Sample records for factors including matrix

  1. Scalable non-negative matrix tri-factorization.

    PubMed

    Čopar, Andrej; Žitnik, Marinka; Zupan, Blaž

    2017-01-01

    Matrix factorization is a well established pattern discovery tool that has seen numerous applications in biomedical data analytics, such as gene expression co-clustering, patient stratification, and gene-disease association mining. Matrix factorization learns a latent data model that takes a data matrix and transforms it into a latent feature space enabling generalization, noise removal and feature discovery. However, factorization algorithms are numerically intensive, and hence there is a pressing challenge to scale current algorithms to work with large datasets. Our focus in this paper is matrix tri-factorization, a popular method that is not limited by the assumption of standard matrix factorization about data residing in one latent space. Matrix tri-factorization solves this by inferring a separate latent space for each dimension in a data matrix, and a latent mapping of interactions between the inferred spaces, making the approach particularly suitable for biomedical data mining. We developed a block-wise approach for latent factor learning in matrix tri-factorization. The approach partitions a data matrix into disjoint submatrices that are treated independently and fed into a parallel factorization system. An appealing property of the proposed approach is its mathematical equivalence with serial matrix tri-factorization. In a study on large biomedical datasets we show that our approach scales well on multi-processor and multi-GPU architectures. On a four-GPU system we demonstrate that our approach can be more than 100-times faster than its single-processor counterpart. A general approach for scaling non-negative matrix tri-factorization is proposed. The approach is especially useful parallel matrix factorization implemented in a multi-GPU environment. We expect the new approach will be useful in emerging procedures for latent factor analysis, notably for data integration, where many large data matrices need to be collectively factorized.

  2. Matrix completion by deep matrix factorization.

    PubMed

    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. Investigation on Constrained Matrix Factorization for Hyperspectral Image Analysis

    DTIC Science & Technology

    2005-07-25

    analysis. Keywords: matrix factorization; nonnegative matrix factorization; linear mixture model ; unsupervised linear unmixing; hyperspectral imagery...spatial resolution permits different materials present in the area covered by a single pixel. The linear mixture model says that a pixel reflectance in...in r. In the linear mixture model , r is considered as the linear mixture of m1, m2, …, mP as nMαr += (1) where n is included to account for

  4. Fast iterative image reconstruction using sparse matrix factorization with GPU acceleration

    NASA Astrophysics Data System (ADS)

    Zhou, Jian; Qi, Jinyi

    2011-03-01

    Statistically based iterative approaches for image reconstruction have gained much attention in medical imaging. An accurate system matrix that defines the mapping from the image space to the data space is the key to high-resolution image reconstruction. However, an accurate system matrix is often associated with high computational cost and huge storage requirement. Here we present a method to address this problem by using sparse matrix factorization and parallel computing on a graphic processing unit (GPU).We factor the accurate system matrix into three sparse matrices: a sinogram blurring matrix, a geometric projection matrix, and an image blurring matrix. The sinogram blurring matrix models the detector response. The geometric projection matrix is based on a simple line integral model. The image blurring matrix is to compensate for the line-of-response (LOR) degradation due to the simplified geometric projection matrix. The geometric projection matrix is precomputed, while the sinogram and image blurring matrices are estimated by minimizing the difference between the factored system matrix and the original system matrix. The resulting factored system matrix has much less number of nonzero elements than the original system matrix and thus substantially reduces the storage and computation cost. The smaller size also allows an efficient implement of the forward and back projectors on GPUs, which have limited amount of memory. Our simulation studies show that the proposed method can dramatically reduce the computation cost of high-resolution iterative image reconstruction. The proposed technique is applicable to image reconstruction for different imaging modalities, including x-ray CT, PET, and SPECT.

  5. Estimating Depolarization with the Jones Matrix Quality Factor

    NASA Astrophysics Data System (ADS)

    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.

  6. Synthetic Division and Matrix Factorization

    ERIC Educational Resources Information Center

    Barabe, Samuel; Dubeau, Franc

    2007-01-01

    Synthetic division is viewed as a change of basis for polynomials written under the Newton form. Then, the transition matrices obtained from a sequence of changes of basis are used to factorize the inverse of a bidiagonal matrix or a block bidiagonal matrix.

  7. Relational Learning via Collective Matrix Factorization

    DTIC Science & Technology

    2008-06-01

    well-known example of such a schema is pLSI- pHITS [13], which models document-word counts and document-document citations: E1 = words and E2 = E3...relational co- clustering include pLSI, pLSI- pHITS , the symmetric block models of Long et. al. [23, 24, 25], and Bregman tensor clustering [5] (which can...to pLSI- pHITS In this section we provide an example where the additional flexibility of collective matrix factorization leads to better results; and

  8. Recovering hidden diagonal structures via non-negative matrix factorization with multiple constraints.

    PubMed

    Yang, Xi; Han, Guoqiang; Cai, Hongmin; Song, Yan

    2017-03-31

    Revealing data with intrinsically diagonal block structures is particularly useful for analyzing groups of highly correlated variables. Earlier researches based on non-negative matrix factorization (NMF) have been shown to be effective in representing such data by decomposing the observed data into two factors, where one factor is considered to be the feature and the other the expansion loading from a linear algebra perspective. If the data are sampled from multiple independent subspaces, the loading factor would possess a diagonal structure under an ideal matrix decomposition. However, the standard NMF method and its variants have not been reported to exploit this type of data via direct estimation. To address this issue, a non-negative matrix factorization with multiple constraints model is proposed in this paper. The constraints include an sparsity norm on the feature matrix and a total variational norm on each column of the loading matrix. The proposed model is shown to be capable of efficiently recovering diagonal block structures hidden in observed samples. An efficient numerical algorithm using the alternating direction method of multipliers model is proposed for optimizing the new model. Compared with several benchmark models, the proposed method performs robustly and effectively for simulated and real biological data.

  9. Estimating gene function with least squares nonnegative matrix factorization.

    PubMed

    Wang, Guoli; Ochs, Michael F

    2007-01-01

    Nonnegative matrix factorization is a machine learning algorithm that has extracted information from data in a number of fields, including imaging and spectral analysis, text mining, and microarray data analysis. One limitation with the method for linking genes through microarray data in order to estimate gene function is the high variance observed in transcription levels between different genes. Least squares nonnegative matrix factorization uses estimates of the uncertainties on the mRNA levels for each gene in each condition, to guide the algorithm to a local minimum in normalized chi2, rather than a Euclidean distance or divergence between the reconstructed data and the data itself. Herein, application of this method to microarray data is demonstrated in order to predict gene function.

  10. Approximate method of variational Bayesian matrix factorization/completion with sparse prior

    NASA Astrophysics Data System (ADS)

    Kawasumi, Ryota; Takeda, Koujin

    2018-05-01

    We derive the analytical expression of a matrix factorization/completion solution by the variational Bayes method, under the assumption that the observed matrix is originally the product of low-rank, dense and sparse matrices with additive noise. We assume the prior of a sparse matrix is a Laplace distribution by taking matrix sparsity into consideration. Then we use several approximations for the derivation of a matrix factorization/completion solution. By our solution, we also numerically evaluate the performance of a sparse matrix reconstruction in matrix factorization, and completion of a missing matrix element in matrix completion.

  11. The Incremental Multiresolution Matrix Factorization Algorithm

    PubMed Central

    Ithapu, Vamsi K.; Kondor, Risi; Johnson, Sterling C.; Singh, Vikas

    2017-01-01

    Multiresolution analysis and matrix factorization are foundational tools in computer vision. In this work, we study the interface between these two distinct topics and obtain techniques to uncover hierarchical block structure in symmetric matrices – an important aspect in the success of many vision problems. Our new algorithm, the incremental multiresolution matrix factorization, uncovers such structure one feature at a time, and hence scales well to large matrices. We describe how this multiscale analysis goes much farther than what a direct “global” factorization of the data can identify. We evaluate the efficacy of the resulting factorizations for relative leveraging within regression tasks using medical imaging data. We also use the factorization on representations learned by popular deep networks, providing evidence of their ability to infer semantic relationships even when they are not explicitly trained to do so. We show that this algorithm can be used as an exploratory tool to improve the network architecture, and within numerous other settings in vision. PMID:29416293

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

    DOEpatents

    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.

  13. Adaptive multi-view clustering based on nonnegative matrix factorization and pairwise co-regularization

    NASA Astrophysics Data System (ADS)

    Zhang, Tianzhen; Wang, Xiumei; Gao, Xinbo

    2018-04-01

    Nowadays, several datasets are demonstrated by multi-view, which usually include shared and complementary information. Multi-view clustering methods integrate the information of multi-view to obtain better clustering results. Nonnegative matrix factorization has become an essential and popular tool in clustering methods because of its interpretation. However, existing nonnegative matrix factorization based multi-view clustering algorithms do not consider the disagreement between views and neglects the fact that different views will have different contributions to the data distribution. In this paper, we propose a new multi-view clustering method, named adaptive multi-view clustering based on nonnegative matrix factorization and pairwise co-regularization. The proposed algorithm can obtain the parts-based representation of multi-view data by nonnegative matrix factorization. Then, pairwise co-regularization is used to measure the disagreement between views. There is only one parameter to auto learning the weight values according to the contribution of each view to data distribution. Experimental results show that the proposed algorithm outperforms several state-of-the-arts algorithms for multi-view clustering.

  14. EPA Positive Matrix Factorization (PMF) 3.0 Fundamentals & User Guide

    EPA Science Inventory

    Positive matrix factorization (PMF) is a multivariate factor analysis tool that decomposes a matrix of ambient data into two matrices - factor contributions and factor profiles - which then need to be interpreted by an analyst as to what source types are represented using measure...

  15. Algorithms for Solvents and Spectral Factors of Matrix Polynomials

    DTIC Science & Technology

    1981-01-01

    spectral factors of matrix polynomials LEANG S. SHIEHt, YIH T. TSAYt and NORMAN P. COLEMANt A generalized Newton method , based on the contracted gradient...of a matrix poly- nomial, is derived for solving the right (left) solvents and spectral factors of matrix polynomials. Two methods of selecting initial...estimates for rapid convergence of the newly developed numerical method are proposed. Also, new algorithms for solving complete sets of the right

  16. THE U.S. ENVIRONMENTAL PROTECTION AGENCY VERSION OF POSITIVE MATRIX FACTORIZATION

    EPA Science Inventory

    The abstract describes some of the special features of the EPA's version of Positive Matrix Factorization that is freely distributed. Features include descriptions of the Graphical User Interface, an approach for estimating errors in the modeled solutions, and future development...

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

    NASA Astrophysics Data System (ADS)

    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.

  18. Matrix heat exchanger including a liquid, thermal couplant

    DOEpatents

    Fewell, Thomas E.; Ward, Charles T.

    1976-01-01

    A tube-to-tube heat exchanger is disclosed with a thermally conductive matrix between and around the tubes to define annuli between the tubes and matrix. The annuli are filled to a level with a molten metal or alloy to provide a conductive heat transfer path from one tube through the matrix to the second tube. A matrix heat exchanger of this type is particularly useful for heat transfer between fluids which would react should one leak into the second.

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

    PubMed

    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.

  20. A quasi-likelihood approach to non-negative matrix factorization

    PubMed Central

    Devarajan, Karthik; Cheung, Vincent C.K.

    2017-01-01

    A unified approach to non-negative matrix factorization based on the theory of generalized linear models is proposed. This approach embeds a variety of statistical models, including the exponential family, within a single theoretical framework and provides a unified view of such factorizations from the perspective of quasi-likelihood. Using this framework, a family of algorithms for handling signal-dependent noise is developed and its convergence proven using the Expectation-Maximization algorithm. In addition, a measure to evaluate the goodness-of-fit of the resulting factorization is described. The proposed methods allow modeling of non-linear effects via appropriate link functions and are illustrated using an application in biomedical signal processing. PMID:27348511

  1. HIGH DIMENSIONAL COVARIANCE MATRIX ESTIMATION IN APPROXIMATE FACTOR MODELS

    PubMed Central

    Fan, Jianqing; Liao, Yuan; Mincheva, Martina

    2012-01-01

    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. PMID:22661790

  2. Sparse nonnegative matrix factorization with ℓ0-constraints

    PubMed Central

    Peharz, Robert; Pernkopf, Franz

    2012-01-01

    Although nonnegative matrix factorization (NMF) favors a sparse and part-based representation of nonnegative data, there is no guarantee for this behavior. Several authors proposed NMF methods which enforce sparseness by constraining or penalizing the ℓ1-norm of the factor matrices. On the other hand, little work has been done using a more natural sparseness measure, the ℓ0-pseudo-norm. In this paper, we propose a framework for approximate NMF which constrains the ℓ0-norm of the basis matrix, or the coefficient matrix, respectively. For this purpose, techniques for unconstrained NMF can be easily incorporated, such as multiplicative update rules, or the alternating nonnegative least-squares scheme. In experiments we demonstrate the benefits of our methods, which compare to, or outperform existing approaches. PMID:22505792

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

    PubMed

    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.

  4. Normalization Of Thermal-Radiation Form-Factor Matrix

    NASA Technical Reports Server (NTRS)

    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.

  5. Cryogenic regenerator including sarancarbon heat conduction matrix

    NASA Technical Reports Server (NTRS)

    Jones, Jack A. (Inventor); Petrick, S. Walter (Inventor); Britcliffe, Michael J. (Inventor)

    1989-01-01

    A saran carbon matrix is employed to conduct heat through the heat storing volume of a cryogenic regenerator. When helium is adsorbed into the saran carbon matrix, the combination exhibits a volumetric specific heat much higher than previously used lead balls. A helium adsorbed saran regenerator should allow much lower refrigerator temperatures than those practically obtainable with lead based regenerators for regenerator type refrigeration systems.

  6. Pattern identification in time-course gene expression data with the CoGAPS matrix factorization.

    PubMed

    Fertig, Elana J; Stein-O'Brien, Genevieve; Jaffe, Andrew; Colantuoni, Carlo

    2014-01-01

    Patterns in time-course gene expression data can represent the biological processes that are active over the measured time period. However, the orthogonality constraint in standard pattern-finding algorithms, including notably principal components analysis (PCA), confounds expression changes resulting from simultaneous, non-orthogonal biological processes. Previously, we have shown that Markov chain Monte Carlo nonnegative matrix factorization algorithms are particularly adept at distinguishing such concurrent patterns. One such matrix factorization is implemented in the software package CoGAPS. We describe the application of this software and several technical considerations for identification of age-related patterns in a public, prefrontal cortex gene expression dataset.

  7. Bayesian Factor Analysis When Only a Sample Covariance Matrix Is Available

    ERIC Educational Resources Information Center

    Hayashi, Kentaro; Arav, Marina

    2006-01-01

    In traditional factor analysis, the variance-covariance matrix or the correlation matrix has often been a form of inputting data. In contrast, in Bayesian factor analysis, the entire data set is typically required to compute the posterior estimates, such as Bayes factor loadings and Bayes unique variances. We propose a simple method for computing…

  8. Spatial operator factorization and inversion of the manipulator mass matrix

    NASA Technical Reports Server (NTRS)

    Rodriguez, Guillermo; Kreutz-Delgado, Kenneth

    1992-01-01

    This paper advances two linear operator factorizations of the manipulator mass matrix. Embedded in the factorizations are many of the techniques that are regarded as very efficient computational solutions to inverse and forward dynamics problems. The operator factorizations provide a high-level architectural understanding of the mass matrix and its inverse, which is not visible in the detailed algorithms. They also lead to a new approach to the development of computer programs or organize complexity in robot dynamics.

  9. Continuous analogues of matrix factorizations

    PubMed Central

    Townsend, Alex; Trefethen, Lloyd N.

    2015-01-01

    Analogues of singular value decomposition (SVD), QR, LU and Cholesky factorizations are presented for problems in which the usual discrete matrix is replaced by a ‘quasimatrix’, continuous in one dimension, or a ‘cmatrix’, continuous in both dimensions. Two challenges arise: the generalization of the notions of triangular structure and row and column pivoting to continuous variables (required in all cases except the SVD, and far from obvious), and the convergence of the infinite series that define the cmatrix factorizations. Our generalizations of triangularity and pivoting are based on a new notion of a ‘triangular quasimatrix’. Concerning convergence of the series, we prove theorems asserting convergence provided the functions involved are sufficiently smooth. PMID:25568618

  10. TRASYS form factor matrix normalization

    NASA Technical Reports Server (NTRS)

    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.

  11. Background recovery via motion-based robust principal component analysis with matrix factorization

    NASA Astrophysics Data System (ADS)

    Pan, Peng; Wang, Yongli; Zhou, Mingyuan; Sun, Zhipeng; He, Guoping

    2018-03-01

    Background recovery is a key technique in video analysis, but it still suffers from many challenges, such as camouflage, lighting changes, and diverse types of image noise. Robust principal component analysis (RPCA), which aims to recover a low-rank matrix and a sparse matrix, is a general framework for background recovery. The nuclear norm is widely used as a convex surrogate for the rank function in RPCA, which requires computing the singular value decomposition (SVD), a task that is increasingly costly as matrix sizes and ranks increase. However, matrix factorization greatly reduces the dimension of the matrix for which the SVD must be computed. Motion information has been shown to improve low-rank matrix recovery in RPCA, but this method still finds it difficult to handle original video data sets because of its batch-mode formulation and implementation. Hence, in this paper, we propose a motion-assisted RPCA model with matrix factorization (FM-RPCA) for background recovery. Moreover, an efficient linear alternating direction method of multipliers with a matrix factorization (FL-ADM) algorithm is designed for solving the proposed FM-RPCA model. Experimental results illustrate that the method provides stable results and is more efficient than the current state-of-the-art algorithms.

  12. Positive Matrix Factorization Model for environmental data analyses

    EPA Pesticide Factsheets

    Positive Matrix Factorization is a receptor model developed by EPA to provide scientific support for current ambient air quality standards and implement those standards by identifying and quantifying the relative contributions of air pollution sources.

  13. 77 FR 12081 - Keithley Instruments Including On-Site Leased Workers from StaffMatrix and ADECCO, Solon, OH...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-02-28

    ... DEPARTMENT OF LABOR Employment and Training Administration [TA-W-80,264] Keithley Instruments Including On-Site Leased Workers from StaffMatrix and ADECCO, Solon, OH; Amended Certification Regarding... Instruments, including on-site leased workers from StaffMatrix and Adecco, Solon, Ohio, who became totally or...

  14. Regular approximate factorization of a class of matrix-function with an unstable set of partial indices

    PubMed Central

    Rogosin, S.

    2018-01-01

    From the classic work of Gohberg & Krein (1958 Uspekhi Mat. Nauk. XIII, 3–72. (Russian).), it is well known that the set of partial indices of a non-singular matrix function may change depending on the properties of the original matrix. More precisely, it was shown that if the difference between the largest and the smallest partial indices is larger than unity then, in any neighbourhood of the original matrix function, there exists another matrix function possessing a different set of partial indices. As a result, the factorization of matrix functions, being an extremely difficult process itself even in the case of the canonical factorization, remains unresolvable or even questionable in the case of a non-stable set of partial indices. Such a situation, in turn, has became an unavoidable obstacle to the application of the factorization technique. This paper sets out to answer a less ambitious question than that of effective factorizing matrix functions with non-stable sets of partial indices, and instead focuses on determining the conditions which, when having known factorization of the limiting matrix function, allow to construct another family of matrix functions with the same origin that preserves the non-stable partial indices and is close to the original set of the matrix functions. PMID:29434502

  15. Regular approximate factorization of a class of matrix-function with an unstable set of partial indices.

    PubMed

    Mishuris, G; Rogosin, S

    2018-01-01

    From the classic work of Gohberg & Krein (1958 Uspekhi Mat. Nauk. XIII , 3-72. (Russian).), it is well known that the set of partial indices of a non-singular matrix function may change depending on the properties of the original matrix. More precisely, it was shown that if the difference between the largest and the smallest partial indices is larger than unity then, in any neighbourhood of the original matrix function, there exists another matrix function possessing a different set of partial indices. As a result, the factorization of matrix functions, being an extremely difficult process itself even in the case of the canonical factorization, remains unresolvable or even questionable in the case of a non-stable set of partial indices. Such a situation, in turn, has became an unavoidable obstacle to the application of the factorization technique. This paper sets out to answer a less ambitious question than that of effective factorizing matrix functions with non-stable sets of partial indices, and instead focuses on determining the conditions which, when having known factorization of the limiting matrix function, allow to construct another family of matrix functions with the same origin that preserves the non-stable partial indices and is close to the original set of the matrix functions.

  16. EPA Positive Matrix Factorization (PMF) 5.0 Fundamentals and User Guide

    EPA Science Inventory

    PMF is a multivariate factor analysis tool that decomposes a matrix of speciated sample data into two matrices: factor contributions (G) and factor profiles (F). These factor profiles need to be interpreted by the user to identify the source types that may be contributing to the ...

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

    NASA Astrophysics Data System (ADS)

    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).

  18. Quantification of various growth factors in different demineralized bone matrix preparations.

    PubMed

    Wildemann, B; Kadow-Romacker, A; Haas, N P; Schmidmaier, G

    2007-05-01

    Besides autografts, allografts, and synthetic materials, demineralized bone matrix (DBM) is used for bone defect filling and treatment of non-unions. Different DBM formulations are introduced in clinic since years. However, little is known about the presents and quantities of growth factors in DBM. Aim of the present study was the quantification of eight growth factors important for bone healing in three different "off the shelf" DBM formulations, which are already in human use: DBX putty, Grafton DBM putty, and AlloMatrix putty. All three DBM formulations are produced from human donor tissue but they differ in the substitutes added. From each of the three products 10 different lots were analyzed. Protein was extracted from the samples with Guanidine HCL/EDTA method and human ELISA kits were used for growth factor quantification. Differences between the three different products were seen in total protein contend and the absolute growth factor values but also a large variability between the different lots was found. The order of the growth factors, however, is almost comparable between the materials. In the three investigated materials FGF basic and BMP-4 were not detectable in any analyzed sample. BMP-2 revealed the highest concentration extractable from the samples with approximately 3.6 microg/g tissue without a significant difference between the three DBM formulations. In DBX putty significantly more TGF-beta1 and FGFa were measurable compared to the two other DBMs. IGF-I revealed the significantly highest value in the AlloMatrix and PDGF in Grafton. No differences were accessed for VEGF. Due to the differences in the growth factor concentration between the individual samples, independently from the product formulation, further analyzes are required to optimize the clinical outcome of the used demineralized bone matrix. Copyright 2006 Wiley Periodicals, Inc.

  19. Identification of Extracellular Matrix Components and Biological Factors in Micronized Dehydrated Human Amnion/Chorion Membrane

    PubMed Central

    Lei, Jennifer; Priddy, Lauren B.; Lim, Jeremy J.; Massee, Michelle; Koob, Thomas J.

    2017-01-01

    Objective: The use of bioactive extracellular matrix (ECM) grafts such as amniotic membranes is an attractive treatment option for enhancing wound repair. In this study, the concentrations, activity, and distribution of matrix components, growth factors, proteases, and inhibitors were evaluated in PURION® Processed, micronized, dehydrated human amnion/chorion membrane (dHACM; MiMedx Group, Inc.). Approach: ECM components in dHACM tissue were assessed by using immunohistochemical staining, and growth factors, cytokines, proteases, and inhibitors were quantified by using single and multiplex ELISAs. The activities of proteases that were native to the tissue were determined via gelatin zymography and EnzChek® activity assay. Results: dHACM tissue contained the ECM components collagens I and IV, hyaluronic acid, heparin sulfate proteoglycans, fibronectin, and laminin. In addition, numerous growth factors, cytokines, chemokines, proteases, and protease inhibitors that are known to play a role in the wound-healing process were quantified in dHACM. Though matrix metalloproteinases (MMPs) were present in dHACM tissues, inhibitors of MMPs overwhelmingly outnumbered the MMP enzymes by an overall molar ratio of 28:1. Protease activity assays revealed that the MMPs in the tissue existed primarily either in their latent form or complexed with inhibitors. Innovation: This is the first study to characterize components that function in wound healing, including inhibitor and protease content and activity, in micronized dHACM. Conclusion: A variety of matrix components and growth factors, as well as proteases and their inhibitors, were identified in micronized dHACM, providing a better understanding of how micronized dHACM tissue can be used to effectively promote wound repair. PMID:28224047

  20. Identification of Extracellular Matrix Components and Biological Factors in Micronized Dehydrated Human Amnion/Chorion Membrane.

    PubMed

    Lei, Jennifer; Priddy, Lauren B; Lim, Jeremy J; Massee, Michelle; Koob, Thomas J

    2017-02-01

    Objective: The use of bioactive extracellular matrix (ECM) grafts such as amniotic membranes is an attractive treatment option for enhancing wound repair. In this study, the concentrations, activity, and distribution of matrix components, growth factors, proteases, and inhibitors were evaluated in PURION ® Processed, micronized, dehydrated human amnion/chorion membrane (dHACM; MiMedx Group, Inc.). Approach: ECM components in dHACM tissue were assessed by using immunohistochemical staining, and growth factors, cytokines, proteases, and inhibitors were quantified by using single and multiplex ELISAs. The activities of proteases that were native to the tissue were determined via gelatin zymography and EnzChek ® activity assay. Results: dHACM tissue contained the ECM components collagens I and IV, hyaluronic acid, heparin sulfate proteoglycans, fibronectin, and laminin. In addition, numerous growth factors, cytokines, chemokines, proteases, and protease inhibitors that are known to play a role in the wound-healing process were quantified in dHACM. Though matrix metalloproteinases (MMPs) were present in dHACM tissues, inhibitors of MMPs overwhelmingly outnumbered the MMP enzymes by an overall molar ratio of 28:1. Protease activity assays revealed that the MMPs in the tissue existed primarily either in their latent form or complexed with inhibitors. Innovation: This is the first study to characterize components that function in wound healing, including inhibitor and protease content and activity, in micronized dHACM. Conclusion: A variety of matrix components and growth factors, as well as proteases and their inhibitors, were identified in micronized dHACM, providing a better understanding of how micronized dHACM tissue can be used to effectively promote wound repair.

  1. Limited-memory fast gradient descent method for graph regularized nonnegative matrix factorization.

    PubMed

    Guan, Naiyang; Wei, Lei; Luo, Zhigang; Tao, Dacheng

    2013-01-01

    Graph regularized nonnegative matrix factorization (GNMF) decomposes a nonnegative data matrix X[Symbol:see text]R(m x n) to the product of two lower-rank nonnegative factor matrices, i.e.,W[Symbol:see text]R(m x r) and H[Symbol:see text]R(r x n) (r < min {m,n}) and aims to preserve the local geometric structure of the dataset by minimizing squared Euclidean distance or Kullback-Leibler (KL) divergence between X and WH. The multiplicative update rule (MUR) is usually applied to optimize GNMF, but it suffers from the drawback of slow-convergence because it intrinsically advances one step along the rescaled negative gradient direction with a non-optimal step size. Recently, a multiple step-sizes fast gradient descent (MFGD) method has been proposed for optimizing NMF which accelerates MUR by searching the optimal step-size along the rescaled negative gradient direction with Newton's method. However, the computational cost of MFGD is high because 1) the high-dimensional Hessian matrix is dense and costs too much memory; and 2) the Hessian inverse operator and its multiplication with gradient cost too much time. To overcome these deficiencies of MFGD, we propose an efficient limited-memory FGD (L-FGD) method for optimizing GNMF. In particular, we apply the limited-memory BFGS (L-BFGS) method to directly approximate the multiplication of the inverse Hessian and the gradient for searching the optimal step size in MFGD. The preliminary results on real-world datasets show that L-FGD is more efficient than both MFGD and MUR. To evaluate the effectiveness of L-FGD, we validate its clustering performance for optimizing KL-divergence based GNMF on two popular face image datasets including ORL and PIE and two text corpora including Reuters and TDT2. The experimental results confirm the effectiveness of L-FGD by comparing it with the representative GNMF solvers.

  2. The nuclear matrix protein NMP-1 is the transcription factor YY1.

    PubMed Central

    Guo, B; Odgren, P R; van Wijnen, A J; Last, T J; Nickerson, J; Penman, S; Lian, J B; Stein, J L; Stein, G S

    1995-01-01

    NMP-1 was initially identified as a nuclear matrix-associated DNA-binding factor that exhibits sequence-specific recognition for the site IV regulatory element of a histone H4 gene. This distal promoter domain is a nuclear matrix interaction site. In the present study, we show that NMP-1 is the multifunctional transcription factor YY1. Gel-shift and Western blot analyses demonstrate that NMP-1 is immunoreactive with YY1 antibody. Furthermore, purified YY1 protein specifically recognizes site IV and reconstitutes the NMP-1 complex. Western blot and gel-shift analyses indicate that YY1 is present within the nuclear matrix. In situ immunofluorescence studies show that a significant fraction of YY1 is localized in the nuclear matrix, principally but not exclusively associated with residual nucleoli. Our results confirm that NMP-1/YY1 is a ubiquitous protein that is present in both human cells and in rat osteosarcoma ROS 17/2.8 cells. The finding that NMP-1 is identical to YY1 suggests that this transcriptional regulator may mediate gene-matrix interactions. Our results are consistent with the concept that the nuclear matrix may functionally compartmentalize the eukaryotic nucleus to support regulation of gene expression. Images Fig. 2 Fig. 3 Fig. 4 Fig. 5 Fig. 6 PMID:7479833

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

    PubMed

    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.

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

    NASA Astrophysics Data System (ADS)

    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.

  5. Discriminant projective non-negative matrix factorization.

    PubMed

    Guan, Naiyang; Zhang, Xiang; Luo, Zhigang; Tao, Dacheng; Yang, Xuejun

    2013-01-01

    Projective non-negative matrix factorization (PNMF) projects high-dimensional non-negative examples X onto a lower-dimensional subspace spanned by a non-negative basis W and considers W(T) X as their coefficients, i.e., X≈WW(T) X. Since PNMF learns the natural parts-based representation Wof X, it has been widely used in many fields such as pattern recognition and computer vision. However, PNMF does not perform well in classification tasks because it completely ignores the label information of the dataset. This paper proposes a Discriminant PNMF method (DPNMF) to overcome this deficiency. In particular, DPNMF exploits Fisher's criterion to PNMF for utilizing the label information. Similar to PNMF, DPNMF learns a single non-negative basis matrix and needs less computational burden than NMF. In contrast to PNMF, DPNMF maximizes the distance between centers of any two classes of examples meanwhile minimizes the distance between any two examples of the same class in the lower-dimensional subspace and thus has more discriminant power. We develop a multiplicative update rule to solve DPNMF and prove its convergence. Experimental results on four popular face image datasets confirm its effectiveness comparing with the representative NMF and PNMF algorithms.

  6. Discriminant Projective Non-Negative Matrix Factorization

    PubMed Central

    Guan, Naiyang; Zhang, Xiang; Luo, Zhigang; Tao, Dacheng; Yang, Xuejun

    2013-01-01

    Projective non-negative matrix factorization (PNMF) projects high-dimensional non-negative examples X onto a lower-dimensional subspace spanned by a non-negative basis W and considers WT X as their coefficients, i.e., X≈WWT X. Since PNMF learns the natural parts-based representation Wof X, it has been widely used in many fields such as pattern recognition and computer vision. However, PNMF does not perform well in classification tasks because it completely ignores the label information of the dataset. This paper proposes a Discriminant PNMF method (DPNMF) to overcome this deficiency. In particular, DPNMF exploits Fisher's criterion to PNMF for utilizing the label information. Similar to PNMF, DPNMF learns a single non-negative basis matrix and needs less computational burden than NMF. In contrast to PNMF, DPNMF maximizes the distance between centers of any two classes of examples meanwhile minimizes the distance between any two examples of the same class in the lower-dimensional subspace and thus has more discriminant power. We develop a multiplicative update rule to solve DPNMF and prove its convergence. Experimental results on four popular face image datasets confirm its effectiveness comparing with the representative NMF and PNMF algorithms. PMID:24376680

  7. A novel edge-preserving nonnegative matrix factorization method for spectral unmixing

    NASA Astrophysics Data System (ADS)

    Bao, Wenxing; Ma, Ruishi

    2015-12-01

    Spectral unmixing technique is one of the key techniques to identify and classify the material in the hyperspectral image processing. A novel robust spectral unmixing method based on nonnegative matrix factorization(NMF) is presented in this paper. This paper used an edge-preserving function as hypersurface cost function to minimize the nonnegative matrix factorization. To minimize the hypersurface cost function, we constructed the updating functions for signature matrix of end-members and abundance fraction respectively. The two functions are updated alternatively. For evaluation purpose, synthetic data and real data have been used in this paper. Synthetic data is used based on end-members from USGS digital spectral library. AVIRIS Cuprite dataset have been used as real data. The spectral angle distance (SAD) and abundance angle distance(AAD) have been used in this research for assessment the performance of proposed method. The experimental results show that this method can obtain more ideal results and good accuracy for spectral unmixing than present methods.

  8. Interactions of cytokines, growth factors, and the extracellular matrix in the cellular biology of uterine leiomyomata.

    PubMed

    Sozen, Ibrahim; Arici, Aydin

    2002-07-01

    To review the available information regarding the role of cytokines, growth factors, and the extracellular matrix in the pathophysiology of uterine leiomyomata and to integrate this information in a suggested model of disease at the cellular level. A thorough literature and MEDLINE search was conducted to identify the relevant studies in the English literature published between January, 1966 and October, 2001. A model of disease at the cellular level was developed using the most likely cytokines to be involved in the pathogenesis of leiomyomata as determined by our assessment of the available literature. A number of cytokines and growth factors, including transforming growth factor-beta (TGF-beta), epidermal growth factor, monocyte chemotactic protein-1, insulin-like growth factors 1 and 2, prolactin, parathyroid-hormone-related peptide, basic fibroblast growth factor, platelet-derived growth factor, interleukin-8, and endothelin, have been investigated in myometrium and leiomyoma. Among these cytokines, TGF-beta appears to be the only growth factor that has been shown to be overexpressed in leiomyoma vs. myometrium, be hormonally-regulated both in vivo and in vitro, and be both mitogenic and fibrogenic in these tissues. In addition to the cytokines, extracellular matrix components such as collagen, fibronectin, proteoglycans, matrix metalloproteinases, and tissue inhibitors of metalloproteinases seem to play pivotal roles in the pathogenesis of leiomyomata. We believe that, given the extent and depth of the current research on the cellular biology of leiomyomata, the cellular mechanisms responsible in the pathogenesis of leiomyomata will be identified clearly within the foreseeable future. This will enable researchers to develop therapy directed against the molecules and mechanisms at the cellular level.

  9. Factors affecting fixation of heavy metals in solidified/stabilized matrix: a review.

    PubMed

    Malviya, Rachana; Chaudhary, Rubina

    2010-07-01

    In this paper, an effort has been made to understand the factors, which affect fixation of heavy metals in solidified/stabilized matrix. Various aspects related to the solidification/stabilization of different heavy metals (Ar, Ba, Cu, Cr, Pb, Zn, Hg) are reviewed. A comparative study of different binders for the fixation of each metal has also been carried out to suggest the most suitable binder, pretreatment required for the metal. Valence, speciation, pH and other factors are also considered while reviewing metal retention capacity of different matrix.

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

    PubMed

    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.

  11. Calabi-Yau structures on categories of matrix factorizations

    NASA Astrophysics Data System (ADS)

    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.

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

    NASA Astrophysics Data System (ADS)

    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.

  13. MPI-FAUN: An MPI-Based Framework for Alternating-Updating Nonnegative Matrix Factorization

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Kannan, Ramakrishnan; Ballard, Grey; Park, Haesun

    Non-negative matrix factorization (NMF) is the problem of determining two non-negative low rank factors W and H, for the given input matrix A, such that A≈WH. 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 parallel algorithms to solve the problem for big data sets. The main contribution of this work is a new, high-performance parallel computational framework for a broad class of NMF algorithms thatmore » iteratively solves alternating non-negative least squares (NLS) subproblems for W and H. 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). The framework is flexible and able to leverage a variety of NMF and NLS algorithms, including Multiplicative Update, Hierarchical Alternating Least Squares, and Block Principal Pivoting. Our implementation allows us to benchmark and compare different algorithms on massive dense and sparse data matrices of size that spans from few hundreds of millions to billions. We demonstrate the scalability of our algorithm and compare it with baseline implementations, showing significant performance improvements. The code and the datasets used for conducting the experiments are available online.« less

  14. MPI-FAUN: An MPI-Based Framework for Alternating-Updating Nonnegative Matrix Factorization

    DOE PAGES

    Kannan, Ramakrishnan; Ballard, Grey; Park, Haesun

    2017-10-30

    Non-negative matrix factorization (NMF) is the problem of determining two non-negative low rank factors W and H, for the given input matrix A, such that A≈WH. 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 parallel algorithms to solve the problem for big data sets. The main contribution of this work is a new, high-performance parallel computational framework for a broad class of NMF algorithms thatmore » iteratively solves alternating non-negative least squares (NLS) subproblems for W and H. 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). The framework is flexible and able to leverage a variety of NMF and NLS algorithms, including Multiplicative Update, Hierarchical Alternating Least Squares, and Block Principal Pivoting. Our implementation allows us to benchmark and compare different algorithms on massive dense and sparse data matrices of size that spans from few hundreds of millions to billions. We demonstrate the scalability of our algorithm and compare it with baseline implementations, showing significant performance improvements. The code and the datasets used for conducting the experiments are available online.« less

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

    PubMed

    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.

  16. Development and Validation of a Job Exposure Matrix for Physical Risk Factors in Low Back Pain

    PubMed Central

    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

    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 other countries

  17. Extracellular Matrix-Inspired Growth Factor Delivery Systems for Skin Wound Healing

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Briquez, Priscilla S.; Hubbell, Jeffrey A.; Martino, Mikaël M.

    2015-08-01

    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 localizationmore » of angiogenic signals in the extracellular matrix (ECM) 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 ECM to optimize the signaling microenvironment of vascular growth factors.« less

  18. Predicting drug-target interactions by dual-network integrated logistic matrix factorization

    NASA Astrophysics Data System (ADS)

    Hao, Ming; Bryant, Stephen H.; Wang, Yanli

    2017-01-01

    In this work, we propose a dual-network integrated logistic matrix factorization (DNILMF) algorithm to predict potential drug-target interactions (DTI). The prediction procedure consists of four steps: (1) inferring new drug/target profiles and constructing profile kernel matrix; (2) diffusing drug profile kernel matrix with drug structure kernel matrix; (3) diffusing target profile kernel matrix with target sequence kernel matrix; and (4) building DNILMF model and smoothing new drug/target predictions based on their neighbors. We compare our algorithm with the state-of-the-art method based on the benchmark dataset. Results indicate that the DNILMF algorithm outperforms the previously reported approaches in terms of AUPR (area under precision-recall curve) and AUC (area under curve of receiver operating characteristic) based on the 5 trials of 10-fold cross-validation. We conclude that the performance improvement depends on not only the proposed objective function, but also the used nonlinear diffusion technique which is important but under studied in the DTI prediction field. In addition, we also compile a new DTI dataset for increasing the diversity of currently available benchmark datasets. The top prediction results for the new dataset are confirmed by experimental studies or supported by other computational research.

  19. Designing Feature and Data Parallel Stochastic Coordinate Descent Method forMatrix and Tensor Factorization

    DTIC Science & Technology

    2016-05-11

    AFRL-AFOSR-JP-TR-2016-0046 Designing Feature and Data Parallel Stochastic Coordinate Descent Method for Matrix and Tensor Factorization U Kang Korea...maintaining the data needed, and completing and reviewing the collection of information. Send comments regarding this burden estimate or   any other aspect...Designing Feature and Data Parallel Stochastic Coordinate Descent Method for Matrix and Tensor Factorization 5a.  CONTRACT NUMBER 5b.  GRANT NUMBER FA2386

  20. Matrix superpotentials

    NASA Astrophysics Data System (ADS)

    Nikitin, Anatoly G.; Karadzhov, Yuri

    2011-07-01

    We present a collection of matrix-valued shape invariant potentials which give rise to new exactly solvable problems of SUSY quantum mechanics. It includes all irreducible matrix superpotentials of the generic form W=kQ+\\frac{1}{k} R+P, where k is a variable parameter, Q is the unit matrix multiplied by a real-valued function of independent variable x, and P and R are the Hermitian matrices depending on x. In particular, we recover the Pron'ko-Stroganov 'matrix Coulomb potential' and all known scalar shape invariant potentials of SUSY quantum mechanics. In addition, five new shape invariant potentials are presented. Three of them admit a dual shape invariance, i.e. the related Hamiltonians can be factorized using two non-equivalent superpotentials. We find discrete spectrum and eigenvectors for the corresponding Schrödinger equations and prove that these eigenvectors are normalizable.

  1. Bone matrix to growth factors: location, location, location

    PubMed Central

    Todorovic, Vesna

    2010-01-01

    The demonstration that fibrillin-1 mutations perturb transforming growth factor (TGF)–β bioavailability/signaling in Marfan syndrome (MFS) changed the view of the extracellular matrix as a passive structural support to a dynamic modulator of cell behavior. In this issue, Nistala et al. (2010. J. Cell Biol. doi: 10.1083/jcb.201003089) advance this concept by demonstrating how fibrillin-1 and -2 regulate TGF-β and bone morphogenetic protein (BMP) action during osteoblast maturation. PMID:20855500

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

    PubMed

    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.

  3. Genetic algorithm and graph theory based matrix factorization method for online friend recommendation.

    PubMed

    Li, Qu; Yao, Min; Yang, Jianhua; Xu, Ning

    2014-01-01

    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.

  4. Implementation of thermal residual stresses in the analysis of fiber bridged matrix crack growth in titanium matrix composites

    NASA Technical Reports Server (NTRS)

    Bakuckas, John G., Jr.; Johnson, W. Steven

    1994-01-01

    In this research, thermal residual stresses were incorporated in an analysis of fiber-bridged matrix cracks in unidirectional and cross-ply titanium matrix composites (TMC) containing center holes or center notches. Two TMC were investigated, namely, SCS-6/Timelal-21S laminates. Experimentally, matrix crack initiation and growth were monitored during tension-tension fatigue tests conducted at room temperature and at an elevated temperature of 200 C. Analytically, thermal residual stresses were included in a fiber bridging (FB) model. The local R-ratio and stress-intensity factor in the matrix due to thermal and mechanical loadings were calculated and used to evaluate the matrix crack growth behavior in the two materials studied. The frictional shear stress term, tau, assumed in this model was used as a curve-fitting parameter to matrix crack growth data. The scatter band in the values of tau used to fit the matrix crack growth data was significantly reduced when thermal residual stresses were included in the fiber bridging analysis. For a given material system, lay-up and temperature, a single value of tau was sufficient to analyze the crack growth data. It was revealed in this study that thermal residual stresses are an important factor overlooked in the original FB models.

  5. Difficulty Factors, Distribution Effects, and the Least Squares Simplex Data Matrix Solution

    ERIC Educational Resources Information Center

    Ten Berge, Jos M. F.

    1972-01-01

    In the present article it is argued that the Least Squares Simplex Data Matrix Solution does not deal adequately with difficulty factors inasmuch as the theoretical foundation is insufficient. (Author/CB)

  6. Multivariate Granger causality: an estimation framework based on factorization of the spectral density matrix

    PubMed Central

    Wen, Xiaotong; Rangarajan, Govindan; Ding, Mingzhou

    2013-01-01

    Granger causality is increasingly being applied to multi-electrode neurophysiological and functional imaging data to characterize directional interactions between neurons and brain regions. For a multivariate dataset, one might be interested in different subsets of the recorded neurons or brain regions. According to the current estimation framework, for each subset, one conducts a separate autoregressive model fitting process, introducing the potential for unwanted variability and uncertainty. In this paper, we propose a multivariate framework for estimating Granger causality. It is based on spectral density matrix factorization and offers the advantage that the estimation of such a matrix needs to be done only once for the entire multivariate dataset. For any subset of recorded data, Granger causality can be calculated through factorizing the appropriate submatrix of the overall spectral density matrix. PMID:23858479

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

    DOE PAGES

    Martino, Mikael M.; Brkic, Sime; Bovo, Emmanuela; ...

    2015-04-01

    In this study, 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,more » the spatial localization of angiogenic signals in the extracellular matrix (ECM) 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 ECM to optimize the signaling microenvironment of vascular growth factors.« less

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Martino, Mikael M.; Brkic, Sime; Bovo, Emmanuela

    In this study, 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,more » the spatial localization of angiogenic signals in the extracellular matrix (ECM) 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 ECM to optimize the signaling microenvironment of vascular growth factors.« less

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Martino, Mikael M.; Brkic, Sime; Bovo, Emmanuela

    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 localizationmore » of angiogenic signals in the extracellular matrix (ECM) 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 ECM to optimize the signaling microenvironment of vascular growth factors.« less

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

    PubMed Central

    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. PMID:26270539

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

    PubMed

    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.

  12. A Study of the Critical Factors Controlling the Synthesis of Ceramic Matrix Composites from Preceramic Polymers.

    DTIC Science & Technology

    1988-04-15

    physical properties of a polycarbosilane preceramic polymer as a function of temperature to derive synthesis methodology for SiC matrix composites , (2...investigate the role of interface modification in creating tough carbon fiber reinforced SiC matrix composites . RESEARCH PROGRESS Preceramic Polymer ...Classfication) A STUDY OF THE CRITICAL FACTORS CONTROLLING THE SYNTHESIS OF CERAMIC MATRIX COMPOSITES FROM PRECERAMIC POLYMERS 12. PERSONAL AUTHOR(S

  13. Matrix factorization-based data fusion for gene function prediction in baker's yeast and slime mold.

    PubMed

    Zitnik, Marinka; Zupan, Blaž

    2014-01-01

    The development of effective methods for the characterization of gene functions that are able to combine diverse data sources in a sound and easily-extendible way is an important goal in computational biology. We have previously developed a general matrix factorization-based data fusion approach for gene function prediction. In this manuscript, we show that this data fusion approach can be applied to gene function prediction and that it can fuse various heterogeneous data sources, such as gene expression profiles, known protein annotations, interaction and literature data. The fusion is achieved by simultaneous matrix tri-factorization that shares matrix factors between sources. We demonstrate the effectiveness of the approach by evaluating its performance on predicting ontological annotations in slime mold D. discoideum and on recognizing proteins of baker's yeast S. cerevisiae that participate in the ribosome or are located in the cell membrane. Our approach achieves predictive performance comparable to that of the state-of-the-art kernel-based data fusion, but requires fewer data preprocessing steps.

  14. Nonnegative Matrix Factorization for Efficient Hyperspectral Image Projection

    NASA Technical Reports Server (NTRS)

    Iacchetta, Alexander S.; Fienup, James R.; Leisawitz, David T.; Bolcar, Matthew R.

    2015-01-01

    Hyperspectral imaging for remote sensing has prompted development of hyperspectral image projectors that can be used to characterize hyperspectral imaging cameras and techniques in the lab. One such emerging astronomical hyperspectral imaging technique is wide-field double-Fourier interferometry. NASA's current, state-of-the-art, Wide-field Imaging Interferometry Testbed (WIIT) uses a Calibrated Hyperspectral Image Projector (CHIP) to generate test scenes and provide a more complete understanding of wide-field double-Fourier interferometry. Given enough time, the CHIP is capable of projecting scenes with astronomically realistic spatial and spectral complexity. However, this would require a very lengthy data collection process. For accurate but time-efficient projection of complicated hyperspectral images with the CHIP, the field must be decomposed both spectrally and spatially in a way that provides a favorable trade-off between accurately projecting the hyperspectral image and the time required for data collection. We apply nonnegative matrix factorization (NMF) to decompose hyperspectral astronomical datacubes into eigenspectra and eigenimages that allow time-efficient projection with the CHIP. Included is a brief analysis of NMF parameters that affect accuracy, including the number of eigenspectra and eigenimages used to approximate the hyperspectral image to be projected. For the chosen field, the normalized mean squared synthesis error is under 0.01 with just 8 eigenspectra. NMF of hyperspectral astronomical fields better utilizes the CHIP's capabilities, providing time-efficient and accurate representations of astronomical scenes to be imaged with the WIIT.

  15. Optical factors determined by the T-matrix method in turbidity measurement of absolute coagulation rate constants.

    PubMed

    Xu, Shenghua; Liu, Jie; Sun, Zhiwei

    2006-12-01

    Turbidity measurement for the absolute coagulation rate constants of suspensions has been extensively adopted because of its simplicity and easy implementation. A key factor in deriving the rate constant from experimental data is how to theoretically evaluate the so-called optical factor involved in calculating the extinction cross section of doublets formed during aggregation. In a previous paper, we have shown that compared with other theoretical approaches, the T-matrix method provides a robust solution to this problem and is effective in extending the applicability range of the turbidity methodology, as well as increasing measurement accuracy. This paper will provide a more comprehensive discussion of the physical insight for using the T-matrix method in turbidity measurement and associated technical details. In particular, the importance of ensuring the correct value for the refractive indices for colloidal particles and the surrounding medium used in the calculation is addressed, because the indices generally vary with the wavelength of the incident light. The comparison of calculated results with experiments shows that the T-matrix method can correctly calculate optical factors even for large particles, whereas other existing theories cannot. In addition, the data of the optical factor calculated by the T-matrix method for a range of particle radii and incident light wavelengths are listed.

  16. Modeling of stress/strain behavior of fiber-reinforced ceramic matrix composites including stress redistribution

    NASA Technical Reports Server (NTRS)

    Mital, Subodh K.; Murthy, Pappu L. N.; Chamis, Christos C.

    1994-01-01

    A computational simulation procedure is presented for nonlinear analyses which incorporates microstress redistribution due to progressive fracture in ceramic matrix composites. This procedure facilitates an accurate simulation of the stress-strain behavior of ceramic matrix composites up to failure. The nonlinearity in the material behavior is accounted for at the constituent (fiber/matrix/interphase) level. This computational procedure is a part of recent upgrades to CEMCAN (Ceramic Matrix Composite Analyzer) computer code. The fiber substructuring technique in CEMCAN is used to monitor the damage initiation and progression as the load increases. The room-temperature tensile stress-strain curves for SiC fiber reinforced reaction-bonded silicon nitride (RBSN) matrix unidirectional and angle-ply laminates are simulated and compared with experimentally observed stress-strain behavior. Comparison between the predicted stress/strain behavior and experimental stress/strain curves is good. Collectively the results demonstrate that CEMCAN computer code provides the user with an effective computational tool to simulate the behavior of ceramic matrix composites.

  17. A Study of Influencing Factors on the Tensile Response of a Titanium Matrix Composite With Weak Interfacial Bonding

    NASA Technical Reports Server (NTRS)

    Goldberg, Robert K.; Arnold, Steven M.

    2000-01-01

    The generalized method of cells micromechanics model is utilized to analyze the tensile stress-strain response of a representative titanium matrix composite with weak interfacial bonding. The fiber/matrix interface is modeled through application of a displacement discontinuity between the fiber and matrix once a critical debonding stress has been exceeded. Unidirectional composites with loading parallel and perpendicular to the fibers are examined, as well as a cross-ply laminate. For each of the laminates studied, analytically obtained results are compared to experimental data. The application of residual stresses through a cool-down process was found to have a significant effect on the tensile response. For the unidirectional laminate with loading applied perpendicular to the fibers, fiber packing and fiber shape were shown to have a significant effect on the predicted tensile response. Furthermore, the interface was characterized through the use of semi-emperical parameters including an interfacial compliance and a "debond stress;" defined as the stress level across the interface which activates fiber/matrix debonding. The results in this paper demonstrate that if architectural factors are correctly accounted for and the interface is appropriately characterized, the macro-level composite behavior can be correctly predicted without modifying any of the fiber or matrix constituent properties.

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

    NASA Astrophysics Data System (ADS)

    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.

  19. THz spectral data analysis and components unmixing based on non-negative matrix factorization methods

    NASA Astrophysics Data System (ADS)

    Ma, Yehao; Li, Xian; Huang, Pingjie; Hou, Dibo; Wang, Qiang; Zhang, Guangxin

    2017-04-01

    In many situations the THz spectroscopic data observed from complex samples represent the integrated result of several interrelated variables or feature components acting together. The actual information contained in the original data might be overlapping and there is a necessity to investigate various approaches for model reduction and data unmixing. The development and use of low-rank approximate nonnegative matrix factorization (NMF) and smooth constraint NMF (CNMF) algorithms for feature components extraction and identification in the fields of terahertz time domain spectroscopy (THz-TDS) data analysis are presented. The evolution and convergence properties of NMF and CNMF methods based on sparseness, independence and smoothness constraints for the resulting nonnegative matrix factors are discussed. For general NMF, its cost function is nonconvex and the result is usually susceptible to initialization and noise corruption, and may fall into local minima and lead to unstable decomposition. To reduce these drawbacks, smoothness constraint is introduced to enhance the performance of NMF. The proposed algorithms are evaluated by several THz-TDS data decomposition experiments including a binary system and a ternary system simulating some applications such as medicine tablet inspection. Results show that CNMF is more capable of finding optimal solutions and more robust for random initialization in contrast to NMF. The investigated method is promising for THz data resolution contributing to unknown mixture identification.

  20. THz spectral data analysis and components unmixing based on non-negative matrix factorization methods.

    PubMed

    Ma, Yehao; Li, Xian; Huang, Pingjie; Hou, Dibo; Wang, Qiang; Zhang, Guangxin

    2017-04-15

    In many situations the THz spectroscopic data observed from complex samples represent the integrated result of several interrelated variables or feature components acting together. The actual information contained in the original data might be overlapping and there is a necessity to investigate various approaches for model reduction and data unmixing. The development and use of low-rank approximate nonnegative matrix factorization (NMF) and smooth constraint NMF (CNMF) algorithms for feature components extraction and identification in the fields of terahertz time domain spectroscopy (THz-TDS) data analysis are presented. The evolution and convergence properties of NMF and CNMF methods based on sparseness, independence and smoothness constraints for the resulting nonnegative matrix factors are discussed. For general NMF, its cost function is nonconvex and the result is usually susceptible to initialization and noise corruption, and may fall into local minima and lead to unstable decomposition. To reduce these drawbacks, smoothness constraint is introduced to enhance the performance of NMF. The proposed algorithms are evaluated by several THz-TDS data decomposition experiments including a binary system and a ternary system simulating some applications such as medicine tablet inspection. Results show that CNMF is more capable of finding optimal solutions and more robust for random initialization in contrast to NMF. The investigated method is promising for THz data resolution contributing to unknown mixture identification. Copyright © 2017 Elsevier B.V. All rights reserved.

  1. Recursive Factorization of the Inverse Overlap Matrix in Linear-Scaling Quantum Molecular Dynamics Simulations.

    PubMed

    Negre, Christian F A; Mniszewski, Susan M; Cawkwell, Marc J; Bock, Nicolas; Wall, Michael E; Niklasson, Anders M N

    2016-07-12

    We present a reduced complexity algorithm to compute the inverse overlap factors required to solve the generalized eigenvalue problem in a quantum-based molecular dynamics (MD) simulation. Our method is based on the recursive, iterative refinement of an initial guess of Z (inverse square root of the overlap matrix S). The initial guess of Z is obtained beforehand by using either an approximate divide-and-conquer technique or dynamical methods, propagated within an extended Lagrangian dynamics from previous MD time steps. With this formulation, we achieve long-term stability and energy conservation even under the incomplete, approximate, iterative refinement of Z. Linear-scaling performance is obtained using numerically thresholded sparse matrix algebra based on the ELLPACK-R sparse matrix data format, which also enables efficient shared-memory parallelization. As we show in this article using self-consistent density-functional-based tight-binding MD, our approach is faster than conventional methods based on the diagonalization of overlap matrix S for systems as small as a few hundred atoms, substantially accelerating quantum-based simulations even for molecular structures of intermediate size. For a 4158-atom water-solvated polyalanine system, we find an average speedup factor of 122 for the computation of Z in each MD step.

  2. Recursive Factorization of the Inverse Overlap Matrix in Linear Scaling Quantum Molecular Dynamics Simulations

    DOE PAGES

    Negre, Christian F. A; Mniszewski, Susan M.; Cawkwell, Marc Jon; ...

    2016-06-06

    We present a reduced complexity algorithm to compute the inverse overlap factors required to solve the generalized eigenvalue problem in a quantum-based molecular dynamics (MD) simulation. Our method is based on the recursive iterative re nement of an initial guess Z of the inverse overlap matrix S. The initial guess of Z is obtained beforehand either by using an approximate divide and conquer technique or dynamically, propagated within an extended Lagrangian dynamics from previous MD time steps. With this formulation, we achieve long-term stability and energy conservation even under incomplete approximate iterative re nement of Z. Linear scaling performance ismore » obtained using numerically thresholded sparse matrix algebra based on the ELLPACK-R sparse matrix data format, which also enables e cient shared memory parallelization. As we show in this article using selfconsistent density functional based tight-binding MD, our approach is faster than conventional methods based on the direct diagonalization of the overlap matrix S for systems as small as a few hundred atoms, substantially accelerating quantum-based simulations even for molecular structures of intermediate size. For a 4,158 atom water-solvated polyalanine system we nd an average speedup factor of 122 for the computation of Z in each MD step.« less

  3. Ceramic matrix composite article and process of fabricating a ceramic matrix composite article

    DOEpatents

    Cairo, Ronald Robert; DiMascio, Paul Stephen; Parolini, Jason Robert

    2016-01-12

    A ceramic matrix composite article and a process of fabricating a ceramic matrix composite are disclosed. The ceramic matrix composite article includes a matrix distribution pattern formed by a manifold and ceramic matrix composite plies laid up on the matrix distribution pattern, includes the manifold, or a combination thereof. The manifold includes one or more matrix distribution channels operably connected to a delivery interface, the delivery interface configured for providing matrix material to one or more of the ceramic matrix composite plies. The process includes providing the manifold, forming the matrix distribution pattern by transporting the matrix material through the manifold, and contacting the ceramic matrix composite plies with the matrix material.

  4. Online blind source separation using incremental nonnegative matrix factorization with volume constraint.

    PubMed

    Zhou, Guoxu; Yang, Zuyuan; Xie, Shengli; Yang, Jun-Mei

    2011-04-01

    Online blind source separation (BSS) is proposed to overcome the high computational cost problem, which limits the practical applications of traditional batch BSS algorithms. However, the existing online BSS methods are mainly used to separate independent or uncorrelated sources. Recently, nonnegative matrix factorization (NMF) shows great potential to separate the correlative sources, where some constraints are often imposed to overcome the non-uniqueness of the factorization. In this paper, an incremental NMF with volume constraint is derived and utilized for solving online BSS. The volume constraint to the mixing matrix enhances the identifiability of the sources, while the incremental learning mode reduces the computational cost. The proposed method takes advantage of the natural gradient based multiplication updating rule, and it performs especially well in the recovery of dependent sources. Simulations in BSS for dual-energy X-ray images, online encrypted speech signals, and high correlative face images show the validity of the proposed method.

  5. Compact Feed Circuit with Quarter Wavelength Transmission Line Matrix Controlling Beams in Three Directions Including Boresight

    NASA Astrophysics Data System (ADS)

    Tsuji, Masatoshi

    A compact feed circuit with a λ/4 transmission line matrix circuit for use in array antennas to control beams in three directions, including boresight, is presented. The feed circuit antenna is composed of five switches and λ/4 transmission lines, and the feeding matrix circuit yields phase differences of ±90° and 0°. The feed circuit can obtain a reliable output signal, as there is only a small degree of deviation of output signal with variations in the line width. The feed circuit is simulated, fabricated, and evaluated for ISM band, and the measured characteristics agree well with the results of the simulation. The size of feed circuit is 45 (H) × 48 (W) × 3 (T) mm.

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

    NASA Astrophysics Data System (ADS)

    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.

  7. Strain intensity factor approach for predicting the strength of continuously reinforced metal matrix composites

    NASA Technical Reports Server (NTRS)

    Poe, Clarence C., Jr.

    1989-01-01

    A method was previously developed to predict the fracture toughness (stress intensity factor at failure) of composites in terms of the elastic constants and the tensile failing strain of the fibers. The method was applied to boron/aluminum composites made with various proportions of 0 deg and +/- 45 deg plies. Predicted values of fracture toughness were in gross error because widespread yielding of the aluminum matrix made the compliance very nonlinear. An alternate method was develolped to predict the strain intensity factor at failure rather than the stress intensity factor because the singular strain field was not affected by yielding as much as the stress field. Far-field strains at failure were calculated from the strain intensity factor, and then strengths were calculated from the far-field strains using uniaxial stress-strain curves. The predicted strengths were in good agreement with experimental values, even for the very nonlinear laminates that contained only +/- 45 deg plies. This approach should be valid for other metal matrix composites that have continuous fibers.

  8. The Exopolysaccharide Matrix

    PubMed Central

    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

  9. Removing non-stationary noise in spectrum sensing using matrix factorization

    NASA Astrophysics Data System (ADS)

    van Bloem, Jan-Willem; Schiphorst, Roel; Slump, Cornelis H.

    2013-12-01

    Spectrum sensing is key to many applications like dynamic spectrum access (DSA) systems or telecom regulators who need to measure utilization of frequency bands. The International Telecommunication Union (ITU) recommends a 10 dB threshold above the noise to decide whether a channel is occupied or not. However, radio frequency (RF) receiver front-ends are non-ideal. This means that the obtained data is distorted with noise and imperfections from the analog front-end. As part of the front-end the automatic gain control (AGC) circuitry mainly affects the sensing performance as strong adjacent signals lift the noise level. To enhance the performance of spectrum sensing significantly we focus in this article on techniques to remove the noise caused by the AGC from the sensing data. In order to do this we have applied matrix factorization techniques, i.e., SVD (singular value decomposition) and NMF (non-negative matrix factorization), which enables signal space analysis. In addition, we use live measurement results to verify the performance and to remove the effects of the AGC from the sensing data using above mentioned techniques, i.e., applied on block-wise available spectrum data. In this article it is shown that the occupancy in the industrial, scientific and medical (ISM) band, obtained by using energy detection (ITU recommended threshold), can be an overestimation of spectrum usage by 60%.

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

    ERIC Educational Resources Information Center

    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),…

  11. MATRIX FACTORIZATION-BASED DATA FUSION FOR GENE FUNCTION PREDICTION IN BAKER’S YEAST AND SLIME MOLD

    PubMed Central

    ŽITNIK, MARINKA; ZUPAN, BLAŽ

    2014-01-01

    The development of effective methods for the characterization of gene functions that are able to combine diverse data sources in a sound and easily-extendible way is an important goal in computational biology. We have previously developed a general matrix factorization-based data fusion approach for gene function prediction. In this manuscript, we show that this data fusion approach can be applied to gene function prediction and that it can fuse various heterogeneous data sources, such as gene expression profiles, known protein annotations, interaction and literature data. The fusion is achieved by simultaneous matrix tri-factorization that shares matrix factors between sources. We demonstrate the effectiveness of the approach by evaluating its performance on predicting ontological annotations in slime mold D. discoideum and on recognizing proteins of baker’s yeast S. cerevisiae that participate in the ribosome or are located in the cell membrane. Our approach achieves predictive performance comparable to that of the state-of-the-art kernel-based data fusion, but requires fewer data preprocessing steps. PMID:24297565

  12. Strain intensity factor approach for predicting the strength of continuously reinforced metal matrix composites

    NASA Technical Reports Server (NTRS)

    Poe, C. C., Jr.

    1988-01-01

    A method was previously developed to predict the fracture toughness (stress intensity factor at failure) of composites in terms of the elastic constants and the tensile failing strain of the fibers. The method was applied to boron/aluminum composites made with various proportions of 0 to + or - 45 deg plies. Predicted values of fracture toughness were in gross error because widespread yielding of the aluminum matrix made the compliance very nonlinear. An alternate method was developed to predict the strain intensity factor at failure rather than the stress intensity factor because the singular strain field was not affected by yielding as much as the stress field. Strengths of specimens containing crack-like slits were calculated from predicted failing strains using uniaxial stress-strain curves. Predicted strengths were in good agreement with experimental values, even for the very nonlinear laminates that contained only + or - 45 deg plies. This approach should be valid for other metal matrix composites that have continuous fibers.

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

    PubMed

    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.

  14. Modeling cometary photopolarimetric characteristics with Sh-matrix method

    NASA Astrophysics Data System (ADS)

    Kolokolova, L.; Petrov, D.

    2017-12-01

    Cometary dust is dominated by particles of complex shape and structure, which are often considered as fractal aggregates. Rigorous modeling of light scattering by such particles, even using parallelized codes and NASA supercomputer resources, is very computer time and memory consuming. We are presenting a new approach to modeling cometary dust that is based on the Sh-matrix technique (e.g., Petrov et al., JQSRT, 112, 2012). This method is based on the T-matrix technique (e.g., Mishchenko et al., JQSRT, 55, 1996) and was developed after it had been found that the shape-dependent factors could be separated from the size- and refractive-index-dependent factors and presented as a shape matrix, or Sh-matrix. Size and refractive index dependences are incorporated through analytical operations on the Sh-matrix to produce the elements of T-matrix. Sh-matrix method keeps all advantages of the T-matrix method, including analytical averaging over particle orientation. Moreover, the surface integrals describing the Sh-matrix elements themselves can be solvable analytically for particles of any shape. This makes Sh-matrix approach an effective technique to simulate light scattering by particles of complex shape and surface structure. In this paper, we present cometary dust as an ensemble of Gaussian random particles. The shape of these particles is described by a log-normal distribution of their radius length and direction (Muinonen, EMP, 72, 1996). Changing one of the parameters of this distribution, the correlation angle, from 0 to 90 deg., we can model a variety of particles from spheres to particles of a random complex shape. We survey the angular and spectral dependencies of intensity and polarization resulted from light scattering by such particles, studying how they depend on the particle shape, size, and composition (including porous particles to simulate aggregates) to find the best fit to the cometary observations.

  15. Hardware Implementation of a MIMO Decoder Using Matrix Factorization Based Channel Estimation

    NASA Astrophysics Data System (ADS)

    Islam, Mohammad Tariqul; Numan, Mostafa Wasiuddin; Misran, Norbahiah; Ali, Mohd Alauddin Mohd; Singh, Mandeep

    2011-05-01

    This paper presents an efficient hardware realization of multiple-input multiple-output (MIMO) wireless communication decoder that utilizes the available resources by adopting the technique of parallelism. The hardware is designed and implemented on Xilinx Virtex™-4 XC4VLX60 field programmable gate arrays (FPGA) device in a modular approach which simplifies and eases hardware update, and facilitates testing of the various modules independently. The decoder involves a proficient channel estimation module that employs matrix factorization on least squares (LS) estimation to reduce a full rank matrix into a simpler form in order to eliminate matrix inversion. This results in performance improvement and complexity reduction of the MIMO system. Performance evaluation of the proposed method is validated through MATLAB simulations which indicate 2 dB improvement in terms of SNR compared to LS estimation. Moreover complexity comparison is performed in terms of mathematical operations, which shows that the proposed approach appreciably outperforms LS estimation at a lower complexity and represents a good solution for channel estimation technique.

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

    PubMed

    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.

  17. Matrix Metalloproteinases in Non-Neoplastic Disorders

    PubMed Central

    Tokito, Akinori; Jougasaki, Michihisa

    2016-01-01

    The matrix metalloproteinases (MMPs) are zinc-dependent endopeptidases belonging to the metzincin superfamily. There are at least 23 members of MMPs ever reported in human, and they and their substrates are widely expressed in many tissues. Recent growing evidence has established that MMP not only can degrade a variety of components of extracellular matrix, but also can cleave and activate various non-matrix proteins, including cytokines, chemokines and growth factors, contributing to both physiological and pathological processes. In normal conditions, MMP expression and activity are tightly regulated via interactions between their activators and inhibitors. Imbalance among these factors, however, results in dysregulated MMP activity, which causes tissue destruction and functional alteration or local inflammation, leading to the development of diverse diseases, such as cardiovascular disease, arthritis, neurodegenerative disease, as well as cancer. This article focuses on the accumulated evidence supporting a wide range of roles of MMPs in various non-neoplastic diseases and provides an outlook on the therapeutic potential of inhibiting MMP action. PMID:27455234

  18. Factorized three-body S-matrix restrained by the Yang–Baxter equation and quantum entanglements

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Yu, Li-Wei, E-mail: NKyulw@gmail.com; Zhao, Qing, E-mail: qzhaoyuping@bit.edu.cn; Ge, Mo-Lin, E-mail: geml@nankai.edu.cn

    2014-09-15

    This paper investigates the physical effects of the Yang–Baxter equation (YBE) to quantum entanglements through the 3-body S-matrix in entangling parameter space. The explicit form of 3-body S-matrix Ř{sub 123}(θ,φ) based on the 2-body S-matrices is given due to the factorization condition of YBE. The corresponding chain Hamiltonian has been obtained and diagonalized, also the Berry phase for 3-body system is given. It turns out that by choosing different spectral parameters the Ř(θ,φ)-matrix gives GHZ and W states respectively. The extended 1-D Kitaev toy model has been derived. Examples of the role of the model in entanglement transfer are discussed.more » - Highlights: • We give the relation between 3-body S-matrix and 3-qubit entanglement. • The relation between 3-qubit and 2-qubit entanglements is investigated via YBE. • 1D Kitaev toy model is derived by the Type-II solution of YBE. • The condition of YBE kills the “Zero boundary mode” in our chain model.« less

  19. Study on the Preparation Process and Influential Factors of Large Area Environment-friendly Molten Carbonate Fuel Cell Matrix

    NASA Astrophysics Data System (ADS)

    Zhang, Ruiyun; Xu, Shisen; Cheng, Jian; Wang, Hongjian; Ren, Yongqiang

    2017-07-01

    Low-cost and high-performance matrix materials used in mass production of molten carbonate fuel cell (MCFC) were prepared by automatic casting machine with α-LiAlO2 powder material synthesized by gel-solid method, and distilled water as solvent. The single cell was assembled for generating test, and the good performance of the matrix was verified. The paper analyzed the factors affecting aqueous tape casting matrix preparation, such as solvent content, dispersant content, milling time, blade height and casting machine running speed, providing a solid basis for the mass production of large area environment-friendly matrix used in molten carbonate fuel cell.

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

    PubMed Central

    Jaeger, Sébastien; Thieffry, Denis

    2017-01-01

    Abstract 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. PMID:28591841

  1. RECEPTOR MODELING OF AMBIENT PARTICULATE MATTER DATA USING POSITIVE MATRIX FACTORIZATION REVIEW OF EXISTING METHODS

    EPA Science Inventory

    Methods for apportioning sources of ambient particulate matter (PM) using the positive matrix factorization (PMF) algorithm are reviewed. Numerous procedural decisions must be made and algorithmic parameters selected when analyzing PM data with PMF. However, few publications docu...

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

    NASA Astrophysics Data System (ADS)

    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. Factors associated with continuance commitment to FAA matrix teams.

    DOT National Transportation Integrated Search

    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...

  4. BASIC Matrix Operations.

    ERIC Educational Resources Information Center

    Digital Equipment Corp., Maynard, MA.

    The curriculum materials and computer programs in this booklet introduce the idea of a matrix. They go on to discuss matrix operations of addition, subtraction, multiplication by a scalar, and matrix multiplication. The last section covers several contemporary applications of matrix multiplication, including problems of communication…

  5. Turbo-SMT: Accelerating Coupled Sparse Matrix-Tensor Factorizations by 200×

    PubMed Central

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

    2015-01-01

    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 accelerate any CMTF solver, so that it runs within a few minutes instead of tens of hours to a day, while maintaining good accuracy? We introduce TURBO-SMT, a meta-method capable of doing exactly that: it boosts the performance of any CMTF algorithm, by up to 200×, along with an up to 65 fold increase in sparsity, with comparable accuracy to the baseline. 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. PMID:26473087

  6. Proposed framework for thermomechanical life modeling of metal matrix composites

    NASA Technical Reports Server (NTRS)

    Halford, Gary R.; Lerch, Bradley A.; Saltsman, James F.

    1993-01-01

    The framework of a mechanics of materials model is proposed for thermomechanical fatigue (TMF) life prediction of unidirectional, continuous-fiber metal matrix composites (MMC's). Axially loaded MMC test samples are analyzed as structural components whose fatigue lives are governed by local stress-strain conditions resulting from combined interactions of the matrix, interfacial layer, and fiber constituents. The metallic matrix is identified as the vehicle for tracking fatigue crack initiation and propagation. The proposed framework has three major elements. First, TMF flow and failure characteristics of in situ matrix material are approximated from tests of unreinforced matrix material, and matrix TMF life prediction equations are numerically calibrated. The macrocrack initiation fatigue life of the matrix material is divided into microcrack initiation and microcrack propagation phases. Second, the influencing factors created by the presence of fibers and interfaces are analyzed, characterized, and documented in equation form. Some of the influences act on the microcrack initiation portion of the matrix fatigue life, others on the microcrack propagation life, while some affect both. Influencing factors include coefficient of thermal expansion mismatch strains, residual (mean) stresses, multiaxial stress states, off-axis fibers, internal stress concentrations, multiple initiation sites, nonuniform fiber spacing, fiber debonding, interfacial layers and cracking, fractured fibers, fiber deflections of crack fronts, fiber bridging of matrix cracks, and internal oxidation along internal interfaces. Equations exist for some, but not all, of the currently identified influencing factors. The third element is the inclusion of overriding influences such as maximum tensile strain limits of brittle fibers that could cause local fractures and ensuing catastrophic failure of surrounding matrix material. Some experimental data exist for assessing the plausibility of the proposed

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

    PubMed

    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.

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

    PubMed

    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.

  9. Practical limits on muscle synergy identification by non-negative matrix factorization in systems with mechanical constraints.

    PubMed

    Burkholder, Thomas J; van Antwerp, Keith W

    2013-02-01

    Statistical decomposition, including non-negative matrix factorization (NMF), is a convenient tool for identifying patterns of structured variability within behavioral motor programs, but it is unclear how the resolved factors relate to actual neural structures. Factors can be extracted from a uniformly sampled, low-dimension command space. In practical application, the command space is limited, either to those activations that perform some task(s) successfully or to activations induced in response to specific perturbations. NMF was applied to muscle activation patterns synthesized from low dimensional, synergy-like control modules mimicking simple task performance or feedback activation from proprioceptive signals. In the task-constrained paradigm, the accuracy of control module recovery was highly dependent on the sampled volume of control space, such that sampling even 50% of control space produced a substantial degradation in factor accuracy. In the feedback paradigm, NMF was not capable of extracting more than four control modules, even in a mechanical model with seven internal degrees of freedom. Reduced access to the low-dimensional control space imposed by physical constraints may result in substantial distortion of an existing low dimensional controller, such that neither the dimensionality nor the composition of the recovered/extracted factors match the original controller.

  10. Factor Analysis and Counseling Research

    ERIC Educational Resources Information Center

    Weiss, David J.

    1970-01-01

    Topics discussed include factor analysis versus cluster analysis, analysis of Q correlation matrices, ipsativity and factor analysis, and tests for the significance of a correlation matrix prior to application of factor analytic techniques. Techniques for factor extraction discussed include principal components, canonical factor analysis, alpha…

  11. Finding imaging patterns of structural covariance via Non-Negative Matrix Factorization.

    PubMed

    Sotiras, Aristeidis; Resnick, Susan M; Davatzikos, Christos

    2015-03-01

    In this paper, we investigate the use of Non-Negative Matrix Factorization (NNMF) for the analysis of structural neuroimaging data. The goal is to identify the brain regions that co-vary across individuals in a consistent way, hence potentially being part of underlying brain networks or otherwise influenced by underlying common mechanisms such as genetics and pathologies. NNMF offers a directly data-driven way of extracting relatively localized co-varying structural regions, thereby transcending limitations of Principal Component Analysis (PCA), Independent Component Analysis (ICA) and other related methods that tend to produce dispersed components of positive and negative loadings. In particular, leveraging upon the well known ability of NNMF to produce parts-based representations of image data, we derive decompositions that partition the brain into regions that vary in consistent ways across individuals. Importantly, these decompositions achieve dimensionality reduction via highly interpretable ways and generalize well to new data as shown via split-sample experiments. We empirically validate NNMF in two data sets: i) a Diffusion Tensor (DT) mouse brain development study, and ii) a structural Magnetic Resonance (sMR) study of human brain aging. We demonstrate the ability of NNMF to produce sparse parts-based representations of the data at various resolutions. These representations seem to follow what we know about the underlying functional organization of the brain and also capture some pathological processes. Moreover, we show that these low dimensional representations favorably compare to descriptions obtained with more commonly used matrix factorization methods like PCA and ICA. Copyright © 2014 Elsevier Inc. All rights reserved.

  12. Finding Imaging Patterns of Structural Covariance via Non-Negative Matrix Factorization

    PubMed Central

    Sotiras, Aristeidis; Resnick, Susan M.; Davatzikos, Christos

    2015-01-01

    In this paper, we investigate the use of Non-Negative Matrix Factorization (NNMF) for the analysis of structural neuroimaging data. The goal is to identify the brain regions that co-vary across individuals in a consistent way, hence potentially being part of underlying brain networks or otherwise influenced by underlying common mechanisms such as genetics and pathologies. NNMF offers a directly data-driven way of extracting relatively localized co-varying structural regions, thereby transcending limitations of Principal Component Analysis (PCA), Independent Component Analysis (ICA) and other related methods that tend to produce dispersed components of positive and negative loadings. In particular, leveraging upon the well known ability of NNMF to produce parts-based representations of image data, we derive decompositions that partition the brain into regions that vary in consistent ways across individuals. Importantly, these decompositions achieve dimensionality reduction via highly interpretable ways and generalize well to new data as shown via split-sample experiments. We empirically validate NNMF in two data sets: i) a Diffusion Tensor (DT) mouse brain development study, and ii) a structural Magnetic Resonance (sMR) study of human brain aging. We demonstrate the ability of NNMF to produce sparse parts-based representations of the data at various resolutions. These representations seem to follow what we know about the underlying functional organization of the brain and also capture some pathological processes. Moreover, we show that these low dimensional representations favorably compare to descriptions obtained with more commonly used matrix factorization methods like PCA and ICA. PMID:25497684

  13. Preferential Enhancement of Sensory and Motor Axon Regeneration by Combining Extracellular Matrix Components with Neurotrophic Factors

    PubMed Central

    Santos, Daniel; González-Pérez, Francisco; Giudetti, Guido; Micera, Silvestro; Udina, Esther; Del Valle, Jaume; Navarro, Xavier

    2016-01-01

    After peripheral nerve injury, motor and sensory axons are able to regenerate but inaccuracy of target reinnervation leads to poor functional recovery. Extracellular matrix (ECM) components and neurotrophic factors (NTFs) exert their effect on different neuronal populations creating a suitable environment to promote axonal growth. Here, we assessed in vitro and in vivo the selective effects of combining different ECM components with NTFs on motor and sensory axons regeneration and target reinnervation. Organotypic cultures with collagen, laminin and nerve growth factor (NGF)/neurotrophin-3 (NT3) or collagen, fibronectin and brain-derived neurotrophic factor (BDNF) selectively enhanced sensory neurite outgrowth of DRG neurons and motor neurite outgrowth from spinal cord slices respectively. For in vivo studies, the rat sciatic nerve was transected and repaired with a silicone tube filled with a collagen and laminin matrix with NGF/NT3 encapsulated in poly(lactic-co-glycolic acid) (PLGA) microspheres (MP) (LM + MP.NGF/NT3), or a collagen and fibronectin matrix with BDNF in PLGA MPs (FN + MP.BDNF). Retrograde labeling and functional tests showed that LM + MP.NGF/NT3 increased the number of regenerated sensory neurons and improved sensory functional recovery, whereas FN + MP.BDNF preferentially increased regenerated motoneurons and enhanced motor functional recovery. Therefore, combination of ECM molecules with NTFs may be a good approach to selectively enhance motor and sensory axons regeneration and promote appropriate target reinnervation. PMID:28036084

  14. Evaluation of non-negative matrix factorization of grey matter in age prediction.

    PubMed

    Varikuti, Deepthi P; Genon, Sarah; Sotiras, Aristeidis; Schwender, Holger; Hoffstaedter, Felix; Patil, Kaustubh R; Jockwitz, Christiane; Caspers, Svenja; Moebus, Susanne; Amunts, Katrin; Davatzikos, Christos; Eickhoff, Simon B

    2018-06-01

    The relationship between grey matter volume (GMV) patterns and age can be captured by multivariate pattern analysis, allowing prediction of individuals' age based on structural imaging. Raw data, voxel-wise GMV and non-sparse factorization (with Principal Component Analysis, PCA) show good performance but do not promote relatively localized brain components for post-hoc examinations. Here we evaluated a non-negative matrix factorization (NNMF) approach to provide a reduced, but also interpretable representation of GMV data in age prediction frameworks in healthy and clinical populations. This examination was performed using three datasets: a multi-site cohort of life-span healthy adults, a single site cohort of older adults and clinical samples from the ADNI dataset with healthy subjects, participants with Mild Cognitive Impairment and patients with Alzheimer's disease (AD) subsamples. T1-weighted images were preprocessed with VBM8 standard settings to compute GMV values after normalization, segmentation and modulation for non-linear transformations only. Non-negative matrix factorization was computed on the GM voxel-wise values for a range of granularities (50-690 components) and LASSO (Least Absolute Shrinkage and Selection Operator) regression were used for age prediction. First, we compared the performance of our data compression procedure (i.e., NNMF) to various other approaches (i.e., uncompressed VBM data, PCA-based factorization and parcellation-based compression). We then investigated the impact of the granularity on the accuracy of age prediction, as well as the transferability of the factorization and model generalization across datasets. We finally validated our framework by examining age prediction in ADNI samples. Our results showed that our framework favorably compares with other approaches. They also demonstrated that the NNMF based factorization derived from one dataset could be efficiently applied to compress VBM data of another dataset and that

  15. Identification of regional activation by factorization of high-density surface EMG signals: A comparison of Principal Component Analysis and Non-negative Matrix factorization.

    PubMed

    Gallina, Alessio; Garland, S Jayne; Wakeling, James M

    2018-05-22

    In this study, we investigated whether principal component analysis (PCA) and non-negative matrix factorization (NMF) perform similarly for the identification of regional activation within the human vastus medialis. EMG signals from 64 locations over the VM were collected from twelve participants while performing a low-force isometric knee extension. The envelope of the EMG signal of each channel was calculated by low-pass filtering (8 Hz) the monopolar EMG signal after rectification. The data matrix was factorized using PCA and NMF, and up to 5 factors were considered for each algorithm. Association between explained variance, spatial weights and temporal scores between the two algorithms were compared using Pearson correlation. For both PCA and NMF, a single factor explained approximately 70% of the variance of the signal, while two and three factors explained just over 85% or 90%. The variance explained by PCA and NMF was highly comparable (R > 0.99). Spatial weights and temporal scores extracted with non-negative reconstruction of PCA and NMF were highly associated (all p < 0.001, mean R > 0.97). Regional VM activation can be identified using high-density surface EMG and factorization algorithms. Regional activation explains up to 30% of the variance of the signal, as identified through both PCA and NMF. Copyright © 2018 Elsevier Ltd. All rights reserved.

  16. Method of forming a ceramic matrix composite and a ceramic matrix component

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    de Diego, Peter; Zhang, James

    A method of forming a ceramic matrix composite component includes providing a formed ceramic member having a cavity, filling at least a portion of the cavity with a ceramic foam. The ceramic foam is deposited on a barrier layer covering at least one internal passage of the cavity. The method includes processing the formed ceramic member and ceramic foam to obtain a ceramic matrix composite component. Also provided is a method of forming a ceramic matrix composite blade and a ceramic matrix composite component.

  17. Physiological Ranges of Matrix Rigidity Modulate Primary Mouse Hepatocyte Function In Part Through Hepatocyte Nuclear Factor 4 Alpha

    PubMed Central

    Desai, Seema S.; Tung, Jason C.; Zhou, Vivian X.; Grenert, James P.; Malato, Yann; Rezvani, Milad; Español-Suñer, Regina; Willenbring, Holger; Weaver, Valerie M.; Chang, Tammy T.

    2016-01-01

    Matrix rigidity has important effects on cell behavior and is increased during liver fibrosis; however, its effect on primary hepatocyte function is unknown. We hypothesized that increased matrix rigidity in fibrotic livers would activate mechanotransduction in hepatocytes and lead to inhibition of hepatic-specific functions. To determine the physiologically relevant ranges of matrix stiffness at the cellular level, we performed detailed atomic force microscopy analysis across liver lobules from normal and fibrotic livers. We determined that normal liver matrix stiffness was around 150Pa and increased to 1–6kPa in areas near fibrillar collagen deposition in fibrotic livers. In vitro culture of primary hepatocytes on collagen matrix of tunable rigidity demonstrated that fibrotic levels of matrix stiffness had profound effects on cytoskeletal tension and significantly inhibited hepatocyte-specific functions. Normal liver stiffness maintained functional gene regulation by hepatocyte nuclear factor 4 alpha (HNF4α) whereas fibrotic matrix stiffness inhibited the HNF4α transcriptional network. Fibrotic levels of matrix stiffness activated mechanotransduction in primary hepatocytes through focal adhesion kinase (FAK). In addition, blockade of the Rho/Rho-associated protein kinase (ROCK) pathway rescued HNF4α expression from hepatocytes cultured on stiff matrix. Conclusion Fibrotic levels of matrix stiffness significantly inhibit hepatocyte-specific functions in part by inhibiting the HNF4α transcriptional network mediated through the Rho/ROCK pathway. Increased appreciation of the role of matrix rigidity in modulating hepatocyte function will advance our understanding of the mechanisms of hepatocyte dysfunction in liver cirrhosis and spur development of novel treatments for chronic liver disease. PMID:26755329

  18. In Spite of Indeterminacy Many Common Factor Score Estimates Yield an Identical Reproduced Covariance Matrix

    ERIC Educational Resources Information Center

    Beauducel, Andre

    2007-01-01

    It was investigated whether commonly used factor score estimates lead to the same reproduced covariance matrix of observed variables. This was achieved by means of Schonemann and Steiger's (1976) regression component analysis, since it is possible to compute the reproduced covariance matrices of the regression components corresponding to different…

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

    PubMed Central

    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 analyzed using the Spearmans correlation test. The levels of TGF-β2 were identified to be positively correlated with the levels of TIMP-1 and TIMP-3 (TIMP-1: r=0.334; P=0.007; TIMP-3: r=0.309; P=0.012). The levels of MMP-2, MMP-3 and TIMP-2 did not significantly correlate with TGF-β2 levels (P>0.05). A positive correlation was identified between TGF-β2 and TIMPs in the aqueous humor of human eyes with elongated axial length. It appears that TGF-β2 stimulates the expression of TIMPs as a compensatory reaction to the development of high myopia. PMID:29188062

  20. Efficient multitasking of Choleski matrix factorization on CRAY supercomputers

    NASA Technical Reports Server (NTRS)

    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.

  1. Inelastic deformation of metal matrix composites

    NASA Technical Reports Server (NTRS)

    Lissenden, C. J.; Herakovich, C. T.; Pindera, M-J.

    1993-01-01

    A theoretical model capable of predicting the thermomechanical response of continuously reinforced metal matrix composite laminates subjected to multiaxial loading was developed. A micromechanical model is used in conjunction with nonlinear lamination theory to determine inelastic laminae response. Matrix viscoplasticity, residual stresses, and damage to the fiber/matrix interfacial zone are explicitly included in the model. The representative cell of the micromechanical model is considered to be in a state of generalized plane strain, enabling a quasi two-dimensional analysis to be performed. Constant strain finite elements are formulated with elastic-viscoplastic constitutive equations. Interfacial debonding is incorporated into the model through interface elements based on the interfacial debonding theory originally presented by Needleman, and modified by Tvergaard. Nonlinear interfacial constitutive equations relate interfacial tractions to displacement discontinuities at the interface. Theoretical predictions are compared with the results of an experimental program conducted on silicon carbide/titanium (SiC/Ti) unidirectional, (O4), and angle-ply, (+34)(sub s), tubular specimens. Multiaxial loading included increments of axial tension, compression, torque, and internal pressure. Loadings were chosen in an effort to distinguish inelastic deformation due to damage from matrix plasticity and separate time-dependent effects from time-independent effects. Results show that fiber/matrix debonding is nonuniform throughout the composite and is a major factor in the effective response. Also, significant creep behavior occurs at relatively low applied stress levels at room temperature.

  2. Hybrid matrix amplifier

    DOEpatents

    Martens, J.S.; Hietala, V.M.; Plut, T.A.

    1995-01-03

    The present invention comprises a novel matrix amplifier. The matrix amplifier includes an active superconducting power divider (ASPD) having N output ports; N distributed amplifiers each operatively connected to one of the N output ports of the ASPD; and a power combiner having N input ports each operatively connected to one of the N distributed amplifiers. The distributed amplifier can included M stages of amplification by cascading superconducting active devices. The power combiner can include N active elements. The resulting (N[times]M) matrix amplifier can produce signals of high output power, large bandwidth, and low noise. 6 figures.

  3. Hybrid matrix amplifier

    DOEpatents

    Martens, Jon S.; Hietala, Vincent M.; Plut, Thomas A.

    1995-01-01

    The present invention comprises a novel matrix amplifier. The matrix amplifier includes an active superconducting power divider (ASPD) having N output ports; N distributed amplifiers each operatively connected to one of the N output ports of the ASPD; and a power combiner having N input ports each operatively connected to one of the N distributed amplifiers. The distributed amplifier can included M stages of amplification by cascading superconducting active devices. The power combiner can include N active elements. The resulting (N.times.M) matrix amplifier can produce signals of high output power, large bandwidth, and low noise.

  4. Identifying Dust Sources by Positive Matrix Factorization (PMF)

    NASA Astrophysics Data System (ADS)

    Engelbrecht, Johann P.

    2010-05-01

    This presentation is on the source attribution by Positive Matrix Factorization (PMF) of aerosol samples collected in Iraq, a major source of mineral dust in the Middle East. Globally transported mineral dust from North Africa, the Middle East, China, and elsewhere are routinely being sampled at high elevation monitoring sites such as those on the Canary Islands and Hawaii, and many ambient monitoring sites worldwide. Chemical results of these filter samples reflect differences in sources impacting at each site, further complicated by the regional geomorphology and meteorology. Trace elements, isotopes, elemental ratios, and mineralogy are generally being used to pinpoint geological source regions of natural and anthropogenic dusts. A receptor site is seldom impacted by only one source at a time. Dust palls are continually being modified by added dust from soils across which they migrate, also by particle segregation in the dust plume, and precipitation of the coarser particles. The result is that dust is a mixture, with contributions from different sources, each with a different chemical and mineralogical signature. PMF is a non-negative factorization procedure that produces only positive factor scores and loadings, in contrast to classical factor analysis (FA) and Principal Components Analysis (PCA). PMF enables us to resolve factors (chemical signatures) for source types contributing to the ambient chemical data set, and also models the source-type contributions to individual ambient samples. The latter can often be related to specific source regions. PMF was applied separately to two ambient data sets collected in Iraq in 2006, the one on Teflon membrane filters and the other on quartz fiber. Each of the filter types were previously analyzed for different chemical species: Teflon membrane for elements, by XRF and ICP-MS, while quartz fiber filters were analyzed for ions and carbon. [Engelbrecht et al. 2009] A set of 392 Teflon filter samples analyzed for 25

  5. Matrix Interdiction Problem

    NASA Astrophysics Data System (ADS)

    Kasiviswanathan, Shiva Prasad; Pan, Feng

    In the matrix interdiction problem, a real-valued matrix and an integer k is given. The objective is to remove a set of k matrix columns that minimizes in the residual matrix the sum of the row values, where the value of a row is defined to be the largest entry in that row. This combinatorial problem is closely related to bipartite network interdiction problem that can be applied to minimize the probability that an adversary can successfully smuggle weapons. After introducing the matrix interdiction problem, we study the computational complexity of this problem. We show that the matrix interdiction problem is NP-hard and that there exists a constant γ such that it is even NP-hard to approximate this problem within an n γ additive factor. We also present an algorithm for this problem that achieves an (n - k) multiplicative approximation ratio.

  6. Closed-form solutions for linear regulator-design of mechanical systems including optimal weighting matrix selection

    NASA Technical Reports Server (NTRS)

    Hanks, Brantley R.; Skelton, Robert E.

    1991-01-01

    This paper addresses the restriction of Linear Quadratic Regulator (LQR) solutions to the algebraic Riccati Equation to design spaces which can be implemented as passive structural members and/or dampers. A general closed-form solution to the optimal free-decay control problem is presented which is tailored for structural-mechanical systems. The solution includes, as subsets, special cases such as the Rayleigh Dissipation Function and total energy. Weighting matrix selection is a constrained choice among several parameters to obtain desired physical relationships. The closed-form solution is also applicable to active control design for systems where perfect, collocated actuator-sensor pairs exist. Some examples of simple spring mass systems are shown to illustrate key points.

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

    PubMed Central

    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

  8. A Hybrid Algorithm for Non-negative Matrix Factorization Based on Symmetric Information Divergence

    PubMed Central

    Devarajan, Karthik; Ebrahimi, Nader; Soofi, Ehsan

    2017-01-01

    The objective of this paper is to provide a hybrid algorithm for non-negative matrix factorization based on a symmetric version of Kullback-Leibler divergence, known as intrinsic information. The convergence of the proposed algorithm is shown for several members of the exponential family such as the Gaussian, Poisson, gamma and inverse Gaussian models. The speed of this algorithm is examined and its usefulness is illustrated through some applied problems. PMID:28868206

  9. Generating favorable growth factor and protease release profiles to enable extracellular matrix accumulation within an in vitro tissue engineering environment.

    PubMed

    Zhang, Xiaoqing; Battiston, Kyle G; Labow, Rosalind S; Simmons, Craig A; Santerre, J Paul

    2017-05-01

    Tissue engineering (particularly for the case of load-bearing cardiovascular and connective tissues) requires the ability to promote the production and accumulation of extracellular matrix (ECM) components (e.g., collagen, glycosaminoglycan and elastin). Although different approaches have been attempted in order to enhance ECM accumulation in tissue engineered constructs, studies of underlying signalling mechanisms that influence ECM deposition and degradation during tissue remodelling and regeneration in multi-cellular culture systems have been limited. The current study investigated vascular smooth muscle cell (VSMC)-monocyte co-culture systems using different VSMC:monocyte ratios, within a degradable polyurethane scaffold, to assess their influence on ECM generation and degradation processes, and to elucidate relevant signalling molecules involved in this in vitro vascular tissue engineering system. It was found that a desired release profile of growth factors (e.g. insulin growth factor-1 (IGF-1)) and hydrolytic proteases (e.g. matrix-metalloproteinases 2, 9, 13 and 14 (MMP2, MMP9, MMP13 and MMP14)), could be achieved in co-culture systems, yielding an accumulation of ECM (specifically for 2:1 and 4:1 VSMC:monocyte culture systems). This study has significant implications for the tissue engineering field (including vascular tissue engineering), not only because it identified important cytokines and proteases that control ECM accumulation/degradation within synthetic tissue engineering scaffolds, but also because the established culture systems could be applied to improve the development of different types of tissue constructs. Sufficient extracellular matrix accumulation within cardiovascular and connective tissue engineered constructs is a prerequisite for their appropriate function in vivo. This study established co-culture systems with tissue specific cells (vascular smooth muscle cells (VSMCs)) and defined ratios of immune cells (monocytes) to investigate

  10. Source apportionment of stack emissions from research and development facilities using positive matrix factorization

    NASA Astrophysics Data System (ADS)

    Ballinger, Marcel Y.; Larson, Timothy V.

    2014-12-01

    Research and development (R&D) facility emissions are difficult to characterize due to their variable processes, changing nature of research, and large number of chemicals. Positive matrix factorization (PMF) was applied to volatile organic compound (VOC) concentrations measured in the main exhaust stacks of four different R&D buildings to identify the number and composition of major contributing sources. PMF identified between 9 and 11 source-related factors contributing to stack emissions, depending on the building. Similar factors between buildings were major contributors to trichloroethylene (TCE), acetone, and ethanol emissions; other factors had similar profiles for two or more buildings but not all four. At least one factor for each building was identified that contained a broad mix of many species and constraints were used in PMF to modify the factors to resemble more closely the off-shift concentration profiles. PMF accepted the constraints with little decrease in model fit.

  11. EFFECT OF GROWTH FACTOR-FIBRONECTIN MATRIX INTERACTION ON RAT TYPE II CELL ADHESION AND DNA SYTHESIS

    EPA Science Inventory

    ABSTRACT

    Type II cells attach, migrate and proliferate on a provisional fibronectin-rich matrix during alveolar wall repair after lung injury. The combination of cell-substratum interactions via integrin receptors and exposure to local growth factors are likely to initiat...

  12. Nonlinear hyperspectral unmixing based on sparse non-negative matrix factorization

    NASA Astrophysics Data System (ADS)

    Li, Jing; Li, Xiaorun; Zhao, Liaoying

    2016-01-01

    Hyperspectral unmixing aims at extracting pure material spectra, accompanied by their corresponding proportions, from a mixed pixel. Owing to modeling more accurate distribution of real material, nonlinear mixing models (non-LMM) are usually considered to hold better performance than LMMs in complicated scenarios. In the past years, numerous nonlinear models have been successfully applied to hyperspectral unmixing. However, most non-LMMs only think of sum-to-one constraint or positivity constraint while the widespread sparsity among real materials mixing is the very factor that cannot be ignored. That is, for non-LMMs, a pixel is usually composed of a few spectral signatures of different materials from all the pure pixel set. Thus, in this paper, a smooth sparsity constraint is incorporated into the state-of-the-art Fan nonlinear model to exploit the sparsity feature in nonlinear model and use it to enhance the unmixing performance. This sparsity-constrained Fan model is solved with the non-negative matrix factorization. The algorithm was implemented on synthetic and real hyperspectral data and presented its advantage over those competing algorithms in the experiments.

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    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-/sup 3/H)proline and (methyl-/sup 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 (/sup 3/H)proline incorporation into collagenase-digestible protein (CDP) and noncollagen protein and on (/sup 3/H)thymidine incorporation into acid-precipitable material (DNA). IGF-Imore » 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.« less

  14. Nonnegative matrix factorization and sparse representation for the automated detection of periodic limb movements in sleep.

    PubMed

    Shokrollahi, Mehrnaz; Krishnan, Sridhar; Dopsa, Dustin D; Muir, Ryan T; Black, Sandra E; Swartz, Richard H; Murray, Brian J; Boulos, Mark I

    2016-11-01

    Stroke is a leading cause of death and disability in adults, and incurs a significant economic burden to society. Periodic limb movements (PLMs) in sleep are repetitive movements involving the great toe, ankle, and hip. Evolving evidence suggests that PLMs may be associated with high blood pressure and stroke, but this relationship remains underexplored. Several issues limit the study of PLMs including the need to manually score them, which is time-consuming and costly. For this reason, we developed a novel automated method for nocturnal PLM detection, which was shown to be correlated with (a) the manually scored PLM index on polysomnography, and (b) white matter hyperintensities on brain imaging, which have been demonstrated to be associated with PLMs. Our proposed algorithm consists of three main stages: (1) representing the signal in the time-frequency plane using time-frequency matrices (TFM), (2) applying K-nonnegative matrix factorization technique to decompose the TFM matrix into its significant components, and (3) applying kernel sparse representation for classification (KSRC) to the decomposed signal. Our approach was applied to a dataset that consisted of 65 subjects who underwent polysomnography. An overall classification of 97 % was achieved for discrimination of the aforementioned signals, demonstrating the potential of the presented method.

  15. Physiological ranges of matrix rigidity modulate primary mouse hepatocyte function in part through hepatocyte nuclear factor 4 alpha.

    PubMed

    Desai, Seema S; Tung, Jason C; Zhou, Vivian X; Grenert, James P; Malato, Yann; Rezvani, Milad; Español-Suñer, Regina; Willenbring, Holger; Weaver, Valerie M; Chang, Tammy T

    2016-07-01

    Matrix rigidity has important effects on cell behavior and is increased during liver fibrosis; however, its effect on primary hepatocyte function is unknown. We hypothesized that increased matrix rigidity in fibrotic livers would activate mechanotransduction in hepatocytes and lead to inhibition of liver-specific functions. To determine the physiologically relevant ranges of matrix stiffness at the cellular level, we performed detailed atomic force microscopy analysis across liver lobules from normal and fibrotic livers. We determined that normal liver matrix stiffness was around 150 Pa and increased to 1-6 kPa in areas near fibrillar collagen deposition in fibrotic livers. In vitro culture of primary hepatocytes on collagen matrix of tunable rigidity demonstrated that fibrotic levels of matrix stiffness had profound effects on cytoskeletal tension and significantly inhibited hepatocyte-specific functions. Normal liver stiffness maintained functional gene regulation by hepatocyte nuclear factor 4 alpha (HNF4α), whereas fibrotic matrix stiffness inhibited the HNF4α transcriptional network. Fibrotic levels of matrix stiffness activated mechanotransduction in primary hepatocytes through focal adhesion kinase. In addition, blockade of the Rho/Rho-associated protein kinase pathway rescued HNF4α expression from hepatocytes cultured on stiff matrix. Fibrotic levels of matrix stiffness significantly inhibit hepatocyte-specific functions in part by inhibiting the HNF4α transcriptional network mediated through the Rho/Rho-associated protein kinase pathway. Increased appreciation of the role of matrix rigidity in modulating hepatocyte function will advance our understanding of the mechanisms of hepatocyte dysfunction in liver cirrhosis and spur development of novel treatments for chronic liver disease. (Hepatology 2016;64:261-275). © 2016 by the American Association for the Study of Liver Diseases.

  16. Hybrid matrix fiber composites

    DOEpatents

    Deteresa, Steven J.; Lyon, Richard E.; Groves, Scott E.

    2003-07-15

    Hybrid matrix fiber composites having enhanced compressive performance as well as enhanced stiffness, toughness and durability suitable for compression-critical applications. The methods for producing the fiber composites using matrix hybridization. The hybrid matrix fiber composites include two chemically or physically bonded matrix materials, whereas the first matrix materials are used to impregnate multi-filament fibers formed into ribbons and the second matrix material is placed around and between the fiber ribbons that are impregnated with the first matrix material and both matrix materials are cured and solidified.

  17. Sparse non-negative matrix factorizations via alternating non-negativity-constrained least squares for microarray data analysis.

    PubMed

    Kim, Hyunsoo; Park, Haesun

    2007-06-15

    Many practical pattern recognition problems require non-negativity constraints. For example, pixels in digital images and chemical concentrations in bioinformatics are non-negative. Sparse non-negative matrix factorizations (NMFs) are useful when the degree of sparseness in the non-negative basis matrix or the non-negative coefficient matrix in an NMF needs to be controlled in approximating high-dimensional data in a lower dimensional space. In this article, we introduce a novel formulation of sparse NMF and show how the new formulation leads to a convergent sparse NMF algorithm via alternating non-negativity-constrained least squares. We apply our sparse NMF algorithm to cancer-class discovery and gene expression data analysis and offer biological analysis of the results obtained. Our experimental results illustrate that the proposed sparse NMF algorithm often achieves better clustering performance with shorter computing time compared to other existing NMF algorithms. The software is available as supplementary material.

  18. Surface presentation of biochemical cues for stem cell expansion - Spatial distribution of growth factors and self-assembly of extracellular matrix

    NASA Astrophysics Data System (ADS)

    Liu, Xingyu

    assembled in order to mimic the stem cell niche in vivo. First, we established assays that allow high-throughput quantification of hESC proliferation and ECM deposition. Human ESC survival was found to be highly sensitive to ECM assembly, and was improved by at least 20 times on substrates with well-assembled ECM. ECM polymerization alone improves clonal efficiency by at least 20 fold, from less than 0.1% to be 3-5%. This ratio is further improved to greater than 35% when combined with ROCK inhibitor, suggesting ECM polymerization underlines another critical factor in dictating hESC survival and growth. Given that many important signaling molecules including growth factors and extracellular matrix are highly enriched and restricted at the stem cell niche, we anticipate that our investigation into these questions provides better insight into the physiological roles of the stem cell niche components, and helps us to rationally direct stem cell fates in future stem cell-based therapeutic interventions.

  19. METCAN-PC - METAL MATRIX COMPOSITE ANALYZER

    NASA Technical Reports Server (NTRS)

    Murthy, P. L.

    1994-01-01

    High temperature metal matrix composites offer great potential for use in advanced aerospace structural applications. The realization of this potential however, requires concurrent developments in (1) a technology base for fabricating high temperature metal matrix composite structural components, (2) experimental techniques for measuring their thermal and mechanical characteristics, and (3) computational methods to predict their behavior. METCAN (METal matrix Composite ANalyzer) is a computer program developed to predict this behavior. METCAN can be used to computationally simulate the non-linear behavior of high temperature metal matrix composites (HT-MMC), thus allowing the potential payoff for the specific application to be assessed. It provides a comprehensive analysis of composite thermal and mechanical performance. METCAN treats material nonlinearity at the constituent (fiber, matrix, and interphase) level, where the behavior of each constituent is modeled accounting for time-temperature-stress dependence. The composite properties are synthesized from the constituent instantaneous properties by making use of composite micromechanics and macromechanics. Factors which affect the behavior of the composite properties include the fabrication process variables, the fiber and matrix properties, the bonding between the fiber and matrix and/or the properties of the interphase between the fiber and matrix. The METCAN simulation is performed as point-wise analysis and produces composite properties which are readily incorporated into a finite element code to perform a global structural analysis. After the global structural analysis is performed, METCAN decomposes the composite properties back into the localized response at the various levels of the simulation. At this point the constituent properties are updated and the next iteration in the analysis is initiated. This cyclic procedure is referred to as the integrated approach to metal matrix composite analysis. METCAN

  20. University Organization. A Matrix Analysis of the Academic Professions.

    ERIC Educational Resources Information Center

    Bess, James L.

    Using the latest research instruments, including questionnaires, interviews, factor analysis, and matrix construction, the present restraints on professorial effectiveness and the contributions of departmental and university structures to professorial malaise is examined for the purpose of improving ways that administrators can increase faculty…

  1. Quantum kinetic expansion in the spin-boson model: Matrix formulation and system-bath factorized initial state.

    PubMed

    Gong, Zhihao; Tang, Zhoufei; Wang, Haobin; Wu, Jianlan

    2017-12-28

    Within the framework of the hierarchy equation of motion (HEOM), the quantum kinetic expansion (QKE) method of the spin-boson model is reformulated in the matrix representation. The equivalence between the two formulations (HEOM matrices and quantum operators) is numerically verified from the calculation of the time-integrated QKE rates. The matrix formulation of the QKE is extended to the system-bath factorized initial state. Following a one-to-one mapping between HEOM matrices and quantum operators, a quantum kinetic equation is rederived. The rate kernel is modified by an extra term following a systematic expansion over the site-site coupling. This modified QKE is numerically tested for its reliability by calculating the time-integrated rate and non-Markovian population kinetics. For an intermediate-to-strong dissipation strength and a large site-site coupling, the population transfer is found to be significantly different when the initial condition is changed from the local equilibrium to system-bath factorized state.

  2. Matrix Theory of Small Oscillations

    ERIC Educational Resources Information Center

    Chavda, L. K.

    1978-01-01

    A complete matrix formulation of the theory of small oscillations is presented. Simple analytic solutions involving matrix functions are found which clearly exhibit the transients, the damping factors, the Breit-Wigner form for resonances, etc. (BB)

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

    PubMed Central

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

    2016-01-01

    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

  4. Biofilm Matrix Proteins.

    PubMed

    Fong, Jiunn N C; Yildiz, Fitnat H

    2015-04-01

    Proteinaceous components of the biofilm matrix include secreted extracellular proteins, cell surface adhesins, and protein subunits of cell appendages such as flagella and pili. Biofilm matrix proteins play diverse roles in biofilm formation and dissolution. They are involved in attaching cells to surfaces, stabilizing the biofilm matrix via interactions with exopolysaccharide and nucleic acid components, developing three-dimensional biofilm architectures, and dissolving biofilm matrix via enzymatic degradation of polysaccharides, proteins, and nucleic acids. In this article, we will review functions of matrix proteins in a selected set of microorganisms, studies of the matrix proteomes of Vibrio cholerae and Pseudomonas aeruginosa, and roles of outer membrane vesicles and of nucleoid-binding proteins in biofilm formation.

  5. High-performance sparse matrix-matrix products on Intel KNL and multicore architectures

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Nagasaka, Y; Matsuoka, S; Azad, A

    Sparse matrix-matrix multiplication (SpGEMM) is a computational primitive that is widely used in areas ranging from traditional numerical applications to recent big data analysis and machine learning. Although many SpGEMM algorithms have been proposed, hardware specific optimizations for multi- and many-core processors are lacking and a detailed analysis of their performance under various use cases and matrices is not available. We firstly identify and mitigate multiple bottlenecks with memory management and thread scheduling on Intel Xeon Phi (Knights Landing or KNL). Specifically targeting multi- and many-core processors, we develop a hash-table-based algorithm and optimize a heap-based shared-memory SpGEMM algorithm. Wemore » examine their performance together with other publicly available codes. Different from the literature, our evaluation also includes use cases that are representative of real graph algorithms, such as multi-source breadth-first search or triangle counting. Our hash-table and heap-based algorithms are showing significant speedups from libraries in the majority of the cases while different algorithms dominate the other scenarios with different matrix size, sparsity, compression factor and operation type. We wrap up in-depth evaluation results and make a recipe to give the best SpGEMM algorithm for target scenario. A critical finding is that hash-table-based SpGEMM gets a significant performance boost if the nonzeros are not required to be sorted within each row of the output matrix.« less

  6. Factors affecting miniature Izod impact strength of tungsten-fiber-metal-matrix

    NASA Technical Reports Server (NTRS)

    Winsa, E. A.; Petrasek, D. W.

    1973-01-01

    The miniature Izod and Charpy impact strengths of copper, copper-nickel, and nickel-base superalloy uniaxially reinforced with continuous tungsten fibers were studied. In most cases, impact strength was increased by increasing fiber or matrix toughness, decreasing fibermatrix reaction, increasing test temperature, hot working, or heat treating. Notch sensitivity was reduced by increasing fiber content or matrix toughness. An equation relating impact strength to fiber and matrix properties and fiber content was developed. Program results imply that tungsten alloy-fiber/superalloy matrix composites can be made with adequate impact resistance for turbine blade or vane applications.

  7. Deep learning and non-negative matrix factorization in recognition of mammograms

    NASA Astrophysics Data System (ADS)

    Swiderski, Bartosz; Kurek, Jaroslaw; Osowski, Stanislaw; Kruk, Michal; Barhoumi, Walid

    2017-02-01

    This paper presents novel approach to the recognition of mammograms. The analyzed mammograms represent the normal and breast cancer (benign and malignant) cases. The solution applies the deep learning technique in image recognition. To obtain increased accuracy of classification the nonnegative matrix factorization and statistical self-similarity of images are applied. The images reconstructed by using these two approaches enrich the data base and thanks to this improve of quality measures of mammogram recognition (increase of accuracy, sensitivity and specificity). The results of numerical experiments performed on large DDSM data base containing more than 10000 mammograms have confirmed good accuracy of class recognition, exceeding the best results reported in the actual publications for this data base.

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

    PubMed

    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.

  9. Application of fiber bridging models to fatigue crack growth in unidirectional titanium matrix composites

    NASA Technical Reports Server (NTRS)

    Bakuckas, J. G., Jr.; Johnson, W. S.

    1992-01-01

    Several fiber bridging models were reviewed and applied to study the matrix fatigue crack growth behavior in center notched (0)(sub 8) SCS-6/Ti-15-3 and (0)(sub 4) SCS-6/Ti-6Al-4V laminates. Observations revealed that fatigue damage consisted primarily of matrix cracks and fiber matrix interfacial failure in the (0)(sub 8) SCS-6/Ti-15-3 laminates. Fiber-matrix interface failure included fracture of the brittle reaction zone and cracking between the two carbon rich fiber coatings. Intact fibers in the wake of the matrix cracks reduce the stress intensity factor range. Thus, an applied stress intensity factor range is inappropriate to characterize matrix crack growth behavior. Fiber bridging models were used to determine the matrix stress intensity factor range in titanium metal matrix composites. In these models, the fibers in the wake of the crack are idealized as a closure pressure. An unknown constant frictional shear stress is assumed to act along the debond or slip length of the bridging fibers. The frictional shear stress was used as a curve fitting parameter to available data (crack growth data, crack opening displacement data, and debond length data). Large variations in the frictional shear stress required to fit the experimental data indicate that the fiber bridging models in their present form lack predictive capabilities. However, these models provide an efficient and relatively simple engineering method for conducting parametric studies of the matrix growth behavior based on constituent properties.

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

    PubMed

    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

  11. The Bioactivity of Cartilage Extracellular Matrix in Articular Cartilage Regeneration

    PubMed Central

    Sutherland, Amanda J.; Converse, Gabriel L.; Hopkins, Richard A.; Detamore, Michael S.

    2014-01-01

    Cartilage matrix is a particularly promising acellular material for cartilage regeneration given the evidence supporting its chondroinductive character. The ‘raw materials’ of cartilage matrix can serve as building blocks and signals for enhanced tissue regeneration. These matrices can be created by chemical or physical methods: physical methods disrupt cellular membranes and nuclei but may not fully remove all cell components and DNA, whereas chemical methods when combined with physical methods are particularly effective in fully decellularizing such materials. Critical endpoints include no detectable residual DNA or immunogenic antigens. It is important to first delineate between the sources of the cartilage matrix, i.e., derived from matrix produced by cells in vitro or from native tissue, and then to further characterize the cartilage matrix based on the processing method, i.e., decellularization or devitalization. With these distinctions, four types of cartilage matrices exist: decellularized native cartilage (DCC), devitalized native cartilage (DVC), decellularized cell derived matrix (DCCM), and devitalized cell derived matrix (DVCM). Delivery of cartilage matrix may be a straightforward approach without the need for additional cells or growth factors. Without additional biological additives, cartilage matrix may be attractive from a regulatory and commercialization standpoint. Source and delivery method are important considerations for clinical translation. Only one currently marketed cartilage matrix medical device is decellularized, although trends in filed patents suggest additional decellularized products may be available in the future. To choose the most relevant source and processing for cartilage matrix, qualifying testing needs to include targeting the desired application, optimizing delivery of the material, identify relevant FDA regulations, assess availability of raw materials, and immunogenic properties of the product. PMID:25044502

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

    PubMed Central

    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. PMID:24982999

  13. GC[Formula: see text]NMF: A Novel Matrix Factorization Framework for Gene-Phenotype Association Prediction.

    PubMed

    Zhang, Yaogong; Liu, Jiahui; Liu, Xiaohu; Hong, Yuxiang; Fan, Xin; Huang, Yalou; Wang, Yuan; Xie, Maoqiang

    2018-04-24

    Gene-phenotype association prediction can be applied to reveal the inherited basis of human diseases and facilitate drug development. Gene-phenotype associations are related to complex biological processes and influenced by various factors, such as relationship between phenotypes and that among genes. While due to sparseness of curated gene-phenotype associations and lack of integrated analysis of the joint effect of multiple factors, existing applications are limited to prediction accuracy and potential gene-phenotype association detection. In this paper, we propose a novel method by exploiting weighted graph constraint learned from hierarchical structures of phenotype data and group prior information among genes by inheriting advantages of Non-negative Matrix Factorization (NMF), called Weighted Graph Constraint and Group Centric Non-negative Matrix Factorization (GC[Formula: see text]NMF). Specifically, first we introduce the depth of parent-child relationships between two adjacent phenotypes in hierarchical phenotypic data as weighted graph constraint for a better phenotype understanding. Second, we utilize intra-group correlation among genes in a gene group as group constraint for gene understanding. Such information provides us with the intuition that genes in a group probably result in similar phenotypes. The model not only allows us to achieve a high-grade prediction performance, but also helps us to learn interpretable representation of genes and phenotypes simultaneously to facilitate future biological analysis. Experimental results on biological gene-phenotype association datasets of mouse and human demonstrate that GC[Formula: see text]NMF can obtain superior prediction accuracy and good understandability for biological explanation over other state-of-the-arts methods.

  14. Recursive mass matrix factorization and inversion: An operator approach to open- and closed-chain multibody dynamics

    NASA Technical Reports Server (NTRS)

    Rodriguez, G.; Kreutz, K.

    1988-01-01

    This report advances a linear operator approach for analyzing the dynamics of systems of joint-connected rigid bodies.It is established that the mass matrix M for such a system can be factored as M=(I+H phi L)D(I+H phi L) sup T. This yields an immediate inversion M sup -1=(I-H psi L) sup T D sup -1 (I-H psi L), where H and phi are given by known link geometric parameters, and L, psi and D are obtained recursively by a spatial discrete-step Kalman filter and by the corresponding Riccati equation associated with this filter. The factors (I+H phi L) and (I-H psi L) are lower triangular matrices which are inverses of each other, and D is a diagonal matrix. This factorization and inversion of the mass matrix leads to recursive algortihms for forward dynamics based on spatially recursive filtering and smoothing. The primary motivation for advancing the operator approach is to provide a better means to formulate, analyze and understand spatial recursions in multibody dynamics. This is achieved because the linear operator notation allows manipulation of the equations of motion using a very high-level analytical framework (a spatial operator algebra) that is easy to understand and use. Detailed lower-level recursive algorithms can readily be obtained for inspection from the expressions involving spatial operators. The report consists of two main sections. In Part 1, the problem of serial chain manipulators is analyzed and solved. Extensions to a closed-chain system formed by multiple manipulators moving a common task object are contained in Part 2. To retain ease of exposition in the report, only these two types of multibody systems are considered. However, the same methods can be easily applied to arbitrary multibody systems formed by a collection of joint-connected regid bodies.

  15. Automatic switching matrix

    DOEpatents

    Schlecht, Martin F.; Kassakian, John G.; Caloggero, Anthony J.; Rhodes, Bruce; Otten, David; Rasmussen, Neil

    1982-01-01

    An automatic switching matrix that includes an apertured matrix board containing a matrix of wires that can be interconnected at each aperture. Each aperture has associated therewith a conductive pin which, when fully inserted into the associated aperture, effects electrical connection between the wires within that particular aperture. Means is provided for automatically inserting the pins in a determined pattern and for removing all the pins to permit other interconnecting patterns.

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

    PubMed

    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.

  17. New intracellular activities of matrix metalloproteinases shine in the moonlight.

    PubMed

    Jobin, Parker G; Butler, Georgina S; Overall, Christopher M

    2017-11-01

    Adaption of a single protein to perform multiple independent functions facilitates functional plasticity of the proteome allowing a limited number of protein-coding genes to perform a multitude of cellular processes. Multifunctionality is achievable by post-translational modifications and by modulating subcellular localization. Matrix metalloproteinases (MMPs), classically viewed as degraders of the extracellular matrix (ECM) responsible for matrix protein turnover, are more recently recognized as regulators of a range of extracellular bioactive molecules including chemokines, cytokines, and their binders. However, growing evidence has convincingly identified select MMPs in intracellular compartments with unexpected physiological and pathological roles. Intracellular MMPs have both proteolytic and non-proteolytic functions, including signal transduction and transcription factor activity thereby challenging their traditional designation as extracellular proteases. This review highlights current knowledge of subcellular location and activity of these "moonlighting" MMPs. Intracellular roles herald a new era of MMP research, rejuvenating interest in targeting these proteases in therapeutic strategies. This article is part of a Special Issue entitled: Matrix Metalloproteinases edited by Rafael Fridman. Copyright © 2017 Elsevier B.V. All rights reserved.

  18. Critical Evaluation of Risk Factors and Early Complications in 564 Consecutive Two-Stage Implant-Based Breast Reconstructions Using Acellular Dermal Matrix at a Single Center.

    PubMed

    Selber, Jesse C; Wren, James H; Garvey, Patrick B; Zhang, Hong; Erickson, Cameron; Clemens, Mark W; Butler, Charles E

    2015-07-01

    Acellular dermal matrix for implant-based breast reconstruction appears to cause higher early complication rates, but long-term outcomes are perceived to be superior. This dichotomy is the subject of considerable debate. The authors hypothesized that patient characteristics and operative variables would have a greater impact on complications than the type of acellular dermal matrix used. A retrospective cohort study was performed of consecutive patients who underwent two-stage, implant-based breast reconstruction with human cadaveric or bovine acellular dermal matrix from 2006 to 2012 at a single institution. Patient characteristics and operative variables were analyzed using logistic regression analyses to identify risk factors for complications. The authors included 564 reconstructions in the study. Radiation therapy and obesity increased the odds of all complications. Every 100-ml increase in preoperative breast volume increased the odds of any complication by 1 percent, the odds of infection by 27 percent, and the risk of explantation by 16 percent. The odds of seroma increased linearly with increasing surface area of acellular dermal matrix. Odds of infection were higher with an intraoperative expander fill volume greater than 50 percent of the total volume. Risk of explantation was twice as high when intraoperative expander fill volume was greater than 300 ml. Radiation therapy, obesity, larger breasts, higher intraoperative fill volumes, and larger acellular dermal matrices are all independent risk factors for early complications. Maximizing the initial mastectomy skin envelope fill must be balanced with the understanding that higher complication rates may result from a larger intraoperative breast mound. Risk, III.

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

    PubMed

    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.

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

    PubMed

    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.

  1. Transforming growth factor-beta stimulates wound healing and modulates extracellular matrix gene expression in pig skin. I. Excisional wound model.

    PubMed

    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.

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

    NASA Astrophysics Data System (ADS)

    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.

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

    PubMed

    Luce, Robert; Hildebrandt, Peter; Kuhlmann, Uwe; Liesen, Jörg

    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 nonnegative matrix factorization that 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 the 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. © The Author(s) 2016.

  4. Applications of a Novel Clustering Approach Using Non-Negative Matrix Factorization to Environmental Research in Public Health

    PubMed Central

    Fogel, Paul; Gaston-Mathé, Yann; Hawkins, Douglas; Fogel, Fajwel; Luta, George; Young, S. Stanley

    2016-01-01

    Often data can be represented as a matrix, e.g., observations as rows and variables as columns, or as a doubly classified contingency table. Researchers may be interested in clustering the observations, the variables, or both. If the data is non-negative, then Non-negative Matrix Factorization (NMF) can be used to perform the clustering. By its nature, NMF-based clustering is focused on the large values. If the data is normalized by subtracting the row/column means, it becomes of mixed signs and the original NMF cannot be used. Our idea is to split and then concatenate the positive and negative parts of the matrix, after taking the absolute value of the negative elements. NMF applied to the concatenated data, which we call PosNegNMF, offers the advantages of the original NMF approach, while giving equal weight to large and small values. We use two public health datasets to illustrate the new method and compare it with alternative clustering methods, such as K-means and clustering methods based on the Singular Value Decomposition (SVD) or Principal Component Analysis (PCA). With the exception of situations where a reasonably accurate factorization can be achieved using the first SVD component, we recommend that the epidemiologists and environmental scientists use the new method to obtain clusters with improved quality and interpretability. PMID:27213413

  5. Applications of a Novel Clustering Approach Using Non-Negative Matrix Factorization to Environmental Research in Public Health.

    PubMed

    Fogel, Paul; Gaston-Mathé, Yann; Hawkins, Douglas; Fogel, Fajwel; Luta, George; Young, S Stanley

    2016-05-18

    Often data can be represented as a matrix, e.g., observations as rows and variables as columns, or as a doubly classified contingency table. Researchers may be interested in clustering the observations, the variables, or both. If the data is non-negative, then Non-negative Matrix Factorization (NMF) can be used to perform the clustering. By its nature, NMF-based clustering is focused on the large values. If the data is normalized by subtracting the row/column means, it becomes of mixed signs and the original NMF cannot be used. Our idea is to split and then concatenate the positive and negative parts of the matrix, after taking the absolute value of the negative elements. NMF applied to the concatenated data, which we call PosNegNMF, offers the advantages of the original NMF approach, while giving equal weight to large and small values. We use two public health datasets to illustrate the new method and compare it with alternative clustering methods, such as K-means and clustering methods based on the Singular Value Decomposition (SVD) or Principal Component Analysis (PCA). With the exception of situations where a reasonably accurate factorization can be achieved using the first SVD component, we recommend that the epidemiologists and environmental scientists use the new method to obtain clusters with improved quality and interpretability.

  6. Nanocrystal doped matrixes

    DOEpatents

    Parce, J. Wallace; Bernatis, Paul; Dubrow, Robert; Freeman, William P.; Gamoras, Joel; Kan, Shihai; Meisel, Andreas; Qian, Baixin; Whiteford, Jeffery A.; Ziebarth, Jonathan

    2010-01-12

    Matrixes doped with semiconductor nanocrystals are provided. In certain embodiments, the semiconductor nanocrystals have a size and composition such that they absorb or emit light at particular wavelengths. The nanocrystals can comprise ligands that allow for mixing with various matrix materials, including polymers, such that a minimal portion of light is scattered by the matrixes. The matrixes of the present invention can also be utilized in refractive index matching applications. In other embodiments, semiconductor nanocrystals are embedded within matrixes to form a nanocrystal density gradient, thereby creating an effective refractive index gradient. The matrixes of the present invention can also be used as filters and antireflective coatings on optical devices and as down-converting layers. Processes for producing matrixes comprising semiconductor nanocrystals are also provided. Nanostructures having high quantum efficiency, small size, and/or a narrow size distribution are also described, as are methods of producing indium phosphide nanostructures and core-shell nanostructures with Group II-VI shells.

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

    PubMed

    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.

  8. Source Apportionment Using Positive Matrix Factorization on Daily Measurements of Inorganic and Organic Speciated PM2.5

    PubMed Central

    Dutton, Steven J.; Vedal, Sverre; Piedrahita, Ricardo; Milford, Jana B.; Miller, Shelly L.; Hannigan, Michael P.

    2012-01-01

    Particulate matter less than 2.5 microns in diameter (PM2.5) has been linked with a wide range of adverse health effects. Determination of the sources of PM2.5 most responsible for these health effects could lead to improved understanding of the mechanisms of such effects and more targeted regulation. This has provided the impetus for the Denver Aerosol Sources and Health (DASH) study, a multi-year source apportionment and health effects study relying on detailed inorganic and organic PM2.5 speciation measurements. In this study, PM2.5 source apportionment is performed by coupling positive matrix factorization (PMF) with daily speciated PM2.5 measurements including inorganic ions, elemental carbon (EC) and organic carbon (OC), and organic molecular markers. A qualitative comparison is made between two models, PMF2 and ME2, commonly used for solving the PMF problem. Many previous studies have incorporated chemical mass balance (CMB) for organic molecular marker source apportionment on limited data sets, but the DASH data set is large enough to use multivariate factor analysis techniques such as PMF. Sensitivity of the PMF2 and ME2 models to the selection of speciated PM2.5 components and model input parameters was investigated in depth. A combination of diagnostics was used to select an optimum, 7-factor model using one complete year of daily data with pointwise measurement uncertainties. The factors included 1) a wintertime/methoxyphenol factor, 2) an EC/sterane factor, 3) a nitrate/polycyclic aromatic hydrocarbon (PAH) factor, 4) a summertime/selective aliphatic factor, 5) an n-alkane factor, 6) a middle oxygenated PAH/alkanoic acid factor and 7) an inorganic ion factor. These seven factors were qualitatively linked with known PM2.5 emission sources with varying degrees of confidence. Mass apportionment using the 7-factor model revealed the contribution of each factor to the mass of OC, EC, nitrate and sulfate. On an annual basis, the majority of OC and EC mass

  9. Engineering a collagen matrix that replicates the biological properties of native extracellular matrix.

    PubMed

    Nam, Kwangwoo; Sakai, Yuuki; Funamoto, Seiichi; Kimura, Tsuyoshi; Kishida, Akio

    2011-01-01

    In this study, we aimed to replicate the function of native tissues that can be used in tissue engineering and regenerative medicine. The key to such replication is the preparation of an artificial collagen matrix that possesses a structure resembling that of the extracellular matrix. We, therefore, prepared a collagen matrix by fibrillogenesis in a NaCl/Na(2)HPO(4) aqueous solution using a dialysis cassette and investigated its biological behavior in vitro and in vivo. The in vitro cell adhesion and proliferation did not show any significant differences. The degradation rate in the living body could be controlled according to the preparation condition, where the collagen matrix with high water content (F-collagen matrix, >98%) showed fast degradation and collagen matrix with lower water content (T-collagen matrix, >80%) showed no degradation for 8 weeks. The degradation did not affect the inflammatory response at all and relatively faster wound healing response was observed. Comparing this result with that of collagen gel and decellularized cornea, it can be concluded that the structural factor is very important and no cell abnormal behavior would be observed for quaternary structured collagen matrix.

  10. Investigation of colloidal graphite as a matrix for matrix-assisted laser desorption/ionisation mass spectrometry of low molecular weight analytes.

    PubMed

    Warren, Alexander D; Conway, Ulric; Arthur, Christopher J; Gates, Paul J

    2016-07-01

    The analysis of low molecular weight compounds by matrix-assisted laser desorption/ionisation mass spectrometry is problematic due to the interference and suppression of analyte ionisation by the matrices typically employed - which are themselves low molecular weight compounds. The application of colloidal graphite is demonstrated here as an easy to use matrix that can promote the ionisation of a wide range of analytes including low molecular weight organic compounds, complex natural products and inorganic complexes. Analyte ionisation with colloidal graphite is compared with traditional organic matrices along with various other sources of graphite (e.g. graphite rods and charcoal pencils). Factors such as ease of application, spectra reproducibility, spot longevity, spot-to-spot reproducibility and spot homogeneity (through single spot imaging) are explored. For some analytes, considerable matrix suppression effects are observed resulting in spectra completely devoid of matrix ions. We also report the observation of radical molecular ions [M(-●) ] in the negative ion mode, particularly with some aromatic analytes. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

  11. Downregulation of connective tissue growth factor by three-dimensional matrix enhances ovarian carcinoma cell invasion.

    PubMed

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

    2009-08-15

    Epithelial ovarian carcinoma (EOC) is a leading cause of death from gynecologic malignancies, due mainly to the prevalence of undetected metastatic disease. The process of cell invasion during intraperitoneal 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 hr of 3D collagen culture) coupled with confirmatory real-time reverse-transcriptase polymerase chain reaction, multiple 3D 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 (3D 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 alpha6beta1 and alpha3beta1 integrins. Together these data suggest that downregulation of CTGF in EOC cells may be important for cell invasion through modulation of cell-matrix adhesion.

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

    PubMed Central

    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

  13. Research on graphite reinforced glass matrix composites

    NASA Technical Reports Server (NTRS)

    Prewo, K. M.; Thompson, E. R.

    1980-01-01

    High levels of mechanical performance in tension, flexure, fatigue, and creep loading situations of graphite fiber reinforced glass matrix composites are discussed. At test temperatures of up to 813 K it was found that the major limiting factor was the oxidative instability of the reinforcing graphite fibers. Particular points to note include the following: (1) a wide variety of graphite fibers were found to be comparable with the glass matrix composite fabrication process; (2) choice of fiber, to a large extent, controlled resultant composite performance; (3) composite fatigue performance was found to be excellent at both 300 K and 703 K; (4) composite creep and stress rupture at temperatures of up to 813 K was limited by the oxidative stability of the fiber; (5) exceptionally low values of composite thermal expansion coefficient were attributable to the dimensional stability of both matrix and fiber; and (6) component fabricability was demonstrated through the hot pressing of hot sections and brazing using glass and metal joining phases.

  14. WALLY 1 ...A large, principal components regression program with varimax rotation of the factor weight matrix

    Treesearch

    James R. Wallis

    1965-01-01

    Written in Fortran IV and MAP, this computer program can handle up to 120 variables, and retain 40 principal components. It can perform simultaneous regression of up to 40 criterion variables upon the varimax rotated factor weight matrix. The columns and rows of all output matrices are labeled by six-character alphanumeric names. Data input can be from punch cards or...

  15. Chemical composition of atmospheric aerosols resolved via positive matrix factorization

    NASA Astrophysics Data System (ADS)

    Äijälä, Mikko; Junninen, Heikki; Heikkinen, Liine; Petäjä, Tuukka; Kulmala, Markku; Worsnop, Douglas; Ehn, Mikael

    2017-04-01

    Atmospheric particulate matter is a complex mixture of various chemical species such as organic compounds, sulfates, nitrates, ammonia, chlorides, black carbon and sea salt. As aerosol chemical composition strongly influences aerosol climate effects (via cloud condensation nucleus activation, hygroscopic properties, aerosol optics, volatility and condensation) as well as health effects (toxicity, carcinogenicity, particle morphology), detailed understanding of atmospheric fine particle composition is widely beneficial for understanding these interactions. Unfortunately the comprehensive, detailed measurement of aerosol chemistry remains difficult due to the wide range of compounds present in the atmosphere as well as for the miniscule mass of the particles themselves compared to their carrier gas. Aerosol mass spectrometer (AMS; Canagaratna et al., 2007) is an instrument often used for characterization of non-refractive aerosol types: the near-universal vaporization and ionisation technique allows for measurement of most atmospheric-relevant compounds (with the notable exception of refractory matter such as sea salt, black carbon, metals and crustal matter). The downside of the hard ionisation applied is extensive fragmentation of sample molecules. However, the apparent loss of information in fragmentation can be partly offset by applying advanced statistical methods to extract information from the fragmentation patterns. In aerosol mass spectrometry statistical analysis methods, such as positive matrix factorization (PMF; Paatero, 1999) are usually applied for aerosol organic component only, to keep the number of factors to be resolved manageable, to retain the inorganic components for solution validation via correlation analysis, and to avoid inorganic species dominating the factor model. However, this practice smears out the interactions between organic and inorganic chemical components, and hinders the understanding of the connections between primary and

  16. Effects of partitioning and scheduling sparse matrix factorization on communication and load balance

    NASA Technical Reports Server (NTRS)

    Venugopal, Sesh; Naik, Vijay K.

    1991-01-01

    A block based, automatic partitioning and scheduling methodology is presented for sparse matrix factorization on distributed memory systems. Using experimental results, this technique is analyzed for communication and load imbalance overhead. To study the performance effects, these overheads were compared with those obtained from a straightforward 'wrap mapped' column assignment scheme. All experimental results were obtained using test sparse matrices from the Harwell-Boeing data set. The results show that there is a communication and load balance tradeoff. The block based method results in lower communication cost whereas the wrap mapped scheme gives better load balance.

  17. Modeling the Nonlinear, Strain Rate Dependent Deformation of Woven Ceramic Matrix Composites With Hydrostatic Stress Effects Included

    NASA Technical Reports Server (NTRS)

    Goldberg, Robert K.; Carney, Kelly S.

    2004-01-01

    An analysis method based on a deformation (as opposed to damage) approach has been developed to model the strain rate dependent, nonlinear deformation of woven ceramic matrix composites with a plain weave fiber architecture. In the developed model, the differences in the tension and compression response have also been considered. State variable based viscoplastic equations originally developed for metals have been modified to analyze the ceramic matrix composites. To account for the tension/compression asymmetry in the material, the effective stress and effective inelastic strain definitions have been modified. The equations have also been modified to account for the fact that in an orthotropic composite the in-plane shear stiffness is independent of the stiffness in the normal directions. The developed equations have been implemented into a commercially available transient dynamic finite element code, LS-DYNA, through the use of user defined subroutines (UMATs). The tensile, compressive, and shear deformation of a representative plain weave woven ceramic matrix composite are computed and compared to experimental results. The computed values correlate well to the experimental data, demonstrating the ability of the model to accurately compute the deformation response of woven ceramic matrix composites.

  18. Hepatocyte growth factor: a regulator of extracellular matrix genes in mouse mesangial cells.

    PubMed

    Laping, N J; Olson, B A; Ho, T; Ziyadeh, F N; Albrightson, C R

    2000-04-01

    The potential role of hepatocyte growth factor (HGF) in regulating extracellular matrix in mouse mesangial cells (MMC) was evaluated. Functional HGF receptors were deed in MMC by HGF-induced extracellular acidification, a response that was inhibited by the HGF inhibitor HGF/NK2, a splice variant expressing the N-terminal domain through the second kringle domain HGF also increased fibronectin and collagen alpha1 (IV) mRNA levels in these cells; the increases were associated with a concentration-dependent increase in transcriptional activity of the collagen alpha1 (IV) gene. HGF also stimulated fibronectin and collagen alpha1 (IV) mRNA levels in primary rabbit proximal tubule epithelial cells To evaluate the potential consequences of chronic elevation of HGF on renal fuction, HGF was administered continuously for 18 days to normal and diabetic C57BLKS/J lepr(db) mice. In the diabetic mice, HGF reduced creatinine clearance and increased microalbuminuria, indicating that chronic exposure to HGF impairs renal function. Thus, chronically elevated HGF may contribute to the progression of chronic renal disease in diabetes by decreasing the glomerular filtration rate and possibly promoting the accumulation of extracellular matrix.

  19. Source apportionment of VOCs in the Los Angeles area using positive matrix factorization

    NASA Astrophysics Data System (ADS)

    Brown, Steven G.; Frankel, Anna; Hafner, Hilary R.

    Eight 3-h speciated hydrocarbon measurements were collected daily by the South Coast Air Quality Management District (SCAQMD) as part of the Photochemical Assessment Monitoring Stations (PAMS) program during the summers of 2001-03 at two sites in the Los Angeles air basin, Azusa and Hawthorne. Over 30 hydrocarbons from over 500 samples at Azusa and 600 samples at Hawthorne were subsequently analyzed using the multivariate receptor model positive matrix factorization (PMF). At Azusa and Hawthorne, five and six factors were identified, respectively, with a good comparison between predicted and measured mass. At Azusa, evaporative emissions (a median of 31% of the total mass), motor vehicle exhaust (22%), liquid/unburned gasoline (27%), coatings (17%), and biogenic emissions (3%) factors were identified. Factors identified at Hawthorne were evaporative emissions (a median of 34% of the total mass), motor vehicle exhaust (24%), industrial process losses (15%), natural gas (13%), liquid/unburned gasoline (13%), and biogenic emissions (1%). Together, the median contribution from mobile source-related factors (exhaust, evaporative emissions, and liquid/unburned gasoline) was 80% and 71% at Azusa and Hawthorne, respectively, similar to previous source apportionment results using the chemical mass balance (CMB) model. There is a difference in the distribution among mobile source factors compared to the CMB work, with an increase in the contribution from evaporative emissions, though the cause (changes in emissions or differences between models) is unknown.

  20. Processing of Antenna-Array Signals on the Basis of the Interference Model Including a Rank-Deficient Correlation Matrix

    NASA Astrophysics Data System (ADS)

    Rodionov, A. A.; Turchin, V. I.

    2017-06-01

    We propose a new method of signal processing in antenna arrays, which is called the Maximum-Likelihood Signal Classification. The proposed method is based on the model in which interference includes a component with a rank-deficient correlation matrix. Using numerical simulation, we show that the proposed method allows one to ensure variance of the estimated arrival angle of the plane wave, which is close to the Cramer-Rao lower boundary and more efficient than the best-known MUSIC method. It is also shown that the proposed technique can be efficiently used for estimating the time dependence of the useful signal.

  1. D-MATRIX: A web tool for constructing weight matrix of conserved DNA motifs

    PubMed Central

    Sen, Naresh; Mishra, Manoj; Khan, Feroz; Meena, Abha; Sharma, Ashok

    2009-01-01

    Despite considerable efforts to date, DNA motif prediction in whole genome remains a challenge for researchers. Currently the genome wide motif prediction tools required either direct pattern sequence (for single motif) or weight matrix (for multiple motifs). Although there are known motif pattern databases and tools for genome level prediction but no tool for weight matrix construction. Considering this, we developed a D-MATRIX tool which predicts the different types of weight matrix based on user defined aligned motif sequence set and motif width. For retrieval of known motif sequences user can access the commonly used databases such as TFD, RegulonDB, DBTBS, Transfac. D­MATRIX program uses a simple statistical approach for weight matrix construction, which can be converted into different file formats according to user requirement. It provides the possibility to identify the conserved motifs in the co­regulated genes or whole genome. As example, we successfully constructed the weight matrix of LexA transcription factor binding site with the help of known sos­box cis­regulatory elements in Deinococcus radiodurans genome. The algorithm is implemented in C-Sharp and wrapped in ASP.Net to maintain a user friendly web interface. D­MATRIX tool is accessible through the CIMAP domain network. Availability http://203.190.147.116/dmatrix/ PMID:19759861

  2. D-MATRIX: a web tool for constructing weight matrix of conserved DNA motifs.

    PubMed

    Sen, Naresh; Mishra, Manoj; Khan, Feroz; Meena, Abha; Sharma, Ashok

    2009-07-27

    Despite considerable efforts to date, DNA motif prediction in whole genome remains a challenge for researchers. Currently the genome wide motif prediction tools required either direct pattern sequence (for single motif) or weight matrix (for multiple motifs). Although there are known motif pattern databases and tools for genome level prediction but no tool for weight matrix construction. Considering this, we developed a D-MATRIX tool which predicts the different types of weight matrix based on user defined aligned motif sequence set and motif width. For retrieval of known motif sequences user can access the commonly used databases such as TFD, RegulonDB, DBTBS, Transfac. D-MATRIX program uses a simple statistical approach for weight matrix construction, which can be converted into different file formats according to user requirement. It provides the possibility to identify the conserved motifs in the co-regulated genes or whole genome. As example, we successfully constructed the weight matrix of LexA transcription factor binding site with the help of known sos-box cis-regulatory elements in Deinococcus radiodurans genome. The algorithm is implemented in C-Sharp and wrapped in ASP.Net to maintain a user friendly web interface. D-MATRIX tool is accessible through the CIMAP domain network. http://203.190.147.116/dmatrix/

  3. SOURCE APPORTIONMENT OF PM 2.5 AND CARBON IN SEATTLE USING CHEMICAL MASS BALANCE AND POSITIVE MATRIX FACTORIZATION

    EPA Science Inventory

    Three years of PM2.5 speciated data were collected and chemically analyzed using the IMPROVE protocol at the Beacon Hill site in Seattle. The data were analyzed by the Chemical Mass Balance Version 8 (CMB8) and Positive Matrix Factorization (PMF) source apportionment models. T...

  4. Considering Horn's Parallel Analysis from a Random Matrix Theory Point of View.

    PubMed

    Saccenti, Edoardo; Timmerman, Marieke E

    2017-03-01

    Horn's parallel analysis is a widely used method for assessing the number of principal components and common factors. We discuss the theoretical foundations of parallel analysis for principal components based on a covariance matrix by making use of arguments from random matrix theory. In particular, we show that (i) for the first component, parallel analysis is an inferential method equivalent to the Tracy-Widom test, (ii) its use to test high-order eigenvalues is equivalent to the use of the joint distribution of the eigenvalues, and thus should be discouraged, and (iii) a formal test for higher-order components can be obtained based on a Tracy-Widom approximation. We illustrate the performance of the two testing procedures using simulated data generated under both a principal component model and a common factors model. For the principal component model, the Tracy-Widom test performs consistently in all conditions, while parallel analysis shows unpredictable behavior for higher-order components. For the common factor model, including major and minor factors, both procedures are heuristic approaches, with variable performance. We conclude that the Tracy-Widom procedure is preferred over parallel analysis for statistically testing the number of principal components based on a covariance matrix.

  5. 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.

    PubMed

    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.

  6. Non-negative Matrix Factorization and Co-clustering: A Promising Tool for Multi-tasks Bearing Fault Diagnosis

    NASA Astrophysics Data System (ADS)

    Shen, Fei; Chen, Chao; Yan, Ruqiang

    2017-05-01

    Classical bearing fault diagnosis methods, being designed according to one specific task, always pay attention to the effectiveness of extracted features and the final diagnostic performance. However, most of these approaches suffer from inefficiency when multiple tasks exist, especially in a real-time diagnostic scenario. A fault diagnosis method based on Non-negative Matrix Factorization (NMF) and Co-clustering strategy is proposed to overcome this limitation. Firstly, some high-dimensional matrixes are constructed using the Short-Time Fourier Transform (STFT) features, where the dimension of each matrix equals to the number of target tasks. Then, the NMF algorithm is carried out to obtain different components in each dimension direction through optimized matching, such as Euclidean distance and divergence distance. Finally, a Co-clustering technique based on information entropy is utilized to realize classification of each component. To verity the effectiveness of the proposed approach, a series of bearing data sets were analysed in this research. The tests indicated that although the diagnostic performance of single task is comparable to traditional clustering methods such as K-mean algorithm and Guassian Mixture Model, the accuracy and computational efficiency in multi-tasks fault diagnosis are improved.

  7. Structure of collagen-glycosaminoglycan matrix and the influence to its integrity and stability.

    PubMed

    Bi, Yuying; Patra, Prabir; Faezipour, Miad

    2014-01-01

    Glycosaminoglycan (GAG) is a chain-like disaccharide that is linked to polypeptide core to connect two collagen fibrils/fibers and provide the intermolecular force in Collagen-GAG matrix (C-G matrix). Thus, the distribution of GAG in C-G matrix contributes to the integrity and mechanical properties of the matrix and related tissue. This paper analyzes the transverse isotropic distribution of GAG in C-G matrix. The angle of GAGs related to collagen fibrils is used as parameters to qualify the GAGs isotropic characteristic in both 3D and 2D rendering. Statistical results included that over one third of GAGs were perpendicular directed to collagen fibril with symmetrical distribution for both 3D matrix and 2D plane cross through collagen fibrils. The three factors tested in this paper: collagen radius, collagen distribution, and GAGs density, were not statistically significant for the strength of Collagen-GAG matrix in 3D rendering. However in 2D rendering, a significant factor found was the radius of collagen in matrix for the GAGs directed to orthogonal plane of Collagen-GAG matrix. Between two cross-section selected from Collagen-GAG matrix model, the plane cross through collagen fibrils was symmetrically distributed but the total percentage of perpendicular directed GAG was deducted by decreasing collagen radius. There were some symmetry features of GAGs angle distribution in selected 2D plane that passed through space between collagen fibrils, but most models showed multiple peaks in GAGs angle distribution. With less GAGs directed to perpendicular of collagen fibril, strength in collagen cross-section weakened. Collagen distribution was also a factor that influences GAGs angle distribution in 2D rendering. True hexagonal collagen packaging is reported in this paper to have less strength at collagen cross-section compared to quasi-hexagonal collagen arrangement. In this work focus is on GAGs matrix within the collagen and its relevance to anisotropy.

  8. Penny-shaped crack in a fiber-reinforced matrix

    NASA Technical Reports Server (NTRS)

    Narayanan, T. V.; Erdogan, F.

    1975-01-01

    Using the slender inclusion model developed earlier the elastostatic interaction problem between a penny-shaped crack and elastic fibers in an elastic matrix is formulated. For a single set and for multiple sets of fibers oriented perpendicularly to the plane of the crack and distributed symmetrically on concentric circles the problem is reduced to a system of singular integral equations. Techniques for the regularization and for the numerical solution of the system are outlined. For various fiber geometries numerical examples are given and distribution of the stress intensity factor along the crack border is obtained. Sample results showing the distribution of the fiber stress and a measure of the fiber-matrix interface shear are also included.

  9. Automatic annotation of histopathological images using a latent topic model based on non-negative matrix factorization

    PubMed Central

    Cruz-Roa, Angel; Díaz, Gloria; Romero, Eduardo; González, Fabio A.

    2011-01-01

    Histopathological images are an important resource for clinical diagnosis and biomedical research. From an image understanding point of view, the automatic annotation of these images is a challenging problem. This paper presents a new method for automatic histopathological image annotation based on three complementary strategies, first, a part-based image representation, called the bag of features, which takes advantage of the natural redundancy of histopathological images for capturing the fundamental patterns of biological structures, second, a latent topic model, based on non-negative matrix factorization, which captures the high-level visual patterns hidden in the image, and, third, a probabilistic annotation model that links visual appearance of morphological and architectural features associated to 10 histopathological image annotations. The method was evaluated using 1,604 annotated images of skin tissues, which included normal and pathological architectural and morphological features, obtaining a recall of 74% and a precision of 50%, which improved a baseline annotation method based on support vector machines in a 64% and 24%, respectively. PMID:22811960

  10. Modulation of keratinocyte motility. Correlation with production of extracellular matrix molecules in response to growth promoting and antiproliferative factors.

    PubMed Central

    Nickoloff, B. J.; Mitra, R. S.; Riser, B. L.; Dixit, V. M.; Varani, J.

    1988-01-01

    Normal human epidermal keratinocytes (KC) grown under conditions that maintain the undifferentiated state are highly motile. Migration of these cells as measured in two different assays (migration out of an agarose drop explant, and into micropore filters in a modified Boyden chamber), is stimulated by fibronectin (FN) and to a lesser extent by thrombospondin (TSP). In contrast, laminin (LN) inhibits KC migration. Cultivation of the cells for 1 day under conditions that induce differentiation (ie, in the presence of 1.4 mM Ca2+) suppresses KC motility. A number of soluble growth modulating polypeptide factors also influence KC migration. Transforming growth factor-beta (TGF-beta) and epidermal growth factor (EGF) stimulate KC motility. These factors simultaneously induce KC production of FN and a significant portion of the stimulated motility can be inhibited with antibodies to FN. EGF and somatomedin-C (SM-C), but not TGF-beta, also stimulate TSP production while EGF and SM-C (but not TGF-beta) induce KC proliferation. In contrast to these factors, interferon-gamma (INF-gamma) inhibits KC production of both FN and TSP and concomitantly inhibits both motility and proliferation. These data suggest that KC properties essential for normal wound healing (ie, motility and proliferation) are regulated by both extracellular matrix molecules and soluble peptide factors. Finally, these effects of various growth promoting and antiproliferative factors on KCs may, in part, be mediated through alteration in the endogenous production of extracellular matrix molecules by KCs. Images Figure 2 PMID:2458044

  11. Hepatocyte growth factor/scatter factor enhances the invasion of mesothelioma cell lines and the expression of matrix metalloproteinases

    PubMed Central

    Harvey, P; Clark, I M; Jaurand, M-C; Warn, R M; Edwards, D R

    2000-01-01

    Hepatocyte growth factor/scatter factor (HGF/SF) is a multifunctional factor involved both in development and tissue repair, as well as pathological processes such as cancer and metastasis. It has been identified in vivo in many types of tumours together with its tyrosine kinase receptor, Met. We show here that exogenous HGF/SF acts as a strong chemoattractant for human mesothelioma cell lines. The factor also enhanced cell adhesion to and invasion into Matrigel. The mesothelioma cell lines synthesized a panel of matrix metalloproteinases critical for tumour progression such as MMP-1, 2, 3, 9 and membrane-bound MT1-MMP. HGF/SF stimulated the expression of MMP-1, 9 and MT1-MMP and had a slight effect on expression of the MMP inhibitor TIMP-1 but not TIMP-2. However, there was no simple correlation between the levels of MMPs and TIMPs of the cell lines and their different invasion properties or between HGF/SF stimulatory effects on MMP expression and invasion. In addition, effects of protease inhibitors on invasion suggested that serine proteases were also expressed in human mesothelioma cell lines and were involved in HGF/SF-induced invasion. The results show a predominant role for HGF/SF in mesothelioma cell invasion, stimulating simultaneously adhesion, motility, invasion and regulation of MMP and TIMP levels. © 2000 Cancer Research Campaign PMID:11027427

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

    PubMed

    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

  13. Matrix metalloproteinases: their functional role in lung cancer.

    PubMed

    Merchant, Neha; Nagaraju, Ganji Purnachandra; Rajitha, Balney; Lammata, Saipriya; Jella, Kishore Kumar; Buchwald, Zachary S; Lakka, Sajani S; Ali, Arif N

    2017-08-01

    Lung malignancy is the foremost cause of cancer-related deaths globally and is frequently related to long-term tobacco smoking. Recent studies reveal that the expression of matrix metalloproteinases (MMPs) is extremely high in lung tumors compared with non-malignant lung tissue. MMPs are zinc-dependent proteases and are involved in the degradation of extracellular matrix (ECM). Several investigations have shown that MMPs manipulate the activity of non-ECM molecules, including cytokines, growth factors and receptors that control the tumor microenvironment. In this review, we have summarized and critically reviewed the published works on the role of MMPs in non-small-cell lung cancer. We have also explored the structure of MMPs, their various types and roles in lung cancer metastasis including invasion, migration and angiogenesis. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  14. Risk Factors for Breast Cancer, Including Occupational Exposures

    PubMed Central

    Meo, Margrethe; Vainio, Harri

    2011-01-01

    The knowledge on the etiology of breast cancer has advanced substantially in recent years, and several etiological factors are now firmly established. However, very few new discoveries have been made in relation to occupational risk factors. The International Agency for Research on Cancer has evaluated over 900 different exposures or agents to-date to determine whether they are carcinogenic to humans. These evaluations are published as a series of Monographs (www.iarc.fr). For breast cancer the following substances have been classified as "carcinogenic to humans" (Group 1): alcoholic beverages, exposure to diethylstilbestrol, estrogen-progestogen contraceptives, estrogen-progestogen hormone replacement therapy and exposure to X-radiation and gamma-radiation (in special populations such as atomic bomb survivors, medical patients, and in-utero exposure). Ethylene oxide is also classified as a Group 1 carcinogen, although the evidence for carcinogenicity in epidemiologic studies, and specifically for the human breast, is limited. The classification "probably carcinogenic to humans" (Group 2A) includes estrogen hormone replacement therapy, tobacco smoking, and shift work involving circadian disruption, including work as a flight attendant. If the association between shift work and breast cancer, the most common female cancer, is confirmed, shift work could become the leading cause of occupational cancer in women. PMID:22953181

  15. Parallel O(log n) algorithms for open- and closed-chain rigid multibody systems based on a new mass matrix factorization technique

    NASA Technical Reports Server (NTRS)

    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.

  16. Recurrence quantity analysis based on matrix eigenvalues

    NASA Astrophysics Data System (ADS)

    Yang, Pengbo; Shang, Pengjian

    2018-06-01

    Recurrence plots is a powerful tool for visualization and analysis of dynamical systems. Recurrence quantification analysis (RQA), based on point density and diagonal and vertical line structures in the recurrence plots, is considered to be alternative measures to quantify the complexity of dynamical systems. In this paper, we present a new measure based on recurrence matrix to quantify the dynamical properties of a given system. Matrix eigenvalues can reflect the basic characteristics of the complex systems, so we show the properties of the system by exploring the eigenvalues of the recurrence matrix. Considering that Shannon entropy has been defined as a complexity measure, we propose the definition of entropy of matrix eigenvalues (EOME) as a new RQA measure. We confirm that EOME can be used as a metric to quantify the behavior changes of the system. As a given dynamical system changes from a non-chaotic to a chaotic regime, the EOME will increase as well. The bigger EOME values imply higher complexity and lower predictability. We also study the effect of some factors on EOME,including data length, recurrence threshold, the embedding dimension, and additional noise. Finally, we demonstrate an application in physiology. The advantage of this measure lies in a high sensitivity and simple computation.

  17. Tissue Engineering Using Transfected Growth-Factor Genes

    NASA Technical Reports Server (NTRS)

    Madry, Henning; Langer, Robert S.; Freed, Lisa E.; Trippel, Stephen; Vunjak-Novakovic, Gordana

    2005-01-01

    A method of growing bioengineered tissues includes, as a major component, the use of mammalian cells that have been transfected with genes for secretion of regulator and growth-factor substances. In a typical application, one either seeds the cells onto an artificial matrix made of a synthetic or natural biocompatible material, or else one cultures the cells until they secrete a desired amount of an extracellular matrix. If such a bioengineered tissue construct is to be used for surgical replacement of injured tissue, then the cells should preferably be the patient s own cells or, if not, at least cells matched to the patient s cells according to a human-leucocyteantigen (HLA) test. The bioengineered tissue construct is typically implanted in the patient's injured natural tissue, wherein the growth-factor genes enhance metabolic functions that promote the in vitro development of functional tissue constructs and their integration with native tissues. If the matrix is biodegradable, then one of the results of metabolism could be absorption of the matrix and replacement of the matrix with tissue formed at least partly by the transfected cells. The method was developed for articular chondrocytes but can (at least in principle) be extended to a variety of cell types and biocompatible matrix materials, including ones that have been exploited in prior tissue-engineering methods. Examples of cell types include chondrocytes, hepatocytes, islet cells, nerve cells, muscle cells, other organ cells, bone- and cartilage-forming cells, epithelial and endothelial cells, connective- tissue stem cells, mesodermal stem cells, and cells of the liver and the pancreas. Cells can be obtained from cell-line cultures, biopsies, and tissue banks. Genes, molecules, or nucleic acids that secrete factors that influence the growth of cells, the production of extracellular matrix material, and other cell functions can be inserted in cells by any of a variety of standard transfection techniques.

  18. Coordinate regulation of estrogen-mediated fibronectin matrix assembly and epidermal growth factor receptor transactivation by the G protein-coupled receptor, GPR30.

    PubMed

    Quinn, Jeffrey A; Graeber, C Thomas; Frackelton, A Raymond; Kim, Minsoo; Schwarzbauer, Jean E; Filardo, Edward J

    2009-07-01

    Estrogen promotes changes in cytoskeletal architecture not easily attributed to the biological action of estrogen receptors, ERalpha and ERbeta. The Gs protein-coupled transmembrane receptor, GPR30, is linked to specific estrogen binding and rapid estrogen-mediated release of heparin-bound epidermal growth factor. Using marker rescue and dominant interfering mutant strategies, we show that estrogen action via GPR30 promotes fibronectin (FN) matrix assembly by human breast cancer cells. Stimulation with 17beta-estradiol or the ER antagonist, ICI 182, 780, results in the recruitment of FN-engaged integrin alpha5beta1 conformers to fibrillar adhesions and the synthesis of FN fibrils. Concurrent with this cellular response, GPR30 promotes the formation of Src-dependent, Shc-integrin alpha5beta1 complexes. Function-blocking antibodies directed against integrin alpha5beta1 or soluble Arg-Gly-Asp peptide fragments derived from FN specifically inhibited GPR30-mediated epidermal growth factor receptor transactivation. Estrogen-mediated FN matrix assembly and epidermal growth factor receptor transactivation were similarly disrupted in integrin beta1-deficient GE11 cells, whereas reintroduction of integrin beta1 into GE11 cells restored these responses. Mutant Shc (317Y/F) blocked GPR30-induced FN matrix assembly and tyrosyl phosphorylation of erbB1. Interestingly, relative to recombinant wild-type Shc, 317Y/F Shc was more readily retained in GPR30-induced integrin alpha5beta1 complexes, yet this mutant did not prevent endogenous Shc-integrin alpha5beta1 complex formation. Our results suggest that GPR30 coordinates estrogen-mediated FN matrix assembly and growth factor release in human breast cancer cells via a Shc-dependent signaling mechanism that activates integrin alpha5beta1.

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

    PubMed

    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.

  20. Evaluation of the Validity of Job Exposure Matrix for Psychosocial Factors at Work

    PubMed Central

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

    2014-01-01

    Objective 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). Materials and Methods 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. Results 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. Conclusions 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. PMID:25268276

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

    PubMed

    Wang, Degao; Tian, Fulin; Yang, Meng; Liu, Chenlin; Li, Yi-Fan

    2009-05-01

    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.

  2. Semi-Supervised Projective Non-Negative Matrix Factorization for Cancer Classification.

    PubMed

    Zhang, Xiang; Guan, Naiyang; Jia, Zhilong; Qiu, Xiaogang; Luo, Zhigang

    2015-01-01

    Advances in DNA microarray technologies have made gene expression profiles a significant candidate in identifying different types of cancers. Traditional learning-based cancer identification methods utilize labeled samples to train a classifier, but they are inconvenient for practical application because labels are quite expensive in the clinical cancer research community. This paper proposes a semi-supervised projective non-negative matrix factorization method (Semi-PNMF) to learn an effective classifier from both labeled and unlabeled samples, thus boosting subsequent cancer classification performance. In particular, Semi-PNMF jointly learns a non-negative subspace from concatenated labeled and unlabeled samples and indicates classes by the positions of the maximum entries of their coefficients. Because Semi-PNMF incorporates statistical information from the large volume of unlabeled samples in the learned subspace, it can learn more representative subspaces and boost classification performance. We developed a multiplicative update rule (MUR) to optimize Semi-PNMF and proved its convergence. The experimental results of cancer classification for two multiclass cancer gene expression profile datasets show that Semi-PNMF outperforms the representative methods.

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

    NASA Astrophysics Data System (ADS)

    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.

  4. Basic Fibroblast Growth Factor Accelerates Matrix Degradation Via a Neuro-Endocrine Pathway in Human Adult Articular Chondrocytes

    PubMed Central

    IM, HEE-JEONG; LI, XIN; MUDDASANI, PRASUNA; KIM, GUN-HEE; DAVIS, FRANCESCA; RANGAN, JAYANTHI; FORSYTH, CHRISTOPHER B.; ELLMAN, MICHAEL; THONAR, EUGENE JMA

    2010-01-01

    Pain-related neuropeptides released from synovial fibroblasts, such as substance P, have been implicated in joint destruction. Substance P-induced inflammatory processes are mediated via signaling through a G-protein-coupled receptor, that is, neurokinin-1 tachykinin receptor (NK1-R). We determined the pathophysiological link between substance P and its receptor in human adult articular cartilage homeostasis. We further examined if catabolic growth factors such as basic fibroblast growth factor (bFGF or FGF-2) or IL-1β accelerate matrix degradation via a neural pathway upregulation of substance P and NK1-R. We show here that substance P stimulates the production of cartilage-degrading enzymes, such as matrix metalloproteinase-13 (MMP-13), and suppresses proteoglycan deposition in human adult articular chondrocytes via NK1-R. Furthermore, we have demonstrated that substance P negates proteoglycan stimulation promoted by bone morphogenetic protein-7, suggesting the dual role of substance P as both a pro-catabolic and anti-anabolic mediator of cartilage homeostasis. We report that bFGF-mediated stimulation of substance P and its receptor NK1-R is, in part, through an IL-1β-dependent pathway. PMID:17960584

  5. Basic fibroblast growth factor accelerates matrix degradation via a neuro-endocrine pathway in human adult articular chondrocytes.

    PubMed

    Im, Hee-Jeong; Li, Xin; Muddasani, Prasuna; Kim, Gun-Hee; Davis, Francesca; Rangan, Jayanthi; Forsyth, Christopher B; Ellman, Michael; Thonar, Eugene J M A

    2008-05-01

    Pain-related neuropeptides released from synovial fibroblasts, such as substance P, have been implicated in joint destruction. Substance P-induced inflammatory processes are mediated via signaling through a G-protein-coupled receptor, that is, neurokinin-1 tachykinin receptor (NK(1)-R). We determined the pathophysiological link between substance P and its receptor in human adult articular cartilage homeostasis. We further examined if catabolic growth factors such as basic fibroblast growth factor (bFGF or FGF-2) or IL-1beta accelerate matrix degradation via a neural pathway upregulation of substance P and NK(1)-R. We show here that substance P stimulates the production of cartilage-degrading enzymes, such as matrix metalloproteinase-13 (MMP-13), and suppresses proteoglycan deposition in human adult articular chondrocytes via NK(1)-R. Furthermore, we have demonstrated that substance P negates proteoglycan stimulation promoted by bone morphogenetic protein-7, suggesting the dual role of substance P as both a pro-catabolic and anti-anabolic mediator of cartilage homeostasis. We report that bFGF-mediated stimulation of substance P and its receptor NK(1)-R is, in part, through an IL-1beta-dependent pathway. (c) 2007 Wiley-Liss, Inc.

  6. Closed-form solutions for linear regulator design of mechanical systems including optimal weighting matrix selection

    NASA Technical Reports Server (NTRS)

    Hanks, Brantley R.; Skelton, Robert E.

    1991-01-01

    Vibration in modern structural and mechanical systems can be reduced in amplitude by increasing stiffness, redistributing stiffness and mass, and/or adding damping if design techniques are available to do so. Linear Quadratic Regulator (LQR) theory in modern multivariable control design, attacks the general dissipative elastic system design problem in a global formulation. The optimal design, however, allows electronic connections and phase relations which are not physically practical or possible in passive structural-mechanical devices. The restriction of LQR solutions (to the Algebraic Riccati Equation) to design spaces which can be implemented as passive structural members and/or dampers is addressed. A general closed-form solution to the optimal free-decay control problem is presented which is tailored for structural-mechanical system. The solution includes, as subsets, special cases such as the Rayleigh Dissipation Function and total energy. Weighting matrix selection is a constrained choice among several parameters to obtain desired physical relationships. The closed-form solution is also applicable to active control design for systems where perfect, collocated actuator-sensor pairs exist.

  7. Matrix diffusion coefficients in volcanic rocks at the Nevada test site: influence of matrix porosity, matrix permeability, and fracture coating minerals.

    PubMed

    Reimus, Paul W; Callahan, Timothy J; Ware, S Doug; Haga, Marc J; Counce, Dale A

    2007-08-15

    Diffusion cell experiments were conducted to measure nonsorbing solute matrix diffusion coefficients in forty-seven different volcanic rock matrix samples from eight different locations (with multiple depth intervals represented at several locations) at the Nevada Test Site. The solutes used in the experiments included bromide, iodide, pentafluorobenzoate (PFBA), and tritiated water ((3)HHO). The porosity and saturated permeability of most of the diffusion cell samples were measured to evaluate the correlation of these two variables with tracer matrix diffusion coefficients divided by the free-water diffusion coefficient (D(m)/D*). To investigate the influence of fracture coating minerals on matrix diffusion, ten of the diffusion cells represented paired samples from the same depth interval in which one sample contained a fracture surface with mineral coatings and the other sample consisted of only pure matrix. The log of (D(m)/D*) was found to be positively correlated with both the matrix porosity and the log of matrix permeability. A multiple linear regression analysis indicated that both parameters contributed significantly to the regression at the 95% confidence level. However, the log of the matrix diffusion coefficient was more highly-correlated with the log of matrix permeability than with matrix porosity, which suggests that matrix diffusion coefficients, like matrix permeabilities, have a greater dependence on the interconnectedness of matrix porosity than on the matrix porosity itself. The regression equation for the volcanic rocks was found to provide satisfactory predictions of log(D(m)/D*) for other types of rocks with similar ranges of matrix porosity and permeability as the volcanic rocks, but it did a poorer job predicting log(D(m)/D*) for rocks with lower porosities and/or permeabilities. The presence of mineral coatings on fracture walls did not appear to have a significant effect on matrix diffusion in the ten paired diffusion cell experiments.

  8. Matrix diffusion coefficients in volcanic rocks at the Nevada test site: Influence of matrix porosity, matrix permeability, and fracture coating minerals

    NASA Astrophysics Data System (ADS)

    Reimus, Paul W.; Callahan, Timothy J.; Ware, S. Doug; Haga, Marc J.; Counce, Dale A.

    2007-08-01

    Diffusion cell experiments were conducted to measure nonsorbing solute matrix diffusion coefficients in forty-seven different volcanic rock matrix samples from eight different locations (with multiple depth intervals represented at several locations) at the Nevada Test Site. The solutes used in the experiments included bromide, iodide, pentafluorobenzoate (PFBA), and tritiated water ( 3HHO). The porosity and saturated permeability of most of the diffusion cell samples were measured to evaluate the correlation of these two variables with tracer matrix diffusion coefficients divided by the free-water diffusion coefficient ( Dm/ D*). To investigate the influence of fracture coating minerals on matrix diffusion, ten of the diffusion cells represented paired samples from the same depth interval in which one sample contained a fracture surface with mineral coatings and the other sample consisted of only pure matrix. The log of ( Dm/ D*) was found to be positively correlated with both the matrix porosity and the log of matrix permeability. A multiple linear regression analysis indicated that both parameters contributed significantly to the regression at the 95% confidence level. However, the log of the matrix diffusion coefficient was more highly-correlated with the log of matrix permeability than with matrix porosity, which suggests that matrix diffusion coefficients, like matrix permeabilities, have a greater dependence on the interconnectedness of matrix porosity than on the matrix porosity itself. The regression equation for the volcanic rocks was found to provide satisfactory predictions of log( Dm/ D*) for other types of rocks with similar ranges of matrix porosity and permeability as the volcanic rocks, but it did a poorer job predicting log( Dm/ D*) for rocks with lower porosities and/or permeabilities. The presence of mineral coatings on fracture walls did not appear to have a significant effect on matrix diffusion in the ten paired diffusion cell experiments.

  9. An Uncertainty Structure Matrix for Models and Simulations

    NASA Technical Reports Server (NTRS)

    Green, Lawrence L.; Blattnig, Steve R.; Hemsch, Michael J.; Luckring, James M.; Tripathi, Ram K.

    2008-01-01

    Software that is used for aerospace flight control and to display information to pilots and crew is expected to be correct and credible at all times. This type of software is typically developed under strict management processes, which are intended to reduce defects in the software product. However, modeling and simulation (M&S) software may exhibit varying degrees of correctness and credibility, depending on a large and complex set of factors. These factors include its intended use, the known physics and numerical approximations within the M&S, and the referent data set against which the M&S correctness is compared. The correctness and credibility of an M&S effort is closely correlated to the uncertainty management (UM) practices that are applied to the M&S effort. This paper describes an uncertainty structure matrix for M&S, which provides a set of objective descriptions for the possible states of UM practices within a given M&S effort. The columns in the uncertainty structure matrix contain UM elements or practices that are common across most M&S efforts, and the rows describe the potential levels of achievement in each of the elements. A practitioner can quickly look at the matrix to determine where an M&S effort falls based on a common set of UM practices that are described in absolute terms that can be applied to virtually any M&S effort. The matrix can also be used to plan those steps and resources that would be needed to improve the UM practices for a given M&S effort.

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

    PubMed

    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.

  11. Carbon Dots and 9AA as a Binary Matrix for the Detection of Small Molecules by Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Chen, Yongli; Gao, Dan; Bai, Hangrui; Liu, Hongxia; Lin, Shuo; Jiang, Yuyang

    2016-07-01

    Application of matrix-assisted laser-desorption/ionization mass spectrometry (MALDI MS) to analyze small molecules have some limitations, due to the inhomogeneous analyte/matrix co-crystallization and interference of matrix-related peaks in low m/z region. In this work, carbon dots (CDs) were for the first time applied as a binary matrix with 9-Aminoacridine (9AA) in MALDI MS for small molecules analysis. By 9AA/CDs assisted desorption/ionization (D/I) process, a wide range of small molecules, including nucleosides, amino acids, oligosaccharides, peptides, and anticancer drugs with a higher sensitivity were demonstrated in the positive ion mode. A detection limit down to 5 fmol was achieved for cytidine. 9AA/CDs matrix also exhibited excellent reproducibility compared with 9AA matrix. Moreover, by exploring the ionization mechanism of the matrix, the influence factors might be attributed to the four parts: (1) the strong UV absorption of 9AA/CDs due to their π-conjugated network; (2) the carboxyl groups modified on the CDs surface act as protonation sites for proton transfer in positive ion mode; (3) the thin layer crystal of 9AA/CDs could reach a high surface temperature more easily and lower transfer energy for LDI MS; (4) CDs could serve as a matrix additive to suppress 9AA ionization. Furthermore, this matrix was allowed for the analysis of glucose as well as nucleosides in human urine, and the level of cytidine was quantified with a linear range of 0.05-5 mM (R2 > 0.99). Therefore, the 9AA/CDs matrix was proven to be an effective MALDI matrix for the analysis of small molecules with improved sensitivity and reproducibility. This work provides an alternative solution for small molecules detection that can be further used in complex samples analysis.

  12. Penny-shaped crack in a fiber-reinforced matrix. [elastostatics

    NASA Technical Reports Server (NTRS)

    Narayanan, T. V.; Erdogan, F.

    1974-01-01

    Using a slender inclusion model developed earlier, the elastostatic interaction problem between a penny-shaped crack and elastic fibers in an elastic matrix is formulated. For a single set and for multiple sets of fibers oriented perpendicularly to the plane of the crack and distributed symmetrically on concentric circles, the problem was reduced to a system of singular integral equations. Techniques for the regularization and for the numerical solution of the system are outlined. For various fiber geometries numerical examples are given, and distribution of the stress intensity factor along the crack border was obtained. Sample results showing the distribution of the fiber stress and a measure of the fiber-matrix interface shear are also included.

  13. Omentin-1 prevents cartilage matrix destruction by regulating matrix metalloproteinases.

    PubMed

    Li, Zhigang; Liu, Baoyi; Zhao, Dewei; Wang, BenJie; Liu, Yupeng; Zhang, Yao; Li, Borui; Tian, Fengde

    2017-08-01

    Matrix metalloproteinases (MMPs) play a crucial role in the degradation of the extracellular matrix and pathological progression of osteoarthritis (OA). Omentin-1 is a newly identified anti-inflammatory adipokine. Little information regarding the protective effects of omentin-1 in OA has been reported before. In the current study, our results indicated that omentin-1 suppressed expression of MMP-1, MMP-3, and MMP-13 induced by the proinflammatory cytokine interleukin-1β (IL-1β) at both the mRNA and protein levels in human chondrocytes. Importantly, administration of omentin-1 abolished IL-1β-induced degradation of type II collagen (Col II) and aggrecan, the two major extracellular matrix components in articular cartilage, in a dose-dependent manner. Mechanistically, omentin-1 ameliorated the expression of interferon regulatory factor 1 (IRF-1) by blocking the JAK-2/STAT3 pathway. Our results indicate that omentin-1 may have a potential chondroprotective therapeutic capacity. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

  14. The exopolysaccharide matrix: a virulence determinant of cariogenic biofilm.

    PubMed

    Koo, H; Falsetta, M L; Klein, M I

    2013-12-01

    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.

  15. Targeting extracellular matrix remodeling in disease: Could resveratrol be a potential candidate?

    PubMed

    Agarwal, Renu; Agarwal, Puneet

    2017-02-01

    Disturbances of extracellular matrix homeostasis are associated with a number of pathological conditions. The ability of extracellular matrix to provide contextual information and hence control the individual or collective cellular behavior is increasingly being recognized. Hence, newer therapeutic approaches targeting extracellular matrix remodeling are widely investigated. We reviewed the current literature showing the effects of resveratrol on various aspects of extracellular matrix remodeling. This review presents a summary of the effects of resveratrol on extracellular matrix deposition and breakdown. Mechanisms of action of resveratrol in extracellular matrix deposition involving growth factors and their signaling pathways are discussed. Involvement of phosphoinositol-3-kinase/Akt and mitogen-activated protein kinase pathways and role of transcription factors and sirtuins on the effects of resveratrol on extracellular matrix homeostasis are summarized. It is evident from the literature presented in this review that resveratrol has significant effects on both the synthesis and breakdown of extracellular matrix. The major molecular targets of the action of resveratrol are growth factors and their signaling pathways, phosphoinositol-3-kinase/Akt and mitogen-activated protein kinase pathways, transcription factors, and SIRT-1. The effects of resveratrol on extracellular matrix and the molecular targets appear to be related to experimental models, experimental environment as well as the doses.

  16. Targeting extracellular matrix remodeling in disease: Could resveratrol be a potential candidate?

    PubMed Central

    Agarwal, Puneet

    2016-01-01

    Disturbances of extracellular matrix homeostasis are associated with a number of pathological conditions. The ability of extracellular matrix to provide contextual information and hence control the individual or collective cellular behavior is increasingly being recognized. Hence, newer therapeutic approaches targeting extracellular matrix remodeling are widely investigated. We reviewed the current literature showing the effects of resveratrol on various aspects of extracellular matrix remodeling. This review presents a summary of the effects of resveratrol on extracellular matrix deposition and breakdown. Mechanisms of action of resveratrol in extracellular matrix deposition involving growth factors and their signaling pathways are discussed. Involvement of phosphoinositol-3-kinase/Akt and mitogen-activated protein kinase pathways and role of transcription factors and sirtuins on the effects of resveratrol on extracellular matrix homeostasis are summarized. It is evident from the literature presented in this review that resveratrol has significant effects on both the synthesis and breakdown of extracellular matrix. The major molecular targets of the action of resveratrol are growth factors and their signaling pathways, phosphoinositol-3-kinase/Akt and mitogen-activated protein kinase pathways, transcription factors, and SIRT-1. The effects of resveratrol on extracellular matrix and the molecular targets appear to be related to experimental models, experimental environment as well as the doses. PMID:27798117

  17. Application of the matrix exponential kernel

    NASA Technical Reports Server (NTRS)

    Rohach, A. F.

    1972-01-01

    A point matrix kernel for radiation transport, developed by the transmission matrix method, has been used to develop buildup factors and energy spectra through slab layers of different materials for a point isotropic source. Combinations of lead-water slabs were chosen for examples because of the extreme differences in shielding properties of these two materials.

  18. Altered bone material properties in HLA-B27 rats include reduced mineral to matrix ratio and altered collagen cross-links.

    PubMed

    Gamsjaeger, Sonja; Srivastava, Apurva K; Wergedal, Jon E; Zwerina, Jochen; Klaushofer, Klaus; Paschalis, Eleftherios P; Tatakis, Dimitris N

    2014-11-01

    Spondyloarthropathy and inflammatory bowel disease (IBD), which includes ulcerative colitis and Crohn's disease, are often associated with severe osteopenia/osteoporosis in both children and adults. HLA-B27 transgenic rats present a phenotype that includes severe colitis and severely accelerated alveolar bone loss. The purpose of this study was to evaluate long bone density status, systemic bone metabolic markers, and intrinsic bone material properties in HLA-B27 transgenic (TG) rats, and compare them with those of age- and sex-matched wild-type (WT) animals. The results indicate that in the HLA-B27 rat, an animal susceptible to both alveolar bone loss (ABL) and long bone osteopenia, there is a statistically significant negative correlation between ABL and long bone bone mineral density (BMD), as well as mineral/matrix ratio at active bone-forming trabecular surfaces. The TG animals had a lower mineral/matrix ratio and higher relative proteoglycan and advanced glycation end product (ϵ-N-Carboxymethyl-L-lysine) content and pyridinoline/divalent collagen cross-link ratio compared with WT. These results may provide better understanding of the interrelationship between osteoporosis and oral bone loss, the underlying causes of the inferior bone strength in the HLA-B27 transgenic animals, and could prove to be a useful model in the elucidation of the pathophysiology of spondyloarthropathy and IBD-associated osteopenia/osteoporosis and in the evaluation of pharmacological intervention(s) against such conditions. © 2014 American Society for Bone and Mineral Research.

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

    PubMed Central

    2012-01-01

    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. PMID:22672618

  20. On non-negative matrix factorization algorithms for signal-dependent noise with application to electromyography data

    PubMed Central

    Devarajan, Karthik; Cheung, Vincent C.K.

    2017-01-01

    Non-negative matrix factorization (NMF) by the multiplicative updates algorithm is a powerful machine learning method for decomposing a high-dimensional nonnegative matrix V into two nonnegative matrices, W and H where V ~ WH. It has been successfully applied in the analysis and interpretation of large-scale data arising in neuroscience, computational biology and natural language processing, among other areas. A distinctive feature of NMF is its nonnegativity constraints that allow only additive linear combinations of the data, thus enabling it to learn parts that have distinct physical representations in reality. In this paper, we describe an information-theoretic approach to NMF for signal-dependent noise based on the generalized inverse Gaussian model. Specifically, we propose three novel algorithms in this setting, each based on multiplicative updates and prove monotonicity of updates using the EM algorithm. In addition, we develop algorithm-specific measures to evaluate their goodness-of-fit on data. Our methods are demonstrated using experimental data from electromyography studies as well as simulated data in the extraction of muscle synergies, and compared with existing algorithms for signal-dependent noise. PMID:24684448

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

    PubMed

    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.

  2. Decomposing Time Series Data by a Non-negative Matrix Factorization Algorithm with Temporally Constrained Coefficients

    PubMed Central

    Cheung, Vincent C. K.; Devarajan, Karthik; Severini, Giacomo; Turolla, Andrea; Bonato, Paolo

    2017-01-01

    The non-negative matrix factorization algorithm (NMF) decomposes a data matrix into a set of non-negative basis vectors, each scaled by a coefficient. In its original formulation, the NMF assumes the data samples and dimensions to be independently distributed, making it a less-than-ideal algorithm for the analysis of time series data with temporal correlations. Here, we seek to derive an NMF that accounts for temporal dependencies in the data by explicitly incorporating a very simple temporal constraint for the coefficients into the NMF update rules. We applied the modified algorithm to 2 multi-dimensional electromyographic data sets collected from the human upper-limb to identify muscle synergies. We found that because it reduced the number of free parameters in the model, our modified NMF made it possible to use the Akaike Information Criterion to objectively identify a model order (i.e., the number of muscle synergies composing the data) that is more functionally interpretable, and closer to the numbers previously determined using ad hoc measures. PMID:26737046

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

    PubMed

    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.

  4. scarlet: Source separation in multi-band images by Constrained Matrix Factorization

    NASA Astrophysics Data System (ADS)

    Melchior, Peter; Moolekamp, Fred; Jerdee, Maximilian; Armstrong, Robert; Sun, Ai-Lei; Bosch, James; Lupton, Robert

    2018-03-01

    SCARLET performs source separation (aka "deblending") on multi-band images. It is geared towards optical astronomy, where scenes are composed of stars and galaxies, but it is straightforward to apply it to other imaging data. Separation is achieved through a constrained matrix factorization, which models each source with a Spectral Energy Distribution (SED) and a non-parametric morphology, or multiple such components per source. The code performs forced photometry (with PSF matching if needed) using an optimal weight function given by the signal-to-noise weighted morphology across bands. The approach works well if the sources in the scene have different colors and can be further strengthened by imposing various additional constraints/priors on each source. Because of its generic utility, this package provides a stand-alone implementation that contains the core components of the source separation algorithm. However, the development of this package is part of the LSST Science Pipeline; the meas_deblender package contains a wrapper to implement the algorithms here for the LSST stack.

  5. Alternative dimensional reduction via the density matrix

    NASA Astrophysics Data System (ADS)

    de Carvalho, C. A.; Cornwall, J. M.; da Silva, A. J.

    2001-07-01

    We give graphical rules, based on earlier work for the functional Schrödinger equation, for constructing the density matrix for scalar and gauge fields in equilibrium at finite temperature T. More useful is a dimensionally reduced effective action (DREA) constructed from the density matrix by further functional integration over the arguments of the density matrix coupled to a source. The DREA is an effective action in one less dimension which may be computed order by order in perturbation theory or by dressed-loop expansions; it encodes all thermal matrix elements. We term the DREA procedure alternative dimensional reduction, to distinguish it from the conventional dimensionally reduced field theory (DRFT) which applies at infinite T. The DREA is useful because it gives a dimensionally reduced theory usable at any T including infinity, where it yields the DRFT, and because it does not and cannot have certain spurious infinities which sometimes occur in the density matrix itself or the conventional DRFT; these come from ln T factors at infinite temperature. The DREA can be constructed to all orders (in principle) and the only regularizations needed are those which control the ultraviolet behavior of the zero-T theory. An example of spurious divergences in the DRFT occurs in d=2+1φ4 theory dimensionally reduced to d=2. We study this theory and show that the rules for the DREA replace these ``wrong'' divergences in physical parameters by calculable powers of ln T; we also compute the phase transition temperature of this φ4 theory in one-loop order. Our density-matrix construction is equivalent to a construction of the Landau-Ginzburg ``coarse-grained free energy'' from a microscopic Hamiltonian.

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

    NASA Astrophysics Data System (ADS)

    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

  7. Preparation and pharmaceutical evaluation of new sustained-release capsule including starch-sponge matrix (SSM).

    PubMed

    Shibata, Nobuhito; Nishumura, Asako; Naruhashi, Kazumasa; Nakao, Yurie; Miura, Rieko

    2010-05-01

    The focus of current study was to demonstrate a new sustained-release capsule including starch-sponge matrix (SSM) and to investigate how the pharmaceutical properties of SSM affect the drug release or its pharmacokinetic properties. Three representative drugs (uranine [UN], indomethacin [IMC] and nifedipine [NFP]) with different physicochemical properties (LogP(ow): 0.10, 1.18 and 3.23, respectively) were selected as model drugs. Model drug was dispersioned in pastelike cornstarch (starch glue) after heating 2.0-3.0% cornstarch suspension with electromagnetic wave at 2450 MHz (700 W) for l min. Then the drug mixture was encapsulated into a gratin capsule by a syringe, and the SSM including drug was prepared by means of a freeze-dried method. Essentially, drug-free SSM has a porous and netlike structure, and the distribution aspect of model drugs in the SSM depends on physicochemical properties between cornstarch glue and drugs. UN with much lower lipophilicity exists in continues phase of SSM, and IMC or NFP with a moderate or a higher lipophilicity exist in continues phase or porous space of the SSM. In the in vitro dissolution study, the release rate of drug from the SSM was mainly dependent on the lipophilicities of drugs, showing a rank order of the release rate of UN>IMC>NFP. In addition, the in vitro release rate for each drug was well regulated by changing the initial concentration of cornstarch suspension. In vivo absorption studies after intraduodenal administration of SSM capsule including model drug revealed that the sustained-release effects also could be regulated by the initial concentration of starch suspension. Moreover, the sustained-release effect of SSM capsule was enhanced with an increase in the lipophilicity of drug, and local-residential and mucoadhesive properties of SSM in the intestine provided stable supply of drugs from the SSM. The SSM capsule we developed here shows promising results as an oral drug delivery system for sustained

  8. A graph regularized non-negative matrix factorization method for identifying microRNA-disease associations.

    PubMed

    Xiao, Qiu; Luo, Jiawei; Liang, Cheng; Cai, Jie; Ding, Pingjian

    2017-09-01

    MicroRNAs (miRNAs) play crucial roles in post-transcriptional regulations and various cellular processes. The identification of disease-related miRNAs provides great insights into the underlying pathogenesis of diseases at a system level. However, most existing computational approaches are biased towards known miRNA-disease associations, which is inappropriate for those new diseases or miRNAs without any known association information. In this study, we propose a new method with graph regularized non-negative matrix factorization in heterogeneous omics data, called GRNMF, to discover potential associations between miRNAs and diseases, especially for new diseases and miRNAs or those diseases and miRNAs with sparse known associations. First, we integrate the disease semantic information and miRNA functional information to estimate disease similarity and miRNA similarity, respectively. Considering that there is no available interaction observed for new diseases or miRNAs, a preprocessing step is developed to construct the interaction score profiles that will assist in prediction. Next, a graph regularized non-negative matrix factorization framework is utilized to simultaneously identify potential associations for all diseases. The results indicated that our proposed method can effectively prioritize disease-associated miRNAs with higher accuracy compared with other recent approaches. Moreover, case studies also demonstrated the effectiveness of GRNMF to infer unknown miRNA-disease associations for those novel diseases and miRNAs. The code of GRNMF is freely available at https://github.com/XIAO-HN/GRNMF/. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

  9. Tendon Functional Extracellular Matrix

    PubMed Central

    Screen, H.R.C.; Birk, D.E.; Kadler, K.E.; Ramirez, F; Young, M.F.

    2015-01-01

    This article is one of a series, summarising views expressed at the Orthopaedic Research Society New Frontiers in Tendon Research Conference. This particular article reviews the three workshops held under the “Functional Extracellular Matrix” stream. The workshops focused on the roles of the tendon extracellular matrix, such as performing the mechanical functions of tendon, creating the local cell environment and providing cellular cues. Tendon is a complex network of matrix and cells, and its biological functions are influenced by widely-varying extrinsic and intrinsic factors such as age, nutrition, exercise levels and biomechanics. Consequently, tendon adapts dynamically during development, ageing and injury. The workshop discussions identified research directions associated with understanding cell-matrix interactions to be of prime importance for developing novel strategies to target tendon healing or repair. PMID:25640030

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

    NASA Astrophysics Data System (ADS)

    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.

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

    NASA Astrophysics Data System (ADS)

    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

  12. GRAY: a program to calculate gray-body radiation heat-transfer view factors from black-body view factors

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Wong, R. L.

    1976-06-14

    Program GRAY is written to perform the matrix manipulations necessary to convert black-body radiation heat-transfer view factors to gray-body view factors as required by thermal analyzer codes. The black-body view factors contain only geometric relationships. Program GRAY allows the effects of multiple gray-body reflections to be included. The resulting effective gray-body factors can then be used with the corresponding fourth-power temperature differences to obtain the net radiative heat flux. The program is written to accept a matrix input or the card image output generated by the black-body view factor program CNVUFAC. The resulting card image output generated by GRAY ismore » in a form usable by the TRUMP thermal analyzer.« less

  13. Effect of reinforcement morphology on matrix microcracking

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Sridhar, N.; Srolovitz, D.J.; Rickman, J.M.

    1996-03-01

    The authors quantitatively examine the conditions under which a particle matrix misfit leads to matrix crack growth as a function of inclusion shape. Such misfit stresses and cracks can be generated by thermal expansion mismatch, generated by cooling a brittle matrix containing ductile inclusions. Using fracture mechanics and perturbation theory, they analyze the case of a penny-shaped crack interacting with a misfitting spheroidal inclusion. A simple and direct relationship is established between the strain energy release rate and the physical and geometrical properties of the system including: the thermal expansion mismatch, temperature change, the crack and inclusion sizes, the elasticmore » properties of the medium and the shape of the inclusion. In particular, the effects of inclusion shape on the stress intensity factors and strain energy release rate are analytically determined for nearly spherical inclusions. The authors use this information to determine the minimum crack size for crack growth to occur and the maximum size to which cracks may grown. The maximum crack size corresponds to the case where the elastic strain energy released upon crack growth is no longer sufficient to compensate for energy expended in extending the crack as the crack is growing into the rapidly decreasing stress field. The authors employ a nominally exact numerical procedure to study the effects of whiskers and platelets (i.e. spheroids very different from spheres) on matrix cracking. It is found that upon cooling a composite containing ductile inclusions, the propensity for matrix cracking is maximized for reinforcement shapes close to that of a sphere.« less

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

    PubMed

    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.

  15. Peak picking NMR spectral data using non-negative matrix factorization.

    PubMed

    Tikole, Suhas; Jaravine, Victor; Rogov, Vladimir; Dötsch, Volker; Güntert, Peter

    2014-02-11

    Simple peak-picking algorithms, such as those based on lineshape fitting, perform well when peaks are completely resolved in multidimensional NMR spectra, but often produce wrong intensities and frequencies for overlapping peak clusters. For example, NOESY-type spectra have considerable overlaps leading to significant peak-picking intensity errors, which can result in erroneous structural restraints. Precise frequencies are critical for unambiguous resonance assignments. To alleviate this problem, a more sophisticated peaks decomposition algorithm, based on non-negative matrix factorization (NMF), was developed. We produce peak shapes from Fourier-transformed NMR spectra. Apart from its main goal of deriving components from spectra and producing peak lists automatically, the NMF approach can also be applied if the positions of some peaks are known a priori, e.g. from consistently referenced spectral dimensions of other experiments. Application of the NMF algorithm to a three-dimensional peak list of the 23 kDa bi-domain section of the RcsD protein (RcsD-ABL-HPt, residues 688-890) as well as to synthetic HSQC data shows that peaks can be picked accurately also in spectral regions with strong overlap.

  16. Peak picking NMR spectral data using non-negative matrix factorization

    PubMed Central

    2014-01-01

    Background Simple peak-picking algorithms, such as those based on lineshape fitting, perform well when peaks are completely resolved in multidimensional NMR spectra, but often produce wrong intensities and frequencies for overlapping peak clusters. For example, NOESY-type spectra have considerable overlaps leading to significant peak-picking intensity errors, which can result in erroneous structural restraints. Precise frequencies are critical for unambiguous resonance assignments. Results To alleviate this problem, a more sophisticated peaks decomposition algorithm, based on non-negative matrix factorization (NMF), was developed. We produce peak shapes from Fourier-transformed NMR spectra. Apart from its main goal of deriving components from spectra and producing peak lists automatically, the NMF approach can also be applied if the positions of some peaks are known a priori, e.g. from consistently referenced spectral dimensions of other experiments. Conclusions Application of the NMF algorithm to a three-dimensional peak list of the 23 kDa bi-domain section of the RcsD protein (RcsD-ABL-HPt, residues 688-890) as well as to synthetic HSQC data shows that peaks can be picked accurately also in spectral regions with strong overlap. PMID:24511909

  17. Selectivity in glycosaminoglycan binding dictates the distribution and diffusion of fibroblast growth factors in the pericellular matrix

    PubMed Central

    Marcello, Marco

    2016-01-01

    The range of biological outcomes generated by many signalling proteins in development and homeostasis is increased by their interactions with glycosaminoglycans, particularly heparan sulfate (HS). This interaction controls the localization and movement of these signalling proteins, but whether such control depends on the specificity of the interactions is not known. We used five fibroblast growth factors with an N-terminal HaloTag (Halo-FGFs) for fluorescent labelling, with well-characterized and distinct HS-binding properties, and measured their binding and diffusion in pericellular matrix of fixed rat mammary 27 fibroblasts. Halo-FGF1, Halo-FGF2 and Halo-FGF6 bound to HS, whereas Halo-FGF10 also interacted with chondroitin sulfate/dermatan sulfate, and FGF20 did not bind detectably. The distribution of bound FGFs in the pericellular matrix was not homogeneous, and for FGF10 exhibited striking clusters. Fluorescence recovery after photobleaching showed that FGF2 and FGF6 diffused faster, whereas FGF1 diffused more slowly, and FGF10 was immobile. The results demonstrate that the specificity of the interactions of proteins with glycosaminoglycans controls their binding and diffusion. Moreover, cells regulate the spatial distribution of different protein-binding sites in glycosaminoglycans independently of each other, implying that the extracellular matrix has long-range structure. PMID:27009190

  18. Matrix Metalloproteinases as Regulators of Periodontal Inflammation

    PubMed Central

    Franco, Cavalla; Patricia, Hernández-Ríos; Timo, Sorsa; Claudia, Biguetti; Marcela, Hernández

    2017-01-01

    Periodontitis are infectious diseases characterized by immune-mediated destruction of periodontal supporting tissues and tooth loss. Matrix metalloproteinases (MMPs) are key proteases involved in destructive periodontal diseases. The study and interest in MMP has been fuelled by emerging evidence demonstrating the broad spectrum of molecules that can be cleaved by them and the myriad of biological processes that they can potentially regulate. The huge complexity of MMP functions within the ‘protease web’ is crucial for many physiologic and pathologic processes, including immunity, inflammation, bone resorption, and wound healing. Evidence points out that MMPs assemble in activation cascades and besides their classical extracellular matrix substrates, they cleave several signalling molecules—such as cytokines, chemokines, and growth factors, among others—regulating their biological functions and/or bioavailability during periodontal diseases. In this review, we provide an overview of emerging evidence of MMPs as regulators of periodontal inflammation. PMID:28218665

  19. Matrix Metalloproteinases as Regulators of Periodontal Inflammation.

    PubMed

    Franco, Cavalla; Patricia, Hernández-Ríos; Timo, Sorsa; Claudia, Biguetti; Marcela, Hernández

    2017-02-17

    Periodontitis are infectious diseases characterized by immune-mediated destruction of periodontal supporting tissues and tooth loss. Matrix metalloproteinases (MMPs) are key proteases involved in destructive periodontal diseases. The study and interest in MMP has been fuelled by emerging evidence demonstrating the broad spectrum of molecules that can be cleaved by them and the myriad of biological processes that they can potentially regulate. The huge complexity of MMP functions within the 'protease web' is crucial for many physiologic and pathologic processes, including immunity, inflammation, bone resorption, and wound healing. Evidence points out that MMPs assemble in activation cascades and besides their classical extracellular matrix substrates, they cleave several signalling molecules-such as cytokines, chemokines, and growth factors, among others-regulating their biological functions and/or bioavailability during periodontal diseases. In this review, we provide an overview of emerging evidence of MMPs as regulators of periodontal inflammation.

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

    PubMed

    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. Platelet-rich fibrin matrix improves wound angiogenesis via inducing endothelial cell proliferation.

    PubMed

    Roy, Sashwati; Driggs, Jason; Elgharably, Haytham; Biswas, Sabyasachi; Findley, Muna; Khanna, Savita; Gnyawali, Urmila; Bergdall, Valerie K; Sen, Chandan K

    2011-11-01

    The economic, social, and public health burden of chronic ulcers and other compromised wounds is enormous and rapidly increasing with the aging population. The growth factors derived from platelets play an important role in tissue remodeling including neovascularization. Platelet-rich plasma (PRP) has been utilized and studied for the last four decades. Platelet gel and fibrin sealant, derived from PRP mixed with thrombin and calcium chloride, have been exogenously applied to tissues to promote wound healing, bone growth, hemostasis, and tissue sealing. In this study, we first characterized recovery and viability of as well as growth factor release from platelets in a novel preparation of platelet gel and fibrin matrix, namely platelet-rich fibrin matrix (PRFM). Next, the effect of PRFM application in a delayed model of ischemic wound angiogenesis was investigated. The study, for the first time, shows the kinetics of the viability of platelet-embedded fibrin matrix. A slow and steady release of growth factors from PRFM was observed. The vascular endothelial growth factor released from PRFM was primarily responsible for endothelial mitogenic response via extracellular signal-regulated protein kinase activation pathway. Finally, this preparation of PRFM effectively induced endothelial cell proliferation and improved wound angiogenesis in chronic wounds, providing evidence of probable mechanisms of action of PRFM in healing of chronic ulcers. 2011 by the Wound Healing Society.

  2. Matrix metalloproteinase-9 and vascular endothelial growth factor expression change in experimental retinal neovascularization.

    PubMed

    Di, Yu; Nie, Qing-Zhu; Chen, Xiao-Long

    2016-01-01

    To investigate the signal transduction mechanism of matrix metalloproteinase-9 (MMP-9) mediated- vascular endothelial growth factor (VEGF) expression and retinal neovascularization (RNV) in oxygen-induced retinopathy (OIR) model. C57BL/6J mice were divided into four groups: control group, OIR group, OIR control group (phosphate-buffered saline by intravitreal injection) and treated group [tissue inhibitor of matrix metalloproteinase-1 (TIMP-1) by intravitreal injection]. OIR model was established in C57BL/6J mice exposed to 75%±2% oxygen for 5d. mRNA level and protein expression of MMP-9, TIMP-1 and VEGF were measured by real-time polymerase chain reaction and Western blotting, and located by immunohistochemistry. Levels of MMP-9 and VEGF in retina were significantly increased in animals with OIR and OIR control group. Levels of TIMP-1 in retina was significantly reduced in animals with OIR and OIR control group. Furthermore, a significant correlation was found between MMP-9 and VEGF. Intravitreal injection of TIMP-1 significantly reduced MMP-9 and VEGF expression of the OIR mouse model (all P<0.05). These results demonstrate that MMP-9-mediated up-regulation of VEGF promotes RNV in retinopathy of prematurity (ROP). TIMP-1 may be a potential target for the prevention and treatment of ROP.

  3. Soy protein preserves basement membrane integrity through a synergistic effect on nephrin, matrix metalloproteinase and vascular endothelial growth factor.

    PubMed

    Palanisamy, Nallasamy; Anuradha, Carani Venkataraman

    2011-01-01

    Soy protein improves renal function and prevents albuminuria in diabetic rats. This study investigates whether the renoprotective effect of soy protein is related to sustenance of basement membrane integrity. Adult male albino rats were randomized into four groups and fed one of the following semi-synthetic diets consisting of corn starch (60%) and casein (20%; CCD), fructose (60%) and casein (20%; FCD), fructose (60%) and soy protein (20%; FSD), or corn starch (60%) and soy protein (20%; CSD). Plasma chemistry and renal changes were analyzed after 60 days. FCD rats displayed metabolic derangements and renal ultrastructural changes. FSD rats showed reduction in type IV collagen, tissue inhibitor for matrix metallo-proteinase-2, vascular endothelial growth factor and tumor necrosis factor-α expression and improved matrix metallo-proteinase expression. Renal architecture was preserved in these rats. Soy protein supplementation not only improved insulin sensitivity but also markedly attenuated renal basement membrane changes in fructose diet-fed rats. These findings provide evidence in support of the use of dietary soy protein in patients with diabetic kidney disease. Copyright © 2011 S. Karger AG, Basel.

  4. A DEIM Induced CUR Factorization

    DTIC Science & Technology

    2015-09-18

    CUR approximate matrix factorization based on the Discrete Empirical Interpolation Method (DEIM). For a given matrix A, such a factorization provides a...CUR approximations based on leverage scores. 1 Introduction This work presents a new CUR matrix factorization based upon the Discrete Empirical...SUPPLEMENTARY NOTES 14. ABSTRACT We derive a CUR approximate matrix factorization based on the Discrete Empirical Interpolation Method (DEIM). For a given

  5. Application of Haddon's matrix in qualitative research methodology: an experience in burns epidemiology.

    PubMed

    Deljavan, Reza; Sadeghi-Bazargani, Homayoun; Fouladi, Nasrin; Arshi, Shahnam; Mohammadi, Reza

    2012-01-01

    Little has been done to investigate the application of injury specific qualitative research methods in the field of burn injuries. The aim of this study was to use an analytical tool (Haddon's matrix) through qualitative research methods to better understand people's perceptions about burn injuries. This study applied Haddon's matrix as a framework and an analytical tool for a qualitative research methodology in burn research. Both child and adult burn injury victims were enrolled into a qualitative study conducted using focus group discussion. Haddon's matrix was used to develop an interview guide and also through the analysis phase. The main analysis clusters were pre-event level/human (including risky behaviors, belief and cultural factors, and knowledge and education), pre-event level/object, pre-event phase/environment and event and post-event phase (including fire control, emergency scald and burn wound management, traditional remedies, medical consultation, and severity indicators). This research gave rise to results that are possibly useful both for future injury research and for designing burn injury prevention plans. Haddon's matrix is applicable in a qualitative research methodology both at data collection and data analysis phases. The study using Haddon's matrix through a qualitative research methodology yielded substantially rich information regarding burn injuries that may possibly be useful for prevention or future quantitative research.

  6. Improving source identification of Atlanta aerosol using temperature resolved carbon fractions in positive matrix factorization

    NASA Astrophysics Data System (ADS)

    Kim, Eugene; Hopke, Philip K.; Edgerton, Eric S.

    Daily integrated PM 2.5 (particulate matter ⩽2.5 μm in aerodynamic diameter) composition data including eight individual carbon fractions collected at the Jefferson Street monitoring site in Atlanta were analyzed with positive matrix factorization (PMF). Particulate carbon was analyzed using the thermal optical reflectance method that divides carbon into four organic carbon (OC), pyrolized organic carbon (OP), and three elemental carbon (EC) fractions. A total of 529 samples and 28 variables were measured between August 1998 and August 2000. PMF identified 11 sources in this study: sulfate-rich secondary aerosol I (50%), on-road diesel emissions (11%), nitrate-rich secondary aerosol (9%), wood smoke (7%), gasoline vehicle (6%), sulfate-rich secondary aerosol II (6%), metal processing (3%), airborne soil (3%), railroad traffic (3%), cement kiln/carbon-rich (2%), and bus maintenance facility/highway traffic (2%). Differences from previous studies using only the traditional OC and EC data (J. Air Waste Manag. Assoc. 53(2003a)731; Atmos Environ. (2003b)) include four traffic-related combustion sources (gasoline vehicle, on-road diesel, railroad, and bus maintenance facility) containing carbon fractions whose abundances were different between the various sources. This study indicates that the temperature resolved fractional carbon data can be utilized to enhance source apportionment study, especially with respect to the separation of diesel emissions from gasoline vehicle sources. Conditional probability functions using surface wind data and identified source contributions aid the identifications of local point sources.

  7. Rephasing invariants of the Cabibbo-Kobayashi- Maskawa matrix

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Pérez R, H.; Kielanowski, P., E-mail: kiel@fis.cinvestav.mx; Juárez W, S. R., E-mail: rebeca@esfm.ipn.mx

    2016-03-15

    The paper is motivated by the importance of the rephasing invariance of the CKM (Cabibbo-Kobayashi-Maskawa) matrix observables. These observables appear in the discussion of the CP violation in the standard model (Jarlskog invariant) and also in the renormalization group equations for the quark Yukawa couplings. Our discussion is based on the general phase invariant monomials built out of the CKM matrix elements and their conjugates. We show that there exist 30 fundamental phase invariant monomials and 18 of them are a product of 4 CKM matrix elements and 12 are a product of 6 CKM matrix elements. In the mainmore » theorem we show that a general rephasing invariant monomial can be expressed as a product of at most five factors: four of them are fundamental phase invariant monomials and the fifth factor consists of powers of squares of absolute values of the CKM matrix elements. We also show that the imaginary part of any rephasing invariant monomial is proportional to the Jarlskog’s invariant J or is 0.« less

  8. Membrane-type matrix metalloproteases as diverse effectors of cancer progression.

    PubMed

    Turunen, S Pauliina; Tatti-Bugaeva, Olga; Lehti, Kaisa

    2017-11-01

    Membrane-type matrix metalloproteases (MT-MMP) are pivotal regulators of cell invasion, growth and survival. Tethered to the cell membranes by a transmembrane domain or GPI-anchor, the six MT-MMPs can exert these functions via cell surface-associated extracellular matrix degradation or proteolytic protein processing, including shedding or release of signaling receptors, adhesion molecules, growth factors and other pericellular proteins. By interactions with signaling scaffold or cytoskeleton, the C-terminal cytoplasmic tail of the transmembrane MT-MMPs further extends their functionality to signaling or structural relay. MT-MMPs are differentially expressed in cancer. The most extensively studied MMP14/MT1-MMP is induced in various cancers along malignant transformation via pathways activated by mutations in tumor suppressors or proto-oncogenes and changes in tumor microenvironment including cellular heterogeneity, extracellular matrix composition, tissue oxygenation, and inflammation. Classically such induction involves transcriptional programs related to epithelial-to-mesenchymal transition. Besides inhibition by endogenous tissue inhibitors, MT-MMP activities are spatially and timely regulated at multiple levels by microtubular vesicular trafficking, dimerization/oligomerization, other interactions and localization in the actin-based invadosomes, in both tumor and the stroma. The functions of MT-MMPs are multifaceted within reciprocal cellular responses in the evolving tumor microenvironment, which poses the importance of these proteases beyond the central function as matrix scissors, and necessitates us to rethink MT-MMPs as dynamic signaling proteases of cancer. This article is part of a Special Issue entitled: Matrix Metalloproteinases edited by Rafael Fridman. Copyright © 2017 Elsevier B.V. All rights reserved.

  9. Novel Entries in a Fungal Biofilm Matrix Encyclopedia

    PubMed Central

    Zarnowski, Robert; Westler, William M.; Lacmbouh, Ghislain Ade; Marita, Jane M.; Bothe, Jameson R.; Bernhardt, Jörg; Lounes-Hadj Sahraoui, Anissa; Fontaine, Joël; Sanchez, Hiram; Hatfield, Ronald D.; Ntambi, James M.; Nett, Jeniel E.; Mitchell, Aaron P.

    2014-01-01

    ABSTRACT Virulence of Candida is linked with its ability to form biofilms. Once established, biofilm infections are nearly impossible to eradicate. Biofilm cells live immersed in a self-produced matrix, a blend of extracellular biopolymers, many of which are uncharacterized. In this study, we provide a comprehensive analysis of the matrix manufactured by Candida albicans both in vitro and in a clinical niche animal model. We further explore the function of matrix components, including the impact on drug resistance. We uncovered components from each of the macromolecular classes (55% protein, 25% carbohydrate, 15% lipid, and 5% nucleic acid) in the C. albicans biofilm matrix. Three individual polysaccharides were identified and were suggested to interact physically. Surprisingly, a previously identified polysaccharide of functional importance, β-1,3-glucan, comprised only a small portion of the total matrix carbohydrate. Newly described, more abundant polysaccharides included α-1,2 branched α-1,6-mannans (87%) associated with unbranched β-1,6-glucans (13%) in an apparent mannan-glucan complex (MGCx). Functional matrix proteomic analysis revealed 458 distinct activities. The matrix lipids consisted of neutral glycerolipids (89.1%), polar glycerolipids (10.4%), and sphingolipids (0.5%). Examination of matrix nucleic acid identified DNA, primarily noncoding sequences. Several of the in vitro matrix components, including proteins and each of the polysaccharides, were also present in the matrix of a clinically relevant in vivo biofilm. Nuclear magnetic resonance (NMR) analysis demonstrated interaction of aggregate matrix with the antifungal fluconazole, consistent with a role in drug impedance and contribution of multiple matrix components. PMID:25096878

  10. Staggered chiral random matrix theory

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Osborn, James C.

    2011-02-01

    We present a random matrix theory for the staggered lattice QCD Dirac operator. The staggered random matrix theory is equivalent to the zero-momentum limit of the staggered chiral Lagrangian and includes all taste breaking terms at their leading order. This is an extension of previous work which only included some of the taste breaking terms. We will also present some results for the taste breaking contributions to the partition function and the Dirac eigenvalues.

  11. Modeling the formation of cell-matrix adhesions on a single 3D matrix fiber.

    PubMed

    Escribano, J; Sánchez, M T; García-Aznar, J M

    2015-11-07

    Cell-matrix adhesions are crucial in different biological processes like tissue morphogenesis, cell motility, and extracellular matrix remodeling. These interactions that link cell cytoskeleton and matrix fibers are built through protein clutches, generally known as adhesion complexes. The adhesion formation process has been deeply studied in two-dimensional (2D) cases; however, the knowledge is limited for three-dimensional (3D) cases. In this work, we simulate different local extracellular matrix properties in order to unravel the fundamental mechanisms that regulate the formation of cell-matrix adhesions in 3D. We aim to study the mechanical interaction of these biological structures through a three dimensional discrete approach, reproducing the transmission pattern force between the cytoskeleton and a single extracellular matrix fiber. This numerical model provides a discrete analysis of the proteins involved including spatial distribution, interaction between them, and study of the different phenomena, such as protein clutches unbinding or protein unfolding. Copyright © 2015 Elsevier Ltd. All rights reserved.

  12. Pseudomonas biofilm matrix composition and niche biology

    PubMed Central

    Mann, Ethan E.; Wozniak, Daniel J.

    2014-01-01

    Biofilms are a predominant form of growth for bacteria in the environment and in the clinic. Critical for biofilm development are adherence, proliferation, and dispersion phases. Each of these stages includes reinforcement by, or modulation of, the extracellular matrix. Pseudomonas aeruginosa has been a model organism for the study of biofilm formation. Additionally, other Pseudomonas species utilize biofilm formation during plant colonization and environmental persistence. Pseudomonads produce several biofilm matrix molecules, including polysaccharides, nucleic acids, and proteins. Accessory matrix components shown to aid biofilm formation and adaptability under varying conditions are also produced by pseudomonads. Adaptation facilitated by biofilm formation allows for selection of genetic variants with unique and distinguishable colony morphology. Examples include rugose small-colony variants and wrinkly spreaders (WS), which over produce Psl/Pel or cellulose, respectively, and mucoid bacteria that over produce alginate. The well-documented emergence of these variants suggests that pseudomonads take advantage of matrix-building subpopulations conferring specific benefits for the entire population. This review will focus on various polysaccharides as well as additional Pseudomonas biofilm matrix components. Discussions will center on structure–function relationships, regulation, and the role of individual matrix molecules in niche biology. PMID:22212072

  13. Interplay of matrix metalloproteinases, tissue inhibitors of metalloproteinases and their regulators in cardiac matrix remodeling.

    PubMed

    Li, Y Y; McTiernan, C F; Feldman, A M

    2000-05-01

    Myocardial fibrosis due to maladaptive extracellular matrix remodeling contributes to dysfunction of the failing heart. Further elucidation of the mechanism by which myocardial fibrosis and dilatation can be prevented or even reversed remains of great interest as a potential means to limit myocardial remodeling and dysfunction. Matrix metalloproteinases (MMPs) are the driving force behind extracellular matrix degradation during remodeling and are increased in the failing human heart. MMPs are regulated by a variety of growth factors, cytokines, and matrix fragments such as matrikines. In the present report, we discuss the regulation of MMPs, the role of MMPs in the development of cardiac fibrosis, and the modulation of MMP activity using gene transfer and knockout technologies. We also present recent findings from our laboratory on the regulation of the extracellular MMP inducer (EMMPRIN), MMPs, and transforming growth factor-beta(1) in the failing human heart before and after left ventricular assist device support, as well as the possibility of preventing ventricular fibrosis using different anti-MMP strategies. Several studies suggest that such modulation of MMP activity can alter ventricular remodeling, myocardial dysfunction, and the progression of heart failure. It is therefore suggested that the interplay of MMPs and their regulators is important in the development of the heart failure phenotype, and myocardial fibrosis in heart failure may be modified by modulating MMP activity.

  14. Necessary and sufficient conditions for the complete controllability and observability of systems in series using the coprime factorization of a rational matrix

    NASA Technical Reports Server (NTRS)

    Callier, F. M.; Nahum, C. D.

    1975-01-01

    The series connection of two linear time-invariant systems that have minimal state space system descriptions is considered. From these descriptions, strict-system-equivalent polynomial matrix system descriptions in the manner of Rosenbrock are derived. They are based on the factorization of the transfer matrix of the subsystems as a ratio of two right or left coprime polynomial matrices. They give rise to a simple polynomial matrix system description of the tandem connection. Theorem 1 states that for the complete controllability and observability of the state space system description of the series connection, it is necessary and sufficient that certain 'denominator' and 'numerator' groups are coprime. Consequences for feedback systems are drawn in Corollary 1. The role of pole-zero cancellations is explained by Lemma 3 and Corollaires 2 and 3.

  15. UTOPIAN: user-driven topic modeling based on interactive nonnegative matrix factorization.

    PubMed

    Choo, Jaegul; Lee, Changhyun; Reddy, Chandan K; Park, Haesun

    2013-12-01

    Topic modeling has been widely used for analyzing text document collections. Recently, there have been significant advancements in various topic modeling techniques, particularly in the form of probabilistic graphical modeling. State-of-the-art techniques such as Latent Dirichlet Allocation (LDA) have been successfully applied in visual text analytics. However, most of the widely-used methods based on probabilistic modeling have drawbacks in terms of consistency from multiple runs and empirical convergence. Furthermore, due to the complicatedness in the formulation and the algorithm, LDA cannot easily incorporate various types of user feedback. To tackle this problem, we propose a reliable and flexible visual analytics system for topic modeling called UTOPIAN (User-driven Topic modeling based on Interactive Nonnegative Matrix Factorization). Centered around its semi-supervised formulation, UTOPIAN enables users to interact with the topic modeling method and steer the result in a user-driven manner. We demonstrate the capability of UTOPIAN via several usage scenarios with real-world document corpuses such as InfoVis/VAST paper data set and product review data sets.

  16. An automatic search of Alzheimer patterns using a nonnegative matrix factorization

    NASA Astrophysics Data System (ADS)

    Giraldo, Diana L.; García-Arteaga, Juan D.; Romero, Eduardo

    2013-11-01

    This paper presents a fully automatic method that condenses relevant morphometric information from a database of magnetic resonance images (MR) labeled as either normal (NC) or Alzheimer's disease (AD). The proposed method generates class templates using Nonnegative Matrix Factorization (NMF) which will be used to develop an NC/AD classi cator. It then nds regions of interest (ROI) with discerning inter-class properties. by inspecting the di erence volume of the two class templates. From these templates local probability distribution functions associated to low level features such as intensities, orientation and edges within the found ROI are calculated. A sample brain volume can then be characterized by a similarity measure in the ROI to both the normal and the pathological templates. These characteristics feed a simple binary SVM classi er which, when tested with an experimental group extracted from a public brain MR dataset (OASIS), reveals an equal error rate measure which is better than the state-of-the-art tested on the same dataset (0:9 in the former and 0:8 in the latter).

  17. Community detection enhancement using non-negative matrix factorization with graph regularization

    NASA Astrophysics Data System (ADS)

    Liu, Xiao; Wei, Yi-Ming; Wang, Jian; Wang, Wen-Jun; He, Dong-Xiao; Song, Zhan-Jie

    2016-06-01

    Community detection is a meaningful task in the analysis of complex networks, which has received great concern in various domains. A plethora of exhaustive studies has made great effort and proposed many methods on community detection. Particularly, a kind of attractive one is the two-step method which first makes a preprocessing for the network and then identifies its communities. However, not all types of methods can achieve satisfactory results by using such preprocessing strategy, such as the non-negative matrix factorization (NMF) methods. In this paper, rather than using the above two-step method as most works did, we propose a graph regularized-based model to improve, specialized, the NMF-based methods for the detection of communities, namely NMFGR. In NMFGR, we introduce the similarity metric which contains both the global and local information of networks, to reflect the relationships between two nodes, so as to improve the accuracy of community detection. Experimental results on both artificial and real-world networks demonstrate the superior performance of NMFGR to some competing methods.

  18. Discriminative non-negative matrix factorization (DNMF) and its application to the fault diagnosis of diesel engine

    NASA Astrophysics Data System (ADS)

    Yang, Yong-sheng; Ming, An-bo; Zhang, You-yun; Zhu, Yong-sheng

    2017-10-01

    Diesel engines, widely used in engineering, are very important for the running of equipments and their fault diagnosis have attracted much attention. In the past several decades, the image based fault diagnosis methods have provided efficient ways for the diesel engine fault diagnosis. By introducing the class information into the traditional non-negative matrix factorization (NMF), an improved NMF algorithm named as discriminative NMF (DNMF) was developed and a novel imaged based fault diagnosis method was proposed by the combination of the DNMF and the KNN classifier. Experiments performed on the fault diagnosis of diesel engine were used to validate the efficacy of the proposed method. It is shown that the fault conditions of diesel engine can be efficiently classified by the proposed method using the coefficient matrix obtained by DNMF. Compared with the original NMF (ONMF) and principle component analysis (PCA), the DNMF can represent the class information more efficiently because the class characters of basis matrices obtained by the DNMF are more visible than those in the basis matrices obtained by the ONMF and PCA.

  19. Novel entries in a fungal biofilm matrix encyclopedia.

    PubMed

    Zarnowski, Robert; Westler, William M; Lacmbouh, Ghislain Ade; Marita, Jane M; Bothe, Jameson R; Bernhardt, Jörg; Lounes-Hadj Sahraoui, Anissa; Fontaine, Joël; Sanchez, Hiram; Hatfield, Ronald D; Ntambi, James M; Nett, Jeniel E; Mitchell, Aaron P; Andes, David R

    2014-08-05

    Virulence of Candida is linked with its ability to form biofilms. Once established, biofilm infections are nearly impossible to eradicate. Biofilm cells live immersed in a self-produced matrix, a blend of extracellular biopolymers, many of which are uncharacterized. In this study, we provide a comprehensive analysis of the matrix manufactured by Candida albicans both in vitro and in a clinical niche animal model. We further explore the function of matrix components, including the impact on drug resistance. We uncovered components from each of the macromolecular classes (55% protein, 25% carbohydrate, 15% lipid, and 5% nucleic acid) in the C. albicans biofilm matrix. Three individual polysaccharides were identified and were suggested to interact physically. Surprisingly, a previously identified polysaccharide of functional importance, β-1,3-glucan, comprised only a small portion of the total matrix carbohydrate. Newly described, more abundant polysaccharides included α-1,2 branched α-1,6-mannans (87%) associated with unbranched β-1,6-glucans (13%) in an apparent mannan-glucan complex (MGCx). Functional matrix proteomic analysis revealed 458 distinct activities. The matrix lipids consisted of neutral glycerolipids (89.1%), polar glycerolipids (10.4%), and sphingolipids (0.5%). Examination of matrix nucleic acid identified DNA, primarily noncoding sequences. Several of the in vitro matrix components, including proteins and each of the polysaccharides, were also present in the matrix of a clinically relevant in vivo biofilm. Nuclear magnetic resonance (NMR) analysis demonstrated interaction of aggregate matrix with the antifungal fluconazole, consistent with a role in drug impedance and contribution of multiple matrix components. Importance: This report is the first to decipher the complex and unique macromolecular composition of the Candida biofilm matrix, demonstrate the clinical relevance of matrix components, and show that multiple matrix components are needed

  20. Phase diagram of matrix compressed sensing

    NASA Astrophysics Data System (ADS)

    Schülke, Christophe; Schniter, Philip; Zdeborová, Lenka

    2016-12-01

    In the problem of matrix compressed sensing, we aim to recover a low-rank matrix from a few noisy linear measurements. In this contribution, we analyze the asymptotic performance of a Bayes-optimal inference procedure for a model where the matrix to be recovered is a product of random matrices. The results that we obtain using the replica method describe the state evolution of the Parametric Bilinear Generalized Approximate Message Passing (P-BiG-AMP) algorithm, recently introduced in J. T. Parker and P. Schniter [IEEE J. Select. Top. Signal Process. 10, 795 (2016), 10.1109/JSTSP.2016.2539123]. We show the existence of two different types of phase transition and their implications for the solvability of the problem, and we compare the results of our theoretical analysis to the numerical performance reached by P-BiG-AMP. Remarkably, the asymptotic replica equations for matrix compressed sensing are the same as those for a related but formally different problem of matrix factorization.

  1. Integrated approach to estimate the ocean's time variable dynamic topography including its covariance matrix

    NASA Astrophysics Data System (ADS)

    Müller, Silvia; Brockmann, Jan Martin; Schuh, Wolf-Dieter

    2015-04-01

    The ocean's dynamic topography as the difference between the sea surface and the geoid reflects many characteristics of the general ocean circulation. Consequently, it provides valuable information for evaluating or tuning ocean circulation models. The sea surface is directly observed by satellite radar altimetry while the geoid cannot be observed directly. The satellite-based gravity field determination requires different measurement principles (satellite-to-satellite tracking (e.g. GRACE), satellite-gravity-gradiometry (GOCE)). In addition, hydrographic measurements (salinity, temperature and pressure; near-surface velocities) provide information on the dynamic topography. The observation types have different representations and spatial as well as temporal resolutions. Therefore, the determination of the dynamic topography is not straightforward. Furthermore, the integration of the dynamic topography into ocean circulation models requires not only the dynamic topography itself but also its inverse covariance matrix on the ocean model grid. We developed a rigorous combination method in which the dynamic topography is parameterized in space as well as in time. The altimetric sea surface heights are expressed as a sum of geoid heights represented in terms of spherical harmonics and the dynamic topography parameterized by a finite element method which can be directly related to the particular ocean model grid. Besides the difficult task of combining altimetry data with a gravity field model, a major aspect is the consistent combination of satellite data and in-situ observations. The particular characteristics and the signal content of the different observations must be adequately considered requiring the introduction of auxiliary parameters. Within our model the individual observation groups are combined in terms of normal equations considering their full covariance information; i.e. a rigorous variance/covariance propagation from the original measurements to the

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

    PubMed

    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.

  3. 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.

    PubMed

    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.

  4. The Progressive Ankylosis Protein Regulates Cementum Apposition and Extracellular Matrix Composition

    PubMed Central

    Foster, B.L.; Nagatomo, K.J.; Bamashmous, S.O.; Tompkins, K.A.; Fong, H.; Dunn, D.; Chu, E.Y.; Guenther, C.; Kingsley, D.M.; Rutherford, R.B.; Somerman, M.J.

    2011-01-01

    Background/Aims Tooth root cementum is sensitive to modulation of inorganic pyrophosphate (PPi), an inhibitor of hydroxyapatite precipitation. Factors increasing PPi include progressive ankylosis protein (ANK) and ectonucleotide pyrophosphatase/phosphodiesterase 1 (NPP1) while tissue nonspecific alkaline phosphatase hydrolyzes PPi. Studies here aimed to define the role of ANK in root and cementum by analyzing tooth development in Ank knock-out (KO) mice versus wild type. Materials and Methods: Periodontal development in KO versus control mice was analyzed by histology, histomorphometry, immunohistochemistry, in situ hybridization, electron microscopy, and nanoindentation. Cementoblast cultures were used in vitro to provide mechanistic underpinnings for PPi modulation of cell function. Results Over the course of root development, Ank KO cervical cementum became 8- to 12-fold thicker than control cervical cementum. Periodontal ligament width was maintained and other dentoalveolar tissues, including apical cementum, were unaltered. Cervical cementum uncharacteristically included numerous cells, from rapid cementogenesis. Ank KO increased osteopontin and dentin matrix protein 1 gene and protein expression, and markedly increased NPP1 protein expression in cementoblasts but not in other cell types. Conditional ablation of Ank in joints and periodontia confirmed a local role for ANK in cementogenesis. In vitro studies employing cementoblasts indicated that Ank and Enpp1 mRNA levels increased in step with mineral nodule formation, supporting a role for these factors in regulation of cementum matrix mineralization. Conclusion: ANK, by modulating local PPi, controls cervical cementum apposition and extracellular matrix. Loss of ANK created a local environment conducive to rapid cementogenesis; therefore, approaches modulating PPi in periodontal tissues have potential to promote cementum regeneration. PMID:21389671

  5. A unified statistical approach to non-negative matrix factorization and probabilistic latent semantic indexing

    PubMed Central

    Wang, Guoli; Ebrahimi, Nader

    2014-01-01

    Non-negative matrix factorization (NMF) is a powerful machine learning method for decomposing a high-dimensional nonnegative matrix V into the product of two nonnegative matrices, W and H, such that V ∼ W H. It has been shown to have a parts-based, sparse representation of the data. NMF has been successfully applied in a variety of areas such as natural language processing, neuroscience, information retrieval, image processing, speech recognition and computational biology for the analysis and interpretation of large-scale data. There has also been simultaneous development of a related statistical latent class modeling approach, namely, probabilistic latent semantic indexing (PLSI), for analyzing and interpreting co-occurrence count data arising in natural language processing. In this paper, we present a generalized statistical approach to NMF and PLSI based on Renyi's divergence between two non-negative matrices, stemming from the Poisson likelihood. Our approach unifies various competing models and provides a unique theoretical framework for these methods. We propose a unified algorithm for NMF and provide a rigorous proof of monotonicity of multiplicative updates for W and H. In addition, we generalize the relationship between NMF and PLSI within this framework. We demonstrate the applicability and utility of our approach as well as its superior performance relative to existing methods using real-life and simulated document clustering data. PMID:25821345

  6. A unified statistical approach to non-negative matrix factorization and probabilistic latent semantic indexing.

    PubMed

    Devarajan, Karthik; Wang, Guoli; Ebrahimi, Nader

    2015-04-01

    Non-negative matrix factorization (NMF) is a powerful machine learning method for decomposing a high-dimensional nonnegative matrix V into the product of two nonnegative matrices, W and H , such that V ∼ W H . It has been shown to have a parts-based, sparse representation of the data. NMF has been successfully applied in a variety of areas such as natural language processing, neuroscience, information retrieval, image processing, speech recognition and computational biology for the analysis and interpretation of large-scale data. There has also been simultaneous development of a related statistical latent class modeling approach, namely, probabilistic latent semantic indexing (PLSI), for analyzing and interpreting co-occurrence count data arising in natural language processing. In this paper, we present a generalized statistical approach to NMF and PLSI based on Renyi's divergence between two non-negative matrices, stemming from the Poisson likelihood. Our approach unifies various competing models and provides a unique theoretical framework for these methods. We propose a unified algorithm for NMF and provide a rigorous proof of monotonicity of multiplicative updates for W and H . In addition, we generalize the relationship between NMF and PLSI within this framework. We demonstrate the applicability and utility of our approach as well as its superior performance relative to existing methods using real-life and simulated document clustering data.

  7. A Glimpse of Matrix Metalloproteinases in Diabetic Nephropathy

    PubMed Central

    Xu, X.; Xiao, L.; Xiao, P.; Yang, S.; Chen, G.; Liu, F.; Kanwar, Y.Y.; Sun, L.

    2014-01-01

    Matrix metalloproteinases (MMPs) are proteolytic enzymes belonging to the family of zinc-dependent endopeptidases that are capable of degrading almost all the proteinaceous components of the extracellular matrix (ECM). It is known that MMPs play a role in a number of renal diseases, such as, various forms of glomerulonephritis and tubular diseases, including some of the inherited kidney diseases. In this regard, ECM accumulation is considered to be a hallmark morphologic finding of diabetic nephropathy, which not only is related to the excessive synthesis of matrix proteins, but also to their decreased degradation by the MMPs. In recent years, increasing evidence suggest that there is a good correlation between the activity or expression of MMPs and progression of renal disease in patients with diabetic nephropathy in humans and in various experimental animal models. In such a diabetic milieu, the expression of MMPs is modulated by high glucose, advanced glycation end products (AGEs), TGF-β, reactive oxygen species (ROS), transcription factors and some of the microRNAs. In this review, we focused on the structure and functions of MMPs, and their role in the pathogenesis of diabetic nephropathy. PMID:25039784

  8. Constructing the matrix

    NASA Astrophysics Data System (ADS)

    Elliott, John

    2012-09-01

    As part of our 'toolkit' for analysing an extraterrestrial signal, the facility for calculating structural affinity to known phenomena must be part of our core capabilities. Without such a resource, we risk compromising our potential for detection and decipherment or at least causing significant delay in the process. To create such a repository for assessing structural affinity, all known systems (language parameters) need to be structurally analysed to 'place' their 'system' within a relational communication matrix. This will need to include all known variants of language structure, whether 'living' (in current use) or ancient; this must also include endeavours to incorporate yet undeciphered scripts and non-human communication, to provide as complete a picture as possible. In creating such a relational matrix, post-detection decipherment will be assisted by a structural 'map' that will have the potential for 'placing' an alien communication with its nearest known 'neighbour', to assist subsequent categorisation of basic parameters as a precursor to decipherment. 'Universal' attributes and behavioural characteristics of known communication structure will form a range of templates (Elliott, 2001 [1] and Elliott et al., 2002 [2]), to support and optimise our attempt at categorising and deciphering the content of an extraterrestrial signal. Detection of the hierarchical layers, which comprise intelligent, complex communication, will then form a matrix of calculations that will ultimately score affinity through a relational matrix of structural comparison. In this paper we develop the rationales and demonstrate functionality with initial test results.

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

    NASA Astrophysics Data System (ADS)

    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).

  10. Fiber pushout and interfacial shear in metal-matrix composites

    NASA Technical Reports Server (NTRS)

    Koss, Donald A.; Hellmann, John R.; Kallas, M. N.

    1993-01-01

    Recent thin-slice pushout tests have suggested that MMC matrix-fiber interface failure processes depend not only on such intrinsic factors as bond strength and toughness, and matrix plasticity, but such extrinsic factors as specimen configuration, thermally-induced residual stresses, and the mechanics associated with a given test. After detailing the contrasts in fiber-pullout and fiber-pushout mechanics, attention is given to selected aspects of thin-slice fiber pushout behavior illustrative of the physical nature of interfacial shear response and its dependence on both intrinsic and extrinsic factors.

  11. Positive matrix factorization of PM2.5 - eliminating the effects of gas/particle partitioning of semivolatile organic compounds.

    PubMed

    Xie, M; Barsanti, K C; Hannigan, M P; Dutton, S J; Vedal, S

    2013-01-01

    Gas-phase concentrations of semi-volatile organic compounds (SVOCs) were calculated from gas/particle (G/P) partitioning theory using their measured particle-phase concentrations. The particle-phase data were obtained from an existing filter measurement campaign (27 January 2003-2 October 2005) as a part of the Denver Aerosol Sources and Health (DASH) study, including 970 observations of 71 SVOCs (Xie et al., 2013). In each compound class of SVOCs, the lighter species (e.g. docosane in n alkanes, fluoranthene in PAHs) had higher total concentrations (gas + particle phase) and lower particle-phase fractions. The total SVOC concentrations were analyzed using positive matrix factorization (PMF). Then the results were compared with source apportionment results where only particle-phase SVOC concentrations were used (particle only-based study; Xie et al., 2013). For the particle only-based PMF analysis, the factors primarily associated with primary or secondary sources ( n alkane, EC/sterane and inorganic ion factors) exhibit similar contribution time series ( r = 0.92-0.98) with their corresponding factors ( n alkane, sterane and nitrate+sulfate factors) in the current work. Three other factors (light n alkane/PAH, PAH and summer/odd n alkane factors) are linked with pollution sources influenced by atmospheric processes (e.g. G/P partitioning, photochemical reaction), and were less correlated ( r = 0.69-0.84) with their corresponding factors (light SVOC, PAH and bulk carbon factors) in the current work, suggesting that the source apportionment results derived from particle-only SVOC data could be affected by atmospheric processes. PMF analysis was also performed on three temperature-stratified subsets of the total SVOC data, representing ambient sampling during cold (daily average temperature < 10 °C), warm (≥ 10 °C and ≤ 20 °C) and hot (> 20 °C) periods. Unlike the particle only-based study, in this work the factor characterized by the low molecular weight (MW

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Gittens, Alex; Kottalam, Jey; Yang, Jiyan

    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 themore » 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.« less

  13. Increased expression of matrix metalloproteinase-10, nerve growth factor and substance P in the painful degenerate intervertebral disc

    PubMed Central

    Richardson, Stephen M; Doyle, Paul; Minogue, Ben M; Gnanalingham, Kanna; Hoyland, Judith A

    2009-01-01

    Introduction Matrix metalloproteinases (MMPs) are known to be involved in the degradation of the nucleus pulposus (NP) during intervertebral disc (IVD) degeneration. This study investigated MMP-10 (stromelysin-2) expression in the NP during IVD degeneration and correlated its expression with pro-inflammatory cytokines and molecules involved in innervation and nociception during degeneration which results in low back pain (LBP). Methods Human NP tissue was obtained at postmortem (PM) from patients without a history of back pain and graded as histologically normal or degenerate. Symptomatic degenerate NP samples were also obtained at surgery for LBP. Expression of MMP-10 mRNA and protein was analysed using real-time polymerase chain reaction and immunohistochemistry. Gene expression for pro-inflammatory cytokines interleukin-1 (IL-1) and tumour necrosis factor-alpha (TNF-α), nerve growth factor (NGF) and the pain-associated neuropeptide substance P were also analysed. Correlations between MMP-10 and IL-1, TNF-α and NGF were assessed along with NGF with substance P. Results MMP-10 mRNA was significantly increased in surgical degenerate NP when compared to PM normal and PM degenerate samples. MMP-10 protein was also significantly higher in degenerate surgical NP samples compared to PM normal. IL-1 and MMP-10 mRNA demonstrated a significant correlation in surgical degenerate samples, while TNF-α was not correlated with MMP-10 mRNA. NGF was significantly correlated with both MMP-10 and substance P mRNA in surgical degenerate NP samples. Conclusions MMP-10 expression is increased in the symptomatic degenerate IVD, where it may contribute to matrix degradation and initiation of nociception. Importantly, this study suggests differences in the pathways involved in matrix degradation between painful and pain-free IVD degeneration. PMID:19695094

  14. Increased expression of matrix metalloproteinase-10, nerve growth factor and substance P in the painful degenerate intervertebral disc.

    PubMed

    Richardson, Stephen M; Doyle, Paul; Minogue, Ben M; Gnanalingham, Kanna; Hoyland, Judith A

    2009-01-01

    Matrix metalloproteinases (MMPs) are known to be involved in the degradation of the nucleus pulposus (NP) during intervertebral disc (IVD) degeneration. This study investigated MMP-10 (stromelysin-2) expression in the NP during IVD degeneration and correlated its expression with pro-inflammatory cytokines and molecules involved in innervation and nociception during degeneration which results in low back pain (LBP). Human NP tissue was obtained at postmortem (PM) from patients without a history of back pain and graded as histologically normal or degenerate. Symptomatic degenerate NP samples were also obtained at surgery for LBP. Expression of MMP-10 mRNA and protein was analysed using real-time polymerase chain reaction and immunohistochemistry. Gene expression for pro-inflammatory cytokines interleukin-1 (IL-1) and tumour necrosis factor-alpha (TNF-alpha), nerve growth factor (NGF) and the pain-associated neuropeptide substance P were also analysed. Correlations between MMP-10 and IL-1, TNF-alpha and NGF were assessed along with NGF with substance P. MMP-10 mRNA was significantly increased in surgical degenerate NP when compared to PM normal and PM degenerate samples. MMP-10 protein was also significantly higher in degenerate surgical NP samples compared to PM normal. IL-1 and MMP-10 mRNA demonstrated a significant correlation in surgical degenerate samples, while TNF-alpha was not correlated with MMP-10 mRNA. NGF was significantly correlated with both MMP-10 and substance P mRNA in surgical degenerate NP samples. MMP-10 expression is increased in the symptomatic degenerate IVD, where it may contribute to matrix degradation and initiation of nociception. Importantly, this study suggests differences in the pathways involved in matrix degradation between painful and pain-free IVD degeneration.

  15. Study on the Algorithm of Judgment Matrix in Analytic Hierarchy Process

    NASA Astrophysics Data System (ADS)

    Lu, Zhiyong; Qin, Futong; Jin, Yican

    2017-10-01

    A new algorithm is proposed for the non-consistent judgment matrix in AHP. A primary judgment matrix is generated firstly through pre-ordering the targeted factor set, and a compared matrix is built through the top integral function. Then a relative error matrix is created by comparing the compared matrix with the primary judgment matrix which is regulated under the control of the relative error matrix and the dissimilar degree of the matrix step by step. Lastly, the targeted judgment matrix is generated to satisfy the requirement of consistence and the least dissimilar degree. The feasibility and validity of the proposed method are verified by simulation results.

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Chennubhotla, Chakra; Castro, Jason

    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.more » 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.« less

  17. New insights into the roles of matrix metalloproteinases in colorectal cancer development and progression.

    PubMed

    Leeman, Matthew F; Curran, Stephanie; Murray, Graeme I

    2003-12-01

    This review outlines new concepts that are emerging for the functions of matrix metalloproteinases in colorectal cancer development and progression. The two main concepts that will be discussed are the role of matrix metalloproteinases in the early stages of colorectal tumour development and the functional mechanisms by which matrix metalloproteinases contribute to colorectal tumour invasion and metastasis. The matrix metalloproteinases are a group of enzymes, which have been best characterized for their ability to degrade extracellular matrix proteins and thus they have been extensively studied in tumour invasion. It is now becoming recognized that the matrix metalloproteinases have key roles in a variety of biological processes that are distinct from their well-defined role in matrix degradation. This group of enzymes has been shown to interact with a broad range of non-matrix proteins including growth factors and their receptors, mediators of apoptosis, and cell adhesion molecules. The elucidation of novel biological roles for the matrix metalloproteinases also challenges the current predominant concept of matrix metalloproteinases as enzymes only involved in matrix degradation. Recent studies have shown that several matrix metalloproteinases, especially matrilysin (MMP-7), interact with the specific molecular genetic and signalling pathways involved in colorectal cancer development. In particular, matrilysin is activated at an early stage of colorectal tumourigenesis by the beta-catenin signalling pathway. Furthermore, studies are now elucidating specific mechanisms by which individual matrix metalloproteinases, especially membrane-type matrix metalloproteinases, interact with specific cell adhesion molecules and cytoskeletal proteins and thus contribute dynamically to colorectal tumour invasion. Copyright 2003 John Wiley & Sons, Ltd.

  18. Exposure matrix development for the Libby cohort.

    PubMed

    Noonan, C W

    2006-11-01

    The Libby, MT, cohort includes current and former residents with potential historical exposure to asbestos-contaminated vermiculite. This cohort includes individuals with a broad range of exposure experiences and work histories. While both occupational and nonoccupational exposure pathways were found to be relevant in recent investigations of health effects among this cohort, there has not been a comprehensive approach to characterizing these varied exposure pathways. Any approach toward assessing historical exposures among this population must account for three general categories: (1) occupational exposures, (2) residential exposures, and (3) exposures related to a variety of nonoccupational activities thought to be associated with vermiculite/asbestos exposure in this community. First, a job exposure matrix is commonly used in occupational epidemiology to assess historical worker exposures, allowing for the incorporation of numerous occupational categories and weighting factors applied to specific jobs for different time periods. Second, residential exposures can best be quantified by integrating individuals' residential histories with data on environmental asbestos contamination in the community. Previous soil or sediment sampling as well as air modeling could inform estimates of time- and spatial-dependent exposure concentrations for a residential exposure matrix. Finally, exposure opportunities due to nonoccupational activities could be weighted by factors such as time, geography, environmental sampling, and an assessment of the relative importance for each pathway. These three matrices for occupational, residential, and activity exposure pathways could be combined or used separately to provide a more comprehensive and quantitative, or semiquantitative, assessment of individual exposure in future epidemiological studies of this cohort.

  19. MATRIX METALLOPROTEINS (MMP)-MEDIATED PHOSPHORYLATION OF THE EPIDERMAL GROWTH FACTOR RECEPTOR (EGFR) IN HUMAN AIRWAY EPITHELIAL CELLS (HAEC) EXPOSED TO ZINC (ZN)

    EPA Science Inventory

    Matrix Metalloproteinase (MMP)-Mediated Phosphorylation of The Epidermal Growth Factor Receptor (EGFR) in Human Airway Epithelial Cells (HAEC) Exposed to Zinc (Zn)
    Weidong Wu, James M. Samet, Robert Silbajoris, Lisa A. Dailey, Lee M. Graves, and Philip A. Bromberg
    Center fo...

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Zhang, Le; Yu, Yu; Zhang, Pengjie, E-mail: lezhang@sjtu.edu.cn

    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-negativemore » 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.« less

  1. Temperature dependent nonlinear metal matrix laminae behavior

    NASA Technical Reports Server (NTRS)

    Barrett, D. J.; Buesking, K. W.

    1986-01-01

    An analytical method is described for computing the nonlinear thermal and mechanical response of laminated plates. The material model focuses upon the behavior of metal matrix materials by relating the nonlinear composite response to plasticity effects in the matrix. The foundation of the analysis is the unidirectional material model which is used to compute the instantaneous properties of the lamina based upon the properties of the fibers and matrix. The unidirectional model assumes that the fibers properties are constant with temperature and assumes that the matrix can be modelled as a temperature dependent, bilinear, kinematically hardening material. An incremental approach is used to compute average stresses in the fibers and matrix caused by arbitrary mechanical and thermal loads. The layer model is incorporated in an incremental laminated plate theory to compute the nonlinear response of laminated metal matrix composites of general orientation and stacking sequence. The report includes comparisons of the method with other analytical approaches and compares theoretical calculations with measured experimental material behavior. A section is included which describes the limitations of the material model.

  2. An inflammation-responsive transcription factor in the pathophysiology of osteoarthritis.

    PubMed

    Ray, Alpana; Ray, Bimal K

    2008-01-01

    A number of risk factors including biomechanical stress on the articular cartilage imposed by joint overloading due to obesity, repetitive damage of the joint tissues by injury of the menisci and ligaments, and abnormal joint alignment play a significant role in the onset of osteoarthritis (OA). Genetic predisposition can also lead to the formation of defective cartilage matrix because of abnormal gene expression in the cartilage-specific cells. Another important biochemical event in OA is the consequence of inflammation. It has been shown that synovial inflammation triggers the synthesis of biological stimuli such as cytokines and growth factors which subsequently reach the chondrocyte cells of the articular cartilage activating inflammatory events in the chondrocytes leading to cartilage destruction. In addition to cartilage degradation, hypertrophy of the subchondral bone and osteophyte formation at the joint margins also takes place in OA. Both processes involve abnormal expression of a number of genes including matrix metalloproteinases (MMPs) for cartilage degradation and those associated with bone formation during osteophyte development. To address how diverse groups of genes are activated in OA chondrocyte, we have studied their induction mechanism. We present evidence for abundant expression of an inflammation-responsive transcription factor, SAF-1, in moderate to severely damaged OA cartilage tissues. In contrast, cells in normal cartilage matrix contain very low level of SAF-1 protein. SAF-1 is identified as a major regulator of increased synthesis of MMP-1 and -9 and pro-angiogenic factor, vascular endothelial growth factor (VEGF). While VEGF by stimulating angiogenesis plays a key role in new bone formation in osteophyte, increase of MMP-1 and -9 is instrumental for cartilage erosion in the pathogenesis of OA. Increased expression in degenerated cartilage matrix and in the osteophytes indicate for a key regulatory role of SAF-1 in directing catabolic

  3. 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.

    PubMed

    Kong, Li; Zhao, Yun-Peng; Tian, Qing-Yun; Feng, Jian-Quan; Kobayashi, Tatsuya; Merregaert, Joseph; Liu, Chuan-Ju

    2016-08-01

    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. © FASEB.

  4. SHIP, a novel factor to ameliorate extracellular matrix accumulation via suppressing PI3K/Akt/CTGF signaling in diabetic kidney disease.

    PubMed

    Li, Fan; Li, Lisha; Cheng, Meijuan; Wang, Xiumin; Hao, Jun; Liu, Shuxia; Duan, Huijun

    2017-01-22

    Tubular interstitial extracellular matrix accumulation, which plays a key role in the pathogenesis and progression of diabetic kidney disease (DKD), is believed to be mediated by activation of PI3K/Akt signal pathway. However, it is still not clear whether SH2 domain-containing inositol 5'-phosphatase (SHIP), known as a negative regulator of PI3K/Akt pathway is also involved in extracellular matrix metabolism of diabetic kidney. In the present study, decreased SHIP and increased phospho-Akt (Ser 473, Thr 308) were found in renal tubular cells of diabetic mice accompanied by overexpression of connective tissue growth factor (CTGF) and extracellular matrix deposition versus normal mice. Again, high glucose attenuated SHIP expression in a time-dependent manner, concomitant with activation of PI3K/Akt signaling and extracellular matrix production in human renal proximal tubular epithelial cells (HK2) cultured in vitro, which was significantly prevented by transfection of M90-SHIP vector. Furthermore, in vivo delivery of rAd-INPP5D vector (SHIP expression vector) via intraperitoneal injection in diabetic mice increased SHIP expression by 3.36 times followed by 65.26%, 70.38% and 46.71% decreases of phospho-Akt (Ser 473), phospho-Akt (Thr 308) and CTGF expression versus diabetic mice receiving rAd-EGFP vector. Meanwhile, increased renal extracellular matrix accumulation of diabetic mice was also inhibited with intraperitoneal injection of rAd-INPP5D vector. These above data suggested that overexpression of SHIP might be a potent method to lessen renal extracellular matrix accumulation via inactivation of PI3K/Akt pathway and suppression of CTGF expression in DKD. Copyright © 2016 Elsevier Inc. All rights reserved.

  5. Encapsulation of Organic Chemicals within a Starch Matrix.

    ERIC Educational Resources Information Center

    Wing, R. E.; Shasha, B. S.

    1983-01-01

    Three experiments demonstrating the feasibility of encapsulating liquids within a starch matrix are described, including encapsulation of linseed oil using the zanthate method and of turpentine and butylate using the calcium adduct procedure. Encapsulated materials, including pesticides, are slowly released from the resulting matrix. Considers…

  6. Expression Levels of Myostatin and Matrix Metalloproteinase 14 mRNAs in Uterine Leiomyoma are Correlated With Dysmenorrhea.

    PubMed

    Tsigkou, Anastasia; Reis, Fernando M; Ciarmela, Pasquapina; Lee, Meng H; Jiang, Bingjie; Tosti, Claudia; Shen, Fang-Rong; Shi, Zhendan; Chen, You-Guo; Petraglia, Felice

    2015-12-01

    Uterine leiomyoma is the most common benign neoplasm of female reproductive system, found in about 50% of women in reproductive age. The mechanisms of leiomyoma growth include cell proliferation, which is modulated by growth factors, and deposition of extracellular matrix (ECM). Activin A and myostatin are growth factors that play a role in proliferation of leiomyoma cells. Matrix metalloproteinases (MMPs) are known for their ability to remodel the ECM in different biological systems. The aim of this study was to evaluate the expression levels of activin βA-subunit, myostatin, and MMP14 messenger RNAs (mRNAs) in uterine leiomyomas and the possible correlation of these factors with clinical features of the disease. Matrix metalloproteinase 14 was highly expressed in uterine leiomyoma and correlated with myostatin and activin A mRNA expression. Moreover, MMP14 and myostatin mRNA expression correlated significantly and directly with the intensity of dysmenorrhea. Overall, the present findings showed that MMP14 mRNA is highly expressed in uterine leiomyoma, where it correlates with the molecular expression of growth factors and is further increased in cases of intense dysmenorrhea. © The Author(s) 2015.

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

    PubMed

    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; p<0.01) with bEPS 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.

  8. FPGA-based coprocessor for matrix algorithms implementation

    NASA Astrophysics Data System (ADS)

    Amira, Abbes; Bensaali, Faycal

    2003-03-01

    Matrix algorithms are important in many types of applications including image and signal processing. These areas require enormous computing power. A close examination of the algorithms used in these, and related, applications reveals that many of the fundamental actions involve matrix operations such as matrix multiplication which is of O (N3) on a sequential computer and O (N3/p) on a parallel system with p processors complexity. This paper presents an investigation into the design and implementation of different matrix algorithms such as matrix operations, matrix transforms and matrix decompositions using an FPGA based environment. Solutions for the problem of processing large matrices have been proposed. The proposed system architectures are scalable, modular and require less area and time complexity with reduced latency when compared with existing structures.

  9. Matrix modulation and heart failure: new concepts question old beliefs.

    PubMed

    Deschamps, Anne M; Spinale, Francis G

    2005-05-01

    Myocardial remodeling is a complex process involving several molecular and cellular factors. Extracellular matrix has been implicated in the remodeling process. Historically, the myocardial extracellular matrix was thought to serve solely as a means to align cells and provide structure to the tissue. Although this is one of its important functions, evidence suggests that the extracellular matrix plays a complex and divergent role in influencing cell behavior. This paper characterizes some of the notable studies on this dynamic entity and on adverse myocardial remodeling that have been published over the past year, which further question the belief that the extracellular matrix is a static structure. Progress has been made in understanding how the extracellular matrix is operative in the three major conditions (myocardial infarction, left ventricular hypertrophy due to overload, and dilated cardiomyopathy) that involve myocardial remodeling. Several studies have examined plasma profiles of matrix metalloproteinases and tissue inhibitors of matrix metalloproteinases following myocardial infarction and during left ventricular hypertrophy as surrogate markers of remodeling/remodeled myocardium. It has been demonstrated that bioactive signaling molecules and growth factors, proteases, and structural proteins influence cell-matrix interactions in the context of left ventricular hypertrophy. Finally, studies that either removed or added tissue inhibitor of metalloproteinases species in the myocardium demonstrated the importance of this regulatory protein in the remodeling process. Understanding the cellular and molecular triggers that in turn give rise to changes in the extracellular matrix could provide opportunities to modify the remodeling process.

  10. Large-scale Cross-modality Search via Collective Matrix Factorization Hashing.

    PubMed

    Ding, Guiguang; Guo, Yuchen; Zhou, Jile; Gao, Yue

    2016-09-08

    By transforming data into binary representation, i.e., Hashing, we can perform high-speed search with low storage cost, and thus Hashing has collected increasing research interest in the recent years. Recently, how to generate Hashcode for multimodal data (e.g., images with textual tags, documents with photos, etc) for large-scale cross-modality search (e.g., searching semantically related images in database for a document query) is an important research issue because of the fast growth of multimodal data in the Web. To address this issue, a novel framework for multimodal Hashing is proposed, termed as Collective Matrix Factorization Hashing (CMFH). The key idea of CMFH is to learn unified Hashcodes for different modalities of one multimodal instance in the shared latent semantic space in which different modalities can be effectively connected. Therefore, accurate cross-modality search is supported. Based on the general framework, we extend it in the unsupervised scenario where it tries to preserve the Euclidean structure, and in the supervised scenario where it fully exploits the label information of data. The corresponding theoretical analysis and the optimization algorithms are given. We conducted comprehensive experiments on three benchmark datasets for cross-modality search. The experimental results demonstrate that CMFH can significantly outperform several state-of-the-art cross-modality Hashing methods, which validates the effectiveness of the proposed CMFH.

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

    PubMed

    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

  12. Structure and function of the interphotoreceptor matrix surrounding retinal photoreceptor cells.

    PubMed

    Ishikawa, Makoto; Sawada, Yu; Yoshitomi, Takeshi

    2015-04-01

    The interphotoreceptor matrix (IPM) is a highly organized structure with interconnected domains surrounding cone and rod photoreceptor cells and extends throughout the subretinal space. Based on known roles of the extracellular matrix in other tissues, the IPM is thought to have several prominent functions including serving as a receptor for growth factors, regulating retinoid transport, participating in cytoskeletal organization in surrounding cells, and regulation of oxygen and nutrient transport. In addition, a number of studies suggest that the IPM also may play a significant role in the etiology of retinal degenerative disorders. In this review, we describe the present knowledge concerning the structure and function of the IPM under physiological and pathological conditions. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

  13. Pirfenidone inhibits transforming growth factor β1-induced extracellular matrix production in nasal polyp-derived fibroblasts.

    PubMed

    Shin, Jae-Min; Park, Joo-Hoo; Park, Il-Ho; Lee, Heung-Man

    2015-01-01

    Pirfenidone has been shown to have antifibrotic and anti-inflammatory effects in the lungs. The purpose of this study was to evaluate the inhibitory effects of pirfenidone on transforming growth factor (TGF)-β1-induced myofibroblast differentiation and extracellular matrix accumulation. We also determined the molecular mechanisms of pirfenidone in nasal polyp-derived fibroblasts (NPDF). NPDFs were isolated from nasal polyps from eight patients who had chronic rhinosinusitis with nasal polyp. Pirfenidone was used to treat TGF-β1-induced NPDFs. Cytotoxicity was evaluated by using a 3-(4,5-dimethylthiazol-2yl)-2,5-diphenyl-tetrazolium bromide assay. Fibroblast migration was evaluated with scratch assays. Expression levels of α-smooth muscle actin (SMA), fibronectin, and phosphorylated Smad2/3 were determined by Western blot and/or reverse transcription-polymerase chain reaction and immunofluorescent staining. Total collagen production was analyzed with the Sircol collagen assay and contractile activity was measured by a collagen gel contraction assay. Pirfenidone (0-2 mg/mL) has no significant cytotoxic effects in TGF-β1-induced NPDFs. Migration of NPDFs was significantly inhibited by pirfenidone treatment. The expression levels of α-SMA and fibronectin were significantly reduced in pirfenidone-treated NPDFs. Collagen contraction and production were also significantly decreased by pirfenidone treatment. Finally, pirfenidone significantly inhibited phosphorylation of the Smad2/3 pathway in TGF-β1-induced NPDFs. Pirfenidone has an inhibitory effect on TGF-β1-induced migration, myofibroblast differentiation (α-SMA), extracellular matrix accumulation, and collagen contraction by blocking the phosphorylation of Smad2/3 pathways in NPDFs. Thus, pirfenidone may inhibit TGF-β1-induced extracellular matrix by regulating Smad2/3.

  14. Factors affecting the microstructure and mechanical properties of Ti-Al3Ti core-shell-structured particle-reinforced Al matrix composites

    NASA Astrophysics Data System (ADS)

    Guo, Baisong; Yi, Jianhong; Ni, Song; Shen, Rujuan; Song, Min

    2016-04-01

    This work studied the effects of matrix powder and sintering temperature on the microstructure and mechanical properties of in situ formed Ti-Al3Ti core-shell-structured particle-reinforced pure Al-based composites. It has been shown that both factors have significant effects on the morphology of the reinforcements and densification behaviour of the composites. Due to the strong interfacial bonding and the limitation of the crack propagation in the intermetallic shell during deformation by soft Al matrix and Ti core, the composite fabricated using fine spherical-shaped Al powder and sintered at 570 °C for 5 h has the optimal combination of the overall mechanical properties. The study provides a direction for the optimum combination of high strength and ductility of the composites by adjusting the fabrication parameters.

  15. Matrix Metalloproteinases in Bone Resorption, Remodeling, and Repair.

    PubMed

    Paiva, Katiucia B S; Granjeiro, José M

    2017-01-01

    Matrix metalloproteinases (MMPs) are the major protease family responsible for the cleavage of the matrisome (global composition of the extracellular matrix (ECM) proteome) and proteins unrelated to the ECM, generating bioactive molecules. These proteins drive ECM remodeling, in association with tissue-specific and cell-anchored inhibitors (TIMPs and RECK, respectively). In the bone, the ECM mediates cell adhesion, mechanotransduction, nucleation of mineralization, and the immobilization of growth factors to protect them from damage or degradation. Since the first description of an MMP in bone tissue, many other MMPs have been identified, as well as their inhibitors. Numerous functions have been assigned to these proteins, including osteoblast/osteocyte differentiation, bone formation, solubilization of the osteoid during bone resorption, osteoclast recruitment and migration, and as a coupling factor in bone remodeling under physiological conditions. In turn, a number of pathologies, associated with imbalanced bone remodeling, arise mainly from MMP overexpression and abnormalities of the ECM, leading to bone osteolysis or bone formation. In this review, we will discuss the functions of MMPs and their inhibitors in bone cells, during bone remodeling, pathological bone resorption (osteoporosis and bone metastasis), bone repair/regeneration, and emergent roles in bone bioengineering. © 2017 Elsevier Inc. All rights reserved.

  16. The Evidence Value Matrix for Diagnostic Imaging.

    PubMed

    Seidel, David; Frank, Richard A; Schmidt, Sebastian

    2016-10-01

    Evidence and value are independent factors that together affect the adoption of diagnostic imaging. For example, noncoverage decisions by reimbursement authorities can be justified by a lack of evidence and/or value. To create transparency and a common understanding among various stakeholders, we have proposed a two-dimensional matrix that allows classification of imaging devices into three distinct categories based on the available evidence and value: "question marks" (low value demonstrated in studies of any evidence level), "candidates" (high value demonstrated in retrospective case-control studies and smaller case series), and "stars" (high value demonstrated in large prospective cohort studies or, preferably, randomized controlled trials). We use several examples to illustrate the application of our matrix. A major benefit of the matrix includes the development of specific strategies for evidence and value generation. High-evidence/low-value studies are expensive and unlikely to convince decision makers, given the uncertainty of the impact on patient management and outcomes. Developing question marks into candidates first and then into stars will often be quicker and less expensive ("success sequence"). Only this more sophisticated and objective approach can justify the additional funding necessary to generate the evidence base to inform reimbursement by payers and adoption by providers. Copyright © 2016 American College of Radiology. Published by Elsevier Inc. All rights reserved.

  17. Matrix computations in MACSYMA

    NASA Technical Reports Server (NTRS)

    Wang, P. S.

    1977-01-01

    Facilities built into MACSYMA for manipulating matrices with numeric or symbolic entries are described. Computations will be done exactly, keeping symbols as symbols. Topics discussed include how to form a matrix and create other matrices by transforming existing matrices within MACSYMA; arithmetic and other computation with matrices; and user control of computational processes through the use of optional variables. Two algorithms designed for sparse matrices are given. The computing times of several different ways to compute the determinant of a matrix are compared.

  18. Pre-form ceramic matrix composite cavity and a ceramic matrix composite component

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Monaghan, Philip Harold; Delvaux, John McConnell; Taxacher, Glenn Curtis

    A pre-form CMC cavity and method of forming pre-form CMC cavity for a ceramic matrix component includes providing a mandrel, applying a base ply to the mandrel, laying-up at least one CMC ply on the base ply, removing the mandrel, and densifying the base ply and the at least one CMC ply. The remaining densified base ply and at least one CMC ply form a ceramic matrix component having a desired geometry and a cavity formed therein. Also provided is a method of forming a CMC component.

  19. Superfund Chemical Data Matrix (SCDM) Query

    EPA Pesticide Factsheets

    This site allows you to to easily query the Superfund Chemical Data Matrix (SCDM) and generate a list of the corresponding Hazard Ranking System (HRS) factor values, benchmarks, and data elements that you need.

  20. [Modern polymers in matrix tablets technology].

    PubMed

    Zimmer, Łukasz; Kasperek, Regina; Poleszak, Ewa

    2014-01-01

    Matrix tablets are the most popular method of oral drug administration, and polymeric materials have been used broadly in matrix formulations to modify and modulate drug release rate. The main goal of the system is to extend drug release profiles to maintain a constant in vivo plasma drug concentration and a consistent pharmacological effect. Polymeric matrix tablets offer a great potential as oral controlled drug delivery systems. Cellulose derivatives, like hydroxypropyl methylcellulose (HPMC) are often used as matrix formers. However, also other types of polymers can be used for this purpose including: Kollidon SR, acrylic acid polymers such as Eudragits and Carbopols. Nevertheless, polymers of natural origin like: carragens, chitosan and alginates widely used in the food and cosmetics industry are now coming to the fore of pharmaceutical research and are used in matrix tablets technology. Modern polymers allow to obtain matrix tablets by 3D printing, which enables to develop new formulation types. In this paper, the polymers used in matrix tablets technology and examples of their applications were described.

  1. Associative Flow Rule Used to Include Hydrostatic Stress Effects in Analysis of Strain-Rate-Dependent Deformation of Polymer Matrix Composites

    NASA Technical Reports Server (NTRS)

    Goldberg, Robert K.; Roberts, Gary D.

    2004-01-01

    designing reliable composite engine cases that are lighter than the metal cases in current use. The types of polymer matrix composites that are likely to be used in such an application have a deformation response that is nonlinear and that varies with strain rate. The nonlinearity and the strain-rate dependence of the composite response are due primarily to the matrix constituent. Therefore, in developing material models to be used in the design of impact-resistant composite engine cases, the deformation of the polymer matrix must be correctly analyzed. However, unlike in metals, the nonlinear response of polymers depends on the hydrostatic stresses, which must be accounted for within an analytical model. By applying micromechanics techniques along with given fiber properties, one can also determine the effects of the hydrostatic stresses in the polymer on the overall composite deformation response. First efforts to account for the hydrostatic stress effects in the composite deformation applied purely empirical methods that relied on composite-level data. In later efforts, to allow polymer properties to be characterized solely on the basis of polymer data, researchers at the NASA Glenn Research Center developed equations to model the polymers that were based on a non-associative flow rule, and efforts to use these equations to simulate the deformation of representative polymer materials were reasonably successful. However, these equations were found to have difficulty in correctly analyzing the multiaxial stress states found in the polymer matrix constituent of a composite material. To correct these difficulties, and to allow for the accurate simulation of the nonlinear strain-rate-dependent deformation analysis of polymer matrix composites, in the efforts reported here Glenn researchers reformulated the polymer constitutive equations from basic principles using the concept of an associative flow rule. These revised equations were characterized and validated in an

  2. The Extracellular Matrix of Fungal Biofilms.

    PubMed

    Mitchell, Kaitlin F; Zarnowski, Robert; Andes, David R

    A key feature of biofilms is their production of an extracellular matrix. This material covers the biofilm cells, providing a protective barrier to the surrounding environment. During an infection setting, this can include such offenses as host cells and products of the immune system as well as drugs used for treatment. Studies over the past two decades have revealed the matrix from different biofilm species to be as diverse as the microbes themselves. This chapter will review the composition and roles of matrix from fungal biofilms, with primary focus on Candida species, Saccharomyces cerevisiae, Aspergillus fumigatus, and Cryptococcus neoformans. Additional coverage will be provided on the antifungal resistance proffered by the Candida albicans matrix, which has been studied in the most depth. A brief section on the matrix produced by bacterial biofilms will be provided for comparison. Current tools for studying the matrix will also be discussed, as well as suggestions for areas of future study in this field.

  3. Qualitative models of seat discomfort including static and dynamic factors.

    PubMed

    Ebe, K; Griffin, M J

    2000-06-01

    Judgements of overall seating comfort in dynamic conditions sometimes correlate better with the static characteristics of a seat than with measures of the dynamic environment. This study developed qualitative models of overall seat discomfort to include both static and dynamic seat characteristics. A dynamic factor that reflected how vibration discomfort increased as vibration magnitude increased was combined with a static seat factor which reflected seating comfort without vibration. The ability of the model to predict the relative and overall importance of dynamic and static seat characteristics on comfort was tested in two experiments. A paired comparison experiment, using four polyurethane foam cushions (50, 70, 100, 120 mm thick), provided different static and dynamic comfort when 12 subjects were exposed to one-third octave band random vertical vibration with centre frequencies of 2.5 and 5.5 Hz, at magnitudes of 0.00, 0.25 and 0.50 m x s(-2) rms measured beneath the foam samples. Subject judgements of the relative discomfort of the different conditions depended on both static and dynamic characteristics in a manner consistent with the model. The effect of static and dynamic seat factors on overall seat discomfort was investigated by magnitude estimation using three foam cushions (of different hardness) and a rigid wooden seat at six vibration magnitudes with 20 subjects. Static seat factors (i.e. cushion stiffness) affected the manner in which vibration influenced the overall discomfort: cushions with lower stiffness were more comfortable and more sensitive to changes in vibration magnitude than those with higher stiffness. The experiments confirm that judgements of overall seat discomfort can be affected by both the static and dynamic characteristics of a seat, with the effect depending on vibration magnitude: when vibration magnitude was low, discomfort was dominated by static seat factors; as the vibration magnitude increased, discomfort became dominated

  4. 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

    PubMed Central

    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

  5. Matrix Remodeling in Pulmonary Fibrosis and Emphysema

    PubMed Central

    O’Reilly, Philip; Antony, Veena B.; Gaggar, Amit

    2016-01-01

    Pulmonary fibrosis and emphysema are chronic lung diseases characterized by a progressive decline in lung function, resulting in significant morbidity and mortality. A hallmark of these diseases is recurrent or persistent alveolar epithelial injury, typically caused by common environmental exposures such as cigarette smoke. We propose that critical determinants of the outcome of the injury-repair processes that result in fibrosis versus emphysema are mesenchymal cell fate and associated extracellular matrix dynamics. In this review, we explore the concept that regulation of mesenchymal cells under the influence of soluble factors, in particular transforming growth factor-β1, and the extracellular matrix determine the divergent tissue remodeling responses seen in pulmonary fibrosis and emphysema. PMID:26741177

  6. Differential effect of extracellular matrix derived from papillary and reticular fibroblasts on epidermal development in vitro.

    PubMed

    Janson, David; Rietveld, Marion; Mahé, Christian; Saintigny, Gaëlle; El Ghalbzouri, Abdoelwaheb

    2017-06-01

    Papillary and reticular fibroblasts have different effects on keratinocyte proliferation and differentiation. The aim of this study was to investigate whether these effects are caused by differential secretion of soluble factors or by differential generation of extracellular matrix from papillary and reticular fibroblasts. To study the effect of soluble factors, keratinocyte monolayer cultures were grown in papillary or reticular fibroblast-conditioned medium. To study the effect of extracellular matrix, keratinocytes were grown on papillary or reticular-derived matrix. Conditioned medium from papillary or reticular fibroblasts did not differentially affect keratinocyte viability or epidermal development. However, keratinocyte viability was increased when grown on matrix derived from papillary, compared with reticular, fibroblasts. In addition, the longevity of the epidermis was increased when cultured on papillary fibroblast-derived matrix skin equivalents compared with reticular-derived matrix skin equivalents. The findings indicate that the matrix secreted by papillary and reticular fibroblasts is the main causal factor to account for the differences in keratinocyte growth and viability observed in our study. Differences in response to soluble factors between both populations were less significant. Matrix components specific to the papillary dermis may account for the preferential growth of keratinocytes on papillary dermis.

  7. Beyond the Matrix: The Many Non-ECM Ligands for Integrins

    PubMed Central

    LaFoya, Bryce; Munroe, Jordan A.; Miyamoto, Alison; Detweiler, Michael A.; Crow, Jacob J.; Gazdik, Tana

    2018-01-01

    The traditional view of integrins portrays these highly conserved cell surface receptors as mediators of cellular attachment to the extracellular matrix (ECM), and to a lesser degree, as coordinators of leukocyte adhesion to the endothelium. These canonical activities are indispensable; however, there is also a wide variety of integrin functions mediated by non-ECM ligands that transcend the traditional roles of integrins. Some of these unorthodox roles involve cell-cell interactions and are engaged to support immune functions such as leukocyte transmigration, recognition of opsonization factors, and stimulation of neutrophil extracellular traps. Other cell-cell interactions mediated by integrins include hematopoietic stem cell and tumor cell homing to target tissues. Integrins also serve as cell-surface receptors for various growth factors, hormones, and small molecules. Interestingly, integrins have also been exploited by a wide variety of organisms including viruses and bacteria to support infectious activities such as cellular adhesion and/or cellular internalization. Additionally, the disruption of integrin function through the use of soluble integrin ligands is a common strategy adopted by several parasites in order to inhibit blood clotting during hematophagy, or by venomous snakes to kill prey. In this review, we strive to go beyond the matrix and summarize non-ECM ligands that interact with integrins in order to highlight these non-traditional functions of integrins. PMID:29393909

  8. Stretching the boundaries of extracellular matrix research.

    PubMed

    Hynes, Richard O

    2014-12-01

    Extracellular matrix (ECM) proteins constitute >1% of the proteome and interact with many modifiers and growth factors to affect most aspects of cellular behaviour during development and normal physiology, as well as in diseases such as fibroses, cancer and many genetic disorders. In addition to biochemical signals provided to cells by ECM proteins, important cell–ECM interactions involve bidirectional mechanotransduction influences, which are dependent on the physical structure and organization of the ECM. These are beginning to be understood using twenty-first-century approaches, including biophysics, nanotechnology, biological engineering and modern microscopy. Articles in this issue of Nature Reviews Molecular Cell Biology review progress in our understanding of the ECM.

  9. [Tissue engineering of urinary bladder using acellular matrix].

    PubMed

    Glybochko, P V; Olefir, Yu V; Alyaev, Yu G; Butnaru, D V; Bezrukov, E A; Chaplenko, A A; Zharikova, T M

    2017-04-01

    Tissue engineering has become a new promising strategy for repairing damaged organs of the urinary system, including the bladder. The basic idea of tissue engineering is to integrate cellular technology and advanced bio-compatible materials to replace or repair tissues and organs. of the study is the objective reflection of the current trends and advances in tissue engineering of the bladder using acellular matrix through a systematic search of preclinical and clinical studies of interest. Relevant studies, including those on methods of tissue engineering of urinary bladder, was retrieved from multiple databases, including Scopus, Web of Science, PubMed, Embase. The reference lists of the retrieved review articles were analyzed for the presence of the missing relevant publications. In addition, a manual search for registered clinical trials was conducted in clinicaltrials.gov. Following the above search strategy, a total of 77 eligible studies were selected for further analysis. Studies differed in the types of animal models, supporting structures, cells and growth factors. Among those, studies using cell-free matrix were selected for a more detailed analysis. Partial restoration of urothelium layer was observed in most studies where acellular grafts were used for cystoplasty, but no the growth of the muscle layer was observed. This is the main reason why cellular structures are more commonly used in clinical practice.

  10. PM 10 metal concentrations and source identification using positive matrix factorization and wind sectoring in a French industrial zone

    NASA Astrophysics Data System (ADS)

    Alleman, Laurent Y.; Lamaison, Laure; Perdrix, Esperanza; Robache, Antoine; Galloo, Jean-Claude

    2010-06-01

    The elemental composition data of ambient aerosols collected upon selected wind sectors in the highly industrialised harbour of Dunkirk (France) were interpreted using pollution roses, elemental ratios, Enrichment Factors (EF), Principal Component Analysis (PCA) and Positive Matrix Factorization (PMF) receptor model. The objective was to identify the possible sources of PM10 aerosols, their respective chemical tracers and to determine their relative contribution at the sampling site. PM10 particles samples were collected from June 2003 to March 2005 in order to analyse up to 35 elements (Ag, Al, As, Ba, Bi, Ca, Cd, Ce, Co, Cr, Cs, Cu, Eu, Fe, K, La, Mg, Mn, Mo, Na, Ni, Pb, Rb, S, Sb, Sc, Si, Sm, Sr, Th, Ti, U, V, Zn and Zr) using Inductively Coupled Plasma (ICP)-Atomic Emission Spectrometry (AES) and ICP-Mass Spectrometry (MS). A significant effort has been made on estimating the total uncertainty of each result by regularly analysing blanks, quality controls and SRM NIST standards. Based on this procedure, a selected set of 24 "robust" elements was compared to the 35-element matrix in order to evaluate the sturdiness of our PMF statistical treatment. Eight source factors were resolved by PCA for all the wind sectors explaining 90% of the total data variance. The PMF results confirmed that eight physically interpretable factors contributed to the ambient particulate pollution at the sampling site: crustal dust (11%), marine aerosols (12%), petrochemistry activities (9.2%), metallurgical sintering plant (8.6%), metallurgical coke plant (12.6%), ferromanganese plant (6.6%), road transport (15%) and a less clearly interpretable profile probably associated to dust resuspension (13%). These weighted contributions against wind direction frequencies demonstrate that industrial sources are the most important contributors to this site (37%) followed by the natural sources (detrital and marine sources) (23%) and the road transport (15%).

  11. Evidence-Based Practice: A Matrix for Predicting Phonological Generalization

    ERIC Educational Resources Information Center

    Gierut, Judith A.; Hulse, Lauren E.

    2010-01-01

    This paper describes a matrix for clinical use in the selection of phonological treatment targets to induce generalization, and in the identification of probe sounds to monitor during the course of intervention. The matrix appeals to a set of factors that have been shown to promote phonological generalization in the research literature, including…

  12. Characterization of Optical Properties of Desert Dust and Other Aerosols Using Postive Matrix Factorization

    NASA Astrophysics Data System (ADS)

    Lihavainen, H.; Alghamdi, M.; Hyvärinen, A.; Hussein, T.; Neitola, K.; Khoder, M.; Abdelmaksoud, A. S.; Al-Jeelani, H.; Shabbaj, I. I.; Almehmadi, F. M.

    2017-12-01

    To derive the comprehensive aerosol in situ characteristics at a rural background area in Saudi Arabia, an aerosol measurements station was established to Hada Al Sham, 60 km east from the Red Sea and the city of Jeddah. The present sturdy describes the observational data from February 2013 to February 2015 of scattering and absorption coefficients, Ångström exponents and single scattering albedo over the measurement period. As expected, the scattering coefficient was dominated by large desert dust particles with low Ångström scattering exponent. Especially from February to June the Ångström scattering exponent was clearly lower and scattering coefficients higher than total averages because of the dust outbreak season. Aerosol optical properties had clear diurnal cycle. The lowest scattering and absorption coefficients and aerosol optical depths were observed around noon. The observed diurnal variation is caused by wind direction and speed, during night time very calm easterly winds are dominating whereas during daytime the stronger westerly winds are dominating (sea breeze). Positive Matrix Factorization mathematical tool was applied to the scattering and absorption coefficients and PM2.5 and coarse mode (PM10- PM2.5) mass concentrations to characterise aerosols from different sources. Analysis revealed three clearly different types of sources, anthropogenic, BC source and desert dust. These factors have clearly different seasonal and diurnal variation. The contribution of desert dust factor was dominating from February to May, whereas the contribution of anthropogenic factor is quite steady over the whole year. We estimated the mass absorption and scattering efficiencies for the factors and they agreed well with earlier observations. Hence, this method could be used to distinguish aerosol source characteristics, at least in fairly simple cases.

  13. Bilinear Factor Matrix Norm Minimization for Robust PCA: Algorithms and Applications.

    PubMed

    Shang, Fanhua; Cheng, James; Liu, Yuanyuan; Luo, Zhi-Quan; Lin, Zhouchen

    2017-09-04

    The heavy-tailed distributions of corrupted outliers and singular values of all channels in low-level vision have proven effective priors for many applications such as background modeling, photometric stereo and image alignment. And they can be well modeled by a hyper-Laplacian. However, the use of such distributions generally leads to challenging non-convex, non-smooth and non-Lipschitz problems, and makes existing algorithms very slow for large-scale applications. Together with the analytic solutions to Lp-norm minimization with two specific values of p, i.e., p=1/2 and p=2/3, we propose two novel bilinear factor matrix norm minimization models for robust principal component analysis. We first define the double nuclear norm and Frobenius/nuclear hybrid norm penalties, and then prove that they are in essence the Schatten-1/2 and 2/3 quasi-norms, respectively, which lead to much more tractable and scalable Lipschitz optimization problems. Our experimental analysis shows that both our methods yield more accurate solutions than original Schatten quasi-norm minimization, even when the number of observations is very limited. Finally, we apply our penalties to various low-level vision problems, e.g. moving object detection, image alignment and inpainting, and show that our methods usually outperform the state-of-the-art methods.

  14. Matrix Management: An Organizational Alternative for Libraries.

    ERIC Educational Resources Information Center

    Johnson, Peggy

    1990-01-01

    Describes various organizational structures and models, presents matrix management as an alternative to traditional hierarchical structures, and suggests matrix management as an appropriate organizational alternative for academic libraries. Benefits that are discussed include increased flexibility, a higher level of professional independence, and…

  15. Matrix precipitation: a general strategy to eliminate matrix interference for pharmaceutical toxic impurities analysis.

    PubMed

    Yang, Xiaojing; Xiong, Xuewu; Cao, Ji; Luan, Baolei; Liu, Yongjun; Liu, Guozhu; Zhang, Lei

    2015-01-30

    Matrix interference, which can lead to false positive/negative results, contamination of injector or separation column, incompatibility between sample solution and the selected analytical instrument, and response inhibition or even quenching, is commonly suffered for the analysis of trace level toxic impurities in drug substance. In this study, a simple matrix precipitation strategy is proposed to eliminate or minimize the above stated matrix interference problems. Generally, a sample of active pharmaceutical ingredients (APIs) is dissolved in an appropriate solvent to achieve the desired high concentration and then an anti-solvent is added to precipitate the matrix substance. As a result, the target analyte is extracted into the mixed solution with very less residual of APIs. This strategy has the characteristics of simple manipulation, high recovery and excellent anti-interference capability. It was found that the precipitation ratio (R, representing the ability to remove matrix substance) and the proportion of solvent (the one used to dissolve APIs) in final solution (P, affecting R and also affecting the method sensitivity) are two important factors of the precipitation process. The correlation between R and P was investigated by performing precipitation with various APIs in different solvent/anti-solvent systems. After a detailed mathematical reasoning process, P=20% was proved to be an effective and robust condition to perform the precipitation strategy. The precipitation method with P=20% can be used as a general strategy for toxic impurity analysis in APIs. Finally, several typical examples are described in this article, where the challenging matrix interference issues have been resolved successfully. Copyright © 2014 Elsevier B.V. All rights reserved.

  16. Organic–inorganic binary mixture matrix for comprehensive laser-desorption ionization mass spectrometric analysis and imaging of medium-size molecules including phospholipids, glycerolipids, and oligosaccharides

    DOE PAGES

    Feenstra, Adam D.; Ames Lab., Ames, IA; O'Neill, Kelly C.; ...

    2016-10-13

    Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) is a widely adopted, versatile technique, especially in high-throughput analysis and imaging. However, matrix-dependent selectivity of analytes is often a severe limitation. In this work, a mixture of organic 2,5-dihydroxybenzoic acid and inorganic Fe 3O 4 nanoparticles is developed as a binary MALDI matrix to alleviate the well-known issue of triacylglycerol (TG) ion suppression by phosphatidylcholine (PC). In application to lipid standards and maize seed cross-sections, the binary matrix not only dramatically reduced the ion suppression of TG, but also efficiently desorbed and ionized a wide variety of lipids such as cationic PC, anionicmore » phosphatidylethanolamine (PE) and phosphatidylinositol (PI), and neutral digalactosyldiacylglycerol (DGDG). The binary matrix was also very efficient for large polysaccharides, which were not detected by either of the individual matrices. As a result, the usefulness of the binary matrix is demonstrated in MS imaging of maize seed sections, successfully visualizing diverse medium-size molecules and acquiring high-quality MS/MS spectra for these compounds.« less

  17. Liarozole inhibits transforming growth factor-β3–mediated extracellular matrix formation in human three-dimensional leiomyoma cultures

    PubMed Central

    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

  18. Assessing the long-range transport of PAH to a sub-Arctic site using positive matrix factorization and potential source contribution function

    NASA Astrophysics Data System (ADS)

    Sofowote, Uwayemi M.; Hung, Hayley; Rastogi, Ankit K.; Westgate, John N.; Deluca, Patrick F.; Su, Yushan; McCarry, Brian E.

    2011-02-01

    Gas-phase and particle-phase atmospheric samples collected in a sparsely populated sub-Arctic environment in the Yukon Territory, Canada were analyzed for a wide range of organic pollutants including polycyclic aromatic hydrocarbons (PAH). Receptor modeling using positive matrix factorization (PMF) was applied to a PAH data set from samples collected between August 2007 and December 2008 to afford four factors. These factors were designated as fossil fuel combustion emissions, particle-phase wood combustion emissions, gas-phase wood combustion emissions, and unburned petroleum/petrogenic emissions. The multiple linear regression-derived average contributions of these factors to the total PAH concentrations were 14% for fossil fuel combustion, 6% for particle-phase wood combustion emissions, 46% for gas-phase wood combustion emissions and 34% for petrogenic emissions. When the total PAH concentrations (defined as the sum of twenty-two PAH) and the PMF-modeled PAH concentrations set were compared, the correlation was excellent ( R2 = 0.97). Ten-day back trajectories starting at four different heights were used in a potential source contribution function analysis (PSCF) to assess the potential source regions of these PAH factors. Mapping the computed PSCF values for the four PMF factors revealed different source regions in the northern hemisphere for each PMF factor. Atmospheric transport of PAH occurred from both relatively short and long distances with both continental (North American) and trans-oceanic (Asian) sources contributing significantly to the total PAH. This study provides evidence of the transport of fossil fuel and wood combustion emissions from Asia, continental North America and northern Europe to sub-Arctic Canada (and by extension to the Canadian Arctic) primarily during cooler (fall-winter) months. This study demonstrates for the first time that the combined PMF-PSCF methodology can be used to identify geographically-disperse PAH source contributors

  19. Robust Programming Problems Based on the Mean-Variance Model Including Uncertainty Factors

    NASA Astrophysics Data System (ADS)

    Hasuike, Takashi; Ishii, Hiroaki

    2009-01-01

    This paper considers robust programming problems based on the mean-variance model including uncertainty sets and fuzzy factors. Since these problems are not well-defined problems due to fuzzy factors, it is hard to solve them directly. Therefore, introducing chance constraints, fuzzy goals and possibility measures, the proposed models are transformed into the deterministic equivalent problems. Furthermore, in order to solve these equivalent problems efficiently, the solution method is constructed introducing the mean-absolute deviation and doing the equivalent transformations.

  20. Pulmonary immunity and extracellular matrix interactions.

    PubMed

    O'Dwyer, David N; Gurczynski, Stephen J; Moore, Bethany B

    2018-04-09

    The lung harbors a complex immune system composed of both innate and adaptive immune cells. Recognition of infection and injury by receptors on lung innate immune cells is crucial for generation of antigen-specific responses by adaptive immune cells. The extracellular matrix of the lung, comprising the interstitium and basement membrane, plays a key role in the regulation of these immune systems. The matrix consists of several hundred assembled proteins that interact to form a bioactive scaffold. This template, modified by enzymes, acts to facilitate cell function and differentiation and changes dynamically with age and lung disease. Herein, we explore relationships between innate and adaptive immunity and the lung extracellular matrix. We discuss the interactions between extracellular matrix proteins, including glycosaminoglycans, with prominent effects on innate immune signaling effectors such as toll-like receptors. We describe the relationship of extracellular matrix proteins with adaptive immunity and leukocyte migration to sites of injury within the lung. Further study of these interactions will lead to greater knowledge of the role of matrix biology in lung immunity. The development of novel therapies for acute and chronic lung disease is dependent on a comprehensive understanding of these complex matrix-immunity interactions. Copyright © 2017 International Society of Matrix Biology. Published by Elsevier B.V. All rights reserved.

  1. Block LU factorization

    NASA Technical Reports Server (NTRS)

    Demmel, James W.; Higham, Nicholas J.; Schreiber, Robert S.

    1992-01-01

    Many of the currently popular 'block algorithms' are scalar algorithms in which the operations have been grouped and reordered into matrix operations. One genuine block algorithm in practical use is block LU factorization, and this has recently been shown by Demmel and Higham to be unstable in general. It is shown here that block LU factorization is stable if A is block diagonally dominant by columns. Moreover, for a general matrix the level of instability in block LU factorization can be founded in terms of the condition number kappa(A) and the growth factor for Gaussian elimination without pivoting. A consequence is that block LU factorization is stable for a matrix A that is symmetric positive definite or point diagonally dominant by rows or columns as long as A is well-conditioned.

  2. Matrix metalloproteinases and epidermal wound repair.

    PubMed

    Martins, Vera L; Caley, Matthew; O'Toole, Edel A

    2013-02-01

    Epidermal wound healing is a complex and highly coordinated process where several different cell types and molecules, such as growth factors and extracellular matrix (ECM) components, play an important role. Among the many proteins that are essential for the restoration of tissue integrity is the metalloproteinase (MMP) family. MMPs can act on ECM and non-ECM components affecting degradation and modulation of the ECM, growth-factor activation and cell-cell and cell-matrix signalling. MMPs are secreted by different cell types such as keratinocytes, fibroblasts and inflammatory cells at different stages and locations during wound healing, thereby regulating this process in a very coordinated and controlled way. In this article, we review the role of MMPs and their inhibitors (TIMPs), as well as the disintegrin and metalloproteinase with the thrombospondin motifs (ADAMs) family, in epithelial wound repair.

  3. Injury Surveillance Among NASA Astronauts Using the Barell Injury Diagnosis Matrix

    NASA Technical Reports Server (NTRS)

    Murray, J. D.; Laughlin, M. S.; Eudy, D. L.; Wear, M. L.; VanBaalen, M. G.

    2014-01-01

    Astronauts perform physically demanding tasks and risk incurring musculoskeletal injuries during both groundbased training and missions. Increased injury rates throughout the history of the U.S. space program have been attributed to numerous factors, including an aging astronaut corps, increased Weightless Environment Training Facility (WETF) and Neutral Buoyancy Laboratory (NBL) training to construct the International Space Station, and improved clinical operations that promote injury prevention and reporting. With NASA program changes through the years (including retirement of the Shuttle program) and an improved training environment (including a new astronaut gym), there is no surveillance program to systematically track injury rates. A limited number of research projects have been conducted over the past 20 years to evaluate musculoskeletal injuries: (1) to evaluate orthopedic injuries from 1987 to 1995, (2) to describe upper extremity injuries, (3) to evaluate EVA spacesuit training related injuries, and (4) to evaluate in-flight musculoskeletal injuries. Nevertheless, there has been no consistently performed comprehensive assessment of musculoskeletal injuries among astronauts. The Barell Injury Diagnosis Matrix was introduced at the 2001 meeting of the International Collaborative Effort (ICE) on Injury Statistics. The Matrix proposes a standardized method of classifying body region by nature of injury. Diagnoses are coded using the International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM) coding system. The purpose of this study is to assess the usefulness and complexity of the Barell Injury Diagnosis Matrix to classify and track musculoskeletal injuries among NASA astronauts.

  4. Understanding the Evolution and Stability of the G-Matrix

    PubMed Central

    Arnold, Stevan J.; Bürger, Reinhard; Hohenlohe, Paul A.; Ajie, Beverley C.; Jones, Adam G.

    2011-01-01

    The G-matrix summarizes the inheritance of multiple, phenotypic traits. The stability and evolution of this matrix are important issues because they affect our ability to predict how the phenotypic traits evolve by selection and drift. Despite the centrality of these issues, comparative, experimental, and analytical approaches to understanding the stability and evolution of the G-matrix have met with limited success. Nevertheless, empirical studies often find that certain structural features of the matrix are remarkably constant, suggesting that persistent selection regimes or other factors promote stability. On the theoretical side, no one has been able to derive equations that would relate stability of the G-matrix to selection regimes, population size, migration, or to the details of genetic architecture. Recent simulation studies of evolving G-matrices offer solutions to some of these problems, as well as a deeper, synthetic understanding of both the G-matrix and adaptive radiations. PMID:18973631

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

    PubMed

    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.

  6. MAGP1, the extracellular matrix, and metabolism

    PubMed Central

    Craft, Clarissa S

    2014-01-01

    Adipose tissue and the extracellular matrix were once considered passive players in regulating physiological processes. Now, both entities are acknowledged for their capacity to engage signal transduction pathways, and for their involvement in maintaining normal tissue homeostasis. We recently published a series of studies that identified a novel mechanism whereby an extracellular matrix molecule, MAGP1 (microfibril associated glycoprotein 1), can regulate energy metabolism in adipose tissue. MAGP1 is a component of extracellular microfibrils and plays a supportive role in maintaining thermoregulation by indirectly regulating expression of the thermogenic uncoupling proteins (UCPs). The focus of this commentary is to draw attention to the role of the extracellular matrix in regulating the bioavailability of signaling molecules, like transforming growth factor β (TGFβ), and exemplify that a better understanding of the extracellular matrix's biological properties could unveil a new source of therapeutic targets for metabolic diseases. PMID:26167404

  7. MAGP1, the extracellular matrix, and metabolism.

    PubMed

    Craft, Clarissa S

    2015-01-01

    Adipose tissue and the extracellular matrix were once considered passive players in regulating physiological processes. Now, both entities are acknowledged for their capacity to engage signal transduction pathways, and for their involvement in maintaining normal tissue homeostasis. We recently published a series of studies that identified a novel mechanism whereby an extracellular matrix molecule, MAGP1 (microfibril associated glycoprotein 1), can regulate energy metabolism in adipose tissue. MAGP1 is a component of extracellular microfibrils and plays a supportive role in maintaining thermoregulation by indirectly regulating expression of the thermogenic uncoupling proteins (UCPs). The focus of this commentary is to draw attention to the role of the extracellular matrix in regulating the bioavailability of signaling molecules, like transforming growth factor β (TGFβ), and exemplify that a better understanding of the extracellular matrix's biological properties could unveil a new source of therapeutic targets for metabolic diseases.

  8. Physical, Spatial, and Molecular Aspects of Extracellular Matrix of In Vivo Niches and Artificial Scaffolds Relevant to Stem Cells Research

    PubMed Central

    Akhmanova, Maria; Osidak, Egor; Domogatsky, Sergey; Rodin, Sergey; Domogatskaya, Anna

    2015-01-01

    Extracellular matrix can influence stem cell choices, such as self-renewal, quiescence, migration, proliferation, phenotype maintenance, differentiation, or apoptosis. Three aspects of extracellular matrix were extensively studied during the last decade: physical properties, spatial presentation of adhesive epitopes, and molecular complexity. Over 15 different parameters have been shown to influence stem cell choices. Physical aspects include stiffness (or elasticity), viscoelasticity, pore size, porosity, amplitude and frequency of static and dynamic deformations applied to the matrix. Spatial aspects include scaffold dimensionality (2D or 3D) and thickness; cell polarity; area, shape, and microscale topography of cell adhesion surface; epitope concentration, epitope clustering characteristics (number of epitopes per cluster, spacing between epitopes within cluster, spacing between separate clusters, cluster patterns, and level of disorder in epitope arrangement), and nanotopography. Biochemical characteristics of natural extracellular matrix molecules regard diversity and structural complexity of matrix molecules, affinity and specificity of epitope interaction with cell receptors, role of non-affinity domains, complexity of supramolecular organization, and co-signaling by growth factors or matrix epitopes. Synergy between several matrix aspects enables stem cells to retain their function in vivo and may be a key to generation of long-term, robust, and effective in vitro stem cell culture systems. PMID:26351461

  9. [In Vitro and In Vivo Biocompatibility of a Novel, 3-Dimensional Cellulose Matrix Structure].

    PubMed

    Dunda, S E; Ranker, M; Pallua, N; Machens, H-G; Ravichandran, A; Schantz, J-T

    2015-12-01

    Biological and physical characteristics of matrices are one essential factor in creating bioartificial tissue. In this study, a new 3-dimensional cellulose matrix (Xellulin(®)) was tested in terms of biocompatibility and applicability for tissue engineering in vitro and in vivo. The tested matrix Xellulin(®) is a natural hydrological gel-matrix containing bacterial cellulose and water. To evaluate the cell biocompatibilty, cell adherence and proliferation characteristics in vitro, the matrix was cultured with human fibroblasts. Further in vivo studies were carried out by transplanting preadipocytes of 4- to 6-week-old Wistar rats with 3 different conditions: a) Xellulin(®) including 500 000 preadipocytes subcutaneous, b) Xellulin(®) including 500 000 preadipocytes within an in vivo bioreactor chamber, c) Xellulin(®) without cells subcutaneous as control. After explantation on day 14 histomorphological and immunohistochemical evaluations were performed. In vitro study revealed an excellent biocompatibility with good cell adherence of the fibroblasts on the matrix and evidence of cell proliferation and creation of a 3-dimensional cell network. In vivo neocapillarisation could be shown in all groups with evidence of erythrocytes (H/E staining) and endothelial vascular cells (RECA-1-staining). A significantly higher vascular density was shown in vascularised bioreactor group (18.4 vessels/100 000 µm(2) (group b) vs. 8.1 (group a), p<0.05). Cell density was the highest in the vascularised group, but without significant values. No immunogenic reaction to the matrix was noticed. The promising in vitro results concerning cell adherence and proliferation on the tested matrix could be confirmed in vivo with an evidence of 3-dimensional neocapillarisation. Cell survival was higher in the vascularised group, but without significance. Long-term tests (28-42 days) need to be carried out to evaluate long-term cell survival and the matrix stability. Furthermore

  10. Thalidomide Accelerates the Degradation of Extracellular Matrix in Rat Hepatic Cirrhosis via Down-Regulation of Transforming Growth Factor-β1

    PubMed Central

    Meng, Qingshun; Liu, Jie; Wang, Chuanfang

    2015-01-01

    Purpose The degradation of the extracellular matrix has been shown to play an important role in the treatment of hepatic cirrhosis. In this study, the effect of thalidomide on the degradation of extracellular matrix was evaluated in a rat model of hepatic cirrhosis. Materials and Methods Cirrhosis was induced in Wistar rats by intraperitoneal injection of carbon tetrachloride (CCl4) three times weekly for 8 weeks. Then CCl4 was discontinued and thalidomide (100 mg/kg) or its vehicle was administered daily by gavage for 6 weeks. Serum hyaluronic acid, laminin, procollagen type III, and collagen type IV were examined by using a radioimmunoassay. Matrix metalloproteinase-13 (MMP-13), tissue inhibitor of metalloproteinase-1 (TIMP-1), and α-smooth muscle actin (α-SMA) protein in the liver, transforming growth factor β1 (TGF-β1) protein in cytoplasm by using immunohistochemistry and Western blot analysis, and MMP-13, TIMP-1, and TGF-β1 mRNA levels in the liver were studied using reverse transcriptase polymerase chain reaction. Results Liver histopathology was significantly better in rats given thalidomide than in the untreated model group. The levels of TIMP-1 and TGF-β1 mRNA and protein expressions were decreased significantly and MMP-13 mRNA and protein in the liver were significantly elevated in the thalidomide-treated group. Conclusion Thalidomide may exert its effects on the regulation of MMP-13 and TIMP-1 via inhibition of the TGF-β1 signaling pathway, which enhances the degradation of extracellular matrix and accelerates the regression of hepatic cirrhosis in rats. PMID:26446639

  11. Plasma Levels of Matrix Metalloproteinase (MMP)-2, MMP-9 and Tumor Necrosis Factor-α in Chronic Hepatitis C Virus Patients.

    PubMed

    Abdel-Latif, Mohamed S

    2015-01-01

    In chronic HCV infection, pathological accumulation of the extracellular matrix is the main feature of liver fibrosis; that indicates the imbalanced rate of increased matrix synthesis to decreased breakdown of connective tissue proteins. Matrix metalloproteinases (MMPs) play a crucial role in remodeling of extracellular matrix. It is known that expression of MMPs is regulated by Tumor necrosis factor (TNF)-α. Also, levels of TNF-α in liver and serum are increased in chronic HCV patient. Accordingly, this study aimed to correlate the plasma levels of MMP-2, MMP-9 and TNF-α in chronic HCV patients with the pathogenesis of the liver. The current study was conducted on 15 fibrotic liver cases with detectable HCV RNA, 10 HCV cirrhotic liver cases, and 15 control subjects of matched age and sex. Plasma MMP-2, MMP-9 and TNF-α were measured by ELISA. Data revealed that the MMP2, MMP9 and TNF-α levels showed a significant elevation in chronic HCV patients compared to control group (p= 0.001). But, no significant correlation was observed in levels of MMP-2, MMP-9, and TNF-α between fibrotic and cirrhotic cases. MMP-2, MMP-9 and TNF-α showed high reproducibility to differentiate chronic HCV patients from control group. On the contrary, MMP-2, MMP-9 and TNF-α were not able to differentiate fibrotic from cirrhotic liver cases. Thus, MMP-2, MMP-9 and TNF-α could not be correlated with the progression of liver disease. Rather they could be used as prognostic markers of liver fibrosis.

  12. Vascular Canals in Permanent Hyaline Cartilage: Development, Corrosion of Nonmineralized Cartilage Matrix, and Removal of Matrix Degradation Products.

    PubMed

    Gabner, Simone; Häusler, Gabriele; Böck, Peter

    2017-06-01

    Core areas in voluminous pieces of permanent cartilage are metabolically supplied via vascular canals (VCs). We studied cartilage corrosion and removal of matrix degradation products during the development of VCs in nose and rib cartilage of piglets. Conventional staining methods were used for glycosaminoglycans, immunohistochemistry was performed to demonstrate collagens types I and II, laminin, Ki-67, von Willebrand factor, VEGF, macrophage marker MAC387, S-100 protein, MMPs -2,-9,-13,-14, and their inhibitors TIMP1 and TIMP2. VCs derived from connective tissue buds that bulged into cartilage matrix ("perichondrial papillae", PPs). Matrix was corroded at the tips of PPs or resulting VCs. Connective tissue stromata in PPs and VCs comprised an axial afferent blood vessel, peripherally located wide capillaries, fibroblasts, newly synthesized matrix, and residues of corroded cartilage matrix (collagen type II, acidic proteoglycans). Multinucleated chondroclasts were absent, and monocytes/macrophages were not seen outside the blood vessels. Vanishing acidity characterized areas of extracellular matrix degradation ("preresorptive layers"), from where the dismantled matrix components diffused out. Leached-out material stained in an identical manner to intact cartilage matrix. It was detected in the stroma and inside capillaries and associated downstream veins. We conclude that the delicate VCs are excavated by endothelial sprouts and fibroblasts, whilst chondroclasts are specialized to remove high volumes of mineralized cartilage. VCs leading into permanent cartilage can be formed by corrosion or inclusion, but most VCs comprise segments that have developed in either of these ways. Anat Rec, 300:1067-1082, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  13. Informed Source Separation of Atmospheric and Surface Signal Contributions in Shortwave Hyperspectral Imagery using Non-negative Matrix Factorization

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

    Current challenges in Earth remote sensing require improved instrument spectral resolution, spectral coverage, and radiometric accuracy. Hyperspectral instruments, deployed on both aircraft and spacecraft, are a growing class of Earth observing sensors designed to meet these challenges. They collect large amounts of spectral data, allowing thorough characterization of both atmospheric and surface properties. The higher accuracy and increased spectral and spatial resolutions of new imagers require new numerical approaches for processing imagery and separating surface and atmospheric signals. One potential approach is source separation, which allows us to determine the underlying physical causes of observed changes. Improved signal separation will allow hyperspectral instruments to better address key science questions relevant to climate change, including land-use changes, trends in clouds and atmospheric water vapor, and aerosol characteristics. In this work, we investigate a Non-negative Matrix Factorization (NMF) method for the separation of atmospheric and land surface signal sources. NMF offers marked benefits over other commonly employed techniques, including non-negativity, which avoids physically impossible results, and adaptability, which allows the method to be tailored to hyperspectral source separation. We adapt our NMF algorithm to distinguish between contributions from different physically distinct sources by introducing constraints on spectral and spatial variability and by using library spectra to inform separation. We evaluate our NMF algorithm with simulated hyperspectral images as well as hyperspectral imagery from several instruments including, the NASA Airborne Visible/Infrared Imaging Spectrometer (AVIRIS), NASA Hyperspectral Imager for the Coastal Ocean (HICO) and National Ecological Observatory Network (NEON) Imaging Spectrometer.

  14. Source Identification of Polycyclic Aromatic Hydrocarbons by Diagnostic Ratios and Positive Matrix Factorization

    NASA Astrophysics Data System (ADS)

    Dvorska, A.; Jarkovsky, J.; Lammel, G.; Klanova, J.

    2009-04-01

    Although polycyclic aromatic hydrocarbons (PAHs) are also of natural origin, in many regions their environmental concentrations have strongly increased due to human activities. These semivolatile organic compounds are generally formed during incomplete combustion. Other sources include volatilization from unburned petroleum or tire abrasion in road traffic. Among all pollutants PAHs pose the highest human health hazard in Europe (WHO, 2003). A multivariate statistical method, positive matrix factorization (PMF; Paatero, 1997), and diagnostic ratios of individual PAHs (e.g. Yunker et al., 2002) are used for PAH source identification in central Europe. To minimise confounding factors such as differences in volatility, water solubility, adsorption etc., diagnostic ratios should be restricted to PAHs of similar molecular mass (Readman et al., 1987). Furthermore, different reactivities are limiting. Nevertheless, the application of PAH diagnostic ratios is often inconclusive, because substance patterns (profiles) have not been reported for all sources and ranges for various sources overlap. The complete profiles are made use of by statistical methods such as factor analysis, UNMIX and PMF (Tauler et al., 2006). However, these methods can be unreliable, because of incomplete knowledge of source profiles and the analysis' sensitivity to the data distribution. A unique 12-year data set of concentrations of PAHs (16 individual substances, 2 phases, weekly) in air, measured at the regional observatory Košetice, Czech Republic, is examined, together with shorter time series from Leipzig (urban background) and Schwartenberg (subalpine mountain background), Germany. Also, retene and coronene as specific source markers measured in Košetice from 2006 on are included into the analysis. An extensive literature search on PAH emission profiles was conducted. This data set was accomplished by measurements at sites in the Zlínsko region, Czech Republic, which are strongly dominated

  15. Transforming growth factor-beta and Forkhead box O transcription factors as cardiac fibroblast regulators.

    PubMed

    Norambuena-Soto, Ignacio; Núñez-Soto, Constanza; Sanhueza-Olivares, Fernanda; Cancino-Arenas, Nicole; Mondaca-Ruff, David; Vivar, Raul; Díaz-Araya, Guillermo; Mellado, Rosemarie; Chiong, Mario

    2017-05-23

    Fibroblasts play several homeostatic roles, including electrical coupling, paracrine signaling and tissue repair after injury. Fibroblasts have low secretory activity. However, in response to injury, they differentiate to myofibroblasts. These cells have an increased extracellular matrix synthesis and secretion, including collagen fibers, providing stiffness to the tissue. In pathological conditions myofibroblasts became resistant to apoptosis, remaining in the tissue, causing excessive extracellular matrix secretion and deposition, which contributes to the progressive tissue remodeling. Therefore, increased myofibroblast content within damaged tissue is a characteristic hallmark of heart, lung, kidney and liver fibrosis. Recently, it was described that cardiac fibroblast to myofibroblast differentiation is triggered by the transforming growth factor β1 (TGF-β1) through a Smad-independent activation of Forkhead box O (FoxO). FoxO proteins are a transcription factor family that includes FoxO1, FoxO3, FoxO4 and FoxO6. In several cells types, they play an important role in cell cycle arrest, oxidative stress resistance, cell survival, energy metabolism, and cell death. Here, we review the role of FoxO family members on the regulation of cardiac fibroblast proliferation and differentiation.

  16. Hypoxic Regulation of Functional Extracellular Matrix Elaboration by Nucleus Pulposus Cells in Long-Term Agarose Culture

    PubMed Central

    Gorth, Deborah J; Lothstein, Katherine E; Chiaro, Joseph A; Farrell, Megan J; Dodge, George R; Elliott, Dawn M; Malhotra, Neil R; Mauck, Robert L; Smith, Lachlan J

    2015-01-01

    Degeneration of the intervertebral discs is strongly implicated as a cause of low back pain. Since current treatments for discogenic low back pain show poor long-term efficacy, a number of new, biological strategies are being pursued. For such therapies to succeed, it is critical that they be validated in conditions that mimic the unique biochemical microenvironment of the nucleus pulposus (NP), which include low oxygen tension. Therefore, the objective of this study was to investigate the effects of oxygen tension on NP cell functional extracellular matrix elaboration in 3D culture. Bovine NP cells were encapsulated in agarose constructs and cultured for 14 or 42 days in either 20% or 2% oxygen in defined media containing transforming growth factor beta-3. At each time point, extracellular matrix composition, biomechanics and mRNA expression of key phenotypic markers were evaluated. Results showed that while bulk mechanics and composition were largely independent of oxygen level, low oxygen promoted improved restoration of the NP phenotype, higher mRNA expression of extracellular matrix and NP specific markers, and more uniform matrix elaboration. These findings indicate that culture under physiological oxygen levels is an important consideration for successful development of cell and growth factor-based regenerative strategies for the disc. PMID:25640328

  17. Convex Banding of the Covariance Matrix.

    PubMed

    Bien, Jacob; Bunea, Florentina; Xiao, Luo

    2016-01-01

    We introduce a new sparse estimator of the covariance matrix for high-dimensional models in which the variables have a known ordering. Our estimator, which is the solution to a convex optimization problem, is equivalently expressed as an estimator which tapers the sample covariance matrix by a Toeplitz, sparsely-banded, data-adaptive matrix. As a result of this adaptivity, the convex banding estimator enjoys theoretical optimality properties not attained by previous banding or tapered estimators. In particular, our convex banding estimator is minimax rate adaptive in Frobenius and operator norms, up to log factors, over commonly-studied classes of covariance matrices, and over more general classes. Furthermore, it correctly recovers the bandwidth when the true covariance is exactly banded. Our convex formulation admits a simple and efficient algorithm. Empirical studies demonstrate its practical effectiveness and illustrate that our exactly-banded estimator works well even when the true covariance matrix is only close to a banded matrix, confirming our theoretical results. Our method compares favorably with all existing methods, in terms of accuracy and speed. We illustrate the practical merits of the convex banding estimator by showing that it can be used to improve the performance of discriminant analysis for classifying sound recordings.

  18. Convex Banding of the Covariance Matrix

    PubMed Central

    Bien, Jacob; Bunea, Florentina; Xiao, Luo

    2016-01-01

    We introduce a new sparse estimator of the covariance matrix for high-dimensional models in which the variables have a known ordering. Our estimator, which is the solution to a convex optimization problem, is equivalently expressed as an estimator which tapers the sample covariance matrix by a Toeplitz, sparsely-banded, data-adaptive matrix. As a result of this adaptivity, the convex banding estimator enjoys theoretical optimality properties not attained by previous banding or tapered estimators. In particular, our convex banding estimator is minimax rate adaptive in Frobenius and operator norms, up to log factors, over commonly-studied classes of covariance matrices, and over more general classes. Furthermore, it correctly recovers the bandwidth when the true covariance is exactly banded. Our convex formulation admits a simple and efficient algorithm. Empirical studies demonstrate its practical effectiveness and illustrate that our exactly-banded estimator works well even when the true covariance matrix is only close to a banded matrix, confirming our theoretical results. Our method compares favorably with all existing methods, in terms of accuracy and speed. We illustrate the practical merits of the convex banding estimator by showing that it can be used to improve the performance of discriminant analysis for classifying sound recordings. PMID:28042189

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

    NASA Astrophysics Data System (ADS)

    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.

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

    PubMed

    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.

  1. Modeling fatigue crack growth in cross ply titanium matrix composites

    NASA Technical Reports Server (NTRS)

    Bakuckas, J. G., Jr.; Johnson, W. S.

    1993-01-01

    In this study, the fatigue crack growth behavior of fiber bridging matrix cracks in cross-ply SCS-6/Ti-15-3 and SCS-6/Timetal-21S laminates containing center holes was investigated. Experimental observations revealed that matrix cracking was far more extensive and wide spread in the SCS-6/Ti-15-3 laminates compared to that in the SCS-6/Timetal-21S laminates. In addition, the fatigue life of the SCS-6/Ti-15-3 laminates was significantly longer than that of the SCS-6/Timetal-21S laminates. The matrix cracking observed in both material systems was analyzed using a fiber bridging (FB) model which was formulated using the boundary correction factors and weight functions for center hole specimen configurations. A frictional shear stress is assumed in the FB model and was used as a curve fitting parameter to model matrix crack growth data. The higher frictional shear stresses calculated in the SCS-6/Timetal-21S laminates resulted in lower stress intensity factors in the matrix and higher axial stresses in the fibers compared to those in the SCS-6/Ti-15-3 laminates at the same applied stress levels.

  2. Nonnegative matrix factorization: a blind sources separation method to extract content of fluorophores mixture media

    NASA Astrophysics Data System (ADS)

    Zhou, Kenneth J.; Chen, Jun

    2014-03-01

    The fluorophores of malignant human breast cells change their compositions that may be exposed in the fluorescence spectroscopy and blind source separation method. The content of the fluorophores mixture media such as tryptophan, collagen, elastin, NADH, and flavin were varied according to the cancer development. The native fluorescence spectra of these key fluorophores mixture media excited by the selective excitation wavelengths of 300 nm and 340 nm were analyzed using a blind source separation method: Nonnegative Matrix Factorization (NMF). The results show that the contribution from tryptophan, NADH and flavin to the fluorescence spectra of the mixture media is proportional to the content of each fluorophore. These data present a possibility that native fluorescence spectra decomposed by NMF can be used as potential native biomarkers for cancer detection evaluation of the cancer.

  3. A micromechanics-based strength prediction methodology for notched metal matrix composites

    NASA Technical Reports Server (NTRS)

    Bigelow, C. A.

    1992-01-01

    An analytical micromechanics based strength prediction methodology was developed to predict failure of notched metal matrix composites. The stress-strain behavior and notched strength of two metal matrix composites, boron/aluminum (B/Al) and silicon-carbide/titanium (SCS-6/Ti-15-3), were predicted. The prediction methodology combines analytical techniques ranging from a three dimensional finite element analysis of a notched specimen to a micromechanical model of a single fiber. In the B/Al laminates, a fiber failure criteria based on the axial and shear stress in the fiber accurately predicted laminate failure for a variety of layups and notch-length to specimen-width ratios with both circular holes and sharp notches when matrix plasticity was included in the analysis. For the SCS-6/Ti-15-3 laminates, a fiber failure based on the axial stress in the fiber correlated well with experimental results for static and post fatigue residual strengths when fiber matrix debonding and matrix cracking were included in the analysis. The micromechanics based strength prediction methodology offers a direct approach to strength prediction by modeling behavior and damage on a constituent level, thus, explicitly including matrix nonlinearity, fiber matrix debonding, and matrix cracking.

  4. A micromechanics-based strength prediction methodology for notched metal-matrix composites

    NASA Technical Reports Server (NTRS)

    Bigelow, C. A.

    1993-01-01

    An analytical micromechanics-based strength prediction methodology was developed to predict failure of notched metal matrix composites. The stress-strain behavior and notched strength of two metal matrix composites, boron/aluminum (B/Al) and silicon-carbide/titanium (SCS-6/Ti-15-3), were predicted. The prediction methodology combines analytical techniques ranging from a three-dimensional finite element analysis of a notched specimen to a micromechanical model of a single fiber. In the B/Al laminates, a fiber failure criteria based on the axial and shear stress in the fiber accurately predicted laminate failure for a variety of layups and notch-length to specimen-width ratios with both circular holes and sharp notches when matrix plasticity was included in the analysis. For the SCS-6/Ti-15-3 laminates, a fiber failure based on the axial stress in the fiber correlated well with experimental results for static and postfatigue residual strengths when fiber matrix debonding and matrix cracking were included in the analysis. The micromechanics-based strength prediction methodology offers a direct approach to strength prediction by modeling behavior and damage on a constituent level, thus, explicitly including matrix nonlinearity, fiber matrix debonding, and matrix cracking.

  5. Non-Abelian integrable hierarchies: matrix biorthogonal polynomials and perturbations

    NASA Astrophysics Data System (ADS)

    Ariznabarreta, Gerardo; García-Ardila, Juan C.; Mañas, Manuel; Marcellán, Francisco

    2018-05-01

    In this paper, Geronimus–Uvarov perturbations for matrix orthogonal polynomials on the real line are studied and then applied to the analysis of non-Abelian integrable hierarchies. The orthogonality is understood in full generality, i.e. in terms of a nondegenerate continuous sesquilinear form, determined by a quasidefinite matrix of bivariate generalized functions with a well-defined support. We derive Christoffel-type formulas that give the perturbed matrix biorthogonal polynomials and their norms in terms of the original ones. The keystone for this finding is the Gauss–Borel factorization of the Gram matrix. Geronimus–Uvarov transformations are considered in the context of the 2D non-Abelian Toda lattice and noncommutative KP hierarchies. The interplay between transformations and integrable flows is discussed. Miwa shifts, τ-ratio matrix functions and Sato formulas are given. Bilinear identities, involving Geronimus–Uvarov transformations, first for the Baker functions, then secondly for the biorthogonal polynomials and its second kind functions, and finally for the τ-ratio matrix functions, are found.

  6. Matrix product operators, matrix product states, and ab initio density matrix renormalization group algorithms

    NASA Astrophysics Data System (ADS)

    Chan, Garnet Kin-Lic; Keselman, Anna; Nakatani, Naoki; Li, Zhendong; White, Steven R.

    2016-07-01

    Current descriptions of the ab initio density matrix renormalization group (DMRG) algorithm use two superficially different languages: an older language of the renormalization group and renormalized operators, and a more recent language of matrix product states and matrix product operators. The same algorithm can appear dramatically different when written in the two different vocabularies. In this work, we carefully describe the translation between the two languages in several contexts. First, we describe how to efficiently implement the ab initio DMRG sweep using a matrix product operator based code, and the equivalence to the original renormalized operator implementation. Next we describe how to implement the general matrix product operator/matrix product state algebra within a pure renormalized operator-based DMRG code. Finally, we discuss two improvements of the ab initio DMRG sweep algorithm motivated by matrix product operator language: Hamiltonian compression, and a sum over operators representation that allows for perfect computational parallelism. The connections and correspondences described here serve to link the future developments with the past and are important in the efficient implementation of continuing advances in ab initio DMRG and related algorithms.

  7. Matrix product operators, matrix product states, and ab initio density matrix renormalization group algorithms.

    PubMed

    Chan, Garnet Kin-Lic; Keselman, Anna; Nakatani, Naoki; Li, Zhendong; White, Steven R

    2016-07-07

    Current descriptions of the ab initio density matrix renormalization group (DMRG) algorithm use two superficially different languages: an older language of the renormalization group and renormalized operators, and a more recent language of matrix product states and matrix product operators. The same algorithm can appear dramatically different when written in the two different vocabularies. In this work, we carefully describe the translation between the two languages in several contexts. First, we describe how to efficiently implement the ab initio DMRG sweep using a matrix product operator based code, and the equivalence to the original renormalized operator implementation. Next we describe how to implement the general matrix product operator/matrix product state algebra within a pure renormalized operator-based DMRG code. Finally, we discuss two improvements of the ab initio DMRG sweep algorithm motivated by matrix product operator language: Hamiltonian compression, and a sum over operators representation that allows for perfect computational parallelism. The connections and correspondences described here serve to link the future developments with the past and are important in the efficient implementation of continuing advances in ab initio DMRG and related algorithms.

  8. Efficient Matrix Models for Relational Learning

    DTIC Science & Technology

    2009-10-01

    74 4.5.3 Comparison to pLSI- pHITS . . . . . . . . . . . . . . . . . . . . 76 5 Hierarchical Bayesian Collective...Behaviour of Newton vs. Stochastic Newton on a three-factor model. 4.5.3 Comparison to pLSI- pHITS Caveat: Collective Matrix Factorization makes no guarantees...leads to better results; and another where a co-clustering model, pLSI- pHITS , has the advantage. pLSI- pHITS [24] is a relational clustering technique

  9. Design and characterization of a composite material based on Sr(II)-loaded clay nanotubes included within a biopolymer matrix.

    PubMed

    Del Buffa, Stefano; Bonini, Massimo; Ridi, Francesca; Severi, Mirko; Losi, Paola; Volpi, Silvia; Al Kayal, Tamer; Soldani, Giorgio; Baglioni, Piero

    2015-06-15

    This paper reports on the preparation, characterization, and cytotoxicity of a hybrid nanocomposite material made of Sr(II)-loaded Halloysite nanotubes included within a biopolymer (3-polyhydroxybutyrate-co-3-hydroxyvalerate) matrix. The Sr(II)-loaded inorganic scaffold is intended to provide mechanical resistance, multi-scale porosity, and to favor the in-situ regeneration of bone tissue thanks to its biocompatibility and bioactivity. The interaction of the hybrid system with the physiological environment is mediated by the biopolymer coating, which acts as a binder, as well as a diffusional barrier to the Sr(II) release. The degradation of the polymer progressively leads to the exposure of the Sr(II)-loaded Halloysite scaffold, tuning its interaction with osteogenic cells. The in vitro biocompatibility of the composite was demonstrated by cytotoxicity tests on L929 fibroblast cells. The results indicate that this composite material could be of interest for multiple strategies in the field of bone tissue engineering. Copyright © 2015 Elsevier Inc. All rights reserved.

  10. Matrix metalloproteinase 2 (MMP-2) levels are increased in active acromegaly patients.

    PubMed

    Karci, Alper Cagri; Canturk, Zeynep; Tarkun, Ilhan; Cetinarslan, Berrin

    2017-07-01

    During follow-up of acromegaly patients, there is a discordance rate of 30% between the measurements of growth hormone and insulin-like growth factor-1 levels. Further tests are required to determine disease activity in patients with discordant results. This study was planned to investigate an association of serum levels of matrix metalloproteinase-2, matrix metalloproteinase-9, and cathepsin B with disease activity in acromegaly patients. In this study, 64 acromegaly patients followed in our clinic were divided into two groups according to the 2010 consensus criteria for cure of acromegaly as patients with active disease (n = 24) and patients with controlled disease (n = 40). Serum matrix metalloproteinase-2, matrix metalloproteinase-9, and cathepsin B levels were measured by the enzyme-linked immunosorbent assay method. The mean serum matrix metalloproteinase-2 level was significantly higher in the active acromegaly patients than in the controlled acromegaly patients (150.1 ± 54.5 ng/mL vs. 100.2 ± 44.6 ng/mL; p < 0.0001). There was no significant difference between the active and controlled acromegaly patients regarding serum matrix metalloproteinase-9 and cathepsin B levels (p = 0.205 and p = 0.598, respectively). Serum matrix metalloproteinase-2 levels of 118.3 ng/mL and higher had a sensitivity of 75% and a specificity of 77.5% in determining active disease. The risk of active acromegaly was 3.3 fold higher in the patients with a matrix metalloproteinase-2 level of >118.3 ng/mL than in the patients with a matrix metalloproteinase-2 level of <118.3 ng/mL. In this study, serum matrix metalloproteinase-2 level is increased in the active acromegaly patients and a threshold value in determining active disease was defined for serum matrix metalloproteinase-2 level. This study is the first to compare acromegaly patients having active or controlled disease in terms of matrix metalloproteinase-2 and matrix metalloproteinase-9

  11. Superfund Chemical Data Matrix (SCDM) Query - Popup

    EPA Pesticide Factsheets

    This site allows you to to easily query the Superfund Chemical Data Matrix (SCDM) and generate a list of the corresponding Hazardous Ranking System (HRS) factor values, benchmarks, and data elements that you need.

  12. Human umbilical cord derived matrix: A scaffold suitable for tissue engineering application.

    PubMed

    Dan, Pan; Velot, Émilie; Mesure, Benjamin; Groshenry, Guillaume; Bacharouche, Jalal; Decot, Véronique; Menu, Patrick

    2017-01-01

    Human tissue derived natural extracellular matrix (ECM) has great potential in tissue engineering. We sought to isolate extracellular matrix derived from human umbilical cord and test its potential in tissue engineering. An enzymatic method was applied to isolate and solubilized complete human umbilical cord derived matrix (hUCM). The obtained solution was analyzed for growth factors, collagen and residual DNA contents, then used to coat 2D and 3D surfaces for cell culture application. The hUCM was successfully isolated with trypsin digestion to acquire a solution containing various growth factors and collagen but no residual DNA. This hUCM solution can form a coating on 2D and 3D substrates suitable cell culture. We developed a new matrix derived from human source that can be further used in tissue engineering.

  13. The Lehmer Matrix and Its Recursive Analogue

    DTIC Science & Technology

    2010-01-01

    LU factorization of matrix A by considering det A = det U = ∏n i=1 2i−1 i2 . The nth Catalan number is given in terms of binomial coefficients by Cn...for failing to comply with a collection of information if it does not display a currently valid OMB control number . 1. REPORT DATE 2010 2. REPORT...TYPE 3. DATES COVERED 00-00-2010 to 00-00-2010 4. TITLE AND SUBTITLE The Lehmer matrix and its recursive analogue 5a. CONTRACT NUMBER 5b

  14. Field-scale effective matrix diffusion coefficient for fractured rock: results from literature survey.

    PubMed

    Zhou, Quanlin; Liu, Hui-Hai; Molz, Fred J; Zhang, Yingqi; Bodvarsson, Gudmundur S

    2007-08-15

    Matrix diffusion is an important mechanism for solute transport in fractured rock. We recently conducted a literature survey on the effective matrix diffusion coefficient, D(m)(e), a key parameter for describing matrix diffusion processes at the field scale. Forty field tracer tests at 15 fractured geologic sites were surveyed and selected for the study, based on data availability and quality. Field-scale D(m)(e) values were calculated, either directly using data reported in the literature, or by reanalyzing the corresponding field tracer tests. The reanalysis was conducted for the selected tracer tests using analytic or semi-analytic solutions for tracer transport in linear, radial, or interwell flow fields. Surveyed data show that the scale factor of the effective matrix diffusion coefficient (defined as the ratio of D(m)(e) to the lab-scale matrix diffusion coefficient, D(m), of the same tracer) is generally larger than one, indicating that the effective matrix diffusion coefficient in the field is comparatively larger than the matrix diffusion coefficient at the rock-core scale. This larger value can be attributed to the many mass-transfer processes at different scales in naturally heterogeneous, fractured rock systems. Furthermore, we observed a moderate, on average trend toward systematic increase in the scale factor with observation scale. This trend suggests that the effective matrix diffusion coefficient is likely to be statistically scale-dependent. The scale-factor value ranges from 0.5 to 884 for observation scales from 5 to 2000 m. At a given scale, the scale factor varies by two orders of magnitude, reflecting the influence of differing degrees of fractured rock heterogeneity at different geologic sites. In addition, the surveyed data indicate that field-scale longitudinal dispersivity generally increases with observation scale, which is consistent with previous studies. The scale-dependent field-scale matrix diffusion coefficient (and dispersivity

  15. Scleraxis is required for cell lineage differentiation and extracellular matrix remodeling during murine heart valve formation in vivo.

    PubMed

    Levay, Agata K; Peacock, Jacqueline D; Lu, Yinhui; Koch, Manuel; Hinton, Robert B; Kadler, Karl E; Lincoln, Joy

    2008-10-24

    Heart valve structures, derived from mesenchyme precursor cells, are composed of differentiated cell types and extracellular matrix arranged to facilitate valve function. Scleraxis (scx) is a transcription factor required for tendon cell differentiation and matrix organization. This study identified high levels of scx expression in remodeling heart valve structures at embryonic day 15.5 through postnatal stages using scx-GFP reporter mice and determined the in vivo function using mice null for scx. Scx(-/-) mice display significantly thickened heart valve structures from embryonic day 17.5, and valves from mutant mice show alterations in valve precursor cell differentiation and matrix organization. This is indicated by decreased expression of the tendon-related collagen type XIV, increased expression of cartilage-associated genes including sox9, as well as persistent expression of mesenchyme cell markers including msx1 and snai1. In addition, ultrastructure analysis reveals disarray of extracellular matrix and collagen fiber organization within the valve leaflet. Thickened valve structures and increased expression of matrix remodeling genes characteristic of human heart valve disease are observed in juvenile scx(-/-) mice. In addition, excessive collagen deposition in annular structures within the atrioventricular junction is observed. Collectively, our studies have identified an in vivo requirement for scx during valvulogenesis and demonstrate its role in cell lineage differentiation and matrix distribution in remodeling valve structures.

  16. Regulation of extracellular matrix vesicles via rapid responses to steroid hormones during endochondral bone formation.

    PubMed

    Asmussen, Niels; Lin, Zhao; McClure, Michael J; Schwartz, Zvi; Boyan, Barbara D

    2017-12-09

    Endochondral bone formation is a precise and highly ordered process whose exact regulatory framework is still being elucidated. Multiple regulatory pathways are known to be involved. In some cases, regulation impacts gene expression, resulting in changes in chondrocyte phenotypic expression and extracellular matrix synthesis. Rapid regulatory mechanisms are also involved, resulting in release of enzymes, factors and micro RNAs stored in extracellular matrisomes called matrix vesicles. Vitamin D metabolites modulate endochondral development via both genomic and rapid membrane-associated signaling pathways. 1α,25-dihydroxyvitamin D3 [1α,25(OH) 2 D 3 ] acts through the vitamin D receptor (VDR) and a membrane associated receptor, protein disulfide isomerase A3 (PDIA3). 24R,25-dihydroxyvitamin D3 [24R,25(OH) 2 D 3 ] affects primarily chondrocytes in the resting zone (RC) of the growth plate, whereas 1α,25(OH) 2 D 3 affects cells in the prehypertrophic and upper hypertrophic cell zones (GC). This includes genomically directing the cells to produce matrix vesicles with zone specific characteristics. In addition, vitamin D metabolites produced by the cells interact directly with the matrix vesicle membrane via rapid signal transduction pathways, modulating their activity in the matrix. The matrix vesicle payload is able to rapidly impact the extracellular matrix via matrix processing enzymes as well as providing a feedback mechanism to the cells themselves via the contained micro RNAs. Copyright © 2017. Published by Elsevier Inc.

  17. The matrix exponential in transient structural analysis

    NASA Technical Reports Server (NTRS)

    Minnetyan, Levon

    1987-01-01

    The primary usefulness of the presented theory is in the ability to represent the effects of high frequency linear response with accuracy, without requiring very small time steps in the analysis of dynamic response. The matrix exponential contains a series approximation to the dynamic model. However, unlike the usual analysis procedure which truncates the high frequency response, the approximation in the exponential matrix solution is in the time domain. By truncating the series solution to the matrix exponential short, the solution is made inaccurate after a certain time. Yet, up to that time the solution is extremely accurate, including all high frequency effects. By taking finite time increments, the exponential matrix solution can compute the response very accurately. Use of the exponential matrix in structural dynamics is demonstrated by simulating the free vibration response of multi degree of freedom models of cantilever beams.

  18. NLTE steady-state response matrix method.

    NASA Astrophysics Data System (ADS)

    Faussurier, G.; More, R. M.

    2000-05-01

    A connection between atomic kinetics and non-equilibrium thermodynamics has been recently established by using a collisional-radiative model modified to include line absorption. The calculated net emission can be expressed as a non-local thermodynamic equilibrium (NLTE) symmetric response matrix. In the paper, this connection is extended to both cases of the average-atom model and the Busquet's model (RAdiative-Dependent IOnization Model, RADIOM). The main properties of the response matrix still remain valid. The RADIOM source function found in the literature leads to a diagonal response matrix, stressing the absence of any frequency redistribution among the frequency groups at this order of calculation.

  19. Health-related quality of life and hand eczema--a comparison of two instruments, including factor analysis.

    PubMed

    Wallenhammar, Lena-Marie; Nyfjäll, Mats; Lindberg, Magnus; Meding, Birgitta

    2004-06-01

    Hand eczema is a disease of long duration, affecting the individual and society. The purpose of this study of 100 patients (51 females and 49 males) at an occupational dermatology clinic was to investigate whether the generic questionnaire Short Form-36 (SF-36), and the dermatology-specific Dermatology Life Quality Index (DLQI) are appropriate for assessing health-related quality of life (HRQL) in patients with hand eczema, and whether gender differences in HRQL could be detected. HRQL was affected by hand eczema, measured with both SF-36 and DLQI. The SF-36 showed more impaired HRQL for females than for males, in the mental health dimension, whereas no gender-related differences were detected with the DLQI. To compare the instruments we used factor analysis, with a polychoric correlation matrix as input, thus taking the ordinal aspect of the data into account. There was a high correlation between the instruments for physical health, but lower for mental health. In this context our interpretation of the factor analysis is that the SF-36 measures mental health better than the DLQI. The SF-36 therefore appears suitable for use in future studies for measuring HRQL, and gender differences in HRQL, in persons with reported hand eczema.

  20. The School Counseling Program Implementation Survey: Initial Instrument Development and Exploratory Factor Analysis

    ERIC Educational Resources Information Center

    Clemens, Elysia V.; Carey, John C.; Harrington, Karen M.

    2010-01-01

    This article details the initial development of the School Counseling Program Implementation Survey and psychometric results including reliability and factor structure. An exploratory factor analysis revealed a three-factor model that accounted for 54% of the variance of the intercorrelation matrix and a two-factor model that accounted for 47% of…

  1. Auto-Bäcklund transformations for a matrix partial differential equation

    NASA Astrophysics Data System (ADS)

    Gordoa, P. R.; Pickering, A.

    2018-07-01

    We derive auto-Bäcklund transformations, analogous to those of the matrix second Painlevé equation, for a matrix partial differential equation. We also then use these auto-Bäcklund transformations to derive matrix equations involving shifts in a discrete variable, a process analogous to the use of the auto-Bäcklund transformations of the matrix second Painlevé equation to derive a discrete matrix first Painlevé equation. The equations thus derived then include amongst other examples a semidiscrete matrix equation which can be considered to be an extension of this discrete matrix first Painlevé equation. The application of this technique to the auto-Bäcklund transformations of the scalar case of our partial differential equation has not been considered before, and so the results obtained here in this scalar case are also new. Other equations obtained here using this technique include a scalar semidiscrete equation which arises in the case of the second Painlevé equation, and which does not seem to have been thus derived previously.

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

    NASA Astrophysics Data System (ADS)

    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.

  3. Studies of fiber-matrix adhesion on compression strength

    NASA Technical Reports Server (NTRS)

    Bascom, Willard D.; Nairn, John A.; Boll, D. J.

    1991-01-01

    A study was initiated on the effect of the matrix polymer and the fiber matrix bond strength of carbon fiber polymer matrix composites. The work includes tests with micro-composites, single ply composites, laminates, and multi-axial loaded cylinders. The results obtained thus far indicate that weak fiber-matrix adhesion dramatically reduces 0 degree compression strength. Evidence is also presented that the flaws in the carbon fiber that govern compression strength differ from those that determine fiber tensile strength. Examination of post-failure damage in the single ply tests indicates kink banding at the crack tip.

  4. Fibroblast growth factor receptor inhibition induces loss of matrix MCL1 and necrosis in cholangiocarcinoma.

    PubMed

    Kabashima, Ayano; Hirsova, Petra; Bronk, Steven F; Hernandez, Matthew C; Truty, Mark J; Rizvi, Sumera; Kaufmann, Scott H; Gores, Gregory J

    2018-03-08

    Myeloid cell leukemia 1 (MCL1), a prosurvival member of the BCL2 protein family, has a pivotal role in human cholangiocarcinoma (CCA) cell survival. We previously reported that fibroblast growth factor receptor (FGFR) signalling mediates MCL1-dependent survival of CCA cells in vitro and in vivo. However, the mode and mechanisms of cell death in this model were not delineated. Human CCA cell lines were treated with the pan-FGFR inhibitor LY2874455 and the mode of cell death examined by several complementary assays. Mitochondrial oxidative metabolism was examined using a XF24 extracellular flux analyser. The efficiency of FGFR inhibition in patient-derived xenografts (PDX) was also assessed. CCA cells expressed two species of MCL1, a full-length form localised to the outer mitochondrial membrane, and an N terminus-truncated species compartmentalised within the mitochondrial matrix. The pan-FGFR inhibitor LY2874455 induced non-apoptotic cell death in the CCA cell lines associated with cellular depletion of both MCL1 species. The cell death was accompanied by failure of mitochondrial oxidative metabolism and was most consistent with necrosis. Enforced expression of N terminus-truncated MCL1 targeted to the mitochondrial matrix, but not full-length MCL1 targeted to the outer mitochondrial membrane, rescued cell death and mitochondrial function. LY2874455 treatment of PDX-bearing mice was associated with tumour cell loss of MCL1 and cell necrosis. FGFR inhibition induces loss of matrix MCL1, resulting in cell necrosis. These observations support a heretofore unidentified, alternative MCL1 survival function, namely prevention of cell necrosis, and have implications for treatment of human CCA. Herein, we report that therapeutic inhibition of a cell receptor expressed by bile duct cancer cells resulted in the loss of a critical survival protein termed MCL1. Cellular depletion of MCL1 resulted in the death of the cancer cells by a process characterised by cell rupture. Cell

  5. Matrix representations of SOn + 2 in an SOn × SO2 basis and some isoscalar factors for SOn + 2 ⊃ SOn × SO2

    NASA Astrophysics Data System (ADS)

    Pan, Feng; Cao, Yu-Fang

    1992-02-01

    Vector coherent state (VCS) theory is applied to the group chain SOn+2⊇SOn×SO2. Matrix elements of SOn+2 generators in the SOn+2⊇SOn×SO2 basis are derived. A new formula for the evaluation of some isoscalar factors for SOn+2⊇SOn×SO2 with branching multiplicity is derived in the VCS framework. As a simple example, a new expression of some isoscalar factors for SO5⊇SO3×SO2, which involves only 6j coefficients and K-normalization factors, are obtained by using this formula.

  6. Streptococcus pyogenes degrades extracellular matrix in chondrocytes via MMP-13

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Sakurai, Atsuo; Okahashi, Nobuo; Maruyama, Fumito

    2008-08-29

    Group A streptococcus (GAS) causes a wide range of human diseases, including bacterial arthritis. The pathogenesis of arthritis is characterized by synovial proliferation and the destruction of cartilage and subchondral bone in joints. We report here that GAS strain JRS4 invaded a chondrogenic cell line ATDC5 and induced the degradation of the extracellular matrix (ECM), whereas an isogenic mutant of JRS4 lacking a fibronectin-binding protein, SAM1, failed to invade the chondrocytes or degrade the ECM. Reverse transcription-PCR and Western blot analysis revealed that the expression of matrix metalloproteinase (MMP)-13 was strongly elevated during the infection with GAS. A reporter assaymore » revealed that the activation of the AP-1 transcription factor and the phosphorylation of c-Jun terminal kinase participated in MMP-13 expression. These results suggest that MMP-13 plays an important role in the destruction of infected joints during the development of septic arthritis.« less

  7. The Baker-Akhiezer Function and Factorization of the Chebotarev-Khrapkov Matrix

    NASA Astrophysics Data System (ADS)

    Antipov, Yuri A.

    2014-10-01

    A new technique is proposed for the solution of the Riemann-Hilbert problem with the Chebotarev-Khrapkov matrix coefficient {G(t) = α1(t)I + α2(t)Q(t)} , {α1(t), α2(t) in H(L)} , I = diag{1, 1}, Q(t) is a {2×2} zero-trace polynomial matrix. This problem has numerous applications in elasticity and diffraction theory. The main feature of the method is the removal of essential singularities of the solution to the associated homogeneous scalar Riemann-Hilbert problem on the hyperelliptic surface of an algebraic function by means of the Baker-Akhiezer function. The consequent application of this function for the derivation of the general solution to the vector Riemann-Hilbert problem requires the finding of the {ρ} zeros of the Baker-Akhiezer function ({ρ} is the genus of the surface). These zeros are recovered through the solution to the associated Jacobi problem of inversion of abelian integrals or, equivalently, the determination of the zeros of the associated degree-{ρ} polynomial and solution of a certain linear algebraic system of {ρ} equations.

  8. Insights into the key roles of epigenetics in matrix macromolecules-associated wound healing.

    PubMed

    Piperigkou, Zoi; Götte, Martin; Theocharis, Achilleas D; Karamanos, Nikos K

    2017-10-24

    Extracellular matrix (ECM) is a dynamic network of macromolecules, playing a regulatory role in cell functions, tissue regeneration and remodeling. Wound healing is a tissue repair process necessary for the maintenance of the functionality of tissues and organs. This highly orchestrated process is divided into four temporally overlapping phases, including hemostasis, inflammation, proliferation and tissue remodeling. The dynamic interplay between ECM and resident cells exerts its critical role in many aspects of wound healing, including cell proliferation, migration, differentiation, survival, matrix degradation and biosynthesis. Several epigenetic regulatory factors, such as the endogenous non-coding microRNAs (miRNAs), are the drivers of the wound healing response. microRNAs have pivotal roles in regulating ECM composition during wound healing and dermal regeneration. Their expression is associated with the distinct phases of wound healing and they serve as target biomarkers and targets for systematic regulation of wound repair. In this article we critically present the importance of epigenetics with particular emphasis on miRNAs regulating ECM components (i.e. glycoproteins, proteoglycans and matrix proteases) that are key players in wound healing. The clinical relevance of miRNA targeting as well as the delivery strategies designed for clinical applications are also presented and discussed. Copyright © 2017 Elsevier B.V. All rights reserved.

  9. Extending the range of real time density matrix renormalization group simulations

    NASA Astrophysics Data System (ADS)

    Kennes, D. M.; Karrasch, C.

    2016-03-01

    We discuss a few simple modifications to time-dependent density matrix renormalization group (DMRG) algorithms which allow to access larger time scales. We specifically aim at beginners and present practical aspects of how to implement these modifications within any standard matrix product state (MPS) based formulation of the method. Most importantly, we show how to 'combine' the Schrödinger and Heisenberg time evolutions of arbitrary pure states | ψ 〉 and operators A in the evaluation of 〈A〉ψ(t) = 〈 ψ | A(t) | ψ 〉 . This includes quantum quenches. The generalization to (non-)thermal mixed state dynamics 〈A〉ρ(t) =Tr [ ρA(t) ] induced by an initial density matrix ρ is straightforward. In the context of linear response (ground state or finite temperature T > 0) correlation functions, one can extend the simulation time by a factor of two by 'exploiting time translation invariance', which is efficiently implementable within MPS DMRG. We present a simple analytic argument for why a recently-introduced disentangler succeeds in reducing the effort of time-dependent simulations at T > 0. Finally, we advocate the python programming language as an elegant option for beginners to set up a DMRG code.

  10. Metal- and intermetallic-matrix composites for aerospace propulsion and power systems

    NASA Astrophysics Data System (ADS)

    Doychak, J.

    1992-06-01

    Successful development and deployment of metal-matrix composites and intermetallic- matrix composites are critical to reaching the goals of many advanced aerospace propulsion and power development programs. The material requirements are based on the aerospace propulsion and power system requirements, economics, and other factors. Advanced military and civilian aircraft engines will require higher specific strength materials that operate at higher temperatures, and the civilian engines will also require long lifetimes. The specific space propulsion and power applications require hightemperature, high-thermal-conductivity, and high-strength materials. Metal-matrix composites and intermetallic-matrix composites either fulfill or have the potential of fulfilling these requirements.

  11. Constrained low-rank matrix estimation: phase transitions, approximate message passing and applications

    NASA Astrophysics Data System (ADS)

    Lesieur, Thibault; Krzakala, Florent; Zdeborová, Lenka

    2017-07-01

    This article is an extended version of previous work of Lesieur et al (2015 IEEE Int. Symp. on Information Theory Proc. pp 1635-9 and 2015 53rd Annual Allerton Conf. on Communication, Control and Computing (IEEE) pp 680-7) on low-rank matrix estimation in the presence of constraints on the factors into which the matrix is factorized. Low-rank matrix factorization is one of the basic methods used in data analysis for unsupervised learning of relevant features and other types of dimensionality reduction. We present a framework to study the constrained low-rank matrix estimation for a general prior on the factors, and a general output channel through which the matrix is observed. We draw a parallel with the study of vector-spin glass models—presenting a unifying way to study a number of problems considered previously in separate statistical physics works. We present a number of applications for the problem in data analysis. We derive in detail a general form of the low-rank approximate message passing (Low-RAMP) algorithm, that is known in statistical physics as the TAP equations. We thus unify the derivation of the TAP equations for models as different as the Sherrington-Kirkpatrick model, the restricted Boltzmann machine, the Hopfield model or vector (xy, Heisenberg and other) spin glasses. The state evolution of the Low-RAMP algorithm is also derived, and is equivalent to the replica symmetric solution for the large class of vector-spin glass models. In the section devoted to result we study in detail phase diagrams and phase transitions for the Bayes-optimal inference in low-rank matrix estimation. We present a typology of phase transitions and their relation to performance of algorithms such as the Low-RAMP or commonly used spectral methods.

  12. The extracellular matrix in myocardial injury, repair, and remodeling

    PubMed Central

    2017-01-01

    The cardiac extracellular matrix (ECM) not only provides mechanical support, but also transduces essential molecular signals in health and disease. Following myocardial infarction, dynamic ECM changes drive inflammation and repair. Early generation of bioactive matrix fragments activates proinflammatory signaling. The formation of a highly plastic provisional matrix facilitates leukocyte infiltration and activates infarct myofibroblasts. Deposition of matricellular proteins modulates growth factor signaling and contributes to the spatial and temporal regulation of the reparative response. Mechanical stress due to pressure and volume overload and metabolic dysfunction also induce profound changes in ECM composition that contribute to the pathogenesis of heart failure. This manuscript reviews the role of the ECM in cardiac repair and remodeling and discusses matrix-based therapies that may attenuate remodeling while promoting repair and regeneration. PMID:28459429

  13. Matrix Representation of Symmetry Operators in Elementary Crystallography

    ERIC Educational Resources Information Center

    Cody, R. D.

    1972-01-01

    Presents the derivation of rotation and reflection matrix representation of symmetry operators as used in the initial discussion of crystal symmetry in elementary mineralogy at Iowa State University. Includes references and an appended list of matrix representations of the important crystallographic symmetry operators, excluding the trigonal and…

  14. Graphene-Reinforced Metal and Polymer Matrix Composites

    NASA Astrophysics Data System (ADS)

    Kasar, Ashish K.; Xiong, Guoping; Menezes, Pradeep L.

    2018-03-01

    Composites have tremendous applicability due to their excellent capabilities. The performance of composites mainly depends on the reinforcing material applied. Graphene is successful as an efficient reinforcing material due to its versatile as well as superior properties. Even at very low content, graphene can dramatically improve the properties of polymer and metal matrix composites. This article reviews the fabrication followed by mechanical and tribological properties of metal and polymer matrix composites filled with different kinds of graphene, including single-layer, multilayer, and functionalized graphene. Results reported to date in literature indicate that functionalized graphene or graphene oxide-polymer composites are promising materials offering significantly improved strength and frictional properties. A similar trend of improved properties has been observed in case of graphene-metal matrix composites. However, achieving higher graphene loading with uniform dispersion in metal matrix composites remains a challenge. Although graphene-reinforced composites face some challenges, such as understanding the graphene-matrix interaction or fabrication techniques, graphene-reinforced polymer and metal matrix composites have great potential for application in various fields due to their outstanding properties.

  15. Graphene-Reinforced Metal and Polymer Matrix Composites

    NASA Astrophysics Data System (ADS)

    Kasar, Ashish K.; Xiong, Guoping; Menezes, Pradeep L.

    2018-06-01

    Composites have tremendous applicability due to their excellent capabilities. The performance of composites mainly depends on the reinforcing material applied. Graphene is successful as an efficient reinforcing material due to its versatile as well as superior properties. Even at very low content, graphene can dramatically improve the properties of polymer and metal matrix composites. This article reviews the fabrication followed by mechanical and tribological properties of metal and polymer matrix composites filled with different kinds of graphene, including single-layer, multilayer, and functionalized graphene. Results reported to date in literature indicate that functionalized graphene or graphene oxide-polymer composites are promising materials offering significantly improved strength and frictional properties. A similar trend of improved properties has been observed in case of graphene-metal matrix composites. However, achieving higher graphene loading with uniform dispersion in metal matrix composites remains a challenge. Although graphene-reinforced composites face some challenges, such as understanding the graphene-matrix interaction or fabrication techniques, graphene-reinforced polymer and metal matrix composites have great potential for application in various fields due to their outstanding properties.

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

    PubMed

    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.

  17. Probabilistic micromechanics for metal matrix composites

    NASA Astrophysics Data System (ADS)

    Engelstad, S. P.; Reddy, J. N.; Hopkins, Dale A.

    A probabilistic micromechanics-based nonlinear analysis procedure is developed to predict and quantify the variability in the properties of high temperature metal matrix composites. Monte Carlo simulation is used to model the probabilistic distributions of the constituent level properties including fiber, matrix, and interphase properties, volume and void ratios, strengths, fiber misalignment, and nonlinear empirical parameters. The procedure predicts the resultant ply properties and quantifies their statistical scatter. Graphite copper and Silicon Carbide Titanlum Aluminide (SCS-6 TI15) unidirectional plies are considered to demonstrate the predictive capabilities. The procedure is believed to have a high potential for use in material characterization and selection to precede and assist in experimental studies of new high temperature metal matrix composites.

  18. Matrix management in hospitals: testing theories of matrix structure and development.

    PubMed

    Burns, L R

    1989-09-01

    A study of 315 hospitals with matrix management programs was used to test several hypotheses concerning matrix management advanced by earlier theorists. The study verifies that matrix management involves several distinctive elements that can be scaled to form increasingly complex types of lateral coordinative devices. The scalability of these elements is evident only cross-sectionally. The results show that matrix complexity is not an outcome of program age, nor does matrix complexity at the time of implementation appear to influence program survival. Matrix complexity, finally, is not determined by the organization's task diversity and uncertainty. The results suggest several modifications in prevailing theories of matrix organization.

  19. The Aarskog-Scott Syndrome Protein Fgd1 Regulates Podosome Formation and Extracellular Matrix Remodeling in Transforming Growth Factor β-Stimulated Aortic Endothelial Cells ▿

    PubMed Central

    Daubon, Thomas; Buccione, Roberto; Génot, Elisabeth

    2011-01-01

    Podosomes are dynamic actin-rich adhesion plasma membrane microdomains endowed with extracellular matrix-degrading activities. In aortic endothelial cells, podosomes are induced by transforming growth factor β (TGF-β), but how this occurs is largely unknown. It is thought that, in endothelial cells, podosomes play a role in vessel remodeling and/or in breaching anatomical barriers. We demonstrate here that, in bovine aortic endothelial cells, that the Cdc42-specific guanine exchange factor (GEF) Fgd1 is expressed and regulated by TGF-β to induce Cdc42-dependent podosome assembly. Within 15 min of TGF-β stimulation, Fgd1, but none of the other tested Cdc42 GEFs, undergoes tyrosine phosphorylation, associates with Cdc42, and translocates to the subcortical cytoskeleton via a cortactin-dependent mechanism. Small interfering RNA-mediated Fgd1 knockdown inhibits TGF-β-induced Cdc42 activation. Fgd1 depletion also reduces podosome formation and associated matrix degradation and these defects are rescued by reexpression of Fgd1. Although overexpression of Fgd1 does not promote podosome formation per se, it enhances TGF-β-induced matrix degradation. Our results identify Fgd1 as a TGF-β-regulated GEF and, as such, the first GEF to be involved in the process of cytokine-induced podosome formation. Our findings reveal the involvement of Fgd1 in endothelial cell biology and open up new avenues to study its role in vascular pathophysiology. PMID:21911474

  20. User's Manual for PCSMS (Parallel Complex Sparse Matrix Solver). Version 1.

    NASA Technical Reports Server (NTRS)

    Reddy, C. J.

    2000-01-01

    PCSMS (Parallel Complex Sparse Matrix Solver) is a computer code written to make use of the existing real sparse direct solvers to solve complex, sparse matrix linear equations. PCSMS converts complex matrices into real matrices and use real, sparse direct matrix solvers to factor and solve the real matrices. The solution vector is reconverted to complex numbers. Though, this utility is written for Silicon Graphics (SGI) real sparse matrix solution routines, it is general in nature and can be easily modified to work with any real sparse matrix solver. The User's Manual is written to make the user acquainted with the installation and operation of the code. Driver routines are given to aid the users to integrate PCSMS routines in their own codes.

  1. BCYCLIC: A parallel block tridiagonal matrix cyclic solver

    NASA Astrophysics Data System (ADS)

    Hirshman, S. P.; Perumalla, K. S.; Lynch, V. E.; Sanchez, R.

    2010-09-01

    A block tridiagonal matrix is factored with minimal fill-in using a cyclic reduction algorithm that is easily parallelized. Storage of the factored blocks allows the application of the inverse to multiple right-hand sides which may not be known at factorization time. Scalability with the number of block rows is achieved with cyclic reduction, while scalability with the block size is achieved using multithreaded routines (OpenMP, GotoBLAS) for block matrix manipulation. This dual scalability is a noteworthy feature of this new solver, as well as its ability to efficiently handle arbitrary (non-powers-of-2) block row and processor numbers. Comparison with a state-of-the art parallel sparse solver is presented. It is expected that this new solver will allow many physical applications to optimally use the parallel resources on current supercomputers. Example usage of the solver in magneto-hydrodynamic (MHD), three-dimensional equilibrium solvers for high-temperature fusion plasmas is cited.

  2. Revealing Slip Bands In A Metal-Matrix/Fiber Composite

    NASA Technical Reports Server (NTRS)

    Lerch, Bradley A.

    1995-01-01

    Experimental procedure includes heat treatments and metallographic techniques developed to facilitate studies of deformation of metal-matrix/fiber composite under stress. Reveals slip bands, indicative of plastic flow occurring in matrix during mechanical tests of specimens of composite.

  3. R-matrix calculations for electron-impact excitation of C(+), N(2+), and O(3+) including fine structure

    NASA Technical Reports Server (NTRS)

    Luo, D.; Pradhan, A. K.

    1990-01-01

    The new R-matrix package for comprehensive close-coupling calculations for electron scattering with the first three ions in the boron isoelectronic sequence, the astrophysically significant C(+), N(2+), and O(3+), is presented. The collision strengths are calculated in the LS coupling approximation, as well as in pair-coupling scheme, for the transitions among the fine-structure sublevels. Calculations are carried out at a large number of energies in order to study the detailed effects of autoionizing resonances.

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

    NASA Astrophysics Data System (ADS)

    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.

  5. Collagen Membranes Adsorb the Transforming Growth Factor-β Receptor I Kinase-Dependent Activity of Enamel Matrix Derivative.

    PubMed

    Stähli, Alexandra; Miron, Richard J; Bosshardt, Dieter D; Sculean, Anton; Gruber, Reinhard

    2016-05-01

    Enamel matrix derivative (EMD) and collagen membranes (CMs) are simultaneously applied in regenerative periodontal surgery. The aim of this study is to evaluate the ability of two CMs and a collagen matrix to adsorb the activity intrinsic to EMD that provokes transforming growth factor (TGF)-β signaling in oral fibroblasts. Three commercially available collagen products were exposed to EMD or recombinant TGF-β1, followed by vigorous washing. Oral fibroblasts were either seeded directly onto collagen products or were incubated with the respective supernatant. Expression of TGF-β target genes interleukin (IL)-11 and proteoglycan 4 (PRG4) was evaluated by real time polymerase chain reaction. Proteomic analysis was used to study the fraction of EMD proteins binding to collagen. EMD or TGF-β1 provoked a significant increase of IL-11 and PRG4 expression of oral fibroblasts when seeded onto collagen products and when incubated with the respective supernatant. Gene expression was blocked by the TGF-β receptor I kinase inhibitor SB431542. Amelogenin bound most abundantly to gelatin-coated culture dishes. However, incubation of palatal fibroblasts with recombinant amelogenin did not alter expression of IL-11 and PRG4. These in vitro findings suggest that collagen products adsorb a TGF-β receptor I kinase-dependent activity of EMD and make it available for potential target cells.

  6. Superfund Chemical Data Matrix (SCDM) Query - April 2016

    EPA Pesticide Factsheets

    This site allows you to to easily query the Superfund Chemical Data Matrix (SCDM) and generate a list of the corresponding Hazardous Ranking System (HRS) factor values, benchmarks, and data elements that you need.

  7. Fibre-matrix bond strength studies of glass, ceramic, and metal matrix composites

    NASA Technical Reports Server (NTRS)

    Grande, D. H.; Mandell, J. F.; Hong, K. C. C.

    1988-01-01

    An indentation test technique for compressively loading the ends of individual fibers to produce debonding has been applied to metal, glass, and glass-ceramic matrix composites; bond strength values at debond initiation are calculated using a finite-element model. Results are correlated with composite longitudinal and interlaminar shear behavior for carbon and Nicalon fiber-reinforced glasses and glass-ceramics including the effects of matrix modifications, processing conditions, and high-temperature oxidation embrittlement. The data indicate that significant bonding to improve off-axis and shear properties can be tolerated before the longitudinal behavior becomes brittle. Residual stress and other mechanical bonding effects are important, but improved analyses and multiaxial interfacial failure criteria are needed to adequately interpret bond strength data in terms of composite performance.

  8. Compensation of matrix effects in gas chromatography-mass spectrometry analysis of pesticides using a combination of matrix matching and multiple isotopically labeled internal standards.

    PubMed

    Tsuchiyama, Tomoyuki; Katsuhara, Miki; Nakajima, Masahiro

    2017-11-17

    In the multi-residue analysis of pesticides using GC-MS, the quantitative results are adversely affected by a phenomenon known as the matrix effect. Although the use of matrix-matched standards is considered to be one of the most practical solutions to this problem, complete removal of the matrix effect is difficult in complex food matrices owing to their inconsistency. As a result, residual matrix effects can introduce analytical errors. To compensate for residual matrix effects, we have developed a novel method that employs multiple isotopically labeled internal standards (ILIS). The matrix effects of ILIS and pesticides were evaluated in spiked matrix extracts of various agricultural commodities, and the obtained data were subjected to simple statistical analysis. Based on the similarities between the patterns of variation in the analytical response, a total of 32 isotopically labeled compounds were assigned to 338 pesticides as internal standards. It was found that by utilizing multiple ILIS, residual matrix effects could be effectively compensated. The developed method exhibited superior quantitative performance compared with the common single-internal-standard method. The proposed method is more feasible for regulatory purposes than that using only predetermined correction factors and is considered to be promising for practical applications. Copyright © 2017 Elsevier B.V. All rights reserved.

  9. Cell and matrix modulation in prenatal and postnatal equine growth cartilage, zones of Ranvier and articular cartilage

    PubMed Central

    Löfgren, Maria; Ekman, Stina; Svala, Emilia; Lindahl, Anders; Ley, Cecilia; Skiöldebrand, Eva

    2014-01-01

    Formation of synovial joints includes phenotypic changes of the chondrocytes and the organisation of their extracellular matrix is regulated by different factors and signalling pathways. Increased knowledge of the normal processes involved in joint development may be used to identify similar regulatory mechanisms during pathological conditions in the joint. Samples of the distal radius were collected from prenatal and postnatal equine growth plates, zones of Ranvier and articular cartilage with the aim of identifying Notch signalling components and cells with stem cell-like characteristics and to follow changes in matrix protein localisation during joint development. The localisation of the Notch signalling components Notch1, Delta4, Hes1, Notch dysregulating protein epidermal growth factor-like domain 7 (EGFL7), the stem cell-indicating factor Stro-1 and the matrix molecules cartilage oligomeric matrix protein (COMP), fibromodulin, matrilin-1 and chondroadherin were studied using immunohistochemistry. Spatial changes in protein localisations during cartilage maturation were observed for Notch signalling components and matrix molecules, with increased pericellular localisation indicating new synthesis and involvement of these proteins in the formation of the joint. However, it was not possible to characterise the phenotype of the chondrocytes based on their surrounding matrix during normal chondrogenesis. The zone of Ranvier was identified in all horses and characterised as an area expressing Stro-1, EGFL7 and chondroadherin with an absence of COMP and Notch signalling. Stro-1 was also present in cells close to the perichondrium, in the articular cartilage and in the fetal resting zone, indicating stem cell-like characteristics of these cells. The presence of stem cells in the articular cartilage will be of importance for the repair of damaged cartilage. Perivascular chondrocytes and hypertrophic cells of the cartilage bone interface displayed positive staining for

  10. In vitro studies to show sequestration of matrix metalloproteinases by silver-containing wound care products.

    PubMed

    Walker, Michael; Bowler, Philip G; Cochrane, Christine A

    2007-09-01

    Excess or "uncontrolled" proteinase activity in the wound bed has been implicated as one factor that may delay or compromise wound healing. One proteinase group--matrix metalloproteinases--includes collagenases, elastase, and gelatinases and can be endogenous (cell) or exogenous (bacterial) in origin. A study was conducted to assess the ability of five silver-containing wound care products to reduce a known matrix metalloproteinase supernatant concentration in vitro. Four silver-containing wound dressings (a carboxy-methyl cellulose, a nanocrystalline, a hydro-alginate, and a collagen/oxidized regenerated cellulose composite dressing), along with a 0.5% aqueous silver nitrate [w/v] solution and controls for matrix metalloproteinase-2 and matrix metalloproteinase-9 sourced from ex vivo dermal tissue and blood monocytes, respectively, were used. Extracts were separated and purified using gelatine-Sepharose column chromatography and dialysis and polyacrylamide gel electrophoretic zymography was used to analyze specific matrix metalloproteinase activity. All dressings and the solution were shown to sequester both matrix metalloproteinases. The silver-containing carboxy-methyl cellulose dressing showed significantly greater sequestration for matrix metalloproteinase-2 at 6 and 24 hours (P< 0.001) compared to the other treatments. For matrix metalloproteinase-9, both the carboxy-methyl cellulose dressing and the oxidized regenerated cellulose dressing achieved significant sequestration when compared to the other treatments at 24 hours (P <0.001), which was maintained to 48 hours (P < 0.001). Results from this study show that silver-containing dressings are effective in sequestering matrix metalloproteinase-2 and -9 and that this can be achieved without a sacrificial protein (eg, collagen). Although the varying ability of wound dressings to sequester matrix metalloproteinases has been shown in vitro, further in vivo evidence is required to confirm these findings.

  11. The anchorless adhesin Eap (extracellular adherence protein) from Staphylococcus aureus selectively recognizes extracellular matrix aggregates but binds promiscuously to monomeric matrix macromolecules.

    PubMed

    Hansen, Uwe; Hussain, Muzaffar; Villone, Daniela; Herrmann, Mathias; Robenek, Horst; Peters, Georg; Sinha, Bhanu; Bruckner, Peter

    2006-05-01

    Besides a number of cell wall-anchored adhesins, the majority of Staphylococcus aureus strains produce anchorless, cell wall-associated proteins, such as Eap (extracellular adherence protein). Eap contains four to six tandem repeat (EAP)-domains. Eap mediates diverse biological functions, including adherence and immunomodulation, thus contributing to S. aureus pathogenesis. Eap binding to host macromolecules is unusually promiscuous and includes matrix or matricellular proteins as well as plasma proteins. The structural basis of this promiscuity is poorly understood. Here, we show that in spite of the preferential location of the binding epitopes within triple helical regions in some collagens there is a striking specificity of Eap binding to different collagen types. Collagen I, but not collagen II, is a binding substrate in monomolecular form. However, collagen I is virtually unrecognized by Eap when incorporated into banded fibrils. By contrast, microfibrils containing collagen VI as well as basement membrane-associated networks containing collagen IV, or aggregates containing fibronectin bound Eap as effectively as the monomeric proteins. Therefore, Eap-binding to extracellular matrix ligands is promiscuous at the molecular level but not indiscriminate with respect to supramolecular structures containing the same macromolecules. In addition, Eap bound to banded fibrils after their partial disintegration by matrix-degrading proteinases, including matrix metalloproteinase 1. Therefore, adherence to matrix suprastructures by S. aureus can be supported by inflammatory reactions.

  12. Oil-free hyaluronic acid matrix for serial femtosecond crystallography

    NASA Astrophysics Data System (ADS)

    Sugahara, Michihiro; Song, Changyong; Suzuki, Mamoru; Masuda, Tetsuya; Inoue, Shigeyuki; Nakane, Takanori; Yumoto, Fumiaki; Nango, Eriko; Tanaka, Rie; Tono, Kensuke; Joti, Yasumasa; Kameshima, Takashi; Hatsui, Takaki; Yabashi, Makina; Nureki, Osamu; Numata, Keiji; Iwata, So

    2016-04-01

    The grease matrix was originally introduced as a microcrystal-carrier for serial femtosecond crystallography and has been expanded to applications for various types of proteins, including membrane proteins. However, the grease-based matrix has limited application for oil-sensitive proteins. Here we introduce a grease-free, water-based hyaluronic acid matrix. Applications for proteinase K and lysozyme proteins were able to produce electron density maps at 2.3-Å resolution.

  13. The successive projection algorithm as an initialization method for brain tumor segmentation using non-negative matrix factorization.

    PubMed

    Sauwen, Nicolas; Acou, Marjan; Bharath, Halandur N; Sima, Diana M; Veraart, Jelle; Maes, Frederik; Himmelreich, Uwe; Achten, Eric; Van Huffel, Sabine

    2017-01-01

    Non-negative matrix factorization (NMF) has become a widely used tool for additive parts-based analysis in a wide range of applications. As NMF is a non-convex problem, the quality of the solution will depend on the initialization of the factor matrices. In this study, the successive projection algorithm (SPA) is proposed as an initialization method for NMF. SPA builds on convex geometry and allocates endmembers based on successive orthogonal subspace projections of the input data. SPA is a fast and reproducible method, and it aligns well with the assumptions made in near-separable NMF analyses. SPA was applied to multi-parametric magnetic resonance imaging (MRI) datasets for brain tumor segmentation using different NMF algorithms. Comparison with common initialization methods shows that SPA achieves similar segmentation quality and it is competitive in terms of convergence rate. Whereas SPA was previously applied as a direct endmember extraction tool, we have shown improved segmentation results when using SPA as an initialization method, as it allows further enhancement of the sources during the NMF iterative procedure.

  14. Nanophosphor composite scintillator with a liquid matrix

    DOEpatents

    McKigney, Edward Allen; Burrell, Anthony Keiran; Bennett, Bryan L.; Cooke, David Wayne; Ott, Kevin Curtis; Bacrania, Minesh Kantilal; Del Sesto, Rico Emilio; Gilbertson, Robert David; Muenchausen, Ross Edward; McCleskey, Thomas Mark

    2010-03-16

    An improved nanophosphor scintillator liquid comprises nanophosphor particles in a liquid matrix. The nanophosphor particles are optionally surface modified with an organic ligand. The surface modified nanophosphor particle is essentially surface charge neutral, thereby preventing agglomeration of the nanophosphor particles during dispersion in a liquid scintillator matrix. The improved nanophosphor scintillator liquid may be used in any conventional liquid scintillator application, including in a radiation detector.

  15. Mimicking the extracellular matrix with functionalized, metal-assembled collagen peptide scaffolds.

    PubMed

    Hernandez-Gordillo, Victor; Chmielewski, Jean

    2014-08-01

    Natural and synthetic three-dimensional (3-D) scaffolds that mimic the microenvironment of the extracellular matrix (ECM), with growth factor storage/release and the display of cell adhesion signals, offer numerous advantages for regenerative medicine and in vitro morphogenesis and oncogenesis modeling. Here we report the design of collagen mimetic peptides (CMPs) that assemble into a highly crosslinked 3-D matrix in response to metal ion stimuli, that may be functionalized with His-tagged cargoes, such as green fluorescent protein (GFP-His8) and human epidermal growth factor (hEGF-His6). The bound hEGF-His6 was found to gradually release from the matrix in vitro and induce cell proliferation in the EGF-dependent cell line MCF10A. The additional incorporation of a cell adhesion sequence (RGDS) at the N-terminus of the CMP creates an environment that facilitated the organization of matrix-encapsulated MCF10A cells into spheroid structures, thus mimicking the ECM environment. Copyright © 2014 Elsevier Ltd. All rights reserved.

  16. Ceramic matrix and resin matrix composites: A comparison

    NASA Technical Reports Server (NTRS)

    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.

  17. Ceramic matrix and resin matrix composites - A comparison

    NASA Technical Reports Server (NTRS)

    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.

  18. Hypercube matrix computation task

    NASA Technical Reports Server (NTRS)

    Calalo, Ruel H.; Imbriale, William A.; Jacobi, Nathan; Liewer, Paulett C.; Lockhart, Thomas G.; Lyzenga, Gregory A.; Lyons, James R.; Manshadi, Farzin; Patterson, Jean E.

    1988-01-01

    A major objective of the Hypercube Matrix Computation effort at the Jet Propulsion Laboratory (JPL) is to investigate the applicability of a parallel computing architecture to the solution of large-scale electromagnetic scattering problems. Three scattering analysis codes are being implemented and assessed on a JPL/California Institute of Technology (Caltech) Mark 3 Hypercube. The codes, which utilize different underlying algorithms, give a means of evaluating the general applicability of this parallel architecture. The three analysis codes being implemented are a frequency domain method of moments code, a time domain finite difference code, and a frequency domain finite elements code. These analysis capabilities are being integrated into an electromagnetics interactive analysis workstation which can serve as a design tool for the construction of antennas and other radiating or scattering structures. The first two years of work on the Hypercube Matrix Computation effort is summarized. It includes both new developments and results as well as work previously reported in the Hypercube Matrix Computation Task: Final Report for 1986 to 1987 (JPL Publication 87-18).

  19. Study of optimal laser parameters for cutting QFN packages by Taguchi's matrix method

    NASA Astrophysics Data System (ADS)

    Li, Chen-Hao; Tsai, Ming-Jong; Yang, Ciann-Dong

    2007-06-01

    This paper reports the study of optimal laser parameters for cutting QFN (Quad Flat No-lead) packages by using a diode pumped solid-state laser system (DPSSL). The QFN cutting path includes two different materials, which are the encapsulated epoxy and a copper lead frame substrate. The Taguchi's experimental method with orthogonal array of L 9(3 4) is employed to obtain optimal combinatorial parameters. A quantified mechanism was proposed for examining the laser cutting quality of a QFN package. The influences of the various factors such as laser current, laser frequency, and cutting speed on the laser cutting quality is also examined. From the experimental results, the factors on the cutting quality in the order of decreasing significance are found to be (a) laser frequency, (b) cutting speed, and (c) laser driving current. The optimal parameters were obtained at the laser frequency of 2 kHz, the cutting speed of 2 mm/s, and the driving current of 29 A. Besides identifying this sequence of dominance, matrix experiment also determines the best level for each control factor. The verification experiment confirms that the application of laser cutting technology to QFN is very successfully by using the optimal laser parameters predicted from matrix experiments.

  20. Implementation of an Associative Flow Rule Including Hydrostatic Stress Effects Into the High Strain Rate Deformation Analysis of Polymer Matrix Composites

    NASA Technical Reports Server (NTRS)

    Goldberg, Robert K.; Roberts, Gary D.; Gilat, Amos

    2003-01-01

    A previously developed analytical formulation has been modified in order to more accurately account for the effects of hydrostatic stresses on the nonlinear, strain rate dependent deformation of polymer matrix composites. State variable constitutive equations originally developed for metals have been modified in order to model the nonlinear, strain rate dependent deformation of polymeric materials. To account for the effects of hydrostatic stresses, which are significant in polymers, the classical J2 plasticity theory definitions of effective stress and effective inelastic strain, along with the equations used to compute the components of the inelastic strain rate tensor, are appropriately modified. To verify the revised formulation, the shear and tensile deformation of two representative polymers are computed across a wide range of strain rates. Results computed using the developed constitutive equations correlate well with experimental data. The polymer constitutive equations are implemented within a strength of materials based micromechanics method to predict the nonlinear, strain rate dependent deformation of polymer matrix composites. The composite mechanics are verified by analyzing the deformation of a representative polymer matrix composite for several fiber orientation angles across a variety of strain rates. The computed values compare well to experimentally obtained results.

  1. Study of the validity of a job-exposure matrix for the job strain model factors: an update and a study of changes over time.

    PubMed

    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.

  2. Uniform-burning matrix burner

    DOEpatents

    Bohn, Mark S.; Anselmo, Mark

    2001-01-01

    Computer simulation was used in the development of an inward-burning, radial matrix gas burner and heat pipe heat exchanger. The burner and exchanger can be used to heat a Stirling engine on cloudy days when a solar dish, the normal source of heat, cannot be used. Geometrical requirements of the application forced the use of the inward burning approach, which presents difficulty in achieving a good flow distribution and air/fuel mixing. The present invention solved the problem by providing a plenum with just the right properties, which include good flow distribution and good air/fuel mixing with minimum residence time. CFD simulations were also used to help design the primary heat exchanger needed for this application which includes a plurality of pins emanating from the heat pipe. The system uses multiple inlet ports, an extended distance from the fuel inlet to the burner matrix, flow divider vanes, and a ring-shaped, porous grid to obtain a high-temperature uniform-heat radial burner. Ideal applications include dish/Stirling engines, steam reforming of hydrocarbons, glass working, and any process requiring high temperature heating of the outside surface of a cylindrical surface.

  3. Regulation of Osteoblast Survival by the Extracellular Matrix and Gravity

    NASA Technical Reports Server (NTRS)

    Globus. Ruth K.; Almeida, Eduardo A. C.; Searby, Nancy D.; Bowley, Susan M. (Technical Monitor)

    2000-01-01

    Spaceflight adversely affects the skeleton, posing a substantial risk to astronaut's health during long duration missions. The reduced bone mass observed in growing animals following spaceflight is due at least in part to inadequate bone formation by osteoblasts. Thus, it is of central importance to identify basic cellular mechanisms underlying normal bone formation. The fundamental ideas underlying our research are that interactions between extracellular matrix proteins, integrin adhesion receptors, cytoplasmic signaling and cytoskeletal proteins are key ingredients for the proper functioning of osteoblasts, and that gravity impacts these interactions. As an in vitro model system we used primary fetal rat calvarial cells which faithfully recapitulate osteoblast differentiation characteristically observed in vivo. We showed that specific integrin receptors ((alpha)3(beta)1), ((alpha)5(beta)1), ((alpha)8(betal)1) and extracellular matrix proteins (fibronectin, laminin) were needed for the differentiation of immature osteoblasts. In the course of maturation, cultured osteoblasts switched from depending on fibronectin and laminin for differentiation to depending on these proteins for their very survival. Furthermore, we found that manipulating the gravity vector using ground-based models resulted in activation of key intracellular survival signals generated by integrin/extracellular matrix interactions. We are currently testing the in vivo relevance of some of these observations using targeted transgenic technology. In conclusion, mechanical factors including gravity may participate in regulating survival via cellular interactions with the extracellular matrix. This leads us to speculate that microgravity adversely affects the survival of osteoblasts and contributes to spaceflight-induced osteoporosis.

  4. Peptide-matrix-mediated gene transfer of an oxygen-insensitive hypoxia-inducible factor-1alpha variant for local induction of angiogenesis.

    PubMed

    Trentin, Diana; Hall, Heike; Wechsler, Sandra; Hubbell, Jeffrey A

    2006-02-21

    Hypoxia-inducible factor (HIF) constitutes a target in therapeutic angiogenesis. HIF-1alpha functions as a sensor of hypoxia and induces expression of vascular endothelial growth factor (VEGF), which then induces angiogenesis. To explore the potential of HIF-1alpha gene therapy in stimulating wound healing, we delivered a gene encoding a stabilized form of HIF-1alpha, lacking the oxygen-sensitive degradation domain, namely HIF-1alpha deltaODD, by using a previously characterized peptide-based gene delivery vector in fibrin as a surgical matrix. The peptide vector consisted of multiple domains: (i) A cysteine-flanked lysine hexamer provided DNA interactions that were stable extracellularly but destabilized intracellularly after reduction of the formed disulfide bonds. This DNA-binding domain was fused to either (ii) a fibrin-binding peptide for entrapment within the matrix or (iii) a nuclear localization sequence for efficient nuclear targeting. The HIF-1alpha deltaODD gene was expressed and translocated to the nucleus under normoxic conditions, leading to up-regulation of vascular endothelial growth factor (VEGF)-A165 mRNA and protein levels in vitro. When the peptide-DNA nanoparticles entrapped in fibrin matrices were applied to full-thickness dermal wounds in the mouse (10 microg per wound in 30 microl of fibrin), angiogenesis was increased comparably strongly to that induced by VEGF-A165 protein (1.25 microg per wound in 30 microl of fibrin). However, the maturity of the vessels induced by HIF-1alpha deltaODD was significantly higher than that induced by VEGF-A165 protein, as shown by stabilization of the neovessels with smooth muscle. Nonviral, local administration of this potent angiogenesis-inducing gene by using this peptide vector represents a powerful approach in tissue engineering and therapeutic angiogenesis.

  5. Source apportionments of PM2.5 organic carbon using molecular marker Positive Matrix Factorization and comparison of results from different receptor models

    NASA Astrophysics Data System (ADS)

    Heo, Jongbae; Dulger, Muaz; Olson, Michael R.; McGinnis, Jerome E.; Shelton, Brandon R.; Matsunaga, Aiko; Sioutas, Constantinos; Schauer, James J.

    2013-07-01

    Four hundred fine particulate matter (PM2.5) samples collected over a 1-year period at two sites in the Los Angeles Basin were analyzed for organic carbon (OC), elemental carbon (EC), water soluble organic carbon (WSOC) and organic molecular markers. The results were used in a Positive Matrix Factorization (PMF) receptor model to obtain daily, monthly and annual average source contributions to PM2.5 OC. Results of the PMF model showed similar source categories with comparable year-long contributions to PM2.5 OC across the sites. Five source categories providing reasonably stable profiles were identified: mobile, wood smoke, primary biogenic, and two types of secondary organic carbon (SOC) (i.e., anthropogenic and biogenic emissions). Total primary emission factors and total SOC factors contributed approximately 60% and 40%, respectively, to the annual-average OC concentrations. Primary sources showed strong seasonal patterns with high winter peaks and low summer peaks, while SOC showed a reverse pattern with highs in the spring and summer in the region. Interestingly, smoke from forest fires which occurred episodically in California during the summer and fall of 2009 was identified and combined with the primary biogenic source as one distinct factor to the OC budget. The PMF resolved factors were further investigated and compared to a chemical mass balance (CMB) model and a second multi-variant receptor model (UNMIX) using molecular markers considered in the PMF. Good agreement between the source contribution from mobile sources and biomass burning for three models were obtained, providing additional weight of evidence that these source apportionment techniques are sufficiently accurate for policy development. However, the CMB model did not quantify primary biogenic emissions, which were included in other sources with the SOC. Both multivariate receptor models, the PMF and the UNMIX, were unable to separate source contributions from diesel and gasoline engines.

  6. Development, implementation, and test results on integrated optics switching matrix

    NASA Technical Reports Server (NTRS)

    Rutz, E.

    1982-01-01

    A small integrated optics switching matrix, which was developed, implemented, and tested, indicates high performance. The matrix serves as a model for the design of larger switching matrices. The larger integrated optics switching matrix should form the integral part of a switching center with high data rate throughput of up to 300 megabits per second. The switching matrix technique can accomplish the design goals of low crosstalk and low distortion. About 50 illustrations help explain and depict the many phases of the integrated optics switching matrix. Many equations used to explain and calculate the experimental data are also included.

  7. Improving the analyte ion signal in matrix-assisted laser desorption/ionization imaging mass spectrometry via electrospray deposition by enhancing incorporation of the analyte in the matrix.

    PubMed

    Malys, Brian J; Owens, Kevin G

    2017-05-15

    Matrix-assisted laser desorption/ionization (MALDI) is widely used as the ionization method in high-resolution chemical imaging studies that seek to visualize the distribution of analytes within sectioned biological tissues. This work extends the use of electrospray deposition (ESD) to apply matrix with an additional solvent spray to incorporate and homogenize analyte within the matrix overlayer. Analytes and matrix are sequentially and independently applied by ESD to create a sample from which spectra are collected, mimicking a MALDI imaging mass spectrometry (IMS) experiment. Subsequently, an incorporation spray consisting of methanol is applied by ESD to the sample and another set of spectra are collected. The spectra prior to and after the incorporation spray are compared to evaluate the improvement in the analyte signal. Prior to the incorporation spray, samples prepared using α-cyano-4-hydroxycinnamic acid (CHCA) and 2,5-dihydroxybenzoic acid (DHB) as the matrix showed low signal while the sample using sinapinic acid (SA) initially exhibited good signal. Following the incorporation spray, the sample using SA did not show an increase in signal; the sample using DHB showed moderate gain factors of 2-5 (full ablation spectra) and 12-336 (raster spectra), while CHCA samples saw large increases in signal, with gain factors of 14-172 (full ablation spectra) and 148-1139 (raster spectra). The use of an incorporation spray to apply solvent by ESD to a matrix layer already deposited by ESD provides an increase in signal by both promoting incorporation of the analyte within and homogenizing the distribution of the incorporated analyte throughout the matrix layer. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

  8. Linearized T-Matrix and Mie Scattering Computations

    NASA Technical Reports Server (NTRS)

    Spurr, R.; Wang, J.; Zeng, J.; Mishchenko, M. I.

    2011-01-01

    We present a new linearization of T-Matrix and Mie computations for light scattering by non-spherical and spherical particles, respectively. In addition to the usual extinction and scattering cross-sections and the scattering matrix outputs, the linearized models will generate analytical derivatives of these optical properties with respect to the real and imaginary parts of the particle refractive index, and (for non-spherical scatterers) with respect to the ''shape'' parameter (the spheroid aspect ratio, cylinder diameter/height ratio, Chebyshev particle deformation factor). These derivatives are based on the essential linearity of Maxwell's theory. Analytical derivatives are also available for polydisperse particle size distribution parameters such as the mode radius. The T-matrix formulation is based on the NASA Goddard Institute for Space Studies FORTRAN 77 code developed in the 1990s. The linearized scattering codes presented here are in FORTRAN 90 and will be made publicly available.

  9. Analysis of IFE, EFE and QSPM matrix on business development strategy

    NASA Astrophysics Data System (ADS)

    Zulkarnain, A.; Wahyuningtias, D.; Putranto, T. S.

    2018-03-01

    IFE matrix, EFE matrix, and QSPM matrix are business strategy tools that can be used to identify the threat, opportunity, weakness, strength as internal, external business factors. The goal of Danti’s Deli Bakery is to provide pastry product and distribute to other food and beverage outlet all around Jakarta. Thus, Danti’s Deli Bakery requires development strategy in order to win the tight competition. Applied descriptive research and data collected from focus group discussion, questionnaire, interview, observation and literature review. The objectives of this paper are (1) to identify and evaluate internal and external factors, (2) to formulate alternative strategy toward business development program, and (3) to give effective recommendation. The result shows that Danti’s Deli Bakery should apply product differentiation strategy. Implementation of this study is providing the recommendation for pastry and bakery industry to establish a successful business.

  10. Characterizing muscular activities using non-negative matrix factorization from EMG channels for driver swings in golf.

    PubMed

    Ozaki, Yasunori; Aoki, Ryosuke; Kimura, Toshitaka; Takashima, Youichi; Yamada, Tomohiro

    2016-08-01

    The goal of this study is to propose a data driven approach method to characterize muscular activities of complex actions in sports such as golf from a lot of EMG channels. Two problems occur in a many channel measurement. The first problem is that it takes a lot of time to check the many channel data because of combinatorial explosion. The second problem is that it is difficult to understand muscle activities related with complex actions. To solve these problems, we propose an analysis method of multi EMG channels using Non-negative Matrix Factorization and adopt the method to driver swings in golf. We measured 26 EMG channels about 4 professional coaches of golf. The results show that the proposed method detected 9 muscle synergies and the activation of each synergy were mostly fitted by sigmoid curve (R2=0.85).

  11. Synthetic design of growth factor sequestering extracellular matrix mimetic hydrogel for promoting in vivo bone formation.

    PubMed

    Yan, Hong Ji; Casalini, Tommaso; Hulsart-Billström, Gry; Wang, Shujiang; Oommen, Oommen P; Salvalaglio, Matteo; Larsson, Sune; Hilborn, Jöns; Varghese, Oommen P

    2018-04-01

    Synthetic scaffolds that possess an intrinsic capability to protect and sequester sensitive growth factors is a primary requisite for developing successful tissue engineering strategies. Growth factors such as recombinant human bone morphogenetic protein-2 (rhBMP-2) is highly susceptible to premature degradation and to provide a meaningful clinical outcome require high doses that can cause serious side effects. We discovered a unique strategy to stabilize and sequester rhBMP-2 by enhancing its molecular interactions with hyaluronic acid (HA), an extracellular matrix (ECM) component. We found that by tuning the initial protonation state of carboxylic acid residues of HA in a covalently crosslinked hydrogel modulate BMP-2 release at physiological pH by minimizing the electrostatic repulsion and maximizing the Van der Waals interactions. At neutral pH, BMP-2 release is primarily governed by Fickian diffusion, whereas at acidic pH both diffusion and electrostatic interactions between HA and BMP-2 become important as confirmed by molecular dynamics simulations. Our results were also validated in an in vivo rat ectopic model with rhBMP-2 loaded hydrogels, which demonstrated superior bone formation with acidic hydrogel as compared to the neutral counterpart. We believe this study provides new insight on growth factor stabilization and highlights the therapeutic potential of engineered matrices for rhBMP-2 delivery and may help to curtail the adverse side effects associated with the high dose of the growth factor. Copyright © 2018 Elsevier Ltd. All rights reserved.

  12. Nonnegative Matrix Factorization for identification of unknown number of sources emitting delayed signals

    PubMed Central

    Iliev, Filip L.; Stanev, Valentin G.; Vesselinov, Velimir V.

    2018-01-01

    Factor analysis is broadly used as a powerful unsupervised machine learning tool for reconstruction of hidden features in recorded mixtures of signals. In the case of a linear approximation, the mixtures can be decomposed by a variety of model-free Blind Source Separation (BSS) algorithms. Most of the available BSS algorithms consider an instantaneous mixing of signals, while the case when the mixtures are linear combinations of signals with delays is less explored. Especially difficult is the case when the number of sources of the signals with delays is unknown and has to be determined from the data as well. To address this problem, in this paper, we present a new method based on Nonnegative Matrix Factorization (NMF) that is capable of identifying: (a) the unknown number of the sources, (b) the delays and speed of propagation of the signals, and (c) the locations of the sources. Our method can be used to decompose records of mixtures of signals with delays emitted by an unknown number of sources in a nondispersive medium, based only on recorded data. This is the case, for example, when electromagnetic signals from multiple antennas are received asynchronously; or mixtures of acoustic or seismic signals recorded by sensors located at different positions; or when a shift in frequency is induced by the Doppler effect. By applying our method to synthetic datasets, we demonstrate its ability to identify the unknown number of sources as well as the waveforms, the delays, and the strengths of the signals. Using Bayesian analysis, we also evaluate estimation uncertainties and identify the region of likelihood where the positions of the sources can be found. PMID:29518126

  13. Nonnegative Matrix Factorization for identification of unknown number of sources emitting delayed signals.

    PubMed

    Iliev, Filip L; Stanev, Valentin G; Vesselinov, Velimir V; Alexandrov, Boian S

    2018-01-01

    Factor analysis is broadly used as a powerful unsupervised machine learning tool for reconstruction of hidden features in recorded mixtures of signals. In the case of a linear approximation, the mixtures can be decomposed by a variety of model-free Blind Source Separation (BSS) algorithms. Most of the available BSS algorithms consider an instantaneous mixing of signals, while the case when the mixtures are linear combinations of signals with delays is less explored. Especially difficult is the case when the number of sources of the signals with delays is unknown and has to be determined from the data as well. To address this problem, in this paper, we present a new method based on Nonnegative Matrix Factorization (NMF) that is capable of identifying: (a) the unknown number of the sources, (b) the delays and speed of propagation of the signals, and (c) the locations of the sources. Our method can be used to decompose records of mixtures of signals with delays emitted by an unknown number of sources in a nondispersive medium, based only on recorded data. This is the case, for example, when electromagnetic signals from multiple antennas are received asynchronously; or mixtures of acoustic or seismic signals recorded by sensors located at different positions; or when a shift in frequency is induced by the Doppler effect. By applying our method to synthetic datasets, we demonstrate its ability to identify the unknown number of sources as well as the waveforms, the delays, and the strengths of the signals. Using Bayesian analysis, we also evaluate estimation uncertainties and identify the region of likelihood where the positions of the sources can be found.

  14. Matrix analysis and risk management to avert depression and suicide among workers

    PubMed Central

    2010-01-01

    Suicide is among the most tragic outcomes of all mental disorders, and the prevalence of suicide has risen dramatically during the last decade, particularly among workers. This paper reviews and proposes strategies to avert suicide and depression with regard to the mind body medicine equation hypothesis, metrics analysis of mental health problems from a public health and clinical medicine view. In occupational fields, the mind body medicine hypothesis has to deal with working environment, working condition, and workers' health. These three factors chosen in this paper were based on the concept of risk control, called San-kanri, which has traditionally been used in Japanese companies, and the causation concepts of host, agent, and environment. Working environment and working condition were given special focus with regard to tackling suicide problems. Matrix analysis was conducted by dividing the problem of working conditions into nine cells: three prevention levels (primary, secondary, and tertiary) were proposed for each of the three factors of the mind body medicine hypothesis (working environment, working condition, and workers' health). After using these main strategies (mind body medicine analysis and matrix analysis) to tackle suicide problems, the paper talks about the versatility of case-method teaching, "Hiyari-Hat activity," routine inspections by professionals, risk assessment analysis, and mandatory health check-up focusing on sleep and depression. In the risk assessment analysis, an exact assessment model was suggested using a formula based on multiplication of the following three factors: (1) severity, (2) frequency, and (3) possibility. Mental health problems, including suicide, are rather tricky to deal with because they involve evaluation of individual cases. The mind body medicine hypothesis and matrix analysis would be appropriate tactics for suicide prevention because they would help the evaluation of this issue as a tangible problem. PMID

  15. Plasma Membrane Factor XIIIA Transglutaminase Activity Regulates Osteoblast Matrix Secretion and Deposition by Affecting Microtubule Dynamics

    PubMed Central

    Al-Jallad, Hadil F.; Myneni, Vamsee D.; Piercy-Kotb, Sarah A.; Chabot, Nicolas; Mulani, Amina; Keillor, Jeffrey W.; Kaartinen, Mari T.

    2011-01-01

    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. PMID:21283799

  16. Improving stochastic estimates with inference methods: calculating matrix diagonals.

    PubMed

    Selig, Marco; Oppermann, Niels; Ensslin, Torsten A

    2012-02-01

    Estimating the diagonal entries of a matrix, that is not directly accessible but only available as a linear operator in the form of a computer routine, is a common necessity in many computational applications, especially in image reconstruction and statistical inference. Here, methods of statistical inference are used to improve the accuracy or the computational costs of matrix probing methods to estimate matrix diagonals. In particular, the generalized Wiener filter methodology, as developed within information field theory, is shown to significantly improve estimates based on only a few sampling probes, in cases in which some form of continuity of the solution can be assumed. The strength, length scale, and precise functional form of the exploited autocorrelation function of the matrix diagonal is determined from the probes themselves. The developed algorithm is successfully applied to mock and real world problems. These performance tests show that, in situations where a matrix diagonal has to be calculated from only a small number of computationally expensive probes, a speedup by a factor of 2 to 10 is possible with the proposed method. © 2012 American Physical Society

  17. Hand-Held Ultrasonic Instrument for Reading Matrix Symbols

    NASA Technical Reports Server (NTRS)

    Schramm, Harry F.; Kula, John P.; Gurney, John W.; Lior, Ephraim D.

    2008-01-01

    A hand-held instrument that would include an ultrasonic camera has been proposed as an efficient means of reading matrix symbols. The proposed instrument could be operated without mechanical raster scanning. All electronic functions from excitation of ultrasonic pulses through final digital processing for decoding matrix symbols would be performed by dedicated circuitry within the single, compact instrument housing.

  18. Brief announcement: Hypergraph parititioning for parallel sparse matrix-matrix multiplication

    DOE PAGES

    Ballard, Grey; Druinsky, Alex; Knight, Nicholas; ...

    2015-01-01

    The performance of parallel algorithms for sparse matrix-matrix multiplication is typically determined by the amount of interprocessor communication performed, which in turn depends on the nonzero structure of the input matrices. In this paper, we characterize the communication cost of a sparse matrix-matrix multiplication algorithm in terms of the size of a cut of an associated hypergraph that encodes the computation for a given input nonzero structure. Obtaining an optimal algorithm corresponds to solving a hypergraph partitioning problem. Furthermore, our hypergraph model generalizes several existing models for sparse matrix-vector multiplication, and we can leverage hypergraph partitioners developed for that computationmore » to improve application-specific algorithms for multiplying sparse matrices.« less

  19. Volatile organic compounds (VOCs) in urban air: How chemistry affects the interpretation of positive matrix factorization (PMF) analysis

    NASA Astrophysics Data System (ADS)

    Yuan, Bin; Shao, Min; de Gouw, Joost; Parrish, David D.; Lu, Sihua; Wang, Ming; Zeng, Limin; Zhang, Qian; Song, Yu; Zhang, Jianbo; Hu, Min

    2012-12-01

    Volatile organic compounds (VOCs) were measured online at an urban site in Beijing in August-September 2010. Diurnal variations of various VOC species indicate that VOCs concentrations were influenced by photochemical removal with OH radicals for reactive species and secondary formation for oxygenated VOCs (OVOCs). A photochemical age-based parameterization method was applied to characterize VOCs chemistry. A large part of the variability in concentrations of both hydrocarbons and OVOCs was explained by this method. The determined emission ratios of hydrocarbons to acetylene agreed within a factor of two between 2005 and 2010 measurements. However, large differences were found for emission ratios of some alkanes and C8 aromatics between Beijing and northeastern United States secondary formation from anthropogenic VOCs generally contributed higher percentages to concentrations of reactive aldehydes than those of inert ketones and alcohols. Anthropogenic primary emissions accounted for the majority of ketones and alcohols concentrations. Positive matrix factorization (PMF) was also used to identify emission sources from this VOCs data set. The four resolved factors were three anthropogenic factors and a biogenic factor. However, the anthropogenic factors are attributed here to a common source at different stages of photochemical processing rather than three independent sources. Anthropogenic and biogenic sources of VOCs concentrations were not separated completely in PMF. This study indicates that photochemistry of VOCs in the atmosphere complicates the information about separated sources that can be extracted from PMF and the influence of photochemical processing must be carefully considered in the interpretation of source apportionment studies based upon PMF.

  20. Effect of transforming growth factor-beta and growth differentiation factor-5 on proliferation and matrix production by human bone marrow stromal cells cultured on braided poly lactic-co-glycolic acid scaffolds for ligament tissue engineering.

    PubMed

    Jenner, J M G Th; van Eijk, F; Saris, D B F; Willems, W J; Dhert, W J A; Creemers, Laura B

    2007-07-01

    Tissue engineering of ligaments based on biomechanically suitable biomaterials combined with autologous cells may provide a solution for the drawbacks associated with conventional graft material. The aim of the present study was to investigate the contribution of recombinant human transforming growth factor beta 1 (rhTGF-beta1) and growth differentiation factor (GDF)-5, known for their role in connective tissue regeneration, to proliferation and matrix production by human bone marrow stromal cells (BMSCs) cultured onto woven, bioabsorbable, 3-dimensional (3D) poly(lactic-co-glycolic acid) scaffolds. Cells were cultured for 12 days in the presence or absence of these growth factors at different concentrations. Human BMSCs attached to the suture material, proliferated, and synthesized extracellular matrix rich in collagen type I and collagen III. No differentiation was demonstrated toward cartilage or bone tissue. The addition of rhTGF-beta1 (1-10 ng/mL) and GDF-5 (10-100 ng/mL) increased cell content (p < 0.05), but only TGF-beta1 also increased total collagen production (p < 0.05) and collagen production per cell, which is a parameter indicating differentiation. In conclusion, stimulation with rhTGF-beta1, and to a lesser extent with GDF-5, can modulate human BMSCs toward collagenous soft tissue when applied to a 3D hybrid construct. The use of growth factors could play an important role in the improvement of ligament tissue engineering.

  1. Matrix effect and recovery terminology issues in regulated drug bioanalysis.

    PubMed

    Huang, Yong; Shi, Robert; Gee, Winnie; Bonderud, Richard

    2012-02-01

    Understanding the meaning of the terms used in the bioanalytical method validation guidance is essential for practitioners to implement best practice. However, terms that have several meanings or that have different interpretations exist within bioanalysis, and this may give rise to differing practices. In this perspective we discuss an important but often confusing term - 'matrix effect (ME)' - in regulated drug bioanalysis. The ME can be interpreted as either the ionization change or the measurement bias of the method caused by the nonanalyte matrix. The ME definition dilemma makes its evaluation challenging. The matrix factor is currently used as a standard method for evaluation of ionization changes caused by the matrix in MS-based methods. Standard additions to pre-extraction samples have been suggested to evaluate the overall effects of a matrix from different sources on the analytical system, because it covers ionization variation and extraction recovery variation. We also provide our personal views on the term 'recovery'.

  2. Massively parallel sparse matrix function calculations with NTPoly

    NASA Astrophysics Data System (ADS)

    Dawson, William; Nakajima, Takahito

    2018-04-01

    We present NTPoly, a massively parallel library for computing the functions of sparse, symmetric matrices. The theory of matrix functions is a well developed framework with a wide range of applications including differential equations, graph theory, and electronic structure calculations. One particularly important application area is diagonalization free methods in quantum chemistry. When the input and output of the matrix function are sparse, methods based on polynomial expansions can be used to compute matrix functions in linear time. We present a library based on these methods that can compute a variety of matrix functions. Distributed memory parallelization is based on a communication avoiding sparse matrix multiplication algorithm. OpenMP task parallellization is utilized to implement hybrid parallelization. We describe NTPoly's interface and show how it can be integrated with programs written in many different programming languages. We demonstrate the merits of NTPoly by performing large scale calculations on the K computer.

  3. Social cognition in schizophrenia: cognitive and affective factors.

    PubMed

    Ziv, Ido; Leiser, David; Levine, Joseph

    2011-01-01

    Social cognition refers to how people conceive, perceive, and draw inferences about mental and emotional states of others in the social world. Previous studies suggest that the concept of social cognition involves several abilities, including those related to affect and cognition. The present study analyses the deficits of individuals with schizophrenia in two areas of social cognition: Theory of Mind (ToM) and emotion recognition and processing. Examining the impairment of these abilities in patients with schizophrenia has the potential to elucidate the neurophysiological regions involved in social cognition and may also have the potential to aid rehabilitation. Two experiments were conducted. Both included the same five tasks: first- and second-level false-belief ToM tasks, emotion inferencing, understanding of irony, and matrix reasoning (a WAIS-R subtest). The matrix reasoning task was administered to evaluate and control for the association of the other tasks with analytic reasoning skills. Experiment 1 involved factor analysis of the task performance of 75 healthy participants. Experiment 2 compared 30 patients with schizophrenia to an equal number of matched controls. Results. (1) The five tasks were clearly divided into two factors corresponding to the two areas of social cognition, ToM and emotion recognition and processing. (2) Schizophrenics' performance was impaired on all tasks, particularly on those loading heavily on the analytic component (matrix reasoning and second-order ToM). (3) Matrix reasoning, second-level ToM (ToM2), and irony were found to distinguish patients from controls, even when all other tasks that revealed significant impairment in the patients' performance were taken into account. The two areas of social cognition examined are related to distinct factors. The mechanism for answering ToM questions (especially ToM2) depends on analytic reasoning capabilities, but the difficulties they present to individuals with schizophrenia are due

  4. Insulin-like growth factor binding proteins initiate cell death and extracellular matrix remodeling in the mammary gland.

    PubMed

    Flint, D J; Boutinaud, M; Tonner, E; Wilde, C J; Hurley, W; Accorsi, P A; Kolb, A F; Whitelaw, C B A; Beattie, J; Allan, G J

    2005-08-01

    We have demonstrated that insulin-like growth factor binding protein-5 (IGFBP-5) production by mammary epithelial cells increases dramatically during forced involution of the mammary gland in rats, mice and pigs. We proposed that growth hormone (GH) increases the survival factor IGF-I, whilst prolactin (PRL) enhances the effects of GH by decreasing the concentration of IGFBP-5, which would otherwise inhibit the actions of IGFs. To demonstrate a causal relationship between IGFBP-5 and cell death, we created transgenic mice expressing IGFBP-5, specifically, in the mammary gland. DNA content in the mammary glands of transgenic mice was decreased as early as day 10 of pregnancy. Mammary cell number and milk synthesis were both decreased by approximately 50% during the first 10 days of lactation. The concentrations of the pro-apoptotic molecule caspase-3 was increased in transgenic animals whilst the concentrations of two pro-survival molecules Bcl-2 and Bcl-x were both decreased. In order to examine whether IGFBP-5 acts by inhibiting the survival effect of IGF-I, we examined IGF receptor- and Akt-phoshorylation and showed that both were inhibited. These studies also indicated that the effects of IGFBP-5 could be mediated in part by IGF-independent effects involving potential interactions with components of the extracellular matrix involved in tissue remodeling, such as components of the plasminogen system, and the matrix metallo-proteinases (MMPs). Mammary development was normalised in transgenic mice by R3-IGF-I, an analogue of IGF-I which binds weakly to IGFBPs, although milk production was only partially restored. In contrast, treatment with prolactin was able to inhibit early involutionary processes in normal mice but was unable to prevent this in mice over-expressing IGFBP-5, although it was able to inhibit activation of MMPs. Thus, IGFBP-5 can simultaneously inhibit IGF action and activate the plasminogen system thereby coordinating cell death and tissue

  5. Extending injury prevention methodology to chemical terrorism preparedness: the Haddon Matrix and sarin.

    PubMed

    Varney, Shawn; Hirshon, Jon Mark; Dischinger, Patricia; Mackenzie, Colin

    2006-01-01

    The Haddon Matrix offers a classic epidemiological model for studying injury prevention. This methodology places the public health concepts of agent, host, and environment within the three sequential phases of an injury-producing incident-pre-event, event, and postevent. This study uses this methodology to illustrate how it could be applied in systematically preparing for a mass casualty disaster such as an unconventional sarin attack in a major urban setting. Nineteen city, state, federal, and military agencies responded to the Haddon Matrix chemical terrorism preparedness exercise and offered feedback in the data review session. Four injury prevention strategies (education, engineering, enforcement, and economics) were applied to the individual factors and event phases of the Haddon Matrix. The majority of factors identified in all phases were modifiable, primarily through educational interventions focused on individual healthcare providers and first responders. The Haddon Matrix provides a viable means of studying an unconventional problem, allowing for the identification of modifiable factors to decrease the type and severity of injuries following a mass casualty disaster such as a sarin release. This strategy could be successfully incorporated into disaster planning for other weapons attacks that could potentially cause mass casualties.

  6. Monocyte-specific Accessibility of a Matrix Attachment Region in the Tumor Necrosis Factor Locus*

    PubMed Central

    Biglione, Sebastian; Tsytsykova, Alla V.; Goldfeld, Anne E.

    2011-01-01

    Regulation of TNF gene expression is cell type- and stimulus-specific. We have previously identified highly conserved noncoding regulatory elements within DNase I-hypersensitive sites (HSS) located 9 kb upstream (HSS−9) and 3 kb downstream (HSS+3) of the TNF gene, which play an important role in the transcriptional regulation of TNF in T cells. They act as enhancers and interact with the TNF promoter and with each other, generating a higher order chromatin structure. Here, we report a novel monocyte-specific AT-rich DNase I-hypersensitive element located 7 kb upstream of the TNF gene (HSS−7), which serves as a matrix attachment region in monocytes. We show that HSS−7 associates with topoisomerase IIα (Top2) in vivo and that induction of endogenous TNF mRNA expression is suppressed by etoposide, a Top2 inhibitor. Moreover, Top2 binds to and cleaves HSS−7 in in vitro analysis. Thus, HSS−7, which is selectively accessible in monocytes, can tether the TNF locus to the nuclear matrix via matrix attachment region formation, potentially promoting TNF gene expression by acting as a Top2 substrate. PMID:22027829

  7. Matrix- and plasma-derived peptides promote tissue-specific injury responses and wound healing in diabetic swine.

    PubMed

    Sheets, Anthony R; Massey, Conner J; Cronk, Stephen M; Iafrati, Mark D; Herman, Ira M

    2016-07-02

    , peptide treatment increases mRNA expression of several pro-angiogenic, epithelializing, and matrix-remodeling factors, importantly including balanced inductions in matrix metalloproteinase-2, -9, and tissue inhibitor of metalloproteinases-1, lending further insight into their mechanisms. Comb1 and UN3 stimulate wound resolution in diabetic Yorkshire swine through upregulation of multiple reparative growth factors and cytokines, especially matrix metalloproteinases and inhibitors that may aid in reversing the proteolytic imbalance characteristic of chronically inflamed non-healing wounds. Together, these peptides should have great therapeutic potential for all patients in need of healing, regardless of injury etiology.

  8. Factorization-based texture segmentation

    DOE PAGES

    Yuan, Jiangye; Wang, Deliang; Cheriyadat, Anil M.

    2015-06-17

    This study introduces a factorization-based approach that efficiently segments textured images. We use local spectral histograms as features, and construct an M × N feature matrix using M-dimensional feature vectors in an N-pixel image. Based on the observation that each feature can be approximated by a linear combination of several representative features, we factor the feature matrix into two matrices-one consisting of the representative features and the other containing the weights of representative features at each pixel used for linear combination. The factorization method is based on singular value decomposition and nonnegative matrix factorization. The method uses local spectral histogramsmore » to discriminate region appearances in a computationally efficient way and at the same time accurately localizes region boundaries. Finally, the experiments conducted on public segmentation data sets show the promise of this simple yet powerful approach.« less

  9. Endocytosis of collagen by hepatic stellate cells regulates extracellular matrix dynamics

    PubMed Central

    Bi, Yan; Mukhopadhyay, Dhriti; Drinane, Mary; Ji, Baoan; Li, Xing; Cao, Sheng

    2014-01-01

    Hepatic stellate cells (HSCs) generate matrix, which in turn may also regulate HSCs function during liver fibrosis. We hypothesized that HSCs may endocytose matrix proteins to sense and respond to changes in microenvironment. Primary human HSCs, LX2, or mouse embryonic fibroblasts (MEFs) [wild-type; c-abl−/−; or Yes, Src, and Fyn knockout mice (YSF−/−)] were incubated with fluorescent-labeled collagen or gelatin. Fluorescence-activated cell sorting analysis and confocal microscopy were used for measuring cellular internalization of matrix proteins. Targeted PCR array and quantitative real-time PCR were used to evaluate gene expression changes. HSCs and LX2 cells endocytose collagens in a concentration- and time-dependent manner. Endocytosed collagen colocalized with Dextran 10K, a marker of macropinocytosis, and 5-ethylisopropyl amiloride, an inhibitor of macropinocytosis, reduced collagen internalization by 46%. Cytochalasin D and ML7 blocked collagen internalization by 47% and 45%, respectively, indicating that actin and myosin are critical for collagen endocytosis. Wortmannin and AKT inhibitor blocked collagen internalization by 70% and 89%, respectively, indicating that matrix macropinocytosis requires phosphoinositide-3-kinase (PI3K)/AKT signaling. Overexpression of dominant-negative dynamin-2 K44A blocked matrix internalization by 77%, indicating a role for dynamin-2 in matrix macropinocytosis. Whereas c-abl−/− MEF showed impaired matrix endocytosis, YSF−/− MEF surprisingly showed increased matrix endocytosis. It was also associated with complex gene regulations that related with matrix dynamics, including increased matrix metalloproteinase 9 (MMP-9) mRNA levels and zymographic activity. HSCs endocytose matrix proteins through macropinocytosis that requires a signaling network composed of PI3K/AKT, dynamin-2, and c-abl. Interaction with extracellular matrix regulates matrix dynamics through modulating multiple gene expressions including MMP-9

  10. Endocytosis of collagen by hepatic stellate cells regulates extracellular matrix dynamics.

    PubMed

    Bi, Yan; Mukhopadhyay, Dhriti; Drinane, Mary; Ji, Baoan; Li, Xing; Cao, Sheng; Shah, Vijay H

    2014-10-01

    Hepatic stellate cells (HSCs) generate matrix, which in turn may also regulate HSCs function during liver fibrosis. We hypothesized that HSCs may endocytose matrix proteins to sense and respond to changes in microenvironment. Primary human HSCs, LX2, or mouse embryonic fibroblasts (MEFs) [wild-type; c-abl(-/-); or Yes, Src, and Fyn knockout mice (YSF(-/-))] were incubated with fluorescent-labeled collagen or gelatin. Fluorescence-activated cell sorting analysis and confocal microscopy were used for measuring cellular internalization of matrix proteins. Targeted PCR array and quantitative real-time PCR were used to evaluate gene expression changes. HSCs and LX2 cells endocytose collagens in a concentration- and time-dependent manner. Endocytosed collagen colocalized with Dextran 10K, a marker of macropinocytosis, and 5-ethylisopropyl amiloride, an inhibitor of macropinocytosis, reduced collagen internalization by 46%. Cytochalasin D and ML7 blocked collagen internalization by 47% and 45%, respectively, indicating that actin and myosin are critical for collagen endocytosis. Wortmannin and AKT inhibitor blocked collagen internalization by 70% and 89%, respectively, indicating that matrix macropinocytosis requires phosphoinositide-3-kinase (PI3K)/AKT signaling. Overexpression of dominant-negative dynamin-2 K44A blocked matrix internalization by 77%, indicating a role for dynamin-2 in matrix macropinocytosis. Whereas c-abl(-/-) MEF showed impaired matrix endocytosis, YSF(-/-) MEF surprisingly showed increased matrix endocytosis. It was also associated with complex gene regulations that related with matrix dynamics, including increased matrix metalloproteinase 9 (MMP-9) mRNA levels and zymographic activity. HSCs endocytose matrix proteins through macropinocytosis that requires a signaling network composed of PI3K/AKT, dynamin-2, and c-abl. Interaction with extracellular matrix regulates matrix dynamics through modulating multiple gene expressions including MMP-9

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

    NASA Astrophysics Data System (ADS)

    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.

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

    PubMed

    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.

  13. Identification of candidate angiogenic inhibitors processed by matrix metalloproteinase 2 (MMP-2) in cell-based proteomic screens: disruption of vascular endothelial growth factor (VEGF)/heparin affin regulatory peptide (pleiotrophin) and VEGF/Connective tissue growth factor angiogenic inhibitory complexes by MMP-2 proteolysis.

    PubMed

    Dean, Richard A; Butler, Georgina S; Hamma-Kourbali, Yamina; Delbé, Jean; Brigstock, David R; Courty, José; Overall, Christopher M

    2007-12-01

    Matrix metalloproteinases (MMPs) exert both pro- and antiangiogenic functions by the release of cytokines or proteolytically generated angiogenic inhibitors from extracellular matrix and basement membrane remodeling. In the Mmp2-/- mouse neovascularization is greatly reduced, but the mechanistic aspects of this remain unclear. Using isotope-coded affinity tag labeling of proteins analyzed by multidimensional liquid chromatography and tandem mass spectrometry we explored proteome differences between Mmp2-/- cells and those rescued by MMP-2 transfection. Proteome signatures that are hallmarks of proteolysis revealed cleavage of many known MMP-2 substrates in the cellular context. Proteomic evidence of MMP-2 processing of novel substrates was found. Insulin-like growth factor binding protein 6, follistatin-like 1, and cystatin C protein cleavage by MMP-2 was biochemically confirmed, and the cleavage sites in heparin affin regulatory peptide (HARP; pleiotrophin) and connective tissue growth factor (CTGF) were sequenced by matrix-assisted laser desorption ionization-time of flight mass spectrometry. MMP-2 processing of HARP and CTGF released vascular endothelial growth factor (VEGF) from angiogenic inhibitory complexes. The cleaved HARP N-terminal domain increased HARP-induced cell proliferation, whereas the HARP C-terminal domain was antagonistic and decreased cell proliferation and migration. Hence the unmasking of cytokines, such as VEGF, by metalloproteinase processing of their binding proteins is a new mechanism in the control of cytokine activation and angiogenesis.

  14. Identification of Candidate Angiogenic Inhibitors Processed by Matrix Metalloproteinase 2 (MMP-2) in Cell-Based Proteomic Screens: Disruption of Vascular Endothelial Growth Factor (VEGF)/Heparin Affin Regulatory Peptide (Pleiotrophin) and VEGF/Connective Tissue Growth Factor Angiogenic Inhibitory Complexes by MMP-2 Proteolysis▿ †

    PubMed Central

    Dean, Richard A.; Butler, Georgina S.; Hamma-Kourbali, Yamina; Delbé, Jean; Brigstock, David R.; Courty, José; Overall, Christopher M.

    2007-01-01

    Matrix metalloproteinases (MMPs) exert both pro- and antiangiogenic functions by the release of cytokines or proteolytically generated angiogenic inhibitors from extracellular matrix and basement membrane remodeling. In the Mmp2−/− mouse neovascularization is greatly reduced, but the mechanistic aspects of this remain unclear. Using isotope-coded affinity tag labeling of proteins analyzed by multidimensional liquid chromatography and tandem mass spectrometry we explored proteome differences between Mmp2−/− cells and those rescued by MMP-2 transfection. Proteome signatures that are hallmarks of proteolysis revealed cleavage of many known MMP-2 substrates in the cellular context. Proteomic evidence of MMP-2 processing of novel substrates was found. Insulin-like growth factor binding protein 6, follistatin-like 1, and cystatin C protein cleavage by MMP-2 was biochemically confirmed, and the cleavage sites in heparin affin regulatory peptide (HARP; pleiotrophin) and connective tissue growth factor (CTGF) were sequenced by matrix-assisted laser desorption ionization-time of flight mass spectrometry. MMP-2 processing of HARP and CTGF released vascular endothelial growth factor (VEGF) from angiogenic inhibitory complexes. The cleaved HARP N-terminal domain increased HARP-induced cell proliferation, whereas the HARP C-terminal domain was antagonistic and decreased cell proliferation and migration. Hence the unmasking of cytokines, such as VEGF, by metalloproteinase processing of their binding proteins is a new mechanism in the control of cytokine activation and angiogenesis. PMID:17908800

  15. Salient Object Detection via Structured Matrix Decomposition.

    PubMed

    Peng, Houwen; Li, Bing; Ling, Haibin; Hu, Weiming; Xiong, Weihua; Maybank, Stephen J

    2016-05-04

    Low-rank recovery models have shown potential for salient object detection, where a matrix is decomposed into a low-rank matrix representing image background and a sparse matrix identifying salient objects. Two deficiencies, however, still exist. First, previous work typically assumes the elements in the sparse matrix are mutually independent, ignoring the spatial and pattern relations of image regions. Second, when the low-rank and sparse matrices are relatively coherent, e.g., when there are similarities between the salient objects and background or when the background is complicated, it is difficult for previous models to disentangle them. To address these problems, we propose a novel structured matrix decomposition model with two structural regularizations: (1) a tree-structured sparsity-inducing regularization that captures the image structure and enforces patches from the same object to have similar saliency values, and (2) a Laplacian regularization that enlarges the gaps between salient objects and the background in feature space. Furthermore, high-level priors are integrated to guide the matrix decomposition and boost the detection. We evaluate our model for salient object detection on five challenging datasets including single object, multiple objects and complex scene images, and show competitive results as compared with 24 state-of-the-art methods in terms of seven performance metrics.

  16. Study of the validity of a job-exposure matrix for psychosocial work factors: results from the national French SUMER survey.

    PubMed

    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.

  17. Uncertainty in positive matrix factorization solutions for PAHs in surface sediments of the Yangtze River Estuary in different seasons.

    PubMed

    Liu, Ruimin; Men, Cong; Yu, Wenwen; Xu, Fei; Wang, Qingrui; Shen, Zhenyao

    2018-01-01

    To examine the variabilities of source contributions in the Yangtze River Estuary (YRE), the uncertainty based on the positive matrix factorization (PMF) was applied to the source apportionment of the 16 priority PAHs in 120 surface sediment samples from four seasons. Based on the signal-to-noise ratios, the PAHs categorized as "Bad" might drop out of the estimation of bootstrap. Next, the spatial variability of residuals was applied to determine which species with non-normal curves should be excluded. The median values from the bootstrapped solutions were chosen as the best estimate of the true factor contributions, and the intervals from 5th to 95th percentile represent the variability in each sample factor contribution. Based on the results, the median factor contributions of wood grass combustion and coke plant emissions were highly correlated with the variability (R 2  = 0.6797-0.9937) in every season. Meanwhile, the factor of coal and gasoline combustion had large variability with lower R 2 values in every season, especially in summer (0.4784) and winter (0.2785). The coefficient of variation (CV) values based on the Bootstrap (BS) simulations were applied to indicate the uncertainties of PAHs in every factor of each season. Acy, NaP and BgP always showed higher CV values, which suggested higher uncertainties in the BS simulations, and the PAH with the lowest concentration among all PAHs usually became the species with higher uncertainties. Copyright © 2017 Elsevier Ltd. All rights reserved.

  18. Matrix Perturbation Techniques in Structural Dynamics

    NASA Technical Reports Server (NTRS)

    Caughey, T. K.

    1973-01-01

    Matrix perturbation are developed techniques which can be used in the dynamical analysis of structures where the range of numerical values in the matrices extreme or where the nature of the damping matrix requires that complex valued eigenvalues and eigenvectors be used. The techniques can be advantageously used in a variety of fields such as earthquake engineering, ocean engineering, aerospace engineering and other fields concerned with the dynamical analysis of large complex structures or systems of second order differential equations. A number of simple examples are included to illustrate the techniques.

  19. Mass Casualty Incidents in the Underground Mining Industry: Applying the Haddon Matrix on an Integrative Literature Review.

    PubMed

    Engström, Karl Gunnar; Angrén, John; Björnstig, Ulf; Saveman, Britt-Inger

    2018-02-01

    Underground mining is associated with obvious risks that can lead to mass casualty incidents. Information about such incidents was analyzed in an integrated literature review. A literature search (1980-2015) identified 564 modern-era underground mining reports from countries sharing similar occupational health legislation. These reports were condensed to 31 reports after consideration of quality grading and appropriateness to the aim. The Haddon matrix was used for structure, separating human factors from technical and environmental details, and timing. Most of the reports were descriptive regarding injury-creating technical and environmental factors. The influence of rock characteristics was an important pre-event environmental factor. The organic nature of coal adds risks not shared in hard-rock mines. A sequence of mechanisms is commonly described, often initiated by a human factor in interaction with technology and step-wise escalation to involve environmental circumstances. Socioeconomic factors introduce heterogeneity. In the Haddon matrix, emergency medical services are mainly a post-event environmental issue, which were not well described in the available literature. The US Quecreek Coal Mine incident of 2002 stands out as a well-planned rescue mission. Evaluation of the preparedness to handle underground mining incidents deserves further scientific attention. Preparedness must include the medical aspects of rescue operations. (Disaster Med Public Health Preparedness. 2018;12:138-146).

  20. Comprehensive T-Matrix Reference Database: A 2012 - 2013 Update

    NASA Technical Reports Server (NTRS)

    Mishchenko, Michael I.; Videen, Gorden; Khlebtsov, Nikolai G.; Wriedt, Thomas

    2013-01-01

    The T-matrix method is one of the most versatile, efficient, and accurate theoretical techniques widely used for numerically exact computer calculations of electromagnetic scattering by single and composite particles, discrete random media, and particles imbedded in complex environments. This paper presents the fifth update to the comprehensive database of peer-reviewed T-matrix publications initiated by us in 2004 and includes relevant publications that have appeared since 2012. It also lists several earlier publications not incorporated in the original database, including Peter Waterman's reports from the 1960s illustrating the history of the T-matrix approach and demonstrating that John Fikioris and Peter Waterman were the true pioneers of the multi-sphere method otherwise known as the generalized Lorenz - Mie theory.

  1. Matrix crack extension at a frictionally constrained fiber

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Selvadurai, A.P.S.

    1994-07-01

    The paper presents the application of a boundary element scheme to the study of the behavior of a penny-shaped matrix crack which occurs at an isolated fiber which is frictionally constrained. An incremental technique is used to examine the progression of self similar extension of the matrix crack due to the axial straining of the composite region. The extension of the crack occurs at the attainment of the critical stress intensity factor in the crack opening mode. Iterative techniques are used to determine the extent to crack enlargement and the occurrence of slip and locked regions in the frictional fiber-matrixmore » interface. The studies illustrate the role of fiber-matrix interface friction on the development of stable cracks in such frictionally constrained zones. The methodologies are applied to typical isolated fiber configurations of interest to fragmentation tests.« less

  2. Modifying Matrix Materials to Increase Wetting and Adhesion

    NASA Technical Reports Server (NTRS)

    Zhong, Katie

    2011-01-01

    In an alternative approach to increasing the degrees of wetting and adhesion between the fiber and matrix components of organic-fiber/polymer matrix composite materials, the matrix resins are modified. Heretofore, it has been common practice to modify the fibers rather than the matrices: The fibers are modified by chemical and/or physical surface treatments prior to combining the fibers with matrix resins - an approach that entails considerable expense and usually results in degradation (typically, weakening) of fibers. The alternative approach of modifying the matrix resins does not entail degradation of fibers, and affords opportunities for improving the mechanical properties of the fiber composites. The alternative approach is more cost-effective, not only because it eliminates expensive fiber-surface treatments but also because it does not entail changes in procedures for manufacturing conventional composite-material structures. The alternative approach is best described by citing an example of its application to a composite of ultra-high-molecular- weight polyethylene (UHMWPE) fibers in an epoxy matrix. The epoxy matrix was modified to a chemically reactive, polarized epoxy nano-matrix to increase the degrees of wetting and adhesion between the fibers and the matrix. The modification was effected by incorporating a small proportion (0.3 weight percent) of reactive graphitic nanofibers produced from functionalized nanofibers into the epoxy matrix resin prior to combining the resin with the UHMWPE fibers. The resulting increase in fiber/matrix adhesion manifested itself in several test results, notably including an increase of 25 percent in the maximum fiber pullout force and an increase of 60-65 percent in fiber pullout energy. In addition, it was conjectured that the functionalized nanofibers became involved in the cross linking reaction of the epoxy resin, with resultant enhancement of the mechanical properties and lower viscosity of the matrix.

  3. LOXL4 Is Induced by Transforming Growth Factor β1 through Smad and JunB/Fra2 and Contributes to Vascular Matrix Remodeling

    PubMed Central

    Busnadiego, Oscar; González-Santamaría, José; Lagares, David; Guinea-Viniegra, Juan; Pichol-Thievend, Cathy; Muller, Laurent

    2013-01-01

    Transforming growth factor β1 (TGF-β1) is a pleiotropic factor involved in the regulation of extracellular matrix (ECM) synthesis and remodeling. In search for novel genes mediating the action of TGF-β1 on vascular ECM, we identified the member of the lysyl oxidase family of matrix-remodeling enzymes, lysyl oxidase-like 4 (LOXL4), as a direct target of TGF-β1 in aortic endothelial cells, and we dissected the molecular mechanism of its induction. Deletion mapping and mutagenesis analysis of the LOXL4 promoter demonstrated the absolute requirement of a distal enhancer containing an activator protein 1 (AP-1) site and a Smad binding element for TGF-β1 to induce LOXL4 expression. Functional cooperation between Smad proteins and the AP-1 complex composed of JunB/Fra2 accounted for the action of TGF-β1, which involved the extracellular signal-regulated kinase (ERK)-dependent phosphorylation of Fra2. We furthermore provide evidence that LOXL4 was extracellularly secreted and significantly contributed to ECM deposition and assembly. These results suggest that TGF-β1-dependent expression of LOXL4 plays a role in vascular ECM homeostasis, contributing to vascular processes associated with ECM remodeling and fibrosis. PMID:23572561

  4. Matrix Treatment of Ray Optics.

    ERIC Educational Resources Information Center

    Quon, W. Steve

    1996-01-01

    Describes a method to combine two learning experiences--optical physics and matrix mathematics--in a straightforward laboratory experiment that allows engineering/physics students to integrate a variety of learning insights and technical skills, including using lasers, studying refraction through thin lenses, applying concepts of matrix…

  5. Paracrine regulation of matrix metalloproteinase expression in the normal human endometrium.

    PubMed

    Osteen, K G; Keller, N R; Feltus, F A; Melner, M H

    1999-01-01

    Endometrial expression of matrix metalloproteinase (MMP)-3, MMP-7 and MMP-11 occurs during menstrual breakdown and subsequent estrogen-mediated growth, but not during the secretory phase. These enzymes are suppressed by progesterone treatment. Paracrine factors, including transforming growth factor-beta (TGF-beta) and retinoic acid, are also critical for MMP regulation in the endometrium. In contrast, inflammatory cytokines such as interleukin-1alpha may block or interfere with steroid-mediated MMP regulation at ectopic sites of growth. Using in vitro models, our laboratory has investigated the complex interactions between progesterone and locally produced cytokines that may affect MMP expression during the development of endometriosis. Our results indicate that targeting the regulation of MMPs may represent an appropriate therapeutic strategy for the treatment of endometriosis. Copyrightz1999S. KargerAG,Basel

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

    PubMed Central

    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 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. PMID:25120710

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

    PubMed

    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.

  8. 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)

    NASA Astrophysics Data System (ADS)

    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

  9. Cladding material, tube including such cladding material and methods of forming the same

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Garnier, John E.; Griffith, George W.

    A multi-layered cladding material including a ceramic matrix composite and a metallic material, and a tube formed from the cladding material. The metallic material forms an inner liner of the tube and enables hermetic sealing of thereof. The metallic material at ends of the tube may be exposed and have an increased thickness enabling end cap welding. The metallic material may, optionally, be formed to infiltrate voids in the ceramic matrix composite, the ceramic matrix composite encapsulated by the metallic material. The ceramic matrix composite includes a fiber reinforcement and provides increased mechanical strength, stiffness, thermal shock resistance and highmore » temperature load capacity to the metallic material of the inner liner. The tube may be used as a containment vessel for nuclear fuel used in a nuclear power plant or other reactor. Methods for forming the tube comprising the ceramic matrix composite and the metallic material are also disclosed.« less

  10. Position Index for the Matrix Light Source

    NASA Astrophysics Data System (ADS)

    Takahashi, Hiroshi; Kobayashi, Yoshinori; Onda, Shou; Irikura, Takashi

    It is expected that in the future white LEDs will be widely used in practical applications including replacing conventional lighting in offices and homes. The white LED light source of matrix arrangement is also considered in it. On the other hand, although now the unified glare rating (UGR) is widely used for evaluation of the discomfort glare of the interior lighting, UGR is a thing for a uniform light source, and its application to the matrix light sources that have non-uniform luminance has not been considered. The aim of this study is to clarify the position index which is one of element of UGR for the matrix light source. In this case, to apply the position index for a matrix light source to UGR, the concept of the revised position index is invented. As the preliminary experiment, method for measuring the position index was conducted, and as the experiment, position index for the matrix light source was conducted and compared with the uniform light source. The results of the experiments show that the position index is decided by the relative angle between line of sight and light source. It is also found that the matrix light source have larger position index than uniform light source. Furthermore, it is shown that the discomfort glare caused by a matrix light source can be evaluated by applying the revised position index to the UGR.

  11. Factor Covariance Analysis in Subgroups.

    ERIC Educational Resources Information Center

    Pennell, Roger

    The problem considered is that of an investigator sampling two or more correlation matrices and desiring to fit a model where a factor pattern matrix is assumed to be identical across samples and we need to estimate only the factor covariance matrix and the unique variance for each sample. A flexible, least squares solution is worked out and…

  12. Mueller matrix imaging study to detect the dental demineralization

    NASA Astrophysics Data System (ADS)

    Chen, Qingguang; Shen, Huanbo; Wang, Binqiang

    2018-01-01

    Mueller matrix is an optical parameter invasively to reveal the structure information of anisotropic material. Dental tissue has the ordered structure including dental enamel prism and dentinal tubule. The ordered structure of teeth surface will be destroyed by demineralization. The structure information has the possibility to reflect the dental demineralization. In the paper, the experiment setup was built to obtain the Mueller matrix images based on the dual- wave plate rotation method. Two linear polarizer and two quarter-wave plate were rotated by electric control revolving stage respectively to capture 16 images at different group of polarization states. Therefore, Mueller matrix image can be calculated from the 16 images. On this basis, depolarization index, the diattenuation index and retardance index of the Mueller matrix were analyzed by Lu-Chipman polarization decomposition method. Mueller matrix images of artificial demineralized enamels at different stages were analyzed and the results show the possibility to detect the dental demineralization using Mueller matrix imaging method.

  13. The use of type 1 collagen scaffold containing stromal cell-derived factor-1 to create a matrix environment conducive to partial-thickness cartilage defects repair.

    PubMed

    Zhang, Wei; Chen, Jialin; Tao, Jiadong; Jiang, Yangzi; Hu, Changchang; Huang, Lu; Ji, Junfeng; Ouyang, Hong Wei

    2013-01-01

    Despite the presence of cartilage-derived mesenchymal stem cells (C-MSCs) and synovial membrane-derived mesenchymal stem cells (SM-MSCs) populations, partial-thickness cartilage defects, in contrast to the full-thickness defects, are devoid of spontaneous repair capacity. This study aims to create an in situ matrix environment conducive to C-MSCs and SM-MSCs to promote cartilage self-repair. Spontaneous repair with MSCs migration into the defect area was observed in full-thickness defects, but not in partial-thickness defects in rabbit model. Ex vivo and in vitro studies showed that subchondral bone or type 1 collagen (col1) scaffold was more permissive for MSCs adhesion than cartilage or type 2 collagen (col2) scaffold and induced robust stromal cell-derived factors-1 (SDF-1) dependent migration of MSCs. Furthermore, creating a matrix environment with col1 scaffold containing SDF-1 enhanced in situ self-repair of partial-thickness defects in rabbit 6 weeks post-injury. Hence, the inferior self-repair capacity in partial-thickness defects is partially owing to the non-permissive matrix environment. Creating an in situ matrix environment conducive to C-MSCs and SM-MSCs migration and adhesion with col1 scaffold containing SDF-1 can be exploited to improve self-repair capacity of cartilage. Copyright © 2012 Elsevier Ltd. All rights reserved.

  14. Source apportionment of 1 h semi-continuous data during the 2005 Study of Organic Aerosols in Riverside (SOAR) using positive matrix factorization

    NASA Astrophysics Data System (ADS)

    Eatough, Delbert J.; Grover, Brett D.; Woolwine, Woods R.; Eatough, Norman L.; Long, Russell; Farber, Robert

    Positive matrix factorization (PMF2) was used to elucidate sources of fine particulate material (PM 2.5) for a study conducted during July and August 2005, in Riverside, CA. One-hour averaged semi-continuous measurements were made with a suite of instruments to provide PM 2.5 mass and chemical composition data. Total PM 2.5 mass concentrations (non-volatile plus semi-volatile) were measured with an R&P filter dynamic measurement system (FDMS TEOM) and a conventional TEOM monitor was used to measure non-volatile mass concentrations. PM 2.5 chemical species monitors included a dual-oven Sunset monitor to measure both non-volatile and semi-volatile carbonaceous material, an ion chromatographic-based monitor to measure sulfate and nitrate and an Anderson Aethalometer to measure black carbon (BC). Gas phase data including CO, NO 2, NO x and O 3 were also collected during the sampling period. In addition, single-particle measurements were made using aerosol time-of-flight mass spectrometry (ATOFMS). Twenty different single-particle types consistent with those observed in previous ATOFMS studies in Riverside were identified for the PMF2 analysis. Finally, time-of-flight aerosol mass spectrometry (ToF-AMS) provided data on markers of primary and secondary organic aerosol. Two distinct PMF2 analyses were performed. In analysis 1, all the data except for the ATOFMS and ToF-AMS data were used in an initial evaluation of sources at Riverside during the study. PMF2 was able to identify six factors from the data set corresponding to both primary and secondary sources, primarily from automobile emissions, diesel emissions, secondary nitrate formation, a secondary photochemical associated source, organic emissions and Basin transported pollutants. In analysis 2, the ATOFMS and ToF-AMS data were included in the analysis. In the second analysis, PMF2 was able to identify 16 factors with a variety of both primary and secondary factors being identified, corresponding to both primary

  15. Does the performance of wet granulation and tablet hardness affect the drug dissolution profile of carvedilol in matrix tablets?

    PubMed

    Košir, Darjan; Ojsteršek, Tadej; Vrečer, Franc

    2018-06-14

    Wet granulation is mostly used process for manufacturing matrix tablets. Compared to the direct compression method, it allows for a better flow and compressibility properties of compression mixtures. Granulation, including process parameters and tableting, can influence critical quality attributes (CQAs) of hydrophilic matrix tablets. One of the most important CQAs is the drug release profile. We studied the influence of granulation process parameters (type of nozzle and water quantity used as granulation liquid) and tablet hardness on the drug release profile. Matrix tablets contained HPMC K4M hydrophilic matrix former and carvedilol as a model drug. The influence of selected HPMC characteristics on the drug release profile was also evaluated using two additional HPMC batches. For statistical evaluation, partial least square (PLS) models were generated for each time point of the drug release profile using the same number of latent factors. In this way, it was possible to evaluate how the importance of factors influencing drug dissolution changes in dependence on time throughout the drug release profile. The results of statistical evaluation show that the granulation process parameters (granulation liquid quantity and type of nozzle) and tablet hardness significantly influence the release profile. On the other hand, the influence of HPMC characteristics is negligible in comparison to the other factors studied. Using a higher granulation liquid quantity and the standard nozzle type results in larger granules with a higher density and lower porosity, which leads to a slower drug release profile. Lower tablet hardness also slows down the release profile.

  16. A Note on the Factor Analysis of Partial Covariance Matrices

    ERIC Educational Resources Information Center

    McDonald, Roderick P.

    1978-01-01

    The relationship between the factor structure of a convariance matrix and the factor structure of a partial convariance matrix when one or more variables are partialled out of the original matrix is given in this brief note. (JKS)

  17. Develop a PWL System for Dense Graded Hot Mix Asphalt Construction, Including Pay Factors

    DOT National Transportation Integrated Search

    2015-01-01

    This research project developed a PWL system that the Nevada DOT can effectively implement on the construction of dense graded HMA mixtures. The PWL system includes pay factors that are based on pavement performance indicators such as rutting and cra...

  18. Two-faced property of a market factor in asset pricing and diversification effect

    NASA Astrophysics Data System (ADS)

    Eom, Cheoljun

    2017-04-01

    This study empirically investigates the test hypothesis that a market factor acting as a representative common factor in the pricing models has a negative influence on constructing a well-diversified portfolio from the Markowitz mean-variance optimization function (MVOF). We use the comparative correlation matrix (C-CM) method to control a single eigenvalue among all eigenvalues included in the sample correlation matrix (S-CM), through the random matrix theory (RMT). In particular, this study observes the effect of the largest eigenvalue that has the property of the market factor. According to the results, the largest eigenvalue has the highest explanatory power on the stock return changes. The C-CM without the largest eigenvalue in the S-CM constructs a more diversified portfolio capable of improving the practical applicability of the MVOF. Moreover, the more diversified portfolio constructed from this C-CM has better out-of-sample performance in the future period. These results support the test hypothesis for the two-faced property of the market factor, defined by the largest eigenvalue.

  19. Effectiveness of metal matrix and ceramic matrix composites as orbital debris shield materials

    NASA Technical Reports Server (NTRS)

    Mcgill, Preston B.; Mount, Angela R.

    1992-01-01

    The effectiveness of two metal matrix composites and one ceramic matrix material in defeating hypervelocity impacts at about 3.8 km/s are evaluated to determine the potential of these composites as spacecraft shield materials. The metal matrix composites investigated consist of SiC particles (70 percent by volume) in an aluminum matrix and Al2O3 particles (50 percent by volume) in an Al matrix. The ceramic composite consists of ZrB2 platelets in a ZrC matrix. Both the metal matrix and ceramic matrix composites are found to perform as well or better than 6061-T6 aluminum, which is presently used in the Whipple type bumper shield of Space Station Freedom. Test results indicate that the composites tested may have applications as micrometeoroid/orbital debris shield materials.

  20. Instruments for Reading Direct-Marked Data-Matrix Symbols

    NASA Technical Reports Server (NTRS)

    Schramm, Harry F.; Corder, Eric L.

    2006-01-01

    Improved optoelectronic instruments (specially configured digital cameras) for reading direct-marked data-matrix symbols on the surfaces of optically reflective objects (including specularly reflective ones) are undergoing development. Data-matrix symbols are two-dimensional binary patterns that are used, like common bar codes, for automated identification of objects. The first data-matrix symbols were checkerboard-like patterns of black-and-white rectangles, typically existing in the forms of paint, ink, or detachable labels. The major advantage of direct marking (the marks are more durable than are painted or printed symbols or detachable labels) is offset by a major disadvantage (the marks generated by some marking methods do not provide sufficient contrast to be readable by optoelectronic instruments designed to read black-and-white data-matrix symbols). Heretofore, elaborate lighting, lensing, and software schemes have been tried in efforts to solve the contrast problem in direct-mark matrix- symbol readers. In comparison with prior readers based on those schemes, the readers now undergoing development are expected to be more effective while costing less. All of the prior direct-mark matrix-symbol readers are designed to be aimed perpendicularly to marked target surfaces, and they tolerate very little angular offset. However, the reader now undergoing development not only tolerates angular offset but depends on angular offset as a means of obtaining the needed contrast, as described below. The prototype reader (see Figure 1) includes an electronic camera in the form of a charge-coupled-device (CCD) image detector equipped with a telecentric lens. It also includes a source of collimated visible light and a source of collimated infrared light for illuminating a target. The visible and infrared illumination complement each other: the visible illumination is more useful for aiming the reader toward a target, while the infrared illumination is more useful for

  1. Estimating the Inertia Matrix of a Spacecraft

    NASA Technical Reports Server (NTRS)

    Acikmese, Behcet; Keim, Jason; Shields, Joel

    2007-01-01

    A paper presents a method of utilizing some flight data, aboard a spacecraft that includes reaction wheels for attitude control, to estimate the inertia matrix of the spacecraft. The required data are digitized samples of (1) the spacecraft attitude in an inertial reference frame as measured, for example, by use of a star tracker and (2) speeds of rotation of the reaction wheels, the moments of inertia of which are deemed to be known. Starting from the classical equations for conservation of angular momentum of a rigid body, the inertia-matrix-estimation problem is formulated as a constrained least-squares minimization problem with explicit bounds on the inertia matrix incorporated as linear matrix inequalities. The explicit bounds reflect physical bounds on the inertia matrix and reduce the volume of data that must be processed to obtain a solution. The resulting minimization problem is a semidefinite optimization problem that can be solved efficiently, with guaranteed convergence to the global optimum, by use of readily available algorithms. In a test case involving a model attitude platform rotating on an air bearing, it is shown that, relative to a prior method, the present method produces better estimates from few data.

  2. Column Subset Selection, Matrix Factorization, and Eigenvalue Optimization

    DTIC Science & Technology

    2008-07-01

    Pietsch and Grothendieck, which are regarded as basic instruments in modern functional analysis [Pis86]. • The methods for computing these... Pietsch factorization and the maxcut semi- definite program [GW95]. 1.2. Overview. We focus on the algorithmic version of the Kashin–Tzafriri theorem...will see that the desired subset is exposed by factoring the random submatrix. This factorization, which was invented by Pietsch , is regarded as a basic

  3. Separating Atmospheric and Surface Contributions in Hyperspectral Imager for the Coastal Ocean (HICO) Scenes using Informed Non-Negative Matrix Factorization

    NASA Astrophysics Data System (ADS)

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

    2016-12-01

    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. These new instruments require novel approaches for processing imagery and separating surface and atmospheric signals. One approach is numerical source separation, which allows the determination of the underlying physical causes of observed signals. Improved source separation will enable hyperspectral imagery to better address key science questions relevant to climate change, including land-use changes, trends in clouds and atmospheric water vapor, and aerosol characteristics. We developed an Informed Non-negative Matrix Factorization (INMF) method for separating atmospheric and surface 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. We also explore methods to produce an initial guess of the spatial separation patterns. 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 conditions, including high and low aerosol optical thickness and cloud cover, with only minor contributions from the ocean surfaces in order to isolate the contributions of the multiple atmospheric

  4. Statistical analysis of latent generalized correlation matrix estimation in transelliptical distribution.

    PubMed

    Han, Fang; Liu, Han

    2017-02-01

    Correlation matrix plays a key role in many multivariate methods (e.g., graphical model estimation and factor analysis). The current state-of-the-art in estimating large correlation matrices focuses on the use of Pearson's sample correlation matrix. Although Pearson's sample correlation matrix enjoys various good properties under Gaussian models, its not an effective estimator when facing heavy-tail distributions with possible outliers. As a robust alternative, Han and Liu (2013b) advocated the use of a transformed version of the Kendall's tau sample correlation matrix in estimating high dimensional latent generalized correlation matrix under the transelliptical distribution family (or elliptical copula). The transelliptical family assumes that after unspecified marginal monotone transformations, the data follow an elliptical distribution. In this paper, we study the theoretical properties of the Kendall's tau sample correlation matrix and its transformed version proposed in Han and Liu (2013b) for estimating the population Kendall's tau correlation matrix and the latent Pearson's correlation matrix under both spectral and restricted spectral norms. With regard to the spectral norm, we highlight the role of "effective rank" in quantifying the rate of convergence. With regard to the restricted spectral norm, we for the first time present a "sign subgaussian condition" which is sufficient to guarantee that the rank-based correlation matrix estimator attains the optimal rate of convergence. In both cases, we do not need any moment condition.

  5. Galaxy two-point covariance matrix estimation for next generation surveys

    NASA Astrophysics Data System (ADS)

    Howlett, Cullan; Percival, Will J.

    2017-12-01

    We perform a detailed analysis of the covariance matrix of the spherically averaged galaxy power spectrum and present a new, practical method for estimating this within an arbitrary survey without the need for running mock galaxy simulations that cover the full survey volume. The method uses theoretical arguments to modify the covariance matrix measured from a set of small-volume cubic galaxy simulations, which are computationally cheap to produce compared to larger simulations and match the measured small-scale galaxy clustering more accurately than is possible using theoretical modelling. We include prescriptions to analytically account for the window function of the survey, which convolves the measured covariance matrix in a non-trivial way. We also present a new method to include the effects of super-sample covariance and modes outside the small simulation volume which requires no additional simulations and still allows us to scale the covariance matrix. As validation, we compare the covariance matrix estimated using our new method to that from a brute-force calculation using 500 simulations originally created for analysis of the Sloan Digital Sky Survey Main Galaxy Sample. We find excellent agreement on all scales of interest for large-scale structure analysis, including those dominated by the effects of the survey window, and on scales where theoretical models of the clustering normally break down, but the new method produces a covariance matrix with significantly better signal-to-noise ratio. Although only formally correct in real space, we also discuss how our method can be extended to incorporate the effects of redshift space distortions.

  6. Human kidney stone matrix: Latent potential to restrain COM induced cytotoxicity and inflammatory response.

    PubMed

    Narula, Shifa; Tandon, Simran; Baligar, Prakash; Singh, Shrawan Kumar; Tandon, Chanderdeep

    2017-12-25

    Kidney stone disease is a multi-factorial disorder resulting from the interplay of various risk factors including lifestyle, environment and genetics along with metabolic activities inside the body. However, it is difficult to determine how these factors converge to promote stone disease. Extensive investigations of kidney stone composition at the molecular level have been carried out however; its impact on the complex mechanism of stone formation is still obscure. Hence, an in vitro study was designed to investigate the attenuation of calcium oxalate toxicity by human kidney stone matrix proteins on NRK-52E cells using flowcytometry, Western blotting, RT-PCR and immunofluorescence assays. Morphological alterations in cell-crystal interaction were assessed using scanning electron microscopy. Microscopic studies showed profound impairment of COM crystal structure as a consequence of protein-crystal interactions. RT-PCR analysis and immunocytochemistry of NRK-52E cells revealed the up-regulation of inflammatory and stress biomarkers OPN and HSP-70, respectively, in response to COM toxicity; which diminished significantly in the presence of kidney stone matrix proteins. The results of present study propose that the mechanism undertaken by matrix proteins to attenuate COM induced cytotoxicity could be attributed to the modulation of crystal structure, which subsequently restraint the inflammatory response and apoptotic cell death. The inference drawn through this study could provide better understanding of the intricate process of kidney stone formation. Copyright © 2017 Elsevier B.V. All rights reserved.

  7. Endothelial cell-derived matrix promotes the metabolic functional maturation of hepatocyte via integrin-Src signalling.

    PubMed

    Guo, Xinyue; Li, Weihong; Ma, Minghui; Lu, Xin; Zhang, Haiyan

    2017-11-01

    The extracellular matrix (ECM) microenvironment is involved in the regulation of hepatocyte phenotype and function. Recently, the cell-derived extracellular matrix has been proposed to represent the bioactive and biocompatible materials of the native ECM. Here, we show that the endothelial cell-derived matrix (EC matrix) promotes the metabolic maturation of human adipose stem cell-derived hepatocyte-like cells (hASC-HLCs) through the activation of the transcription factor forkhead box protein A2 (FOXA2) and the nuclear receptors hepatocyte nuclear factor 4 alpha (HNF4α) and pregnane X receptor (PXR). Reducing the fibronectin content in the EC matrix or silencing the expression of α5 integrin in the hASC-HLCs inhibited the effect of the EC matrix on Src phosphorylation and hepatocyte maturation. The inhibition of Src phosphorylation using the inhibitor PP2 or silencing the expression of Src in hASC-HLCs also attenuated the up-regulation of the metabolic function of hASC-HLCs in a nuclear receptor-dependent manner. These data elucidate integrin-Src signalling linking the extrinsic EC matrix signals and metabolic functional maturation of hepatocyte. This study provides a model for studying the interaction between hepatocytes and non-parenchymal cell-derived matrix. © 2017 The Authors. Journal of Cellular and Molecular Medicine published by John Wiley & Sons Ltd and Foundation for Cellular and Molecular Medicine.

  8. Electrolyte matrix for molten carbonate fuel cells

    DOEpatents

    Huang, C.M.; Yuh, C.Y.

    1999-02-09

    A matrix is described for a carbonate electrolyte including a support material and an additive constituent having a relatively low melting temperature and a relatively high coefficient of thermal expansion. The additive constituent is from 3 to 45 weight percent of the matrix and is formed from raw particles whose diameter is in a range of 0.1 {micro}m to 20 {micro}m and whose aspect ratio is in a range of 1 to 50. High energy intensive milling is used to mix the support material and additive constituent during matrix formation. Also disclosed is the use of a further additive constituent comprising an alkaline earth containing material. The further additive is mixed with the support material using high energy intensive milling. 5 figs.

  9. Electrolyte matrix for molten carbonate fuel cells

    DOEpatents

    Huang, Chao M.; Yuh, Chao-Yi

    1999-01-01

    A matrix for a carbonate electrolyte including a support material and an additive constituent having a relatively low melting temperature and a relatively high coefficient of thermal expansion. The additive constituent is from 3 to 45 weight percent of the matrix and is formed from raw particles whose diameter is in a range of 0.1 .mu.m to 20 .mu.m and whose aspect ratio is in a range of 1 to 50. High energy intensive milling is used to mix the support material and additive constituent during matrix formation. Also disclosed is the use of a further additive constituent comprising an alkaline earth containing material. The further additive is mixed with the support material using high energy intensive milling.

  10. Airbreathing Hypersonic Vision-Operational-Vehicles Design Matrix

    NASA Technical Reports Server (NTRS)

    Hunt, James L.; Pegg, Robert J.; Petley, Dennis H.

    1999-01-01

    This paper presents the status of the airbreathing hypersonic airplane and space-access vision-operational-vehicle design matrix, with emphasis on horizontal takeoff and landing systems being studied at Langley; it reflects the synergies and issues, and indicates the thrust of the effort to resolve the design matrix including Mach 5 to 10 airplanes with global-reach potential, pop-up and dual-role transatmospheric vehicles and airbreathing launch systems. The convergence of several critical systems/technologies across the vehicle matrix is indicated. This is particularly true for the low speed propulsion system for large unassisted horizontal takeoff vehicles which favor turbines and/or perhaps pulse detonation engines that do not require LOX which imposes loading concerns and mission flexibility restraints.

  11. Airbreathing Hypersonic Vision-Operational-Vehicles Design Matrix

    NASA Technical Reports Server (NTRS)

    Hunt, James L.; Pegg, Robert J.; Petley, Dennis H.

    1999-01-01

    This paper presents the status of the airbreathing hypersonic airplane and space-access vision-operational-vehicle design matrix, with emphasis on horizontal takeoff and landing systems being, studied at Langley, it reflects the synergies and issues, and indicates the thrust of the effort to resolve the design matrix including Mach 5 to 10 airplanes with global-reach potential, pop-up and dual-role transatmospheric vehicles and airbreathing launch systems. The convergence of several critical systems/technologies across the vehicle matrix is indicated. This is particularly true for the low speed propulsion system for large unassisted horizontal takeoff vehicles which favor turbines and/or perhaps pulse detonation engines that do not require LOX which imposes loading concerns and mission Flexibility restraints.

  12. Computing row and column counts for sparse QR and LU factorization

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Gilbert, John R.; Li, Xiaoye S.; Ng, Esmond G.

    2001-01-01

    We present algorithms to determine the number of nonzeros in each row and column of the factors of a sparse matrix, for both the QR factorization and the LU factorization with partial pivoting. The algorithms use only the nonzero structure of the input matrix, and run in time nearly linear in the number of nonzeros in that matrix. They may be used to set up data structures or schedule parallel operations in advance of the numerical factorization. The row and column counts we compute are upper bounds on the actual counts. If the input matrix is strong Hall and theremore » is no coincidental numerical cancellation, the counts are exact for QR factorization and are the tightest bounds possible for LU factorization. These algorithms are based on our earlier work on computing row and column counts for sparse Cholesky factorization, plus an efficient method to compute the column elimination tree of a sparse matrix without explicitly forming the product of the matrix and its transpose.« less

  13. Stability-driven nonnegative matrix factorization to interpret spatial gene expression and build local gene networks.

    PubMed

    Wu, Siqi; Joseph, Antony; Hammonds, Ann S; Celniker, Susan E; Yu, Bin; Frise, Erwin

    2016-04-19

    Spatial gene expression patterns enable the detection of local covariability and are extremely useful for identifying local gene interactions during normal development. The abundance of spatial expression data in recent years has led to the modeling and analysis of regulatory networks. The inherent complexity of such data makes it a challenge to extract biological information. We developed staNMF, a method that combines a scalable implementation of nonnegative matrix factorization (NMF) with a new stability-driven model selection criterion. When applied to a set ofDrosophilaearly embryonic spatial gene expression images, one of the largest datasets of its kind, staNMF identified 21 principal patterns (PP). Providing a compact yet biologically interpretable representation ofDrosophilaexpression patterns, PP are comparable to a fate map generated experimentally by laser ablation and show exceptional promise as a data-driven alternative to manual annotations. Our analysis mapped genes to cell-fate programs and assigned putative biological roles to uncharacterized genes. Finally, we used the PP to generate local transcription factor regulatory networks. Spatially local correlation networks were constructed for six PP that span along the embryonic anterior-posterior axis. Using a two-tail 5% cutoff on correlation, we reproduced 10 of the 11 links in the well-studied gap gene network. The performance of PP with theDrosophiladata suggests that staNMF provides informative decompositions and constitutes a useful computational lens through which to extract biological insight from complex and often noisy gene expression data.

  14. Engineering Three-dimensional Epithelial Tissues Embedded within Extracellular Matrix.

    PubMed

    Piotrowski-Daspit, Alexandra S; Nelson, Celeste M

    2016-07-10

    The architecture of branched organs such as the lungs, kidneys, and mammary glands arises through the developmental process of branching morphogenesis, which is regulated by a variety of soluble and physical signals in the microenvironment. Described here is a method created to study the process of branching morphogenesis by forming engineered three-dimensional (3D) epithelial tissues of defined shape and size that are completely embedded within an extracellular matrix (ECM). This method enables the formation of arrays of identical tissues and enables the control of a variety of environmental factors, including tissue geometry, spacing, and ECM composition. This method can also be combined with widely used techniques such as traction force microscopy (TFM) to gain more information about the interactions between cells and their surrounding ECM. The protocol can be used to investigate a variety of cell and tissue processes beyond branching morphogenesis, including cancer invasion.

  15. BSR: B-spline atomic R-matrix codes

    NASA Astrophysics Data System (ADS)

    Zatsarinny, Oleg

    2006-02-01

    BSR is a general program to calculate atomic continuum processes using the B-spline R-matrix method, including electron-atom and electron-ion scattering, and radiative processes such as bound-bound transitions, photoionization and polarizabilities. The calculations can be performed in LS-coupling or in an intermediate-coupling scheme by including terms of the Breit-Pauli Hamiltonian. New version program summaryTitle of program: BSR Catalogue identifier: ADWY Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADWY Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Computers on which the program has been tested: Microway Beowulf cluster; Compaq Beowulf cluster; DEC Alpha workstation; DELL PC Operating systems under which the new version has been tested: UNIX, Windows XP Programming language used: FORTRAN 95 Memory required to execute with typical data: Typically 256-512 Mwords. Since all the principal dimensions are allocatable, the available memory defines the maximum complexity of the problem No. of bits in a word: 8 No. of processors used: 1 Has the code been vectorized or parallelized?: no No. of lines in distributed program, including test data, etc.: 69 943 No. of bytes in distributed program, including test data, etc.: 746 450 Peripherals used: scratch disk store; permanent disk store Distribution format: tar.gz Nature of physical problem: This program uses the R-matrix method to calculate electron-atom and electron-ion collision processes, with options to calculate radiative data, photoionization, etc. The calculations can be performed in LS-coupling or in an intermediate-coupling scheme, with options to include Breit-Pauli terms in the Hamiltonian. Method of solution: The R-matrix method is used [P.G. Burke, K.A. Berrington, Atomic and Molecular Processes: An R-Matrix Approach, IOP Publishing, Bristol, 1993; P.G. Burke, W.D. Robb, Adv. At. Mol. Phys. 11 (1975) 143; K.A. Berrington, W.B. Eissner, P.H. Norrington, Comput

  16. Comprehensive T-Matrix Reference Database: A 2007-2009 Update

    NASA Technical Reports Server (NTRS)

    Mishchenko, Michael I.; Zakharova, Nadia T.; Videen, Gorden; Khlebtsov, Nikolai G.; Wriedt, Thomas

    2010-01-01

    The T-matrix method is among the most versatile, efficient, and widely used theoretical techniques for the numerically exact computation of electromagnetic scattering by homogeneous and composite particles, clusters of particles, discrete random media, and particles in the vicinity of an interface separating two half-spaces with different refractive indices. This paper presents an update to the comprehensive database of T-matrix publications compiled by us previously and includes the publications that appeared since 2007. It also lists several earlier publications not included in the original database.

  17. Comprehensive T-matrix Reference Database: A 2009-2011 Update

    NASA Technical Reports Server (NTRS)

    Zakharova, Nadezhda T.; Videen, G.; Khlebtsov, Nikolai G.

    2012-01-01

    The T-matrix method is one of the most versatile and efficient theoretical techniques widely used for the computation of electromagnetic scattering by single and composite particles, discrete random media, and particles in the vicinity of an interface separating two half-spaces with different refractive indices. This paper presents an update to the comprehensive database of peer-reviewed T-matrix publications compiled by us previously and includes the publications that appeared since 2009. It also lists several earlier publications not included in the original database.

  18. Neutron Multiplicity: LANL W Covariance Matrix for Curve Fitting

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Wendelberger, James G.

    2016-12-08

    In neutron multiplicity counting one may fit a curve by minimizing an objective function, χmore » $$2\\atop{n}$$. The objective function includes the inverse of an n by n matrix of covariances, W. The inverse of the W matrix has a closed form solution. In addition W -1 is a tri-diagonal matrix. The closed form and tridiagonal nature allows for a simpler expression of the objective function χ$$2\\atop{n}$$. Minimization of this simpler expression will provide the optimal parameters for the fitted curve.« less

  19. A Study of the Critical Factors Controlling the Synthesis of Ceramic Matrix Composites from Preceramic Polymers

    DTIC Science & Technology

    1990-12-15

    THE SYNTHESIS OF CERAMIC MATRIX COMPOSITES PE - 61102F FROM PRECERAMIC POLYMERS PR -9999 6. AUTHOR(S) TA - 99 J. R. Strife(l), J. P. Wesson(1 ), and H...stability at temperatures up to 15000 C. 14. SUBJECT TERMS 15. NUMBER OF PAGES 49 C- SiC composites vinylmethylsilane 16. PRICE CODE polymer precursor...vapor infiltration of fibrous preforms. More recently, the conversion of preceramic polymers as a matrix synthesis process is being considered. This

  20. Osteoblast Differentiation and Bone Matrix Formation In Vivo and In Vitro.

    PubMed

    Blair, Harry C; Larrouture, Quitterie C; Li, Yanan; Lin, Hang; Beer-Stoltz, Donna; Liu, Li; Tuan, Rocky S; Robinson, Lisa J; Schlesinger, Paul H; Nelson, Deborah J

    2017-06-01

    We review the characteristics of osteoblast differentiation and bone matrix synthesis. Bone in air breathing vertebrates is a specialized tissue that developmentally replaces simpler solid tissues, usually cartilage. Bone is a living organ bounded by a layer of osteoblasts that, because of transport and compartmentalization requirements, produce bone matrix exclusively as an organized tight epithelium. With matrix growth, osteoblasts are reorganized and incorporated into the matrix as living cells, osteocytes, which communicate with each other and surface epithelium by cell processes within canaliculi in the matrix. The osteoblasts secrete the organic matrix, which are dense collagen layers that alternate parallel and orthogonal to the axis of stress loading. Into this matrix is deposited extremely dense hydroxyapatite-based mineral driven by both active and passive transport and pH control. As the matrix matures, hydroxyapatite microcrystals are organized into a sophisticated composite in the collagen layer by nucleation in the protein lattice. Recent studies on differentiating osteoblast precursors revealed a sophisticated proton export network driving mineralization, a gene expression program organized with the compartmentalization of the osteoblast epithelium that produces the mature bone matrix composite, despite varying serum calcium and phosphate. Key issues not well defined include how new osteoblasts are incorporated in the epithelial layer, replacing those incorporated in the accumulating matrix. Development of bone in vitro is the subject of numerous projects using various matrices and mesenchymal stem cell-derived preparations in bioreactors. These preparations reflect the structure of bone to variable extents, and include cells at many different stages of differentiation. Major challenges are production of bone matrix approaching the in vivo density and support for trabecular bone formation. In vitro differentiation is limited by the organization and

  1. Osteoblast Differentiation and Bone Matrix Formation In Vivo and In Vitro

    PubMed Central

    Larrouture, Quitterie C.; Li, Yanan; Lin, Hang; Beer-Stoltz, Donna; Liu, Li; Tuan, Rocky S.; Robinson, Lisa J.; Schlesinger, Paul H.; Nelson, Deborah J.

    2017-01-01

    We review the characteristics of osteoblast differentiation and bone matrix synthesis. Bone in air breathing vertebrates is a specialized tissue that developmentally replaces simpler solid tissues, usually cartilage. Bone is a living organ bounded by a layer of osteoblasts that, because of transport and compartmentalization requirements, produce bone matrix exclusively as an organized tight epithelium. With matrix growth, osteoblasts are reorganized and incorporated into the matrix as living cells, osteocytes, which communicate with each other and surface epithelium by cell processes within canaliculi in the matrix. The osteoblasts secrete the organic matrix, which are dense collagen layers that alternate parallel and orthogonal to the axis of stress loading. Into this matrix is deposited extremely dense hydroxyapatite-based mineral driven by both active and passive transport and pH control. As the matrix matures, hydroxyapatite microcrystals are organized into a sophisticated composite in the collagen layer by nucleation in the protein lattice. Recent studies on differentiating osteoblast precursors revealed a sophisticated proton export network driving mineralization, a gene expression program organized with the compartmentalization of the osteoblast epithelium that produces the mature bone matrix composite, despite varying serum calcium and phosphate. Key issues not well defined include how new osteoblasts are incorporated in the epithelial layer, replacing those incorporated in the accumulating matrix. Development of bone in vitro is the subject of numerous projects using various matrices and mesenchymal stem cell-derived preparations in bioreactors. These preparations reflect the structure of bone to variable extents, and include cells at many different stages of differentiation. Major challenges are production of bone matrix approaching the in vivo density and support for trabecular bone formation. In vitro differentiation is limited by the organization and

  2. Extraction of food consumption systems by nonnegative matrix factorization (NMF) for the assessment of food choices.

    PubMed

    Zetlaoui, Mélanie; Feinberg, Max; Verger, Philippe; Clémençon, Stephan

    2011-12-01

    In Western countries where food supply is satisfactory, consumers organize their diets around a large combination of foods. It is the purpose of this article to examine how recent nonnegative matrix factorization (NMF) techniques can be applied to food consumption data to understand these combinations. Such data are nonnegative by nature and of high dimension. The NMF model provides a representation of consumption data through latent vectors with nonnegative coefficients, that we call consumption systems (CS), in a small number. As the NMF approach may encourage sparsity of the data representation produced, the resulting CS are easily interpretable. Beyond the illustration of its properties we provide through a simple simulation result, the NMF method is applied to data issued from a French consumption survey. The numerical results thus obtained are displayed and thoroughly discussed. A clustering based on the k-means method is also achieved in the resulting latent consumption space, to recover food consumption patterns easily usable for nutritionists. © 2011, The International Biometric Society.

  3. Fibroblasts and the extracellular matrix in right ventricular disease.

    PubMed

    Frangogiannis, Nikolaos G

    2017-10-01

    Right ventricular failure predicts adverse outcome in patients with pulmonary hypertension (PH), and in subjects with left ventricular heart failure and is associated with interstitial fibrosis. This review manuscript discusses the cellular effectors and molecular mechanisms implicated in right ventricular fibrosis. The right ventricular interstitium contains vascular cells, fibroblasts, and immune cells, enmeshed in a collagen-based matrix. Right ventricular pressure overload in PH is associated with the expansion of the fibroblast population, myofibroblast activation, and secretion of extracellular matrix proteins. Mechanosensitive transduction of adrenergic signalling and stimulation of the renin-angiotensin-aldosterone cascade trigger the activation of right ventricular fibroblasts. Inflammatory cytokines and chemokines may contribute to expansion and activation of macrophages that may serve as a source of fibrogenic growth factors, such as transforming growth factor (TGF)-β. Endothelin-1, TGF-βs, and matricellular proteins co-operate to activate cardiac myofibroblasts, and promote synthesis of matrix proteins. In comparison with the left ventricle, the RV tolerates well volume overload and ischemia; whether the right ventricular interstitial cells and matrix are implicated in these favourable responses remains unknown. Expansion of fibroblasts and extracellular matrix protein deposition are prominent features of arrhythmogenic right ventricular cardiomyopathies and may be implicated in the pathogenesis of arrhythmic events. Prevailing conceptual paradigms on right ventricular remodelling are based on extrapolation of findings in models of left ventricular injury. Considering the unique embryologic, morphological, and physiologic properties of the RV and the clinical significance of right ventricular failure, there is a need further to dissect RV-specific mechanisms of fibrosis and interstitial remodelling. Published on behalf of the European Society of

  4. Hyaluronan Induces the Selective Accumulation of Matrix- and Cell-Associated Proteoglycans by Mesangial Cells

    PubMed Central

    Kastner, Sabine; Thomas, Gareth J.; Jenkins, Robert H.; Davies, Malcolm; Steadman, Robert

    2007-01-01

    Mesangial cells (MCs) are essential for normal renal function through the synthesis of their own extracellular matrix, which forms the structural support of the renal glomerulus. In many renal diseases this matrix is reorganized in response to a variety of cytokines and growth factors. This study examines proteoglycan and hyaluronan (HA) synthesis by MCs triggered by proinflammatory agents and investigates the effect of an exogenous HA matrix on matrix synthesis by MCs. Metabolic labeling, ion exchange and size exclusion chromatography, Western blotting, and immunocytochemistry were used to identify changes in matrix accumulation. When incubated with interleukin-1, platelet-derived growth factor, or fetal calf serum, MCs initiated rapid HA synthesis associated with the up-regulation of HA synthase-2 and increased the synthesis of versican, perlecan, and decorin/biglycan. HA was both released into the medium and incorporated into extensive pericellular coats. Adding exogenous HA to unstimulated cells that had undetectable pericellular coats of HA selectively reduced perlecan and versican turnover, whereas other proteoglycans were unaffected. These results suggest that high levels of HA in the mesangium in disease is a mechanism controlling the accumulation of specific mesangial matrix components. HA may thus be an attractive target for therapeutic intervention. PMID:17974600

  5. Modification of natural matrix lac-bagasse for matrix composite films

    NASA Astrophysics Data System (ADS)

    Nurhayati, Nanik Dwi; Widjaya, Karna; Triyono

    2016-02-01

    Material technology continues to be developed in order to a material that is more efficient with composite technology is a combination of two or more materials to obtain the desired material properties. The objective of this research was to modification and characterize the natural matrix lac-bagasse as composite films. The first step, natural matrix lac was changed from solid to liquid using an ethanol as a solvent so the matrix homogenly. Natural matrix lac was modified by adding citric acid with concentration variation. Secondly, the bagasse delignification using acid hydrolysis method. The composite films natural matrix lac-bagasse were prepared with optimum modified the addition citric acid 5% (v/v) and delignification bagasse optimum at 1,5% (v/v) in hot press at 80°C 6 Kg/cm-1. Thirdly, composite films without and with modification were characterized functional group analysis using FTIR spectrophotometer and mechanical properties using Universal Testing Machine. The result of research showed natural matrix lac can be modified by reaction with citric acid. FTIR spectra showed without and with modification had functional groups wide absorption 3448 cm-1 group -OH, C=O ester strong on 1712 cm-1 and the methylene group -CH2 on absorption 1465 cm-1. The mechanical properties showed tensile strength 0,55 MPa and elongation at break of 0,95 %. So that composite films natural matrix lac can be made with reinforcement bagasse for material application.

  6. Space Shuttle communications RF switch matrix

    NASA Technical Reports Server (NTRS)

    Winch, R.

    1979-01-01

    The Shuttle Orbiter communications equipment includes phase modulation (PM) and frequency modulation (FM) channels. The PM section has the capability of routing high levels of energy (175 W) from any one of four transmitters to any one of four antennas, mutually exclusive. The FM channel uses a maximum of 15-W power routed from either of two transmitters to one of two antennas, mutually exclusive. The paper describes the design and the theory of a logic-controlled RF switch matrix devised for the purposes cited. Both PM and FM channels are computer-controlled with manual overrides. The logic interface is realized with CMOS logic for low power consumption and high noise immunity. The interior of the switch matrix is maintained at a pressure of 15 psi (90% nitrogen, 10% helium) by an electron beam-welded encapsulation. The computational results confirm the viability of the RF switch matrix concept.

  7. Extracellular matrix metalloproteinase inducer (EMMPRIN) expression correlates positively with active angiogenesis and negatively with basic fibroblast growth factor expression in epithelial ovarian cancer.

    PubMed

    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. Scale-Free Nonparametric Factor Analysis: A User-Friendly Introduction with Concrete Heuristic Examples.

    ERIC Educational Resources Information Center

    Mittag, Kathleen Cage

    Most researchers using factor analysis extract factors from a matrix of Pearson product-moment correlation coefficients. A method is presented for extracting factors in a non-parametric way, by extracting factors from a matrix of Spearman rho (rank correlation) coefficients. It is possible to factor analyze a matrix of association such that…

  9. Modeling for Matrix Multicracking Evolution of Cross-ply Ceramic-Matrix Composites Using Energy Balance Approach

    NASA Astrophysics Data System (ADS)

    Longbiao, Li

    2015-12-01

    The matrix multicracking evolution of cross-ply ceramic-matrix composites (CMCs) has been investigated using energy balance approach. The multicracking of cross-ply CMCs was classified into five modes, i.e., (1) mode 1: transverse multicracking; (2) mode 2: transverse multicracking and matrix multicracking with perfect fiber/matrix interface bonding; (3) mode 3: transverse multicracking and matrix multicracking with fiber/matrix interface debonding; (4) mode 4: matrix multicracking with perfect fiber/matrix interface bonding; and (5) mode 5: matrix multicracking with fiber/matrix interface debonding. The stress distributions of four cracking modes, i.e., mode 1, mode 2, mode 3 and mode 5, are analysed using shear-lag model. The matrix multicracking evolution of mode 1, mode 2, mode 3 and mode 5, has been determined using energy balance approach. The effects of ply thickness and fiber volume fraction on matrix multicracking evolution of cross-ply CMCs have been investigated.

  10. Multi-contrast imaging of human posterior eye by Jones matrix optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Yasuno, Yoshiaki

    2017-04-01

    A multi-contrast imaging of pathologic posterior eyes is demonstrated by Jones matrix optical coherence tomography (Jones matrix OCT). The Jones matrix OCT provides five tomographies, which includes scattering, local attenuation, birefringence, polarization uniformity, and optical coherence angiography, by a single scan. The hardware configuration, algorithms of the Jones matrix OCT as well as its application to ophthalmology is discussed.

  11. DNA Damage Response Factors from Diverse Pathways, Including DNA Crosslink Repair, Mediate Alternative End Joining

    PubMed Central

    Howard, Sean M.; Yanez, Diana A.; Stark, Jeremy M.

    2015-01-01

    Alternative end joining (Alt-EJ) chromosomal break repair involves bypassing classical non-homologous end joining (c-NHEJ), and such repair causes mutations often with microhomology at the repair junction. Since the mediators of Alt-EJ are not well understood, we have sought to identify DNA damage response (DDR) factors important for this repair event. Using chromosomal break reporter assays, we surveyed an RNAi library targeting known DDR factors for siRNAs that cause a specific decrease in Alt-EJ, relative to an EJ event that is a composite of Alt-EJ and c-NHEJ (Distal-EJ between two tandem breaks). From this analysis, we identified several DDR factors that are specifically important for Alt-EJ relative to Distal-EJ. While these factors are from diverse pathways, we also found that most of them also promote homologous recombination (HR), including factors important for DNA crosslink repair, such as the Fanconi Anemia factor, FANCA. Since bypass of c-NHEJ is likely important for both Alt-EJ and HR, we disrupted the c-NHEJ factor Ku70 in Fanca-deficient mouse cells and found that Ku70 loss significantly diminishes the influence of Fanca on Alt-EJ. In contrast, an inhibitor of poly ADP-ribose polymerase (PARP) causes a decrease in Alt-EJ that is enhanced by Ku70 loss. Additionally, the helicase/nuclease DNA2 appears to have distinct effects from FANCA and PARP on both Alt-EJ, as well as end resection. Finally, we found that the proteasome inhibitor Bortezomib, a cancer therapeutic that has been shown to disrupt FANC signaling, causes a significant reduction in both Alt-EJ and HR, relative to Distal-EJ, as well as a substantial loss of end resection. We suggest that several distinct DDR functions are important for Alt-EJ, which include promoting bypass of c-NHEJ and end resection. PMID:25629353

  12. Mitochondrial unfolded protein response controls matrix pre-RNA processing and translation.

    PubMed

    Münch, Christian; Harper, J Wade

    2016-06-30

    The mitochondrial matrix is unique in that it must integrate the folding and assembly of proteins derived from the nuclear and mitochondrial genomes. In Caenorhabditis elegans, the mitochondrial unfolded protein response (UPRmt) senses matrix protein misfolding and induces a program of nuclear gene expression, including mitochondrial chaperonins, to promote mitochondrial proteostasis. While misfolded mitochondrial-matrix-localized ornithine transcarbamylase induces chaperonin expression, our understanding of mammalian UPRmt is rudimentary, reflecting a lack of acute triggers for UPRmt activation. This limitation has prevented analysis of the cellular responses to matrix protein misfolding and the effects of UPRmt on mitochondrial translation to control protein folding loads. Here we combine pharmacological inhibitors of matrix-localized HSP90/TRAP1 (ref. 8) or LON protease, which promote chaperonin expression, with global transcriptional and proteomic analysis to reveal an extensive and acute response of human cells to UPRmt. This response encompasses widespread induction of nuclear genes, including matrix-localized proteins involved in folding, pre-RNA processing and translation. Functional studies revealed rapid but reversible translation inhibition in mitochondria occurring concurrently with defects in pre-RNA processing caused by transcriptional repression and LON-dependent turnover of the mitochondrial pre-RNA processing nuclease MRPP3 (ref. 10). This study reveals that acute mitochondrial protein folding stress activates both increased chaperone availability within the matrix and reduced matrix-localized protein synthesis through translational inhibition, and provides a framework for further dissection of mammalian UPRmt.

  13. Matrix differentiation formulas

    NASA Technical Reports Server (NTRS)

    Usikov, D. A.; Tkhabisimov, D. K.

    1983-01-01

    A compact differentiation technique (without using indexes) is developed for scalar functions that depend on complex matrix arguments which are combined by operations of complex conjugation, transposition, addition, multiplication, matrix inversion and taking the direct product. The differentiation apparatus is developed in order to simplify the solution of extremum problems of scalar functions of matrix arguments.

  14. Application of positive matrix factorization to on-road measurements for source apportionment of diesel- and gasoline-powered vehicle emissions in Mexico City

    NASA Astrophysics Data System (ADS)

    Thornhill, D. A.; Williams, A. E.; Onasch, T. B.; Wood, E.; Herndon, S. C.; Kolb, C. E.; Knighton, W. B.; Zavala, M.; Molina, L. T.; Marr, L. C.

    2009-12-01

    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 responsible for 97% of mobile source emissions of CO, 22% of NOx, 95-97% of aromatics, 72-85% of carbonyls, 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. Nevertheless, the fuel-based inventory suggests that mobile source emissions of CO and NOx are overstated in the official inventory while

  15. Streptococcus mutans-derived extracellular matrix in cariogenic oral biofilms.

    PubMed

    Klein, Marlise I; Hwang, Geelsu; Santos, Paulo H S; Campanella, Osvaldo H; Koo, Hyun

    2015-01-01

    Biofilms are highly structured microbial communities that are enmeshed in a self-produced extracellular matrix. Within the complex oral microbiome, Streptococcus mutans is a major producer of extracellular polymeric substances including exopolysaccharides (EPS), eDNA, and lipoteichoic acid (LTA). EPS produced by S. mutans-derived exoenzymes promote local accumulation of microbes on the teeth, while forming a spatially heterogeneous and diffusion-limiting matrix that protects embedded bacteria. The EPS-rich matrix provides mechanical stability/cohesiveness and facilitates the creation of highly acidic microenvironments, which are critical for the pathogenesis of dental caries. In parallel, S. mutans also releases eDNA and LTA, which can contribute with matrix development. eDNA enhances EPS (glucan) synthesis locally, increasing the adhesion of S. mutans to saliva-coated apatitic surfaces and the assembly of highly cohesive biofilms. eDNA and other extracellular substances, acting in concert with EPS, may impact the functional properties of the matrix and the virulence of cariogenic biofilms. Enhanced understanding about the assembly principles of the matrix may lead to efficacious approaches to control biofilm-related diseases.

  16. Streptococcus mutans-derived extracellular matrix in cariogenic oral biofilms

    PubMed Central

    Klein, Marlise I.; Hwang, Geelsu; Santos, Paulo H. S.; Campanella, Osvaldo H.; Koo, Hyun

    2015-01-01

    Biofilms are highly structured microbial communities that are enmeshed in a self-produced extracellular matrix. Within the complex oral microbiome, Streptococcus mutans is a major producer of extracellular polymeric substances including exopolysaccharides (EPS), eDNA, and lipoteichoic acid (LTA). EPS produced by S. mutans-derived exoenzymes promote local accumulation of microbes on the teeth, while forming a spatially heterogeneous and diffusion-limiting matrix that protects embedded bacteria. The EPS-rich matrix provides mechanical stability/cohesiveness and facilitates the creation of highly acidic microenvironments, which are critical for the pathogenesis of dental caries. In parallel, S. mutans also releases eDNA and LTA, which can contribute with matrix development. eDNA enhances EPS (glucan) synthesis locally, increasing the adhesion of S. mutans to saliva-coated apatitic surfaces and the assembly of highly cohesive biofilms. eDNA and other extracellular substances, acting in concert with EPS, may impact the functional properties of the matrix and the virulence of cariogenic biofilms. Enhanced understanding about the assembly principles of the matrix may lead to efficacious approaches to control biofilm-related diseases. PMID:25763359

  17. Extracellular matrix structure governs invasion resistance in bacterial biofilms.

    PubMed

    Nadell, Carey D; Drescher, Knut; Wingreen, Ned S; Bassler, Bonnie L

    2015-08-01

    Many bacteria are highly adapted for life in communities, or biofilms. A defining feature of biofilms is the production of extracellular matrix that binds cells together. The biofilm matrix provides numerous fitness benefits, including protection from environmental stresses and enhanced nutrient availability. Here we investigate defense against biofilm invasion using the model bacterium Vibrio cholerae. We demonstrate that immotile cells, including those identical to the biofilm resident strain, are completely excluded from entry into resident biofilms. Motile cells can colonize and grow on the biofilm exterior, but are readily removed by shear forces. Protection from invasion into the biofilm interior is mediated by the secreted protein RbmA, which binds mother-daughter cell pairs to each other and to polysaccharide components of the matrix. RbmA, and the invasion protection it confers, strongly localize to the cell lineages that produce it.

  18. Thermal and mechanical behavior of metal matrix and ceramic matrix composites

    NASA Technical Reports Server (NTRS)

    Kennedy, John M. (Editor); Moeller, Helen H. (Editor); Johnson, W. S. (Editor)

    1990-01-01

    The present conference discusses local stresses in metal-matrix composites (MMCs) subjected to thermal and mechanical loads, the computational simulation of high-temperature MMCs' cyclic behavior, an analysis of a ceramic-matrix composite (CMC) flexure specimen, and a plasticity analysis of fibrous composite laminates under thermomechanical loads. Also discussed are a comparison of methods for determining the fiber-matrix interface frictional stresses of CMCs, the monotonic and cyclic behavior of an SiC/calcium aluminosilicate CMC, the mechanical and thermal properties of an SiC particle-reinforced Al alloy MMC, the temperature-dependent tensile and shear response of a graphite-reinforced 6061 Al-alloy MMC, the fiber/matrix interface bonding strength of MMCs, and fatigue crack growth in an Al2O3 short fiber-reinforced Al-2Mg matrix MMC.

  19. Geometric control of capillary architecture via cell-matrix mechanical interactions.

    PubMed

    Sun, Jian; Jamilpour, Nima; Wang, Fei-Yue; Wong, Pak Kin

    2014-03-01

    Capillary morphogenesis is a multistage, multicellular activity that plays a pivotal role in various developmental and pathological situations. In-depth understanding of the regulatory mechanism along with the capability of controlling the morphogenic process will have direct implications on tissue engineering and therapeutic angiogenesis. Extensive research has been devoted to elucidate the biochemical factors that regulate capillary morphogenesis. The roles of geometric confinement and cell-matrix mechanical interactions on the capillary architecture, nevertheless, remain largely unknown. Here, we show geometric control of endothelial network topology by creating physical confinements with microfabricated fences and wells. Decreasing the thickness of the matrix also results in comparable modulation of the network architecture, supporting the boundary effect is mediated mechanically. The regulatory role of cell-matrix mechanical interaction on the network topology is further supported by alternating the matrix stiffness by a cell-inert PEG-dextran hydrogel. Furthermore, reducing the cell traction force with a Rho-associated protein kinase inhibitor diminishes the boundary effect. Computational biomechanical analysis delineates the relationship between geometric confinement and cell-matrix mechanical interaction. Collectively, these results reveal a mechanoregulation scheme of endothelial cells to regulate the capillary network architecture via cell-matrix mechanical interactions. Copyright © 2014 Elsevier Ltd. All rights reserved.

  20. Dynamics of VEGF matrix-retention in vascular network patterning

    NASA Astrophysics Data System (ADS)

    Köhn-Luque, A.; de Back, W.; Yamaguchi, Y.; Yoshimura, K.; Herrero, M. A.; Miura, T.

    2013-12-01

    Vascular endothelial growth factor (VEGF) is a central regulator of blood vessel morphogenesis, although its role in patterning of endothelial cells into vascular networks is not fully understood. It has been suggested that binding of soluble VEGF to extracellular matrix components causes spatially restricted cues that guide endothelial cells into network patterns. Yet, current evidence for such a mechanism remains indirect. In this study, we quantitatively analyse the dynamics of VEGF retention in a controlled in vitro situation of human umbilical vascular endothelial cells (HUVECs) in Matrigel. We show that fluorescent VEGF accumulates in pericellular areas and colocalizes with VEGF binding molecules. Analysis of fluorescence recovery after photobleaching reveals that binding/unbinding to matrix molecules dominates VEGF dynamics in the pericellular region. Computational simulations using our experimental measurements of kinetic parameters show that matrix retention of chemotactic signals can lead to the formation of reticular cellular networks on a realistic timescale. Taken together, these results show that VEGF binds to matrix molecules in proximity of HUVECs in Matrigel, and suggest that bound VEGF drives vascular network patterning.

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