentage of similarity (POS). Four essential DNA version of the amino acids that emphasize the importance of proteomic functionalities are chosen as patterns and matching is performed with the known and given DNA sequences to determine the similarity between them. The ratio of amino acid counts between the two sequences is estimated and the results are compared with that of the POS value. It is found from the experimental results that higher the POS value and the pattern matching higher are the similarity between the two DNA sequences. The optimal block is also identified based on the POS value and amino acids count.

  19. 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.

  20. 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.

  1. 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

  2. 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.

  3. 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

  4. Gene therapy in peripheral nerve reconstruction approaches.

    Science.gov (United States)

    Haastert, Kirsten; Grothe, Claudia

    2007-06-01

    Gene transfer to a transected peripheral nerve or avulsed nerve root is discussed to be helpful where neurosurgical peripheral nerve reconstruction alone will not result in full recovery of function. Axonal regeneration is supposed to be facilitated by this new therapeutic approach via delivery of specific regeneration promoting molecules as well as survival proteins for the injured sensory and motor neurons. Therefore gene therapy aims in long-term and site-specific delivery of those neurotrophic factors. This paper reviews methods and perspectives for gene therapy to promote functional recovery of severely injured and thereafter reconstructed peripheral nerves. Experimental in vivo and ex vivo gene therapy approaches are reported by different groups. In vivo gene therapy generally uses direct injection of cDNA vectors to injured peripheral nerves. Ex vivo gene therapy is based on the isolation of autologous cells followed by genetic modification of these cells in vitro and re-transplantation of the modified cells to the patient as part of tissue engineered nerve transplants. Vectors of different origin are published to be suitable for peripheral nerve gene therapy and this review discusses the different strategies with regard to their efficiency in gene transfer, their risks and their potential relevance for clinical application.

  5. A new approach of QRS complex detection based on matched filtering and triangle character analysis.

    Science.gov (United States)

    Li, Yanjun; Yan, Hong; Hong, Feng; Song, Jinzhong

    2012-09-01

    QRS complex detection usually provides the fundamentals to automated electrocardiogram (ECG) analysis. In this paper, a new approach of QRS complex detection without the stage of noise suppression was developed and evaluated, which was based on the combination of two techniques: matched filtering and triangle character analysis. Firstly, a template of QRS complex was selected automatically by the triangle character in ECG, and then it was time-reversed after removing its direct current component. Secondly, matched filtering was implemented at low computational cost by finite impulse response, which further enhanced QRS complex and attenuated non-QRS regions containing P-wave, T-wave and various noise components. Subsequently, triangle structure-based threshold decision was processed to detect QRS complexes. And RR intervals and triangle structures were further analyzed for the reduction of false-positive and false-negative detections. Finally, the performance of the proposed algorithm was tested on all 48 records of the MIT-BIH Arrhythmia Database. The results demonstrated that the detection rate reached 99.62 %, the sensitivity got 99.78 %, and the positive prediction was 99.85 %. In addition, the proposed method was able to identify QRS complexes reliably even under the condition of poor signal quality.

  6. CLARREO Approach for Reference Intercalibration of Reflected Solar Sensors: On-Orbit Data Matching and Sampling

    Science.gov (United States)

    Roithmayr, Carlos; Lukashin, Constantine; Speth, Paul W.; Kopp, Gregg; Thome, Kurt; Wielicki, Bruce A.; Young, David F.

    2014-01-01

    The implementation of the Climate Absolute Radiance and Refractivity Observatory (CLARREO) mission was recommended by the National Research Council in 2007 to provide an on-orbit intercalibration standard with accuracy of 0.3% (k = 2) for relevant Earth observing sensors. The goal of reference intercalibration, as established in the Decadal Survey, is to enable rigorous high-accuracy observations of critical climate change parameters, including reflected broadband radiation [Clouds and Earth's Radiant Energy System (CERES)], cloud properties [Visible Infrared Imaging Radiometer Suite (VIIRS)], and changes in surface albedo, including snow and ice albedo feedback. In this paper, we describe the CLARREO approach for performing intercalibration on orbit in the reflected solar (RS) wavelength domain. It is based on providing highly accurate spectral reflectance and reflected radiance measurements from the CLARREO Reflected Solar Spectrometer (RSS) to establish an on-orbit reference for existing sensors, namely, CERES and VIIRS on Joint Polar Satellite System satellites, Advanced Very High Resolution Radiometer and follow-on imagers on MetOp, Landsat imagers, and imagers on geostationary platforms. One of two fundamental CLARREO mission goals is to provide sufficient sampling of high-accuracy observations that are matched in time, space, and viewing angles with measurements made by existing instruments, to a degree that overcomes the random error sources from imperfect data matching and instrument noise. The data matching is achieved through CLARREO RSS pointing operations on orbit that align its line of sight with the intercalibrated sensor. These operations must be planned in advance; therefore, intercalibration events must be predicted by orbital modeling. If two competing opportunities are identified, one target sensor must be given priority over the other. The intercalibration method is to monitor changes in targeted sensor response function parameters: effective

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. Gene therapy in glaucoma-3: Therapeutic approaches.

    Science.gov (United States)

    Mahdy, Mohamed Abdel-Monem Soliman

    2010-09-01

    Despite new and improving diagnostic and therapeutic options for glaucoma, blindness from glaucoma is increasing and glaucoma remains a major public health problem. The role of heredity in ocular disease including glaucoma is attracting greater attention as the knowledge and recent advances of Human Genome Project and the HapMap Project have made genetic analysis of many human disorders possible.Glaucoma offers a variety of potential targets for gene therapy. All risk factors for glaucoma and their underlying causes are potentially susceptible to modulation by gene transfer. As genetic defects responsible for glaucoma are identified and the biochemical mechanisms underlying the disease are recognized, new methods of therapy can be developed. Genetic tests are indicated for treatment, diagnosis, prognosis, counseling, and research purposes; however, there is significant overlap among them. One of the important genetic tests for glaucoma is OcuGene. Therefore, it is of utmost importance for the glaucoma specialists to be familiar with and understand the basic molecular mechanisms, genes responsible for glaucoma, and the ways of genetic treatment.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.

  15. 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.

  16. 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.

  17. A Match-based approach to the estimation of polar stratospheric ozone loss using Aura Microwave Limb Sounder observations

    Directory of Open Access Journals (Sweden)

    N. J. Livesey

    2015-04-01

    Full Text Available The well-established "Match" approach to quantifying chemical destruction of ozone in the polar lower stratosphere is applied to ozone observations from the Microwave Limb Sounder (MLS on NASA's Aura spacecraft. Quantification of ozone loss requires distinguishing transport- and chemically induced changes in ozone abundance. This is accomplished in the Match approach by examining cases where trajectories indicate that the same airmass has been observed on multiple occasions. The method was pioneered using ozone sonde observations, for which hundreds of matched ozone observations per winter are typically available. The dense coverage of the MLS measurements, particularly at polar latitudes, allows matches to be made to thousands of observations each day. This study is enabled by recently developed MLS Lagrangian Trajectory Diagnostic (LTD support products. Sensitivity studies indicate that the largest influence on the ozone loss estimates are the value of potential vorticity (PV used to define the edge of the polar vortex (within which matched observations must lie and the degree to which the PV of an airmass is allowed to vary between matched observations. Applying Match calculations to MLS observations of nitrous oxide, a long-lived tracer whose expected rate of change on these timescales is negligible, enables quantification of the impact of transport errors on the Match-based ozone loss estimates. Our loss estimates are generally in agreement with previous estimates for selected Arctic winters, though indicating smaller losses than many other studies. Arctic ozone losses are greatest during the 2010/11 winter, as seen in prior studies, with 2.0 ppmv (parts per million by volume loss estimated at 450 K potential temperature. As expected, Antarctic winter ozone losses are consistently greater than those for the Arctic, with less interannual variability (e.g., ranging between 2.3 and 3.0 ppmv at 450 K. This study exemplifies the insights into

  18. A Match-based approach to the estimation of polar stratospheric ozone loss using Aura Microwave Limb Sounder observations

    Science.gov (United States)

    Livesey, N. J.; Santee, M. L.; Manney, G. L.

    2015-09-01

    The well-established "Match" approach to quantifying chemical destruction of ozone in the polar lower stratosphere is applied to ozone observations from the Microwave Limb Sounder (MLS) on NASA's Aura spacecraft. Quantification of ozone loss requires distinguishing transport- and chemically induced changes in ozone abundance. This is accomplished in the Match approach by examining cases where trajectories indicate that the same air mass has been observed on multiple occasions. The method was pioneered using ozonesonde observations, for which hundreds of matched ozone observations per winter are typically available. The dense coverage of the MLS measurements, particularly at polar latitudes, allows matches to be made to thousands of observations each day. This study is enabled by recently developed MLS Lagrangian trajectory diagnostic (LTD) support products. Sensitivity studies indicate that the largest influence on the ozone loss estimates are the value of potential vorticity (PV) used to define the edge of the polar vortex (within which matched observations must lie) and the degree to which the PV of an air mass is allowed to vary between matched observations. Applying Match calculations to MLS observations of nitrous oxide, a long-lived tracer whose expected rate of change is negligible on the weekly to monthly timescales considered here, enables quantification of the impact of transport errors on the Match-based ozone loss estimates. Our loss estimates are generally in agreement with previous estimates for selected Arctic winters, though indicating smaller losses than many other studies. Arctic ozone losses are greatest during the 2010/11 winter, as seen in prior studies, with 2.0 ppmv (parts per million by volume) loss estimated at 450 K potential temperature (~ 18 km altitude). As expected, Antarctic winter ozone losses are consistently greater than those for the Arctic, with less interannual variability (e.g., ranging between 2.3 and 3.0 ppmv at 450 K). This

  19. A Match-based approach to the estimation of polar stratospheric ozone loss using Aura Microwave Limb Sounder observations

    Directory of Open Access Journals (Sweden)

    N. J. Livesey

    2015-09-01

    Full Text Available The well-established "Match" approach to quantifying chemical destruction of ozone in the polar lower stratosphere is applied to ozone observations from the Microwave Limb Sounder (MLS on NASA's Aura spacecraft. Quantification of ozone loss requires distinguishing transport- and chemically induced changes in ozone abundance. This is accomplished in the Match approach by examining cases where trajectories indicate that the same air mass has been observed on multiple occasions. The method was pioneered using ozonesonde observations, for which hundreds of matched ozone observations per winter are typically available. The dense coverage of the MLS measurements, particularly at polar latitudes, allows matches to be made to thousands of observations each day. This study is enabled by recently developed MLS Lagrangian trajectory diagnostic (LTD support products. Sensitivity studies indicate that the largest influence on the ozone loss estimates are the value of potential vorticity (PV used to define the edge of the polar vortex (within which matched observations must lie and the degree to which the PV of an air mass is allowed to vary between matched observations. Applying Match calculations to MLS observations of nitrous oxide, a long-lived tracer whose expected rate of change is negligible on the weekly to monthly timescales considered here, enables quantification of the impact of transport errors on the Match-based ozone loss estimates. Our loss estimates are generally in agreement with previous estimates for selected Arctic winters, though indicating smaller losses than many other studies. Arctic ozone losses are greatest during the 2010/11 winter, as seen in prior studies, with 2.0 ppmv (parts per million by volume loss estimated at 450 K potential temperature (~ 18 km altitude. As expected, Antarctic winter ozone losses are consistently greater than those for the Arctic, with less interannual variability (e.g., ranging between 2.3 and 3.0 ppmv at

  20. 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...

  1. The matching pursuit approach based on the modulated Gaussian pulse for efficient guided-wave damage inspection

    Science.gov (United States)

    Hong, Jin-Chul; Sun, Kyung Ho; Kim, Yoon Young

    2005-08-01

    The success of the guided-wave damage inspection technology depends not only on the generation and measurement of desired waveforms but also on the signal processing of the measured waves, but less attention has been paid to the latter. This research aims to develop an efficient signal processing technique especially suitable for the current guided-wave technology. To achieve this objective, the use of a two-stage matching pursuit approach based on the Gabor dictionary is proposed. Instead of truncated sine pulses commonly used in waveguide inspection, Gabor pulses, the modulated Gaussian pulses, are chosen as the elastic energy carrier to facilitate the matching pursuit algorithm. To extract meaningful waves out of noisy signals, a two-stage matching pursuit strategy is developed, which consists of the following: rough approximations with a set of predetermined parameters characterizing the Gabor pulse, and fine adjustments of the parameters by optimization. The parameters estimated from measured longitudinal elastic waves can be then directly used to assess not only the location but also the size of a crack in a rod. For the estimation of the crack size, in particular, Love's theory is incorporated in the matching pursuit analysis. Several experiments were conducted to verify the validity of the proposed approach in damage assessment.

  2. 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…

  3. 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.

  4. 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

  5. A zero-one programming approach to Gulliksen's matched random subtests method

    NARCIS (Netherlands)

    Linden, van der Wim J.; Boekkooi-Timminga, Ellen

    1988-01-01

    Gulliksen’s matched random subtests method is a graphical method to split a test into parallel test halves. The method has practical relevance because it maximizes coefficient α as a lower bound to the classical test reliability coefficient. In this paper the same problem is formulated as a zero-one

  6. 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

  7. A robust data-driven approach for gene ontology annotation.

    Science.gov (United States)

    Li, Yanpeng; Yu, Hong

    2014-01-01

    Gene ontology (GO) and GO annotation are important resources for biological information management and knowledge discovery, but the speed of manual annotation became a major bottleneck of database curation. BioCreative IV GO annotation task aims to evaluate the performance of system that automatically assigns GO terms to genes based on the narrative sentences in biomedical literature. This article presents our work in this task as well as the experimental results after the competition. For the evidence sentence extraction subtask, we built a binary classifier to identify evidence sentences using reference distance estimator (RDE), a recently proposed semi-supervised learning method that learns new features from around 10 million unlabeled sentences, achieving an F1 of 19.3% in exact match and 32.5% in relaxed match. In the post-submission experiment, we obtained 22.1% and 35.7% F1 performance by incorporating bigram features in RDE learning. In both development and test sets, RDE-based method achieved over 20% relative improvement on F1 and AUC performance against classical supervised learning methods, e.g. support vector machine and logistic regression. For the GO term prediction subtask, we developed an information retrieval-based method to retrieve the GO term most relevant to each evidence sentence using a ranking function that combined cosine similarity and the frequency of GO terms in documents, and a filtering method based on high-level GO classes. The best performance of our submitted runs was 7.8% F1 and 22.2% hierarchy F1. We found that the incorporation of frequency information and hierarchy filtering substantially improved the performance. In the post-submission evaluation, we obtained a 10.6% F1 using a simpler setting. Overall, the experimental analysis showed our approaches were robust in both the two tasks.

  8. The active disturbance rejection control approach to stabilisation of coupled heat and ODE system subject to boundary control matched disturbance

    Science.gov (United States)

    Guo, Bao-Zhu; Liu, Jun-Jun; AL-Fhaid, A. S.; Younas, Arshad Mahmood M.; Asiri, Asim

    2015-08-01

    We consider stabilisation for a linear ordinary differential equation system with input dynamics governed by a heat equation, subject to boundary control matched disturbance. The active disturbance rejection control approach is applied to estimate, in real time, the disturbance with both constant high gain and time-varying high gain. The disturbance is cancelled in the feedback loop. The closed-loop systems with constant high gain and time-varying high gain are shown, respectively, to be practically stable and asymptotically stable.

  9. 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.

  10. Output feedback model matching in linear impulsive systems with control feedthrough: a structural approach

    Science.gov (United States)

    Zattoni, Elena

    2017-01-01

    This paper investigates the problem of structural model matching by output feedback in linear impulsive systems with control feedthrough. Namely, given a linear impulsive plant, possibly featuring an algebraic link from the control input to the output, and given a linear impulsive model, the problem consists in finding a linear impulsive regulator that achieves exact matching between the respective forced responses of the linear impulsive plant and of the linear impulsive model, for all the admissible input functions and all the admissible sequences of jump times, by means of a dynamic feedback of the plant output. The problem solvability is characterized by a necessary and sufficient condition. The regulator synthesis is outlined through the proof of sufficiency, which is constructive.

  11. Different approaches to generate matching effects using arrays in contact with superconducting films.

    Science.gov (United States)

    del Valle, J.; Gomez, A.; Luis-Hita, J.; Rollano, V.; Gonzalez, E. M.; Vicent, J. L.

    2017-02-01

    Superconducting films in contact with non-superconducting regular arrays can exhibit commensurability effects between the vortex lattice and the unit cell of the pinning array. These matching effects yield a slowdown of the vortex flow and the corresponding dissipation decrease. The superconducting samples are Nb films grown on Si substrates. We have studied these matching effects with the array on top, embedded or threading the Nb superconducting films and using different materials (Si, Cu, Ni, Py dots and dots fabricated with Co/Pd multilayers). These hybrids allow for studying the contribution of different pinning potentials to the matching effects. The main findings are: (i) Periodic roughness induced in the superconducting film is enough to generate resistivity minima; (ii) A minor effect is achieved by magnetic pinning from periodic magnetic field potentials obtained by dots with out of plane magnetization grown on top of the superconducting film, (iii) In the case of array of magnetic dots embedded in the films, vortex flow probes the magnetic state; i.e. magnetoresistance measurements detect the magnetic state of very small nanomagnets. In addition, we have studied the role played by the local order in the commensurability effects. This was attained using an array that mimics a smectic crystal. We have found that preserving the local order is crucial. If the local order is not retained the magnetoresistance minima vanish.

  12. Online tuning of impedance matching circuit for long pulse inductively coupled plasma source operation--an alternate approach.

    Science.gov (United States)

    Sudhir, Dass; Bandyopadhyay, M; Kraus, W; Gahlaut, A; Bansal, G; Chakraborty, A

    2014-01-01

    Impedance matching circuit between radio frequency (RF) generator and the plasma load, placed between them, determines the RF power transfer from RF generator to the plasma load. The impedance of plasma load depends on the plasma parameters through skin depth and plasma conductivity or resistivity. Therefore, for long pulse operation of inductively coupled plasmas, particularly for high power (∼100 kW or more) where plasma load condition may vary due to different reasons (e.g., pressure, power, and thermal), online tuning of impedance matching circuit is necessary through feedback. In fusion grade ion source operation, such online methodology through feedback is not present but offline remote tuning by adjusting the matching circuit capacitors and tuning the driving frequency of the RF generator between the ion source operation pulses is envisaged. The present model is an approach for remote impedance tuning methodology for long pulse operation and corresponding online impedance matching algorithm based on RF coil antenna current measurement or coil antenna calorimetric measurement may be useful in this regard.

  13. 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.

  14. Gene transfer approaches in cancer immunotherapy.

    Science.gov (United States)

    Larin, S S; Georgiev, G P; Kiselev, S L

    2004-10-01

    The idea of enhancing or establishing effective immune response against endogenously developed tumor cells is not novel. More than a hundred years ago, bacterial components were used to develop antitumor immune response. Later, when a number of immune system-effecting cytokines had been discovered, they were used for systemic treatment of cancer patients. However, systemic treatment often resulted in even negative outcome. Recent developments of genetic approaches of cell modifications allowed developing of modern techniques of targeted tumor cell elimination. In the present paper, we review modern trends of the antitumor response enhancement based on immunoregulatory gene transfer into different cell types both in vivo and in vitro. Almost all these approaches are based on the activation of the adaptive arm of the immune system in response to tumor cells. However, recent studies indicate that the innate arm of the immune system, as well as adaptive arm, is involved in tumor suppression. The innate immune system uses nonrearranging germline receptors, which could trigger cellular effector responses that are conditional (or instructive) to the subsequent adaptive immune response. Last years' viewpoints on 'self' and 'non-self' recognition and primary induction of the immune response have changed. The key role of lymphocytes is pathogen recognition and, following immune response induction, switched on the central role of dendritic cells in 'non-self' recognition and induction of both innate and adaptive responses. Moreover, innate response is supposed to be an essential starting point in induction of successful and effective acquired response. Most cancer vaccines do not have 'non-self' marks presentation due to their endogenous origin, thus lacking their effectiveness in the induction of the specific long-lasting immune response. Taking this point into consideration, we can conclude that to make cancer vaccine more effective we have to present tumor antigens

  15. 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

  16. 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

  17. 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...

  18. Appraisal, coping, emotion, and performance during elite fencing matches: a random coefficient regression model approach.

    Science.gov (United States)

    Doron, J; Martinent, G

    2016-06-23

    Understanding more about the stress process is important for the performance of athletes during stressful situations. Grounded in Lazarus's (1991, 1999, 2000) CMRT of emotion, this study tracked longitudinally the relationships between cognitive appraisal, coping, emotions, and performance in nine elite fencers across 14 international matches (representing 619 momentary assessments) using a naturalistic, video-assisted methodology. A series of hierarchical linear modeling analyses were conducted to: (a) explore the relationships between cognitive appraisals (challenge and threat), coping strategies (task- and disengagement oriented coping), emotions (positive and negative) and objective performance; (b) ascertain whether the relationship between appraisal and emotion was mediated by coping; and (c) examine whether the relationship between appraisal and objective performance was mediated by emotion and coping. The results of the random coefficient regression models showed: (a) positive relationships between challenge appraisal, task-oriented coping, positive emotions, and performance, as well as between threat appraisal, disengagement-oriented coping and negative emotions; (b) that disengagement-oriented coping partially mediated the relationship between threat and negative emotions, whereas task-oriented coping partially mediated the relationship between challenge and positive emotions; and (c) that disengagement-oriented coping mediated the relationship between threat and performance, whereas task-oriented coping and positive emotions partially mediated the relationship between challenge and performance. As a whole, this study furthered knowledge during sport performance situations of Lazarus's (1999) claim that these psychological constructs exist within a conceptual unit. Specifically, our findings indicated that the ways these constructs are inter-related influence objective performance within competitive settings.

  19. Matching for the nonconventional MHC-I MICA gene significantly reduces the incidence of acute and chronic GVHD.

    Science.gov (United States)

    Carapito, Raphael; Jung, Nicolas; Kwemou, Marius; Untrau, Meiggie; Michel, Sandra; Pichot, Angélique; Giacometti, Gaëlle; Macquin, Cécile; Ilias, Wassila; Morlon, Aurore; Kotova, Irina; Apostolova, Petya; Schmitt-Graeff, Annette; Cesbron, Anne; Gagne, Katia; Oudshoorn, Machteld; van der Holt, Bronno; Labalette, Myriam; Spierings, Eric; Picard, Christophe; Loiseau, Pascale; Tamouza, Ryad; Toubert, Antoine; Parissiadis, Anne; Dubois, Valérie; Lafarge, Xavier; Maumy-Bertrand, Myriam; Bertrand, Frédéric; Vago, Luca; Ciceri, Fabio; Paillard, Catherine; Querol, Sergi; Sierra, Jorge; Fleischhauer, Katharina; Nagler, Arnon; Labopin, Myriam; Inoko, Hidetoshi; von dem Borne, Peter A; Kuball, Jürgen; Ota, Masao; Katsuyama, Yoshihiko; Michallet, Mauricette; Lioure, Bruno; Peffault de Latour, Régis; Blaise, Didier; Cornelissen, Jan J; Yakoub-Agha, Ibrahim; Claas, Frans; Moreau, Philippe; Milpied, Noël; Charron, Dominique; Mohty, Mohamad; Zeiser, Robert; Socié, Gérard; Bahram, Seiamak

    2016-10-13

    Graft-versus-host disease (GVHD) is among the most challenging complications in unrelated donor hematopoietic cell transplantation (HCT). The highly polymorphic MHC class I chain-related gene A, MICA, encodes a stress-induced glycoprotein expressed primarily on epithelia. MICA interacts with the invariant activating receptor NKG2D, expressed by cytotoxic lymphocytes, and is located in the MHC, next to HLA-B Hence, MICA has the requisite attributes of a bona fide transplantation antigen. Using high-resolution sequence-based genotyping of MICA, we retrospectively analyzed the clinical effect of MICA mismatches in a multicenter cohort of 922 unrelated donor HLA-A, HLA-B, HLA-C, HLA-DRB1, and HLA-DQB1 10/10 allele-matched HCT pairs. Among the 922 pairs, 113 (12.3%) were mismatched in MICA MICA mismatches were significantly associated with an increased incidence of grade III-IV acute GVHD (hazard ratio [HR], 1.83; 95% confidence interval [CI], 1.50-2.23; P < .001), chronic GVHD (HR, 1.50; 95% CI, 1.45-1.55; P < .001), and nonelapse mortality (HR, 1.35; 95% CI, 1.24-1.46; P < .001). The increased risk for GVHD was mirrored by a lower risk for relapse (HR, 0.50; 95% CI, 0.43-0.59; P < .001), indicating a possible graft-versus-leukemia effect. In conclusion, when possible, selecting a MICA-matched donor significantly influences key clinical outcomes of HCT in which a marked reduction of GVHD is paramount. The tight linkage disequilibrium between MICA and HLA-B renders identifying a MICA-matched donor readily feasible in clinical practice.

  20. 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

  1. 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

  2. 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.

  3. A predictive approach to identify genes differentially expressed

    Science.gov (United States)

    Saraiva, Erlandson F.; Louzada, Francisco; Milan, Luís A.; Meira, Silvana; Cobre, Juliana

    2012-10-01

    The main objective of gene expression data analysis is to identify genes that present significant changes in expression levels between a treatment and a control biological condition. In this paper, we propose a Bayesian approach to identify genes differentially expressed calculating credibility intervals from predictive densities which are constructed using 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 indicate 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 publicly available data set on Escherichia coli bacteria.

  4. Pattern matching

    NARCIS (Netherlands)

    A. Hak (Tony); J. Dul (Jan)

    2009-01-01

    textabstractPattern matching is comparing two patterns in order to determine whether they match (i.e., that they are the same) or do not match (i.e., that they differ). Pattern matching is the core procedure of theory-testing with cases. Testing consists of matching an “observed pattern” (a pattern

  5. Matching diagnosis and management of diabetes in pregnancy to local priorities and resources: an international approach.

    Science.gov (United States)

    McIntyre, H David; Oats, Jeremy J N; Zeck, Willibald; Seshiah, V; Hod, Moshe

    2011-11-01

    The International Association of the Diabetes and Pregnancy Study Groups' (IADPSG) criteria for the diagnosis and classification of hyperglycemia in pregnancy are described and application of these in differing healthcare contexts on a worldwide basis is reported. Existing local protocols and known epidemiologic and clinical data regarding the detection and management of overt diabetes and gestational diabetes in the context of human pregnancy are considered. Although the IADPSG criteria are uniform, their introduction poses a variety of practical and technical challenges in differing healthcare contexts, both between and within countries. Knowledge of local factors will be vital in the implementation of the new guidelines and will require extensive liaison with local clinical and health policy groups. Resource availability will be critical in determining the type of treatment available in this context. The IADPSG criteria offer an important opportunity for a uniform approach to diabetes in pregnancy. Scaled implementation of these criteria adapted to a variety of local healthcare contexts should improve both research endeavors and patient care.

  6. A DSRPCL-SVM Approach to Informative Gene Analysis

    Institute of Scientific and Technical Information of China (English)

    Wei Xiong; Zhibin Cai; Jinwen Ma

    2008-01-01

    Microarray data based tumor diagnosis is a very interesting topic in bioinformatics. One of the key problems is the discovery and analysis of informative genes of a tumor. Although there are many elaborate approaches to this problem, it is still difficult to select a reasonable set of informative genes for tumor diagnosis only with microarray data. In this paper, we classify the genes expressed through microarray data into a number of clusters via the distance sensitive rival penalized competitive learning (DSRPCL) algorithm and then detect the informative gene cluster or set with the help of support vector machine (SVM). Moreover, the critical or powerful informative genes can be found through further classifications and detections on the obtained informative gene clusters. It is well demonstrated by experiments on the colon, leukemia, and breast cancer datasets that our proposed DSRPCL-SVM approach leads to a reasonable selection of informative genes for tumor diagnosis.

  7. 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.

  8. 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.

  9. Matching Through Position Auctions

    OpenAIRE

    Terence Johnson

    2009-01-01

    This paper studies how an intermediary should design two-sided matching markets when agents are privately informed about their quality as a partner and can make payments to the intermediary. Using a mechanism design approach, I derive sufficient conditions for assortative matching to be profit- or welfare-maximizing, and then show how to implement the optimal match and payments through two-sided position auctions. This sharpens our understanding of intermediated matching markets by clarifying...

  10. Gene therapy in glaucoma-3: Therapeutic approaches

    OpenAIRE

    Mohamed Abdel-Monem Soliman Mahdy

    2010-01-01

    Despite new and improving diagnostic and therapeutic options for glaucoma, blindness from glaucoma is increasing and glaucoma remains a major public health problem. The role of heredity in ocular disease including glaucoma is attracting greater attention as the knowledge and recent advances of Human Genome Project and the HapMap Project have made genetic analysis of many human disorders possible. Glaucoma offers a variety of potential targets for gene therapy. All risk factors for glaucom...

  11. Pattern matching

    OpenAIRE

    Hak, Tony; Dul, Jan

    2009-01-01

    textabstractPattern matching is comparing two patterns in order to determine whether they match (i.e., that they are the same) or do not match (i.e., that they differ). Pattern matching is the core procedure of theory-testing with cases. Testing consists of matching an “observed pattern” (a pattern of measured values) with an “expected pattern” (a hypothesis), and deciding whether these patterns match (resulting in a confirmation of the hypothesis) or do not match (resulting in a disconfirmat...

  12. 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

  13. 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.

  14. 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

  15. 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.

  16. 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.

  17. 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.

  18. Computing gene expression data with a knowledge-based gene clustering approach.

    Science.gov (United States)

    Rosa, Bruce A; Oh, Sookyung; Montgomery, Beronda L; Chen, Jin; Qin, Wensheng

    2010-01-01

    Computational analysis methods for gene expression data gathered in microarray experiments can be used to identify the functions of previously unstudied genes. While obtaining the expression data is not a difficult task, interpreting and extracting the information from the datasets is challenging. In this study, a knowledge-based approach which identifies and saves important functional genes before filtering based on variability and fold change differences was utilized to study light regulation. Two clustering methods were used to cluster the filtered datasets, and clusters containing a key light regulatory gene were located. The common genes to both of these clusters were identified, and the genes in the common cluster were ranked based on their coexpression to the key gene. This process was repeated for 11 key genes in 3 treatment combinations. The initial filtering method reduced the dataset size from 22,814 probes to an average of 1134 genes, and the resulting common cluster lists contained an average of only 14 genes. These common cluster lists scored higher gene enrichment scores than two individual clustering methods. In addition, the filtering method increased the proportion of light responsive genes in the dataset from 1.8% to 15.2%, and the cluster lists increased this proportion to 18.4%. The relatively short length of these common cluster lists compared to gene groups generated through typical clustering methods or coexpression networks narrows the search for novel functional genes while increasing the likelihood that they are biologically relevant.

  19. 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.

  20. [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…

  1. 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).

  2. 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.

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

    OpenAIRE

    2015-01-01

    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) cy...

  4. 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

  5. Signature-Discovery Approach for Sample Matching of a Nerve-Agent Precursor using Liquid Chromatography–Mass Spectrometry, XCMS, and Chemometrics

    Energy Technology Data Exchange (ETDEWEB)

    Fraga, Carlos G.; Clowers, Brian H.; Moore, Ronald J.; Zink, Erika M.

    2010-05-15

    This report demonstrates the use of bioinformatic and chemometric tools on liquid chromatography mass spectrometry (LC-MS) data for the discovery of ultra-trace forensic signatures for sample matching of various stocks of the nerve-agent precursor known as methylphosphonic dichloride (dichlor). The use of the bioinformatic tool known as XCMS was used to comprehensively search and find candidate LC-MS peaks in a known set of dichlor samples. These candidate peaks were down selected to a group of 34 impurity peaks. Hierarchal cluster analysis and factor analysis demonstrated the potential of these 34 impurities peaks for matching samples based on their stock source. Only one pair of dichlor stocks was not differentiated from one another. An acceptable chemometric approach for sample matching was determined to be variance scaling and signal averaging of normalized duplicate impurity profiles prior to classification by k-nearest neighbors. Using this approach, a test set of dichlor samples were all correctly matched to their source stock. The sample preparation and LC-MS method permitted the detection of dichlor impurities presumably in the parts-per-trillion (w/w). The detection of a common impurity in all dichlor stocks that were synthesized over a 14-year period and by different manufacturers was an unexpected discovery. Our described signature-discovery approach should be useful in the development of a forensic capability to help in criminal investigations following chemical attacks.

  6. 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.

  7. A Novel Multi-Purpose Matching Representation of Local 3D Surfaces: A Rotationally Invariant, Efficient, and Highly Discriminative Approach With an Adjustable Sensitivity.

    Science.gov (United States)

    Al-Osaimi, Faisal R

    2016-02-01

    In this paper, a novel approach to local 3D surface matching representation suitable for a range of 3D vision applications is introduced. Local 3D surface patches around key points on the 3D surface are represented by 2D images such that the representing 2D images enjoy certain characteristics which positively impact the matching accuracy, robustness, and speed. First, the proposed representation is complete, in the sense, there is no information loss during their computation. Second, the 3DoF 2D representations are strictly invariant to all the 3DoF rotations. To optimally avail surface information, the sensitivity of the representations to surface information is adjustable. This also provides the proposed matching representation with the means to optimally adjust to a particular class of problems/applications or an acquisition technology. Each 2D matching representation is a sequence of adjustable integral kernels, where each kernel is efficiently computed from a triple of precise 3D curves (profiles) formed by intersecting three concentric spheres with the 3D surface. Robust techniques for sampling the profiles and establishing correspondences among them were devised. Based on the proposed matching representation, two techniques for the detection of key points were presented. The first is suitable for static images, while the second is suitable for 3D videos. The approach was tested on the face recognition grand challenge v2.0, the 3D twins expression challenge, and the Bosphorus data sets, and a superior face recognition performance was achieved. In addition, the proposed approach was used in object class recognition and tested on a Kinect data set.

  8. Liver resection for hepatocellular carcinoma within a fast-track management:a propensity-score matched analysis between open and laparoscopic approach

    Institute of Scientific and Technical Information of China (English)

    Francesca Ratti; Federica Cipriani; Raffaella Reineke; Marco Catena; Michele Paganelli; Luigi Beretta; Luca Aldrighetti

    2016-01-01

    Aim: The study was designed to assess the implications of enhanced recovery after surgery (ERAS) approach in patients submitted to open liver resection for hepatocellular carcinoma (HCC) comparing their short term outcome with patients treated by laparoscopic approach, in a case-matched design.Methods: The open-group (n = 60) was matched in a ratio of 1:1 with patients undergoing laparoscopic liver resection for HCC (Lap-group,n= 60), with a matching achieved on a basis of propensity scores including 6 covariates representing patients characteristics and severity of the disease. Primary outcome analysis was performed in terms of ERAS-speciifc items and postoperative morbidity and mortality.Results: Overall morbidity and mortality were comparable between groups. Incidence of ascites was slightly higher in the open- compared with the Lap-group (respectively 11.7% and 13.3%), without statistical signiifcance. The need for introduction or increase of chronic diuretic therapy was signiifcantly higher in the open-compared with the Lap-group (16.7%vs. 11.7%,P = 0.046). Furthermore, ascites more frequently required percutaneous drainage in the open-compared with the Lap-group (5%vs. 1.7% respectively,P = 0.041).Conclusion: In patients who can’t beneift from minimally-invasive approach because of disease characteristics, ERAS management seems to be associated with an improved postoperative functional recovery and postoperative outcomes, comparable to those of the minimally invasive approach.

  9. 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...

  10. A preclinical approach for gene therapy of β-thalassemia

    Science.gov (United States)

    Breda, Laura; Kleinert, Dorothy A.; Casu, Carla; Casula, Laura; Cartegni, Luca; Fibach, Eitan; Mancini, Irene; Giardina, Patricia J.; Gambari, Roberto; Rivella, Stefano

    2011-01-01

    Lentiviral-mediated β-globin gene transfer successfully treated β-thalassemic mice. Based on this result, clinical trials were initiated. To date, however, no study has investigated the efficacy of gene therapy in relation to the nature of the different β-globin mutations found in patients. Most mutations can be classified as β0 or β+, based on the amount of β-globin protein produced. Therefore, we propose that a screening in vitro is necessary to verify the efficacy of gene transfer prior to treatment of individual patients. We used a two-phase liquid culture system to expand and differentiate erythroid progenitor cells (ErPCs) transduced with lentiviral vectors. We propose the use of this system to test the efficiency of lentiviral vectors carrying the human β-globin gene, to correct the phenotype of ErPCs from patients preparing for gene therapy. This new approach might have profound implications for designing gene therapy and for understanding the genotype/phenotype variability observed in Cooley’s anemia patients. PMID:20712784

  11. A preclinical approach for gene therapy of beta-thalassemia.

    Science.gov (United States)

    Breda, Laura; Kleinert, Dorothy A; Casu, Carla; Casula, Laura; Cartegni, Luca; Fibach, Eitan; Mancini, Irene; Giardina, Patricia J; Gambari, Roberto; Rivella, Stefano

    2010-08-01

    Lentiviral-mediated beta-globin gene transfer successfully treated beta-thalassemic mice. Based on this result, clinical trials were initiated. To date, however, no study has investigated the efficacy of gene therapy in relation to the nature of the different beta-globin mutations found in patients. Most mutations can be classified as beta(0) or beta(+), based on the amount of beta-globin protein produced. Therefore, we propose that a screening in vitro is necessary to verify the efficacy of gene transfer prior to treatment of individual patients. We used a two-phase liquid culture system to expand and differentiate erythroid progenitor cells (ErPCs) transduced with lentiviral vectors. We propose the use of this system to test the efficiency of lentiviral vectors carrying the human beta-globin gene, to correct the phenotype of ErPCs from patients preparing for gene therapy. This new approach might have profound implications for designing gene therapy and for understanding the genotype/phenotype variability observed in Cooley's anemia patients.

  12. 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.

  13. Design and Simulation for Producing Two Amplitude Matched Anti-phase Sine Waveforms Using ±2.5 V CMOS Current-Mode Approach

    OpenAIRE

    Anil Kumar Sharma; Dipankar Pal

    2010-01-01

    In this paper the current mode approach called “Current Conveyor (CCII+)” has been incorporated to design and simulate the circuit for producing two amplitude matched anti-phase sine waveforms which are frequently used in various communication and instrumentation systems. PSpice simulation has been used to depict the output waveforms. The power supply used is ±2.5 V which can be easily incorporated with CMOS IC technology. The designed circuit has been simulated at variousfrequency ranges and...

  14. Candidate genes, pathways and mechanisms for alcoholism: an expanded convergent functional genomics approach.

    Science.gov (United States)

    Rodd, Z A; Bertsch, B A; Strother, W N; Le-Niculescu, H; Balaraman, Y; Hayden, E; Jerome, R E; Lumeng, L; Nurnberger, J I; Edenberg, H J; McBride, W J; Niculescu, A B

    2007-08-01

    We describe a comprehensive translational approach for identifying candidate genes for alcoholism. The approach relies on the cross-matching of animal model brain gene expression data with human genetic linkage data, as well as human tissue data and biological roles data, an approach termed convergent functional genomics. An analysis of three animal model paradigms, based on inbred alcohol-preferring (iP) and alcohol-non-preferring (iNP) rats, and their response to treatments with alcohol, was used. A comprehensive analysis of microarray gene expression data from five key brain regions (frontal cortex, amygdala, caudate-putamen, nucleus accumbens and hippocampus) was carried out. The Bayesian-like integration of multiple independent lines of evidence, each by itself lacking sufficient discriminatory power, led to the identification of high probability candidate genes, pathways and mechanisms for alcoholism. These data reveal that alcohol has pleiotropic effects on multiple systems, which may explain the diverse neuropsychiatric and medical pathology in alcoholism. Some of the pathways identified suggest avenues for pharmacotherapy of alcoholism with existing agents, such as angiotensin-converting enzyme (ACE) inhibitors. Experiments we carried out in alcohol-preferring rats with an ACE inhibitor show a marked modulation of alcohol intake. Other pathways are new potential targets for drug development. The emergent overall picture is that physical and physiological robustness may permit alcohol-preferring individuals to withstand the aversive effects of alcohol. In conjunction with a higher reactivity to its rewarding effects, they may able to ingest enough of this nonspecific drug for a strong hedonic and addictive effect to occur.

  15. 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.

  16. Intraoperative cone-beam CT for correction of periaxial malrotation of the femoral shaft: a surface-matching approach.

    Science.gov (United States)

    Khoury, Amal; Whyne, Cari M; Daly, Michael; Moseley, Douglas; Bootsma, Greg; Skrinskas, Tomas; Siewerdsen, Jeffrey; Jaffray, David

    2007-04-01

    Limb length, alignment and rotation can be difficult to determine in femoral shaft fractures. Shaft axis rotation is particularly difficult to assess intraoperatively. Femoral malpositioning can cause deformity, pain and secondary degenerative joint damage. The aim of this study is to develop an intraoperative method based on cone-beam computed tomography (CBCT) to guide alignment of femoral shaft fractures. We hypothesize that bone surface matching can predict malrotation even with severe comminution. A cadaveric femur was imaged at 16 femoral periaxial malrotations (-51.2 degrees to 60.1 degrees). The images were processed resulting in an unwrapped bone surface plot consisting of a pattern of ridges and valleys. Fracture gaps were simulated by removing midline CT slices. The gaps were reconstituted by extrapolating the existing proximal and distal fragments to the midline of the fracture. The two bone surfaces were then shifted to align bony features. Periaxial malrotation was accurately assessed using surface matching (r2 = 0.99, slope 1.0). The largest mean error was 2.20 degrees and the average difference between repeated measurements was 0.49 degrees. CBCT can provide intraoperative high-resolution images with a large field of view. This quality of imaging enables surface matching algorithms to be utilized even with large areas of comminution.

  17. 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.

  18. 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

  19. 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.

  20. Cell- and gene-based approaches to tendon regeneration.

    Science.gov (United States)

    Nixon, Alan J; Watts, Ashlee E; Schnabel, Lauren V

    2012-02-01

    Repair of rotator cuff tears in experimental models has been significantly improved by the use of enhanced biologic approaches, including platelet-rich plasma, bone marrow aspirate, growth factor supplements, and cell- and gene-modified cell therapy. Despite added complexity, cell-based therapies form an important part of enhanced repair, and combinations of carrier vehicles, growth factors, and implanted cells provide the best opportunity for robust repair. Bone marrow-derived mesenchymal stem cells provide a stimulus for repair in flexor tendons, but application in rotator cuff repair has not shown universally positive results. The use of scaffolds such as platelet-rich plasma, fibrin, and synthetic vehicles and the use of gene priming for stem cell differentiation and local anabolic and anti-inflammatory impact have both provided essential components for enhanced tendon and tendon-to-bone repair in rotator cuff disruption. Application of these research techniques in human rotator cuff injury has generally been limited to autologous platelet-rich plasma, bone marrow concentrate, or bone marrow aspirates combined with scaffold materials. Cultured mesenchymal progenitor therapy and gene-enhanced function have not yet reached clinical trials in humans. Research in several animal species indicates that the concept of gene-primed stem cells, particularly embryonic stem cells, combined with effective culture conditions, transduction with long-term integrating vectors carrying anabolic growth factors, and development of cells conditioned by use of RNA interference gene therapy to resist matrix metalloproteinase degradation, may constitute potential advances in rotator cuff repair. This review summarizes cell- and gene-enhanced cell research for tendon repair and provides future directions for rotator cuff repair using biologic composites.

  1. Liver-targeted gene therapy: Approaches and challenges.

    Science.gov (United States)

    Aravalli, Rajagopal N; Belcher, John D; Steer, Clifford J

    2015-06-01

    The liver plays a major role in many inherited and acquired genetic disorders. It is also the site for the treatment of certain inborn errors of metabolism that do not directly cause injury to the liver. The advancement of nucleic acid-based therapies for liver maladies has been severely limited because of the myriad untoward side effects and methodological limitations. To address these issues, research efforts in recent years have been intensified toward the development of targeted gene approaches using novel genetic tools, such as zinc-finger nucleases, transcription activator-like effector nucleases, and clustered regularly interspaced short palindromic repeats as well as various nonviral vectors such as Sleeping Beauty transposons, PiggyBac transposons, and PhiC31 integrase. Although each of these methods uses a distinct mechanism of gene modification, all of them are dependent on the efficient delivery of DNA and RNA molecules into the cell. This review provides an overview of current and emerging therapeutic strategies for liver-targeted gene therapy and gene repair.

  2. Gene Therapy Approaches For The Treatment Of Retinal Disorders

    Science.gov (United States)

    Petit, Lolita; Punzo, Claudio

    2016-01-01

    There is an impelling need to develop effective therapeutic strategies for patients with retinal disorders. Gleaning from the large quantity of information gathered over the past two decades on the mechanisms governing degeneration of the retina, it is now possible to devise innovative therapies based on retinal gene transfer. Different gene-based approaches are under active investigation. They include strategies to correct the specific genetic defect in inherited retinal diseases, strategies to delay the onset of blindness independently of the disease-causing mutations and strategies to reactivate residual cells at late stages of the diseases. In this review, we discuss the status of application of these technologies, outlining the future therapeutic potential for many forms of retinal blinding diseases. PMID:27875674

  3. 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.

  4. One-Match and All-Match Categories for Keywords Matching in Chatbot

    Directory of Open Access Journals (Sweden)

    Abbas S. Lokman

    2010-01-01

    Full Text Available Problem statement: Artificial intelligence chatbot is a technology that makes interactions between men and machines using natural language possible. From literature of chatbots keywords/pattern matching techniques, potential issues for improvement had been discovered. The discovered issues are in the context of keywords arrangement for matching precedence and keywords variety for matching flexibility. Approach: Combining previous techniques/mechanisms with some additional adjustment, new technique to be used for keywords matching process is proposed. Using newly developed chatbot named ViDi (abbreviation for Virtual Diabetes physician which is a chatbot for diabetes education activity as a testing medium, the proposed technique named One-Match and All-Match Categories (OMAMC is being used to test the creation of possible keywords surrounding one sample input sentence. The result for possible keywords created by this technique then being compared to possible keywords created by previous chatbots techniques surrounding the same sample sentence in matching precedence and matching flexibility context. Results: OMAMC technique is found to be improving previous matching techniques in matching precedence and flexibility context. This improvement is seen to be useful for shortening matching time and widening matching flexibility within the chatbots keywords matching process. Conclusion: OMAMC for keywords matching in chatbot is shown to be an improvement over previous techniques in the context of keywords arrangement for matching precedence and keywords variety for matching flexibility.

  5. Targeted gene repair: the ups and downs of a promising gene therapy approach.

    Science.gov (United States)

    de Semir, David; Aran, Josep M

    2006-08-01

    As a novel form of molecular medicine based on direct actions over the genes, targeted gene repair has raised consideration recently above classical gene therapy strategies based on genetic augmentation or complementation. Targeted gene repair relies on the local induction of the cell's endogenous DNA repair mechanisms to attain a therapeutic gene conversion event within the genome of the diseased cell. Successful repair has been achieved both in vitro and in vivo with a variety of corrective molecules ranging from oligonucleotides (chimeraplasts, modified single-stranded oligonucleotides, triplex-forming oligonucleotides), to small DNA fragments (small fragment homologous replacement (SFHR)), and even viral vectors (AAV-based). However, controversy on the consistency and lack of reproducibility of early experiments regarding frequencies and persistence of targeted gene repair, particularly for chimeraplasty, has flecked the field. Nevertheless, several hurdles such as inefficient nuclear uptake of the corrective molecules, and misleading assessment of targeted repair frequencies have been identified and are being addressed. One of the key bottlenecks for exploiting the overall potential of the different targeted gene repair modalities is the lack of a detailed knowledge of their mechanisms of action at the molecular level. Several studies are now focusing on the assessment of the specific repair pathway(s) involved (homologous recombination, mismatch repair, etc.), devising additional strategies to increase their activity (using chemotherapeutic drugs, chimeric nucleases, etc.), and assessing the influence of the cell cycle in the regulation of the repair process. Until therapeutic correction frequencies for single gene disorders are reached both in cellular and animal models, precision and undesired side effects of this promising gene therapy approach will not be thoroughly evaluated.

  6. 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.

  7. 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.

  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. Matching for the non-conventional MHC-I MICA gene significantly reduces the incidence of acute and chronic GVHD

    NARCIS (Netherlands)

    Carapito, Raphael; Jung, Nicolas; Kwemou, Marius; Untrau, Meiggie; Michel, Sandra; Pichot, Angélique; Giacometti, Gaëlle; Macquin, Cécile; Ilias, Wassila; Morlon, Aurore; Kotova, Irina; Apostolova, Petya; Schmitt-Graeff, Annette; Cesbron, Anne; Gagne, Katia; Oudshoorn, Machteld; van der Holt, Bronno; Labalette, Myriam; Spierings, Eric; Picard, Christophe; Loiseau, Pascale; Tamouza, Ryad; Toubert, Antoine; Parissiadis, Anne; Dubois, Valérie; Lafarge, Xavier; Maumy-Bertrand, Myriam; Bertrand, Frédéric; Vago, Luca; Ciceri, Fabio; Paillard, Catherine; Querol, Sergi; Sierra, Jorge; Fleischhauer, Katharina; Nagler, Arnon; Labopin, Myriam; Inoko, Hidetoshi; von dem Borne, Peter A; Kuball, Jürgen H E; Ota, Masao; Katsuyama, Yoshihiko; Michallet, Mauricette; Lioure, Bruno; Peffault de Latour, Régis; Blaise, Didier; Cornelissen, Jan J; Yakoub-Agha, Ibrahim; Claas, Frans; Moreau, Philippe; Milpied, Noël; Charron, Dominique; Mohty, Mohamad; Zeiser, Robert; Socié, Gérard; Bahram, Seiamak

    2016-01-01

    Graft-versus-host disease (GVHD) is among the most challenging complications in unrelated donor hematopoietic cell transplantation (HCT). The highly polymorphic "MHC class I chain-related gene A", MICA, encodes a stress-induced glycoprotein expressed primarily on epithelia. MICA interacts with the i

  10. Matching for the nonconventional MHC-I MICA gene significantly reduces the incidence of acute and chronic GVHD

    NARCIS (Netherlands)

    Carapito, R. (Raphael); Jung, N. (Nicolas); Kwemou, M. (Marius); Untrau, M. (Meiggie); Michel, S. (Sandra); Pichot, A. (Angélique); Giacometti, G. (Gaëlle); Macquin, C. (Cécile); Ilias, W. (Wassila); Morlon, A. (Aurore); Kotova, I. (Irina); Apostolova, P. (Petya); Schmitt-Graeff, A. (Annette); Cesbron, A. (Anne); K. Gagne (Katia); M. Oudshoorn (Machteld); B. van der Holt (Bronno); Labalette, M. (Myriam); E. Spierings (E.); Picard, C. (Christophe); P. Loiseau (Pascale); Tamouza, R. (Ryad); Toubert, A. (Antoine); Parissiadis, A. (Anne); V. Dubois (Valerie); Lafarge, X. (Xavier); Maumy-Bertrand, M. (Myriam); Bertrand, F. (Frédéric); Vago, L. (Luca); F. Ciceri (Fabio); Paillard, C. (Catherine); Querol, S. (Sergi); J. Sierra (Jorge); Fleischhauer, K. (Katharina); A. Nagler (Arnon); M. Labopin (Myriam); H. Inoko (Hidetoshi); P.A. von dem Borne (P. A.); J. Kuball (Jürgen); Ota, M. (Masao); Katsuyama, Y. (Yoshihiko); M. Michallet (M.); B. Lioure; De Latour, R.P. (Régis Peffault); D. Blaise (Didier); J.J. Cornelissen (Jan); I. Yakoub-Agha (Ibrahim); F.H.J. Claas (Frans); P. Moreau; N. Milpied; Charron, D. (Dominique); M. Mohty (Mohamad); Zeiser, R. (Robert); G. Socie (Gerard); Bahram, S. (Seiamak)

    2016-01-01

    textabstractGraft-versus-host disease (GVHD) is among the most challenging complications in unrelated donor hematopoietic cell transplantation (HCT). The highly polymorphic MHC class I chain-related gene A, MICA, encodes a stress-induced glycoprotein expressed primarily on epithelia. MICA interacts

  11. Automatic Tuning Matching Cycler (ATMC) In Situ NMR Spectroscopy as a Novel Approach for Real-Time Investigations of Li- and Na-Ion Batteries

    OpenAIRE

    2016-01-01

    This is the author accepted manuscript. The final version is available from Elsevier via http://dx.doi.org/10.1016/j.jmr.2016.02.008 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., sign...

  12. Design and Simulation for Producing Two Amplitude Matched Anti-phase Sine Waveforms Using ±2.5 V CMOS Current-Mode Approach

    Directory of Open Access Journals (Sweden)

    Anil Kumar Sharma,

    2010-08-01

    Full Text Available In this paper the current mode approach called “Current Conveyor (CCII+” has been incorporated to design and simulate the circuit for producing two amplitude matched anti-phase sine waveforms which are frequently used in various communication and instrumentation systems. PSpice simulation has been used to depict the output waveforms. The power supply used is ±2.5 V which can be easily incorporated with CMOS IC technology. The designed circuit has been simulated at variousfrequency ranges and the waveforms are obtained after the circuit is optimized.

  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. 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).

    Science.gov (United States)

    Grötzinger, Stefan W; Alam, Intikhab; Ba Alawi, Wail; Bajic, Vladimir B; Stingl, Ulrich; Eppinger, Jörg

    2014-01-01

    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

  16. 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

  17. 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.

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

    Science.gov (United States)

    Xiang, Menglong; Sun, Lei; Dong, Xiaomei; Yang, Huan; Liu, Wen-bin; Zhou, Niya; Han, Xue; Zhou, Ziyuan; Cui, Zhihong; Liu, Jing-yi; Cao, Jia; Ao, Lin

    2015-01-01

    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.

  19. 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.

  20. 'Wiggle matching' radiocarbon dates

    NARCIS (Netherlands)

    Ramsey, CB; van der Plicht, J; Weninger, B

    2001-01-01

    This paper covers three different methods of matching radiocarbon dates to the 'wiggles' of the calibration curve in those situations where the age difference between the C-14 dates is known. These methods are most often applied to tree-ring sequences. The simplest approach is to use a classical Chi

  1. Donor killer immunoglobulin-like receptor genes and reactivation of cytomegalovirus after HLA-matched hematopoietic stem-cell transplantation: HLA-C allotype is an essential cofactor

    Directory of Open Access Journals (Sweden)

    Carolyn E. Behrendt

    2013-02-01

    Full Text Available Natural Killer (NK cells whose killer immunoglobulin-like receptors (KIR recognize human leukocyte antigen (HLA ligand are licensed for activity. In contrast, non-licensed NK cells display KIRs for which ligand is absent from the self genotype and are usually hyporesponsive. Surprisingly, non-licensed cells are active in tumor control after hematopoietic stem-cell transplantation (HSCT and dominate NK response to murine cytomegalovirus (CMV infection. From those reports, we hypothesized that control of human CMV early after HSCT is influenced by donor KIR genes whose HLA ligand is absent-from-genotype of HLA-matched donor and recipient. To investigate, we studied CMV reactivation through Day 100 after grafts involving CMV-seropositive donor and/or recipient. A multivariate proportional rates model controlled for variability in surveillance and established covariates including acute graft-versus-host disease; statistical significance was adjusted for testing of multiple KIRs with identified HLA class I ligand (2DL1, 2DL2/3, 2DS1, 2DS2, full-length 2DS4, 3DL1/3DS1, 3DL2. Among HSCT recipients (n=286, CMV reactivation-free survival time varied with individual donor KIR genes evolutionarily-specific for HLA-C: when ligand was absent from the donor/recipient genotype, inhibitory KIRs 2DL2 (P<0.0001 and 2DL1 (P=0.015 each predicted inferior outcome, and activating KIRs 2DS2 (P<0.0001, 2DS1 (P=0.016, and 2DS4 (P=0.016 each predicted superior outcome. Otherwise, with ligand present-in-genotype, donor KIR genes had no effect. In conclusion, early after HLA-matched HSCT, individual inhibitory and activating KIR genes have qualitatively different effects on risk of CMV reactivation; unexpectedly, absence of HLA-C ligand from the donor/recipient genotype constitutes an essential cofactor in these associations. Being KIR and HLA-C specific, these findings are independent of licensing via alternate NK cell receptors (NKG2A, NKG2C that recognize HLA-E.

  2. 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.

  3. Incremental pattern matching for regular expressions

    NARCIS (Netherlands)

    Jalali, Arash; Ghamarian, Amir Hossein; Rensink, Arend; Fish, Andrew; Lambers, Leen

    2012-01-01

    Graph pattern matching lies at the heart of any graph transformation-based system. Incremental pattern matching is one approach proposed for reducingthe overall cost of pattern matching over successive transformations by preserving the matches that stay relevant after a rule application. An importan

  4. 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

  5. Relaxation matching algorithm for moving photogrammetry

    Science.gov (United States)

    Guo, Lei; Liu, Ke; Miao, Yinxiao; Zhu, Jigui

    2015-02-01

    Moving photogrammetry is an application of close range photogrammetry in industrial measurement to realize threedimensional coordinate measurement within large-scale volume. This paper describes an approach of relaxation matching algorithm applicable to moving photogrammetry according to the characteristics of accurate matching result of different measuring images. This method uses neighborhood matching support to improve the matching rate after coarse matching based on epipolar geometry constraint and precise matching using three images. It reflects the overall matching effect of all points, that means when a point is matched correctly, the matching results of those points round it must be correct. So for one point considered, the matching results of points round it are calculated to judge whether its result is correct. Analysis indicates that relaxation matching can eliminate the mismatching effectively and acquire 100% rate of correct matching. It will play a very important role in moving photogrammetry to ensure the following implement of ray bundle adjustment.

  6. New approaches to gene and cell therapy for hemophilia.

    Science.gov (United States)

    Ohmori, T; Mizukami, H; Ozawa, K; Sakata, Y; Nishimura, S

    2015-06-01

    Hemophilia is considered suitable for gene therapy because it is caused by a single gene abnormality, and therapeutic coagulation factor levels may vary across a broad range. Recent success of hemophilia B gene therapy with an adeno-associated virus (AAV) vector in a clinical trial showed the real prospect that, through gene therapy, a cure for hemophilia may become a reality. However, AAV-mediated gene therapy is not applicable to patients with hemophilia A at present, and neutralizing antibodies against AAV reduce the efficacy of AAV-mediated strategies. Because patients that benefit from AAV treatment (hemophilia B without neutralizing antibodies) are estimated to represent only 15% of total patients with hemophilia, the development of basic technologies for hemophilia A and those that result in higher therapeutic effects are critical. In this review, we present an outline of gene therapy methods for hemophilia, including the transition of technical developments thus far and our novel techniques.

  7. 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...

  8. Navigating the complex path between the oxytocin receptor gene (OXTR) and cooperation: an endophenotype approach

    OpenAIRE

    Haas, Brian W.; Anderson, Ian W.; Smith, Jessica M.

    2013-01-01

    Although cooperation represents a core facet of human social behavior there exists considerable variability across people in terms of the tendency to cooperate. One factor that may contribute to individual differences in cooperation is a key gene within the oxytocin (OT) system, the OT reception gene (OXTR). In this article, we aim to bridge the gap between the OXTR gene and cooperation by using an endophenotype approach. We present evidence that the association between the OXTR gene and coop...

  9. Identification of ovarian cancer associated genes using an integrated approach in a Boolean framework

    Science.gov (United States)

    2013-01-01

    Background Cancer is a complex disease where molecular mechanism remains elusive. A systems approach is needed to integrate diverse biological information for the prognosis and therapy risk assessment using mechanistic approach to understand gene interactions in pathways and networks and functional attributes to unravel the biological behaviour of tumors. Results We weighted the functional attributes based on various functional properties observed between cancerous and non-cancerous genes reported from literature. This weighing schema was then encoded in a Boolean logic framework to rank differentially expressed genes. We have identified 17 genes to be differentially expressed from a total of 11,173 genes, where ten genes are reported to be down-regulated via epigenetic inactivation and seven genes are up-regulated. Here, we report that the overexpressed genes IRAK1, CHEK1 and BUB1 may play an important role in ovarian cancer. We also show that these 17 genes can be used to form an ovarian cancer signature, to distinguish normal from ovarian cancer subjects and that the set of three genes, CHEK1, AR, and LYN, can be used to classify good and poor prognostic tumors. Conclusion We provided a workflow using a Boolean logic schema for the identification of differentially expressed genes by integrating diverse biological information. This integrated approach resulted in the identification of genes as potential biomarkers in ovarian cancer. PMID:23383610

  10. A robust data-driven approach for gene ontology annotation

    OpenAIRE

    2014-01-01

    Gene ontology (GO) and GO annotation are important resources for biological information management and knowledge discovery, but the speed of manual annotation became a major bottleneck of database curation. BioCreative IV GO annotation task aims to evaluate the performance of system that automatically assigns GO terms to genes based on the narrative sentences in biomedical literature. This article presents our work in this task as well as the experimental results after the competition. For th...

  11. 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.

  12. 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.

  13. Longevity, genes and efforts: an optimal taxation approach to prevention.

    Science.gov (United States)

    Leroux, M-L; Pestieau, P; Ponthiere, G

    2011-01-01

    This paper applies the analytical tools of optimal taxation theory to the design of the optimal subsidy on preventive behaviours, in an economy where longevity varies across agents, and depends on preventive expenditures and on longevity genes. Public intervention can be here justified on three grounds: corrections for misperceptions of the survival process and for externalities related to individual preventive behaviour, and redistribution across both earnings and genetic dimensions. The optimal subsidy on preventive expenditures is shown to depend on the combined impacts of misperception, externalities and self-selection. It is generally optimal to subsidize preventive efforts to an extent depending on the degree of individual myopia, on how productivity and genes are correlated, and on the complementarity of genes and preventive efforts in the survival function.

  14. [Approach to depressogenic genes from genetic analyses of animal models].

    Science.gov (United States)

    Yoshikawa, Takeo

    2004-01-01

    Human depression or mood disorder is defined as a complex disease, making positional cloning of susceptibility genes a formidable task. We have undertaken genetic analyses of three different animal models for depression, comparing our results with advanced database resources. We first performed quantitative trait loci (QTL) analysis on two mouse models of "despair", namely, the forced swim test (FST) and tail suspension test (TST), and detected multiple chromosomal loci that control immobility time in these tests. Since one QTL detected on mouse chromosome 11 harbors the GABA A receptor subunit genes, we tested these genes for association in human mood disorder patients. We obtained significant associations of the alpha 1 and alpha 6 subunit genes with the disease, particularly in females. This result was striking, because we had previously detected an epistatic interaction between mouse chromosomes 11 and X that regulates immobility time in these animals. Next, we performed genome-wide expression analyses using a rat model of depression, learned helplessness (LH). We found that in the frontal cortex of LH rats, a disease implicated region, the LIM kinase 1 gene (Limk 1) showed greatest alteration, in this case down-regulation. By combining data from the QTL analysis of FST/TST and DNA microarray analysis of mouse frontal cortex, we identified adenylyl cyclase-associated CAP protein 1 (Cap 1) as another candidate gene for depression susceptibility. Both Limk 1 and Cap 1 are key players in the modulation of actin G-F conversion. In summary, our current study using animal models suggests disturbances of GABAergic neurotransmission and actin turnover as potential pathophysiologies for mood disorder.

  15. 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…

  16. 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.

  17. 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.

  18. 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...

  19. 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.

  20. 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

  1. 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.

  2. Approaches and methods in gene therapy for kidney disease

    NARCIS (Netherlands)

    van der Wouden, Els A; Sandovici, Maria; Henning, Robert H; de Zeeuw, Dick; Deelman, Leo E

    2004-01-01

    Renal gene therapy may offer new strategies to treat diseases of native and transplanted kidneys. Several experimental techniques have been developed and employed using nonviral, viral, and cellular vectors. The most efficient vector for in vivo transfection appears to be adenovirus. Glomeruli, bloo

  3. 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.

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

    DEFF Research Database (Denmark)

    Peña-Diaz, Javier; Rasmussen, Lene Juel

    2016-01-01

    (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...... 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...

  5. Gene silencing: a therapeutic approach to combat influenza virus infections.

    Science.gov (United States)

    Khanna, Madhu; Saxena, Latika; Rajput, Roopali; Kumar, Binod; Prasad, Rajendra

    2015-01-01

    Selective gene silencing technologies such as RNA interference (RNAi) and nucleic acid enzymes have shown therapeutic potential for treating viral infections. Influenza virus is one of the major public health concerns around the world and its management is challenging due to a rapid increase in antiviral resistance. Influenza vaccine also has its limitations due to the emergence of new strains that may escape the immunity developed by the previous year's vaccine. Antiviral drugs are the primary mode of prevention and control against a pandemic and there is an urgency to develop novel antiviral strategies against influenza virus. In this review, we discuss the potential utility of several gene silencing mechanisms and their prophylactic and therapeutic potential against the influenza virus.

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

    OpenAIRE

    Jayashree Sadasivam; Ramesh, N.; K. Vijayalakshmi; 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...

  7. Gene therapy as a therapeutic approach for the treatment of rheumatoid arthritis: innovative vectors and therapeutic genes.

    Science.gov (United States)

    Adriaansen, J; Vervoordeldonk, M J B M; Tak, P P

    2006-06-01

    In recent years, significant progress has been made in the treatment of rheumatoid arthritis (RA). In addition to conventional therapy, novel biologicals targeting tumour necrosis factor-alpha have successfully entered the clinic. However, the majority of the patients still has some actively inflamed joints and some patients suffer from side-effects associated with the high systemic dosages needed to achieve therapeutic levels in the joints. In addition, due to of the short half-life of these proteins there is a need for continuous, multiple injections of the recombinant protein. An alternative approach might be the use of gene transfer to deliver therapeutic genes locally at the site of inflammation. Several viral and non-viral vectors are being used in animal models of RA. The first gene therapy trials for RA have already entered the clinic. New vectors inducing long-term and regulated gene expression in specific tissue are under development, resulting in more efficient gene transfer, for example by using distinct serotypes of viral vectors such as adeno-associated virus. This review gives an overview of some promising vectors used in RA research. Furthermore, several therapeutic genes are discussed that could be used for gene therapy in RA patients.

  8. 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.

  9. Gene function hypotheses for the Campylobacter jejuni glycome generated by a logic-based approach.

    Science.gov (United States)

    Sternberg, Michael J E; Tamaddoni-Nezhad, Alireza; Lesk, Victor I; Kay, Emily; Hitchen, Paul G; Cootes, Adrian; van Alphen, Lieke B; Lamoureux, Marc P; Jarrell, Harold C; Rawlings, Christopher J; Soo, Evelyn C; Szymanski, Christine M; Dell, Anne; Wren, Brendan W; Muggleton, Stephen H

    2013-01-09

    Increasingly, experimental data on biological systems are obtained from several sources and computational approaches are required to integrate this information and derive models for the function of the system. Here, we demonstrate the power of a logic-based machine learning approach to propose hypotheses for gene function integrating information from two diverse experimental approaches. Specifically, we use inductive logic programming that automatically proposes hypotheses explaining the empirical data with respect to logically encoded background knowledge. We study the capsular polysaccharide biosynthetic pathway of the major human gastrointestinal pathogen Campylobacter jejuni. We consider several key steps in the formation of capsular polysaccharide consisting of 15 genes of which 8 have assigned function, and we explore the extent to which functions can be hypothesised for the remaining 7. Two sources of experimental data provide the information for learning-the results of knockout experiments on the genes involved in capsule formation and the absence/presence of capsule genes in a multitude of strains of different serotypes. The machine learning uses the pathway structure as background knowledge. We propose assignments of specific genes to five previously unassigned reaction steps. For four of these steps, there was an unambiguous optimal assignment of gene to reaction, and to the fifth, there were three candidate genes. Several of these assignments were consistent with additional experimental results. We therefore show that the logic-based methodology provides a robust strategy to integrate results from different experimental approaches and propose hypotheses for the behaviour of a biological system.

  10. Robust modeling of differential gene expression data using normal/independent distributions: a Bayesian approach.

    Directory of Open Access Journals (Sweden)

    Mojtaba Ganjali

    Full Text Available In this paper, the problem of identifying differentially expressed genes under different conditions using gene expression microarray data, in the presence of outliers, is discussed. For this purpose, the robust modeling of gene expression data using some powerful distributions known as normal/independent distributions is considered. These distributions include the Student's t and normal distributions which have been used previously, but also include extensions such as the slash, the contaminated normal and the Laplace distributions. The purpose of this paper is to identify differentially expressed genes by considering these distributional assumptions instead of the normal distribution. A Bayesian approach using the Markov Chain Monte Carlo method is adopted for parameter estimation. Two publicly available gene expression data sets are analyzed using the proposed approach. The use of the robust models for detecting differentially expressed genes is investigated. This investigation shows that the choice of model for differentiating gene expression data is very important. This is due to the small number of replicates for each gene and the existence of outlying data. Comparison of the performance of these models is made using different statistical criteria and the ROC curve. The method is illustrated using some simulation studies. We demonstrate the flexibility of these robust models in identifying differentially expressed genes.

  11. 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

  12. 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

  13. 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.

  14. A Double Selection Approach to Achieve Specific Expression of Toxin Genes for Ovarian Cancer Gene Therapy

    Science.gov (United States)

    2005-11-01

    therapy vectors. .. OE +04 I.OE+02 ri . OE +03t 0E+0)1 .0E+02 Discussion I) 100 100) I I 100 xp/cell %,p/ccll A major obstacle to be overcome in Ad5-based can...4,11,20]. Thus, Ad gene ther- 1. OE +03 i.E+04, apy vectors with CAR-independent and/or expanded I 01-+2 I.OE+03 tropism may prove valuable for maximal...Tsurutaa, Seiji Yamamotoa, Yosuke Kawakami’, Joanne T. Douglas" b, Kenzaburo Tanid , David T. Curiel,’b and Joel N. Glasgowa* a Division of Human Gene

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

    Science.gov (United States)

    Liscombe, David K; O'Connor, Sarah E

    2011-11-01

    The anticancer agents vinblastine and vincristine are bisindole alkaloids derived from coupling vindoline and catharanthine, monoterpenoid indole alkaloids produced exclusively by the Madagascar periwinkle (Catharanthus roseus). 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 either 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. A VIGS method was developed herein 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.

  16. 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.

  17. Generalized Orthogonal Matching Pursuit

    CERN Document Server

    Wang, Jian; Shim, Byonghyo

    2011-01-01

    As a greedy algorithm to recover sparse signals from compressed measurements, the orthogonal matching pursuit (OMP) algorithm has received much attention in recent years. In this paper, we introduce an extension of the orthogonal matching pursuit (gOMP) for pursuing efficiency in reconstructing sparse signals. Our approach, henceforth referred to as generalized OMP (gOMP), is literally a generalization of the OMP in the sense that multiple indices are identified per iteration. Owing to the selection of multiple "correct" indices, the gOMP algorithm is finished with much smaller number of iterations compared to the OMP. We show that the gOMP can perfectly reconstruct any $K$-sparse signals ($K > 1$), provided that the sensing matrix satisfies the RIP with $\\delta_{NK} < \\frac{\\sqrt{N}}{\\sqrt{K} + 2 \\sqrt{N}}$. We also demonstrate by empirical simulations that the gOMP has excellent recovery performance comparable to $\\ell_1$-minimization technique with fast processing speed and competitive computational com...

  18. 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.

  19. 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.

  20. Nucleic acid modulation of gene expression: approaches for nucleic acid therapeutics against cancer.

    Science.gov (United States)

    Nakata, Yuji; Kim, Tae-Kon; Shetzline, Susan; Gewirtz, Alan M

    2005-01-01

    Most cancers are characterized by abnormal gene expression, which is thought to contribute to the pathogenesis and maintenance of the malignant phenotype; abnormal proliferation, maturation, and apoptosis. Silencing such genes would appear to be a rational approach to the therapy of cancer, and some preliminary clinical studies support this concept. Of the strategies available, the anti-mRNA gene silencing approach has attracted much attention and is the focus of this review. This strategy includes three types of agents: (1) single-stranded antisense oligonucleotides; (2) catalytically active oligonucleotides, such as ribozymes, and DNAzymes that possess inherent RNA cleaving activity; and (3) small interfering RNA (siRNA) molecules that induce RNA interference (RNAi). Among these agents, antisense oligonucleotides, especially phosphorothioate (PS) oligonucleotides, have been the most frequently used in clinical trials. In this article, we provide an overview of anti-mRNA gene silencing agents and their development for use as cancer therapeutics.

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

    Science.gov (United States)

    He, Qinbin; Xia, Zhile; Lin, Bin

    2016-11-07

    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.

  2. 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.

  3. An Analysis of Gene Expression Data using Penalized Fuzzy C-Means Approach

    OpenAIRE

    Banu, P. K. Nizar; Inbarani, H. Hannah

    2013-01-01

    With the rapid advances of microarray technologies, large amounts of high-dimensional gene expression data are being generated, which poses significant computational challenges. A first step towards addressing this challenge is the use of clustering techniques, which is essential in the data mining process to reveal natural structures and identify interesting patterns in the underlying data. A robust gene expression clustering approach to minimize undesirable clustering is proposed. In this p...

  4. Interactive Naive Bayesian network: A new approach of constructing gene-gene interaction network for cancer classification.

    Science.gov (United States)

    Tian, Xue W; Lim, Joon S

    2015-01-01

    Naive Bayesian (NB) network classifier is a simple and well-known type of classifier, which can be easily induced from a DNA microarray data set. However, a strong conditional independence assumption of NB network sometimes can lead to weak classification performance. In this paper, we propose a new approach of interactive naive Bayesian (INB) network to weaken the conditional independence of NB network and classify cancers using DNA microarray data set. We selected the differently expressed genes (DEGs) to reduce the dimension of the microarray data set. Then, an interactive parent which has the biggest influence among all DEGs is searched for each DEG. And then we calculate a weight to represent the interactive relationship between a DEG and its parent. Finally, the gene-gene interaction network is constructed. We experimentally test the INB network in terms of classification accuracy using leukemia and colon DNA microarray data sets, then we compare it with the NB network. The INB network can get higher classification accuracies than NB network. And INB network can show the gene-gene interactions visually.

  5. 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

  6. 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.

  7. RNA Interference (RNAi) Induced Gene Silencing: A Promising Approach of Hi-Tech Plant Breeding.

    Science.gov (United States)

    Younis, Adnan; Siddique, Muhammad Irfan; Kim, Chang-Kil; Lim, Ki-Byung

    2014-01-01

    RNA interference (RNAi) is a promising gene regulatory approach in functional genomics that has significant impact on crop improvement which permits down-regulation in gene expression with greater precise manner without affecting the expression of other genes. RNAi mechanism is expedited by small molecules of interfering RNA to suppress a gene of interest effectively. RNAi has also been exploited in plants for resistance against pathogens, insect/pest, nematodes, and virus that cause significant economic losses. Keeping beside the significance in the genome integrity maintenance as well as growth and development, RNAi induced gene syntheses are vital in plant stress management. Modifying the genes by the interference of small RNAs is one of the ways through which plants react to the environmental stresses. Hence, investigating the role of small RNAs in regulating gene expression assists the researchers to explore the potentiality of small RNAs in abiotic and biotic stress management. This novel approach opens new avenues for crop improvement by developing disease resistant, abiotic or biotic stress tolerant, and high yielding elite varieties.

  8. 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.

  9. 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,

  10. 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.

  11. Megathrust Earthquake Swarms Contemporaneous to Slow Slip and Non-Volcanic Tremor in Southern Mexico, Detected and Analyzed through a Template Matching Approach

    Science.gov (United States)

    Holtkamp, S.; Brudzinski, M. R.; Cabral-Cano, E.; Arciniega-Ceballos, A.

    2012-12-01

    An outstanding question in geophysics is the degree to which the newly discovered types of slow fault slip are related to their destructive cousin - the earthquake. Here, we utilize a local network along the Oaxacan segment of the Middle American subduction zone to investigate the potential relationship between slow slip, non-volcanic tremor (NVT), and earthquakes along the subduction megathrust. We have developed a multi-station "template matching" waveform cross correlation technique which is able to detect and locate events several orders of magnitude smaller than would be possible using more traditional techniques. Also, our template matching procedure is capable of consistently locate events which occur during periods of increased background activity (e.g., during productive NVT, loud cultural noise, or after larger earthquakes) because the multi-station detector is finely tuned to events with similar hypocentral location and focal mechanism. The local network in the Oaxaca region allows us to focus on documented megathrust earthquake swarms, which we focus on because slow slip is hypothesized to be the cause for earthquake swarms in some tectonic environments. We identify a productive earthquake swarm in July 2006 (~600 similar earthquakes detected), which occurred during a week-long episode of productive tremor and slow slip. Families of events in this sequence were also active during larger and longer slow slip events, which provides a potential link between slow slip in the transition zone and earthquakes at the downdip end of the seismogenic portion of the megathrust. Because template matching techniques only detect similar signals, detected waveforms can be stacked together to produce higher signal to noise ratios or cross correlated against each other to produce precise relative phase arrival times. We are using the refined signals to look for evidence of expansion or propagation of hypocenters during these earthquake swarms, which could be used as a

  12. A new approach to quantify the adaptive potential of gene expression variation in gymnosperms.

    Science.gov (United States)

    Renaut, Sébastien

    2013-05-01

    Variation in patterns of gene expression contributes to phenotypic diversity and can ultimately predict adaptive responses. However, in many cases, the consequences of regulatory mutations on patterns of gene expression and ultimately phenotypic differences remain elusive. A standard way to study the genetic architecture of expression variation in model systems has been to map gene expression variation to genetic loci (Fig. 1a). At the same time, in many nonmodel species, especially for long-lived organisms, controlled crosses are not feasible. If we are to expand our understanding of the role of regulatory mutations on phenotypes, we need to develop new methodologies to study species under ecologically relevant conditions. In this issue of Molecular Ecology, Verta et al. (2013) present a new approach to analyse gene expression variation and regulatory networks in gymnosperms (Fig. 1b). They capitalized on the fact that gymnosperm seeds contain an energy storage tissue (the megagametophyte) that is directly derived from a single haploid cell (the megaspore). The authors identified over 800 genes for which expression segregated in this maternally inherited haploid tissue. Based on the observed segregation patterns, these genes (Mendelian Expression Traits) are most probably controlled by biallelic variants at a single locus. Most of these genes also belonged to different regulatory networks, except for one large group of 180 genes under the control of a putative trans-acting factor. In addition, the approach developed here may also help to uncover the effect of rare recessive mutations, which usually remain hidden in a heterozygous state in diploid individuals. The appeal of the work by Verta et al. (2013) to study gene expression variation is in its simplicity, which circumvents several of the hurdles behind traditional expression quantitative trait locus (eQTL) studies, and could potentially be applied to a large number of species.

  13. 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.

  14. 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

  15. 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.

  16. Best matching theory & applications

    CERN Document Server

    Moghaddam, Mohsen

    2017-01-01

    Mismatch or best match? This book demonstrates that best matching of individual entities to each other is essential to ensure smooth conduct and successful competitiveness in any distributed system, natural and artificial. Interactions must be optimized through best matching in planning and scheduling, enterprise network design, transportation and construction planning, recruitment, problem solving, selective assembly, team formation, sensor network design, and more. Fundamentals of best matching in distributed and collaborative systems are explained by providing: § Methodical analysis of various multidimensional best matching processes § Comprehensive taxonomy, comparing different best matching problems and processes § Systematic identification of systems’ hierarchy, nature of interactions, and distribution of decision-making and control functions § Practical formulation of solutions based on a library of best matching algorithms and protocols, ready for direct applications and apps development. Design...

  17. 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...

  18. 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

    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 transcriptome, and may reveal novel genes affecting complex diseases. Integration of genomic and transcriptomic variation (expression quantitative trait loci [eQTL] mapping) has identified causal variants that affect complex diseases. We integrated transcriptomic data from adipose tissue and genomic data from...... a porcine model to investigate the mechanisms involved in obesity using a systems genetics approach. METHODS: Using a selective gene expression profiling approach, we selected 36 animals based on a previously created genomic Obesity Index for RNA sequencing of subcutaneous adipose tissue. Differential...

  19. 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.

  20. Gene editing in hematopoietic stem cells: a potential therapeutic approach for Fanconi anemia

    Energy Technology Data Exchange (ETDEWEB)

    Diez Cabezas, B.

    2015-07-01

    Gene therapy nowadays constitutes a safe and efficient treatment for a number of monogenic diseases affecting the hematopoietic system. Risks of insertional mutagenesis derived from the use of integrative vectors cannot, however, be completely excluded. Therefore, gene targeting has been proposed as a safer alternative, since the insertion of the herapeutic gene is driven to a specific locus in the genome. Gene targeting approaches are based on the use of specific nucleases which generate double strand breaks (DSBs) in a specific site of the genome,markedly enhancing the efficacy of homologous recombination (HR) with donor constructs harboring the gene of interest flanked by the corresponding homology arms. In this study we have optimized the conditions to target human lymphoblastic cell lines (LCLs) and also hematopoietic stem cells (HSCs) from healthy donors, with the final aim of correcting by gene editing the hematopoietic progenitor cells from Fanconi anemia subtype A (FA-A) patients. In particular, we have established a robust method to target both LCLs and HSCs in a safe harbor site in the genome, the AAVS1 locus. Our approach is based on the transduction of these cells with integrase-defective lentiviral vectors carrying a donor with the gene of interest, followed by the nucleofection of these cells with zinc finger nucleases used as mRNA. Using a control donor vector carrying the GFP reporter gene we have obtained, on average, 9.43% gene targeting efficiency in cord blood CD34+ cells from healthy donors. Moreover, we confirmed that gene targeting was also efficient in HSCs with long term and multipotent repopulation capacity, as demonstrated by transplants into immunodeficient mice. To improve the gene targeting efficiency, we investigated the feasibility of using gold nanoparticles, which were shown to improve the transduction efficiency of integrase-defective and competent lentiviral vectors in HSCs. This increment, however, did not lead to a higher gene

  1. Navigating the complex path between the oxytocin receptor gene (OXTR) and cooperation: an endophenotype approach.

    Science.gov (United States)

    Haas, Brian W; Anderson, Ian W; Smith, Jessica M

    2013-11-28

    Although cooperation represents a core facet of human social behavior there exists considerable variability across people in terms of the tendency to cooperate. One factor that may contribute to individual differences in cooperation is a key gene within the oxytocin (OT) system, the OT reception gene (OXTR). In this article, we aim to bridge the gap between the OXTR gene and cooperation by using an endophenotype approach. We present evidence that the association between the OXTR gene and cooperation may in part be due to how the OXTR gene affects brain systems involved in emotion recognition, empathy/theory of mind, social communication and social reward seeking. There is evidence that the OXTR gene is associated with the functional anatomy of the amygdala, visual cortex (VC), anterior cingulate and superior temporal gyrus (STG). However, it is currently unknown how the OXTR gene may be linked to the functional anatomy of other relevant brain regions that include the fusiform gyrus (FG), superior temporal sulcus (STS), ventromedial prefrontal cortex (VMPFC), temporoparietal junction (TPJ) and nucleus accumbens (NAcc). We conclude by highlighting potential future research directions that may elucidate the path between OXTR and complex behaviors such as cooperation.

  2. Navigating the complex path between the oxytocin receptor gene (OXTR and cooperation: an endophenotype approach

    Directory of Open Access Journals (Sweden)

    Brian W. Haas

    2013-11-01

    Full Text Available Although cooperation represents a core facet of human social behavior there exists considerable variability across people in terms of the tendency to cooperate. One factor that may contribute to individual differences in cooperation is a key gene within the oxytocin system, the oxytocin reception gene (OXTR. In this article, we aim to bridge the gap between the OXTR gene and cooperation by using an endophenotype approach. We present evidence that the association between the OXTR gene and cooperation may in part be due to how the OXTR gene affects brain systems involved in emotion recognition, empathy/theory of mind, social communication and social reward seeking. There is evidence that the OXTR gene may influence the functional anatomy of the amygdala, visual cortex, anterior cingulate and superior temporal gyrus. However, it is currently unknown how the OXTR gene may be linked to the functional anatomy of other relevant brain regions that include the fusiform gyrus, superior temporal sulcus, ventromedial prefrontal cortex, temporoparietal junction and nucleus accumbens. We conclude by highlighting potential future research directions that may elucidate the path between OXTR and complex behaviors such as cooperation.

  3. 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.

  4. Bioinformatics approach of salt tolerance gene in mangrove plant Rhizophora stylosa

    Science.gov (United States)

    Basyuni, M.; Sumardi

    2017-01-01

    This study descibes bioinformatics approach on the analyze of the salt tolerance genes in mangrove plant, Rhizophora stylosa on DDBJ/EMBL/GenBank as well as similarity, phylogenetic, potential peptide, and subcellular localization. The DNA sequence between salt tolerance gene from R. stylosa exhibited 42-11% between themselves The target peptide value of mitochondria varied from 0.163 to 0.430, indicated it was possible to exist. These results suggested the importance of understanding the diversity and functional of properties of the different amino acids in mangrove OSC genes. To clarify the relationship among the salt-tolerant genes in R. stylosa, a phylogenetic tree was constructed. The phylogenetic tree shows that there are three clusters, first branch of Cu/Zn SOD and reverse transcriptase genes, the second branch consists of the majority genes and the last group was MAP3K alpha protein kinase only. The present study, therefore, suggested that salt tolerance genes form distinct clusters in the tree.

  5. 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.

  6. 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

  7. A recursive network approach can identify constitutive regulatory circuits in gene expression data

    Science.gov (United States)

    Blasi, Monica Francesca; Casorelli, Ida; Colosimo, Alfredo; Blasi, Francesco Simone; Bignami, Margherita; Giuliani, Alessandro

    2005-03-01

    The activity of the cell is often coordinated by the organisation of proteins into regulatory circuits that share a common function. Genome-wide expression profiles might contain important information on these circuits. Current approaches for the analysis of gene expression data include clustering the individual expression measurements and relating them to biological functions as well as modelling and simulation of gene regulation processes by additional computer tools. The identification of the regulative programmes from microarray experiments is limited, however, by the intrinsic difficulty of linear methods to detect low-variance signals and by the sensitivity of the different approaches. Here we face the problem of recognising invariant patterns of correlations among gene expression reminiscent of regulation circuits. We demonstrate that a recursive neural network approach can identify genetic regulation circuits from expression data for ribosomal and genome stability genes. The proposed method, by greatly enhancing the sensitivity of microarray studies, allows the identification of important aspects of genetic regulation networks and might be useful for the discrimination of the different players involved in regulation circuits. Our results suggest that the constitutive regulatory networks involved in the generic organisation of the cell display a high degree of clustering depending on a modular architecture.

  8. 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

  9. 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

  10. Information content-based gene ontology semantic similarity approaches: toward a unified framework theory.

    Science.gov (United States)

    Mazandu, Gaston K; Mulder, Nicola J

    2013-01-01

    Several approaches have been proposed for computing term information content (IC) and semantic similarity scores within the gene ontology (GO) directed acyclic graph (DAG). These approaches contributed to improving protein analyses at the functional level. Considering the recent proliferation of these approaches, a unified theory in a well-defined mathematical framework is necessary in order to provide a theoretical basis for validating these approaches. We review the existing IC-based ontological similarity approaches developed in the context of biomedical and bioinformatics fields to propose a general framework and unified description of all these measures. We have conducted an experimental evaluation to assess the impact of IC approaches, different normalization models, and correction factors on the performance of a functional similarity metric. Results reveal that considering only parents or only children of terms when assessing information content or semantic similarity scores negatively impacts the approach under consideration. This study produces a unified framework for current and future GO semantic similarity measures and provides theoretical basics for comparing different approaches. The experimental evaluation of different approaches based on different term information content models paves the way towards a solution to the issue of scoring a term's specificity in the GO DAG.

  11. Information Content-Based Gene Ontology Semantic Similarity Approaches: Toward a Unified Framework Theory

    Science.gov (United States)

    Mazandu, Gaston K.; Mulder, Nicola J.

    2013-01-01

    Several approaches have been proposed for computing term information content (IC) and semantic similarity scores within the gene ontology (GO) directed acyclic graph (DAG). These approaches contributed to improving protein analyses at the functional level. Considering the recent proliferation of these approaches, a unified theory in a well-defined mathematical framework is necessary in order to provide a theoretical basis for validating these approaches. We review the existing IC-based ontological similarity approaches developed in the context of biomedical and bioinformatics fields to propose a general framework and unified description of all these measures. We have conducted an experimental evaluation to assess the impact of IC approaches, different normalization models, and correction factors on the performance of a functional similarity metric. Results reveal that considering only parents or only children of terms when assessing information content or semantic similarity scores negatively impacts the approach under consideration. This study produces a unified framework for current and future GO semantic similarity measures and provides theoretical basics for comparing different approaches. The experimental evaluation of different approaches based on different term information content models paves the way towards a solution to the issue of scoring a term's specificity in the GO DAG. PMID:24078912

  12. Matchings in hexagonal cacti

    Directory of Open Access Journals (Sweden)

    E. J. Farrell

    1987-01-01

    Full Text Available Explicit recurrences are derived for the matching polynomials of the basic types of hexagonal cacti, the linear cactus and the star cactus and also for an associated graph, called the hexagonal crown. Tables of the polynomials are given for each type of graph. Explicit formulae are then obtained for the number of defect-d matchings in the graphs, for various values of d. In particular, formulae are derived for the number of perfect matchings in all three types of graphs. Finally, results are given for the total number of matchings in the graphs.

  13. To control false positives in gene-gene interaction analysis: two novel conditional entropy-based approaches.

    Directory of Open Access Journals (Sweden)

    Xiaoyu Zuo

    Full Text Available Genome-wide analysis of gene-gene interactions has been recognized as a powerful avenue to identify the missing genetic components that can not be detected by using current single-point association analysis. Recently, several model-free methods (e.g. the commonly used information based metrics and several logistic regression-based metrics were developed for detecting non-linear dependence between genetic loci, but they are potentially at the risk of inflated false positive error, in particular when the main effects at one or both loci are salient. In this study, we proposed two conditional entropy-based metrics to challenge this limitation. Extensive simulations demonstrated that the two proposed metrics, provided the disease is rare, could maintain consistently correct false positive rate. In the scenarios for a common disease, our proposed metrics achieved better or comparable control of false positive error, compared to four previously proposed model-free metrics. In terms of power, our methods outperformed several competing metrics in a range of common disease models. Furthermore, in real data analyses, both metrics succeeded in detecting interactions and were competitive with the originally reported results or the logistic regression approaches. In conclusion, the proposed conditional entropy-based metrics are promising as alternatives to current model-based approaches for detecting genuine epistatic effects.

  14. 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.

  15. 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.

  16. Understanding Y haplotype matching probability.

    Science.gov (United States)

    Brenner, Charles H

    2014-01-01

    The Y haplotype population-genetic terrain is better explored from a fresh perspective rather than by analogy with the more familiar autosomal ideas. For haplotype matching probabilities, versus for autosomal matching probabilities, explicit attention to modelling - such as how evolution got us where we are - is much more important while consideration of population frequency is much less so. This paper explores, extends, and explains some of the concepts of "Fundamental problem of forensic mathematics - the evidential strength of a rare haplotype match". That earlier paper presented and validated a "kappa method" formula for the evidential strength when a suspect matches a previously unseen haplotype (such as a Y-haplotype) at the crime scene. Mathematical implications of the kappa method are intuitive and reasonable. Suspicions to the contrary raised in rest on elementary errors. Critical to deriving the kappa method or any sensible evidential calculation is understanding that thinking about haplotype population frequency is a red herring; the pivotal question is one of matching probability. But confusion between the two is unfortunately institutionalized in much of the forensic world. Examples make clear why (matching) probability is not (population) frequency and why uncertainty intervals on matching probabilities are merely confused thinking. Forensic matching calculations should be based on a model, on stipulated premises. The model inevitably only approximates reality, and any error in the results comes only from error in the model, the inexactness of the approximation. Sampling variation does not measure that inexactness and hence is not helpful in explaining evidence and is in fact an impediment. Alternative haplotype matching probability approaches that various authors have considered are reviewed. Some are based on no model and cannot be taken seriously. For the others, some evaluation of the models is discussed. Recent evidence supports the adequacy of

  17. 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.

  18. Whole genome phylogeny of Prochlorococcus marinus group of cyanobacteria: genome alignment and overlapping gene approach.

    Science.gov (United States)

    Prabha, Ratna; Singh, Dhananjaya P; Gupta, Shailendra K; Rai, Anil

    2014-06-01

    Prochlorococcus is the smallest known oxygenic phototrophic marine cyanobacterium dominating the mid-latitude oceans. Physiologically and genetically distinct P. marinus isolates from many oceans in the world were assigned two different groups, a tightly clustered high-light (HL)-adapted and a divergent low-light (LL-) adapted clade. Phylogenetic analysis of this cyanobacterium on the basis of 16S rRNA and other conserved genes did not show consistency with its phenotypic behavior. We analyzed phylogeny of this genus on the basis of complete genome sequences through genome alignment, overlapping-gene content and gene-order approach. Phylogenetic tree of P. marinus obtained by comparing whole genome sequences in contrast to that based on 16S rRNA gene, corresponded well with the HL/LL ecotypic distinction of twelve strains and showed consistency with phenotypic classification of P. marinus. Evidence for the horizontal descent and acquisition of genes within and across the genus was observed. Many genes involved in metabolic functions were found to be conserved across these genomes and many were continuously gained by different strains as per their needs during the course of their evolution. Consistency in the physiological and genetic phylogeny based on whole genome sequence is established. These observations improve our understanding about the adaptation and diversification of these organisms under evolutionary pressure.

  19. 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.

  20. Ontology Matching Across Domains

    Science.gov (United States)

    2010-05-01

    matching include GMO [1], Anchor-Prompt [2], and Similarity Flooding [3]. GMO is an iterative structural matcher, which uses RDF bipartite graphs to...AFRL under contract# FA8750-09-C-0058. References [1] Hu, W., Jian, N., Qu, Y., Wang, Y., “ GMO : a graph matching for ontologies”, in: Proceedings of

  1. A cellular genetics approach identifies gene-drug interactions and pinpoints drug toxicity pathway nodes

    Directory of Open Access Journals (Sweden)

    Oscar Takeo Suzuki

    2014-08-01

    Full Text Available New approaches to toxicity testing have incorporated high-throughput screening across a broad-range of in vitro assays to identify potential key events in response to chemical or drug treatment. To date, these approaches have primarily utilized repurposed drug discovery assays. In this study, we describe an approach that combines in vitro screening with genetic approaches for the experimental identification of genes and pathways involved in chemical or drug toxicity. Primary embryonic fibroblasts isolated from 32 genetically-characterized inbred mouse strains were treated in concentration-response format with 65 compounds, including pharmaceutical drugs, environmental chemicals, and compounds with known modes-of-action. Integrated cellular responses were measured at 24 and 72 hours using high-content imaging and included cell loss, membrane permeability, mitochondrial function, and apoptosis. Genetic association analysis of cross-strain differences in the cellular responses resulted in a collection of candidate loci potentially underlying the variable strain response to each chemical. As a demonstration of the approach, one candidate gene involved in rotenone sensitivity, Cybb, was experimentally validated in vitro and in vivo. Pathway analysis on the combined list of candidate loci across all chemicals identified a number of over-connected nodes that may serve as core regulatory points in toxicity pathways.

  2. Investigating meta-approaches for reconstructing gene networks in a mammalian cellular context.

    Directory of Open Access Journals (Sweden)

    Azree Nazri

    Full Text Available The output of state-of-the-art reverse-engineering methods for biological networks is often based on the fitting of a mathematical model to the data. Typically, different datasets do not give single consistent network predictions but rather an ensemble of inconsistent networks inferred under the same reverse-engineering method that are only consistent with the specific experimentally measured data. Here, we focus on an alternative approach for combining the information contained within such an ensemble of inconsistent gene networks called meta-analysis, to make more accurate predictions and to estimate the reliability of these predictions. We review two existing meta-analysis approaches; the Fisher transformation combined coefficient test (FTCCT and Fisher's inverse combined probability test (FICPT; and compare their performance with five well-known methods, ARACNe, Context Likelihood or Relatedness network (CLR, Maximum Relevance Minimum Redundancy (MRNET, Relevance Network (RN and Bayesian Network (BN. We conducted in-depth numerical ensemble simulations and demonstrated for biological expression data that the meta-analysis approaches consistently outperformed the best gene regulatory network inference (GRNI methods in the literature. Furthermore, the meta-analysis approaches have a low computational complexity. We conclude that the meta-analysis approaches are a powerful tool for integrating different datasets to give more accurate and reliable predictions for biological networks.

  3. Advanced targeted, cell and gene therapy approaches for pediatric hematological malignancies: results and future perspectives

    Directory of Open Access Journals (Sweden)

    Chiara Francesca Magnani

    2013-04-01

    Full Text Available Despite the survival of pediatric patients affected by hematological malignancies being improved in the last 20 years by chemotherapy and hematopoietic stem cell transplantation (HSCT, a significant amount of patients still relapses. Treatment intensification is limited by toxic side effects and is constrained by the plateau of efficacy, while the pipeline of new chemotherapeutic drugs is running short. Therefore, novel therapeutic strategies are essential and researchers around the world are testing in clinical trials immune and gene therapy approaches as second-line treatments. The aim of this review is to give a glance at these novel promising strategies of advanced medicine in the field of pediatric leukemias. Results from clinical protocols using new targeted smart drugs, immunotherapy and gene therapy are summarized, and important considerations regarding the combination of these novel approaches with standard treatments to promote safe and long-term cure are discussed.

  4. Shortening trinucleotide repeats using highly specific endonucleases: a possible approach to gene therapy?

    Science.gov (United States)

    Richard, Guy-Franck

    2015-04-01

    Trinucleotide repeat expansions are involved in more than two dozen neurological and developmental disorders. Conventional therapeutic approaches aimed at regulating the expression level of affected genes, which rely on drugs, oligonucleotides, and/or transgenes, have met with only limited success so far. An alternative approach is to shorten repeats to non-pathological lengths using highly specific nucleases. Here, I review early experiments using meganucleases, zinc-finger nucleases (ZFN), and transcription-activator like effector nucleases (TALENs) to contract trinucleotide repeats, and discuss the possibility of using CRISPR-Cas nucleases to the same end. Although this is a nascent field, I explore the possibility of designing nucleases and effectively delivering them in the context of gene therapy.

  5. 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.

  6. Matched-pair classification

    Energy Technology Data Exchange (ETDEWEB)

    Theiler, James P [Los Alamos National Laboratory

    2009-01-01

    Following an analogous distinction in statistical hypothesis testing, we investigate variants of machine learning where the training set comes in matched pairs. We demonstrate that even conventional classifiers can exhibit improved performance when the input data has a matched-pair structure. Online algorithms, in particular, converge quicker when the data is presented in pairs. In some scenarios (such as the weak signal detection problem), matched pairs can be generated from independent samples, with the effect not only doubling the nominal size of the training set, but of providing the structure that leads to better learning. A family of 'dipole' algorithms is introduced that explicitly takes advantage of matched-pair structure in the input data and leads to further performance gains. Finally, we illustrate the application of matched-pair learning to chemical plume detection in hyperspectral imagery.

  7. Learning Graph Matching

    CERN Document Server

    Caetano, Tiberio S; Cheng, Li; Le, Quoc V; Smola, Alex J

    2008-01-01

    As a fundamental problem in pattern recognition, graph matching has applications in a variety of fields, from computer vision to computational biology. In graph matching, patterns are modeled as graphs and pattern recognition amounts to finding a correspondence between the nodes of different graphs. Many formulations of this problem can be cast in general as a quadratic assignment problem, where a linear term in the objective function encodes node compatibility and a quadratic term encodes edge compatibility. The main research focus in this theme is about designing efficient algorithms for approximately solving the quadratic assignment problem, since it is NP-hard. In this paper we turn our attention to a different question: how to estimate compatibility functions such that the solution of the resulting graph matching problem best matches the expected solution that a human would manually provide. We present a method for learning graph matching: the training examples are pairs of graphs and the `labels' are ma...

  8. A Hybrid One-Way ANOVA Approach for the Robust and Efficient Estimation of Differential Gene Expression with Multiple Patterns

    OpenAIRE

    Mohammad Manir Hossain Mollah; Rahman Jamal; Norfilza Mohd Mokhtar; Roslan Harun; Md. Nurul Haque Mollah

    2015-01-01

    Background Identifying genes that are differentially expressed (DE) between two or more conditions with multiple patterns of expression is one of the primary objectives of gene expression data analysis. Several statistical approaches, including one-way analysis of variance (ANOVA), are used to identify DE genes. However, most of these methods provide misleading results for two or more conditions with multiple patterns of expression in the presence of outlying genes. In this paper, an attempt ...

  9. 一种用于无源UHF RFID应答器的阻抗匹配方法%A Novel Impedance Matching Approach for Passive UHF RFID Transponder ICs

    Institute of Scientific and Technical Information of China (English)

    陈力颖; 毛陆虹; 吴顺华; 郑轩

    2008-01-01

    This paper presents a novel impedance matching approach for passive UHF RFID transponder ICs, which are compatible with the ISO/IEC 18000-6B standard and operate in the 915MHz ISM band. The passive UHF RFID transpon- der with complex impedances is powered by received RF energy. The approach uses the parasitic inductance of the antenna to implement ASK modulation by adjusting the capacitive reactance of the matching network, which changes with the backscatter circuit. The impedance matching achieves maximum power transfer between the reader, antenna, and tran- sponder. The transponder IC, whose operating distance is more than 4m with the impedance matching approach, is fabrica- ted using a Chartered 0. 35μm two-poly four-metal CMOS process that supports Schottkv diodes and EEPROM.%提出了一种可以在915MHz ISM频带下工作的、符合ISO/IEC 18000-6B标准的无源UHF RFID应答器的阻抗匹配方法.该UHF RFID应答器具有复数阻抗并从射频电磁场接收能量.该阻抗匹配方法利用天线的寄生电感,通过调整反向散射电路的电容来改变匹配网络的容抗,从而实现ASK调制.而且,该阻抗匹配方法在阅读器、天线与应答器之间达到了最大的功率传输.采用该阻抗匹配方法的应答器芯片通过支持肖特基二极管和EEPROM的Chartered 0.35μm 2P4M CMOS工艺进行流片,经测试其工作距离约为4m.

  10. 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.

  11. 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.

  12. 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

  13. 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

  14. Machine learning approaches to supporting the identification of photoreceptor-enriched genes based on expression data

    Directory of Open Access Journals (Sweden)

    Simpson David

    2006-03-01

    Full Text Available Abstract Background Retinal photoreceptors are highly specialised cells, which detect light and are central to mammalian vision. Many retinal diseases occur as a result of inherited dysfunction of the rod and cone photoreceptor cells. Development and maintenance of photoreceptors requires appropriate regulation of the many genes specifically or highly expressed in these cells. Over the last decades, different experimental approaches have been developed to identify photoreceptor enriched genes. Recent progress in RNA analysis technology has generated large amounts of gene expression data relevant to retinal development. This paper assesses a machine learning methodology for supporting the identification of photoreceptor enriched genes based on expression data. Results Based on the analysis of publicly-available gene expression data from the developing mouse retina generated by serial analysis of gene expression (SAGE, this paper presents a predictive methodology comprising several in silico models for detecting key complex features and relationships encoded in the data, which may be useful to distinguish genes in terms of their functional roles. In order to understand temporal patterns of photoreceptor gene expression during retinal development, a two-way cluster analysis was firstly performed. By clustering SAGE libraries, a hierarchical tree reflecting relationships between developmental stages was obtained. By clustering SAGE tags, a more comprehensive expression profile for photoreceptor cells was revealed. To demonstrate the usefulness of machine learning-based models in predicting functional associations from the SAGE data, three supervised classification models were compared. The results indicated that a relatively simple instance-based model (KStar model performed significantly better than relatively more complex algorithms, e.g. neural networks. To deal with the problem of functional class imbalance occurring in the dataset, two data re

  15. 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.

  16. 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.

  17. 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.

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

    Science.gov (United States)

    Tamas, Ivica; Hodges, Emily; Dessi, Patrick; Johnsen, Robert; Vaz Gomes, Ana

    2005-01-01

    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. PMID:15877817

  19. Learning graph matching.

    Science.gov (United States)

    Caetano, Tibério S; McAuley, Julian J; Cheng, Li; Le, Quoc V; Smola, Alex J

    2009-06-01

    As a fundamental problem in pattern recognition, graph matching has applications in a variety of fields, from computer vision to computational biology. In graph matching, patterns are modeled as graphs and pattern recognition amounts to finding a correspondence between the nodes of different graphs. Many formulations of this problem can be cast in general as a quadratic assignment problem, where a linear term in the objective function encodes node compatibility and a quadratic term encodes edge compatibility. The main research focus in this theme is about designing efficient algorithms for approximately solving the quadratic assignment problem, since it is NP-hard. In this paper we turn our attention to a different question: how to estimate compatibility functions such that the solution of the resulting graph matching problem best matches the expected solution that a human would manually provide. We present a method for learning graph matching: the training examples are pairs of graphs and the 'labels' are matches between them. Our experimental results reveal that learning can substantially improve the performance of standard graph matching algorithms. In particular, we find that simple linear assignment with such a learning scheme outperforms Graduated Assignment with bistochastic normalisation, a state-of-the-art quadratic assignment relaxation algorithm.

  20. Latent fingerprint matching.

    Science.gov (United States)

    Jain, Anil K; Feng, Jianjiang

    2011-01-01

    Latent fingerprint identification is of critical importance to law enforcement agencies in identifying suspects: Latent fingerprints are inadvertent impressions left by fingers on surfaces of objects. While tremendous progress has been made in plain and rolled fingerprint matching, latent fingerprint matching continues to be a difficult problem. Poor quality of ridge impressions, small finger area, and large nonlinear distortion are the main difficulties in latent fingerprint matching compared to plain or rolled fingerprint matching. We propose a system for matching latent fingerprints found at crime scenes to rolled fingerprints enrolled in law enforcement databases. In addition to minutiae, we also use extended features, including singularity, ridge quality map, ridge flow map, ridge wavelength map, and skeleton. We tested our system by matching 258 latents in the NIST SD27 database against a background database of 29,257 rolled fingerprints obtained by combining the NIST SD4, SD14, and SD27 databases. The minutiae-based baseline rank-1 identification rate of 34.9 percent was improved to 74 percent when extended features were used. In order to evaluate the relative importance of each extended feature, these features were incrementally used in the order of their cost in marking by latent experts. The experimental results indicate that singularity, ridge quality map, and ridge flow map are the most effective features in improving the matching accuracy.

  1. 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

  2. AN EVEN ODD MULTIPLE PATTERN MATCHING ALGORITHM

    OpenAIRE

    Raju Bhukya; DVLN Somayajulu

    2011-01-01

    Pattern matching plays an important role in various applications ranging from text searching in word processors to identification of functional and structural behavior in proteins and genes. Pattern matching is one of the fundamental areas in the field of computational biology. Currently research in life science area is producing large amount of genetic data. Due to this large and use full information can be gained by finding valuable information available from the genomic sequences. Many alg...

  3. 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...

  4. 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...

  5. Cognitive Levels Matching.

    Science.gov (United States)

    Brooks, Martin; And Others

    1983-01-01

    The Cognitive Levels Matching Project trains teachers to guide students' skill acquisition and problem-solving processes by assessing students' cognitive levels and adapting their teaching materials accordingly. (MLF)

  6. 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.

  7. SEMI-GLOBAL MATCHING IN OBJECT SPACE

    Directory of Open Access Journals (Sweden)

    F. Bethmann

    2015-03-01

    Full Text Available Semi-Global Matching (SGM is a widespread algorithm for image matching which is used for very different applications, ranging from real-time applications (e.g. for generating 3D data for driver assistance systems to aerial image matching. Originally developed for stereo-image matching, several extensions have been proposed to use more than two images within the matching process (multi-baseline matching, multi-view stereo. These extensions still perform the image matching in (rectified stereo images and combine the pairwise results afterwards to create the final solution. This paper proposes an alternative approach which is suitable for the introduction of an arbitrary number of images into the matching process and utilizes image matching by using non-rectified images. The new method differs from the original SGM method mainly in two aspects: Firstly, the cost calculation is formulated in object space within a dense voxel raster by using the grey (or colour values of all images instead of pairwise cost calculation in image space. Secondly, the semi-global (path-wise minimization process is transferred into object space as well, so that the result of semi-global optimization leads to index maps (instead of disparity maps which directly indicate the 3D positions of the best matches. Altogether, this yields to an essential simplification of the matching process compared to multi-view stereo (MVS approaches. After a description of the new method, results achieved from two different datasets (close-range and aerial are presented and discussed.

  8. PUMA: The Positional Update and Matching Algorithm

    Science.gov (United States)

    Line, J. L. B.; Webster, R. L.; Pindor, B.; Mitchell, D. A.; Trott, C. M.

    2017-01-01

    We present new software to cross-match low-frequency radio catalogues: the Positional Update and Matching Algorithm. The Positional Update and Matching Algorithm combines a positional Bayesian probabilistic approach with spectral matching criteria, allowing for confusing sources in the matching process. We go on to create a radio sky model using Positional Update and Matching Algorithm based on the Murchison Widefield Array Commissioning Survey, and are able to automatically cross-match 98.5% of sources. Using the characteristics of this sky model, we create simple simulated mock catalogues on which to test the Positional Update and Matching Algorithm, and find that Positional Update and Matching Algorithm can reliably find the correct spectral indices of sources, along with being able to recover ionospheric offsets. Finally, we use this sky model to calibrate and remove foreground sources from simulated interferometric data, generated using OSKAR (the Oxford University visibility generator). We demonstrate that there is a substantial improvement in foreground source removal when using higher frequency and higher resolution source positions, even when correcting positions by an average of 0.3 arcmin given a synthesised beam-width of 2.3 arcmin.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. Research advances in gene therapy approaches for the treatment of amyotrophic lateral sclerosis.

    Science.gov (United States)

    Nizzardo, Monica; Simone, Chiara; Falcone, Marianna; Riboldi, Giulietta; Rizzo, Federica; Magri, Francesca; Bresolin, Nereo; Comi, Giacomo P; Corti, Stefania

    2012-05-01

    Amyotrophic lateral sclerosis (ALS) is a devastating neurodegenerative disease of motor neurons that causes progressive muscle weakness, paralysis, and premature death. No effective therapy is available. Research in the motor neuron field continues to grow, and recent breakthroughs have demonstrated the possibility of completely achieving rescue in animal models of spinal muscular atrophy, a genetic motor neuron disease. With adeno-associated virus (AAV) vectors, gene transfer can be achieved with systemic non-invasive injection and minimal toxicity. In the context of this success, we review gene therapy approaches for ALS, considering what has been done and the possible future directions for effective application of the latest generation of vectors for clinical translation. We focus on recent developments in the areas of RNA/antisense-mediated silencing of specific ALS causative genes like superoxide dismutase-1 and other molecular pathogenetic targets, as well as the administration of neuroprotective factors with viral vectors. We argue that gene therapy offers new opportunities to open the path for clinical progress in treating ALS.

  14. A simple approach for estimating gene expression in Candida albicans directly from a systemic infection site.

    Science.gov (United States)

    Andes, D; Lepak, A; Pitula, A; Marchillo, K; Clark, J

    2005-09-01

    Gene expression analysis after the host-pathogen interaction is revolutionizing our understanding of the host response to infection. Numerous studies have utilized microarray analysis to follow host cell transcriptome alterations in response to interactions with infectious pathogens. However, similar analyses of pathogen transcriptional adaptation at the infection site have been limited. Understanding the nature of this interaction from the pathogen perspective at different sites and stages of infection is central to strategies for development of new anti-infective therapies. Toward this end, we developed a protocol to analyze changes in gene expression for a eukaryotic pathogen, Candida albicans, during systemic infection in mice. The experimental approach takes advantage of the resistance of the cell wall of many fungal pathogens to cell lysis, relative to mammalian cells. After lysis of mammalian cells, the tissue mixture containing fungal cells is depleted of mammalian RNA by centrifugation, followed by enzymatic digestion. RNA-digesting enzymes are then inhibited before eukaryotic cell lysis and RNA isolation. The protocol provides a reproducible quantity of RNA based on pathogen cell number. The quality of the RNA allowed reliable downstream transcriptional analysis using reverse-transcription polymerase chain reaction and microarrays. The in vivo gene expression data confirmed involvement of several putative pathogenesis genes. More importantly, the results provided a wealth of biologically interesting hypotheses to direct future investigation.

  15. 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

  16. Epigenetic phenomena, chromatin dynamics, and gene expression. New theoretical approaches in the study of living systems.

    Science.gov (United States)

    Boi, Luciano

    2008-01-01

    This paper is aimed at exploring the genome at the level beyond that of DNA sequence alone. We stress the fact that the level of genes is not the sole "reality" in the living world, for there are different epigenetic processes that profoundly affect change in living systems. Moreover, epigenetics very likely influences the course of evolution and the unfolding of life. We further attempt to investigate how the genome is dynamically organized into the nuclear space within the cell. We mainly focus on analyses of higher order nuclear architecture and the dynamic interactions of chromatin with other nuclear components. We especially want to know how epigenetic phenomena influences genes expression and chromosome functions. The proper understanding of these processes require new concepts and approaches be introduced and developed. In particular, we think that research in biology has to shift from only describing molecular and local features of living systems to studying the regulatory networks of interactions among gene pathways, the folding and dynamics of chromatin structure and how environmental factors affects the behavior of organisms. There are essential components of biological information on living organisms which cannot be portrayed in the DNA sequence alone. In a post-genomic era, the importance of chromatin/epigenetic interface has become increasingly apparent. One of the purposes of current research should be to highlight the enormous impact of chromatin organization and dynamics on epigenetic phenomena, and, conversely, to emphasize the important role that epigenetic phenomena play in gene expression and cell regulation.

  17. Gene editing and genetic engineering approaches for advanced probiotics: A Review.

    Science.gov (United States)

    Yadav, Ruby; Kumar, Vishal; Baweja, Mehak; Shukla, Pratyoosh

    2017-01-10

    The applications of probiotics are significant and thus resulted in need of genome analysis of probiotic strains. Various omics methods and systems biology approaches enables us to understand and optimize the metabolic processes. These techniques have increased the researcher's attention towards gut microbiome and provided a new source for the revelation of uncharacterized biosynthetic pathways which enables novel metabolic engineering approaches. In recent years, the broad and quantitative analysis of modified strains relies on systems biology tools such as in silico design which are commonly used methods for improving strain performance. The genetic manipulation of probiotic microorganisms is crucial for defining their role in intestinal microbiota and exploring their beneficial properties. This review describes an overview of gene editing and system biology approaches, highlighting the advent of omics methods which allows the study of new routes for studying probiotic bacteria. We have also summarized gene editing tools like TALEN, ZFNs and CRISPR-Cas that edits or cleave the specific target DNA. Furthermore, in this review an overview of proposed design of advanced customized probiotic is also hypothesized to improvise the probiotics.

  18. 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.

  19. 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.

  20. 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.

  1. An approach towards bronchoscopic-based gene therapy using electrical field accelerated plasmid droplets.

    Science.gov (United States)

    Hradetzky, D; Boehringer, S; Geiser, Th; Gazdhar, A

    2012-01-01

    Idiopathic pulmonary fibrosis (IPF) is a devastating disease affecting the distal lung, due to failure of the alveolar epithelium to heal after micro-injuries, leading to inefficient gas exchange and resulting in death. Therapeutic options are very limited. A new therapeutic approach based on gene therapy restores the self-healing process within the lung in the experimental setup. A basic requirement of this therapy is the successful transduction of genes into the alveolar epithelium in the distal part of the lung, for which a new therapeutic instrument is required. In this paper we present the concept and first experimental results of a device which uses an electrical field to accelerate the charged droplets of plasmid suspension toward the tissue and which overcomes cell membrane with its impact energy. The aim is to develop a therapeutic device capable of being integrated into minimally invasive procedures such as bronchoscopy.

  2. 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.

  3. Stochastic Boolean networks: An efficient approach to modeling gene regulatory networks

    Directory of Open Access Journals (Sweden)

    Liang Jinghang

    2012-08-01

    network inferred from a T cell immune response dataset. An SBN can also implement the function of an asynchronous PBN and is potentially useful in a hybrid approach in combination with a continuous or single-molecule level stochastic model. Conclusions Stochastic Boolean networks (SBNs are proposed as an efficient approach to modelling gene regulatory networks (GRNs. The SBN approach is able to recover biologically-proven regulatory behaviours, such as the oscillatory dynamics of the p53-Mdm2 network and the dynamic attractors in a T cell immune response network. The proposed approach can further predict the network dynamics when the genes are under perturbation, thus providing biologically meaningful insights for a better understanding of the dynamics of GRNs. The algorithms and methods described in this paper have been implemented in Matlab packages, which are attached as Additional files.

  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. PUMA: The Positional Update and Matching Algorithm

    CERN Document Server

    Line, J L B; Pindor, B; Mitchell, D A; Trott, C M

    2016-01-01

    We present new software to cross-match low-frequency radio catalogues: the Positional Update and Matching Algorithm (PUMA). PUMA combines a positional Bayesian probabilistic approach with spectral matching criteria, allowing for confusing sources in the matching process. We go on to create a radio sky model using PUMA based on the Murchison Widefield Array Commissioning Survey, and are able to automatically cross-match 98.5% of sources. Using the characteristics of this sky model, we create simple simulated mock catalogues on which to test PUMA, and find that PUMA can reliably find the correct spectral indices of sources, along with being able to recover ionospheric offsets. Finally, we use this sky model to calibrate and remove foreground sources from simulated interferometric data, generated using OSKAR (the Oxford University visibility generator). We demonstrate that there is a substantial improvement in foreground source removal when using higher frequency and higher resolution source positions, even when...

  6. 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

  7. Evaluating the effects of genetic variants of DNA repair genes using cytogenetic mutagen sensitivity approaches.

    Science.gov (United States)

    Abdel-Rahman, Sherif Z; El-Zein, Randa A

    2011-08-01

    Mutagen sensitivity, measured in short-term cultures of peripheral blood lymphocytes by cytogenetic endpoints, is an indirect measure for DNA repair capacity and has been used for many years as a biomarker for intrinsic susceptibility for cancer. In this article, we briefly give an overview of the different cytogenetic mutagen sensitivity approaches that have been used successfully to evaluate the biological effects of polymorphisms in DNA repair genes based on a current review of the literature and based on the need for biomarkers that would allow the characterization of the biological and functional significance of such polymorphisms. We also address some of the future challenges facing this emerging area of research.

  8. 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.

  9. 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.

  10. 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...

  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...... nodes and the arc prior models variations in row and column spacing across the grid. Grid matching is done by placing an initial rough grid over the image and applying an ensemble annealing scheme to maximize the posterior distribution of the grid. The method can be applied to noisy images with missing...

  12. Middle matching mining algorithm

    Institute of Scientific and Technical Information of China (English)

    GUO Ping; CHEN Li

    2003-01-01

    A new algorithm for fast discovery of sequential patterns to solve the problems of too many candidate sets made by SPADE is presented, which is referred to as middle matching algorithm. Experiments on a large customer transaction database consisting of customer_id, transaction time, and transaction items demonstrate that the proposed algorithm performs better than SPADE attributed to its philosophy to generate a candidate set by matching two sequences in the middle place so as to reduce the number of the candidate sets.

  13. 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

  14. 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.

  15. A top-down approach for construction of hybrid polymer-virus gene delivery vectors.

    Science.gov (United States)

    Ramsey, Joshua D; Vu, Halong N; Pack, Daniel W

    2010-05-21

    Safe and efficient delivery of therapeutic nucleic acids remains the primary hurdle for human gene therapy. While many researchers have attempted to re-engineer viruses to be suited for gene delivery, others have sought to develop non-viral alternatives. We have developed a complementary approach in which viral and synthetic components are combined to form hybrid nanoparticulate vectors. In particular, we complexed non-infectious retrovirus-like particles lacking a viral envelope protein, from Moloney murine leukemia virus (M-VLP) or human immunodeficiency virus (H-VLP), with poly-L-lysine (PLL) or polyethylenimine (PEI) over a range of polymer/VLP ratios. At appropriate stoichiometry (75-250 microg polymer/10(6) VLP), the polymers replace the function of the viral envelope protein and interact with the target cell membrane, initiate cellular uptake and facilitate escape from endocytic vesicles. The viral particle, once in the cytosol, efficiently completes its normal infection process including integration of viral genes with the host genome as demonstrated by long-term (at least 5 weeks) transgene expression. In addition, hybrid vectors comprising H-VLP were shown to be capable of infecting non-dividing cells.

  16. Detecting the existence of gene flow between Spanish and North African goats through a coalescent approach.

    Science.gov (United States)

    Martínez, Amparo; Manunza, Arianna; Delgado, Juan Vicente; Landi, Vincenzo; Adebambo, Ayotunde; Ismaila, Muritala; Capote, Juan; El Ouni, Mabrouk; Elbeltagy, Ahmed; Abushady, Asmaa M; Galal, Salah; Ferrando, Ainhoa; Gómez, Mariano; Pons, Agueda; Badaoui, Bouabid; Jordana, Jordi; Vidal, Oriol; Amills, Marcel

    2016-12-14

    Human-driven migrations are one of the main processes shaping the genetic diversity and population structure of domestic species. However, their magnitude and direction have been rarely analysed in a statistical framework. We aimed to estimate the impact of migration on the population structure of Spanish and African goats. To achieve this goal, we analysed a dataset of 1,472 individuals typed with 23 microsatellites. Population structure of African and Spanish goats was moderate (mean FST = 0.07), with the exception of the Canarian and South African breeds that displayed a significant differentiation when compared to goats from North Africa and Nigeria. Measurement of gene flow with Migrate-n and IMa coalescent genealogy samplers supported the existence of a bidirectional gene flow between African and Spanish goats. Moreover, IMa estimates of the effective number of migrants were remarkably lower than those calculated with Migrate-n and classical approaches. Such discrepancies suggest that recent divergence, rather than extensive gene flow, is the main cause of the weak population structure observed in caprine breeds.

  17. Detecting the existence of gene flow between Spanish and North African goats through a coalescent approach

    Science.gov (United States)

    Martínez, Amparo; Manunza, Arianna; Delgado, Juan Vicente; Landi, Vincenzo; Adebambo, Ayotunde; Ismaila, Muritala; Capote, Juan; El Ouni, Mabrouk; Elbeltagy, Ahmed; Abushady, Asmaa M.; Galal, Salah; Ferrando, Ainhoa; Gómez, Mariano; Pons, Agueda; Badaoui, Bouabid; Jordana, Jordi; Vidal, Oriol; Amills, Marcel

    2016-01-01

    Human-driven migrations are one of the main processes shaping the genetic diversity and population structure of domestic species. However, their magnitude and direction have been rarely analysed in a statistical framework. We aimed to estimate the impact of migration on the population structure of Spanish and African goats. To achieve this goal, we analysed a dataset of 1,472 individuals typed with 23 microsatellites. Population structure of African and Spanish goats was moderate (mean FST = 0.07), with the exception of the Canarian and South African breeds that displayed a significant differentiation when compared to goats from North Africa and Nigeria. Measurement of gene flow with Migrate-n and IMa coalescent genealogy samplers supported the existence of a bidirectional gene flow between African and Spanish goats. Moreover, IMa estimates of the effective number of migrants were remarkably lower than those calculated with Migrate-n and classical approaches. Such discrepancies suggest that recent divergence, rather than extensive gene flow, is the main cause of the weak population structure observed in caprine breeds. PMID:27966592

  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. Detection and isolation of selected genes of interest from metagenomic libraries by a DNA microarray approach.

    Science.gov (United States)

    Pathak, Gopal P; Gärtner, Wolfgang

    2010-01-01

    A DNA microarray-based approach is described for screening metagenomic libraries for the presence of selected genes. The protocol is exemplified for the identification of flavin-binding, blue-light-sensitive biological photoreceptors (BL), based on a homology search in already sequenced, annotated genomes. The microarray carried 149 different 54-mer oligonucleotides, derived from consensus sequences of BL photoreceptors. The array could readily identify targets carrying 4% sequence mismatch, and allowed unambiguous identification of a positive cosmid clone of as little as 10 ng against a background of 25 μg of cosmid DNA. The protocol allows screening up to 1,200 library clones in concentrations as low as ca. 20 ng, each with a ca. 40 kb insert size readily in a single batch. Calibration and control conditions are outlined. This protocol, when applied to the thermophilic fraction of a soil sample, yielded the identification and functional characterization of a novel, BL-encoding gene that showed a 58% similarity to a known, BL-encoding gene from Kineococcus radiotolerans SRS30216 (similarity values refer to the respective LOV domains).

  20. [Recent progress in gene mapping through high-throughput sequencing technology and forward genetic approaches].

    Science.gov (United States)

    Lu, Cairui; Zou, Changsong; Song, Guoli

    2015-08-01

    Traditional gene mapping using forward genetic approaches is conducted primarily through construction of a genetic linkage map, the process of which is tedious and time-consuming, and often results in low accuracy of mapping and large mapping intervals. With the rapid development of high-throughput sequencing technology and decreasing cost of sequencing, a variety of simple and quick methods of gene mapping through sequencing have been developed, including direct sequencing of the mutant genome, sequencing of selective mutant DNA pooling, genetic map construction through sequencing of individuals in population, as well as sequencing of transcriptome and partial genome. These methods can be used to identify mutations at the nucleotide level and has been applied in complex genetic background. Recent reports have shown that sequencing mapping could be even done without the reference of genome sequence, hybridization, and genetic linkage information, which made it possible to perform forward genetic study in many non-model species. In this review, we summarized these new technologies and their application in gene mapping.

  1. AN EVEN ODD MULTIPLE PATTERN MATCHING ALGORITHM

    Directory of Open Access Journals (Sweden)

    Raju Bhukya,

    2011-03-01

    Full Text Available Pattern matching plays an important role in various applications ranging from text searching in word processors to identification of functional and structural behavior in proteins and genes. Pattern matching is one of the fundamental areas in the field of computational biology. Currently research in life science area is producing large amount of genetic data. Due to this large and use full information can be gained by finding valuable information available from the genomic sequences. Many algorithms have been proposed but more efficient and robust methods are needed for the multiple pattern matching algorithms for better use. We introduce a new indexing technique called an Index based even odd multiple pattern matching, which gives very good performance when compared with some of the existing popular algorithms. The current technique avoids unnecessary DNA comparisons as a result the number of comparisons and CPC ratio gradually decreases and overall performance increases accordingly.

  2. Consilient research approaches in studying gene x environment interactions in alcohol research.

    Science.gov (United States)

    Sher, Kenneth J; Dick, Danielle M; Crabbe, John C; Hutchison, Kent E; O'Malley, Stephanie S; Heath, Andrew C

    2010-04-01

    This review article discusses the importance of identifying gene-environment interactions for understanding the etiology and course of alcohol use disorders and related conditions. A number of critical challenges are discussed, including the fact that there is no organizing typology for classifying different types of environmental exposures, many key human environmental risk factors for alcohol dependence have no clear equivalents in other species, much of the genetic variance of alcohol dependence in human is not 'alcohol specific', and the potential range of gene-environment interactions that could be considered is so vast that maintaining statistical control of Type 1 errors is a daunting task. Despite these and other challenges, there appears to be a number of promising approaches that could be taken in order to achieve consilience and ecologically valid translation between human alcohol dependence and animal models. Foremost among these is to distinguish environmental exposures that are thought to have enduring effects on alcohol use motivation (and self-regulation) from situational environmental exposures that facilitate the expression of such motivations but do not, by themselves, have enduring effects. In order to enhance consilience, various domains of human approach motivation should be considered so that relevant environmental exposures can be sampled, as well as the appropriate species to study them in (i.e. where such motivations are ecologically relevant). Foremost among these are social environments, which are central to the initiation and escalation of human alcohol consumption. The value of twin studies, human laboratory studies and pharmacogenetic studies is also highlighted.

  3. Broadband electrical impedance matching for piezoelectric ultrasound transducers.

    Science.gov (United States)

    Huang, Haiying; Paramo, Daniel

    2011-12-01

    This paper presents a systematic method for designing broadband electrical impedance matching networks for piezoelectric ultrasound transducers. The design process involves three steps: 1) determine the equivalent circuit of the unmatched piezoelectric transducer based on its measured admittance; 2) design a set of impedance matching networks using a computerized Smith chart; and 3) establish the simulation model of the matched transducer to evaluate the gain and bandwidth of the impedance matching networks. The effectiveness of the presented approach is demonstrated through the design, implementation, and characterization of impedance matching networks for a broadband acoustic emission sensor. The impedance matching network improved the power of the acquired signal by 9 times.

  4. Theory of fractional order elements based impedance matching networks

    KAUST Repository

    Radwan, Ahmed G.

    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. Polytypic pattern matching

    NARCIS (Netherlands)

    Jeuring, J.T.

    2007-01-01

    The pattern matching problem can be informally specified as follows: given a pattern and a text, find all occurrences of the pattern in the text. The pattern and the text may both be lists, or they may both be trees, or they may both be multi-dimensional arrays, etc. This paper describes a general p

  6. 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…

  7. 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...

  8. Factorized Graph Matching.

    Science.gov (United States)

    Zhou, Feng; de la Torre, Fernando

    2015-11-19

    Graph matching (GM) is a fundamental problem in computer science, and it plays a central role to solve correspondence problems in computer vision. GM problems that incorporate pairwise constraints can be formulated as a quadratic assignment problem (QAP). Although widely used, solving the correspondence problem through GM has two main limitations: (1) the QAP is NP-hard and difficult to approximate; (2) GM algorithms do not incorporate geometric constraints between nodes that are natural in computer vision problems. To address aforementioned problems, this paper proposes factorized graph matching (FGM). FGM factorizes the large pairwise affinity matrix into smaller matrices that encode the local structure of each graph and the pairwise affinity between edges. Four are the benefits that follow from this factorization: (1) There is no need to compute the costly (in space and time) pairwise affinity matrix; (2) The factorization allows the use of a path-following optimization algorithm, that leads to improved optimization strategies and matching performance; (3) Given the factorization, it becomes straight-forward to incorporate geometric transformations (rigid and non-rigid) to the GM problem. (4) Using a matrix formulation for the GM problem and the factorization, it is easy to reveal commonalities and differences between different GM methods. The factorization also provides a clean connection with other matching algorithms such as iterative closest point; Experimental results on synthetic and real databases illustrate how FGM outperforms state-of-the-art algorithms for GM. The code is available at http://humansensing.cs.cmu.edu/fgm.

  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. Matching Supernovae to Galaxies

    Science.gov (United States)

    Kohler, Susanna

    2016-12-01

    developed a new automated algorithm for matching supernovae to their host galaxies. Their work builds on currently existing algorithms and makes use of information about the nearby galaxies, accounts for the uncertainty of the match, and even includes a machine learning component to improve the matching accuracy.Gupta and collaborators test their matching algorithm on catalogs of galaxies and simulated supernova events to quantify how well the algorithm is able to accurately recover the true hosts.Successful MatchingThe matching algorithms accuracy (purity) as a function of the true supernova-host separation, the supernova redshift, the true hosts brightness, and the true hosts size. [Gupta et al. 2016]The authors find that when the basic algorithm is run on catalog data, it matches supernovae to their hosts with 91% accuracy. Including the machine learning component, which is run after the initial matching algorithm, improves the accuracy of the matching to 97%.The encouraging results of this work which was intended as a proof of concept suggest that methods similar to this could prove very practical for tackling future survey data. And the method explored here has use beyond matching just supernovae to their host galaxies: it could also be applied to other extragalactic transients, such as gamma-ray bursts, tidal disruption events, or electromagnetic counterparts to gravitational-wave detections.CitationRavi R. Gupta et al 2016 AJ 152 154. doi:10.3847/0004-6256/152/6/154

  11. Target gene approaches: Gene expression in Daphnia magna exposed to predator-borne kairomones or to microcystin-producing and microcystin-free Microcystis aeruginosa

    Directory of Open Access Journals (Sweden)

    Courts Cornelius

    2009-11-01

    Full Text Available Abstract Background Two major biological stressors of freshwater zooplankton of the genus Daphnia are predation and fluctuations in food quality. Here we use kairomones released from a planktivorous fish (Leucaspius delineatus and from an invertebrate predator (larvae of Chaoborus flavicans to simulate predation pressure; a microcystin-producing culture of the cyanobacterium Microcystis aeruginosa and a microcystin-deficient mutant are used to investigate effects of low food quality. Real-time quantitative polymerase chain reaction (QPCR allows quantification of the impact of biotic stressors on differential gene activity. The draft genome sequence for Daphnia pulex facilitates the use of candidate genes by precisely identifying orthologs to functionally characterized genes in other model species. This information is obtained by constructing phylogenetic trees of candidate genes with the knowledge that the Daphnia genome is composed of many expanded gene families. Results We evaluated seven candidate reference genes for QPCR in Daphnia magna after exposure to kairomones. As a robust approach, a combination normalisation factor (NF was calculated based on the geometric mean of three of these seven reference genes: glyceraldehyde-3-phosphate dehydrogenase, TATA-box binding protein and succinate dehydrogenase. Using this NF, expression of the target genes actin and alpha-tubulin were revealed to be unchanged in the presence of the tested kairomones. The presence of fish kairomone up-regulated one gene (cyclophilin involved in the folding of proteins, whereas Chaoborus kairomone down-regulated the same gene. We evaluated the same set of candidate reference genes for QPCR in Daphnia magna after exposure to a microcystin-producing and a microcystin-free strain of the cyanobacterium Microcystis aeruginosa. The NF was calculated based on the reference genes 18S ribosomal RNA, alpha-tubulin and TATA-box binding protein. We found glyceraldehyde-3

  12. 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...... into mesoangioblasts did not interfere with the myogenic properties of mesoangioblasts in culture or in vivo. Mesoangioblasts are able to function as retroviral packaging cells in vitro. While a possible therapeutic application of this new gene delivery system will require further detailed analysis of the long...

  13. 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.

  14. A Pareto Approach to Lossy Matching

    Science.gov (United States)

    2006-09-01

    provided by Pozar [16, Eq. 11.13]: GT = |s21|2 (1− |sG|2)(1− |sL|2) |1− sGs1|2|1− s22sL|2 . (3) The transducer power gain is tightly linked to the power...York, NY. [16] Pozar , David M. [1998] Microwave Engineering, third edition, Prentice- Hall, Upper Saddle River, NJ. [17] Schwartz, David F. and J. C

  15. 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.

  16. 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.

  17. 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.

  18. Resurgence matches quantization

    Science.gov (United States)

    Couso-Santamaría, Ricardo; Mariño, Marcos; Schiappa, Ricardo

    2017-04-01

    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 {{{P}}2} toric Calabi–Yau threefold, the present work shows how the Borel–Padé–Écalle 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.

  19. Characteristic Evolution and Matching

    Directory of Open Access Journals (Sweden)

    Winicour Jeffrey

    2005-12-01

    Full Text Available I review the development of numerical evolution codes for general relativity based upon the characteristic initial value problem. Progress is traced from the early stage of 1D feasibility studies to 2D axisymmetric codes that accurately simulate the oscillations and gravitational collapse of relativistic stars and to current 3D codes that provide pieces of a binary black hole spacetime. A prime application of characteristic evolution is to compute waveforms via Cauchy-characteristic matching, which is also reviewed.

  20. Graphical models and point pattern matching.

    Science.gov (United States)

    Caetano, Tibério S; Caelli, Terry; Schuurmans, Dale; Barone, Dante A C

    2006-10-01

    This paper describes a novel solution to the rigid point pattern matching problem in Euclidean spaces of any dimension. Although we assume rigid motion, jitter is allowed. We present a noniterative, polynomial time algorithm that is guaranteed to find an optimal solution for the noiseless case. First, we model point pattern matching as a weighted graph matching problem, where weights correspond to Euclidean distances between nodes. We then formulate graph matching as a problem of finding a maximum probability configuration in a graphical model. By using graph rigidity arguments, we prove that a sparse graphical model yields equivalent results to the fully connected model in the noiseless case. This allows us to obtain an algorithm that runs in polynomial time and is provably optimal for exact matching between noiseless point sets. For inexact matching, we can still apply the same algorithm to find approximately optimal solutions. Experimental results obtained by our approach show improvements in accuracy over current methods, particularly when matching patterns of different sizes.

  1. 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.

  2. 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.

  3. [MATCHE: Management Approach to Teaching Consumer and Homemaking Education.] Consumer Approach Strand: Textiles and Clothing. Module I-D-4: Applications and Implications of New Technology in Textiles and Clothing.

    Science.gov (United States)

    Joseph, Marjory

    This competency-based preservice home economics teacher education module on applications and implications of new technology in textiles and clothing is the fourth 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…

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. A hybrid dynamic Bayesian network approach for modelling temporal associations of gene expressions for hypertension diagnosis.

    Science.gov (United States)

    Akutekwe, Arinze; Seker, Huseyin

    2014-01-01

    Computational and machine learning techniques have been applied in identifying biomarkers and constructing predictive models for diagnosis of hypertension. Strategies such as improved classification rules based on decision trees have been proposed. Other techniques such as Fuzzy Expert Systems (FES) and Neuro-Fuzzy Systems (NFS) have recently been applied. However, these methods lack the ability to detect temporal relationships among biomarker genes that will aid better understanding of the mechanism of hypertension disease. In this paper we apply a proposed two-stage bio-network construction approach that combines the power and computational efficiency of classification methods with the well-established predictive ability of Dynamic Bayesian Network. We demonstrate our method using the analysis of male young-onset hypertension microarray dataset. Four key genes were identified by the Least Angle Shrinkage and Selection Operator (LASSO) and three Support Vector Machine Recursive Feature Elimination (SVM-RFE) methods. Results show that cell regulation FOXQ1 may inhibit the expression of focusyltransferase-6 (FUT6) and that ABCG1 ATP-binding cassette sub-family G may also play inhibitory role against NR2E3 nuclear receptor sub-family 2 and CGB2 Chromatin Gonadotrophin.

  9. Integrating Environmental Genomics and Biogeochemical Models: a Gene-centric Approach

    Science.gov (United States)

    Reed, D. C.; Algar, C. K.; Huber, J. A.; Dick, G.

    2013-12-01

    Rapid advances in molecular microbial ecology have yielded an unprecedented amount of data about the evolutionary relationships and functional traits of microbial communities that regulate global geochemical cycles. Biogeochemical models, however, are trailing in the wake of the environmental genomics revolution and such models rarely incorporate explicit representations of bacteria and archaea, nor are they compatible with nucleic acid or protein sequence data. Here, we present a functional gene-based framework for describing microbial communities in biogeochemical models that uses genomics data and provides predictions that are readily testable using cutting-edge molecular tools. To demonstrate the approach in practice, nitrogen cycling in the Arabian Sea oxygen minimum zone (OMZ) was modelled to examine key questions about cryptic sulphur cycling and dinitrogen production pathways in OMZs. By directly linking geochemical dynamics to the genetic composition of microbial communities, the method provides mechanistic insights into patterns and biogeochemical consequences of marine microbes. Such an approach is critical for informing our understanding of the key role microbes play in modulating Earth's biogeochemistry.

  10. Differential subtraction display: a unified approach for isolation of cDNAs from differentially expressed genes.

    Science.gov (United States)

    Pardinas, J R; Combates, N J; Prouty, S M; Stenn, K S; Parimoo, S

    1998-03-15

    We have developed a novel efficient approach, termed differential subtraction display, for the identification of differentially expressed genes. Several critical parameters for the reproducibility and enhanced sensitivity of display, as well as steps to reduce the number of false positive cDNA species, have been defined. These include- (a) use of standardized oligo(dT)-primed cDNA pools rather than total RNA as the starting material for differential display, (b) critical role of optimal cDNA input for each distinct class of primers, (c) phenomena of primer dominance and interference, and (d) design of a novel set of enhanced specificity anchor primers. Introduction of an efficient subtractive hybridization step prior to cloning of cDNA species enriches the bona fide cDNA species that are either exclusively present in one sample (+/-) or show altered expression (up-/down-regulation) in RNA samples from two different tissues or cell types. This approach, in comparison to differential display, has several advantages in terms of reproducibility and enhanced sensitivity of display coupled to the cloning of enriched bona fide cDNA species corresponding to differentially expressed RNAs.

  11. 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.

  12. 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.

  13. 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.

  14. Matching a wavelet to ECG signal.

    Science.gov (United States)

    Takla, George F; Nair, Bala G; Loparo, Kenneth A

    2006-01-01

    In this paper we develop an approach to synthesize a wavelet that matches the ECG signal. Matching a wavelet to a signal of interest has potential advantages in extracting signal features with greater accuracy, particularly when the signal is contaminated with noise. The approach that we have taken is based on the theoretical work done by Chapa and Rao. We have applied their technique to a noise-free ECG signal representing one cardiac cycle. Results indicate that a matched wavelet, that was able to capture the broad ECG features, could be obtained. Such a wavelet could be used to extract ECG features such as QRS complexes and P&T waves with greater accuracy.

  15. 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.

  16. 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.

  17. 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.

  18. Novel therapeutic approaches for various cancer types using a modified sleeping beauty-based gene delivery system.

    Science.gov (United States)

    Hong, In-Sun; Lee, Hwa-Yong; Kim, Hyun-Pyo

    2014-01-01

    Successful gene therapy largely depends on the selective introduction of therapeutic genes into the appropriate target cancer cells. One of the most effective and promising approaches for targeting tumor tissue during gene delivery is the use of viral vectors, which allow for high efficiency gene delivery. However, the use of viral vectors is not without risks and safety concerns, such as toxicities, a host immune response towards the viral antigens or potential viral recombination into the host's chromosome; these risks limit the clinical application of viral vectors. The Sleeping Beauty (SB) transposon-based system is an attractive, non-viral alternative to viral delivery systems. SB may be less immunogenic than the viral vector system due to its lack of viral sequences. The SB-based gene delivery system can stably integrate into the host cell genome to produce the therapeutic gene product over the lifetime of a cell. However, when compared to viral vectors, the non-viral SB-based gene delivery system still has limited therapeutic efficacy due to the lack of long-lasting gene expression potential and tumor cell specific gene transfer ability. These limitations could be overcome by modifying the SB system through the introduction of the hTERT promoter and the SV40 enhancer. In this study, a modified SB delivery system, under control of the hTERT promoter in conjunction with the SV40 enhancer, was able to successfully transfer the suicide gene (HSV-TK) into multiple types of cancer cells. The modified SB transfected cancer cells exhibited a significantly increased cancer cell specific death rate. These data suggest that our modified SB-based gene delivery system can be used as a safe and efficient tool for cancer cell specific therapeutic gene transfer and stable long-term expression.

  19. Improved electromagnetic induction processing with novel adaptive matched filter and matched subspace detection

    Science.gov (United States)

    Hayes, Charles E.; McClellan, James H.; Scott, Waymond R.; Kerr, Andrew J.

    2016-05-01

    This work introduces two advances in wide-band electromagnetic induction (EMI) processing: a novel adaptive matched filter (AMF) and matched subspace detection methods. Both advances make use of recent work with a subspace SVD approach to separating the signal, soil, and noise subspaces of the frequency measurements The proposed AMF provides a direct approach to removing the EMI self-response while improving the signal to noise ratio of the data. Unlike previous EMI adaptive downtrack filters, this new filter will not erroneously optimize the EMI soil response instead of the EMI target response because these two responses are projected into separate frequency subspaces. The EMI detection methods in this work elaborate on how the signal and noise subspaces in the frequency measurements are ideal for creating the matched subspace detection (MSD) and constant false alarm rate matched subspace detection (CFAR) metrics developed by Scharf The CFAR detection metric has been shown to be the uniformly most powerful invariant detector.

  20. 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…

  1. Matching Expectations for Successful University Student Volunteering

    Science.gov (United States)

    Paull, Megan; Omari, Maryam; MacCallum, Judith; Young, Susan; Walker, Gabrielle; Holmes, Kirsten; Haski-Leventha, Debbie; Scott, Rowena

    2017-01-01

    Purpose: The purpose of this paper is to demonstrate the importance of expectation formation and matching for university student volunteers and their hosts. Design/methodology/approach: This research involved a multi-stage data collection process including interviews with student volunteers, and university and host representatives from six…

  2. Investigation on the role of nsSNPs in HNPCC genes – a bioinformatics approach

    Directory of Open Access Journals (Sweden)

    Sethumadhavan Rao

    2009-04-01

    Full Text Available Abstract Background A central focus of cancer genetics is the study of mutations that are causally implicated in tumorigenesis. The identification of such causal mutations not only provides insight into cancer biology but also presents anticancer therapeutic targets and diagnostic markers. Missense mutations are nucleotide substitutions that change an amino acid in a protein, the deleterious effects of these mutations are commonly attributed to their impact on primary amino acid sequence and protein structure. Methods The method to identify functional SNPs from a pool, containing both functional and neutral SNPs is challenging by experimental protocols. To explore possible relationships between genetic mutation and phenotypic variation, we employed different bioinformatics algorithms like Sorting Intolerant from Tolerant (SIFT, Polymorphism Phenotyping (PolyPhen, and PupaSuite to predict the impact of these amino acid substitutions on protein activity of mismatch repair (MMR genes causing hereditary nonpolyposis colorectal cancer (HNPCC. Results SIFT classified 22 of 125 variants (18% as 'Intolerant." PolyPhen classified 40 of 125 amino acid substitutions (32% as "Probably or possibly damaging". The PupaSuite predicted the phenotypic effect of SNPs on the structure and function of the affected protein. Based on the PolyPhen scores and availability of three-dimensional structures, structure analysis was carried out with the major mutations that occurred in the native protein coded by MSH2 and MSH6 genes. The amino acid residues in the native and mutant model protein were further analyzed for solvent accessibility and secondary structure to check the stability of the proteins. Conclusion Based on this approach, we have shown that four nsSNPs, which were predicted to have functional consequences (MSH2-Y43C, MSH6-Y538S, MSH6-S580L, and MSH6-K854M, were already found to be associated with cancer risk. Our study demonstrates the presence of other

  3. 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.

  4. Phylogeny of haemosporidian blood parasites revealed by a multi-gene approach.

    Science.gov (United States)

    Borner, Janus; Pick, Christian; Thiede, Jenny; Kolawole, Olatunji Matthew; Kingsley, Manchang Tanyi; Schulze, Jana; Cottontail, Veronika M; Wellinghausen, Nele; Schmidt-Chanasit, Jonas; Bruchhaus, Iris; Burmester, Thorsten

    2016-01-01

    The apicomplexan order Haemosporida is a clade of unicellular blood parasites that infect a variety of reptilian, avian and mammalian hosts. Among them are the agents of human malaria, parasites of the genus Plasmodium, which pose a major threat to human health. Illuminating the evolutionary history of Haemosporida may help us in understanding their enormous biological diversity, as well as tracing the multiple host switches and associated acquisitions of novel life-history traits. However, the deep-level phylogenetic relationships among major haemosporidian clades have remained enigmatic because the datasets employed in phylogenetic analyses were severely limited in either gene coverage or taxon sampling. Using a PCR-based approach that employs a novel set of primers, we sequenced fragments of 21 nuclear genes from seven haemosporidian parasites of the genera Leucocytozoon, Haemoproteus, Parahaemoproteus, Polychromophilus and Plasmodium. After addition of genomic data from 25 apicomplexan species, the unreduced alignment comprised 20,580 bp from 32 species. Phylogenetic analyses were performed based on nucleotide, codon and amino acid data employing Bayesian inference, maximum likelihood and maximum parsimony. All analyses resulted in highly congruent topologies. We found consistent support for a basal position of Leucocytozoon within Haemosporida. In contrast to all previous studies, we recovered a sister group relationship between the genera Polychromophilus and Plasmodium. Within Plasmodium, the sauropsid and mammal-infecting lineages were recovered as sister clades. Support for these relationships was high in nearly all trees, revealing a novel phylogeny of Haemosporida, which is robust to the choice of the outgroup and the method of tree inference.

  5. Antenna impedance matching with neural networks.

    Science.gov (United States)

    Hemminger, Thomas L

    2005-10-01

    Impedance matching between transmission lines and antennas is an important and fundamental concept in electromagnetic theory. One definition of antenna impedance is the resistance and reactance seen at the antenna terminals or the ratio of electric to magnetic fields at the input. The primary intent of this paper is real-time compensation for changes in the driving point impedance of an antenna due to frequency deviations. In general, the driving point impedance of an antenna or antenna array is computed by numerical methods such as the method of moments or similar techniques. Some configurations do lend themselves to analytical solutions, which will be the primary focus of this work. This paper employs a neural control system to match antenna feed lines to two common antennas during frequency sweeps. In practice, impedance matching is performed off-line with Smith charts or relatively complex formulas but they rarely perform optimally over a large bandwidth. There have been very few attempts to compensate for matching errors while the transmission system is in operation and most techniques have been targeted to a relatively small range of frequencies. The approach proposed here employs three small neural networks to perform real-time impedance matching over a broad range of frequencies during transmitter operation. Double stub tuners are being explored in this paper but the approach can certainly be applied to other methodologies. The ultimate purpose of this work is the development of an inexpensive microcontroller-based system.

  6. 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

  7. 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

  8. Optimizing Transmission Line Matching Circuits

    OpenAIRE

    Novak, S.

    1996-01-01

    When designing transmission line matching circuits, there exist often overlooked, additional, not much used, degree of choice in the selection of the transmission line impedance. In this work are presented results of CAD analysis for the two element transmission line matching networks, demonstrating that selecting matching circuits transmission lines with higher impedance, than usually used 50 or 75 ohms, can in most cases substantially decrease the physical dimension of the final matching ci...

  9. 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

  10. The earliest matches.

    Directory of Open Access Journals (Sweden)

    Naama Goren-Inbar

    Full Text Available Cylindrical objects made usually of fired clay but sometimes of stone were found at the Yarmukian Pottery Neolithic sites of Sha'ar HaGolan and Munhata (first half of the 8(th millennium BP in the Jordan Valley. Similar objects have been reported from other Near Eastern Pottery Neolithic sites. Most scholars have interpreted them as cultic objects in the shape of phalli, while others have referred to them in more general terms as "clay pestles," "clay rods," and "cylindrical clay objects." Re-examination of these artifacts leads us to present a new interpretation of their function and to suggest a reconstruction of their technology and mode of use. We suggest that these objects were components of fire drills and consider them the earliest evidence of a complex technology of fire ignition, which incorporates the cylindrical objects in the role of matches.

  11. The earliest matches.

    Science.gov (United States)

    Goren-Inbar, Naama; Freikman, Michael; Garfinkel, Yosef; Goring-Morris, A Nigel; Goring-Morris, Nigel A; Grosman, Leore

    2012-01-01

    Cylindrical objects made usually of fired clay but sometimes of stone were found at the Yarmukian Pottery Neolithic sites of Sha'ar HaGolan and Munhata (first half of the 8(th) millennium BP) in the Jordan Valley. Similar objects have been reported from other Near Eastern Pottery Neolithic sites. Most scholars have interpreted them as cultic objects in the shape of phalli, while others have referred to them in more general terms as "clay pestles," "clay rods," and "cylindrical clay objects." Re-examination of these artifacts leads us to present a new interpretation of their function and to suggest a reconstruction of their technology and mode of use. We suggest that these objects were components of fire drills and consider them the earliest evidence of a complex technology of fire ignition, which incorporates the cylindrical objects in the role of matches.

  12. Matching with Commitments

    CERN Document Server

    Costello, Kevin; Tripathi, Pushkar

    2012-01-01

    We consider the following stochastic optimization problem first introduced by Chen et al. in \\cite{chen}. We are given a vertex set of a random graph where each possible edge is present with probability p_e. We do not know which edges are actually present unless we scan/probe an edge. However whenever we probe an edge and find it to be present, we are constrained to picking the edge and both its end points are deleted from the graph. We wish to find the maximum matching in this model. We compare our results against the optimal omniscient algorithm that knows the edges of the graph and present a 0.573 factor algorithm using a novel sampling technique. We also prove that no algorithm can attain a factor better than 0.898 in this model.

  13. Characteristic Evolution and Matching

    Directory of Open Access Journals (Sweden)

    Winicour Jeffrey

    2009-04-01

    Full Text Available I review the development of numerical evolution codes for general relativity based upon the characteristic initial value problem. Progress is traced from the early stage of 1D feasibility studies to 2D axisymmetric codes that accurately simulate the oscillations and gravitational collapse of relativistic stars and to current 3D codes that provide pieces of a binary black hole spacetime. Cauchy codes have now been successful at simulating all aspects of the binary black hole problem inside an artificially constructed outer boundary. A prime application of characteristic evolution is to eliminate the role of this artificial outer boundary via Cauchy-characteristic matching, by which the radiated waveform can be computed at null infinity. Progress in this direction is discussed.

  14. Changes in winter depression phenotype correlate with white blood cell gene expression profiles : A combined metagene and gene ontology approach

    NARCIS (Netherlands)

    Bosker, Fokko J.; Terpstra, Peter; Gladkevich, Anatoliy V.; Dijck-Brouwer, D. A. Janneke; te Meerman, Gerard; Nolen, Willem A.; Schoevers, Robert A.; Meesters, Ybe

    2015-01-01

    In the present study we evaluate the feasibility of gene expression in white blood cells as a peripheral marker for winter depression. Sixteen patients with winter type seasonal affective disorder were included in the study. Blood was taken by venous puncture at three time points; in winter prior an

  15. 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.

  16. 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

  17. 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.

  18. 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.

  19. Update of the Gene Discovery Program in Schistosoma mansoni with the Expressed Sequence Tag Approach

    Directory of Open Access Journals (Sweden)

    Élida ML Rabelo

    1997-09-01

    Full Text Available Continuing the Schistosoma mansoni Genome Project 363 new templates were sequenced generating 205 more ESTs corresponding to 91 genes. Seventy four of these genes (81% had not previously been described in S. mansoni. Among the newly discovered genes there are several of significant biological interest such as synaptophysin, NIFs-like and rho-GDP dissociation inhibitor

  20. Exploring drought stress-regulated genes in senna (Cassia angustifolia Vahl.): a transcriptomic approach.

    Science.gov (United States)

    Mehta, Rucha Harishbhai; Ponnuchamy, Manivel; Kumar, Jitendra; Reddy, Nagaraja Reddy Rama

    2017-01-01

    De novo assembly of reads produced by next-generation sequencing (NGS) technologies offers a rapid approach to obtain expressed gene sequences for non-model organisms. Senna (Cassia angustifolia Vahl.) is a drought-tolerant annual undershrub of Caesalpiniaceae, a subfamily of Fabaceae. There are insufficient transcriptomic and genomic data in public databases for understanding the molecular mechanism underlying the drought tolerance of senna. Therefore, the main purpose of this study was to know the transcriptome profile of senna, with special reference to drought stress. RNA from two different stages of leaf development was extracted and sequenced separately using the Illumina technology. A total of 200 million reads were generated, and a de novo assembly of processed reads in the pooled transcriptome using Trinity yielded 43,413 transcripts which were further annotated using NCBI BLAST with "green plant database (txid 33090)," Swiss Prot, Kyoto Encyclopedia of Genes and Genomes (KEGG), Clusters of Orthologous Groups (COG), and Gene Ontology (GO). Out of the total transcripts, 42,280 (95.0 %) were annotated by BLASTX against the green plant database of NCBI. Senna transcriptome showed the highest similarity to Glycine max (41 %), followed by Phaseolus vulgaris (16 %), Cicer arietinum (15 %), and Medicago trancatula (5 %). The highest number of GO terms were enriched for the molecular functions category; of these "catalytic activity" (GO: 0003824) (25.10 %) and "binding activity" (GO: 0005488) (20.10 %) were most abundantly represented. We used InterProscan to see protein similarity at domain level; a total of 33,256 transcripts were annotated against the Pfam domains. The transcripts were assigned with various KEGG pathways. Coding DNA sequences (CDS) encoding various drought stress-regulated pathways such as signaling factors, protein-modifying/degrading enzymes, biosynthesis of phytohormone, phytohormone signaling, osmotically active compounds, free radical

  1. Identifying New Candidate Genes and Chemicals Related to Prostate Cancer Using a Hybrid Network and Shortest Path Approach

    Science.gov (United States)

    Yuan, Fei; Zhou, You; Wang, Meng; Yang, Jing; Wu, Kai; Lu, Changhong; Kong, Xiangyin; Cai, Yu-Dong

    2015-01-01

    Prostate cancer is a type of cancer that occurs in the male prostate, a gland in the male reproductive system. Because prostate cancer cells may spread to other parts of the body and can influence human reproduction, understanding the mechanisms underlying this disease is critical for designing effective treatments. The identification of as many genes and chemicals related to prostate cancer as possible will enhance our understanding of this disease. In this study, we proposed a computational method to identify new candidate genes and chemicals based on currently known genes and chemicals related to prostate cancer by applying a shortest path approach in a hybrid network. The hybrid network was constructed according to information concerning chemical-chemical interactions, chemical-protein interactions, and protein-protein interactions. Many of the obtained genes and chemicals are associated with prostate cancer. PMID:26504486

  2. Genes and longevity: a genetic-demographic approach reveals sex- and age-specific gene effects not shown by the case-control approach (APOE and HSP70.1 loci).

    Science.gov (United States)

    Dato, S; Carotenuto, L; De Benedictis, G

    2007-02-01

    Association analyses between gene variability and human longevity carried out by comparing gene frequencies between population samples of different ages (case/control design) may provide information on genes and pathways playing a role in modulating survival at old ages. However, by dealing with cross-sectional data, the gene-frequency (GF) approach ignores cohort effects in population mortality changes. The genetic-demographic (GD) approach adds demographic information to genetic data and allows the estimation of hazard rates and survival functions for candidate alleles and genotypes. Thus mortality changes in the cohort to which the cross-sectional sample belongs are taken into account. In this work, we applied the GD method to a dataset relevant to two genes, APOE and HSP70.1, previously shown to be related to longevity by the GF method. We show that the GD method reveals sex- and age-specific allelic effects not shown by the GF analysis. In addition, we provide an algorithm for the implementation of a non-parametric GD analysis.

  3. Voice Matching Using Genetic Algorithm

    Directory of Open Access Journals (Sweden)

    Abhishek Bal

    2014-03-01

    Full Text Available In this paper, the use of Genetic Algorithm (GA for voice recognition is described. The practical application of Genetic Algorithm (GA to the solution of engineering problem is a rapidly emerging approach in the field of control engineering and signal processing. Genetic algorithms are useful for searching a space in multi-directional way from large spaces and poorly defined space. Voice is a signal of infinite information. Digital processing of voice signal is very important for automatic voice recognition technology. Nowadays, voice processing is very much important in security mechanism due to mimicry characteristic. So studying the voice feature extraction in voice processing is very necessary in military, hospital, telephone system, investigation bureau and etc. In order to extract valuable information from the voice signal, make decisions on the process, and obtain results, the data needs to be manipulated and analyzed. In this paper, if the instant voice is not matched with same person’s reference voices in the database, then Genetic Algorithm (GA is applied between two randomly chosen reference voices. Again the instant voice is compared with the result of Genetic Algorithm (GA which is used, including its three main steps: selection, crossover and mutation. We illustrate our approach with different sample of voices from human in our institution.

  4. Design Pattern Mining Using Graph Matching

    Institute of Scientific and Technical Information of China (English)

    LI Qing-hua; ZHANG Zhi-xiang; BEN Ke-rong

    2004-01-01

    The identification of design pattern instances is important for program understanding and software maintenance. Aiming at the mining of design patterns in existing systems, this paper proposes a sub-graph isomorphism approach to discover several design patterns in a legacy system at a time. The attributed relational graph is used to describe design patterns and legacy systems. The sub-graph isomorphism approach consists of decomposition and composition process. During the decomposition process, graphs corresponding to the design patterns are decomposed into sub-graphs, some of which are graphs corresponding to the elemental design patterns. The composition process tries to get sub-graph isomorphism of the matched graph if sub-graph isomorphism of each sub-graph is obtained. Due to the common structures between design patterns, the proposed approach can reduce the matching times of entities and relations. Compared with the existing methods, the proposed algorithm is not linearly dependent on the number of design pattern graphs.

  5. Heritable and inducible gene knockdown in astrocytes or neurons in vivo by a combined lentiviral and RNAi approach.

    Directory of Open Access Journals (Sweden)

    Fabrice eHeitz

    2014-03-01

    Full Text Available Gene knockout by homologous recombination is a popular method to study gene functions in the mouse in vivo. However, its lack of temporal control has limited the interpretation of knockout studies because the complete elimination of a gene product often alters developmental processes, and can induce severe malformations or lethality. Conditional gene knockdown has emerged as a compelling alternative to gene knockout, an approach well established in vitro but that remains challenging in vivo, especially in the adult brain. Here, we report a method for conditional and cell-specific gene knockdown in the mouse brain in vivo that combines Cre-mediated RNA interference (RNAi with classical and lentivirus-mediated transgenesis. The method is based on the inducible expression of a silencing short hairpin RNA (shRNA introduced in mice by lentivirus-mediated transgenesis, and on its activation by excision of a floxed stop EGFP reporter with an inducible Cre recombinase expressed in astrocytes or in neurons. This dual system should be of broad utility for comparative studies of gene functions in these two cell types in vivo.

  6. 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.

  7. Sidescan Sonar Image Matching Using Cross Correlation

    DEFF Research Database (Denmark)

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

    2003-01-01

    When surveying an area for sea mines with a sidescan sonar, the ability to find the same object in two different sonar images is helpful to determine the nature of the object. The main problem with matching two sidescan sonar images is that a scene changes appearance when viewed from different...... 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...... displacements of the relative objects position as a result of the ground registration, the object position is given an area of influence. The method is compared to an existing method for matching sidescan sonar images based on hypothetical reasoning. The two methods are compared on a number of real sidescan...

  8. 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.

  9. Characteristic Evolution and Matching

    Directory of Open Access Journals (Sweden)

    Jeffrey Winicour

    2012-01-01

    Full Text Available I review the development of numerical evolution codes for general relativity based upon the characteristic initial-value problem. Progress in characteristic evolution is traced from the early stage of 1D feasibility studies to 2D-axisymmetric codes that accurately simulate the oscillations and gravitational collapse of relativistic stars and to current 3D codes that provide pieces of a binary black-hole spacetime. Cauchy codes have now been successful at simulating all aspects of the binary black-hole problem inside an artificially constructed outer boundary. A prime application of characteristic evolution is to extend such simulations to null infinity where the waveform from the binary inspiral and merger can be unambiguously computed. This has now been accomplished by Cauchy-characteristic extraction, where data for the characteristic evolution is supplied by Cauchy data on an extraction worldtube inside the artificial outer boundary. The ultimate application of characteristic evolution is to eliminate the role of this outer boundary by constructing a global solution via Cauchy-characteristic matching. Progress in this direction is discussed.

  10. 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.

  11. 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.

  12. Multi-Parametric Profiling Network Based on Gene Expression and Phenotype Data: A Novel Approach to Developmental Neurotoxicity Testing

    Directory of Open Access Journals (Sweden)

    Hideko Sone

    2011-12-01

    Full Text Available The establishment of more efficient approaches for developmental neurotoxicity testing (DNT has been an emerging issue for children’s environmental health. Here we describe a systematic approach for DNT using the neuronal differentiation of mouse embryonic stem cells (mESCs as a model of fetal programming. During embryoid body (EB formation, mESCs were exposed to 12 chemicals for 24 h and then global gene expression profiling was performed using whole genome microarray analysis. Gene expression signatures for seven kinds of gene sets related to neuronal development and neuronal diseases were selected for further analysis. At the later stages of neuronal cell differentiation from EBs, neuronal phenotypic parameters were determined using a high-content image analyzer. Bayesian network analysis was then performed based on global gene expression and neuronal phenotypic data to generate comprehensive networks with a linkage between early events and later effects. Furthermore, the probability distribution values for the strength of the linkage between parameters in each network was calculated and then used in principal component analysis. The characterization of chemicals according to their neurotoxic potential reveals that the multi-parametric analysis based on phenotype and gene expression profiling during neuronal differentiation of mESCs can provide a useful tool to monitor fetal programming and to predict developmentally neurotoxic compounds.

  13. 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.

  14. 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.

  15. Tuning Schema Matching Systems using Parallel Genetic Algorithms on GPU

    Directory of Open Access Journals (Sweden)

    Yuting Feng

    2010-11-01

    Full Text Available Most recent schema matching systems combine multiple components, each of which employs a particular matching technique with several knobs. The multi-component nature has brought a tuning problem, that is to determine which components to execute and how to adjust the knobs (e.g., thresholds, weights, etc. of these components for domain users. In this paper, we present an approach to automatically tune schema matching systems using genetic algorithms. We match a given schema S against generated matching scenarios, for which the ground truth matches are known, and find a configuration that effectively improves the performance of matching S against real schemas. To search the huge space of configuration candidates efficiently, we adopt genetic algorithms (GAs during the tuning process. To promote the performance of our approach, we implement parallel genetic algorithms on graphic processing units (GPUs based on NVIDIA’s Compute Unified Device Architecture (CUDA. Experiments over four real-world domains with two main matching systems demonstrate that our approach provides more qualified matches over different domains.

  16. 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...... gene coexpression and protein-protein interaction networks that were strongly associated with islet insulin secretion and HbA(1c). We integrated our data to form a rank list of putative T2D genes, of which CHL1, LRFN2, RASGRP1, and PPM1K were validated in INS-1 cells to influence insulin secretion...... of genes potentially involved in T2D....

  17. 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

    2013-05-01

    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.

  18. A feature selection approach for identification of signature genes from SAGE data

    Directory of Open Access Journals (Sweden)

    Silva Paulo JS

    2007-05-01

    Full Text Available Abstract Background One goal of gene expression profiling is to identify signature genes that robustly distinguish different types or grades of tumors. Several tumor classifiers based on expression profiling have been proposed using microarray technique. Due to important differences in the probabilistic models of microarray and SAGE technologies, it is important to develop suitable techniques to select specific genes from SAGE measurements. Results A new framework to select specific genes that distinguish different biological states based on the analysis of SAGE data is proposed. The new framework applies the bolstered error for the identification of strong genes that separate the biological states in a feature space defined by the gene expression of a training set. Credibility intervals defined from a probabilistic model of SAGE measurements are used to identify the genes that distinguish the different states with more reliability among all gene groups selected by the strong genes method. A score taking into account the credibility and the bolstered error values in order to rank the groups of considered genes is proposed. Results obtained using SAGE data from gliomas are presented, thus corroborating the introduced methodology. Conclusion The model representing counting data, such as SAGE, provides additional statistical information that allows a more robust analysis. The additional statistical information provided by the probabilistic model is incorporated in the methodology described in the paper. The introduced method is suitable to identify signature genes that lead to a good separation of the biological states using SAGE and may be adapted for other counting methods such as Massive Parallel Signature Sequencing (MPSS or the recent Sequencing-By-Synthesis (SBS technique. Some of such genes identified by the proposed method may be useful to generate classifiers.

  19. Comparing partial least square approaches in a gene- or region-based association study for multiple quantitative phenotypes.

    Science.gov (United States)

    Yuan, Zhongshang; Zhang, Xiaoshuai; Li, Fangyu; Zhao, Jinghua; Xue, Fuzhong

    2014-01-01

    On thinking quantitatively of complex diseases, there are at least three statistical strategies for association studies: one single-nucleotide polymorphism (SNP) on a single trait, gene or region (with multiple SNPs) on a single trait, and gene or region on multiple traits. The third approach is the most general in dissecting genetic mechanisms underlying complex diseases underpinning multiple quantitative traits. Gene or region association methods based on partial least square (PLS) approaches have been shown to have apparent power advantage. However, few approaches have been developed for multiple quantitative phenotypes or traits underlying a condition or disease, and the performance of various PLS approaches used in association studies for multiple quantitative traits have not been assessed. Here we exploit association between multiple SNPs and multiple phenotypes or traits, from a regression perspective, through exhaustive scan statistics (sliding window) using PLS and sparse PLS regressions. Simulations were conducted to assess the performance of the proposed scan statistics and compare them with existing methods. The proposed methods were applied to 12 regions of genome-wide association study data from the European Prospective Investigation of Cancer-Norfolk study.

  20. Sequence Matching Analysis for Curriculum Development

    Directory of Open Access Journals (Sweden)

    Liem Yenny Bendatu

    2015-06-01

    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.

  1. Identifying overrepresented concepts in gene lists from literature: a statistical approach based on Poisson mixture model

    Directory of Open Access Journals (Sweden)

    Zhai Chengxiang

    2010-05-01

    Full Text Available Abstract Background Large-scale genomic studies often identify large gene lists, for example, the genes sharing the same expression patterns. The interpretation of these gene lists is generally achieved by extracting concepts overrepresented in the gene lists. This analysis often depends on manual annotation of genes based on controlled vocabularies, in particular, Gene Ontology (GO. However, the annotation of genes is a labor-intensive process; and the vocabularies are generally incomplete, leaving some important biological domains inadequately covered. Results We propose a statistical method that uses the primary literature, i.e. free-text, as the source to perform overrepresentation analysis. The method is based on a statistical framework of mixture model and addresses the methodological flaws in several existing programs. We implemented this method within a literature mining system, BeeSpace, taking advantage of its analysis environment and added features that facilitate the interactive analysis of gene sets. Through experimentation with several datasets, we showed that our program can effectively summarize the important conceptual themes of large gene sets, even when traditional GO-based analysis does not yield informative results. Conclusions We conclude that the current work will provide biologists with a tool that effectively complements the existing ones for overrepresentation analysis from genomic experiments. Our program, Genelist Analyzer, is freely available at: http://workerbee.igb.uiuc.edu:8080/BeeSpace/Search.jsp

  2. Enhancing the Lasso Approach for Developing a Survival Prediction Model Based on Gene Expression Data

    Directory of Open Access Journals (Sweden)

    Shuhei Kaneko

    2015-01-01

    Full Text Available In the past decade, researchers in oncology have sought to develop survival prediction models using gene expression data. The least absolute shrinkage and selection operator (lasso has been widely used to select genes that truly correlated with a patient’s survival. The lasso selects genes for prediction by shrinking a large number of coefficients of the candidate genes towards zero based on a tuning parameter that is often determined by a cross-validation (CV. However, this method can pass over (or fail to identify true positive genes (i.e., it identifies false negatives in certain instances, because the lasso tends to favor the development of a simple prediction model. Here, we attempt to monitor the identification of false negatives by developing a method for estimating the number of true positive (TP genes for a series of values of a tuning parameter that assumes a mixture distribution for the lasso estimates. Using our developed method, we performed a simulation study to examine its precision in estimating the number of TP genes. Additionally, we applied our method to a real gene expression dataset and found that it was able to identify genes correlated with survival that a CV method was unable to detect.

  3. A novel computational approach for the prediction of networked transcription factors of aryl hydrocarbon-receptor-regulated genes.

    Science.gov (United States)

    Kel, Alexander; Reymann, Susanne; Matys, Volker; Nettesheim, Paul; Wingender, Edgar; Borlak, Jürgen

    2004-12-01

    A novel computational method based on a genetic algorithm was developed to study composite structure of promoters of coexpressed genes. Our method enabled an identification of combinations of multiple transcription factor binding sites regulating the concerted expression of genes. In this article, we study genes whose expression is regulated by a ligand-activated transcription factor, aryl hydrocarbon receptor (AhR), that mediates responses to a variety of toxins. AhR-mediated change in expression of AhR target genes was measured by oligonucleotide microarrays and by reverse transcription-polymerase chain reaction in human and rat hepatocytes. Promoters and long-distance regulatory regions (>10 kb) of AhR-responsive genes were analyzed by the genetic algorithm and a variety of other computational methods. Rules were established on the local oligonucleotide context in the flanks of the AhR binding sites, on the occurrence of clusters of AhR recognition elements, and on the presence in the promoters of specific combinations of multiple binding sites for the transcription factors cooperating in the AhR regulatory network. Our rules were applied to search for yet unknown Ah-receptor target genes. Experimental evidence is presented to demonstrate high fidelity of this novel in silico approach.

  4. 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.

  5. Cross-species transcriptomic approach reveals genes in hamster implantation sites.

    Science.gov (United States)

    Lei, Wei; Herington, Jennifer; Galindo, Cristi L; Ding, Tianbing; Brown, Naoko; Reese, Jeff; Paria, Bibhash C

    2014-12-01

    The mouse model has greatly contributed to understanding molecular mechanisms involved in the regulation of progesterone (P4) plus estrogen (E)-dependent blastocyst implantation process. However, little is known about contributory molecular mechanisms of the P4-only-dependent blastocyst implantation process that occurs in species such as hamsters, guineapigs, rabbits, pigs, rhesus monkeys, and perhaps humans. We used the hamster as a model of P4-only-dependent blastocyst implantation and carried out cross-species microarray (CSM) analyses to reveal differentially expressed genes at the blastocyst implantation site (BIS), in order to advance the understanding of molecular mechanisms of implantation. Upregulation of 112 genes and downregulation of 77 genes at the BIS were identified using a mouse microarray platform, while use of the human microarray revealed 62 up- and 38 down-regulated genes at the BIS. Excitingly, a sizable number of genes (30 up- and 11 down-regulated genes) were identified as a shared pool by both CSMs. Real-time RT-PCR and in situ hybridization validated the expression patterns of several up- and down-regulated genes identified by both CSMs at the hamster and mouse BIS to demonstrate the merit of CSM findings across species, in addition to revealing genes specific to hamsters. Functional annotation analysis found that genes involved in the spliceosome, proteasome, and ubiquination pathways are enriched at the hamster BIS, while genes associated with tight junction, SAPK/JNK signaling, and PPARα/RXRα signalings are repressed at the BIS. Overall, this study provides a pool of genes and evidence of their participation in up- and down-regulated cellular functions/pathways at the hamster BIS.

  6. 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

  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. 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…

  9. 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.

  10. 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...

  11. A novel reverse-genetic approach (SIMF) identifies Mutator insertions in new Myb genes.

    Science.gov (United States)

    Rabinowicz, P D; Grotewold, E

    2000-11-01

    We have developed a new strategy designated SIMF (Systematic Insertional Mutagenesis of Families), to identify DNA insertions in many members of a gene family simultaneously. This method requires only a short amino acid sequence conserved in all members of the family to make a degenerate oligonucleotide, and a sequence from the end of the DNA insertion. The SIMF strategy was successfully applied to the large maize R2R3 Myb family of regulatory genes, and Mutator insertions in several novel Myb genes were identified. Application of this technique to identify insertions in other large gene families could significantly decrease the effort involved in screening at the same time for insertions in all members of groups of genes that share a limited sequence identity.

  12. A Hybrid One-Way ANOVA Approach for the Robust and Efficient Estimation of Differential Gene Expression with Multiple Patterns.

    Directory of Open Access Journals (Sweden)

    Mohammad Manir Hossain Mollah

    Full Text Available Identifying genes that are differentially expressed (DE between two or more conditions with multiple patterns of expression is one of the primary objectives of gene expression data analysis. Several statistical approaches, including one-way analysis of variance (ANOVA, are used to identify DE genes. However, most of these methods provide misleading results for two or more conditions with multiple patterns of expression in the presence of outlying genes. In this paper, an attempt is made to develop a hybrid one-way ANOVA approach that unifies the robustness and efficiency of estimation using the minimum β-divergence method to overcome some problems that arise in the existing robust methods for both small- and large-sample cases with multiple patterns of expression.The proposed method relies on a β-weight function, which produces values between 0 and 1. The β-weight function with β = 0.2 is used as a measure of outlier detection. It assigns smaller weights (≥ 0 to outlying expressions and larger weights (≤ 1 to typical expressions. The distribution of the β-weights is used to calculate the cut-off point, which is compared to the observed β-weight of an expression to determine whether that gene expression is an outlier. This weight function plays a key role in unifying the robustness and efficiency of estimation in one-way ANOVA.Analyses of simulated gene expression profiles revealed that all eight methods (ANOVA, SAM, LIMMA, EBarrays, eLNN, KW, robust BetaEB and proposed perform almost identically for m = 2 conditions in the absence of outliers. However, the robust BetaEB method and the proposed method exhibited considerably better performance than the other six methods in the presence of outliers. In this case, the BetaEB method exhibited slightly better performance than the proposed method for the small-sample cases, but the the proposed method exhibited much better performance than the BetaEB method for both the small- and large

  13. 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

  14. A supervised learning approach for taxonomic classification of core-photosystem-II genes and transcripts in the marine environment

    Directory of Open Access Journals (Sweden)

    Polz Martin F

    2009-05-01

    Full Text Available Abstract Background Cyanobacteria of the genera Synechococcus and Prochlorococcus play a key role in marine photosynthesis, which contributes to the global carbon cycle and to the world oxygen supply. Recently, genes encoding the photosystem II reaction center (psbA and psbD were found in cyanophage genomes. This phenomenon suggested that the horizontal transfer of these genes may be involved in increasing phage fitness. To date, a very small percentage of marine bacteria and phages has been cultured. Thus, mapping genomic data extracted directly from the environment to its taxonomic origin is necessary for a better understanding of phage-host relationships and dynamics. Results To achieve an accurate and rapid taxonomic classification, we employed a computational approach combining a multi-class Support Vector Machine (SVM with a codon usage position specific scoring matrix (cuPSSM. Our method has been applied successfully to classify core-photosystem-II gene fragments, including partial sequences coming directly from the ocean, to seven different taxonomic classes. Applying the method on a large set of DNA and RNA psbA clones from the Mediterranean Sea, we studied the distribution of cyanobacterial psbA genes and transcripts in their natural environment. Using our approach, we were able to simultaneously examine taxonomic and ecological distributions in the marine environment. Conclusion The ability to accurately classify the origin of individual genes and transcripts coming directly from the environment is of great importance in studying marine ecology. The classification method presented in this paper could be applied further to classify other genes amplified from the environment, for which training data is available.

  15. 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.

  16. Message passing with relaxed moment matching

    OpenAIRE

    Qi, Yuan; Guo, Yandong

    2012-01-01

    Bayesian learning is often hampered by large computational expense. As a powerful generalization of popular belief propagation, expectation propagation (EP) efficiently approximates the exact Bayesian computation. Nevertheless, EP can be sensitive to outliers and suffer from divergence for difficult cases. To address this issue, we propose a new approximate inference approach, relaxed expectation propagation (REP). It relaxes the moment matching requirement of expectation propagation by addin...

  17. Application of Multi-SOM clustering approach to macrophage gene expression analysis.

    Science.gov (United States)

    Ghouila, Amel; Yahia, Sadok Ben; Malouche, Dhafer; Jmel, Haifa; Laouini, Dhafer; Guerfali, Fatma Z; Abdelhak, Sonia

    2009-05-01

    The production of increasingly reliable and accessible gene expression data has stimulated the development of computational tools to interpret such data and to organize them efficiently. The clustering techniques are largely recognized as useful exploratory tools for gene expression data analysis. Genes that show similar expression patterns over a wide range of experimental conditions can be clustered together. This relies on the hypothesis that genes that belong to the same cluster are coregulated and involved in related functions. Nevertheless, clustering algorithms still show limits, particularly for the estimation of the number of clusters and the interpretation of hierarchical dendrogram, which may significantly influence the outputs of the analysis process. We propose here a multi level SOM based clustering algorithm named Multi-SOM. Through the use of clustering validity indices, Multi-SOM overcomes the problem of the estimation of clusters number. To test the validity of the proposed clustering algorithm, we first tested it on supervised training data sets. Results were evaluated by computing the number of misclassified samples. We have then used Multi-SOM for the analysis of macrophage gene expression data generated in vitro from the same individual blood infected with 5 different pathogens. This analysis led to the identification of sets of tightly coregulated genes across different pathogens. Gene Ontology tools were then used to estimate the biological significance of the clustering, which showed that the obtained clusters are coherent and biologically significant.

  18. 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.

  19. 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…

  20. Robust spatiotemporal matching of electronic slides to presentation videos.

    Science.gov (United States)

    Fan, Quanfu; Barnard, Kobus; Amir, Arnon; Efrat, Alon

    2011-08-01

    We describe a robust and efficient method for automatically matching and time-aligning electronic slides to videos of corresponding presentations. Matching electronic slides to videos provides new methods for indexing, searching, and browsing videos in distance-learning applications. However, robust automatic matching is challenging due to varied frame composition, slide distortion, camera movement, low-quality video capture, and arbitrary slides sequence. Our fully automatic approach combines image-based matching of slide to video frames with a temporal model for slide changes and camera events. To address these challenges, we begin by extracting scale-invariant feature-transformation (SIFT) keypoints from both slides and video frames, and matching them subject to a consistent projective transformation (homography) by using random sample consensus (RANSAC). We use the initial set of matches to construct a background model and a binary classifier for separating video frames showing slides from those without. We then introduce a new matching scheme for exploiting less distinctive SIFT keypoints that enables us to tackle more difficult images. Finally, we improve upon the matching based on visual information by using estimated matching probabilities as part of a hidden Markov model (HMM) that integrates temporal information and detected camera operations. Detailed quantitative experiments characterize each part of our approach and demonstrate an average accuracy of over 95% in 13 presentation videos.

  1. Towards optimal packed string matching

    DEFF Research Database (Denmark)

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

    2014-01-01

    -size string-matching instruction wssm is available in contemporary commodity processors. The other word-size maximum-suffix instruction wslm is only required during the pattern pre-processing. Benchmarks show that our solution can be efficiently implemented, unlike some prior theoretical packed string......In the packed string matching problem, it is assumed that each machine word can accommodate up to α characters, thus an n-character string occupies n/α memory words.(a) We extend the Crochemore–Perrin constant-space O(n)-time string-matching algorithm to run in optimal O(n/α) time and even in real...... matching work.(b) We also consider the complexity of the packed string matching problem in the classical word-RAM model in the absence of the specialized micro-level instructions wssm and wslm. We propose micro-level algorithms for the theoretically efficient emulation using parallel algorithms techniques...

  2. 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.

  3. 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.

  4. 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.

  5. Identification and Cloning of Differentially Expressed SOUL and ELIP Genes in Saffron Stigmas Using a Subtractive Hybridization Approach

    Science.gov (United States)

    Ahrazem, Oussama; Argandoña, Javier; Castillo, Raquel; Rubio-Moraga, Ángela

    2016-01-01

    Using a subtractive hybridization approach, differentially expressed genes involved in the light response in saffron stigmas were identified. Twenty-two differentially expressed transcript-derived fragments were cloned and sequenced. Two of them were highly induced by light and had sequence similarity to early inducible proteins (ELIP) and SOUL heme-binding proteins. Using these sequences, we searched for other family members expressed in saffron stigma. ELIP and SOUL are represented by small gene families in saffron, with four and five members, respectively. The expression of these genes was analyzed during the development of the stigma and in light and dark conditions. ELIP transcripts were detected in all the developmental stages showing much higher expression levels in the developed stigmas of saffron and all were up-regulated by light but at different levels. By contrast, only one SOUL gene was up-regulated by light and was highly expressed in the stigma at anthesis. Both the ELIP and SOUL genes induced by light in saffron stigmas might be associated with the structural changes affecting the chromoplast of the stigma, as a result of light exposure, which promotes the development and increases the number of plastoglobules, specialized in the recruitment of specific proteins, which enables them to act in metabolite synthesis and disposal under changing environmental conditions and developmental stages. PMID:28030614

  6. 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.

  7. 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.

  8. 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,...

  9. 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

  10. 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.

  11. A Promising Approach to Gene Confinement and Breeding for Genetically Modified Bioenergy Crops

    OpenAIRE

    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...

  12. 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.

  13. 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

  14. Genetic Susceptibility to Vitiligo: GWAS Approaches for Identifying Vitiligo Susceptibility Genes and Loci

    OpenAIRE

    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-wid...

  15. Genetic Susceptibility to Vitiligo: GWAS Approaches for Identifying Vitiligo Susceptibility Genes and Loci

    OpenAIRE

    Chang eShen; Jing eGao; Yu Jun Sheng; Jinfa eDou; Fusheng eZhou; Xiaodong eZheng; Randy eKo; Xianfa eTang; Caihong Hong Zhu; Xianyong Yong Yin; Liangdan Dan Sun; Yong eCui; Xue Jun Zhang

    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 and family studies. Previously, vitiligo susceptibility genes were mainly revealed through linkage analysis and candidate gene studies. Our understanding of the genetic basis of vitiligo has been rapidly advancing through genome-wide association stud...

  16. A computational approach to identify predictive gene signatures in Triple Negative Breast Cancer

    OpenAIRE

    Nuzzo, Simona

    2014-01-01

    Microarray technology has been extensively used to detect patterns in gene expression that stem from regulatory interactions. Seminal studies demonstrated that the synergistic use of microarray-based techniques and bioinformatics analysis of genomic data might not only further the understanding of pathological phenotypes, but also provide lists of genes to dissect a disease into distinct groups, with different diagnostic or prognostic characteristics. Nonetheless, optimism for microarray-base...

  17. Searching for “monogenic diabetes” in dogs using a candidate gene approach

    OpenAIRE

    Short, Andrea D.; Holder, Angela; Rothwell, Simon; Massey, Jonathan; Scholey, Rachel; Kennedy, Lorna J.; Catchpole, Brian; Ollier, William ER

    2014-01-01

    Background Canine diabetes is a common endocrine disorder with an estimated breed-related prevalence ranging from 0.005% to 1.5% in pet dogs. Increased prevalence in some breeds suggests that diabetes in dogs is influenced by genetic factors and similarities between canine and human diabetes phenotypes suggest that the same genes might be associated with disease susceptibility in both species. Between 1-5% of human diabetes cases result from mutations in a single gene, including maturity onse...

  18. Bridging the gap between genes and language deficits in schizophrenia: an oscillopathic approach

    Directory of Open Access Journals (Sweden)

    Elliot Murphy

    2016-08-01

    Full Text Available Schizophrenia is characterised 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 aetiology of schizophrenia, its clinical/linguistic profile, and its high prevalence among modern populations.

  19. 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.

  20. A large-scale functional approach to uncover human genes and pathways in Drosophila

    Institute of Scientific and Technical Information of China (English)

    Rong Xu; Yuan Zhuang; Tian Xu; Kejing Deng; Yi Zhu; Yue Wu; Jing Ren; Min Wan; Shouyuan Zhao; Xiaohui Wu; Min Han

    2008-01-01

    We demonstrate the feasibility of performing a systematic screen for human gene functions in Drosophila by assay-ing for their ability to induce overexpression phenotypes. Over 1 500 transgenic fly lines corresponding to 236 human genes have been established. In all, 51 lines are capable of eliciting a phenotype suggesting that the human genes are functional. These heterologous genes are functionally relevant as we have found a similar mutant phenotype caused either by a dominant negative mutant form of the human ribosomal protein L8 gene or by RNAi downregulation of the Drosophila RPL8. Significantly, the Drosophila RPL8 mutant can be rescued by wild-type human RPL8. We also provide genetic evidence that Drosophila RPL8 is a new member of the insulin signaling pathway. In summary, the functions of many human genes appear to be highly conserved, and the ability to identify them in Drosophila repre-sents a powerful genetic tool for large-scale analysis of human transcripts in vivo.

  1. Optimal Control of Gene Regulatory Networks with Effectiveness of Multiple Drugs: A Boolean Network Approach

    Science.gov (United States)

    Kobayashi, Koichi; Hiraishi, Kunihiko

    2013-01-01

    Developing control theory of gene regulatory networks is one of the significant topics in the field of systems biology, and it is expected to apply the obtained results to gene therapy technologies in the future. In this paper, a control method using a Boolean network (BN) is studied. A BN is widely used as a model of gene regulatory networks, and gene expression is expressed by a binary value (0 or 1). In the control problem, we assume that the concentration level of a part of genes is arbitrarily determined as the control input. However, there are cases that no gene satisfying this assumption exists, and it is important to consider structural control via external stimuli. Furthermore, these controls are realized by multiple drugs, and it is also important to consider multiple effects such as duration of effect and side effects. In this paper, we propose a BN model with two types of the control inputs and an optimal control method with duration of drug effectiveness. First, a BN model and duration of drug effectiveness are discussed. Next, the optimal control problem is formulated and is reduced to an integer linear programming problem. Finally, numerical simulations are shown. PMID:24058904

  2. 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.

  3. Accuracy and robustness evaluation in stereo matching

    Science.gov (United States)

    Nguyen, Duc M.; Hanca, Jan; Lu, Shao-Ping; Schelkens, Peter; Munteanu, Adrian

    2016-09-01

    Stereo matching has received a lot of attention from the computer vision community, thanks to its wide range of applications. Despite of the large variety of algorithms that have been proposed so far, it is not trivial to select suitable algorithms for the construction of practical systems. One of the main problems is that many algorithms lack sufficient robustness when employed in various operational conditions. This problem is due to the fact that most of the proposed methods in the literature are usually tested and tuned to perform well on one specific dataset. To alleviate this problem, an extensive evaluation in terms of accuracy and robustness of state-of-the-art stereo matching algorithms is presented. Three datasets (Middlebury, KITTI, and MPEG FTV) representing different operational conditions are employed. Based on the analysis, improvements over existing algorithms have been proposed. The experimental results show that our improved versions of cross-based and cost volume filtering algorithms outperform the original versions with large margins on Middlebury and KITTI datasets. In addition, the latter of the two proposed algorithms ranks itself among the best local stereo matching approaches on the KITTI benchmark. Under evaluations using specific settings for depth-image-based-rendering applications, our improved belief propagation algorithm is less complex than MPEG's FTV depth estimation reference software (DERS), while yielding similar depth estimation performance. Finally, several conclusions on stereo matching algorithms are also presented.

  4. Expression of nisin genes in cheese--a quantitative real-time polymerase chain reaction approach.

    Science.gov (United States)

    Trmčić, A; Monnet, C; Rogelj, I; Bogovič Matijašić, B

    2011-01-01

    The role of bacteriocins in different environments has not been thoroughly explained, mainly because of the difficulties related to the detection of their production. Nisin, an antimicrobial peptide produced by Lactococcus lactis has a long history of safe use in food products and has been studied from many aspects of genetics, biosynthesis, immunity, regulation, and mode of action. Still, some aspects concerning the dynamics of nisin gene expression remain unknown, especially in complex media like cheese. The main objective of the present study was to quantify in a cheese-like medium the expression of nisin genes in L. lactis M78, a well-characterized nisin A producer isolated from raw milk. The expression of all 11 genes involved in nisin biosynthesis was evaluated during cheese production by real-time reverse transcription-PCR. Total RNA was extracted from cheeses using a direct extraction method without prior separation of microbial cells. The M78 strain grew well in experimental cheeses, producing detectable amounts of nisin after 4 h of fermentation. The presence of nisin as an activator modified both the expression of nisin genes and the accumulation of active nisin. Four groups could be distinguished based on gene expression as a function of time: nisA, nisFEG, nisRK and nisBTCIP. Based on nisin-producing strain growth, nisin activity, function of nisin genes, and their location, correlations were established that contribute to the explanation of regulation of nisin biosynthesis and immunity. This study is the first in which the evolution of bacteriocin gene transcripts has been quantified rigorously in a cheese-like medium.

  5. 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.

  6. 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.

  7. Embryonic stem cell gene expression signatures in the canine mammary tumor: a bioinformatics approach.

    Science.gov (United States)

    Zamani-Ahmadmahmudi, Mohamad

    2016-08-01

    Canine breast cancer was considered as an ideal model of comparative oncology for the human breast cancer, as there is significant overlap between biological and clinical characteristics of the human and canine breast cancer. We attempt to clarify expression profile of the embryonic stem cell (ES) gene signatures in canine breast cancer. Using microarray datasets (GSE22516 and GSE20718), expression of the three major ES gene signatures (modules or gene-sets), including Myc, ESC-like, and PRC modules, was primarily analyzed through Gene-Set Enrichment Analysis (GSEA) method in tumor and healthy datasets. For confirmation of the primary results, an additional 13 ES gene-sets which were categorized into four groups including ES expressed (ES exp1 and ES exp2), NOS targets (Nanog targets, Oct4 targets, Sox2 targets, NOS targets, and NOS TFs), Polycomb targets (Suz12 targets, Eed targets, H3K27 bound, and PRC2 targets), and Myc targets (Myc targets1, and Myc targets2) were tested in the tumor and healthy datasets. Our results revealed that there is a valuable overlap between canine and human breast cancer ES gene-sets expression profile, where Myc and ESC-like modules were up-regulated and PRC module was down-regulated in metastatic canine mammary gland tumors. Further analysis of the secondary gene-sets indicated overexpression of the ES expressed, NOS targets (Nanog targets, Oct4 targets, Sox2 targets, and NOS targets), and Myc targets and underexpression of the Polycomb targets in metastatic canine breast cancer.

  8. 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

  9. 49 CFR 173.186 - Matches.

    Science.gov (United States)

    2010-10-01

    ...) Wax “Vesta” matches are matches that can be ignited by friction either on a prepared surface or on a solid surface. (c) Safety matches and wax “Vesta” matches must be tightly packed in securely closed... packaging with any material other than safety matches or wax “Vesta” matches, which must be packed...

  10. Pattern Matching in Multiple Streams

    CERN Document Server

    Clifford, Raphael; Porat, Ely; Sach, Benjamin

    2012-01-01

    We investigate the problem of deterministic pattern matching in multiple streams. In this model, one symbol arrives at a time and is associated with one of s streaming texts. The task at each time step is to report if there is a new match between a fixed pattern of length m and a newly updated stream. As is usual in the streaming context, the goal is to use as little space as possible while still reporting matches quickly. We give almost matching upper and lower space bounds for three distinct pattern matching problems. For exact matching we show that the problem can be solved in constant time per arriving symbol and O(m+s) words of space. For the k-mismatch and k-differences problems we give O(k) time solutions that require O(m+ks) words of space. In all three cases we also give space lower bounds which show our methods are optimal up to a single logarithmic factor. Finally we set out a number of open problems related to this new model for pattern matching.

  11. 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.......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...... matching dækker over arbejdsprocessen, hvor de fysiske parametre i en reservoirsimuleringsmodel bliver justeret således, at en simulering af olieproduktionen stemmer overens med egentlige målte produktionsdata. Mange history matching metoder er baseret på et geostatistisk fundament, hvilket også gør sig...

  12. 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.

  13. MATCHING IN INFORMAL FINANCIAL INSTITUTIONS.

    Science.gov (United States)

    Eeckhout, Jan; Munshi, Kaivan

    2010-09-01

    This paper analyzes an informal financial institution that brings heterogeneous agents together in groups. We analyze decentralized matching into these groups, and the equilibrium composition of participants that consequently arises. We find that participants sort remarkably well across the competing groups, and that they re-sort immediately following an unexpected exogenous regulatory change. These findings suggest that the competitive matching model might have applicability and bite in other settings where matching is an important equilibrium phenomenon. (JEL: O12, O17, G20, D40).

  14. 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.

  15. Variants of the HNF1α gene: a molecular approach concerning diabetic patients from southern Brazil

    Directory of Open Access Journals (Sweden)

    Naieli Bonatto

    2012-01-01

    Full Text Available Maturity Onset Diabetes of the Young (MODY presents monogenic inheritance and mutation factors which have already been identified in six different genes. Given the wide molecular variation present in the hepatocyte nuclear factor-1α gene (HNF1α MODY3, the aimof this study was to amplify and sequence the coding regions of this gene in seven patients from the Campos Gerais region, Paraná State, Brazil, presenting clinical MODY3 features. Besides the synonymous variations, A15A, L17L, Q141Q, G288G and T515T, two missense mutations, I27L and A98V, were also detected. Clinical and laboratory data obtained from patients were compared with the molecular findings, including the I27L polymorphism that was revealed in some overweight/obese diabetic patients of this study, this corroborating with the literature. We found certain DNA variations that could explain the hyperglycemic phenotype of the patients.

  16. 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...

  17. 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

    genes with evidence of linkage: ENPP1 (P = 0.003), IGFBP3 (P = 0.006), DHCR7 (P = 0.009), and TRAF2 (P = 0.01). DNA sequence analysis of the coding exons and splice sites for CRHR1 and TRAF2 identified no new likely etiologic variants.Conclusion:These findings suggest the involvement of six genes acting...... used. Premature infants and mothers of premature infants were defined as affected cases in independent analyses.Results:Analyses with the infant as the case identified two genes with evidence of linkage: CRHR1 (P = 0.0012) and CYP2E1 (P = 0.0011). Analyses with the mother as the case identified four...

  18. 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.

  19. 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.

  20. 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

  1. Discovering gene annotations in biomedical text databases

    Directory of Open Access Journals (Sweden)

    Ozsoyoglu Gultekin

    2008-03-01

    Full Text Available Abstract Background Genes and gene products are frequently annotated with Gene Ontology concepts based on the evidence provided in genomics articles. Manually locating and curating information about a genomic entity from the biomedical literature requires vast amounts of human effort. Hence, there is clearly a need forautomated computational tools to annotate the genes and gene products with Gene Ontology concepts by computationally capturing the related knowledge embedded in textual data. Results In this article, we present an automated genomic entity annotation system, GEANN, which extracts information about the characteristics of genes and gene products in article abstracts from PubMed, and translates the discoveredknowledge into Gene Ontology (GO concepts, a widely-used standardized vocabulary of genomic traits. GEANN utilizes textual "extraction patterns", and a semantic matching framework to locate phrases matching to a pattern and produce Gene Ontology annotations for genes and gene products. In our experiments, GEANN has reached to the precision level of 78% at therecall level of 61%. On a select set of Gene Ontology concepts, GEANN either outperforms or is comparable to two other automated annotation studies. Use of WordNet for semantic pattern matching improves the precision and recall by 24% and 15%, respectively, and the improvement due to semantic pattern matching becomes more apparent as the Gene Ontology terms become more general. Conclusion GEANN is useful for two distinct purposes: (i automating the annotation of genomic entities with Gene Ontology concepts, and (ii providing existing annotations with additional "evidence articles" from the literature. The use of textual extraction patterns that are constructed based on the existing annotations achieve high precision. The semantic pattern matching framework provides a more flexible pattern matching scheme with respect to "exactmatching" with the advantage of locating approximate

  2. iSLIM: a comprehensive approach to mapping and characterizing gene regulatory networks.

    Science.gov (United States)

    Rockel, Sylvie; Geertz, Marcel; Hens, Korneel; Deplancke, Bart; Maerkl, Sebastian J

    2013-02-01

    Mapping gene regulatory networks is a significant challenge in systems biology, yet only a few methods are currently capable of systems-level identification of transcription factors (TFs) that bind a specific regulatory element. We developed a microfluidic method for integrated systems-level interaction mapping of TF-DNA interactions, generating and interrogating an array of 423 full-length Drosophila TFs. With integrated systems-level interaction mapping, it is now possible to rapidly and quantitatively map gene regulatory networks of higher eukaryotes.

  3. 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.

  4. 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.

  5. Perturbation Detection Through Modeling of Gene Expression on a Latent Biological Pathway Network: A Bayesian hierarchical approach.

    Science.gov (United States)

    Pham, Lisa M; Carvalho, Luis; Schaus, Scott; Kolaczyk, Eric D

    Cellular response to a perturbation is the result of a dynamic system of biological variables linked in a complex network. A major challenge in drug and disease studies is identifying the key factors of a biological network that are essential in determining the cell's fate. Here our goal is the identification of perturbed pathways from high-throughput gene expression data. We develop a three-level hierarchical model, where (i) the first level captures the relationship between gene expression and biological pathways using confirmatory factor analysis, (ii) the second level models the behavior within an underlying network of pathways induced by an unknown perturbation using a conditional autoregressive model, and (iii) the third level is a spike-and-slab prior on the perturbations. We then identify perturbations through posterior-based variable selection. We illustrate our approach using gene transcription drug perturbation profiles from the DREAM7 drug sensitivity predication challenge data set. Our proposed method identified regulatory pathways that are known to play a causative role and that were not readily resolved using gene set enrichment analysis or exploratory factor models. Simulation results are presented assessing the performance of this model relative to a network-free variant and its robustness to inaccuracies in biological databases.

  6. PATE, a gene expressed in prostate cancer, normal prostate, and testis, identified by a functional genomic approach

    Science.gov (United States)

    Bera, Tapan K.; Maitra, Rangan; Iavarone, Carlo; Salvatore, Giuliana; Kumar, Vasantha; Vincent, James J.; Sathyanarayana, B. K.; Duray, Paul; Lee, B. K.; Pastan, Ira

    2002-03-01

    To identify target antigens for prostate cancer therapy, we have combined computer-based screening of the human expressed sequence tag database and experimental expression analysis to identify genes that are expressed in normal prostate and prostate cancer but not in essential human tissues. Using this approach, we identified a gene that is expressed specifically in prostate cancer, normal prostate, and testis. The gene has a 1.5-kb transcript that encodes a protein of 14 kDa. We named this gene PATE (expressed in prostate and testis). In situ hybridization shows that PATE mRNA is expressed in the epithelial cells of prostate cancers and in normal prostate. Transfection of the PATE cDNA with a Myc epitope tag into NIH 3T3 cells and subsequent cell fractionation analysis shows that the PATE protein is localized in the membrane fraction of the cell. Analysis of the amino acid sequence of PATE shows that it has structural similarities to a group of proteins known as three-finger toxins, which includes the extracellular domain of the type transforming growth factor receptor. Restricted expression of PATE makes it a potential candidate for the immunotherapy of prostate cancer.

  7. 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....

  8. 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.

  9. 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.

  10. 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 ...

  11. 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

    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...

  12. Use of linkage disequilibrium approaches to map genes for bipolar disorder in the Costa Rican population

    NARCIS (Netherlands)

    Escamilla, MA; Spesny, M; Reus, [No Value; Gallegos, A; Meza, L; Molina, J; Sandkuijl, LA; Fournier, E; Leon, PE; Smith, LB; Freimer, NB

    1996-01-01

    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, s

  13. 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.

  14. Genetic Susceptibility to Vitiligo: GWAS Approaches for Identifying Vitiligo Susceptibility Genes and Loci

    Directory of Open Access Journals (Sweden)

    Chang eShen

    2016-02-01

    Full Text Available 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 and family studies. Previously, vitiligo susceptibility genes were mainly revealed through linkage analysis and candidate gene studies. Our understanding of the genetic basis of vitiligo has been rapidly advancing through genome-wide association studies (GWASs. More than 40 robust susceptible loci have been identified and confirmed to be associated with vitiligo by using GWASs. Most of these associated genes participate in important pathways involved in the pathogenesis of vitiligo, such as immunoregulatory function, melanocyte regulation and so on. A number of 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 vitiligo development.

  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. Candidate fire blight resistance genes in Malus identified with the use of genomic tools and approaches

    Science.gov (United States)

    The goal of this research is to utilize current advances in Rosaceae genomics to identify DNA markers for use in marker-assisted selection of durable resistance to fire blight. Candidate fire blight resistance genes were selected and ranked based upon differential expression after inoculation with ...

  17. A complementary bioinformatics approach to identify potential plant cell wall glycosytransferase 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...

  18. 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.

  19. 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.

  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. Antibodies against Human Cytomegalovirus in the Pathogenesis of Systemic Sclerosis: A Gene Array Approach.

    Directory of Open Access Journals (Sweden)

    2005-12-01

    Full Text Available BACKGROUND: Systemic sclerosis is an autoimmune disease characterized by immunological abnormalities, vascular damage, and fibroblast proliferation. We have previously shown that a molecular mimicry mechanism links antibodies against the human-cytomegalovirus-derived protein UL94 to the pathogenesis of systemic sclerosis. The UL94 epitope shows homology with NAG-2, a surface molecule highly expressed on endothelial cells. Anti-UL94 peptide antibodies purified from patients' sera induce apoptosis of endothelial cells upon engagement of the NAG-2-integrin complex. METHODS AND FINDINGS: We show here that NAG-2 is expressed on dermal fibroblasts and that anti-UL94 antibodies bind to fibroblasts. We have used the gene array strategy (Affimetrix oligonucleotide microarrays to analyze the transcriptional profile in response to a 4-h and an 8-h treatment with antibodies against the UL94 peptide in endothelial cells and dermal fibroblasts. Exposure of endothelial cells to anti-UL94 antibodies had a profound impact on gene expression, resulting in the upregulation of 1,645 transcripts. Several gene clusters were upregulated including genes encoding adhesion molecules, chemokines, colony-stimulating factors (CSFs, growth factors, and molecules involved in apoptosis. Following antibody stimulation, dermal fibroblasts showed an upregulation of 989 transcripts and acquired a "scleroderma-like" phenotype. Indeed, genes involved in extracellular matrix deposition, growth factors, chemokines, and cytokines were upregulated. We confirmed the microarray results by real-time quantitative polymerase chain reaction and by measuring some of the corresponding proteins with ELISA and Western blotting. CONCLUSION: Our results show that anti-human-cytomegalovirus antibodies may be linked to the pathogenesis of systemic sclerosis not only by inducing endothelial cell activation and apoptosis but also by causing activation of fibroblasts, one of the hallmarks of the disease.

  2. Antibodies against human cytomegalovirus in the pathogenesis of systemic sclerosis: a gene array approach.

    Directory of Open Access Journals (Sweden)

    Claudio Lunardi

    2006-01-01

    Full Text Available BACKGROUND: Systemic sclerosis is an autoimmune disease characterized by immunological abnormalities, vascular damage, and fibroblast proliferation. We have previously shown that a molecular mimicry mechanism links antibodies against the human-cytomegalovirus-derived protein UL94 to the pathogenesis of systemic sclerosis. The UL94 epitope shows homology with NAG-2, a surface molecule highly expressed on endothelial cells. Anti-UL94 peptide antibodies purified from patients' sera induce apoptosis of endothelial cells upon engagement of the NAG-2-integrin complex. METHODS AND FINDINGS: We show here that NAG-2 is expressed on dermal fibroblasts and that anti-UL94 antibodies bind to fibroblasts. We have used the gene array strategy (Affimetrix oligonucleotide microarrays to analyze the transcriptional profile in response to a 4-h and an 8-h treatment with antibodies against the UL94 peptide in endothelial cells and dermal fibroblasts. Exposure of endothelial cells to anti-UL94 antibodies had a profound impact on gene expression, resulting in the upregulation of 1,645 transcripts. Several gene clusters were upregulated including genes encoding adhesion molecules, chemokines, colony-stimulating factors (CSFs, growth factors, and molecules involved in apoptosis. Following antibody stimulation, dermal fibroblasts showed an upregulation of 989 transcripts and acquired a "scleroderma-like" phenotype. Indeed, genes involved in extracellular matrix deposition, growth factors, chemokines, and cytokines were upregulated. We confirmed the microarray results by real-time quantitative polymerase chain reaction and by measuring some of the corresponding proteins with ELISA and Western blotting. CONCLUSION: Our results show that anti-human-cytomegalovirus antibodies may be linked to the pathogenesis of systemic sclerosis not only by inducing endothelial cell activation and apoptosis but also by causing activation of fibroblasts, one of the hallmarks of the disease.

  3. 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.

  4. Shape-Based Image Matching Using Heat Kernels and Diffusion Maps

    Science.gov (United States)

    Vizilter, Yu. V.; Gorbatsevich, V. S.; Rubis, A. Yu.; Zheltov, S. Yu.

    2014-08-01

    2D image matching problem is often stated as an image-to-shape or shape-to-shape matching problem. Such shape-based matching techniques should provide the matching of scene image fragments registered in various lighting, weather and season conditions or in different spectral bands. Most popular shape-to-shape matching technique is based on mutual information approach. Another wellknown approach is a morphological image-to-shape matching proposed by Pytiev. In this paper we propose the new image-to-shape matching technique based on heat kernels and diffusion maps. The corresponding Diffusion Morphology is proposed as a new generalization of Pytiev morphological scheme. The fast implementation of morphological diffusion filtering is described. Experimental comparison of new and aforementioned shape-based matching techniques is reported applying to the TV and IR image matching problem.

  5. 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.

  6. 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.

  7. A culture-independent approach to unravel uncultured bacteria and functional genes in a complex microbial community.

    Directory of Open Access Journals (Sweden)

    Yun Wang

    Full Text Available Most microorganisms in nature are uncultured with unknown functionality. Sequence-based metagenomics alone answers 'who/what are there?' but not 'what are they doing and who is doing it and how?'. Function-based metagenomics reveals gene function but is usually limited by the specificity and sensitivity of screening strategies, especially the identification of clones whose functional gene expression has no distinguishable activity or phenotypes. A 'biosensor-based genetic transducer' (BGT technique, which employs a whole-cell biosensor to quantitatively detect expression of inserted genes encoding designated functions, is able to screen for functionality of unknown genes from uncultured microorganisms. In this study, BGT was integrated with Stable isotope probing (SIP-enabled Metagenomics to form a culture-independent SMB toolbox. The utility of this approach was demonstrated in the discovery of a novel functional gene cluster in naphthalene contaminated groundwater. Specifically, metagenomic sequencing of the (13C-DNA fraction obtained by SIP indicated that an uncultured Acidovorax sp. was the dominant key naphthalene degrader in-situ, although three culturable Pseudomonas sp. degraders were also present in the same groundwater. BGT verified the functionality of a new nag2 operon which co-existed with two other nag and two nah operons for naphthalene biodegradation in the same microbial community. Pyrosequencing analysis showed that the nag2 operon was the key functional operon in naphthalene degradation in-situ, and shared homology with both nag operons in Ralstonia sp. U2 and Polaromonas naphthalenivorans CJ2. The SMB toolbox will be useful in providing deep insights into uncultured microorganisms and unravelling their ecological roles in natural environments.

  8. 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.

  9. 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.

  10. Metagenomic approach reveals variation of microbes with arsenic and antimony metabolism genes from highly contaminated soil.

    Science.gov (United States)

    Luo, Jinming; Bai, Yaohui; Liang, Jinsong; Qu, Jiuhui

    2014-01-01

    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.

  11. 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.

  12. May I Cut in? Gene Editing Approaches in Human Induced Pluripotent Stem Cells

    Science.gov (United States)

    Brookhouser, Nicholas; Raman, Sreedevi; Potts, Christopher; Brafman, David. A.

    2017-01-01

    In the decade since Yamanaka and colleagues described methods to reprogram somatic cells into a pluripotent state, human induced pluripotent stem cells (hiPSCs) have demonstrated tremendous promise in numerous disease modeling, drug discovery, and regenerative medicine applications. More recently, the development and refinement of advanced gene transduction and editing technologies have further accelerated the potential of hiPSCs. In this review, we discuss the various gene editing technologies that are being implemented with hiPSCs. Specifically, we describe the emergence of technologies including zinc-finger nuclease (ZFN), transcription activator-like effector nuclease (TALEN), and clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 that can be used to edit the genome at precise locations, and discuss the strengths and weaknesses of each of these technologies. In addition, we present the current applications of these technologies in elucidating the mechanisms of human development and disease, developing novel and effective therapeutic molecules, and engineering cell-based therapies. Finally, we discuss the emerging technological advances in targeted gene editing methods. PMID:28178187

  13. May I Cut in? Gene Editing Approaches in Human Induced Pluripotent Stem Cells.

    Science.gov (United States)

    Brookhouser, Nicholas; Raman, Sreedevi; Potts, Christopher; Brafman, David A

    2017-02-06

    In the decade since Yamanaka and colleagues described methods to reprogram somatic cells into a pluripotent state, human induced pluripotent stem cells (hiPSCs) have demonstrated tremendous promise in numerous disease modeling, drug discovery, and regenerative medicine applications. More recently, the development and refinement of advanced gene transduction and editing technologies have further accelerated the potential of hiPSCs. In this review, we discuss the various gene editing technologies that are being implemented with hiPSCs. Specifically, we describe the emergence of technologies including zinc-finger nuclease (ZFN), transcription activator-like effector nuclease (TALEN), and clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 that can be used to edit the genome at precise locations, and discuss the strengths and weaknesses of each of these technologies. In addition, we present the current applications of these technologies in elucidating the mechanisms of human development and disease, developing novel and effective therapeutic molecules, and engineering cell-based therapies. Finally, we discuss the emerging technological advances in targeted gene editing methods.

  14. May I Cut in? Gene Editing Approaches in Human Induced Pluripotent Stem Cells

    Directory of Open Access Journals (Sweden)

    Nicholas Brookhouser

    2017-02-01

    Full Text Available In the decade since Yamanaka and colleagues described methods to reprogram somatic cells into a pluripotent state, human induced pluripotent stem cells (hiPSCs have demonstrated tremendous promise in numerous disease modeling, drug discovery, and regenerative medicine applications. More recently, the development and refinement of advanced gene transduction and editing technologies have further accelerated the potential of hiPSCs. In this review, we discuss the various gene editing technologies that are being implemented with hiPSCs. Specifically, we describe the emergence of technologies including zinc-finger nuclease (ZFN, transcription activator-like effector nuclease (TALEN, and clustered regularly interspaced short palindromic repeats (CRISPR/Cas9 that can be used to edit the genome at precise locations, and discuss the strengths and weaknesses of each of these technologies. In addition, we present the current applications of these technologies in elucidating the mechanisms of human development and disease, developing novel and effective therapeutic molecules, and engineering cell-based therapies. Finally, we discuss the emerging technological advances in targeted gene editing methods.

  15. 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.

  16. 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.

  17. 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.

  18. 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

  19. Matching illumination of solid objects.

    Science.gov (United States)

    Pont, Sylvia C; Koenderink, Jan J

    2007-04-01

    The appearance of objects is determined by their surface reflectance and roughness and by the light field. Conversely, human observers might derive properties of the light field from the appearance of objects. The inverse problem has no unique solution, so perceptual interactions between reflectance, roughness, and lightfield are to be expected. In two separate experiments, we tested whether observers are able to match the illumination of spheres under collimated illumination only (matching of illumination direction) and under more or less diffuse illumination (matching of illumination direction and directedness of the beam). We found that observers are quite able to match collimated illumination directions of two rendered Lambertian spheres. Matching of the collimated beam directions of a Lambertian sphere and that of a real object with arbitrary reflectance and roughness properties resulted in similar results for the azimuthal angle, but in higher variance for the polar angle. Translucent objects and a tennis ball were found to be systematic outliers. If the directedness of the beam was also varied, the direction settings showed larger variance for more diffuse illumination. The directedness settings showed an overall quite large variance and, interestingly, interacted with the polar angle settings. We discuss possible photometrical mechanisms behind these effects.

  20. 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

  1. 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.

  2. Gold-nanorod-based colorimetric and fluorescent approach for sensitive and specific assay of disease-related gene and mutation.

    Science.gov (United States)

    Wang, Wenhong; Zhao, Yina; Jin, Yan

    2013-11-27

    Sensitive and specific detection of disease-related gene and single nucleotide polymorphism (SNP) is of great importance in cancer diagnosis. Here, a colorimetric and fluorescent approach is described for detection of the p53 gene and SNP in homogeneous solution by using gold nanorods (GNRs) as both colorimetric probe and fluorescence quencher. Hairpin oligonucleotide was utilized as DNA probe to ensure highly sequence-specific detection of target DNA. In the presence of target DNA, the formation of DNA duplex greatly changed the electrostatic interaction between GNR and DNAs, leading to an obvious change in fluorescence and colorimetric response. The detection limit of fluorescent and colorimetric assay is 0.26 pM and 0.3 nM, respectively. Both fluorescence and colorimetric strategies were able to effectively discriminate complementary DNA from single-base mismatched DNA, which is meaningful for cancer diagnosis. More important, target DNA can be detected as low as 10 nM by the naked eye. Furthermore, transmission electron microscopy and fluorescence anisotropy measurements demonstrated that the color change as well as fluorescence quenching is ascribed to the DNA hybridization-induced aggregation of GNRs. Therefore, the assay provided a fast, sensitive, cost-effective, and specific sensing platform for detecting disease-related gene and SNP.

  3. Lambda exonuclease-based subtractive hybridization approach to isolate differentially expressed genes from leaf cultures of Paulownia kawakamii.

    Science.gov (United States)

    Low, R K; Prakash, A P; Swarup, S; Goh, C J; Kumar, P P

    2001-08-15

    Genes that are preferentially expressed in a particular developmental pathway can be isolated by subtractive hybridization (SH). We developed a PCR-based approach coupled with lambda exonuclease digestion that allows for generating single-stranded tester and driver nucleic acids suitable for SH starting from cDNA libraries. An efficient subtraction strategy was developed to overcome some of the problems in the previously described SH protocols, such as the need for large amounts of experimental tissue, RNase contamination during solution hybridization, and postsubtraction recovery of nucleic acids. We used this method to obtain cDNA corresponding to genes expressed during adventitious shoot regeneration from excised leaf cultures of the fast-growing tree Paulownia kawakamii. Over 36 cDNA clones were isolated and 1 of the differentially expressed clones codes for a leucine zipper transcription factor. This clone showed about sixfold higher level of expression in the shoot-forming tissues (tester) compared to that in the callus-forming tissues (driver) of Paulownia, suggesting that differentially expressed genes can be efficiently isolated using this simple lambda exonuclease-based subtractive hybridization method.

  4. A combinational CRISPR/Cas9 gene-editing approach can halt HIV replication and prevent viral escape

    Science.gov (United States)

    Lebbink, Robert Jan; de Jong, Dorien C. M.; Wolters, Femke; Kruse, Elisabeth M.; van Ham, Petra M.; Wiertz, Emmanuel J. H. J.; Nijhuis, Monique

    2017-01-01

    HIV presents one of the highest evolutionary rates ever detected and combination antiretroviral therapy is needed to overcome the plasticity of the virus population and control viral replication. Conventional treatments lack the ability to clear the latent reservoir, which remains the major obstacle towards a cure. Novel strategies, such as CRISPR/Cas9 gRNA-based genome-editing, can permanently disrupt the HIV genome. However, HIV genome-editing may accelerate viral escape, questioning the feasibility of the approach. Here, we demonstrate that CRISPR/Cas9 targeting of single HIV loci, only partially inhibits HIV replication and facilitates rapid viral escape at the target site. A combinatorial approach of two strong gRNAs targeting different regions of the HIV genome can completely abrogate viral replication and prevent viral escape. Our data shows that the accelerating effect of gene-editing on viral escape can be overcome and as such gene-editing may provide a future alternative for control of HIV-infection. PMID:28176813

  5. Integrating Molecular Imaging Approaches to Monitor Prostate Targeted Suicide and Anti-angiogenic Gene Therapy

    Science.gov (United States)

    2005-02-01

    clinical trials. The ad- vantages of using adenovirus are severalfold: (1) ease of ge- netic manipulation ( Chartier et al., 1996; Kanerva et al...located upstream of an immediate early gene of human cytomegalovirus. Cell 41, 521–530. CHARTIER , C., DEGRYSE, E., GANTZER, M., DIETERLE, A., PAVIRANI, A...Hemminki, A., Belousova, N., Zinn, K.R., Liu, B., Wang, M., Chaudhuri, T.R., Rogers , B.E., Buchsbaum, D.J., Siegal, G.P., Barnes, M.N., Go- mez-Navarro

  6. 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.

  7. 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.

  8. 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.)

  9. 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.

  10. Large-Scale Collective Entity Matching

    CERN Document Server

    Rastogi, Vibhor; Garofalakis, Minos

    2011-01-01

    There have been several recent advancements in Machine Learning community on the Entity Matching (EM) problem. However, their lack of scalability has prevented them from being applied in practical settings on large real-life datasets. Towards this end, we propose a principled framework to scale any generic EM algorithm. Our technique consists of running multiple instances of the EM algorithm on small neighborhoods of the data and passing messages across neighborhoods to construct a global solution. We prove formal properties of our framework and experimentally demonstrate the effectiveness of our approach in scaling EM algorithms.

  11. Antennas with non-foster matching networks

    CERN Document Server

    Aberle, James T

    2007-01-01

    Most antenna engineers are likely to believe that antennas are one technology that is more or less impervious to the rapidly advancing semiconductor industry. However, as demonstrated in this lecture, there is a way to incorporate active components into an antenna and transform it into a new kind of radiating structure that can take advantage of the latest advances in analog circuit design. The approach for making this transformation is to make use of non-Foster circuit elements in the matching network of the antenna. By doing so, we are no longer constrained by the laws of physics that apply

  12. Error-tolerant Tree Matching

    CERN Document Server

    Oflazer, K

    1996-01-01

    This paper presents an efficient algorithm for retrieving from a database of trees, all trees that match a given query tree approximately, that is, within a certain error tolerance. It has natural language processing applications in searching for matches in example-based translation systems, and retrieval from lexical databases containing entries of complex feature structures. The algorithm has been implemented on SparcStations, and for large randomly generated synthetic tree databases (some having tens of thousands of trees) it can associatively search for trees with a small error, in a matter of tenths of a second to few seconds.

  13. Memristor-based pattern matching

    Science.gov (United States)

    Klimo, Martin; Such, Ondrej; Skvarek, Ondrej; Fratrik, Milan

    2014-10-01

    Pattern matching is a machine learning area that requires high-performance hardware. It has been hypothesized that massively parallel designs, which avoid von Neumann architecture, could provide a significant performance boost. Such designs can advantageously use memristive switches. This paper discusses a two-stage design that implements the induced ordered weighted average (IOWA) method for pattern matching. We outline the circuit structure and discuss how a functioning circuit can be achieved using metal oxide devices. We describe our simulations of memristive circuits and illustrate their performance on a vowel classification task.

  14. Robust and accurate multi-view reconstruction by prioritized matching

    DEFF Research Database (Denmark)

    Ylimaki, Markus; Kannala, Juho; Holappa, Jukka;

    2012-01-01

    a 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 input images. Our experiments show that matching the most promising seeds first provides very robust point cloud reconstructions efficiently with just a single expansion step. A comparison to the current state-of-the-art shows that our method produces reconstructions of similar quality but significantly...

  15. Spectral feature matching based on partial least squares

    Institute of Scientific and Technical Information of China (English)

    Weidong Yan; Zheng Tian; Lulu Pan; Mingtao Ding

    2009-01-01

    We investigate the spectral approaches to the problem of point pattern matching, and present a spectral feature descriptors based on partial least square (PLS). Given keypoints of two images, we define the position similarity matrices respectively, and extract the spectral features from the matrices by PLS, which indicate geometric distribution and inner relationships of the keypoints. Then the keypoints matching is done by bipartite graph matching. The experiments on both synthetic and real-world data corroborate the robustness and invariance of the algorithm.

  16. 2-Jump DNA Search Multiple Pattern Matching Algorithm

    OpenAIRE

    Raju Bhukya; D. V. L. N. Somayajulu

    2011-01-01

    Pattern matching in a DNA sequence or searching a pattern from a large data base is a major research area in computational biology. To extract pattern match 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 in the sequence. As performance plays a major role in extracting patterns from a given DNA sequence or from a database independent of the size of the sequence....

  17. A biology-driven approach identifies the hypoxia gene signature as a predictor of the outcome of neuroblastoma patients

    Directory of Open Access Journals (Sweden)

    Fardin Paolo

    2010-07-01

    Full Text Available Abstract Background Hypoxia is a condition of low oxygen tension occurring in the tumor microenvironment and it is related to poor prognosis in human cancer. To examine the relationship between hypoxia and neuroblastoma, we generated and tested an in vitro derived hypoxia gene signature for its ability to predict patients' outcome. Results We obtained the gene expression profile of 11 hypoxic neuroblastoma cell lines and we derived a robust 62 probesets signature (NB-hypo taking advantage of the strong discriminating power of the l1-l2 feature selection technique combined with the analysis of differential gene expression. We profiled gene expression of the tumors of 88 neuroblastoma patients and divided them according to the NB-hypo expression values by K-means clustering. The NB-hypo successfully stratifies the neuroblastoma patients into good and poor prognosis groups. Multivariate Cox analysis revealed that the NB-hypo is a significant independent predictor after controlling for commonly used risk factors including the amplification of MYCN oncogene. NB-hypo increases the resolution of the MYCN stratification by dividing patients with MYCN not amplified tumors in good and poor outcome suggesting that hypoxia is associated with the aggressiveness of neuroblastoma tumor independently from MYCN amplification. Conclusions Our results demonstrate that the NB-hypo is a novel and independent prognostic factor for neuroblastoma and support the view that hypoxia is negatively correlated with tumors' outcome. We show the power of the biology-driven approach in defining hypoxia as a critical molecular program in neuroblastoma and the potential for improvement in the current criteria for risk stratification.

  18. Targeted SNP discovery in Atlantic salmon (Salmo salar genes using a 3'UTR-primed SNP detection approach

    Directory of Open Access Journals (Sweden)

    Høyheim Bjørn

    2010-12-01

    Full Text Available Abstract Background Single nucleotide polymorphisms (SNPs represent the most widespread type of DNA variation in vertebrates and may be used as genetic markers for a range of applications. This has led to an increased interest in identification of SNP markers in non-model species and farmed animals. The in silico SNP mining method used for discovery of most known SNPs in Atlantic salmon (Salmo salar has applied a global (genome-wide approach. In this study we present a targeted 3'UTR-primed SNP discovery strategy that utilizes sequence data from Salmo salar full length sequenced cDNAs (FLIcs. We compare the efficiency of this new strategy to the in silico SNP mining method when using both methods for targeted SNP discovery. Results The SNP discovery efficiency of the two methods was tested in a set of FLIc target genes. The 3'UTR-primed SNP discovery method detected novel SNPs in 35% of the target genes while the in silico SNP mining method detected novel SNPs in 15% of the target genes. Furthermore, the 3'UTR-primed SNP discovery strategy was the less labor intensive one and revealed a higher success rate than the in silico SNP mining method in the initial amplification step. When testing the methods we discovered 112 novel bi-allelic polymorphisms (type I markers in 88 salmon genes [dbSNP: ss179319972-179320081, ss250608647-250608648], and three of the SNPs discovered were missense substitutions. Conclusions Full length insert cDNAs (FLIcs are important genomic resources that have been developed in many farmed animals. The 3'UTR-primed SNP discovery strategy successfully utilized FLIc data to detect novel SNPs in the partially tetraploid Atlantic salmon. This strategy may therefore be useful for targeted SNP discovery in several species, and particularly useful in species that, like salmonids, have duplicated genomes.

  19. 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.

  20. 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.

  1. 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

  2. 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.

  3. Online matching on a line

    NARCIS (Netherlands)

    Fuchs, Bernard; Hochstättler, Winfried; Kern, Walter

    2005-01-01

    Given a set S c R of points on the line, we consider the task of matching a sequence (r1,r2,…) of requests in R to points in S. It has been conjectured [Online Algorithms: The State of the Art, Lecture Notes in Computer Science, Vol. 1442, Springer, Berlin, 1998, pp. 268–280] that there exists a 9-c

  4. Matchings with Externalities and Attitudes

    DEFF Research Database (Denmark)

    Branzei, Simina; Michalak, Tomasz; Rahwan, Talal;

    2013-01-01

    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 ...

  5. Topics in combinatorial pattern matching

    DEFF Research Database (Denmark)

    Vildhøj, Hjalte Wedel

    This dissertation studies problems in the general theme of combinatorial pattern matching. More specifically, we study the following topics: Longest Common Extensions. We revisit the longest common extension (LCE) problem, that is, preprocess a string T into a compact data structure that supports...

  6. An Implementation of Bigraph Matching

    DEFF Research Database (Denmark)

    Glenstrup, Arne John; Damgaard, Troels Christoffer; Birkedal, Lars

    We describe a provably sound and complete matching algorithm for bigraphical reactive systems. The algorithm has been implemented in our BPL Tool, a first implementation of bigraphical reactive systems. We describe the tool and present a concrete example of how it can be used to simulate a model...

  7. Micro-PET/CT Monitoring of Herpes Thymidine Kinase Suicide Gene Therapy in a Prostate Cancer Xenograft: The Advantage of a Cell-specific Transcriptional Targeting Approach

    Directory of Open Access Journals (Sweden)

    Mai Johnson

    2005-10-01

    Full Text Available Cancer gene therapy based on tissue-restricted expression of cytotoxic gene should achieve superior therapeutic index over an unrestricted method. This study compared the therapeutic effects of a highly augmented, prostate-specific gene expression method to a strong constitutive promoter-driven approach. Molecular imaging was coupled to gene therapy to ascertain real-time therapeutic activity. The imaging reporter gene (luciferase and the cytotoxic gene (herpes simplex thymidine kinase were delivered by adenoviral vectors injected directly into human prostate tumors grafted in SCID mice. Serial bioluminescence imaging, positron emission tomography, and computed tomography revealed restriction of gene expression to the tumors when prostate-specific vector was employed. In contrast, administration of constitutive active vector resulted in strong signals in the liver. Liver serology, tissue histology, and frail condition of animals confirmed liver toxicity suffered by the constitutive active cohorts, whereas the prostate-targeted group was unaffected. The extent of tumor killing was analyzed by apoptotic staining and human prostate marker (prostate-specific antigen. Overall, the augmented prostate-specific expression system was superior to the constitutive approach in safeguarding against systemic toxicity, while achieving effective tumor killing. Integrating noninvasive imaging into cytotoxic gene therapy will provide a useful strategy to monitor gene expression and therapeutic efficacy in future clinical protocols.

  8. Debt-maturity structures should match risk preferences.

    Science.gov (United States)

    Gapenski, L C

    1999-12-01

    Key to any debt-maturity matching strategy is financing assets with the appropriate debt structure. Financial managers need to establish an optimal capital structure and then choose the best maturity-matching structure for their debt. Two maturity-matching strategies that are available to healthcare financial managers are the accounting approach and the finance approach. The accounting approach, which defines asset maturities as current or fixed, is a riskier financing strategy than the finance approach, which defines asset maturities as permanent or temporary. The added risk occurs because of the accounting approach's heavy reliance on short-term debt. The accounting approach offers the potential for lower costs at the expense of higher risk. Healthcare financial managers who believe the financing function should support the organization's operations without adding undue risk should use the finance approach to maturity matching. Asset maturities in those organizations then should be considered permanent or temporary rather than current or fixed, and the debt-maturity structure should reflect this.

  9. Integrative microRNA and proteomic approaches identify novel osteoarthritis genes and their collaborative metabolic and inflammatory networks.

    Directory of Open Access Journals (Sweden)

    Dimitrios Iliopoulos

    Full Text Available BACKGROUND: Osteoarthritis is a multifactorial disease characterized by destruction of the articular cartilage due to genetic, mechanical and environmental components affecting more than 100 million individuals all over the world. Despite the high prevalence of the disease, the absence of large-scale molecular studies limits our ability to understand the molecular pathobiology of osteoathritis and identify targets for drug development. METHODOLOGY/PRINCIPAL FINDINGS: In this study we integrated genetic, bioinformatic and proteomic approaches in order to identify new genes and their collaborative networks involved in osteoarthritis pathogenesis. MicroRNA profiling of patient-derived osteoarthritic cartilage in comparison to normal cartilage, revealed a 16 microRNA osteoarthritis gene signature. Using reverse-phase protein arrays in the same tissues we detected 76 differentially expressed proteins between osteoarthritic and normal chondrocytes. Proteins such as SOX11, FGF23, KLF6, WWOX and GDF15 not implicated previously in the genesis of osteoarthritis were identified. Integration of microRNA and proteomic data with microRNA gene-target prediction algorithms, generated a potential "interactome" network consisting of 11 microRNAs and 58 proteins linked by 414 potential functional associations. Comparison of the molecular and clinical data, revealed specific microRNAs (miR-22, miR-103 and proteins (PPARA, BMP7, IL1B to be highly correlated with Body Mass Index (BMI. Experimental validation revealed that miR-22 regulated PPARA and BMP7 expression and its inhibition blocked inflammatory and catabolic changes in osteoarthritic chondrocytes. CONCLUSIONS/SIGNIFICANCE: Our findings indicate that obesity and inflammation are related to osteoarthritis, a metabolic disease affected by microRNA deregulation. Gene network approaches provide new insights for elucidating the complexity of diseases such as osteoarthritis. The integration of microRNA, proteomic

  10. Gene expression in teratogenic exposures: a new approach to understanding individual risk.

    Science.gov (United States)

    Kappen, Claudia; Salbaum, J Michael

    2014-06-01

    The phenomenon of partial or incomplete penetrance is common to many paradigms of exposure to teratogens, where only some of the exposed individuals exhibit developmental defects. We here argue that the most widely used experimental approaches in reproductive toxicology do not take partial penetrance into account, and are thus likely to miss differences between affected and unaffected individuals that contribute to susceptibility for teratogenesis. We propose that focus on the variation between exposed individuals could help to discover factors that may play a causative role for abnormal developmental processes that occur with incomplete penetrance.

  11. Feature Matching in Time Series Modelling

    CERN Document Server

    Xia, Yingcun

    2011-01-01

    Using a time series model to mimic an observed time series has a long history. However, with regard to this objective, conventional estimation methods for discrete-time dynamical models are frequently found to be wanting. In the absence of a true model, we prefer an alternative approach to conventional model fitting that typically involves one-step-ahead prediction errors. Our primary aim is to match the joint probability distribution of the observable time series, including long-term features of the dynamics that underpin the data, such as cycles, long memory and others, rather than short-term prediction. For want of a better name, we call this specific aim {\\it feature matching}. The challenges of model mis-specification, measurement errors and the scarcity of data are forever present in real time series modelling. In this paper, by synthesizing earlier attempts into an extended-likelihood, we develop a systematic approach to empirical time series analysis to address these challenges and to aim at achieving...

  12. 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

  13. A Therapeutic Approach to Nasopharyngeal Carcinomas by DNAzymes Targeting EBV LMP-1 Gene

    Directory of Open Access Journals (Sweden)

    Lun-Quan Sun

    2010-09-01

    Full Text Available Epstein-Barr virus (EBV-encoded latent membrane protein 1 (LMP1 has been known to have oncogenic properties during latent infection in nasopharyngeal carcinoma (NPC. Genetic manipulation of LMP1 expression may provide a novel strategy for the treatment of NPC. DNAzymes are synthetic, single-stranded DNA catalysts that can be engineered to bind and cleave the target mRNA of a disease-causing gene. By targeting the LMP1 mRNA, we successfully obtained a phosphorothioate-modified ‘‘10–23’’ DNAzyme namely DZ1, through screening a series of DNAzymes. DZ1 could significantly down-regulate the expression of LMP1 in NPC cells, inhibit cell proliferation, metastasis, promote apoptosis and enhance radiosensitivity of NPC through interfering signal pathways which are abnormally activated by LMP1, including NF-κB, AP-1 and STAT3 signal pathways. Together, interfering LMP1 signaling pathway could be a promising strategy to target the malignant phenotypes of NPC.

  14. Inactivation of tumor suppressor genes and cancer therapy: An evolutionary game theory approach.

    Science.gov (United States)

    Khadem, Heydar; Kebriaei, Hamed; Veisi, Zahra

    2017-03-06

    Inactivation of alleles in tumor suppressor genes (TSG) is one of the important issues resulting in evolution of cancerous cells. In this paper, the evolution of healthy, one and two missed allele cells is modeled using the concept of evolutionary game theory and replicator dynamics. The proposed model also takes into account the interaction rates of the cells as designing parameters of the system. Different combinations of the equilibrium points of the parameterized nonlinear system is studied and categorized into some cases. In each case, the interaction rates' values are suggested in a way that the equilibrium points of the replicator dynamics are located on an appropriate region of the state space. Based on the suggested interaction rates, it is proved that the system doesn't have any undesirable interior equilibrium point as well. Therefore, the system will converge to the desirable region, where there is a scanty level of cancerous cells. In addition, the proposed conditions for interaction rates guarantee that, when a trajectory of the system reaches the boundaries, then it will stay there forever which is a desirable property since the equilibrium points have been already located on the boundaries, appropriately. The simulation results show the effectiveness of the suggestions in the elimination of the cancerous cells in different scenarios.

  15. Controlling HIV-1: Non-Coding RNA Gene Therapy Approaches to a Functional Cure.

    Science.gov (United States)

    Ahlenstiel, Chantelle L; Suzuki, Kazuo; Marks, Katherine; Symonds, Geoff P; Kelleher, Anthony D

    2015-01-01

    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 develop alternate treatment strategies, which impact upon the reservoir and provide a path toward 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 (si)RNA and short hairpin (sh)RNA, targeting molecular mechanisms of HIV-1 transcription, which may represent potential future therapeutics. It will also briefly address animal models for testing potential therapeutics and current gene therapy clinical trials.

  16. 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.

  17. A matched crossover design for clinical trials.

    Science.gov (United States)

    Simon, Laura J; Chinchilli, Vernon M

    2007-09-01

    Two design principles are used frequently in clinical trials: 1) A subject is "matched" or "paired" with a similar subject to reduce the chance that other variables obscure the primary comparison of interest. 2) A subject serves as his/her own control by "crossing over" from one treatment to another during the course of an experiment. There are situations in which it may be advantageous to use the two design principles - crossing over and <