WorldWideScience

Sample records for matrix factorization comparison

  1. Matrix comparison, Part 2

    DEFF Research Database (Denmark)

    Schneider, Jesper Wiborg; Borlund, Pia

    2007-01-01

    The present two-part article introduces matrix comparison as a formal means for evaluation purposes in informetric studies such as cocitation analysis. In the first part, the motivation behind introducing matrix comparison to informetric studies, as well as two important issues influencing such c...

  2. Matrix completion by deep matrix factorization.

    Science.gov (United States)

    Fan, Jicong; Cheng, Jieyu

    2018-02-01

    Conventional methods of matrix completion are linear methods that are not effective in handling data of nonlinear structures. Recently a few researchers attempted to incorporate nonlinear techniques into matrix completion but there still exists considerable limitations. In this paper, a novel method called deep matrix factorization (DMF) is proposed for nonlinear matrix completion. Different from conventional matrix completion methods that are based on linear latent variable models, DMF is on the basis of a nonlinear latent variable model. DMF is formulated as a deep-structure neural network, in which the inputs are the low-dimensional unknown latent variables and the outputs are the partially observed variables. In DMF, the inputs and the parameters of the multilayer neural network are simultaneously optimized to minimize the reconstruction errors for the observed entries. Then the missing entries can be readily recovered by propagating the latent variables to the output layer. DMF is compared with state-of-the-art methods of linear and nonlinear matrix completion in the tasks of toy matrix completion, image inpainting and collaborative filtering. The experimental results verify that DMF is able to provide higher matrix completion accuracy than existing methods do and DMF is applicable to large matrices. Copyright © 2017 Elsevier Ltd. All rights reserved.

  3. TRASYS form factor matrix normalization

    Science.gov (United States)

    Tsuyuki, Glenn T.

    1992-01-01

    A method has been developed for adjusting a TRASYS enclosure form factor matrix to unity. This approach is not limited to closed geometries, and in fact, it is primarily intended for use with open geometries. The purpose of this approach is to prevent optimistic form factors to space. In this method, nodal form factor sums are calculated within 0.05 of unity using TRASYS, although deviations as large as 0.10 may be acceptable, and then, a process is employed to distribute the difference amongst the nodes. A specific example has been analyzed with this method, and a comparison was performed with a standard approach for calculating radiation conductors. In this comparison, hot and cold case temperatures were determined. Exterior nodes exhibited temperature differences as large as 7 C and 3 C for the hot and cold cases, respectively when compared with the standard approach, while interior nodes demonstrated temperature differences from 0 C to 5 C. These results indicate that temperature predictions can be artificially biased if the form factor computation error is lumped into the individual form factors to space.

  4. Matrix Factorizations at Scale: a Comparison of Scientific Data Analytics in Spark and C+MPI Using Three Case Studies

    Energy Technology Data Exchange (ETDEWEB)

    Gittens, Alex; Devarakonda, Aditya; Racah, Evan; Ringenburg, Michael; Gerhardt, Lisa; Kottalam, Jey; Liu, Jialin; Maschhoff, Kristyn; Canon, Shane; Chhugani, Jatin; Sharma, Pramod; Yang, Jiyan; Demmel, James; Harrell, Jim; Krishnamurthy, Venkat; Mahoney, Michael; Prabhat, Mr

    2016-05-12

    We explore the trade-offs of performing linear algebra using Apache Spark, compared to traditional C and MPI implementations on HPC platforms. Spark is designed for data analytics on cluster computing platforms with access to local disks and is optimized for data-parallel tasks. We examine three widely-used and important matrix factorizations: NMF (for physical plausibility), PCA (for its ubiquity) and CX (for data interpretability). We apply these methods to 1.6TB particle physics, 2.2TB and 16TB climate modeling and 1.1TB bioimaging data. The data matrices are tall-and-skinny which enable the algorithms to map conveniently into Spark’s data parallel model. We perform scaling experiments on up to 1600 Cray XC40 nodes, describe the sources of slowdowns, and provide tuning guidance to obtain high performance.

  5. Convex nonnegative matrix factorization with manifold regularization.

    Science.gov (United States)

    Hu, Wenjun; Choi, Kup-Sze; Wang, Peiliang; Jiang, Yunliang; Wang, Shitong

    2015-03-01

    Nonnegative Matrix Factorization (NMF) has been extensively applied in many areas, including computer vision, pattern recognition, text mining, and signal processing. However, nonnegative entries are usually required for the data matrix in NMF, which limits its application. Besides, while the basis and encoding vectors obtained by NMF can represent the original data in low dimension, the representations do not always reflect the intrinsic geometric structure embedded in the data. Motivated by manifold learning and Convex NMF (CNMF), we propose a novel matrix factorization method called Graph Regularized and Convex Nonnegative Matrix Factorization (GCNMF) by introducing a graph regularized term into CNMF. The proposed matrix factorization technique not only inherits the intrinsic low-dimensional manifold structure, but also allows the processing of mixed-sign data matrix. Clustering experiments on nonnegative and mixed-sign real-world data sets are conducted to demonstrate the effectiveness of the proposed method. Copyright © 2014 Elsevier Ltd. All rights reserved.

  6. Ceramic matrix and resin matrix composites - A comparison

    Science.gov (United States)

    Hurwitz, Frances I.

    1987-01-01

    The underlying theory of continuous fiber reinforcement of ceramic matrix and resin matrix composites, their fabrication, microstructure, physical and mechanical properties are contrasted. The growing use of organometallic polymers as precursors to ceramic matrices is discussed as a means of providing low temperature processing capability without the fiber degradation encountered with more conventional ceramic processing techniques. Examples of ceramic matrix composites derived from particulate-filled, high char yield polymers and silsesquioxane precursors are provided.

  7. Ceramic matrix and resin matrix composites: A comparison

    Science.gov (United States)

    Hurwitz, Frances I.

    1987-01-01

    The underlying theory of continuous fiber reinforcement of ceramic matrix and resin matrix composites, their fabrication, microstructure, physical and mechanical properties are contrasted. The growing use of organometallic polymers as precursors to ceramic matrices is discussed as a means of providing low temperature processing capability without the fiber degradation encountered with more conventional ceramic processing techniques. Examples of ceramic matrix composites derived from particulate-filled, high char yield polymers and silsesquioxane precursors are provided.

  8. Massive Asynchronous Parallelization of Sparse Matrix Factorizations

    Energy Technology Data Exchange (ETDEWEB)

    Chow, Edmond [Georgia Inst. of Technology, Atlanta, GA (United States)

    2018-01-08

    Solving sparse problems is at the core of many DOE computational science applications. We focus on the challenge of developing sparse algorithms that can fully exploit the parallelism in extreme-scale computing systems, in particular systems with massive numbers of cores per node. Our approach is to express a sparse matrix factorization as a large number of bilinear constraint equations, and then solving these equations via an asynchronous iterative method. The unknowns in these equations are the matrix entries of the factorization that is desired.

  9. On affine non-negative matrix factorization

    DEFF Research Database (Denmark)

    Laurberg, Hans; Hansen, Lars Kai

    2007-01-01

    We generalize the non-negative matrix factorization (NMF) generative model to incorporate an explicit offset. Multiplicative estimation algorithms are provided for the resulting sparse affine NMF model. We show that the affine model has improved uniqueness properties and leads to more accurate id...

  10. A hierarchical model for ordinal matrix factorization

    DEFF Research Database (Denmark)

    Paquet, Ulrich; Thomson, Blaise; Winther, Ole

    2012-01-01

    This paper proposes a hierarchical probabilistic model for ordinal matrix factorization. Unlike previous approaches, we model the ordinal nature of the data and take a principled approach to incorporating priors for the hidden variables. Two algorithms are presented for inference, one based...

  11. Enforced Sparse Non-Negative Matrix Factorization

    Science.gov (United States)

    2016-01-23

    proposals quotas opec legislation revenue england ico iraq vote passenger yen producer iranian surplus Figure 4. Example NMF with and without sparsity...preprint arXiv:1007.0380, 2010. [22] A. Cichocki and P. Anh-Huy, “Fast local algorithms for large scale nonnegative matrix and tensor factorizations

  12. Shifted Non-negative Matrix Factorization

    DEFF Research Database (Denmark)

    Mørup, Morten; Madsen, Kristoffer Hougaard; Hansen, Lars Kai

    2007-01-01

    Non-negative matrix factorization (NMF) has become a widely used blind source separation technique due to its part based representation and ease of interpretability. We currently extend the NMF model to allow for delays between sources and sensors. This is a natural extension for spectrometry data...

  13. Matrix factorization on a hypercube multiprocessor

    International Nuclear Information System (INIS)

    Geist, G.A.; Heath, M.T.

    1985-08-01

    This paper is concerned with parallel algorithms for matrix factorization on distributed-memory, message-passing multiprocessors, with special emphasis on the hypercube. Both Cholesky factorization of symmetric positive definite matrices and LU factorization of nonsymmetric matrices using partial pivoting are considered. The use of the resulting triangular factors to solve systems of linear equations by forward and back substitutions is also considered. Efficiencies of various parallel computational approaches are compared in terms of empirical results obtained on an Intel iPSC hypercube. 19 refs., 6 figs., 2 tabs

  14. Max–min distance nonnegative matrix factorization

    KAUST Repository

    Wang, Jim Jing-Yan; Gao, Xin

    2014-01-01

    Nonnegative Matrix Factorization (NMF) has been a popular representation method for pattern classification problems. It tries to decompose a nonnegative matrix of data samples as the product of a nonnegative basis matrix and a nonnegative coefficient matrix. The columns of the coefficient matrix can be used as new representations of these data samples. However, traditional NMF methods ignore class labels of the data samples. In this paper, we propose a novel supervised NMF algorithm to improve the discriminative ability of the new representation by using the class labels. Using the class labels, we separate all the data sample pairs into within-class pairs and between-class pairs. To improve the discriminative ability of the new NMF representations, we propose to minimize the maximum distance of the within-class pairs in the new NMF space, and meanwhile to maximize the minimum distance of the between-class pairs. With this criterion, we construct an objective function and optimize it with regard to basis and coefficient matrices, and slack variables alternatively, resulting in an iterative algorithm. The proposed algorithm is evaluated on three pattern classification problems and experiment results show that it outperforms the state-of-the-art supervised NMF methods.

  15. Max–min distance nonnegative matrix factorization

    KAUST Repository

    Wang, Jim Jing-Yan

    2014-10-26

    Nonnegative Matrix Factorization (NMF) has been a popular representation method for pattern classification problems. It tries to decompose a nonnegative matrix of data samples as the product of a nonnegative basis matrix and a nonnegative coefficient matrix. The columns of the coefficient matrix can be used as new representations of these data samples. However, traditional NMF methods ignore class labels of the data samples. In this paper, we propose a novel supervised NMF algorithm to improve the discriminative ability of the new representation by using the class labels. Using the class labels, we separate all the data sample pairs into within-class pairs and between-class pairs. To improve the discriminative ability of the new NMF representations, we propose to minimize the maximum distance of the within-class pairs in the new NMF space, and meanwhile to maximize the minimum distance of the between-class pairs. With this criterion, we construct an objective function and optimize it with regard to basis and coefficient matrices, and slack variables alternatively, resulting in an iterative algorithm. The proposed algorithm is evaluated on three pattern classification problems and experiment results show that it outperforms the state-of-the-art supervised NMF methods.

  16. Incremental Nonnegative Matrix Factorization for Face Recognition

    Directory of Open Access Journals (Sweden)

    Wen-Sheng Chen

    2008-01-01

    Full Text Available Nonnegative matrix factorization (NMF is a promising approach for local feature extraction in face recognition tasks. However, there are two major drawbacks in almost all existing NMF-based methods. One shortcoming is that the computational cost is expensive for large matrix decomposition. The other is that it must conduct repetitive learning, when the training samples or classes are updated. To overcome these two limitations, this paper proposes a novel incremental nonnegative matrix factorization (INMF for face representation and recognition. The proposed INMF approach is based on a novel constraint criterion and our previous block strategy. It thus has some good properties, such as low computational complexity, sparse coefficient matrix. Also, the coefficient column vectors between different classes are orthogonal. In particular, it can be applied to incremental learning. Two face databases, namely FERET and CMU PIE face databases, are selected for evaluation. Compared with PCA and some state-of-the-art NMF-based methods, our INMF approach gives the best performance.

  17. Matrix factorizations, minimal models and Massey products

    International Nuclear Information System (INIS)

    Knapp, Johanna; Omer, Harun

    2006-01-01

    We present a method to compute the full non-linear deformations of matrix factorizations for ADE minimal models. This method is based on the calculation of higher products in the cohomology, called Massey products. The algorithm yields a polynomial ring whose vanishing relations encode the obstructions of the deformations of the D-branes characterized by these matrix factorizations. This coincides with the critical locus of the effective superpotential which can be computed by integrating these relations. Our results for the effective superpotential are in agreement with those obtained from solving the A-infinity relations. We point out a relation to the superpotentials of Kazama-Suzuki models. We will illustrate our findings by various examples, putting emphasis on the E 6 minimal model

  18. Decoding the encoding of functional brain networks: An fMRI classification comparison of non-negative matrix factorization (NMF), independent component analysis (ICA), and sparse coding algorithms.

    Science.gov (United States)

    Xie, Jianwen; Douglas, Pamela K; Wu, Ying Nian; Brody, Arthur L; Anderson, Ariana E

    2017-04-15

    Brain networks in fMRI are typically identified using spatial independent component analysis (ICA), yet other mathematical constraints provide alternate biologically-plausible frameworks for generating brain networks. Non-negative matrix factorization (NMF) would suppress negative BOLD signal by enforcing positivity. Spatial sparse coding algorithms (L1 Regularized Learning and K-SVD) would impose local specialization and a discouragement of multitasking, where the total observed activity in a single voxel originates from a restricted number of possible brain networks. The assumptions of independence, positivity, and sparsity to encode task-related brain networks are compared; the resulting brain networks within scan for different constraints are used as basis functions to encode observed functional activity. These encodings are then decoded using machine learning, by using the time series weights to predict within scan whether a subject is viewing a video, listening to an audio cue, or at rest, in 304 fMRI scans from 51 subjects. The sparse coding algorithm of L1 Regularized Learning outperformed 4 variations of ICA (pcoding algorithms. Holding constant the effect of the extraction algorithm, encodings using sparser spatial networks (containing more zero-valued voxels) had higher classification accuracy (pcoding algorithms suggests that algorithms which enforce sparsity, discourage multitasking, and promote local specialization may capture better the underlying source processes than those which allow inexhaustible local processes such as ICA. Negative BOLD signal may capture task-related activations. Copyright © 2017 Elsevier B.V. All rights reserved.

  19. Multiple graph regularized nonnegative matrix factorization

    KAUST Repository

    Wang, Jim Jing-Yan

    2013-10-01

    Non-negative matrix factorization (NMF) has been widely used as a data representation method based on components. To overcome the disadvantage of NMF in failing to consider the manifold structure of a data set, graph regularized NMF (GrNMF) has been proposed by Cai et al. by constructing an affinity graph and searching for a matrix factorization that respects graph structure. Selecting a graph model and its corresponding parameters is critical for this strategy. This process is usually carried out by cross-validation or discrete grid search, which are time consuming and prone to overfitting. In this paper, we propose a GrNMF, called MultiGrNMF, in which the intrinsic manifold is approximated by a linear combination of several graphs with different models and parameters inspired by ensemble manifold regularization. Factorization metrics and linear combination coefficients of graphs are determined simultaneously within a unified object function. They are alternately optimized in an iterative algorithm, thus resulting in a novel data representation algorithm. Extensive experiments on a protein subcellular localization task and an Alzheimer\\'s disease diagnosis task demonstrate the effectiveness of the proposed algorithm. © 2013 Elsevier Ltd. All rights reserved.

  20. Multithreading for synchronization tolerance in matrix factorization

    International Nuclear Information System (INIS)

    Buttari, Alfredo; Dongarra, Jack; Husbands, Parry; Kurzak, Jakub; Yelick, Katherine

    2007-01-01

    Physical constraints such as power, leakage and pin bandwidth are currently driving the HPC industry to produce systems with unprecedented levels of concurrency. In these parallel systems, synchronization and memory operations are becoming considerably more expensive than before. In this work we study parallel matrix factorization codes and conclude that they need to be re-engineered to avoid unnecessary (and expensive) synchronization. We propose the use of multithreading combined with intelligent schedulers and implement representative algorithms in this style. Our results indicate that this strategy can significantly outperform traditional codes

  1. Comparison of transition-matrix sampling procedures

    DEFF Research Database (Denmark)

    Yevick, D.; Reimer, M.; Tromborg, Bjarne

    2009-01-01

    We compare the accuracy of the multicanonical procedure with that of transition-matrix models of static and dynamic communication system properties incorporating different acceptance rules. We find that for appropriate ranges of the underlying numerical parameters, algorithmically simple yet high...... accurate procedures can be employed in place of the standard multicanonical sampling algorithm....

  2. Multiple Kernel Learning for adaptive graph regularized nonnegative matrix factorization

    KAUST Repository

    Wang, Jim Jing-Yan; AbdulJabbar, Mustafa Abdulmajeed

    2012-01-01

    Nonnegative Matrix Factorization (NMF) has been continuously evolving in several areas like pattern recognition and information retrieval methods. It factorizes a matrix into a product of 2 low-rank non-negative matrices that will define parts-based, and linear representation of non-negative data. Recently, Graph regularized NMF (GrNMF) is proposed to find a compact representation, which uncovers the hidden semantics and simultaneously respects the intrinsic geometric structure. In GNMF, an affinity graph is constructed from the original data space to encode the geometrical information. In this paper, we propose a novel idea which engages a Multiple Kernel Learning approach into refining the graph structure that reflects the factorization of the matrix and the new data space. The GrNMF is improved by utilizing the graph refined by the kernel learning, and then a novel kernel learning method is introduced under the GrNMF framework. Our approach shows encouraging results of the proposed algorithm in comparison to the state-of-the-art clustering algorithms like NMF, GrNMF, SVD etc.

  3. Non-negative Matrix Factorization for Binary Data

    DEFF Research Database (Denmark)

    Larsen, Jacob Søgaard; Clemmensen, Line Katrine Harder

    We propose the Logistic Non-negative Matrix Factorization for decomposition of binary data. Binary data are frequently generated in e.g. text analysis, sensory data, market basket data etc. A common method for analysing non-negative data is the Non-negative Matrix Factorization, though...... this is in theory not appropriate for binary data, and thus we propose a novel Non-negative Matrix Factorization based on the logistic link function. Furthermore we generalize the method to handle missing data. The formulation of the method is compared to a previously proposed method (Tome et al., 2015). We compare...... the performance of the Logistic Non-negative Matrix Factorization to Least Squares Non-negative Matrix Factorization and Kullback-Leibler (KL) Non-negative Matrix Factorization on sets of binary data: a synthetic dataset, a set of student comments on their professors collected in a binary term-document matrix...

  4. Low-Rank Matrix Factorization With Adaptive Graph Regularizer.

    Science.gov (United States)

    Lu, Gui-Fu; Wang, Yong; Zou, Jian

    2016-05-01

    In this paper, we present a novel low-rank matrix factorization algorithm with adaptive graph regularizer (LMFAGR). We extend the recently proposed low-rank matrix with manifold regularization (MMF) method with an adaptive regularizer. Different from MMF, which constructs an affinity graph in advance, LMFAGR can simultaneously seek graph weight matrix and low-dimensional representations of data. That is, graph construction and low-rank matrix factorization are incorporated into a unified framework, which results in an automatically updated graph rather than a predefined one. The experimental results on some data sets demonstrate that the proposed algorithm outperforms the state-of-the-art low-rank matrix factorization methods.

  5. Proper comparison among methods using a confusion matrix

    CSIR Research Space (South Africa)

    Salmon

    2015-07-01

    Full Text Available -1 IGARSS 2015, Milan, Italy, 26-31 July 2015 Proper comparison among methods using a confusion matrix 1,2 B.P. Salmon, 2,3 W. Kleynhans, 2,3 C.P. Schwegmann and 1J.C. Olivier 1School of Engineering and ICT, University of Tasmania, Australia 2...

  6. A flexible R package for nonnegative matrix factorization

    Directory of Open Access Journals (Sweden)

    Seoighe Cathal

    2010-07-01

    Full Text Available Abstract Background Nonnegative Matrix Factorization (NMF is an unsupervised learning technique that has been applied successfully in several fields, including signal processing, face recognition and text mining. Recent applications of NMF in bioinformatics have demonstrated its ability to extract meaningful information from high-dimensional data such as gene expression microarrays. Developments in NMF theory and applications have resulted in a variety of algorithms and methods. However, most NMF implementations have been on commercial platforms, while those that are freely available typically require programming skills. This limits their use by the wider research community. Results Our objective is to provide the bioinformatics community with an open-source, easy-to-use and unified interface to standard NMF algorithms, as well as with a simple framework to help implement and test new NMF methods. For that purpose, we have developed a package for the R/BioConductor platform. The package ports public code to R, and is structured to enable users to easily modify and/or add algorithms. It includes a number of published NMF algorithms and initialization methods and facilitates the combination of these to produce new NMF strategies. Commonly used benchmark data and visualization methods are provided to help in the comparison and interpretation of the results. Conclusions The NMF package helps realize the potential of Nonnegative Matrix Factorization, especially in bioinformatics, providing easy access to methods that have already yielded new insights in many applications. Documentation, source code and sample data are available from CRAN.

  7. Comparison of linear and non-linear monotonicity-based shape reconstruction using exact matrix characterizations

    DEFF Research Database (Denmark)

    Garde, Henrik

    2018-01-01

    . For a fair comparison, exact matrix characterizations are used when probing the monotonicity relations to avoid errors from numerical solution to PDEs and numerical integration. Using a special factorization of the Neumann-to-Dirichlet map also makes the non-linear method as fast as the linear method...

  8. Efficient multitasking of Choleski matrix factorization on CRAY supercomputers

    Science.gov (United States)

    Overman, Andrea L.; Poole, Eugene L.

    1991-01-01

    A Choleski method is described and used to solve linear systems of equations that arise in large scale structural analysis. The method uses a novel variable-band storage scheme and is structured to exploit fast local memory caches while minimizing data access delays between main memory and vector registers. Several parallel implementations of this method are described for the CRAY-2 and CRAY Y-MP computers demonstrating the use of microtasking and autotasking directives. A portable parallel language, FORCE, is used for comparison with the microtasked and autotasked implementations. Results are presented comparing the matrix factorization times for three representative structural analysis problems from runs made in both dedicated and multi-user modes on both computers. CPU and wall clock timings are given for the parallel implementations and are compared to single processor timings of the same algorithm.

  9. Nonnegative Matrix Factorizations Performing Object Detection and Localization

    Directory of Open Access Journals (Sweden)

    G. Casalino

    2012-01-01

    Full Text Available We study the problem of detecting and localizing objects in still, gray-scale images making use of the part-based representation provided by nonnegative matrix factorizations. Nonnegative matrix factorization represents an emerging example of subspace methods, which is able to extract interpretable parts from a set of template image objects and then to additively use them for describing individual objects. In this paper, we present a prototype system based on some nonnegative factorization algorithms, which differ in the additional properties added to the nonnegative representation of data, in order to investigate if any additional constraint produces better results in general object detection via nonnegative matrix factorizations.

  10. Convergence Improvement of Response Matrix Method with Large Discontinuity Factors

    International Nuclear Information System (INIS)

    Yamamoto, Akio

    2003-01-01

    In the response matrix method, a numerical divergence problem has been reported when extremely small or large discontinuity factors are utilized in the calculations. In this paper, an alternative response matrix formulation to solve the divergence problem is discussed, and properties of iteration matrixes are investigated through eigenvalue analyses. In the conventional response matrix formulation, partial currents between adjacent nodes are assumed to be discontinuous, and outgoing partial currents are converted into incoming partial currents by the discontinuity factor matrix. Namely, the partial currents of the homogeneous system (i.e., homogeneous partial currents) are treated in the conventional response matrix formulation. In this approach, the spectral radius of an iteration matrix for the partial currents may exceed unity when an extremely small or large discontinuity factor is used. Contrary to this, an alternative response matrix formulation using heterogeneous partial currents is discussed in this paper. In the latter approach, partial currents are assumed to be continuous between adjacent nodes, and discontinuity factors are directly considered in the coefficients of a response matrix. From the eigenvalue analysis of the iteration matrix for the one-group, one-dimensional problem, the spectral radius for the heterogeneous partial current formulation does not exceed unity even if an extremely small or large discontinuity factor is used in the calculation; numerical stability of the alternative formulation is superior to the conventional one. The numerical stability of the heterogeneous partial current formulation is also confirmed by the two-dimensional light water reactor core analysis. Since the heterogeneous partial current formulation does not require any approximation, the converged solution exactly reproduces the reference solution when the discontinuity factors are directly derived from the reference calculation

  11. Multiplicative algorithms for constrained non-negative matrix factorization

    KAUST Repository

    Peng, Chengbin; Wong, Kachun; Rockwood, Alyn; Zhang, Xiangliang; Jiang, Jinling; Keyes, David E.

    2012-01-01

    Non-negative matrix factorization (NMF) provides the advantage of parts-based data representation through additive only combinations. It has been widely adopted in areas like item recommending, text mining, data clustering, speech denoising, etc

  12. Normalization Of Thermal-Radiation Form-Factor Matrix

    Science.gov (United States)

    Tsuyuki, Glenn T.

    1994-01-01

    Report describes algorithm that adjusts form-factor matrix in TRASYS computer program, which calculates intraspacecraft radiative interchange among various surfaces and environmental heat loading from sources such as sun.

  13. An Elementary Proof of the Polynomial Matrix Spectral Factorization Theorem

    OpenAIRE

    Ephremidze, Lasha

    2010-01-01

    A very simple and short proof of the polynomial matrix spectral factorization theorem (on the unit circle as well as on the real line) is presented, which relies on elementary complex analysis and linear algebra.

  14. Matrix factorizations and homological mirror symmetry on the torus

    International Nuclear Information System (INIS)

    Knapp, Johanna; Omer, Harun

    2007-01-01

    We consider matrix factorizations and homological mirror symmetry on the torus T 2 using a Landau-Ginzburg description. We identify the basic matrix factorizations of the Landau-Ginzburg superpotential and compute the full spectrum taking into account the explicit dependence on bulk and boundary moduli. We verify homological mirror symmetry by comparing three-point functions in the A-model and the B-model

  15. Parallelized preconditioned model building algorithm for matrix factorization

    OpenAIRE

    Kaya, Kamer; Birbil, İlker; Birbil, Ilker; Öztürk, Mehmet Kaan; Ozturk, Mehmet Kaan; Gohari, Amir

    2017-01-01

    Matrix factorization is a common task underlying several machine learning applications such as recommender systems, topic modeling, or compressed sensing. Given a large and possibly sparse matrix A, we seek two smaller matrices W and H such that their product is as close to A as possible. The objective is minimizing the sum of square errors in the approximation. Typically such problems involve hundreds of thousands of unknowns, so an optimizer must be exceptionally efficient. In this study, a...

  16. HIGH DIMENSIONAL COVARIANCE MATRIX ESTIMATION IN APPROXIMATE FACTOR MODELS.

    Science.gov (United States)

    Fan, Jianqing; Liao, Yuan; Mincheva, Martina

    2011-01-01

    The variance covariance matrix plays a central role in the inferential theories of high dimensional factor models in finance and economics. Popular regularization methods of directly exploiting sparsity are not directly applicable to many financial problems. Classical methods of estimating the covariance matrices are based on the strict factor models, assuming independent idiosyncratic components. This assumption, however, is restrictive in practical applications. By assuming sparse error covariance matrix, we allow the presence of the cross-sectional correlation even after taking out common factors, and it enables us to combine the merits of both methods. We estimate the sparse covariance using the adaptive thresholding technique as in Cai and Liu (2011), taking into account the fact that direct observations of the idiosyncratic components are unavailable. The impact of high dimensionality on the covariance matrix estimation based on the factor structure is then studied.

  17. Strong factor in the SO(2,3) S matrix

    International Nuclear Information System (INIS)

    Amado, R.D.; Sparrow, D.A.

    1986-01-01

    The group theoretic S matrix of Alhassid, Iachello, and Wu is factorable into a product of Coulomb and strong factors. The strong factor is examined with a view to relating it to more fa- miliar potential and phase shift descriptions. We find simple approximate expressions for the phase shifts which are very accurate for heavy-ion-type applications. For peripheral scattering it is possible to obtain simple expressions relating the strong factor to an effective potential

  18. Data fusion in metabolomics using coupled matrix and tensor factorizations

    DEFF Research Database (Denmark)

    Evrim, Acar Ataman; Bro, Rasmus; Smilde, Age Klaas

    2015-01-01

    of heterogeneous (i.e., in the form of higher order tensors and matrices) data sets with shared/unshared factors. In order to jointly analyze such heterogeneous data sets, we formulate data fusion as a coupled matrix and tensor factorization (CMTF) problem, which has already proved useful in many data mining...

  19. Estimating Depolarization with the Jones Matrix Quality Factor

    Science.gov (United States)

    Hilfiker, James N.; Hale, Jeffrey S.; Herzinger, Craig M.; Tiwald, Tom; Hong, Nina; Schöche, Stefan; Arwin, Hans

    2017-11-01

    Mueller matrix (MM) measurements offer the ability to quantify the depolarization capability of a sample. Depolarization can be estimated using terms such as the depolarization index or the average degree of polarization. However, these calculations require measurement of the complete MM. We propose an alternate depolarization metric, termed the Jones matrix quality factor, QJM, which does not require the complete MM. This metric provides a measure of how close, in a least-squares sense, a Jones matrix can be found to the measured Mueller matrix. We demonstrate and compare the use of QJM to other traditional calculations of depolarization for both isotropic and anisotropic depolarizing samples; including non-uniform coatings, anisotropic crystal substrates, and beetle cuticles that exhibit both depolarization and circular diattenuation.

  20. Implicit vs. Explicit Trust in Social Matrix Factorization

    NARCIS (Netherlands)

    Fazeli, Soude; Loni, Babak; Bellogin, Alejandro; Drachsler, Hendrik; Sloep, Peter

    2014-01-01

    Incorporating social trust in Matrix Factorization (MF) methods demonstrably improves accuracy of rating prediction. Such approaches mainly use the trust scores explicitly expressed by users. However, it is often challenging to have users provide explicit trust scores of each other. There exist

  1. Sparse-matrix factorizations for fast symmetric Fourier transforms

    International Nuclear Information System (INIS)

    Sequel, J.

    1987-01-01

    This work proposes new fast algorithms computing the discrete Fourier transform of certain families of symmetric sequences. Sequences commonly found in problems of structure determination by x-ray crystallography and in numerical solutions of boundary-value problems in partial differential equations are dealt with. In the algorithms presented, the redundancies in the input and output data, due to the presence of symmetries in the input data sequence, were eliminated. Using ring-theoretical methods a matrix representation is obtained for the remaining calculations; which factors as the product of a complex block-diagonal matrix times as integral matrix. A basic two-step algorithm scheme arises from this factorization with a first step consisting of pre-additions and a second step containing the calculations involved in computing with the blocks in the block-diagonal factor. These blocks are structured as block-Hankel matrices, and two sparse-matrix factoring formulas are developed in order to diminish their arithmetic complexity

  2. An integrating factor matrix method to find first integrals

    International Nuclear Information System (INIS)

    Saputra, K V I; Quispel, G R W; Van Veen, L

    2010-01-01

    In this paper we develop an integrating factor matrix method to derive conditions for the existence of first integrals. We use this novel method to obtain first integrals, along with the conditions for their existence, for two- and three-dimensional Lotka-Volterra systems with constant terms. The results are compared to previous results obtained by other methods.

  3. An interlaboratory comparison of methods for measuring rock matrix porosity

    International Nuclear Information System (INIS)

    Rasilainen, K.; Hellmuth, K.H.; Kivekaes, L.; Ruskeeniemi, T.; Melamed, A.; Siitari-Kauppi, M.

    1996-09-01

    An interlaboratory comparison study was conducted for the available Finnish methods of rock matrix porosity measurements. The aim was first to compare different experimental methods for future applications, and second to obtain quality assured data for the needs of matrix diffusion modelling. Three different versions of water immersion techniques, a tracer elution method, a helium gas through-diffusion method, and a C-14-PMMA method were tested. All methods selected for this study were established experimental tools in the respective laboratories, and they had already been individually tested. Rock samples for the study were obtained from a homogeneous granitic drill core section from the natural analogue site at Palmottu. The drill core section was cut into slabs that were expected to be practically identical. The subsamples were then circulated between the different laboratories using a round robin approach. The circulation was possible because all methods were non-destructive, except the C-14-PMMA method, which was always the last method to be applied. The possible effect of drying temperature on the measured porosity was also preliminarily tested. These measurements were done in the order of increasing drying temperature. Based on the study, it can be concluded that all methods are comparable in their accuracy. The selection of methods for future applications can therefore be based on practical considerations. Drying temperature seemed to have very little effect on the measured porosity, but a more detailed study is needed for definite conclusions. (author) (4 refs.)

  4. Extracellular matrix organization modulates fibroblast growth and growth factor responsiveness.

    Science.gov (United States)

    Nakagawa, S; Pawelek, P; Grinnell, F

    1989-06-01

    To learn more about the relationship between extracellular matrix organization, cell shape, and cell growth control, we studied DNA synthesis by fibroblasts in collagen gels that were either attached to culture dishes or floating in culture medium during gel contraction. After 4 days of contraction, the collagen density (initially 1.5 mg/ml) reached 22 mg/ml in attached gels and 55 mg/ml in floating gels. After contraction, attached collagen gels were well organized; collagen fibrils were aligned in the plane of cell spreading; and fibroblasts had an elongated, bipolar morphology. Floating collagen gels, however, were unorganized; collagen fibrils were arranged randomly; and fibroblasts had a stellate morphology. DNA synthesis by fibroblasts in contracted collagen gels was suppressed if the gels were floating in medium but not if the gels were attached, and inhibition was independent of the extent of gel contraction. Therefore, growth of fibroblasts in contracted collagen gels could be regulated by differences in extracellular matrix organization and cell shape independently of extracellular matrix density. We also compared the responses of fibroblasts in contracted collagen gels and monolayer culture to peptide growth factors including fibroblast growth factor, platelet-derived growth factor, transforming growth factor-beta, and interleukin 1. Cells in floating collagen gels were generally unresponsive to any of the growth factors. Cells in attached collagen gels and monolayer culture were affected similarly by fibroblast growth factor but not by the others. Our results indicate that extracellular matrix organization influenced not only cell growth, but also fibroblast responsiveness to peptide growth factors.

  5. Calabi-Yau structures on categories of matrix factorizations

    Science.gov (United States)

    Shklyarov, Dmytro

    2017-09-01

    Using tools of complex geometry, we construct explicit proper Calabi-Yau structures, that is, non-degenerate cyclic cocycles on differential graded categories of matrix factorizations of regular functions with isolated critical points. The formulas involve the Kapustin-Li trace and its higher corrections. From the physics perspective, our result yields explicit 'off-shell' models for categories of topological D-branes in B-twisted Landau-Ginzburg models.

  6. Metal matrix composites: History, status, factors and future

    Science.gov (United States)

    Cyriac, Ajith James

    The history, status, and future of metal matrix composites are presented by evaluating the progression of available literature through time. The trends that existed and issues that still prevail are discussed and a prediction of the future for MMCs is presented. The factors that govern the performance of metal matrix composites are also discussed. In many developed countries and in several developing countries there exists continued interest in MMCs. Researchers tried numerous combinations of matrices and reinforcements since work strictly on MMCs began in the 1950s. This led to developments for aerospace and defense applications, but resultant commercial applications were limited. The introduction of ceramic whiskers as reinforcement and the development of 'in-situ' eutectics in the 1960s aided high temperature applications in aircraft engines. In the late 1970s the automobile industries started to take MMCs seriously. In the last 20 years, MMCs evolved from laboratories to a class of materials with numerous applications and commercial markets. After the collapse of the Berlin Wall, prevailing order in the world changed drastically. This effect was evident in the progression of metal matrix composites. The internet connected the world like never before and tremendous information was available for researchers around the world. Globalization and the internet resulted in the transformation of the world to a more level playing field, and this effect is evident in the nature and source of research on metal matrix composites happening around the world.

  7. Comparison of matrix exponential methods for fuel burnup calculations

    International Nuclear Information System (INIS)

    Oh, Hyung Suk; Yang, Won Sik

    1999-01-01

    Series expansion methods to compute the exponential of a matrix have been compared by applying them to fuel depletion calculations. Specifically, Taylor, Pade, Chebyshev, and rational Chebyshev approximations have been investigated by approximating the exponentials of bum matrices by truncated series of each method with the scaling and squaring algorithm. The accuracy and efficiency of these methods have been tested by performing various numerical tests using one thermal reactor and two fast reactor depletion problems. The results indicate that all the four series methods are accurate enough to be used for fuel depletion calculations although the rational Chebyshev approximation is relatively less accurate. They also show that the rational approximations are more efficient than the polynomial approximations. Considering the computational accuracy and efficiency, the Pade approximation appears to be better than the other methods. Its accuracy is better than the rational Chebyshev approximation, while being comparable to the polynomial approximations. On the other hand, its efficiency is better than the polynomial approximations and is similar to the rational Chebyshev approximation. In particular, for fast reactor depletion calculations, it is faster than the polynomial approximations by a factor of ∼ 1.7. (author). 11 refs., 4 figs., 2 tabs

  8. Nonnegative Matrix Factorization with Rank Regularization and Hard Constraint.

    Science.gov (United States)

    Shang, Ronghua; Liu, Chiyang; Meng, Yang; Jiao, Licheng; Stolkin, Rustam

    2017-09-01

    Nonnegative matrix factorization (NMF) is well known to be an effective tool for dimensionality reduction in problems involving big data. For this reason, it frequently appears in many areas of scientific and engineering literature. This letter proposes a novel semisupervised NMF algorithm for overcoming a variety of problems associated with NMF algorithms, including poor use of prior information, negative impact on manifold structure of the sparse constraint, and inaccurate graph construction. Our proposed algorithm, nonnegative matrix factorization with rank regularization and hard constraint (NMFRC), incorporates label information into data representation as a hard constraint, which makes full use of prior information. NMFRC also measures pairwise similarity according to geodesic distance rather than Euclidean distance. This results in more accurate measurement of pairwise relationships, resulting in more effective manifold information. Furthermore, NMFRC adopts rank constraint instead of norm constraints for regularization to balance the sparseness and smoothness of data. In this way, the new data representation is more representative and has better interpretability. Experiments on real data sets suggest that NMFRC outperforms four other state-of-the-art algorithms in terms of clustering accuracy.

  9. Sparse Nonnegative Matrix Factorization Strategy for Cochlear Implants

    Directory of Open Access Journals (Sweden)

    Hongmei Hu

    2015-12-01

    Full Text Available Current cochlear implant (CI strategies carry speech information via the waveform envelope in frequency subbands. CIs require efficient speech processing to maximize information transfer to the brain, especially in background noise, where the speech envelope is not robust to noise interference. In such conditions, the envelope, after decomposition into frequency bands, may be enhanced by sparse transformations, such as nonnegative matrix factorization (NMF. Here, a novel CI processing algorithm is described, which works by applying NMF to the envelope matrix (envelopogram of 22 frequency channels in order to improve performance in noisy environments. It is evaluated for speech in eight-talker babble noise. The critical sparsity constraint parameter was first tuned using objective measures and then evaluated with subjective speech perception experiments for both normal hearing and CI subjects. Results from vocoder simulations with 10 normal hearing subjects showed that the algorithm significantly enhances speech intelligibility with the selected sparsity constraints. Results from eight CI subjects showed no significant overall improvement compared with the standard advanced combination encoder algorithm, but a trend toward improvement of word identification of about 10 percentage points at +15 dB signal-to-noise ratio (SNR was observed in the eight CI subjects. Additionally, a considerable reduction of the spread of speech perception performance from 40% to 93% for advanced combination encoder to 80% to 100% for the suggested NMF coding strategy was observed.

  10. Comparison of matrix methods for elastic wave scattering problems

    International Nuclear Information System (INIS)

    Tsao, S.J.; Varadan, V.K.; Varadan, V.V.

    1983-01-01

    This article briefly describes the T-matrix method and the MOOT (method of optimal truncation) of elastic wave scattering as they apply to A-D, SH- wave problems as well as 3-D elastic wave problems. Two methods are compared for scattering by elliptical cylinders as well as oblate spheroids of various eccentricity as a function of frequency. Convergence, and symmetry of the scattering cross section are also compared for ellipses and spheroidal cavities of different aspect ratios. Both the T-matrix approach and the MOOT were programmed on an AMDHL 470 computer using double precision arithmetic. Although the T-matrix method and MOOT are not always in agreement, it is in no way implied that any of the published results using MOOT are in error

  11. Factors associated with continuance commitment to FAA matrix teams.

    Science.gov (United States)

    1993-11-01

    Several organizations within the FAA employ matrix teams to achieve cross-functional coordination. Matrix team members typically represent different organizational functions required for project accomplishment (e.g., research and development, enginee...

  12. Symmetric nonnegative matrix factorization: algorithms and applications to probabilistic clustering.

    Science.gov (United States)

    He, Zhaoshui; Xie, Shengli; Zdunek, Rafal; Zhou, Guoxu; Cichocki, Andrzej

    2011-12-01

    Nonnegative matrix factorization (NMF) is an unsupervised learning method useful in various applications including image processing and semantic analysis of documents. This paper focuses on symmetric NMF (SNMF), which is a special case of NMF decomposition. Three parallel multiplicative update algorithms using level 3 basic linear algebra subprograms directly are developed for this problem. First, by minimizing the Euclidean distance, a multiplicative update algorithm is proposed, and its convergence under mild conditions is proved. Based on it, we further propose another two fast parallel methods: α-SNMF and β -SNMF algorithms. All of them are easy to implement. These algorithms are applied to probabilistic clustering. We demonstrate their effectiveness for facial image clustering, document categorization, and pattern clustering in gene expression.

  13. SHMF: Interest Prediction Model with Social Hub Matrix Factorization

    Directory of Open Access Journals (Sweden)

    Chaoyuan Cui

    2017-01-01

    Full Text Available With the development of social networks, microblog has become the major social communication tool. There is a lot of valuable information such as personal preference, public opinion, and marketing in microblog. Consequently, research on user interest prediction in microblog has a positive practical significance. In fact, how to extract information associated with user interest orientation from the constantly updated blog posts is not so easy. Existing prediction approaches based on probabilistic factor analysis use blog posts published by user to predict user interest. However, these methods are not very effective for the users who post less but browse more. In this paper, we propose a new prediction model, which is called SHMF, using social hub matrix factorization. SHMF constructs the interest prediction model by combining the information of blogs posts published by both user and direct neighbors in user’s social hub. Our proposed model predicts user interest by integrating user’s historical behavior and temporal factor as well as user’s friendships, thus achieving accurate forecasts of user’s future interests. The experimental results on Sina Weibo show the efficiency and effectiveness of our proposed model.

  14. Multiplicative algorithms for constrained non-negative matrix factorization

    KAUST Repository

    Peng, Chengbin

    2012-12-01

    Non-negative matrix factorization (NMF) provides the advantage of parts-based data representation through additive only combinations. It has been widely adopted in areas like item recommending, text mining, data clustering, speech denoising, etc. In this paper, we provide an algorithm that allows the factorization to have linear or approximatly linear constraints with respect to each factor. We prove that if the constraint function is linear, algorithms within our multiplicative framework will converge. This theory supports a large variety of equality and inequality constraints, and can facilitate application of NMF to a much larger domain. Taking the recommender system as an example, we demonstrate how a specialized weighted and constrained NMF algorithm can be developed to fit exactly for the problem, and the tests justify that our constraints improve the performance for both weighted and unweighted NMF algorithms under several different metrics. In particular, on the Movielens data with 94% of items, the Constrained NMF improves recall rate 3% compared to SVD50 and 45% compared to SVD150, which were reported as the best two in the top-N metric. © 2012 IEEE.

  15. A Comparison of Methods for Estimating the Determinant of High-Dimensional Covariance Matrix

    KAUST Repository

    Hu, Zongliang

    2017-09-27

    The determinant of the covariance matrix for high-dimensional data plays an important role in statistical inference and decision. It has many real applications including statistical tests and information theory. Due to the statistical and computational challenges with high dimensionality, little work has been proposed in the literature for estimating the determinant of high-dimensional covariance matrix. In this paper, we estimate the determinant of the covariance matrix using some recent proposals for estimating high-dimensional covariance matrix. Specifically, we consider a total of eight covariance matrix estimation methods for comparison. Through extensive simulation studies, we explore and summarize some interesting comparison results among all compared methods. We also provide practical guidelines based on the sample size, the dimension, and the correlation of the data set for estimating the determinant of high-dimensional covariance matrix. Finally, from a perspective of the loss function, the comparison study in this paper may also serve as a proxy to assess the performance of the covariance matrix estimation.

  16. A Comparison of Methods for Estimating the Determinant of High-Dimensional Covariance Matrix.

    Science.gov (United States)

    Hu, Zongliang; Dong, Kai; Dai, Wenlin; Tong, Tiejun

    2017-09-21

    The determinant of the covariance matrix for high-dimensional data plays an important role in statistical inference and decision. It has many real applications including statistical tests and information theory. Due to the statistical and computational challenges with high dimensionality, little work has been proposed in the literature for estimating the determinant of high-dimensional covariance matrix. In this paper, we estimate the determinant of the covariance matrix using some recent proposals for estimating high-dimensional covariance matrix. Specifically, we consider a total of eight covariance matrix estimation methods for comparison. Through extensive simulation studies, we explore and summarize some interesting comparison results among all compared methods. We also provide practical guidelines based on the sample size, the dimension, and the correlation of the data set for estimating the determinant of high-dimensional covariance matrix. Finally, from a perspective of the loss function, the comparison study in this paper may also serve as a proxy to assess the performance of the covariance matrix estimation.

  17. A Comparison of Methods for Estimating the Determinant of High-Dimensional Covariance Matrix

    KAUST Repository

    Hu, Zongliang; Dong, Kai; Dai, Wenlin; Tong, Tiejun

    2017-01-01

    The determinant of the covariance matrix for high-dimensional data plays an important role in statistical inference and decision. It has many real applications including statistical tests and information theory. Due to the statistical and computational challenges with high dimensionality, little work has been proposed in the literature for estimating the determinant of high-dimensional covariance matrix. In this paper, we estimate the determinant of the covariance matrix using some recent proposals for estimating high-dimensional covariance matrix. Specifically, we consider a total of eight covariance matrix estimation methods for comparison. Through extensive simulation studies, we explore and summarize some interesting comparison results among all compared methods. We also provide practical guidelines based on the sample size, the dimension, and the correlation of the data set for estimating the determinant of high-dimensional covariance matrix. Finally, from a perspective of the loss function, the comparison study in this paper may also serve as a proxy to assess the performance of the covariance matrix estimation.

  18. Interface discontinuity factors in the modal Eigenspace of the multigroup diffusion matrix

    International Nuclear Information System (INIS)

    Garcia-Herranz, N.; Herrero, J.J.; Cuervo, D.; Ahnert, C.

    2011-01-01

    Interface discontinuity factors based on the Generalized Equivalence Theory are commonly used in nodal homogenized diffusion calculations so that diffusion average values approximate heterogeneous higher order solutions. In this paper, an additional form of interface correction factors is presented in the frame of the Analytic Coarse Mesh Finite Difference Method (ACMFD), based on a correction of the modal fluxes instead of the physical fluxes. In the ACMFD formulation, implemented in COBAYA3 code, the coupled multigroup diffusion equations inside a homogenized region are reduced to a set of uncoupled modal equations through diagonalization of the multigroup diffusion matrix. Then, physical fluxes are transformed into modal fluxes in the Eigenspace of the diffusion matrix. It is possible to introduce interface flux discontinuity jumps as the difference of heterogeneous and homogeneous modal fluxes instead of introducing interface discontinuity factors as the ratio of heterogeneous and homogeneous physical fluxes. The formulation in the modal space has been implemented in COBAYA3 code and assessed by comparison with solutions using classical interface discontinuity factors in the physical space. (author)

  19. Comparison between phase shift derived and exactly calculated nucleon--nucleon interaction matrix elements

    International Nuclear Information System (INIS)

    Gregersen, A.W.

    1977-01-01

    A comparison is made between matrix elements calculated using the uncoupled channel Sussex approach to second order in DWBA and matrix elements calculated using a square well potential. The square well potential illustrated the problem of the determining parameter independence balanced with the concept of phase shift difference. The super-soft core potential was used to discuss the systematics of the Sussex approach as a function of angular momentum as well as the relation between Sussex generated and effective interaction matrix elements. In the uncoupled channels the original Sussex method of extracting effective interaction matrix elements was found to be satisfactory. In the coupled channels emphasis was placed upon the 3 S 1 -- 3 D 1 coupled channel matrix elements. Comparison is made between exactly calculated matrix elements, and matrix elements derived using an extended formulation of the coupled channel Sussex method. For simplicity the potential used is a nonseparable cut-off oscillator. The eigenphases of this potential can be made to approximate the realistic nucleon--nucleon phase shifts at low energies. By using the cut-off oscillator test potential, the original coupled channel Sussex method of determining parameter independence was shown to be incapable of accurately reproducing the exact cut-off oscillator matrix elements. The extended Sussex method was found to be accurate to within 10 percent. The extended method is based upon more general coupled channel DWBA and a noninfinite oscillator wave function solution to the cut-off oscillator auxiliary potential. A comparison is made in the coupled channels between matrix elements generated using the original Sussex method and the extended method. Tables of matrix elements generated using the original uncoupled channel Sussex method and the extended coupled channel Sussex method are presented for all necessary angular momentum channels

  20. Drug-Target Interaction Prediction with Graph Regularized Matrix Factorization.

    Science.gov (United States)

    Ezzat, Ali; Zhao, Peilin; Wu, Min; Li, Xiao-Li; Kwoh, Chee-Keong

    2017-01-01

    Experimental determination of drug-target interactions is expensive and time-consuming. Therefore, there is a continuous demand for more accurate predictions of interactions using computational techniques. Algorithms have been devised to infer novel interactions on a global scale where the input to these algorithms is a drug-target network (i.e., a bipartite graph where edges connect pairs of drugs and targets that are known to interact). However, these algorithms had difficulty predicting interactions involving new drugs or targets for which there are no known interactions (i.e., "orphan" nodes in the network). Since data usually lie on or near to low-dimensional non-linear manifolds, we propose two matrix factorization methods that use graph regularization in order to learn such manifolds. In addition, considering that many of the non-occurring edges in the network are actually unknown or missing cases, we developed a preprocessing step to enhance predictions in the "new drug" and "new target" cases by adding edges with intermediate interaction likelihood scores. In our cross validation experiments, our methods achieved better results than three other state-of-the-art methods in most cases. Finally, we simulated some "new drug" and "new target" cases and found that GRMF predicted the left-out interactions reasonably well.

  1. Data Reduction Algorithm Using Nonnegative Matrix Factorization with Nonlinear Constraints

    Science.gov (United States)

    Sembiring, Pasukat

    2017-12-01

    Processing ofdata with very large dimensions has been a hot topic in recent decades. Various techniques have been proposed in order to execute the desired information or structure. Non- Negative Matrix Factorization (NMF) based on non-negatives data has become one of the popular methods for shrinking dimensions. The main strength of this method is non-negative object, the object model by a combination of some basic non-negative parts, so as to provide a physical interpretation of the object construction. The NMF is a dimension reduction method thathasbeen used widely for numerous applications including computer vision,text mining, pattern recognitions,and bioinformatics. Mathematical formulation for NMF did not appear as a convex optimization problem and various types of algorithms have been proposed to solve the problem. The Framework of Alternative Nonnegative Least Square(ANLS) are the coordinates of the block formulation approaches that have been proven reliable theoretically and empirically efficient. This paper proposes a new algorithm to solve NMF problem based on the framework of ANLS.This algorithm inherits the convergenceproperty of the ANLS framework to nonlinear constraints NMF formulations.

  2. Link Prediction via Convex Nonnegative Matrix Factorization on Multiscale Blocks

    Directory of Open Access Journals (Sweden)

    Enming Dong

    2014-01-01

    Full Text Available Low rank matrices approximations have been used in link prediction for networks, which are usually global optimal methods and lack of using the local information. The block structure is a significant local feature of matrices: entities in the same block have similar values, which implies that links are more likely to be found within dense blocks. We use this insight to give a probabilistic latent variable model for finding missing links by convex nonnegative matrix factorization with block detection. The experiments show that this method gives better prediction accuracy than original method alone. Different from the original low rank matrices approximations methods for link prediction, the sparseness of solutions is in accord with the sparse property for most real complex networks. Scaling to massive size network, we use the block information mapping matrices onto distributed architectures and give a divide-and-conquer prediction method. The experiments show that it gives better results than common neighbors method when the networks have a large number of missing links.

  3. Z4-symmetric factorized S-matrix in two space-time dimensions

    International Nuclear Information System (INIS)

    Zamolodchikov, A.B.

    1979-01-01

    The factorized S-matrix with internal symmetry Z 4 is constructed in two space-time dimensions. The two-particle amplitudes are obtained by means of solving the factorization, unitarity and analyticity equations. The solution of factorization equations can be expressed in terms of elliptic functions. The S-matrix cotains the resonance poles naturally. The simple formal relation between the general factorized S-matrices and the Baxter-type lattice transfer matrices is found. In the sense of this relation the Z 4 -symmetric S-matrix corresponds to the Baxter transfer matrix itself. (orig.)

  4. Angiogenic Type I Collagen Extracellular Matrix Integrated with Recombinant Bacteriophages Displaying Vascular Endothelial Growth Factors.

    Science.gov (United States)

    Yoon, Junghyo; Korkmaz Zirpel, Nuriye; Park, Hyun-Ji; Han, Sewoon; Hwang, Kyung Hoon; Shin, Jisoo; Cho, Seung-Woo; Nam, Chang-Hoon; Chung, Seok

    2016-01-21

    Here, a growth-factor-integrated natural extracellular matrix of type I collagen is presented that induces angiogenesis. The developed matrix adapts type I collagen nanofibers integrated with synthetic colloidal particles of recombinant bacteriophages that display vascular endothelial growth factor (VEGF). The integration is achieved during or after gelation of the type I collagen and the matrix enables spatial delivery of VEGF into a desired region. Endothelial cells that contact the VEGF are found to invade into the matrix to form tube-like structures both in vitro and in vivo, proving the angiogenic potential of the matrix. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. Manifold regularized discriminative nonnegative matrix factorization with fast gradient descent.

    Science.gov (United States)

    Guan, Naiyang; Tao, Dacheng; Luo, Zhigang; Yuan, Bo

    2011-07-01

    Nonnegative matrix factorization (NMF) has become a popular data-representation method and has been widely used in image processing and pattern-recognition problems. This is because the learned bases can be interpreted as a natural parts-based representation of data and this interpretation is consistent with the psychological intuition of combining parts to form a whole. For practical classification tasks, however, NMF ignores both the local geometry of data and the discriminative information of different classes. In addition, existing research results show that the learned basis is unnecessarily parts-based because there is neither explicit nor implicit constraint to ensure the representation parts-based. In this paper, we introduce the manifold regularization and the margin maximization to NMF and obtain the manifold regularized discriminative NMF (MD-NMF) to overcome the aforementioned problems. The multiplicative update rule (MUR) can be applied to optimizing MD-NMF, but it converges slowly. In this paper, we propose a fast gradient descent (FGD) to optimize MD-NMF. FGD contains a Newton method that searches the optimal step length, and thus, FGD converges much faster than MUR. In addition, FGD includes MUR as a special case and can be applied to optimizing NMF and its variants. For a problem with 165 samples in R(1600), FGD converges in 28 s, while MUR requires 282 s. We also apply FGD in a variant of MD-NMF and experimental results confirm its efficiency. Experimental results on several face image datasets suggest the effectiveness of MD-NMF.

  6. Multi-view clustering via multi-manifold regularized non-negative matrix factorization.

    Science.gov (United States)

    Zong, Linlin; Zhang, Xianchao; Zhao, Long; Yu, Hong; Zhao, Qianli

    2017-04-01

    Non-negative matrix factorization based multi-view clustering algorithms have shown their competitiveness among different multi-view clustering algorithms. However, non-negative matrix factorization fails to preserve the locally geometrical structure of the data space. In this paper, we propose a multi-manifold regularized non-negative matrix factorization framework (MMNMF) which can preserve the locally geometrical structure of the manifolds for multi-view clustering. MMNMF incorporates consensus manifold and consensus coefficient matrix with multi-manifold regularization to preserve the locally geometrical structure of the multi-view data space. We use two methods to construct the consensus manifold and two methods to find the consensus coefficient matrix, which leads to four instances of the framework. Experimental results show that the proposed algorithms outperform existing non-negative matrix factorization based algorithms for multi-view clustering. Copyright © 2017 Elsevier Ltd. All rights reserved.

  7. Form factors in quantum integrable models with GL(3)-invariant R-matrix

    Energy Technology Data Exchange (ETDEWEB)

    Pakuliak, S., E-mail: pakuliak@theor.jinr.ru [Laboratory of Theoretical Physics, JINR, 141980 Dubna, Moscow Reg. (Russian Federation); Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Moscow Reg. (Russian Federation); Institute of Theoretical and Experimental Physics, 117259 Moscow (Russian Federation); Ragoucy, E., E-mail: eric.ragoucy@lapth.cnrs.fr [Laboratoire de Physique Théorique LAPTH, CNRS and Université de Savoie, BP 110, 74941 Annecy-le-Vieux Cedex (France); Slavnov, N.A., E-mail: nslavnov@mi.ras.ru [Steklov Mathematical Institute, Moscow (Russian Federation)

    2014-04-15

    We study integrable models solvable by the nested algebraic Bethe ansatz and possessing GL(3)-invariant R-matrix. We obtain determinant representations for form factors of off-diagonal entries of the monodromy matrix. These representations can be used for the calculation of form factors and correlation functions of the XXX SU(3)-invariant Heisenberg chain.

  8. Non-negative matrix factorization in texture feature for classification of dementia with MRI data

    Science.gov (United States)

    Sarwinda, D.; Bustamam, A.; Ardaneswari, G.

    2017-07-01

    This paper investigates applications of non-negative matrix factorization as feature selection method to select the features from gray level co-occurrence matrix. The proposed approach is used to classify dementia using MRI data. In this study, texture analysis using gray level co-occurrence matrix is done to feature extraction. In the feature extraction process of MRI data, we found seven features from gray level co-occurrence matrix. Non-negative matrix factorization selected three features that influence of all features produced by feature extractions. A Naïve Bayes classifier is adapted to classify dementia, i.e. Alzheimer's disease, Mild Cognitive Impairment (MCI) and normal control. The experimental results show that non-negative factorization as feature selection method able to achieve an accuracy of 96.4% for classification of Alzheimer's and normal control. The proposed method also compared with other features selection methods i.e. Principal Component Analysis (PCA).

  9. Direct comparison of phosphate uptake by adnate and loosely attached microalgae within an intact biofilm matrix

    International Nuclear Information System (INIS)

    Burkholder, J.M.; Wetzel, R.G.; Klomparens, K.L.

    1990-01-01

    We report a direct comparison of phosphate uptake by adnate and loosely attached microalgae in an intact biofilm matrix, with resolution at the level of individual cells. Track scanning electron microscope autoradiography enabled assay of [ 33 P]phosphate uptake from the overlying water by adnate algae left undisturbed on mature leaves of the macrophyte Potamogeton illinoensis or on artificial plant mimics. The epiphyte communities developed in either phosphate-poor or moderately phosphate-enriched water, and they were assayed on both natural and artificial plants. All adnate taxa examined from both natural and artificial plants in both habitats took up significantly less radiolabel when assayed beneath the overlying matrix than when they were exposed to the water upon removal of the overstory material. Track scanning electron microscope autoradiography and track light microscope autoradiography were intercalibrated to enable comparison of [ 33 P]phosphate uptake by adnate and loosely attached components of the epiphyte matrix. Loosley attached cells on substrata from both habitats took up significantly more radiolabel than did underlying adnate cells, indicating that access to phosphate supplies from the water depended on the position of microbial cells in the matrix. In this short-term assay, the adnate microalgae were relatively isolated from the water column nutrient source

  10. Semi-Supervised Half-Quadratic Nonnegative Matrix Factorization for Face Recognition

    KAUST Repository

    Alghamdi, Masheal M.

    2014-01-01

    complications to the face recognition research. Many algorithms are devoted to solving the face recognition problem, among which the family of nonnegative matrix factorization (NMF) algorithms has been widely used as a compact data representation method

  11. Angiogenesis in vestibular schwannomas: expression of extracellular matrix factors MMP-2, MMP-9, and TIMP-1

    DEFF Research Database (Denmark)

    Møller, Martin Nue; Werther, Kim; Nalla, Amarnadh

    2010-01-01

    Vascular endothelial growth factor (VEGF) and matrix metalloproteinases (MMPs) are potent mediators of tumor angiogenesis. It has been demonstrated that vestibular schwannoma VEGF expression correlates with tumor growth pattern, whereas knowledge on the expression of MMPs is lacking. This study...

  12. On the Road to Genetic Boolean Matrix Factorization

    Czech Academy of Sciences Publication Activity Database

    Snášel, V.; Platoš, J.; Krömer, P.; Húsek, Dušan; Frolov, A.

    2007-01-01

    Roč. 17, č. 6 (2007), s. 675-688 ISSN 1210-0552 Institutional research plan: CEZ:AV0Z10300504 Keywords : data mining * genetic algorithms * Boolean factorization * binary data * machine learning * feature extraction Subject RIV: IN - Informatics, Computer Science Impact factor: 0.280, year: 2007

  13. Calculation of the Cholesky factor directly from the stiffness matrix of the structural element

    International Nuclear Information System (INIS)

    Prates, C.L.M.; Soriano, H.L.

    1978-01-01

    The analysis of the structures of nuclear power plants requires the evaluation of the internal forces. This is attained by the solution of a system of equations. This solution takes most of the computing time and memory. One of the ways it can be achieved is based on the Cholesky factor. The structural matrix of the coeficients is transformed into an upper triangular matrix by the Cholesky decomposition. Cholesky factor can be obtained directly from the stiffness matrix of the structural element. The result can thus be obtained in a more precise and quick way. (Author)

  14. Space Vector Modulation for an Indirect Matrix Converter with Improved Input Power Factor

    Directory of Open Access Journals (Sweden)

    Nguyen Dinh Tuyen

    2017-04-01

    Full Text Available Pulse width modulation strategies have been developed for indirect matrix converters (IMCs in order to improve their performance. In indirect matrix converters, the LC input filter is used to remove input current harmonics and electromagnetic interference problems. Unfortunately, due to the existence of the input filter, the input power factor is diminished, especially during operation at low voltage outputs. In this paper, a new space vector modulation (SVM is proposed to compensate for the input power factor of the indirect matrix converter. Both computer simulation and experimental studies through hardware implementation were performed to verify the effectiveness of the proposed modulation strategy.

  15. Fast matrix factorization algorithm for DOSY based on the eigenvalue decomposition and the difference approximation focusing on the size of observed matrix

    International Nuclear Information System (INIS)

    Tanaka, Yuho; Uruma, Kazunori; Furukawa, Toshihiro; Nakao, Tomoki; Izumi, Kenya; Utsumi, Hiroaki

    2017-01-01

    This paper deals with an analysis problem for diffusion-ordered NMR spectroscopy (DOSY). DOSY is formulated as a matrix factorization problem of a given observed matrix. In order to solve this problem, a direct exponential curve resolution algorithm (DECRA) is well known. DECRA is based on singular value decomposition; the advantage of this algorithm is that the initial value is not required. However, DECRA requires a long calculating time, depending on the size of the given observed matrix due to the singular value decomposition, and this is a serious problem in practical use. Thus, this paper proposes a new analysis algorithm for DOSY to achieve a short calculating time. In order to solve matrix factorization for DOSY without using singular value decomposition, this paper focuses on the size of the given observed matrix. The observed matrix in DOSY is also a rectangular matrix with more columns than rows, due to limitation of the measuring time; thus, the proposed algorithm transforms the given observed matrix into a small observed matrix. The proposed algorithm applies the eigenvalue decomposition and the difference approximation to the small observed matrix, and the matrix factorization problem for DOSY is solved. The simulation and a data analysis show that the proposed algorithm achieves a lower calculating time than DECRA as well as similar analysis result results to DECRA. (author)

  16. A multi-platform evaluation of the randomized CX low-rank matrix factorization in Spark

    Energy Technology Data Exchange (ETDEWEB)

    Gittens, Alex; Kottalam, Jey; Yang, Jiyan; Ringenburg, Michael, F.; Chhugani, Jatin; Racah, Evan; Singh, Mohitdeep; Yao, Yushu; Fischer, Curt; Ruebel, Oliver; Bowen, Benjamin; Lewis, Norman, G.; Mahoney, Michael, W.; Krishnamurthy, Venkat; Prabhat, Mr

    2017-07-27

    We investigate the performance and scalability of the randomized CX low-rank matrix factorization and demonstrate its applicability through the analysis of a 1TB mass spectrometry imaging (MSI) dataset, using Apache Spark on an Amazon EC2 cluster, a Cray XC40 system, and an experimental Cray cluster. We implemented this factorization both as a parallelized C implementation with hand-tuned optimizations and in Scala using the Apache Spark high-level cluster computing framework. We obtained consistent performance across the three platforms: using Spark we were able to process the 1TB size dataset in under 30 minutes with 960 cores on all systems, with the fastest times obtained on the experimental Cray cluster. In comparison, the C implementation was 21X faster on the Amazon EC2 system, due to careful cache optimizations, bandwidth-friendly access of matrices and vector computation using SIMD units. We report these results and their implications on the hardware and software issues arising in supporting data-centric workloads in parallel and distributed environments.

  17. Investigation of occupational health and safety application using the internal and external factor assessment matrix: SWOT

    Directory of Open Access Journals (Sweden)

    2012-09-01

    Material and Method: IIn this study, the threats, opportunities, weaknesses and strengths were evaluated by one of the tools named SWOT, in one of the assembly industries company in Iran, in order to controlling the operations in this company considering to safety and health standard (OHSAS18001. A comparison of the company’s performance in implementing the safety and health standards was done between years 1387 and 1388 contain in the Company considered, and weighted scoring weaknesses, strengths, threats and opportunities using the matrix of internal factors (strengths and weaknesses and external factors (treats and opportunities then, the importance of each factor were determined in the company’s implementation and enforcement of those standards. . Result: Focusing on the strengths and weaknesses, opportunities and threats, some strategies to improve the implementation were presented. Any points were weighted based on the most important weaknesses identified as the lack of monitoring contractors, lack of management commitment for implementation of OHSAS18001, no attempt to identify the risks of change, lack of training needs assessment, main strengths identified in the context of adequate budget health and safety, environmental efforts, identify risk for abnormal conditions, the most important threats for immediate delivery customer orders and the opportunity to support the safety and health plans, were determined. . Conclusion: Sum of the weighted scores in year 87 were obtained for the external factors (opportunities and threats, 2.16 and internal factors (strengths and weaknesses 1.66. Both of these scores were less than 2.5 (minimum amount of the acceptable rate so, the company has been poor performance in the implementation of this standard for the year 87 and a weak reaction in the use of opportunities and the minimize threats has. In case of internal factors, it was worse than external one and the situation was more bold of the weaknesses companies to

  18. Dictionary Learning Based on Nonnegative Matrix Factorization Using Parallel Coordinate Descent

    Directory of Open Access Journals (Sweden)

    Zunyi Tang

    2013-01-01

    Full Text Available Sparse representation of signals via an overcomplete dictionary has recently received much attention as it has produced promising results in various applications. Since the nonnegativities of the signals and the dictionary are required in some applications, for example, multispectral data analysis, the conventional dictionary learning methods imposed simply with nonnegativity may become inapplicable. In this paper, we propose a novel method for learning a nonnegative, overcomplete dictionary for such a case. This is accomplished by posing the sparse representation of nonnegative signals as a problem of nonnegative matrix factorization (NMF with a sparsity constraint. By employing the coordinate descent strategy for optimization and extending it to multivariable case for processing in parallel, we develop a so-called parallel coordinate descent dictionary learning (PCDDL algorithm, which is structured by iteratively solving the two optimal problems, the learning process of the dictionary and the estimating process of the coefficients for constructing the signals. Numerical experiments demonstrate that the proposed algorithm performs better than the conventional nonnegative K-SVD (NN-KSVD algorithm and several other algorithms for comparison. What is more, its computational consumption is remarkably lower than that of the compared algorithms.

  19. Nonnegative Matrix Factor 2-D Deconvolution for Blind Single Channel Source Separation

    DEFF Research Database (Denmark)

    Schmidt, Mikkel N.; Mørup, Morten

    2006-01-01

    We present a novel method for blind separation of instruments in polyphonic music based on a non-negative matrix factor 2-D deconvolution algorithm. Using a model which is convolutive in both time and frequency we factorize a spectrogram representation of music into components corresponding...

  20. Validation of Spectral Unmixing Results from Informed Non-Negative Matrix Factorization (INMF) of Hyperspectral Imagery

    Science.gov (United States)

    Wright, L.; Coddington, O.; Pilewskie, P.

    2017-12-01

    Hyperspectral instruments are a growing class of Earth observing sensors designed to improve remote sensing capabilities beyond discrete multi-band sensors by providing tens to hundreds of continuous spectral channels. Improved spectral resolution, range and radiometric accuracy allow the collection of large amounts of spectral data, facilitating thorough characterization of both atmospheric and surface properties. We describe the development of an Informed Non-Negative Matrix Factorization (INMF) spectral unmixing method to exploit this spectral information and separate atmospheric and surface signals based on their physical sources. INMF offers marked benefits over other commonly employed techniques including non-negativity, which avoids physically impossible results; and adaptability, which tailors the method to hyperspectral source separation. The INMF algorithm is adapted to separate contributions from physically distinct sources using constraints on spectral and spatial variability, and library spectra to improve the initial guess. Using this INMF algorithm we decompose hyperspectral imagery from the NASA Hyperspectral Imager for the Coastal Ocean (HICO), with a focus on separating surface and atmospheric signal contributions. HICO's coastal ocean focus provides a dataset with a wide range of atmospheric and surface conditions. These include atmospheres with varying aerosol optical thicknesses and cloud cover. HICO images also provide a range of surface conditions including deep ocean regions, with only minor contributions from the ocean surfaces; and more complex shallow coastal regions with contributions from the seafloor or suspended sediments. We provide extensive comparison of INMF decomposition results against independent measurements of physical properties. These include comparison against traditional model-based retrievals of water-leaving, aerosol, and molecular scattering radiances and other satellite products, such as aerosol optical thickness from

  1. General factorization relations and consistency conditions in the sudden approximation via infinite matrix inversion

    International Nuclear Information System (INIS)

    Chan, C.K.; Hoffman, D.K.; Evans, J.W.

    1985-01-01

    Local, i.e., multiplicative, operators satisfy well-known linear factorization relations wherein matrix elements (between states associated with a complete set of wave functions) can be obtained as a linear combination of those out of the ground state (the input data). Analytic derivation of factorization relations for general state input data results in singular integral expressions for the coefficients, which can, however, be regularized using consistency conditions between matrix elements out of a single (nonground) state. Similar results hold for suitable ''symmetry class'' averaged matrix elements where the symmetry class projection operators are ''complete.'' In several cases where the wave functions or projection operators incorporate orthogonal polynomial dependence, we show that the ground state factorization relations have a simplified structure allowing an alternative derivation of the general factorization relations via an infinite matrix inversion procedure. This form is shown to have some advantages over previous versions. In addition, this matrix inversion procedure obtains all consistency conditions (which is not always the case from regularization of singular integrals)

  2. Followee recommendation in microblog using matrix factorization model with structural regularization.

    Science.gov (United States)

    Yu, Yan; Qiu, Robin G

    2014-01-01

    Microblog that provides us a new communication and information sharing platform has been growing exponentially since it emerged just a few years ago. To microblog users, recommending followees who can serve as high quality information sources is a competitive service. To address this problem, in this paper we propose a matrix factorization model with structural regularization to improve the accuracy of followee recommendation in microblog. More specifically, we adapt the matrix factorization model in traditional item recommender systems to followee recommendation in microblog and use structural regularization to exploit structure information of social network to constrain matrix factorization model. The experimental analysis on a real-world dataset shows that our proposed model is promising.

  3. Single-channel source separation using non-negative matrix factorization

    DEFF Research Database (Denmark)

    Schmidt, Mikkel Nørgaard

    -determined and its solution relies on making appropriate assumptions concerning the sources. This dissertation is concerned with model-based probabilistic single-channel source separation based on non-negative matrix factorization, and consists of two parts: i) three introductory chapters and ii) five published...... papers. The first part introduces the single-channel source separation problem as well as non-negative matrix factorization and provides a comprehensive review of existing approaches, applications, and practical algorithms. This serves to provide context for the second part, the published papers......, in which a number of methods for single-channel source separation based on non-negative matrix factorization are presented. In the papers, the methods are applied to separating audio signals such as speech and musical instruments and separating different types of tissue in chemical shift imaging....

  4. Technique for information retrieval using enhanced latent semantic analysis generating rank approximation matrix by factorizing the weighted morpheme-by-document matrix

    Science.gov (United States)

    Chew, Peter A; Bader, Brett W

    2012-10-16

    A technique for information retrieval includes parsing a corpus to identify a number of wordform instances within each document of the corpus. A weighted morpheme-by-document matrix is generated based at least in part on the number of wordform instances within each document of the corpus and based at least in part on a weighting function. The weighted morpheme-by-document matrix separately enumerates instances of stems and affixes. Additionally or alternatively, a term-by-term alignment matrix may be generated based at least in part on the number of wordform instances within each document of the corpus. At least one lower rank approximation matrix is generated by factorizing the weighted morpheme-by-document matrix and/or the term-by-term alignment matrix.

  5. Source contributions to PM10 and arsenic concentrations in Central Chile using positive matrix factorization

    Science.gov (United States)

    Hedberg, Emma; Gidhagen, Lars; Johansson, Christer

    Sampling of particles (PM10) was conducted during a one-year period at two rural sites in Central Chile, Quillota and Linares. The samples were analyzed for elemental composition. The data sets have undergone source-receptor analyses in order to estimate the sources and their abundance's in the PM10 size fraction, by using the factor analytical method positive matrix factorization (PMF). The analysis showed that PM10 was dominated by soil resuspension at both sites during the summer months, while during winter traffic dominated the particle mass at Quillota and local wood burning dominated the particle mass at Linares. Two copper smelters impacted the Quillota station, and contributed to 10% and 16% of PM10 as an average during summer and winter, respectively. One smelter impacted Linares by 8% and 19% of PM10 in the summer and winter, respectively. For arsenic the two smelters accounted for 87% of the monitored arsenic levels at Quillota and at Linares one smelter contributed with 72% of the measured mass. In comparison with PMF, the use of a dispersion model tended to overestimate the smelter contribution to arsenic levels at both sites. The robustness of the PMF model was tested by using randomly reduced data sets, where 85%, 70%, 50% and 33% of the samples were included. In this way the ability of the model to reconstruct the sources initially found by the original data set could be tested. On average for all sources the relative standard deviation increased from 7% to 25% for the variables identifying the sources, when decreasing the data set from 85% to 33% of the samples, indicating that the solution initially found was very stable to begin with. But it was also noted that sources due to industrial or combustion processes were more sensitive for the size of the data set, compared to the natural sources as local soil and sea spray sources.

  6. Genetic Algorithm and Graph Theory Based Matrix Factorization Method for Online Friend Recommendation

    Directory of Open Access Journals (Sweden)

    Qu Li

    2014-01-01

    Full Text Available Online friend recommendation is a fast developing topic in web mining. In this paper, we used SVD matrix factorization to model user and item feature vector and used stochastic gradient descent to amend parameter and improve accuracy. To tackle cold start problem and data sparsity, we used KNN model to influence user feature vector. At the same time, we used graph theory to partition communities with fairly low time and space complexity. What is more, matrix factorization can combine online and offline recommendation. Experiments showed that the hybrid recommendation algorithm is able to recommend online friends with good accuracy.

  7. Development and validation of a job exposure matrix for physical risk factors in low back pain.

    Directory of Open Access Journals (Sweden)

    Svetlana Solovieva

    Full Text Available OBJECTIVES: The aim was to construct and validate a gender-specific job exposure matrix (JEM for physical exposures to be used in epidemiological studies of low back pain (LBP. MATERIALS AND METHODS: We utilized two large Finnish population surveys, one to construct the JEM and another to test matrix validity. The exposure axis of the matrix included exposures relevant to LBP (heavy physical work, heavy lifting, awkward trunk posture and whole body vibration and exposures that increase the biomechanical load on the low back (arm elevation or those that in combination with other known risk factors could be related to LBP (kneeling or squatting. Job titles with similar work tasks and exposures were grouped. Exposure information was based on face-to-face interviews. Validity of the matrix was explored by comparing the JEM (group-based binary measures with individual-based measures. The predictive validity of the matrix against LBP was evaluated by comparing the associations of the group-based (JEM exposures with those of individual-based exposures. RESULTS: The matrix includes 348 job titles, representing 81% of all Finnish job titles in the early 2000s. The specificity of the constructed matrix was good, especially in women. The validity measured with kappa-statistic ranged from good to poor, being fair for most exposures. In men, all group-based (JEM exposures were statistically significantly associated with one-month prevalence of LBP. In women, four out of six group-based exposures showed an association with LBP. CONCLUSIONS: The gender-specific JEM for physical exposures showed relatively high specificity without compromising sensitivity. The matrix can therefore be considered as a valid instrument for exposure assessment in large-scale epidemiological studies, when more precise but more labour-intensive methods are not feasible. Although the matrix was based on Finnish data we foresee that it could be applicable, with some modifications, in

  8. Development and validation of a job exposure matrix for physical risk factors in low back pain.

    Science.gov (United States)

    Solovieva, Svetlana; Pehkonen, Irmeli; Kausto, Johanna; Miranda, Helena; Shiri, Rahman; Kauppinen, Timo; Heliövaara, Markku; Burdorf, Alex; Husgafvel-Pursiainen, Kirsti; Viikari-Juntura, Eira

    2012-01-01

    The aim was to construct and validate a gender-specific job exposure matrix (JEM) for physical exposures to be used in epidemiological studies of low back pain (LBP). We utilized two large Finnish population surveys, one to construct the JEM and another to test matrix validity. The exposure axis of the matrix included exposures relevant to LBP (heavy physical work, heavy lifting, awkward trunk posture and whole body vibration) and exposures that increase the biomechanical load on the low back (arm elevation) or those that in combination with other known risk factors could be related to LBP (kneeling or squatting). Job titles with similar work tasks and exposures were grouped. Exposure information was based on face-to-face interviews. Validity of the matrix was explored by comparing the JEM (group-based) binary measures with individual-based measures. The predictive validity of the matrix against LBP was evaluated by comparing the associations of the group-based (JEM) exposures with those of individual-based exposures. The matrix includes 348 job titles, representing 81% of all Finnish job titles in the early 2000s. The specificity of the constructed matrix was good, especially in women. The validity measured with kappa-statistic ranged from good to poor, being fair for most exposures. In men, all group-based (JEM) exposures were statistically significantly associated with one-month prevalence of LBP. In women, four out of six group-based exposures showed an association with LBP. The gender-specific JEM for physical exposures showed relatively high specificity without compromising sensitivity. The matrix can therefore be considered as a valid instrument for exposure assessment in large-scale epidemiological studies, when more precise but more labour-intensive methods are not feasible. Although the matrix was based on Finnish data we foresee that it could be applicable, with some modifications, in other countries with a similar level of technology.

  9. KEY COMPARISON: CCQM-K27-Subsequent: Key Comparison (subsequent) for the determination of ethanol in aqueous matrix

    Science.gov (United States)

    Schantz, Michele M.; Duewer, David L.; Parris, Reenie M.; May, Willie E.; Archer, Marcellé; Mussell, Chris; Carter, David; Konopelko, Leonid A.; Kustikov, Yury A.; Krylov, Anatoli I.; Fatina, Olga V.

    2005-01-01

    Ethanol is important both forensically ('drunk driving' or driving while under the influence, 'DWI', regulations) and commercially (alcoholic beverages). Blood- and breath-alcohol testing can be imposed on individuals operating private vehicles such as cars, boats, or snowmobiles, or operators of commercial vehicles like trucks, planes, and ships. The various levels of blood alcohol that determine whether these operators are considered legally impaired vary depending on the circumstances and locality. Accurate calibration and validation of instrumentation is critical in areas of forensic testing where quantitative analysis directly affects the outcome of criminal prosecutions, as is the case with the determination of ethanol in blood and breath. Additionally, the accurate assessment of the alcoholic content of beverages is a commercially important commodity. In 2002, the CCQM conducted a Key Comparison (CCQM-K27) for the determination of ethanol in aqueous matrix with nine participants. A report on this project has been approved by the CCQM and can be found at the BIPM website and in this Technical Supplement. CCQM-K27 comprised three samples, one at low mass fraction of ethanol in water (nominal concentration of 0.8 mg/g), one at high level (nominal concentration of 120 mg/g), and one wine matrix (nominal concentration of 81 mg/g). Overall agreement among eight participants using gas chromatography with flame ionization detection (GC-FID), titrimetry, isotope dilution gas chromatography/mass spectrometry (GC-IDMS), and gas chromatography-combustion-isotope ratio mass spectrometry (ID-GC-C-IRMS) was good. The ninth participant used a headspace GC-FID method that had not been validated in an earlier pilot study (CCQM-P35). A follow-on Key Comparison, CCQM-K27-Subsequent, was initiated in 2003 to accommodate laboratories that had not been ready to benchmark their methods in the original CCQM-K27 study or that wished to benchmark a different method. Four levels of

  10. Robust Nonnegative Matrix Factorization via Joint Graph Laplacian and Discriminative Information for Identifying Differentially Expressed Genes

    Directory of Open Access Journals (Sweden)

    Ling-Yun Dai

    2017-01-01

    Full Text Available Differential expression plays an important role in cancer diagnosis and classification. In recent years, many methods have been used to identify differentially expressed genes. However, the recognition rate and reliability of gene selection still need to be improved. In this paper, a novel constrained method named robust nonnegative matrix factorization via joint graph Laplacian and discriminative information (GLD-RNMF is proposed for identifying differentially expressed genes, in which manifold learning and the discriminative label information are incorporated into the traditional nonnegative matrix factorization model to train the objective matrix. Specifically, L2,1-norm minimization is enforced on both the error function and the regularization term which is robust to outliers and noise in gene data. Furthermore, the multiplicative update rules and the details of convergence proof are shown for the new model. The experimental results on two publicly available cancer datasets demonstrate that GLD-RNMF is an effective method for identifying differentially expressed genes.

  11. High performance matrix inversion based on LU factorization for multicore architectures

    KAUST Repository

    Dongarra, Jack

    2011-01-01

    The goal of this paper is to present an efficient implementation of an explicit matrix inversion of general square matrices on multicore computer architecture. The inversion procedure is split into four steps: 1) computing the LU factorization, 2) inverting the upper triangular U factor, 3) solving a linear system, whose solution yields inverse of the original matrix and 4) applying backward column pivoting on the inverted matrix. Using a tile data layout, which represents the matrix in the system memory with an optimized cache-aware format, the computation of the four steps is decomposed into computational tasks. A directed acyclic graph is generated on the fly which represents the program data flow. Its nodes represent tasks and edges the data dependencies between them. Previous implementations of matrix inversions, available in the state-of-the-art numerical libraries, are suffer from unnecessary synchronization points, which are non-existent in our implementation in order to fully exploit the parallelism of the underlying hardware. Our algorithmic approach allows to remove these bottlenecks and to execute the tasks with loose synchronization. A runtime environment system called QUARK is necessary to dynamically schedule our numerical kernels on the available processing units. The reported results from our LU-based matrix inversion implementation significantly outperform the state-of-the-art numerical libraries such as LAPACK (5x), MKL (5x) and ScaLAPACK (2.5x) on a contemporary AMD platform with four sockets and the total of 48 cores for a matrix of size 24000. A power consumption analysis shows that our high performance implementation is also energy efficient and substantially consumes less power than its competitors. © 2011 ACM.

  12. Large-Scale Distributed Bayesian Matrix Factorization using Stochastic Gradient MCMC

    NARCIS (Netherlands)

    Ahn, S.; Korattikara, A.; Liu, N.; Rajan, S.; Welling, M.

    2015-01-01

    Despite having various attractive qualities such as high prediction accuracy and the ability to quantify uncertainty and avoid ovrfitting, Bayesian Matrix Factorization has not been widely adopted because of the prohibitive cost of inference. In this paper, we propose a scalable distributed Bayesian

  13. A Transfer Learning Approach for Applying Matrix Factorization to Small ITS Datasets

    Science.gov (United States)

    Voß, Lydia; Schatten, Carlotta; Mazziotti, Claudia; Schmidt-Thieme, Lars

    2015-01-01

    Machine Learning methods for Performance Prediction in Intelligent Tutoring Systems (ITS) have proven their efficacy; specific methods, e.g. Matrix Factorization (MF), however suffer from the lack of available information about new tasks or new students. In this paper we show how this problem could be solved by applying Transfer Learning (TL),…

  14. Sparse Non-negative Matrix Factor 2-D Deconvolution for Automatic Transcription of Polyphonic Music

    DEFF Research Database (Denmark)

    Schmidt, Mikkel N.; Mørup, Morten

    2006-01-01

    We present a novel method for automatic transcription of polyphonic music based on a recently published algorithm for non-negative matrix factor 2-D deconvolution. The method works by simultaneously estimating a time-frequency model for an instrument and a pattern corresponding to the notes which...... are played based on a log-frequency spectrogram of the music....

  15. Structure constrained semi-nonnegative matrix factorization for EEG-based motor imagery classification.

    Science.gov (United States)

    Lu, Na; Li, Tengfei; Pan, Jinjin; Ren, Xiaodong; Feng, Zuren; Miao, Hongyu

    2015-05-01

    Electroencephalogram (EEG) provides a non-invasive approach to measure the electrical activities of brain neurons and has long been employed for the development of brain-computer interface (BCI). For this purpose, various patterns/features of EEG data need to be extracted and associated with specific events like cue-paced motor imagery. However, this is a challenging task since EEG data are usually non-stationary time series with a low signal-to-noise ratio. In this study, we propose a novel method, called structure constrained semi-nonnegative matrix factorization (SCS-NMF), to extract the key patterns of EEG data in time domain by imposing the mean envelopes of event-related potentials (ERPs) as constraints on the semi-NMF procedure. The proposed method is applicable to general EEG time series, and the extracted temporal features by SCS-NMF can also be combined with other features in frequency domain to improve the performance of motor imagery classification. Real data experiments have been performed using the SCS-NMF approach for motor imagery classification, and the results clearly suggest the superiority of the proposed method. Comparison experiments have also been conducted. The compared methods include ICA, PCA, Semi-NMF, Wavelets, EMD and CSP, which further verified the effectivity of SCS-NMF. The SCS-NMF method could obtain better or competitive performance over the state of the art methods, which provides a novel solution for brain pattern analysis from the perspective of structure constraint. Copyright © 2015 Elsevier Ltd. All rights reserved.

  16. arXiv On Matrix Factorizations, Residue Pairings and Homological Mirror Symmetry

    CERN Document Server

    Lerche, Wolfgang

    We argue how boundary B-type Landau-Ginzburg models based on matrix factorizations can be used to compute exact superpotentials for intersecting D-brane configurations on compact Calabi-Yau spaces. In this paper, we consider the dependence of open-string, boundary changing correlators on bulk moduli. This determines, via mirror symmetry, non-trivial disk instanton corrections in the A-model. As crucial ingredient we propose a differential equation that involves matrix analogs of Saito's higher residue pairings. As example, we compute from this for the elliptic curve certain quantum products m_2 and m_3, which reproduce genuine boundary changing, open Gromov-Witten invariants.

  17. Matrix completion via a low rank factorization model and an Augmented Lagrangean Succesive Overrelaxation Algorithm

    Directory of Open Access Journals (Sweden)

    Hugo Lara

    2014-12-01

    Full Text Available The matrix completion problem (MC has been approximated by using the nuclear norm relaxation. Some algorithms based on this strategy require the computationally expensive singular value decomposition (SVD at each iteration. One way to avoid SVD calculations is to use alternating methods, which pursue the completion through matrix factorization with a low rank condition. In this work an augmented Lagrangean-type alternating algorithm is proposed. The new algorithm uses duality information to define the iterations, in contrast to the solely primal LMaFit algorithm, which employs a Successive Over Relaxation scheme. The convergence result is studied. Some numerical experiments are given to compare numerical performance of both proposals.

  18. Compound nucleus in Livsic open-system theory: Factorization of the S matrix

    International Nuclear Information System (INIS)

    Avishai, Y.

    1988-01-01

    The compound-nucleus system fits into a mathematical theory of open systems in physics developed by the mathematician M. Livsic [Translations of Mathematical Monographs (American Mathematical Society, Providence, Rhode Island, 1973), Vol. 34]. In this article we review some basic concepts of the above theory and apply it to study the structure of the compound-nucleus S matrix. One of the results is a factorization of the S matrix in the form S(ω) = S +iA/sub k//(tau/sub k/-ω)], where A/sub k/ are known matrices and tau/sub k/ are the complex resonance energies

  19. Constructing the tree-level Yang-Mills S-matrix using complex factorization

    Science.gov (United States)

    Schuster, Philip C.; Toro, Natalia

    2009-06-01

    A remarkable connection between BCFW recursion relations and constraints on the S-matrix was made by Benincasa and Cachazo in 0705.4305, who noted that mutual consistency of different BCFW constructions of four-particle amplitudes generates non-trivial (but familiar) constraints on three-particle coupling constants — these include gauge invariance, the equivalence principle, and the lack of non-trivial couplings for spins > 2. These constraints can also be derived with weaker assumptions, by demanding the existence of four-point amplitudes that factorize properly in all unitarity limits with complex momenta. From this starting point, we show that the BCFW prescription can be interpreted as an algorithm for fully constructing a tree-level S-matrix, and that complex factorization of general BCFW amplitudes follows from the factorization of four-particle amplitudes. The allowed set of BCFW deformations is identified, formulated entirely as a statement on the three-particle sector, and using only complex factorization as a guide. Consequently, our analysis based on the physical consistency of the S-matrix is entirely independent of field theory. We analyze the case of pure Yang-Mills, and outline a proof for gravity. For Yang-Mills, we also show that the well-known scaling behavior of BCFW-deformed amplitudes at large z is a simple consequence of factorization. For gravity, factorization in certain channels requires asymptotic behavior ~ 1/z2.

  20. Constructing the tree-level Yang-Mills S-matrix using complex factorization

    International Nuclear Information System (INIS)

    Schuster, Philip C.; Toro, Natalia

    2009-01-01

    A remarkable connection between BCFW recursion relations and constraints on the S-matrix was made by Benincasa and Cachazo in 0705.4305, who noted that mutual consistency of different BCFW constructions of four-particle amplitudes generates non-trivial (but familiar) constraints on three-particle coupling constants - these include gauge invariance, the equivalence principle, and the lack of non-trivial couplings for spins > 2. These constraints can also be derived with weaker assumptions, by demanding the existence of four-point amplitudes that factorize properly in all unitarity limits with complex momenta. From this starting point, we show that the BCFW prescription can be interpreted as an algorithm for fully constructing a tree-level S-matrix, and that complex factorization of general BCFW amplitudes follows from the factorization of four-particle amplitudes. The allowed set of BCFW deformations is identified, formulated entirely as a statement on the three-particle sector, and using only complex factorization as a guide. Consequently, our analysis based on the physical consistency of the S-matrix is entirely independent of field theory. We analyze the case of pure Yang-Mills, and outline a proof for gravity. For Yang-Mills, we also show that the well-known scaling behavior of BCFW-deformed amplitudes at large z is a simple consequence of factorization. For gravity, factorization in certain channels requires asymptotic behavior ∼ 1/z 2 .

  1. Factorizations of rational matrix functions with application to discrete isomonodromic transformations and difference Painleve equations

    International Nuclear Information System (INIS)

    Dzhamay, Anton

    2009-01-01

    We study factorizations of rational matrix functions with simple poles on the Riemann sphere. For the quadratic case (two poles) we show, using multiplicative representations of such matrix functions, that a good coordinate system on this space is given by a mix of residue eigenvectors of the matrix and its inverse. Our approach is motivated by the theory of discrete isomonodromic transformations and their relationship with difference Painleve equations. In particular, in these coordinates, basic isomonodromic transformations take the form of the discrete Euler-Lagrange equations. Secondly we show that dPV equations, previously obtained in this context by D Arinkin and A Borodin, can be understood as simple relationships between the residues of such matrices and their inverses.

  2. All-at-once Optimization for Coupled Matrix and Tensor Factorizations

    DEFF Research Database (Denmark)

    Evrim, Acar Ataman; Kolda, Tamara G.; Dunlavy, Daniel M.

    2011-01-01

    .g., the person by person social network matrix or the restaurant by category matrix, and higher-order tensors, e.g., the "ratings" tensor of the form restaurant by meal by person. In this paper, we are particularly interested in fusing data sets with the goal of capturing their underlying latent structures. We...... formulate this problem as a coupled matrix and tensor factorization (CMTF) problem where heterogeneous data sets are modeled by fitting outer-product models to higher-order tensors and matrices in a coupled manner. Unlike traditional approaches solving this problem using alternating algorithms, we propose...... an all-at-once optimization approach called CMTF-OPT (CMTF-OPTimization), which is a gradient-based optimization approach for joint analysis of matrices and higher-order tensors. We also extend the algorithm to handle coupled incomplete data sets. Using numerical experiments, we demonstrate...

  3. Wiener-Hopf factorization of piecewise meromorphic matrix-valued functions

    International Nuclear Information System (INIS)

    Adukov, Victor M

    2009-01-01

    Let D + be a multiply connected domain bounded by a contour Γ, let D - be the complement of D + union Γ in C-bar=C union {∞}, and a(t) be a continuous invertible matrix-valued function on Γ which can be meromorphically extended into the open disconnected set D - (as a piecewise meromorphic matrix-valued function). An explicit solution of the Wiener-Hopf factorization problem for a(t) is obtained and the partial factorization indices of a(t) are calculated. Here an explicit solution of a factorization problem is meant in the sense of reducing it to the investigation of finitely many systems of linear algebraic equations with matrices expressed in closed form, that is, in quadratures. Bibliography: 15 titles.

  4. ENDMEMBER EXTRACTION OF HIGHLY MIXED DATA USING L1 SPARSITY-CONSTRAINED MULTILAYER NONNEGATIVE MATRIX FACTORIZATION

    Directory of Open Access Journals (Sweden)

    H. Fang

    2018-04-01

    Full Text Available Due to the limited spatial resolution of remote hyperspectral sensors, pixels are usually highly mixed in the hyperspectral images. Endmember extraction refers to the process identifying the pure endmember signatures from the mixture, which is an important step towards the utilization of hyperspectral data. Nonnegative matrix factorization (NMF is a widely used method of endmember extraction due to its effectiveness and convenience. While most NMF-based methods have single-layer structures, which may have difficulties in effectively learning the structures of highly mixed and complex data. On the other hand, multilayer algorithms have shown great advantages in learning data features and been widely studied in many fields. In this paper, we presented a L1 sparsityconstrained multilayer NMF method for endmember extraction of highly mixed data. Firstly, the multilayer NMF structure was obtained by unfolding NMF into a certain number of layers. In each layer, the abundance matrix was decomposed into the endmember matrix and abundance matrix of the next layer. Besides, to improve the performance of NMF, we incorporated sparsity constraints to the multilayer NMF model by adding a L1 regularizer of the abundance matrix to each layer. At last, a layer-wise optimization method based on NeNMF was proposed to train the multilayer NMF structure. Experiments were conducted on both synthetic data and real data. The results demonstrate that our proposed algorithm can achieve better results than several state-of-art approaches.

  5. RSAT matrix-clustering: dynamic exploration and redundancy reduction of transcription factor binding motif collections.

    Science.gov (United States)

    Castro-Mondragon, Jaime Abraham; Jaeger, Sébastien; Thieffry, Denis; Thomas-Chollier, Morgane; van Helden, Jacques

    2017-07-27

    Transcription factor (TF) databases contain multitudes of binding motifs (TFBMs) from various sources, from which non-redundant collections are derived by manual curation. The advent of high-throughput methods stimulated the production of novel collections with increasing numbers of motifs. Meta-databases, built by merging these collections, contain redundant versions, because available tools are not suited to automatically identify and explore biologically relevant clusters among thousands of motifs. Motif discovery from genome-scale data sets (e.g. ChIP-seq) also produces redundant motifs, hampering the interpretation of results. We present matrix-clustering, a versatile tool that clusters similar TFBMs into multiple trees, and automatically creates non-redundant TFBM collections. A feature unique to matrix-clustering is its dynamic visualisation of aligned TFBMs, and its capability to simultaneously treat multiple collections from various sources. We demonstrate that matrix-clustering considerably simplifies the interpretation of combined results from multiple motif discovery tools, and highlights biologically relevant variations of similar motifs. We also ran a large-scale application to cluster ∼11 000 motifs from 24 entire databases, showing that matrix-clustering correctly groups motifs belonging to the same TF families, and drastically reduced motif redundancy. matrix-clustering is integrated within the RSAT suite (http://rsat.eu/), accessible through a user-friendly web interface or command-line for its integration in pipelines. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  6. Doubly Nonparametric Sparse Nonnegative Matrix Factorization Based on Dependent Indian Buffet Processes.

    Science.gov (United States)

    Xuan, Junyu; Lu, Jie; Zhang, Guangquan; Xu, Richard Yi Da; Luo, Xiangfeng

    2018-05-01

    Sparse nonnegative matrix factorization (SNMF) aims to factorize a data matrix into two optimized nonnegative sparse factor matrices, which could benefit many tasks, such as document-word co-clustering. However, the traditional SNMF typically assumes the number of latent factors (i.e., dimensionality of the factor matrices) to be fixed. This assumption makes it inflexible in practice. In this paper, we propose a doubly sparse nonparametric NMF framework to mitigate this issue by using dependent Indian buffet processes (dIBP). We apply a correlation function for the generation of two stick weights associated with each column pair of factor matrices while still maintaining their respective marginal distribution specified by IBP. As a consequence, the generation of two factor matrices will be columnwise correlated. Under this framework, two classes of correlation function are proposed: 1) using bivariate Beta distribution and 2) using Copula function. Compared with the single IBP-based NMF, this paper jointly makes two factor matrices nonparametric and sparse, which could be applied to broader scenarios, such as co-clustering. This paper is seen to be much more flexible than Gaussian process-based and hierarchial Beta process-based dIBPs in terms of allowing the two corresponding binary matrix columns to have greater variations in their nonzero entries. Our experiments on synthetic data show the merits of this paper compared with the state-of-the-art models in respect of factorization efficiency, sparsity, and flexibility. Experiments on real-world data sets demonstrate the efficiency of this paper in document-word co-clustering tasks.

  7. Hessian regularization based symmetric nonnegative matrix factorization for clustering gene expression and microbiome data.

    Science.gov (United States)

    Ma, Yuanyuan; Hu, Xiaohua; He, Tingting; Jiang, Xingpeng

    2016-12-01

    Nonnegative matrix factorization (NMF) has received considerable attention due to its interpretation of observed samples as combinations of different components, and has been successfully used as a clustering method. As an extension of NMF, Symmetric NMF (SNMF) inherits the advantages of NMF. Unlike NMF, however, SNMF takes a nonnegative similarity matrix as an input, and two lower rank nonnegative matrices (H, H T ) are computed as an output to approximate the original similarity matrix. Laplacian regularization has improved the clustering performance of NMF and SNMF. However, Laplacian regularization (LR), as a classic manifold regularization method, suffers some problems because of its weak extrapolating ability. In this paper, we propose a novel variant of SNMF, called Hessian regularization based symmetric nonnegative matrix factorization (HSNMF), for this purpose. In contrast to Laplacian regularization, Hessian regularization fits the data perfectly and extrapolates nicely to unseen data. We conduct extensive experiments on several datasets including text data, gene expression data and HMP (Human Microbiome Project) data. The results show that the proposed method outperforms other methods, which suggests the potential application of HSNMF in biological data clustering. Copyright © 2016. Published by Elsevier Inc.

  8. Extracellular matrix and growth factor engineering for controlled angiogenesis in regenerative medicine

    Directory of Open Access Journals (Sweden)

    Mikaël M Martino

    2015-04-01

    Full Text Available Blood vessel growth plays a key role in regenerative medicine, both to restore blood supply to ischemic tissues and to ensure rapid vascularization of clinical-size tissue-engineered grafts. For example, vascular endothelial growth factor (VEGF is the master regulator of physiological blood vessel growth and is one of the main molecular targets of therapeutic angiogenesis approaches. However, angiogenesis is a complex process and there is a need to develop rational therapeutic strategies based on a firm understanding of basic vascular biology principles, as evidenced by the disappointing results of initial clinical trials of angiogenic factor delivery. In particular, the spatial localization of angiogenic signals in the extracellular matrix is crucial to ensure the proper assembly and maturation of new vascular structures. Here we discuss the therapeutic implications of matrix interactions of angiogenic factors, with a special emphasis on VEGF, as well as provide an overview of current approaches, based on protein and biomaterial engineering that mimic the regulatory functions of extracellular matrix to optimize the signaling microenvironment of vascular growth factors.

  9. Insulin-like growth factor I has independent effects on bone matrix formation and cell replication

    International Nuclear Information System (INIS)

    Hock, J.M.; Centrella, M.; Canalis, E.

    1988-01-01

    The effects of insulin-like growth factor-I (IGF-I) and insulin on bone matrix synthesis and bone cell replication were studied in cultured 21-day-old fetal rat calvariae. Histomorphometry techniques were developed to measure the incorporation of [2,3- 3 H]proline and [methyl- 3 H]thymidine into bone matrix and bone cell nuclei, respectively, using autoradiographs of sagittal sections of calvariae cultured with IGF-I, insulin, or vehicle for up to 96 h. To confirm an effect on bone formation, IGF-I was also studied for its effects on [ 3 H]proline incorporation into collagenase-digestible protein (CDP) and noncollagen protein and on [ 3 H]thymidine incorporation into acid-precipitable material (DNA). IGF-I at 10(-9)-10(-7) M significantly increased the rate of bone matrix apposition and CDP after 24 h by 45-50% and increased cell labeling by 8-fold in the osteoprogenitor cell zone, by 4-fold in the osteoblast cell zone, and by 2-fold in the periosteal fibroblast zone. Insulin at 10(-9)-10(-6) M also increased matrix apposition rate and CDP by 40-50%, but increased cell labeling by 2-fold only at a concentration of 10(-7) M or higher and then only in the osteoprogenitor cell zone. When hydroxyurea was added to IGF-I-treated bones, the effects of IGF-I on DNA synthesis were abolished, but the increase in bone matrix apposition induced by IGF-I was only partly diminished. In conclusion, IGF-I stimulates matrix synthesis in calvariae, an effect that is partly, although not completely, dependent on its stimulatory effect on DNA synthesis

  10. Role of Matrix Metalloproteinase-2, Matrix Metalloproteinase-9, and Vascular Endothelial Growth Factor in the Development of Chronic Subdural Hematoma

    Science.gov (United States)

    Hua, Cong; Feng, Yan; Yuan, Hongyan; Song, Hongmei

    2016-01-01

    Abstract Chronic subdural hematoma (CSDH) is an inflammatory and angiogenic disease. Vascular endothelial growth factor (VEGF) has an important effect on the pathological progression of CSDH. The matrix metalloproteinases (MMPs) and VEGF also play a significant role in pathological angiogenesis. Our research was to investigate the level of MMPs and VEGF in serum and hematoma fluid. Magnetic Resonance Imaging (MRI) shows the characteristics of different stages of CSDH. We also analyzed the relationship between the level of VEGF in subdural hematoma fluid and the appearances of the patients' MRI. We performed a study comparing serum and hematoma fluid in 37 consecutive patients with primary CSDHs using enzyme-linked immunosorbent assay (ELISA). MMP-2 and MMP-9 activity was assayed by the gelatin zymography method. The patients were divided into five groups according to the appearance of the hematomas on MRI: group 1 (T1-weighted low, T2-weighted low, n=4), group 2 (T1-weighted high, T2-weighted low, n=11), group 3 (T1-weighted mixed, T2-weighted mixed, n=9), group 4 (T1-weighted high, T2-weighted high, n=5), and group 5 (T1-weighted low, T2-weighted high, n=8). Neurological status was assessed by Markwalder score on admission and at follow-up. The mean age, sex, and Markwalder score were not significantly different among groups. The mean concentration of VEGF, MMP-2, and MMP-9 were significantly higher in hematoma fluid than in serum (phematoma fluid (phematoma fluid (phematoma fluid, suggesting that the MMPs/VEGF system may be involved in the angiogenesis of CSDH. We also demonstrate a significant correlation between the concentrations of VEGF and MRI appearance. This finding supports the hypothesis that high VEGF concentration in the hematoma fluid is of major pathophysiological importance in the generation and steady increase of the hematoma volume, as well as the determination of MRI appearance. PMID:25646653

  11. Dynamic SPECT reconstruction from few projections: a sparsity enforced matrix factorization approach

    Science.gov (United States)

    Ding, Qiaoqiao; Zan, Yunlong; Huang, Qiu; Zhang, Xiaoqun

    2015-02-01

    The reconstruction of dynamic images from few projection data is a challenging problem, especially when noise is present and when the dynamic images are vary fast. In this paper, we propose a variational model, sparsity enforced matrix factorization (SEMF), based on low rank matrix factorization of unknown images and enforced sparsity constraints for representing both coefficients and bases. The proposed model is solved via an alternating iterative scheme for which each subproblem is convex and involves the efficient alternating direction method of multipliers (ADMM). The convergence of the overall alternating scheme for the nonconvex problem relies upon the Kurdyka-Łojasiewicz property, recently studied by Attouch et al (2010 Math. Oper. Res. 35 438) and Attouch et al (2013 Math. Program. 137 91). Finally our proof-of-concept simulation on 2D dynamic images shows the advantage of the proposed method compared to conventional methods.

  12. Alternating optimization method based on nonnegative matrix factorizations for deep neural networks

    OpenAIRE

    Sakurai, Tetsuya; Imakura, Akira; Inoue, Yuto; Futamura, Yasunori

    2016-01-01

    The backpropagation algorithm for calculating gradients has been widely used in computation of weights for deep neural networks (DNNs). This method requires derivatives of objective functions and has some difficulties finding appropriate parameters such as learning rate. In this paper, we propose a novel approach for computing weight matrices of fully-connected DNNs by using two types of semi-nonnegative matrix factorizations (semi-NMFs). In this method, optimization processes are performed b...

  13. Factors that impact the stability of vitamin C at intermediate temperatures in a food matrix

    OpenAIRE

    Herbig, Anna-Lena

    2017-01-01

    The study comprises a systematic and quantitative evaluation of potential intrinsic and extrinsic factors that impact vitamin C degradation in a real food matrix. The supernatant of centrifuged apple purée was fortified in vitamin C, and degradation was followed without stirring. Model discrimination indicated better fit for the zero order model than the first order model which was hence chosen for determination of rate constants. pH influenced strongly vitamin C degradation in citrate-phosph...

  14. Augmenting matrix factorization technique with the combination of tags and genres

    Science.gov (United States)

    Ma, Tinghuai; Suo, Xiafei; Zhou, Jinjuan; Tang, Meili; Guan, Donghai; Tian, Yuan; Al-Dhelaan, Abdullah; Al-Rodhaan, Mznah

    2016-11-01

    Recommender systems play an important role in our daily life and are becoming popular tools for users to find what they are really interested in. Matrix factorization methods, which are popular recommendation methods, have gained high attention these years. With the rapid growth of the Internet, lots of information has been created, like social network information, tags and so on. Along with these, a few matrix factorization approaches have been proposed which incorporate the personalized information of users or items. However, except for ratings, most of the matrix factorization models have utilized only one kind of information to understand users' interests. Considering the sparsity of information, in this paper, we try to investigate the combination of different information, like tags and genres, to reveal users' interests accurately. With regard to the generalization of genres, a constraint is added when genres are utilized to find users' similar ;soulmates;. In addition, item regularizer is also considered based on latent semantic indexing (LSI) method with the item tags. Our experiments are conducted on two real datasets: Movielens dataset and Douban dataset. The experimental results demonstrate that the combination of tags and genres is really helpful to reveal users' interests.

  15. Non-negative matrix factorization by maximizing correntropy for cancer clustering

    KAUST Repository

    Wang, Jim Jing-Yan; Wang, Xiaolei; Gao, Xin

    2013-01-01

    Background: Non-negative matrix factorization (NMF) has been shown to be a powerful tool for clustering gene expression data, which are widely used to classify cancers. NMF aims to find two non-negative matrices whose product closely approximates the original matrix. Traditional NMF methods minimize either the l2 norm or the Kullback-Leibler distance between the product of the two matrices and the original matrix. Correntropy was recently shown to be an effective similarity measurement due to its stability to outliers or noise.Results: We propose a maximum correntropy criterion (MCC)-based NMF method (NMF-MCC) for gene expression data-based cancer clustering. Instead of minimizing the l2 norm or the Kullback-Leibler distance, NMF-MCC maximizes the correntropy between the product of the two matrices and the original matrix. The optimization problem can be solved by an expectation conditional maximization algorithm.Conclusions: Extensive experiments on six cancer benchmark sets demonstrate that the proposed method is significantly more accurate than the state-of-the-art methods in cancer clustering. 2013 Wang et al.; licensee BioMed Central Ltd.

  16. Non-negative matrix factorization by maximizing correntropy for cancer clustering

    KAUST Repository

    Wang, Jim Jing-Yan

    2013-03-24

    Background: Non-negative matrix factorization (NMF) has been shown to be a powerful tool for clustering gene expression data, which are widely used to classify cancers. NMF aims to find two non-negative matrices whose product closely approximates the original matrix. Traditional NMF methods minimize either the l2 norm or the Kullback-Leibler distance between the product of the two matrices and the original matrix. Correntropy was recently shown to be an effective similarity measurement due to its stability to outliers or noise.Results: We propose a maximum correntropy criterion (MCC)-based NMF method (NMF-MCC) for gene expression data-based cancer clustering. Instead of minimizing the l2 norm or the Kullback-Leibler distance, NMF-MCC maximizes the correntropy between the product of the two matrices and the original matrix. The optimization problem can be solved by an expectation conditional maximization algorithm.Conclusions: Extensive experiments on six cancer benchmark sets demonstrate that the proposed method is significantly more accurate than the state-of-the-art methods in cancer clustering. 2013 Wang et al.; licensee BioMed Central Ltd.

  17. Minimally invasive esthetic ridge preservation with growth-factor enhanced bone matrix.

    Science.gov (United States)

    Nevins, Marc L; Said, Sherif

    2017-12-28

    Extraction socket preservation procedures are critical to successful esthetic implant therapy. Conventional surgical approaches are technique sensitive and often result in alteration of the soft tissue architecture, which then requires additional corrective surgical procedures. This case series report presents the ability of flapless surgical techniques combined with a growth factor-enhanced bone matrix to provide esthetic ridge preservation at the time of extraction for compromised sockets. When considering esthetic dental implant therapy, preservation, or further enhancement of the available tissue support at the time of tooth extraction may provide an improved esthetic outcome with reduced postoperative sequelae and decreased treatment duration. Advances in minimally invasive surgical techniques combined with recombinant growth factor technology offer an alternative for bone reconstruction while maintaining the gingival architecture for enhanced esthetic outcome. The combination of freeze-dried bone allograft (FDBA) and rhPDGF-BB (platelet-derived growth factor-BB) provides a growth-factor enhanced matrix to induce bone and soft tissue healing. The use of a growth-factor enhanced matrix is an option for minimally invasive ridge preservation procedures for sites with advanced bone loss. Further studies including randomized clinical trials are needed to better understand the extent and limits of these procedures. The use of minimally invasive techniques with growth factors for esthetic ridge preservation reduces patient morbidity associated with more invasive approaches and increases the predictability for enhanced patient outcomes. By reducing the need for autogenous bone grafts the use of this technology is favorable for patient acceptance and ease of treatment process for esthetic dental implant therapy. © 2017 Wiley Periodicals, Inc.

  18. Quantitative evaluation of the matrix effect in bioanalytical methods based on LC-MS: A comparison of two approaches.

    Science.gov (United States)

    Rudzki, Piotr J; Gniazdowska, Elżbieta; Buś-Kwaśnik, Katarzyna

    2018-06-05

    Liquid chromatography coupled to mass spectrometry (LC-MS) is a powerful tool for studying pharmacokinetics and toxicokinetics. Reliable bioanalysis requires the characterization of the matrix effect, i.e. influence of the endogenous or exogenous compounds on the analyte signal intensity. We have compared two methods for the quantitation of matrix effect. The CVs(%) of internal standard normalized matrix factors recommended by the European Medicines Agency were evaluated against internal standard normalized relative matrix effects derived from Matuszewski et al. (2003). Both methods use post-extraction spiked samples, but matrix factors require also neat solutions. We have tested both approaches using analytes of diverse chemical structures. The study did not reveal relevant differences in the results obtained with both calculation methods. After normalization with the internal standard, the CV(%) of the matrix factor was on average 0.5% higher than the corresponding relative matrix effect. The method adopted by the European Medicines Agency seems to be slightly more conservative in the analyzed datasets. Nine analytes of different structures enabled a general overview of the problem, still, further studies are encouraged to confirm our observations. Copyright © 2018 Elsevier B.V. All rights reserved.

  19. A regularized matrix factorization approach to induce structured sparse-low-rank solutions in the EEG inverse problem

    DEFF Research Database (Denmark)

    Montoya-Martinez, Jair; Artes-Rodriguez, Antonio; Pontil, Massimiliano

    2014-01-01

    We consider the estimation of the Brain Electrical Sources (BES) matrix from noisy electroencephalographic (EEG) measurements, commonly named as the EEG inverse problem. We propose a new method to induce neurophysiological meaningful solutions, which takes into account the smoothness, structured...... sparsity, and low rank of the BES matrix. The method is based on the factorization of the BES matrix as a product of a sparse coding matrix and a dense latent source matrix. The structured sparse-low-rank structure is enforced by minimizing a regularized functional that includes the ℓ21-norm of the coding...... matrix and the squared Frobenius norm of the latent source matrix. We develop an alternating optimization algorithm to solve the resulting nonsmooth-nonconvex minimization problem. We analyze the convergence of the optimization procedure, and we compare, under different synthetic scenarios...

  20. Fibroblast growth factor receptor 4 regulates tumor invasion by coupling fibroblast growth factor signaling to extracellular matrix degradation

    DEFF Research Database (Denmark)

    Sugiyama, Nami; Varjosalo, Markku; Meller, Pipsa

    2010-01-01

    /stroma border and tumor invasion front. The strongest overall coexpression was found in prostate carcinoma. Studies with cultured prostate carcinoma cell lines showed that the FGFR4-R388 variant, which has previously been associated with poor cancer prognosis, increased MT1-MMP-dependent collagen invasion......Aberrant expression and polymorphism of fibroblast growth factor receptor 4 (FGFR4) has been linked to tumor progression and anticancer drug resistance. We describe here a novel mechanism of tumor progression by matrix degradation involving epithelial-to-mesenchymal transition in response...... to membrane-type 1 matrix metalloproteinase (MT1-MMP, MMP-14) induction at the edge of tumors expressing the FGFR4-R388 risk variant. Both FGFR4 and MT1-MMP were upregulated in tissue biopsies from several human cancer types including breast adenocarcinomas, where they were partially coexpressed at the tumor...

  1. Link predication based on matrix factorization by fusion of multi class organizations of the network.

    Science.gov (United States)

    Jiao, Pengfei; Cai, Fei; Feng, Yiding; Wang, Wenjun

    2017-08-21

    Link predication aims at forecasting the latent or unobserved edges in the complex networks and has a wide range of applications in reality. Almost existing methods and models only take advantage of one class organization of the networks, which always lose important information hidden in other organizations of the network. In this paper, we propose a link predication framework which makes the best of the structure of networks in different level of organizations based on nonnegative matrix factorization, which is called NMF 3 here. We first map the observed network into another space by kernel functions, which could get the different order organizations. Then we combine the adjacency matrix of the network with one of other organizations, which makes us obtain the objective function of our framework for link predication based on the nonnegative matrix factorization. Third, we derive an iterative algorithm to optimize the objective function, which converges to a local optimum, and we propose a fast optimization strategy for large networks. Lastly, we test the proposed framework based on two kernel functions on a series of real world networks under different sizes of training set, and the experimental results show the feasibility, effectiveness, and competitiveness of the proposed framework.

  2. Matrix diffusion studies by electrical conductivity methods. Comparison between laboratory and in-situ measurements

    International Nuclear Information System (INIS)

    Ohlsson, Y.; Neretnieks, I.

    1998-01-01

    Traditional laboratory diffusion experiments in rock material are time consuming, and quite small samples are generally used. Electrical conductivity measurements, on the other hand, provide a fast means for examining transport properties in rock and allow measurements on larger samples as well. Laboratory measurements using electrical conductivity give results that compare well to those from traditional diffusion experiments. The measurement of the electrical resistivity in the rock surrounding a borehole is a standard method for the detection of water conducting fractures. If these data could be correlated to matrix diffusion properties, in-situ diffusion data from large areas could be obtained. This would be valuable because it would make it possible to obtain data very early in future investigations of potentially suitable sites for a repository. This study compares laboratory electrical conductivity measurements with in-situ resistivity measurements from a borehole at Aespoe. The laboratory samples consist mainly of Aespoe diorite and fine-grained granite and the rock surrounding the borehole of Aespoe diorite, Smaaland granite and fine-grained granite. The comparison shows good agreement between laboratory measurements and in-situ data

  3. Regulation of proliferation of embryonic heart mesenchyme: Role of transforming growth factor-beta 1 and the interstitial matrix

    International Nuclear Information System (INIS)

    Choy, M.; Armstrong, M.T.; Armstrong, P.B.

    1990-01-01

    Proliferation of atrioventricular cushion mesenchyme of the embryonic avian heart maintained in three-dimensional aggregate culture is stimulated by interaction with the interstitial matrix. Chicken serum or transforming growth factor-beta 1, which stimulates proliferation, induces matrix deposition in regions of the aggregate showing high labeling indices with tritiated thymidine. Dispersed heart mesenchyme interstitial matrix introduced into serum-free culture is incorporated into the aggregate and stimulates cellular proliferation similar to serum or transforming growth factor-beta 1. Proliferation is reversibly inhibited by the peptide Gly-Arg-Gly-Asp-Ser-Pro. It is suggested that transforming growth factor-beta 1 stimulates the production of interstitial matrix and that a sufficient stimulus for proliferation in this system is the presence of the matrix, which acts as the adhesive support for cellular anchorage

  4. Human aqueous humor levels of transforming growth factor-β2: Association with matrix metalloproteinases/tissue inhibitors of matrix metalloproteinases

    OpenAIRE

    Jia, Yan; Yue, Yu; Hu, Dan-Ning; Chen, Ji-Li; Zhou, Ji-Bo

    2017-01-01

    The present study aims to investigate the association of transforming growth factor-β2 (TGF-β2) and matrix metalloproteinases (MMPs), MMP-2 and MMP-3, and tissue inhibitors of matrix metalloproteinases (TIMPs), TIMP-1, TIMP-2 and TIMP-3 in the aqueous humor of patients with high myopia or cataracts. The levels of TGF-β2 and MMPs/TIMPs were measured with the Luminex xMAP Technology using commercially available Milliplex xMAP kits. The association between TGF-β2 and MMPs/TIMPs levels was analyz...

  5. Predicting protein-protein interactions from multimodal biological data sources via nonnegative matrix tri-factorization.

    Science.gov (United States)

    Wang, Hua; Huang, Heng; Ding, Chris; Nie, Feiping

    2013-04-01

    Protein interactions are central to all the biological processes and structural scaffolds in living organisms, because they orchestrate a number of cellular processes such as metabolic pathways and immunological recognition. Several high-throughput methods, for example, yeast two-hybrid system and mass spectrometry method, can help determine protein interactions, which, however, suffer from high false-positive rates. Moreover, many protein interactions predicted by one method are not supported by another. Therefore, computational methods are necessary and crucial to complete the interactome expeditiously. In this work, we formulate the problem of predicting protein interactions from a new mathematical perspective--sparse matrix completion, and propose a novel nonnegative matrix factorization (NMF)-based matrix completion approach to predict new protein interactions from existing protein interaction networks. Through using manifold regularization, we further develop our method to integrate different biological data sources, such as protein sequences, gene expressions, protein structure information, etc. Extensive experimental results on four species, Saccharomyces cerevisiae, Drosophila melanogaster, Homo sapiens, and Caenorhabditis elegans, have shown that our new methods outperform related state-of-the-art protein interaction prediction methods.

  6. Sparse modeling of EELS and EDX spectral imaging data by nonnegative matrix factorization

    Energy Technology Data Exchange (ETDEWEB)

    Shiga, Motoki, E-mail: shiga_m@gifu-u.ac.jp [Department of Electrical, Electronic and Computer Engineering, Gifu University, 1-1, Yanagido, Gifu 501-1193 (Japan); Tatsumi, Kazuyoshi; Muto, Shunsuke [Advanced Measurement Technology Center, Institute of Materials and Systems for Sustainability, Nagoya University, Chikusa-ku, Nagoya 464-8603 (Japan); Tsuda, Koji [Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa 277-8561 (Japan); Center for Materials Research by Information Integration, National Institute for Materials Science, 1-2-1 Sengen, Tsukuba 305-0047 (Japan); Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi Koto-ku, Tokyo 135-0064 (Japan); Yamamoto, Yuta [High-Voltage Electron Microscope Laboratory, Institute of Materials and Systems for Sustainability, Nagoya University, Chikusa-ku, Nagoya 464-8603 (Japan); Mori, Toshiyuki [Environment and Energy Materials Division, National Institute for Materials Science, 1-1 Namiki, Tsukuba 305-0044 (Japan); Tanji, Takayoshi [Division of Materials Research, Institute of Materials and Systems for Sustainability, Nagoya University, Chikusa-ku, Nagoya 464-8603 (Japan)

    2016-11-15

    Advances in scanning transmission electron microscopy (STEM) techniques have enabled us to automatically obtain electron energy-loss (EELS)/energy-dispersive X-ray (EDX) spectral datasets from a specified region of interest (ROI) at an arbitrary step width, called spectral imaging (SI). Instead of manually identifying the potential constituent chemical components from the ROI and determining the chemical state of each spectral component from the SI data stored in a huge three-dimensional matrix, it is more effective and efficient to use a statistical approach for the automatic resolution and extraction of the underlying chemical components. Among many different statistical approaches, we adopt a non-negative matrix factorization (NMF) technique, mainly because of the natural assumption of non-negative values in the spectra and cardinalities of chemical components, which are always positive in actual data. This paper proposes a new NMF model with two penalty terms: (i) an automatic relevance determination (ARD) prior, which optimizes the number of components, and (ii) a soft orthogonal constraint, which clearly resolves each spectrum component. For the factorization, we further propose a fast optimization algorithm based on hierarchical alternating least-squares. Numerical experiments using both phantom and real STEM-EDX/EELS SI datasets demonstrate that the ARD prior successfully identifies the correct number of physically meaningful components. The soft orthogonal constraint is also shown to be effective, particularly for STEM-EELS SI data, where neither the spatial nor spectral entries in the matrices are sparse. - Highlights: • Automatic resolution of chemical components from spectral imaging is considered. • We propose a new non-negative matrix factorization with two new penalties. • The first penalty is sparseness to choose the number of components from data. • Experimental results with real data demonstrate effectiveness of our method.

  7. ImWalkMF: Joint matrix factorization and implicit walk integrative learning for recommendation

    KAUST Repository

    Zhang, Chuxu

    2018-01-15

    Data sparsity and cold-start problems are prevalent in recommender systems. To address such problems, both the observable explicit social information (e.g., user-user trust connections) and the inferable implicit correlations (e.g., implicit neighbors computed by similarity measurement) have been introduced to complement user-item ratings data for improving the performances of traditional model-based recommendation algorithms such as matrix factorization. Although effective, (1) the utilization of the explicit user-user social relationships suffers from the weakness of unavailability in real systems such as Netflix or the issue of sparse observable content like 0.03% trust density in Epinions, thus there is no or little explicit social information that can be employed to improve baseline model in real applications; (2) the current similarity measurement approaches focus on inferring implicit correlations between a user (item) and their direct neighbors or top-k similar neighbors based on user-item ratings bipartite network, so that they fail to comprehensively unfold the indirect potential relationships among users and items. To solve these issues regarding both explicit/implicit social recommendation algorithms, we design a joint model of matrix factorization and implicit walk integrative learning, i.e., ImWalkMF, which only uses explicit ratings information yet models both direct rating feedbacks and multiple direct/indirect implicit correlations among users and items from a random walk perspective. We further propose a combined strategy for training two independent components in the proposed model based on sampling. The experimental results on two real-world sparse datasets demonstrate that ImWalkMF outperforms the traditional regularized/probabilistic matrix factorization models as well as other competitive baselines that utilize explicit/implicit social information.

  8. A Recursive Formulation of Cholesky Factorization of a Matrix in Packed Storage Format

    DEFF Research Database (Denmark)

    Andersen, Bjarne Stig; Gustavson, Fred; Wasniewski, Jerzy

    2001-01-01

    . Algorithm RPC is based on level-3 BLAS and requires variants of algorithms {\\$\\backslash\\$bf TRSM} and {\\$\\backslash\\$bf SYRK} that work on RPF. We call these {\\$\\backslash\\$bf RP\\$\\backslash\\$\\_TRSM} and {\\$\\backslash\\$bf RP\\$\\backslash\\$\\_SYRK} and find that they do most of their work by calling...... matrix. Second, RPC gives a level-3 implementation of Cholesky factorization whereas standard packed implementations are only level 2. Hence, the performance of our RPC implementation is decidedly superior. Third, unlike fixed block size algorithms, RPC requires no block size tuning parameter. We present...

  9. On the Equivalence of Nonnegative Matrix Factorization and K-means- Spectral Clustering

    Energy Technology Data Exchange (ETDEWEB)

    Ding, Chris; He, Xiaofeng; Simon, Horst D.; Jin, Rong

    2005-12-04

    We provide a systematic analysis of nonnegative matrix factorization (NMF) relating to data clustering. We generalize the usual X = FG{sup T} decomposition to the symmetric W = HH{sup T} and W = HSH{sup T} decompositions. We show that (1) W = HH{sup T} is equivalent to Kernel K-means clustering and the Laplacian-based spectral clustering. (2) X = FG{sup T} is equivalent to simultaneous clustering of rows and columns of a bipartite graph. We emphasizes the importance of orthogonality in NMF and soft clustering nature of NMF. These results are verified with experiments on face images and newsgroups.

  10. Source apportionment of atmospheric bulk deposition in the Belgrade urban area using Positive Matrix factorization

    Science.gov (United States)

    Tasić, M.; Mijić, Z.; Rajšić, S.; Stojić, A.; Radenković, M.; Joksić, J.

    2009-04-01

    The primary objective of the present study was to assess anthropogenic impacts of heavy metals to the environment by determination of total atmospheric deposition of heavy metals. Atmospheric depositions (wet + dry) were collected monthly, from June 2002 to December 2006, at three urban locations in Belgrade, using bulk deposition samplers. Concentrations of Fe, Al, Pb, Zn, Cu, Ni, Mn, Cr, V, As and Cd were analyzed using atomic absorption spectrometry. Based upon these results, the study attempted to examine elemental associations in atmospheric deposition and to elucidate the potential sources of heavy metal contaminants in the region by the use of multivariate receptor model Positive Matrix Factorization (PMF).

  11. Source apportionment of atmospheric bulk deposition in the Belgrade urban area using Positive Matrix factorization

    International Nuclear Information System (INIS)

    Tasic, M; Mijic, Z; Rajsic, S; Stojic, A; Radenkovic, M; Joksic, J

    2009-01-01

    The primary objective of the present study was to assess anthropogenic impacts of heavy metals to the environment by determination of total atmospheric deposition of heavy metals. Atmospheric depositions (wet + dry) were collected monthly, from June 2002 to December 2006, at three urban locations in Belgrade, using bulk deposition samplers. Concentrations of Fe, Al, Pb, Zn, Cu, Ni, Mn, Cr, V, As and Cd were analyzed using atomic absorption spectrometry. Based upon these results, the study attempted to examine elemental associations in atmospheric deposition and to elucidate the potential sources of heavy metal contaminants in the region by the use of multivariate receptor model Positive Matrix Factorization (PMF).

  12. Performance and stochastic stability of the adaptive fading extended Kalman filter with the matrix forgetting factor

    Directory of Open Access Journals (Sweden)

    Biçer Cenker

    2016-01-01

    Full Text Available In this paper, the stability of the adaptive fading extended Kalman filter with the matrix forgetting factor when applied to the state estimation problem with noise terms in the non–linear discrete–time stochastic systems has been analysed. The analysis is conducted in a similar manner to the standard extended Kalman filter’s stability analysis based on stochastic framework. The theoretical results show that under certain conditions on the initial estimation error and the noise terms, the estimation error remains bounded and the state estimation is stable.

  13. Absence of particle production and factorization of the s-matrix in 1 + 1 dimensional models

    International Nuclear Information System (INIS)

    Parke, S.

    1980-01-01

    In massive, 1 + 1 dimensional, local, quantum field theories the existence of two conserved charges is shown to be a sufficient condition for the absence of particle production and factorization of the s-matrix. These charges must commute and be integrals of local current densities. Their transformation properties under the Lorentz group must be different and also different from the transformation properties under the Lorentz group must be different and also different from the transformation properties pf a vector or a scalar. Also, they must not annihilate any single-particle momentum eigenstate. (orig.)

  14. Comparison of Damage Models for Predicting the Non-Linear Response of Laminates Under Matrix Dominated Loading Conditions

    Science.gov (United States)

    Schuecker, Clara; Davila, Carlos G.; Rose, Cheryl A.

    2010-01-01

    Five models for matrix damage in fiber reinforced laminates are evaluated for matrix-dominated loading conditions under plane stress and are compared both qualitatively and quantitatively. The emphasis of this study is on a comparison of the response of embedded plies subjected to a homogeneous stress state. Three of the models are specifically designed for modeling the non-linear response due to distributed matrix cracking under homogeneous loading, and also account for non-linear (shear) behavior prior to the onset of cracking. The remaining two models are localized damage models intended for predicting local failure at stress concentrations. The modeling approaches of distributed vs. localized cracking as well as the different formulations of damage initiation and damage progression are compared and discussed.

  15. Nonselective matrix metalloproteinase but not tumor necrosis factor-a inhibition effectively preserves the early critical colon anastomotic integrity

    DEFF Research Database (Denmark)

    Ågren, Magnus S.; Andersen, Thomas L.; Andersen, Line

    2011-01-01

    Increased matrix metalloproteinase (MMP) activity has been implicated in the pathogenesis of colorectal anastomotic leakage. Tumor necrosis factor-a (TNF-a) induces MMPs and may influence anastomosis repair....

  16. Comparison of Transcription Factor Binding Site Models

    KAUST Repository

    Bhuyan, Sharifulislam

    2012-05-01

    Modeling of transcription factor binding sites (TFBSs) and TFBS prediction on genomic sequences are important steps to elucidate transcription regulatory mechanism. Dependency of transcription regulation on a great number of factors such as chemical specificity, molecular structure, genomic and epigenetic characteristics, long distance interaction, makes this a challenging problem. Different experimental procedures generate evidence that DNA-binding domains of transcription factors show considerable DNA sequence specificity. Probabilistic modeling of TFBSs has been moderately successful in identifying patterns from a family of sequences. In this study, we compare performances of different probabilistic models and try to estimate their efficacy over experimental TFBSs data. We build a pipeline to calculate sensitivity and specificity from aligned TFBS sequences for several probabilistic models, such as Markov chains, hidden Markov models, Bayesian networks. Our work, containing relevant statistics and evaluation for the models, can help researchers to choose the most appropriate model for the problem at hand.

  17. A network and visual quality aware N-screen content recommender system using joint matrix factorization.

    Science.gov (United States)

    Ullah, Farman; Sarwar, Ghulam; Lee, Sungchang

    2014-01-01

    We propose a network and visual quality aware N-Screen content recommender system. N-Screen provides more ways than ever before to access multimedia content through multiple devices and heterogeneous access networks. The heterogeneity of devices and access networks present new questions of QoS (quality of service) in the realm of user experience with content. We propose, a recommender system that ensures a better visual quality on user's N-screen devices and the efficient utilization of available access network bandwidth with user preferences. The proposed system estimates the available bandwidth and visual quality on users N-Screen devices and integrates it with users preferences and contents genre information to personalize his N-Screen content. The objective is to recommend content that the user's N-Screen device and access network are capable of displaying and streaming with the user preferences that have not been supported in existing systems. Furthermore, we suggest a joint matrix factorization approach to jointly factorize the users rating matrix with the users N-Screen device similarity and program genres similarity. Finally, the experimental results show that we also enhance the prediction and recommendation accuracy, sparsity, and cold start issues.

  18. Neighborhood Regularized Logistic Matrix Factorization for Drug-Target Interaction Prediction.

    Science.gov (United States)

    Liu, Yong; Wu, Min; Miao, Chunyan; Zhao, Peilin; Li, Xiao-Li

    2016-02-01

    In pharmaceutical sciences, a crucial step of the drug discovery process is the identification of drug-target interactions. However, only a small portion of the drug-target interactions have been experimentally validated, as the experimental validation is laborious and costly. To improve the drug discovery efficiency, there is a great need for the development of accurate computational approaches that can predict potential drug-target interactions to direct the experimental verification. In this paper, we propose a novel drug-target interaction prediction algorithm, namely neighborhood regularized logistic matrix factorization (NRLMF). Specifically, the proposed NRLMF method focuses on modeling the probability that a drug would interact with a target by logistic matrix factorization, where the properties of drugs and targets are represented by drug-specific and target-specific latent vectors, respectively. Moreover, NRLMF assigns higher importance levels to positive observations (i.e., the observed interacting drug-target pairs) than negative observations (i.e., the unknown pairs). Because the positive observations are already experimentally verified, they are usually more trustworthy. Furthermore, the local structure of the drug-target interaction data has also been exploited via neighborhood regularization to achieve better prediction accuracy. We conducted extensive experiments over four benchmark datasets, and NRLMF demonstrated its effectiveness compared with five state-of-the-art approaches.

  19. A Network and Visual Quality Aware N-Screen Content Recommender System Using Joint Matrix Factorization

    Directory of Open Access Journals (Sweden)

    Farman Ullah

    2014-01-01

    Full Text Available We propose a network and visual quality aware N-Screen content recommender system. N-Screen provides more ways than ever before to access multimedia content through multiple devices and heterogeneous access networks. The heterogeneity of devices and access networks present new questions of QoS (quality of service in the realm of user experience with content. We propose, a recommender system that ensures a better visual quality on user’s N-screen devices and the efficient utilization of available access network bandwidth with user preferences. The proposed system estimates the available bandwidth and visual quality on users N-Screen devices and integrates it with users preferences and contents genre information to personalize his N-Screen content. The objective is to recommend content that the user’s N-Screen device and access network are capable of displaying and streaming with the user preferences that have not been supported in existing systems. Furthermore, we suggest a joint matrix factorization approach to jointly factorize the users rating matrix with the users N-Screen device similarity and program genres similarity. Finally, the experimental results show that we also enhance the prediction and recommendation accuracy, sparsity, and cold start issues.

  20. An Extended-Tag-Induced Matrix Factorization Technique for Recommender Systems

    Directory of Open Access Journals (Sweden)

    Huirui Han

    2018-06-01

    Full Text Available Social tag information has been used by recommender systems to handle the problem of data sparsity. Recently, the relationships between users/items and tags are considered by most tag-induced recommendation methods. However, sparse tag information is challenging to most existing methods. In this paper, we propose an Extended-Tag-Induced Matrix Factorization technique for recommender systems, which exploits correlations among tags derived by co-occurrence of tags to improve the performance of recommender systems, even in the case of sparse tag information. The proposed method integrates coupled similarity between tags, which is calculated by the co-occurrences of tags in the same items, to extend each item’s tags. Finally, item similarity based on extended tags is utilized as an item relationship regularization term to constrain the process of matrix factorization. MovieLens dataset and Book-Crossing dataset are adopted to evaluate the performance of the proposed algorithm. The results of experiments show that the proposed method can alleviate the impact of tag sparsity and improve the performance of recommender systems.

  1. Impact of the Choice of Normalization Method on Molecular Cancer Class Discovery Using Nonnegative Matrix Factorization.

    Science.gov (United States)

    Yang, Haixuan; Seoighe, Cathal

    2016-01-01

    Nonnegative Matrix Factorization (NMF) has proved to be an effective method for unsupervised clustering analysis of gene expression data. By the nonnegativity constraint, NMF provides a decomposition of the data matrix into two matrices that have been used for clustering analysis. However, the decomposition is not unique. This allows different clustering results to be obtained, resulting in different interpretations of the decomposition. To alleviate this problem, some existing methods directly enforce uniqueness to some extent by adding regularization terms in the NMF objective function. Alternatively, various normalization methods have been applied to the factor matrices; however, the effects of the choice of normalization have not been carefully investigated. Here we investigate the performance of NMF for the task of cancer class discovery, under a wide range of normalization choices. After extensive evaluations, we observe that the maximum norm showed the best performance, although the maximum norm has not previously been used for NMF. Matlab codes are freely available from: http://maths.nuigalway.ie/~haixuanyang/pNMF/pNMF.htm.

  2. Graph regularized nonnegative matrix factorization for temporal link prediction in dynamic networks

    Science.gov (United States)

    Ma, Xiaoke; Sun, Penggang; Wang, Yu

    2018-04-01

    Many networks derived from society and nature are temporal and incomplete. The temporal link prediction problem in networks is to predict links at time T + 1 based on a given temporal network from time 1 to T, which is essential to important applications. The current algorithms either predict the temporal links by collapsing the dynamic networks or collapsing features derived from each network, which are criticized for ignoring the connection among slices. to overcome the issue, we propose a novel graph regularized nonnegative matrix factorization algorithm (GrNMF) for the temporal link prediction problem without collapsing the dynamic networks. To obtain the feature for each network from 1 to t, GrNMF factorizes the matrix associated with networks by setting the rest networks as regularization, which provides a better way to characterize the topological information of temporal links. Then, the GrNMF algorithm collapses the feature matrices to predict temporal links. Compared with state-of-the-art methods, the proposed algorithm exhibits significantly improved accuracy by avoiding the collapse of temporal networks. Experimental results of a number of artificial and real temporal networks illustrate that the proposed method is not only more accurate but also more robust than state-of-the-art approaches.

  3. Identifying sources of atmospheric fine particles in Havana City using Positive Matrix Factorization technique

    International Nuclear Information System (INIS)

    Pinnera, I.; Perez, G.; Ramos, M.; Guibert, R.; Aldape, F.; Flores M, J.; Martinez, M.; Molina, E.; Fernandez, A.

    2011-01-01

    In previous study a set of samples of fine and coarse airborne particulate matter collected in a urban area of Havana City were analyzed by Particle-Induced X-ray Emission (PIXE) technique. The concentrations of 14 elements (S, Cl, K, Ca, Ti, V, Cr, Mn, Fe, Ni, Cu, Zn, Br and Pb) were consistently determined in both particle sizes. The analytical database provided by PIXE was statistically analyzed in order to determine the local pollution sources. The Positive Matrix Factorization (PMF) technique was applied to fine particle data in order to identify possible pollution sources. These sources were further verified by enrichment factor (EF) calculation. A general discussion about these results is presented in this work. (Author)

  4. Assessment of algorithms for inferring positional weight matrix motifs of transcription factor binding sites using protein binding microarray data.

    Directory of Open Access Journals (Sweden)

    Yaron Orenstein

    Full Text Available The new technology of protein binding microarrays (PBMs allows simultaneous measurement of the binding intensities of a transcription factor to tens of thousands of synthetic double-stranded DNA probes, covering all possible 10-mers. A key computational challenge is inferring the binding motif from these data. We present a systematic comparison of four methods developed specifically for reconstructing a binding site motif represented as a positional weight matrix from PBM data. The reconstructed motifs were evaluated in terms of three criteria: concordance with reference motifs from the literature and ability to predict in vivo and in vitro bindings. The evaluation encompassed over 200 transcription factors and some 300 assays. The results show a tradeoff between how the methods perform according to the different criteria, and a dichotomy of method types. Algorithms that construct motifs with low information content predict PBM probe ranking more faithfully, while methods that produce highly informative motifs match reference motifs better. Interestingly, in predicting high-affinity binding, all methods give far poorer results for in vivo assays compared to in vitro assays.

  5. Comparison of two matrix data structures for advanced CSM testbed applications

    Science.gov (United States)

    Regelbrugge, M. E.; Brogan, F. A.; Nour-Omid, B.; Rankin, C. C.; Wright, M. A.

    1989-01-01

    The first section describes data storage schemes presently used by the Computational Structural Mechanics (CSM) testbed sparse matrix facilities and similar skyline (profile) matrix facilities. The second section contains a discussion of certain features required for the implementation of particular advanced CSM algorithms, and how these features might be incorporated into the data storage schemes described previously. The third section presents recommendations, based on the discussions of the prior sections, for directing future CSM testbed development to provide necessary matrix facilities for advanced algorithm implementation and use. The objective is to lend insight into the matrix structures discussed and to help explain the process of evaluating alternative matrix data structures and utilities for subsequent use in the CSM testbed.

  6. Extracellular Matrix and Growth Factors Improve the Efficacy of Intramuscular Islet Transplantation.

    Directory of Open Access Journals (Sweden)

    Haruyuki Tsuchiya

    Full Text Available The efficacy of intramuscular islet transplantation is poor despite being technically simple, safe, and associated with reduced rates of severe complications. We evaluated the efficacy of combined treatment with extracellular matrix (ECM and growth factors in intramuscular islet transplantation.Male BALB/C mice were used for the in vitro and transplantation studies. The following three groups were evaluated: islets without treatment (islets-only group, islets embedded in ECM with growth factors (Matrigel group, and islets embedded in ECM without growth factors [growth factor-reduced (GFR Matrigel group]. The viability and insulin-releasing function of islets cultured for 96 h were significantly improved in Matrigel and GFR Matrigel groups compared with the islets-only group.Blood glucose and serum insulin levels immediately following transplantation were significantly improved in the Matrigel and GFR Matrigel groups and remained significantly improved in the Matrigel group at postoperative day (POD 28. On histological examination, significantly decreased numbers of TdT-mediated deoxyuridine triphosphate-biotin nick end labeling-positive islet cells and significantly increased numbers of Ki67-positive cells were observed in the Matrigel and GFR Matrigel groups at POD 3. Peri-islet revascularization was most prominent in the Matrigel group at POD 14.The efficacy of intramuscular islet transplantation was improved by combination treatment with ECM and growth factors through the inhibition of apoptosis, increased proliferation of islet cells, and promotion of revascularization.

  7. Extracellular Matrix and Growth Factors Improve the Efficacy of Intramuscular Islet Transplantation.

    Science.gov (United States)

    Tsuchiya, Haruyuki; Sakata, Naoaki; Yoshimatsu, Gumpei; Fukase, Masahiko; Aoki, Takeshi; Ishida, Masaharu; Katayose, Yu; Egawa, Shinichi; Unno, Michiaki

    2015-01-01

    The efficacy of intramuscular islet transplantation is poor despite being technically simple, safe, and associated with reduced rates of severe complications. We evaluated the efficacy of combined treatment with extracellular matrix (ECM) and growth factors in intramuscular islet transplantation. Male BALB/C mice were used for the in vitro and transplantation studies. The following three groups were evaluated: islets without treatment (islets-only group), islets embedded in ECM with growth factors (Matrigel group), and islets embedded in ECM without growth factors [growth factor-reduced (GFR) Matrigel group]. The viability and insulin-releasing function of islets cultured for 96 h were significantly improved in Matrigel and GFR Matrigel groups compared with the islets-only group. Blood glucose and serum insulin levels immediately following transplantation were significantly improved in the Matrigel and GFR Matrigel groups and remained significantly improved in the Matrigel group at postoperative day (POD) 28. On histological examination, significantly decreased numbers of TdT-mediated deoxyuridine triphosphate-biotin nick end labeling-positive islet cells and significantly increased numbers of Ki67-positive cells were observed in the Matrigel and GFR Matrigel groups at POD 3. Peri-islet revascularization was most prominent in the Matrigel group at POD 14. The efficacy of intramuscular islet transplantation was improved by combination treatment with ECM and growth factors through the inhibition of apoptosis, increased proliferation of islet cells, and promotion of revascularization.

  8. Interpretation of organic components from Positive Matrix Factorization of aerosol mass spectrometric data

    Directory of Open Access Journals (Sweden)

    I. M. Ulbrich

    2009-05-01

    Full Text Available The organic aerosol (OA dataset from an Aerodyne Aerosol Mass Spectrometer (Q-AMS collected at the Pittsburgh Air Quality Study (PAQS in September 2002 was analyzed with Positive Matrix Factorization (PMF. Three components – hydrocarbon-like organic aerosol OA (HOA, a highly-oxygenated OA (OOA-1 that correlates well with sulfate, and a less-oxygenated, semi-volatile OA (OOA-2 that correlates well with nitrate and chloride – are identified and interpreted as primary combustion emissions, aged SOA, and semivolatile, less aged SOA, respectively. The complexity of interpreting the PMF solutions of unit mass resolution (UMR AMS data is illustrated by a detailed analysis of the solutions as a function of number of components and rotational forcing. A public web-based database of AMS spectra has been created to aid this type of analysis. Realistic synthetic data is also used to characterize the behavior of PMF for choosing the best number of factors, and evaluating the rotations of non-unique solutions. The ambient and synthetic data indicate that the variation of the PMF quality of fit parameter (Q, a normalized chi-squared metric vs. number of factors in the solution is useful to identify the minimum number of factors, but more detailed analysis and interpretation are needed to choose the best number of factors. The maximum value of the rotational matrix is not useful for determining the best number of factors. In synthetic datasets, factors are "split" into two or more components when solving for more factors than were used in the input. Elements of the "splitting" behavior are observed in solutions of real datasets with several factors. Significant structure remains in the residual of the real dataset after physically-meaningful factors have been assigned and an unrealistic number of factors would be required to explain the remaining variance. This residual structure appears to be due to variability in the spectra of the components

  9. Evaluation of the validity of job exposure matrix for psychosocial factors at work.

    Directory of Open Access Journals (Sweden)

    Svetlana Solovieva

    Full Text Available To study the performance of a developed job exposure matrix (JEM for the assessment of psychosocial factors at work in terms of accuracy, possible misclassification bias and predictive ability to detect known associations with depression and low back pain (LBP.We utilized two large population surveys (the Health 2000 Study and the Finnish Work and Health Surveys, one to construct the JEM and another to test matrix performance. In the first study, information on job demands, job control, monotonous work and social support at work was collected via face-to-face interviews. Job strain was operationalized based on job demands and job control using quadrant approach. In the second study, the sensitivity and specificity were estimated applying a Bayesian approach. The magnitude of misclassification error was examined by calculating the biased odds ratios as a function of the sensitivity and specificity of the JEM and fixed true prevalence and odds ratios. Finally, we adjusted for misclassification error the observed associations between JEM measures and selected health outcomes.The matrix showed a good accuracy for job control and job strain, while its performance for other exposures was relatively low. Without correction for exposure misclassification, the JEM was able to detect the association between job strain and depression in men and between monotonous work and LBP in both genders.Our results suggest that JEM more accurately identifies occupations with low control and high strain than those with high demands or low social support. Overall, the present JEM is a useful source of job-level psychosocial exposures in epidemiological studies lacking individual-level exposure information. Furthermore, we showed the applicability of a Bayesian approach in the evaluation of the performance of the JEM in a situation where, in practice, no gold standard of exposure assessment exists.

  10. Evaluation of the validity of job exposure matrix for psychosocial factors at work.

    Science.gov (United States)

    Solovieva, Svetlana; Pensola, Tiina; Kausto, Johanna; Shiri, Rahman; Heliövaara, Markku; Burdorf, Alex; Husgafvel-Pursiainen, Kirsti; Viikari-Juntura, Eira

    2014-01-01

    To study the performance of a developed job exposure matrix (JEM) for the assessment of psychosocial factors at work in terms of accuracy, possible misclassification bias and predictive ability to detect known associations with depression and low back pain (LBP). We utilized two large population surveys (the Health 2000 Study and the Finnish Work and Health Surveys), one to construct the JEM and another to test matrix performance. In the first study, information on job demands, job control, monotonous work and social support at work was collected via face-to-face interviews. Job strain was operationalized based on job demands and job control using quadrant approach. In the second study, the sensitivity and specificity were estimated applying a Bayesian approach. The magnitude of misclassification error was examined by calculating the biased odds ratios as a function of the sensitivity and specificity of the JEM and fixed true prevalence and odds ratios. Finally, we adjusted for misclassification error the observed associations between JEM measures and selected health outcomes. The matrix showed a good accuracy for job control and job strain, while its performance for other exposures was relatively low. Without correction for exposure misclassification, the JEM was able to detect the association between job strain and depression in men and between monotonous work and LBP in both genders. Our results suggest that JEM more accurately identifies occupations with low control and high strain than those with high demands or low social support. Overall, the present JEM is a useful source of job-level psychosocial exposures in epidemiological studies lacking individual-level exposure information. Furthermore, we showed the applicability of a Bayesian approach in the evaluation of the performance of the JEM in a situation where, in practice, no gold standard of exposure assessment exists.

  11. Correlation Between Placental Matrix Metalloproteinase 9 and Tumor Necrosis Factor-α Protein Expression Throughout Gestation in Normal Human Pregnancy.

    Science.gov (United States)

    Basu, Jayasri; Agamasu, Enyonam; Bendek, Bolek; Salafia, Carolyn M; Mishra, Aruna; Lopez, Julia Vasquez; Kroes, Jessica; Dragich, Sharon Claire; Thakur, Ashley; Mikhail, Magdy

    2018-04-01

    Matrix metalloproteinases (MMPs), specifically MMP-9 plays a role in human placentation. The enzyme confers an invasive ability to cytotrophoblasts and degrades the endometrial matrix as the cells infiltrate the decidua to keep up with placental growth. Since tumor necrosis factor-α (TNF-α) can induce the synthesis of MMP-9, we investigated the patterns of changes in and correlation between placental villous MMP-9 and TNF-α expressions throughout normal human gestation. Placentas were obtained from 179 normal pregnant women who underwent elective abortion or term delivery. Chorionic villi isolated from placental samples were grouped as first, second, and third trimester (7 0/7 -13 0/7 , 13 1/7 -23 6/7 , and 37 0/7 -42 4/7 weeks, respectively). Chorionic villous TNF-α and MMP-9 proteins were assayed using enzyme immunoassay kits. There were significant differences in MMP-9 and TNF-α protein expressions among the trimester groups ( P = .001). The MMP-9 protein increased progressively with an increase in gestational age (GA), but TNF-α peaked in the second trimester. Within each trimester group, we searched for the effects of variation of GA in days on the 2 variables. A significant positive correlation between MMP-9 and GA was noted in the first trimester ( r = 0.364, P = .005). No other comparisons were significant. When GA was controlled for, partial correlation revealed a significant positive correlation between TNF-α and MMP-9 only in the second trimester ( r = 0.300, P = .018). We hypothesize that the TNF-α peak and the positive correlation between TNF-α and MMP-9 in the second trimester of normal human gestation could contribute toward a successful pregnancy outcome.

  12. Calculation of the fast multiplication factor by the fission matrix method

    International Nuclear Information System (INIS)

    Naumov, V.A.; Rozin, S.G.; Ehl'perin, T.I.

    1976-01-01

    A variation of the Monte Carlo method to calculate an effective breeding factor of a nuclear reactor is described. The evaluation procedure of reactivity perturbations by the Monte Carlo method in the first order perturbation theory is considered. The method consists in reducing an integral neutron transport equation to a set of linear algebraic equations. The coefficients of this set are elements of a fission matrix. The fission matrix being a Grin function of the neutron transport equation, is evaluated by the Monte Carlo method. In the program realizing the suggested algorithm, the game for initial neutron energy of a fission spectrum and then for the region of neutron birth, ΔVsub(f)sup(i)has been played in proportion to the product of Σsub(f)sup(i)ΔVsub(f)sup(i), where Σsub(f)sup(i) is a macroscopic cross section in the region numbered at the birth energy. Further iterations of a space distribution of neutrons in the system are performed by the generation method. In the adopted scheme of simulation of neutron histories the emission of secondary neutrons is controlled by weights; it occurs at every collision and not only in the end on the history. The breeding factor is calculated simultaneously with the space distribution of neutron worth in the system relative to the fission process and neutron flux. Efficiency of the described procedure has been tested on the calculation of the breeding factor for the Godiva assembly, simulating a fast reactor with a hard spectrum. A high accuracy of calculations at moderate number of zones in the core and reasonable statistics has been stated

  13. Turbo-SMT: Parallel Coupled Sparse Matrix-Tensor Factorizations and Applications

    Science.gov (United States)

    Papalexakis, Evangelos E.; Faloutsos, Christos; Mitchell, Tom M.; Talukdar, Partha Pratim; Sidiropoulos, Nicholas D.; Murphy, Brian

    2016-01-01

    How can we correlate the neural activity in the human brain as it responds to typed words, with properties of these terms (like ’edible’, ’fits in hand’)? In short, we want to find latent variables, that jointly explain both the brain activity, as well as the behavioral responses. This is one of many settings of the Coupled Matrix-Tensor Factorization (CMTF) problem. Can we enhance any CMTF solver, so that it can operate on potentially very large datasets that may not fit in main memory? We introduce Turbo-SMT, a meta-method capable of doing exactly that: it boosts the performance of any CMTF algorithm, produces sparse and interpretable solutions, and parallelizes any CMTF algorithm, producing sparse and interpretable solutions (up to 65 fold). Additionally, we improve upon ALS, the work-horse algorithm for CMTF, with respect to efficiency and robustness to missing values. We apply Turbo-SMT to BrainQ, a dataset consisting of a (nouns, brain voxels, human subjects) tensor and a (nouns, properties) matrix, with coupling along the nouns dimension. Turbo-SMT is able to find meaningful latent variables, as well as to predict brain activity with competitive accuracy. Finally, we demonstrate the generality of Turbo-SMT, by applying it on a Facebook dataset (users, ’friends’, wall-postings); there, Turbo-SMT spots spammer-like anomalies. PMID:27672406

  14. Factors that impact the stability of vitamin C at intermediate temperatures in a food matrix.

    Science.gov (United States)

    Herbig, Anna-Lena; Renard, Catherine M G C

    2017-04-01

    The study comprises a systematic and quantitative evaluation of potential intrinsic and extrinsic factors that impact vitamin C degradation in a real food matrix. The supernatant of centrifuged apple purée was fortified in vitamin C, and degradation was followed without stirring. Model discrimination indicated better fit for the zero order model than the first order model which was hence chosen for determination of rate constants. pH influenced strongly vitamin C degradation in citrate-phosphate buffer but not in the apple purée serum. To get an idea of the impact of the food matrix, stability in apple purée serum was compared with that in carrot purée. In the latter, stability was slightly higher. Vitamin C degradation rates were not influenced by its initial concentration. The temperature effect was only marked in the temperature range 40-60°C. In the range 60-80°C, filling height of tubes had the greatest impact. Copyright © 2016 Elsevier Ltd. All rights reserved.

  15. Exploring Mixed Membership Stochastic Block Models via Non-negative Matrix Factorization

    KAUST Repository

    Peng, Chengbin

    2014-12-01

    Many real-world phenomena can be modeled by networks in which entities and connections are represented by nodes and edges respectively. When certain nodes are highly connected with each other, those nodes forms a cluster, which is called community in our context. It is usually assumed that each node belongs to one community only, but evidences in biology and social networks reveal that the communities often overlap with each other. In other words, one node can probably belong to multiple communities. In light of that, mixed membership stochastic block models (MMB) have been developed to model those networks with overlapping communities. Such a model contains three matrices: two incidence matrices indicating in and out connections and one probability matrix. When the probability of connections for nodes between communities are significantly small, the parameter inference problem to this model can be solved by a constrained non-negative matrix factorization (NMF) algorithm. In this paper, we explore the connection between the two models and propose an algorithm based on NMF to infer the parameters of MMB. The proposed algorithms can detect overlapping communities regardless of knowing or not the number of communities. Experiments show that our algorithm can achieve a better community detection performance than the traditional NMF algorithm. © 2014 IEEE.

  16. Beyond cross-domain learning: Multiple-domain nonnegative matrix factorization

    KAUST Repository

    Wang, Jim Jing-Yan; Gao, Xin

    2014-01-01

    Traditional cross-domain learning methods transfer learning from a source domain to a target domain. In this paper, we propose the multiple-domain learning problem for several equally treated domains. The multiple-domain learning problem assumes that samples from different domains have different distributions, but share the same feature and class label spaces. Each domain could be a target domain, while also be a source domain for other domains. A novel multiple-domain representation method is proposed for the multiple-domain learning problem. This method is based on nonnegative matrix factorization (NMF), and tries to learn a basis matrix and coding vectors for samples, so that the domain distribution mismatch among different domains will be reduced under an extended variation of the maximum mean discrepancy (MMD) criterion. The novel algorithm - multiple-domain NMF (MDNMF) - was evaluated on two challenging multiple-domain learning problems - multiple user spam email detection and multiple-domain glioma diagnosis. The effectiveness of the proposed algorithm is experimentally verified. © 2013 Elsevier Ltd. All rights reserved.

  17. Beyond cross-domain learning: Multiple-domain nonnegative matrix factorization

    KAUST Repository

    Wang, Jim Jing-Yan

    2014-02-01

    Traditional cross-domain learning methods transfer learning from a source domain to a target domain. In this paper, we propose the multiple-domain learning problem for several equally treated domains. The multiple-domain learning problem assumes that samples from different domains have different distributions, but share the same feature and class label spaces. Each domain could be a target domain, while also be a source domain for other domains. A novel multiple-domain representation method is proposed for the multiple-domain learning problem. This method is based on nonnegative matrix factorization (NMF), and tries to learn a basis matrix and coding vectors for samples, so that the domain distribution mismatch among different domains will be reduced under an extended variation of the maximum mean discrepancy (MMD) criterion. The novel algorithm - multiple-domain NMF (MDNMF) - was evaluated on two challenging multiple-domain learning problems - multiple user spam email detection and multiple-domain glioma diagnosis. The effectiveness of the proposed algorithm is experimentally verified. © 2013 Elsevier Ltd. All rights reserved.

  18. Clinicopathological correlation of keratinocyte growth factor and matrix metalloproteinase-9 expression in human gastric cancer.

    Science.gov (United States)

    Zhang, Qing; Wang, Ping; Shao, Ming; Chen, Shi-Wen; Xu, Zhi-Feng; Xu, Feng; Yang, Zhong-Yin; Liu, Bing-Ya; Gu, Qin-Long; Zhang, Wen-Jian; Li, Yong

    2015-01-01

    Keratinocyte growth factor (KGF) is reported to be implicated in the growth of some cancer cells. Matrix metalloproteinase 9 (MMP-9) is thought to enhance the tumor invasion and metastasis ability. This study was aimed at analyzing the relationship between KGF and MMP-9 expression and patients' clinicopathological characteristics to clarify the clinical significance of the expression of KGF and MMP-9 in gastric cancer. Tissue samples from 161 patients with primary gastric cancer were investigated using immunohistochemistry. The relationship between KGF and/or MMP-9 expression and clinicopathological characteristics was analyzed. KGF expression and MMP-9 expression in gastric cancer tissue were observed in 62 cases (38.5%) and 97 cases (60.2%), respectively. MMP-9 was significantly associated with depth of invasion, lymph node metastasis and TNM stage. The prognosis of MMP-9-positive patients was significantly poorer than that of MMP-9-negative patients (p = 0.009). KGF expression was positively correlated with MMP-9 expression in gastric cancer, and the prognosis of patients with both KGF- and MMP-9-positive tumors was significantly worse than that of patients with negative tumors for either factor (p = 0.045). Expression of MMP-9 was revealed to be an independent prognostic factor (p = 0.026). Coexpression of KGF and MMP-9 in gastric cancer could be a useful prognostic factor, and MMP-9 might also serve as a novel target for both prognostic prediction and therapeutics.

  19. Application of positive matrix factorization to identify potential sources of PAHs in soil of Dalian, China

    International Nuclear Information System (INIS)

    Wang Degao; Tian Fulin; Yang Meng; Liu Chenlin; Li Yifan

    2009-01-01

    Soil derived sources of polycyclic aromatic hydrocarbons (PAHs) in the region of Dalian, China were investigated using positive matrix factorization (PMF). Three factors were separated based on PMF for the statistical investigation of the datasets both in summer and winter. These factors were dominated by the pattern of single sources or groups of similar sources, showing seasonal and regional variations. The main sources of PAHs in Dalian soil in summer were the emissions from coal combustion average (46%), diesel engine (30%), and gasoline engine (24%). In winter, the main sources were the emissions from coal-fired boiler (72%), traffic average (20%), and gasoline engine (8%). These factors with strong seasonality indicated that coal combustion in winter and traffic exhaust in summer dominated the sources of PAHs in soil. These results suggested that PMF model was a proper approach to identify the sources of PAHs in soil. - PMF model is a proper approach to identify potential sources of PAHs in soil based on the PAH profiles measured in the field and those published in the literature.

  20. Attributed community mining using joint general non-negative matrix factorization with graph Laplacian

    Science.gov (United States)

    Chen, Zigang; Li, Lixiang; Peng, Haipeng; Liu, Yuhong; Yang, Yixian

    2018-04-01

    Community mining for complex social networks with link and attribute information plays an important role according to different application needs. In this paper, based on our proposed general non-negative matrix factorization (GNMF) algorithm without dimension matching constraints in our previous work, we propose the joint GNMF with graph Laplacian (LJGNMF) to implement community mining of complex social networks with link and attribute information according to different application needs. Theoretical derivation result shows that the proposed LJGNMF is fully compatible with previous methods of integrating traditional NMF and symmetric NMF. In addition, experimental results show that the proposed LJGNMF can meet the needs of different community minings by adjusting its parameters, and the effect is better than traditional NMF in the community vertices attributes entropy.

  1. Categorical dimensions of human odor descriptor space revealed by non-negative matrix factorization

    Energy Technology Data Exchange (ETDEWEB)

    Chennubhotla, Chakra [University of Pittsburgh School of Medicine, Pittsburgh PA; Castro, Jason [Bates College

    2013-01-01

    In contrast to most other sensory modalities, the basic perceptual dimensions of olfaction remain un- clear. Here, we use non-negative matrix factorization (NMF) - a dimensionality reduction technique - to uncover structure in a panel of odor profiles, with each odor defined as a point in multi-dimensional descriptor space. The properties of NMF are favorable for the analysis of such lexical and perceptual data, and lead to a high-dimensional account of odor space. We further provide evidence that odor di- mensions apply categorically. That is, odor space is not occupied homogenously, but rather in a discrete and intrinsically clustered manner. We discuss the potential implications of these results for the neural coding of odors, as well as for developing classifiers on larger datasets that may be useful for predicting perceptual qualities from chemical structures.

  2. Adhesion properties of Lactobacillus rhamnosus mucus-binding factor to mucin and extracellular matrix proteins.

    Science.gov (United States)

    Nishiyama, Keita; Nakamata, Koichi; Ueno, Shintaro; Terao, Akari; Aryantini, Ni Putu Desy; Sujaya, I Nengah; Fukuda, Kenji; Urashima, Tadasu; Yamamoto, Yuji; Mukai, Takao

    2015-01-01

    We previously described potential probiotic Lactobacillus rhamnosus strains, isolated from fermented mare milk produced in Sumbawa Island, Indonesia, which showed high adhesion to porcine colonic mucin (PCM) and extracellular matrix (ECM) proteins. Recently, mucus-binding factor (MBF) was found in the GG strain of L. rhamnosus as a mucin-binding protein. In this study, we assessed the ability of recombinant MBF protein from the FSMM22 strain, one of the isolates of L. rhamnosus from fermented Sumbawa mare milk, to adhere to PCM and ECM proteins by overlay dot blot and Biacore assays. MBF bound to PCM, laminin, collagen IV, and fibronectin with submicromolar dissociation constants. Adhesion of the FSMM22 mbf mutant strain to PCM and ECM proteins was significantly less than that of the wild-type strain. Collectively, these results suggested that MBF contribute to L. rhamnosus host colonization via mucin and ECM protein binding.

  3. Approximate L0 constrained Non-negative Matrix and Tensor Factorization

    DEFF Research Database (Denmark)

    Mørup, Morten; Madsen, Kristoffer Hougaard; Hansen, Lars Kai

    2008-01-01

    Non-negative matrix factorization (NMF), i.e. V = WH where both V, W and H are non-negative has become a widely used blind source separation technique due to its part based representation. The NMF decomposition is not in general unique and a part based representation not guaranteed. However...... constraint. In general, solving for a given L0 norm is an NP hard problem thus convex relaxatin to regularization by the L1 norm is often considered, i.e., minimizing ( 1/2 ||V-WHk||^2+lambda|H|_1). An open problem is to control the degree of sparsity imposed. We here demonstrate that a full regularization......, the L1 regularization strength lambda that best approximates a given L0 can be directly accessed and in effect used to control the sparsity of H. The MATLAB code for the NLARS algorithm is available for download....

  4. Molecular interactions between chondroitin-dermatan sulfate and growth factors/receptors/matrix proteins.

    Science.gov (United States)

    Mizumoto, Shuji; Yamada, Shuhei; Sugahara, Kazuyuki

    2015-10-01

    Recent functional studies on chondroitin sulfate-dermatan sulfate (CS-DS) demonstrated its indispensable roles in various biological events including brain development and cancer. CS-DS proteoglycans exert their physiological activity through interactions with specific proteins including growth factors, cell surface receptors, and matrix proteins. The characterization of these interactions is essential for regulating the biological functions of CS-DS proteoglycans. Although amino acid sequences on the bioactive proteins required for these interactions have already been elucidated, the specific saccharide sequences involved in the binding of CS-DS to target proteins have not yet been sufficiently identified. In this review, recent findings are described on the interaction between CS-DS and some proteins which are especially involved in the central nervous system and cancer development/metastasis. Copyright © 2015. Published by Elsevier Ltd.

  5. Tumor Necrosis Factors, Interferons and Matrix Metalloproteinase-9 in Sera of Non-Hodgkin's Lymphoma Patients

    International Nuclear Information System (INIS)

    Abdel Malak, C.A.; Karawya, E.M.; Hammouda, G.A.; Zakhary, N.I.

    2003-01-01

    In the present study, the serum levels of some cytokines and the matrix metalloproteinase-9 (MMP-9) were studied in an attempt to find suitable markers for early diagnosis of non- Hodgkin's lymphoma (NHL) and to assess their role in differentiating between disseminated and non disseminated cases. The present study was conducted on 60 patients with non disseminated NHL, 14 patients with disseminated NHL, in addition to 10 healthy controls. Their sera were used to determine tumor necrosis factor-α (TNF--α), tumor necrosis factor--β (TNF-β), interferon---α), (IFN--α), interferon-γ (IFN--γ) and Matrix Metalloproteinase-9 (MMP-9) using the ELISA technique. The results showed that the serum level of TNF---α), and IFN---α), can be used to differentiate between the control group and the group of NHL patients. However, they could not differentiate between non disseminated NHL (nd- NHL) and disseminated NHL (d- NHL). On the other hand, the serum level of TNF-β) can be used to differentiate between nd- NHL and d- NHL, but not between the control group and nd-NHL. Each of [FN--γ and MMP-9 were not useful in discrimination between the control group and the diseased ones. Our data revealed no correlation between serum level of the parameters investigated and the gender of the patients. The present results revealed that TNF-α) and INF-α), can be used as diagnostic tools for NHL. On the other hand, TNF-β) is useful in the differentiation between nd-NHL and d-NHL

  6. Matrix factorization-based data fusion for the prediction of lncRNA-disease associations.

    Science.gov (United States)

    Fu, Guangyuan; Wang, Jun; Domeniconi, Carlotta; Yu, Guoxian

    2018-05-01

    Long non-coding RNAs (lncRNAs) play crucial roles in complex disease diagnosis, prognosis, prevention and treatment, but only a small portion of lncRNA-disease associations have been experimentally verified. Various computational models have been proposed to identify lncRNA-disease associations by integrating heterogeneous data sources. However, existing models generally ignore the intrinsic structure of data sources or treat them as equally relevant, while they may not be. To accurately identify lncRNA-disease associations, we propose a Matrix Factorization based LncRNA-Disease Association prediction model (MFLDA in short). MFLDA decomposes data matrices of heterogeneous data sources into low-rank matrices via matrix tri-factorization to explore and exploit their intrinsic and shared structure. MFLDA can select and integrate the data sources by assigning different weights to them. An iterative solution is further introduced to simultaneously optimize the weights and low-rank matrices. Next, MFLDA uses the optimized low-rank matrices to reconstruct the lncRNA-disease association matrix and thus to identify potential associations. In 5-fold cross validation experiments to identify verified lncRNA-disease associations, MFLDA achieves an area under the receiver operating characteristic curve (AUC) of 0.7408, at least 3% higher than those given by state-of-the-art data fusion based computational models. An empirical study on identifying masked lncRNA-disease associations again shows that MFLDA can identify potential associations more accurately than competing models. A case study on identifying lncRNAs associated with breast, lung and stomach cancers show that 38 out of 45 (84%) associations predicted by MFLDA are supported by recent biomedical literature and further proves the capability of MFLDA in identifying novel lncRNA-disease associations. MFLDA is a general data fusion framework, and as such it can be adopted to predict associations between other biological

  7. A Normalized Transfer Matrix Method for the Free Vibration of Stepped Beams: Comparison with Experimental and FE(3D Methods

    Directory of Open Access Journals (Sweden)

    Tamer Ahmed El-Sayed

    2017-01-01

    Full Text Available The exact solution for multistepped Timoshenko beam is derived using a set of fundamental solutions. This set of solutions is derived to normalize the solution at the origin of the coordinates. The start, end, and intermediate boundary conditions involve concentrated masses and linear and rotational elastic supports. The beam start, end, and intermediate equations are assembled using the present normalized transfer matrix (NTM. The advantage of this method is that it is quicker than the standard method because the size of the complete system coefficient matrix is 4 × 4. In addition, during the assembly of this matrix, there are no inverse matrix steps required. The validity of this method is tested by comparing the results of the current method with the literature. Then the validity of the exact stepped analysis is checked using experimental and FE(3D methods. The experimental results for stepped beams with single step and two steps, for sixteen different test samples, are in excellent agreement with those of the three-dimensional finite element FE(3D. The comparison between the NTM method and the finite element method results shows that the modal percentage deviation is increased when a beam step location coincides with a peak point in the mode shape. Meanwhile, the deviation decreases when a beam step location coincides with a straight portion in the mode shape.

  8. A Poisson nonnegative matrix factorization method with parameter subspace clustering constraint for endmember extraction in hyperspectral imagery

    Science.gov (United States)

    Sun, Weiwei; Ma, Jun; Yang, Gang; Du, Bo; Zhang, Liangpei

    2017-06-01

    A new Bayesian method named Poisson Nonnegative Matrix Factorization with Parameter Subspace Clustering Constraint (PNMF-PSCC) has been presented to extract endmembers from Hyperspectral Imagery (HSI). First, the method integrates the liner spectral mixture model with the Bayesian framework and it formulates endmember extraction into a Bayesian inference problem. Second, the Parameter Subspace Clustering Constraint (PSCC) is incorporated into the statistical program to consider the clustering of all pixels in the parameter subspace. The PSCC could enlarge differences among ground objects and helps finding endmembers with smaller spectrum divergences. Meanwhile, the PNMF-PSCC method utilizes the Poisson distribution as the prior knowledge of spectral signals to better explain the quantum nature of light in imaging spectrometer. Third, the optimization problem of PNMF-PSCC is formulated into maximizing the joint density via the Maximum A Posterior (MAP) estimator. The program is finally solved by iteratively optimizing two sub-problems via the Alternating Direction Method of Multipliers (ADMM) framework and the FURTHESTSUM initialization scheme. Five state-of-the art methods are implemented to make comparisons with the performance of PNMF-PSCC on both the synthetic and real HSI datasets. Experimental results show that the PNMF-PSCC outperforms all the five methods in Spectral Angle Distance (SAD) and Root-Mean-Square-Error (RMSE), and especially it could identify good endmembers for ground objects with smaller spectrum divergences.

  9. Extracellular Matrix-Regulated Gene Expression RequiresCooperation of SWI/SNF and Transcription Factors

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Ren; Spencer, Virginia A.; Bissell, Mina J.

    2006-05-25

    Extracellular cues play crucial roles in the transcriptional regulation of tissue-specific genes, but whether and how these signals lead to chromatin remodeling is not understood and subject to debate. Using chromatin immunoprecipitation (ChIP) assays and mammary-specific genes as models, we show here that extracellular matrix (ECM) molecules and prolactin cooperate to induce histone acetylation and binding of transcription factors and the SWI/SNF complex to the {beta}- and ?-casein promoters. Introduction of a dominant negative Brg1, an ATPase subunit of SWI/SNF complex, significantly reduced both {beta}- and ?-casein expression, suggesting that SWI/SNF-dependent chromatin remodeling is required for transcription of mammary-specific genes. ChIP analyses demonstrated that the ATPase activity of SWI/SNF is necessary for recruitment of RNA transcriptional machinery, but not for binding of transcription factors or for histone acetylation. Coimmunoprecipitation analyses showed that the SWI/SNF complex is associated with STAT5, C/EBP{beta}, and glucocorticoid receptor (GR). Thus, ECM- and prolactin-regulated transcription of the mammary-specific casein genes requires the concerted action of chromatin remodeling enzymes and transcription factors.

  10. Source apportionment and location by selective wind sampling and Positive Matrix Factorization.

    Science.gov (United States)

    Venturini, Elisa; Vassura, Ivano; Raffo, Simona; Ferroni, Laura; Bernardi, Elena; Passarini, Fabrizio

    2014-10-01

    In order to determine the pollution sources in a suburban area and identify the main direction of their origin, PM2.5 was collected with samplers coupled with a wind select sensor and then subjected to Positive Matrix Factorization (PMF) analysis. In each sample, soluble ions, organic carbon, elemental carbon, levoglucosan, metals, and Polycyclic Aromatic Hydrocarbons (PAHs) were determined. PMF results identified six main sources affecting the area: natural gas home appliances, motor vehicles, regional transport, biomass combustion, manufacturing activities, and secondary aerosol. The connection of factor temporal trends with other parameters (i.e., temperature, PM2.5 concentration, and photochemical processes) confirms factor attributions. PMF analysis indicated that the main source of PM2.5 in the area is secondary aerosol. This should be mainly due to regional contributions, owing to both the secondary nature of the source itself and the higher concentration registered in inland air masses. The motor vehicle emission source contribution is also important. This source likely has a prevalent local origin. The most toxic determined components, i.e., PAHs, Cd, Pb, and Ni, are mainly due to vehicular traffic. Even if this is not the main source in the study area, it is the one of greatest concern. The application of PMF analysis to PM2.5 collected with this new sampling technique made it possible to obtain more detailed results on the sources affecting the area compared to a classical PMF analysis.

  11. Factorization of J-unitary matrix polynomials on the line and a Schur algorithm for generalized Nevanlinna functions

    NARCIS (Netherlands)

    Alpay, D.; Dijksma, A.; Langer, H.

    2004-01-01

    We prove that a 2 × 2 matrix polynomial which is J-unitary on the real line can be written as a product of normalized elementary J-unitary factors and a J-unitary constant. In the second part we give an algorithm for this factorization using an analog of the Schur transformation.

  12. Comparison of Material Behavior of Matrix Graphite for HTGR Fuel Elements upon Irradiation: A literature Survey

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Young-Woo; Yeo, Seunghwan; Cho, Moon Sung [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

    2015-05-15

    The fuel elements for the HTGRs (i.e., spherical fuel element in pebble-bed type core design and fuel compact in prismatic core design) consists of coated fuel particles dispersed and bonded in a closely packed array within a carbonaceous matrix. This matrix is generally made by mixing fully graphitized natural and needle- or pitchcoke originated powders admixed with a binder material (pitch or phenolic resin), The resulting resinated graphite powder mixture, when compacted, may influence a number of material properties as well as its behavior under neutron irradiation during reactor operation. In the fabrication routes of these two different fuel element forms, different consolidation methods are employed; a quasi-isostatic pressing method is generally adopted to make pebbles while fuel compacts are fabricated by uni-axial pressing mode. The result showed that the hardness values obtained from the two directions showed an anisotropic behavior: The values obtained from the perpendicular section showed much higher micro hardness (176.6±10.5MPa in average) than from the parallel section ((125.6±MPa in average). This anisotropic behavior was concluded to be related to the microstructure of the matrix graphite. This may imply that the uni-axial pressing method to make compacts influence the microstructure of the matrix and hence the material properties of the matrix graphite.

  13. Comparison of hemostatic matrix and standard hemostasis in patients undergoing primary TKA.

    Science.gov (United States)

    Comadoll, James L; Comadoll, Shea; Hutchcraft, Audrey; Krishnan, Sangeeta; Farrell, Kelly; Kreuwel, Huub T C; Bechter, Mark

    2012-06-01

    Bleeding after total knee arthroplasty increases the risk of pain, delayed rehabilitation, blood transfusion, and transfusion-associated complications. The authors compared pre- and postoperative decreases in hemoglobin as a surrogate for blood loss in consecutive patients treated at a single institution by the same surgeon (J.L.C.) using conventional hemostatic methods (electrocautery, suturing, or manual compression) or a gelatin and thrombin-based hemostatic matrix during total knee arthroplasty. Data were collected retrospectively by chart review. The population comprised 165 controls and 184 patients treated with hemostatic matrix. Median age was 66 years (range, 28-89 years); 66% were women. The arithmetic mean ± SD for the maximal postoperative decrease in hemoglobin was 3.18 ± 0.94 g/dL for controls and 2.19 ± 0.83 g/dL for the hemostatic matrix group. Least squares means estimates of the group difference (controls-hemostatic matrix) in the maximal decrease in hemoglobin was 0.96 g/dL (95% confidence interval, 0.77-1.14 mg/dL; Pmatrix, 84%). In both groups, overall mean tourniquet time was approximately 1 hour, and the most common length of stay was 3 to 5 days. No serious complications related to the hemostatic agent were observed. These data demonstrate that the use of a flowable hemostatic matrix results in less reduction in hemoglobin than the use of conventional hemostatic methods in patient undergoing total knee arthroplasty. Copyright 2012, SLACK Incorporated.

  14. Using Dynamic Multi-Task Non-Negative Matrix Factorization to Detect the Evolution of User Preferences in Collaborative Filtering.

    Directory of Open Access Journals (Sweden)

    Bin Ju

    Full Text Available Predicting what items will be selected by a target user in the future is an important function for recommendation systems. Matrix factorization techniques have been shown to achieve good performance on temporal rating-type data, but little is known about temporal item selection data. In this paper, we developed a unified model that combines Multi-task Non-negative Matrix Factorization and Linear Dynamical Systems to capture the evolution of user preferences. Specifically, user and item features are projected into latent factor space by factoring co-occurrence matrices into a common basis item-factor matrix and multiple factor-user matrices. Moreover, we represented both within and between relationships of multiple factor-user matrices using a state transition matrix to capture the changes in user preferences over time. The experiments show that our proposed algorithm outperforms the other algorithms on two real datasets, which were extracted from Netflix movies and Last.fm music. Furthermore, our model provides a novel dynamic topic model for tracking the evolution of the behavior of a user over time.

  15. Using Dynamic Multi-Task Non-Negative Matrix Factorization to Detect the Evolution of User Preferences in Collaborative Filtering.

    Science.gov (United States)

    Ju, Bin; Qian, Yuntao; Ye, Minchao; Ni, Rong; Zhu, Chenxi

    2015-01-01

    Predicting what items will be selected by a target user in the future is an important function for recommendation systems. Matrix factorization techniques have been shown to achieve good performance on temporal rating-type data, but little is known about temporal item selection data. In this paper, we developed a unified model that combines Multi-task Non-negative Matrix Factorization and Linear Dynamical Systems to capture the evolution of user preferences. Specifically, user and item features are projected into latent factor space by factoring co-occurrence matrices into a common basis item-factor matrix and multiple factor-user matrices. Moreover, we represented both within and between relationships of multiple factor-user matrices using a state transition matrix to capture the changes in user preferences over time. The experiments show that our proposed algorithm outperforms the other algorithms on two real datasets, which were extracted from Netflix movies and Last.fm music. Furthermore, our model provides a novel dynamic topic model for tracking the evolution of the behavior of a user over time.

  16. Comparison of experimental methods for estimating matrix diffusion coefficients for contaminant transport modeling

    Science.gov (United States)

    Telfeyan, Katherine; Ware, S. Doug; Reimus, Paul W.; Birdsell, Kay H.

    2018-02-01

    Diffusion cell and diffusion wafer experiments were conducted to compare methods for estimating effective matrix diffusion coefficients in rock core samples from Pahute Mesa at the Nevada Nuclear Security Site (NNSS). A diffusion wafer method, in which a solute diffuses out of a rock matrix that is pre-saturated with water containing the solute, is presented as a simpler alternative to the traditional through-diffusion (diffusion cell) method. Both methods yielded estimates of effective matrix diffusion coefficients that were within the range of values previously reported for NNSS volcanic rocks. The difference between the estimates of the two methods ranged from 14 to 30%, and there was no systematic high or low bias of one method relative to the other. From a transport modeling perspective, these differences are relatively minor when one considers that other variables (e.g., fracture apertures, fracture spacings) influence matrix diffusion to a greater degree and tend to have greater uncertainty than effective matrix diffusion coefficients. For the same relative random errors in concentration measurements, the diffusion cell method yields effective matrix diffusion coefficient estimates that have less uncertainty than the wafer method. However, the wafer method is easier and less costly to implement and yields estimates more quickly, thus allowing a greater number of samples to be analyzed for the same cost and time. Given the relatively good agreement between the methods, and the lack of any apparent bias between the methods, the diffusion wafer method appears to offer advantages over the diffusion cell method if better statistical representation of a given set of rock samples is desired.

  17. Downregulation of Connective Tissue Growth Factor by Three-Dimensional Matrix Enhances Ovarian Carcinoma Cell Invasion

    Science.gov (United States)

    Barbolina, Maria V.; Adley, Brian P.; Kelly, David L.; Shepard, Jaclyn; Fought, Angela J.; Scholtens, Denise; Penzes, Peter; Shea, Lonnie D.; Sharon Stack, M

    2010-01-01

    Epithelial ovarian carcinoma (EOC) is a leading cause of death from gynecologic malignancy, due mainly to the prevalence of undetected metastatic disease. The process of cell invasion during intra-peritoneal anchoring of metastatic lesions requires concerted regulation of many processes, including modulation of adhesion to the extracellular matrix and localized invasion. Exploratory cDNA microarray analysis of early response genes (altered after 4 hours of 3-dimensional collagen culture) coupled with confirmatory real-time RT-PCR, multiple three-dimensional cell culture matrices, Western blot, immunostaining, adhesion, migration, and invasion assays were used to identify modulators of adhesion pertinent to EOC progression and metastasis. cDNA microarray analysis indicated a dramatic downregulation of connective tissue growth factor (CTGF) in EOC cells placed in invasion-mimicking conditions (3-dimensional type I collagen). Examination of human EOC specimens revealed that CTGF expression was absent in 46% of the tested samples (n=41), but was present in 100% of normal ovarian epithelium samples (n=7). Reduced CTGF expression occurs in many types of cells and may be a general phenomenon displayed by cells encountering a 3D environment. CTGF levels were inversely correlated with invasion such that downregulation of CTGF increased, while its upregulation reduced, collagen invasion. Cells adhered preferentially to a surface comprised of both collagen I and CTGF relative to either component alone using α6β1 and α3β1 integrins. Together these data suggest that downregulation of CTGF in EOC cells may be important for cell invasion through modulation of cell-matrix adhesion. PMID:19382180

  18. Plasma membrane factor XIIIA transglutaminase activity regulates osteoblast matrix secretion and deposition by affecting microtubule dynamics.

    Directory of Open Access Journals (Sweden)

    Hadil F Al-Jallad

    2011-01-01

    Full Text Available Transglutaminase activity, arising potentially from transglutaminase 2 (TG2 and Factor XIIIA (FXIIIA, has been linked to osteoblast differentiation where it is required for type I collagen and fibronectin matrix deposition. In this study we have used an irreversible TG-inhibitor to 'block -and-track' enzyme(s targeted during osteoblast differentiation. We show that the irreversible TG-inhibitor is highly potent in inhibiting osteoblast differentiation and mineralization and reduces secretion of both fibronectin and type I collagen and their release from the cell surface. Tracking of the dansyl probe by Western blotting and immunofluorescence microscopy demonstrated that the inhibitor targets plasma membrane-associated FXIIIA. TG2 appears not to contribute to crosslinking activity on the osteoblast surface. Inhibition of FXIIIA with NC9 resulted in defective secretory vesicle delivery to the plasma membrane which was attributable to a disorganized microtubule network and decreased microtubule association with the plasma membrane. NC9 inhibition of FXIIIA resulted in destabilization of microtubules as assessed by cellular Glu-tubulin levels. Furthermore, NC9 blocked modification of Glu-tubulin into 150 kDa high-molecular weight Glu-tubulin form which was specifically localized to the plasma membrane. FXIIIA enzyme and its crosslinking activity were colocalized with plasma membrane-associated tubulin, and thus, it appears that FXIIIA crosslinking activity is directed towards stabilizing the interaction of microtubules with the plasma membrane. Our work provides the first mechanistic cues as to how transglutaminase activity could affect protein secretion and matrix deposition in osteoblasts and suggests a novel function for plasma membrane FXIIIA in microtubule dynamics.

  19. Matrix metalloproteinase-3, vitamin D receptor gene polymorphisms, and occupational risk factors in lumbar disc degeneration.

    Science.gov (United States)

    Zawilla, N H; Darweesh, H; Mansour, N; Helal, S; Taha, F M; Awadallah, M; El Shazly, R

    2014-06-01

    Lumbar disc degeneration (LDD) is a process that begins early in life, contributing to the development of low back pain. LDD is a consequence of a variety of factors, and its etiology remains poorly understood. Objectives to investigate occupational and genetic risk factors inducing lumbar disc degeneration, and to evaluate the possible association of genetic polymorphisms of matrix metalloproteinase 3 (MMP-3) and vitamin D receptor (VDR) with the severity of LDD in an Egyptian population. A case control study involving 84 LDD and 60 controls was carried out. Five types of work related factors were investigated by questionnaire, complete neurological examination for all subjects and MRI for the cases. Polymerase chain reaction and restriction fragment length polymorphism methods were applied to detect polymorphisms in MMP-3 Promoter (-1,171 6A/5A) (rs 731236) and VDR-Apa (rs 35068180). We found that family history, back injury, smoking, high level of sitting, bending/twisting, physical workload, lifting, whole body vibration, mutant allele 5A of MMP-3 and mutant allele T of VDR were significantly associated with LDD (OR = 2.9, 3.1, 2.1, 11.1, 15.9, 11.7, 8.2, 12.6, 2.5 and 3.1 respectively, p < 0.05). Cases that carry allele 5A and/or allele T were associated with LDD severity. LDD is closely associated in occurrence and severity with occupational, environmental risk factors and susceptibility genes namely MMP-3, and VDR (ApaI). This study throws light on the importance of screening for early detection of susceptible individuals and disease prevention.

  20. Gene Ranking of RNA-Seq Data via Discriminant Non-Negative Matrix Factorization.

    Science.gov (United States)

    Jia, Zhilong; Zhang, Xiang; Guan, Naiyang; Bo, Xiaochen; Barnes, Michael R; Luo, Zhigang

    2015-01-01

    RNA-sequencing is rapidly becoming the method of choice for studying the full complexity of transcriptomes, however with increasing dimensionality, accurate gene ranking is becoming increasingly challenging. This paper proposes an accurate and sensitive gene ranking method that implements discriminant non-negative matrix factorization (DNMF) for RNA-seq data. To the best of our knowledge, this is the first work to explore the utility of DNMF for gene ranking. When incorporating Fisher's discriminant criteria and setting the reduced dimension as two, DNMF learns two factors to approximate the original gene expression data, abstracting the up-regulated or down-regulated metagene by using the sample label information. The first factor denotes all the genes' weights of two metagenes as the additive combination of all genes, while the second learned factor represents the expression values of two metagenes. In the gene ranking stage, all the genes are ranked as a descending sequence according to the differential values of the metagene weights. Leveraging the nature of NMF and Fisher's criterion, DNMF can robustly boost the gene ranking performance. The Area Under the Curve analysis of differential expression analysis on two benchmarking tests of four RNA-seq data sets with similar phenotypes showed that our proposed DNMF-based gene ranking method outperforms other widely used methods. Moreover, the Gene Set Enrichment Analysis also showed DNMF outweighs others. DNMF is also computationally efficient, substantially outperforming all other benchmarked methods. Consequently, we suggest DNMF is an effective method for the analysis of differential gene expression and gene ranking for RNA-seq data.

  1. Analysis of risk factors for hydrocephalus development in newborn infants with germinal matrix hemorrhage.

    Science.gov (United States)

    Romero, L; Ros, B; Arráez, M A; Ríus, F; González, L; Martín, A; Carrasco, A; Segura, M

    2015-10-01

    The aim of this study was to analyze risk factors for the development of hydrocephalus in newborn infants with germinal matrix (GM) hemorrhage. The study comprised 271 patients admitted to Carlos Haya University Hospital in Malaga with GM hemorrhage. The following data were recorded: gestational age, gender, twin birth, head circumference at birth, weight at birth, and Papile grade. Severe obstetrical (abruption, chorioamnionitis, pregnancy-induced hypertension, tocolytic treatment) and neonatal disorders (respiratory distress syndrome, neonatal infection, coagulation disorder, patent ductus arteriosus, necrotizing enterocolitis) were also recorded. Symptomatic hydrocephalus was diagnosed in the event of a progressive increase in head circumference and ventricular indices requiring shunting. Of the 271 patients, 139 (51%) developed posthemorrhagic ventriculomegaly; 47 patients (17%) developed symptomatic hydrocephalus and needed shunt implantation. We found a significant relationship between the development of symptomatic hydrocephalus and Papile grade, lower gestational age, lower birth weight, twin birth, and neonatal infection. Awareness of risk factors for the development of hydrocephalus in newborn infants with GM hemorrhage should be emphasized in order to enable an early diagnosis of ventriculomegaly and symptomatic hydrocephalus and thus make a correct therapeutic decision.

  2. The interplay of matrix metalloproteinases, morphogens and growth factors is necessary for branching of mammary epithelial cells

    OpenAIRE

    Simian, Marina; Hirai, Yohei; Navre, Marc; Werb, Zena; Lochter, Andre; Bissell, Mina J.

    2001-01-01

    The mammary gland develops its adult form by a process referred to as branching morphogenesis. Many factors have been reported to affect this process. We have used cultured primary mammary epithelial organoids and mammary epithelial cell lines in three-dimensional collagen gels to elucidate which growth factors, matrix metalloproteinases (MMPs) and mammary morphogens interact in branching morphogenesis. Branching stimulated by stromal fibroblasts, epidermal growth factor, fibroblast growth fa...

  3. A comparison of likelihood ratio tests and Rao's score test for three separable covariance matrix structures.

    Science.gov (United States)

    Filipiak, Katarzyna; Klein, Daniel; Roy, Anuradha

    2017-01-01

    The problem of testing the separability of a covariance matrix against an unstructured variance-covariance matrix is studied in the context of multivariate repeated measures data using Rao's score test (RST). The RST statistic is developed with the first component of the separable structure as a first-order autoregressive (AR(1)) correlation matrix or an unstructured (UN) covariance matrix under the assumption of multivariate normality. It is shown that the distribution of the RST statistic under the null hypothesis of any separability does not depend on the true values of the mean or the unstructured components of the separable structure. A significant advantage of the RST is that it can be performed for small samples, even smaller than the dimension of the data, where the likelihood ratio test (LRT) cannot be used, and it outperforms the standard LRT in a number of contexts. Monte Carlo simulations are then used to study the comparative behavior of the null distribution of the RST statistic, as well as that of the LRT statistic, in terms of sample size considerations, and for the estimation of the empirical percentiles. Our findings are compared with existing results where the first component of the separable structure is a compound symmetry (CS) correlation matrix. It is also shown by simulations that the empirical null distribution of the RST statistic converges faster than the empirical null distribution of the LRT statistic to the limiting χ 2 distribution. The tests are implemented on a real dataset from medical studies. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. Identification of the sources of PM10 in a subway tunnel using positive matrix factorization.

    Science.gov (United States)

    Park, Duckshin; Lee, Taejeong; Hwang, Doyeon; Jung, Wonseok; Lee, Yongil; Cho, KiChul; Kim, Dongsool; Lees, Kiyoung

    2014-12-01

    The level of particulate matter of less than 10 μm diameter (PM10) at subway platforms can be significantly reduced by installing a platform screen-door system. However, both workers and passengers might be exposed to higher PM10 levels while the cars are within the tunnel because it is a more confined environment. This study determined the PM10 levels in a subway tunnel, and identified the sources of PM10 using elemental analysis and receptor modeling. Forty-four PM10 samples were collected in the tunnel between the Gireum and Mia stations on Line 4 in metropolitan Seoul and analyzed using inductively coupled plasma-atomic emission spectrometry and ion chromatography. The major PM10 sources were identified using positive matrix factorization (PMF). The average PM10 concentration in the tunnels was 200.8 ± 22.0 μg/m3. Elemental analysis indicated that the PM10 consisted of 40.4% inorganic species, 9.1% anions, 4.9% cations, and 45.6% other materials. Iron was the most abundant element, with an average concentration of 72.5 ± 10.4 μg/m3. The PM10 sources characterized by PMF included rail, wheel, and brake wear (59.6%), soil combustion (17.0%), secondary aerosols (10.0%), electric cable wear (8.1%), and soil and road dust (5.4%). Internal sources comprising rail, wheel, brake, and electric cable wear made the greatest contribution to the PM10 (67.7%) in tunnel air. Implications: With installation of a platform screen door, PM10 levels in subway tunnels were higher than those on platforms. Tunnel PM10 levels exceeded 150 µg/m3 of the Korean standard for subway platform. Elemental analysis of PM10 in a tunnel showed that Fe was the most abundant element. Five PM10 sources in tunnel were identified by positive matrix factorization. Railroad-related sources contributed 68% of PM10 in the subway tunnel.

  5. Source apportionment of ambient particle number concentrations in central Los Angeles using positive matrix factorization (PMF

    Directory of Open Access Journals (Sweden)

    M. H. Sowlat

    2016-04-01

    Full Text Available In this study, the positive matrix factorization (PMF receptor model (version 5.0 was used to identify and quantify major sources contributing to particulate matter (PM number concentrations, using PM number size distributions in the range of 13 nm to 10 µm combined with several auxiliary variables, including black carbon (BC, elemental and organic carbon (EC/OC, PM mass concentrations, gaseous pollutants, meteorological, and traffic counts data, collected for about 9 months between August 2014 and 2015 in central Los Angeles, CA. Several parameters, including particle number and volume size distribution profiles, profiles of auxiliary variables, contributions of different factors in different seasons to the total number concentrations, diurnal variations of each of the resolved factors in the cold and warm phases, weekday/weekend analysis for each of the resolved factors, and correlation between auxiliary variables and the relative contribution of each of the resolved factors, were used to identify PM sources. A six-factor solution was identified as the optimum for the aforementioned input data. The resolved factors comprised nucleation, traffic 1, traffic 2 (with a larger mode diameter than traffic 1 factor, urban background aerosol, secondary aerosol, and soil/road dust. Traffic sources (1 and 2 were the major contributor to PM number concentrations, collectively making up to above 60 % (60.8–68.4 % of the total number concentrations during the study period. Their contribution was also significantly higher in the cold phase compared to the warm phase. Nucleation was another major factor significantly contributing to the total number concentrations (an overall contribution of 17 %, ranging from 11.7 to 24 %, with a larger contribution during the warm phase than in the cold phase. The other identified factors were urban background aerosol, secondary aerosol, and soil/road dust, with relative contributions of approximately 12

  6. A comparison of companion matrix methods to find roots of a trigonometric polynomial

    Science.gov (United States)

    Boyd, John P.

    2013-08-01

    A trigonometric polynomial is a truncated Fourier series of the form fN(t)≡∑j=0Naj cos(jt)+∑j=1N bj sin(jt). It has been previously shown by the author that zeros of such a polynomial can be computed as the eigenvalues of a companion matrix with elements which are complex valued combinations of the Fourier coefficients, the "CCM" method. However, previous work provided no examples, so one goal of this new work is to experimentally test the CCM method. A second goal is introduce a new alternative, the elimination/Chebyshev algorithm, and experimentally compare it with the CCM scheme. The elimination/Chebyshev matrix (ECM) algorithm yields a companion matrix with real-valued elements, albeit at the price of usefulness only for real roots. The new elimination scheme first converts the trigonometric rootfinding problem to a pair of polynomial equations in the variables (c,s) where c≡cos(t) and s≡sin(t). The elimination method next reduces the system to a single univariate polynomial P(c). We show that this same polynomial is the resultant of the system and is also a generator of the Groebner basis with lexicographic ordering for the system. Both methods give very high numerical accuracy for real-valued roots, typically at least 11 decimal places in Matlab/IEEE 754 16 digit floating point arithmetic. The CCM algorithm is typically one or two decimal places more accurate, though these differences disappear if the roots are "Newton-polished" by a single Newton's iteration. The complex-valued matrix is accurate for complex-valued roots, too, though accuracy decreases with the magnitude of the imaginary part of the root. The cost of both methods scales as O(N3) floating point operations. In spite of intimate connections of the elimination/Chebyshev scheme to two well-established technologies for solving systems of equations, resultants and Groebner bases, and the advantages of using only real-valued arithmetic to obtain a companion matrix with real-valued elements

  7. Comparison of Experimental Methods for Estimating Matrix Diffusion Coefficients for Contaminant Transport Modeling

    Energy Technology Data Exchange (ETDEWEB)

    Telfeyan, Katherine Christina [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Ware, Stuart Douglas [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Reimus, Paul William [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Birdsell, Kay Hanson [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2017-11-06

    Diffusion cell and diffusion wafer experiments were conducted to compare methods for estimating matrix diffusion coefficients in rock core samples from Pahute Mesa at the Nevada Nuclear Security Site (NNSS). A diffusion wafer method, in which a solute diffuses out of a rock matrix that is pre-saturated with water containing the solute, is presented as a simpler alternative to the traditional through-diffusion (diffusion cell) method. Both methods yielded estimates of matrix diffusion coefficients that were within the range of values previously reported for NNSS volcanic rocks. The difference between the estimates of the two methods ranged from 14 to 30%, and there was no systematic high or low bias of one method relative to the other. From a transport modeling perspective, these differences are relatively minor when one considers that other variables (e.g., fracture apertures, fracture spacings) influence matrix diffusion to a greater degree and tend to have greater uncertainty than diffusion coefficients. For the same relative random errors in concentration measurements, the diffusion cell method yields diffusion coefficient estimates that have less uncertainty than the wafer method. However, the wafer method is easier and less costly to implement and yields estimates more quickly, thus allowing a greater number of samples to be analyzed for the same cost and time. Given the relatively good agreement between the methods, and the lack of any apparent bias between the methods, the diffusion wafer method appears to offer advantages over the diffusion cell method if better statistical representation of a given set of rock samples is desired.

  8. Correlation between matrix metalloproteinase-9 and vascular endothelial growth factor expression in lung adenocarcinoma.

    Science.gov (United States)

    Wen, Y L; Li, L

    2015-12-29

    The aim of this study was to investigate the correlation between the expression of matrix metalloproteinase-9 (MMP-9) and vascular endothelial growth factor (VEGF) and clinicopathological features of lung adenocarcinoma. The expression of MMP-9 and VEGF was evaluated by immunohistochemistry of 30 samples from lung adenocarcinoma patients and 12 paratumoral (normal) tissue samples. In addition, the change in VEGF or MMP-9 expression after MMP-9 or VEGF blockade, respectively, was measured using western blot in lung adenocarcinoma A549 cells. High expression of MMP-9 was found in 63.3% of adenocarcinoma tissues versus 16.7% in normal tissues (P correlation was identified between MMP-9 and VEGF expression (correlation coefficient = 0.7094, P < 0.001), and their mutual overexpression was associated with clinical staging and lymph node status (P < 0.05). In addition, an decrease in VEGF protein expression was observed after MMP-9 blockade by an MMP-9-specific monoclonal antibody. Similarly, a decrease in MMP-9 protein expression was found after VEGF blockade by a VEGF-specific monoclonal antibody. In conclusion, VEGF and MMP-9 are overexpressed in lung adenocarcinoma tissues, and they have a synergistic effect on the invasion and metastasis of adenocarcinoma.

  9. Source Apportionment of PM10 by Positive Matrix Factorization in Urban Area of Mumbai, India

    Directory of Open Access Journals (Sweden)

    Indrani Gupta

    2012-01-01

    Full Text Available Particulate Matter (PM10 has been one of the main air pollutants exceeding the ambient standards in most of the major cities in India. During last few years, receptor models such as Chemical Mass Balance, Positive Matrix Factorization (PMF, PCA–APCS and UNMIX have been used to provide solutions to the source identification and contributions which are accepted for developing effective and efficient air quality management plans. Each site poses different complexities while resolving PM10 contributions. This paper reports the variability of four sites within Mumbai city using PMF. Industrial area of Mahul showed sources such as residual oil combustion and paved road dust (27%, traffic (20%, coal fired boiler (17%, nitrate (15%. Residential area of Khar showed sources such as residual oil combustion and construction (25%, motor vehicles (23%, marine aerosol and nitrate (19%, paved road dust (18% compared to construction and natural dust (27%, motor vehicles and smelting work (25%, nitrate (16% and biomass burning and paved road dust (15% in Dharavi, a low income slum residential area. The major contributors of PM10 at Colaba were marine aerosol, wood burning and ammonium sulphate (24%, motor vehicles and smelting work (22%, Natural soil (19%, nitrate and oil burning (18%.

  10. Using Separable Nonnegative Matrix Factorization Techniques for the Analysis of Time-Resolved Raman Spectra

    Science.gov (United States)

    Luce, R.; Hildebrandt, P.; Kuhlmann, U.; Liesen, J.

    2016-09-01

    The key challenge of time-resolved Raman spectroscopy is the identification of the constituent species and the analysis of the kinetics of the underlying reaction network. In this work we present an integral approach that allows for determining both the component spectra and the rate constants simultaneously from a series of vibrational spectra. It is based on an algorithm for non-negative matrix factorization which is applied to the experimental data set following a few pre-processing steps. As a prerequisite for physically unambiguous solutions, each component spectrum must include one vibrational band that does not significantly interfere with vibrational bands of other species. The approach is applied to synthetic "experimental" spectra derived from model systems comprising a set of species with component spectra differing with respect to their degree of spectral interferences and signal-to-noise ratios. In each case, the species involved are connected via monomolecular reaction pathways. The potential and limitations of the approach for recovering the respective rate constants and component spectra are discussed.

  11. Feature selection and multi-kernel learning for adaptive graph regularized nonnegative matrix factorization

    KAUST Repository

    Wang, Jim Jing-Yan

    2014-09-20

    Nonnegative matrix factorization (NMF), a popular part-based representation technique, does not capture the intrinsic local geometric structure of the data space. Graph regularized NMF (GNMF) was recently proposed to avoid this limitation by regularizing NMF with a nearest neighbor graph constructed from the input data set. However, GNMF has two main bottlenecks. First, using the original feature space directly to construct the graph is not necessarily optimal because of the noisy and irrelevant features and nonlinear distributions of data samples. Second, one possible way to handle the nonlinear distribution of data samples is by kernel embedding. However, it is often difficult to choose the most suitable kernel. To solve these bottlenecks, we propose two novel graph-regularized NMF methods, AGNMFFS and AGNMFMK, by introducing feature selection and multiple-kernel learning to the graph regularized NMF, respectively. Instead of using a fixed graph as in GNMF, the two proposed methods learn the nearest neighbor graph that is adaptive to the selected features and learned multiple kernels, respectively. For each method, we propose a unified objective function to conduct feature selection/multi-kernel learning, NMF and adaptive graph regularization simultaneously. We further develop two iterative algorithms to solve the two optimization problems. Experimental results on two challenging pattern classification tasks demonstrate that the proposed methods significantly outperform state-of-the-art data representation methods.

  12. Hyperspectral and multispectral data fusion based on linear-quadratic nonnegative matrix factorization

    Science.gov (United States)

    Benhalouche, Fatima Zohra; Karoui, Moussa Sofiane; Deville, Yannick; Ouamri, Abdelaziz

    2017-04-01

    This paper proposes three multisharpening approaches to enhance the spatial resolution of urban hyperspectral remote sensing images. These approaches, related to linear-quadratic spectral unmixing techniques, use a linear-quadratic nonnegative matrix factorization (NMF) multiplicative algorithm. These methods begin by unmixing the observable high-spectral/low-spatial resolution hyperspectral and high-spatial/low-spectral resolution multispectral images. The obtained high-spectral/high-spatial resolution features are then recombined, according to the linear-quadratic mixing model, to obtain an unobservable multisharpened high-spectral/high-spatial resolution hyperspectral image. In the first designed approach, hyperspectral and multispectral variables are independently optimized, once they have been coherently initialized. These variables are alternately updated in the second designed approach. In the third approach, the considered hyperspectral and multispectral variables are jointly updated. Experiments, using synthetic and real data, are conducted to assess the efficiency, in spatial and spectral domains, of the designed approaches and of linear NMF-based approaches from the literature. Experimental results show that the designed methods globally yield very satisfactory spectral and spatial fidelities for the multisharpened hyperspectral data. They also prove that these methods significantly outperform the used literature approaches.

  13. Contribution of non-negative matrix factorization to the classification of remote sensing images

    Science.gov (United States)

    Karoui, M. S.; Deville, Y.; Hosseini, S.; Ouamri, A.; Ducrot, D.

    2008-10-01

    Remote sensing has become an unavoidable tool for better managing our environment, generally by realizing maps of land cover using classification techniques. The classification process requires some pre-processing, especially for data size reduction. The most usual technique is Principal Component Analysis. Another approach consists in regarding each pixel of the multispectral image as a mixture of pure elements contained in the observed area. Using Blind Source Separation (BSS) methods, one can hope to unmix each pixel and to perform the recognition of the classes constituting the observed scene. Our contribution consists in using Non-negative Matrix Factorization (NMF) combined with sparse coding as a solution to BSS, in order to generate new images (which are at least partly separated images) using HRV SPOT images from Oran area, Algeria). These images are then used as inputs of a supervised classifier integrating textural information. The results of classifications of these "separated" images show a clear improvement (correct pixel classification rate improved by more than 20%) compared to classification of initial (i.e. non separated) images. These results show the contribution of NMF as an attractive pre-processing for classification of multispectral remote sensing imagery.

  14. Label-Informed Non-negative Matrix Factorization with Manifold Regularization for Discriminative Subnetwork Detection.

    Science.gov (United States)

    Watanabe, Takanori; Tunc, Birkan; Parker, Drew; Kim, Junghoon; Verma, Ragini

    2016-10-01

    In this paper, we present a novel method for obtaining a low dimensional representation of a complex brain network that: (1) can be interpreted in a neurobiologically meaningful way, (2) emphasizes group differences by accounting for label information, and (3) captures the variation in disease subtypes/severity by respecting the intrinsic manifold structure underlying the data. Our method is a supervised variant of non-negative matrix factorization (NMF), and achieves dimensionality reduction by extracting an orthogonal set of subnetworks that are interpretable, reconstructive of the original data, and also discriminative at the group level. In addition, the method includes a manifold regularizer that encourages the low dimensional representations to be smooth with respect to the intrinsic geometry of the data, allowing subjects with similar disease-severity to share similar network representations. While the method is generalizable to other types of non-negative network data, in this work we have used structural connectomes (SCs) derived from diffusion data to identify the cortical/subcortical connections that have been disrupted in abnormal neurological state. Experiments on a traumatic brain injury (TBI) dataset demonstrate that our method can identify subnetworks that can reliably classify TBI from controls and also reveal insightful connectivity patterns that may be indicative of a biomarker.

  15. Hessian regularization based non-negative matrix factorization for gene expression data clustering.

    Science.gov (United States)

    Liu, Xiao; Shi, Jun; Wang, Congzhi

    2015-01-01

    Since a key step in the analysis of gene expression data is to detect groups of genes that have similar expression patterns, clustering technique is then commonly used to analyze gene expression data. Data representation plays an important role in clustering analysis. The non-negative matrix factorization (NMF) is a widely used data representation method with great success in machine learning. Although the traditional manifold regularization method, Laplacian regularization (LR), can improve the performance of NMF, LR still suffers from the problem of its weak extrapolating power. Hessian regularization (HR) is a newly developed manifold regularization method, whose natural properties make it more extrapolating, especially for small sample data. In this work, we propose the HR-based NMF (HR-NMF) algorithm, and then apply it to represent gene expression data for further clustering task. The clustering experiments are conducted on five commonly used gene datasets, and the results indicate that the proposed HR-NMF outperforms LR-based NMM and original NMF, which suggests the potential application of HR-NMF for gene expression data.

  16. A Global Sampling Based Image Matting Using Non-Negative Matrix Factorization

    Directory of Open Access Journals (Sweden)

    NAVEED ALAM

    2017-10-01

    Full Text Available Image matting is a technique in which a foreground is separated from the background of a given image along with the pixel wise opacity. This foreground can then be seamlessly composited in a different background to obtain a novel scene. This paper presents a global non-parametric sampling algorithm over image patches and utilizes a dimension reduction technique known as NMF (Non-Negative Matrix Factorization. Although some existing non-parametric approaches use large nearby foreground and background regions to sample patches but these approaches fail to take the whole image to sample patches. It is because of the high memory and computational requirements. The use of NMF in the proposed algorithm allows the dimension reduction which reduces the computational cost and memory requirement. The use of NMF also allow the proposed approach to use the whole foreground and background region in the image and reduces the patch complexity and help in efficient patch sampling. The use of patches not only allows the incorporation of the pixel colour but also the local image structure. The use of local structures in the image is important to estimate a high-quality alpha matte especially in the images which have regions containing high texture. The proposed algorithm is evaluated on the standard data set and obtained results are comparable to the state-of-the-art matting techniques

  17. A global sampling based image matting using non-negative matrix factorization

    International Nuclear Information System (INIS)

    Alam, N.; Sarim, M.; Shaikh, A.B.

    2017-01-01

    Image matting is a technique in which a foreground is separated from the background of a given image along with the pixel wise opacity. This foreground can then be seamlessly composited in a different background to obtain a novel scene. This paper presents a global non-parametric sampling algorithm over image patches and utilizes a dimension reduction technique known as NMF (Non-Negative Matrix Factorization). Although some existing non-parametric approaches use large nearby foreground and background regions to sample patches but these approaches fail to take the whole image to sample patches. It is because of the high memory and computational requirements. The use of NMF in the proposed algorithm allows the dimension reduction which reduces the computational cost and memory requirement. The use of NMF also allow the proposed approach to use the whole foreground and background region in the image and reduces the patch complexity and help in efficient patch sampling. The use of patches not only allows the incorporation of the pixel colour but also the local image structure. The use of local structures in the image is important to estimate a high-quality alpha matte especially in the images which have regions containing high texture. The proposed algorithm is evaluated on the standard data set and obtained results are comparable to the state-of-the-art matting techniques. (author)

  18. ARMA Cholesky Factor Models for the Covariance Matrix of Linear Models.

    Science.gov (United States)

    Lee, Keunbaik; Baek, Changryong; Daniels, Michael J

    2017-11-01

    In longitudinal studies, serial dependence of repeated outcomes must be taken into account to make correct inferences on covariate effects. As such, care must be taken in modeling the covariance matrix. However, estimation of the covariance matrix is challenging because there are many parameters in the matrix and the estimated covariance matrix should be positive definite. To overcomes these limitations, two Cholesky decomposition approaches have been proposed: modified Cholesky decomposition for autoregressive (AR) structure and moving average Cholesky decomposition for moving average (MA) structure, respectively. However, the correlations of repeated outcomes are often not captured parsimoniously using either approach separately. In this paper, we propose a class of flexible, nonstationary, heteroscedastic models that exploits the structure allowed by combining the AR and MA modeling of the covariance matrix that we denote as ARMACD. We analyze a recent lung cancer study to illustrate the power of our proposed methods.

  19. Adaptive Multiview Nonnegative Matrix Factorization Algorithm for Integration of Multimodal Biomedical Data

    Directory of Open Access Journals (Sweden)

    Bisakha Ray

    2017-08-01

    Full Text Available The amounts and types of available multimodal tumor data are rapidly increasing, and their integration is critical for fully understanding the underlying cancer biology and personalizing treatment. However, the development of methods for effectively integrating multimodal data in a principled manner is lagging behind our ability to generate the data. In this article, we introduce an extension to a multiview nonnegative matrix factorization algorithm (NNMF for dimensionality reduction and integration of heterogeneous data types and compare the predictive modeling performance of the method on unimodal and multimodal data. We also present a comparative evaluation of our novel multiview approach and current data integration methods. Our work provides an efficient method to extend an existing dimensionality reduction method. We report rigorous evaluation of the method on large-scale quantitative protein and phosphoprotein tumor data from the Clinical Proteomic Tumor Analysis Consortium (CPTAC acquired using state-of-the-art liquid chromatography mass spectrometry. Exome sequencing and RNA-Seq data were also available from The Cancer Genome Atlas for the same tumors. For unimodal data, in case of breast cancer, transcript levels were most predictive of estrogen and progesterone receptor status and copy number variation of human epidermal growth factor receptor 2 status. For ovarian and colon cancers, phosphoprotein and protein levels were most predictive of tumor grade and stage and residual tumor, respectively. When multiview NNMF was applied to multimodal data to predict outcomes, the improvement in performance is not overall statistically significant beyond unimodal data, suggesting that proteomics data may contain more predictive information regarding tumor phenotypes than transcript levels, probably due to the fact that proteins are the functional gene products and therefore a more direct measurement of the functional state of the tumor. Here, we

  20. Nonnegative matrix factorization with the Itakura-Saito divergence: with application to music analysis.

    Science.gov (United States)

    Févotte, Cédric; Bertin, Nancy; Durrieu, Jean-Louis

    2009-03-01

    This letter presents theoretical, algorithmic, and experimental results about nonnegative matrix factorization (NMF) with the Itakura-Saito (IS) divergence. We describe how IS-NMF is underlaid by a well-defined statistical model of superimposed gaussian components and is equivalent to maximum likelihood estimation of variance parameters. This setting can accommodate regularization constraints on the factors through Bayesian priors. In particular, inverse-gamma and gamma Markov chain priors are considered in this work. Estimation can be carried out using a space-alternating generalized expectation-maximization (SAGE) algorithm; this leads to a novel type of NMF algorithm, whose convergence to a stationary point of the IS cost function is guaranteed. We also discuss the links between the IS divergence and other cost functions used in NMF, in particular, the Euclidean distance and the generalized Kullback-Leibler (KL) divergence. As such, we describe how IS-NMF can also be performed using a gradient multiplicative algorithm (a standard algorithm structure in NMF) whose convergence is observed in practice, though not proven. Finally, we report a furnished experimental comparative study of Euclidean-NMF, KL-NMF, and IS-NMF algorithms applied to the power spectrogram of a short piano sequence recorded in real conditions, with various initializations and model orders. Then we show how IS-NMF can successfully be employed for denoising and upmix (mono to stereo conversion) of an original piece of early jazz music. These experiments indicate that IS-NMF correctly captures the semantics of audio and is better suited to the representation of music signals than NMF with the usual Euclidean and KL costs.

  1. Predicting and understanding comprehensive drug-drug interactions via semi-nonnegative matrix factorization.

    Science.gov (United States)

    Yu, Hui; Mao, Kui-Tao; Shi, Jian-Yu; Huang, Hua; Chen, Zhi; Dong, Kai; Yiu, Siu-Ming

    2018-04-11

    Drug-drug interactions (DDIs) always cause unexpected and even adverse drug reactions. It is important to identify DDIs before drugs are used in the market. However, preclinical identification of DDIs requires much money and time. Computational approaches have exhibited their abilities to predict potential DDIs on a large scale by utilizing pre-market drug properties (e.g. chemical structure). Nevertheless, none of them can predict two comprehensive types of DDIs, including enhancive and degressive DDIs, which increases and decreases the behaviors of the interacting drugs respectively. There is a lack of systematic analysis on the structural relationship among known DDIs. Revealing such a relationship is very important, because it is able to help understand how DDIs occur. Both the prediction of comprehensive DDIs and the discovery of structural relationship among them play an important guidance when making a co-prescription. In this work, treating a set of comprehensive DDIs as a signed network, we design a novel model (DDINMF) for the prediction of enhancive and degressive DDIs based on semi-nonnegative matrix factorization. Inspiringly, DDINMF achieves the conventional DDI prediction (AUROC = 0.872 and AUPR = 0.605) and the comprehensive DDI prediction (AUROC = 0.796 and AUPR = 0.579). Compared with two state-of-the-art approaches, DDINMF shows it superiority. Finally, representing DDIs as a binary network and a signed network respectively, an analysis based on NMF reveals crucial knowledge hidden among DDIs. Our approach is able to predict not only conventional binary DDIs but also comprehensive DDIs. More importantly, it reveals several key points about the DDI network: (1) both binary and signed networks show fairly clear clusters, in which both drug degree and the difference between positive degree and negative degree show significant distribution; (2) the drugs having large degrees tend to have a larger difference between positive degree

  2. Improving the robustness of Surface Enhanced Raman Spectroscopy based sensors by Bayesian Non-negative Matrix Factorization

    DEFF Research Database (Denmark)

    Alstrøm, Tommy Sonne; Frøhling, Kasper Bayer; Larsen, Jan

    2014-01-01

    a Bayesian Non-negative Matrix Factorization (NMF) approach to identify locations of target molecules. The proposed method is able to successfully analyze the spectra and extract the target spectrum. A visualization of the loadings of the basis vector is created and the results show a clear SNR enhancement...

  3. Integral transport multiregion geometrical shadowing factor for the approximate collision probability matrix calculation of infinite closely packed lattices

    International Nuclear Information System (INIS)

    Jowzani-Moghaddam, A.

    1981-01-01

    An integral transport method of calculating the geometrical shadowing factor in multiregion annular cells for infinite closely packed lattices in cylindrical geometry is developed. This analytical method has been programmed in the TPGS code. This method is based upon a consideration of the properties of the integral transport method for a nonuniform body, which together with Bonalumi's approximations allows the determination of the approximate multiregion collision probability matrix for infinite closely packed lattices with sufficient accuracy. The multiregion geometrical shadowing factors have been calculated for variations in fuel pin annular segment rings in a geometry of annular cells. These shadowing factors can then be used in the calculation of neutron transport from one annulus to another in an infinite lattice. The result of this new geometrical shadowing and collision probability matrix are compared with the Dancoff-Ginsburg correction and the probability matrix using constant shadowing on Yankee fuel elements in an infinite lattice. In these cases the Dancoff-Ginsburg correction factor and collision probability matrix using constant shadowing are in difference by at most 6.2% and 6%, respectively

  4. ℓ2,1 Norm and Hessian Regularized Non-Negative Matrix Factorization with Discriminability for Data Representation

    Directory of Open Access Journals (Sweden)

    Peng Luo

    2017-09-01

    Full Text Available Matrix factorization based methods have widely been used in data representation. Among them, Non-negative Matrix Factorization (NMF is a promising technique owing to its psychological and physiological interpretation of spontaneously occurring data. On one hand, although traditional Laplacian regularization can enhance the performance of NMF, it still suffers from the problem of its weak extrapolating ability. On the other hand, standard NMF disregards the discriminative information hidden in the data and cannot guarantee the sparsity of the factor matrices. In this paper, a novel algorithm called ℓ 2 , 1 norm and Hessian Regularized Non-negative Matrix Factorization with Discriminability (ℓ 2 , 1 HNMFD, is developed to overcome the aforementioned problems. In ℓ 2 , 1 HNMFD, Hessian regularization is introduced in the framework of NMF to capture the intrinsic manifold structure of the data. ℓ 2 , 1 norm constraints and approximation orthogonal constraints are added to assure the group sparsity of encoding matrix and characterize the discriminative information of the data simultaneously. To solve the objective function, an efficient optimization scheme is developed to settle it. Our experimental results on five benchmark data sets have demonstrated that ℓ 2 , 1 HNMFD can learn better data representation and provide better clustering results.

  5. Reduction in the Number of Comparisons Required to Create Matrix of Expert Judgment in the Comet Method

    Directory of Open Access Journals (Sweden)

    Sałabun Wojciech

    2014-09-01

    Full Text Available Multi-criteria decision-making (MCDM methods are associated with the ranking of alternatives based on expert judgments made using a number of criteria. In the MCDM field, the distance-based approach is one popular method for receiving a final ranking. One of the newest MCDM method, which uses the distance-based approach, is the Characteristic Objects Method (COMET. In this method, the preferences of each alternative are obtained on the basis of the distance from the nearest characteristic ob jects and their values. For this purpose, the domain and fuzzy numbers set for all the considered criteria are determined. The characteristic objects are obtained as the combination of the crisp values of all the fuzzy numbers. The preference values of all the characteristic ob ject are determined based on the tournament method and the principle of indifference. Finally, the fuzzy model is constructed and is used to calculate preference values of the alternatives. In this way, a multi-criteria model is created and it is free of rank reversal phenomenon. In this approach, the matrix of expert judgment is necessary to create. For this purpose, an expert has to compare all the characteristic ob jects with each other. The number of necessary comparisons depends squarely to the number of ob jects. This study proposes the improvement of the COMET method by using the transitivity of pairwise comparisons. Three numerical examples are used to illustrate the efficiency of the proposed improvement with respect to results from the original approach. The proposed improvement reduces significantly the number of necessary comparisons to create the matrix of expert judgment.

  6. Thermometric determination of cartilage matrix temperatures during thermal chondroplasty: comparison of bipolar and monopolar radiofrequency devices.

    Science.gov (United States)

    Edwards, Ryland B; Lu, Yan; Rodriguez, Edwin; Markel, Mark D

    2002-04-01

    To compare cartilage matrix temperatures between monopolar radiofrequency energy (mRFE) and bipolar RFE (bRFE) at 3 depths under the articular surface during thermal chondroplasty. We hypothesized that cartilage temperatures would be higher at all cartilage depths for the bRFE device than for the mRFE device. Randomized trial using bovine cartilage. Sixty osteochondral sections from the femoropatellar joint of 15 adult cattle were used for this study. Using a custom jig, fluoroptic thermometry probes were placed at one of the following depths under the articular surface: 200 microm, 500 microm, or 2,000 microm. RF treatment was performed either with fluid flow (F) (120 mL/min) or without fluid flow (NF) (n = 5/depth/RFE device/flow; total specimens, 60). Irrigation fluid temperature was room temperature (22 degrees C). Thermometry data were acquired at 4 Hz for 5 seconds with the RF probe off, for 20 seconds with the RF probe on, and then for 15 seconds with the RF probe off. During RF treatment, a 0.79-cm2 area (1.0-cm diameter) of the articular surface centered over the thermometry probe was treated in a paintbrush manner in noncontact (bRFE) or light contact (mRFE). Thermal chondroplasty with bRFE resulted in higher cartilage matrix temperatures compared with mRFE for all depths and regardless of fluid flow. Bipolar RFE resulted in temperatures of 95 degrees C to 100 degrees C at 200 microm and 500 microm under the surface, with temperatures of 75 degrees C to 78 degrees C at 2,000 microm. Fluid flow during bRFE application had no effect at 200 microm. Monopolar RFE resulted in temperatures of 61 degrees C to 68 degrees C at 200 microm, 54 degrees C to 70 degrees C at 500 microm under the surface, and 28 degrees C to 30 degrees C at 2,000 microm below the surface. A significant effect of fluid flow during mRFE application occurred at 200 microm (NF, 61 degrees C; F, 63 degrees C) and 500 microm (NF, 53 degrees C; F, 68 degrees C). In this study, we found

  7. Comparison of dechlorination rates for field DNAPL vs synthetic samples: effect of sample matrix

    Science.gov (United States)

    O'Carroll, D. M.; Sakulchaicharoen, N.; Herrera, J. E.

    2015-12-01

    Nanometals have received significant attention in recent years due to their ability to rapidly destroy numerous priority source zone contaminants in controlled laboratory studies. This has led to great optimism surrounding nanometal particle injection for insitu remediation. Reported dechlorination rates vary widely among different investigators. These differences have been ascribed to differences in the iron types (granular, micro, or nano-sized iron), matrix solution chemistry and the morphology of the nZVI surface. Among these, the effects of solution chemistry on rates of reductive dechlorination of various chlorinated compounds have been investigated in several short-term laboratory studies. Variables investigated include the effect of anions or groundwater solutes such as SO4-2, Cl-, NO3-, pH, natural organic matters (NOM), surfactant, and humic acid on dechlorination reaction of various chlorinated compounds such as TCE, carbon tetrachloride (CT), and chloroform (CF). These studies have normally centered on the assessment of nZVI reactivity toward dechlorination of an isolated individual contaminant spiked into a ground water sample under ideal conditions, with limited work conducted using real field samples. In this work, the DNAPL used for the dechlorination study was obtained from a contaminatied site. This approach was selected to adequately simulate a condition where the nZVI suspension was in direct contact with DNAPL and to isolate the dechlorination activity shown by the nZVI from the groundwater matrix effects. An ideal system "synthetic DNAPL" composed of a mixture of chlorinated compounds mimicking the composition of the actual DNAPL was also dechlorinated to evaluate the DNAPL "matrix effect" on NZVI dechlorination activity. This approach allowed us to evaluate the effect of the presence of different types of organic compounds (volatile fatty acids and humic acids) found in the actual DNAPL on nZVI dechlorination activity. This presentation will

  8. Chronic mild stress influences nerve growth factor through a matrix metalloproteinase-dependent mechanism.

    Science.gov (United States)

    Kucharczyk, Mateusz; Kurek, Anna; Detka, Jan; Slusarczyk, Joanna; Papp, Mariusz; Tota, Katarzyna; Basta-Kaim, Agnieszka; Kubera, Marta; Lason, Wladyslaw; Budziszewska, Bogusława

    2016-04-01

    Stress is generally a beneficial experience that motivates an organism to action to overcome the stressful challenge. In particular situations, when stress becomes chronic might be harmful and devastating. The hypothalamus is a critical coordinator of stress and the metabolic response; therefore, disruptions in this structure may be a significant cause of the hormonal and metabolic disturbances observed in depression. Chronic stress induces adverse changes in the morphology of neural cells that are often associated with a deficiency of neurotrophic factors (NTFs); additionally, many studies indicate that insufficient NTF synthesis may participate in the pathogenesis of depression. The aim of the present study was to determine the expression of the nerve growth factor (NGF) in the hypothalamus of male rats subjected to chronic mild stress (CMS) or to prenatal stress (PS) and to PS in combination with an acute stress event (AS). It has been found that chronic mild stress, but not prenatal stress, acute stress or a combination of PS with AS, decreased the concentration of the mature form of NGF (m-NGF) in the rat hypothalamus. A discrepancy between an increase in the Ngf mRNA and a decrease in the m-NGF levels suggested that chronic mild stress inhibited NGF maturation or enhanced the degradation of this factor. We have shown that NGF degradation in the hypothalamus of rats subjected to chronic mild stress is matrix metalloproteinase-dependent and related to an increase in the active forms of some metalloproteinases (MMP), including MMP2, MMP3, MMP9 and MMP13, while the NGF maturation process does not seem to be changed. We suggested that activated MMP2 and MMP9 potently cleave the mature but not the pro- form of NGF into biologically inactive products, which is the reason for m-NGF decomposition. In turn, the enhanced expression of Ngf in the hypothalamus of these rats is an attempt to overcome the reduced levels of m-NGF. Additionally, the decreased level of m

  9. Effect Of Neutron Activation Factor On The Physico-Chemical Properties Of Hydrophilic And Hydrophobic Polymer Formulation Of Matrix Tablets

    International Nuclear Information System (INIS)

    Ibrahim Ijang; Bohari Yaacob; Nordiana, N.R.

    2011-01-01

    This study was to investigate effect of neutron activation on the physicochemical properties and in vitro dissolution of sustained-release matrix tablets. The tablets incorporation of Samarium oxide (Sm 2 O 3 ) and were compared before and after irradiation with thermal neutron for 5 minutes at 1.2 x 10 12 neutron cm -2 s -1 . The neutron activation factor did not influence the compression properties of the tablets. The dissolution tests showed that irradiation increased the release of the model drug ketoprofen from the tablets. This effect might be explained by polymer degradation. Incorporation of Sm 2 O 3 in the matrix tablets did not influence the release. (author)

  10. Expression of extracellular matrix components and related growth factors in human tendon and muscle after acute exercise

    DEFF Research Database (Denmark)

    Heinemeier, K M; Bjerrum, S S; Schjerling, P

    2013-01-01

    Acute kicking exercise induces collagen synthesis in both tendon and muscle in humans, but it is not known if this relates to increased collagen transcription and if other matrix genes are regulated. Young men performed 1 h of one-leg kicking at 67% of max workload. Biopsies were taken from...... the patellar tendon and vastus lateralis muscle of each leg at 2 (n = 10), 6 (n = 11), or 26 h (n = 10) after exercise. Levels of messenger ribonucleic acid mRNA for collagens, noncollagenous matrix proteins, and growth factors were measured with real-time reverse transcription polymerase chain reaction...

  11. Comparison of ethylcellulose matrix characteristics prepared by solid dispersion technique or physical mixing

    Directory of Open Access Journals (Sweden)

    Fatemeh Sadeghi

    2003-07-01

    Full Text Available The characteristics of ethylcellulose matrices prepared from solid dispersion systems were compared with those prepared from physical mixture of drug and polymer. Sodium diclofenac was used as a model drug and the effect of the drug:polymer ratio and the method of matrix production on tablet crushing strength, friability, drug release profile and drug release mechanism were evaluated. The results showed that increasing the polymer content in matrices increased the crushing strengths of tablets. However the friability of tablets was independent of polymer content. Drug release rate was greatly affected by the amount of polymer in the matrices and considerable decrease in release rate was observed by increasing the polymer content. It was also found that the type of mixture used for matrix production had great influence on the tablet crushing strength and drug release rate. Matrices prepared from physical mixtures of drug and polymer was harder than those prepared from solid dispersion systems, but their release rates were considerably faster. This phenomenon was attributed to the encapsulation of drug particles by polymer in matrices prepared from solid dispersion system which caused a great delay in diffusion of the drug through polymer and made diffusion as a rate retarding process in drug release mechanism.

  12. Semi-Supervised Half-Quadratic Nonnegative Matrix Factorization for Face Recognition

    KAUST Repository

    Alghamdi, Masheal M.

    2014-05-01

    Face recognition is a challenging problem in computer vision. Difficulties such as slight differences between similar faces of different people, changes in facial expressions, light and illumination condition, and pose variations add extra complications to the face recognition research. Many algorithms are devoted to solving the face recognition problem, among which the family of nonnegative matrix factorization (NMF) algorithms has been widely used as a compact data representation method. Different versions of NMF have been proposed. Wang et al. proposed the graph-based semi-supervised nonnegative learning (S2N2L) algorithm that uses labeled data in constructing intrinsic and penalty graph to enforce separability of labeled data, which leads to a greater discriminating power. Moreover the geometrical structure of labeled and unlabeled data is preserved through using the smoothness assumption by creating a similarity graph that conserves the neighboring information for all labeled and unlabeled data. However, S2N2L is sensitive to light changes, illumination, and partial occlusion. In this thesis, we propose a Semi-Supervised Half-Quadratic NMF (SSHQNMF) algorithm that combines the benefits of S2N2L and the robust NMF by the half- quadratic minimization (HQNMF) algorithm.Our algorithm improves upon the S2N2L algorithm by replacing the Frobenius norm with a robust M-Estimator loss function. A multiplicative update solution for our SSHQNMF algorithmis driven using the half- 4 quadratic (HQ) theory. Extensive experiments on ORL, Yale-A and a subset of the PIE data sets for nine M-estimator loss functions for both SSHQNMF and HQNMF algorithms are investigated, and compared with several state-of-the-art supervised and unsupervised algorithms, along with the original S2N2L algorithm in the context of classification, clustering, and robustness against partial occlusion. The proposed algorithm outperformed the other algorithms. Furthermore, SSHQNMF with Maximum Correntropy

  13. Spatiotemporal variations of ambient PM10 source contributions in Beijing in 2004 using positive matrix factorization

    Directory of Open Access Journals (Sweden)

    T. Chen

    2008-05-01

    Full Text Available Source contributions to ambient PM10 (particles with an aerodynamic diameter of 10 μm or less in Beijing, China were determined with positive matrix factorization (PMF based on ambient PM10 composition data including concentrations of organic carbon (OC, elemental carbon (EC, ions and metal elements, which were simultaneously obtained at six sites through January, April, July and October in 2004. Results from PMF indicated that seven major sources of ambient PM10 were urban fugitive dust, crustal soil, coal combustion, secondary sulfate, secondary nitrate, biomass burning with municipal incineration, and vehicle emission, respectively. In paticular, urban fugitive dust and crustal soil as two types of dust sources with similar chemical characteristics were differentiated by PMF. Urban fugitive dust contributed the most, accounting for 34.4% of total PM10 mass on an annual basis, with relatively high contributions in all four months, and even covered 50% in April. It also showed higher contributions in southwestern and southeastern areas than in central urban areas. Coal combustion was found to be the primary contributor in January, showing higher contributions in urban areas than in suburban areas with seasonal variation peaking in winter, which accounted for 15.5% of the annual average PM10 concentration. Secondary sulfate and secondary nitrate combined as the largest contributor to PM10 in July and October, with strong seasonal variation peaking in summer, accounting for 38.8% and 31.5% of the total PM10 mass in July and October, respectively. Biomass burning with municipal incineration contributions were found in all four months and accounted for 9.8% of the annual average PM10 mass concentration, with obviously higher contribution in October than in other months. Incineration sources were probably located in southwestern Beijing. Contribution from vehicle emission accounted for 5.0% and exhibited no significant seasonal variation. In sum

  14. Effect of fisetin supplementation on inflammatory factors and matrix metalloproteinase enzymes in colorectal cancer patients.

    Science.gov (United States)

    Farsad-Naeimi, Alireza; Alizadeh, Mohammad; Esfahani, Ali; Darvish Aminabad, Esmaeil

    2018-04-25

    A growing body of evidence indicates that inflammation is associated with tumorigenesis, metastasis and chemotherapeutic resistance in patients with colorectal cancer (CRC). Natural flavonoids are promising agents for inflammation-related tumor progression in patients with CRC. This study aimed to assess the efficacy of flavonoid fisetin supplementation on the inflammatory status and matrix metalloproteinase (MMP) levels in these patients. In this double-blind, randomized placebo-controlled clinical trial, 37 CRC patients undergoing chemotherapy were assigned to receive either 100 mg fisetin (n = 18) or placebo (n = 19) for seven consecutive weeks. The supplementation began one week before chemotherapy and continued until the end of the second chemotherapy cycle. Levels of interleukin (IL)-8, IL-10, high-sensitivity C-reactive protein (hs-CRP), MMP-7, and MMP-9 were measured in plasma using ELISA, before and after the intervention. The trial was registered at http://www.irct.ir (code: IRCT2015110511288N9). The participants were 55.59 ± 15.46 years old with 62.16% being male. After the intervention, the plasma levels of IL-8 and hs-CRP reduced significantly in the fisetin group (p < 0.04 and p < 0.01, respectively). Additionally, fisetin supplementation suppressed the values of MMP-7 levels (p < 0.02). However, significant changes were observed only in IL-8 concentrations in the fisetin group when compared with the placebo group (p < 0.03). The changes in the levels of other metabolic factors were not statistically significant. According to the results, fisetin could improve the inflammatory status in CRC patients, suggesting it as a novel complementary antitumor agent for these patients and warranting further studies.

  15. Positive semidefinite tensor factorizations of the two-electron integral matrix for low-scaling ab initio electronic structure.

    Science.gov (United States)

    Hoy, Erik P; Mazziotti, David A

    2015-08-14

    Tensor factorization of the 2-electron integral matrix is a well-known technique for reducing the computational scaling of ab initio electronic structure methods toward that of Hartree-Fock and density functional theories. The simplest factorization that maintains the positive semidefinite character of the 2-electron integral matrix is the Cholesky factorization. In this paper, we introduce a family of positive semidefinite factorizations that generalize the Cholesky factorization. Using an implementation of the factorization within the parametric 2-RDM method [D. A. Mazziotti, Phys. Rev. Lett. 101, 253002 (2008)], we study several inorganic molecules, alkane chains, and potential energy curves and find that this generalized factorization retains the accuracy and size extensivity of the Cholesky factorization, even in the presence of multi-reference correlation. The generalized family of positive semidefinite factorizations has potential applications to low-scaling ab initio electronic structure methods that treat electron correlation with a computational cost approaching that of the Hartree-Fock method or density functional theory.

  16. Positive semidefinite tensor factorizations of the two-electron integral matrix for low-scaling ab initio electronic structure

    Energy Technology Data Exchange (ETDEWEB)

    Hoy, Erik P.; Mazziotti, David A., E-mail: damazz@uchicago.edu [Department of Chemistry and The James Franck Institute, The University of Chicago, Chicago, Illinois 60637 (United States)

    2015-08-14

    Tensor factorization of the 2-electron integral matrix is a well-known technique for reducing the computational scaling of ab initio electronic structure methods toward that of Hartree-Fock and density functional theories. The simplest factorization that maintains the positive semidefinite character of the 2-electron integral matrix is the Cholesky factorization. In this paper, we introduce a family of positive semidefinite factorizations that generalize the Cholesky factorization. Using an implementation of the factorization within the parametric 2-RDM method [D. A. Mazziotti, Phys. Rev. Lett. 101, 253002 (2008)], we study several inorganic molecules, alkane chains, and potential energy curves and find that this generalized factorization retains the accuracy and size extensivity of the Cholesky factorization, even in the presence of multi-reference correlation. The generalized family of positive semidefinite factorizations has potential applications to low-scaling ab initio electronic structure methods that treat electron correlation with a computational cost approaching that of the Hartree-Fock method or density functional theory.

  17. Comparison of matrix method and ray tracing in the study of complex optical systems

    Science.gov (United States)

    Anterrieu, Eric; Perez, Jose-Philippe

    2000-06-01

    In the context of the classical study of optical systems within the geometrical Gauss approximation, the cardinal elements are efficiently obtained with the aid of the transfer matrix between the input and output planes of the system. In order to take into account the geometrical aberrations, a ray tracing approach, using the Snell- Descartes laws, has been implemented in an interactive software. Both methods are applied for measuring the correction to be done to a human eye suffering from ametropia. This software may be used by optometrists and ophthalmologists for solving the problems encountered when considering this pathology. The ray tracing approach gives a significant improvement and could be very helpful for a better understanding of an eventual surgical act.

  18. Comparison of various tool wear prediction methods during end milling of metal matrix composite

    Science.gov (United States)

    Wiciak, Martyna; Twardowski, Paweł; Wojciechowski, Szymon

    2018-02-01

    In this paper, the problem of tool wear prediction during milling of hard-to-cut metal matrix composite Duralcan™ was presented. The conducted research involved the measurements of acceleration of vibrations during milling with constant cutting conditions, and evaluation of the flank wear. Subsequently, the analysis of vibrations in time and frequency domain, as well as the correlation of the obtained measures with the tool wear values were conducted. The validation of tool wear diagnosis in relation to selected diagnostic measures was carried out with the use of one variable and two variables regression models, as well as with the application of artificial neural networks (ANN). The comparative analysis of the obtained results enable.

  19. Elements of comparison between different inert matrix fuels towards plutonium use and safety coefficients

    International Nuclear Information System (INIS)

    Baldi, St.; Porta, J.

    2000-08-01

    This work deals with the CERMET fuels, chosen for their good behaviour under irradiation and their high thermal conductivity. The kinetic coefficients have been particularly studied. Comparisons have been made with other solutions using other composite fuels in particular the solid solutions and the ROX solution. The core control requiring an heterogeneous assembly, we propose an assembly whose characteristics are compared with those of the APA reference. (O.M.)

  20. Testing the usability of the Rapid Impact Assessment Matrix (RIAM) method for comparison of EIA and SEA results

    International Nuclear Information System (INIS)

    Kuitunen, Markku; Jalava, Kimmo; Hirvonen, Kimmo

    2008-01-01

    This study examines how the results of Environmental Impact Assessment (EIA) and Strategic Environmental Assessment (SEA) could be compared using the Rapid Impact Assessment Matrix (RIAM) method. There are many tools and techniques that have been developed for use in impact assessment processes, including scoping, checklists, matrices, qualitative and quantitative models, literature reviews, and decision-support systems. While impact assessment processes have become more technically complicated, it is recognized that approaches including simpler applications of available tools and techniques are also appropriate. The Rapid Impact Assessment Matrix (RIAM) is a tool for organizing, analysing and presenting the results of a holistic EIA. RIAM was originally developed to compare the impact of alternative procedures in a single project. In this study, we used RIAM to compare the environmental and social impact of different projects, plans and programs realized within the same geographical area. RIAM scoring is based on five separate criteria. The RIAM criteria were applied to the impact that was considered to be the most significant in the evaluated cases, and scores were given both on environmental and social impact. Our results revealed that the RIAM method could be used for comparison and ranking of separate and distinct projects, plans, programs and policies, based on their negative or positive impact. Our data included 142 cases from the area of Central Finland that is covered by the Regional Council of Central Finland. This sample consisted of various types of projects, ranging from road construction to education programs that applied for EU funding

  1. TRENDS OF THE FACTORING TURNOVER IN INTERNATIONAL COMPARISONS

    Directory of Open Access Journals (Sweden)

    Éva DARABOS

    2017-05-01

    Full Text Available The factoring scheme was developed by the competition between the market operators and the need for the most favourable conditions of sale. The seller is constrained to provide loans on a broad scale therefore the seller may have liquidity problems. In cases of this kind, the seller can apply to a factoring company in order to access sources, instead of a bank loan. The factoring service has a price. Decision of the financial managers can largely contribute to choosing the appropriate funding form to retain the continuous liquidity situation of an enterprise. Aim of the article is to present the main tendencies of the factoring turnover in international comparisons, highlighting the characteristics of the financial service by its direction, sectorial distribution and customer size in Hungary. It has been estimated that the factoring financing approaches 10% of the short-term loan stocks of SMEs required from banks which indicates that the factoring is now far beyond the marginal financial service but it is an essential element of the short-term financing toolkit.

  2. Constructing stage-structured matrix population models from life tables: comparison of methods

    Directory of Open Access Journals (Sweden)

    Masami Fujiwara

    2017-10-01

    Full Text Available A matrix population model is a convenient tool for summarizing per capita survival and reproduction rates (collectively vital rates of a population and can be used for calculating an asymptotic finite population growth rate (λ and generation time. These two pieces of information can be used for determining the status of a threatened species. The use of stage-structured population models has increased in recent years, and the vital rates in such models are often estimated using a life table analysis. However, potential bias introduced when converting age-structured vital rates estimated from a life table into parameters for a stage-structured population model has not been assessed comprehensively. The objective of this study was to investigate the performance of methods for such conversions using simulated life histories of organisms. The underlying models incorporate various types of life history and true population growth rates of varying levels. The performance was measured by comparing differences in λ and the generation time calculated using the Euler-Lotka equation, age-structured population matrices, and several stage-structured population matrices that were obtained by applying different conversion methods. The results show that the discretization of age introduces only small bias in λ or generation time. Similarly, assuming a fixed age of maturation at the mean age of maturation does not introduce much bias. However, aggregating age-specific survival rates into a stage-specific survival rate and estimating a stage-transition rate can introduce substantial bias depending on the organism’s life history type and the true values of λ. In order to aggregate survival rates, the use of the weighted arithmetic mean was the most robust method for estimating λ. Here, the weights are given by survivorship curve after discounting with λ. To estimate a stage-transition rate, matching the proportion of individuals transitioning, with λ used

  3. NMF-mGPU: non-negative matrix factorization on multi-GPU systems.

    Science.gov (United States)

    Mejía-Roa, Edgardo; Tabas-Madrid, Daniel; Setoain, Javier; García, Carlos; Tirado, Francisco; Pascual-Montano, Alberto

    2015-02-13

    In the last few years, the Non-negative Matrix Factorization ( NMF ) technique has gained a great interest among the Bioinformatics community, since it is able to extract interpretable parts from high-dimensional datasets. However, the computing time required to process large data matrices may become impractical, even for a parallel application running on a multiprocessors cluster. In this paper, we present NMF-mGPU, an efficient and easy-to-use implementation of the NMF algorithm that takes advantage of the high computing performance delivered by Graphics-Processing Units ( GPUs ). Driven by the ever-growing demands from the video-games industry, graphics cards usually provided in PCs and laptops have evolved from simple graphics-drawing platforms into high-performance programmable systems that can be used as coprocessors for linear-algebra operations. However, these devices may have a limited amount of on-board memory, which is not considered by other NMF implementations on GPU. NMF-mGPU is based on CUDA ( Compute Unified Device Architecture ), the NVIDIA's framework for GPU computing. On devices with low memory available, large input matrices are blockwise transferred from the system's main memory to the GPU's memory, and processed accordingly. In addition, NMF-mGPU has been explicitly optimized for the different CUDA architectures. Finally, platforms with multiple GPUs can be synchronized through MPI ( Message Passing Interface ). In a four-GPU system, this implementation is about 120 times faster than a single conventional processor, and more than four times faster than a single GPU device (i.e., a super-linear speedup). Applications of GPUs in Bioinformatics are getting more and more attention due to their outstanding performance when compared to traditional processors. In addition, their relatively low price represents a highly cost-effective alternative to conventional clusters. In life sciences, this results in an excellent opportunity to facilitate the

  4. Learning Microbial Community Structures with Supervised and Unsupervised Non-negative Matrix Factorization.

    Science.gov (United States)

    Cai, Yun; Gu, Hong; Kenney, Toby

    2017-08-31

    Learning the structure of microbial communities is critical in understanding the different community structures and functions of microbes in distinct individuals. We view microbial communities as consisting of many subcommunities which are formed by certain groups of microbes functionally dependent on each other. The focus of this paper is on methods for extracting the subcommunities from the data, in particular Non-Negative Matrix Factorization (NMF). Our methods can be applied to both OTU data and functional metagenomic data. We apply the existing unsupervised NMF method and also develop a new supervised NMF method for extracting interpretable information from classification problems. The relevance of the subcommunities identified by NMF is demonstrated by their excellent performance for classification. Through three data examples, we demonstrate how to interpret the features identified by NMF to draw meaningful biological conclusions and discover hitherto unidentified patterns in the data. Comparing whole metagenomes of various mammals, (Muegge et al., Science 332:970-974, 2011), the biosynthesis of macrolides pathway is found in hindgut-fermenting herbivores, but not carnivores. This is consistent with results in veterinary science that macrolides should not be given to non-ruminant herbivores. For time series microbiome data from various body sites (Caporaso et al., Genome Biol 12:50, 2011), a shift in the microbial communities is identified for one individual. The shift occurs at around the same time in the tongue and gut microbiomes, indicating that the shift is a genuine biological trait, rather than an artefact of the method. For whole metagenome data from IBD patients and healthy controls (Qin et al., Nature 464:59-65, 2010), we identify differences in a number of pathways (some known, others new). NMF is a powerful tool for identifying the key features of microbial communities. These identified features can not only be used to perform difficult

  5. A Damage Resistance Comparison Between Candidate Polymer Matrix Composite Feedline Materials

    Science.gov (United States)

    Nettles, A. T

    2000-01-01

    As part of NASAs focused technology programs for future reusable launch vehicles, a task is underway to study the feasibility of using the polymer matrix composite feedlines instead of metal ones on propulsion systems. This is desirable to reduce weight and manufacturing costs. The task consists of comparing several prototype composite feedlines made by various methods. These methods are electron-beam curing, standard hand lay-up and autoclave cure, solvent assisted resin transfer molding, and thermoplastic tape laying. One of the critical technology drivers for composite components is resistance to foreign objects damage. This paper presents results of an experimental study of the damage resistance of the candidate materials that the prototype feedlines are manufactured from. The materials examined all have a 5-harness weave of IM7 as the fiber constituent (except for the thermoplastic, which is unidirectional tape laid up in a bidirectional configuration). The resin tested were 977-6, PR 520, SE-SA-1, RS-E3 (e-beam curable), Cycom 823 and PEEK. The results showed that the 977-6 and PEEK were the most damage resistant in all tested cases.

  6. Effective Factors in Severity of Traffic Accident-Related Traumas; an Epidemiologic Study Based on the Haddon Matrix.

    Science.gov (United States)

    Masoumi, Kambiz; Forouzan, Arash; Barzegari, Hassan; Asgari Darian, Ali; Rahim, Fakher; Zohrevandi, Behzad; Nabi, Somayeh

    2016-01-01

    Traffic accidents are the 8(th) cause of mortality in different countries and are expected to rise to the 3(rd) rank by 2020. Based on the Haddon matrix numerous factors such as environment, host, and agent can affect the severity of traffic-related traumas. Therefore, the present study aimed to evaluate the effective factors in severity of these traumas based on Haddon matrix. In the present 1-month cross-sectional study, all the patients injured in traffic accidents, who were referred to the ED of Imam Khomeini and Golestan Hospitals, Ahvaz, Iran, during March 2013 were evaluated. Based on the Haddon matrix, effective factors in accident occurrence were defined in 3 groups of host, agent, and environment. Demographic data of the patients and data regarding Haddon risk factors were extracted and analyzed using SPSS version 20. 700 injured people with the mean age of 29.66 ± 12.64 years (3-82) were evaluated (92.4% male). Trauma mechanism was car-pedestrian in 308 (44%) of the cases and car-motorcycle in 175 (25%). 610 (87.1%) cases were traffic accidents and 371 (53%) occurred in the time between 2 pm and 8 pm. Violation of speed limit was the most common violation with 570 (81.4%) cases, followed by violation of right-of-way in 57 (8.1%) patients. 59.9% of the severe and critical injuries had occurred on road accidents, while 61.3% of the injuries caused by traffic accidents were mild to moderate (p accidents (p severity of traffic accident-related traumas were age over 50, not using safety tools, and undertaking among host-related factors; insufficient environment safety, road accidents and time between 2 pm and 8 pm among environmental factors; and finally, rollover, car-pedestrian, and motorcycle-pedestrian accidents among the agent factors.

  7. Human macrophages primed with angiogenic factors show dynamic plasticity, irrespective of extracellular matrix components

    NARCIS (Netherlands)

    Ploeger, Diana T. A.; van Putten, Sander M.; Koerts, Jasper A.; van Luyn, Marja J. A.; Harmsen, Martin C.

    Macrophages are important in inflammation as well as in tissue repair processes. They can be activated by various stimuli and classified into two major groups: M1 (classically activated) or M2 (alternatively activated). Inflammation, angiogenesis and matrix remodeling play a major role in tissue

  8. BJUT at TREC 2015 Microblog Track: Real-Time Filtering Using Non-negative Matrix Factorization

    Science.gov (United States)

    2015-11-20

    query accurate ambiguity intergration Tweets Vector Preprocessing W-d matrix Feature vector Similarity ranking Recommended twittres Get...recommendation tech- nique based on product category attributes[J]. Expert Systems with Applications, 2009, 36(9): 11480-11488. [5] Sobecki J, Babiak E,Sanina M

  9. High performance matrix inversion based on LU factorization for multicore architectures

    KAUST Repository

    Dongarra, Jack; Faverge, Mathieu; Ltaief, Hatem; Luszczek, Piotr R.

    2011-01-01

    on the available processing units. The reported results from our LU-based matrix inversion implementation significantly outperform the state-of-the-art numerical libraries such as LAPACK (5x), MKL (5x) and ScaLAPACK (2.5x) on a contemporary AMD platform with four

  10. Factors affecting alcohol-water pervaporation performance of hydrophobic zeolite-silicone rubber mixed matrix membranes

    Science.gov (United States)

    Mixed matrix membranes (MMMs) consisting of ZSM-5 zeolite particles dispersed in silicone rubber exhibited ethanol-water pervaporation permselectivities up to 5 times that of silicone rubber alone and 3 times higher than simple vapor-liquid equilibrium (VLE). A number of conditi...

  11. Matrix metalloproteinase-2 is a consistent prognostic factor in gastric cancer.

    NARCIS (Netherlands)

    Kubben, F.J.G.M.; Sier, C.F.M.; Duijn, W. van; Griffioen, G.; Hanemaaijer, R.; Velde, C.J. van de; Krieken, J.H.J.M. van; Lamers, C.B.H.W.; Verspaget, H.W.

    2006-01-01

    In a pioneer study, we showed 10 years ago that enhanced tissue levels of the matrix metalloproteinases (MMPs) MMP-2 and MMP-9 in gastric cancers, as determined by zymography, were related with worse overall survival of the patients. To corroborate these observations, we now assessed MMP-2 and MMP-9

  12. Matrix metalloproteinase-2 is a consistent prognostic factor in gastric cancer

    NARCIS (Netherlands)

    Kubben, F.J.G.M.; Sier, C.F.M.; Duijn, W. van; Griffioen, G.; Hanemaaijer, R.; Velde, C.J.H. van de; Krieken, J.H.J.M. van; Lamers, C.B.H.W.; Verspaget, H.W.

    2006-01-01

    In a pioneer study, we showed 10 years ago that enhanced tissue levels of the matrix metalloproteinases (MMPs) MMP-2 and MMP-9 in gastric cancers, as determined by zymography, were related with worse overall survival of the patients. To corroborate these observations, we now assessed MMP-2 and MMP-9

  13. IgE-mediated basophil tumour necrosis factor alpha induces matrix metalloproteinase-9 from monocytes

    DEFF Research Database (Denmark)

    Falkencrone, Sidsel; Poulsen, Lars K.; Bindslev-Jensen, Carsten

    2013-01-01

    IgE-mediated activation of mast cells has been reported to induce the release of tumour necrosis alpha (TNF-α), which may display autocrine effects on these cells by inducing the generation of the tissue remodelling protease matrix metalloproteinase-9 (MMP-9). While mast cells and basophils have...

  14. Optical Properties of Biomass Burning Aerosols: Comparison of Experimental Measurements and T-Matrix Calculations

    Directory of Open Access Journals (Sweden)

    Samin Poudel

    2017-11-01

    Full Text Available The refractive index (RI is an important parameter in describing the radiative impacts of aerosols. It is important to constrain the RI of aerosol components, since there is still significant uncertainty regarding the RI of biomass burning aerosols. Experimentally measured extinction cross-sections, scattering cross-sections, and single scattering albedos for white pine biomass burning (BB aerosols under two different burning and sampling conditions were modeled using T-matrix theory. The refractive indices were extracted from these calculations. Experimental measurements were conducted using a cavity ring-down spectrometer to measure the extinction, and a nephelometer to measure the scattering of size-selected aerosols. BB aerosols were obtained by burning white pine using (1 an open fire in a burn drum, where the aerosols were collected in distilled water using an impinger, and then re-aerosolized after several days, and (2 a tube furnace to directly introduce the BB aerosols into an indoor smog chamber, where BB aerosols were then sampled directly. In both cases, filter samples were also collected, and electron microscopy images were used to obtain the morphology and size information used in the T-matrix calculations. The effective radius of the particles collected on filter media from the open fire was approximately 245 nm, whereas it was approximately 76 nm for particles from the tube furnace burns. For samples collected in distilled water, the real part of the RI increased with increasing particle size, and the imaginary part decreased. The imaginary part of the RI was also significantly larger than the reported values for fresh BB aerosol samples. For the particles generated in the tube furnace, the real part of the RI decreased with particle size, and the imaginary part was much smaller and nearly constant. The RI is sensitive to particle size and sampling method, but there was no wavelength dependence over the range considered (500

  15. Canonical polyadic decomposition of third-order semi-nonnegative semi-symmetric tensors using LU and QR matrix factorizations

    Science.gov (United States)

    Wang, Lu; Albera, Laurent; Kachenoura, Amar; Shu, Huazhong; Senhadji, Lotfi

    2014-12-01

    Semi-symmetric three-way arrays are essential tools in blind source separation (BSS) particularly in independent component analysis (ICA). These arrays can be built by resorting to higher order statistics of the data. The canonical polyadic (CP) decomposition of such semi-symmetric three-way arrays allows us to identify the so-called mixing matrix, which contains the information about the intensities of some latent source signals present in the observation channels. In addition, in many applications, such as the magnetic resonance spectroscopy (MRS), the columns of the mixing matrix are viewed as relative concentrations of the spectra of the chemical components. Therefore, the two loading matrices of the three-way array, which are equal to the mixing matrix, are nonnegative. Most existing CP algorithms handle the symmetry and the nonnegativity separately. Up to now, very few of them consider both the semi-nonnegativity and the semi-symmetry structure of the three-way array. Nevertheless, like all the methods based on line search, trust region strategies, and alternating optimization, they appear to be dependent on initialization, requiring in practice a multi-initialization procedure. In order to overcome this drawback, we propose two new methods, called [InlineEquation not available: see fulltext.] and [InlineEquation not available: see fulltext.], to solve the problem of CP decomposition of semi-nonnegative semi-symmetric three-way arrays. Firstly, we rewrite the constrained optimization problem as an unconstrained one. In fact, the nonnegativity constraint of the two symmetric modes is ensured by means of a square change of variable. Secondly, a Jacobi-like optimization procedure is adopted because of its good convergence property. More precisely, the two new methods use LU and QR matrix factorizations, respectively, which consist in formulating high-dimensional optimization problems into several sequential polynomial and rational subproblems. By using both LU

  16. Link predication based on matrix factorization by fusion of multi class organizations of the network

    OpenAIRE

    Jiao, Pengfei; Cai, Fei; Feng, Yiding; Wang, Wenjun

    2017-01-01

    Link predication aims at forecasting the latent or unobserved edges in the complex networks and has a wide range of applications in reality. Almost existing methods and models only take advantage of one class organization of the networks, which always lose important information hidden in other organizations of the network. In this paper, we propose a link predication framework which makes the best of the structure of networks in different level of organizations based on nonnegative matrix fac...

  17. Quantification of uncertainties in turbulence modeling: A comparison of physics-based and random matrix theoretic approaches

    International Nuclear Information System (INIS)

    Wang, Jian-Xun; Sun, Rui; Xiao, Heng

    2016-01-01

    Highlights: • Compared physics-based and random matrix methods to quantify RANS model uncertainty. • Demonstrated applications of both methods in channel ow over periodic hills. • Examined the amount of information introduced in the physics-based approach. • Discussed implications to modeling turbulence in both near-wall and separated regions. - Abstract: Numerical models based on Reynolds-Averaged Navier-Stokes (RANS) equations are widely used in engineering turbulence modeling. However, the RANS predictions have large model-form uncertainties for many complex flows, e.g., those with non-parallel shear layers or strong mean flow curvature. Quantification of these large uncertainties originating from the modeled Reynolds stresses has attracted attention in the turbulence modeling community. Recently, a physics-based Bayesian framework for quantifying model-form uncertainties has been proposed with successful applications to several flows. Nonetheless, how to specify proper priors without introducing unwarranted, artificial information remains challenging to the current form of the physics-based approach. Another recently proposed method based on random matrix theory provides the prior distributions with maximum entropy, which is an alternative for model-form uncertainty quantification in RANS simulations. This method has better mathematical rigorousness and provides the most non-committal prior distributions without introducing artificial constraints. On the other hand, the physics-based approach has the advantages of being more flexible to incorporate available physical insights. In this work, we compare and discuss the advantages and disadvantages of the two approaches on model-form uncertainty quantification. In addition, we utilize the random matrix theoretic approach to assess and possibly improve the specification of priors used in the physics-based approach. The comparison is conducted through a test case using a canonical flow, the flow past

  18. Evaluating the Effectiveness of Cryopreserved Acellular Dermal Matrix in Immediate Expander-Based Breast Reconstruction: A Comparison Study

    Directory of Open Access Journals (Sweden)

    So-Young Kim

    2015-05-01

    Full Text Available BackgroundCGCryoDerm was first introduced in 2010 and offers a different matrix preservation processes for freezing without drying preparation. From a theoretical perspective, CGCryoDerm has a more preserved dermal structure and more abundant growth factors for angiogenesis and recellularization. In the current study, the authors performed a retrospective study to evaluate freezing- and freeze-drying-processed acellular dermal matrix (ADM to determine whether any differences were present in an early complication profile.MethodsPatients who underwent ADM-assisted tissue expander placement for two stage breast reconstruction between January of 2013 and March of 2014 were retrospectively reviewed and divided into two groups based on the types of ADM-assisted expander reconstruction (CGDerm vs. CGCryoDerm. Complications were divided into four main categories and recorded as follows: seroma, hematoma, infection, and mastectomy skin flap necrosis.ResultsIn a total of 82 consecutive patients, the CGCryoDerm group had lower rates of seroma when compared to the CGDerm group without statistical significance (3.0% vs. 10.2%, P=0.221, respectively. Other complications were similar in both groups. Reconstructions with CGCryoDerm were found to have a significantly longer period of drainage when compared to reconstructions with CGDerm (11.91 days vs. 10.41 days, P=0.043.ConclusionsPreliminary findings indicate no significant differences in early complications between implant/expander-based reconstructions using CGCryoderm and those using CGDerm.

  19. Development of Normalization Factors for Canada and the United States and Comparison with European Factors

    DEFF Research Database (Denmark)

    Lautier, Anne; Rosenbaum, Ralph K.; Margni, Manuele

    2010-01-01

    In Life Cycle Assessment (LCA), normalization calculates the magnitude of an impact (midpoint or endpoint) relative to the total effect of a given reference. The goal of this work is to calculate normalization factors for Canada and the US and to compare them with existing European normalization...... factors. The differences between geographical areas were highlighted by identifying and comparing the main contributors to a given impact category in Canada, the US and Europe. This comparison verified that the main contributors in Europe and in the US are also present in the Canadian inventory. It also...

  20. Pro-inflammatory stimulation of meniscus cells increases production of matrix metalloproteinases and additional catabolic factors involved in osteoarthritis pathogenesis

    Science.gov (United States)

    Stone, Austin V.; Loeser, Richard F.; Vanderman, Kadie S.; Long, David L.; Clark, Stephanie C.; Ferguson, Cristin M.

    2014-01-01

    Objective Meniscus injury increases the risk of osteoarthritis; however, the biologic mechanism remains unknown. We hypothesized that pro-inflammatory stimulation of meniscus would increase production of matrix-degrading enzymes, cytokines and chemokines which cause joint tissue destruction and could contribute to osteoarthritis development. Design Meniscus and cartilage tissue from healthy tissue donors and total knee arthroplasties was cultured. Primary cell cultures were stimulated with pro-inflammatory factors [IL-1β, IL-6, or fibronectin fragments (FnF)] and cellular responses were analyzed by real-time PCR, protein arrays and immunoblots. To determine if NF-κB was required for MMP production, meniscus cultures were treated with inflammatory factors with and without the NF-κB inhibitor, hypoestoxide. Results Normal and osteoarthritic meniscus cells increased their MMP secretion in response to stimulation, but specific patterns emerged that were unique to each stimulus with the greatest number of MMPs expressed in response to FnF. Meniscus collagen and connective tissue growth factor gene expression was reduced. Expression of cytokines (IL-1α, IL-1β, IL-6), chemokines (IL-8, CXCL1, CXCL2, CSF1) and components of the NF-κB and tumor necrosis factor (TNF) family were significantly increased. Cytokine and chemokine protein production was also increased by stimulation. When primary cell cultures were treated with hypoestoxide in conjunction with pro-inflammatory stimulation, p65 activation was reduced as were MMP-1 and MMP-3 production. Conclusions Pro-inflammatory stimulation of meniscus cells increased matrix metalloproteinase production and catabolic gene expression. The meniscus could have an active biologic role in osteoarthritis development following joint injury through increased production of cytokines, chemokines, and matrix-degrading enzymes. PMID:24315792

  1. A parton shower based on factorization of the quantum density matrix

    OpenAIRE

    Nagy, Zoltan; Soper, Davison E.

    2014-01-01

    We present first results from a new parton shower event generator, D eductor . Anticipating a need for an improved treatment of parton color and spin, the structure of the generator is based on the quantum density matrix in color and spin space. So far, D eductor implements only a standard spin-averaged treatment of spin in parton splittings. Although D eductor implements an improved treatment of color, in this paper we present results in the standard leading color approximation so that we ca...

  2. Remembrance of Dead Cells Past: Discovering That the Extracellular Matrix Is a Cell Survival Factor

    OpenAIRE

    Schwartz, Martin A.

    2010-01-01

    In 1992, Jere Meredith and I followed up on a serendipitous observation and showed that matrix deprivation can lead to apoptosis. Our article in Molecular Biology of the Cell, together with work form Steve Frisch's lab, helped establish the paradigm that integrin signals control cell survival in a variety of systems. It has been a pleasure to watch that work take on a life of its own as other investigators have explored its role in processes such as cavitation, regression of the mammary gland...

  3. A parton shower based on factorization of the quantum density matrix

    International Nuclear Information System (INIS)

    Nagy, Zoltan; Soper, Davison E.

    2014-01-01

    We present rst results from a new parton shower event generator, DEDUCTOR. Anticipating a need for an improved treatment of parton color and spin, the structure of the generator is based on the quantum density matrix in color and spin space. So far, DEDUCTOR implements only a standard spin-averaged treatment of spin in parton splittings. Although DEDUCTOR implements an improved treatment of color, in this paper we present results in the standard leading color approximation so that we can compare to the generator PYTHIA. The algorithms used incorporate a virtuality based shower ordering parameter and massive initial state bottom and charm quarks.

  4. Solving symmetric-definite quadratic lambda-matrix problems without factorization

    International Nuclear Information System (INIS)

    Scott, D.S.; Ward, R.C.

    1982-01-01

    Algorithms are presented for computing some of the eigenvalues and their associated eigenvectors of the quadratic lambda-matrix M lambda 2 C lambda + K. M, C, and K are assumed to have special symmetry-type properties which insure that theory analogous to the standard symmetric eigenproblem exists. The algorithms are based on a generalization of the Rayleigh quotient and the Lanczos method for computing eigenpairs of standard symmetric eigenproblems. Monotone quadratic convergence of the basic method is proved. Test examples are presented

  5. Quantitative comparison of some aesthetic factors among rivers

    Science.gov (United States)

    Leopold, Luna Bergere

    1969-01-01

    It is difficult to evaluate the factors contributing to aesthetic or nonmonetary aspects of a landscape. In contrast, aspects which lend themselves to cost-benefit comparisons are now treated in a routine way. As a result, nonmonetary values are described either in emotion-loaded words or else are mentioned and thence forgotten.The present report is a preliminary attempt to quantify some elements of aesthetic appeal while eliminating, insofar as possible, value judgments or personal preferences. If methods of recording such factors can be developed, the results promise to be a useful, new kind of basic data needed in many planning and decision-making circumstances. Such data would be especially useful when choices must be made among alternative courses of action. Such data would tend to provide a more prominent consideration of the nonmonetary aspects of a landscape.Assignment of quantitative estimates to aesthetic factors leads not so much to ratios of value as to relative rank positions. In fact, value itself tends to carry a connotation of preference, whereas ranking can more easily be used for categorization without attribution of preference and thus it tends to a void the introduction at too early a stage of differences in preference. Because the Federal Power Commission has been studying an application for a permit to construct one or more additional hydropower dams in the vicinity of Hells Canyon of the Snake River, the localities studied for the present discussion are in that region of Idaho. Hopefully, the data collected will provide some useful information on factors related to nonmonetary values in the region. The present discussion has been kept free of the preference judgments of the writer, and throughout the discussions observations are treated as facts.

  6. Effective Factors in Severity of Traffic Accident-Related Traumas; an Epidemiologic Study Based on the Haddon Matrix

    Directory of Open Access Journals (Sweden)

    Kambiz Masoumi

    2016-04-01

    Full Text Available Introduction: Traffic accidents are the 8th cause of mortality in different countries and are expected to rise to the 3rd rank by 2020. Based on the Haddon matrix numerous factors such as environment, host, and agent can affect the severity of traffic-related traumas. Therefore, the present study aimed to evaluate the effective factors in severity of these traumas based on Haddon matrix. Methods: In the present 1-month cross-sectional study, all the patients injured in traffic accidents, who were referred to the ED of Imam Khomeini and Golestan Hospitals, Ahvaz, Iran, during March 2013 were evaluated. Based on the Haddon matrix, effective factors in accident occurrence were defined in 3 groups of host, agent, and environment. Demographic data of the patients and data regarding Haddon risk factors were extracted and analyzed using SPSS version 20. Results: 700 injured people with the mean age of 29.66 ± 12.64 years (3-82 were evaluated (92.4% male. Trauma mechanism was car-pedestrian in 308 (44% of the cases and car-motorcycle in 175 (25%. 610 (87.1% cases were traffic accidents and 371 (53% occurred in the time between 2 pm and 8 pm. Violation of speed limit was the most common violation with 570 (81.4% cases, followed by violation of right-of-way in 57 (8.1% patients. 59.9% of the severe and critical injuries had occurred on road accidents, while 61.3% of the injuries caused by traffic accidents were mild to moderate (p < 0.001. The most common mechanisms of trauma for critical injuries were rollover (72.5%, motorcycle-pedestrian (23.8%, and car-motorcycle (13.14% accidents (p < 0.001. Conclusion: Based on the results of the present study, the most important effective factors in severity of traffic accident-related traumas were age over 50, not using safety tools, and undertaking among host-related factors; insufficient environment safety, road accidents and time between 2 pm and 8 pm among environmental factors; and finally, rollover, car

  7. Non-adiabatic quantum evolution: The S matrix as a geometrical phase factor

    Energy Technology Data Exchange (ETDEWEB)

    Saadi, Y., E-mail: S_yahiadz@yahoo.fr [Laboratoire de Physique Quantique et Systèmes Dynamiques, Faculté des Sciences, Université Ferhat Abbas de Sétif, Sétif 19000 (Algeria); Maamache, M. [Laboratoire de Physique Quantique et Systèmes Dynamiques, Faculté des Sciences, Université Ferhat Abbas de Sétif, Sétif 19000 (Algeria)

    2012-03-19

    We present a complete derivation of the exact evolution of quantum mechanics for the case when the underlying spectrum is continuous. We base our discussion on the use of the Weyl eigendifferentials. We show that a quantum system being in an eigenstate of an invariant will remain in the subspace generated by the eigenstates of the invariant, thereby acquiring a generalized non-adiabatic or Aharonov–Anandan geometric phase linked to the diagonal element of the S matrix. The modified Pöschl–Teller potential and the time-dependent linear potential are worked out as illustrations. -- Highlights: ► In this Letter we study the exact quantum evolution for continuous spectra problems. ► We base our discussion on the use of the Weyl eigendifferentials. ► We give a generalized Lewis and Riesenfeld phase for continuous spectra. ► This generalized phase or Aharonov–Anandan geometric phase is linked to the S matrix. ► The modified Pöschl–Teller and the linear potential are worked out as illustrations.

  8. Decomposing the time-frequency representation of EEG using non-negative matrix and multi-way factorization

    DEFF Research Database (Denmark)

    Mørup, Morten; Hansen, Lars Kai; Parnas, Josef

    2006-01-01

    We demonstrate how non-negative matrix factorization (NMF) can be used to decompose the inter trial phase coherence (ITPC) of multi-channel EEG to yield a unique decomposition of time-frequency signatures present in various degrees in the recording channels. The NMF optimization is easily...... generalized to a parallel factor (PARAFAC) model to form a non-negative multi-way factorization (NMWF). While the NMF can examine subject specific activities the NMWF can effectively extract the most similar activities across subjects and or conditions. The methods are tested on a proprioceptive stimulus...... consisting of a weight change in a handheld load. While somatosensory gamma oscillations have previously only been evoked by electrical stimuli we hypothesized that a natural proprioceptive stimulus also would be able to evoke gamma oscillations. ITPC maxima were determined by visual inspection...

  9. Assessment of the influence of anthropogenic factors on elements of the ecological network in Vojvodina (Serbia using the Leopold matrix

    Directory of Open Access Journals (Sweden)

    Kicošev Vesna

    2015-01-01

    Full Text Available Salt steppes and marshes represent the most valuable ecosystems in the world, providing numerous ecosystem services that are extremely vulnerable to anthropogenic influences. These types of habitat in the territory of Serbia are most dominant in Banat and a significant portion of them is under protection or in the process of becoming protected. The section surrounding the protected areas of Slano Kopovo Special Nature Reserve, Rusanda Nature Park and Okanj Bara Special Nature Reserve with the non-building area of Novi Bečej, Kumane, Melenci, Elemir and Taraš cadastral municipalities, has been chosen for the analysis. The aim of this paper was to assess the influence of specific anthropogenic factors on the elements of an ecological network using the analytical method that can generate the required results in a manner suitable for presentation to various stakeholders. To achieve this aim, the Leopold matrix model, used for assessing anthropogenic influence on the environment, has been chosen. The specificity of this issue of protecting and preserving elements of an ecological network resulted in the need to isolate and evaluate the factors affecting the preservation of habitats and functionality of ecosystems, unlike the concept of Leopold matrix, which treats all factors as equally important in the process of evaluation. Evaluation results indicate significant effects of historical, perennial manner of using the area and other resources in the non-building area.

  10. Monitoring organic loading to swimming pools by fluorescence excitation–emission matrix with parallel factor analysis (PARAFAC)

    DEFF Research Database (Denmark)

    Seredynska-Sobecka, Bozena; Stedmon, Colin; Boe-Hansen, Rasmus

    2011-01-01

    Fluorescence Excitation–Emission Matrix spectroscopy combined with parallel factor analysis was employed to monitor water quality and organic contamination in swimming pools. The fluorescence signal of the swimming pool organic matter was low but increased slightly through the day. The analysis...... revealed that the organic matter fluorescence was characterised by five different components, one of which was unique to swimming pool organic matter and one which was specific to organic contamination. The latter component had emission peaks at 420nm and was found to be a sensitive indicator of organic...... loading in swimming pool water. The fluorescence at 420nm gradually increased during opening hours and represented material accumulating through the day....

  11. The interplay of matrix metalloproteinases, morphogens and growth factors is necessary for branching of mammary epithelial cells

    Energy Technology Data Exchange (ETDEWEB)

    Simian, M.; Harail, Y.; Navre, M.; Werb, Z.; Lochter, A.; Bissell, M.J.

    2002-03-06

    The mammary gland develops its adult form by a process referred to as branching morphogenesis. Many factors have been reported to affect this process. We have used cultured primary mammary epithelial organoids and mammary epithelial cell lines in three-dimensional collagen gels to elucidate which growth factors, matrix metalloproteinases (MMPs) and mammary morphogens interact in branching morphogenesis. Branching stimulated by stromal fibroblasts, epidermal growth factor, fibroblast growth factor 7, fibroblast growth factor 2 and hepatocyte growth factor was strongly reduced by inhibitors of MMPs, indicating the requirement of MMPs for three-dimensional growth involved in morphogenesis. Recombinant stromelysin 1/MMP-3 alone was sufficient to drive branching in the absence of growth factors in the organoids. Plasmin also stimulated branching; however, plasmin-dependent branching was abolished by both inhibitors of plasmin and MMPs, suggesting that plasmin activates MMPs. To differentiate between signals for proliferation and morphogenesis, we used a cloned mammary epithelial cell line that lacks epimorphin, an essential mammary morphogen. Both epimorphin and MMPs were required for morphogenesis, but neither was required for epithelial cell proliferation. These results provide direct evidence for a critical role of MMPs in branching in mammary epithelium and suggest that, in addition to epimorphin, MMP activity is a minimum requirement for branching morphogenesis in the mammary gland.

  12. The interplay of matrix metalloproteinases, morphogens and growth factors is necessary for branching of mammary epithelial cells

    International Nuclear Information System (INIS)

    Simian, Marina; Hirai, Yohei; Navre, Marc; Werb, Zena; Lochter, Andre; Bissell, Mina J.

    2002-01-01

    The mammary gland develops its adult form by a process referred to as branching morphogenesis. Many factors have been reported to affect this process. We have used cultured primary mammary epithelial organoids and mammary epithelial cell lines in three-dimensional collagen gels to elucidate which growth factors, matrix metalloproteinases (MMPs) and mammary morphogens interact in branching morphogenesis. Branching stimulated by stromal fibroblasts, epidermal growth factor, fibroblast growth factor 7, fibroblast growth factor 2 and hepatocyte growth factor was strongly reduced by inhibitors of MMPs, indicating the requirement of MMPs for three-dimensional growth involved in morphogenesis. Recombinant stromelysin 1/MMP-3 alone was sufficient to drive branching in the absence of growth factors in the organoids. Plasmin also stimulated branching; however, plasmin-dependent branching was abolished by both inhibitors of plasmin and MMPs, suggesting that plasmin activates MMPs. To differentiate between signals for proliferation and morphogenesis, we used a cloned mammary epithelial cell line that lacks epimorphin, an essential mammary morphogen. Both epimorphin and MMPs were required for morphogenesis, but neither was required for epithelial cell proliferation. These results provide direct evidence for a critical role of MMPs in branching in mammary epithelium and suggest that, in addition to epimorphin, MMP activity is a minimum requirement for branching morphogenesis in the mammary gland

  13. Effect of cannabidiol on human gingival fibroblast extracellular matrix metabolism: MMP production and activity, and production of fibronectin and transforming growth factor β.

    Science.gov (United States)

    Rawal, S Y; Dabbous, M Kh; Tipton, D A

    2012-06-01

    Marijuana (Cannabis sativa) use may be associated with gingival enlargement, resembling that caused by phenytoin. Cannabidiol (CBD), a nonpsychotropic Cannabis derivative, is structurally similar to phenytoin. While there are many reports on effects of phenytoin on human gingival fibroblasts, there is no information on effects of Cannabis components on these cells. The objective of this study was to determine effects of CBD on human gingival fibroblast fibrogenic and matrix-degrading activities. Fibroblasts were incubated with CBD in serum-free medium for 1-6 d. The effect of CBD on cell viability was determined by measuring activity of a mitochondrial enzyme. The fibrogenic molecule transforming growth factor β and the extracellular matrix molecule fibronectin were measured by ELISA. Pro-MMP-1 and total MMP-2 were measured by ELISA. Activity of MMP-2 was determined via a colorimetric assay in which a detection enzyme is activated by active MMP-2. Data were analysed using ANOVA and Scheffe's F procedure for post hoc comparisons. Cannabidiol had little or no significant effect on cell viability. Low CBD concentrations increased transforming growth factor β production by as much as 40% (p Cannabidiol increased fibronectin production by as much as approximately 100% (p < 0.001). Lower CBD concentrations increased MMP production, but the highest concentrations decreased production of both MMPs (p < 0.05) and decreased MMP-2 activity (p < 0.02). The data suggest that the CBD may promote fibrotic gingival enlargement by increasing gingival fibroblast production of transforming growth factor β and fibronectin, while decreasing MMP production and activity. © 2011 John Wiley & Sons A/S.

  14. Estudio de factores de riesgo para la hemorragia de la matriz germinal del prematuro Risk factors for germinal matrix hemorrhage in preterm infants

    Directory of Open Access Journals (Sweden)

    Gladys P. Arango

    1997-01-01

    Full Text Available Con el propósito de facilitar el diagnóstico clínico de la hemorragia de la matriz germinal del prematuro, se diseñó un estudio de casos (n: 56 y controles (n: 66 para determinar los factores de riesgo de la madre y del niño; también se buscó asociación entre dichos factores y la gravedad del evento. No se halló relación entre los factores de riesgo maternos y la presencia o gravedad de la hemorragia. En cuanto a los niños, la edad gestacional menor de 31 semanas, el uso de ventilación mecánica y la persistencia del ductus arterioso mostraron una relación estadística con el evento (p < 0.05, mientras que la sumatoria de tres o más riesgos la tuvo con la gravedad del mismo (p < 0.05. Se concluye que los mencionados factores de riesgo pueden ser indicativos del desarrollo de la hemorragia de la matriz germinal en el prematuro. To facilitate clinical diagnosis of germinal matrix hemorrhage In preterm infants, a study of cases {n: 56 and controls {n: 66 was carried out. Association was investigated between hemorrhage and maternal and neonatal risk factors; also included was the correlation between such factors and seriousness of the hemorrhagic episode. No correlation was found between maternal risk factors and hemorrhage or its seriousness. Concerning neonatal risks, gestational age under 31 weeks, the use of mechanical ventilation and persistence of ductus arteriosus, independently, showed statistical correlation with the hemorrhage {p < 0.05, whereas the simultaneous presence of three or more risks correlated with intensity of hemorrhage {p < 0.05. We conclude that the abovementioned neonatal risk factors can be suggestive of the development of germinal matrix hemorrhage in preterm Infants.

  15. Natural gas in Brazil's energy matrix: demand for 1995-2010 and usage factors

    International Nuclear Information System (INIS)

    Fernandes, Elton; Fonseca, Marcus Vinicius de A; Alonso, P.S.R.

    2005-01-01

    This paper describes and analyzes the constraints hampering achievement of the 12% share planned for natural gas in Brazil's energy matrix by 2010, and advises policies for reaching that goal on the basis of forecasts and three probable scenarios for the development of the Brazilian economy. The 12% share goal was established in 1993 by the Ministry of Mines and Energy and confirmed in 2000, and is now in full development. The figures used to represent the estimates of natural gas demands in the three scenarios were obtained from the Integrated Energy Planning Model (MIPE--Modelo Integrado de Planejamento Energetico), which is a technical and economic forecasting model developed by a group of researchers linked to the Energy Planning Program run by the Graduate Engineering Programs Coordination Unit at the Rio de Janeiro Federal University (COPPE-UFRJ) under the sponsorship of Petrobras (a Brazilian enterprise operating in the oil and gas segment) and Eletrobras (a Brazilian enterprise in charge of electricity demand planning). The analysis of the constraints take place under the aegis of the objective proposed by the Brazilian Government. The authors suggest specific actions to be taken in four application areas of natural gas: industrial, electric power generation, domestic distribution and vehicular fleet conversions. All the actions proposed encourage the use of a fuel with low environmental impacts and high calorie power, replacing firewood and other polluting fuels and are evaluated relative to the impacts occurring in society, especially from the standpoint of social welfare in a developing country. The necessity of developing the goods and services infrastructure in the country to support the natural gas insertion in the Brazilian energy matrix is also addressed

  16. Extracellular Matrix Hydrogel Derived from Human Umbilical Cord as a Scaffold for Neural Tissue Repair and Its Comparison with Extracellular Matrix from Porcine Tissues

    Czech Academy of Sciences Publication Activity Database

    Kočí, Zuzana; Výborný, Karel; Dubišová, Jana; Vacková, Irena; Jäger, Aleš; Lunov, Oleg; Jiráková, Klára; Kubinová, Šárka

    2017-01-01

    Roč. 23, č. 6 (2017), s. 333-345 ISSN 1937-3384 R&D Projects: GA ČR(CZ) GA15-01396S; GA MŠk(CZ) LO1309; GA MŠk(CZ) ED1.1.00/02.0109; GA MŠk(CZ) EF15_003/0000419 Grant - others:AV ČR(CZ) Fellowship J. E. Purkyně Institutional support: RVO:68378041 ; RVO:68378271 Keywords : extracellular matrix * hydrogel * umbilical cord Subject RIV: FH - Neurology; EB - Genetics ; Molecular Biology (FZU-D) OBOR OECD: Neurosciences (including psychophysiology; Biophysics (FZU-D)

  17. Exploring syndrome differentiation using non-negative matrix factorization and cluster analysis in patients with atopic dermatitis.

    Science.gov (United States)

    Yun, Younghee; Jung, Wonmo; Kim, Hyunho; Jang, Bo-Hyoung; Kim, Min-Hee; Noh, Jiseong; Ko, Seong-Gyu; Choi, Inhwa

    2017-08-01

    Syndrome differentiation (SD) results in a diagnostic conclusion based on a cluster of concurrent symptoms and signs, including pulse form and tongue color. In Korea, there is a strong interest in the standardization of Traditional Medicine (TM). In order to standardize TM treatment, standardization of SD should be given priority. The aim of this study was to explore the SD, or symptom clusters, of patients with atopic dermatitis (AD) using non-negative factorization methods and k-means clustering analysis. We screened 80 patients and enrolled 73 eligible patients. One TM dermatologist evaluated the symptoms/signs using an existing clinical dataset from patients with AD. This dataset was designed to collect 15 dermatologic and 18 systemic symptoms/signs associated with AD. Non-negative matrix factorization was used to decompose the original data into a matrix with three features and a weight matrix. The point of intersection of the three coordinates from each patient was placed in three-dimensional space. With five clusters, the silhouette score reached 0.484, and this was the best silhouette score obtained from two to nine clusters. Patients were clustered according to the varying severity of concurrent symptoms/signs. Through the distribution of the null hypothesis generated by 10,000 permutation tests, we found significant cluster-specific symptoms/signs from the confidence intervals in the upper and lower 2.5% of the distribution. Patients in each cluster showed differences in symptoms/signs and severity. In a clinical situation, SD and treatment are based on the practitioners' observations and clinical experience. SD, identified through informatics, can contribute to development of standardized, objective, and consistent SD for each disease. Copyright © 2017. Published by Elsevier Ltd.

  18. Robust extraction of basis functions for simultaneous and proportional myoelectric control via sparse non-negative matrix factorization

    Science.gov (United States)

    Lin, Chuang; Wang, Binghui; Jiang, Ning; Farina, Dario

    2018-04-01

    Objective. This paper proposes a novel simultaneous and proportional multiple degree of freedom (DOF) myoelectric control method for active prostheses. Approach. The approach is based on non-negative matrix factorization (NMF) of surface EMG signals with the inclusion of sparseness constraints. By applying a sparseness constraint to the control signal matrix, it is possible to extract the basis information from arbitrary movements (quasi-unsupervised approach) for multiple DOFs concurrently. Main Results. In online testing based on target hitting, able-bodied subjects reached a greater throughput (TP) when using sparse NMF (SNMF) than with classic NMF or with linear regression (LR). Accordingly, the completion time (CT) was shorter for SNMF than NMF or LR. The same observations were made in two patients with unilateral limb deficiencies. Significance. The addition of sparseness constraints to NMF allows for a quasi-unsupervised approach to myoelectric control with superior results with respect to previous methods for the simultaneous and proportional control of multi-DOF. The proposed factorization algorithm allows robust simultaneous and proportional control, is superior to previous supervised algorithms, and, because of minimal supervision, paves the way to online adaptation in myoelectric control.

  19. Enhancer of rudimentary homologue interacts with scaffold attachment factor B at the nuclear matrix to regulate SR protein phosphorylation.

    Science.gov (United States)

    Drakouli, Sotiria; Lyberopoulou, Aggeliki; Papathanassiou, Maria; Mylonis, Ilias; Georgatsou, Eleni

    2017-08-01

    Scaffold attachment factor B1 (SAFB1) is an integral component of the nuclear matrix of vertebrate cells. It binds to DNA on scaffold/matrix attachment region elements, as well as to RNA and a multitude of different proteins, affecting basic cellular activities such as transcription, splicing and DNA damage repair. In the present study, we show that enhancer of rudimentary homologue (ERH) is a new molecular partner of SAFB1 and its 70% homologous paralogue, scaffold attachment factor B2 (SAFB2). ERH interacts directly in the nucleus with the C-terminal Arg-Gly-rich region of SAFB1/2 and co-localizes with it in the insoluble nuclear fraction. ERH, a small ubiquitous protein with striking homology among species and a unique structure, has also been implicated in fundamental cellular mechanisms. Our functional analyses suggest that the SAFB/ERH interaction does not affect SAFB1/2 function in transcription (e.g. as oestrogen receptor α co-repressors), although it reverses the inhibition exerted by SAFB1/2 on the splicing kinase SR protein kinase 1 (SRPK1), which also binds on the C-terminus of SAFB1/2. Accordingly, ERH silencing decreases lamin B receptor and SR protein phosphorylation, which are major SRPK1 substrates, further substantiating the role of SAFB1 and SAFB2 in the co-ordination of nuclear function. © 2017 Federation of European Biochemical Societies.

  20. Positive matrix factorization as source apportionment of soil lead and cadmium around a battery plant (Changxing County, China).

    Science.gov (United States)

    Xue, Jian-long; Zhi, Yu-you; Yang, Li-ping; Shi, Jia-chun; Zeng, Ling-zao; Wu, Lao-sheng

    2014-06-01

    Chemical compositions of soil samples are multivariate in nature and provide datasets suitable for the application of multivariate factor analytical techniques. One of the analytical techniques, the positive matrix factorization (PMF), uses a weighted least square by fitting the data matrix to determine the weights of the sources based on the error estimates of each data point. In this research, PMF was employed to apportion the sources of heavy metals in 104 soil samples taken within a 1-km radius of a lead battery plant contaminated site in Changxing County, Zhejiang Province, China. The site is heavily contaminated with high concentrations of lead (Pb) and cadmium (Cd). PMF successfully partitioned the variances into sources related to soil background, agronomic practices, and the lead battery plants combined with a geostatistical approach. It was estimated that the lead battery plants and the agronomic practices contributed 55.37 and 29.28%, respectively, for soil Pb of the total source. Soil Cd mainly came from the lead battery plants (65.92%), followed by the agronomic practices (21.65%), and soil parent materials (12.43%). This research indicates that PMF combined with geostatistics is a useful tool for source identification and apportionment.

  1. Factors associated with multidisciplinary case conference outcomes in children admitted to a regional hospital in Hong Kong with suspected child abuse: a retrospective case series with internal comparison.

    Science.gov (United States)

    Lo, W C; Fung, G Pg; Cheung, P Ch

    2017-10-01

    In all cases of suspected child abuse, accurate risk assessment is vital to guide further management. This study examined the relationship between risk factors in a risk assessment matrix and child abuse case conference outcomes. Records of all children hospitalised at United Christian Hospital in Hong Kong for suspected child abuse from January 2012 to December 2014 were reviewed. Outcomes of the hospital abuse work-up as concluded in the Multi-Disciplinary Case Conference were categorised as 'established', 'high risk', or 'not established'. All cases of 'established' and 'high risk' were included in the positive case conference outcome group and all cases of 'not established' formed the comparison group. On the other hand, using the Risk Assessment Matrix developed by the California State University, Fresno in 1990, each case was allotted a matrix score of low, intermediate, or high risk in each of 15 matrix domains, and an aggregate matrix score was derived. The effect of individual matrix domain on case conference outcome was analysed. Receiver operating characteristic curve analysis was used to examine the relationship between case conference outcome and aggregate matrix score. In this study, 265 children suspected of being abused were included, with 198 in the positive case conference outcome group and 67 in the comparison group. Three matrix domains (severity and frequency of abuse, location of injuries, and strength of family support systems) were significantly associated with case conference outcome. An aggregate cut-off score of 23 yielded a sensitivity of 91.4% and specificity of 38.2% in relation to outcome of abuse categorisation. Risk assessment should be performed when handling suspected child abuse cases. A high aggregate score should arouse suspicion in all disciplines managing child abuse cases.

  2. Comparison of Bloodmeal Digestion and the Peritrophic Matrix in Four Sand Fly Species Differing in Susceptibility to Leishmania donovani.

    Science.gov (United States)

    Pruzinova, Katerina; Sadlova, Jovana; Seblova, Veronika; Homola, Miroslav; Votypka, Jan; Volf, Petr

    2015-01-01

    The early stage of Leishmania development in sand flies is closely connected with bloodmeal digestion. Here we compared various parameters of bloodmeal digestion in sand flies that are either susceptible (Phlebotomus argentipes and P. orientalis) or refractory (P. papatasi and Sergentomyia schwetzi) to Leishmania donovani, to study the effects on vector competence. The volume of the bloodmeal ingested, time of defecation of bloodmeal remnants, timing of formation and degradation of the peritrophic matrix (PM) and dynamics of proteolytic activities were compared in four sand fly species. Both proven vectors of L. donovani showed lower trypsin activity and slower PM formation than refractory species. Interestingly, the two natural L. donovani vectors strikingly differed from each other in secretion of the PM and midgut proteases, with P. argentipes possessing fast bloodmeal digestion with a very high peak of chymotrypsin activity and rapid degradation of the PM. Experimental infections of P. argentipes did not reveal any differences in vector competence in comparison with previously studied P. orientalis; even the very low initial dose (2×103 promastigotes/ml) led to fully developed late-stage infections with colonization of the stomodeal valve in about 40% of females. We hypothesise that the period between the breakdown of the PM and defecation of the bloodmeal remnants, i.e. the time frame when Leishmania attach to the midgut in order to prevent defecation, could be one of crucial parameters responsible for the establishment of Leishmania in the sand fly midgut. In both natural L. donovani vectors this period was significantly longer than in S. schwetzi. Both vectors are equally susceptible to L. donovani; as average bloodmeal volumes taken by females of P. argentipes and P. orientalis were 0.63 μl and 0.59 μl, respectively, an infective dose corresponding to 1-2 parasites was enough to initiate mature infections.

  3. Transcriptional factor DLX3 promotes the gene expression of enamel matrix proteins during amelogenesis.

    Science.gov (United States)

    Zhang, Zhichun; Tian, Hua; Lv, Ping; Wang, Weiping; Jia, Zhuqing; Wang, Sainan; Zhou, Chunyan; Gao, Xuejun

    2015-01-01

    Mutation of distal-less homeobox 3 (DLX3) is responsible for human tricho-dento-osseous syndrome (TDO) with amelogenesis imperfecta, indicating a crucial role of DLX3 in amelogenesis. However, the expression pattern of DLX3 and its specific function in amelogenesis remain largely unknown. The aim of this study was to investigate the effects of DLX3 on enamel matrix protein (EMP) genes. By immunohistochemistry assays of mouse tooth germs, stronger immunostaining of DLX3 protein was identified in ameloblasts in the secretory stage than in the pre-secretory and maturation stages, and the same pattern was found for Dlx3 mRNA using Realtime PCR. In a mouse ameloblast cell lineage, forced expression of DLX3 up-regulated the expression of the EMP genes Amelx, Enam, Klk4, and Odam, whereas knockdown of DLX3 down-regulated these four EMP genes. Further, bioinformatics, chromatin immunoprecipitation, and luciferase assays revealed that DLX3 transactivated Enam, Amelx, and Odam through direct binding to their enhancer regions. Particularly, over-expression of mutant-DLX3 (c.571_574delGGGG, responsible for TDO) inhibited the activation function of DLX3 on expression levels and promoter activities of the Enam, Amelx, and Odam genes. Together, our data show that DLX3 promotes the expression of the EMP genes Amelx, Enam, Klk4, and Odam in amelogenesis, while mutant-DLX3 disrupts this regulatory function, thus providing insights into the molecular mechanisms underlying the enamel defects of TDO disease.

  4. Efficient fully 3D list-mode TOF PET image reconstruction using a factorized system matrix with an image domain resolution model

    International Nuclear Information System (INIS)

    Zhou, Jian; Qi, Jinyi

    2014-01-01

    A factorized system matrix utilizing an image domain resolution model is attractive in fully 3D time-of-flight PET image reconstruction using list-mode data. In this paper, we study a factored model based on sparse matrix factorization that is comprised primarily of a simplified geometrical projection matrix and an image blurring matrix. Beside the commonly-used Siddon’s ray-tracer, we propose another more simplified geometrical projector based on the Bresenham’s ray-tracer which further reduces the computational cost. We discuss in general how to obtain an image blurring matrix associated with a geometrical projector, and provide theoretical analysis that can be used to inspect the efficiency in model factorization. In simulation studies, we investigate the performance of the proposed sparse factorization model in terms of spatial resolution, noise properties and computational cost. The quantitative results reveal that the factorization model can be as efficient as a non-factored model, while its computational cost can be much lower. In addition we conduct Monte Carlo simulations to identify the conditions under which the image resolution model can become more efficient in terms of image contrast recovery. We verify our observations using the provided theoretical analysis. The result offers a general guide to achieve the optimal reconstruction performance based on a sparse factorization model with an image domain resolution model. (paper)

  5. Occupancy classification of position weight matrix-inferred transcription factor binding sites.

    Directory of Open Access Journals (Sweden)

    Hollis Wright

    Full Text Available BACKGROUND: Computational prediction of Transcription Factor Binding Sites (TFBS from sequence data alone is difficult and error-prone. Machine learning techniques utilizing additional environmental information about a predicted binding site (such as distances from the site to particular chromatin features to determine its occupancy/functionality class show promise as methods to achieve more accurate prediction of true TFBS in silico. We evaluate the Bayesian Network (BN and Support Vector Machine (SVM machine learning techniques on four distinct TFBS data sets and analyze their performance. We describe the features that are most useful for classification and contrast and compare these feature sets between the factors. RESULTS: Our results demonstrate good performance of classifiers both on TFBS for transcription factors used for initial training and for TFBS for other factors in cross-classification experiments. We find that distances to chromatin modifications (specifically, histone modification islands as well as distances between such modifications to be effective predictors of TFBS occupancy, though the impact of individual predictors is largely TF specific. In our experiments, Bayesian network classifiers outperform SVM classifiers. CONCLUSIONS: Our results demonstrate good performance of machine learning techniques on the problem of occupancy classification, and demonstrate that effective classification can be achieved using distances to chromatin features. We additionally demonstrate that cross-classification of TFBS is possible, suggesting the possibility of constructing a generalizable occupancy classifier capable of handling TFBS for many different transcription factors.

  6. Normalization of the parameterized Courant-Snyder matrix for symplectic factorization of a parameterized Taylor map

    International Nuclear Information System (INIS)

    Yan, Y.T.

    1991-01-01

    The transverse motion of charged particles in a circular accelerator can be well represented by a one-turn high-order Taylor map. For particles without energy deviation, the one-turn Taylor map is a 4-dimensional polynomials of four variables. The four variables are the transverse canonical coordinates and their conjugate momenta. To include the energy deviation (off-momentum) effects, the map has to be parameterized with a smallness factor representing the off-momentum and so the Taylor map becomes a 4-dimensional polynomials of five variables. It is for this type of parameterized Taylor map that a mehtod is presented for converting it into a parameterized Dragt-Finn factorization map. Parameterized nonlinear normal form and parameterized kick factorization can thus be obtained with suitable modification of the existing technique

  7. HPC-NMF: A High-Performance Parallel Algorithm for Nonnegative Matrix Factorization

    Energy Technology Data Exchange (ETDEWEB)

    2016-08-22

    NMF is a useful tool for many applications in different domains such as topic modeling in text mining, background separation in video analysis, and community detection in social networks. Despite its popularity in the data mining community, there is a lack of efficient distributed algorithms to solve the problem for big data sets. We propose a high-performance distributed-memory parallel algorithm that computes the factorization by iteratively solving alternating non-negative least squares (NLS) subproblems for $\\WW$ and $\\HH$. It maintains the data and factor matrices in memory (distributed across processors), uses MPI for interprocessor communication, and, in the dense case, provably minimizes communication costs (under mild assumptions). As opposed to previous implementation, our algorithm is also flexible: It performs well for both dense and sparse matrices, and allows the user to choose any one of the multiple algorithms for solving the updates to low rank factors $\\WW$ and $\\HH$ within the alternating iterations.

  8. Comparison of Matrix Frequency-Doubling Technology (FDT) Perimetry with the SWEDISH Interactive Thresholding Algorithm (SITA) Standard Automated Perimetry (SAP) in Mild Glaucoma.

    Science.gov (United States)

    Doozandeh, Azadeh; Irandoost, Farnoosh; Mirzajani, Ali; Yazdani, Shahin; Pakravan, Mohammad; Esfandiari, Hamed

    2017-01-01

    This study aimed to compare second-generation frequency-doubling technology (FDT) perimetry with standard automated perimetry (SAP) in mild glaucoma. Forty-seven eyes of 47 participants who had mild visual field defect by SAP were included in this study. All participants were examined using SITA 24-2 (SITA-SAP) and matrix 24-2 (Matrix-FDT). The correlations of global indices and the number of defects on pattern deviation (PD) plots were determined. Agreement between two sets regarding the stage of visual field damage was assessed. Pearson's correlation, intra-cluster comparison, paired t-test, and 95% limit of agreement were calculated. Although there was no significant difference between global indices, the agreement between the two devices regarding the global indices was weak (the limit of agreement for mean deviation was -6.08 to 6.08 and that for pattern standard deviation was -4.42 to 3.42). The agreement between SITA-SAP and Matrix-FDT regarding the Glaucoma Hemifield Test (GHT) and the number of defective points in each quadrant and staging of the visual field damage was also weak. Because the correlation between SITA-SAP and Matrix-FDT regarding global indices, GHT, number of defective points, and stage of the visual field damage in mild glaucoma is weak, Matrix-FDT cannot be used interchangeably with SITA-SAP in the early stages of glaucoma.

  9. Comparison of four decontamination treatments on porcine renal decellularized extracellular matrix structure, composition, and support of human renal cortical tubular epithelium cells.

    Science.gov (United States)

    Poornejad, Nafiseh; Nielsen, Jeffery J; Morris, Ryan J; Gassman, Jason R; Reynolds, Paul R; Roeder, Beverly L; Cook, Alonzo D

    2016-03-01

    Engineering whole organs from porcine decellularized extracellular matrix and human cells may lead to a plentiful source of implantable organs. Decontaminating the porcine decellularized extracellular matrix scaffolds is an essential step prior to introducing human cells. However, decontamination of whole porcine kidneys is a major challenge because the decontamination agent or irradiation needs to diffuse deep into the structure to eliminate all microbial contamination while minimizing damage to the structure and composition of the decellularized extracellular matrix. In this study, we compared four decontamination treatments that could be applicable to whole porcine kidneys: 70% ethanol, 0.2% peracetic acid in 1 M NaCl, 0.2% peracetic acid in 4% ethanol, and gamma (γ)-irradiation. Porcine kidneys were decellularized by perfusion of 0.5% (w/v) aqueous solution of sodium dodecyl sulfate and the four decontamination treatments were optimized using segments (n = 60) of renal tissue to ensure a consistent comparison. Although all four methods were successful in decontamination, γ-irradiation was very damaging to collagen fibers and glycosaminoglycans, leading to less proliferation of human renal cortical tubular epithelium cells within the porcine decellularized extracellular matrix. The effectiveness of the other three optimized solution treatments were then all confirmed using whole decellularized porcine kidneys (n = 3). An aqueous solution of 0.2% peracetic acid in 1 M NaCl was determined to be the best method for decontamination of porcine decellularized extracellular matrix. © The Author(s) 2015.

  10. Inhibition of Matrix Metalloproteinase Activity Prevents Increases in Myocardial Tumor Necrosis Factor

    Science.gov (United States)

    Murray, David B.; Levick, Scott P; Brower, Gregory L.; Janicki, Joseph S.

    2010-01-01

    Aim TNF-α is known to cause adverse myocardial remodeling. While we have previously shown a role for cardiac mast cells in mediating myocardial TNF-α, matrix metalloproteinases (MMP) activation of TNF-α may also be contributory. We sought to determine the relative roles of MMPs and cardiac mast cells in the activation of TNF-α in the hearts of rats subjected to chronic volume overload. Methods Interventions with the broad spectrum MMP inhibitor, GM6001, or the mast cell stabilizer, nedocromil, were performed in the rat aortocaval fistula (ACF) model of volume overload. Results Myocardial TNF-α levels were significantly increased in the ACF. This increase was prevented by MMP inhibition with GM6001 (p ≤ 0.001 vs. ACF). Conversely, myocardial TNF-α levels were increased in the ACF + nedocromil treated fistula groups (p ≤ 0.001 vs. sham). The degradation of interstitial collagen volume fraction seen in the untreated ACF group was prevented in both the GM6001 and nedocromil treated hearts. Significant increases in LV myocardial ET-1 levels also occurred in the ACF group at 3 days post-fistula. Whereas administration of GM6001 significantly attenuated this increase, mast cell stabilization with nedocromil markedly exacerbated the increase, producing ET-1 levels 6.5 fold and 2 fold greater than that in the sham-operated control and ACF group, respectively. Conclusion The efficacy of the MMP inhibitor, GM6001, to prevent increased levels of myocardial TNF-α is indicative of MMP-mediated cleavage of latent extracellular membrane bound TNF-α protein as the primary source of bioactive TNF-α in the myocardium of the volume-overload heart. PMID:20403361

  11. Transcriptional factor DLX3 promotes the gene expression of enamel matrix proteins during amelogenesis.

    Directory of Open Access Journals (Sweden)

    Zhichun Zhang

    Full Text Available Mutation of distal-less homeobox 3 (DLX3 is responsible for human tricho-dento-osseous syndrome (TDO with amelogenesis imperfecta, indicating a crucial role of DLX3 in amelogenesis. However, the expression pattern of DLX3 and its specific function in amelogenesis remain largely unknown. The aim of this study was to investigate the effects of DLX3 on enamel matrix protein (EMP genes. By immunohistochemistry assays of mouse tooth germs, stronger immunostaining of DLX3 protein was identified in ameloblasts in the secretory stage than in the pre-secretory and maturation stages, and the same pattern was found for Dlx3 mRNA using Realtime PCR. In a mouse ameloblast cell lineage, forced expression of DLX3 up-regulated the expression of the EMP genes Amelx, Enam, Klk4, and Odam, whereas knockdown of DLX3 down-regulated these four EMP genes. Further, bioinformatics, chromatin immunoprecipitation, and luciferase assays revealed that DLX3 transactivated Enam, Amelx, and Odam through direct binding to their enhancer regions. Particularly, over-expression of mutant-DLX3 (c.571_574delGGGG, responsible for TDO inhibited the activation function of DLX3 on expression levels and promoter activities of the Enam, Amelx, and Odam genes. Together, our data show that DLX3 promotes the expression of the EMP genes Amelx, Enam, Klk4, and Odam in amelogenesis, while mutant-DLX3 disrupts this regulatory function, thus providing insights into the molecular mechanisms underlying the enamel defects of TDO disease.

  12. Exploring matrix factorization techniques for significant genes identification of Alzheimer’s disease microarray gene expression data

    Directory of Open Access Journals (Sweden)

    Hu Xiaohua

    2011-07-01

    Full Text Available Abstract Background The wide use of high-throughput DNA microarray technology provide an increasingly detailed view of human transcriptome from hundreds to thousands of genes. Although biomedical researchers typically design microarray experiments to explore specific biological contexts, the relationships between genes are hard to identified because they are complex and noisy high-dimensional data and are often hindered by low statistical power. The main challenge now is to extract valuable biological information from the colossal amount of data to gain insight into biological processes and the mechanisms of human disease. To overcome the challenge requires mathematical and computational methods that are versatile enough to capture the underlying biological features and simple enough to be applied efficiently to large datasets. Methods Unsupervised machine learning approaches provide new and efficient analysis of gene expression profiles. In our study, two unsupervised knowledge-based matrix factorization methods, independent component analysis (ICA and nonnegative matrix factorization (NMF are integrated to identify significant genes and related pathways in microarray gene expression dataset of Alzheimer’s disease. The advantage of these two approaches is they can be performed as a biclustering method by which genes and conditions can be clustered simultaneously. Furthermore, they can group genes into different categories for identifying related diagnostic pathways and regulatory networks. The difference between these two method lies in ICA assume statistical independence of the expression modes, while NMF need positivity constrains to generate localized gene expression profiles. Results In our work, we performed FastICA and non-smooth NMF methods on DNA microarray gene expression data of Alzheimer’s disease respectively. The simulation results shows that both of the methods can clearly classify severe AD samples from control samples, and

  13. Non-negative Matrix Factorization for Self-calibration of Photometric Redshift Scatter in Weak-lensing Surveys

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Le; Yu, Yu; Zhang, Pengjie, E-mail: lezhang@sjtu.edu.cn [Department of Astronomy, Shanghai Jiao Tong University, Shanghai, 200240 (China)

    2017-10-10

    Photo- z error is one of the major sources of systematics degrading the accuracy of weak-lensing cosmological inferences. Zhang et al. proposed a self-calibration method combining galaxy–galaxy correlations and galaxy–shear correlations between different photo- z bins. Fisher matrix analysis shows that it can determine the rate of photo- z outliers at a level of 0.01%–1% merely using photometric data and do not rely on any prior knowledge. In this paper, we develop a new algorithm to implement this method by solving a constrained nonlinear optimization problem arising in the self-calibration process. Based on the techniques of fixed-point iteration and non-negative matrix factorization, the proposed algorithm can efficiently and robustly reconstruct the scattering probabilities between the true- z and photo- z bins. The algorithm has been tested extensively by applying it to mock data from simulated stage IV weak-lensing projects. We find that the algorithm provides a successful recovery of the scatter rates at the level of 0.01%–1%, and the true mean redshifts of photo- z bins at the level of 0.001, which may satisfy the requirements in future lensing surveys.

  14. Using Matrix and Tensor Factorizations for the Single-Trial Analysis of Population Spike Trains.

    Directory of Open Access Journals (Sweden)

    Arno Onken

    2016-11-01

    Full Text Available Advances in neuronal recording techniques are leading to ever larger numbers of simultaneously monitored neurons. This poses the important analytical challenge of how to capture compactly all sensory information that neural population codes carry in their spatial dimension (differences in stimulus tuning across neurons at different locations, in their temporal dimension (temporal neural response variations, or in their combination (temporally coordinated neural population firing. Here we investigate the utility of tensor factorizations of population spike trains along space and time. These factorizations decompose a dataset of single-trial population spike trains into spatial firing patterns (combinations of neurons firing together, temporal firing patterns (temporal activation of these groups of neurons and trial-dependent activation coefficients (strength of recruitment of such neural patterns on each trial. We validated various factorization methods on simulated data and on populations of ganglion cells simultaneously recorded in the salamander retina. We found that single-trial tensor space-by-time decompositions provided low-dimensional data-robust representations of spike trains that capture efficiently both their spatial and temporal information about sensory stimuli. Tensor decompositions with orthogonality constraints were the most efficient in extracting sensory information, whereas non-negative tensor decompositions worked well even on non-independent and overlapping spike patterns, and retrieved informative firing patterns expressed by the same population in response to novel stimuli. Our method showed that populations of retinal ganglion cells carried information in their spike timing on the ten-milliseconds-scale about spatial details of natural images. This information could not be recovered from the spike counts of these cells. First-spike latencies carried the majority of information provided by the whole spike train about fine

  15. Decomposing tensors with structured matrix factors reduces to rank-1 approximations

    DEFF Research Database (Denmark)

    Comon, Pierre; Sørensen, Mikael; Tsigaridas, Elias

    2010-01-01

    Tensor decompositions permit to estimate in a deterministic way the parameters in a multi-linear model. Applications have been already pointed out in antenna array processing and digital communications, among others, and are extremely attractive provided some diversity at the receiver is availabl....... As opposed to the widely used ALS algorithm, non-iterative algorithms are proposed in this paper to compute the required tensor decomposition into a sum of rank-1 terms, when some factor matrices enjoy some structure, such as block-Hankel, triangular, band, etc....

  16. The impact of initialization procedures on unsupervised unmixing of hyperspectral imagery using the constrained positive matrix factorization

    Science.gov (United States)

    Masalmah, Yahya M.; Vélez-Reyes, Miguel

    2007-04-01

    The authors proposed in previous papers the use of the constrained Positive Matrix Factorization (cPMF) to perform unsupervised unmixing of hyperspectral imagery. Two iterative algorithms were proposed to compute the cPMF based on the Gauss-Seidel and penalty approaches to solve optimization problems. Results presented in previous papers have shown the potential of the proposed method to perform unsupervised unmixing in HYPERION and AVIRIS imagery. The performance of iterative methods is highly dependent on the initialization scheme. Good initialization schemes can improve convergence speed, whether or not a global minimum is found, and whether or not spectra with physical relevance are retrieved as endmembers. In this paper, different initializations using random selection, longest norm pixels, and standard endmembers selection routines are studied and compared using simulated and real data.

  17. Early alterations in extracellular matrix and transforming growth factor β gene expression in mouse lung indicative of late radiation fibrosis

    International Nuclear Information System (INIS)

    Finkelstein, J.N.; Johnston, C.J.; Baggs, R.; Rubin, P.

    1994-01-01

    Fibrosis, characterized by the accumulation of collagen, is a late result of thoracic irradiation. The expression of late radiation injury can be found immediately after irradiation by measuring messenger RNA (mRNA) abundance. To determine if extracellular matrix mRNA and transforming growth factor beta abundance was affected acutely after irradiation, the authors measured mRNA levels of collagen I (CI), collagen III (CIII), collagen IV (CIV), fibronectin (FN), and transforming growth factor β (TGFβ 1,2ampersand3 ) in mouse lungs on day 1 and day 14 after graded doses of radiation. C57BL/6 female mice were irradiated with a single dose to the thorax of 5 or 12.5 Gy. Total lung RNA was prepared and immobilized by Northern and slot blotting and hybridized with radiolabelled cDNA probes for CI, CIII, CIV, FN, TGFβ 1,2ampersand3 and a control probe encoding for glyceraldehyde-3-phosphate dehydrogenase (GAPDH). Autoradiographic data were quantified by video densitometry and results normalized to GAPDH. Changes in the expression of CI, CIII, CIV, FN and TGFβ 1,2ampersand3 were observed as early as 1 day after exposure. Through 14 days, changes in mRNA up to 5-fold were seen for any one dose. Dose related changes as high as 10-fold were also evident. The CI:CIII ratio increased gradually for the 5 Gy dose at 14 days postirradiation while the CI:CII ratio for the 12.5 Gy dose decreased by approximately 4-fold as compared to the control. These studies suggest that alterations in expression of extracellular matrix and TGFβ mRNA occur very early after radiation injury even at low doses and may play a role in the development of chronic fibrosis. 37 refs., 6 figs

  18. Effects of extracellular matrix proteins on macrophage differentiation, growth, and function: comparison of liquid and agar culture systems

    Science.gov (United States)

    Armstrong, J. W.; Chapes, S. K.; Spooner, B. S. (Principal Investigator)

    1994-01-01

    Both spaceflight and skeletal unloading suppress the haematopoietic differentiation of macrophages (Sonnenfeld et al., Aviat. Space Environ. Med., 61:648-653, 1990; Armstrong et al., J. Appl. Physiol., 75:2734-2739, 1993). The mechanism behind this reduction in haematopoiesis has yet to be elucidated. However, changes in bone marrow extracellular matrix (ECM) may be involved. To further understand the role of ECM products in macrophage differentiation, we have performed experiments evaluating the effects of fibronectin, laminin, collagen type I, and collagen type IV on macrophage development and function. Bone marrow-derived macrophages cultured on four different ECM substrates in liquid culture medium showed less growth than those cultured on plastic. Significant morphological differences were seen on each of the substrates used. Phenotypically and functionally, as measured by class II major histocompatibility molecule (MHCII) expression, MAC-2 expression, and the secretion of interleukin-6 (IL-6) and tumor necrosis factor-alpha (TNF-alpha), these macrophages were similar. In contrast, bone marrow-derived macrophages cultured in suspension, using agar, showed no difference in growth when exposed to ECM proteins. However, IL-6 and TNF-alpha secretion was affected by fibronectin, laminin, collagen type I, and collagen type IV in a concentration-dependent manner. We conclude that the ECM products fibronectin, laminin, collagen type I, and collagen type IV have profound effects on macrophage development and function. Additionally, we suggest that an ECM-supplemented agar culture system provides an environment more analogous to in vivo bone marrow than does a traditional liquid culture system.

  19. Adipose Extracellular Matrix/Stromal Vascular Fraction Gel Secretes Angiogenic Factors and Enhances Skin Wound Healing in a Murine Model

    Directory of Open Access Journals (Sweden)

    Mingliang Sun

    2017-01-01

    Full Text Available Mesenchymal stem cells are an attractive cell type for cytotherapy in wound healing. The authors recently developed a novel, adipose-tissue-derived, injectable extracellular matrix/stromal vascular fraction gel (ECM/SVF-gel for stem cell therapy. This study was designed to assess the therapeutic effects of ECM/SVF-gel on wound healing and potential mechanisms. ECM/SVF-gel was prepared for use in nude mouse excisional wound healing model. An SVF cell suspension and phosphate-buffered saline injection served as the control. The expression levels of vascular endothelial growth factor (VEGF, basic fibroblast growth factor (bFGF, and monocyte chemotactic protein-1 (MCP-1 in ECM/SVF-gel were analyzed at different time points. Angiogenesis (tube formation assays of ECM/SVF-gel extracts were evaluated, and vessels density in skin was determined. The ECM/SVF-gel extract promoted tube formation in vitro and increased the expression of the angiogenic factors VEGF and bFGF compared with those in the control. The expression of the inflammatory chemoattractant MCP-1 was high in ECM/SVF-gel at the early stage and decreased sharply during the late stage of wound healing. The potent angiogenic effects exerted by ECM/SVF-gel may contribute to the improvement of wound healing, and these effects could be related to the enhanced inflammatory response in ECM/SVF-gel during the early stage of wound healing.

  20. Decreased expression of extracellular matrix proteins and trophic factors in the amygdala complex of depressed mice after chronic immobilization stress

    Directory of Open Access Journals (Sweden)

    Jung Soonwoong

    2012-06-01

    Full Text Available Abstract Background The amygdala plays an essential role in controlling emotional behaviors and has numerous connections to other brain regions. The functional role of the amygdala has been highlighted by various studies of stress-induced behavioral changes. Here we investigated gene expression changes in the amygdala in the chronic immobilization stress (CIS-induced depression model. Results Eight genes were decreased in the amygdala of CIS mice, including genes for neurotrophic factors and extracellular matrix proteins. Among these, osteoglycin, fibromodulin, insulin-like growth factor 2 (Igf2, and insulin-like growth factor binding protein 2 (Igfbp2 were further analyzed for histological expression changes. The expression of osteoglycin and fibromodulin simultaneously decreased in the medial, basolateral, and central amygdala regions. However, Igf2 and Igfbp2 decreased specifically in the central nucleus of the amygdala. Interestingly, this decrease was found only in the amygdala of mice showing higher immobility, but not in mice displaying lower immobility, although the CIS regimen was the same for both groups. Conclusions These results suggest that the responsiveness of the amygdala may play a role in the sensitivity of CIS-induced behavioral changes in mice.

  1. A New EM CKM Matrix: Implications of the Nucleon Strange Quark Content, Anomalous Magnetic Moments of Nucleons and Electric and Magnetic Nucleon Form Factors

    Science.gov (United States)

    Ward, Thomas

    2013-10-01

    A new electromagnetic neutral-current quark mixing matrix, analog to the well-known Cabibbo-Kobayashi-Maskawa (CKM) weak charge-current matrix, is proposed to account for the strange quark content of the neutron and proton and part of the anomalous axial vector magnetic moments. The EM-CKM matrix is shown to be equivalent to the weak-CKM matrix following an EM to weak gauge symmetry transformation, demonstrating the universality of the Standard Model (SM) CKM quark mixing matrix. The electric and magnetic form factors are reformulated using a new QCD three quark nucleon gyromagnetic factor, Dirac and Pauli form factors and anomalous kappa factors. The old 1943 Jauch form factors which have been systematically used and developed for many years is shown to be in stark disagreement with the new global set of experimental polarized electron-proton scattering data whereas the reformulated SM parameter set of this study is shown to agree very well, lending strong support for this new EM SM approach.

  2. Right ventricular function after repair of tetralogy of Fallot: a comparison between bovine pericardium and porcine small intestinal extracellular matrix.

    Science.gov (United States)

    Naik, Ronak; Johnson, Jason; Kumar, T K S; Philip, Ranjit; Boston, Umar; Knott-Craig, Christopher J

    2017-05-29

    The porcine small intestinal extracellular matrix reportedly has the potential to differentiate into viable myocardial cells. When used in tetralogy of Fallot repair, it may improve right ventricular function. We evaluated right ventricular function after repair of tetralogy of Fallot with extracellular matrix versus bovine pericardium. Subjects with non-transannular repair of tetralogy of Fallot with at least 1 year of follow-up were selected. The extracellular matrix and bovine pericardium groups were compared. We used three-dimensional right ventricular ejection fraction, right ventricle global longitudinal strain, and tricuspid annular plane systolic excursion to assess right ventricular function. The extracellular matrix group had 11 patients, whereas the bovine pericardium group had 10 patients. No differences between the groups were found regarding sex ratio, age at surgery, and cardiopulmonary bypass time. The follow-up period was 28±12.6 months in the extracellular matrix group and 50.05±17.6 months in the bovine pericardium group (p=0.001). The mean three-dimensional right ventricular ejection fraction (55.7±5.0% versus 55.3±5.2%, p=0.73), right ventricular global longitudinal strain (-18.5±3.0% versus -18.0±2.2%, p=0.44), and tricuspid annular plane systolic excursions (1.59±0.16 versus 1.59±0.2, p=0.93) were similar in the extracellular matrix group and in the bovine pericardium group, respectively. Right ventricular global longitudinal strain in healthy children is reported at -29±3% in literature. In a small cohort of the patients undergoing non-transannular repair of tetralogy of Fallot, there was no significant difference in right ventricular function between groups having extracellular matrix versus bovine pericardium patches followed-up for more than 1 year. Lower right ventricular longitudinal strain noted in both the groups compared to healthy children.

  3. A Comparison of Factors that Influence the Lyophilization Process

    OpenAIRE

    Mnerie, Dumitru; Anghel, Gabriela Victoria; Mnerie, Alin Vasile; Cheveresan, Constantin

    2007-01-01

    The lyophilization (or freeze drying) process for agro-foods products depends on a series of technological factors that are in an inter-dependence with the process performance. This paper presents an expert method and its application. This method characterizes the influence factors of the lyophilization process, after the importance level of some factors in correlation with other factors, is defined. Only the most important factors were considered; influence considerations were made in relati...

  4. Icotinib inhibits the invasion of Tca8113 cells via downregulation of nuclear factor κB-mediated matrix metalloproteinase expression.

    Science.gov (United States)

    Yang, Cailing; Yan, Jianguo; Yuan, Guoyan; Zhang, Yinghua; Lu, Derong; Ren, Mingxin; Cui, Weigang

    2014-09-01

    Icotinib is an epidermal growth factor receptor tyrosine kinase inhibitor, which has been revealed to inhibit proliferation in tumor cells. However, the effect of icotinib on cancer cell metastasis remains to be explained. This study examines the effect of icotinib on the migration and invasion of squamous cells of tongue carcinoma (Tca8113 cells) in vitro . The results of the Boyden chamber invasion assay demonstrated that icotinib reduced cell invasion, suppressed the protein levels of matrix metalloproteinases (MMPs), MMP-2 and MMP-9, and increased the expression of tissue inhibitor of metalloproteinase-1. In addition, icotinib was found to significantly decrease the protein levels of nuclear factor κB (NF-κB) p65, which suggested that icotinib inhibits NF-κB activity. Furthermore, treatment with the NF-κB inhibitor, pyrrolidine dithiocarbamate, suppressed cell invasion and MMP-2 expression. These results suggested that icotinib inhibits the invasion of Tca8113 cells by downregulating MMP via the inactivation of the NF-κB signaling pathways.

  5. Discovering perturbation of modular structure in HIV progression by integrating multiple data sources through non-negative matrix factorization.

    Science.gov (United States)

    Ray, Sumanta; Maulik, Ujjwal

    2016-12-20

    Detecting perturbation in modular structure during HIV-1 disease progression is an important step to understand stage specific infection pattern of HIV-1 virus in human cell. In this article, we proposed a novel methodology on integration of multiple biological information to identify such disruption in human gene module during different stages of HIV-1 infection. We integrate three different biological information: gene expression information, protein-protein interaction information and gene ontology information in single gene meta-module, through non negative matrix factorization (NMF). As the identified metamodules inherit those information so, detecting perturbation of these, reflects the changes in expression pattern, in PPI structure and in functional similarity of genes during the infection progression. To integrate modules of different data sources into strong meta-modules, NMF based clustering is utilized here. Perturbation in meta-modular structure is identified by investigating the topological and intramodular properties and putting rank to those meta-modules using a rank aggregation algorithm. We have also analyzed the preservation structure of significant GO terms in which the human proteins of the meta-modules participate. Moreover, we have performed an analysis to show the change of coregulation pattern of identified transcription factors (TFs) over the HIV progression stages.

  6. A stromal cell-derived factor-1 releasing matrix enhances the progenitor cell response and blood vessel growth in ischaemic skeletal muscle

    Directory of Open Access Journals (Sweden)

    D Kuraitis

    2011-09-01

    Full Text Available Although many regenerative cell therapies are being developed to replace or regenerate ischaemic muscle, the lack of vasculature and poor persistence of the therapeutic cells represent major limiting factors to successful tissue restoration. In response to ischaemia, stromal cell-derived factor-1 (SDF-1 is up-regulated by the affected tissue to stimulate stem cell-mediated regenerative responses. Therefore, we encapsulated SDF-1 into alginate microspheres and further incorporated these into an injectable collagen-based matrix in order to improve local delivery. Microsphere-matrix impregnation reduced the time for matrix thermogelation, and also increased the viscosity reached. This double-incorporation prolonged the release of SDF-1, which maintained adhesive and migratory bioactivity, attributed to chemotaxis in response to SDF-1. In vivo, treatment of ischaemic hindlimb muscle with microsphere-matrix led to increased mobilisation of bone marrow-derived progenitor cells, and also improved recruitment of angiogenic cells expressing the SDF-1 receptor (CXCR4 from bone marrow and local tissues. Both matrix and SDF-1-releasing matrix were successful at restoring perfusion, but SDF-1 treatment appeared to play an earlier role, as evidenced by arterioles that are phenotypically older and by increased angiogenic cytokine production, stimulating the generation of a qualitative microenvironment for a rapid and therefore more efficient regeneration. These results support the release of implanted SDF-1 as a promising method for enhancing progenitor cell responses and restoring perfusion to ischaemic tissues via neovascularisation.

  7. Positive matrix factorization and trajectory modelling for source identification: A new look at Indian Ocean Experiment ship observations

    Science.gov (United States)

    Bhanuprasad, S. G.; Venkataraman, Chandra; Bhushan, Mani

    The sources of aerosols on a regional scale over India have only recently received attention in studies using back trajectory analysis and chemical transport modelling. Receptor modelling approaches such as positive matrix factorization (PMF) and the potential source contribution function (PSCF) are effective tools in source identification of urban and regional-scale pollution. In this work, PMF and PSCF analysis is applied to identify categories and locations of sources that influenced surface concentrations of aerosols in the Indian Ocean Experiment (INDOEX) domain measured on-board the research vessel Ron Brown [Quinn, P.K., Coffman, D.J., Bates, T.S., Miller, T.L., Johnson, J.E., Welton, E.J., et al., 2002. Aerosol optical properties during INDOEX 1999: means, variability, and controlling factors. Journal of Geophysical Research 107, 8020, doi:10.1029/2000JD000037]. Emissions inventory information is used to identify sources co-located with probable source regions from PSCF. PMF analysis identified six factors influencing PM concentrations during the INDOEX cruise of the Ron Brown including a biomass combustion factor (35-40%), three industrial emissions factors (35-40%), primarily secondary sulphate-nitrate, balance trace elements and Zn, and two dust factors (20-30%) of Si- and Ca-dust. The identified factors effectively predict the measured submicron PM concentrations (slope of regression line=0.90±0.20; R2=0.76). Probable source regions shifted based on changes in surface and elevated flows during different times in the ship cruise. They were in India in the early part of the cruise, but in west Asia, south-east Asia and Africa, during later parts of the cruise. Co-located sources include coal-fired electric utilities, cement, metals and petroleum production in India and west Asia, biofuel combustion for energy and crop residue burning in India, woodland/forest burning in north sub-Saharan Africa and forest burning in south-east Asia. Significant findings

  8. Platelet-derived growth factor-D modulates extracellular matrix homeostasis and remodeling through TIMP-1 induction and attenuation of MMP-2 and MMP-9 gelatinase activities

    International Nuclear Information System (INIS)

    Borkham-Kamphorst, Erawan; Alexi, Pascal; Tihaa, Lidia; Haas, Ute; Weiskirchen, Ralf

    2015-01-01

    Platelet-derived growth factor-D (PDGF-D) is a more recent recognized growth factor involved in the regulation of several cellular processes, including cell proliferation, transformation, invasion, and angiogenesis by binding to and activating its cognate receptor PDGFR-β. After bile duct ligation or in the carbon tetrachloride-induced hepatic fibrosis model , PDGF-D showed upregulation comparable to PDGF-B. Moreover, adenoviral PDGF-D gene transfer induced hepatic stellate cell proliferation and liver fibrosis. We here investigated the molecular mechanism of PDGF-D involvement in liver fibrogenesis. Therefore, the GRX mouse cell line was stimulated with PDGF-D and evaluated for fibrotic markers and PDGF-D signaling pathways in comparison to the other PDGF isoforms. We found that PDGF-D failed to enhance Col I and α-smooth muscle actin (α-SMA) production but has capacity to upregulate expression of the tissue inhibitor of metalloprotease 1 (TIMP-1) resulting in attenuation of MMP-2 and MMP-9 gelatinase activity as indicated by gelatinase zymography. This phenomenon was restored through application of a PDGF-D neutralizing antibody. Unexpectedly, PDGF-D incubation decreased both PDGFR-α and -β in mRNA and protein levels, and PDGF-D phosphorylated typrosines specific for PDGFR-α and -β. We conclude that PDGF-D intensifies fibrogenesis by interfering with the fibrolytic activity of the TIMP-1/MMP system and that PDGF-D signaling is mediated through both PDGF-α and -β receptors. - Highlights: • PDGF-D signals through PDGF receptor type α and β. • PDGF-D modulates extracellular matrix homeostasis and remodeling. • Like PDGF-B, PDGF-D triggers phosphorylation of PLC-γ, Akt/PKB, JNK, ERK1/2, and p38. • PDGF-D induces TIMP-1 expression through ERK and p38 MAPK. • PDGF-D attenuates MMP-2 and MMP-9 gelatinase activities

  9. Comparison of Conjugate Gradient Density Matrix Search and Chebyshev Expansion Methods for Avoiding Diagonalization in Large-Scale Electronic Structure Calculations

    Science.gov (United States)

    Bates, Kevin R.; Daniels, Andrew D.; Scuseria, Gustavo E.

    1998-01-01

    We report a comparison of two linear-scaling methods which avoid the diagonalization bottleneck of traditional electronic structure algorithms. The Chebyshev expansion method (CEM) is implemented for carbon tight-binding calculations of large systems and its memory and timing requirements compared to those of our previously implemented conjugate gradient density matrix search (CG-DMS). Benchmark calculations are carried out on icosahedral fullerenes from C60 to C8640 and the linear scaling memory and CPU requirements of the CEM demonstrated. We show that the CPU requisites of the CEM and CG-DMS are similar for calculations with comparable accuracy.

  10. Monte Carlo determination of the infinite matrix dose rate correction factors for 250 μm quartz and TLD500 chip

    International Nuclear Information System (INIS)

    Baly, L.; Martín, G.; Quesada, I.; Padilla, F.; Arteche, R.

    2015-01-01

    A new approach based on the Monte Carlo simulation is used to calculate the infinite matrix dose rate correction factors of gamma, beta and internal conversion radiations for 250 μm diameter grains of quartz and TLD500 chips. Here, the dependence of the correction factor on the radiation energy is initially calculated for each type of emitted particle and with this result the correction factors for the 232 Th and 238 U series and 40 K are determined. This analysis is made for dry soil and also for different levels of water content in it. The obtained beta correction factors for quartz are in good agreement with those previously reported. For the TLD500 chip certain differences with previously reported data are found. The analysis of the gamma water correction factor for quartz based on Zimmerman equation shows the correspondence with the similar correction factor for electrons. In the case of TLD500 chip a gamma water correction factor value of 1.0 was found. - Highlights: • A new approach based on Monte Carlo simulation is used to compute infinite matrix dose rate correction factors. • Infinite matrix models with real dimensions were analyzed within 3% uncertainties. • The dependence of grain size attenuation on particle energy is determined. • The same dependence for water correction factors is also analyzed

  11. Expression of early transcription factors Oct-4, Sox-2 and Nanog by porcine umbilical cord (PUC matrix cells

    Directory of Open Access Journals (Sweden)

    Schultz Bruce

    2006-02-01

    Full Text Available Abstract Background Three transcription factors that are expressed at high levels in embryonic stem cells (ESCs are Nanog, Oct-4 and Sox-2. These transcription factors regulate the expression of other genes during development and are found at high levels in the pluripotent cells of the inner cell mass. The downregulation of these three transcription factors correlates with the loss of pluripotency and self-renewal, and the beginning of subsequent differentiation steps. The roles of Nanog, Oct-4 and Sox-2 have not been fully elucidated. They are important in embryonic development and maintenance of pluripotency in ESCs. We studied the expression of these transcription factors in porcine umbilical cord (PUC matrix cells. Methods Cells were isolated from Wharton's jelly of porcine umbilical cords (PUC and histochemically assayed for the presence of alkaline phosphatase and the presence of Nanog, Oct-4 and Sox-2 mRNA and protein. PCR amplicons were sequenced and compared with known sequences. The synthesis of Oct-4 and Nanog protein was analyzed using immunocytochemistry. FACS analysis was utilized to evaluate Hoechst 33342 dye-stained cells. Results PUC isolates were maintained in culture and formed colonies that express alkaline phosphatase. FACS analysis revealed a side population of Hoechst dye-excluding cells, the Hoechst exclusion was verapamil sensitive. Quantitative and non-quantitative RT-PCR reactions revealed expression of Nanog, Oct-4 and Sox-2 in day 15 embryonic discs, PUC cell isolates and porcine fibroblasts. Immunocytochemical analysis detected Nanog immunoreactivity in PUC cell nuclei, and faint labeling in fibroblasts. Oct-4 immunoreactivity was detected in the nuclei of some PUC cells, but not in fibroblasts. Conclusion Cells isolated from PUC express three transcription factors found in pluripotent stem cell markers both at the mRNA and protein level. The presence of these transcription factors, along with the other

  12. A composite demineralized bone matrix--self assembling peptide scaffold for enhancing cell and growth factor activity in bone marrow.

    Science.gov (United States)

    Hou, Tianyong; Li, Zhiqiang; Luo, Fei; Xie, Zhao; Wu, Xuehui; Xing, Junchao; Dong, Shiwu; Xu, Jianzhong

    2014-07-01

    The need for suitable bone grafts is high; however, there are limitations to all current graft sources, such as limited availability, the invasive harvest procedure, insufficient osteoinductive properties, poor biocompatibility, ethical problems, and degradation properties. The lack of osteoinductive properties is a common problem. As an allogenic bone graft, demineralized bone matrix (DBM) can overcome issues such as limited sources and comorbidities caused by invasive harvest; however, DBM is not sufficiently osteoinductive. Bone marrow has been known to magnify osteoinductive components for bone reconstruction because it contains osteogenic cells and factors. Mesenchymal stem cells (MSCs) derived from bone marrow are the gold standard for cell seeding in tissue-engineered biomaterials for bone repair, and these cells have demonstrated beneficial effects. However, the associated high cost and the complicated procedures limit the use of tissue-engineered bone constructs. To easily enrich more osteogenic cells and factors to DBM by selective cell retention technology, DBM is modified by a nanoscale self-assembling peptide (SAP) to form a composite DBM/SAP scaffold. By decreasing the pore size and increasing the charge interaction, DBM/SAP scaffolds possess a much higher enriching yield for osteogenic cells and factors compared with DBM alone scaffolds. At the same time, SAP can build a cellular microenvironment for cell adhesion, proliferation, and differentiation that promotes bone reconstruction. As a result, a suitable bone graft fabricated by DBM/SAP scaffolds and bone marrow represents a new strategy and product for bone transplantation in the clinic. Copyright © 2014 Elsevier Ltd. All rights reserved.

  13. Discrimination Factors and Incorporation Rates for Organic Matrix in Shark Teeth Based on a Captive Feeding Study.

    Science.gov (United States)

    Zeichner, S S; Colman, A S; Koch, P L; Polo-Silva, C; Galván-Magaña, F; Kim, S L

    Sharks migrate annually over large distances and occupy a wide variety of habitats, complicating analysis of lifestyle and diet. A biogeochemical technique often used to reconstruct shark diet and environment preferences is stable isotope analysis, which is minimally invasive and integrates through time and space. There are previous studies that focus on isotopic analysis of shark soft tissues, but there are limited applications to shark teeth. However, shark teeth offer an advantage of multiple ecological snapshots and minimum invasiveness during removal because of their distinct conveyor belt tooth replacement system. In this study, we analyze δ 13 C and δ 15 N values of the organic matrix in leopard shark teeth (Triakis semifasciata) from a captive experiment and report discrimination factors as well as incorporation rates. We found differences in tooth discrimination factors for individuals fed different prey sources (mean ± SD; Δ 13 C squid = 4.7‰ ± 0.5‰, Δ 13 C tilapia = 3.1‰ ± 1.0‰, Δ 15 N squid = 2.0‰ ± 0.7‰, Δ 15 N tilapia = 2.8‰ ± 0.6‰). In addition, these values differed from previously published discrimination factors for plasma, red blood cells, and muscle of the same leopard sharks. Incorporation rates of shark teeth were similar for carbon and nitrogen (mean ± SE; λ C = 0.021 ± 0.009, λ N = 0.024 ± 0.007) and comparable to those of plasma. We emphasize the difference in biological parameters on the basis of tissue substrate and diet items to interpret stable isotope data and apply our results to stable isotope values from blue shark (Prionace glauca) teeth to illustrate the importance of biological parameters to interpret the complex ecology of a migratory shark.

  14. Joint refinement model for the spin resolved one-electron reduced density matrix of YTiO3 using magnetic structure factors and magnetic Compton profiles data.

    Science.gov (United States)

    Gueddida, Saber; Yan, Zeyin; Kibalin, Iurii; Voufack, Ariste Bolivard; Claiser, Nicolas; Souhassou, Mohamed; Lecomte, Claude; Gillon, Béatrice; Gillet, Jean-Michel

    2018-04-28

    In this paper, we propose a simple cluster model with limited basis sets to reproduce the unpaired electron distributions in a YTiO 3 ferromagnetic crystal. The spin-resolved one-electron-reduced density matrix is reconstructed simultaneously from theoretical magnetic structure factors and directional magnetic Compton profiles using our joint refinement algorithm. This algorithm is guided by the rescaling of basis functions and the adjustment of the spin population matrix. The resulting spin electron density in both position and momentum spaces from the joint refinement model is in agreement with theoretical and experimental results. Benefits brought from magnetic Compton profiles to the entire spin density matrix are illustrated. We studied the magnetic properties of the YTiO 3 crystal along the Ti-O 1 -Ti bonding. We found that the basis functions are mostly rescaled by means of magnetic Compton profiles, while the molecular occupation numbers are mainly modified by the magnetic structure factors.

  15. Development of Positive Matrix Factorization Model (PMF) to Annual Study of the PM2.5 Organic Composition in ChapinerIa

    International Nuclear Information System (INIS)

    Pindado, O.; Perez, R. M.; Garcia, S.

    2013-01-01

    The Positive Matrix Factorization (PMF) application to a set of PM2.5 data collected in a rural area of Madrid for a period of 1 year has been developed. Results has let describing the particulate faction of atmospheric aerosol collected in Chapineria according to 7 factor, among them fossil fuel combustion by traffic, wax plants, primary emissions of organic carbon, crustal material, and secondary organic aerosol. Five of these factors are related to primary particles; meanwhile only one factor has been associated to secondary particles. Finally, a factor has not been associated to any known source of particulate matter. (Author)

  16. Membrane Type-1 Matrix Metalloproteinase Expression in Acute Myeloid Leukemia and Its Upregulation by Tumor Necrosis Factor

    Directory of Open Access Journals (Sweden)

    Anna Janowska-Wieczorek

    2012-07-01

    Full Text Available Membrane type-1 matrix metalloproteinase (MT1-MMP has been implicated in tumor invasion, as well as trafficking of normal hematopoietic cells, and acts as a physiologic activator of proMMP-2. In this study we examined MT1-MMP expression in primary acute myeloid leukemia (AML cells. Because tumor necrosis factor (TNF-α is known to be elevated in AML, we also investigated the effect of TNF-α on MT1-MMP expression. We found (i MT1-MMP mRNA expression in 41 out of 43 primary AML samples tested; (ii activation of proMMP-2 in co-cultures of AML cells with normal bone marrow stromal cells; and (iii inhibition of proMMP-2 activation and trans-Matrigel migration of AML cells by gene silencing using MT1-MMP siRNA. Moreover, recombinant human TNF-α upregulated MT1-MMP expression in AML cells resulting in enhanced proMMP-2 activation and trans-Matrigel migration. Thus, AML cells express MT1-MMP and TNF-α enhances it leading to increased MMP-2 activation and most likely contributing to the invasive phenotype. We suggest that MT1-MMP, together with TNF-α, should be investigated as potential therapeutic targets in AML.

  17. Membrane Type-1 Matrix Metalloproteinase Expression in Acute Myeloid Leukemia and Its Upregulation by Tumor Necrosis Factor

    International Nuclear Information System (INIS)

    Marquez-Curtis, Leah A.; Shirvaikar, Neeta; Turner, A. Robert; Mirza, Imran; Surmawala, Amir; Larratt, Loree M.; Janowska-Wieczorek, Anna

    2012-01-01

    Membrane type-1 matrix metalloproteinase (MT1-MMP) has been implicated in tumor invasion, as well as trafficking of normal hematopoietic cells, and acts as a physiologic activator of proMMP-2. In this study we examined MT1-MMP expression in primary acute myeloid leukemia (AML) cells. Because tumor necrosis factor (TNF)-α is known to be elevated in AML, we also investigated the effect of TNF-α on MT1-MMP expression. We found (i) MT1-MMP mRNA expression in 41 out of 43 primary AML samples tested; (ii) activation of proMMP-2 in co-cultures of AML cells with normal bone marrow stromal cells; and (iii) inhibition of proMMP-2 activation and trans-Matrigel migration of AML cells by gene silencing using MT1-MMP siRNA. Moreover, recombinant human TNF-α upregulated MT1-MMP expression in AML cells resulting in enhanced proMMP-2 activation and trans-Matrigel migration. Thus, AML cells express MT1-MMP and TNF-α enhances it leading to increased MMP-2 activation and most likely contributing to the invasive phenotype. We suggest that MT1-MMP, together with TNF-α, should be investigated as potential therapeutic targets in AML

  18. [Application of excitation-emission matrix spectrum combined with parallel factor analysis in dissolved organic matter in East China Sea].

    Science.gov (United States)

    Lü, Li-Sha; Zhao, Wei-Hong; Miao, Hui

    2013-03-01

    Using excitation-emission matrix spectrum(EEMs) combined with parallel factor analysis (PARAFAC) examine the fluorescent components feature of dissolved organic matter (DOM) sampled from East China Sea in the summer and autumn was examined. The type, distribution and origin of the fluorescence dissolved organic matter were also discussed. Three fluorescent components were identified by PARAFAC, including protein-like component C1 (235, 280/330), terrestrial or marine humic-like component C2 (255, 330/400) and terrestrial humic-like component C3 (275, 360/480). The good linearity of the two humic-like components showed the same source or some relationship between the chemical constitutions. As a whole, the level of the fluorescence intensity in coastal ocean was higher than that of the open ocean in different water layers in two seasons. The relationship of three components with chlorophyll-a and salinity showed the DOM in the study area is almost not influenced by the living algal matter, but the fresh water outflow of the Yangtze River might be the source of them in the Yangtze River estuary in Summer. From what has been discussed above, we can draw the conclusion that the application of EEM-PARAFAC modeling will exert a profound influence upon the research of the dissolved organic matter.

  19. Modulation of extracellular matrix by nutritional hepatotrophic factors in thioacetamide-induced liver cirrhosis in the rat

    Directory of Open Access Journals (Sweden)

    R.R. Guerra

    2009-11-01

    Full Text Available Nutritional substances associated to some hormones enhance liver regeneration when injected intraperitoneally, being denominated hepatotrophic factors (HF. Here we verified if a solution of HF (glucose, vitamins, salts, amino acids, glucagon, insulin, and triiodothyronine can revert liver cirrhosis and how some extracellular matrices are affected. Cirrhosis was induced for 14 weeks in 45 female Wistar rats (200 mg by intraperitoneal injections of thioacetamide (200 mg/kg. Twenty-five rats received intraperitoneal HF twice a day for 10 days (40 mL·kg-1·day-1 and 20 rats received physiological saline. Fifteen rats were used as control. The HF applied to cirrhotic rats significantly: a reduced the relative mRNA expression of the genes: Col-α1 (-53%, TIMP-1 (-31.7%, TGF-β1 (-57.7%, and MMP-2 (-41.6%, whereas Plau mRNA remained unchanged; b reduced GGT (-43.1%, ALT (-17.6%, and AST (-12.2% serum levels; c increased liver weight (11.3%, and reduced liver collagen (-37.1%, regenerative nodules size (-22.1%, and fibrous septum thickness. Progranulin protein (immunohistochemistry and mRNA (in situ hybridization were found in fibrous septa and areas of bile duct proliferation in cirrhotic livers. Concluding, HF improved the histology and serum biochemistry of liver cirrhosis, with an important reduction of interstitial collagen and increased extracelullar matrix degradation by reducing profibrotic gene expression.

  20. [Resolving excitation emission matrix spectroscopy of estuarine CDOM with parallel factor analysis and its application in organic pollution monitoring].

    Science.gov (United States)

    Guo, Wei-Dong; Huang, Jian-Ping; Hong, Hua-Sheng; Xu, Jing; Deng, Xun

    2010-06-01

    The distribution and estuarine behavior of fluorescent components of chromophoric dissolved organic matter (CDOM) from Jiulong Estuary were determined by fluorescence excitation emission matrix spectroscopy (EEMs) combined with parallel factor analysis (PARAFAC). The feasibility of these components as tracers for organic pollution in estuarine environments was also evaluated. Four separate fluorescent components were identified by PARAFAC, including three humic-like components (C1: 240, 310/382 nm; C2: 230, 250, 340/422 nm; C4: 260, 390/482 nm) and one protein-like components (C3: 225, 275/342 nm). These results indicated that UV humic-like peak A area designated by traditional "peak-picking method" was not a single peak but actually a combination of several fluorescent components, and it also had inherent links to so-called marine humic-like peak M or terrestrial humic-like peak C. Component C2 which include peak M decreased with increase of salinity in Jiulong Estuary, demonstrating that peak M can not be thought as the specific indicator of the "marine" humic-like component. Two humic-like components C1 and C2 showed additional behavior in the turbidity maximum region (salinity CDOM may provide a fast in-situ way to monitor the variation of the degree of organic pollution in estuarine environments.

  1. Transforming growth factor. beta. sub 1 is present at sites of extracellular matrix gene expression in human pulmonary fibrosis

    Energy Technology Data Exchange (ETDEWEB)

    Broekelmann, T.J.; Limper, A.H.; McDonald, J.A. (Washington Univ., St. Louis, MO (United States)); Colby, T.V. (Mayo Clinic, Rochester, MN (United States))

    1991-08-01

    Idiopathic pulmonary fibrosis is an inexorably fatal disorder characterized by connective tissue deposition within the terminal air spaces resulting in loss of lung function and eventual respiratory failure. Previously, the authors demonstrated that foci of activated fibroblasts expressing high levels of fibronectin, procollagen, and smooth muscle actin and thus resembling those found in healing wounds are responsible for the connective tissue deposition and scarring in idiopathic pulmonary fibrosis. Using in situ hybridization and immunohistochemistry, they now demonstrate the presence of transforming growth factor {beta}{sub 1} (TGF-{beta}{sub 1}), a potent profibrotic cytokine, in the foci containing these activated fibroblasts. These results suggest that matrix-associated TGF-{beta}{sub 1} may serve as a stimulus for the persistent expression of connective tissue genes. One potential source of the TGF-{beta}{sub 1} is the alveolar macrophage, and they demonstrate the expression of abundant TGF-{beta}{sub 1} mRNA in alveolar macrophages in lung tissue from patients with idiopathic pulmonary fibrosis.

  2. Size-resolved particle number emission patterns under real-world driving conditions using positive matrix factorization.

    Science.gov (United States)

    Domínguez-Sáez, Aida; Viana, Mar; Barrios, Carmen C; Rubio, Jose R; Amato, Fulvio; Pujadas, Manuel; Querol, Xavier

    2012-10-16

    A novel on-board system was tested to characterize size-resolved particle number emission patterns under real-world driving conditions, running in a EURO4 diesel vehicle and in a typical urban circuit in Madrid (Spain). Emission profiles were determined as a function of driving conditions. Source apportionment by Positive Matrix Factorization (PMF) was carried out to interpret the real-world driving conditions. Three emission patterns were identified: (F1) cruise conditions, with medium-high speeds, contributing in this circuit with 60% of total particle number and a particle size distribution dominated by particles >52 nm and around 60 nm; (F2) transient conditions, stop-and-go conditions at medium-high speed, contributing with 25% of the particle number and mainly emitting particles in the nucleation mode; and (F3) creep-idle conditions, representing traffic congestion and frequent idling periods, contributing with 14% to the total particle number and with particles in the nucleation mode (emissions depending on particle size and driving conditions. Differences between real-world emission patterns and regulatory cycles (NEDC) are also presented, which evidence that detecting particle number emissions real-world driving conditions.

  3. Decorin-transforming growth factor- interaction regulates matrix organization and mechanical characteristics of three-dimensional collagen matrices.

    Science.gov (United States)

    Ferdous, Zannatul; Wei, Victoria Mariko; Iozzo, Renato; Höök, Magnus; Grande-Allen, Kathryn Jane

    2007-12-07

    The small leucine-rich proteoglycan decorin has been demonstrated to be a key regulator of collagen fibrillogenesis; decorin deficiencies lead to irregularly shaped collagen fibrils and weakened material behavior in postnatal murine connective tissues. In an in vitro investigation of the contributions of decorin to tissue organization and material behavior, model tissues were engineered by seeding embryonic fibroblasts, harvested from 12.5-13.5 days gestational aged decorin null (Dcn(-/-)) or wild-type mice, within type I collagen gels. The resulting three-dimensional collagen matrices were cultured for 4 weeks under static tension. The collagen matrices seeded with Dcn(-/-) cells exhibited greater contraction, cell density, ultimate tensile strength, and elastic modulus than those seeded with wild-type cells. Ultrastructurally, the matrices seeded with Dcn(-/-) cells contained a greater density of collagen. The decorin-null tissues contained more biglycan than control tissues, suggesting that this related proteoglycan compensated for the absence of decorin. The effect of transforming growth factor-beta (TGF-beta), which is normally sequestered by decorin, was also investigated in this study. The addition of TGF-beta1 to the matrices seeded with wild-type cells improved their contraction and mechanical strength, whereas blocking TGF-beta1 in the Dcn(-/-) cell-seeded matrices significantly reduced the collagen gel contraction. These results indicate that the inhibitory interaction between decorin and TGF-beta1 significantly influenced the matrix organization and material behavior of these in vitro model tissues.

  4. Local hyperspectral data multisharpening based on linear/linear-quadratic nonnegative matrix factorization by integrating lidar data

    Science.gov (United States)

    Benhalouche, Fatima Zohra; Karoui, Moussa Sofiane; Deville, Yannick; Ouamri, Abdelaziz

    2015-10-01

    In this paper, a new Spectral-Unmixing-based approach, using Nonnegative Matrix Factorization (NMF), is proposed to locally multi-sharpen hyperspectral data by integrating a Digital Surface Model (DSM) obtained from LIDAR data. In this new approach, the nature of the local mixing model is detected by using the local variance of the object elevations. The hyper/multispectral images are explored using small zones. In each zone, the variance of the object elevations is calculated from the DSM data in this zone. This variance is compared to a threshold value and the adequate linear/linearquadratic spectral unmixing technique is used in the considered zone to independently unmix hyperspectral and multispectral data, using an adequate linear/linear-quadratic NMF-based approach. The obtained spectral and spatial information thus respectively extracted from the hyper/multispectral images are then recombined in the considered zone, according to the selected mixing model. Experiments based on synthetic hyper/multispectral data are carried out to evaluate the performance of the proposed multi-sharpening approach and literature linear/linear-quadratic approaches used on the whole hyper/multispectral data. In these experiments, real DSM data are used to generate synthetic data containing linear and linear-quadratic mixed pixel zones. The DSM data are also used for locally detecting the nature of the mixing model in the proposed approach. Globally, the proposed approach yields good spatial and spectral fidelities for the multi-sharpened data and significantly outperforms the used literature methods.

  5. Matrix protein of vesicular stomatitis virus: a potent inhibitor of vascular endothelial growth factor and malignant ascites formation.

    Science.gov (United States)

    Zhou, Y; Wen, F; Zhang, P; Tang, R; Li, Q

    2013-03-01

    Malignant ascites is common in various types of cancers and is difficult to manage. Vascular endothelial growth factor (VEGF) has a pivotal role in malignant ascites. The matrix protein of vesicular stomatitis virus (VSVMP) has been shown to inhibit host gene expression and induce the apoptosis of cancer cells. The present study was designed to determine whether VSVMP suppresses the formation of ascites in ascites-producing peritoneal carcinomatosis. BALB/c female mice, 6-8 weeks old, bearing peritoneal tumors of H22 or MethA cells received an intraperitoneal administration of 50 μg VSVMP/250 μg liposome complexes, 50 μg empty plasmid/250 μg liposome complexes or 0.9% NaCl solution, respectively, every 2 days for 3 weeks. Administration of VSVMP resulted in a significant inhibition in ascites formation, improvement in health condition and prolonged survival of the treated mice. Decreased peritoneum osmolarity and reduced tumor vascularity coincided with dramatic reductions in the VEGF level in ascites fluid and plasma. Examination of floating tumor cells collected from the peritoneal wash revealed an apparently increased number of apoptotic cells and profound downregulation of VEGF mRNA in the VSVMP-treated mice. Our data indicate for the first time that in BALB/c mice bearing H22 or MethA cell peritoneal tumors, VSVMP may inhibit VEGF production and suppress angiogenesis, consequently abolishing ascites formation.

  6. Characterizing fluorescent dissolved organic matter in a membrane bioreactor via excitation-emission matrix combined with parallel factor analysis.

    Science.gov (United States)

    Maqbool, Tahir; Quang, Viet Ly; Cho, Jinwoo; Hur, Jin

    2016-06-01

    In this study, we successfully tracked the dynamic changes in different constitutes of bound extracellular polymeric substances (bEPS), soluble microbial products (SMP), and permeate during the operation of bench scale membrane bioreactors (MBRs) via fluorescence excitation-emission matrix (EEM) combined with parallel factor analysis (PARAFAC). Three fluorescent groups were identified, including two protein-like (tryptophan-like C1 and tyrosine-like C2) and one microbial humic-like components (C3). In bEPS, protein-like components were consistently more dominant than C3 during the MBR operation, while their relative abundance in SMP depended on aeration intensities. C1 of bEPS exhibited a linear correlation (R(2)=0.738; pbEPS amounts in sludge, and C2 was closely related to the stability of sludge. The protein-like components were more greatly responsible for membrane fouling. Our study suggests that EEM-PARAFAC can be a promising monitoring tool to provide further insight into process evaluation and membrane fouling during MBR operation. Copyright © 2016 Elsevier Ltd. All rights reserved.

  7. [Expression and clinical significance of kisspeptin-1, matrix metalloproteinase-2 and vascular endothelial growth factor in tissue of colon cancer].

    Science.gov (United States)

    Wang, Wenhui; Qi, Yuanling; Xu, Qian; Ren, Haipeng

    2016-03-01

    To detect the expression of kisspeptin-1 (KISS-1), matrix metalloproteinase-2 (MMP-2) and vascular endothelial growth factor (VEGF) in the tissue of colon cancer, and analyze the relativity between KISS-1, MMP-2, VEGF and pathological characteristics of colon cancer. A total of 60 colon cancer patients and 60 patients with benign colorectal disease who received surgical treatment in our hospital from January 2009 to June 2010 were selected as observation group and control group respectively. The cancer tissue samples and excision samples collected from them were used to detect KISS-1, MMP-2 and VEGF with immunohistochemistry. The positive rates of KISS-1, MMP-2 and VEGF were 31.7%, 58.3% and 78.3% in observation group, and 73.3%, 16.7% and 33.3% in control group. The positive rate of KISS-1 in observation group was lower than that in control group (χ(2)=23.489, Pcolon cancer (χ(2)=8.997, P=0.011; χ(2)=6.163, P=0.013; χ(2)=8.519, P=0.014; χ(2)=9.160, P=0.002; χ(2)=16.577, Pclinical stage of colon cancer and provide evidence for clinical diagnosis and prognosis prediction by detecting KISS-1, MMP-2 and VEGF.

  8. Membrane Type-1 Matrix Metalloproteinase Expression in Acute Myeloid Leukemia and Its Upregulation by Tumor Necrosis Factor

    Energy Technology Data Exchange (ETDEWEB)

    Marquez-Curtis, Leah A.; Shirvaikar, Neeta [Canadian Blood Services R& D, Edmonton, Alberta T6G 2R8 (Canada); Turner, A. Robert [Departments of Medicine and Oncology, University of Alberta, Edmonton, Alberta T6G 2G3 (Canada); Mirza, Imran [Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta T6G 2B7 (Canada); Surmawala, Amir; Larratt, Loree M. [Departments of Medicine and Oncology, University of Alberta, Edmonton, Alberta T6G 2G3 (Canada); Janowska-Wieczorek, Anna, E-mail: anna.janowska@blood.ca [Canadian Blood Services R& D, Edmonton, Alberta T6G 2R8 (Canada); Departments of Medicine and Oncology, University of Alberta, Edmonton, Alberta T6G 2G3 (Canada)

    2012-07-25

    Membrane type-1 matrix metalloproteinase (MT1-MMP) has been implicated in tumor invasion, as well as trafficking of normal hematopoietic cells, and acts as a physiologic activator of proMMP-2. In this study we examined MT1-MMP expression in primary acute myeloid leukemia (AML) cells. Because tumor necrosis factor (TNF)-α is known to be elevated in AML, we also investigated the effect of TNF-α on MT1-MMP expression. We found (i) MT1-MMP mRNA expression in 41 out of 43 primary AML samples tested; (ii) activation of proMMP-2 in co-cultures of AML cells with normal bone marrow stromal cells; and (iii) inhibition of proMMP-2 activation and trans-Matrigel migration of AML cells by gene silencing using MT1-MMP siRNA. Moreover, recombinant human TNF-α upregulated MT1-MMP expression in AML cells resulting in enhanced proMMP-2 activation and trans-Matrigel migration. Thus, AML cells express MT1-MMP and TNF-α enhances it leading to increased MMP-2 activation and most likely contributing to the invasive phenotype. We suggest that MT1-MMP, together with TNF-α, should be investigated as potential therapeutic targets in AML.

  9. A comparison study of different physical treatments on cartilage matrix derived porous scaffolds for tissue engineering applications

    International Nuclear Information System (INIS)

    Moradi, Ali; Pramanik, Sumit; Ataollahi, Forough; Pingguan-Murphy, Belinda; Abdul Khalil, Alizan; Kamarul, Tunku

    2014-01-01

    Native cartilage matrix derived (CMD) scaffolds from various animal and human sources have drawn attention in cartilage tissue engineering due to the demonstrable presence of bioactive components. Different chemical and physical treatments have been employed to enhance the micro-architecture of CMD scaffolds. In this study we have assessed the typical effects of physical cross-linking methods, namely ultraviolet (UV) light, dehydrothermal (DHT) treatment, and combinations of them on bovine articular CMD porous scaffolds with three different matrix concentrations (5%, 15% and 30%) to assess the relative strengths of each treatment. Our findings suggest that UV and UV–DHT treatments on 15% CMD scaffolds can yield architecturally optimal scaffolds for cartilage tissue engineering. (paper)

  10. KEY COMPARISON: CCQM-K61: Quantitation of a linearised plasmid DNA, based on a matched standard in a matrix of non-target DNA

    Science.gov (United States)

    Woolford, Alison; Holden, Marcia; Salit, Marc; Burns, Malcolm; Ellison, Stephen L. R.

    2009-01-01

    Key comparison CCQM-K61 was performed to demonstrate and document the capability of interested national metrology institutes in the determination of the quantity of specific DNA target in an aqueous solution. The study provides support for the following measurement claim: "Quantitation of a linearised plasmid DNA, based on a matched standard in a matrix of non-target DNA". The comparison was an activity of the Bioanalysis Working Group (BAWG) of the Comité Consultatif pour la Quantité de Matière and was coordinated by NIST (Gaithersburg, USA) and LGC (Teddington, UK). The following laboratories (in alphabetical order) participated in this key comparison. DMSC (Thailand); IRMM (European Union); KRISS (Republic of Korea); LGC (UK); NIM (China); NIST (USA); NMIA (Australia); NMIJ (Japan); VNIIM (Russian Federation) Good agreement was observed between the reported results of all nine of the participants. Uncertainty estimates did not account fully for the dispersion of results even after allowance for possible inhomogeneity in calibration materials. Preliminary studies suggest that the effects of fluorescence threshold setting might contribute to the excess dispersion, and further study of this topic is suggested Main text. To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/. The final report has been peer-reviewed and approved for publication by the CCQM, according to the provisions of the CIPM Mutual Recognition Arrangement (MRA).

  11. Higher Expression of Epidermal Growth Factor Receptor Is Associated with Extracellular Matrix Metalloprotease Inducer in Colorectal Adenocarcinoma: Tissue Microarray Analysis of Immunostaining Score with Clinicopathological Parameters

    Directory of Open Access Journals (Sweden)

    Jong-Shiaw Jin

    2006-01-01

    Full Text Available Aim: Extracellular matrix metalloprotease inducer (EMMPRIN expression was demonstrated in several cancers, but its expression profile in colorectal cancers remains unclear. Epidermal growth factor receptor (EGFR was reported to regulate EMMPRIN expression in human epithelial cancers. Our purpose was to determine EMMPRIN expression and its relationship with EGFR in colorectal cancers.

  12. Characterization of O-glycosylated precursors of insulin-like growth factor II by matrix-assisted laser desorption/ionization mass spectrometry

    NARCIS (Netherlands)

    Jespersen, S.; Koedam, J.A.; Hoogerbrugge, C.M.; Tjaden, U.R.; Greef, J. van der; Brande, J.L. van den

    1996-01-01

    High molecular weight precursors of insulin-like growth factor II (IGF-II) were isolated from Cohn fraction IV of human plasma by ultrafiltration, affinity chromatography and reversed-phase high-performance liquid chromatography. Molecular weight determination by matrix-assisted laser

  13. Vascular endothelial growth factors: A comparison between invertebrates and vertebrates.

    Science.gov (United States)

    Kipryushina, Yulia O; Yakovlev, Konstantin V; Odintsova, Nelly A

    2015-12-01

    This review aims to summarize recent data concerning the structure and role of the members of the vascular endothelial growth factor (VEGF) and vascular endothelial growth factor receptor (VEGFR) families in the context of early development, organogenesis and regeneration, with a particular emphasis on the role of these factors in the development of invertebrates. Homologs of VEGF and/or VEGFR have been found in all Eumetazoa, in both Radiata and Bilateria, where they are expressed in the descendants of different germ layers and play a pivotal role in the development of animals with and without a vascular system. VEGF is a well-known angiogenesis regulator, but this factor also control cell migration during neurogenesis and the development of branching organs (the trachea) in invertebrate and vertebrate species. A possible explanation for the origin of Vegf/Vegfr in the animal kingdom and a pathway of Vegf/Vegfr evolution are discussed. Copyright © 2015 Elsevier Ltd. All rights reserved.

  14. Mass closure and source apportionment of PM2.5 by Positive Matrix Factorization analysis in urban Mediterranean environment

    Science.gov (United States)

    Mantas, E.; Remoundaki, E.; Halari, I.; Kassomenos, P.; Theodosi, C.; Hatzikioseyian, A.; Mihalopoulos, N.

    2014-09-01

    A systematic monitoring of PM2.5 was carried out during a period of three years (from February 2010 to April 2013) at an urban site, at the National Technical University of Athens campus. Two types of 24-h PM2.5 samples have been collected: 271 samples on PTFE and 116 samples on quartz filters. Daily PM2.5 concentrations were determined for both types of samples. Total sulfur, crustal origin elements and elements of a major crustal component (Al, Si, Fe, Ca, K, Mg, Ti) trace elements (Zn, Pb, Cu, Ni, P, V, Cr, Mn) and water soluble ions (Cl-, NO3-, SO42-, Na+, K+, NH4+, Ca2+, Mg2+) were determined on the PTFE samples. Organic carbon (OC), elemental carbon (EC) and water soluble ions were determined on the quartz samples. For the mass closure six components were considered: Secondary Inorganic Aerosol (SIA), Organic Matter (OM), Elemental Carbon (EC), Dust, Mineral anthropogenic component (MIN) and Sea Salt (SS). SIA and OM contributed in the mass of PM2.5 almost equally: 30-36% and 30% respectively. EC, SS and MIN accounted for 5, 4 and 3% respectively of the total PM2.5 mass. Dust accounted for about 3-5% in absence of dust transport event and reached a much higher percentage in case of dust transport event. These contributions justify at least 80% of the PM2.5 mass. Source apportionment analysis has been performed by Positive Matrix Factorization. The combination of the PMF results obtained by both data sets lead to the definition of six factors: 1. SO42-, NH4+, OC (industrial/regional sources, secondary aerosol) 2. EC, OC, K and trace metals (traffic and heating by biomass burning, locally emitted aerosol). 3. Ca, EC, OC and trace metals (urban-resuspended road dust reflecting exhaust emissions), 4. Secondary nitrates 5. Na, Cl (marine source) 6. Si, Al, Ti, Ca, Fe (Dust transported from Sahara). These factors reflect not only main sources contributions but also underline the key role of atmospheric dynamics and aerosol ageing processes in this Mediterranean

  15. Matrix Organization and Merit Factor Evaluation as a Method to Address the Challenge of Finding a Polymer Material for Roll Coated Polymer Solar Cells

    DEFF Research Database (Denmark)

    Bundgaard, Eva; Livi, Francesco; Hagemann, Ole

    2015-01-01

    The results presented demonstrate how the screening of 104 light-absorbing low band gap polymers for suitability in roll coated polymer solar cells can be accomplished through rational synthesis according to a matrix where 8 donor and 13 acceptor units are organized in rows and columns. Synthesis...... silver comb back electrode structure. The matrix organization enables fast identification of active layer materials according to a weighted merit factor that includes more than simply the power conversion efficiency and is used as a method to identify the lead candidates. Based on several characteristics...

  16. A matrix of social accounting for Asturias

    Directory of Open Access Journals (Sweden)

    Margarita Argüelles

    2003-01-01

    Full Text Available A Social Accounting Matrix is an integrated system of accounts that presents in a double-entry table all the transactions made in an economy among productive sectors, production factors, institutional sectors and the rest of the world. In comparison with an Input-Output Table, it offers a greater deal of information and shows completely the circular process of income, captivating more precisely the effects of exogenous changes. One of the main profits of a Social Accounting Matrix is to serve as a database for the development and application of a computable general equilibrium model. This is, in fact, the aim pursued with the elaboration of the Social Accounting Matrix for the Asturian economy presented here. This Matrix has been constructed with data from the 1995 Regional Accounts of Asturias, and its structure has been adapted to its future use as a database for a computable general equilibrium model of this regional economy.

  17. Source apportionment of NMVOCs in the Kathmandu Valley during the SusKat-ABC international field campaign using positive matrix factorization

    Directory of Open Access Journals (Sweden)

    C. Sarkar

    2017-07-01

    Full Text Available A positive matrix factorization model (US EPA PMF version 5.0 was applied for the source apportionment of the dataset of 37 non-methane volatile organic compounds (NMVOCs measured from 19 December 2012 to 30 January 2013 during the SusKat-ABC international air pollution measurement campaign using a proton-transfer-reaction time-of-flight mass spectrometer in the Kathmandu Valley. In all, eight source categories were identified with the PMF model using the new constrained model operation mode. Unresolved industrial emissions and traffic source factors were the major contributors to the total measured NMVOC mass loading (17.9 and 16.8 %, respectively followed by mixed industrial emissions (14.0 %, while the remainder of the source was split approximately evenly between residential biofuel use and waste disposal (10.9 %, solvent evaporation (10.8 %, biomass co-fired brick kilns (10.4 %, biogenic emissions (10.0 % and mixed daytime factor (9.2 %. Conditional probability function (CPF analyses were performed to identify the physical locations associated with different sources. Source contributions to individual NMVOCs showed that biomass co-fired brick kilns significantly contribute to the elevated concentrations of several health relevant NMVOCs such as benzene. Despite the highly polluted conditions, biogenic emissions had the largest contribution (24.2 % to the total daytime ozone production potential, even in winter, followed by solvent evaporation (20.2 %, traffic (15.0 % and unresolved industrial emissions (14.3 %. Secondary organic aerosol (SOA production had approximately equal contributions from biomass co-fired brick kilns (28.9 % and traffic (28.2 %. Comparison of PMF results based on the in situ data versus REAS v2.1 and EDGAR v4.2 emission inventories showed that both the inventories underestimate the contribution of traffic and do not take the contribution of brick kilns into account. In addition, the REAS

  18. Comparison of the Economic Factors that Influence Foreign Direct ...

    African Journals Online (AJOL)

    The study determined the compound growth rate of FDI and the factors ... India attracted more FDI than Nigeria due to its large GDP, higher real interest rate and trade openness; it is suggested that a further depreciated currency would ...

  19. Joint Dictionary Learning-Based Non-Negative Matrix Factorization for Voice Conversion to Improve Speech Intelligibility After Oral Surgery.

    Science.gov (United States)

    Fu, Szu-Wei; Li, Pei-Chun; Lai, Ying-Hui; Yang, Cheng-Chien; Hsieh, Li-Chun; Tsao, Yu

    2017-11-01

    Objective: This paper focuses on machine learning based voice conversion (VC) techniques for improving the speech intelligibility of surgical patients who have had parts of their articulators removed. Because of the removal of parts of the articulator, a patient's speech may be distorted and difficult to understand. To overcome this problem, VC methods can be applied to convert the distorted speech such that it is clear and more intelligible. To design an effective VC method, two key points must be considered: 1) the amount of training data may be limited (because speaking for a long time is usually difficult for postoperative patients); 2) rapid conversion is desirable (for better communication). Methods: We propose a novel joint dictionary learning based non-negative matrix factorization (JD-NMF) algorithm. Compared to conventional VC techniques, JD-NMF can perform VC efficiently and effectively with only a small amount of training data. Results: The experimental results demonstrate that the proposed JD-NMF method not only achieves notably higher short-time objective intelligibility (STOI) scores (a standardized objective intelligibility evaluation metric) than those obtained using the original unconverted speech but is also significantly more efficient and effective than a conventional exemplar-based NMF VC method. Conclusion: The proposed JD-NMF method may outperform the state-of-the-art exemplar-based NMF VC method in terms of STOI scores under the desired scenario. Significance: We confirmed the advantages of the proposed joint training criterion for the NMF-based VC. Moreover, we verified that the proposed JD-NMF can effectively improve the speech intelligibility scores of oral surgery patients. Objective: This paper focuses on machine learning based voice conversion (VC) techniques for improving the speech intelligibility of surgical patients who have had parts of their articulators removed. Because of the removal of parts of the articulator, a patient

  20. Epidermal growth factor-containing fibulin-like extracellular matrix protein 1 expression and regulation in uterine leiomyoma.

    Science.gov (United States)

    Marsh, Erica E; Chibber, Shani; Wu, Ju; Siegersma, Kendra; Kim, Julie; Bulun, Serdar

    2016-04-01

    To determine the presence, differential expression, and regulation of epidermal growth factor-containing fibulin-like extracellular matrix protein 1 (EFEMP1) in uterine leiomyomas. Laboratory in vivo and in vitro study with the use of human leiomyoma and myometrial tissue and primary cells. Academic medical center. Leiomyoma and myometrial tissue samples and cultured cells. 5-Aza-2'-deoxycytidine (5-aza-dC) treatment. Fold-change difference between EFEMP1 and fibulin-3 expression in leiomyoma tissue and cells compared with matched myometrial samples, and fold-change difference in EFEMP1 expression with 5-Aza-dC treatment. In vivo, EFEMP1 expression was 3.19-fold higher in myometrial tissue than in leiomyoma tissue. EFEMP1 expression in vitro was 5.03-fold higher in myometrial cells than in leiomyoma cells. Western blot and immunohistochemistry staining of tissue and cells confirmed similar findings in protein expression. Treatment of leiomyoma cells with 5-Aza-dC resulted in increased expression of EFEMP1 in vitro. The EFEMP1 gene and its protein product, fibulin-3, are both significantly down-regulated in leiomyoma compared with myometrium when studied both in vivo and in vitro. The increase in EFEMP1 expression in leiomyoma cells with 5-Aza-dC treatment suggest that differential methylation is responsible, in part, for the differences seen in gene expression. Copyright © 2016 American Society for Reproductive Medicine. Published by Elsevier Inc. All rights reserved.

  1. Application of Positive Matrix Factorization in the Identification of the Sources of PM2.5 in Taipei City

    Directory of Open Access Journals (Sweden)

    Wen-Yuan Ho

    2018-06-01

    Full Text Available Fine particulate matter (PM2.5 has a small particle size, which allows it to directly enter the respiratory mucosa and reach the alveoli and even the blood. Many countries are already aware of the adverse effects of PM2.5, and determination of the sources of PM2.5 is a critical step in reducing its concentration to protect public health. This study monitored PM2.5 in the summer (during the southwest monsoon season of 2017. Three online monitoring systems were used to continuously collect hourly concentrations of key chemical components of PM2.5, including anions, cations, carbon, heavy metals, and precursor gases, for 24 h per day. The sum of the concentrations of each compound obtained from the online monitoring systems is similar to the actual PM2.5 concentration (98.75%. This result suggests that the on-line monitoring system of this study covers relatively complete chemical compounds. Positive matrix factorization (PMF was adopted to explore and examine the proportion of each source that contributed to the total PM2.5 concentration. According to the source contribution analysis, 55% of PM2.5 can be attributed to local pollutant sources, and the remaining 45% can be attributed to pollutants emitted outside Taipei City. During the high-PM2.5-concentration (episode period, the pollutant conversion rates were higher than usual due to the occurrence of vigorous photochemical reactions. Moreover, once pollutants are emitted by external stationary pollutant sources, they move with pollution air masses and undergo photochemical reactions, resulting in increases in the secondary pollutant concentrations of PM2.5. The vertical monitoring data indicate that there is a significant increase in PM2.5 concentration at high altitudes. High-altitude PM2.5 will descend to the ground and thereby affect the ground-level PM2.5 concentration.

  2. Size-resolved source apportionment of ambient particles by positive matrix factorization at Gosan background site in East Asia

    Directory of Open Access Journals (Sweden)

    J. S. Han

    2006-01-01

    Full Text Available Size- and time-resolved aerosol samples were collected using an eight-stage Davis rotating unit for monitoring (DRUM sampler from 29 March to 29 May in 2002 at Gosan, Jeju Island, Korea, which is one of the representative background sites in East Asia. These samples were analyzed using synchrotron X-ray fluorescence for 3-h average concentrations of 19 elements consisting of S, Si, Al, Fe, Ca, Cl, Cu, Zn, Ti, K, Mn, Pb, Ni, V, Se, As, Rb, Cr, Br. The size-resolved data sets were then analyzed using the positive matrix factorization (PMF technique in order to identify possible sources and estimate their contribution to particulate matter mass. PMF analysis uses the uncertainty of the measured data to provide an optimal weighting. Fifteen sources were resolved in eight size ranges (0.07~12 μm and included continental soil, local soil, sea salt, biomass/biofuel burning, coal combustion, oil heating furnace, residual oil fired boiler, municipal incineration, nonferrous metal source, ferrous metal source, gasoline vehicle, diesel vehicle, copper smelter and volcanic emission. PMF analysis of size-resolved source contributions showed that natural sources represented by local soil, sea salt and continental soil contributed about 79% to the predicted primary particulate matter (PM mass in the coarse size range (1.15~12 μm. On the other hand, anthropogenic sources such as coal combustion and biomass/biofuel burning contributed about 60% in the fine size range (0.56~2.5 μm. The diesel vehicle source contributed the most in the ultra-fine size range (0.07~0.56 μm and was responsible for about 52% of the primary PM mass.

  3. Basic fibroblast growth factor binds to subendothelial extracellular matrix and is released by heparitinase and heparin-like molecules

    International Nuclear Information System (INIS)

    Bashkin, P.; Doctrow, S.; Klagsbrun, M.; Svahn, C.M.; Folkman, J.; Vlodavsky, I.

    1989-01-01

    Basic fibroblast growth factor (bFGF) exhibits specific binding to the extracellular matrix (ECM) produced by cultured endothelial cells. Binding was saturable as a function both of time and of concentration of 125 I-bFGF. Scatchard analysis of FGF binding revealed the presence of about 1.5 x 10 12 binding sites/mm 2 ECM with an apparent k D of 610 nM. FGF binds to heparan sulfate (HS) in ECM as evidenced by (i) inhibition of binding in the presence of heparin or HS at 0.1-1 μg/mL, but not by chondroitin sulfate, keratan sulfate, or hyaluronic acid at 10 μg/mL, (ii) lack of binding to ECM pretreated with heparitinase, but not with chondroitinase ABC, and (iii) rapid release of up to 90% of ECM-bound FGF by exposure to heparin, HS, or heparitinase, but not to chondroitin sulfate, keratan sulfate, hyaluronic acid, or chondroitinase ABC. Oligosaccharides derived from depolymerized heparin, and as small as the tetrasaccharide, released the ECM-bound FGF, but there was little or no release of FGF by modified nonanticoagulant heparins such as totally desulfated heparin, N-desulfated heparin, and N-acetylated heparin. FGF released from ECM was biologically active, as indicated by its stimulation of cell proliferation and DNA synthesis in vascular endothelial cells and 3T3 fibroblasts. Similar results were obtained in studies on release of endogenous FGF-like mitogenic activity from Descement's membranes of bovine corneas. It is suggested that ECM storage and release of bFGF provide a novel mechanism for regulation of capillary blood vessel growth. Whereas ECM-bound FGF may be prevented from acting on endothelial cells, its displacement by heparin-like molecules and/or HS-degrading enzymes may elicit a neovascular response

  4. Vascular endothelial growth factor-A, matrix metalloproteinase-1, and macrophage migration inhibition factor changes in the porcine remnant kidney model: Evaluation by MRI

    Science.gov (United States)

    Misra, Sanjay; Misra, Khamal D; Glockner, James F.

    2010-01-01

    Purpose To determine the expression of vascular endothelial growth factor-A (VEGF-A), macrophage migration inhibition factor (MIF), and matrix metalloproteinase-1 (MMP-1) in the porcine remnant kidney model and quantify renal blood flow and volume using phase contrast magnetic resonance imaging with magnetic resonance angiography (PC MRI/MRA). Material and methods In 23 pigs, the left renal artery was completely embolized using polyvinyl acrylide (PVA) particles and the right kidney partially embolized (remnant kidney) while six pigs served as controls. The animals were sacrificed early (day 3, 7, and 14, N=3), day 24 (D24, N=5), day 37 (D37, N=3), day 42 (D42, N=9), and day 84 (D84, N=3). MRI/PC MRA of the kidneys was performed prior to sacrifice. The remnant and control kidneys were harvested for Western blotting of VEGF-A, MMP-1, and MIF. Blood was removed for BUN and creatinine prior to embolization and at time of sacrifice. Results The kidney function after the embolization was characterized by chronic renal insufficiency. The renal artery blood flow, volume, and weight of the remnant kidney increased significantly over time when compared to controls. At early time points, there was increased expression of MIF and MMP-1 followed by an increase in the expression of VEGF-A by day 37 (P<0.05 when compared to control). Masson's trichrome staining of the remnant kidney revealed scarring in the tubulointerstitial space. Conclusions In this model, renal blood flow and volume increase as the remnant kidney hypertrophies and scars. There is increased expression of MIF, VEGF-A, and MMP-1 in the remnant kidney. PMID:20610182

  5. Tribological Properties of AlSi12-Al₂O₃ Interpenetrating Composite Layers in Comparison with Unreinforced Matrix Alloy.

    Science.gov (United States)

    Dolata, Anna Janina

    2017-09-06

    Alumina-Aluminum composites with interpenetrating network structures are a new class of advanced materials with potentially better properties than composites reinforced by particles or fibers. Local casting reinforcement was proposed to take into account problems with the machinability of this type of materials and the shaping of the finished products. The centrifugal infiltration process fabricated composite castings in the form of locally reinforced shafts. The main objective of the research presented in this work was to compare the tribological properties (friction coefficient, wear resistance) of AlSi12/Al₂O₃ interpenetrating composite layers with unreinforced AlSi12 matrix areas. Profilometric tests enabled both quantitative and qualitative analyses of the wear trace that formed on investigated surfaces. It has been shown that interpenetrating composite layers are characterized by lower and more stable coefficients of friction (μ), as well as higher wear resistance than unreinforced matrix areas. At the present stage, the study confirmed that the tribological properties of the composite layers depend on the spatial structure of the ceramic reinforcement, and primarily the volume and size of alumina foam cells.

  6. In vitro comparison of new bisphosphonic acids and zoledronate effects on human gingival fibroblasts viability, inflammation and matrix turnover.

    Science.gov (United States)

    De Colli, Marianna; Tortorella, Paolo; Marconi, Guya Diletta; Agamennone, Mariangela; Campestre, Cristina; Tauro, Marilena; Cataldi, Amelia; Zara, Susi

    2016-11-01

    Bisphosphonates (BPs) are drugs clinically used in resorptive diseases. It was already proved that some clinically relevant BPs can inhibit a class of enzymes called matrix metalloproteinases (MMPs), required during tissue remodelling. Combining the arylsulfonamide function with the bisphosphonic group, several compounds were synthesized to obtain selective inhibitors of MMPs. The aim of the present study was to compare the effect of zoledronic acid (ZA), the most potent bisphosphonate available as therapy, with new sulfonamide containing BPs in an in vitro model of human gingival fibroblasts (HGFs). Western blot was used to measure procollagen I, β1 integrin MMP-8 and MMP-9, phase contrast and MTT for cell viability; L-lactate-dehydrogenase (LDH) measurement was performed for toxicity evaluation and ELISA for prostaglandin E 2 (PGE 2 ) secretion assessment. When compared with ZA, the treatment with the newly synthesized compounds shows increasing viability, procollagen I expression and decreased expression of β1 integrin in HGFs. Higher levels of released LDH, PGE 2 and MMP-9 expression are recorded in ZA-treated HGFs. Increased levels of MMP-8 are recorded in newly synthesized compounds-treated samples. These findings allowed to conclude that new tested BPs did not affect HGFs viability and adhesion, did not induce cellular toxicity, were not responsible for inflammatory event induction and could preserve the physiological matrix turnover. It could be hypothesized that the new molecules were better tolerated by soft tissues, resulting in lesser side effects.

  7. Comparison of colorectal and gastric cancer: Survival and prognostic factors

    International Nuclear Information System (INIS)

    Moghimi-Dehkordi, Bijan; Safaee, Azadeh; Zali, Mohammad R

    2009-01-01

    Gastric and colorectal cancers are the most common gastrointestinal malignancies in Iran. We aim to compare the survival rates and prognostic factors between these two cancers. We studied 1873 patients with either gastric or colorectal cancer who were registered in one referral cancer registry center in Tehran, Iran. All patients were followed from their time of diagnosis until December 2006 (as failure time). Survival curves were calculated according to the Kaplan-Meier Method and compared by the Log-rank test. Multivariate analysis of prognostic factors was carried out using the Cox proportional hazard model. Of 1873 patients, there were 746 with gastric cancer and 1138 with colorectal cancer. According to the Kaplan-Meier method 1, 3, 5, and 7-year survival rates were 71.2, 37.8, 25.3, and 19.5%, respectively, in gastric cancer patients and 91.1, 73.1, 61, and 54.9%, respectively, in patients with colorectal cancer. Also, univariate analysis showed that age at diagnosis, sex, grade of tumor, and distant metastasis were of prognostic significance in both cancers ( P < 0.0001). However, in multivariate analysis, only distant metastasis in colorectal cancer and age at diagnosis, grade of tumor, and distant metastasis in colorectal cancer were identified as independent prognostic factors influencing survival. According to our findings, survival is significantly related to histological differentiation of tumor and distant metastasis in colorectal cancer patients and only to distant metastasis in gastric cancer patients. (author)

  8. Comparisons of treatment means when factors do not interact in two-factorial studies

    KAUST Repository

    Wei, Jiawei; Carroll, Raymond J.; Harden, Kathryn K.; Wu, Guoyao

    2011-01-01

    Scientists in the fields of nutrition and other biological sciences often design factorial studies to test the hypotheses of interest and importance. In the case of two-factorial studies, it is widely recognized that the analysis of factor effects is generally based on treatment means when the interaction of the factors is statistically significant, and involves multiple comparisons of treatment means. However, when the two factors do not interact, a common understanding among biologists is that comparisons among treatment means cannot or should not be made. Here, we bring this misconception into the attention of researchers. Additionally, we indicate what kind of comparisons among the treatment means can be performed when there is a nonsignificant interaction among two factors. Such information should be useful in analyzing the experimental data and drawing meaningful conclusions.

  9. Identification and comparison of structural factors of innovation capability in ESCO with desirable status

    Directory of Open Access Journals (Sweden)

    Fatemeh Jalali

    2014-12-01

    Full Text Available The present study describes the identification and comparison of structural factors of innovation capability in Esfahan Steel Company (ESCO. Innovation is a crucial factor in growth, success, and survival of organizations. Since the innovation for organizations is not possible without the level of innovation capabilities and the need for steel products and imports of goods from developed countries has greatly increased, this study intends to investigate the factors affecting the subject that may be able to increase the production and reduce the need to import it. Evaluation of the innovation capability factors of ESCO compared with its desired status in industry can help companies develop innovative strategies and also achieve organizational goals. Statistical analysis methods and mean comparison test by examining the structure of the innovation capability in the form of a standard questionnaire was employed. The findings suggest that the innovation capability in the existing situation of ESCO in comparison with the desired situation is significantly different.

  10. Comparisons of treatment means when factors do not interact in two-factorial studies

    KAUST Repository

    Wei, Jiawei

    2011-05-06

    Scientists in the fields of nutrition and other biological sciences often design factorial studies to test the hypotheses of interest and importance. In the case of two-factorial studies, it is widely recognized that the analysis of factor effects is generally based on treatment means when the interaction of the factors is statistically significant, and involves multiple comparisons of treatment means. However, when the two factors do not interact, a common understanding among biologists is that comparisons among treatment means cannot or should not be made. Here, we bring this misconception into the attention of researchers. Additionally, we indicate what kind of comparisons among the treatment means can be performed when there is a nonsignificant interaction among two factors. Such information should be useful in analyzing the experimental data and drawing meaningful conclusions.

  11. Triiodothyronine radioimmunoassay. Comparison of the different factors between two technics

    International Nuclear Information System (INIS)

    Gehin-Fouque, F.; Etling, N.; Pradelles, P.; Bornet, H.

    1980-01-01

    Triiodothyronine concentration was determined in human serum and in thyroid extracts by two radioimmunoassay technics. Both antibodies, radioactive T 3 , stable T 3 , protein-binding-hormone inhibitors, methods used to separate the free from the bound fractions were different. Each factor from a method was substituted to the homologue of the other method. The results occasionnally showed a variation of 32% in the first method and 50% in the second one. However the results gave a correct interpretation of the triiodothyronine values measured in human serum and in thyroid extracts [fr

  12. Free-free Gaunt factors: comparison of various models

    International Nuclear Information System (INIS)

    Collins, L.A.; Merts, A.L.

    1986-01-01

    We develop the general theory of free-free absorption processes in terms of basic quantum mechanical principles. We perform calculations of the free-free Gaunt factor for several models of the electron-atom (ion) interaction in a variety of systems including rare gases, alkali, and aluminum. In addition, we investigate plasma-screening effects in such models as the Yukawa potential. Our calculations compare well with those of other authors, and our comparative study of various models allows a more thorough understanding of their range of validity. 38 refs., 2 figs., 14 tabs

  13. Topical photodynamic therapy following excisional wounding of human skin increases production of transforming growth factor-β3 and matrix metalloproteinases 1 and 9, with associated improvement in dermal matrix organization.

    Science.gov (United States)

    Mills, S J; Farrar, M D; Ashcroft, G S; Griffiths, C E M; Hardman, M J; Rhodes, L E

    2014-07-01

    Animal studies report photodynamic therapy (PDT) to improve healing of excisional wounds; the mechanism is uncertain and equivalent human studies are lacking. To explore the impact of methyl aminolaevulinate (MAL)-PDT on clinical and microscopic parameters of human cutaneous excisional wound healing, examining potential modulation through production of transforming growth factor (TGF)-β isoforms. In 27 healthy older men (60-77 years), a 4-mm punch biopsy wound was created in skin of the upper inner arm and treated with MAL-PDT three times over 5 days. An identical control wound to the contralateral arm was untreated and both wounds left to heal by secondary intention. Wounds were re-excised during the inflammatory phase (7 days, n = 10), matrix remodelling (3 weeks, n = 8) and cosmetic outcome/dermal structure (9 months, n = 9). Production of TGF-β1, TGF-β3 and matrix metalloproteinases (MMPs) was assessed by immunohistochemistry alongside microscopic measurement of wound size/area and clinical assessment of wound appearance. MAL-PDT delayed re-epithelialization at 7 days, associated with increased inflammation. However, 3 weeks postwounding, treated wounds were smaller with higher production of MMP-1 (P = 0·01), MMP-9 (P = 0·04) and TGF-β3 (P = 0·03). TGF-β1 was lower than control at 7 days and higher at 3 weeks (both P = 0·03). At 9 months, MAL-PDT-treated wounds showed greater, more ordered deposition of collagen I, collagen III and elastin (all P < 0·05). MAL-PDT increases MMP-1, MMP-9 and TGF-β3 production during matrix remodelling, ultimately producing scars with improved dermal matrix architecture. © 2014 British Association of Dermatologists.

  14. Transforming growth factor-beta stimulates wound healing and modulates extracellular matrix gene expression in pig skin. I. Excisional wound model.

    Science.gov (United States)

    Quaglino, D; Nanney, L B; Kennedy, R; Davidson, J M

    1990-09-01

    The effect of transforming growth factor-beta 1 (TGF-beta 1) on matrix gene expression has been investigated during the process of wound repair, where the formation of new connective tissue represents a critical step in restoring tissue integrity. Split-thickness excisional wounds in the pig were studied by in situ hybridization in order to obtain subjective findings on the activity and location of cells involved in matrix gene expression after the administration of recombinant TGF-beta 1. Data focus on the stimulatory role of this growth factor in granulation tissue formation, on the enhanced mRNA content of collagen types I and III, fibronectin, TGF-beta 1 itself, and on the reduction in stromelysin mRNA, suggesting that increased matrix formation measured after treatment with TGF-beta 1 is due to fibroplasia regulated by the abundance of mRNAs for several different structural, matrix proteins as well as inhibition of proteolytic phenomena elicited by metalloproteinases. These studies reveal elastin mRNA early in the repair process, and elastin mRNA expression is enhanced by administration of TGF-beta 1. Moreover, we show that TGF-beta 1 was auto-stimulating in wounds, accounting, at least in part, for the persistent effects of single doses of this multipotential cytokine.

  15. Platelet-derived growth factor-D modulates extracellular matrix homeostasis and remodeling through TIMP-1 induction and attenuation of MMP-2 and MMP-9 gelatinase activities

    Energy Technology Data Exchange (ETDEWEB)

    Borkham-Kamphorst, Erawan, E-mail: ekamphorst@ukaachen.de; Alexi, Pascal; Tihaa, Lidia; Haas, Ute; Weiskirchen, Ralf, E-mail: rweiskirchen@ukaachen.de

    2015-02-13

    Platelet-derived growth factor-D (PDGF-D) is a more recent recognized growth factor involved in the regulation of several cellular processes, including cell proliferation, transformation, invasion, and angiogenesis by binding to and activating its cognate receptor PDGFR-β. After bile duct ligation or in the carbon tetrachloride-induced hepatic fibrosis model{sub ,} PDGF-D showed upregulation comparable to PDGF-B. Moreover, adenoviral PDGF-D gene transfer induced hepatic stellate cell proliferation and liver fibrosis. We here investigated the molecular mechanism of PDGF-D involvement in liver fibrogenesis. Therefore, the GRX mouse cell line was stimulated with PDGF-D and evaluated for fibrotic markers and PDGF-D signaling pathways in comparison to the other PDGF isoforms. We found that PDGF-D failed to enhance Col I and α-smooth muscle actin (α-SMA) production but has capacity to upregulate expression of the tissue inhibitor of metalloprotease 1 (TIMP-1) resulting in attenuation of MMP-2 and MMP-9 gelatinase activity as indicated by gelatinase zymography. This phenomenon was restored through application of a PDGF-D neutralizing antibody. Unexpectedly, PDGF-D incubation decreased both PDGFR-α and -β in mRNA and protein levels, and PDGF-D phosphorylated typrosines specific for PDGFR-α and -β. We conclude that PDGF-D intensifies fibrogenesis by interfering with the fibrolytic activity of the TIMP-1/MMP system and that PDGF-D signaling is mediated through both PDGF-α and -β receptors. - Highlights: • PDGF-D signals through PDGF receptor type α and β. • PDGF-D modulates extracellular matrix homeostasis and remodeling. • Like PDGF-B, PDGF-D triggers phosphorylation of PLC-γ, Akt/PKB, JNK, ERK1/2, and p38. • PDGF-D induces TIMP-1 expression through ERK and p38 MAPK. • PDGF-D attenuates MMP-2 and MMP-9 gelatinase activities.

  16. Interleukin-1β attenuates myofibroblast formation and extracellular matrix production in dermal and lung fibroblasts exposed to transforming growth factor-β1.

    Directory of Open Access Journals (Sweden)

    Masum M Mia

    Full Text Available One of the most potent pro-fibrotic cytokines is transforming growth factor (TGFβ. TGFβ is involved in the activation of fibroblasts into myofibroblasts, resulting in the hallmark of fibrosis: the pathological accumulation of collagen. Interleukin-1β (IL1β can influence the severity of fibrosis, however much less is known about the direct effects on fibroblasts. Using lung and dermal fibroblasts, we have investigated the effects of IL1β, TGFβ1, and IL1β in combination with TGFβ1 on myofibroblast formation, collagen synthesis and collagen modification (including prolyl hydroxylase, lysyl hydroxylase and lysyl oxidase, and matrix metalloproteinases (MMPs. We found that IL1β alone has no obvious pro-fibrotic effect on fibroblasts. However, IL1β is able to inhibit the TGFβ1-induced myofibroblast formation as well as collagen synthesis. Glioma-associated oncogene homolog 1 (GLI1, the Hedgehog transcription factor that is involved in the transformation of fibroblasts into myofibroblasts is upregulated by TGFβ1. The addition of IL1β reduced the expression of GLI1 and thereby also indirectly inhibits myofibroblast formation. Other potentially anti-fibrotic effects of IL1β that were observed are the increased levels of MMP1, -2, -9 and -14 produced by fibroblasts exposed to TGFβ1/IL1β in comparison with fibroblasts exposed to TGFβ1 alone. In addition, IL1β decreased the TGFβ1-induced upregulation of lysyl oxidase, an enzyme involved in collagen cross-linking. Furthermore, we found that lung and dermal fibroblasts do not always behave identically towards IL1β. Suppression of COL1A1 by IL1β in the presence of TGFβ1 is more pronounced in lung fibroblasts compared to dermal fibroblasts, whereas a higher upregulation of MMP1 is seen in dermal fibroblasts. The role of IL1β in fibrosis should be reconsidered, and the differences in phenotypical properties of fibroblasts derived from different organs should be taken into account in future

  17. Comparison of the iterated equation of motion approach and the density matrix formalism for the quantum Rabi model

    Science.gov (United States)

    Kalthoff, Mona; Keim, Frederik; Krull, Holger; Uhrig, Götz S.

    2017-05-01

    The density matrix formalism and the equation of motion approach are two semi-analytical methods that can be used to compute the non-equilibrium dynamics of correlated systems. While for a bilinear Hamiltonian both formalisms yield the exact result, for any non-bilinear Hamiltonian a truncation is necessary. Due to the fact that the commonly used truncation schemes differ for these two methods, the accuracy of the obtained results depends significantly on the chosen approach. In this paper, both formalisms are applied to the quantum Rabi model. This allows us to compare the approximate results and the exact dynamics of the system and enables us to discuss the accuracy of the approximations as well as the advantages and the disadvantages of both methods. It is shown to which extent the results fulfill physical requirements for the observables and which properties of the methods lead to unphysical results.

  18. Development Status and Performance Comparisons of Environmental Barrier Coating Systems for SiCSiC Ceramic Matrix Composites

    Science.gov (United States)

    Zhu, Dongming; Harder, Bryan

    2016-01-01

    Environmental barrier coatings (EBC) and SiCSiC ceramic matrix composites (CMCs) will play a crucial role in future aircraft turbine engine systems, because of their ability to significantly increase engine operating temperatures, reduce engine weight and cooling requirements. This paper presents current NASA EBC-CMC development emphases including: the coating composition and processing improvements, laser high heat flux-thermal gradient thermo-mechanical fatigue - environmental testing methodology development, and property evaluations for next generation EBC-CMC systems. EBCs processed with various deposition techniques including Plasma Spray, Electron Beam - Physical Vapor Deposition, and Plasma Spray Physical Vapor Deposition (PS-PVD) will be particularly discussed. The testing results and demonstrations of advanced EBCs-CMCs in complex simulated engine thermal gradient cyclic fatigue, oxidizing-steam and CMAS environments will help provide insights into the coating development strategies to meet long-term engine component durability goals.

  19. (60)Co in cast steel matrix: A European interlaboratory comparison for the characterisation of new activity standards for calibration of gamma-ray spectrometers in metallurgy.

    Science.gov (United States)

    Tzika, Faidra; Burda, Oleksiy; Hult, Mikael; Arnold, Dirk; Marroyo, Belén Caro; Dryák, Pavel; Fazio, Aldo; Ferreux, Laurent; García-Toraño, Eduardo; Javornik, Andrej; Klemola, Seppo; Luca, Aurelian; Moser, Hannah; Nečemer, Marijan; Peyrés, Virginia; Reis, Mario; Silva, Lidia; Šolc, Jaroslav; Svec, Anton; Tyminski, Zbigniew; Vodenik, Branko; Wätjen, Uwe

    2016-08-01

    Two series of activity standards of (60)Co in cast steel matrix, developed for the calibration of gamma-ray spectrometry systems in the metallurgical sector, were characterised using a European interlaboratory comparison among twelve National Metrology Institutes and one international organisation. The first standard, consisting of 14 disc shaped samples, was cast from steel contaminated during production ("originally"), and the second, consisting of 15 similar discs, from artificially-contaminated ("spiked") steel. The reference activity concentrations of (60)Co in the cast steel standards were (1.077±0.019) Bqg(-1) on 1 January 2013 12h00 UT and (1.483±0.022) Bqg(-1) on 1 June 2013 12h00 UT, respectively. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

  20. A Comparison on Gas Separation between PES(polyethersulfone)/MMT (Na-montmorillonite) and PES/TiO2 Mixed Matrix Membranes

    Czech Academy of Sciences Publication Activity Database

    Liang, Ch.-Y.; Uchytil, Petr; Petričkovič, Roman; Lai, Y.-Ch.; Friess, K.; Šípek, M.; Reddy, M.M.; Suen, S.-Y.

    2012-01-01

    Roč. 92, MAY 18 (2012), s. 57-63 ISSN 1383-5866 R&D Projects: GA ČR GCP106/10/J038 Grant - others:NSCT(TW) NSC:99-2911-I-005-002; NSCT(TW) NSC:99-2923-E-005-001-MY2 Institutional research plan: CEZ:AV0Z40720504 Keywords : mixed matrix membrane * polyethersulfone membrane * sodium montmorillonite Subject RIV: CB - Analytical Chemistry, Separation Impact factor: 2.894, year: 2012

  1. Role of tissue factor pathway inhibitor-2 in the expressions of matrix metallopro- teinases in keratocytes in vitro

    Directory of Open Access Journals (Sweden)

    Jing Yuan

    2013-04-01

    Full Text Available AIM:To elucidate the relation between tissue factor pathway inhibitor-2(TFPI-2expression and the expression of matrix metalloproteinases(MMPsin keratocytes. METHODS: Primary culture and subculture of rabbit keratocytes were established in vitro. Plasmid vector pBos-Cite-neo/TFPI-2 was transfected into keratocytes with Lipofectamine 2000. After being selected by G418, three groups of cells including TFPI-2 gene transfected cells K-TFPI-2, empty vector transfected cells K-V and non-transfected cells K-P were screened for TFPI-2 mRNA and protein by reverse transcription-polymerase chain reaction and Western blot analysis, respectively. The activity of MMPs in the three groups of cells was detected by substrate zymography and compared by ANOVA. RESULTS: Expression of mRNA and protein of TFPI-2 was more in the cells of K-TFPI-2 than in the other cells of K-P and K-V with a significant difference(mRNA:0.79±0.02 vs 0.51±0.03 and 0.48±0.02, P=0.000 and P=0.000; Protein:24.5±0.8 vs 15.5±0.5 and 14.9±0.9,P=0.000 and P=0.000. Compared with the two groups of K-P and K-V, the cells of K-TFPI-2 had a significant decreased activity of MMP1(12.3±0.7 vs 16.7±1.2 and 15.9±0.7, P=0.001 and P=0.003and MMP2(15.4±1.3 vs 18.2±1.1 and 17.8±1.1, P=0.027 and P=0.046. CONCLUSION: It is suggested that the expression of TFPI-2 may strongly inhibit the activity of MMPs in keratocytes in vitro, which provides an experimental basis for curing CNV with gene therapy.

  2. Transforming growth factor β1, matrix metalloproteinase-2 and its tissue inhibitor in patients with pseudoexfoliation glaucoma/syndrome

    Directory of Open Access Journals (Sweden)

    Đorđević-Jocić Jasmina

    2012-01-01

    Full Text Available Background/Aim. Transforming growth factor-b1 (TGF-b1, oxidative stress and imbalance between matrix metalloproteinases (MMPs and their tissue inhibitors (TIMPs may play an important role in pathogenesis of pseudoexfoliation syndrome/glaucoma (PEX Sy/Gl. The aim of the study was to measure concentrations of TGF- b1, MMP-2, TIMP-2 in the aqueous humor in the examined group, as well as to compare the biochemical findings with the following clinical parameters: degree of chamber angle pigmantation, presence of pseudoexfoliation and the value of intraocular pressure (IOP. Methods. Aqueous samples from 30 patients with cataract, 30 patients with PEX Sy, 36 patients with PEX Gl, and 42 patients with primary open-angle glaucoma (POAG were collected during phacoemulsification cataract surgery. TGF b1, MMP-2, TIMP-2 Fluotokine Multi Analyze Profiling kits and Luminex technology were used to simultaneously measure TGF b1, MMP-2 and TIMP-2. Results. TGF- β1, MMP-2, TIMP-2 were detected in human aqueous from all the groups with the highest level in the group with PEX Gl. Statistically, a significant correlation between the levels of TGF b1, MMP-2, TIMP-2 in the aqueous humor of the patients with PEX Gl and the IOP value was confirmed (p < 0.05. In this group, the positive correlations between the TGF b1 concentration in the aqueous humor and the presence of pseudoexfoliation (p < 0.01, on the one hand, and between the TIMP-2 level and the presence of pseudoexfoliation (p < 0.05, on the other, were reported. A statistically significant positive correlation of TGF-b1 and MMP-2, and the degree of chamber angle pigmentation in the PEX Gl group was confirmed (p < 0.05. In the POAG group, TIMP-2 values were in a negative correlation with the degree of pigmentation (p < 0.05, and the IOP value (p < 0.05. Conclusion. TGF b1 and MMP-2 affect the degree of chamber angle pigmentation and the degree of pseudoexfoliation in patients with pseudoexfoliative glaucoma.

  3. Experimental comparison between total calibration factors and components calibration factors of reference dosemeters used in secondary standard laboratory dosemeters

    International Nuclear Information System (INIS)

    Silva, T.A. da.

    1981-06-01

    A quantitative comparison of component calibration factors with the corresponding overall calibration factor was used to evaluate the adopted component calibration procedure in regard to parasitic elements. Judgement of significance is based upon the experimental uncertainty of a well established procedure for determination of the overall calibration factor. The experimental results obtained for different ionization chambers and different electrometers demonstrate that for one type of electrometer the parasitic elements have no influence on its sensitivity considering the experimental uncertainty of the calibration procedures. In this case the adopted procedure for determination of component calibration factors is considered to be equivalent to the procedure of determination of the overall calibration factor and thus might be used as a strong quality control measure in routine calibration. (Author) [pt

  4. Tumor necrosis factor-α-accelerated degradation of type I collagen in human skin is associated with elevated matrix metalloproteinase (MMP)-1 and MMP-3 ex vivo

    DEFF Research Database (Denmark)

    Ågren, Magnus S; Schnabel, Reinhild; Christensen, Lise H

    2015-01-01

    Tumor necrosis factor (TNF)-α induces matrix metalloproteinases (MMPs) that may disrupt skin integrity. We have investigated the effects and mechanisms of exogenous TNF-α on collagen degradation by incubating human skin explants in defined serum-free media with or without TNF-α (10ng/ml) in the a......Tumor necrosis factor (TNF)-α induces matrix metalloproteinases (MMPs) that may disrupt skin integrity. We have investigated the effects and mechanisms of exogenous TNF-α on collagen degradation by incubating human skin explants in defined serum-free media with or without TNF-α (10ng...... tissue-derived collagenolytic activity with TNF-α exposure was blocked by neutralizing MMP-1 monoclonal antibody and was not due to down-regulation of tissue inhibitor of metalloproteinase-1. TNF-α increased production (pendogenous MMP-1...

  5. A comparison study on detection of key geochemical variables and factors through three different types of factor analysis

    Science.gov (United States)

    Hoseinzade, Zohre; Mokhtari, Ahmad Reza

    2017-10-01

    Large numbers of variables have been measured to explain different phenomena. Factor analysis has widely been used in order to reduce the dimension of datasets. Additionally, the technique has been employed to highlight underlying factors hidden in a complex system. As geochemical studies benefit from multivariate assays, application of this method is widespread in geochemistry. However, the conventional protocols in implementing factor analysis have some drawbacks in spite of their advantages. In the present study, a geochemical dataset including 804 soil samples collected from a mining area in central Iran in order to search for MVT type Pb-Zn deposits was considered to outline geochemical analysis through various fractal methods. Routine factor analysis, sequential factor analysis, and staged factor analysis were applied to the dataset after opening the data with (additive logratio) alr-transformation to extract mineralization factor in the dataset. A comparison between these methods indicated that sequential factor analysis has more clearly revealed MVT paragenesis elements in surface samples with nearly 50% variation in F1. In addition, staged factor analysis has given acceptable results while it is easy to practice. It could detect mineralization related elements while larger factor loadings are given to these elements resulting in better pronunciation of mineralization.

  6. Pipeline for Efficient Mapping of Transcription Factor Binding Sites and Comparison of Their Models

    KAUST Repository

    Ba alawi, Wail

    2011-06-01

    The control of genes in every living organism is based on activities of transcription factor (TF) proteins. These TFs interact with DNA by binding to the TF binding sites (TFBSs) and in that way create conditions for the genes to activate. Of the approximately 1500 TFs in human, TFBSs are experimentally derived only for less than 300 TFs and only in generally limited portions of the genome. To be able to associate TF to genes they control we need to know if TFs will have a potential to interact with the control region of the gene. For this we need to have models of TFBS families. The existing models are not sufficiently accurate or they are too complex for use by ordinary biologists. To remove some of the deficiencies of these models, in this study we developed a pipeline through which we achieved the following: 1. Through a comparison analysis of the performance we identified the best models with optimized thresholds among the four different types of models of TFBS families. 2. Using the best models we mapped TFBSs to the human genome in an efficient way. The study shows that a new scoring function used with TFBS models based on the position weight matrix of dinucleotides with remote dependency results in better accuracy than the other three types of the TFBS models. The speed of mapping has been improved by developing a parallelized code and shows a significant speed up of 4x when going from 1 CPU to 8 CPUs. To verify if the predicted TFBSs are more accurate than what can be expected with the conventional models, we identified the most frequent pairs of TFBSs (for TFs E4F1 and ATF6) that appeared close to each other (within the distance of 200 nucleotides) over the human genome. We show unexpectedly that the genes that are most close to the multiple pairs of E4F1/ATF6 binding sites have a co-expression of over 90%. This indirectly supports our hypothesis that the TFBS models we use are more accurate and also suggests that the E4F1/ATF6 pair is exerting the

  7. Assessment of chronic spontaneous urticaria by serum-induced tumor necrosis factor alpha and matrix metalloproteinase-9 release

    DEFF Research Database (Denmark)

    Falkencrone, Sidsel; Bindslev-Jensen, Carsten; Skov, Per Stahl

    BACKGROUND Previous studies from our group have demonstrated that IgE-mediated basophil activation leads to release of TNFα that in turn can induce matrix metallo-proteinase-9 (MMP-9) release from monocytes. We wished to investigate if serum from chronic spontaneous urticaria-patients with auto-a...

  8. Extracellular matrix protein 1, a direct targeting molecule of parathyroid hormone–related peptide, negatively regulates chondrogenesis and endochondral ossification via associating with progranulin growth factor

    Science.gov (United States)

    Kong, Li; Zhao, Yun-Peng; Tian, Qing-Yun; Feng, Jian-Quan; Kobayashi, Tatsuya; Merregaert, Joseph; Liu, Chuan-Ju

    2016-01-01

    Chondrogenesis and endochondral ossification are precisely controlled by cellular interactions with surrounding matrix proteins and growth factors that mediate cellular signaling pathways. Here, we report that extracellular matrix protein 1 (ECM1) is a previously unrecognized regulator of chondrogenesis. ECM1 is induced in the course of chondrogenesis and its expression in chondrocytes strictly depends on parathyroid hormone–related peptide (PTHrP) signaling pathway. Overexpression of ECM1 suppresses, whereas suppression of ECM1 enhances, chondrocyte differentiation and hypertrophy in vitro and ex vivo. In addition, target transgene of ECM1 in chondrocytes or osteoblasts in mice leads to striking defects in cartilage development and endochondral bone formation. Of importance, ECM1 seems to be critical for PTHrP action in chondrogenesis, as blockage of ECM1 nearly abolishes PTHrP regulation of chondrocyte hypertrophy, and overexpression of ECM1 rescues disorganized growth plates of PTHrP-null mice. Furthermore, ECM1 and progranulin chondrogenic growth factor constitute an interaction network and act in concert in the regulation of chondrogenesis.—Kong, L., Zhao, Y.-P., Tian, Q.-Y., Feng, J.-Q., Kobayashi, T., Merregaert, J., Liu, C.-J. Extracellular matrix protein 1, a direct targeting molecule of parathyroid hormone–related peptide, negatively regulates chondrogenesis and endochondral ossification via associating with progranulin growth factor. PMID:27075243

  9. Biological Assessment of a Calcium Silicate Incorporated Hydroxyapatite-Gelatin Nanocomposite: A Comparison to Decellularized Bone Matrix

    Directory of Open Access Journals (Sweden)

    Dong Joon Lee

    2014-01-01

    Full Text Available Our laboratory utilized biomimicry to develop a synthetic bone scaffold based on hydroxyapatite-gelatin-calcium silicate (HGCS. Here, we evaluated the potential of HGCS scaffold in bone formation in vivo using the rat calvarial critical-sized defect (CSD. Twelve Sprague-Dawley rats were randomized to four groups: control (defect only, decellularized bone matrix (DECBM, and HGCS with and without multipotent adult progenitor cells (MAPCs. DECBM was prepared by removing all the cells using SDS and NH4OH. After 12 weeks, the CSD specimens were harvested to evaluate radiographical, histological, and histomorphometrical outcomes. The in vitro osteogenic effects of the materials were studied by focal adhesion, MTS, and alizarin red. Micro-CT analysis indicated that the DECBM and the HGCS scaffold groups developed greater radiopaque areas than the other groups. Bone regeneration, assessed using histological analysis and fluorochrome labeling, was the highest in the HGCS scaffold seeded with MAPCs. The DECBM group showed limited osteoinductivity, causing a gap between the implant and host tissue. The group grafted with HGCS+MAPCs resulting in twice as much new bone formation seems to indicate a role for effective bone regeneration. In conclusion, the novel HGCS scaffold could improve bone regeneration and is a promising carrier for stem cell-mediated bone regeneration.

  10. Using heavy atom rare gas matrix to control the reactivity of 4-methoxybenzaldehyde: A comparison with benzaldehyde

    Energy Technology Data Exchange (ETDEWEB)

    Kus, Nihal [Department of Chemistry, University of Coimbra, 3004-535 Coimbra (Portugal); Department of Physics, Anadolu University, 26470 Eskisehir (Turkey); Sharma, Archna; Reva, Igor; Fausto, Rui [Department of Chemistry, University of Coimbra, 3004-535 Coimbra (Portugal); Lapinski, Leszek [Institute of Physics, Polish Academy of Sciences, Warsaw (Poland)

    2012-04-14

    Different patterns of photochemical behavior were observed for 4-methoxybenzaldehyde (p-anisaldehyde) isolated in xenon and in argon matrices. Monomers of the compound isolated in solid Xe decarbonylate upon middle ultraviolet irradiation, yielding methoxybenzene (anisole), and CO. On the other hand, p-anisaldehyde isolated in an Ar matrix and subjected to identical irradiation, predominantly isomerizes to the closed-ring isomeric ketene (4-methoxycyclohexa-2,4-dien-1-ylidene) methanone. Experimental detection of a closed-ring ketene photoproduct, generated from an aromatic aldehyde, constitutes a rare observation. The difference between the patterns of photochemical transformations of p-anisaldehyde isolated in argon and xenon environments can be attributed to the external heavy-atom effect, where xenon enhances the rate of intersystem crossing from the singlet to the triplet manifold in which decarbonylation (via p-methoxybenzoyl radical) takes place. The parent compound, benzaldehyde, decarbonylates (to benzene + CO) when subjected to middle ultraviolet irradiation in both argon and xenon matrices. This demonstrates the role of the methoxy p-anisaldehyde substituent in activation of the reaction channel leading to the formation of the ketene photoproduct.

  11. Assessment and Comparison of Vitreous Humor as an Alternative Matrix for Forensic Toxicology Screening by GC-MS.

    Science.gov (United States)

    Metushi, Imir G; Fitzgerald, Robert L; McIntyre, Iain M

    2016-05-01

    Alternative specimens have been occasionally considered as substitutes for whole blood for postmortem toxicology testing. We studied the applicability of vitreous humor, and evaluated whether it would be suitable to replace (or augment) whole blood for routine drug screening. Results showed that from 51 autopsy cases, we were able to identify an aggregate of 209 findings in whole blood compared with 169 in vitreous. The total number of compounds identified was 71 for whole blood and 60 for vitreous humor. Quantitative analysis showed that whole-blood concentrations of trazodone were several fold higher than vitreous humor concentrations (1.42 ± 0.57 vs. 0.15 ± 0.05 mg/L, respectively) and similar results were also obtained for diazepam (0.37 ± 0.06 vs. 0.13 ± 0.01, respectively). For other drugs such as oxycodone, hydrocodone and doxylamine, a trend suggesting higher concentrations in vitreous humor vs. whole blood was observed; however, this was not significant. Our results are consistent with the limited work of other investigators, and suggest that vitreous humor could be an appropriate matrix for drug screening in postmortem toxicology. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  12. Formulation of bi-layer matrix tablets of tramadol hydrochloride: Comparison of rate retarding ability of the incorporated hydrophilic polymers.

    Science.gov (United States)

    Arif, Hasanul; Al-Masum, Abdullah; Sharmin, Florida; Reza, Selim; Sm Islam, Sm Ashraful

    2015-05-01

    Bi-layer tablets of tramadol hydrochloride were prepared by direct compression technique. Each tablet contains an instant release layer with a sustained release layer. The instant release layer was found to release the initial dose immediately within minutes. The instant release layer was combined with sustained release matrix made of varying quantity of Methocel K4M, Methocel K15MCR and Carbomer 974P. Bi-layer tablets were evaluated for various physical tests including weight variation, thickness and diameter, hardness and percent friability. Drug release from bi-layer tablet was studied in acidic medium and buffer medium for two and six hours respectively. Sustained release of tramadol hydrochloride was observed with a controlled fashion that was characteristic to the type and extent of polymer used. % Drug release from eight-hour dissolution study was fitted with several kinetic models. Mean dissolution time (MDT) and fractional dissolution values (T25%, T50% and T80%) were also calculated as well, to compare the retarding ability of the polymers. Methocel K15MCR was found to be the most effective in rate retardation of freely water-soluble tramadol hydrochloride compared to Methocel K4M and Capbomer 974P, when incorporated at equal ratio in the formulation.

  13. Performance Comparison of a Matrix Solver on a Heterogeneous Network Using Two Implementations of MPI: MPICH and LAM

    Science.gov (United States)

    Phillips, Jennifer K.

    1995-01-01

    Two of the current and most popular implementations of the Message-Passing Standard, Message Passing Interface (MPI), were contrasted: MPICH by Argonne National Laboratory, and LAM by the Ohio Supercomputer Center at Ohio State University. A parallel skyline matrix solver was adapted to be run in a heterogeneous environment using MPI. The Message-Passing Interface Forum was held in May 1994 which lead to a specification of library functions that implement the message-passing model of parallel communication. LAM, which creates it's own environment, is more robust in a highly heterogeneous network. MPICH uses the environment native to the machine architecture. While neither of these free-ware implementations provides the performance of native message-passing or vendor's implementations, MPICH begins to approach that performance on the SP-2. The machines used in this study were: IBM RS6000, 3 Sun4, SGI, and the IBM SP-2. Each machine is unique and a few machines required specific modifications during the installation. When installed correctly, both implementations worked well with only minor problems.

  14. Matrix theory

    CERN Document Server

    Franklin, Joel N

    2003-01-01

    Mathematically rigorous introduction covers vector and matrix norms, the condition-number of a matrix, positive and irreducible matrices, much more. Only elementary algebra and calculus required. Includes problem-solving exercises. 1968 edition.

  15. Standard Errors for Matrix Correlations.

    Science.gov (United States)

    Ogasawara, Haruhiko

    1999-01-01

    Derives the asymptotic standard errors and intercorrelations for several matrix correlations assuming multivariate normality for manifest variables and derives the asymptotic standard errors of the matrix correlations for two factor-loading matrices. (SLD)

  16. Final report on CCQM-K79: Comparison of value-assigned CRMs and PT materials: Ethanol in aqueous matrix

    Science.gov (United States)

    Hein, Sebastian; Philipp, Rosemarie; Duewer, David L.; Gasca Aragon, Hugo; Lippa, Katrice A.; Toman, Blaza

    2013-01-01

    The 2010 CCQM-K79 'Comparison of value-assigned CRMs and PT materials: Ethanol in aqueous media' is the second key comparison directly testing the chemical measurement services provided to customers by National Metrology Institutes (NMIs) and Designated Institutes (DIs). CCQM-K79 compared the assigned ethanol values of proficiency test (PT) and certified reference materials (CRMs) using measurements made on these materials under repeatability conditions. Nine NMIs submitted 27 CRM or value-assigned PT materials for evaluation. These materials represent many of the higher-order reference materials then available for this commercially and forensically important measurand. The assigned ethanol mass fraction in the materials ranged from 0.1 mg/kg to 334 mg/kg. All materials were stored and prepared according the specifications provided by each NMI. Samples were processed and analyzed under repeatability conditions by one analytical team using a gas chromatography with flame ionization detection (GC-FID) method of demonstrated trueness and precision. Given the number of materials and the time required for each analysis, the majority of the measurements were made in two measurement campaigns ('runs'). Due to a shipping delay from one NMI, an unanticipated third campaign was required. In all three campaigns, replicate analyses (three injections of one preparation separated in time) were made for one randomly selected unit of each of the 27 materials. Nine of the 27 materials were gravimetrically diluted before measurement to provide solutions with ethanol mass fraction in the established linear range of the GC-FID method. The repeatability measurement value for each analyzed solution was estimated as the mean of all replicate values. The within- and between-campaign variance components were estimated using one-way ANOVA. Markov Chain Monte Carlo Bayesian analysis was used to estimate 95% level-of-confidence coverage intervals for the mean values. Uncertainty

  17. Comparison of the effects of semicarbazide and β-aminopropionitrile on the arterial extracellular matrix in the Brown Norway rat

    International Nuclear Information System (INIS)

    Mercier, Nathalie; Kakou, Augustine; Challande, Pascal; Lacolley, Patrick; Osborne-Pellegrin, Mary

    2009-01-01

    To investigate a putative role for semicarbazide-sensitive amine oxidase (SSAO) in arterial extracellular matrix (ECM) organization, we compared arteries of growing Brown Norway (BN) rats after chronic administration of semicarbazide (SCZ) and β-aminopropionitrile (BAPN), two inhibitors with different properties and relative specificities for SSAO and lysyl oxidase (LOX). The BN model is particularly well adapted to evaluating effects of toxic compounds on the arterial elastic network. We measured aortic LOX and SSAO activities and quantified several ECM parameters. After a pilot study comparing doses previously studied and testing for additivity, we studied low and high equimolar doses of SCZ and BAPN. Both compounds similarly inhibited LOX, whereas SCZ inhibited SSAO far more effectively than BAPN. Both decreased carotid wall rupture pressure, increased tail tendon collagen solubility, decreased aortic insoluble elastin (% dry weight) and dose-dependently increased defects in the internal elastic lamina of abdominal aorta, iliac and renal arteries. Our results suggest that either these effects are mediated by LOX inhibition, SCZ being slightly more effective than BAPN in our conditions, or SSAO acts similarly to and in synergy with LOX on ECM, the greater SCZ effect reflecting the simultaneous inhibition of both enzymes. However, the high SCZ dose increased aortic collagen and ECM proteins other than insoluble elastin markedly more than did equimolar BAPN, possibly revealing a specific effect of SSAO inhibition. To discriminate between the two above possibilities, and to demonstrate unequivocally a specific effect of SSAO inhibition on ECM formation or organization, we must await availability of more specific inhibitors.

  18. Source identification of water-soluble organic aerosols at a roadway site using a positive matrix factorization analysis.

    Science.gov (United States)

    Park, Seungshik; Cho, Sung Yong; Bae, Min-Suk

    2015-11-15

    Daily PM2.5 measurements were carried out at a local roadway every sixth day from May 2011 to August 2013 to obtain seasonal quantitative information on the primary and secondary sources of two water-soluble organic carbon (WSOC) fractions. Filter samples were analyzed for OC, elemental carbon (EC), WSOC, hydrophilic and hydrophobic WSOC fractions (WSOC(HPI) and WSOC(HPO)), and ionic species. An XAD solid phase extraction method and a total organic carbon analyzer were used to isolate the two WSOC fractions and determine their amounts, respectively. The WSOC/OC and WSOC(HPI)/WSOC ratios were 0.62±0.13 and 0.47±0.14, respectively. Similar seasonal profiles in EC, OC, and WSOC concentrations were observed, with higher concentrations occurring in the cold season and lower concentrations in the warm season. However, opposite results were obtained in WSOC/OC and WSOC(HPI)/WSOC ratios, with the higher in the warm season and the lower in the cold season. Correlation analyses indicated that two WSOC fractions in winter were likely attributed to secondary formation processes, biomass burning (BB), and traffic emissions, while WSOC(HPI) observed in other seasons were associated with secondary formation processes similar to those of oxalate and secondary inorganic species. A positive matrix factorization (PMF) model was employed to investigate the sources of two WSOC fractions. PMF indicated that concentrations of WSOC fractions were affected by five sources: secondary NO3(-) related, secondary SO4(2-) and oxalate related, traffic emissions, BB emissions, and sea-salt. Throughout the study period, secondary organic aerosols were estimated to be the most dominant contributor of WSOC fractions, with higher contributions occurring in the warm seasons. The contribution of secondary aerosol formation processes (NO3(-) related+SO4(2-) and oxalate related) to WSOC(HPI) and WSOC(HPO) was on an average 56.2% (45.0-73.8%) and 47.7% (39.6-52.1%), respectively. The seasonal average

  19. Knockdown of asporin affects transforming growth factor-β1-induced matrix synthesis in human intervertebral annulus cells

    Directory of Open Access Journals (Sweden)

    Xu Jiang

    2016-10-01

    Conclusion: Our results have verified a functional feedback loop between TGF-β1 and asporin in human intervertebral annulus cells indicating that TGF-β1-induced annulus matrix biosynthesis can be significantly upregulated by knockdown of asporin. Therefore, asporin could be a potential new therapeutic target and inhibition of asporin could be adopted to enhance the anabolic effect of TGF-β1 in human intervertebral annulus cells in degenerative IVD diseases.

  20. Student and School Factors Affecting Mathematics Achievement: International Comparisons between Korea, Japan and the USA

    Science.gov (United States)

    Shin, Jongho; Lee, Hyunjoo; Kim, Yongnam

    2009-01-01

    The purpose of the study was to comparatively investigate student- and school-level factors affecting mathematics achievement of Korean, Japanese and American students. For international comparisons, the PISA 2003 data were analysed by using the Hierarchical Linear Modeling method. The variables of competitive-learning preference, instrumental…

  1. Growth Factors and Breast Tumors, Comparison of Selected Growth Factors with Traditional Tumor Markers

    Czech Academy of Sciences Publication Activity Database

    Kučera, R.; Černá, M.; Ňaršanská, A.; Svobodová, Š.; Straková, M.; Vrzalová, J.; Fuchsová, R.; Třešková, I.; Kydlíček, T.; Třeška, V.; Pecen, Ladislav; Topolčan, O.; Padziora, P.

    2011-01-01

    Roč. 31, č. 12 (2011), s. 4653-4656 ISSN 0250-7005 Grant - others:GA MZd(CZ) NS9727; GA MZd(CZ) NS10238; GA MZd(CZ) NS10253 Institutional research plan: CEZ:AV0Z10300504 Keywords : growth factor * breast cancer * tumor markers * CA 15-3 * CEA * IGF1 * EGF * HGF Subject RIV: FD - Oncology ; Hematology Impact factor: 1.725, year: 2011

  2. Investigation of plasma-related matrix effects in inductively coupled plasma-atomic emission spectrometry caused by matrices with low second ionization potentials-identification of the secondary factor

    International Nuclear Information System (INIS)

    Chan, George C.-Y.; Hieftje, Gary M.

    2006-01-01

    Plasma-related matrix effects induced by a comprehensive list of matrix elements (a total of fifty-one matrices) in inductively coupled plasma-atomic emission spectrometry were investigated and used to confirm that matrix effects caused by elements with a low second ionization potential are more severe than those from matrix elements having a low first ionization potential. Although the matrix effect is correlated unambiguously with the second ionization potential of a matrix, the correlation is not monotonic, which suggests that at least one other factor is operative. Through study of a large pool of matrix elements, it becomes possible to identify another critical parameter that defines the magnitude of the matrix effect; namely the presence of low-lying energy levels in the doubly charged matrix ion. Penning ionization by Ar excited states is proposed as the dominant mechanism for both analyte ionization/excitation and matrix effects; matrices with a low second ionization potential can effectively quench the population of Ar excited states through successive Penning ionization followed by ion-electron recombination and lead to more severe matrix effects

  3. Parallel O(log n) algorithms for open- and closed-chain rigid multibody systems based on a new mass matrix factorization technique

    Science.gov (United States)

    Fijany, Amir

    1993-01-01

    In this paper, parallel O(log n) algorithms for computation of rigid multibody dynamics are developed. These parallel algorithms are derived by parallelization of new O(n) algorithms for the problem. The underlying feature of these O(n) algorithms is a drastically different strategy for decomposition of interbody force which leads to a new factorization of the mass matrix (M). Specifically, it is shown that a factorization of the inverse of the mass matrix in the form of the Schur Complement is derived as M(exp -1) = C - B(exp *)A(exp -1)B, wherein matrices C, A, and B are block tridiagonal matrices. The new O(n) algorithm is then derived as a recursive implementation of this factorization of M(exp -1). For the closed-chain systems, similar factorizations and O(n) algorithms for computation of Operational Space Mass Matrix lambda and its inverse lambda(exp -1) are also derived. It is shown that these O(n) algorithms are strictly parallel, that is, they are less efficient than other algorithms for serial computation of the problem. But, to our knowledge, they are the only known algorithms that can be parallelized and that lead to both time- and processor-optimal parallel algorithms for the problem, i.e., parallel O(log n) algorithms with O(n) processors. The developed parallel algorithms, in addition to their theoretical significance, are also practical from an implementation point of view due to their simple architectural requirements.

  4. Comparison of Efficacy of Endogenous and Exogenous IGF-I in Stimulating Matrix Production in Neonatal and Mature Chondrocytes.

    Science.gov (United States)

    Aguilar, Izath N; Trippel, Stephen B; Shi, Shuiliang; Bonassar, Lawrence J

    2015-10-01

    The goal of this study was to compare the efficacy of endogenous upregulation of IGF-I by gene therapy and exogenous addition of insulin-like growth factor I (IGF-I) in enhancing proteoglycan synthesis by skeletally mature and neonatal chondrocytes. Chondrocyte transplantation therapy is a common treatment for focal cartilage lesions, with both mature and neonatal chondrocytes used as a cell source. Additionally, gene therapy strategies to upregulate growth factors such as IGF-I have been proposed to augment chondrocyte transplantation therapies. Both skeletally mature and neonatal chondrocytes were exposed to either an adeno-associated virus-based plasmid containing the IGF-I gene or exogenous IGF-I. Analysis of IGF-I and glycosaminoglycan production using a 4-parameter dose-response model established a clear connection between the amount of IGF-I produced by cells and their biosynthetic response. Both neonatal and mature chondrocytes showed this relationship, but the sensitivities were quite different, with EC50 of 0.57 ng/mL for neonatal chondrocytes and EC50 of 8.70 ng/mL IGF-I for skeletally mature chondrocytes. These data suggest that IGF-I gene therapy may be more effective with younger cell sources. Both cell types were less sensitive to exogenous IGF-I than endogenous IGF-I.

  5. A comparison of confirmatory factor analysis methods : Oblique multiple group method versus confirmatory common factor method

    NARCIS (Netherlands)

    Stuive, Ilse

    2007-01-01

    Confirmatieve Factor Analyse (CFA) is een vaak gebruikte methode wanneer onderzoekers een bepaalde veronderstelling hebben over de indeling van items in één of meerdere subtests en willen onderzoeken of deze indeling ook wordt ondersteund door verzamelde onderzoeksgegevens. De meest gebruikte

  6. Effects of transforming growth factor-beta1 on cell motility, collagen gel contraction, myofibroblastic differentiation, and extracellular matrix expression of human adipose-derived stem cell.

    Science.gov (United States)

    Kakudo, Natsuko; Kushida, Satoshi; Suzuki, Kenji; Ogura, Tsunetaka; Notodihardjo, Priscilla Valentin; Hara, Tomoya; Kusumoto, Kenji

    2012-12-01

    Human adipose-derived stem cells (ASCs) are adult pluripotent stem cells, and their usefulness in plastic surgery has garnered attention in recent years. Although, there have been expectations that ASCs might function in wound repair and regeneration, no studies to date have examined the role of ASCs in the mechanism that promotes wound-healing. Transforming growth factor-beta1 (TGF-β1) is a strong candidate cytokine for the triggering of mesenchymal stem cell migration, construction of extracellular matrices, and differentiation of ASCs into myofibroblasts. Cell proliferation, motility, and differentiation, as well as extracellular matrix production, play an important role in wound-healing. We have evaluated the capacity of ASCs to proliferate and their potential to differentiate into phenotypic myofibroblasts, as well as their cell motility and collagen gel contraction ability, when cultured with TGF-β1. Cell motility was analyzed using a wound-healing assay. ASCs that differentiated into myofibroblasts expressed the gene for alpha-smooth muscle actin, and its protein expression was detected immunohistochemically. The extracellular matrix expression in ASCs was evaluated using real-time RT-PCR. Based on the results, we conclude that human ASCs have the potential for cell motility, extracellular matrix gene expression, gel contraction, and differentiation into myofibroblasts and, therefore, may play an important role in the wound-healing process.

  7. Significance of soluble growth factors in the chondrogenic response of human umbilical cord matrix stem cells in a porous three dimensional scaffold

    Directory of Open Access Journals (Sweden)

    RS Nirmal

    2013-11-01

    Full Text Available Stem cell based tissue engineering has emerged as a promising strategy for articular cartilage regeneration. Foetal derived mesenchymal stem cells (MSCs with their ease of availability, pluripotency and high expansion potential have been demonstrated to be an attractive cell source over adult MSCs. However, there is a need for optimisation of chondrogenic signals to direct the differentiation of these multipotent MSCs to chondrogenic lineage. In this study we have demonstrated the in vitro chondrogenesis of human umbilical cord matrix MSCs in three dimensional PVA-PCL (polyvinyl alcohol-polycaprolactone scaffolds in the presence of the individual growth factors TGFβ1, TGFβ3, IGF, BMP2 and their combination with BMP2. Gene expression, histology and immunohistology were evaluated after 28 d culture. The induced cells showed the feature of chondrocytes in their morphology and expression of typical chondrogenic extracellular matrix molecules. Moreover, the real-time PCR assay has shown the expression of gene markers of chondrogenesis, SOX9, collagen type II and aggrecan. The expression of collagen type I and collagen type X was also evaluated. This study has demonstrated the successful chondrogenic induction of human umbilical cord MSCs in 3D scaffolds. Interestingly, the growth factor combination of TGF-β3 and BMP-2 was found to be more effective for chondrogenesis as shown by the real-time PCR studies. The findings of this study suggest the importance of using growth factor combinations for successful chondrogenic differentiation of umbilical cord MSCs.

  8. GGA+U study of uranium mononitride: A comparison of the U-ramping and occupation matrix schemes and incorporation energies of fission products

    Energy Technology Data Exchange (ETDEWEB)

    Claisse, Antoine, E-mail: claisse@kth.se [KTH Royal Institute of Technology, Reactor Physics, AlbaNova University Centre, 106 91 Stockholm (Sweden); Klipfel, Marco [European Commission, Joint Research Centre, Institute for Transuranium Elements, P.O. Box 2340, D-76125 Karlsruhe (Germany); Lindbom, Niclas [KTH Royal Institute of Technology, Reactor Physics, AlbaNova University Centre, 106 91 Stockholm (Sweden); Freyss, Michel [CEA, DEN, DEC, Centre de Cadarache, 13108 Saint-Paul-lez-Durance (France); Olsson, Pär [KTH Royal Institute of Technology, Reactor Physics, AlbaNova University Centre, 106 91 Stockholm (Sweden)

    2016-09-15

    Uranium mononitride is studied in the DFT + U framework. Its ground state is investigated and a study of the incorporation of diverse fission products in the crystal is conducted. The U-ramping and occupation matrix control (OMC) schemes are used to eliminate metastable states. Beyond a certain amount of introduced correlation, the OMC scheme starts to find a lower total energy. The OMC scheme is chosen for the second part of this study. Furthermore, the influence of the magnetic ordering is studied using the U-ramping method, showing that antiferromagnetic order is the most stable one when the U parameter is larger than 1.75 eV. The effect on the density of states is investigated and elastic constants are provided for comparison with other methods and experiments. The incorporation energies of fission products in different defect configurations are calculated and these energies are corrected to take into account the limited size of the supercell. - Highlights: • We studied bulk uranium nitride with means of DFT+U with the U-ramping scheme and the OMC scheme. • We produces a density of states plot and calculated the elastic constants of UN. • We calculated the incorporation energy of many fission products in UN, and corrected them to take into account the elastic interactions. • The OMC scheme should be used over the U-ramping scheme. • Fission products go to larger crystal sites.

  9. Cell wall matrix polysaccharide distribution and cortical microtubule organization: two factors controlling mesophyll cell morphogenesis in land plants.

    Science.gov (United States)

    Sotiriou, P; Giannoutsou, E; Panteris, E; Apostolakos, P; Galatis, B

    2016-03-01

    This work investigates the involvement of local differentiation of cell wall matrix polysaccharides and the role of microtubules in the morphogenesis of mesophyll cells (MCs) of three types (lobed, branched and palisade) in the dicotyledon Vigna sinensis and the fern Asplenium nidus. Homogalacturonan (HGA) epitopes recognized by the 2F4, JIM5 and JIM7 antibodies and callose were immunolocalized in hand-made leaf sections. Callose was also stained with aniline blue. We studied microtubule organization by tubulin immunofluorescence and transmission electron microscopy. In both plants, the matrix cell wall polysaccharide distribution underwent definite changes during MC differentiation. Callose constantly defined the sites of MC contacts. The 2F4 HGA epitope in V. sinensis first appeared in MC contacts but gradually moved towards the cell wall regions facing the intercellular spaces, while in A. nidus it was initially localized at the cell walls delimiting the intercellular spaces, but finally shifted to MC contacts. In V. sinensis, the JIM5 and JIM7 HGA epitopes initially marked the cell walls delimiting the intercellular spaces and gradually shifted in MC contacts, while in A. nidus they constantly enriched MC contacts. In all MC types examined, the cortical microtubules played a crucial role in their morphogenesis. In particular, in palisade MCs, cortical microtubule helices, by controlling cellulose microfibril orientation, forced these MCs to acquire a truncated cone-like shape. Unexpectedly in V. sinensis, the differentiation of colchicine-affected MCs deviated completely, since they developed a cell wall ingrowth labyrinth, becoming transfer-like cells. The results of this work and previous studies on Zea mays (Giannoutsou et al., Annals of Botany 2013; 112: : 1067-1081) revealed highly controlled local cell wall matrix differentiation in MCs of species belonging to different plant groups. This, in coordination with microtubule-dependent cellulose microfibril

  10. Low-rank matrix approximation with manifold regularization.

    Science.gov (United States)

    Zhang, Zhenyue; Zhao, Keke

    2013-07-01

    This paper proposes a new model of low-rank matrix factorization that incorporates manifold regularization to the matrix factorization. Superior to the graph-regularized nonnegative matrix factorization, this new regularization model has globally optimal and closed-form solutions. A direct algorithm (for data with small number of points) and an alternate iterative algorithm with inexact inner iteration (for large scale data) are proposed to solve the new model. A convergence analysis establishes the global convergence of the iterative algorithm. The efficiency and precision of the algorithm are demonstrated numerically through applications to six real-world datasets on clustering and classification. Performance comparison with existing algorithms shows the effectiveness of the proposed method for low-rank factorization in general.

  11. The Relationship between Self-Leadership and Personality: A Comparison of Hierarchical Factor Structures

    OpenAIRE

    Houghton, Jeffery D.

    2000-01-01

    This study examined the relationship between self-leadership and personality through an analysis and comparison of hierarchical factor structures. More specifically, this study examined the relationships between the self-leadership dimensions of behavior-focused strategies, natural reward strategies, and constructive thought strategies, and the personality dimensions of extraversion, emotional stability, and conscientiousness. The results of the study provide evidence that the self-leadershi...

  12. A Study on Influencing Factors of Knowledge Management Systems Adoption: Models Comparison Approach

    OpenAIRE

    Mei-Chun Yeh; Ming-Shu Yuan

    2007-01-01

    Using Linear Structural Relation model (LISREL model) as analysis method and technology acceptance model and decomposed theory of planned behavior as research foundation, this study approachesmainly from the angle of behavioral intention to examine the influential factors of 421 employees adopting knowledge management systems and in the meantime to compare the two method models mentioned on the top. According to the research, there is no, in comparison with technology acceptance model anddeco...

  13. Comparison of different boost transformations for the calculation of form factors in relativistic quantum mechanics

    International Nuclear Information System (INIS)

    Theussl, L.; Noguera, S.; Amghar, A.; Desplanques, B.

    2003-01-01

    The effect of different boost expressions, pertinent to the instant, front and point forms of relativistic quantum mechanics, is considered for the calculation of the ground-state form factor of a two-body system in simple scalar models. Results with a Galilean boost as well as an explicitly covariant calculation based on the Bethe-Salpeter approach are given for comparison. It is found that the present so-called point-form calculations of form factors strongly deviate from all the other ones. This suggests that the formalism which underlies them requires further elaboration. A proposition in this sense is made. (author)

  14. Comparison of cardiovascular risk factors in maintenance hemodialysis patients based on phase angle of bioimpedance analysis

    Science.gov (United States)

    Muzasti, R. A.; Lubis, H. R.

    2018-03-01

    Mortality and morbidity rate, especially from cardiovascular disease in hemodialysis patients in Indonesia is still quite high. One of indicator to assess the predictive value of mortality is the phase angle (PhA) of bioimpedance analysis (BIA) scan examination. Determining the comparison of BMI and laboratory data as cardiovascular risk factors in hemodialysis patients based on PhA.A cross-sectional analytical study was done on 155 outpatientsin RasyidaRenal Hospital, Medan in 2016. Patients were two groups, namely PhAcardiovascular risk factors of hemodialysis patients were determined by age, BMI, and hemoglobin.

  15. Source apportionment of PAH in Hamilton Harbour suspended sediments: comparison of two factor analysis methods.

    Science.gov (United States)

    Sofowote, Uwayemi M; McCarry, Brian E; Marvin, Christopher H

    2008-08-15

    A total of 26 suspended sediment samples collected over a 5-year period in Hamilton Harbour, Ontario, Canada and surrounding creeks were analyzed for a suite of polycyclic aromatic hydrocarbons and sulfur heterocycles. Hamilton Harbour sediments contain relatively high levels of polycyclic aromatic compounds and heavy metals due to emissions from industrial and mobile sources. Two receptor modeling methods using factor analyses were compared to determine the profiles and relative contributions of pollution sources to the harbor; these methods are principal component analyses (PCA) with multiple linear regression analysis (MLR) and positive matrix factorization (PMF). Both methods identified four factors and gave excellent correlation coefficients between predicted and measured levels of 25 aromatic compounds; both methods predicted similar contributions from coal tar/coal combustion sources to the harbor (19 and 26%, respectively). One PCA factor was identified as contributions from vehicular emissions (61%); PMF was able to differentiate vehicular emissions into two factors, one attributed to gasoline emissions sources (28%) and the other to diesel emissions sources (24%). Overall, PMF afforded better source identification than PCA with MLR. This work constitutes one of the few examples of the application of PMF to the source apportionment of sediments; the addition of sulfur heterocycles to the analyte list greatly aided in the source identification process.

  16. Amino acids supply in culture media is not a limiting factor in the matrix synthesis of engineered cartilage tissue

    Science.gov (United States)

    Ng, K. W.; DeFrancis, J. G.; Kugler, L. E.; Kelly, T.-A. N.; Ho, M. M.; O’Conor, C. J.; Ateshian, G. A.; Hung, C. T.

    2013-01-01

    Summary Increased amino acid supplementation (0.5×, 1.0×, and 5.0× recommended concentrations or additional proline) was hypothesized to increase the collagen content in engineered cartilage. No significant differences were found between groups in matrix content or dynamic modulus. Control constructs possessed the highest compressive Young’s modulus on day 42. On day 42, compared to controls, decreased type II collagen was found with 0.5×, 1.0×, and 5.0× supplementation and significantly increased DNA content found in 1.0× and 5.0×. No effects were observed on these measures with added proline. These results lead us to reject our hypothesis and indicate that the low collagen synthesis in engineered cartilage is not due to a limited supply of amino acids in media but may require a further stimulatory signal. The results of this study also highlight the impact that culture environment can play on the development of engineered cartilage. PMID:17713744

  17. Matrix calculus

    CERN Document Server

    Bodewig, E

    1959-01-01

    Matrix Calculus, Second Revised and Enlarged Edition focuses on systematic calculation with the building blocks of a matrix and rows and columns, shunning the use of individual elements. The publication first offers information on vectors, matrices, further applications, measures of the magnitude of a matrix, and forms. The text then examines eigenvalues and exact solutions, including the characteristic equation, eigenrows, extremum properties of the eigenvalues, bounds for the eigenvalues, elementary divisors, and bounds for the determinant. The text ponders on approximate solutions, as well

  18. Intercultural comparison of patient satisfaction with physiotherapy care in Australia and Korea: an exploratory factor analysis.

    Science.gov (United States)

    Hush, Julia M; Lee, Haejung; Yung, Vivian; Adams, Roger; Mackey, Martin; Wand, Benedict M; Nelson, Roger; Beattie, Paul

    2013-05-01

    The aim of this study was to conduct a cross-cultural comparison of the factors that influence patient satisfaction with musculoskeletal physiotherapy care in Australia and Korea. Prospective studies were conducted in Australia and Korea. Patient satisfaction data were collected using the MedRisk Instrument for Measuring Patient Satisfaction with Physical Therapy Care (MRPS) from a total of 1666 patients who were attending clinics for physiotherapy treatment of a musculoskeletal condition. Exploratory factor analysis was conducted to identify factors determining patient satisfaction in each cohort. A four-factor solution for the MRPS was found for the Australian and Korean data sets, explaining 61 and 55% of the variance respectively. Communication and respect, convenience and quality time and person-focused care were factors common to both countries. One factor unique to Korea was courtesy and propriety. For both cultures, global patient satisfaction was significantly but weakly correlated with the outcome of treatment. The interpersonal aspect of care, namely effective communication and respect from the therapist, appears to be the predominant and universal factor that influences patient satisfaction with physiotherapy care, although other culturally specific factors were identified. Physiotherapists can maximize patient satisfaction with care by addressing those features that uniquely contribute to patient satisfaction in the cultural context in which they are working.

  19. Intercultural comparison of patient satisfaction with physiotherapy care in Australia and Korea: an exploratory factor analysis

    Science.gov (United States)

    Hush, Julia M; Lee, Haejung; Yung, Vivian; Adams, Roger; Mackey, Martin; Wand, Benedict M; Nelson, Roger; Beattie, Paul

    2013-01-01

    Objectives: The aim of this study was to conduct a cross-cultural comparison of the factors that influence patient satisfaction with musculoskeletal physiotherapy care in Australia and Korea. Methods: Prospective studies were conducted in Australia and Korea. Patient satisfaction data were collected using the MedRisk Instrument for Measuring Patient Satisfaction with Physical Therapy Care (MRPS) from a total of 1666 patients who were attending clinics for physiotherapy treatment of a musculoskeletal condition. Exploratory factor analysis was conducted to identify factors determining patient satisfaction in each cohort. Results: A four-factor solution for the MRPS was found for the Australian and Korean data sets, explaining 61 and 55% of the variance respectively. Communication and respect, convenience and quality time and person-focused care were factors common to both countries. One factor unique to Korea was courtesy and propriety. For both cultures, global patient satisfaction was significantly but weakly correlated with the outcome of treatment. Conclusions: The interpersonal aspect of care, namely effective communication and respect from the therapist, appears to be the predominant and universal factor that influences patient satisfaction with physiotherapy care, although other culturally specific factors were identified. Physiotherapists can maximize patient satisfaction with care by addressing those features that uniquely contribute to patient satisfaction in the cultural context in which they are working. PMID:24421620

  20. Competitive Promoter-Associated Matrix Attachment Region Binding of the Arid3a and Cux1 Transcription Factors

    Directory of Open Access Journals (Sweden)

    Dongkyoon Kim

    2017-12-01

    Full Text Available Arid3a/Bright/Dril1 is a B cell-specific transactivator that regulates immunoglobulin heavy chain (IgH gene transcription by binding promoter and enhancer-associated matrix attachment regions (MARs within the IgH gene locus. Promoter MAR-mediated Arid3a transactivation is antagonized by direct competition of MAR binding by Cux1/CDP—a ubiquitously expressed repressor originally termed NF-μNR. We report that the NF-μNR complex includes Arid3a in B cells but not in non-B cells through mobility shift assays. The binding activity of NF-μNR and Arid3a in B cells is reciprocally altered during the cell division cycle and by the B cell mitogen lipopolysaccharide LPS. LPS treatment had no effect on Arid3a localization but increased its total abundance within the nucleus and cytoplasm. We show that this increased level of Arid3a is capable of displacing Cux from the MARs to facilitate IgH gene transcription. Finally, we showed that the MARs (termed Bf150 and Tx125 associated with the VH1 rearranged variable region expressed in the S107 murine plasmacytoma, can repress reporter gene transcription in non-B cells and that they can relieve the repression mediated by Eμ enhancer in B cells. These results have significant implications for early human development and demonstrate that MARs in IgH locus, NF-µNR and Arid3a regulate IgH gene expression in a concerted fashion. This paves the way for future studies examining the misregulation of this pathway in pediatric disease.

  1. Comparison of the two different standard flux-to-dose rate conversion factors

    International Nuclear Information System (INIS)

    Metghalchi, M.; Ashrafi, R.

    1983-01-01

    A very useful and simple way of obtaining the dose rate associated with neutron or photon fluxes is to multiply these fluxes by the appropriate flux-to-dose rate conversion factors. Two basic standard flux-to-dose rate conversion factors. are being used in all over the world, those recommended by the International Commission on Radiation Protection (ICRP) and the American National Standars (ANS). The purpose of this paper is to compare these two standard with each other. The comparison proved that the dose rate associated with a specific neutron flux, obtained by the ANS flux-to-dose rate conversion factors is usually higher than those calculated by the ICRP's conversion factors. Whereas in the case of the photon, in all energies, the difference between the dose rates obtained by these two standard flux-to-dose rate conversion factors are noticeable, and the ANS results are higher than the ICRP ones. So, it should be noted that for a specific neutron or photon flux the dose rate obtained by the ANS flux-to-dose rate conversion factors are more conservative than those obtained by the ICRP's. Therefore, in order to establish a more reasonable new standard flux-to-dose rate conversion factors, more work should be done. (author)

  2. Liarozole inhibits transforming growth factor-β3–mediated extracellular matrix formation in human three-dimensional leiomyoma cultures

    Science.gov (United States)

    Levy, Gary; Malik, Minnie; Britten, Joy; Gilden, Melissa; Segars, James; Catherino, William H.

    2014-01-01

    Objective To investigate the impact of liarozole on transforming growth factor-β3 (TGF-β3) expression, TGF-β3 controlled profibrotic cytokines, and extracellular matrix formation in a three-dimensional (3D) leiomyoma model system. Design Molecular and immunohistochemical analysis in a cell line evaluated in a three-dimensional culture. Setting Laboratory study. Patient(s) None. Intervention(s) Treatment of leiomyoma and myometrial cells with liarozole and TGF-β3 in a three-dimensional culture system. Main Outcome Measure(s) Quantitative real-time reverse-transcriptase polymerase chain reaction and Western blotting to assess fold gene and protein expression of TGF-β3 and TGF-β3 regulated fibrotic cytokines: collagen 1A1 (COL1A1), fibronectin, and versican before and after treatment with liarozole, and confirmatory immunohistochemical stains of treated three-dimensional cultures. Result(s) Both TGF-β3 gene and protein expression were elevated in leiomyoma cells compared with myometrium in two-dimensional and 3D cultures. Treatment with liarozole decreased TGF-β3 gene and protein expression. Extracellular matrix components versican, COL1A1, and fibronectin were also decreased by liarozole treatment in 3D cultures. Treatment of 3D cultures with TGF-β3 increased gene expression and protein production of COL1A1, fibronectin, and versican. Conclusion(s) Liarozole decreased TGF-β3 and TGF-β3–mediated extracellular matrix expression in a 3D uterine leiomyoma culture system. PMID:24825427

  3. Biomedical Application of Low Molecular Weight Heparin/Protamine Nano/Micro Particles as Cell- and Growth Factor-Carriers and Coating Matrix

    Directory of Open Access Journals (Sweden)

    Masayuki Ishihara

    2015-05-01

    Full Text Available Low molecular weight heparin (LMWH/protamine (P nano/micro particles (N/MPs (LMWH/P N/MPs were applied as carriers for heparin-binding growth factors (GFs and for adhesive cells including adipose-derived stromal cells (ADSCs and bone marrow-derived mesenchymal stem cells (BMSCs. A mixture of LMWH and P yields a dispersion of N/MPs (100 nm–3 μm in diameter. LMWH/P N/MPs can be immobilized onto cell surfaces or extracellular matrix, control the release, activate GFs and protect various GFs. Furthermore, LMWH/P N/MPs can also bind to adhesive cell surfaces, inducing cells and LMWH/P N/MPs-aggregate formation. Those aggregates substantially promoted cellular viability, and induced vascularization and fibrous tissue formation in vivo. The LMWH/P N/MPs, in combination with ADSCs or BMSCs, are effective cell-carriers and are potential promising novel therapeutic agents for inducing vascularization and fibrous tissue formation in ischemic disease by transplantation of the ADSCs and LMWH/P N/MPs-aggregates. LMWH/P N/MPs can also bind to tissue culture plates and adsorb exogenous GFs or GFs from those cells. The LMWH/P N/MPs-coated matrix in the presence of GFs may provide novel biomaterials that can control cellular activity such as growth and differentiation. Furthermore, three-dimensional (3D cultures of cells including ADSCs and BMSCs using plasma-medium gel with LMWH/P N/MPs exhibited efficient cell proliferation. Thus, LMWH/P N/MPs are an adequate carrier both for GFs and for stromal cells such as ADSCs and BMSCs, and are a functional coating matrix for their cultures.

  4. Analysis of the transforming growth factor-beta1 pathway and extracellular matrix formation as a hybrid system

    NARCIS (Netherlands)

    Musters, M.W.J.M.; Riel, van N.A.W.

    2004-01-01

    It is generally accepted that aging of the vascular system plays an important role in cardiovascular disease (CVD). Recent experimental findings have indicated the involvement of the cytokine transforming growth factor-/spl beta//sub 1/ (TGF-/spl beta//sub 1/) in these vascular aging processes. This

  5. Recovery of heat treated Bacillus cereus spores is affected by matrix composition and factors with putative functions in damage repair

    NARCIS (Netherlands)

    Warda, A.K.; Tempelaars, M.H.; Abee, T.; Nierop Groot, M.N.

    2016-01-01

    The ability of spores to recover and grow out after food processing is affected by cellular factors and by the outgrowth conditions. In the current communication we studied the recovery and outgrowth of individually sorted spores in BHI and rice broth media and on agar plates using flow cytometry.

  6. 3-Way characterization of soils by Procrustes rotation, matrix-augmented principal components analysis and parallel factor analysis

    Czech Academy of Sciences Publication Activity Database

    Andrade, J.M.; Kubista, Mikael; Carlosena, A.; Prada, D.

    2007-01-01

    Roč. 603, č. 1 (2007), s. 20-29 ISSN 0003-2670 Institutional research plan: CEZ:AV0Z50520514 Keywords : PCA * heavy metals * soil Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.186, year: 2007

  7. Comparison of approaches to deal with matrix effects in LC-MS/MS based determinations of mycotoxins in food and feed

    NARCIS (Netherlands)

    Fabregat-Cabello, N.; Zomer, P.; Sancho, J.V.; Roig-Navarro, A.F.; Mol, H.G.J.

    2016-01-01

    This study deals with one of the major concerns in mycotoxin determinations: The matrix effect related to LC-MS/ MS systems with electrospray ionization sources. To this end, in a first approach, the matrix effect has been evaluated in two ways: monitoring the signal of a compound (added to the

  8. Electromagnetic Compatibility of Matrix Converter System

    Directory of Open Access Journals (Sweden)

    S. Fligl

    2006-12-01

    Full Text Available The presented paper deals with matrix converters pulse width modulation strategies design with emphasis on the electromagnetic compatibility. Matrix converters provide an all-silicon solution to the problem of converting AC power from one frequency to another, offering almost all the features required of an ideal static frequency changer. They possess many advantages compared to the conventional voltage or current source inverters. A matrix converter does not require energy storage components as a bulky capacitor or an inductance in the DC-link, and enables the bi-directional power flow between the power supply and load. The most of the contemporary modulation strategies are able to provide practically sinusoidal waveforms of the input and output currents with negligible low order harmonics, and to control the input displacement factor. The perspective of matrix converters regarding EMC in comparison with other types of converters is brightly evident because it is no need to use any equipment for power factor correction and current and voltage harmonics reduction. Such converter with proper control is properly compatible both with the supply mains and with the supplied load. A special digital control system was developed for the realized experimental test bed which makes it possible to achieve greater throughput of the digital control system and its variability.

  9. A new method to quantify the health risks from sources of perfluoroalkyl substances, combined with positive matrix factorization and risk assessment models.

    Science.gov (United States)

    Xu, Jiao; Shi, Guo-Liang; Guo, Chang-Sheng; Wang, Hai-Ting; Tian, Ying-Ze; Huangfu, Yan-Qi; Zhang, Yuan; Feng, Yin-Chang; Xu, Jian

    2018-01-01

    A hybrid model based on the positive matrix factorization (PMF) model and the health risk assessment model for assessing risks associated with sources of perfluoroalkyl substances (PFASs) in water was established and applied at Dianchi Lake to test its applicability. The new method contains 2 stages: 1) the sources of PFASs were apportioned by the PMF model and 2) the contribution of health risks from each source was calculated by the new hybrid model. Two factors were extracted by PMF, with factor 1 identified as aqueous fire-fighting foams source and factor 2 as fluoropolymer manufacturing and processing and perfluorooctanoic acid production source. The health risk of PFASs in the water assessed by the health risk assessment model was 9.54 × 10 -7  a -1 on average, showing no obvious adverse effects to human health. The 2 sources' risks estimated by the new hybrid model ranged from 2.95 × 10 -10 to 6.60 × 10 -6  a -1 and from 1.64 × 10 -7 to 1.62 × 10 -6  a -1 , respectively. The new hybrid model can provide useful information on the health risks of PFAS sources, which is helpful for pollution control and environmental management. Environ Toxicol Chem 2018;37:107-115. © 2017 SETAC. © 2017 SETAC.

  10. Icotinib inhibits the invasion of Tca8113 cells via downregulation of nuclear factor κB-mediated matrix metalloproteinase expression

    OpenAIRE

    YANG, CAILING; YAN, JIANGUO; YUAN, GUOYAN; ZHANG, YINGHUA; LU, DERONG; REN, MINGXIN; CUI, WEIGANG

    2014-01-01

    Icotinib is an epidermal growth factor receptor tyrosine kinase inhibitor, which has been revealed to inhibit proliferation in tumor cells. However, the effect of icotinib on cancer cell metastasis remains to be explained. This study examines the effect of icotinib on the migration and invasion of squamous cells of tongue carcinoma (Tca8113 cells) in vitro. The results of the Boyden chamber invasion assay demonstrated that icotinib reduced cell invasion, suppressed the protein levels of matri...

  11. Importance-performance matrix analysis of the factors influencing international students’ psychological and sociocultural adaptations using SmartPLS

    OpenAIRE

    Shafaei, Azadeh; Razak, Nordin Abd

    2015-01-01

    With the increase in international mobility in higher education especially in Asia, the issue of cross-cultural adaptation becomes paramount since international students try to overcome challenges and flourish psychologically and socioculturally in a new environment. Therefore, this study is conducted to identify the factors influencing international postgraduate students’ psychological and sociocultural adaptations in Malaysian public universities, an emerging education hub in the region. It...

  12. The transcription factor SOX18 regulates the expression of matrix metalloproteinase 7 and guidance molecules in human endothelial cells.

    Directory of Open Access Journals (Sweden)

    Martina Hoeth

    Full Text Available Mutations in the transcription factor SOX18 are responsible for specific cardiovascular defects in humans and mice. In order to gain insight into the molecular basis of its action, we identified target genes of SOX18 and analyzed one, MMP7, in detail.SOX18 was expressed in HUVEC using a recombinant adenoviral vector and the altered gene expression profile was analyzed using microarrays. Expression of several regulated candidate SOX18 target genes was verified by real-time PCR. Knock-down of SOX18 using RNA interference was then used to confirm the effect of the transcription factor on selected genes that included the guidance molecules ephrin B2 and semaphorin 3G. One gene, MMP7, was chosen for further analysis, including detailed promoter studies using reporter gene assays, electrophoretic mobility shift analysis and chromatin-immunoprecipitation, revealing that it responds directly to SOX18. Immunohistochemical analysis demonstrated the co-expression of SOX18 and MMP7 in blood vessels of human skin.The identification of MMP7 as a direct SOX18 target gene as well as other potential candidates including guidance molecules provides a molecular basis for the proposed function of this transcription factor in the regulation of vessel formation.

  13. Comparison of lifestyle risk factors by family history for gastric, breast, lung and colorectal cancer.

    Science.gov (United States)

    Huang, Xin-En; Hirose, Kaoru; Wakai, Kenji; Matsuo, Keitaro; Ito, Hidemi; Xiang, Jin; Takezaki, Toshiro; Tajima, Kazuo

    2004-01-01

    To assess the theoretical impact of lifestyle of a cancer family history in first-degree relatives (CFH) and clarify interactions between CFH and lifestyle factors, hospital-based comparison and case-reference studies were conducted in Nagoya, Japan. Totals of 1988 gastric, 2455 breast, 1398 lung and 1352 colorectal cancer patients, as well as 50,706 non-cancer outpatients collected from 1988 to 1998, were checked for lifestyle factors, which included dietary and physical exercise habits, as well as smoking/drinking status. General lifestyle factors with non-cancer outpatients did not differ by the CFH status. Case-reference analyses showed that frequent intake of fruits, raw vegetables, carrots, pumpkin, cabbage and lettuce, as well as frequent physical exercise, were associated with decreased risk for all four sites of cancer, while habitual smoking increasing the risk of gastric, and more particularly, lung cancer. Interestingly, the study revealed the magnitude of odds ratios for the above lifestyle factors obtained from CFH positives to be similar to those from CFH negatives for these four sites of cancer. There were no significant interactions between CFH and any particular lifestyle factor. In conclusion, our results suggest no appreciable influence of CFH on lifestyle related risk factors for gastric, breast, lung, and colorectal cancer. Habitual smoking increased, while frequent physical exercise and raw vegetables intake decreased cancer risk, regardless of the CFH status.

  14. Arabian, Asian, western: a cross-cultural comparison of aircraft accidents from human factor perspectives.

    Science.gov (United States)

    Al-Wardi, Yousuf

    2017-09-01

    Rates of aviation accident differ in different regions; and national culture has been implicated as a factor. This invites a discussion about the role of national culture in aviation accidents. This study makes a cross-cultural comparison between Oman, Taiwan and the USA. A cross-cultural comparison was acquired using data from three studies, including this study, by applying the Human Factors Analysis and Classification System (HFACS) framework. The Taiwan study presented 523 mishaps with 1762 occurrences of human error obtained from the Republic of China Air Force. The study from the USA carried out for commercial aviation had 119 accidents with 245 instances of human error. This study carried out in Oman had a total of 40 aircraft accidents with 129 incidences. Variations were found between Oman, Taiwan and the USA at the levels of organisational influence and unsafe supervision. Seven HFACS categories showed significant differences between the three countries (p culture can have an impact on aviation safety. This study revealed that national culture plays a role in aircraft accidents related to human factors that cannot be disregarded.

  15. Sources identification of the atmospheric aerosol at urban and suburban sites in Indonesia by positive matrix factorization

    International Nuclear Information System (INIS)

    Santoso, Muhayatun; Hopke, Philip K.; Hidayat, Achmad; Diah Dwiana L

    2008-01-01

    Samples of fine and coarse fractions of airborne particulate matter were collected in Indonesia (west central Java) at an urban site in Bandung and in suburban Lembang from January 2002 to December 2004. The samples were collected using a Gent stacked filter sampler in two size fractions of 2.5-10 mass at both sites comes from soil dust and road dust. The biomass burning factor contributes about 40% of the PM 2.5 mass in case of suburban Lembang and about 20% in urban Bandung

  16. Encoding of rat working memory by power of multi-channel local field potentials via sparse non-negative matrix factorization

    Institute of Scientific and Technical Information of China (English)

    Xu Liu; Tiao-Tiao Liu; Wen-Wen Bai; Hu Yi; Shuang-Yan Li; Xin Tian

    2013-01-01

    Working memory plays an important role in human cognition.This study investigated how working memory was encoded by the power of multi-channel local field potentials (LFPs) based on sparse nonnegative matrix factorization (SNMF).SNMF was used to extract features from LFPs recorded from the prefrontal cortex of four Sprague-Dawley rats during a memory task in a Y maze,with 10 trials for each rat.Then the power-increased LFP components were selected as working memory-related features and the other components were removed.After that,the inverse operation of SNMF was used to study the encoding of working memory in the timefrequency domain.We demonstrated that theta and gamma power increased significantly during the working memory task.The results suggested that postsynaptic activity was simulated well by the sparse activity model.The theta and gamma bands were meaningful for encoding working memory.

  17. Source Apportionment of PM2.5 Mass and Optical Attenuation Over an Ecologically Sensitive Zone in Central India by Positive Matrix Factorization

    Science.gov (United States)

    Nirmalkar, J.; Raman, R. S.

    2016-12-01

    Ambient PM2.5 samples (N=366) were collected over an ecologically sensitive zone (Van Vihar National Park) in Bhopal, Central India for two years (01 January, 2012 to 31 December, 2013). Samples were collected using three co-located Mini-Vol® samplers on Teflon, Nylon, and Quartz filter substrates. The aerosol was then chemically characterized for water-soluble inorganic ions, elements, and carbon fractions (elemental carbon and organic carbon) using ion chromatography, ED-XRF, and thermal-optical EC/OC analyzer, respectively. The optical attenuation (at 370 nm and 800 nm) of PM2.5 aerosols was also determined by optical transmissometry (OT-21). The application of Positive matrix factorization (PMF) to a combination of PM2.5 mass, its ions, elements, carbon fractions, and optical attenuation and its outcomes will be discussed.

  18. Study of the validity of a job-exposure matrix for psychosocial work factors: results from the national French SUMER survey.

    Science.gov (United States)

    Niedhammer, Isabelle; Chastang, Jean-François; Levy, David; David, Simone; Degioanni, Stéphanie; Theorell, Töres

    2008-10-01

    To construct and evaluate the validity of a job-exposure matrix (JEM) for psychosocial work factors defined by Karasek's model using national representative data of the French working population. National sample of 24,486 men and women who filled in the Job Content Questionnaire (JCQ) by Karasek measuring the scores of psychological demands, decision latitude, and social support (individual scores) in 2003 (response rate 96.5%). Median values of the three scores in the total sample of men and women were used to define high demands, low latitude, and low support (individual binary exposures). Job title was defined by both occupation and economic activity that were coded using detailed national classifications (PCS and NAF/NACE). Two JEM measures were calculated from the individual scores of demands, latitude and support for each job title: JEM scores (mean of the individual score) and JEM binary exposures (JEM score dichotomized at the median). The analysis of the variance of the individual scores of demands, latitude, and support explained by occupations and economic activities, of the correlation and agreement between individual measures and JEM measures, and of the sensitivity and specificity of JEM exposures, as well as the study of the associations with self-reported health showed a low validity of JEM measures for psychological demands and social support, and a relatively higher validity for decision latitude compared with individual measures. Job-exposure matrix measure for decision latitude might be used as a complementary exposure assessment. Further research is needed to evaluate the validity of JEM for psychosocial work factors.

  19. Effect of DEM resolution and comparison between different weighting factors for hydrologic connectivity index

    Science.gov (United States)

    Cantreul, Vincent; Cavalli, Marco; Degré, Aurore

    2016-04-01

    zones. On the contrary, areas up to very well connected zones (roads, paths…) are higher and much more connected than downstream areas. For the Manning's factor, the values are very low and not very well contrasted. This factor is not enough discriminant for this study. In conclusion, high resolution DEM (1 meter or higher) is needed for the IC calculation (precison, impact of connections…). Very high resolution permits to identify very well disconnected areas but it multiplies the calculation time. For the weighting factor, rugosity index and C factor have each some advantages. It is planned to test other approaches for the IC calculation. Key-words: hydrological connectivity index, DEM, resolution, weighting factor, comparison

  20. Matrix thermalization

    International Nuclear Information System (INIS)

    Craps, Ben; Evnin, Oleg; Nguyen, Kévin

    2017-01-01

    Matrix quantum mechanics offers an attractive environment for discussing gravitational holography, in which both sides of the holographic duality are well-defined. Similarly to higher-dimensional implementations of holography, collapsing shell solutions in the gravitational bulk correspond in this setting to thermalization processes in the dual quantum mechanical theory. We construct an explicit, fully nonlinear supergravity solution describing a generic collapsing dilaton shell, specify the holographic renormalization prescriptions necessary for computing the relevant boundary observables, and apply them to evaluating thermalizing two-point correlation functions in the dual matrix theory.

  1. Matrix thermalization

    Science.gov (United States)

    Craps, Ben; Evnin, Oleg; Nguyen, Kévin

    2017-02-01

    Matrix quantum mechanics offers an attractive environment for discussing gravitational holography, in which both sides of the holographic duality are well-defined. Similarly to higher-dimensional implementations of holography, collapsing shell solutions in the gravitational bulk correspond in this setting to thermalization processes in the dual quantum mechanical theory. We construct an explicit, fully nonlinear supergravity solution describing a generic collapsing dilaton shell, specify the holographic renormalization prescriptions necessary for computing the relevant boundary observables, and apply them to evaluating thermalizing two-point correlation functions in the dual matrix theory.

  2. Matrix thermalization

    Energy Technology Data Exchange (ETDEWEB)

    Craps, Ben [Theoretische Natuurkunde, Vrije Universiteit Brussel (VUB), and International Solvay Institutes, Pleinlaan 2, B-1050 Brussels (Belgium); Evnin, Oleg [Department of Physics, Faculty of Science, Chulalongkorn University, Thanon Phayathai, Pathumwan, Bangkok 10330 (Thailand); Theoretische Natuurkunde, Vrije Universiteit Brussel (VUB), and International Solvay Institutes, Pleinlaan 2, B-1050 Brussels (Belgium); Nguyen, Kévin [Theoretische Natuurkunde, Vrije Universiteit Brussel (VUB), and International Solvay Institutes, Pleinlaan 2, B-1050 Brussels (Belgium)

    2017-02-08

    Matrix quantum mechanics offers an attractive environment for discussing gravitational holography, in which both sides of the holographic duality are well-defined. Similarly to higher-dimensional implementations of holography, collapsing shell solutions in the gravitational bulk correspond in this setting to thermalization processes in the dual quantum mechanical theory. We construct an explicit, fully nonlinear supergravity solution describing a generic collapsing dilaton shell, specify the holographic renormalization prescriptions necessary for computing the relevant boundary observables, and apply them to evaluating thermalizing two-point correlation functions in the dual matrix theory.

  3. Comparison of AB2588 multipathway risk factors for California fossil-fuel power stations

    International Nuclear Information System (INIS)

    Gratt, L.B.; Levin, L.

    1997-01-01

    Substances released from power plants may travel through various exposure pathways resulting in human health and environmental risks. The stack air emission's primary pathway is inhalation from the ambient air. Multipathway factors (adjustment factors to the inhalation risk) are used to evaluate the importance of non-inhalation pathways (such as ingestion and dermal contact). The multipathway factor for a specific substance is the health risk by all pathways divided by the inhalation health risk for that substance. These factors are compared for fossil fuel power stations that submitted regulatory risk assessments in compliance with California Toxic Hot Spots Act (AB2588). Substances representing the largest contributions to the cancer risk are of primary concern: arsenic, beryllium, cadmium, chromium (+6), formaldehyde, nickel, lead, selenium, and PAHs. Comparisons of the chemical-specific multipathway factors show the impacts of regulatory policy decisions on the estimated health risk for trace substances. As an example, point estimates of the soil mixing depth, varying from 1 cm to 15 cm, relate to the relative importance of the pathway. For the deeper mixing depths, the root-zone uptake by homegrown tomato plants (for assumed consumption rate of 15% for San Diego) may result in high multipathway factors for several trace metals. For shallower mixing depths, soil ingestion may become the dominant non-inhalation pathway. These differences may lead to significantly different risk estimates for similar facilities located at different California locations such as to be under local regulatory authorities. The overall multipathway factor for the total cancer risk is about 2, much smaller than some of the chemical-specific factors. Science-based multipathway analysis should reduce much of the concern that may be due to policy-based decisions on pathway selection and high-value point-estimates of the parameters

  4. Buildup factors for multilayer shieldings in deterministic methods and their comparison with Monte Carlo

    International Nuclear Information System (INIS)

    Listjak, M.; Slavik, O.; Kubovcova, D.; Vermeersch, F.

    2008-01-01

    In general there are two ways how to calculate effective doses. The first way is by use of deterministic methods like point kernel method which is implemented in Visiplan or Microshield. These kind of calculations are very fast, but they are not very convenient for a complex geometry with shielding composed of more then one material in meaning of result precision. In spite of this that programs are sufficient for ALARA optimisation calculations. On other side there are Monte Carlo methods which can be used for calculations. This way of calculation is quite precise in comparison with reality but calculation time is usually very large. Deterministic method like programs have one disadvantage -usually there is option to choose buildup factor (BUF) only for one material in multilayer stratified slabs shielding calculation problems even if shielding is composed from different materials. In literature there are proposed different formulas for multilayer BUF approximation. Aim of this paper was to examine these different formulas and their comparison with MCNP calculations. At first ware compared results of Visiplan and Microshield. Simple geometry was modelled - point source behind single and double slab shielding. For Build-up calculations was chosen Geometric Progression method (feature of the newest version of Visiplan) because there are lower deviations in comparison with Taylor fitting. (authors)

  5. Buildup factors for multilayer shieldings in deterministic methods and their comparison with Monte Carlo

    International Nuclear Information System (INIS)

    Listjak, M.; Slavik, O.; Kubovcova, D.; Vermeersch, F.

    2009-01-01

    In general there are two ways how to calculate effective doses. The first way is by use of deterministic methods like point kernel method which is implemented in Visiplan or Microshield. These kind of calculations are very fast, but they are not very convenient for a complex geometry with shielding composed of more then one material in meaning of result precision. In spite of this that programs are sufficient for ALARA optimisation calculations. On other side there are Monte Carlo methods which can be used for calculations. This way of calculation is quite precise in comparison with reality but calculation time is usually very large. Deterministic method like programs have one disadvantage -usually there is option to choose buildup factor (BUF) only for one material in multilayer stratified slabs shielding calculation problems even if shielding is composed from different materials. In literature there are proposed different formulas for multilayer BUF approximation. Aim of this paper was to examine these different formulas and their comparison with MCNP calculations. At first ware compared results of Visiplan and Microshield. Simple geometry was modelled - point source behind single and double slab shielding. For Build-up calculations was chosen Geometric Progression method (feature of the newest version of Visiplan) because there are lower deviations in comparison with Taylor fitting. (authors)

  6. Synergistic action of protease-modulating matrix and autologous growth factors in healing of diabetic foot ulcers. A prospective randomized trial.

    Science.gov (United States)

    Kakagia, Despoina D; Kazakos, Konstantinos J; Xarchas, Konstantinos C; Karanikas, Michael; Georgiadis, George S; Tripsiannis, Gregory; Manolas, Constantinos

    2007-01-01

    This study tests the hypothesis that addition of a protease-modulating matrix enhances the efficacy of autologous growth factors in diabetic ulcers. Fifty-one patients with chronic diabetic foot ulcers were managed as outpatients at the Democritus University Hospital of Alexandroupolis and followed up for 8 weeks. All target ulcers were > or = 2.5 cm in any one dimension and had been previously treated only with moist gauze. Patients were randomly allocated in three groups of 17 patients each: Group A was treated only with the oxidized regenerated cellulose/collagen biomaterial (Promogran, Johnson & Johnson, New Brunswick, NJ), Group B was treated only with autologous growth factors delivered by Gravitational Platelet Separation System (GPS, Biomet), and Group C was managed by a combination of both. All ulcers were digitally photographed at initiation of the study and then at change of dressings once weekly. Computerized planimetry (Texas Health Science Center ImageTool, Version 3.0) was used to assess ulcer dimensions that were analyzed for homogeneity and significance using the Statistical Package for Social Sciences, Version 13.0. Post hoc analysis revealed that there was significantly greater reduction of all three dimensions of the ulcers in Group C compared to Groups A and B (all P<.001). Although reduction of ulcer dimensions was greater in Group A than in Group B, these differences did not reach statistical significance. It is concluded that protease-modulating dressings act synergistically with autologous growth factors and enhance their efficacy in diabetic foot ulcers.

  7. Extracellular matrix metalloproteinase inducer (EMMPRIN) expression correlates positively with active angiogenesis and negatively with basic fibroblast growth factor expression in epithelial ovarian cancer.

    Science.gov (United States)

    Szubert, Sebastian; Szpurek, Dariusz; Moszynski, Rafal; Nowicki, Michal; Frankowski, Andrzej; Sajdak, Stefan; Michalak, Slawomir

    2014-03-01

    The primary aim of this paper was to evaluate the expression of extracellular matrix metalloproteinase inducer (EMMPRIN) and its relationship with proangiogenic factors and microvessel density (MVD) in ovarian cancer. The study group included 58 epithelial ovarian cancers (EOCs), 35 benign ovarian tumors, and 21 normal ovaries. The expression of EMMPRIN, vascular endothelial growth factor (VEGF), and basic fibroblast growth factor (bFGF) was assessed by ELISA of tissue homogenates. Antibodies against CD105, CD31, and CD34 were used to immunohistochemically assess MVD. We have found significantly higher EMMPRIN expression in EOC than in benign ovarian tumors and normal ovaries. Similarly, the VEGF expression was higher in EOC than in benign ovarian tumors and normal ovaries. By contrast, bFGF expression was lower in EOC than in benign ovarian tumors and ovary samples. EMMPRIN expression in EOC was directly correlated with VEGF expression and CD105-MVD, but inversely correlated with bFGF expression. Grade 2/3 ovarian cancers had increased expression of EMMPRIN and VEGF, increased CD105-MVD, and lowered expression of bFGF compared to grade 1 ovarian cancers. Moreover, EMMPRIN expression was higher in advanced (FIGO III and IV) ovarian cancer. The upregulation of EMMPRIN and VEGF expression is correlated with increased CD105-MVD and silenced bFGF, which suggests early and/or reactivated angiogenesis in ovarian cancer. Aggressive EOC is characterized by the following: high expression of EMMPRIN and VEGF, high CD105-MVD, and low expression of bFGF.

  8. Clonorchis sinensis excretory-secretory products regulate migration and invasion in cholangiocarcinoma cells via extracellular signal-regulated kinase 1/2/nuclear factor-κB-dependent matrix metalloproteinase-9 expression.

    Science.gov (United States)

    Pak, Jhang Ho; Shin, Jimin; Song, In-Sung; Shim, Sungbo; Jang, Sung-Wuk

    2017-01-01

    Matrix metalloproteinase-9 plays an important role in the invasion and metastasis of various types of cancer cells. We have previously reported that excretory-secretory products from Clonorchis sinensis increases matrix metalloproteinase-9 expression. However, the regulatory mechanisms through which matrix metalloproteinase-9 expression affects cholangiocarcinoma development remain unclear. In the current study, we examined the potential role of excretory-secretory products in regulating the migration and invasion of various cholangiocarcinoma cell lines. We demonstrated that excretory-secretory products significantly induced matrix metalloproteinase-9 expression and activity in a concentration-dependent manner. Reporter gene and chromatin immunoprecipitation assays showed that excretory-secretory products induced matrix metalloproteinase-9 expression by enhancing the activity of nuclear factor-kappa B. Moreover, excretory-secretory products induced the degradation and phosphorylation of IκBα and stimulated nuclear factor-kappa B p65 nuclear translocation, which was regulated by extracellular signal-regulated kinase 1/2. Taken together, our findings indicated that the excretory-secretory product-dependent enhancement of matrix metalloproteinase-9 activity and subsequent induction of IκBα and nuclear factor-kappa B activities may contribute to the progression of cholangiocarcinoma. Copyright © 2016 Australian Society for Parasitology. Published by Elsevier Ltd. All rights reserved.

  9. Roles of pro-angiogenic and anti-angiogenic factors as well as matrix metalloproteinases in healing of NSAID-induced small intestinal ulcers in rats.

    Science.gov (United States)

    Gyenge, Melinda; Amagase, Kikuko; Kunimi, Shino; Matsuoka, Rie; Takeuchi, Koji

    2013-10-06

    We examined changes in the expression of a pro-angiogenic factor, vascular endothelial growth factor (VEGF), and an anti-angiogenic factor, endostatin, as well as matrix metalloproteinase (MMP)-2 and MMP-9 in the rat small intestine after administration of indomethacin and investigated the roles of these factors in the healing of indomethacin-induced small intestinal ulcers. Male SD rats were given indomethacin (10mg/kg) p.o. and euthanized at various time points (3-24h and 2-7days) after the administration. To impair the healing of these lesions, low-dose of indomethacin (2mg/kg) was given p.o. once daily for 6days starting 1day after ulceration. Levels of VEGF, endostatin, MMP-2 and MMP-9 were determined by Western blotting. The expression of both VEGF and endostatin was upregulated after the ulceration. Repeated administration of low-dose indomethacin impaired the ulcer healing with a decrease of VEGF expression and a further increase of endostatin expression, resulting in a marked decrease in the ratio of VEGF/endostatin expression. The levels of MMP-2 and MMP-9 were both significantly increased after the ulceration, but these responses were suppressed by the repeated indomethacin treatment. The healing of these ulcers was significantly delayed by the repeated administration of MMP inhibitors such as ARP-101 and SB-3CT. The results confirm the importance of the balance between pro-angiogenic and anti-angiogenic activities in the healing of indomethacin-induced small intestinal damage and further suggest that the increased expression of MMP-2 and MMP-9 is another important factor for ulcer healing in the small intestine. © 2013.

  10. Study of the validity of a job-exposure matrix for the job strain model factors: an update and a study of changes over time.

    Science.gov (United States)

    Niedhammer, Isabelle; Milner, Allison; LaMontagne, Anthony D; Chastang, Jean-François

    2018-03-08

    The objectives of the study were to construct a job-exposure matrix (JEM) for psychosocial work factors of the job strain model, to evaluate its validity, and to compare the results over time. The study was based on national representative data of the French working population with samples of 46,962 employees (2010 SUMER survey) and 24,486 employees (2003 SUMER survey). Psychosocial work factors included the job strain model factors (Job Content Questionnaire): psychological demands, decision latitude, social support, job strain and iso-strain. Job title was defined by three variables: occupation and economic activity coded using standard classifications, and company size. A JEM was constructed using a segmentation method (Classification and Regression Tree-CART) and cross-validation. The best quality JEM was found using occupation and company size for social support. For decision latitude and psychological demands, there was not much difference using occupation and company size with or without economic activity. The validity of the JEM estimates was higher for decision latitude, job strain and iso-strain, and lower for social support and psychological demands. Differential changes over time were observed for psychosocial work factors according to occupation, economic activity and company size. This study demonstrated that company size in addition to occupation may improve the validity of JEMs for psychosocial work factors. These matrices may be time-dependent and may need to be updated over time. More research is needed to assess the validity of JEMs given that these matrices may be able to provide exposure assessments to study a range of health outcomes.

  11. Public beliefs about causes and risk factors for mental disorders: a comparison of Japan and Australia

    Directory of Open Access Journals (Sweden)

    Nakane Hideyuki

    2005-09-01

    Full Text Available Abstract Background Surveys of the public in a range of Western countries have shown a predominant belief in social stressors as causes of mental disorders. However, there has been little direct cross-cultural comparison. Here we report a comparison of public beliefs about the causes of mental disorders in Japan and Australia. Methods Surveys of the public were carried out in each country using as similar a methodology as feasible. In both countries, household interviews were carried out concerning beliefs about causes and risk factors in relation to one of four case vignettes, describing either depression, depression with suicidal thoughts, early schizophrenia or chronic schizophrenia. In Japan, the survey involved 2000 adults aged between 20 and 69 from 25 regional sites spread across the country. In Australia, the survey involved a national sample of 3998 adults aged 18 years or over. Results In both countries, both social and personal vulnerability causes were commonly endorsed across all vignettes. The major differences in causal beliefs were that Australians were more likely to believe in infection, allergy and genetics, while Japanese were more likely to endorse "nervous person" and "weakness of character". For risk factors, Australians tended to believe that women, the young and the poor were more at risk of depression, but these were not seen as higher risk groups by Japanese. Conclusion In both Japan and Australia, the public has a predominant belief in social causes and risk factors, with personal vulnerability factors also seen as important. However, there are also some major differences between the countries. The belief in weakness of character as a cause, which was stronger in Japan, is of particular concern because it may reduce the likelihood of seeking professional help and support from others.

  12. Matrix interdiction problem

    Energy Technology Data Exchange (ETDEWEB)

    Pan, Feng [Los Alamos National Laboratory; Kasiviswanathan, Shiva [Los Alamos National Laboratory

    2010-01-01

    In the matrix interdiction problem, a real-valued matrix and an integer k is given. The objective is to remove k columns such that the sum over all rows of the maximum entry in each row is minimized. This combinatorial problem is closely related to bipartite network interdiction problem which can be applied to prioritize the border checkpoints in order to minimize the probability that an adversary can successfully cross the border. After introducing the matrix interdiction problem, we will prove the problem is NP-hard, and even NP-hard to approximate with an additive n{gamma} factor for a fixed constant {gamma}. We also present an algorithm for this problem that achieves a factor of (n-k) mUltiplicative approximation ratio.

  13. Comparison of Some Cardiovascular Risk Factors between Active and Sedentary Elderly Men

    Directory of Open Access Journals (Sweden)

    H. Najafgholizadeh

    2017-04-01

    Full Text Available Background: One of the major problems threatening the world’s people are cardiovascular diseases, accounting for 30% of the deaths. The factors exposing people to this danger are called risk factors. Objective: This study aimed to compare the cardiovascular risk factors and C-reactive protein between active and sedentary elderly men. Methods: The study was a descriptive comparison of two groups that were conducted in Rasht city in 2015. The subjects of this study consist of 30 active elderly men and 30 sedentary elderly men who were selected non-randomly and purposefully. Inclusion criteria of research for active subjects were have regular physical activity at least six months and don’t use cigarette and pills that affect profile lipids and inclusion criteria for sedentary subjects were don’t have regular physical activity and also don’t use cigarette and pills that affect profile lipids. The measured cardiovascular risk factors of subjects include fasting blood sugar (FBS, triglyceride (TG, total cholesterol (TC, highdensity lipoprotein (HDL, low-density lipoprotein (LDL, very low-density lipoprotein (VLDL, glycated haemoglobinA1c (HbA1c, and C-reactive protein (CRP. The statistical methods used for data analysis are Kolmogorov-Smirnov test, t-student, and U Mann-Whitney with significance level less than 0.05. Findings: The t-student exam shows that cardiovascular risk factors, including FBS, TG, TC, HDL, VLDL, HbA1c, and CRP, in active elderly men are lower than sedentary elderly men. This difference is also statistically significant (P≤0/01. Conclusion: The study showed that cardiovascular risk factors in active elderly men are less than sedentary ones. However, 80% of active elderly men had still at least one or several cardiovascular risk factors.

  14. The Exopolysaccharide Matrix

    Science.gov (United States)

    Koo, H.; Falsetta, M.L.; Klein, M.I.

    2013-01-01

    Many infectious diseases in humans are caused or exacerbated by biofilms. Dental caries is a prime example of a biofilm-dependent disease, resulting from interactions of microorganisms, host factors, and diet (sugars), which modulate the dynamic formation of biofilms on tooth surfaces. All biofilms have a microbial-derived extracellular matrix as an essential constituent. The exopolysaccharides formed through interactions between sucrose- (and starch-) and Streptococcus mutans-derived exoenzymes present in the pellicle and on microbial surfaces (including non-mutans) provide binding sites for cariogenic and other organisms. The polymers formed in situ enmesh the microorganisms while forming a matrix facilitating the assembly of three-dimensional (3D) multicellular structures that encompass a series of microenvironments and are firmly attached to teeth. The metabolic activity of microbes embedded in this exopolysaccharide-rich and diffusion-limiting matrix leads to acidification of the milieu and, eventually, acid-dissolution of enamel. Here, we discuss recent advances concerning spatio-temporal development of the exopolysaccharide matrix and its essential role in the pathogenesis of dental caries. We focus on how the matrix serves as a 3D scaffold for biofilm assembly while creating spatial heterogeneities and low-pH microenvironments/niches. Further understanding on how the matrix modulates microbial activity and virulence expression could lead to new approaches to control cariogenic biofilms. PMID:24045647

  15. Chemical characterization of PM1.0 aerosol in Delhi and source apportionment using positive matrix factorization.

    Science.gov (United States)

    Jaiprakash; Singhai, Amrita; Habib, Gazala; Raman, Ramya Sunder; Gupta, Tarun

    2017-01-01

    Fine aerosol fraction (particulate matter with aerodynamic diameter <= 1.0 μm (PM) 1.0 ) over the Indian Institute of Technology Delhi campus was monitored day and night (10 h each) at 30 m height from November 2009 to March 2010. The samples were analyzed for 5 ions (NH 4 + , NO 3 - , SO 4 2- , F - , and Cl - ) and 12 trace elements (Na, K, Mg, Ca, Pb, Zn, Fe, Mn, Cu, Cd, Cr, and Ni). Importantly, secondary aerosol (sulfate and nitrate) formation was observed during dense foggy events, supporting the fog-smog-fog cycle. A total of 76 samples were used for source apportionment of PM mass. Six factors were resolved by PMF analyses and were identified as secondary aerosol, secondary chloride, biomass burning, soil dust, iron-rich source, and vehicular emission. The geographical location of the sources and/or preferred transport pathways was identified by conditional probability function (for local sources) and potential source contribution function (for regional sources) analyses. Medium- and small-scale metal processing (e.g. steel sheet rolling) industries in Haryana and National Capital Region (NCR) Delhi, coke and petroleum refining in Punjab, and thermal power plants in Pakistan, Punjab, and NCR Delhi were likely contributors to secondary sulfate, nitrate, and secondary chloride at the receptor site. The agricultural residue burning after harvesting season (Sept-Dec and Feb-Apr) in Punjab, and Haryana contributed to potassium at receptor site during November-December and March 2010. The soil dust from North and East Pakistan, and Rajasthan, North-East Punjab, and Haryana along with the local dust contributed to soil dust at the receptor site, during February and March 2010. A combination of temporal behavior and air parcel trajectory ensemble analyses indicated that the iron-rich source was most likely a local source attributed to emissions from metal processing facilities. Further, as expected, the vehicular emissions source did not show any seasonality and

  16. Transforming growth factor beta 1 modulates extracellular matrix organization and cell-cell junctional complex formation during in vitro angiogenesis.

    Science.gov (United States)

    Merwin, J R; Anderson, J M; Kocher, O; Van Itallie, C M; Madri, J A

    1990-01-01

    Transforming growth factor-beta 1 (TGF-beta 1) is angiogenic in vivo. In two-dimensional (2-D) culture systems microvascular endothelial cell proliferation is inhibited up to 80% by TGF-beta 1; however, in three-dimensional (3-D) collagen gels TGF-beta 1 is found to have no effect on proliferation while eliciting the formation of calcium and magnesium dependent tube-like structures mimicking angiogenesis. DNA analyses performed on 3-D cell cultures reveal no significant difference in the amount of DNA or cell number in control versus TGF-beta 1 treated cultures. In 2-D cultures TGF-beta 1 is known to increase cellular fibronectin accumulation; however, in 3-D cultures no difference is seen between control and TGF-beta 1 treated cells as established by ELISA testing for type IV collagen, fibronectin, and laminin. In 3-D cultures there is increased synthesis and secretion of type V collagen in both control and TGF-beta 1 treated cultures over 2-D cultures. Even though an equal amount of type V collagen is seen in both 3-D conditions, there is a reorganization of the protein with concentration along an organizing basal lamina in TGF-beta 1 treated cultures. EM morphological analyses on 3-D cultures illustrate quiescent, control cells lacking cell contacts. In contrast, TGF-beta 1 treated cells show increased pseudopod formation, cell-cell contact, and organized basal lamina-like material closely apposed to the "abluminal" plasma membranes. TGF-beta 1 treated cells also appear to form junctional complexes between adjoining cells. Immunofluorescence using specific antibodies to the tight junction protein ZO-1 results in staining at apparent cell-cell junctions in the 3-D cultures. Northern blots of freshly isolated microvascular endothelium, 2-D and 3-D cultures, using cDNA and cRNA probes specific for the ZO-1 tight junction protein, reveal the presence of the 7.8 kb mRNA. Western blots of rat epididymal fat pad endothelial cells (RFC) monolayer lysates probed with

  17. COMPARISON OF SEVERITY AFFECTING FACTORS BETWEEN YOUNG AND OLDER DRIVERS INVOLVED IN SINGLE VEHICLE CRASHES

    Directory of Open Access Journals (Sweden)

    Sunanda DISSANAYAKE, Ph.D., P.E.

    2004-01-01

    Full Text Available Single vehicle crashes contribute to a significant amount of fatalities in the United States. At the same time, fatality crash involvement rates of young and older drivers are well above the average and both groups are identified as critical groups when it comes to highway safety. Therefore, the study described in this paper developed separate models to predict crash severity of single vehicle crashes by young and older drivers. By using the models, factors affecting towards increased crash severity were identified for each group and comparisons were made. Almost all the common identified factors influenced both driver groups in the same manner except in the case of alcohol and drug usage, which indicated an interesting finding in the case of crash severity of older drivers. Speeding and non-usage of a restraint device were the two most important factors affecting towards increased crash severity for both driver groups at all severity levels. Additionally, ejection and existence of curve/grade were determinants of higher young driver crash severity at all levels. For older drivers, having a frontal impact point was a severity determinant at all levels. County of residence and weather condition were not effective in making any changes with respect to crash severity at any level, while some other factors had a minimal affect. Findings of this study are beneficial in investigating the potential ways of reducing crash severity, which could also be influential in reducing the occurrence of crashes as well.

  18. Matrix metalloproteinase 9 (MMP-9) mediated release of MMP-9 resistant stromal cell-derived factor 1α (SDF-1α) from surface modified polymer films.

    Science.gov (United States)

    Steinhagen, Max; Hoffmeister, Peter-Georg; Nordsieck, Karoline; Hötzel, Rudi; Baumann, Lars; Hacker, Michael C; Schulz-Siegmund, Michaela; Beck-Sickinger, Annette G

    2014-04-23

    Preparation of smart materials by coatings of established surfaces with biomolecules will lead to the next generation of functionalized biomaterials. Rejection of implants is still a major problem in medical applications but masking the implant material with protein coatings is a promising approach. These layers not only disguise the material but also equip it with a certain biological function. The anti-inflammatory chemokine stromal cell-derived factor 1α (SDF-1α) is well suited to take over this function, because it efficiently attracts stem cells and promotes their differentiation and proliferation. At least the initial stem cell homing requires the formation of a concentration gradient. Thus, a reliable and robust release mechanism of SDF-1α from the material is essential. Several proteases, most notably matrix metalloproteinases, are upregulated during inflammation, which, in principle, can be exploited for a tightly controlled release of SDF-1α. Herein, we present the covalent immobilization of M-[S4V]-SDF-1α on novel biodegradable polymer films, which consist of heterobifunctional poly(ethylene glycol) and oligolactide-based functionalized macromers. A peptidic linker with a trimeric matrix metalloproteinase 9 (MMP-9) cleavage site (MCS) was used as connection and the linkage between the three components was achieved by combination of expressed protein ligation and Cu(I) catalyzed azide/alkyne cycloaddition. The MCS was used for MMP-9 mediated release of M-[S4V]-SDF-1α from the biomaterial and the released SDF-1α derivative was biologically active and induced strong cell migration, which demonstrates the great potential of this system.

  19. Comparison of risk factors of CHD in the men and women with MI.

    Science.gov (United States)

    Ilali, E; Taraghi, Z

    2010-04-01

    The purpose of this study is comparison of risk factors of MI in hospitalized men and women patients in CCU. The CHD is the most important cause of mortality in the industry countries. Different environmental and race in each location can affect on frequency of risk factors of MI. In this cross sectional study, comparison was done between men and women who have involved in MI. The random sampling method was used Blood sugar, cholesterol and homocystein, LPa, BMI, family history, skin color, smoking and the amount of activity were assessed with variables such as age. The data was collected via questionnaire from September until March 2004-2005. Finally the data were analyzed with using t-test, Chi square and pearson correlation. In this research 169 patients who involved in MI (114 men and 55 women) have participated. The mean of age in the men was 55.4 and in the women was 61.02. All patients had risk factors. In the men, smoking (52.6%) and family history (41.1%) were the most common risk factors of MI. In the women, hyperlipidemia (66.4%), diabetes (62%) and hypertension (58.2%) were the most common risk factors of MI. The mean of BMI in the men was 25.9 +/- 4.25 and in the women was 27.6 +/- 4.71. The mean of LPa in the men was 59.2 +/- 4.21 and in the women was 50.9 +/- 4.25. the mean of homocystein in the men was 10.7 +/- 7.67 and in the women was 8.9 +/- 14.45. Diabetes, hyperlipidemia, hypertension and smoking had significant relationship with age and sex (p homocystein, LPa, job, personality type and mobility didn't have significant relationship with age and sex. In this study the most common risk factors of MI in the men were smoking and positive family history and in the women were known hyperlipidemia and diabetes.

  20. Apoptosis Signal-Regulating Kinase 1 Is Involved in Brain-Derived Neurotrophic Factor (BDNF)-Enhanced Cell Motility and Matrix Metalloproteinase 1 Expression in Human Chondrosarcoma Cells

    Science.gov (United States)

    Lin, Chih-Yang; Chang, Sunny Li-Yun; Fong, Yi-Chin; Hsu, Chin-Jung; Tang, Chih-Hsin

    2013-01-01

    Chondrosarcoma is the primary malignancy of bone that is characterized by a potent capacity to invade locally and cause distant metastasis, and is therefore associated with poor prognoses. Chondrosarcoma further shows a predilection for metastasis to the lungs. The brain-derived neurotrophic factor (BDNF) is a small molecule in the neurotrophin family of growth factors that is associated with the disease status and outcome of cancers. However, the effect of BDNF on cell motility in human chondrosarcoma cells is mostly unknown. Here, we found that human chondrosarcoma cell lines had significantly higher cell motility and BDNF expression compared to normal chondrocytes. We also found that BDNF increased cell motility and expression of matrix metalloproteinase-1 (MMP-1) in human chondrosarcoma cells. BDNF-mediated cell motility and MMP-1 up-regulation were attenuated by Trk inhibitor (K252a), ASK1 inhibitor (thioredoxin), JNK inhibitor (SP600125), and p38 inhibitor (SB203580). Furthermore, BDNF also promoted Sp1 activation. Our results indicate that BDNF enhances the migration and invasion activity of chondrosarcoma cells by increasing MMP-1 expression through a signal transduction pathway that involves the TrkB receptor, ASK1, JNK/p38, and Sp1. BDNF thus represents a promising new target for treating chondrosarcoma metastasis. PMID:23892595

  1. Application of the positive matrix factorization approach to identify heavy metal sources in sediments. A case study on the Mexican Pacific Coast.

    Science.gov (United States)

    González-Macías, C; Sánchez-Reyna, G; Salazar-Coria, L; Schifter, I

    2014-01-01

    During the last two decades, sediments collected in different sources of water bodies of the Tehuantepec Basin, located in the southeast of the Mexican Pacific Coast, showed that concentrations of heavy metals may pose a risk to the environment and human health. The extractable organic matter, geoaccumulation index, and enrichment factors were quantified for arsenic, cadmium, copper, chromium, nickel, lead, vanadium, zinc, and the fine-grained sediment fraction. The non-parametric SiZer method was applied to assess the statistical significance of the reconstructed metal variation along time. This inference method appears to be particularly natural and well suited to temperature and other environmental reconstructions. In this approach, a collection of smooth of the reconstructed metal concentrations is considered simultaneously, and inferences about the significance of the metal trends can be made with respect to time. Hence, the database represents a consolidated set of available and validated water and sediment data of an urban industrialized area, which is very useful as case study site. The positive matrix factorization approach was used in identification and source apportionment of the anthropogenic heavy metals in the sediments. Regionally, metals and organic matter are depleted relative to crustal abundance in a range of 45-55 %, while there is an inorganic enrichment from lithogenous/anthropogenic sources of around 40 %. Only extractable organic matter, Pb, As, and Cd can be related with non-crustal sources, suggesting that additional input cannot be explained by local runoff or erosion processes.

  2. Buddleja officinalis suppresses high glucose-induced vascular smooth muscle cell proliferation: role of mitogen-activated protein kinases, nuclear factor-kappaB and matrix metalloproteinases.

    Science.gov (United States)

    Lee, Yun Jung; Kim, Jin Sook; Kang, Dae Gill; Lee, Ho Sub

    2010-02-01

    Diabetes mellitus is a well-established risk factor for vascular diseases caused by atherosclerosis. In the development of diabetic atherogenesis, vascular smooth muscle cell proliferation is recognized as a key event. Thus, we aimed to investigate whether an ethanol extract of Buddleja officinalis (EBO) suppresses high glucose-induced proliferation in primary cultured human aortic smooth muscle cells (HASMC). [(3)H]-thymidine incorporation revealed that incubation of HASMC with a high concentration of glucose (25 mmol/L) increased cell proliferation. The expression levels of cell cycle protein were also increased by treatment with high glucose concentration. Pretreatment of HASMC with EBO significantly attenuated the increase of high glucose-induced cell proliferation as well as p38 mitogen-activated protein kinases (MAPK) and JNK phosphorylation. EBO suppressed high glucose-induced matrix metalloproteinase (MMP)-9 activity in a dose-dependent manner. In addition, EBO suppressed nuclear factor-kappaB (NF-kappaB) nuclear translocation and transcriptional activity in high glucose conditions. Taken together, the present data suggest that EBO could suppress high glucose-induced atherosclerotic processes through inhibition of p38, JNK, NF-kappaB and MMP signal pathways in HASMC.

  3. Fisetin Ameliorated Photodamage by Suppressing the Mitogen-Activated Protein Kinase/Matrix Metalloproteinase Pathway and Nuclear Factor-κB Pathways.

    Science.gov (United States)

    Chiang, Hsiu-Mei; Chan, Shih-Yun; Chu, Yin; Wen, Kuo-Ching

    2015-05-13

    Ultraviolet (UV) irradiation is one of the most important extrinsic factors contributing to skin photodamage. After UV irradiation, a series of signal transductions in the skin will be activated, leading to inflammatory response and photoaged skin. In this study, fisetin, a flavonol that exists in fruits and vegetables, was investigated for its photoprotective effects. The results revealed that 5-25 μM fisetin inhibits cyclooxygenase-2 (COX-2) and matrix metalloproteinase (MMP)-1, MMP-3, MMP-9 expression induced by ultraviolet B (UVB) irradiation in human skin fibroblasts. In addition, fisetin suppressed UVB-induced collagen degradation. With regard to its effect on upper-stream signal transduction, we found that fisetin reduced the expression of ultraviolet (UV)-induced ERK, JNK, and p38 phosphorylation in the mitogen-activated protein kinase (MAP kinase) pathway. Furthermore, fisetin reduced inhibitor κB (IκB) degradation and increased the amount of p65, which is a major subunit of nuclear factor-κB (NF-κB), in cytoplasm. It also suppressed NF-κB translocated to the nucleus and inhibited cAMP response element-binding protein (CREB) Ser-133 phosphorylation level in the phosphoinositide 3-kinase/protein kinase B/CREB (PI3K/AKT/CREB) pathway. Finally, fisetin inhibited UV-induced intracellular reactive oxygen species (ROS), prostaglandin E2 (PGE2), and nitric oxide (NO) generation. The mentioned effects and mechanisms suggest that fisetin can be used in the development of photoprotective agents.

  4. Exploiting Data Sparsity for Large-Scale Matrix Computations

    KAUST Repository

    Akbudak, Kadir; Ltaief, Hatem; Mikhalev, Aleksandr; Charara, Ali; Keyes, David E.

    2018-01-01

    Exploiting data sparsity in dense matrices is an algorithmic bridge between architectures that are increasingly memory-austere on a per-core basis and extreme-scale applications. The Hierarchical matrix Computations on Manycore Architectures (HiCMA) library tackles this challenging problem by achieving significant reductions in time to solution and memory footprint, while preserving a specified accuracy requirement of the application. HiCMA provides a high-performance implementation on distributed-memory systems of one of the most widely used matrix factorization in large-scale scientific applications, i.e., the Cholesky factorization. It employs the tile low-rank data format to compress the dense data-sparse off-diagonal tiles of the matrix. It then decomposes the matrix computations into interdependent tasks and relies on the dynamic runtime system StarPU for asynchronous out-of-order scheduling, while allowing high user-productivity. Performance comparisons and memory footprint on matrix dimensions up to eleven million show a performance gain and memory saving of more than an order of magnitude for both metrics on thousands of cores, against state-of-the-art open-source and vendor optimized numerical libraries. This represents an important milestone in enabling large-scale matrix computations toward solving big data problems in geospatial statistics for climate/weather forecasting applications.

  5. Exploiting Data Sparsity for Large-Scale Matrix Computations

    KAUST Repository

    Akbudak, Kadir

    2018-02-24

    Exploiting data sparsity in dense matrices is an algorithmic bridge between architectures that are increasingly memory-austere on a per-core basis and extreme-scale applications. The Hierarchical matrix Computations on Manycore Architectures (HiCMA) library tackles this challenging problem by achieving significant reductions in time to solution and memory footprint, while preserving a specified accuracy requirement of the application. HiCMA provides a high-performance implementation on distributed-memory systems of one of the most widely used matrix factorization in large-scale scientific applications, i.e., the Cholesky factorization. It employs the tile low-rank data format to compress the dense data-sparse off-diagonal tiles of the matrix. It then decomposes the matrix computations into interdependent tasks and relies on the dynamic runtime system StarPU for asynchronous out-of-order scheduling, while allowing high user-productivity. Performance comparisons and memory footprint on matrix dimensions up to eleven million show a performance gain and memory saving of more than an order of magnitude for both metrics on thousands of cores, against state-of-the-art open-source and vendor optimized numerical libraries. This represents an important milestone in enabling large-scale matrix computations toward solving big data problems in geospatial statistics for climate/weather forecasting applications.

  6. Matrix inequalities

    CERN Document Server

    Zhan, Xingzhi

    2002-01-01

    The main purpose of this monograph is to report on recent developments in the field of matrix inequalities, with emphasis on useful techniques and ingenious ideas. Among other results this book contains the affirmative solutions of eight conjectures. Many theorems unify or sharpen previous inequalities. The author's aim is to streamline the ideas in the literature. The book can be read by research workers, graduate students and advanced undergraduates.

  7. Gully erosion: A comparison of contributing factors in two catchments in South Africa

    Science.gov (United States)

    Mararakanye, Ndifelani; Sumner, Paul D.

    2017-07-01

    Gully erosion is an environmental, agricultural and social problem requiring extensive research and mitigation actions to control. This study assesses the influence of factors contributing to gully erosion using Geographic Information System (GIS) and Information Value (InfVal) statistics from two catchments coded X12 and W55 in the Mpumalanga province of South Africa. Existing spatial data representing contributing factors; soil, geology, vegetation and land use were analyzed. Topographic variables were extracted from a 10 m Digital Elevation Model (DEM) interpolated from map contours, and gullies were mapped from aerial photos with 0.5 m spatial resolution. A zonal approach was used to extract the proportion of gullies in each of the contributing factor classes using GIS software packages, and InfVal weighting was performed to determine the influence of each class. Comparison of the results shows the variation in the level of influence of factors contributing to gully erosion. The findings in catchment X12 support a commonly held assumption that gully formation is influenced by duplex soils underlain by colluvium and alluvial deposits on a lower slope position where overland flow converges and accumulates, resulting in high soil moisture. Gullies were also influenced by soils developed over weathered granite, gneiss and ultramafic rocks. The influence of a granite rock was further highlighted in catchment W55 where there is a variable thickness of very deep Hutton dominant soil form and shallow Lithosols with sandy texture, on an area of moderate to steep slopes where overland flow converges and accumulates, with high stream power in overgrazed grassland. An understanding of these factors will assist future modelling of the vulnerability to gully erosion over a wider geographical area.

  8. Source apportionment of organic compounds in Berlin using positive matrix factorization - assessing the impact of biogenic aerosol and biomass burning on urban particulate matter.

    Science.gov (United States)

    Wagener, Sandra; Langner, Marcel; Hansen, Ute; Moriske, Heinz-Jörn; Endlicher, Wilfried R

    2012-10-01

    Source apportionment of 13 organic compounds, elemental carbon and organic carbon of ambient PM(10) and PM(1) was performed with positive matrix factorization (PMF). Samples were collected at three sites characterized by different vegetation influences in Berlin, Germany in 2010. The aim was to determine organic, mainly biogenic sources and their impact on urban aerosol collected in a densely populated region. A 6-factor solution provided the best data fit for both PM-fractions, allowing the sources isoprene- and α-pinene-derived secondary organic aerosol (SOA), bio primary, primarily attributable to fungal spores, bio/urban primary including plant fragments in PM(10) and cooking and traffic emissions in PM(1), biomass burning and combustion fossil to be identified. With mean concentrations up to 2.6 μg Cm(-3), biomass burning dominated the organic fraction in cooler months. Concentrations for α-pinene-derived SOA exceeded isoprene-derived concentrations. Estimated secondary organic carbon contributions to total organic carbon (OC) were between 7% and 42% in PM(10) and between 11% and 60% in PM(1), which is slightly lower than observed for US- or Asian cities. Primary biogenic emissions reached up to 33% of OC in the PM(10)-fraction in the late summer and autumn months. Temperature-dependence was found for both SOA-factors, correlations with ozone and mix depth only for the α-pinene-derived SOA-factor. Latter indicated input of α-pinene from the borders, highlighting differences in the origin of the precursors of both factors. Most factors were regionally distributed. High regional distribution was found to be associated with stronger influence of ambient parameters and higher concentrations at the background station. A significant contribution of biogenic emissions and biomass burning to urban organic aerosol could be stated. This indicates a considerable impact on PM concentrations also in cities in a densely populated area, and should draw the attention

  9. Factors of Public Procurement: Evaluation of an Influence into the International Comparison

    Directory of Open Access Journals (Sweden)

    Melnikov Vladimir, V.

    2016-07-01

    Full Text Available There was a tendency to expand the using of state regulation tools and increasing the scale of the public sector of economy In XX century. Statistically, it is characterized by increasing of indicators of public expenditures and procurement of products for public use. The amazing thing is that countries which are different from each other in terms of the formed institutional environment, reflect the same trends of maintaining the scale of public purchases market. Analysis of the factors influencing on purchases for public use, allows to identify the causes of the government’s interests in expanding of government intervention in the economy and the use of this tool in the development of economic policy. In the paper reviewed the impact of a number of institutional and technological factors such as The Corruption Perceptions Index, government debt, the percentage of water surface area, Gini coefficient, unemployment and Ease of Doing Business Index on public purchases. Assessment of the impact of these factors was carried out on the volume of public purchases in the framework of an international comparison of procurement practices. Justification of the results was suggested in terms of the existing approaches to macroeconomic policy.

  10. M2 macrophages induce ovarian cancer cell proliferation via a heparin binding epidermal growth factor/matrix metalloproteinase 9 intercellular feedback loop.

    Science.gov (United States)

    Carroll, Molly J; Kapur, Arvinder; Felder, Mildred; Patankar, Manish S; Kreeger, Pamela K

    2016-12-27

    In ovarian cancer, a high ratio of anti-inflammatory M2 to pro-inflammatory M1 macrophages correlates with poor patient prognosis. The mechanisms driving poor tumor outcome as a result of the presence of M2 macrophages in the tumor microenvironment remain unclear and are challenging to study with current techniques. Therefore, in this study we utilized a micro-culture device previously developed by our lab to model concentrated paracrine signaling in order to address our hypothesis that interactions between M2 macrophages and ovarian cancer cells induce tumor cell proliferation. Using the micro-culture device, we determined that co-culture with M2-differentiated primary macrophages or THP-1 increased OVCA433 proliferation by 10-12%. This effect was eliminated with epidermal growth factor receptor (EGFR) or heparin-bound epidermal growth factor (HB-EGF) neutralizing antibodies and HBEGF expression in peripheral blood mononuclear cells from ovarian cancer patients was 9-fold higher than healthy individuals, suggesting a role for HB-EGF in tumor progression. However, addition of HB-EGF at levels secreted by macrophages or macrophage-conditioned media did not induce proliferation to the same extent, indicating a role for other factors in this process. Matrix metalloproteinase-9, MMP-9, which cleaves membrane-bound HB-EGF, was elevated in co-culture and its inhibition decreased proliferation. Utilizing inhibitors and siRNA against MMP9 in each population, we determined that macrophage-secreted MMP-9 released HB-EGF from macrophages, which increased MMP9 in OVCA433, resulting in a positive feedback loop to drive HB-EGF release and increase proliferation in co-culture. Identification of multi-cellular interactions such as this may provide insight into how to most effectively control ovarian cancer progression.

  11. Efficacy comparison of Accell Evo3 and Grafton demineralized bone matrix putties against autologous bone in a rat posterolateral spine fusion model.

    Science.gov (United States)

    Brecevich, Antonio T; Kiely, Paul D; Yoon, B Victor; Nguyen, Joseph T; Cammisa, Frank P; Abjornson, Celeste

    2017-06-01

    Spinal fusion procedures are intended to stabilize the spinal column for a multitude of disorders including abnormal curvature, traumatic instability, degenerative instability, and damage from infections or tumors. As an aid in the bone healing response, bone graft materials are used to bridge joints for arthrodesis and promote unions in pseudoarthrosis. Currently, the gold standard for stabilizing fusion masses in spinal procedures involves using the osteogenic, osteoinductive, and osteoconductive properties of autologous iliac crest corticocancellous bone. However, considerable morbidity is associated with harvesting the autologous graft. Donor site complications including infection, large hematomas, and pain have been reported at rates as high as 50% (Boden and Jeffrey, 1995). Biologically, the rate of bone repair dictates the rate at which the fusion mass will unite under autologous graft conditions. The purpose of this study is to compare the quality and rate of fusion between Accell Evo3 and Grafton demineralized bone matrix (DBM), with the gold standard iliac crest bone graft (ICBG) as the control, in athymic rat posterolateral fusion. This study was a randomized, controlled study in a laboratory setting at the Hospital for Special Surgery in New York City. Blinded observations were made, which created an assessment of outcomes for successful fusions between each method. Forty-eight (48) athymic rats were used in this study and underwent posterolateral lumbar fusion. They were assessed at either 3 weeks or 9 weeks to see the rate and efficacy of fusion. Outcome measures will be the efficacy of the different bone grafts and their success rates of fusion in the rats. A comparison of the quality and rate of fusion between Accell Evo3® (DBM A) and Grafton (DBM B), with the gold standard iliac crest bone graft (ICBG) as the control, was performed using the established posterolateral intertransverse process on an athymic rat model. Materials were evaluated for

  12. Migration of bone marrow and cord blood mesenchymal stem cells in vitro is regulated by stromal-derived factor-1-CXCR4 and hepatocyte growth factor-c-met axes and involves matrix metalloproteinases.

    Science.gov (United States)

    Son, Bo-Ra; Marquez-Curtis, Leah A; Kucia, Magda; Wysoczynski, Marcin; Turner, A Robert; Ratajczak, Janina; Ratajczak, Mariusz Z; Janowska-Wieczorek, Anna

    2006-05-01

    Human mesenchymal stem cells (MSCs) are increasingly being considered in cell-based therapeutic strategies for regeneration of various organs/tissues. However, the signals required for their homing and recruitment to injured sites are not yet fully understood. Because stromal-derived factor (SDF)-1 and hepatocyte growth factor (HGF) become up-regulated during tissue/organ damage, in this study we examined whether these factors chemoattract ex vivo-expanded MSCs derived from bone marrow (BM) and umbilical cord blood (CB). Specifically, we investigated the expression by MSCs of CXCR4 and c-met, the cognate receptors of SDF-1 and HGF, and their functionality after early and late passages of MSCs. We also determined whether MSCs express matrix metalloproteinases (MMPs), including membrane type 1 (MT1)-MMP, matrix-degrading enzymes that facilitate the trafficking of hematopoietic stem cells. We maintained expanded BM- or CB-derived MSCs for up to 15-18 passages with monitoring of the expression of 1) various tissue markers (cardiac and skeletal muscle, neural, liver, and endothelial cells), 2) functional CXCR4 and c-met, and 3) MMPs. We found that for up to 15-18 passages, both BM- and CB-derived MSCs 1) express mRNA for cardiac, muscle, neural, and liver markers, as well as the vascular endothelial (VE) marker VE-cadherin; 2) express CXCR4 and c-met receptors and are strongly attracted by SDF-1 and HGF gradients; 3) express MMP-2 and MT1-MMP transcripts and proteins; and 4) are chemo-invasive across the reconstituted basement membrane Matrigel. These in vitro results suggest that the SDF-1-CXCR4 and HGF-c-met axes, along with MMPs, may be involved in recruitment of expanded MSCs to damaged tissues.

  13. Trust and Product/Sellers Reviews as Factors Influencing Online Product Comparison Sites Usage by Young Consumers

    OpenAIRE

    Radoslaw Macik; Dorota Macik

    2016-01-01

    Paper describes young consumers’ behaviour connected with online product comparison sites usage as an example of online decision shopping aids. Authors’ main goal is to check whether or not such factors as: previous experience in such sites usage, personal innovativeness in domain of information technology – PIIT, and particularly cognitive trust (in several subdimensions), as well as affective trust toward online product comparison site, influence purchase intention via men...

  14. Application of positive matrix factorization to on-road measurements for source apportionment of diesel- and gasoline-powered vehicle emissions in Mexico City

    Directory of Open Access Journals (Sweden)

    D. A. Thornhill

    2010-04-01

    Full Text Available The goal of this research is to quantify diesel- and gasoline-powered motor vehicle emissions within the Mexico City Metropolitan Area (MCMA using on-road measurements captured by a mobile laboratory combined with positive matrix factorization (PMF receptor modeling. During the MCMA-2006 ground-based component of the MILAGRO field campaign, the Aerodyne Mobile Laboratory (AML measured many gaseous and particulate pollutants, including carbon dioxide, carbon monoxide (CO, nitrogen oxides (NOx, benzene, toluene, alkylated aromatics, formaldehyde, acetaldehyde, acetone, ammonia, particle number, fine particulate mass (PM2.5, and black carbon (BC. These serve as inputs to the receptor model, which is able to resolve three factors corresponding to gasoline engine exhaust, diesel engine exhaust, and the urban background. Using the source profiles, we calculate fuel-based emission factors for each type of exhaust. The MCMA's gasoline-powered vehicles are considerably dirtier, on average, than those in the US with respect to CO and aldehydes. Its diesel-powered vehicles have similar emission factors of NOx and higher emission factors of aldehydes, particle number, and BC. In the fleet sampled during AML driving, gasoline-powered vehicles are found to be responsible for 97% of total vehicular emissions of CO, 22% of NOx, 95–97% of each aromatic species, 72–85% of each carbonyl species, 74% of ammonia, negligible amounts of particle number, 26% of PM2.5, and 2% of BC; diesel-powered vehicles account for the balance. Because the mobile lab spent 17% of its time waiting at stoplights, the results may overemphasize idling conditions, possibly resulting in an underestimate of NOx and overestimate of CO emissions. On the other hand, estimates of the inventory that do not correctly account for emissions during idling are likely to produce bias in the opposite direction.The resulting fuel

  15. Involvement of matrix metalloproteinases and their inhibitors in peripheral synovitis and down-regulation by tumor necrosis factor alpha blockade in spondylarthropathy

    NARCIS (Netherlands)

    Vandooren, Bernard; Kruithof, Elli; Yu, David T. Y.; Rihl, Markus; Gu, Jieruo; de Rycke, Leen; van den Bosch, Filip; Veys, Eric M.; de Keyser, Filip; Baeten, Dominique

    2004-01-01

    OBJECTIVE: To investigate the role of matrix metalloproteinases (MMPs) and tissue inhibitors of matrix metalloproteinases (TIMPs) in spondylarthropathy (SpA) synovitis. METHODS: Paired samples of synovial biopsy tissue as well as serum and synovial fluid (SF) from 41 patients with SpA and 20

  16. Analytic matrix elements with shifted correlated Gaussians

    DEFF Research Database (Denmark)

    Fedorov, D. V.

    2017-01-01

    Matrix elements between shifted correlated Gaussians of various potentials with several form-factors are calculated analytically. Analytic matrix elements are of importance for the correlated Gaussian method in quantum few-body physics.......Matrix elements between shifted correlated Gaussians of various potentials with several form-factors are calculated analytically. Analytic matrix elements are of importance for the correlated Gaussian method in quantum few-body physics....

  17. Seasonal characterization of CDOM for lakes in semiarid regions of Northeast China using excitation-emission matrix fluorescence and parallel factor analysis (EEM-PARAFAC)

    Science.gov (United States)

    Zhao, Ying; Song, Kaishan; Wen, Zhidan; Li, Lin; Zang, Shuying; Shao, Tiantian; Li, Sijia; Du, Jia

    2016-03-01

    The seasonal characteristics of fluorescent components in chromophoric dissolved organic matter (CDOM) for lakes in the semiarid region of Northeast China were examined by excitation-emission matrix (EEM) spectra and parallel factor analysis (PARAFAC). Two humic-like (C1 and C2) and protein-like (C3 and C4) components were identified using PARAFAC. The average fluorescence intensity of the four components differed under seasonal variation from June and August 2013 to February and April 2014. Components 1 and 2 exhibited a strong linear correlation (R2 = 0.628). Significantly positive linear relationships between CDOM absorption coefficients a(254) (R2 = 0.72, 0.46, p DOC). However, almost no obvious correlation was found between salinity and EEM-PARAFAC-extracted components except for C3 (R2 = 0.469). Results from this investigation demonstrate that the EEM-PARAFAC technique can be used to evaluate the seasonal dynamics of CDOM fluorescent components for inland waters in the semiarid regions of Northeast China, and to quantify CDOM components for other waters with similar environmental conditions.

  18. Genetic polymorphism in matrix metalloproteinase-9 and transforming growth factor-β1 and susceptibility to combined pulmonary fibrosis and emphysema in a Chinese population.

    Science.gov (United States)

    Xu, Ling; Bian, Wei; Gu, Xiao-Hua; Shen, Ce

    2017-03-01

    In this study, we aimed to explore the association of genetic polymorphism in matrix metalloproteinase-9 (MMP-9) and transforming growth factor-β1 (TGF-β1) and the susceptibility to combined pulmonary fibrosis and emphysema (CPFE). We examined the polymorphisms of the MMP-9 C-1562T and TGF-β1 T869C in 38 CPFE patients, 50 pulmonary emphysema patients, and 34 idiopathic pulmonary fibrosis (IPF) patients. The frequencies of polymorphic genotypes in MMP-9 were 78.95% CC and 21.05% CT in CPFE group, 76.0% CC and 24.0% CT in emphysema group, and 100.0% CC in IPF group. There were highly statistically significant increased frequencies of the CT genotype and T allele in CPFE and emphysema groups compared with IPF group (p emphysema group, and 5.88% CC, 41.18% CT, 52.94% TT in IPF group. Significant increases in the TT genotype and T allele frequencies were observed in emphysema group compared with IPF group (p pulmonary emphysema. The T allele in MMP-9 (C-1562T) possibly predisposes patients with pulmonary fibrosis to develop emphysema. Copyright © 2017. Published by Elsevier Taiwan.

  19. Plasma levels of mature brain-derived neurotrophic factor (BDNF) and matrix metalloproteinase-9 (MMP-9) in treatment-resistant schizophrenia treated with clozapine.

    Science.gov (United States)

    Yamamori, Hidenaga; Hashimoto, Ryota; Ishima, Tamaki; Kishi, Fukuko; Yasuda, Yuka; Ohi, Kazutaka; Fujimoto, Michiko; Umeda-Yano, Satomi; Ito, Akira; Hashimoto, Kenji; Takeda, Masatoshi

    2013-11-27

    Brain-derived neurotrophic factor (BDNF) regulates the survival and growth of neurons, and influences synaptic efficiency and plasticity. Peripheral BDNF levels in patients with schizophrenia have been widely reported in the literature. However, it is still controversial whether peripheral levels of BDNF are altered in patients with schizophrenia. The peripheral BDNF levels previously reported in patients with schizophrenia were total BDNF (proBDNF and mature BDNF) as it was unable to specifically measure mature BDNF due to limited BDNF antibody specificity. In this study, we examined whether peripheral levels of mature BDNF were altered in patients with treatment-resistant schizophrenia. Matrix metalloproteinase-9 (MMP-9) levels were also measured, as MMP-9 plays a role in the conversion of proBDNF to mature BDNF. Twenty-two patients with treatment-resistant schizophrenia treated with clozapine and 22 age- and sex-matched healthy controls were enrolled. The plasma levels of mature BDNF and MMP-9 were measured using ELISA kits. No significant difference was observed for mature BDNF however, MMP-9 was significantly increased in patients with schizophrenia. The significant correlation was observed between mature BDNF and MMP-9 plasma levels. Neither mature BDNF nor MMP-9 plasma levels were associated clinical variables. Our results do not support the view that peripheral BDNF levels are associated with schizophrenia. MMP-9 may play a role in the pathophysiology of schizophrenia and serve as a biomarker for schizophrenia. Copyright © 2013 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

  20. The Effector Protein BPE005 from Brucella abortus Induces Collagen Deposition and Matrix Metalloproteinase 9 Downmodulation via Transforming Growth Factor β1 in Hepatic Stellate Cells.

    Science.gov (United States)

    Arriola Benitez, Paula Constanza; Rey Serantes, Diego; Herrmann, Claudia Karina; Pesce Viglietti, Ayelén Ivana; Vanzulli, Silvia; Giambartolomei, Guillermo Hernán; Comerci, Diego José; Delpino, María Victoria

    2016-02-01

    The liver is frequently affected in patients with active brucellosis. In the present study, we identified a virulence factor involved in the modulation of hepatic stellate cell function and consequent fibrosis during Brucella abortus infection. This study assessed the role of BPE005 protein from B. abortus in the fibrotic phenotype induced on hepatic stellate cells during B. abortus infection in vitro and in vivo. We demonstrated that the fibrotic phenotype induced by B. abortus on hepatic stellate (LX-2) cells was dependent on BPE005, a protein associated with the type IV secretion system (T4SS) VirB from B. abortus. Our results indicated that B. abortus inhibits matrix metalloproteinase 9 (MMP-9) secretion through the activity of the BPE005-secreted protein and induces concomitant collagen deposition by LX-2 cells. BPE005 is a small protein containing a cyclic nucleotide monophosphate binding domain (cNMP) that modulates the LX-2 cell phenotype through a mechanism that is dependent on the cyclic AMP (cAMP)/protein kinase A (PKA) signaling pathway. Altogether, these results indicate that B. abortus tilts LX-2 cells to a profibrogenic phenotype employing a functional T4SS and the secreted BPE005 protein through a mechanism that involves the cAMP and PKA signaling pathway. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  1. Detection of Copper (II) and Cadmium (II) binding to dissolved organic matter from macrophyte decomposition by fluorescence excitation-emission matrix spectra combined with parallel factor analysis

    International Nuclear Information System (INIS)

    Yuan, Dong-hai; Guo, Xu-jing; Wen, Li; He, Lian-sheng; Wang, Jing-gang; Li, Jun-qi

    2015-01-01

    Fluorescence excitation-emission matrix (EEM) spectra coupled with parallel factor analysis (PARAFAC) was used to characterize dissolved organic matter (DOM) derived from macrophyte decomposition, and to study its complexation with Cu (II) and Cd (II). Both the protein-like and the humic-like components showed a marked quenching effect by Cu (II). Negligible quenching effects were found for Cd (II) by components 1, 5 and 6. The stability constants and the fraction of the binding fluorophores for humic-like components and Cu (II) can be influenced by macrophyte decomposition of various weight gradients in aquatic plants. Macrophyte decomposition within the scope of the appropriate aquatic phytomass can maximize the stability constant of DOM-metal complexes. A large amount of organic matter was introduced into the aquatic environment by macrophyte decomposition, suggesting that the potential risk of DOM as a carrier of heavy metal contamination in macrophytic lakes should not be ignored. - Highlights: • Macrophyte decomposition increases fluorescent DOM components in the upper sediment. • Protein-like components are quenched or enhanced by adding Cu (II) and Cd (II). • Macrophyte decomposition DOM can impact the affinity of Cu (II) and Cd (II). • The log K M and f values showed a marked change due to macrophyte decomposition. • Macrophyte decomposition can maximize the stability constant of DOM-Cu (II) complexes. - Macrophyte decomposition DOM can influence on the binding affinity of metal ions in macrophytic lakes

  2. Heterogeneous adsorption behavior of landfill leachate on granular activated carbon revealed by fluorescence excitation emission matrix (EEM)-parallel factor analysis (PARAFAC).

    Science.gov (United States)

    Lee, Sonmin; Hur, Jin

    2016-04-01

    Heterogeneous adsorption behavior of landfill leachate on granular activated carbon (GAC) was investigated by fluorescence excitation-emission matrix (EEM) combined with parallel factor analysis (PARAFAC). The equilibrium adsorption of two leachates on GAC was well described by simple Langmuir and Freundlich isotherm models. More nonlinear isotherm and a slower adsorption rate were found for the leachate with the higher values of specific UV absorbance and humification index, suggesting that the leachate containing more aromatic content and condensed structures might have less accessible sites of GAC surface and a lower degree of diffusive adsorption. Such differences in the adsorption behavior were found even within the bulk leachate as revealed by the dissimilarity in the isotherm and kinetic model parameters between two identified PARAFAC components. For both leachates, terrestrial humic-like fluorescence (C1) component, which is likely associated with relatively large sized and condensed aromatic structures, exhibited a higher isotherm nonlinearity and a slower kinetic rate for GAC adsorption than microbial humic-like (C2) component. Our results were consistent with size exclusion effects, a well-known GAC adsorption mechanism. This study demonstrated the promising benefit of using EEM-PARAFAC for GAC adsorption processes of landfill leachate through fast monitoring of the influent and treated leachate, which can provide valuable information on optimizing treatment processes and predicting further environmental impacts of the treated effluent. Copyright © 2016 Elsevier Ltd. All rights reserved.

  3. Characterization of CDOM from urban waters in Northern-Northeastern China using excitation-emission matrix fluorescence and parallel factor analysis.

    Science.gov (United States)

    Zhao, Ying; Song, Kaishan; Li, Sijia; Ma, Jianhang; Wen, Zhidan

    2016-08-01

    Chromophoric dissolved organic matter (CDOM) plays an important role in aquatic systems, but high concentrations of organic materials are considered pollutants. The fluorescent component characteristics of CDOM in urban waters sampled from Northern and Northeastern China were examined by excitation-emission matrix fluorescence and parallel factor analysis (EEM-PARAFAC) to investigate the source and compositional changes of CDOM on both space and pollution levels. One humic-like (C1), one tryptophan-like component (C2), and one tyrosine-like component (C3) were identified by PARAFAC. Mean fluorescence intensities of the three CDOM components varied spatially and by pollution level in cities of Northern and Northeastern China during July-August, 2013 and 2014. Principal components analysis (PCA) was conducted to identify the relative distribution of all water samples. Cluster analysis (CA) was also used to categorize the samples into groups of similar pollution levels within a study area. Strong positive linear relationships were revealed between the CDOM absorption coefficients a(254) (R (2) = 0.89, p CDOM components can be applied to monitor water quality in real time compared to that of traditional approaches. These results demonstrate that EEM-PARAFAC is useful to evaluate the dynamics of CDOM fluorescent components in urban waters from Northern and Northeastern China and this method has potential applications for monitoring urban water quality in different regions with various hydrological conditions and pollution levels.

  4. Extracellular Matrix (ECM) Multilayer Membrane as a Sustained Releasing Growth Factor Delivery System for rhTGF-β3 in Articular Cartilage Repair

    Science.gov (United States)

    Park, Sang-Hyug; Kim, Moon Suk; Kim, Young Jick; Choi, Byung Hyune; Lee, Chun Tek; Park, So Ra; Min, Byoung-Hyun

    2016-01-01

    Recombinant human transforming growth factor beta-3 (rhTGF-β3) is a key regulator of chondrogenesis in stem cells and cartilage formation. We have developed a novel drug delivery system that continuously releases rhTGF-β3 using a multilayered extracellular matrix (ECM) membrane. We hypothesize that the sustained release of rhTGF-β3 could activate stem cells and result in enhanced repair of cartilage defects. The properties and efficacy of the ECM multilayer-based delivery system (EMLDS) are investigated using rhTGF-β3 as a candidate drug. The bioactivity of the released rhTGF-ß3 was evaluated through chondrogenic differentiation of mesenchymal stem cells (MSCs) using western blot and circular dichroism (CD) analyses in vitro. The cartilage reparability was evaluated through implanting EMLDS with endogenous and exogenous MSC in both in vivo and ex vivo models, respectively. In the results, the sustained release of rhTGF-ß3 was clearly observed over a prolonged period of time in vitro and the released rhTGF-β3 maintained its structural stability and biological activity. Successful cartilage repair was also demonstrated when rabbit MSCs were treated with rhTGF-β3-loaded EMLDS ((+) rhTGF-β3 EMLDS) in an in vivo model and when rabbit chondrocytes and MSCs were treated in ex vivo models. Therefore, the multilayer ECM membrane could be a useful drug delivery system for cartilage repair. PMID:27258120

  5. CS5931, a Novel Polypeptide in Ciona savignyi, Represses Angiogenesis via Inhibiting Vascular Endothelial Growth Factor (VEGF and Matrix Metalloproteinases (MMPs

    Directory of Open Access Journals (Sweden)

    Ge Liu

    2014-03-01

    Full Text Available CS5931 is a novel polypeptide from Ciona savignyi with anticancer activities. Previous study in our laboratory has shown that CS5931 can induce cell death via mitochondrial apoptotic pathway. In the present study, we found that the polypeptide could inhibit angiogenesis both in vitro and in vivo. CS5931 inhibited the proliferation, migration and formation of capillary-like structures of HUVECs (Human Umbilical Vein Endothelial Cell in a dose-dependent manner. Additionally, CS5931 repressed spontaneous angiogenesis of the zebrafish vessels. Further studies showed that CS5931 also blocked vascular endothelial growth factor (VEGF production but without any effect on its mRNA expression. Moreover, CS5931 reduced the expression of matrix metalloproteinases (MMP-2 and MMP-9 both on protein and mRNA levels in HUVEC cells. We demonstrated that CS5931 possessed strong anti-angiogenic activity both in vitro and in vivo, possible via VEGF and MMPs. This study indicates that CS5931 has the potential to be developed as a novel therapeutic agent as an inhibitor of angiogenesis for the treatment of cancer.

  6. Source apportionment for indoor PM2.5 and elemental concentrations using by a positive matrix factorization and an instrumental neutron activation analysis

    International Nuclear Information System (INIS)

    Lim, Jong Myoung; Moon, Jong Hwa; Chung, Yong Sam; Jung, Byoung Won; Lee, Jin Hong

    2009-01-01

    Airborne particulate matters, especially the PM2.5 (aerodynamic equivalent diameter, AED, less than 2.5 μm) fraction has been important. This is because of their potential for deposition on to the human respiratory system being accompanied by many harmful trace metals (such as As, Cd, Cr, Cu, Mn, Pb, Se, and Zn). The indoor air quality has become a great concern since late 1980s, because the population spends a majority of their time in various indoor environments. The indoor particulate matter may be influenced from outdoor environment and indoor sources such as environmental tobacco smoke (ETS), combustion devices, cooking, etc. In this study, we undertake the measurements of about 26 elements using instrumental neutron activation analysis (INAA). Based on our measurement data, we characterize concentration status and mutual relationship between indoor and adjacent outdoor air quality. Next, sources at indoor/outdoor environment were identified and the contributions of each source were quantified by positive matrix factorization (PMF)

  7. Expression of toll-like receptor 4, tumor necrosis factor- alpha, matrix metalloproteinase-9 and effects of benazepril in patients with acute coronary syndromes.

    Science.gov (United States)

    Xie, Ping; Cao, Yun-Shan; Su, Peng; Li, Yu-Hong; Gao, Zhi-Ling; Borst, Mathias M

    2010-10-11

    The study aims to explore the relationship between expressions of toll-like receptor 4 (TLR4) on peripheral blood monocytes, serum tumor necrosis factor-alpha (TNF-α) and matrix metalloproteinase-9 (MMP-9) in patients with acute coronary syndromes(ACS), and to investigate the possible mechanisms of Benazepril stabilizing atherosclerosis plaques. 70 patients selected were randomly divided into Benazepril treatment group (35 patients) and regular treatment group (35 patients). Meanwhile, Stable angina pectoris (SAP) group of 32 patients and control group of 22 patients were also set up. With the help of flow-cytometry, expressions of TLR4 on peripheral blood monocytes of the four groups were analyzed and compared to show differences, correlations and changes of the above mentioned indicators. The concentration of TNF-α and MMP-9 in serum were measured by enzyme linked immunosorbent assay (ELISA). (1) Expressions of TLR4, levels of TNF-α and MMP-9 were increased and the rate was rising from the control group, to SAP group and then to ACS group. All these indicators in ACS group are significantly higher than those in other groups (P Benazepril treatment group and regular treatment group before treatment (P > 0.05) while they all fell after treatment (P Benazepril can inhibit over-expression of TLR4 and reduce serum levels of TNF-α and MMP-9, thus stabilize the vulnerable plaques and improve the condition of the patients with ACS.

  8. Extracellular Matrix (ECM Multilayer Membrane as a Sustained Releasing Growth Factor Delivery System for rhTGF-β3 in Articular Cartilage Repair.

    Directory of Open Access Journals (Sweden)

    Soon Sim Yang

    Full Text Available Recombinant human transforming growth factor beta-3 (rhTGF-β3 is a key regulator of chondrogenesis in stem cells and cartilage formation. We have developed a novel drug delivery system that continuously releases rhTGF-β3 using a multilayered extracellular matrix (ECM membrane. We hypothesize that the sustained release of rhTGF-β3 could activate stem cells and result in enhanced repair of cartilage defects. The properties and efficacy of the ECM multilayer-based delivery system (EMLDS are investigated using rhTGF-β3 as a candidate drug. The bioactivity of the released rhTGF-ß3 was evaluated through chondrogenic differentiation of mesenchymal stem cells (MSCs using western blot and circular dichroism (CD analyses in vitro. The cartilage reparability was evaluated through implanting EMLDS with endogenous and exogenous MSC in both in vivo and ex vivo models, respectively. In the results, the sustained release of rhTGF-ß3 was clearly observed over a prolonged period of time in vitro and the released rhTGF-β3 maintained its structural stability and biological activity. Successful cartilage repair was also demonstrated when rabbit MSCs were treated with rhTGF-β3-loaded EMLDS ((+ rhTGF-β3 EMLDS in an in vivo model and when rabbit chondrocytes and MSCs were treated in ex vivo models. Therefore, the multilayer ECM membrane could be a useful drug delivery system for cartilage repair.

  9. Inferring Aggregated Functional Traits from Metagenomic Data Using Constrained Non-negative Matrix Factorization: Application to Fiber Degradation in the Human Gut Microbiota.

    Science.gov (United States)

    Raguideau, Sébastien; Plancade, Sandra; Pons, Nicolas; Leclerc, Marion; Laroche, Béatrice

    2016-12-01

    Whole Genome Shotgun (WGS) metagenomics is increasingly used to study the structure and functions of complex microbial ecosystems, both from the taxonomic and functional point of view. Gene inventories of otherwise uncultured microbial communities make the direct functional profiling of microbial communities possible. The concept of community aggregated trait has been adapted from environmental and plant functional ecology to the framework of microbial ecology. Community aggregated traits are quantified from WGS data by computing the abundance of relevant marker genes. They can be used to study key processes at the ecosystem level and correlate environmental factors and ecosystem functions. In this paper we propose a novel model based approach to infer combinations of aggregated traits characterizing specific ecosystemic metabolic processes. We formulate a model of these Combined Aggregated Functional Traits (CAFTs) accounting for a hierarchical structure of genes, which are associated on microbial genomes, further linked at the ecosystem level by complex co-occurrences or interactions. The model is completed with constraints specifically designed to exploit available genomic information, in order to favor biologically relevant CAFTs. The CAFTs structure, as well as their intensity in the ecosystem, is obtained by solving a constrained Non-negative Matrix Factorization (NMF) problem. We developed a multicriteria selection procedure for the number of CAFTs. We illustrated our method on the modelling of ecosystemic functional traits of fiber degradation by the human gut microbiota. We used 1408 samples of gene abundances from several high-throughput sequencing projects and found that four CAFTs only were needed to represent the fiber degradation potential. This data reduction highlighted biologically consistent functional patterns while providing a high quality preservation of the original data. Our method is generic and can be applied to other metabolic processes in

  10. Inferring Aggregated Functional Traits from Metagenomic Data Using Constrained Non-negative Matrix Factorization: Application to Fiber Degradation in the Human Gut Microbiota.

    Directory of Open Access Journals (Sweden)

    Sébastien Raguideau

    2016-12-01

    Full Text Available Whole Genome Shotgun (WGS metagenomics is increasingly used to study the structure and functions of complex microbial ecosystems, both from the taxonomic and functional point of view. Gene inventories of otherwise uncultured microbial communities make the direct functional profiling of microbial communities possible. The concept of community aggregated trait has been adapted from environmental and plant functional ecology to the framework of microbial ecology. Community aggregated traits are quantified from WGS data by computing the abundance of relevant marker genes. They can be used to study key processes at the ecosystem level and correlate environmental factors and ecosystem functions. In this paper we propose a novel model based approach to infer combinations of aggregated traits characterizing specific ecosystemic metabolic processes. We formulate a model of these Combined Aggregated Functional Traits (CAFTs accounting for a hierarchical structure of genes, which are associated on microbial genomes, further linked at the ecosystem level by complex co-occurrences or interactions. The model is completed with constraints specifically designed to exploit available genomic information, in order to favor biologically relevant CAFTs. The CAFTs structure, as well as their intensity in the ecosystem, is obtained by solving a constrained Non-negative Matrix Factorization (NMF problem. We developed a multicriteria selection procedure for the number of CAFTs. We illustrated our method on the modelling of ecosystemic functional traits of fiber degradation by the human gut microbiota. We used 1408 samples of gene abundances from several high-throughput sequencing projects and found that four CAFTs only were needed to represent the fiber degradation potential. This data reduction highlighted biologically consistent functional patterns while providing a high quality preservation of the original data. Our method is generic and can be applied to other

  11. Phosphorylated hepatocyte growth factor receptor/c-Met is associated with tumor growth and prognosis in patients with bladder cancer: correlation with matrix metalloproteinase-2 and -7 and E-cadherin.

    Science.gov (United States)

    Miyata, Yasuyoshi; Sagara, Yuji; Kanda, Shigeru; Hayashi, Tomayoshi; Kanetake, Hiroshi

    2009-04-01

    Hepatocyte growth factor receptor/c-Met is associated with malignant aggressiveness and survival in various cancers including bladder cancer. Although phosphorylation of hepatocyte growth factor receptor/c-Met is essential for its function, the pathologic significance of phosphorylated hepatocyte growth factor receptor/c-Met in bladder cancer remains elusive. We investigated the clinical significance of its expression, and its correlation with cancer cell progression-related molecules. The expression levels of 2 tyrosine residues of hepatocyte growth factor receptor/c-Met (pY1234/1235 and pY1349) were examined immunohistochemically in 133 specimens with nonmetastatic bladder cancer. We also investigated their correlation with matrix metalloproteinase-1, -2, -7, and -14; urokinase-type plasminogen activator; E-cadherin; CD44 standard, variant 3, and variant 6; and vascular endothelial growth factor. Expression of phosphorylated hepatocyte growth factor receptor/c-Met was detected in cancer cells, but was rare in normal urothelial cells. Although hepatocyte growth factor receptor/c-Met, pY1234/1235 hepatocyte growth factor receptor/c-Met, and pY1349 hepatocyte growth factor receptor/c-Met were associated with pT stage, multivariate analysis identified pY1349 hepatocyte growth factor receptor/c-met expression only as a significant factor for high pT stage. Expression of pY1349 hepatocyte growth factor receptor/c-Met was a marker of metastasis and (P = .001) and cause-specific survival (P = .003). Expressions of matrix metalloproteinase-2, matrix metalloproteinase-7, and E-cadherin correlated with pY1349 hepatocyte growth factor receptor/c-Met expression. Our results demonstrated that pY1349 hepatocyte growth factor receptor/c-Met plays an important role in tumor development, and its expression is a significant predictor of metastasis and survival of patients with bladder cancer. The results suggest that these activities are mediated, at least in part, by matrix

  12. Comparison of cardiovascular risk factors between Sri Lankans living in Kandy and Oslo.

    Science.gov (United States)

    Tennakoon, Sampath U B; Kumar, Bernadette N; Nugegoda, Danasela B; Meyer, Haakon E

    2010-10-29

    South Asians living in western countries are known to have unfavourable cardiovascular risk profiles. Studies indicate migrants are worse off when compared to those living in country of origin. The purpose of this study was to compare selected cardiovascular risk factors between migrant Sri Lankans living in Oslo, Norway and Urban dwellers from Kandy, Sri Lanka. Data on non fasting serum lipids, blood pressure, anthropometrics and socio demographics of Sri Lankan Tamils from two almost similar population based cross sectional studies in Oslo, Norway between 2000 and 2002 (1145 participants) and Kandy, Sri Lanka in 2005 (233 participants) were compared. Combined data were analyzed using linear regression analyses. Men and women in Oslo had higher HDL cholesterol. Men and women from Kandy had higher Total/HDL cholesterol ratios. Mean waist circumference and body mass index was higher in Oslo. Smoking among men was low (19.2% Oslo, 13.1% Kandy, P = 0.16). None of the women smoked. Mean systolic and diastolic blood pressure was significantly higher in Kandy than in Oslo. Our comparison showed unexpected differences in risk factors between Sri Lankan migrants living in Oslo and those living in Kandy Sri Lanka. Sri Lankans in Oslo had favorable lipid profiles and blood pressure levels despite being more obese.

  13. Parental Separation and Cardiometabolic Risk Factors in Late Adolescence: A Cross-Cohort Comparison.

    Science.gov (United States)

    Soares, Ana Luiza Gonçalves; Gonçalves, Helen; Matijasevich, Alicia; Sequeira, Maija; Smith, George Davey; Menezes, Ana M B; Assunção, Maria Cecília; Wehrmeister, Fernando C; Fraser, Abigail; Howe, Laura D

    2017-05-15

    The aim of this study was to explore the association between parental separation during childhood (up to 18 years of age) and cardiometabolic risk factors (body mass index, fat mass index, blood pressure, physical activity, smoking, and alcohol consumption) in late adolescence using a cross-cohort comparison and to explore whether associations differ according to the age at which the parental separation occurred and the presence or absence of parental conflict prior to separation. Data from the Avon Longitudinal Study of Parents and Children (ALSPAC, United Kingdom) (1991-2011) and the 1993 Pelotas Birth Cohort (Brazil) (1993-2011) were used. The associations of parental separation with children's cardiometabolic risk factors were largely null. Higher odds of daily smoking were observed in both cohorts for those adolescents whose parents separated (for ALSPAC, odds ratio = 1.46; for Pelotas Birth Cohort, odds ratio = 1.98). Some additional associations were observed in the Pelotas Birth Cohort but were generally in the opposite direction to our a priori hypothesis: Parental separation was associated with lower blood pressure and fat mass index, and with more physical activity. No consistent differences were observed when analyses were stratified by child's age at parental separation or parental conflict. © The Author 2017. Published by Oxford University Press on behalf of the Johns Hopkins Bloomberg School of Public Health.

  14. Diurnal and seasonal trends and source apportionment of redox-active metals in Los Angeles using a novel online metal monitor and Positive Matrix Factorization (PMF)

    Science.gov (United States)

    Mousavi, Amirhosein; Sowlat, Mohammad H.; Sioutas, Constantinos

    2018-02-01

    In the present study, we identified the sources of four redox-active metals, including Iron (Fe), Chromium (Cr), Cupper (Cu), and Manganese (Mn) and quantified the contribution of these sources to PM2.5 concentrations in central Los Angeles, California, by employing time-resolved measurements (i.e., a time resolution of 2 h) with a recently developed online metal monitor and Positive Matrix Factorization (PMF). Size distribution of ambient PM (14 nm-10 μm) was measured using the Scanning Mobility Particle Sizer (SMPS) and Optical Particle Sizer (OPS). Auxiliary variables were also collected, including elemental (EC) and organic carbon (OC), gaseous pollutants (NO2 and O3), meteorological parameters (including relative humidity (RH) and temperature), and traffic data (for heavy- (HDVs) and light-duty vehicles (LDVs)). A 4-factor solution was found to be optimum for the chemically-speciated dataset, whereas a 5-factor solution appeared to be most plausible for the size distribution data. The factors included fresh traffic, soil/road dust, urban background aerosol, secondary aerosol, and nucleation (only resolved for the size distribution data). Fresh traffic was the major contributor to Fe and Cu concentrations, whereas Cr was mostly found in the urban background aerosol (reflecting a mixture of small local sources as well as aged traffic emissions), and Mn mostly came from both soil/road dust and was to a lesser degree found in urban background aerosol. Secondary aerosol did not contribute to the concentrations of any of these metals, but was associated with very high loading of OC, as expected. Even though the urban background aerosol and secondary aerosol appeared to be characterized by "aged" particles and have a rather homogeneous spatial distribution, the reactions and processes involved in their formation are entirely different. Our results provide insights into the sources of redox-active metals in central Los Angeles. They also underscore the benefits of

  15. Matrix analysis

    CERN Document Server

    Bhatia, Rajendra

    1997-01-01

    A good part of matrix theory is functional analytic in spirit. This statement can be turned around. There are many problems in operator theory, where most of the complexities and subtleties are present in the finite-dimensional case. My purpose in writing this book is to present a systematic treatment of methods that are useful in the study of such problems. This book is intended for use as a text for upper division and gradu­ ate courses. Courses based on parts of the material have been given by me at the Indian Statistical Institute and at the University of Toronto (in collaboration with Chandler Davis). The book should also be useful as a reference for research workers in linear algebra, operator theory, mathe­ matical physics and numerical analysis. A possible subtitle of this book could be Matrix Inequalities. A reader who works through the book should expect to become proficient in the art of deriving such inequalities. Other authors have compared this art to that of cutting diamonds. One first has to...

  16. Electromagnetic matrix elements in baryons

    International Nuclear Information System (INIS)

    Lipkin, H.J.; Moinester, M.A.

    1992-01-01

    Some simple symmetry relations between matrix elements of electromagnetic operators are investigated. The implications are discussed for experiments to study hyperon radiative transitions and polarizabilities and form factors. (orig.)

  17. Stratification of surgical site infection by operative factors and comparison of infection rates after hernia repair.

    Science.gov (United States)

    Olsen, Margaret A; Nickel, Katelin B; Wallace, Anna E; Mines, Daniel; Fraser, Victoria J; Warren, David K

    2015-03-01

    To investigate whether operative factors are associated with risk of surgical site infection (SSI) after hernia repair. Retrospective cohort study. Patients Commercially insured enrollees aged 6 months-64 years with International Classification of Diseases, Ninth Revision, Clinical Modification procedure or Current Procedural Terminology, fourth edition, codes for inguinal/femoral, umbilical, and incisional/ventral hernia repair procedures from January 1, 2004, through December 31, 2010. SSIs within 90 days after hernia repair were identified by diagnosis codes. The χ2 and Fisher exact tests were used to compare SSI incidence by operative factors. A total of 119,973 hernia repair procedures were analyzed. The incidence of SSI differed significantly by anatomic site, with rates of 0.45% (352/77,666) for inguinal/femoral, 1.16% (288/24,917) for umbilical, and 4.11% (715/17,390) for incisional/ventral hernia repair. Within anatomic sites, the incidence of SSI was significantly higher for open versus laparoscopic inguinal/femoral (0.48% [295/61,142] vs 0.34% [57/16,524], P=.020) and incisional/ventral (4.20% [701/16,699] vs 2.03% [14/691], P=.005) hernia repairs. The rate of SSI was higher following procedures with bowel obstruction/necrosis than procedures without obstruction/necrosis for open inguinal/femoral (0.89% [48/5,422] vs 0.44% [247/55,720], Poperative factors may facilitate accurate comparison of SSI rates between facilities.

  18. Comparison of visual field test results obtained through Humphrey matrix frequency doubling technology perimetry versus standard automated perimetry in healthy children.

    Science.gov (United States)

    Kocabeyoglu, Sibel; Uzun, Salih; Mocan, Mehmet Cem; Bozkurt, Banu; Irkec, Murat; Orhan, Mehmet

    2013-10-01

    The aim of this study was to compare the visual field test results in healthy children obtained via the Humphrey matrix 24-2 threshold program and standard automated perimetry (SAP) using the Swedish interactive threshold algorithm (SITA)-Standard 24-2 test. This prospective study included 55 healthy children without ocular or systemic disorders who underwent both SAP and frequency doubling technology (FDT) perimetry visual field testing. Visual field test reliability indices, test duration, global indices (mean deviation [MD], and pattern standard deviation [PSD]) were compared between the 2 tests using the Wilcoxon signed-rank test and paired t-test. The performance of the Humphrey field analyzer (HFA) 24-2 SITA-standard and frequency-doubling technology Matrix 24-2 tests between genders were compared with Mann-Whitney U-test. Fifty-five healthy children with a mean age of 12.2 ± 1.9 years (range from 8 years to 16 years) were included in this prospective study. The test durations of SAP and FDT were similar (5.2 ± 0.5 and 5.1 ± 0.2 min, respectively, P = 0.651). MD and the PSD values obtained via FDT Matrix were significantly higher than those obtained via SAP (P tests in terms of MD (r = 0.352, P = 0.008) and PSD (r = 0.329, P = 0.014) was observed. Children were able to complete both the visual test algorithms successfully within 6 min. However, SAP testing appears to be associated with less depression of the visual field indices of healthy children. FDT Matrix and SAP should not be used interchangeably in the follow-up of children.

  19. Comparison of visual field test results obtained through Humphrey matrix frequency doubling technology perimetry versus standard automated perimetry in healthy children

    Directory of Open Access Journals (Sweden)

    Sibel Kocabeyoglu

    2013-01-01

    Full Text Available Aims : The aim of this study was to compare the visual field test results in healthy children obtained via the Humphrey matrix 24-2 threshold program and standard automated perimetry (SAP using the Swedish interactive threshold algorithm (SITA-Standard 24-2 test. Materials and Methods: This prospective study included 55 healthy children without ocular or systemic disorders who underwent both SAP and frequency doubling technology (FDT perimetry visual field testing. Visual field test reliability indices, test duration, global indices (mean deviation [MD], and pattern standard deviation [PSD] were compared between the 2 tests using the Wilcoxon signed-rank test and paired t-test. The performance of the Humphrey field analyzer (HFA 24-2 SITA-standard and frequency-doubling technology Matrix 24-2 tests between genders were compared with Mann-Whitney U-test. Results: Fifty-five healthy children with a mean age of 12.2 ± 1.9 years (range from 8 years to 16 years were included in this prospective study. The test durations of SAP and FDT were similar (5.2 ± 0.5 and 5.1 ± 0.2 min, respectively, P = 0.651. MD and the PSD values obtained via FDT Matrix were significantly higher than those obtained via SAP (P < 0.001, and fixation losses and false negative errors were significantly less with SAP (P < 0.05. A weak positive correlation between the two tests in terms of MD (r = 0.352, P = 0.008 and PSD (r = 0.329, P = 0.014 was observed. Conclusion: Children were able to complete both the visual test algorithms successfully within 6 min. However, SAP testing appears to be associated with less depression of the visual field indices of healthy children. FDT Matrix and SAP should not be used interchangeably in the follow-up of children.

  20. Ecological risk assessment of agricultural soils for the definition of soil screening values: A comparison between substance-based and matrix-based approaches.

    Science.gov (United States)

    Pivato, Alberto; Lavagnolo, Maria Cristina; Manachini, Barbara; Vanin, Stefano; Raga, Roberto; Beggio, Giovanni

    2017-04-01

    The Italian legislation on contaminated soils does not include the Ecological Risk Assessment (ERA) and this deficiency has important consequences for the sustainable management of agricultural soils. The present research compares the results of two ERA procedures applied to agriculture (i) one based on the "substance-based" approach and (ii) a second based on the "matrix-based" approach. In the former the soil screening values (SVs) for individual substances were derived according to institutional foreign guidelines. In the latter, the SVs characterizing the whole-matrix were derived originally by the authors by means of experimental activity. The results indicate that the "matrix-based" approach can be efficiently implemented in the Italian legislation for the ERA of agricultural soils. This method, if compared to the institutionalized "substance based" approach is (i) comparable in economic terms and in testing time, (ii) is site specific and assesses the real effect of the investigated soil on a battery of bioassays, (iii) accounts for phenomena that may radically modify the exposure of the organisms to the totality of contaminants and (iv) can be considered sufficiently conservative.

  1. Ecological risk assessment of agricultural soils for the definition of soil screening values: A comparison between substance-based and matrix-based approaches

    Directory of Open Access Journals (Sweden)

    Alberto Pivato

    2017-04-01

    Full Text Available The Italian legislation on contaminated soils does not include the Ecological Risk Assessment (ERA and this deficiency has important consequences for the sustainable management of agricultural soils. The present research compares the results of two ERA procedures applied to agriculture (i one based on the “substance-based” approach and (ii a second based on the “matrix-based” approach. In the former the soil screening values (SVs for individual substances were derived according to institutional foreign guidelines. In the latter, the SVs characterizing the whole-matrix were derived originally by the authors by means of experimental activity.The results indicate that the “matrix-based” approach can be efficiently implemented in the Italian legislation for the ERA of agricultural soils. This method, if compared to the institutionalized “substance based” approach is (i comparable in economic terms and in testing time, (ii is site specific and assesses the real effect of the investigated soil on a battery of bioassays, (iii accounts for phenomena that may radically modify the exposure of the organisms to the totality of contaminants and (iv can be considered sufficiently conservative. Keyword: Environmental science

  2. Matrix pentagons

    Science.gov (United States)

    Belitsky, A. V.

    2017-10-01

    The Operator Product Expansion for null polygonal Wilson loop in planar maximally supersymmetric Yang-Mills theory runs systematically in terms of multi-particle pentagon transitions which encode the physics of excitations propagating on the color flux tube ending on the sides of the four-dimensional contour. Their dynamics was unraveled in the past several years and culminated in a complete description of pentagons as an exact function of the 't Hooft coupling. In this paper we provide a solution for the last building block in this program, the SU(4) matrix structure arising from internal symmetry indices of scalars and fermions. This is achieved by a recursive solution of the Mirror and Watson equations obeyed by the so-called singlet pentagons and fixing the form of the twisted component in their tensor decomposition. The non-singlet, or charged, pentagons are deduced from these by a limiting procedure.

  3. Matrix pentagons

    Directory of Open Access Journals (Sweden)

    A.V. Belitsky

    2017-10-01

    Full Text Available The Operator Product Expansion for null polygonal Wilson loop in planar maximally supersymmetric Yang–Mills theory runs systematically in terms of multi-particle pentagon transitions which encode the physics of excitations propagating on the color flux tube ending on the sides of the four-dimensional contour. Their dynamics was unraveled in the past several years and culminated in a complete description of pentagons as an exact function of the 't Hooft coupling. In this paper we provide a solution for the last building block in this program, the SU(4 matrix structure arising from internal symmetry indices of scalars and fermions. This is achieved by a recursive solution of the Mirror and Watson equations obeyed by the so-called singlet pentagons and fixing the form of the twisted component in their tensor decomposition. The non-singlet, or charged, pentagons are deduced from these by a limiting procedure.

  4. Jasmonate-dependent modifications of the pectin matrix during potato development function as a defense mechanism targeted by Dickeya dadantii virulence factors.

    Science.gov (United States)

    Taurino, Marco; Abelenda, Jose A; Río-Alvarez, Isabel; Navarro, Cristina; Vicedo, Begonya; Farmaki, Theodora; Jiménez, Pedro; García-Agustín, Pilar; López-Solanilla, Emilia; Prat, Salomé; Rojo, Enrique; Sánchez-Serrano, José J; Sanmartín, Maite

    2014-02-01

    The plant cell wall constitutes an essential protection barrier against pathogen attack. In addition, cell-wall disruption leads to accumulation of jasmonates (JAs), which are key signaling molecules for activation of plant inducible defense responses. However, whether JAs in return modulate the cell-wall composition to reinforce this defensive barrier remains unknown. The enzyme 13-allene oxide synthase (13-AOS) catalyzes the first committed step towards biosynthesis of JAs. In potato (Solanum tuberosum), there are two putative St13-AOS genes, which we show here to be differentially induced upon wounding. We also determine that both genes complement an Arabidopsis aos null mutant, indicating that they encode functional 13-AOS enzymes. Indeed, transgenic potato plants lacking both St13-AOS genes (CoAOS1/2 lines) exhibited a significant reduction of JAs, a concomitant decrease in wound-responsive gene activation, and an increased severity of soft rot disease symptoms caused by Dickeya dadantii. Intriguingly, a hypovirulent D. dadantii pel strain lacking the five major pectate lyases, which causes limited tissue maceration on wild-type plants, regained infectivity in CoAOS1/2 plants. In line with this, we found differences in pectin methyl esterase activity and cell-wall pectin composition between wild-type and CoAOS1/2 plants. Importantly, wild-type plants had pectins with a lower degree of methyl esterification, which are the substrates of the pectate lyases mutated in the pel strain. These results suggest that, during development of potato plants, JAs mediate modification of the pectin matrix to form a defensive barrier that is counteracted by pectinolytic virulence factors from D. dadantii. © 2013 The Authors The Plant Journal © 2013 John Wiley & Sons Ltd.

  5. Quantification of endogenous metabolites by the postcolumn infused-internal standard method combined with matrix normalization factor in liquid chromatography-electrospray ionization tandem mass spectrometry.

    Science.gov (United States)

    Liao, Hsiao-Wei; Chen, Guan-Yuan; Wu, Ming-Shiang; Liao, Wei-Chih; Tsai, I-Lin; Kuo, Ching-Hua

    2015-01-02

    Quantification of endogenous metabolites has enabled the discovery of biomarkers for diagnosis and provided for an understanding of disease etiology. The standard addition and stable isotope labeled-internal standard (SIL-IS) methods are currently the most widely used approaches to quantifying endogenous metabolites, but both have some limitations for clinical measurement. In this study, we developed a new approach for endogenous metabolite quantification by the postcolumn infused-internal standard (PCI-IS) method combined with the matrix normalization factor (MNF) method. MNF was used to correct the difference in MEs between standard solution and biofluids, and PCI-IS additionally tailored the correction of the MEs for individual samples. Androstenedione and testosterone were selected as test articles to verify this new approach to quantifying metabolites in plasma. The repeatability (n=4 runs) and intermediate precision (n=3 days) in terms of the peak area of androstenedione and testosterone at all tested concentrations were all less than 11% relative standard deviation (RSD). The accuracy test revealed that the recoveries were between 95.72% and 113.46%. The concentrations of androstenedione and testosterone in fifty plasma samples obtained from healthy volunteers were quantified by the PCI-IS combined with the MNF method, and the quantification results were compared with the results of the SIL-IS method. The Pearson correlation test showed that the correlation coefficient was 0.98 for both androstenedione and testosterone. We demonstrated that the PCI-IS combined with the MNF method is an effective and accurate method for quantifying endogenous metabolites. Copyright © 2014 Elsevier B.V. All rights reserved.

  6. Interaction with extracellular matrix proteins influences Lsh/Ity/Bcg (candidate Nramp) gene regulation of macrophage priming/activation for tumour necrosis factor-alpha and nitrite release.

    Science.gov (United States)

    Formica, S; Roach, T I; Blackwell, J M

    1994-05-01

    The murine resistance gene Lsh/Ity/Bcg regulates activation of macrophages for tumour necrosis factor-alpha (TNF-alpha)-dependent production of nitric oxide mediating antimicrobial activity against Leishmania, Salmonella and Mycobacterium. As Lsh is differentially expressed in macrophages from different tissue sites, experiments were performed to determine whether interaction with extracellular matrix (ECM) proteins would influence the macrophage TNF-alpha response. Plating of bone marrow-derived macrophages onto purified fibrinogen or fibronectin-rich L929 cell-derived matrices, but not onto mannan, was itself sufficient to stimulate TNF-alpha release, with significantly higher levels released from congenic B10.L-Lshr compared to C57BL/10ScSn (Lshs) macrophages. Only macrophages plated onto fibrinogen also released measurable levels of nitrites, again higher in Lshr compared to Lshs macrophages. Addition of interferon-gamma (IFN-gamma), but not bacterial lipopolysaccharide or mycobacterial lipoarabinomannan, as a second signal enhanced the TNF-alpha and nitrite responses of macrophages plated onto fibrinogen, particularly in the Lshr macrophages. Interaction with fibrinogen and fibronectin also primed macrophages for an enhanced TNF-alpha response to leishmanial parasites, but this was only translated into enhanced nitrite responses in the presence of IFN-gamma. In these experiments, Lshr macrophages remained superior in their TNF-alpha responses throughout, but to a degree which reflected the magnitude of the difference observed on ECM alone. Hence, the specificity for the enhanced TNF-alpha responses of Lshr macrophages lay in their interaction with fibrinogen and fibronectin ECM, while a differential nitrite response was only observed with fibrinogen and/or IFN-gamma. The results are discussed in relation to the possible function of the recently cloned candidate gene Nramp, which has structural identity to eukaryote transporters and an N-terminal cytoplasmic

  7. Presence of Insulin-Like Growth Factor Binding Proteins Correlates With Tumor-Promoting Effects of Matrix Metalloproteinase 9 in Breast Cancer

    Directory of Open Access Journals (Sweden)

    Jae-Hyun Park

    2015-05-01

    Full Text Available The stroma of breast cancer can promote the disease’s progression, but whether its composition and functions are shared among different subtypes is poorly explored. We compared stromal components of a luminal [mouse mammary tumor virus (MMTV–Neu] and a triple-negative/basal-like [C3(1–Simian virus 40 large T antigen (Tag] genetically engineered breast cancer mouse model. The types of cytokines and their expression levels were very different in the two models, as was the extent of innate immune cell infiltration; however, both models showed infiltration of innate immune cells that expressed matrix metalloproteinase 9 (MMP9, an extracellular protease linked to the progression of many types of cancer. By intercrossing with Mmp9 null mice, we found that the absence of MMP9 delayed tumor onset in the C3(1-Tag model but had no effect on tumor onset in the MMTV-Neu model. We discovered that protein levels of insulin-like growth factor binding protein-1 (IGFBP-1, an MMP9 substrate, were increased in C3(1-Tag;Mmp9−/− compared to C3(1-Tag;Mmp9+/+ tumors. In contrast, IGFBP-1 protein expression was low in MMTV-Neu tumors regardless of Mmp9 status. IGFBP-1 binds and antagonizes IGFs, preventing them from activating their receptors to promote cell proliferation and survival. Tumors from C3(1-Tag;Mmp9−/− mice had reduced IGF-1 receptor phosphorylation, consistent with slower tumor onset. Finally, gene expression analysis of human breast tumors showed that high expression of IGFBP mRNA was strongly correlated with good prognosis but not when MMP9 mRNA was also highly expressed. In conclusion, MMP9 has different effects on breast cancer progression depending on whether IGFBPs are expressed.

  8. Chromophoric dissolved organic matter (CDOM) variability in Barataria Basin using excitation-emission matrix (EEM) fluorescence and parallel factor analysis (PARAFAC).

    Science.gov (United States)

    Singh, Shatrughan; D'Sa, Eurico J; Swenson, Erick M

    2010-07-15

    Chromophoric dissolved organic matter (CDOM) variability in Barataria Basin, Louisiana, USA,was examined by excitation emission matrix (EEM) fluorescence combined with parallel factor analysis (PARAFAC). CDOM optical properties of absorption and fluorescence at 355nm along an axial transect (36 stations) during March, April, and May 2008 showed an increasing trend from the marine end member to the upper basin with mean CDOM absorption of 11.06 + or - 5.01, 10.05 + or - 4.23, 11.67 + or - 6.03 (m(-)(1)) and fluorescence 0.80 + or - 0.37, 0.78 + or - 0.39, 0.75 + or - 0.51 (RU), respectively. PARAFAC analysis identified two terrestrial humic-like (component 1 and 2), one non-humic like (component 3), and one soil derived humic acid like (component 4) components. The spatial variation of the components showed an increasing trend from station 1 (near the mouth of basin) to station 36 (end member of bay; upper basin). Deviations from this increasing trend were observed at a bayou channel with very high chlorophyll-a concentrations especially for component 3 in May 2008 that suggested autochthonous production of CDOM. The variability of components with salinity indicated conservative mixing along the middle part of the transect. Component 1 and 4 were found to be relatively constant, while components 2 and 3 revealed an inverse relationship for the sampling period. Total organic carbon showed increasing trend for each of the components. An increase in humification and a decrease in fluorescence indices along the transect indicated an increase in terrestrial derived organic matter and reduced microbial activity from lower to upper basin. The use of these indices along with PARAFAC results improved dissolved organic matter characterization in the Barataria Basin. Copyright 2010 Elsevier B.V. All rights reserved.

  9. Characterizing chromophoric dissolved organic matter in Lake Tianmuhu and its catchment basin using excitation-emission matrix fluorescence and parallel factor analysis.

    Science.gov (United States)

    Zhang, Yunlin; Yin, Yan; Feng, Longqing; Zhu, Guangwei; Shi, Zhiqiang; Liu, Xiaohan; Zhang, Yuanzhi

    2011-10-15

    Chromophoric dissolved organic matter (CDOM) is an important optically active substance that transports nutrients, heavy metals, and other pollutants from terrestrial to aquatic systems and is used as a measure of water quality. To investigate how the source and composition of CDOM changes in both space and time, we used chemical, spectroscopic, and fluorescence analyses to characterize CDOM in Lake Tianmuhu (a drinking water source) and its catchment in China. Parallel factor analysis (PARAFAC) identified three individual fluorophore moieties that were attributed to humic-like and protein-like materials in 224 water samples collected between December 2008 and September 2009. The upstream rivers contained significantly higher concentrations of CDOM than did the lake water (a(350) of 4.27±2.51 and 2.32±0.59 m(-1), respectively), indicating that the rivers carried a substantial load of organic matter to the lake. Of the three main rivers that flow into Lake Tianmuhu, the Pingqiao River brought in the most CDOM from the catchment to the lake. CDOM absorption and the microbial and terrestrial humic-like components, but not the protein-like component, were significantly higher in the wet season than in other seasons, indicating that the frequency of rainfall and runoff could significantly impact the quantity and quality of CDOM collected from the catchment. The different relationships between the maximum fluorescence intensities of the three PARAFAC components, CDOM absorption, and chemical oxygen demand (COD) concentration in riverine and lake water indicated the difference in the composition of CDOM between Lake Tianmuhu and the rivers that feed it. This study demonstrates the utility of combining excitation-emission matrix fluorescence and PARAFAC to study CDOM dynamics in inland waters. Copyright © 2011 Elsevier Ltd. All rights reserved.

  10. Pollution sources for indoor PM2.5 at the platform in subway station using a positive matrix factorization and an instrumental neutron activation analysis

    Energy Technology Data Exchange (ETDEWEB)

    Lim, Jong Myoung; Moon, Jong Hwa; Chung, Yong Sam [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of); Lee, Jin Hong [Chungnam National University, Daejeon (Korea, Republic of)

    2010-05-15

    Airborne particulate matters, especially the PM2.5 (aerodynamic equivalent diameter, AED, less than 2.5 )m) fraction has been important. This is because of their potential for deposition on to the human respiratory system being accompanied by many harmful trace metals (such as As, Cd, Cr, Cu, Mn, Pb, Se, and Zn). As most people spend more than 80% of their time indoors, indoor air quality (IAQ) can exert a considerable impact on the inhalation condition of toxic substances. Therefore, assessment of the absolute concentration levels and elemental composition of PM in an indoor environment such as subway station can be used as a practical barometer of IAQ. The contaminants originated from the indoor pollution sources as well as various outdoor sources are easily accumulated in indoor environment dissimilar to the outdoor. Especially, since the natural ventilation is nearly impossible in the subway station, its pollution status can be worsened under the circumstance that contaminants are constantly originated and circulated inside of station by the repetitive action of subway trains. In this study, a total of 60 PM2.5 samples were collected for 4 seasonal campaigns in 2009 with a low-volume air sampler at one subway station in Daejeon, Korea. We undertook the measurements of up to 25 elements in PM2.5 using an instrumental neutron activation analysis (INAA) and X-ray fluorescence (XRF). And inorganic ion species (SO{sub 4}{sup 2-}, NO{sub 3}{sup -}, NH{sub 4}{sup +}) also were determined by ion chromatography (IC). Next, sources at indoor/outdoor environment were identified and the contributions of each source were quantified by positive matrix factorization (PMF).

  11. Pollution sources for indoor PM2.5 at the platform in subway station using a positive matrix factorization and an instrumental neutron activation analysis

    International Nuclear Information System (INIS)

    Lim, Jong Myoung; Moon, Jong Hwa; Chung, Yong Sam; Lee, Jin Hong

    2010-01-01

    Airborne particulate matters, especially the PM2.5 (aerodynamic equivalent diameter, AED, less than 2.5 )m) fraction has been important. This is because of their potential for deposition on to the human respiratory system being accompanied by many harmful trace metals (such as As, Cd, Cr, Cu, Mn, Pb, Se, and Zn). As most people spend more than 80% of their time indoors, indoor air quality (IAQ) can exert a considerable impact on the inhalation condition of toxic substances. Therefore, assessment of the absolute concentration levels and elemental composition of PM in an indoor environment such as subway station can be used as a practical barometer of IAQ. The contaminants originated from the indoor pollution sources as well as various outdoor sources are easily accumulated in indoor environment dissimilar to the outdoor. Especially, since the natural ventilation is nearly impossible in the subway station, its pollution status can be worsened under the circumstance that contaminants are constantly originated and circulated inside of station by the repetitive action of subway trains. In this study, a total of 60 PM2.5 samples were collected for 4 seasonal campaigns in 2009 with a low-volume air sampler at one subway station in Daejeon, Korea. We undertook the measurements of up to 25 elements in PM2.5 using an instrumental neutron activation analysis (INAA) and X-ray fluorescence (XRF). And inorganic ion species (SO 4 2- , NO 3 - , NH 4 + ) also were determined by ion chromatography (IC). Next, sources at indoor/outdoor environment were identified and the contributions of each source were quantified by positive matrix factorization (PMF).

  12. Insight into the heterogeneous adsorption of humic acid fluorescent components on multi-walled carbon nanotubes by excitation-emission matrix and parallel factor analysis.

    Science.gov (United States)

    Yang, Chenghu; Liu, Yangzhi; Cen, Qiulin; Zhu, Yaxian; Zhang, Yong

    2018-02-01

    The heterogeneous adsorption behavior of commercial humic acid (HA) on pristine and functionalized multi-walled carbon nanotubes (MWCNTs) was investigated by fluorescence excitation-emission matrix and parallel factor (EEM- PARAFAC) analysis. The kinetics, isotherms, thermodynamics and mechanisms of adsorption of HA fluorescent components onto MWCNTs were the focus of the present study. Three humic-like fluorescent components were distinguished, including one carboxylic-like fluorophore C1 (λ ex /λ em = (250, 310) nm/428nm), and two phenolic-like fluorophores, C2 (λ ex /λ em = (300, 460) nm/552nm) and C3 (λ ex /λ em = (270, 375) nm/520nm). The Lagergren pseudo-second-order model can be used to describe the adsorption kinetics of the HA fluorescent components. In addition, both the Freundlich and Langmuir models can be suitably employed to describe the adsorption of the HA fluorescent components onto MWCNTs with significantly high correlation coefficients (R 2 > 0.94, Padsorption affinity (K d ) and nonlinear adsorption degree from the HA fluorescent components to MWCNTs was clearly observed. The adsorption mechanism suggested that the π-π electron donor-acceptor (EDA) interaction played an important role in the interaction between HA fluorescent components and the three MWCNTs. Furthermore, the values of the thermodynamic parameters, including the Gibbs free energy change (ΔG°), enthalpy change (ΔH°) and entropy change (ΔS°), showed that the adsorption of the HA fluorescent components on MWCNTs was spontaneous and exothermic. Copyright © 2017 Elsevier Inc. All rights reserved.

  13. Sirtuin 1 regulates matrix metalloproteinase-13 expression induced by Porphyromonas endodontalis lipopolysaccharide via targeting nuclear factor-κB in osteoblasts.

    Science.gov (United States)

    Qu, Liu; Yu, Yaqiong; Qiu, Lihong; Yang, Di; Yan, Lu; Guo, Jiajie; Jahan, Rabita

    2017-01-01

    Porphyromonas endodontalis lipopolysaccharide (P.e LPS) is an important initiating factor for periapical inflammation and bone destruction. Matrix metalloproteinase-13 (MMP-13) has been shown to participate in the formation and diffusion of periapical bone lesion in chronic apical periodontitis. Sirtuin 1 (SIRT1) is a key regulator of inflammation in mammalian cells which suppresses the release of inflammatory mediators. This study aimed to explore the role of SIRT1 in regulating MMP-13 expression induced by P.e LPS in osteoblasts. P.e LPS stimulated MMP-13 expression in MC3T3-E1 cells. Knockdown of SIRT1 reinforced the increase of MMP-13mRNA expression induced by P.e LPS. SIRT1 activator resveratrol significantly reduced the expression of MMP-13 and SIRT1 inhibitor EX-527 enhanced the expression of MMP-13. Moreover, SIRT1 activation with resveratrol inhibited acetylation of NF-κB p65 and NF-κB transcriptional activity, which were enhanced by P.e LPS. In addition, NF-κB p65 was involved in P.e LPS-induced MMP-13 expression via directly binding to the MMP-13 promoter. However, SIRT1 activation significantly interfered with this binding. These findings strongly suggest that P.e LPS induces MMP-13 expression in osteoblasts, and SIRT1 suppresses this expression of MMP-13 through targeting NF-κB p65. This provides new insights into understanding the actions of SIRT1 on anti-inflammatory and anti-bone resorption activity.

  14. Expression of vascular endothelial growth factor and matrix metalloproteinase-9 in Apis mellifera Lawang propolis extract gel-treated traumatic ulcers in diabetic rats

    Directory of Open Access Journals (Sweden)

    Diah Savitri Ernawati

    2018-03-01

    Full Text Available Aim: The aim of this study was to determine the effect of Apis mellifera propolis extract gel on vascular endothelial growth factor (VEGF and matrix metalloproteinase-9 (MMP-9 expression in the traumatic ulcers of rats afflicted with diabetes mellitus (DM. Materials and Methods: The study was conducted on 24 male Wistar rats (Rattus norvegicus induced with DM by injecting 50 mg/kg of Streptozotocin, intraperitoneally, and a traumatic ulcer on their lower lip mucosa. These were divided into eight groups: Four each for control and treatment groups. Each control and treatment group consisted of three rats. The control groups treated with hydroxypropyl methylcellulose 5% gel and treatment groups were administered with propolis extract gel. The expression of VEGF and MMP-9 was observed on days 3, 5, 7, and 9. Furthermore, mice sacrificed and the lower lip labial mucosa tissue of mice has been taken to make the histopathology anatomy preparation by means of immunohistochemical examination with monoclonal antibodies anti-VEGF and anti-MMP-9. Results: This experiment revealed higher VEGF expression and lower MMP-9 expression in the treatment group as compared to that of the control group. Analysis of Variance showed significant differences (p<0.01 of both VEGF expression and MMP-9 expression between the two groups. A Tukey's analysis did not find strong contrasts in VEGF and MMP-9 expressions between various treatment groups. However, those between treatment and control groups were found to be considerable. Conclusion: Propolis extract gel increased the expression of VEGF and decreased that of MMP-9 during the healing process of traumatic ulcers on the oral mucosa of diabetes afflicted Wistar rats (R. norvegicus.

  15. A forecasting performance comparison of dynamic factor models based on static and dynamic methods

    Directory of Open Access Journals (Sweden)

    Marra Fabio Della

    2017-03-01

    Full Text Available We present a comparison of the forecasting performances of three Dynamic Factor Models on a large monthly data panel of macroeconomic and financial time series for the UE economy. The first model relies on static principal-component and was introduced by Stock and Watson (2002a, b. The second is based on generalized principal components and it was introduced by Forni, Hallin, Lippi and Reichlin (2000, 2005. The last model has been recently proposed by Forni, Hallin, Lippi and Zaffaroni (2015, 2016. The data panel is split into two parts: the calibration sample, from February 1986 to December 2000, is used to select the most performing specification for each class of models in a in- sample environment, and the proper sample, from January 2001 to November 2015, is used to compare the performances of the selected models in an out-of-sample environment. The metholodogical approach is analogous to Forni, Giovannelli, Lippi and Soccorsi (2016, but also the size of the rolling window is empirically estimated in the calibration process to achieve more robustness. We find that, on the proper sample, the last model is the most performing for the Inflation. However, mixed evidencies appear over the proper sample for the Industrial Production.

  16. Meniscal tear evaluation. Comparison of a conventional spin-echo proton density sequence with a fast spin-echo sequence utilizing a 512x358 matrix size

    International Nuclear Information System (INIS)

    Hopper, M.A.; Robinson, P.; Grainger, A.J.

    2011-01-01

    Aim: To determine the sensitivities, specificities, and receiver-operating characteristics (ROCs) for sagittal conventional spin-echo proton density (SE-PD) and fast spin-echo proton density (FSE-PD) sequences in the diagnosis of meniscal tears when compared to arthroscopic findings utilizing increased FSE matrix acquisition size. Method and materials: Magnetic resonance imaging (MRI) studies of 97 knees (194 menisci) were independently and prospectively interpreted by two experienced musculoskeletal radiologists over four separate readings at least 3 weeks apart. Readings 1 and 2 included images in all three planes in accordance with the standard protocol with either a SE or FSE sagittal PD, at readings 3 and 4 just the SE or FSE sagittal PD sequences were reported. The FSE sequence was acquired with an increased matrix size, compared to the SE sequence, to provide increased resolution. Menisci were graded for the presence of a tear and statistical analysis to calculate sensitivity and specificity was performed comparing to arthroscopy as the reference standard. ROC analysis for the diagnosis of meniscal tears on the SE and FSE sagittal sequences was also evaluated. Reader concordance for the SE and FSE sequences was calculated. Results: Sixty-seven tears were noted at arthroscopy; 60 were detected on SE and 56 on FSE. The sensitivity and specificity for SE was 90 and 90%, and for FSE was 84 and 94%, respectively, with no significant difference. ROC analysis showed no significant difference between the two sequences and kappa values demonstrated a higher level of reader agreement for the FSE than for the SE reading. Conclusion: Use of a FSE sagittal PD sequence with an increased matrix size provides comparable performance to conventional SE sagittal PD when evaluating meniscal disease with a modern system. The present study indicates an increased level of concordance between readers for the FSE sagittal sequence compared to the conventional SE.

  17. Meniscal tear evaluation. Comparison of a conventional spin-echo proton density sequence with a fast spin-echo sequence utilizing a 512x358 matrix size

    Energy Technology Data Exchange (ETDEWEB)

    Hopper, M.A.; Robinson, P. [Leeds Teaching Hospitals NHS Trust, Leeds (United Kingdom); Grainger, A.J., E-mail: andrew.grainger@leedsth.nhs.u [Leeds Teaching Hospitals NHS Trust, Leeds (United Kingdom)

    2011-04-15

    Aim: To determine the sensitivities, specificities, and receiver-operating characteristics (ROCs) for sagittal conventional spin-echo proton density (SE-PD) and fast spin-echo proton density (FSE-PD) sequences in the diagnosis of meniscal tears when compared to arthroscopic findings utilizing increased FSE matrix acquisition size. Method and materials: Magnetic resonance imaging (MRI) studies of 97 knees (194 menisci) were independently and prospectively interpreted by two experienced musculoskeletal radiologists over four separate readings at least 3 weeks apart. Readings 1 and 2 included images in all three planes in accordance with the standard protocol with either a SE or FSE sagittal PD, at readings 3 and 4 just the SE or FSE sagittal PD sequences were reported. The FSE sequence was acquired with an increased matrix size, compared to the SE sequence, to provide increased resolution. Menisci were graded for the presence of a tear and statistical analysis to calculate sensitivity and specificity was performed comparing to arthroscopy as the reference standard. ROC analysis for the diagnosis of meniscal tears on the SE and FSE sagittal sequences was also evaluated. Reader concordance for the SE and FSE sequences was calculated. Results: Sixty-seven tears were noted at arthroscopy; 60 were detected on SE and 56 on FSE. The sensitivity and specificity for SE was 90 and 90%, and for FSE was 84 and 94%, respectively, with no significant difference. ROC analysis showed no significant difference between the two sequences and kappa values demonstrated a higher level of reader agreement for the FSE than for the SE reading. Conclusion: Use of a FSE sagittal PD sequence with an increased matrix size provides comparable performance to conventional SE sagittal PD when evaluating meniscal disease with a modern system. The present study indicates an increased level of concordance between readers for the FSE sagittal sequence compared to the conventional SE.

  18. Species identification of clinical isolates of anaerobic bacteria: a comparison of two matrix-assisted laser desorption ionization-time of flight mass spectrometry systems

    DEFF Research Database (Denmark)

    Justesen, Ulrik Stenz; Holm, Anette; Knudsen, Elisa

    2011-01-01

    We compared two matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) systems (Shimadzu/SARAMIS and Bruker) on a collection of consecutive clinically important anaerobic bacteria (n = 290). The Bruker system had more correct identifications to the species level...... (67.2% versus 49.0%), but also more incorrect identifications (7.9% versus 1.4%). The system databases need to be optimized to increase identification levels. However, MALDI-TOF MS in its present version seems to be a fast and inexpensive method for identification of most clinically important...

  19. Rovibrational matrix elements of the multipole moments

    Indian Academy of Sciences (India)

    Rovibrational matrix elements of the multipole moments ℓ up to rank 10 and of the linear polarizability of the H2 molecule in the condensed phase have been computed taking into account the effect of the intermolecular potential. Comparison with gas phase matrix elements shows that the effect of solid state interactions is ...

  20. Comparison of friction and wear performances of brake materials containing different amounts of ZrSiO4 dry sliding against SiCp reinforced Al matrix composites

    International Nuclear Information System (INIS)

    Zhang Shaoyang; Wang Fuping

    2007-01-01

    Low friction levels for brake materials dry sliding against Al matrix composites (Al-MMCs) were observed. Al matrix composites reinforced with 30 vol.% SiC p (34 μm) were used first to fabricate a new brake drum in place of the conventional cast iron brake drum for a Chase Machine. Experimental studies on the brake materials differing in amounts of zirconium silicate (0 wt%, 4 wt%, 8 wt%, and 12 wt% ZrSiO 4 ) dry sliding against the Al-MMCs drum were performed on the Chase Machine in order to examine their effects on friction and wear performances. The test procedures include friction fade and recovery, load and speed sensitivities at 177 deg. C and 316 deg. C, and wear. Experimental results show that the brake material containing 8 wt% ZrSiO 4 had the best wear resistance and higher friction level. The brake material containing 12 wt% ZrSiO 4 had the highest friction level, but wear increased rapidly. The deterioration of the latter wear suggests that this brake material is unreliable in commercial applications

  1. Occupational exposures and chronic obstructive pulmonary disease (COPD): comparison of a COPD-specific job exposure matrix and expert-evaluated occupational exposures.

    Science.gov (United States)

    Kurth, Laura; Doney, Brent; Weinmann, Sheila

    2017-03-01

    To compare the occupational exposure levels assigned by our National Institute for Occupational Safety and Health chronic obstructive pulmonary disease-specific job exposure matrix (NIOSH COPD JEM) and by expert evaluation of detailed occupational information for various jobs held by members of an integrated health plan in the Northwest USA. We analysed data from a prior study examining COPD and occupational exposures. Jobs were assigned exposure levels using 2 methods: (1) the COPD JEM and (2) expert evaluation. Agreement (Cohen's κ coefficients), sensitivity and specificity were calculated to compare exposure levels assigned by the 2 methods for 8 exposure categories. κ indicated slight to moderate agreement (0.19-0.51) between the 2 methods and was highest for organic dust and overall exposure. Sensitivity of the matrix ranged from 33.9% to 68.5% and was highest for sensitisers, diesel exhaust and overall exposure. Specificity ranged from 74.7% to 97.1% and was highest for fumes, organic dust and mineral dust. This COPD JEM was compared with exposures assigned by experts and offers a generalisable approach to assigning occupational exposure. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

  2. Comparison of Regenerative Tissue Quality following Matrix-Associated Cell Implantation Using Amplified Chondrocytes Compared to Synovium-Derived Stem Cells in a Rabbit Model for Cartilage Lesions

    DEFF Research Database (Denmark)

    Schmal, Hagen; Kowal, Justyna M; Kassem, Moustapha

    2018-01-01

    Known problems of the autologous chondrocyte implantation motivate the search for cellular alternatives. The aim of the study was to test the potential of synovium-derived stem cells (SMSC) to regenerate cartilage using a matrix-associated implantation. In an osteochondral defect model of the med......Known problems of the autologous chondrocyte implantation motivate the search for cellular alternatives. The aim of the study was to test the potential of synovium-derived stem cells (SMSC) to regenerate cartilage using a matrix-associated implantation. In an osteochondral defect model...... of the medial femoral condyle in a rabbit, a collagen membrane was seeded with either culture-expanded allogenic chondrocytes or SMSC and then transplanted into the lesion. A tailored piece synovium served as a control. Rabbit SMSC formed typical cartilage in vitro. Macroscopic evaluation of defect healing...... and the thickness of the regenerated tissue did not reveal a significant difference between the intervention groups. However, instantaneous and shear modulus, reflecting the biomechanical strength of the repair tissue, was superior in the implantation group using allogenic chondrocytes (p

  3. Form of multicomponent Fickian diffusion coefficients matrix

    International Nuclear Information System (INIS)

    Wambui Mutoru, J.; Firoozabadi, Abbas

    2011-01-01

    Highlights: → Irreversible thermodynamics establishes form of multicomponent diffusion coefficients. → Phenomenological coefficients and thermodynamic factors affect sign of diffusion coefficients. → Negative diagonal elements of diffusion coefficients matrix can occur in non-ideal mixtures. → Eigenvalues of the matrix of Fickian diffusion coefficients may not be all real. - Abstract: The form of multicomponent Fickian diffusion coefficients matrix in thermodynamically stable mixtures is established based on the form of phenomenological coefficients and thermodynamic factors. While phenomenological coefficients form a symmetric positive definite matrix, the determinant of thermodynamic factors matrix is positive. As a result, the Fickian diffusion coefficients matrix has a positive determinant, but its elements - including diagonal elements - can be negative. Comprehensive survey of reported diffusion coefficients data for ternary and quaternary mixtures, confirms that invariably the determinant of the Fickian diffusion coefficients matrix is positive.

  4. International comparison of the factors influencing reimbursement of targeted anti-cancer drugs.

    Science.gov (United States)

    Lim, Carol Sunghye; Lee, Yun-Gyoo; Koh, Youngil; Heo, Dae Seog

    2014-11-29

    Reimbursement policies for anti-cancer drugs vary among countries even though they rely on the same clinical evidence. We compared the pattern of publicly funded drug programs and analyzed major factors influencing the differences. We investigated reimbursement policies for 19 indications with targeted anti-cancer drugs that are used variably across ten countries. The available incremental cost-effectiveness ratio (ICER) data were retrieved for each indication. Based on the comparison between actual reimbursement decisions and the ICERs, we formulated a reimbursement adequacy index (RAI): calculating the proportion of cost-effective decisions, either reimbursement of cost-effective indications or non-reimbursement of cost-ineffective indications, out of the total number of indications for each country. The relationship between RAI and other indices were analyzed, including governmental dependency on health technology assessment, as well as other parameters for health expenditure. All the data used in this study were gathered from sources publicly available online. Japan and France were the most likely to reimburse indications (16/19), whereas Sweden and the United Kingdom were the least likely to reimburse them (5/19 and 6/19, respectively). Indications with high cost-effectiveness values were more likely to be reimbursed (ρ = -0.68, P = 0.001). The three countries with high RAI scores each had a healthcare system that was financed by general taxation. Although reimbursement policies for anti-cancer drugs vary among countries, we found a strong correlation of reimbursements for those indications with lower ICERs. Countries with healthcare systems financed by general taxation demonstrated greater cost-effectiveness as evidenced by reimbursement decisions of anti-cancer drugs.

  5. A comparison of usability factors of four mobile devices for accessing healthcare information by adolescents.

    Science.gov (United States)

    Sheehan, B; Lee, Y; Rodriguez, M; Tiase, V; Schnall, R

    2012-01-01

    Mobile health (mHealth) is a growing field aimed at developing mobile information and communication technologies for healthcare. Adolescents are known for their ubiquitous use of mobile technologies in everyday life. However, the use of mHealth tools among adolescents is not well described. We examined the usability of four commonly used mobile devices (an iPhone, an Android with touchscreen keyboard, an Android with built-in keyboard, and an iPad) for accessing healthcare information among a group of urban-dwelling adolescents. Guided by the FITT (Fit between Individuals, Task, and Technology) framework, a thinkaloud protocol was combined with a questionnaire to describe usability on three dimensions: 1) task-technology fit; 2) individual-technology fit; and 3) individual-task fit. For task-technology fit, we compared the efficiency, and effectiveness of each of the devices tested and found that the iPhone was the most usable had the fewest errors and prompts and had the lowest mean overall task time For individual-task fit, we compared efficiency and learnability measures by website tasks and found no statistically significant effect on tasks steps, task time and number of errors. Following our comparison of success rates by website tasks, we compared the difference between two mobile applications which were used for diet tracking and found statistically significant effect on tasks steps, task time and number of errors. For individual-technology fit, interface quality was significantly different across devices indicating that this is an important factor to be considered in developing future mobile devices. All of our users were able to complete all of the tasks, however the time needed to complete the tasks was significantly different by mobile device and mHealth application. Future design of mobile technology and mHealth applications should place particular importance on interface quality.

  6. Expression and clinical significance of extracellular matrix protein 1 and vascular endothelial growth factor-C in lymphatic metastasis of human breast cancer

    International Nuclear Information System (INIS)

    Wu, Qiu-Wan; She, Hong-Qiang; Liang, Jing; Huang, Yu-Fan; Yang, Qing-Mo; Yang, Qiao-Lu; Zhang, Zhi-Ming

    2012-01-01

    Extracellular matrix protein 1 (ECM1) and vascular endothelial growth factor-C (VEGF-C) are secretory glycoproteins that are associated with lymphangiogenesis; these proteins could, therefore, play important roles in the lymphatic dissemination of tumors. However, very little is known about their potential roles in lymphangiogenesis. The aim of this study was to investigate whether correlations exist between ECM1 and VEGF-C in human breast cancer, lymphangiogenesis, and the clinicopathological characteristics of the disease. ECM1 and VEGF-C mRNA and protein expression levels in 41 patients were investigated using real-time reverse transcriptase polymerase chain reaction (RT-PCR), or immunohistochemical (IHC) staining of breast cancer tissue, matched noncancerous breast epithelial tissues, and suspicious metastatic axillary lymph nodes. D2-40 labelled lymph vessels and lymphatic microvessel density (LMVD) were counted. Correlations between ECM1 or VEGF-C protein expression levels, LMVD, and clinicopathological parameters were statistically tested. The rate of ECM1 positive staining in breast cancer tissues was higher (31/41, 75.6%) than that in the corresponding epithelial tissues (4/41, 9.8%, P < 0.001) and lymph nodes (13/41, 31.7%, P < 0.001). Similarly, the VEGF-C expression rate in cancer specimens was higher (33/41, 80.5%) than in epithelial tissues (19/41, 46.3%, P < 0.01) or lymph nodes (15/41, 36.6%, P < 0.01). Higher ECM1 and VEGF-C mRNA expression levels were also detected in the tumor tissues, compared to the non-cancerous tissue types or lymph nodes (P < 0.05). ECM1 protein expression was positively correlated with the estrogen receptor status (P < 0.05) and LMVD (P < 0.05). LMVD in the ECM1- and VEGF-C-positive tumor specimens was higher than that in the tissue types with negative staining (P < 0.05). Both ECM1 and VEGF-C were overexpressed in breast cancer tissue samples. ECM1 expression was positively correlated with estrogen responsiveness and the

  7. [Resolving characteristic of CDOM by excitation-emission matrix spectroscopy combined with parallel factor analysis in the seawater of outer Yangtze Estuary in Autumn in 2010].

    Science.gov (United States)

    Yan, Li-Hong; Chen, Xue-Jun; Su, Rong-Guo; Han, Xiu-Rong; Zhang, Chuan-Song; Shi, Xiao-Yong

    2013-01-01

    The distribution and estuarine behavior of fluorescent components of chromophoric dissolved organic matter in the seawater of outer Yangtze Estuary were determined by fluorescence excitation emission matrix spectra combined with parallel factor analysis. Six individual fluorescent components were identified by PARAFAC models, including three terrestrial humic-like components C1 [330 nm/390(430) nm], C2 (390 nm/480 nm), C3 (360 nm/440 nm), marine biological production component C5 (300 nm/400 nm) and protein-like components C4 (290 nm/350 nm) and C6 (275 nm/300 nm). The results indicated that C1, C2, and C3 showed a conservative mixing behavior in the whole estuarine region, especially in high-salinity region. And the fluorescence intensity proportion of C1 and C3 decreased with increase of salinity and fluorescence intensity proportion of C2 kept constant with increase of salinity in the whole estuarine region. While C4 showed conservative mixing behavior in low-salinity region and non-conservative mixing behavior in high-salinity region, and fluorescence intensity proportion of C4 increased with increase of salinity. However, C5 and C6 showed a non-conservative mixing behavior and fluorescence intensity proportion increased with increase of salinity in high-salinity region. Significantly spatial difference was recorded for CDOM absorption coefficient in the coastal region and in the open water areas with the highest value in coastal region and the lowest value in the open water areas. The scope of absorption coefficient and absorption slope was higher in coastal region than that in the open water areas. Significantly positive correlations were found between CDOM absorption coefficient and the fluorescence intensities of C1, C2, C3, and C4, but no significant correlation was found between C5 and C6, suggesting that the river inputs contributed to the coastal areas, while CDOM in the open water areas was affected by terrestrial inputs and phytoplankton degradation.

  8. Green tea polyphenol epigallocatechin-3-gallate inhibits advanced glycation end product-induced expression of tumor necrosis factor-alpha and matrix metalloproteinase-13 in human chondrocytes.

    Science.gov (United States)

    Rasheed, Zafar; Anbazhagan, Arivarasu N; Akhtar, Nahid; Ramamurthy, Sangeetha; Voss, Frank R; Haqqi, Tariq M

    2009-01-01

    The major risk factor for osteoarthritis (OA) is aging, but the mechanisms underlying this risk are only partly understood. Age-related accumulation of advanced glycation end products (AGEs) can activate chondrocytes and induce the production of proinf