Recursive inverse factorization.

PubMed

Rubensson, Emanuel H; Bock, Nicolas; Holmström, Erik; Niklasson, Anders M N

2008-03-14

A recursive algorithm for the inverse factorization S(-1)=ZZ(*) of Hermitian positive definite matrices S is proposed. The inverse factorization is based on iterative refinement [A.M.N. Niklasson, Phys. Rev. B 70, 193102 (2004)] combined with a recursive decomposition of S. As the computational kernel is matrix-matrix multiplication, the algorithm can be parallelized and the computational effort increases linearly with system size for systems with sufficiently sparse matrices. Recent advances in network theory are used to find appropriate recursive decompositions. We show that optimization of the so-called network modularity results in an improved partitioning compared to other approaches. In particular, when the recursive inverse factorization is applied to overlap matrices of irregularly structured three-dimensional molecules.

Intelligence and Semen Quality Are Positively Correlated

ERIC Educational Resources Information Center

Arden, Rosalind; Gottfredson, Linda S.; Miller, Geoffrey; Pierce, Arand

2009-01-01

Human cognitive abilities inter-correlate to form a positive matrix, from which a large first factor, called "Spearman's g" or general intelligence, can be extracted. General intelligence itself is correlated with many important health outcomes including cardio-vascular function and longevity. However, the important evolutionary question of…

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.

Factor Analytic Approach to Transitive Text Mining using Medline Descriptors

NASA Astrophysics Data System (ADS)

Stegmann, J.; Grohmann, G.

Matrix decomposition methods were applied to examples of noninteractive literature sets sharing implicit relations. Document-by-term matrices were created from downloaded PubMed literature sets, the terms being the Medical Subject Headings (MeSH descriptors) assigned to the documents. The loadings of the factors derived from singular value or eigenvalue matrix decomposition were sorted according to absolute values and subsequently inspected for positions of terms relevant to the discovery of hidden connections. It was found that only a small number of factors had to be screened to find key terms in close neighbourhood, being separated by a small number of terms only.

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.

SIMS of Organic Materials—Interface Location in Argon Gas Cluster Depth Profiles Using Negative Secondary Ions

NASA Astrophysics Data System (ADS)

Havelund, R.; Seah, M. P.; Tiddia, M.; Gilmore, I. S.

2018-02-01

A procedure has been established to define the interface position in depth profiles accurately when using secondary ion mass spectrometry and the negative secondary ions. The interface position varies strongly with the extent of the matrix effect and so depends on the secondary ion measured. Intensity profiles have been measured at both fluorenylmethyloxycarbonyl-uc(l)-pentafluorophenylalanine (FMOC) to Irganox 1010 and Irganox 1010 to FMOC interfaces for many secondary ions. These profiles show separations of the two interfaces that vary over some 10 nm depending on the secondary ion selected. The shapes of these profiles are strongly governed by matrix effects, slightly weakened by a long wavelength roughening. The matrix effects are separately measured using homogeneous, known mixtures of these two materials. Removal of the matrix and roughening effects give consistent compositional profiles for all ions that are described by an integrated exponentially modified Gaussian (EMG) profile. Use of a simple integrated Gaussian may lead to significant errors. The average interface positions in the compositional profiles are determined to standard uncertainties of 0.19 and 0.14 nm, respectively, using the integrated EMG function. Alternatively, and more simply, it is shown that interface positions and profiles may be deduced from data for several secondary ions with measured matrix factors by simply extrapolating the result to Ξ = 0. Care must be taken in quoting interface resolutions since those measured for predominantly Gaussian interfaces with Ξ above or below zero, without correction, appear significantly better than the true resolution.

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

PubMed

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

2017-10-01

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

Source Apportionment of PM2.5 Mass and Optical Attenuation Over an Ecologically Sensitive Zone in Central India by Positive Matrix Factorization

NASA Astrophysics Data System (ADS)

Nirmalkar, J.; Raman, R. S.

2016-12-01

Ambient PM2.5 samples (N=366) were collected over an ecologically sensitive zone (Van Vihar National Park) in Bhopal, Central India for two years (01 January, 2012 to 31 December, 2013). Samples were collected using three co-located Mini-Vol® samplers on Teflon, Nylon, and Quartz filter substrates. The aerosol was then chemically characterized for water-soluble inorganic ions, elements, and carbon fractions (elemental carbon and organic carbon) using ion chromatography, ED-XRF, and thermal-optical EC/OC analyzer, respectively. The optical attenuation (at 370 nm and 800 nm) of PM2.5 aerosols was also determined by optical transmissometry (OT-21). The application of Positive matrix factorization (PMF) to a combination of PM2.5 mass, its ions, elements, carbon fractions, and optical attenuation and its outcomes will be discussed.

Communication requirements of sparse Cholesky factorization with nested dissection ordering

NASA Technical Reports Server (NTRS)

Naik, Vijay K.; Patrick, Merrell L.

1989-01-01

Load distribution schemes for minimizing the communication requirements of the Cholesky factorization of dense and sparse, symmetric, positive definite matrices on multiprocessor systems are presented. The total data traffic in factoring an n x n sparse symmetric positive definite matrix representing an n-vertex regular two-dimensional grid graph using n exp alpha, alpha not greater than 1, processors are shown to be O(n exp 1 + alpha/2). It is O(n), when n exp alpha, alpha not smaller than 1, processors are used. Under the conditions of uniform load distribution, these results are shown to be asymptotically optimal.

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.

Effect of molecular anisotropy on the intensity and degree of polarization of light scattered from model atmospheres

NASA Technical Reports Server (NTRS)

Bahethi, O. P.; Fraser, R. S.

1975-01-01

Computations of the intensity, flux, degree of polarization, and the positions of neutral points are presented for models of the terrestrial gaseous and hazy atmospheres by incorporating the molecular anisotropy due to air in the Rayleigh scattering optical thickness and phase matrix. Molecular anisotropy causes significant changes in the intensity, flux and the degree of polarization of the scattered light. The positions of neutral points do not change significantly. When the Rayleigh scattering optical thickness is kept constant and the molecular anisotropy factor is included only in the Rayleigh phase matrix, the flux does not change and the intensity and positions of neutron points change by a small amount. The changes in the degree of polarization are still significant.

Fragment quality and matrix affect epiphytic performance in a Mediterranean forest landscape.

PubMed

Belinchón, Rocío; Martínez, Isabel; Otálora, Mónica A G; Aragón, Gregorio; Dimas, Jesús; Escudero, Adrián

2009-11-01

Destruction and fragmentation of habitats represent one of the most important threats for biodiversity. Here, we examined the effects of fragmentation in Mediterranean forests on the epiphytic lichen Lobaria pulmonaria (Lobariaceae). We tested the hypothesis that not only the level of fragmentation affects L. pulmonaria populations, but also the quality of the habitat and the nature of the surrounding matrix affect them. The presence and abundance of the lichen was recorded on 2039 trees in a total of 31 stands. We recorded habitat quality and landscape variables at three hierarchical levels: tree, plot, and patch. We found that L. pulmonaria tends to occur in trees with larger diameters in two types of surveyed forests. In Quercus pyrenaica patches, the mean diameter of colonized trees was smaller, suggesting the importance of bark roughness. Factors affecting the presence and cover of the lichen in each type of forest were different. There was a strong positive influence of distance from a river in beech forests, whereas proximity to forest edge positively affected in oak forests. The influence of the surrounding matrix was also an important factor explaining the epiphytic lichen abundance.

SOURCE APPORTIONMENT RESULTS, UNCERTAINTIES, AND MODELING TOOLS

EPA Science Inventory

Advanced multivariate receptor modeling tools are available from the U.S. Environmental Protection Agency (EPA) that use only speciated sample data to identify and quantify sources of air pollution. EPA has developed both EPA Unmix and EPA Positive Matrix Factorization (PMF) and ...

Evaluating the MSCEIT V2.0 via CFA: comment on Mayer et al. (2003).

PubMed

Gignac, Gilles E

2005-06-01

This investigation uncovered several substantial errors in the confirmatory factor analysis results reported by J. D. Mayer, P. Salovey, D. R. Caruso, and G. Sitarenios (see record 2003-02341-015). Specifically, the values associated with the close-fit indices (normed fit index, Tucker-Lewis Index, and root-mean-square error of approximation) are inaccurate. A reanalysis of the Mayer et al. subscale intercorrelation matrix provided accurate values of the close-fit indices, which resulted in different evaluations of the models tested by J. D. Mayer et al. Contrary to J. D. Mayer et al., the 1-factor model and the 2-factor model did not provide good fit. Although the 4-factor model was still considered good fitting, the non-constrained 4-factor model yielded a non-positive definite matrix, which was interpreted to be due to the fact that two of the branch-level factors (Perceiving and Facilitating) were collinear, suggesting that a model with 4 factors was implausible.

ORACLE INEQUALITIES FOR THE LASSO IN THE COX MODEL

PubMed Central

Huang, Jian; Sun, Tingni; Ying, Zhiliang; Yu, Yi; Zhang, Cun-Hui

2013-01-01

We study the absolute penalized maximum partial likelihood estimator in sparse, high-dimensional Cox proportional hazards regression models where the number of time-dependent covariates can be larger than the sample size. We establish oracle inequalities based on natural extensions of the compatibility and cone invertibility factors of the Hessian matrix at the true regression coefficients. Similar results based on an extension of the restricted eigenvalue can be also proved by our method. However, the presented oracle inequalities are sharper since the compatibility and cone invertibility factors are always greater than the corresponding restricted eigenvalue. In the Cox regression model, the Hessian matrix is based on time-dependent covariates in censored risk sets, so that the compatibility and cone invertibility factors, and the restricted eigenvalue as well, are random variables even when they are evaluated for the Hessian at the true regression coefficients. Under mild conditions, we prove that these quantities are bounded from below by positive constants for time-dependent covariates, including cases where the number of covariates is of greater order than the sample size. Consequently, the compatibility and cone invertibility factors can be treated as positive constants in our oracle inequalities. PMID:24086091

ORACLE INEQUALITIES FOR THE LASSO IN THE COX MODEL.

PubMed

Huang, Jian; Sun, Tingni; Ying, Zhiliang; Yu, Yi; Zhang, Cun-Hui

2013-06-01

We study the absolute penalized maximum partial likelihood estimator in sparse, high-dimensional Cox proportional hazards regression models where the number of time-dependent covariates can be larger than the sample size. We establish oracle inequalities based on natural extensions of the compatibility and cone invertibility factors of the Hessian matrix at the true regression coefficients. Similar results based on an extension of the restricted eigenvalue can be also proved by our method. However, the presented oracle inequalities are sharper since the compatibility and cone invertibility factors are always greater than the corresponding restricted eigenvalue. In the Cox regression model, the Hessian matrix is based on time-dependent covariates in censored risk sets, so that the compatibility and cone invertibility factors, and the restricted eigenvalue as well, are random variables even when they are evaluated for the Hessian at the true regression coefficients. Under mild conditions, we prove that these quantities are bounded from below by positive constants for time-dependent covariates, including cases where the number of covariates is of greater order than the sample size. Consequently, the compatibility and cone invertibility factors can be treated as positive constants in our oracle inequalities.

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.

DEVELOPMENT AND EVALUATION OF PM 2.5 SOURCE APPORTIONMENT METHODOLOGIES

EPA Science Inventory

The receptor model called Positive Matrix Factorization (PMF) has been extensively used to apportion sources of ambient fine particulate matter (PM_2.5), but the accuracy of source apportionment results currently remains unknown. In addition, air quality forecast model...

Guidance Document for PMF Applications with the Multilinear Engine

EPA Science Inventory

This document serves as a guide for users of the Multilinear Engine version 2 (ME-2) for source apportionment applications utilizing positive matrix factorization (PMF). It aims to educate experienced source apportionment analysts on available ME rotational tools and provides gui...

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.

A Chess-Like Game for Teaching Engineering Students to Solve Large System of Simultaneous Linear Equations

NASA Technical Reports Server (NTRS)

Nguyen, Duc T.; Mohammed, Ahmed Ali; Kadiam, Subhash

2010-01-01

Solving large (and sparse) system of simultaneous linear equations has been (and continues to be) a major challenging problem for many real-world engineering/science applications [1-2]. For many practical/large-scale problems, the sparse, Symmetrical and Positive Definite (SPD) system of linear equations can be conveniently represented in matrix notation as [A] {x} = {b} , where the square coefficient matrix [A] and the Right-Hand-Side (RHS) vector {b} are known. The unknown solution vector {x} can be efficiently solved by the following step-by-step procedures [1-2]: Reordering phase, Matrix Factorization phase, Forward solution phase, and Backward solution phase. In this research work, a Game-Based Learning (GBL) approach has been developed to help engineering students to understand crucial details about matrix reordering and factorization phases. A "chess-like" game has been developed and can be played by either a single player, or two players. Through this "chess-like" open-ended game, the players/learners will not only understand the key concepts involved in reordering algorithms (based on existing algorithms), but also have the opportunities to "discover new algorithms" which are better than existing algorithms. Implementing the proposed "chess-like" game for matrix reordering and factorization phases can be enhanced by FLASH [3] computer environments, where computer simulation with animated human voice, sound effects, visual/graphical/colorful displays of matrix tables, score (or monetary) awards for the best game players, etc. can all be exploited. Preliminary demonstrations of the developed GBL approach can be viewed by anyone who has access to the internet web-site [4]!

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.

Organic Aerosol Composition and Sources in Pasadena, California during the 2010 CalNex Campaign

EPA Science Inventory

Organic aerosols (OA) in Pasadena are characterized using multiple measurements from the California Research at the Nexus of Air Quality and Climate Change (CalNex) campaign. Five OA components are identified using positive matrix factorization including hydrocarbon-like OA (HOA) ...

Source identification of coarse particles in the Desert Southwest, USA using Positive Matrix Factorization

EPA Science Inventory

The Desert Southwest Coarse Particulate Matter Study was undertaken to further our understanding of the spatial and temporal variability and sources of fine and coarse particulate matter (PM) in rural, arid, desert environments. Sampling was conducted between February 2009 and Fe...

NOVEL STATISTICAL APPROACH TO EVALUATE SPATIAL DISTRIBUTION OF PM FROM SPECIFIC SOURCE CATEGORIES

EPA Science Inventory

This task addresses aspects of NRC recommendations 10A and 10B. Positive matrix factorization (PMF) is a new statistical techniques for determining the daily contribution to PM mass of specific source categories (auto exhaust, smelters, suspended soil, secondary sulfate, etc.). I...

An Evaluation of Unit and ½ Mass Correction Approaches as a ...

EPA Pesticide Factsheets

Rare earth elements (REE) and certain alkaline earths can produce M+2 interferences in ICP-MS because they have sufficiently low second ionization energies. Four REEs (150Sm, 150Nd, 156Gd and 156Dy) produce false positives on 75As and 78Se and 132Ba can produce a false positive on 66Zn. Currently, US EPA Method 200.8 does not address these as sources of false positives. Additionally, these M+2 false positives are typically enhanced if collision cell technology is utilized to reduce polyatomic interferences associated with ICP-MS detection. A preliminary evaluation indicates that instrumental tuning conditions can impact the observed M+2/M+1 ratio and in turn the false positives generated on Zn, As and Se. Both unit and ½ mass approaches will be evaluated to correct for these false positives relative to the benchmark concentrations estimates from a triple quadrupole ICP-MS using standard solutions. The impact of matrix on these M+2 corrections will be evaluated over multiple analysis days with a focus on evaluating internal standards that mirror the matrix induced shifts in the M+2 ion transmission. The goal of this evaluation is to move away from fixed M+2 corrective approaches and move towards sample specific approaches that mimic the sample matrix induced variability while attempting to address intra-day variability of the M+2 correction factors through the use of internal standards. Oral Presentation via webinar for EPA Laboratory Technical Informati

Positional information in axolotl and mouse limb extracellular matrix is mediated via heparan sulfate and fibroblast growth factor during limb regeneration in the axolotl (Ambystoma mexicanum).

PubMed

Phan, Anne Q; Lee, Jangwoo; Oei, Michelle; Flath, Craig; Hwe, Caitlyn; Mariano, Rachele; Vu, Tiffany; Shu, Cynthia; Dinh, Andrew; Simkin, Jennifer; Muneoka, Ken; Bryant, Susan V; Gardiner, David M

2015-08-01

Urodele amphibians are unique among adult vertebrates in their ability to regenerate complex body structures after traumatic injury. In salamander regeneration, the cells maintain a memory of their original position and use this positional information to recreate the missing pattern. We used an in vivo gain-of-function assay to determine whether components of the extracellular matrix (ECM) have positional information required to induce formation of new limb pattern during regeneration. We discovered that salamander limb ECM has a position-specific ability to either inhibit regeneration or induce de novo limb structure, and that this difference is dependent on heparan sulfates that are associated with differential expression of heparan sulfate sulfotransferases. We also discovered that an artificial ECM containing only heparan sulfate was sufficient to induce de novo limb pattern in salamander limb regeneration. Finally, ECM from mouse limbs is capable of inducing limb pattern in axolotl blastemas in a position-specific, developmental-stage-specific, and heparan sulfate-dependent manner. This study demonstrates a mechanism for positional information in regeneration and establishes a crucial functional link between salamander regeneration and mammals.

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.

Source Apportionment of Primary and Secondary Organic Aerosol Using Positive Matrix Factorization (PMF) of Molecular Markers

EPA Science Inventory

Monthly average ambient concentrations of more than eighty particle-phase organic compounds, as well as total organic carbon (OC) and elemental carbon (EC), were measured from March 2004 through February 2005 in five cities in the Midwestern United States. A multi-variant source...

On Schrödinger's bridge problem

NASA Astrophysics Data System (ADS)

Friedland, S.

2017-11-01

In the first part of this paper we generalize Georgiou-Pavon's result that a positive square matrix can be scaled uniquely to a column stochastic matrix which maps a given positive probability vector to another given positive probability vector. In the second part we prove that a positive quantum channel can be scaled to another positive quantum channel which maps a given positive definite density matrix to another given positive definite density matrix using Brouwer's fixed point theorem. This result proves the Georgiou-Pavon conjecture for two positive definite density matrices, made in their recent paper. We show that the fixed points are unique for certain pairs of positive definite density matrices. Bibliography: 15 titles.

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.

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.

Connes' embedding problem and Tsirelson's problem

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

Junge, M.; Palazuelos, C.; Navascues, M.

2011-01-15

We show that Tsirelson's problem concerning the set of quantum correlations and Connes' embedding problem on finite approximations in von Neumann algebras (known to be equivalent to Kirchberg's QWEP conjecture) are essentially equivalent. Specifically, Tsirelson's problem asks whether the set of bipartite quantum correlations generated between tensor product separated systems is the same as the set of correlations between commuting C{sup *}-algebras. Connes' embedding problem asks whether any separable II{sub 1} factor is a subfactor of the ultrapower of the hyperfinite II{sub 1} factor. We show that an affirmative answer to Connes' question implies a positive answer to Tsirelson's. Conversely,more » a positive answer to a matrix valued version of Tsirelson's problem implies a positive one to Connes' problem.« less

Using Chebyshev polynomials and approximate inverse triangular factorizations for preconditioning the conjugate gradient method

NASA Astrophysics Data System (ADS)

Kaporin, I. E.

2012-02-01

In order to precondition a sparse symmetric positive definite matrix, its approximate inverse is examined, which is represented as the product of two sparse mutually adjoint triangular matrices. In this way, the solution of the corresponding system of linear algebraic equations (SLAE) by applying the preconditioned conjugate gradient method (CGM) is reduced to performing only elementary vector operations and calculating sparse matrix-vector products. A method for constructing the above preconditioner is described and analyzed. The triangular factor has a fixed sparsity pattern and is optimal in the sense that the preconditioned matrix has a minimum K-condition number. The use of polynomial preconditioning based on Chebyshev polynomials makes it possible to considerably reduce the amount of scalar product operations (at the cost of an insignificant increase in the total number of arithmetic operations). The possibility of an efficient massively parallel implementation of the resulting method for solving SLAEs is discussed. For a sequential version of this method, the results obtained by solving 56 test problems from the Florida sparse matrix collection (which are large-scale and ill-conditioned) are presented. These results show that the method is highly reliable and has low computational costs.

Method and apparatus for optimized processing of sparse matrices

DOEpatents

Taylor, Valerie E.

1993-01-01

A computer architecture for processing a sparse matrix is disclosed. The apparatus stores a value-row vector corresponding to nonzero values of a sparse matrix. Each of the nonzero values is located at a defined row and column position in the matrix. The value-row vector includes a first vector including nonzero values and delimiting characters indicating a transition from one column to another. The value-row vector also includes a second vector which defines row position values in the matrix corresponding to the nonzero values in the first vector and column position values in the matrix corresponding to the column position of the nonzero values in the first vector. The architecture also includes a circuit for detecting a special character within the value-row vector. Matrix-vector multiplication is executed on the value-row vector. This multiplication is performed by multiplying an index value of the first vector value by a column value from a second matrix to form a matrix-vector product which is added to a previous matrix-vector product.

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

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.

Estimation of positive semidefinite correlation matrices by using convex quadratic semidefinite programming.

PubMed

Fushiki, Tadayoshi

2009-07-01

The correlation matrix is a fundamental statistic that is used in many fields. For example, GroupLens, a collaborative filtering system, uses the correlation between users for predictive purposes. Since the correlation is a natural similarity measure between users, the correlation matrix may be used in the Gram matrix in kernel methods. However, the estimated correlation matrix sometimes has a serious defect: although the correlation matrix is originally positive semidefinite, the estimated one may not be positive semidefinite when not all ratings are observed. To obtain a positive semidefinite correlation matrix, the nearest correlation matrix problem has recently been studied in the fields of numerical analysis and optimization. However, statistical properties are not explicitly used in such studies. To obtain a positive semidefinite correlation matrix, we assume the approximate model. By using the model, an estimate is obtained as the optimal point of an optimization problem formulated with information on the variances of the estimated correlation coefficients. The problem is solved by a convex quadratic semidefinite program. A penalized likelihood approach is also examined. The MovieLens data set is used to test our approach.

Bone resorption analysis of platelet-derived growth factor type BB application on collagen for bone grafts secured by titanium mesh over a pig jaw defect model

PubMed Central

Herford, Alan Scott; Cicciù, Marco

2012-01-01

Purpose: The aim of this investigation was to evaluate whether the addition of the platelet derived growth factor type BB (PDGF-BB) to a collagen matrix applied on a titanium mesh would favor healing and resorption onto the grafted bone. A histologic and radiographic study of two different groups (test and control) was performed. Designs: A surgical procedure was performed on 8 pigs to obtain 16 bilateral mandibular alveolar defects. All the defects were then reconstructed with a mixture of autogenous bovine bone using titanium mesh positioning. Two groups, with a total of 16 defects were created: The first to study collagen sponge and PDGF-BB and the second to control collagen only. The collagen matrix was positioned directly over the mesh and soft tissue was closed without tensions onto both groups without attempting to obtain primary closure. Possible exposure of the titanium mesh as well as the height and volume of the new bone was recorded. Results: New bone formation averaged about 6.68 mm in the test group studied; the control group had less regenerated bone at 4.62 mm. Conclusion: PDGF-BB addition to the collagen matrix induced a strong increase in hard and soft tissue healing and favored bone formation, reducing bone resorption even if the mesh was exposed. PMID:23833493

Serum levels of matrix metalloproteinase-3 and autoantibodies related to rheumatoid arthritis in the general Japanese population and their association with osteoporosis and osteoarthritis: the ROAD study.

PubMed

Kodama, Rie; Muraki, Shigeyuki; Iidaka, Toshiko; Oka, Hiroyuki; Teraguchi, Masatoshi; Kagotani, Ryohei; Asai, Yoshiki; Hashizume, Hiroshi; Yoshida, Munehito; Kawaguchi, Hiroshi; Nakamura, Kozo; Akune, Toru; Tanaka, Sakae; Yoshimura, Noriko

2018-03-01

To purpose of this study was to reveal the mean levels and positive proportion of serological markers related to rheumatoid arthritis, and clarify their relationship with osteoporosis and hand osteoarthritis (OA). A total of 1546 participants from the third survey of the research on osteoarthritis/osteoporosis against disability study were enrolled in the current study. Using participant blood samples, the levels of anti-cyclic citrullinated protein (CCP) antibody, rheumatoid factor (RF), matrix metalloproteinase-3 (MMP-3), C-reactive protein (CRP), and high-sensitivity CRP (hsCRP) were measured. Subjects with higher than normal levels were defined as being positive. Osteoporosis was defined according to the recommendations set by World Health Organization criteria in 1994. Radiographic hand OA was evaluated using the modified Kellgren-Lawrence (KL) scale. The positive proportion of anti-CCP antibody, RF, MMP-3, CRP, and hsCRP was 1.8, 7.1, 15.0, 6.7, and 6.4%, respectively. MMP-3 was associated with age, and was significantly higher in men than in women. Positive MMP-3 was not significantly related to osteoporosis or severe hand OA (KL grade ≥3) after adjustment for other factors including age, sex, and body mass index. The results from this study clarified the values and positive proportion of RA-related markers and revealed their relationship with osteoporosis and hand OA.

The Impact of Select Pollutant Sources on Air Quality and the Moravian-Silesian Metropolitan Region by the Positive Matrix Factorization Model

EPA Science Inventory

The National Exposure Research Laboratory (NERL) Human Exposure and Atmospheric Sciences Division (HEASD) conducts research in support of EPA mission to protect human health and the environment. HEASD research program supports Goal 1 (Clean Air) and Goal 4 (Healthy People) of EP...

SOURCE APPORTIONMENT OF PM2.5 AT AN URBAN IMPROVE SITE IN SEATTLE, WA

EPA Science Inventory

The multivariate receptor models Positive Matrix Factorization (PMF) and Unmix were used along with EPA's Chemical Mass Balance model to deduce the sources of PM2.5 at a centrally located urban site in Seattle, Washington. A total of 289 filter samples were obtained with an IM...

SOURCE IDENTIFICATION OF PM2.5 IN AN ARID NORTHWEST U.S. CITY BY POSITIVE MATRIX FACTORIZATION. (R827355C008)

EPA Science Inventory

Spokane, WA is prone to frequent particulate pollution episodes due to dust storms, biomass burning, and periods of stagnant meteorological conditions. Spokane is the location of a long-term study examining the association between health effects and chemical or physical consti...

Application of a self-organizing map and positive matrix factorization to investigate the spatial distributions and sources of polycyclic aromatic hydrocarbons in soils from Xiangfen County, northern China.

PubMed

Tao, Shi-Yang; Zhong, Bu-Qing; Lin, Yan; Ma, Jin; Zhou, Yongzhang; Hou, Hong; Zhao, Long; Sun, Zaijin; Qin, Xiaopeng; Shi, Huading

2017-07-01

The concentrations of 16 priority polycyclic aromatic hydrocarbons (PAHs) were measured in 128 surface soil samples from Xiangfen County, northern China. The total mass concentration of these PAHs ranged from 52 to 10,524ng/g, with a mean of 723ng/g. Four-ring PAHs contributed almost 50% of the total PAH burden. A self-organizing map and positive matrix factorization were applied to investigate the spatial distribution and source apportionment of PAHs. Three emission sources of PAHs were identified, namely, coking ovens (21.9%), coal/biomass combustion (60.1%), and anthracene oil (18.0%). High concentrations of low-molecular-weight PAHs were particularly apparent in the coking plant zone in the region around Gucheng Town. High-molecular-weight PAHs mainly originated from coal/biomass combustion around Gucheng Town, Xincheng Town, and Taosi Town. PAHs in the soil of Xiangfen County are unlikely to pose a significant cancer risk for the population. Copyright © 2017 Elsevier Inc. All rights reserved.

Motif discovery and motif finding from genome-mapped DNase footprint data.

PubMed

Kulakovskiy, Ivan V; Favorov, Alexander V; Makeev, Vsevolod J

2009-09-15

Footprint data is an important source of information on transcription factor recognition motifs. However, a footprinting fragment can contain no sequences similar to known protein recognition sites. Inspection of genome fragments nearby can help to identify missing site positions. Genome fragments containing footprints were supplied to a pipeline that constructed a position weight matrix (PWM) for different motif lengths and selected the optimal PWM. Fragments were aligned with the SeSiMCMC sampler and a new heuristic algorithm, Bigfoot. Footprints with missing hits were found for approximately 50% of factors. Adding only 2 bp on both sides of a footprinting fragment recovered most hits. We automatically constructed motifs for 41 Drosophila factors. New motifs can recognize footprints with a greater sensitivity at the same false positive rate than existing models. Also we discuss possible overfitting of constructed motifs. Software and the collection of regulatory motifs are freely available at http://line.imb.ac.ru/DMMPMM.

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 EGFL7, which is a novel finding and suggests a role of EGFL7 in the vascular infiltration of growth cartilage. PMID:25175365

Osteoblastic differentiation of human stem cells derived from bone marrow and periodontal ligament under the effect of enamel matrix derivative and transforming growth factor-beta.

PubMed

Houshmand, Behzad; Behnia, Hossein; Khoshzaban, Ahad; Morad, Golnaz; Behrouzi, Gholamreza; Dashti, Seyedeh Ghazaleh; Khojasteh, Arash

2013-01-01

To increase the understanding of the applicability of biomaterials and growth factors in enhancing stem cell-based bone regeneration modalities, this study evaluated the effects of enamel matrix derivative (EMD) and recombinant human transforming growth factor-beta (rhTGF-β) on osteoblastic differentiation of human bone marrow mesenchymal stem cells (hBMSCs) as well as human periodontal ligament stem cells (hPDLSCs). hBMSCs and hPDLSCs were obtained, and identification of stem cell surface markers was performed according to the criteria of the International Society for Cellular Therapy. Each group of stem cells was separately treated with a serial dilution of EMD (10, 50, and 100 μg/mL) or rhTGF-β (10 ng/mL). Osteoblastic differentiation was examined through in vitro matrix mineralization by alizarin red staining, and mRNA expression of osteopontin and osteonectin was determined by quantitative reverse-transcriptase polymerase chain reaction. hPDLSCs were further assessed for osteocalcin mRNA expression. Stem cells cultured in osteogenic medium were employed as a standard positive control group. In none of the experimental groups were bone-related mRNAs detected subsequent to treatment with EMD for 5, 10, and 15 days. Alizarin red staining on day 21 was negative in EMD-treated BMSC and PDLSC cultures. In rhTGF-β-supplemented BMSC culture, expression of osteonectin mRNA was demonstrated on day 15, which was statistically comparable to the positive control group. Nevertheless, extracellular matrix mineralization was inhibited in both groups of stem cells. Within the limitations of this study, it could be concluded that EMD with a concentration of 10, 50, or 100 μg/mL has no appreciable effect on osteoblastic differentiation of BMSCs and PDLSCs. Application of rhTGF-β increased osteonectin mRNA expression in BMSCs. This finding corroborates the hypothesis that TGF-β might be involved in early osteoblastic maturation.

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.

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.

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.

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%).

TM4SF5 promotes metastatic behavior of cells in 3D extracellular matrix gels by reducing dependency on environmental cues

PubMed Central

Nam, Seo Hee; Cheong, Jin-Gyu; Jeong, Doyoung; Lee, Seo-Jin; Pan, Cheol-Ho; Jung, Jae Woo; Kim, Hye-Jin; Ryu, Jihye; Kim, Ji Eon; Kim, Somi; Cho, Chang Yun; Kang, Min-Kyung; Lee, Kyung-Min; Lee, Jung Weon

2017-01-01

Transmembrane 4 L six family member 5 (TM4SF5) is highly expressed in hepatocellular carcinoma tissues and enhances migration in two-dimensional environments. Here, we investigated how TM4SF5 is involved in diverse pro-metastatic phenotypes in in vivo-like three-dimensional (3D) extracellular matrix gels. TM4SF5-positive cells aggressively formed invasive foci in 3D Matrigel, depending on TM4SF5-mediated signaling activity, cytoskeletal organization, and matrix metallopeptidase (MMP) 2-mediated extracellular remodeling, whereas TM4SF5-null cells did not. The TM4SF5-null cells did, however, form invasive foci in 3D Matrigel following inhibition of Rho-associated protein kinase or addition of collagen I, suggesting that collagen I compensated for TM4SF5 expression. Similarly, TM4SF5-positive cells expressing vascular endothelial-cadherin formed network-like vasculogenic mimicry in 3D Matrigel and collagen I mixture gels, whereas TM4SF5-negative cells in the mixture gels displayed the network structures only upon further treatment with epidermal growth factor. The foci formation also required MMP2-mediated remodeling of the extracellular matrix. Co-cultures exhibited TM4SF5-positive or cancer-associated fibroblasts at the outward edges of TM4SF5-null cell clusters. Compared with TM4SF5-null cells, TM4SF5-positive cells in 3D collagen gels showed a more invasive outgrowth with dramatic invadopodia. These observations suggest that TM4SF5 plays roles in the promotion of diverse metastatic properties with fewer environmental requirements than TM4SF5-negative cells. PMID:29137358

Changing sources of polychlorinated dibenzo-p-dioxins and furans in sediments and ecological risk for nekton in the lower Passaic River and Newark Bay, New Jersey, USA.

PubMed

Khairy, Mohammed; Barrett, Kirk; Lohmann, Rainer

2016-03-01

Polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs) were measured in sediments (surface and deeper sediments) and porewater of the lower Passaic River and Newark Bay (New Jersey, USA) to apportion their sources and conduct an ecological risk assessment. Positive matrix factorization was applied to identify sources of PCDD/Fs. Five source profiles were extracted from the positive matrix factorization model applied to the sediment samples including chloranil, combustion, polychlorinated biphenyl impurities, mixed urban sources, and the historical contamination from the former Diamond Alkali plant. The ecological risk assessment was estimated using several lines of evidence depending on site-specific data (blue crab and fish samples representing different feeding habits and positions in the trophic wood web of the river). Porewater concentrations gave the best estimates of lipid concentrations especially in the blue crab samples (with an average factor difference of 3.8). Calculated hazard quotients (HQs) for the fish samples and blue crab were >1 based on the no-effect concentration and tissue screening concentration approaches. At the same time, calculated porewater toxic units were >1. Sediment concentrations exceeded the published sediment quality guidelines for the protection of fish and benthic species, indicating the existence of significant risk to the aquatic life in the Passaic River. Accordingly, further actions and control measures are needed to reduce the emission of PCDD/Fs from ongoing sources. © 2015 SETAC.

Effects of forest fragmentation on the beetle assemblage at the relict forest of Fray Jorge, Chile.

PubMed

Barbosa, Olga; Marquet, Pablo A

2002-07-01

Habitat fragmentation is recognized as one of the main factors associated with species extinction and is particularly acute in South American forest habitats. In this study, we examined the effects of forest fragmentation on the beetle assemblage at the relict temperate forest of Fray Jorge (Chile). We evaluated the following hypotheses: (1) there is a strong edge effect, so that the number of beetle species and individuals increases away from the edge, towards the inner part of each fragment, (2) this pattern should be apparent in the larger fragments but not in the smaller ones, where edge effects are expected to be stronger, and (3) there should be a significant interaction between number of species/individuals found inside and outside fragments (i.e., in the matrix) and season, because of an increase in aridity and water stress during austral summer months. We found that the relationship between the number of individuals and number of species vs distance from the matrix towards the forest interior was affected by fragment size and season. In general, both number of species and individuals tended to increase from the matrix towards the forest edge and then either decrease, increase or maintain a constant level, depending on fragment size and season. The result of an ANOVA analysis, which used season, size, and position (inside vs outside fragments) as factors and number of individuals as the response variable, showed a significant effect of fragment size, position, and season and a significant interaction between fragment size and season, season and position, and size and position. ANOVA analysis using number of species as the response variable showed that area, season, and position all had significant effects. The results also showed a significant interaction between size and season and between season and position. Our results emphasize the existence of strong fragment-size and seasonal effects modulating both the response of beetles to fragmentation and their abundance and distribution in temperate areas. Thus, seasonal dynamic effects can be of paramount importance to demonstrate and understand the effect of habitat fragmentation upon arthropod assemblages in temperate areas.

A new method to quantify the health risks from sources of perfluoroalkyl substances, combined with positive matrix factorization and risk assessment models.

PubMed

Xu, Jiao; Shi, Guo-Liang; Guo, Chang-Sheng; Wang, Hai-Ting; Tian, Ying-Ze; Huangfu, Yan-Qi; Zhang, Yuan; Feng, Yin-Chang; Xu, Jian

2018-01-01

A hybrid model based on the positive matrix factorization (PMF) model and the health risk assessment model for assessing risks associated with sources of perfluoroalkyl substances (PFASs) in water was established and applied at Dianchi Lake to test its applicability. The new method contains 2 stages: 1) the sources of PFASs were apportioned by the PMF model and 2) the contribution of health risks from each source was calculated by the new hybrid model. Two factors were extracted by PMF, with factor 1 identified as aqueous fire-fighting foams source and factor 2 as fluoropolymer manufacturing and processing and perfluorooctanoic acid production source. The health risk of PFASs in the water assessed by the health risk assessment model was 9.54 × 10 -7  a -1 on average, showing no obvious adverse effects to human health. The 2 sources' risks estimated by the new hybrid model ranged from 2.95 × 10 -10 to 6.60 × 10 -6  a -1 and from 1.64 × 10 -7 to 1.62 × 10 -6  a -1 , respectively. The new hybrid model can provide useful information on the health risks of PFAS sources, which is helpful for pollution control and environmental management. Environ Toxicol Chem 2018;37:107-115. © 2017 SETAC. © 2017 SETAC.

Positional information in axolotl and mouse limb extracellular matrix is mediated via heparan sulfate and fibroblast growth factor during limb regeneration in the axolotl (Ambystoma mexicanum)

PubMed Central

Phan, Anne Q.; Lee, Jangwoo; Oei, Michelle; Flath, Craig; Hwe, Caitlyn; Mariano, Rachele; Vu, Tiffany; Shu, Cynthia; Dinh, Andrew; Simkin, Jennifer; Muneoka, Ken; Bryant, Susan V.

2015-01-01

Abstract Urodele amphibians are unique among adult vertebrates in their ability to regenerate complex body structures after traumatic injury. In salamander regeneration, the cells maintain a memory of their original position and use this positional information to recreate the missing pattern. We used an in vivo gain‐of‐function assay to determine whether components of the extracellular matrix (ECM) have positional information required to induce formation of new limb pattern during regeneration. We discovered that salamander limb ECM has a position‐specific ability to either inhibit regeneration or induce de novo limb structure, and that this difference is dependent on heparan sulfates that are associated with differential expression of heparan sulfate sulfotransferases. We also discovered that an artificial ECM containing only heparan sulfate was sufficient to induce de novo limb pattern in salamander limb regeneration. Finally, ECM from mouse limbs is capable of inducing limb pattern in axolotl blastemas in a position‐specific, developmental‐stage‐specific, and heparan sulfate‐dependent manner. This study demonstrates a mechanism for positional information in regeneration and establishes a crucial functional link between salamander regeneration and mammals. PMID:27499874

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

Source apportionment with uncertainty estimates of fine particulate matter in Ostrava, Czech Republic using Positive Matrix Factorization

EPA Science Inventory

A 14-week investigation during a warm and cold seasons was conducted to improve understanding of air pollution sources that might be impacting air quality in Ostrava, the Czech Republic. Fine particulate matter (PM2.5) samples were collected in consecutive 12-h day and night incr...

SOURCE APPORTIONMENT OF INDOOR, OUTDOOR, AND PERSONAL PM2.5 IN SEATTLE, WASHINGTON, USING POSITIVE MATRIX FACTORIZATION

EPA Science Inventory

As part of a large exposure assessment and health effects panel study, 33 trace elements and light-absorbing carbon were measured on 24-hr particulate matter with an aero-dynamic diameter <2.5 um (PM2.5) fixed-site filter samples collected between September 26, 2000, and May 25, ...

The occurrence and behavior of radium in saline formation water of the U.S. Gulf Coast region

USGS Publications Warehouse

Kraemer, T.F.; Reid, D.F.

1984-01-01

Radium has been measured in deep saline formation waters produced from a variety of U.S. Gulf Coast subsurface environments, including oil reservoirs, gas reservoirs and water-producing geopressured aquifers. A strong positive correlation has been found between formation-water salinity and Ra activity, resulting from the interaction of formation water with aquifer matrix. Ra isotopes enter the fluid phase after being produced by the decay of parent elements U and Th, which are located at sites on and within the solid matrix. Processes that are belived to be primarily responsible for transferring Ra from matrix to formation water are chemical leaching and alpha-particle recoil. Factors controlling the observed salinity-Ra relationship may be one or a combination of the following factors: (a) ion exchange; (b) increased solubility of matrix silica surrounding Ra atoms, coupled with a salinity-controlled rate of reequilibration of silica between solution and quartz grains; and (c) the equilibration of Ra in solution with detrial barite within the aquifer. No difference was found in the brine-Ra relation in water produced from oil or gas wells and water produced from wells penetrating only water-bearing aquifers, although the relation was more highly correlated for water-bearing aquifers than hydrocarbon-containing reservoirs. ?? 1984.

Unsupervised Bayesian linear unmixing of gene expression microarrays.

PubMed

Bazot, Cécile; Dobigeon, Nicolas; Tourneret, Jean-Yves; Zaas, Aimee K; Ginsburg, Geoffrey S; Hero, Alfred O

2013-03-19

This paper introduces a new constrained model and the corresponding algorithm, called unsupervised Bayesian linear unmixing (uBLU), to identify biological signatures from high dimensional assays like gene expression microarrays. The basis for uBLU is a Bayesian model for the data samples which are represented as an additive mixture of random positive gene signatures, called factors, with random positive mixing coefficients, called factor scores, that specify the relative contribution of each signature to a specific sample. The particularity of the proposed method is that uBLU constrains the factor loadings to be non-negative and the factor scores to be probability distributions over the factors. Furthermore, it also provides estimates of the number of factors. A Gibbs sampling strategy is adopted here to generate random samples according to the posterior distribution of the factors, factor scores, and number of factors. These samples are then used to estimate all the unknown parameters. Firstly, the proposed uBLU method is applied to several simulated datasets with known ground truth and compared with previous factor decomposition methods, such as principal component analysis (PCA), non negative matrix factorization (NMF), Bayesian factor regression modeling (BFRM), and the gradient-based algorithm for general matrix factorization (GB-GMF). Secondly, we illustrate the application of uBLU on a real time-evolving gene expression dataset from a recent viral challenge study in which individuals have been inoculated with influenza A/H3N2/Wisconsin. We show that the uBLU method significantly outperforms the other methods on the simulated and real data sets considered here. The results obtained on synthetic and real data illustrate the accuracy of the proposed uBLU method when compared to other factor decomposition methods from the literature (PCA, NMF, BFRM, and GB-GMF). The uBLU method identifies an inflammatory component closely associated with clinical symptom scores collected during the study. Using a constrained model allows recovery of all the inflammatory genes in a single factor.

Localization of matrix metalloproteinases, (MMPs) their tissue inhibitors, and vascular endothelial growth factor (VEGF) in growth plates of children and adolescents indicates a role for MMPs in human postnatal growth and skeletal maturation.

PubMed

Haeusler, G; Walter, I; Helmreich, M; Egerbacher, M

2005-05-01

Numerous studies have focused on the expression, regulation, and biological significance of matrix metalloproteinases (MMPs) in the growth plate. Findings in mouse knockout models and in vitro data from various species indicate that MMPs not only degrade extracellular matrix components but may regulate the activity of local growth factors. In this study we investigated the presence, distribution, and activity of various MMPs and inhibitors, tissue transglutaminase (tTG or TG2) and vascular endothelial growth factor (VEGF) in the human child and adolescent growth plates by means of immunohistochemistry and gelatin zymography. Tissue was derived during orthopedic surgery (epiphysiodesis) in two prepubertal and four pubertal patients.MMP-2 and MMP-14 were present in reserve cell chondrocytes. MMP-14 was the most prominent MMP within all zones of the growth plate including proliferating chondrocytes. MMP-1 and MMP-13 (collagenases 1 and 3), MMP-9 (gelatinases B), MMP-10, and MMP-11 (stromelysins) and VEGF were positive in hypertrophic chondrocytes and osteoblasts. MMP-2 showed the same expression pattern but was negative in osteoblasts. Osteoclasts stained positive for MMP-9, MMP-2, and TG2. Tissue inhibitor of MMP (TIMP)-1 was present in all zones of the growth plate, osteoblasts, and osteoclasts; TIMP-2 was found in hypertrophic chondrocytes and osteoblasts. In summary, the presence of MMPs, TIMPs, TG2, and VEGF in our study indicated that the MMPs are relevant in growth plate physiology during the postnatal period in humans. The specific location of MMP expression within the growth plate may be the basis for further studies on the role of MMPs in the local regulation of chondrocyte differentiation, proliferation, and ossification at the chondroosseus junction.

CD147 and matrix-metalloproteinase-2 expression in metastatic and non-metastatic uveal melanomas.

PubMed

Lüke, Julia; Vukoja, Vlatka; Brandenbusch, Tim; Nassar, Khaled; Rohrbach, Jens Martin; Grisanti, Salvatore; Lüke, Matthias; Tura, Aysegül

2016-06-03

Extracellular matrix remodelling regulated by matrix-metalloproteinase (MMP) inducer (CD147) is a crucial process during tumor cell invasion and regulation of blood supply. In this study, we evaluated the correlation of CD147 and MMP-2 expression with major prognostic factors for uveal melanoma and the development of metastasis. The expression of CD147 and MMP-2 was analyzed in 49 samples of uveal melanomas. Triple immunofluorescence stainings using markers against glial cells (GFAP), endothelial cells (CD34) and macrophages (CD68) were performed to further analyse the exact localisation of CD147 and MMP-2 positivity. In 28 cases clinical metastatic disease were found. The remaining 21 cases showed no signs of metastatic disease for an average follow-up of 10 years. Correlation analysis (Pearson correlation) was performed to analyse the association of CD147 and MMP-2 expression with known prognostic factors, vasculogenic mimicry (VM), the mature vasculature (von Willebrand Factor) and tumor induced angiogenesis (by means of Endoglin expression). CD147 and MMP-2 were expressed in 47 (96.0 %) of the uveal melanomas. CD147 up-regulation was significantly correlated with a higher MMP-2 expression. The overall expression analysis revealed no significant difference in the metastatic (p = 0.777) and non-metastatic subgroup (p = 0.585). No correlation of CD147 expression and any system of blood supply was evident. In the non-metastatic sub-group a significant correlation of clustered CD147 positive cells with largest basal diameter (p = 0.039), height (p = 0.047) and TNM-stage (p = 0.013) was evident. These data may indicate that CD147 regulates MMP-2 expression in uveal melanoma cells.

Prothymosin α overexpression contributes to the development of pulmonary emphysema.

PubMed

Su, Bing-Hua; Tseng, Yau-Lin; Shieh, Gia-Shing; Chen, Yi-Cheng; Shiang, Ya-Chieh; Wu, Pensee; Li, Kuo-Jung; Yen, Te-Hsin; Shiau, Ai-Li; Wu, Chao-Liang

2013-01-01

Emphysema is one of the disease conditions that comprise chronic obstructive pulmonary disease. Prothymosin α transgenic mice exhibit an emphysema phenotype, but the pathophysiological role of prothymosin α in emphysema remains unclear. Here we show that prothymosin α contributes to the pathogenesis of emphysema by increasing acetylation of histones and nuclear factor-kappaB, particularly upon cigarette smoke exposure. We find a positive correlation between prothymosin α levels and the severity of emphysema in prothymosin α transgenic mice and emphysema patients. Prothymosin α overexpression increases susceptibility to cigarette smoke-induced emphysema, and cigarette smoke exposure further enhances prothymosin α expression. We show that prothymosin α inhibits the association of histone deacetylases with histones and nuclear factor-kappaB, and that prothymosin α overexpression increases expression of nuclear factor-kappaB-dependent matrix metalloproteinase 2 and matrix metalloproteinase 9, which are found in the lungs of patients with chronic obstructive pulmonary disease. These results demonstrate the clinical relevance of prothymosin α in regulating acetylation events during the pathogenesis of emphysema.

Prothymosin α overexpression contributes to the development of pulmonary emphysema

PubMed Central

Su, Bing-Hua; Tseng, Yau-Lin; Shieh, Gia-Shing; Chen, Yi-Cheng; Shiang, Ya-Chieh; Wu, Pensee; Li, Kuo-Jung; Yen, Te-Hsin; Shiau, Ai-Li; Wu, Chao-Liang

2013-01-01

Emphysema is one of the disease conditions that comprise chronic obstructive pulmonary disease. Prothymosin α transgenic mice exhibit an emphysema phenotype, but the pathophysiological role of prothymosin α in emphysema remains unclear. Here we show that prothymosin α contributes to the pathogenesis of emphysema by increasing acetylation of histones and nuclear factor-kappaB, particularly upon cigarette smoke exposure. We find a positive correlation between prothymosin α levels and the severity of emphysema in prothymosin α transgenic mice and emphysema patients. Prothymosin α overexpression increases susceptibility to cigarette smoke-induced emphysema, and cigarette smoke exposure further enhances prothymosin α expression. We show that prothymosin α inhibits the association of histone deacetylases with histones and nuclear factor-kappaB, and that prothymosin α overexpression increases expression of nuclear factor-kappaB-dependent matrix metalloproteinase 2 and matrix metalloproteinase 9, which are found in the lungs of patients with chronic obstructive pulmonary disease. These results demonstrate the clinical relevance of prothymosin α in regulating acetylation events during the pathogenesis of emphysema. PMID:23695700

An on-line calibration algorithm for external parameters of visual system based on binocular stereo cameras

NASA Astrophysics Data System (ADS)

Wang, Liqiang; Liu, Zhen; Zhang, Zhonghua

2014-11-01

Stereo vision is the key in the visual measurement, robot vision, and autonomous navigation. Before performing the system of stereo vision, it needs to calibrate the intrinsic parameters for each camera and the external parameters of the system. In engineering, the intrinsic parameters remain unchanged after calibrating cameras, and the positional relationship between the cameras could be changed because of vibration, knocks and pressures in the vicinity of the railway or motor workshops. Especially for large baselines, even minute changes in translation or rotation can affect the epipolar geometry and scene triangulation to such a degree that visual system becomes disabled. A technology including both real-time examination and on-line recalibration for the external parameters of stereo system becomes particularly important. This paper presents an on-line method for checking and recalibrating the positional relationship between stereo cameras. In epipolar geometry, the external parameters of cameras can be obtained by factorization of the fundamental matrix. Thus, it offers a method to calculate the external camera parameters without any special targets. If the intrinsic camera parameters are known, the external parameters of system can be calculated via a number of random matched points. The process is: (i) estimating the fundamental matrix via the feature point correspondences; (ii) computing the essential matrix from the fundamental matrix; (iii) obtaining the external parameters by decomposition of the essential matrix. In the step of computing the fundamental matrix, the traditional methods are sensitive to noise and cannot ensure the estimation accuracy. We consider the feature distribution situation in the actual scene images and introduce a regional weighted normalization algorithm to improve accuracy of the fundamental matrix estimation. In contrast to traditional algorithms, experiments on simulated data prove that the method improves estimation robustness and accuracy of the fundamental matrix. Finally, we take an experiment for computing the relationship of a pair of stereo cameras to demonstrate accurate performance of the algorithm.

Chromatographic behavior of co-eluted plasma compounds and effect on screening of drugs by APCI-LC-MS(/MS): Applications to selected cardiovascular drugs.

PubMed

Tahboub, Yahya R

2014-12-01

Chromatographic behavior of co-eluted compounds from un-extracted drug-free plasma samples was studied by LC-MS and LC-MS/MS with positive APCI. Under soft gradient, total ion chromatogram (TIC) consisted of two major peaks separated by a constant lower intensity region. Early peak (0.15-0.4 min) belongs to polar plasma compounds and consisted of smaller mass ions ( m / z <250); late peak (3.6-4.6 min) belongs to thermally unstable phospholipids and consisted of fragments with m / z <300. Late peak is more sensitive to variations in chromatographic and MS parameters. Screening of most targeted cardiovascular drugs at levels lower than 50 ng/mL has been possible by LC-MS for drugs with retention factors larger than three. Matrix effects and recovery, at 20 and 200 ng/mL, were evaluated for spiked plasma samples with 15 cardiovascular drugs, by MRM-LC-MS/MS. Average recoveries were above 90% and matrix effects expressed as percent matrix factor (% MF) were above 100%, indicating enhancement character for APCI. Large uncertainties were significant for drugs with smaller masses ( m / z <250) and retention factors lower than two.

A Regional Assessment of Marine Vessel PM2.5 Impacts in the U.S. Pacific Northwest Using a Receptor Based Source Apportionment Method

EPA Science Inventory

This work reports the results of a regional receptor-based source apportionment analysis using the Positive Matrix Factorization (PMF) model on chemically speciated PM2.5 data from 36 urban and rural monitoring sites within the U.S. Pacific Northwest. The approach taken is to mo...

Expression of POEM, a positive regulator of osteoblast differentiation, is suppressed by TNF-{alpha}

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

Tsukasaki, Masayuki; Yamada, Atsushi, E-mail: yamadaa@dent.showa-u.ac.jp; Suzuki, Dai

2011-07-15

Highlights: {yields} TNF-{alpha} inhibits POEM gene expression. {yields} Inhibition of POEM gene expression is caused by NF-{kappa}B activation by TNF-{alpha}. {yields} Over-expression of POEM recovers inhibition of osteoblast differentiation by TNF-{alpha}. -- Abstract: POEM, also known as nephronectin, is an extracellular matrix protein considered to be a positive regulator of osteoblast differentiation. In the present study, we found that tumor necrosis factor-{alpha} (TNF-{alpha}), a key regulator of bone matrix properties and composition that also inhibits terminal osteoblast differentiation, strongly inhibited POEM expression in the mouse osteoblastic cell line MC3T3-E1. TNF-{alpha}-induced down-regulation of POEM gene expression occurred in both time- andmore » dose-dependent manners through the nuclear factor kappa B (NF-{kappa}B) pathway. In addition, expressions of marker genes in differentiated osteoblasts were down-regulated by TNF-{alpha} in a manner consistent with our findings for POEM, while over-expression of POEM recovered TNF-{alpha}-induced inhibition of osteoblast differentiation. These results suggest that TNF-{alpha} inhibits POEM expression through the NF-{kappa}B signaling pathway and down-regulation of POEM influences the inhibition of osteoblast differentiation by TNF-{alpha}.« less

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.

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.

TETRA-COM: a comprehensive SPSS program for estimating the tetrachoric correlation.

PubMed

Lorenzo-Seva, Urbano; Ferrando, Pere J

2012-12-01

We provide an SPSS program that implements descriptive and inferential procedures for estimating tetrachoric correlations. These procedures have two main purposes: (1) bivariate estimation in contingency tables and (2) constructing a correlation matrix to be used as input for factor analysis (in particular, the SPSS FACTOR procedure). In both cases, the program computes accurate point estimates, as well as standard errors and confidence intervals that are correct for any population value. For purpose (1), the program computes the contingency table together with five other measures of association. For purpose (2), the program checks the positive definiteness of the matrix, and if it is found not to be Gramian, performs a nonlinear smoothing procedure at the user's request. The SPSS syntax, a short manual, and data files related to this article are available as supplemental materials from brm.psychonomic-journals.org/content/supplemental.

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

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.

Two overlapping domains of a lyssavirus matrix protein that acts on different cell death pathways.

PubMed

Larrous, Florence; Gholami, Alireza; Mouhamad, Shahul; Estaquier, Jérôme; Bourhy, Hervé

2010-10-01

The lyssavirus matrix (M) protein induces apoptosis. The regions of the M protein that are essential for triggering cell death pathways are not yet clearly defined. We therefore compared the M proteins from two viruses that have contrasting characteristics in terms of cellular apoptosis: a genotype 3 lyssavirus, Mokola virus (MOK), and a genotype 1 rabies virus isolated from a dog from Thailand (THA). We identified a 20-amino-acid fragment (corresponding to positions 67 to 86) that retained the cell death activities of the full-length M protein from MOK via both the tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) and inhibition of cytochrome c oxidase (CcO) activity. We found that the amino acids at positions 77 and 81 have an essential role in triggering these two cell death pathways. Directed mutagenesis demonstrated that the amino acid at position 77 affects CcO activity, whereas the amino acid at position 81 affects TRAIL-dependent apoptosis. Mutations in the full-length M protein that compromised induction of either of these two pathways resulted in delayed apoptosis compared with the time to apoptosis for the nonmutated control.

Two Overlapping Domains of a Lyssavirus Matrix Protein That Acts on Different Cell Death Pathways ▿

PubMed Central

Larrous, Florence; Gholami, Alireza; Mouhamad, Shahul; Estaquier, Jérôme; Bourhy, Hervé

2010-01-01

The lyssavirus matrix (M) protein induces apoptosis. The regions of the M protein that are essential for triggering cell death pathways are not yet clearly defined. We therefore compared the M proteins from two viruses that have contrasting characteristics in terms of cellular apoptosis: a genotype 3 lyssavirus, Mokola virus (MOK), and a genotype 1 rabies virus isolated from a dog from Thailand (THA). We identified a 20-amino-acid fragment (corresponding to positions 67 to 86) that retained the cell death activities of the full-length M protein from MOK via both the tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) and inhibition of cytochrome c oxidase (CcO) activity. We found that the amino acids at positions 77 and 81 have an essential role in triggering these two cell death pathways. Directed mutagenesis demonstrated that the amino acid at position 77 affects CcO activity, whereas the amino acid at position 81 affects TRAIL-dependent apoptosis. Mutations in the full-length M protein that compromised induction of either of these two pathways resulted in delayed apoptosis compared with the time to apoptosis for the nonmutated control. PMID:20631119

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…

Can positive matrix factorization help to understand patterns of organic trace gases at the continental Global Atmosphere Watch site Hohenpeissenberg?

NASA Astrophysics Data System (ADS)

Leuchner, M.; Gubo, S.; Schunk, C.; Wastl, C.; Kirchner, M.; Menzel, A.; Plass-Dülmer, C.

2015-02-01

From the rural Global Atmosphere Watch (GAW) site Hohenpeissenberg in the pre-alpine area of southern Germany, a data set of 24 C2-C8 non-methane hydrocarbons over a period of 7 years was analyzed. Receptor modeling was performed by positive matrix factorization (PMF) and the resulting factors were interpreted with respect to source profiles and photochemical aging. Differing from other studies, no direct source attribution was intended because, due to chemistry along transport, mass conservation from source to receptor is not given. However, at remote sites such as Hohenpeissenberg, the observed patterns of non-methane hydrocarbons can be derived from combinations of factors determined by PMF. A six-factor solution showed high stability and the most plausible results. In addition to a biogenic and a background factor of very stable compounds, four additional anthropogenic factors were resolved that could be divided into two short- and two long-lived patterns from evaporative sources/natural gas leakage and incomplete combustion processes. The volume or mass contribution at the site over the entire period was, in decreasing order, from the following factor categories: background, gas leakage and long-lived evaporative, residential heating and long-lived combustion, short-lived evaporative, short-lived combustion, and biogenic. The importance with respect to reactivity contribution was generally in reverse order, with the biogenic and the short-lived combustion factors contributing most. The seasonality of the factors was analyzed and compared to results of a simple box model using constant emissions and the photochemical decay calculated from the measured annual cycles of OH radicals and ozone. Two of the factors, short-lived combustion and gas leakage/long-lived evaporative, showed winter/summer ratios of about 9 and 7, respectively, as expected from constant source estimations. Contrarily, the short-lived evaporative emissions were about 3 times higher in summer than in winter, while residential heating/long-lived combustion emissions were about 2 times higher in winter than in summer.

Machine learning with quantum relative entropy

NASA Astrophysics Data System (ADS)

Tsuda, Koji

2009-12-01

Density matrices are a central tool in quantum physics, but it is also used in machine learning. A positive definite matrix called kernel matrix is used to represent the similarities between examples. Positive definiteness assures that the examples are embedded in an Euclidean space. When a positive definite matrix is learned from data, one has to design an update rule that maintains the positive definiteness. Our update rule, called matrix exponentiated gradient update, is motivated by the quantum relative entropy. Notably, the relative entropy is an instance of Bregman divergences, which are asymmetric distance measures specifying theoretical properties of machine learning algorithms. Using the calculus commonly used in quantum physics, we prove an upperbound of the generalization error of online learning.

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

Distributed Matrix Completion: Application to Cooperative Positioning in Noisy Environments

DTIC Science & Technology

2013-12-11

positioning, and a gossip version of low-rank approximation were developed. A convex relaxation for positioning in the presence of noise was shown to...of a large data matrix through gossip algorithms. A new algorithm is proposed that amounts to iteratively multiplying a vector by independent random...sparsification of the original matrix and averaging the resulting normalized vectors. This can be viewed as a generalization of gossip algorithms for

The discrete hungry Lotka Volterra system and a new algorithm for computing matrix eigenvalues

NASA Astrophysics Data System (ADS)

Fukuda, Akiko; Ishiwata, Emiko; Iwasaki, Masashi; Nakamura, Yoshimasa

2009-01-01

The discrete hungry Lotka-Volterra (dhLV) system is a generalization of the discrete Lotka-Volterra (dLV) system which stands for a prey-predator model in mathematical biology. In this paper, we show that (1) some invariants exist which are expressed by dhLV variables and are independent from the discrete time and (2) a dhLV variable converges to some positive constant or zero as the discrete time becomes sufficiently large. Some characteristic polynomial is then factorized with the help of the dhLV system. The asymptotic behaviour of the dhLV system enables us to design an algorithm for computing complex eigenvalues of a certain band matrix.

Detection of Amine Impurity and Quality Assessment of the MALDI Matrix α-Cyano-4-Hydroxy-Cinnamic Acid for Peptide Analysis in the amol Range

NASA Astrophysics Data System (ADS)

Rechthaler, Justyna; Pittenauer, Ernst; Schaub, Tanner M.; Allmaier, Günter

2013-05-01

We have studied sample preparation conditions to increase the reproducibility of positive UV-MALDI-TOF mass spectrometry of peptides in the amol range. By evaluating several α-cyano-4-hydroxy-cinnamic acid (CHCA) matrix batches and preparation protocols, it became apparent that two factors have a large influence on the reproducibility and the quality of the generated peptide mass spectra: (1) the selection of the CHCA matrix, which allows the most sensitive measurements and an easier finding of the "sweet spots," and (2) the amount of the sample volume deposited onto the thin crystalline matrix layer. We have studied in detail the influence of a contaminant, coming from commercial CHCA matrix batches, on sensitivity of generated peptide mass spectra in the amol as well as fmol range of a tryptic peptide mixture. The structure of the contaminant, N, N-dimethylbutyl amine, was determined by applying MALDI-FT-ICR mass spectrometry experiments for elemental composition and MALDI high energy CID experiments utilizing a tandem mass spectrometer (TOF/RTOF). A recrystallization of heavily contaminated CHCA batches that reduces or eliminates the determined impurity is described. Furthermore, a fast and reliable method for the assessment of CHCA matrix batches prior to tryptic peptide MALDI mass spectrometric analyses is presented.

Efficient system modeling for a small animal PET scanner with tapered DOI detectors.

PubMed

Zhang, Mengxi; Zhou, Jian; Yang, Yongfeng; Rodríguez-Villafuerte, Mercedes; Qi, Jinyi

2016-01-21

A prototype small animal positron emission tomography (PET) scanner for mouse brain imaging has been developed at UC Davis. The new scanner uses tapered detector arrays with depth of interaction (DOI) measurement. In this paper, we present an efficient system model for the tapered PET scanner using matrix factorization and a virtual scanner geometry. The factored system matrix mainly consists of two components: a sinogram blurring matrix and a geometrical matrix. The geometric matrix is based on a virtual scanner geometry. The sinogram blurring matrix is estimated by matrix factorization. We investigate the performance of different virtual scanner geometries. Both simulation study and real data experiments are performed in the fully 3D mode to study the image quality under different system models. The results indicate that the proposed matrix factorization can maintain image quality while substantially reduce the image reconstruction time and system matrix storage cost. The proposed method can be also applied to other PET scanners with DOI measurement.

Analytic tools for investigating the structure of network reliability measures with regard to observation correlations

NASA Astrophysics Data System (ADS)

Prószyński, W.; Kwaśniak, M.

2018-03-01

A global measure of observation correlations in a network is proposed, together with the auxiliary indices related to non-diagonal elements of the correlation matrix. Based on the above global measure, a specific representation of the correlation matrix is presented, being the result of rigorously proven theorem formulated within the present research. According to the theorem, each positive definite correlation matrix can be expressed by a scale factor and a so-called internal weight matrix. Such a representation made it possible to investigate the structure of the basic reliability measures with regard to observation correlations. Numerical examples carried out for two test networks illustrate the structure of those measures that proved to be dependent on global correlation index. Also, the levels of global correlation are proposed. It is shown that one can readily find an approximate value of the global correlation index, and hence the correlation level, for the expected values of auxiliary indices being the only knowledge about a correlation matrix of interest. The paper is an extended continuation of the previous study of authors that was confined to the elementary case termed uniform correlation. The extension covers arbitrary correlation matrices and a structure of correlation effect.

Dependence of matrix effect on ionization polarity during LC-ESI-MS analysis of derivatized amino acids in some natural samples.

PubMed

Oldekop, Maarja-Liisa; Rebane, Riin; Herodes, Koit

2017-10-01

Matrix effect, the influence of co-eluting components on the ionization efficiency of the analyte, affects the trueness and precision of the LC-ESI-MS analysis. Derivatization can reduce or eliminate matrix effect, for example, diethyl ethoxymethylenemalonate (DEEMM) derivatives have shown less matrix effect compared to other derivatives. Moreover, the use of negative ion mode can further reduce matrix effect. In order to investigate the combination of derivatization and different ionization modes, an LC-ESI-MS/MS method using alternating positive/negative ion mode was developed and validated. The analyses in positive and negative ion modes had comparable limit of quantitation values. The influence of ESI polarity on matrix effect was investigated during the analysis of 22 DEEMM-derivatized amino acids in herbal extracts and honeys. Sample dilution approach was used for the evaluation of the presence of matrix effect. Altogether, 4 honeys and 11 herbal extracts were analyzed, and the concentrations of 22 amino acids in the samples are presented. In the positive ion mode, matrix effect was observed for several amino acid derivatives and the matrix effect was stronger in honey samples compared to the herbal extracts. The negative ion mode was free from matrix effect, with only few exceptions in honeys (average relative standard deviation over all analytes and matrices was 8%; SD = 7%). The matrix effect was eliminated in the positive ion mode by sample dilution and agreement between concentrations from the two ion modes was achieved for most amino acids. In conclusion, it was shown that the combination of derivatization and negative ion mode can be a powerful tool for minimizing matrix effect in more complicated applications.

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)

Sources and drains: Major controls of hydrothermal fluid flow in the Kokanee Range, British Columbia, Canada

NASA Astrophysics Data System (ADS)

Beaudoin, Georges; Therrien, René

1999-10-01

Vein fields are fractured domains of the lithosphere that have been infiltrated by hydrothermal fluids, which deposited minerals in response to changing physico-chemical conditions. Because oxygen is a major component of the infiltrating fluid and the surrounding rock matrix, the oxygen isotope composition of minerals found in veins is used to decipher ancient fluid flow within the lithosphere. We use a numerical model to simulate oxygen isotope transport in the Kokanee Range silver-lead-zinc vein field. The model considers advective, dispersive, and reactive transport in a three-dimensional porous rock matrix intersected by high-permeability planes representing fracture zones. Here we show that it is the geometrical configuration of the sources and of the drains of hydrothermal fluids, combined with the fracture pattern, that exerts the main control on the oxygen isotope distribution. Other factors that affect, to a lesser extent, the values and positions of oxygen isopleths are the fluids and rock-matrix isotopic compositions, the isotopic fractionation, the reaction rate constant, and hydraulic conductivities of the rock matrix and fracture zones.

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.

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…

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

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 on a hemispherical scale.

Fast polar decomposition of an arbitrary matrix

NASA Technical Reports Server (NTRS)

Higham, Nicholas J.; Schreiber, Robert S.

1988-01-01

The polar decomposition of an m x n matrix A of full rank, where m is greater than or equal to n, can be computed using a quadratically convergent algorithm. The algorithm is based on a Newton iteration involving a matrix inverse. With the use of a preliminary complete orthogonal decomposition the algorithm can be extended to arbitrary A. How to use the algorithm to compute the positive semi-definite square root of a Hermitian positive semi-definite matrix is described. A hybrid algorithm which adaptively switches from the matrix inversion based iteration to a matrix multiplication based iteration due to Kovarik, and to Bjorck and Bowie is formulated. The decision when to switch is made using a condition estimator. This matrix multiplication rich algorithm is shown to be more efficient on machines for which matrix multiplication can be executed 1.5 times faster than matrix inversion.

Multi-ray-based system matrix generation for 3D PET reconstruction

NASA Astrophysics Data System (ADS)

Moehrs, Sascha; Defrise, Michel; Belcari, Nicola; DelGuerra, Alberto; Bartoli, Antonietta; Fabbri, Serena; Zanetti, Gianluigi

2008-12-01

Iterative image reconstruction algorithms for positron emission tomography (PET) require a sophisticated system matrix (model) of the scanner. Our aim is to set up such a model offline for the YAP-(S)PET II small animal imaging tomograph in order to use it subsequently with standard ML-EM (maximum-likelihood expectation maximization) and OSEM (ordered subset expectation maximization) for fully three-dimensional image reconstruction. In general, the system model can be obtained analytically, via measurements or via Monte Carlo simulations. In this paper, we present the multi-ray method, which can be considered as a hybrid method to set up the system model offline. It incorporates accurate analytical (geometric) considerations as well as crystal depth and crystal scatter effects. At the same time, it has the potential to model seamlessly other physical aspects such as the positron range. The proposed method is based on multiple rays which are traced from/to the detector crystals through the image volume. Such a ray-tracing approach itself is not new; however, we derive a novel mathematical formulation of the approach and investigate the positioning of the integration (ray-end) points. First, we study single system matrix entries and show that the positioning and weighting of the ray-end points according to Gaussian integration give better results compared to equally spaced integration points (trapezoidal integration), especially if only a small number of integration points (rays) are used. Additionally, we show that, for a given variance of the single matrix entries, the number of rays (events) required to calculate the whole matrix is a factor of 20 larger when using a pure Monte-Carlo-based method. Finally, we analyse the quality of the model by reconstructing phantom data from the YAP-(S)PET II scanner.

Coupling chemical transport model source attributions with positive matrix factorization: application to two IMPROVE sites impacted by wildfires.

PubMed

Sturtz, Timothy M; Schichtel, Bret A; Larson, Timothy V

2014-10-07

Source contributions to total fine particle carbon predicted by a chemical transport model (CTM) were incorporated into the positive matrix factorization (PMF) receptor model to form a receptor-oriented hybrid model. The level of influence of the CTM versus traditional PMF was varied using a weighting parameter applied to an object function as implemented in the Multilinear Engine (ME-2). The methodology provides the ability to separate features that would not be identified using PMF alone, without sacrificing fit to observations. The hybrid model was applied to IMPROVE data taken from 2006 through 2008 at Monture and Sula Peak, Montana. It was able to separately identify major contributions of total carbon (TC) from wildfires and minor contributions from biogenic sources. The predictions of TC had a lower cross-validated RMSE than those from either PMF or CTM alone. Two unconstrained, minor features were identified at each site, a soil derived feature with elevated summer impacts and a feature enriched in sulfate and nitrate with significant, but sporadic contributions across the sampling period. The respective mean TC contributions from wildfires, biogenic emissions, and other sources were 1.18, 0.12, and 0.12 ugC/m(3) at Monture and 1.60, 0.44, and 0.06 ugC/m(3) at Sula Peak.

Source apportionment of PM10 by positive matrix factorization in urban area of Mumbai, India.

PubMed

Gupta, Indrani; Salunkhe, Abhaysinh; Kumar, Rakesh

2012-01-01

Particulate Matter (PM(10)) has been one of the main air pollutants exceeding the ambient standards in most of the major cities in India. During last few years, receptor models such as Chemical Mass Balance, Positive Matrix Factorization (PMF), PCA-APCS and UNMIX have been used to provide solutions to the source identification and contributions which are accepted for developing effective and efficient air quality management plans. Each site poses different complexities while resolving PM(10) contributions. This paper reports the variability of four sites within Mumbai city using PMF. Industrial area of Mahul showed sources such as residual oil combustion and paved road dust (27%), traffic (20%), coal fired boiler (17%), nitrate (15%). Residential area of Khar showed sources such as residual oil combustion and construction (25%), motor vehicles (23%), marine aerosol and nitrate (19%), paved road dust (18%) compared to construction and natural dust (27%), motor vehicles and smelting work (25%), nitrate (16%) and biomass burning and paved road dust (15%) in Dharavi, a low income slum residential area. The major contributors of PM(10) at Colaba were marine aerosol, wood burning and ammonium sulphate (24%), motor vehicles and smelting work (22%), Natural soil (19%), nitrate and oil burning (18%).

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

PubMed

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

2012-10-16

A novel on-board system was tested to characterize size-resolved particle number emission patterns under real-world driving conditions, running in a EURO4 diesel vehicle and in a typical urban circuit in Madrid (Spain). Emission profiles were determined as a function of driving conditions. Source apportionment by Positive Matrix Factorization (PMF) was carried out to interpret the real-world driving conditions. Three emission patterns were identified: (F1) cruise conditions, with medium-high speeds, contributing in this circuit with 60% of total particle number and a particle size distribution dominated by particles >52 nm and around 60 nm; (F2) transient conditions, stop-and-go conditions at medium-high speed, contributing with 25% of the particle number and mainly emitting particles in the nucleation mode; and (F3) creep-idle conditions, representing traffic congestion and frequent idling periods, contributing with 14% to the total particle number and with particles in the nucleation mode (<29.4 nm) and around 98 nm. We suggest potential approaches to reduce particle number emissions depending on particle size and driving conditions. Differences between real-world emission patterns and regulatory cycles (NEDC) are also presented, which evidence that detecting particle number emissions <40 nm is only possible under real-world driving conditions.

Positioning matrix of economic efficiency and complexity: a case study in a university hospital.

PubMed

Ippolito, Adelaide; Viggiani, Vincenzo

2014-01-01

At the end of 2010, the Federico II University Hospital in Naples, Italy, initiated a series of discussions aimed at designing and applying a positioning matrix to its departments. This analysis was developed to create a tool able to extract meaningful information both to increase knowledge about individual departments and to inform the choices of general management during strategic planning. The name given to this tool was the positioning matrix of economic efficiency and complexity. In the matrix, the x-axis measures the ratio between revenues and costs, whereas the y-axis measures the index of complexity, thus showing "profitability" while bearing in mind the complexity of activities. By using the positioning matrix, it was possible to conduct a critical analysis of the characteristics of the Federico II University Hospital and to extract useful information for general management to use during strategic planning at the end of 2010 when defining medium-term objectives. Copyright © 2013 John Wiley & Sons, Ltd.

Convergence of moment expansions for expectation values with embedded random matrix ensembles and quantum chaos

NASA Astrophysics Data System (ADS)

Kota, V. K. B.

2003-07-01

Smoothed forms for expectation values < K> E of positive definite operators K follow from the K-density moments either directly or in many other ways each giving a series expansion (involving polynomials in E). In large spectroscopic spaces one has to partition the many particle spaces into subspaces. Partitioning leads to new expansions for expectation values. It is shown that all the expansions converge to compact forms depending on the nature of the operator K and the operation of embedded random matrix ensembles and quantum chaos in many particle spaces. Explicit results are given for occupancies < ni> E, spin-cutoff factors < JZ2> E and strength sums < O†O> E, where O is a one-body transition operator.

Temporal growth factor release from platelet-rich plasma, trehalose lyophilized platelets, and bone marrow aspirate and their effect on tendon and ligament gene expression.

PubMed

McCarrel, Taralyn; Fortier, Lisa

2009-08-01

Platelet-rich plasma (PRP) has generated substantial interest for tendon and ligament regeneration because of the high concentrations of growth factors in platelet alpha-granules. This study compared the temporal release of growth factors from bone marrow aspirate (BMA), PRP, and lyophilized platelet product (PP), and measured their effects on tendon and ligament gene expression. Blood and BMA were collected and processed to yield PRP and plasma. Flexor digitorum superficialis tendon (FDS) and suspensory ligament (SL) explants were cultured in 10% plasma in DMEM (control), BMA, PRP, or PP. TGF-beta1 and PDGF-BB concentrations were determined at 0, 24, and 96 h of culture using ELISA. Quantitative RT-PCR for collagen types I and III (COL1A1, COL3A1), cartilage oligomeric matrix protein (COMP), decorin, and matrix metalloproteinases-3 and 13 (MMP-3, MMP-13) was performed. TGF-beta1 and PDGF-BB concentrations were highest in PRP and PP. Growth factor quantity was unchanged in BMA, increased in PRP, and decreased in PP over 4 days. TGF-beta1 and platelet concentrations were positively correlated. Lyophilized PP and PRP resulted in increased COL1A1:COL3A1 ratio, increased COMP, and decreased MMP-13 expression. BMA resulted in decreased COMP and increased MMP-3 and MMP-13 gene expression. Platelet concentration was positively correlated with COL1A1, ratio of COL1A1:COL3A1, and COMP, and negatively correlated with COL3A1, MMP-13, and MMP-3. White blood cell concentration was positively correlated with COL3A1, MMP3, and MMP13, and negatively correlated with a ratio of COL1A1:COL3A1, COMP, and decorin. These findings support further in vivo investigation of PRP and PP for treatment of tendonitis and desmitis. Copyright 2009 Orthopaedic Research Society. Published by Wiley Periodicals, Inc.

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.

Reduction of matrix interferences in furnace atomic absorption with the L'vov Platform

USGS Publications Warehouse

Kaiser, M.L.; Koirtyohann, S.R.; Hinderberger, E.J.; Taylor, Howard E.

1981-01-01

Use of a modified L'vov Platform and ammonium phosphate as a matrix modifier greatly reduced matrix interferences in a commercial Massmann-type atomic absorption furnace. Platforms were readily fabricated from furnace tubes and, once positioned in the furnace, caused no inconvenience in operation. Two volatile elements (Pb, Cd), two of intermediate volatility (Co, Cr) and two which form stable oxides (Al, Sn) were tested in natural water and selected synthetic matrices. In every case for which there was a significant matrix effect during atomization from the tube wall, the platform and platform plus modifier gave improved performance. With lead, for example, an average ratio of 0.48 ?? 0.11 was found when the slope of the standard additions plot for six different natural water samples was compared to the slope of the standard working curve in dilute acid. The average slope ratio between the natural water matrices and the dilute acid matrix was 0.94 ?? 0.03 with the L'vov Platform and 0.96 ?? 0.03 with the platform and matrix modifier. In none of the cases studied did the use of the platform or platform plus modifier cause an interference problem where none existed while atomizing from the tube wall. An additional benefit of the platform was a factor of about two improvement in peak height precision. ?? 1981.

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) compounds (light SVOC factor) exhibited strong correlations ( r = 0.82-0.98) between the full data set and each sub-data set solution, indicating that the impacts of G/P partitioning on receptor-based source apportionment could be eliminated by using total SVOC concentrations.

Cell stiffness, contractile stress and the role of extracellular matrix

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

An, Steven S., E-mail: san@jhsph.edu; Kim, Jina; Ahn, Kwangmi

Here we have assessed the effects of extracellular matrix (ECM) composition and rigidity on mechanical properties of the human airway smooth muscle (ASM) cell. Cell stiffness and contractile stress showed appreciable changes from the most relaxed state to the most contracted state: we refer to the maximal range of these changes as the cell contractile scope. The contractile scope was least when the cell was adherent upon collagen V, followed by collagen IV, laminin, and collagen I, and greatest for fibronectin. Regardless of ECM composition, upon adherence to increasingly rigid substrates, the ASM cell positively regulated expression of antioxidant genesmore » in the glutathione pathway and heme oxygenase, and disruption of a redox-sensitive transcription factor, nuclear erythroid 2 p45-related factor (Nrf2), culminated in greater contractile scope. These findings provide biophysical evidence that ECM differentially modulates muscle contractility and, for the first time, demonstrate a link between muscle contractility and Nrf2-directed responses.« less

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.

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.

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.

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.

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

Histopathological and Immunohistochemical Evaluation of Pannus Tissue in Patients with Prosthetic Valve Dysfunction.

PubMed

Karakoyun, Süleyman; Ozan Gürsoy, Mustafa; Yesin, Mahmut; Kalçık, Macit; Astarcıoğlu, Mehmet Ali; Gündüz, Sabahattin; Emrah Oğuz, Ali; Çoban Kökten, Şermin; Nimet Karadayı, Ayşe; Tuncer, Altuğ; Köksal, Cengiz; Gökdeniz, Tayyar; Özkan, Mehmet

2016-01-01

Prosthetic valve dysfunction due to pannus formation is a rare but serious complication. Currently, limited data are available concerning the pathogenesis and immunohistochemical properties of pannus. The study aim was to investigate the morphological, histopathological and immunohistochemical characteristics of pannus formation in patients with prosthetic valve dysfunction. A total of 35 patients (10 males, 25 females; mean age 44 ± 16 years) who had undergone re-do valve surgery due to prosthetic valve obstruction was enrolled in the study. Immunohistochemical studies were aimed at evaluating the expression of alphasmooth muscle actin (α-SMA) and desmin in myofibroblasts and smooth muscle cells; epithelial membrane antigen (EMA) in epithelial cells; and CD34, Factor VIII and vascular endothelial growth factor (VEGF) in endothelial cells. Matrix metalloproteinases (MMPs) -2 and -9, and transforming growth factor-beta (TGF-β) were used to demonstrate cytokine release from macrophages, leukocytes, fibroblasts and myofibroblasts. Pannus appeared as a tough and thick tissue hyperplasia which began from outside the suture ring in the periannular region and extended to the inflow and outflow surfaces of the prosthetic valves. Histopathological analysis showed the pannus tissue to consist of chronic inflammatory cells (lymphocytes, plasma cells, macrophages and foreign body giant cells), spindle cells such as myofibroblasts, capillary blood vessels and endothelial cells laying down the lumens. Calcification was present in the pannus tissue of 19 explanted prostheses. Immunohistochemical studies revealed positive α-SMA expression in all patients, whereas 60.5% of patients were positive for desmin, 50% for EMA, 42.1% for VEGF, 39.5% for TBF-β, 42.1% for MMP-2, 86.8% for CD34, and 97.4% for Factor VIII. MMP-9 was negative in all patients. Pannus tissue appears to be formed as the result of a neointimal response in periannular regions of prosthetic valves that consist of periannular tissue migration, myofibroblast and extracellular matrix proliferation with vascular components. It is a chronic active process in which mediators such as TGF-β, VEGF and MMP-2 play roles in both matrix formation and degradation.

An Improved DOA Estimation Approach Using Coarray Interpolation and Matrix Denoising

PubMed Central

Guo, Muran; Chen, Tao; Wang, Ben

2017-01-01

Co-prime arrays can estimate the directions of arrival (DOAs) of O(MN) sources with O(M+N) sensors, and are convenient to analyze due to their closed-form expression for the locations of virtual lags. However, the number of degrees of freedom is limited due to the existence of holes in difference coarrays if subspace-based algorithms such as the spatial smoothing multiple signal classification (MUSIC) algorithm are utilized. To address this issue, techniques such as positive definite Toeplitz completion and array interpolation have been proposed in the literature. Another factor that compromises the accuracy of DOA estimation is the limitation of the number of snapshots. Coarray-based processing is particularly sensitive to the discrepancy between the sample covariance matrix and the ideal covariance matrix due to the finite number of snapshots. In this paper, coarray interpolation based on matrix completion (MC) followed by a denoising operation is proposed to detect more sources with a higher accuracy. The effectiveness of the proposed method is based on the capability of MC to fill in holes in the virtual sensors and that of MC denoising operation to reduce the perturbation in the sample covariance matrix. The results of numerical simulations verify the superiority of the proposed approach. PMID:28509886

An Improved DOA Estimation Approach Using Coarray Interpolation and Matrix Denoising.

PubMed

Guo, Muran; Chen, Tao; Wang, Ben

2017-05-16

Co-prime arrays can estimate the directions of arrival (DOAs) of O ( M N ) sources with O ( M + N ) sensors, and are convenient to analyze due to their closed-form expression for the locations of virtual lags. However, the number of degrees of freedom is limited due to the existence of holes in difference coarrays if subspace-based algorithms such as the spatial smoothing multiple signal classification (MUSIC) algorithm are utilized. To address this issue, techniques such as positive definite Toeplitz completion and array interpolation have been proposed in the literature. Another factor that compromises the accuracy of DOA estimation is the limitation of the number of snapshots. Coarray-based processing is particularly sensitive to the discrepancy between the sample covariance matrix and the ideal covariance matrix due to the finite number of snapshots. In this paper, coarray interpolation based on matrix completion (MC) followed by a denoising operation is proposed to detect more sources with a higher accuracy. The effectiveness of the proposed method is based on the capability of MC to fill in holes in the virtual sensors and that of MC denoising operation to reduce the perturbation in the sample covariance matrix. The results of numerical simulations verify the superiority of the proposed approach.

Mitochondrial function in engineered cardiac tissues is regulated by extracellular matrix elasticity and tissue alignment.

PubMed

Lyra-Leite, Davi M; Andres, Allen M; Petersen, Andrew P; Ariyasinghe, Nethika R; Cho, Nathan; Lee, Jezell A; Gottlieb, Roberta A; McCain, Megan L

2017-10-01

Mitochondria in cardiac myocytes are critical for generating ATP to meet the high metabolic demands associated with sarcomere shortening. Distinct remodeling of mitochondrial structure and function occur in cardiac myocytes in both developmental and pathological settings. However, the factors that underlie these changes are poorly understood. Because remodeling of tissue architecture and extracellular matrix (ECM) elasticity are also hallmarks of ventricular development and disease, we hypothesize that these environmental factors regulate mitochondrial function in cardiac myocytes. To test this, we developed a new procedure to transfer tunable polydimethylsiloxane disks microcontact-printed with fibronectin into cell culture microplates. We cultured Sprague-Dawley neonatal rat ventricular myocytes within the wells, which consistently formed tissues following the printed fibronectin, and measured oxygen consumption rate using a Seahorse extracellular flux analyzer. Our data indicate that parameters associated with baseline metabolism are predominantly regulated by ECM elasticity, whereas the ability of tissues to adapt to metabolic stress is regulated by both ECM elasticity and tissue alignment. Furthermore, bioenergetic health index, which reflects both the positive and negative aspects of oxygen consumption, was highest in aligned tissues on the most rigid substrate, suggesting that overall mitochondrial function is regulated by both ECM elasticity and tissue alignment. Our results demonstrate that mitochondrial function is regulated by both ECM elasticity and myofibril architecture in cardiac myocytes. This provides novel insight into how extracellular cues impact mitochondrial function in the context of cardiac development and disease. NEW & NOTEWORTHY A new methodology has been developed to measure O 2 consumption rates in engineered cardiac tissues with independent control over tissue alignment and matrix elasticity. This led to the findings that matrix elasticity regulates basal mitochondrial function, whereas both matrix elasticity and tissue alignment regulate mitochondrial stress responses. Copyright © 2017 the American Physiological Society.

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).

The association between MMP2 -1306 C > T (rs243865) polymorphism and risk of prostate cancer.

PubMed

Shajarehpoor Salavati, L; Tafvizi, F; Manjili, H K

2017-02-01

Prostate cancer is the second most common cancer in men. Matrix metalloproteinase-2 (MMP2) is the most important member of the matrix metalloproteinase family. MMP2 digests the basement membrane and causes changes in the extracellular matrix which in turn facilitate cancer invasion. It, therefore, has a major role in tumor angiogenesis. Previous studies have identified a single-nucleotide polymorphism C/T at position -1306 of MMP2 gene promoter which is a key regulatory factor in cancer progression. The present study aimed to determine the association between MMP2 polymorphism and the risk of prostate cancer in Iranian men. This case-control study was performed on 50 paraffin-embedded prostate cancer tissue samples and 54 blood samples from healthy men. Genotyping of the samples was performed using high-resolution melting analysis (HRM). Finally, 20 % of the genotypes were confirmed by sequencing. No significant associations were found between CT and TT genotypes and the risk of prostate cancer. However, there were no significant relationships between the genotypes and the studied factors, e.g., age, pathological stage, and Gleason Score. MMP2 -1306 C > T (rs243865) polymorphism was not significantly related with prostate cancer susceptibility in Iranian men.

Residue 41 of the Eurasian Avian-Like Swine Influenza A Virus Matrix Protein Modulates Virion Filament Length and Efficiency of Contact Transmission

PubMed Central

Campbell, Patricia J.; Kyriakis, Constantinos S.; Marshall, Nicolle; Suppiah, Suganthi; Seladi-Schulman, Jill; Danzy, Shamika; Lowen, Anice C.

2014-01-01

ABSTRACT Position 41 of the influenza A virus matrix protein encodes a highly conserved alanine in human and avian lineages. Nonetheless, strains of the Eurasian avian-like swine (Easw) lineage contain a change at this position: position 41 of A/swine/Spain/53207/04 (H1N1) (SPN04) encodes a proline. To assess the impact of this naturally occurring polymorphism on viral fitness, we utilized reverse genetics to produce recombinant viruses encoding wild-type M1 41P (rSPN04-P) and consensus 41A (rSPN04-A) residues. Relative to rSPN04-A, rSPN04-P virus displayed reduced growth in vitro. In the guinea pig model, rSPN04-P was transmitted to fewer contact animals than rSPN04-A and failed to infect guinea pigs that received a low-dose inoculum. Moreover, the P41A change altered virion morphology, reducing the number and length of filamentous virions, as well as reducing the neuraminidase activity of virions. The lab-adapted human isolate, A/PR/8/34 (H1N1) (PR8), is nontransmissible in the guinea pig model, making it a useful background in which to identify certain viral factors that enhance transmissibility. We assessed transmission in the context of single-, double-, and triple-reassortant viruses between PR8 and SPN04; PR8/SPN04 M, PR8/SPN04 M+NA, and PR8/SPN04 M+NA+HA, encoding either matrix 41 A or P, were generated. In each case, the virus possessing 41P transmitted less well than the corresponding 41A-encoding virus. In summary, we have identified a naturally occurring mutation in the influenza A virus matrix protein that impacts transmission efficiency and can alter virion morphology and neuraminidase activity. IMPORTANCE We have developed a practical model for examining the genetics underlying transmissibility of the Eurasian avian-like swine lineage viruses, which contributed M and NA segments to the 2009 pandemic strain. Here, we use our system to investigate the impact on viral fitness of a naturally occurring polymorphism at matrix (M1) position 41 in an Easw isolate. Position 41 has been implicated previously in adaptation to laboratory substrates and to mice. Here we show that the polymorphism at M1 41 has a limited effect on growth in vitro but changes the morphology of the virus and impacts growth and transmission in the guinea pig model. PMID:24760887

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

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

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.

[Sorption properties of various polysaccharide matrixes to Lactobacillus plantarum 8RA-3 bacteria].

PubMed

Bondarenko, V M; Larionov, I V; Rybal'chenko, O V; Potokin, I L; Ryzhankova, A V

2011-01-01

Study of sorption properties of various spherical polysaccharide matrixes designated as Spherocell to probiotic Lactobacillus plantarum 8RA-3 bacteria. Industrial strain of L. plantarum 8PA-3 was used. The process of immobilization of lactobacilli on 3 variants of spherical sorbents was studied. The first sorbent - neutral, composed of nonpolar cellulose matrix with ("0") charge, the second--DEAE obtained by modification of cellulose by diethylaminoethyl groups with positive ("+") charge and the third--CM (carboxymethyl) with negative ("-") charge. Cellulose matrixes were designated by us by the term Spherocell. Immobilization of bacterial cells on Spherocell was performed by addition of suspension containing 1.0 x 10(9) CFU/ml. The effect of bacterial immobilization was evaluated by CFU/ ml titration and by electron microscopy. The dependence on matrix charge of adsorption immobilization on sorbent granules of lactobacilli cells was shown. At certain equal parameters (granule size, surface characteristics, charge value) the positively charged matrix sorbed 3-10 times more cells than neutral and 20-25 times more than negatively charged matrix. Each 100-180 microm Spherocell DEAE particle could sorb more than 1000 viable bacterial cells. Positively charged polysaccharide matrix Spherocell DEAE obtained by modification of cellulose by diethylaminoethyl groups is promising for creation of immobilized probiotic preparations.

Landscape attributes as drivers of the geographical variation in density of Sapajus nigritus Kerr, 1792, a primate endemic to the Atlantic Forest

NASA Astrophysics Data System (ADS)

Hendges, Carla D.; Melo, Geruza L.; Gonçalves, Alberto S.; Cerezer, Felipe O.; Cáceres, Nilton C.

2017-10-01

Neotropical primates are among the most well studied forest mammals concerning their population densities. However, few studies have evaluated the factors that influence the spatial variation in the population density of primates, which limits the possibility of inferences towards this animal group, especially at the landscape-level. Here, we compiled density data of Sapajus nigritus from 21 forest patches of the Brazilian Atlantic Forest. We tested the effects of climatic variables (temperature, precipitation), landscape attributes (number of patches, mean inter-patch isolation distance, matrix modification index) and patch size on the population density using linear models and the Akaike information criterion. Our findings showed that the density of S. nigritus is influenced by landscape attributes, particularly by fragmentation and matrix modification. Overall, moderately fragmented landscapes and those surrounded by matrices with intermediate indexes of temporal modification (i.e., crop plantations, forestry) are related to high densities of this species. These results support the assumptions that ecologically flexible species respond positively to forest fragmentation. However, the non-linear relationship between S. nigritus density and number of patches suggests that even the species that are most tolerant to forest cover changes seem to respond positively only at an intermediate level of habitat fragmentation, being dependent of both a moderate degree of forest cover and a high quality matrix. The results we found here can be a common response to fragmentation for those forest dweller species that are able to use the matrix as complementary foraging sites.

Monitoring of the alignment in developing tissue-engineered constructs by elastic scattering spectroscopy

NASA Astrophysics Data System (ADS)

Kostyuk, Oksana P.; Brown, Robert A.

2004-07-01

Elastic light scattering spectroscopy was applied to monitor the development of alignment in fibroblast-populated collagen gels. Gels were seeded with human dermal fibroblasts in rectangular moulds so uniaxial tension was generated in the central zone of the gels due to cell contraction. There was a gradual transition from a disorganized matrix with round cells to highly organized cell/collagen matrix, aligned in the direction of the principal strain developed during gel contraction (observed with light microscopy under phase contrast). Spectra of the backscattered light (320 - 850 nm) were acquired via an optical probe with 2.75-mm source-detector separation, positioned perpendicularly to the gel surface, at 0, 17, 24, 41, 47, 65 and 72h. Spectra were registered for light propagating along, perpendicular and at intermediate angles relative to the cell/collagen matrix alignment, at 45° intervals. Backscatter was isotropic for non-contracted gels. However, as gels contracted, anisotropy of backscatter gradually increased. This was characterized by an 'anisotropy factor,' AF (500 nm), calculated as the ratio of backscatter intensities at 90° and 0° positions of the probe, at 500 nm. AF (500nm) increased from 1.2 +/- 0.1 at 0h up to 2.6 +/- 0.4 at 72h of contraction, with more backscatter detected perpendicular to the cell/collagen matrix alignment than in parallel direction. Thus, backscatter anisotropy allows determination of the direction of the preferential alignment and quantitative monitoring of its development during gel contraction. It is possible to use measurements of this type to quantify a proportion of oriented fibrils in the gel using modeling.

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.

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.

Lipopolysaccharide and hypoxia significantly alters interleukin-8 and macrophage chemoattractant protein-1 production by human fibroblasts but not fibrosis related factors.

PubMed

Eleftheriadis, T; Liakopoulos, V; Lawson, B; Antoniadi, G; Stefanidis, I; Galaktidou, G

2011-07-01

Besides extracellular matrix production, fibroblasts are able to produce various cytokines. Their ubiquitous position makes fibroblasts appropriate cells for sensing various noxious stimuli and for attracting immune cells in the affected area. In the present study the effect of lipopolysaccharide (LPS) and cobalt chloride (CoCl(2)) on the above fibroblasts functions were evaluated in primary human skin fibroblasts cultures. Collagen, matrix metalloproteinase-1, tissue inhibitor of metalloproteinases-1, transforming growth factor-β1, interleukin-8 (IL-8) and macrophage chemoattractant protein-1 (MCP-1) were measured in fibroblasts culture supernatants. Fibroblasts proliferation and viability were assessed as well. Hypoxia inducible factor-1α and the phosphorylated p65 portion of NF-κB were assessed in fibroblasts protein extracts. LPS and CoCl(2) had a minor effect on fibrosis related factors in human primary fibroblasts, possibly due to the absence of interplay with other cell types in the used experimental system. On the contrary both LPS and CoCl(2) increased significantly IL-8. LPS also increased considerably MCP-1, but CoCl(2) decreased it. Thus LPS and CoCl(2) induce a sentinel, nevertheless not identical, phenotype in primary human fibroblasts. The last disparity could result in different body response to infectious or hypoxic noxious stimuli.

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.

Distributed Matrix Completion: Applications to Cooperative Positioning in Noisy Environments

DTIC Science & Technology

2013-12-11

positioning, and a gossip version of low-rank approximation were developed. A convex relaxation for positioning in the presence of noise was shown...computing the leading eigenvectors of a large data matrix through gossip algorithms. A new algorithm is proposed that amounts to iteratively multiplying...generalization of gossip algorithms for consensus. The algorithms outperform state-of-the-art methods in a communication-limited scenario. Positioning via

Fuzzy Mathematical Models To Remove Poverty Of Gypsies In Tamilnadu

NASA Astrophysics Data System (ADS)

Chandrasekaran, A. D.; Ramkumar, C.; Siva, E. P.; Balaji, N.

2018-04-01

In the society there are several poor people are living. One of the sympathetic poor people is gypsies. They are moving from one place to another place towards survive of life because of not having any permanent place to live. In this paper we have interviewed 895 gypsies in Tamilnadu using a linguistic questionnaire. As the problems faced by them to improve their life at large involve so much of feeling, uncertainties and unpredictabilitys. I felt that it deem fit to use fuzzy theory in general and fuzzy matrix in particular. Fuzzy matrix is the best suitable tool where the data is an unsupervised one. Further the fuzzy matrix is so powerful to identify the main development factor of gypsies.This paper has three sections. In section one the method of application of CEFD matrix. In section two, we describe the development factors of gypsies. In section three, we apply these factors to the CEFD matrix and derive our conclusions. Key words: RD matrix, AFD matrix, CEFD matrix.

Data traffic reduction schemes for sparse Cholesky factorizations

NASA Technical Reports Server (NTRS)

Naik, Vijay K.; Patrick, Merrell L.

1988-01-01

Load distribution schemes are presented which minimize the total data traffic in the Cholesky factorization of dense and sparse, symmetric, positive definite matrices on multiprocessor systems with local and shared memory. The total data traffic in factoring an n x n sparse, symmetric, positive definite matrix representing an n-vertex regular 2-D grid graph using n (sup alpha), alpha is equal to or less than 1, processors are shown to be O(n(sup 1 + alpha/2)). It is O(n(sup 3/2)), when n (sup alpha), alpha is equal to or greater than 1, processors are used. Under the conditions of uniform load distribution, these results are shown to be asymptotically optimal. The schemes allow efficient use of up to O(n) processors before the total data traffic reaches the maximum value of O(n(sup 3/2)). The partitioning employed within the scheme, allows a better utilization of the data accessed from shared memory than those of previously published methods.

Direct Assistance: USAID Has Taken Positive Action to Assess Afghan Ministries’ Ability to Manage Donor Funds, but Concerns Remain

DTIC Science & Technology

2014-01-01

with the adverse event’s potential impact , ranging from negligible to catastrophic. Appendix V includes a matrix of how USAID/Afghanistan assigns risk...International Development (USAID) assigns risk ratings based on potential impact and probability of occurrence of an identified risk. The impact measures...frequent. Combining impact and probability factors categorize risk clusters of critical, high, medium and low categories. Although subjective, it is

A Review of Positive Ion Sensitivities for the SIMS Analysis of CMT

DTIC Science & Technology

1991-05-01

microprobe. Inter-laboratory exercises organised by NRL using standardised glasses and steels’ s showed considerable agreement usually within a factor...would be sufficient oxygen to convert all the remaining matrix atoms to oxides, TeO2 and CdO. Any general theory of the lonisation of sputtered particles...Eggert equation which works well for many other matrices, such as metals, glasses and ceramics. Despite decades of basic studies there is still no

Analysis of ligand-receptor cross-linked fragments by mass spectrometry

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

Son, C.D.; Sargsyan, H.; Hurst, Gregory

G-protein coupled receptors (GPCRs) are a class of integral membrane receptor proteins that are characterized by a signature seven-transmembrane (7-TM) configuration. The a-factor receptor (Ste2p) from Saccharomyces cerevisiae is a GPCR that, upon binding of a peptide ligand, transduces a signal to initiate a cascade of events leading to the mating of haploid yeast cells. This study summarizes the application of affinity purification and of matrix-assisted laser-desorption ionization time-of-flight (MALDI-TOF) experiments using biotinylated photoactivatable a-factor analogs. Affinity purification and enrichment of biotinylated peptides by monomeric avidin beads resulted in mass spectrometric detection of specific signals corresponding to crosslinked fragments ofmore » Ste2p. Data obtained from cyanogen bromide (CNBr) fragments of receptor cross-linked to an a-factor analog with the photoaffinity group p-benzoyl-L-phenylalanine on position 1 were in agreement with the previous results reported by our laboratory suggesting the cross-linking between position 1 of a-factor and a region of Ste2p covering residues 251 294.« less

Uncertainty of relative sensitivity factors in glow discharge mass spectrometry

NASA Astrophysics Data System (ADS)

Meija, Juris; Methven, Brad; Sturgeon, Ralph E.

2017-10-01

The concept of the relative sensitivity factors required for the correction of the measured ion beam ratios in pin-cell glow discharge mass spectrometry is examined in detail. We propose a data-driven model for predicting the relative response factors, which relies on a non-linear least squares adjustment and analyte/matrix interchangeability phenomena. The model provides a self-consistent set of response factors for any analyte/matrix combination of any element that appears as either an analyte or matrix in at least one known response factor.

Large Covariance Estimation by Thresholding Principal Orthogonal Complements

PubMed Central

Fan, Jianqing; Liao, Yuan; Mincheva, Martina

2012-01-01

This paper deals with the estimation of a high-dimensional covariance with a conditional sparsity structure and fast-diverging eigenvalues. By assuming sparse error covariance matrix in an approximate factor model, we allow for the presence of some cross-sectional correlation even after taking out common but unobservable factors. We introduce the Principal Orthogonal complEment Thresholding (POET) method to explore such an approximate factor structure with sparsity. The POET estimator includes the sample covariance matrix, the factor-based covariance matrix (Fan, Fan, and Lv, 2008), the thresholding estimator (Bickel and Levina, 2008) and the adaptive thresholding estimator (Cai and Liu, 2011) as specific examples. We provide mathematical insights when the factor analysis is approximately the same as the principal component analysis for high-dimensional data. The rates of convergence of the sparse residual covariance matrix and the conditional sparse covariance matrix are studied under various norms. It is shown that the impact of estimating the unknown factors vanishes as the dimensionality increases. The uniform rates of convergence for the unobserved factors and their factor loadings are derived. The asymptotic results are also verified by extensive simulation studies. Finally, a real data application on portfolio allocation is presented. PMID:24348088

Large Covariance Estimation by Thresholding Principal Orthogonal Complements.

PubMed

Fan, Jianqing; Liao, Yuan; Mincheva, Martina

2013-09-01

This paper deals with the estimation of a high-dimensional covariance with a conditional sparsity structure and fast-diverging eigenvalues. By assuming sparse error covariance matrix in an approximate factor model, we allow for the presence of some cross-sectional correlation even after taking out common but unobservable factors. We introduce the Principal Orthogonal complEment Thresholding (POET) method to explore such an approximate factor structure with sparsity. The POET estimator includes the sample covariance matrix, the factor-based covariance matrix (Fan, Fan, and Lv, 2008), the thresholding estimator (Bickel and Levina, 2008) and the adaptive thresholding estimator (Cai and Liu, 2011) as specific examples. We provide mathematical insights when the factor analysis is approximately the same as the principal component analysis for high-dimensional data. The rates of convergence of the sparse residual covariance matrix and the conditional sparse covariance matrix are studied under various norms. It is shown that the impact of estimating the unknown factors vanishes as the dimensionality increases. The uniform rates of convergence for the unobserved factors and their factor loadings are derived. The asymptotic results are also verified by extensive simulation studies. Finally, a real data application on portfolio allocation is presented.

Application of the positive matrix factorization approach to identify heavy metal sources in sediments. A case study on the Mexican Pacific Coast.

PubMed

González-Macías, C; Sánchez-Reyna, G; Salazar-Coria, L; Schifter, I

2014-01-01

During the last two decades, sediments collected in different sources of water bodies of the Tehuantepec Basin, located in the southeast of the Mexican Pacific Coast, showed that concentrations of heavy metals may pose a risk to the environment and human health. The extractable organic matter, geoaccumulation index, and enrichment factors were quantified for arsenic, cadmium, copper, chromium, nickel, lead, vanadium, zinc, and the fine-grained sediment fraction. The non-parametric SiZer method was applied to assess the statistical significance of the reconstructed metal variation along time. This inference method appears to be particularly natural and well suited to temperature and other environmental reconstructions. In this approach, a collection of smooth of the reconstructed metal concentrations is considered simultaneously, and inferences about the significance of the metal trends can be made with respect to time. Hence, the database represents a consolidated set of available and validated water and sediment data of an urban industrialized area, which is very useful as case study site. The positive matrix factorization approach was used in identification and source apportionment of the anthropogenic heavy metals in the sediments. Regionally, metals and organic matter are depleted relative to crustal abundance in a range of 45-55 %, while there is an inorganic enrichment from lithogenous/anthropogenic sources of around 40 %. Only extractable organic matter, Pb, As, and Cd can be related with non-crustal sources, suggesting that additional input cannot be explained by local runoff or erosion processes.

Tissue Inhibitor of Metalloproteinase-2 (TIMP-2) expression is regulated by multiple neural differentiation signals

PubMed Central

Jaworski, Diane M.; Pérez-Martínez, Leonor

2010-01-01

Neuronal differentiation requires exquisitely timed cell cycle arrest for progenitors to acquire an appropriate neuronal cell fate and is achieved by communication between soluble signals, such as growth factors and extracellular matrix molecules. Here we report that the expression of TIMP-2, a matrix metalloproteinase inhibitor, is up-regulated by signals that control proliferation (bFGF and EGF) and differentiation (retinoic acid and NGF) in neural progenitor and neuroblastoma cell lines. TIMP-2 expression coincides with the appearance of neurofilament-positive neurons, indicating that TIMP-2 may play a role in neurogenesis. The up-regulation of TIMP-2 expression by proliferative signals suggests a role in the transition from proliferation to neuronal differentiation. Live labeling experiments demonstrate TIMP-2 expression only on α3 integrin-positive cells. Thus, TIMP-2 function may be mediated via interaction with integrin receptor(s). We propose that TIMP-2 represents a component of the neurogenic signaling cascade induced by mitogenic stimuli that may withdraw progenitor cells from the cell cycle permitting their terminal neuronal differentiation. PMID:16805810

On the Relations among Regular, Equal Unique Variances, and Image Factor Analysis Models.

ERIC Educational Resources Information Center

Hayashi, Kentaro; Bentler, Peter M.

2000-01-01

Investigated the conditions under which the matrix of factor loadings from the factor analysis model with equal unique variances will give a good approximation to the matrix of factor loadings from the regular factor analysis model. Extends the results to the image factor analysis model. Discusses implications for practice. (SLD)

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.

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

Matrix method for acoustic levitation simulation.

PubMed

Andrade, Marco A B; Perez, Nicolas; Buiochi, Flavio; Adamowski, Julio C

2011-08-01

A matrix method is presented for simulating acoustic levitators. A typical acoustic levitator consists of an ultrasonic transducer and a reflector. The matrix method is used to determine the potential for acoustic radiation force that acts on a small sphere in the standing wave field produced by the levitator. The method is based on the Rayleigh integral and it takes into account the multiple reflections that occur between the transducer and the reflector. The potential for acoustic radiation force obtained by the matrix method is validated by comparing the matrix method results with those obtained by the finite element method when using an axisymmetric model of a single-axis acoustic levitator. After validation, the method is applied in the simulation of a noncontact manipulation system consisting of two 37.9-kHz Langevin-type transducers and a plane reflector. The manipulation system allows control of the horizontal position of a small levitated sphere from -6 mm to 6 mm, which is done by changing the phase difference between the two transducers. The horizontal position of the sphere predicted by the matrix method agrees with the horizontal positions measured experimentally with a charge-coupled device camera. The main advantage of the matrix method is that it allows simulation of non-symmetric acoustic levitators without requiring much computational effort.

A reassessment of the taxonomic position of mesosaurs, and a surprising phylogeny of early amniotes

NASA Astrophysics Data System (ADS)

Laurin, Michel; Piñeiro, Graciela H.

2017-11-01

We reassess the phylogenetic position of mesosaurs by using a data matrix that is updated and slightly expanded from a matrix that the first author published in 1995 with his former thesis advisor. The revised matrix, which incorporates anatomical information published in the last twenty years and observations on several mesosaur specimens (mostly from Uruguay) includes seventeen terminal taxa and 129 characters (four more taxa and five more characters than the original matrix from 1995). The new matrix also differs by incorporating more ordered characters (all morphoclines were ordered). Parsimony analyses in PAUP 4 using the branch and bound algorithm show that the new matrix supports a position of mesosaurs at the very base of Sauropsida, as suggested by the first author in 1995. The exclusion of mesosaurs from a less inclusive clade of sauropsids is supported by a Bremer (Decay) index of 4 and a bootstrap frequency of 66%, both of which suggest that this result is moderately robust. The most parsimonious trees include some unexpected results, such as placing the anapsid reptile Paleothyris near the base of diapsids, and all of parareptiles as the sister-group of younginiforms (the most crownward diapsids included in the analyses). Turtles are placed among parareptiles, as the sister-group of pareiasaurs (and in diapsids, given that parareptiles are nested within diapsids). This unexpected result offers a potential solution to the long-lasting controversy about the position of turtles because previous studies viewed a position among diapsids and among parareptiles as mutually exclusive alternatives.

An Upper Bound on Orbital Debris Collision Probability When Only One Object has Position Uncertainty Information

NASA Technical Reports Server (NTRS)

Frisbee, Joseph H., Jr.

2015-01-01

Upper bounds on high speed satellite collision probability, P (sub c), have been investigated. Previous methods assume an individual position error covariance matrix is available for each object. The two matrices being combined into a single, relative position error covariance matrix. Components of the combined error covariance are then varied to obtain a maximum P (sub c). If error covariance information for only one of the two objects was available, either some default shape has been used or nothing could be done. An alternative is presented that uses the known covariance information along with a critical value of the missing covariance to obtain an approximate but useful P (sub c) upper bound. There are various avenues along which an upper bound on the high speed satellite collision probability has been pursued. Typically, for the collision plane representation of the high speed collision probability problem, the predicted miss position in the collision plane is assumed fixed. Then the shape (aspect ratio of ellipse), the size (scaling of standard deviations) or the orientation (rotation of ellipse principal axes) of the combined position error ellipse is varied to obtain a maximum P (sub c). Regardless as to the exact details of the approach, previously presented methods all assume that an individual position error covariance matrix is available for each object and the two are combined into a single, relative position error covariance matrix. This combined position error covariance matrix is then modified according to the chosen scheme to arrive at a maximum P (sub c). But what if error covariance information for one of the two objects is not available? When error covariance information for one of the objects is not available the analyst has commonly defaulted to the situation in which only the relative miss position and velocity are known without any corresponding state error covariance information. The various usual methods of finding a maximum P (sub c) do no good because the analyst defaults to no knowledge of the combined, relative position error covariance matrix. It is reasonable to think, given an assumption of no covariance information, an analyst might still attempt to determine the error covariance matrix that results in an upper bound on the P (sub c). Without some guidance on limits to the shape, size and orientation of the unknown covariance matrix, the limiting case is a degenerate ellipse lying along the relative miss vector in the collision plane. Unless the miss position is exceptionally large or the at-risk object is exceptionally small, this method results in a maximum P (sub c) too large to be of practical use. For example, assuming that the miss distance is equal to the current ISS alert volume along-track (+ or -) distance of 25 kilometers and that the at-risk area has a 70 meter radius. The maximum (degenerate ellipse) P (sub c) is about 0.00136. At 40 kilometers, the maximum P (sub c) would be 0.00085 which is still almost an order of magnitude larger than the ISS maneuver threshold of 0.0001. In fact, a miss distance of almost 340 kilometers is necessary to reduce the maximum P (sub c) associated with this degenerate ellipse to the ISS maneuver threshold value. Such a result is frequently of no practical value to the analyst. Some improvement may be made with respect to this problem by realizing that while the position error covariance matrix of one of the objects (usually the debris object) may not be known the position error covariance matrix of the other object (usually the asset) is almost always available. Making use of the position error covariance information for the one object provides an improvement in finding a maximum P (sub c) which, in some cases, may offer real utility. The equations to be used are presented and their use discussed.

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.

Nanomechanical Contribution of Collagen and von Willebrand Factor A in Marine Underwater Adhesion and Its Implication for Collagen Manipulation.

PubMed

Yoo, Hee Young; Huang, Jun; Li, Lin; Foo, Mathias; Zeng, Hongbo; Hwang, Dong Soo

2016-03-14

Recent works on mussel adhesion have identified a load bearing matrix protein (PTMP1) containing von Willebrand factor (vWF) with collagen binding capability that contributes to the mussel holdfast by manipulating mussel collagens. Using a surface forces apparatus, we investigate for the first time, the nanomechanical properties of vWF-collagen interaction using homologous proteins of mussel byssus, PTMP1 and preCollagens (preCols), as collagen. Mimicking conditions similar to mussel byssus secretion (pH < 5.0) and seawater condition (pH 8.0), PTMP1 and preCol interact weakly in the "positioning" phase based on vWF-collagen binding and strengthen in "locked" phase due to the combined effects of electrostatic attraction, metal binding, and mechanical shearing. The progressive enhancement of binding between PTMP1 with porcine collagen under the aforementioned conditions is also observed. The binding mechanisms of PTMP1-preCols provide insights into the molecular interaction of the mammalian collagen system and the development of an artificial extracellular matrix based on collagens.

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.

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.

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

Attractive electron-electron interactions within robust local fitting approximations.

PubMed

Merlot, Patrick; Kjærgaard, Thomas; Helgaker, Trygve; Lindh, Roland; Aquilante, Francesco; Reine, Simen; Pedersen, Thomas Bondo

2013-06-30

An analysis of Dunlap's robust fitting approach reveals that the resulting two-electron integral matrix is not manifestly positive semidefinite when local fitting domains or non-Coulomb fitting metrics are used. We present a highly local approximate method for evaluating four-center two-electron integrals based on the resolution-of-the-identity (RI) approximation and apply it to the construction of the Coulomb and exchange contributions to the Fock matrix. In this pair-atomic resolution-of-the-identity (PARI) approach, atomic-orbital (AO) products are expanded in auxiliary functions centered on the two atoms associated with each product. Numerical tests indicate that in 1% or less of all Hartree-Fock and Kohn-Sham calculations, the indefinite integral matrix causes nonconvergence in the self-consistent-field iterations. In these cases, the two-electron contribution to the total energy becomes negative, meaning that the electronic interaction is effectively attractive, and the total energy is dramatically lower than that obtained with exact integrals. In the vast majority of our test cases, however, the indefiniteness does not interfere with convergence. The total energy accuracy is comparable to that of the standard Coulomb-metric RI method. The speed-up compared with conventional algorithms is similar to the RI method for Coulomb contributions; exchange contributions are accelerated by a factor of up to eight with a triple-zeta quality basis set. A positive semidefinite integral matrix is recovered within PARI by introducing local auxiliary basis functions spanning the full AO product space, as may be achieved by using Cholesky-decomposition techniques. Local completion, however, slows down the algorithm to a level comparable with or below conventional calculations. Copyright © 2013 Wiley Periodicals, Inc.

Investigation into Text Classification With Kernel Based Schemes

DTIC Science & Technology

2010-03-01

Document Matrix TDMs Term-Document Matrices TMG Text to Matrix Generator TN True Negative TP True Positive VSM Vector Space Model xxii THIS PAGE...are represented as a term-document matrix, common evaluation metrics, and the software package Text to Matrix Generator ( TMG ). The classifier...AND METRICS This chapter introduces the indexing capabilities of the Text to Matrix Generator ( TMG ) Toolbox. Specific attention is placed on the

Convergence analysis of modulus-based matrix splitting iterative methods for implicit complementarity problems.

PubMed

Wang, An; Cao, Yang; Shi, Quan

2018-01-01

In this paper, we demonstrate a complete version of the convergence theory of the modulus-based matrix splitting iteration methods for solving a class of implicit complementarity problems proposed by Hong and Li (Numer. Linear Algebra Appl. 23:629-641, 2016). New convergence conditions are presented when the system matrix is a positive-definite matrix and an [Formula: see text]-matrix, respectively.

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.

Joint estimation of 2D-DOA and frequency based on space-time matrix and conformal array.

PubMed

Wan, Liang-Tian; Liu, Lu-Tao; Si, Wei-Jian; Tian, Zuo-Xi

2013-01-01

Each element in the conformal array has a different pattern, which leads to the performance deterioration of the conventional high resolution direction-of-arrival (DOA) algorithms. In this paper, a joint frequency and two-dimension DOA (2D-DOA) estimation algorithm for conformal array are proposed. The delay correlation function is used to suppress noise. Both spatial and time sampling are utilized to construct the spatial-time matrix. The frequency and 2D-DOA estimation are accomplished based on parallel factor (PARAFAC) analysis without spectral peak searching and parameter pairing. The proposed algorithm needs only four guiding elements with precise positions to estimate frequency and 2D-DOA. Other instrumental elements can be arranged flexibly on the surface of the carrier. Simulation results demonstrate the effectiveness of the proposed algorithm.

Simple Derivation of the Lindblad Equation

ERIC Educational Resources Information Center

Pearle, Philip

2012-01-01

The Lindblad equation is an evolution equation for the density matrix in quantum theory. It is the general linear, Markovian, form which ensures that the density matrix is Hermitian, trace 1, positive and completely positive. Some elementary examples of the Lindblad equation are given. The derivation of the Lindblad equation presented here is…

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 elemental species was modeled by PMF. A five factor solution identified three soil factors, a silicate soil, limestone soil, and a gypsum soil, as well as a salt factor and an anthropogenic metal factor. Similarly, a set of 362 quartz filter samples analyzed for 10 selected chemical species was modeled by PMF. A five factor solution provided a limestone-gypsum soil, diesel combustion, secondary ammonium sulfate, salt and agricultural-burnpit combustion source type. Examples of time series plots of PMF factor contributions for each of six sampling sites (Balad, Baghdad, Tallil, Tikrit, Taji, and Al Asad) will be discussed. Engelbrecht , J. P., McDonald, E. V., Gillies, J. A., Jayanty, R. K. M., Casuccio, G., and Gertler, A. W., 2009, Characterizing mineral dusts and other aerosols from the Middle East - Part 1: Ambient sampling: Inhalation Toxicology, v. 21, p. 297-326.

Battery element and method for making same

NASA Technical Reports Server (NTRS)

Clough, Thomas J. (Inventor); Pinsky, Naum (Inventor)

1989-01-01

In a method for producing a battery element useful as at least a positive plate in a lead-acid battery, the element comprising a fluid impervious, electrically conductive matrix having mutually opposing first and second surfaces and positive active electrode material associated with the first surface of the matrix, the improvement which comprises: conditioning the first surface to enhance the association of the positive active electrode material and the first surface; and applying and associating the positive active electrode material to the first surface.

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.

Information of group-correlations in Korean financial market

NASA Astrophysics Data System (ADS)

Choi, Jaewon; Lim, Gyuchang; Kim, Soo Yong; Kim, Kyungsik

2011-01-01

We study two sides of the KOSPI, classified as an emerging market. First, the evolutionary property is examined in terms of overlapping matrix and survival ratios. To this end, we apply the random matrix theory (RMT) and the one-factor model to analyzing correlation matrix and finding business clusters. Second, we examine the relations between the market capitalization and the business. For the well-developed markets such as NYSE, the contribution of the firms to the second-largest eigenvector shows an exponential function of the market capitalizations while no clue is observed for the KOSPI. We confirm that the market capitalization is distributed in a power-law with the exponent 1.2 like a Pareto's distribution. Particulary, the KOSPI shows a different behavior compared to the mature market, that is, one or two companies lead a number of companies with the little money and big companies competed to win each other. The clusters also represent by largest eigenstates show a weak affiliation compared to smaller ones. These results imply that the KOSPI is the target for the short-positioned investors.

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 was associated with the summertime/selective aliphatic factor and the EC/sterane factor, respectively, while nitrate and sulfate mass were both dominated by the inorganic ion factor. This apportionment was found to vary substantially by season. Several of the factors identified in this study agree well with similar assessments conducted in St. Louis, MO and Pittsburgh, PA using PMF and organic molecular markers. PMID:22768005

Cytokine Response to Diet and Exercise Affects Atheromatous Matrix Metalloproteinase-2/9 Activity in Mice.

PubMed

Shon, Soo-Min; Jang, Hee Jeong; Schellingerhout, Dawid; Kim, Jeong-Yeon; Ryu, Wi-Sun; Lee, Su-Kyoung; Kim, Jiwon; Park, Jin-Yong; Oh, Ji Hye; Kang, Jeong Wook; Je, Kang-Hoon; Park, Jung E; Kim, Kwangmeyung; Kwon, Ick Chan; Lee, Juneyoung; Nahrendorf, Matthias; Park, Jong-Ho; Kim, Dong-Eog

2017-09-25

The aim of this study is to identify the principal circulating factors that modulate atheromatous matrix metalloproteinase (MMP) activity in response to diet and exercise.Methods and Results:Apolipoprotein-E knock-out (ApoE -/- ) mice (n=56) with pre-existing plaque, fed either a Western diet (WD) or normal diet (ND), underwent either 10 weeks of treadmill exercise or had no treatment. Atheromatous MMP activity was visualized using molecular imaging with a MMP-2/9 activatable near-infrared fluorescent (NIRF) probe. Exercise did not significantly reduce body weight, visceral fat, and plaque size in either WD-fed animals or ND-fed animals. However, atheromatous MMP-activity was different; ND animals that did or did not exercise had similarly low MMP activities, WD animals that did not exercise had high MMP activity, and WD animals that did exercise had reduced levels of MMP activity, close to the levels of ND animals. Factor analysis and path analysis showed that soluble vascular cell adhesion molecule (sVCAM)-1 was directly positively correlated to atheromatous MMP activity. Adiponectin was indirectly negatively related to atheromatous MMP activity by way of sVCAM-1. Resistin was indirectly positively related to atheromatous MMP activity by way of sVCAM-1. Visceral fat amount was indirectly positively associated with atheromatous MMP activity, by way of adiponectin reduction and resistin elevation. MMP-2/9 imaging of additional mice (n=18) supported the diet/exercise-related anti-atherosclerotic roles for sVCAM-1. Diet and exercise affect atheromatous MMP activity by modulating the systemic inflammatory milieu, with sVCAM-1, resistin, and adiponectin closely interacting with each other and with visceral fat.

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

Source apportionment of organic compounds in Berlin using positive matrix factorization - assessing the impact of biogenic aerosol and biomass burning on urban particulate matter.

PubMed

Wagener, Sandra; Langner, Marcel; Hansen, Ute; Moriske, Heinz-Jörn; Endlicher, Wilfried R

2012-10-01

Source apportionment of 13 organic compounds, elemental carbon and organic carbon of ambient PM(10) and PM(1) was performed with positive matrix factorization (PMF). Samples were collected at three sites characterized by different vegetation influences in Berlin, Germany in 2010. The aim was to determine organic, mainly biogenic sources and their impact on urban aerosol collected in a densely populated region. A 6-factor solution provided the best data fit for both PM-fractions, allowing the sources isoprene- and α-pinene-derived secondary organic aerosol (SOA), bio primary, primarily attributable to fungal spores, bio/urban primary including plant fragments in PM(10) and cooking and traffic emissions in PM(1), biomass burning and combustion fossil to be identified. With mean concentrations up to 2.6 μg Cm(-3), biomass burning dominated the organic fraction in cooler months. Concentrations for α-pinene-derived SOA exceeded isoprene-derived concentrations. Estimated secondary organic carbon contributions to total organic carbon (OC) were between 7% and 42% in PM(10) and between 11% and 60% in PM(1), which is slightly lower than observed for US- or Asian cities. Primary biogenic emissions reached up to 33% of OC in the PM(10)-fraction in the late summer and autumn months. Temperature-dependence was found for both SOA-factors, correlations with ozone and mix depth only for the α-pinene-derived SOA-factor. Latter indicated input of α-pinene from the borders, highlighting differences in the origin of the precursors of both factors. Most factors were regionally distributed. High regional distribution was found to be associated with stronger influence of ambient parameters and higher concentrations at the background station. A significant contribution of biogenic emissions and biomass burning to urban organic aerosol could be stated. This indicates a considerable impact on PM concentrations also in cities in a densely populated area, and should draw the attention concerning health aspects not only to cardio-vascular diseases but also to allergy issues. Copyright © 2012 Elsevier B.V. All rights reserved.

Uncertainty assessment of source attribution of PM(2.5) and its water-soluble organic carbon content using different biomass burning tracers in positive matrix factorization analysis--a case study in Beijing, China.

PubMed

Tao, Jun; Zhang, Leiming; Zhang, Renjian; Wu, Yunfei; Zhang, Zhisheng; Zhang, Xiaoling; Tang, Yixi; Cao, Junji; Zhang, Yuanhang

2016-02-01

Daily PM2.5 samples were collected at an urban site in Beijing during four one-month periods in 2009-2010, with each period in a different season. Samples were subject to chemical analysis for various chemical components including major water-soluble ions, organic carbon (OC) and water-soluble organic carbon (WSOC), element carbon (EC), trace elements, anhydrosugar levoglucosan (LG), and mannosan (MN). Three sets of source profiles of PM2.5 were first identified through positive matrix factorization (PMF) analysis using single or combined biomass tracers - non-sea salt potassium (nss-K(+)), LG, and a combination of nss-K(+) and LG. The six major source factors of PM2.5 included secondary inorganic aerosol, industrial pollution, soil dust, biomass burning, traffic emission, and coal burning, which were estimated to contribute 31±37%, 39±28%, 14±14%, 7±7%, 5±6%, and 4±8%, respectively, to PM2.5 mass if using the nss-K(+) source profiles, 22±19%, 29±17%, 20±20%, 13±13%, 12±10%, and 4±6%, respectively, if using the LG source profiles, and 21±17%, 31±18%, 19±19%, 11±12%, 14±11%, and 4±6%, respectively, if using the combined nss-K(+) and LG source profiles. The uncertainties in the estimation of biomass burning contributions to WSOC due to the different choices of biomass burning tracers were around 3% annually and up to 24% seasonally in terms of absolute percentage contributions, or on a factor of 1.7 annually and up to a factor of 3.3 seasonally in terms of the actual concentrations. The uncertainty from the major source (e.g. industrial pollution) was on a factor of 1.9 annually and up to a factor of 2.5 seasonally in the estimated WSOC concentrations. Copyright © 2015 Elsevier B.V. All rights reserved.

Continued-fraction representation of the Kraus map for non-Markovian reservoir damping

NASA Astrophysics Data System (ADS)

van Wonderen, A. J.; Suttorp, L. G.

2018-04-01

Quantum dissipation is studied for a discrete system that linearly interacts with a reservoir of harmonic oscillators at thermal equilibrium. Initial correlations between system and reservoir are assumed to be absent. The dissipative dynamics as determined by the unitary evolution of system and reservoir is described by a Kraus map consisting of an infinite number of matrices. For all Laplace-transformed Kraus matrices exact solutions are constructed in terms of continued fractions that depend on the pair correlation functions of the reservoir. By performing factorizations in the Kraus map a perturbation theory is set up that conserves in arbitrary perturbative order both positivity and probability of the density matrix. The latter is determined by an integral equation for a bitemporal matrix and a finite hierarchy for Kraus matrices. In the lowest perturbative order this hierarchy reduces to one equation for one Kraus matrix. Its solution is given by a continued fraction of a much simpler structure as compared to the non-perturbative case. In the lowest perturbative order our non-Markovian evolution equations are applied to the damped Jaynes–Cummings model. From the solution for the atomic density matrix it is found that the atom may remain in the state of maximum entropy for a significant time span that depends on the initial energy of the radiation field.

The occurrence and behavior of radium in saline formation water of the U.S. Gulf Coast region.

USGS Publications Warehouse

Kraemer, T.F.; Reid, D.F.

1984-01-01

Ra was measured in deep saline formation waters produced from a variety of US Gulf Coast subsurface environments, including oil and gas reservoirs, and water-producing geopressured aquifers. A strong positive correlation was found between formation-water salinity and Ra activity, resulting from the interaction of formation water with aquifer matrix. Ra isotopes enter the fluid phase after being produced by the decay of parent elements U and Th on and within the solid matrix. The processes believed to be primarily responsible for transfering Ra from matrix to formation water are chemical leaching and alpha -particle recoil. Factors controlling the observed salinity-Ra relationship may be one or a combination of the following: 1) ion exchange; 2) increased solubility of matrix silica surrounding Ra atoms, coupled with a salinity-controlled rate of re-equilibration of silica between solution and quartz grains; and 3) the equilibration of Ra in solution with detrital baryte within the aquifer. No difference was found in the brine-Ra relation in water produced from oil or gas wells and water produced from wells penetrating only water-bearing aquifers, although the relation was more highly correlated for water-bearing aquifers than hydrocarbon-containing reservoirs.-P.Br.

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.

Distributed Cooperative Control of Multiple Nonlinear Systems with Nonholonomic Constraints and Uncertainty

DTIC Science & Technology

2015-04-04

system j, Mj(q∗j) is a 3×3 positive- definite symmetric matrix, Cj(q∗j , q̇∗j)q̇∗j represents centripetal and Coriolis force, Gj(q∗j) is the...states of system j, Mj(q∗j) is a 3×3 positive- definite symmetric matrix, Cj(q∗j , q̇∗j)q̇∗j represents centripetal and Coriolis force, Gj(q∗j) is the...positive- definite symmetric matrix, Cj(q∗j , q̇∗j)q̇∗j is cen- tripetal and Coriolis force, Gj(q∗j) is gravitational force, Bj(q∗j) is an 4 × 2 input

Convergence Results on Iteration Algorithms to Linear Systems

PubMed Central

Wang, Zhuande; Yang, Chuansheng; Yuan, Yubo

2014-01-01

In order to solve the large scale linear systems, backward and Jacobi iteration algorithms are employed. The convergence is the most important issue. In this paper, a unified backward iterative matrix is proposed. It shows that some well-known iterative algorithms can be deduced with it. The most important result is that the convergence results have been proved. Firstly, the spectral radius of the Jacobi iterative matrix is positive and the one of backward iterative matrix is strongly positive (lager than a positive constant). Secondly, the mentioned two iterations have the same convergence results (convergence or divergence simultaneously). Finally, some numerical experiments show that the proposed algorithms are correct and have the merit of backward methods. PMID:24991640

Topical application of substance P promotes wound healing in streptozotocin-induced diabetic rats.

PubMed

Kant, Vinay; Kumar, Dinesh; Kumar, Dhirendra; Prasad, Raju; Gopal, Anu; Pathak, Nitya N; Kumar, Pawan; Tandan, Surender K

2015-05-01

Substance P (SP) is known to stimulate angiogenesis, fibroblasts proliferation and expressions of cytokines and growth factors involved in wound healing. However, SP level reduces in dermis in diabetics and, hence, it was hypothesized that exogenously applied SP could be helpful in improving wound healing in diabetic rats. Excision skin wound was created on the back of diabetic rats and rats were divided into three groups i.e. (i) saline-, (ii) gel- and (iii) SP-treated. Normal saline, pluronic gel and SP (10(-6)M) in gel were topically applied once daily for 19days. SP treatment significantly increased the wound closure, levels of interleukin-10, and expressions of vascular endothelial growth factor, transforming growth factor-beta1, heme oxygenase-1 and endothelial nitric oxide synthase, whereas it significantly decreased the expression of tumor necrosis factor-alpha, interleukin-1beta and matrix metalloproteinases-9 in the granulation/healing tissue. The inflammatory cells were present for long time in normal saline-treated group. Histological evaluation revealed better extracellular matrix formation with marked fibroblast proliferation and collagen deposition in SP-treated group. Early epithelial layer formation, increased microvessel density and greater growth associated protein-43 positive nerve fibers were also evidenced in SP-treated group. In conclusion, SP treatment markedly accelerated cutaneous wound healing in diabetic rats. Copyright © 2014 Elsevier Ltd. All rights reserved.

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.

A tight and explicit representation of Q in sparse QR factorization

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

Ng, E.G.; Peyton, B.W.

1992-05-01

In QR factorization of a sparse m{times}n matrix A (m {ge} n) the orthogonal factor Q is often stored implicitly as a lower trapezoidal matrix H known as the Householder matrix. This paper presents a simple characterization of the row structure of Q, which could be used as the basis for a sparse data structure that can store Q explicitly. The new characterization is a simple extension of a well known row-oriented characterization of the structure of H. Hare, Johnson, Olesky, and van den Driessche have recently provided a complete sparsity analysis of the QR factorization. Let U be themore » matrix consisting of the first n columns of Q. Using results from, we show that the data structures for H and U resulting from our characterizations are tight when A is a strong Hall matrix. We also show that H and the lower trapezoidal part of U have the same sparsity characterization when A is strong Hall. We then show that this characterization can be extended to any weak Hall matrix that has been permuted into block upper triangular form. Finally, we show that permuting to block triangular form never increases the fill incurred during the factorization.« less

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.

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.

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

Genome-wide inference of transcription factor-DNA binding specificity in cell regeneration using a combination strategy.

PubMed

Wang, Xiaofeng; Zhang, Aiqun; Ren, Weizheng; Chen, Caiyu; Dong, Jiahong

2012-11-01

The cell growth, development, and regeneration of tissue and organ are associated with a large number of gene regulation events, which are mediated in part by transcription factors (TFs) binding to cis-regulatory elements involved in the genome. Predicting the binding affinity and inferring the binding specificity of TF-DNA interactions at the genomic level would be fundamentally helpful for our understanding of the molecular mechanism and biological implication underlying sequence-specific TF-DNA recognition. In this study, we report the development of a combination method to characterize the interaction behavior of a 11-mer oligonucleotide segment and its mutations with the Gcn4p protein, a homodimeric, basic leucine zipper TF, and to predict the binding affinity and specificity of potential Gcn4p binders in the genome-wide scale. In this procedure, a position-mutated energy matrix is created based on molecular modeling analysis of native and mutated Gcn4p-DNA complex structures to describe the position-independent interaction energy profile of Gcn4p with different nucleotide types at each position of the oligonucleotide, and the energy terms extracted from the matrix and their interactives are then correlated with experimentally measured affinities of 19268 distinct oligonucleotides using statistical modeling methodology. Subsequently, the best one of built regression models is successfully applied to screen those of potential high-affinity Gcn4p binders from the complete genome. The findings arising from this study are briefly listed below: (i) The 11 positions of oligonucleotides are highly interactive and non-additive in contribution to Gcn4p-DNA binding affinity; (ii) Indirect conformational effects upon nucleotide mutations as well as associated subtle changes in interfacial atomic contacts, but not the direct nonbonded interactions, are primarily responsible for the sequence-specific recognition; (iii) The intrinsic synergistic effects among the sequence positions of oligonucleotides determine Gcn4p-DNA binding affinity and specificity; (iv) Linear regression models in conjunction with variable selection seem to perform fairly well in capturing the internal dependences hidden in the Gcn4p-DNA system, albeit ignoring nonlinear factors may lead the models to systematically underestimate and overestimate high- and low-affinity samples, respectively. © 2012 John Wiley & Sons A/S.

The "Box"ing Match: Narratives from Queer Adults Growing up through the Heterosexual Matrix

ERIC Educational Resources Information Center

Leonardi, Bethy

2017-01-01

Using queer theories of sexuality and gender, this study centers on "coming out" stories of ten queer adults. Engaging Butler's heterosexual matrix (1990) as an analytic tool, stories are analyzed with respect to agency and positioning. Findings suggest that participants' positioning and agency were largely affected by gender identity…

PM10 source apportionment in Milan (Italy) using time-resolved data.

PubMed

Bernardoni, Vera; Vecchi, Roberta; Valli, Gianluigi; Piazzalunga, Andrea; Fermo, Paola

2011-10-15

In this work Positive Matrix Factorization (PMF) was applied to 4-hour resolved PM10 data collected in Milan (Italy) during summer and winter 2006. PM10 characterisation included elements (Mg-Pb), main inorganic ions (NH(4)(+), NO(3)(-), SO(4)(2-)), levoglucosan and its isomers (mannosan and galactosan), and organic and elemental carbon (OC and EC). PMF resolved seven factors that were assigned to construction works, re-suspended dust, secondary sulphate, traffic, industry, secondary nitrate, and wood burning. Multi Linear Regression was applied to obtain the PM10 source apportionment. The 4-hour temporal resolution allowed the estimation of the factor contributions during peculiar episodes, which would have not been detected with the traditional 24-hour sampling strategy. Copyright © 2011 Elsevier B.V. All rights reserved.

Synovial chondromatosis of the temporomandibular joint: Immunohistochemical examinations regarding the role of insulin-like growth factors and their binding proteins in the etiology of this disease.

PubMed

Wilms, Christian T; Heim, Nils; Teschke, Marcus; Reich, Rudolf R; Götz, Werner

2017-02-01

Synovial chondromatosis (SC) is a benign disease of the joints without a known cause. It sometimes affects the temporomandibular joint (TMJ) and is accompanied by pain, swelling, malocclusion, and crepitation. It has been divided into three stages by Milgram and is supposed to originate from the synovia and cartilage of a joint (Milgram, 1977b). The aim of this study was to examine an involvement of the insulin-like growth factors (IGF-I/-II) and their binding proteins (IGFBP-1 to -6) in the etiology of this disease. Therefore 23 specimen of SC from 16 patients were immunohistochemically stained and microscopically examined. Staining was assessed semiquantitatively: negative (-), weakly positive ((+)), moderately positive (+), strongly positive (++) and very strongly positive (+++). It could be seen that especially the chondro- and fibrocytes and the synovia showed positive staining for almost all IGFs and IGFBPs. The underlying tissue, consisting of connective tissue or chondroid matrix, was stained as well but more weakly so. We conclude that the IGF/IGFBP system seems to contribute to the pathogenesis of SC, especially IGF-I and -II, and their effects enhancing binding protein 5. Copyright © 2016 European Association for Cranio-Maxillo-Facial Surgery. Published by Elsevier Ltd. All rights reserved.

A Gaussian random field model for similarity-based smoothing in Bayesian disease mapping.

PubMed

Baptista, Helena; Mendes, Jorge M; MacNab, Ying C; Xavier, Miguel; Caldas-de-Almeida, José

2016-08-01

Conditionally specified Gaussian Markov random field (GMRF) models with adjacency-based neighbourhood weight matrix, commonly known as neighbourhood-based GMRF models, have been the mainstream approach to spatial smoothing in Bayesian disease mapping. In the present paper, we propose a conditionally specified Gaussian random field (GRF) model with a similarity-based non-spatial weight matrix to facilitate non-spatial smoothing in Bayesian disease mapping. The model, named similarity-based GRF, is motivated for modelling disease mapping data in situations where the underlying small area relative risks and the associated determinant factors do not vary systematically in space, and the similarity is defined by "similarity" with respect to the associated disease determinant factors. The neighbourhood-based GMRF and the similarity-based GRF are compared and accessed via a simulation study and by two case studies, using new data on alcohol abuse in Portugal collected by the World Mental Health Survey Initiative and the well-known lip cancer data in Scotland. In the presence of disease data with no evidence of positive spatial correlation, the simulation study showed a consistent gain in efficiency from the similarity-based GRF, compared with the adjacency-based GMRF with the determinant risk factors as covariate. This new approach broadens the scope of the existing conditional autocorrelation models. © The Author(s) 2016.

Positioning patient-perceived medical services to develop a marketing strategy.

PubMed

Jung, Minsoo; Hong, Myung-Sun

2012-01-01

In today's medical market, marketing philosophy is being rapidly transformed from customer searching to patient satisfaction and service improvement. The principal objective of this study was to contribute to the establishment of a desirable medical marketing strategy, through the factors of customer satisfaction and the positioning of patients' perceptions by marketing institutions. The data were collected from 282 students of the College of Public Health and Medicine in Seoul. The survey tools were developed using the SERVQUAL scale. Analysis in this study involved both statistical and network analysis. The former was used to verify the determinants of service satisfaction as perceived by respondents, via factor analysis and multiple regression analysis. The latter was obtained using a positioning map and 2-mode network analysis with the matrix data converted from raw data. The determining factors for patient satisfaction were identified as facilities, accessibility, process, physicians, and medical staff. The regression equation was significant (R = 0.606), and the most influential variable was the service quality of physicians (β = .569). According to multidimensional scaling, the positioning of medical institutions indicated that patients' perceptions were affected by hospital size and specialization. By recognizing and managing patient satisfaction, medical institutions are able to foster customer loyalty and, in turn, to enhance service quality. It is necessary to develop an adequate marketing mix to provide better medical services and to overcome medical competition among institutions.

Source identification of PM10 pollution in subway passenger cabins using positive matrix factorization

NASA Astrophysics Data System (ADS)

Park, Duckshin; Oh, Miseok; Yoon, Younghun; Park, Eunyoung; Lee, Kiyoung

2012-03-01

Monitoring the air quality in subway passenger cabins is important because of the large number of passengers and potentially high levels of air pollution. This report characterized PM10 levels in subway cabins in Seoul, Korea, and identified PM10 sources using elemental analysis and receptor modeling. PM10 levels in subway cabins were continuously measured using a light scattering monitor during rush and non-rush hours. A total of 41 measurements were taken during rush and non-rush hours, and the measurements were repeated in all four seasons. Filter samples were also collected for elemental composition analysis. Major PM10 sources were identified using positive matrix factorization (PMF). The in-cabin PM10 concentrations were the highest in the winter at 152.8 μg m-3 during rush hours and 90.2 μg m-3 during non-rush hours. While PM10 levels were higher during rush hours than during non-rush hours in three seasons (excluding summer), these levels were not associated with number of passenger. Elemental analysis showed that the PM10 was composed of 52.5% inorganic elements, 10.2% anions, and 37.3% other. Fe was the most abundant element and significantly correlated (p < 0.01) with Mn (r = 0.97), Ti (r = 0.91), Cr (r = 0.88), Ni (r = 0.89), and Cu (r = 0.88). Fe, Mn, Cr, and Cu are indicators of railroad-related PM10 sources. The PM10 sources characterized by PMF were soil and road dust sources (27.2%), railroad-related sources (47.6%), secondary nitrate sources (16.2%), and a chlorine factor mixed with a secondary sulfate source (9.1%). Overall, railroad-related sources contributed the most PM10 to subway cabin air.

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

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.

Physician trust in the patient: development and validation of a new measure.

PubMed

Thom, David H; Wong, Sabrina T; Guzman, David; Wu, Amery; Penko, Joanne; Miaskowski, Christine; Kushel, Margot

2011-01-01

Mutual trust is an important aspect of the patient-physician relationship with positive consequences for both parties. Previous measures have been limited to patient trust in the physician. We set out to develop and validate a measure of physician trust in the patient. We identified candidate items for the scale by content analysis of a previous qualitative study of patient-physician trust and developed and validated a scale among 61 primary care clinicians (50 physicians and 11 nonphysicians) with respect to 168 patients as part of a community-based study of prescription opioid use for chronic, nonmalignant pain in HIV-positive adults. Polychoric factor structure analysis using the Pratt D matrix was used to reduce the number of items and describe the factor structure. Construct validity was tested by comparing mean clinician trust scores for patients by clinician and patient behaviors expected to be associated with clinician trust using a generalized linear mixed model. The final 12-item scale had high internal reliability (Cronbach α =.93) and a distinct 2-factor pattern with the Pratt matrix D. Construct validity was demonstrated with respect to clinician-reported self-behaviors including toxicology screening (P <.001), and refusal to prescribe opioids (P <.001) and with patient behaviors including reporting opioids lost or stolen (P=.008), taking opioids to get high (P <.001), and selling opioids (P<.001). If validated in other populations, this measure of physician trust in the patient will be useful in investigating the antecedents and consequences of mutual trust, and the relationship between mutual trust and processes of care, which can help improve the delivery of clinical care.

Functional disorders of the temporomandibular joints: Internal derangement of the temporomandibular joint.

PubMed

Chang, Chih-Ling; Wang, Ding-Han; Yang, Mu-Chen; Hsu, Wun-Eng; Hsu, Ming-Lun

2018-04-01

Temporomandibular joint (TMJ) is one of the most complex joints of the human body. Due to its unique movement, in terms of combination of rotation and translator movement, disc of the joint plays an important role to maintain its normal function. In order to sustain the normal function of the TMJ, disc must be kept in proper position as well as maintain normal shape in all circumstances. Once the disc is not any more in its normal position during function of the joint, disturbance of the joint can be occurred which will lead to subsequent distortion of the disc. Shape of the disc can be influenced by many factors i.e.: abnormal function or composition of the disc itself. Etiology of the internal derangement of the disc remains controversial. Multifactorial theory has been postulated in most of previous manuscripts. Disc is composed of mainly extracellular matrix. Abnormal proportion of collagen type I & III may also leads to joint hypermobility which may be also a predisposing factor of this disorder. Thus it can be recognized as local manifestation of a systemic disorder. Different treatment modalities with from conservative treatment to surgical intervention distinct success rate have been reported. Recently treatment with extracellular matrix injection becomes more and more popular to strengthen the joint itself. Since multifactorial in character, the best solution of the treatment modalities should be aimed to resolve possible etiology from different aspects. Team work may be indication to reach satisfied results. Copyright © 2018. Published by Elsevier Taiwan.

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.

High Glucose Forces a Positive Feedback Loop Connecting Akt Kinase and FoxO1 Transcription Factor to Activate mTORC1 Kinase for Mesangial Cell Hypertrophy and Matrix Protein Expression*

PubMed Central

Das, Falguni; Ghosh-Choudhury, Nandini; Dey, Nirmalya; Bera, Amit; Mariappan, Meenalakshmi M.; Kasinath, Balakuntalam S.; Ghosh Choudhury, Goutam

2014-01-01

High glucose-induced Akt acts as a signaling hub for mesangial cell hypertrophy and matrix expansion, which are recognized as cardinal signatures for the development of diabetic nephropathy. How mesangial cells sustain the activated state of Akt is not clearly understood. Here we show Akt-dependent phosphorylation of the transcription factor FoxO1 by high glucose. Phosphorylation-deficient, constitutively active FoxO1 inhibited the high glucose-induced phosphorylation of Akt to suppress the phosphorylation/inactivation of PRAS40 and mTORC1 activity. In contrast, dominant negative FoxO1 increased the phosphorylation of Akt, resulting in increased mTORC1 activity similar to high glucose treatment. Notably, FoxO1 regulates high glucose-induced protein synthesis, hypertrophy, and expression of fibronectin and PAI-1. High glucose paves the way for complications of diabetic nephropathy through the production of reactive oxygen species (ROS). We considered whether the FoxO1 target antioxidant enzyme catalase contributes to sustained activation of Akt. High glucose-inactivated FoxO1 decreases the expression of catalase to increase the production of ROS. Moreover, we show that catalase blocks high glucose-stimulated Akt phosphorylation to attenuate the inactivation of FoxO1 and PRAS40, resulting in the inhibition of mTORC1 and mesangial cell hypertrophy and fibronectin and PAI-1 expression. Finally, using kidney cortices from type 1 diabetic OVE26 mice, we show that increased FoxO1 phosphorylation is associated with decreased catalase expression and increased fibronectin and PAI-1 expression. Together, our results provide the first evidence for the presence of a positive feedback loop for the sustained activation of Akt involving inactivated FoxO1 and a decrease in catalase expression, leading to increased ROS and mesangial cell hypertrophy and matrix protein expression. PMID:25288788

Fast calculation of the `ILC norm' in iterative learning control

NASA Astrophysics Data System (ADS)

Rice, Justin K.; van Wingerden, Jan-Willem

2013-06-01

In this paper, we discuss and demonstrate a method for the exploitation of matrix structure in computations for iterative learning control (ILC). In Barton, Bristow, and Alleyne [International Journal of Control, 83(2), 1-8 (2010)], a special insight into the structure of the lifted convolution matrices involved in ILC is used along with a modified Lanczos method to achieve very fast computational bounds on the learning convergence, by calculating the 'ILC norm' in ? computational complexity. In this paper, we show how their method is equivalent to a special instance of the sequentially semi-separable (SSS) matrix arithmetic, and thus can be extended to many other computations in ILC, and specialised in some cases to even faster methods. Our SSS-based methodology will be demonstrated on two examples: a linear time-varying example resulting in the same ? complexity as in Barton et al., and a linear time-invariant example where our approach reduces the computational complexity to ?, thus decreasing the computation time, for an example, from the literature by a factor of almost 100. This improvement is achieved by transforming the norm computation via a linear matrix inequality into a check of positive definiteness - which allows us to further exploit the almost-Toeplitz properties of the matrix, and additionally provides explicit upper and lower bounds on the norm of the matrix, instead of the indirect Ritz estimate. These methods are now implemented in a MATLAB toolbox, freely available on the Internet.

Recursive inverse kinematics for robot arms via Kalman filtering and Bryson-Frazier smoothing

NASA Technical Reports Server (NTRS)

Rodriguez, G.; Scheid, R. E., Jr.

1987-01-01

This paper applies linear filtering and smoothing theory to solve recursively the inverse kinematics problem for serial multilink manipulators. This problem is to find a set of joint angles that achieve a prescribed tip position and/or orientation. A widely applicable numerical search solution is presented. The approach finds the minimum of a generalized distance between the desired and the actual manipulator tip position and/or orientation. Both a first-order steepest-descent gradient search and a second-order Newton-Raphson search are developed. The optimal relaxation factor required for the steepest descent method is computed recursively using an outward/inward procedure similar to those used typically for recursive inverse dynamics calculations. The second-order search requires evaluation of a gradient and an approximate Hessian. A Gauss-Markov approach is used to approximate the Hessian matrix in terms of products of first-order derivatives. This matrix is inverted recursively using a two-stage process of inward Kalman filtering followed by outward smoothing. This two-stage process is analogous to that recently developed by the author to solve by means of spatial filtering and smoothing the forward dynamics problem for serial manipulators.

Fuzzy Adaptive Cubature Kalman Filter for Integrated Navigation Systems.

PubMed

Tseng, Chien-Hao; Lin, Sheng-Fuu; Jwo, Dah-Jing

2016-07-26

This paper presents a sensor fusion method based on the combination of cubature Kalman filter (CKF) and fuzzy logic adaptive system (FLAS) for the integrated navigation systems, such as the GPS/INS (Global Positioning System/inertial navigation system) integration. The third-degree spherical-radial cubature rule applied in the CKF has been employed to avoid the numerically instability in the system model. In processing navigation integration, the performance of nonlinear filter based estimation of the position and velocity states may severely degrade caused by modeling errors due to dynamics uncertainties of the vehicle. In order to resolve the shortcoming for selecting the process noise covariance through personal experience or numerical simulation, a scheme called the fuzzy adaptive cubature Kalman filter (FACKF) is presented by introducing the FLAS to adjust the weighting factor of the process noise covariance matrix. The FLAS is incorporated into the CKF framework as a mechanism for timely implementing the tuning of process noise covariance matrix based on the information of degree of divergence (DOD) parameter. The proposed FACKF algorithm shows promising accuracy improvement as compared to the extended Kalman filter (EKF), unscented Kalman filter (UKF), and CKF approaches.

Fuzzy Adaptive Cubature Kalman Filter for Integrated Navigation Systems

PubMed Central

Tseng, Chien-Hao; Lin, Sheng-Fuu; Jwo, Dah-Jing

2016-01-01

This paper presents a sensor fusion method based on the combination of cubature Kalman filter (CKF) and fuzzy logic adaptive system (FLAS) for the integrated navigation systems, such as the GPS/INS (Global Positioning System/inertial navigation system) integration. The third-degree spherical-radial cubature rule applied in the CKF has been employed to avoid the numerically instability in the system model. In processing navigation integration, the performance of nonlinear filter based estimation of the position and velocity states may severely degrade caused by modeling errors due to dynamics uncertainties of the vehicle. In order to resolve the shortcoming for selecting the process noise covariance through personal experience or numerical simulation, a scheme called the fuzzy adaptive cubature Kalman filter (FACKF) is presented by introducing the FLAS to adjust the weighting factor of the process noise covariance matrix. The FLAS is incorporated into the CKF framework as a mechanism for timely implementing the tuning of process noise covariance matrix based on the information of degree of divergence (DOD) parameter. The proposed FACKF algorithm shows promising accuracy improvement as compared to the extended Kalman filter (EKF), unscented Kalman filter (UKF), and CKF approaches. PMID:27472336

The synergic role of sociotechnical and personal characteristics on work injuries in mines.

PubMed

Paul, P S; Maiti, J

2008-05-01

Occupational injuries in mines are attributed to many factors. In this study, an attempt was made to identify the various factors related to work injuries in mines and to estimate their effects on work injuries to mine workers. An accident path model was developed to estimate the pattern and strength of relationships amongst the personal and sociotechnical variables in accident/injury occurrences. The input data for the model were the correlation matrix of 18 variables, which were collected from the case study mines. The case study results showed that there are sequential interactions amongst the sociotechnical and personal factors leading to accidents/injuries in mines. Amongst the latent endogenous constructs, job dissatisfaction and safe work behaviour show a significant positive and negative direct relationship with work injury, respectively. However, the construct safety environment has a significant negative indirect relationship with work injury. The safety environment is negatively affected by work hazards and positively affected by social support. The safety environment also shows a significant negative relationship with job stress and job dissatisfaction. However, negative personality has no significant direct or indirect effect on work injury, but it has a significant negative relationship with safe work behaviour. The endogenous construct negative personality is positively influenced by job stress and negatively influenced by social support.

Production and characterization of hyaluronic acid microparticles for the controlled delivery of growth factors using a spray/dehydration method.

PubMed

Babo, Pedro S; Reis, Rui L; Gomes, Manuela E

2016-11-01

Hyaluronic acid is the main polysaccharide present in the connective tissue. Besides its structural function as backbone of the extracellular matrix, hyaluronic acid plays staple roles in several biological processes including the modulation of inflammation and wound healing processes. The application of hyaluronic acid in regenerative medicine, either as cells and/or drug/growth factors delivery vehicles, relies on its ability to be cross-linked using a plethora of reactions, producing stable hydrogels. In this work, we propose a novel method for the production of hyaluronic acid microparticles that presents several advantages over others that have been used. Basically, droplets of hyaluronic acid solution produced with a nozzle are collected in an isopropanol dehydration bath, and stabilized after crosslinking with adipic acid dihydrazide, using a cabodiimide-based chemistry. The size and morphology of the hyaluronic acid microparticles produced by this method varied with the molecular weight and concentration of the hyaluronic acid solution, the nozzle chamber pressure, the distance between the nozzle and the crosslinking solution, and the number of crosslinking steps. The degree of crosslinking of the hyaluronic acid microparticles produced was tunable and allowed to control the rate of the degradation promoted by hyaluronidase. Moreover, the particles were loaded with platelet lysate, a hemoderivative rich in cytokines with interest for regenerative medicine applications. The hyaluronic acid microparticles showed potential to bind selectively to positively charged molecules, as the factors present in the platelet lysate. It is envisioned that these can be further released in a sustained manner by ion exchange or by the degradation of the hyaluronic acid microparticles matrix promoted by extracellular matrix remodeling. © The Author(s) 2016.

Extracellular matrix metalloproteinase inducer (EMMPRIN) is a potential biomarker of angiogenesis in proliferative diabetic retinopathy.

PubMed

Abu El-Asrar, Ahmed M; Ahmad, Ajmal; Alam, Kaiser; Siddiquei, Mohammad Mairaj; Mohammad, Ghulam; Hertogh, Gert De; Mousa, Ahmed; Opdenakker, Ghislain

2017-11-01

Extracellular matrix metalloproteinase inducer (EMMPRIN) promotes angiogenesis through matrix metalloproteinases (MMPs) and vascular endothelial growth factor (VEGF) production. We investigated the expression levels of EMMPRIN and correlated these levels with VEGF, MMP-1 and MMP-9 in proliferative diabetic retinopathy (PDR). In addition, we examined the expression of EMMPRIN in the retinas of diabetic rats and the effect of EMMPRIN on the induction of angiogenesis regulatory factors in human retinal microvascular endothelial cells (HRMECs). Vitreous samples from 40 PDR and 19 non-diabetic patients, epiretinal membranes from 12 patients with PDR, retinas of rats and HRMECs were studied by enzyme-linked immunosorbent assay (ELISA), immunohistochemistry, Western blot analysis, zymography analysis and RT-PCR. We showed a significant increase in the expression of EMMPRIN, VEGF, MMP-1 and MMP-9 in vitreous samples from PDR patients compared with non-diabetic controls (p < 0.0001; p = 0.001; p = 0.009; p < 0.0001, respectively). Significant positive correlations were found between the levels of EMMPRIN and the levels of VEGF (r = 0.38; p = 0.003), MMP-1 (r = 0.36; p = 0.005) and MMP-9 (r = 0.46; p = 0.003). In epiretinal membranes, EMMPRIN was expressed in vascular endothelial cells and stromal cells. Significant increase of EMMPRIN mRNA was detected in rat retinas after induction of diabetes. EMMPRIN induced hypoxia-inducible factor-1α, VEGF and MMP-1 expression in HRMEC. These results suggest that EMMPRIN/MMPs/VEGF pathway is involved in PDR angiogenesis. © 2016 Acta Ophthalmologica Scandinavica Foundation. Published by John Wiley & Sons Ltd.

Marketing Strategy Analysis for Small and Medium Scale Business Enterprise (SMEs) for Home Industry Furniture in Leilem, the Regency of Minahasa

NASA Astrophysics Data System (ADS)

Pangemanan, S. A.; Walukow, I. M.

2018-01-01

Leilem is a small village located in Minahasa Regency. This village is well known for furniture products made of Timber. Eventhough the village has been producing various furniture products with high quality since many decades ago, it has not been able to compete with other new entries such furniture from Java, Synthetic Ratan, Plywood and plastic based furniture. The monotonous design and the finishing works done on the furniture have been some of the major issues in the decline of home furniture. The research explores problems and challenges faced by the furniture home Industry. It will also aim at identifying the internal and external factors that prevent the home industry to compete and survive. In the end the research will develop the strategic positioning of the home industry in the midst of competition. The research methodology employs descriptive analysis in which data are collected through observation, interview, and questionnaire. This methodology is combined with IFE (Internal Factor Evaluation) and EFE (External Factor Evaluation) Matrix, SPACE Matrix and SWOT Analysis and QSPM (Quantitative Strategic Planning Matrix). The sample is 66 business people, of 823 craftsmen who are working in this business. The result shows this home industry is very competitive in terms of consistency, but in terms of promotion, product quality, price, product diversification, design training of furniture, management and economic scale, it is lagging behind. The home industry should be able to develop marketing networking, improve design and product quality, promotion and cost control, product diversification and these can only be done by intensive training in managing business and investment.

Correlation of pretreatment 18F-FDG PET tumor textural features with gene expression in pharyngeal cancer and implications for radiotherapy-based treatment outcomes.

PubMed

Chen, Shang-Wen; Shen, Wei-Chih; Lin, Ying-Chun; Chen, Rui-Yun; Hsieh, Te-Chun; Yen, Kuo-Yang; Kao, Chia-Hung

2017-04-01

This study investigated the correlation of the matrix heterogeneity of tumors on 18 F-fluorodeoxyglucose positron emission tomography-computed tomography (PET-CT) with gene-expression profiling in patients with pharyngeal cancer and determined the prognostic factors for radiotherapy-based treatment outcomes. We retrospectively reviewed the records of 57 patients with stage III-IV oropharyngeal or hypopharyngeal cancer who had completed definitive therapy. Four groups of the textural features as well as 31 indices were studied in addition to maximum standard uptake value, metastatic tumor volume, and total lesion glycolysis. Immunohistochemical data from pretreatment biopsy specimens (Glut1, CAIX, VEGF, HIF-1α, EGFR, Ki-67, Bcl-2, CLAUDIN-4, YAP-1, c-Met, and p16) were analyzed. The relationships between the indices and genomic expression were studied, and the robustness of various textural features relative to cause-specific survival and primary relapse-free survival was analyzed. The overexpression of VEGF was positively associated with the increased values of the matrix heterogeneity obtained using gray-level nonuniformity for zone (GLNUz) and run-length nonuniformity (RLNU). Advanced T stage (p = 0.01, hazard ratio [HR] = 3.38), a VEGF immunoreactive score of >2 (p = 0.03, HR = 2.79), and a higher GLNUz value (p = 0.04, HR = 2.51) were prognostic factors for low cause-specific survival, whereas advanced T stage, a HIF-1α staining percentage of ≥80%, and a higher GLNUz value were prognostic factors for low primary-relapse free survival. The overexpression of VEGF was associated with the increased matrix index of GLNUz and RLNU. For patients with pharyngeal cancer requiring radiotherapy, the treatment outcome can be stratified according to the textural features, T stage, and biomarkers.

Toda hierarchies and their applications

NASA Astrophysics Data System (ADS)

Takasaki, Kanehisa

2018-05-01

The 2D Toda hierarchy occupies a central position in the family of integrable hierarchies of the Toda type. The 1D Toda hierarchy and the Ablowitz–Ladik (aka relativistic Toda) hierarchy can be derived from the 2D Toda hierarchy as reductions. These integrable hierarchies have been applied to various problems of mathematics and mathematical physics since 1990s. A recent example is a series of studies on models of statistical mechanics called the melting crystal model. This research has revealed that the aforementioned two reductions of the 2D Toda hierarchy underlie two different melting crystal models. Technical clues are a fermionic realization of the quantum torus algebra, special algebraic relations therein called shift symmetries, and a matrix factorization problem. The two melting crystal models thus exhibit remarkable similarity with the Hermitian and unitary matrix models for which the two reductions of the 2D Toda hierarchy play the role of fundamental integrable structures.

Large scale nanoparticle screening for small molecule analysis in laser desorption ionization mass spectrometry

DOE PAGES

Yagnik, Gargey B.; Hansen, Rebecca L.; Korte, Andrew R.; ...

2016-08-30

Nanoparticles (NPs) have been suggested as efficient matrixes for small molecule profiling and imaging by laser-desorption ionization mass spectrometry (LDI-MS), but so far there has been no systematic study comparing different NPs in the analysis of various classes of small molecules. Here, we present a large scale screening of 13 NPs for the analysis of two dozen small metabolite molecules. Many NPs showed much higher LDI efficiency than organic matrixes in positive mode and some NPs showed comparable efficiencies for selected analytes in negative mode. Our results suggest that a thermally driven desorption process is a key factor for metalmore » oxide NPs, but chemical interactions are also very important, especially for other NPs. Furthermore, the screening results provide a useful guideline for the selection of NPs in the LDI-MS analysis of small molecules.« less

Large scale nanoparticle screening for small molecule analysis in laser desorption ionization mass spectrometry

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

Yagnik, Gargey B.; Hansen, Rebecca L.; Korte, Andrew R.

Nanoparticles (NPs) have been suggested as efficient matrixes for small molecule profiling and imaging by laser-desorption ionization mass spectrometry (LDI-MS), but so far there has been no systematic study comparing different NPs in the analysis of various classes of small molecules. Here, we present a large scale screening of 13 NPs for the analysis of two dozen small metabolite molecules. Many NPs showed much higher LDI efficiency than organic matrixes in positive mode and some NPs showed comparable efficiencies for selected analytes in negative mode. Our results suggest that a thermally driven desorption process is a key factor for metalmore » oxide NPs, but chemical interactions are also very important, especially for other NPs. Furthermore, the screening results provide a useful guideline for the selection of NPs in the LDI-MS analysis of small molecules.« less

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 emissions of VOCs may be understated. For NOx, the fuel-based inventory is lower for gasoline-powered vehicles but higher for diesel-powered ones compared to the official inventory.

Recursive flexible multibody system dynamics using spatial operators

NASA Technical Reports Server (NTRS)

Jain, A.; Rodriguez, G.

1992-01-01

This paper uses spatial operators to develop new spatially recursive dynamics algorithms for flexible multibody systems. The operator description of the dynamics is identical to that for rigid multibody systems. Assumed-mode models are used for the deformation of each individual body. The algorithms are based on two spatial operator factorizations of the system mass matrix. The first (Newton-Euler) factorization of the mass matrix leads to recursive algorithms for the inverse dynamics, mass matrix evaluation, and composite-body forward dynamics for the systems. The second (innovations) factorization of the mass matrix, leads to an operator expression for the mass matrix inverse and to a recursive articulated-body forward dynamics algorithm. The primary focus is on serial chains, but extensions to general topologies are also described. A comparison of computational costs shows that the articulated-body, forward dynamics algorithm is much more efficient than the composite-body algorithm for most flexible multibody systems.

Direct Solve of Electrically Large Integral Equations for Problem Sizes to 1M Unknowns

NASA Technical Reports Server (NTRS)

Shaeffer, John

2008-01-01

Matrix methods for solving integral equations via direct solve LU factorization are presently limited to weeks to months of very expensive supercomputer time for problems sizes of several hundred thousand unknowns. This report presents matrix LU factor solutions for electromagnetic scattering problems for problem sizes to one million unknowns with thousands of right hand sides that run in mere days on PC level hardware. This EM solution is accomplished by utilizing the numerical low rank nature of spatially blocked unknowns using the Adaptive Cross Approximation for compressing the rank deficient blocks of the system Z matrix, the L and U factors, the right hand side forcing function and the final current solution. This compressed matrix solution is applied to a frequency domain EM solution of Maxwell's equations using standard Method of Moments approach. Compressed matrix storage and operations count leads to orders of magnitude reduction in memory and run time.

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.

Development of a methodology examining the behaviours of VOCs source apportionment with micro-meteorology analysis in an urban and industrial area.

PubMed

Xiang, Yang; Delbarre, Hervé; Sauvage, Stéphane; Léonardis, Thierry; Fourmentin, Marc; Augustin, Patrick; Locoge, Nadine

2012-03-01

During summer 2009, online measurements of 25 Volatile Organic Compounds (VOCs) from C6 to C10 as well as micro-meteorological parameters were simultaneously performed in the industrial city of Dunkerque. With the obtained data set, we developed a methodology to examine how the contributions of different source categories depend on atmospheric turbulences, and the results provided identification of emission modes. Eight factors were resolved by using Positive Matrix Factorization model and three of them were associated with mixed sources. The observed behaviours of contributions with turbulences lead to attribute some factors with sources at ground level, and some other factors with sources in the upper part of surface layer. The impact of vertical turbulence on the pollutant dispersion is also affected by the distance between sources and receptor site. Copyright © 2011 Elsevier Ltd. All rights reserved.

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)

Searching for transcription factor binding sites in vector spaces

PubMed Central

2012-01-01

Background Computational approaches to transcription factor binding site identification have been actively researched in the past decade. Learning from known binding sites, new binding sites of a transcription factor in unannotated sequences can be identified. A number of search methods have been introduced over the years. However, one can rarely find one single method that performs the best on all the transcription factors. Instead, to identify the best method for a particular transcription factor, one usually has to compare a handful of methods. Hence, it is highly desirable for a method to perform automatic optimization for individual transcription factors. Results We proposed to search for transcription factor binding sites in vector spaces. This framework allows us to identify the best method for each individual transcription factor. We further introduced two novel methods, the negative-to-positive vector (NPV) and optimal discriminating vector (ODV) methods, to construct query vectors to search for binding sites in vector spaces. Extensive cross-validation experiments showed that the proposed methods significantly outperformed the ungapped likelihood under positional background method, a state-of-the-art method, and the widely-used position-specific scoring matrix method. We further demonstrated that motif subtypes of a TF can be readily identified in this framework and two variants called the k NPV and k ODV methods benefited significantly from motif subtype identification. Finally, independent validation on ChIP-seq data showed that the ODV and NPV methods significantly outperformed the other compared methods. Conclusions We conclude that the proposed framework is highly flexible. It enables the two novel methods to automatically identify a TF-specific subspace to search for binding sites. Implementations are available as source code at: http://biogrid.engr.uconn.edu/tfbs_search/. PMID:23244338

Matrix Metalloproteinase (MMP) 9 Transcription in Mouse Brain Induced by Fear Learning*

PubMed Central

Ganguly, Krishnendu; Rejmak, Emilia; Mikosz, Marta; Nikolaev, Evgeni; Knapska, Ewelina; Kaczmarek, Leszek

2013-01-01

Memory formation requires learning-based molecular and structural changes in neurons, whereas matrix metalloproteinase (MMP) 9 is involved in the synaptic plasticity by cleaving extracellular matrix proteins and, thus, is associated with learning processes in the mammalian brain. Because the mechanisms of MMP-9 transcription in the brain are poorly understood, this study aimed to elucidate regulation of MMP-9 gene expression in the mouse brain after fear learning. We show here that contextual fear conditioning markedly increases MMP-9 transcription, followed by enhanced enzymatic levels in the three major brain structures implicated in fear learning, i.e. the amygdala, hippocampus, and prefrontal cortex. To reveal the role of AP-1 transcription factor in MMP-9 gene expression, we have used reporter gene constructs with specifically mutated AP-1 gene promoter sites. The constructs were introduced into the medial prefrontal cortex of neonatal mouse pups by electroporation, and the regulation of MMP-9 transcription was studied after contextual fear conditioning in the adult animals. Specifically, −42/-50- and −478/-486-bp AP-1 binding motifs of the mouse MMP-9 promoter sequence have been found to play a major role in MMP-9 gene activation. Furthermore, increases in MMP-9 gene promoter binding by the AP-1 transcription factor proteins c-Fos and c-Jun have been demonstrated in all three brain structures under investigation. Hence, our results suggest that AP-1 acts as a positive regulator of MMP-9 transcription in the brain following fear learning. PMID:23720741

Matrix metalloproteinase (MMP) 9 transcription in mouse brain induced by fear learning.

PubMed

Ganguly, Krishnendu; Rejmak, Emilia; Mikosz, Marta; Nikolaev, Evgeni; Knapska, Ewelina; Kaczmarek, Leszek

2013-07-19

Memory formation requires learning-based molecular and structural changes in neurons, whereas matrix metalloproteinase (MMP) 9 is involved in the synaptic plasticity by cleaving extracellular matrix proteins and, thus, is associated with learning processes in the mammalian brain. Because the mechanisms of MMP-9 transcription in the brain are poorly understood, this study aimed to elucidate regulation of MMP-9 gene expression in the mouse brain after fear learning. We show here that contextual fear conditioning markedly increases MMP-9 transcription, followed by enhanced enzymatic levels in the three major brain structures implicated in fear learning, i.e. the amygdala, hippocampus, and prefrontal cortex. To reveal the role of AP-1 transcription factor in MMP-9 gene expression, we have used reporter gene constructs with specifically mutated AP-1 gene promoter sites. The constructs were introduced into the medial prefrontal cortex of neonatal mouse pups by electroporation, and the regulation of MMP-9 transcription was studied after contextual fear conditioning in the adult animals. Specifically, -42/-50- and -478/-486-bp AP-1 binding motifs of the mouse MMP-9 promoter sequence have been found to play a major role in MMP-9 gene activation. Furthermore, increases in MMP-9 gene promoter binding by the AP-1 transcription factor proteins c-Fos and c-Jun have been demonstrated in all three brain structures under investigation. Hence, our results suggest that AP-1 acts as a positive regulator of MMP-9 transcription in the brain following fear learning.

EMMPRIN co-expressed with matrix metalloproteinases predicts poor prognosis in patients with osteosarcoma.

PubMed

Futamura, Naohisa; Nishida, Yoshihiro; Urakawa, Hiroshi; Kozawa, Eiji; Ikuta, Kunihiro; Hamada, Shunsuke; Ishiguro, Naoki

2014-06-01

Several studies have focused on the relationships between the expression of extracellular matrix metalloproteinase inducer (EMMPRIN) and the prognosis of patients with malignant tumors. However, few of these have investigated the expression of EMMPRIN in osteosarcoma. We examined expression levels of EMMPRIN immunohistochemically in 53 cases of high-grade osteosarcoma of the extremities and analyzed the correlation of its expression with patient prognosis. The correlation between matrix metalloproteinases (MMPs) and EMMPRIN expression and the prognostic value of co-expression were also analyzed. Staining positivity for EMMPRIN was negative in 7 cases, low in 17, moderate in 19, and strong in 10. The overall and disease-free survivals (OS and DFS) in patients with higher EMMPRIN expression (strong-moderate) were significantly lower than those in the lower (weak-negative) group (0.037 and 0.024, respectively). In multivariate analysis, age (P=0.004), location (P=0.046), and EMMPRIN expression (P=0.038) were significant prognostic factors for overall survival. EMMPRIN expression (P=0.024) was also a significant prognostic factor for disease-free survival. Co-expression analyses of EMMPRIN and MMPs revealed that strong co-expression of EMMPRIN and membrane-type 1 (MT1)-MMP had a poor prognostic value (P=0.056 for DFS, P=0.006 for OS). EMMPRIN expression and co-expression with MMPs well predict the prognosis of patients with extremity osteosarcoma, making EMMPRIN a possible therapeutic target in these patients.

Designing Hyperchaotic Cat Maps With Any Desired Number of Positive Lyapunov Exponents.

PubMed

Hua, Zhongyun; Yi, Shuang; Zhou, Yicong; Li, Chengqing; Wu, Yue

2018-02-01

Generating chaotic maps with expected dynamics of users is a challenging topic. Utilizing the inherent relation between the Lyapunov exponents (LEs) of the Cat map and its associated Cat matrix, this paper proposes a simple but efficient method to construct an -dimensional ( -D) hyperchaotic Cat map (HCM) with any desired number of positive LEs. The method first generates two basic -D Cat matrices iteratively and then constructs the final -D Cat matrix by performing similarity transformation on one basic -D Cat matrix by the other. Given any number of positive LEs, it can generate an -D HCM with desired hyperchaotic complexity. Two illustrative examples of -D HCMs were constructed to show the effectiveness of the proposed method, and to verify the inherent relation between the LEs and Cat matrix. Theoretical analysis proves that the parameter space of the generated HCM is very large. Performance evaluations show that, compared with existing methods, the proposed method can construct -D HCMs with lower computation complexity and their outputs demonstrate strong randomness and complex ergodicity.

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.

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.

Carbon nanodots as a matrix for the analysis of low-molecular-weight molecules in both positive- and negative-ion matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and quantification of glucose and uric acid in real samples.

PubMed

Chen, Suming; Zheng, Huzhi; Wang, Jianing; Hou, Jian; He, Qing; Liu, Huihui; Xiong, Caiqiao; Kong, Xianglei; Nie, Zongxiu

2013-07-16

Carbon nanodots were applied for the first time as a new matrix for the analysis of low-molecular-weight compounds by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) in both positive- and negative-ion modes. A wide range of small molecules including amino acids, peptides, fatty acids, as well as β-agonists and neutral oligosaccharides were analyzed by MALDI MS with carbon nanodots as the matrix, and the lowest 0.2 fmol limits-of-detection were obtained for octadecanoic acid. Clear sodium and potassium adducts and deprotonated signals were produced in positive- and negative-ion modes. Furthermore, the glucose and uric acid in real samples were quantitatively determined by the internal standard method with the linear range of 0.5-9 mM and 0.1-1.8 mM (R(2) > 0.999), respectively. This work gives new insight into the application of carbon nanodots and provides a general approach for rapid analysis of low-molecular-weight compounds.

Classification and identification of molecules through factor analysis method based on terahertz spectroscopy

NASA Astrophysics Data System (ADS)

Huang, Jianglou; Liu, Jinsong; Wang, Kejia; Yang, Zhengang; Liu, Xiaming

2018-06-01

By means of factor analysis approach, a method of molecule classification is built based on the measured terahertz absorption spectra of the molecules. A data matrix can be obtained by sampling the absorption spectra at different frequency points. The data matrix is then decomposed into the product of two matrices: a weight matrix and a characteristic matrix. By using the K-means clustering to deal with the weight matrix, these molecules can be classified. A group of samples (spirobenzopyran, indole, styrene derivatives and inorganic salts) has been prepared, and measured via a terahertz time-domain spectrometer. These samples are classified with 75% accuracy compared to that directly classified via their molecular formulas.

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.

Moving-Bank Multiple Model Adaptive Estimation and Control Applied to a Large Flexible Space Structure

DTIC Science & Technology

1990-12-01

was determined from the difference between the 24-state matrix product, HtP (t’)HT, and the six-state matrix product, HfPf (tT)HT’. For this...The true position for node 7, which represents the rigid body position of the structure, is not damped and can be interpreted as a rigid body...application, considering the same issues as explored in this research. Continue with a physical interpretation of the structure positions for determining the

Simple derivation of the Lindblad equation

NASA Astrophysics Data System (ADS)

Pearle, Philip

2012-07-01

The Lindblad equation is an evolution equation for the density matrix in quantum theory. It is the general linear, Markovian, form which ensures that the density matrix is Hermitian, trace 1, positive and completely positive. Some elementary examples of the Lindblad equation are given. The derivation of the Lindblad equation presented here is ‘simple’ in that all it uses is the expression of a Hermitian matrix in terms of its orthonormal eigenvectors and real eigenvalues. Thus, it is appropriate for students who have learned the algebra of quantum theory. Where helpful, arguments are first given in a two-dimensional Hilbert space.

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…

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

EMMPRIN Is an Independent Negative Prognostic Factor for Patients with Astrocytic Glioma

PubMed Central

Chen, Yu; Cai, Min; Dong, Hailong; Xiong, Lize

2013-01-01

Extracellular matrix metalloproteinase inducer (EMMPRIN), also known as CD147, is a member of the immunoglobulin superfamily that is present on the surface of tumor cells and stimulates adjacent fibroblasts to produce matrix metalloproteinases (MMPs). It has been proved to be associated with tumor invasion and metastasis in various human malignancies. In our study, the protein expression level of EMMPRIN in 306 cases of astrocytic glioma is investigated by immunohistochemistry assay. Statistical analysis was utilized to evaluate the association of EMMPRIN with clinicopathological characteristics and prognosis of patients. It was proved that EMMPRIN protein expression was increased in glioma compared with that in normal brain tissue. Moreover, EMMPRIN immunohistochemical staining was correlated with WHO grade and Karnofsky performance score for strong positive EMMPRIN staining is more frequently detected in glioma of advanced grade or low KPS score. It is also demonstrated that EMMPRIN could be an independent negative prognostic factor in glioma for patients with glioma of strong EMMPRIN staining tend to have high risk of death. These results proved that EMMPRIN is associated with prognosis of glioma, which may also suggest the potential role of EMMPRIN in glioma management. PMID:23516431

EMMPRIN is an independent negative prognostic factor for patients with astrocytic glioma.

PubMed

Tian, Li; Zhang, Yang; Chen, Yu; Cai, Min; Dong, Hailong; Xiong, Lize

2013-01-01

Extracellular matrix metalloproteinase inducer (EMMPRIN), also known as CD147, is a member of the immunoglobulin superfamily that is present on the surface of tumor cells and stimulates adjacent fibroblasts to produce matrix metalloproteinases (MMPs). It has been proved to be associated with tumor invasion and metastasis in various human malignancies. In our study, the protein expression level of EMMPRIN in 306 cases of astrocytic glioma is investigated by immunohistochemistry assay. Statistical analysis was utilized to evaluate the association of EMMPRIN with clinicopathological characteristics and prognosis of patients. It was proved that EMMPRIN protein expression was increased in glioma compared with that in normal brain tissue. Moreover, EMMPRIN immunohistochemical staining was correlated with WHO grade and Karnofsky performance score for strong positive EMMPRIN staining is more frequently detected in glioma of advanced grade or low KPS score. It is also demonstrated that EMMPRIN could be an independent negative prognostic factor in glioma for patients with glioma of strong EMMPRIN staining tend to have high risk of death. These results proved that EMMPRIN is associated with prognosis of glioma, which may also suggest the potential role of EMMPRIN in glioma management.

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 are equivalent contributions of biomass combustion and industrial emissions to the measured aerosol surface concentrations, the origin of carbonaceous aerosols largely from biomass combustion and the identification of probable source regions in Africa, west Asia, the Arabian peninsula and south-east Asia, in addition to India, which affected particulate matter concentrations over parts of the INDOEX domain covered by the Ron Brown cruise.

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) may have significant implications for assessing long-term, large-scale radionuclide and contaminant transport events in fractured rock, both for nuclear waste disposal and contaminant remediation.

A novel image encryption algorithm based on the chaotic system and DNA computing

NASA Astrophysics Data System (ADS)

Chai, Xiuli; Gan, Zhihua; Lu, Yang; Chen, Yiran; Han, Daojun

A novel image encryption algorithm using the chaotic system and deoxyribonucleic acid (DNA) computing is presented. Different from the traditional encryption methods, the permutation and diffusion of our method are manipulated on the 3D DNA matrix. Firstly, a 3D DNA matrix is obtained through bit plane splitting, bit plane recombination, DNA encoding of the plain image. Secondly, 3D DNA level permutation based on position sequence group (3DDNALPBPSG) is introduced, and chaotic sequences generated from the chaotic system are employed to permutate the positions of the elements of the 3D DNA matrix. Thirdly, 3D DNA level diffusion (3DDNALD) is given, the confused 3D DNA matrix is split into sub-blocks, and XOR operation by block is manipulated to the sub-DNA matrix and the key DNA matrix from the chaotic system. At last, by decoding the diffused DNA matrix, we get the cipher image. SHA 256 hash of the plain image is employed to calculate the initial values of the chaotic system to avoid chosen plaintext attack. Experimental results and security analyses show that our scheme is secure against several known attacks, and it can effectively protect the security of the images.

Beta-palmitate - a natural component of human milk in supplemental milk formulas.

PubMed

Havlicekova, Zuzana; Jesenak, Milos; Banovcin, Peter; Kuchta, Milan

2016-03-17

The composition and function of human milk is unique and gives a basis for the development of modern artificial milk formulas that can provide an appropriate substitute for non-breastfed infants. Although human milk is not fully substitutable, modern milk formulas are attempting to mimic human milk and partially substitute its complex biological positive effects on infants. Besides the immunomodulatory factors from human milk, research has been focused on the composition and structure of human milk fat with a high content of β-palmitic acid (sn-2 palmitic acid, β-palmitate). According to the available studies, increasing the content of β-palmitate added to milk formulas promotes several beneficial physiological functions. β-palmitate positively influences fatty acid metabolism, increases calcium absorption, improves bone matrix quality and the stool consistency, and has a positive effect on the development of the intestinal microbiome.

A Study on Dielectric Properties of Cadmium Sulfide-Zinc Sulfide Core-Shell Nanocomposites for Application as Nanoelectronic Filter Component in the Microwave Domain

NASA Astrophysics Data System (ADS)

Devi, Jutika; Datta, Pranayee

2018-07-01

Complex permittivities of cadmium sulfide (CdS), zinc sulfide (ZnS), and of cadmium sulfide-zinc sulfide (CdS/ZnS) core-shell nanoparticles embedded in a polyvinyl alcohol matrix (PVA) were measured in liquid phase using a VectorNetwork Analyzer in the frequency range of 500 MHz-10 GHz. These nanocomposites are modeled as an embedded capacitor, and their electric field distribution and polarization have been studied using COMSOL Multiphysics software. By varying the thickness of the shell and the number of inclusions, the capacitance values were estimated. It was observed that CdS, ZnS and CdS/ZnS core-shell nanoparticles embedded in a polyvinyl alcohol matrix show capacitive behavior. There is a strong influence of the dielectric properties in the capacitive behavior of the embedded nanocapacitor. The capping matrix, position and filling factors of nanoinclusions all affect the capacitive behavior of the tested nanocomposites. Application of the CdS, ZnS and CdS/ZnS core-shell nanocomposite as the passive low-pass filter circuit has also been investigated. From the present study, it has been found that CdS/ZnS core-shell nanoparticles embedded in PVA matrix are potential structures for application as nanoelectronic filter components in different areas of communication.

A Study on Dielectric Properties of Cadmium Sulfide-Zinc Sulfide Core-Shell Nanocomposites for Application as Nanoelectronic Filter Component in the Microwave Domain

NASA Astrophysics Data System (ADS)

Devi, Jutika; Datta, Pranayee

2018-03-01

Complex permittivities of cadmium sulfide (CdS), zinc sulfide (ZnS), and of cadmium sulfide-zinc sulfide (CdS/ZnS) core-shell nanoparticles embedded in a polyvinyl alcohol matrix (PVA) were measured in liquid phase using a VectorNetwork Analyzer in the frequency range of 500 MHz-10 GHz. These nanocomposites are modeled as an embedded capacitor, and their electric field distribution and polarization have been studied using COMSOL Multiphysics software. By varying the thickness of the shell and the number of inclusions, the capacitance values were estimated. It was observed that CdS, ZnS and CdS/ZnS core-shell nanoparticles embedded in a polyvinyl alcohol matrix show capacitive behavior. There is a strong influence of the dielectric properties in the capacitive behavior of the embedded nanocapacitor. The capping matrix, position and filling factors of nanoinclusions all affect the capacitive behavior of the tested nanocomposites. Application of the CdS, ZnS and CdS/ZnS core-shell nanocomposite as the passive low-pass filter circuit has also been investigated. From the present study, it has been found that CdS/ZnS core-shell nanoparticles embedded in PVA matrix are potential structures for application as nanoelectronic filter components in different areas of communication.

A real time spectrum to dose conversion system

NASA Technical Reports Server (NTRS)

Farmer, B. J.; Johnson, J. H.; Bagwell, R. G.

1972-01-01

A system has been developed which permits the determination of dose in real time or near real time directly from the pulse-height output of a radiation spectrometer. The technique involves the use of the resolution matrix of a spectrometer, the radiation energy-to-dose conversion function, and the geometrical factors, although the order of matrix operations is reversed. The new technique yields a result which is mathematically identical to the standard method while requiring no matrix manipulations or resolution matrix storage in the remote computer. It utilizes only a single function for each type dose required and each geometric factor involved.

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...

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)

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 framework.

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.

Epimorphin expression in interstitial pneumonia

PubMed Central

Terasaki, Yasuhiro; Fukuda, Yuh; Suga, Moritaka; Ikeguchi, Naoki; Takeya, Motohiro

2005-01-01

Epimorphin modulates epithelial morphogenesis in embryonic mouse organs. We previously suggested that epimorphin contributes to repair of bleomycin-induced pulmonary fibrosis in mice via epithelium-mesenchyme interactions. To clarify the role of epimorphin in human lungs, we evaluated epimorphin expression and localization in normal lungs, lungs with nonspecific interstitial pneumonia (NSIP), and lungs with usual interstitial pneumonia (UIP); we also studied the effect of recombinant epimorphin on cultured human alveolar epithelial cells in vitro. Northern and Western blotting analyses revealed that epimorphin expression in NSIP samples were significantly higher than those in control lungs and lungs with UIP. Immunohistochemistry showed strong epimorphin expression in mesenchymal cells of early fibrotic lesions and localization of epimorphin protein on mesenchymal cells and extracellular matrix of early fibrotic lesions in the nonspecific interstitial pneumonia group. Double-labeled fluorescent images revealed expression of matrix metalloproteinase 2 in re-epithelialized cells overlying epimorphin-positive early fibrotic lesions. Immunohistochemistry and metalloproteinase activity assay demonstrated augmented expression of metalloproteinase induced by recombinant epimorphin in human alveolar epithelial cells. These findings suggest that epimorphin contributes to repair of pulmonary fibrosis in nonspecific interstitial pneumonia, perhaps partly by inducing expression of matrix metalloproteinase 2, which is an important proteolytic factor in lung remodeling. PMID:15651999

Environmental impact assessment of the industrial estate development plan with the geographical information system and matrix methods.

PubMed

Ghasemian, Mohammad; Poursafa, Parinaz; Amin, Mohammad Mehdi; Ziarati, Mohammad; Ghoddousi, Hamid; Momeni, Seyyed Alireza; Rezaei, Amir Hossein

2012-01-01

The purpose of this study is environmental impact assessment of the industrial estate development planning. This cross-sectional study was conducted in 2010 in Isfahan province, Iran. GIS and matrix methods were applied. Data analysis was done to identify the current situation of the region, zoning vulnerable areas, and scoping the region. Quantitative evaluation was done by using matrix of Wooten and Rau. The net score for impact of industrial units operation on air quality of the project area was (-3). According to the transition of industrial estate pollutants, residential places located in the radius of 2500 meters of the city were expected to be affected more. The net score for impact of construction of industrial units on plant species of the project area was (-2). Environmental protected areas were not affected by the air and soil pollutants because of their distance from industrial estate. Positive effects of project activities outweigh the drawbacks and the sum scores allocated to the project activities on environmental factor was (+37). Totally it does not have detrimental effects on the environment and residential neighborhood. EIA should be considered as an anticipatory, participatory environmental management tool before determining a plan application.

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

The matrix effect in secondary ion mass spectrometry

NASA Astrophysics Data System (ADS)

Seah, M. P.; Shard, A. G.

2018-05-01

Matrix effects in the secondary ion mass spectrometry (SIMS) of selected elemental systems have been analyzed to investigate the applicability of a mathematical description of the matrix effect, called here the charge transfer (CT) model. This model was originally derived for proton exchange and organic positive secondary ions, to characterise the enhancement or suppression of intensities in organic binary systems. In the systems considered in this paper protons are specifically excluded, which enables an assessment of whether the model applies for electrons as well. The present importance is in organic systems but, here we analyse simpler inorganic systems. Matrix effects in elemental systems cannot involve proton transfer if there are no protons present but may be caused by electron transfer and so electron transfer may also be involved in the matrix effects for organic systems. There are general similarities in both the magnitudes of the ion intensities as well as the matrix effects for both positive and negative secondary ions in both systems and so the CT model may be more widely applicable. Published SIMS analyses of binary elemental mixtures are analyzed. The data of Kim et al., for the Pt/Co system, provide, with good precision, data for such a system. This gives evidence for the applicability of the CT model, where electron, rather than proton, transfer is the matrix enhancing and suppressing mechanism. The published data of Prudon et al., for the important Si/Ge system, provides further evidence for the effects for both positive and negative secondary ions and allows rudimentary rules to be developed for the enhancing and suppressing species.

New Factorization Techniques and Fast Serial and Parrallel Algorithms for Operational Space Control of Robot Manipulators

NASA Technical Reports Server (NTRS)

Fijany, Amir; Djouani, Karim; Fried, George; Pontnau, Jean

1997-01-01

In this paper a new factorization technique for computation of inverse of mass matrix, and the operational space mass matrix, as arising in implementation of the operational space control scheme, is presented.

Osteogenic potential of mesenchymal cells embedded in the provisional matrix after a 6-week healing period in augmented and non-augmented extraction sockets: an immunohistochemical prospective pilot study in humans.

PubMed

Heberer, Susanne; Wustlich, Alexander; Lage, Hermann; Nelson, John J; Nelson, Katja

2012-01-01

The aim of the present clinical study was the evaluation of the osteogenic potential of mesenchymal cells embedded in the provisional matrix of non-augmented and with Bio-Oss collagen-augmented human extraction sockets after 6 weeks of healing time. Twenty-five patients with 47 extraction sites participated in the present study. After tooth removal, the extraction sockets were augmented with Bio-Oss collagen or not augmented. At implant placement, bone biopsies of the extraction sockets were obtained. The immunohistochemical analysis of the osteogenic potential of the mesenchymal cells in the provisional matrix was performed using three monoclonal antibodies: core-binding factor α1 (Cbfa1)/runt-related protein (Runx)2, osteonectin (OSN/secreted protein acidic and rich in cyst [SPARC]) and osteocalcin (OC). The statistical analysis was performed using two-factorial analysis for repeated measures, Mann-Whitney U-test and Spearman's rank-order correlation coefficient. Of 47 extraction sockets examined, 17 sockets demonstrated an almost complete ossification. Hence, the provisional matrix of the 30 remaining extraction sockets (21 non-augmented, 9 augmented) was immunohistochemically investigated. No evidence of acute or chronic inflammation was noted in any of the specimens. In the provisional matrix of the non-grafted socket, the median amount of Cbfa1/Runx2-positive cells was 72.3%, of OSN (SPARC) 66.9% and of OC 23.4%, whereas in the grafted sockets the median rate of immunopositive cells staining with Cbfa1/Runx2 was 73.3%, of OSN (SPARC) 61.4% and of OC 20.1%. There was no significant difference in the proportion of positive cells expressed by Cbfa1/Runx2, OSN/SPARC and OC between the grafted and non-grafted socket. Furthermore, the cell density did not correlate to the quantity of stained cells independent of the used proteins. After a 6-week healing period, the provisional matrix was demonstrated to have a high proportion of cells displaying a maturation of mature osteoprogenitor cells to osteoblasts. The grafting procedure did not influence the quantity of osteogenic cells in the extraction socket. © 2011 John Wiley & Sons A/S.

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.

Trust in Leadership DEOCS 4.1 Construct Validity Summary

DTIC Science & Technology

2017-08-01

Item Corrected Item- Total Correlation Cronbach’s Alpha if Item Deleted Four-point Scale Items I can depend on my immediate supervisor to meet...1974) were used to assess the fit between the data and the factor. The BTS hypothesizes that the correlation matrix is an identity matrix. The...to reject the null hypothesis that the correlation matrix is an identity, and to conclude that the factor analysis is an appropriate method to

Metal chloride cathode for a battery

NASA Technical Reports Server (NTRS)

Bugga, Ratnakumar V. (Inventor); Distefano, Salvador (Inventor); Bankston, C. Perry (Inventor)

1991-01-01

A method of fabricating a rechargeable battery is disclosed which includes a positive electrode which contains a chloride of a selected metal when the electrode is in its active state. The improvement comprises fabricating the positive electrode by: providing a porous matrix composed of a metal; providing a solution of the chloride of the selected metal; and impregnating the matrix with the chloride from the solution.

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.

Transplantation of an alginate-matrigel matrix containing isolated ovarian cells: first step in developing a biodegradable scaffold to transplant isolated preantral follicles and ovarian cells.

PubMed

Vanacker, Julie; Luyckx, Valérie; Dolmans, Marie-Madeleine; Des Rieux, Anne; Jaeger, Jonathan; Van Langendonckt, Anne; Donnez, Jacques; Amorim, Christiani A

2012-09-01

For women diagnosed with leukemia, transplantation of cryopreserved ovarian tissue after disease remission is not advisable. Therefore, to restore fertility in these patients, we aim to develop a biodegradable artificial ovary that offers an environment where isolated follicles and ovarian cells (OCs) can survive and grow. Four NMRI mice were ovariectomized and their ovaries used to isolate OCs. Groups of 50,000 OCs were embedded in an alginate-matrigel matrix for further fixation (fresh controls), one week of in vitro culture (IVC) or heterotopic autografting. OC proliferation (Ki67), apoptosis (TUNEL), scaffold degradation, vessel formation (CD34) and inflammation (CD45) were analyzed. Ki67-positive OCs were found in 2.3%, 9.0% and 15.5% cells of cases in fresh, IVC and grafted beads respectively, while cells were TUNEL-positive in 0%, 1.5% and 6.9% of cases. After IVC or grafting, the beads degraded, losing their original round aspect, and infiltrating blood capillaries could be observed in the grafted beads. CD34-positive cells and 22% CD45-positive cells were found around and inside the matrix. In conclusion, our results demonstrate that an alginate-based matrix is a promising proposition to graft isolated OCs. After transplantation, this matrix was able to degrade, allowed vascularization and elicited a low inflammatory response. Copyright © 2012 Elsevier Ltd. All rights reserved.

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.

Transformed PANSS Factors Intended to Reduce Pseudospecificity Among Symptom Domains and Enhance Understanding of Symptom Change in Antipsychotic-Treated Patients With Schizophrenia

PubMed Central

Hopkins, Seth C; Ogirala, Ajay; Loebel, Antony; Koblan, Kenneth S

2018-01-01

Abstract Positive and Negative Syndrome Scale (PANSS) total score is the standard primary efficacy measure in acute treatment studies of schizophrenia. However, PANSS factors that have been derived from factor analytic approaches over the past several decades have uncertain clinical and regulatory status as they are, to varying degrees, intercorrelated. As a consequence of cross-factor correlations, the apparent improvement in key clinical domains (eg, negative symptoms, disorganized thinking/behavior) may largely be attributable to improvement in a related clinical domain, such as positive symptoms, a problem often referred to as pseudospecificity. Here, we analyzed correlations among PANSS items, at baseline and change post-baseline, in a pooled sample of 5 placebo-controlled clinical trials (N = 1710 patients), using clustering and factor analysis to identify an uncorrelated PANSS score matrix (UPSM) that minimized the degree of correlation between each resulting transformed PANSS factor. The transformed PANSS factors corresponded well with discrete symptom domains described by prior factor analyses, but between-factor change-scores correlations were markedly lower. We then used the UPSM to transform PANSS in data from 4657 unique schizophrenia patients included in 12 additional lurasidone clinical trials. The results confirmed that transformed PANSS factors retained a high degree of specificity, thus validating that low between-factor correlations are a reliable property of the USPM when transforming PANSS data from a variety of clinical trial data sets. These results provide a more robust understanding of the structure of symptom change in schizophrenia and suggest a means to evaluate the specificity of antipsychotic treatment effects. PMID:28981857

Bioengineering a highly vascularized matrix for the ectopic transplantation of islets

PubMed Central

Ellis, Cara E; Suuronen, Erik; Yeung, Telford; Seeberger, Karen; Korbutt, Gregory S

2013-01-01

Islet transplantation is a promising treatment for Type 1 diabetes; however limitations of the intra-portal site and poor revascularization of islets must be overcome. We hypothesize that engineering a highly vascularized collagen-based construct will allow islet graft survival and function in alternative sites. In this study, we developed such a collagen-based biomaterial. Neonatal porcine islets (NPIs) were embedded in collagen matrices crosslinked with 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide and N-hydroxysuccinimide containing combinations of chondroitin-6-sulfate, chitosan, and laminin, and compared with controls cultured in standard media. Islets were examined for insulin secretory activity after 24 h and 4 d and for apoptotic cell death and matrix integrity after 7 d in vitro. These same NPI/collagen constructs were transplanted subcutaneously in immunoincompetent B6.Rag−/− mice and then assessed for islet survival and vascularization. At all time points assessed during in vitro culture there were no significant differences in insulin secretory activity between control islets and those embedded in the collagen constructs, indicating that the collagen matrix had no adverse effect on islet function. Less cell death was observed in the matrix with all co-polymers compared with the other matrices tested. Immunohistochemical analysis of the grafts post-transplant confirmed the presence of intact insulin-positive islets; grafts were also shown to be vascularized by von Willebrand factor staining. This study demonstrates that a collagen, chondroitin-6-sulfate, chitosan, and laminin matrix supports islet function in vitro and moreover allows islet survival and vascularization post-transplantation; therefore, this bio-engineered vascularized construct is capable of supporting islet survival. PMID:24262950

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

A Deep Stochastic Model for Detecting Community in Complex Networks

NASA Astrophysics Data System (ADS)

Fu, Jingcheng; Wu, Jianliang

2017-01-01

Discovering community structures is an important step to understanding the structure and dynamics of real-world networks in social science, biology and technology. In this paper, we develop a deep stochastic model based on non-negative matrix factorization to identify communities, in which there are two sets of parameters. One is the community membership matrix, of which the elements in a row correspond to the probabilities of the given node belongs to each of the given number of communities in our model, another is the community-community connection matrix, of which the element in the i-th row and j-th column represents the probability of there being an edge between a randomly chosen node from the i-th community and a randomly chosen node from the j-th community. The parameters can be evaluated by an efficient updating rule, and its convergence can be guaranteed. The community-community connection matrix in our model is more precise than the community-community connection matrix in traditional non-negative matrix factorization methods. Furthermore, the method called symmetric nonnegative matrix factorization, is a special case of our model. Finally, based on the experiments on both synthetic and real-world networks data, it can be demonstrated that our algorithm is highly effective in detecting communities.

Angiogenesis in mucous retention cyst: a human in vivo-like model of endothelial cell differentiation in mucous substrate.

PubMed

Swelam, Wael; Ida-Yonemochi, Hiroko; Saku, Takashi

2005-01-01

Mucous retention cysts contain a mucous pool in the lumina, in which pure angiogenic processes are occasionally observed. By using this unique human material, our aim was to understand the in vivo angiogenic process. Fifteen surgical tissue samples of mucous retention cysts of the lip were examined for expression of vascular endothelial markers and extracellular matrix molecules by immunohistochemistry and in situ hybridization (ISH). Endothelial cells forming new vascular channels showed immunopositivities for CD31, CD34, vascular endothelial growth factor (VEGF), and von Willebrand factor (vWF). These newly formed capillaries were surrounded by tenascin-positive matrices and further by a dense infiltration of CD68-positive cells with foamy to epitheloid appearances. Some of these cells were simultaneously positive for CD34, VEGF, and one of its receptors, Flk-1, and they showed definite mRNA as well as protein signals for tenascin. In addition, these cells often tended to be aligned, which suggested tubule formation. The results suggest that monocyte/macrophage lineage cells are a major source for endothelial cells at least in mucous retention cysts and that tenascin produced by those cells plays an important role in differentiation of endothelial cells.

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

Parworth, Caroline; Tilp, Alison; Fast, Jerome

In this study the long-term trends of non-refractory submicrometer aerosol (NR-PM1) composition and mass concentration measured by an Aerosol Chemical Speciation Monitor (ACSM) at the Atmospheric Radiation Measurement (ARM) program's Southern Great Plains (SGP) site are discussed. NR-PM1 data was recorded at ~30 min intervals over a period of 19 months between November 2010 and June 2012. Positive Matrix Factorization (PMF) was performed on the measured organic mass spectral matrix using a rolling window technique to derive factors associated with distinct sources, evolution processes, and physiochemical properties. The rolling window approach also allows us to capture the dynamic variations ofmore » the chemical properties in the organic aerosol (OA) factors over time. Three OA factors were obtained including two oxygenated OA (OOA) factors, differing in degrees of oxidation, and a biomass burning OA (BBOA) factor. Back trajectory analyses were performed to investigate possible sources of major NR-PM1 species at the SGP site. Organics dominated NR-PM1 mass concentration for the majority of the study with the exception of winter, when ammonium nitrate increases due to transport of precursor species from surrounding urban and agricultural areas and also due to cooler temperatures. Sulfate mass concentrations have little seasonal variation with mixed regional and local sources. In the spring BBOA emissions increase and are mainly associated with local fires. Isoprene and carbon monoxide emission rates were obtained by the Model of Emissions of Gases and Aerosols from Nature (MEGAN) and the 2011 U.S. National Emissions Inventory to represent the spatial distribution of biogenic and anthropogenic sources, respectively. The combined spatial distribution of isoprene emissions and air mass trajectories suggest that biogenic emissions from the southeast contribute to SOA formation at the SGP site during the summer.« less

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.

Vortex manipulation in a superconducting matrix with view on applications

NASA Astrophysics Data System (ADS)

Milošević, M. V.; Peeters, F. M.

2010-05-01

We show how a single flux quantum can be effectively manipulated in a superconducting film with a matrix of blind holes. Such a sample can serve as a basic memory element, where the position of the vortex in a k ×l matrix of pinning sites defines the desired combination of n bits of information (2n=k×l). Vortex placement is achieved by strategically applied current and the resulting position is read out via generated voltage between metallic contacts on the sample. Such a device can also act as a controllable source of a nanoengineered local magnetic field for, e.g., spintronics applications.

Representation learning via Dual-Autoencoder for recommendation.

PubMed

Zhuang, Fuzhen; Zhang, Zhiqiang; Qian, Mingda; Shi, Chuan; Xie, Xing; He, Qing

2017-06-01

Recommendation has provoked vast amount of attention and research in recent decades. Most previous works employ matrix factorization techniques to learn the latent factors of users and items. And many subsequent works consider external information, e.g., social relationships of users and items' attributions, to improve the recommendation performance under the matrix factorization framework. However, matrix factorization methods may not make full use of the limited information from rating or check-in matrices, and achieve unsatisfying results. Recently, deep learning has proven able to learn good representation in natural language processing, image classification, and so on. Along this line, we propose a new representation learning framework called Recommendation via Dual-Autoencoder (ReDa). In this framework, we simultaneously learn the new hidden representations of users and items using autoencoders, and minimize the deviations of training data by the learnt representations of users and items. Based on this framework, we develop a gradient descent method to learn hidden representations. Extensive experiments conducted on several real-world data sets demonstrate the effectiveness of our proposed method compared with state-of-the-art matrix factorization based methods. Copyright © 2017 Elsevier Ltd. All rights reserved.

Postconcussive Symptoms in OEF-OIF Veterans: Factor Structure and Impact of Posttraumatic Stress

DTIC Science & Technology

2009-06-03

correlations between NSI full items are presented in Appendix A. Visual inspection of the correlation matrix, the Kaiser - Meyer - Olkin coefficient of .92, and...Spearman rho correlations between NSI residuals are pre- sented in Appendix B. Again, visual inspection of the correla- tion matrix, the Kaiser - Meyer ... Olkin coefficient of .83, and Bartlett’s test of sphericity (x2 5 1,936.0, p , .01) suggested that the matrix could be factored. Principal-components

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

A System for Discovering Bioengineered Threats by Knowledge Base Driven Mining of Toxin Data

DTIC Science & Technology

2004-08-01

RMSD cut - off and select a residue substitution matrix. The user is also allowed...in the sense that after super-positioning, the RMSD between the substructures is no more than the cut - off RMSD . * Residue substitutions are allowed...during super-positioning. Default RMSD cut - off and residue substitution matrix are provided. Users can specify their own RMSD cut - offs as well as

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.

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.

Selection of representative embankments based on rough set - fuzzy clustering method

NASA Astrophysics Data System (ADS)

Bin, Ou; Lin, Zhi-xiang; Fu, Shu-yan; Gao, Sheng-song

2018-02-01

The premise condition of comprehensive evaluation of embankment safety is selection of representative unit embankment, on the basis of dividing the unit levee the influencing factors and classification of the unit embankment are drafted.Based on the rough set-fuzzy clustering, the influence factors of the unit embankment are measured by quantitative and qualitative indexes.Construct to fuzzy similarity matrix of standard embankment then calculate fuzzy equivalent matrix of fuzzy similarity matrix by square method. By setting the threshold of the fuzzy equivalence matrix, the unit embankment is clustered, and the representative unit embankment is selected from the classification of the embankment.

3D tensor-based blind multispectral image decomposition for tumor demarcation

NASA Astrophysics Data System (ADS)

Kopriva, Ivica; Peršin, Antun

2010-03-01

Blind decomposition of multi-spectral fluorescent image for tumor demarcation is formulated exploiting tensorial structure of the image. First contribution of the paper is identification of the matrix of spectral responses and 3D tensor of spatial distributions of the materials present in the image from Tucker3 or PARAFAC models of 3D image tensor. Second contribution of the paper is clustering based estimation of the number of the materials present in the image as well as matrix of their spectral profiles. 3D tensor of the spatial distributions of the materials is recovered through 3-mode multiplication of the multi-spectral image tensor and inverse of the matrix of spectral profiles. Tensor representation of the multi-spectral image preserves its local spatial structure that is lost, due to vectorization process, when matrix factorization-based decomposition methods (such as non-negative matrix factorization and independent component analysis) are used. Superior performance of the tensor-based image decomposition over matrix factorization-based decompositions is demonstrated on experimental red-green-blue (RGB) image with known ground truth as well as on RGB fluorescent images of the skin tumor (basal cell carcinoma).

Engineering Human TMJ Discs with Protein-Releasing 3D-Printed Scaffolds.

PubMed

Legemate, K; Tarafder, S; Jun, Y; Lee, C H

2016-07-01

The temporomandibular joint (TMJ) disc is a heterogeneous fibrocartilaginous tissue positioned between the mandibular condyle and glenoid fossa of the temporal bone, with important roles in TMJ functions. Tissue engineering TMJ discs has emerged as an alternative approach to overcoming limitations of current treatments for TMJ disorders. However, the anisotropic collagen orientation and inhomogeneous fibrocartilaginous matrix distribution present challenges in the tissue engineering of functional TMJ discs. Here, we developed 3-dimensional (3D)-printed anatomically correct scaffolds with region-variant microstrand alignment, mimicking anisotropic collagen alignment in the TMJ disc and corresponding mechanical properties. Connective tissue growth factor (CTGF) and transforming growth factor beta 3 (TGFβ3) were then delivered in the scaffolds by spatially embedding CTGF- or TGFβ3-encapsulated microspheres (µS) to reconstruct the regionally variant fibrocartilaginous matrix in the native TMJ disc. When cultured with human mesenchymal stem/progenitor cells (MSCs) for 6 wk, 3D-printed scaffolds with CTGF/TGFβ3-µS resulted in a heterogeneous fibrocartilaginous matrix with overall distribution of collagen-rich fibrous structure in the anterior/posterior (AP) bands and fibrocartilaginous matrix in the intermediate zone, reminiscent of the native TMJ disc. High dose of CTGF/TGFβ3-µS (100 mg µS/g of scaffold) showed significantly more collagen II and aggrecan in the intermediate zone than a low dose (50 mg µS/g of scaffold). Similarly, a high dose of CTGF/TGFβ3-µS yielded significantly higher collagen I expression in the AP bands compared with the low-dose and empty µS. From stress relaxation tests, the ratio of relaxation modulus to instantaneous modulus was significantly smaller with CTGF/TGFβ3-µS than empty µS. Similarly, a significantly higher coefficient of viscosity was achieved with the high dose of CTGF/TGFβ3-µS compared with the low-dose and empty µS, suggesting the dose effect of CTGF and TGFβ3 on fibrocartilage formation. Together, our findings may represent an efficient approach to engineering the TMJ disc graft with anisotropic scaffold microstructure, heterogeneous fibrocartilaginous matrix, and region-dependent viscoelastic properties. © International & American Associations for Dental Research 2016.

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.

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.

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

Understanding the pathogenesis of abdominal aortic aneurysms

PubMed Central

Kuivaniemi, Helena; Ryer, Evan J.; Elmore, James R.; Tromp, Gerard

2016-01-01

Summary An aortic aneurysm is a dilatation in which the aortic diameter is ≥ 3.0 cm. If left untreated, the aortic wall continues to weaken and becomes unable to withstand the forces of the luminal blood pressure resulting in progressive dilatation and rupture, a catastrophic event associated with a mortality of 50 – 80%. Smoking and positive family history are important risk factors for the development of abdominal aortic aneurysms (AAA). Several genetic risk factors have also been identified. On the histological level, visible hallmarks of AAA pathogenesis include inflammation, smooth muscle cell apoptosis, extracellular matrix degradation, and oxidative stress. We expect that large genetic, genomic, epigenetic, proteomic and metabolomic studies will be undertaken by international consortia to identify additional risk factors and biomarkers, and to enhance our understanding of the pathobiology of AAA. Collaboration between different research groups will be important in overcoming the challenges to develop pharmacological treatments for AAA. PMID:26308600

Weighted graph based ordering techniques for preconditioned conjugate gradient methods

NASA Technical Reports Server (NTRS)

Clift, Simon S.; Tang, Wei-Pai

1994-01-01

We describe the basis of a matrix ordering heuristic for improving the incomplete factorization used in preconditioned conjugate gradient techniques applied to anisotropic PDE's. Several new matrix ordering techniques, derived from well-known algorithms in combinatorial graph theory, which attempt to implement this heuristic, are described. These ordering techniques are tested against a number of matrices arising from linear anisotropic PDE's, and compared with other matrix ordering techniques. A variation of RCM is shown to generally improve the quality of incomplete factorization preconditioners.

Temperature effects on ash physical and chemical properties. A laboratory study.

NASA Astrophysics Data System (ADS)

Pereira, Paulo; Úbeda, Xavier; Martin, Deborah

2010-05-01

Fire temperatures have different impacts on ash physical and chemical properties that depend mainly of the specie affected and time of exposition. In a real prescribed or wildland fire, the temperatures produce ash with different characteristics. Know the impacts of a specific temperature or a gradient on a certain element and specie is very difficult in real fires, especially in wildland fires, where temperatures achieve higher values and the burning conditions are not controlled. Hence, laboratory studies revealed to be an excellent methodology to understand the effects of fire temperatures in ash physical and chemical. The aim of this study is study the effects of a temperature gradient (150, 200, 250, 300, 350, 400, 450, 500 and 550°C) on ash physical and chemical properties. For this study we collected litter of Quercus suber, Pinus pinea and Pinus pinaster in a plot located in Portugal. The selected species are the most common in the ecosystem. We submitted samples to the mentioned temperatures throughout a time of two hours and we analysed several parameters, namely, Loss on Ignition (LOI%), ash colour - through the Croma Value (CV) observed in Munsell color chart - CaCO3, Total Nitrogen (TN), Total Carbon (TC), C/N ratio, ash pH, Electrical Conductivity (EC), extractable Calcium (Ca2+), Magnesium (Mg2+), Sodium (Na+), Potassium (K+), Aluminium (Al3+), Manganese (Mn2+), Iron (Fe2+), Zinc (Zn2+), Total Phosphorous (TP), Sulphur (S) and Silica (SiO2). Since we considered many elements, in order to obtain a better explanation of all dataset, we applied a Factorial Analysis (FA), based on the correlation matrix and the Factors were extracted according to the Principle Components method. To obtain a better relation between the variables with a specific Factor we rotated the matrix according to the VARIMAX NORMALIZED method. FA identified 5 Factors that explained a total of 95% of the variance. We retained in each Factor the variables that presented an eigenvalue >0.7. Factor 1 explained the majority of the variance (60.05%). LOI(%), CV, CaCO3, pH, Na+, K+, S (these last tree elements only in both Pinus) and SiO2, showed positive loadings. Inversely, TC, C/N ratio, Al3+, Fe2+ (these last tree elements for Quercus suber and Pinus pinaster ash) and Mn2+ (In the case of Quercus suber) presented negative loadings. Factor 2 explained 19.89% of the variance and showed higher loadings in TN, Ca2+ and Mg2+ (in the case of the ions only in both Pinus). Factor 3 explains only 6.69% of the variance and we identified higher loadings in Mg2+, Na+ and K+ of Quercus suber. Factor 4 explains less then the last Factor, only 4.60% of the variance and presented negative loadings above -0.7 in TP of Quercus suber and Pinus pinea. Factor 5 explained 3.93% of the variance, less than all other Factors and showed in Al3+, Mn2+ and Zn2+ of Pinus pinea and in the case of the last element, also in Pinus pinaster. The observation of the scores matrix allowed us to understand the major concentration of these elements according the temperature of exposition. Hence, the elements that showed higher positive loadings in Factor 1, have a major concentration at 450, 500 and 550°C, and the ones with higher negative loadings presented higher concentration at 200 and 250°C. The nutrients that presented higher positive loadings in Factor 2 have higher concentrations at 400°C. The elements with higher positive loadings in Factor 3 have bigger amounts in the ash slurries produced at 350°C and the ones with higher negative loadings in the Factor 4 showed greater concentrations in the ash produced at 300°C. The elements with higher negative loadings in the Factor 5 showed higher amounts in the ash created at 150°C of exposition. The results obtained showed that nutrients concentration is a function of the burned specie and temperature reached in the considered exposure time. Micronutrients and TC and C/N showed higher values at lower temperatures, TN, Ca2+, Mg2+ and TP at temperatures between 300-400°C. The other variables in study have major concentrations at temperatures higher than 450°C. Some differences between species can be identified and this is a result of the different litter vulnerabilities to the same temperature, producing diverse fire severities. This and other reasons for this behaviour will be discussed in the communication.

PWMScan: a fast tool for scanning entire genomes with a position-specific weight matrix.

PubMed

Ambrosini, Giovanna; Groux, Romain; Bucher, Philipp

2018-03-05

Transcription factors (TFs) regulate gene expression by binding to specific short DNA sequences of 5 to 20-bp to regulate the rate of transcription of genetic information from DNA to messenger RNA. We present PWMScan, a fast web-based tool to scan server-resident genomes for matches to a user-supplied PWM or TF binding site model from a public database. The web server and source code are available at http://ccg.vital-it.ch/pwmscan and https://sourceforge.net/projects/pwmscan, respectively. giovanna.ambrosini@epfl.ch. SUPPLEMENTARY DATA ARE AVAILABLE AT BIOINFORMATICS ONLINE.

Growth factor transgenes interactively regulate articular chondrocytes.

PubMed

Shi, Shuiliang; Mercer, Scott; Eckert, George J; Trippel, Stephen B

2013-04-01

Adult articular chondrocytes lack an effective repair response to correct damage from injury or osteoarthritis. Polypeptide growth factors that stimulate articular chondrocyte proliferation and cartilage matrix synthesis may augment this response. Gene transfer is a promising approach to delivering such factors. Multiple growth factor genes regulate these cell functions, but multiple growth factor gene transfer remains unexplored. We tested the hypothesis that multiple growth factor gene transfer selectively modulates articular chondrocyte proliferation and matrix synthesis. We tested the hypothesis by delivering combinations of the transgenes encoding insulin-like growth factor I (IGF-I), fibroblast growth factor-2 (FGF-2), transforming growth factor beta1 (TGF-β1), bone morphogenetic protein-2 (BMP-2), and bone morphogenetic protien-7 (BMP-7) to articular chondrocytes and measured changes in the production of DNA, glycosaminoglycan, and collagen. The transgenes differentially regulated all these chondrocyte activities. In concert, the transgenes interacted to generate widely divergent responses from the cells. These interactions ranged from inhibitory to synergistic. The transgene pair encoding IGF-I and FGF-2 maximized cell proliferation. The three-transgene group encoding IGF-I, BMP-2, and BMP-7 maximized matrix production and also optimized the balance between cell proliferation and matrix production. These data demonstrate an approach to articular chondrocyte regulation that may be tailored to stimulate specific cell functions, and suggest that certain growth factor gene combinations have potential value for cell-based articular cartilage repair. Copyright © 2012 Wiley Periodicals, Inc.

Leukocyte- and platelet-rich fibrin (L-PRF) for long-term delivery of growth factor in rotator cuff repair: review, preliminary results and future directions.

PubMed

Zumstein, Matthias A; Berger, Simon; Schober, Martin; Boileau, Pascal; Nyffeler, Richard W; Horn, Michael; Dahinden, Clemens A

2012-06-01

Surgical repair of the rotator cuff repair is one of the most common procedures in orthopedic surgery. Despite it being the focus of much research, the physiological tendon-bone insertion is not recreated following repair and there is an anatomic non-healing rate of up to 94%. During the healing phase, several growth factors are upregulated that induce cellular proliferation and matrix deposition. Subsequently, this provisional matrix is replaced by the definitive matrix. Leukocyte- and platelet-rich fibrin (L-PRF) contain growth factors and has a stable dense fibrin matrix. Therefore, use of LPRF in rotator cuff repair is theoretically attractive. The aim of the present study was to determine 1) the optimal protocol to achieve the highest leukocyte content; 2) whether L-PRF releases growth factors in a sustained manner over 28 days; 3) whether standard/gelatinous or dry/compressed matrix preparation methods result in higher growth factor concentrations. 1) The standard L-PRF centrifugation protocol with 400 x g showed the highest concentration of platelets and leukocytes. 2) The L-PRF clots cultured in medium showed a continuous slow release with an increase in the absolute release of growth factors TGF-β1, VEGF and MPO in the first 7 days, and for IGF1, PDGF-AB and platelet activity (PF4=CXCL4) in the first 8 hours, followed by a decrease to close to zero at 28 days. Significantly higher levels of growth factor were expressed relative to the control values of normal blood at each culture time point. 3) Except for MPO and the TGFβ-1, there was always a tendency towards higher release of growth factors (i.e., CXCL4, IGF-1, PDGF-AB, and VEGF) in the standard/gelatinous- compared to the dry/compressed group. L-PRF in its optimal standard/gelatinous-type matrix can store and deliver locally specific healing growth factors for up to 28 days and may be a useful adjunct in rotator cuff repair.

Risk Management using Dependency Stucture Matrix

NASA Astrophysics Data System (ADS)

Petković, Ivan

2011-09-01

An efficient method based on dependency structure matrix (DSM) analysis is given for ranking risks in a complex system or process whose entities are mutually dependent. This rank is determined according to the element's values of the unique positive eigenvector which corresponds to the matrix spectral radius modeling the considered engineering system. For demonstration, the risk problem of NASA's robotic spacecraft is analyzed.

A density functional approach to ferrogels

NASA Astrophysics Data System (ADS)

Cremer, P.; Heinen, M.; Menzel, A. M.; Löwen, H.

2017-07-01

Ferrogels consist of magnetic colloidal particles embedded in an elastic polymer matrix. As a consequence, their structural and rheological properties are governed by a competition between magnetic particle-particle interactions and mechanical matrix elasticity. Typically, the particles are permanently fixed within the matrix, which makes them distinguishable by their positions. Over time, particle neighbors do not change due to the fixation by the matrix. Here we present a classical density functional approach for such ferrogels. We map the elastic matrix-induced interactions between neighboring colloidal particles distinguishable by their positions onto effective pairwise interactions between indistinguishable particles similar to a ‘pairwise pseudopotential’. Using Monte-Carlo computer simulations, we demonstrate for one-dimensional dipole-spring models of ferrogels that this mapping is justified. We then use the pseudopotential as an input into classical density functional theory of inhomogeneous fluids and predict the bulk elastic modulus of the ferrogel under various conditions. In addition, we propose the use of an ‘external pseudopotential’ when one switches from the viewpoint of a one-dimensional dipole-spring object to a one-dimensional chain embedded in an infinitely extended bulk matrix. Our mapping approach paves the way to describe various inhomogeneous situations of ferrogels using classical density functional concepts of inhomogeneous fluids.

Gas chromatography/matrix-isolation apparatus

DOEpatents

Reedy, G.T.

1986-06-10

A gas-sample collection device provides matrix isolation of individual gas bands from a gas chromatographic separation and for the spectroscopic analysis of the individual sample bands. The device includes a vacuum chamber containing a rotatably supported, specular carousel having at least one reflecting surface for holding a sample deposited thereon. A gas inlet is provided for depositing a mixture of sample and matrix material on the reflecting surface which is maintained at a sufficiently low temperature to cause solidification. A first parabolic mirror directs an incident beam of electromagnetic radiation, such as in the infrared (IR) spectrum, from a source onto the sample/matrix mixture while a second parabolic mirror directs a second beam of electromagnetic radiation reflected by the specular surface to an IR spectrometer for determining the absorption spectra of the sample material deposited on the reflecting surface. The pair of off-axis parabolic mirrors having a common focal point are positioned outside of the vacuum chamber and may be displaced in combination for improved beam positioning and alignment. The carousel is provided with an aperture for each reflecting surface to facilitate accurate positioning of the incident beam relative to the gas-samples under analysis. Improved gas-sample deposition is insured by the use of a long focal length stereomicroscope positioned outside of the vacuum chamber for monitoring sample formation through a window, while the sample collector is positioned outside of the zone bounded by the incident and reflected electromagnetic beams for improved sample access and monitoring. 10 figs.

Gas chromatography/matrix-isolation apparatus

DOEpatents

Reedy, Gerald T.

1986-01-01

A gas-sample collection device provides matrix isolation of individual gas bands from a gas chromatographic separation and for the spectroscopic analysis of the individual sample bands. The device includes a vacuum chamber containing a rotatably supported, specular carousel having at least one reflecting surface for holding a sample deposited thereon. A gas inlet is provided for depositing a mixture of sample and matrix material on the reflecting surface which is maintained at a sufficiently low temperature to cause solidification. A first parabolic mirror directs an incident beam of electromagnetic radiation, such as in the infrared (IR) spectrum, from a source onto the sample/matrix mixture while a second parabolic mirror directs a second beam of electromagnetic radiation reflected by the specular surface to an IR spectrometer for determining the absorption spectra of the sample material deposited on the reflecting surface. The pair of off-axis parabolic mirrors having a common focal point are positioned outside of the vacuum chamber and may be displaced in combination for improved beam positioning and alignment. The carousel is provided with an aperture for each reflecting surface to facilitate accurate positioning of the incident beam relative to the gas-samples under analysis. Improved gas-sample deposition is insured by the use of a long focal length stereomicroscope positioned outside of the vacuum chamber for monitoring sample formation through a window, while the sample collector is positioned outside of the zone bounded by the incident and reflected electromagnetic beams for improved sample access and monitoring.

Manifold Preserving: An Intrinsic Approach for Semisupervised Distance Metric Learning.

PubMed

Ying, Shihui; Wen, Zhijie; Shi, Jun; Peng, Yaxin; Peng, Jigen; Qiao, Hong

2017-05-18

In this paper, we address the semisupervised distance metric learning problem and its applications in classification and image retrieval. First, we formulate a semisupervised distance metric learning model by considering the metric information of inner classes and interclasses. In this model, an adaptive parameter is designed to balance the inner metrics and intermetrics by using data structure. Second, we convert the model to a minimization problem whose variable is symmetric positive-definite matrix. Third, in implementation, we deduce an intrinsic steepest descent method, which assures that the metric matrix is strictly symmetric positive-definite at each iteration, with the manifold structure of the symmetric positive-definite matrix manifold. Finally, we test the proposed algorithm on conventional data sets, and compare it with other four representative methods. The numerical results validate that the proposed method significantly improves the classification with the same computational efficiency.

Factor Analysis by Generalized Least Squares.

ERIC Educational Resources Information Center

Joreskog, Karl G.; Goldberger, Arthur S.

Aitkin's generalized least squares (GLS) principle, with the inverse of the observed variance-covariance matrix as a weight matrix, is applied to estimate the factor analysis model in the exploratory (unrestricted) case. It is shown that the GLS estimates are scale free and asymptotically efficient. The estimates are computed by a rapidly…

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...

UDU/T/ covariance factorization for Kalman filtering

NASA Technical Reports Server (NTRS)

Thornton, C. L.; Bierman, G. J.

1980-01-01

There has been strong motivation to produce numerically stable formulations of the Kalman filter algorithms because it has long been known that the original discrete-time Kalman formulas are numerically unreliable. Numerical instability can be avoided by propagating certain factors of the estimate error covariance matrix rather than the covariance matrix itself. This paper documents filter algorithms that correspond to the covariance factorization P = UDU(T), where U is a unit upper triangular matrix and D is diagonal. Emphasis is on computational efficiency and numerical stability, since these properties are of key importance in real-time filter applications. The history of square-root and U-D covariance filters is reviewed. Simple examples are given to illustrate the numerical inadequacy of the Kalman covariance filter algorithms; these examples show how factorization techniques can give improved computational reliability.

Quantum-inspired algorithm for estimating the permanent of positive semidefinite matrices

NASA Astrophysics Data System (ADS)

Chakhmakhchyan, L.; Cerf, N. J.; Garcia-Patron, R.

2017-08-01

We construct a quantum-inspired classical algorithm for computing the permanent of Hermitian positive semidefinite matrices by exploiting a connection between these mathematical structures and the boson sampling model. Specifically, the permanent of a Hermitian positive semidefinite matrix can be expressed in terms of the expected value of a random variable, which stands for a specific photon-counting probability when measuring a linear-optically evolved random multimode coherent state. Our algorithm then approximates the matrix permanent from the corresponding sample mean and is shown to run in polynomial time for various sets of Hermitian positive semidefinite matrices, achieving a precision that improves over known techniques. This work illustrates how quantum optics may benefit algorithm development.

Fuel cell having electrolyte

DOEpatents

Wright, Maynard K.

1989-01-01

A fuel cell having an electrolyte control volume includes a pair of porous opposed electrodes. A maxtrix is positioned between the pair of electrodes for containing an electrolyte. A first layer of backing paper is positioned adjacent to one of the electrodes. A portion of the paper is substantially previous to the acceptance of the electrolyte so as to absorb electrolyte when there is an excess in the matrix and to desorb electrolyte when there is a shortage in the matrix. A second layer of backing paper is positioned adjacent to the first layer of paper and is substantially impervious to the acceptance of electrolyte.

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 and negative degree; (3) though the binary DDI network contains no information about enhancive and degressive DDIs at all, it implies some of their relationship in the comprehensive DDI matrix; (4) the occurrence of signs indicating enhancive and degressive DDIs is not random because the comprehensive DDI network is equipped with a structural balance.

Do factors in the psychosocial work environment mediate the effect of socioeconomic position on the risk of myocardial infarction? Study from the Copenhagen Centre for Prospective Population Studies

PubMed Central

Andersen, I; Burr, H; Kristensen, T; Gamborg, M; Osler, M; Prescott, E; Diderichsen, F

2004-01-01

Aim: To investigate whether the effect of socioeconomic position on risk of myocardial infarction (MI) is mediated by differential exposure or differential susceptibility to psychosocial work environment. Methods: Data were used from three prospective population studies conducted in Copenhagen. A total of 16 214 employees, 44% women, aged 20–75 years, with initial examination between 1974 and 1992 were followed until 1996 for incident (hospital admission or death) MI. Register based information on job categories was used. Psychosocial job exposures were measured indirectly by means of a job exposure matrix based on the Danish Work Environment Cohort Study 1990. Results: During follow up, 731 subjects were diagnosed with an MI: 610 men and 121 women (35% fatal). The hazards by socioeconomic position showed a graded effect with a hazard ratio (HR) of 1.57 (95% CI 1.23 to 2.03) for unskilled workers compared to executive managers. Despite a strong and graded association in risk of MI related to decision authority and skill discretion, only skill discretion mediated the effect of socioeconomic position. The HR for unskilled workers was reduced to 1.47 (0.93 to 2.31) after adjustment for decision authority and other cardiovascular risk factors, and to 1.07 (0.72 to 1.60) after adjustment for skill discretion and cardiovascular risk factors. No sign of synergy was found. Conclusions: Decision authority and skill discretion were strongly related to socioeconomic position; and the effect on risk of MI was partially mediated by skill discretion. Improvements in psychosocial work environment, especially possibilities for skill discretion, might contribute to reducing the incidence of MI and social inequality in MI. PMID:15477281

ECM microenvironment unlocks brown adipogenic potential of adult human bone marrow-derived MSCs.

PubMed

Lee, Michelle H; Goralczyk, Anna G; Kriszt, Rókus; Ang, Xiu Min; Badowski, Cedric; Li, Ying; Summers, Scott A; Toh, Sue-Anne; Yassin, M Shabeer; Shabbir, Asim; Sheppard, Allan; Raghunath, Michael

2016-02-17

Key to realizing the diagnostic and therapeutic potential of human brown/brite adipocytes is the identification of a renewable, easily accessible and safe tissue source of progenitor cells, and an efficacious in vitro differentiation protocol. We show that macromolecular crowding (MMC) facilitates brown adipocyte differentiation in adult human bone marrow mesenchymal stem cells (bmMSCs), as evidenced by substantially upregulating uncoupling protein 1 (UCP1) and uncoupled respiration. Moreover, MMC also induced 'browning' in bmMSC-derived white adipocytes. Mechanistically, MMC creates a 3D extracellular matrix architecture enshrouding maturing adipocytes in a collagen IV cocoon that is engaged by paxillin-positive focal adhesions also at the apical side of cells, without contact to the stiff support structure. This leads to an enhanced matrix-cell signaling, reflected by increased phosphorylation of ATF2, a key transcription factor in UCP1 regulation. Thus, tuning the dimensionality of the microenvironment in vitro can unlock a strong brown potential dormant in bone marrow.

Serum matrix metalloproteinase 3 in detecting remitting seronegative symmetrical synovitis with pitting edema syndrome: A case report.

PubMed

Kenzaka, Tsuneaki; Goda, Ken

2018-05-16

We report a case of remitting seronegative symmetrical synovitis with pitting edema (RS3PE) syndrome in a 71-year-old woman. She referred to our hospital with finger stiffness, edema of both hands and feet, pain of bilateral shoulder, wrist, metacarpophalangeal, proximal interphalangeal, and ankle joints. Rheumatoid factor was negative, human leukocyte antigen -B7 antigen was positive. Moreover, matrix metalloproteinase 3 (MMP-3) was high. She was diagnosed with RS3PE syndrome, and treatment with prednisolone (15 mg/d) was started. One week after prednisolone treatment initiation, CRP decreased to negative, and joint pain was almost completely resolved. However, hand stiffness persisted, and MMP-3 level was still high. Thus, prednisolone dose was increased to 20 mg/d, and the stiffness resolved. Twenty days after treatment initiation, MMP-3 was normalized. MMP-3 was more indicative of RS3PE syndrome symptoms than CRP. Thus, MMP-3 seems to be more sensitive to RS3PE syndrome symptoms.

Serum matrix metalloproteinase 3 in detecting remitting seronegative symmetrical synovitis with pitting edema syndrome: A case report

PubMed Central

Kenzaka, Tsuneaki; Goda, Ken

2018-01-01

We report a case of remitting seronegative symmetrical synovitis with pitting edema (RS3PE) syndrome in a 71-year-old woman. She referred to our hospital with finger stiffness, edema of both hands and feet, pain of bilateral shoulder, wrist, metacarpophalangeal, proximal interphalangeal, and ankle joints. Rheumatoid factor was negative, human leukocyte antigen -B7 antigen was positive. Moreover, matrix metalloproteinase 3 (MMP-3) was high. She was diagnosed with RS3PE syndrome, and treatment with prednisolone (15 mg/d) was started. One week after prednisolone treatment initiation, CRP decreased to negative, and joint pain was almost completely resolved. However, hand stiffness persisted, and MMP-3 level was still high. Thus, prednisolone dose was increased to 20 mg/d, and the stiffness resolved. Twenty days after treatment initiation, MMP-3 was normalized. MMP-3 was more indicative of RS3PE syndrome symptoms than CRP. Thus, MMP-3 seems to be more sensitive to RS3PE syndrome symptoms. PMID:29774220

Self-sensing of elastic strain, matrix yielding and plasticity in multiwall carbon nanotube/vinyl ester composites

NASA Astrophysics Data System (ADS)

Ku-Herrera, J. J.; Avilés, F.; Seidel, G. D.

2013-08-01

The piezoresistive response of multiwalled carbon nanotube/vinyl ester composites containing 0.3, 0.5 and 1% w/w carbon nanotubes (CNTs) loaded in tension and compression is investigated. The change in electrical resistance (ΔR) under tension loading was positive and showed a linear relationship with the applied strain up to failure, with slightly increased sensitivity for decreased CNT content. In compression, a nonlinear and non-monotonic piezoresistive behavior was observed, with ΔR initially decreasing in the elastic regime, leveling off at the onset of yielding and increasing after matrix yielding. The piezoresistive response of the composite is more sensitive to the CNT content for compression than for tension, and the calculated gage factors are higher in the compressive plastic regime. The results show that the piezoresistive signal is dependent on the CNT concentration, loading type and material elastoplastic behavior, and that recording ΔR during mechanical loading can allow self-identification of the elastic and plastic regimes of the composite.

Realizability of a model in infinite statistics

NASA Astrophysics Data System (ADS)

Zagier, Don

1992-06-01

Following Greenberg and others, we study a space with a collection of operators a(k) satisfying the “ q-mutator relations” a(l)a † (k)a(l)=δ k,l (corresponding for q=±1 to classical Bose and Fermi statistics). We show that the n!×n! matrix A n (q) representing the scalar products of n-particle states is positive definite for all n if q lies between -1 and +1, so that the commutator relations have a Hilbert space representation in this case (this has also been proved by Fivel and by Bozejko and Speicher). We also give an explicit factorization of A n (q) as a product of matrices of the form (1-q jT)±1 with 1≦ j≦ n and T a permutation matrix. In particular, A n (q) is singular if and only if q M=1 for some integer M of the form k 2- k, 2≦ k≦ n.

Insulin and insulin-like growth factor-1 induce pronounced hypertrophy of skeletal myofibers in tissue culture

NASA Technical Reports Server (NTRS)

Vandenburgh, Herman H.; Karlisch, Patricia; Shansky, Janet

1990-01-01

Skeletal myofibers differentiated from primary avian myoblasts in tissue culture can be maintained in positive nitrogen balance in a serum-free medium for at least 6 to 7 days when embedded in a three dimensional collagen gel matrix. The myofibers are metabolically sensitive to physiological concentrations of insulin but these concentrations do not stimulate cell growth. Higher insulin concentrations stimulate both cell hyperplasia and myofiber hypertrophy. Cell growth results from a long term 42 percent increase in total protein synthesis and a 38 percent increase in protein degradation. Myofiber diameters increase by 71 to 98 percent after 6 to 7 days in insulin-containing medium. Insulin-like growth factor-1 but not insulin-like growth factor-2, at 250 ng/ml, is as effective as insulin in stimulating cell hyperplasia and myofiber hypertrophy. This model system provides a new method for studying the long-term anabolic effects of insulin and insulin-like growth factors on myofiber hypertrophy under defined tissue culture conditions.

Orthogonal Simulation Experiment for Flow Characteristics of Ore in Ore Drawing and Influencing Factors in a Single Funnel Under a Flexible Isolation Layer

NASA Astrophysics Data System (ADS)

Chen, Qingfa; Zhao, Fuyu; Chen, Qinglin; Wang, Yuding; Zhong, Yu; Niu, Wenjing

2017-12-01

A study on the flow characteristics of ore and factors that influence these characteristics is important to master ore flow laws. An orthogonal ore-drawing numerical model was established and the flow characteristics were explored. A weight matrix was obtained and the effect of the factors was determined. It was found that (1) the entire isolation-layer interface presents a Gaussian curve morphology and marked particles in each layer show a funnel morphology; (2) the drawing amount, Q, and the isolation layer half-width, W, are correlated positively with the fall depth, H, of the isolation layer; (3) factors that affect the characteristics sequentially include the particle friction coefficient, the interface friction coefficient, the isolation layer thickness, and the particle radius, and (4) the optimal combination is an isolation layer thickness of 0.005 m, an interface friction coefficient of 0.8, a particle friction coefficient of 0.2, and a particle radius of 0.007 m.

Factorization and fitting of molecular scattering information

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

Goldflam, R.; Kouri, D.J.; Green, S.

1977-12-15

The factorization of cross sections of various kinds resulting from the infinite order sudden approximation is considered in detail. Unlike the earlier study of Goldflam, Green, and Kouri, we base the present analysis on the factored IOS T-matrix rather than on the S-matrix. This enables us to obtain somewhat simpler expressions. For example, we show that the factored IOS approximation to the Arthurs--Dalgarno T-matrix involves products of dynamical coefficients T/sup L//sub l/ and Percival--Seaton coefficients f/sub L/(jlvertical-barj/sub 0/l/sub 0/vertical-barJ). It is shown that an optical theorem exists for the T/sub l//sup L/ dynamical coefficients of the T-matrix. The differential scatteringmore » amplitudes are shown to factor into dynamical coefficients q/sub L/(chi) times spectroscopic factors that are independent of the dynamics (potential). Then a generalized form of the Parker--Pack result for ..sigma../sub j/(dsigma/dR)(j/sub 0/..-->..j) is derived. It is also shown that the IOS approximation for (dsigma/dR)(j/sub 0/..-->..j) factors into sums of spectroscopic coefficients times the differential cross sections out of j/sub 0/=0. The IOS integral cross sections factor into spectroscopic coefficients times the integral cross sections out of j/sub 0/=0. The factored IOS general phenomenological cross sections are rederived using the T-matrix approach and are shown to equal sums of Percival--Seaton coefficients timesthe inelastic integral cross section out of initial rotor state j/sub 0/ = 0. This suggests that experimental measurements of line shapes and/or NMR spin--lattice relaxation can be used to directly give inelastic state-to-state degeneracy averaged integral cross sections whenever the IOS is a good approximation. Factored IOS expressions for viscosity and diffusion are derived and shown to potentially yield additional information beyond that contained in line shapes.« less

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.

Fibronectin alters the rate of formation and structure of the fibrin matrix.

PubMed

Ramanathan, Anand; Karuri, Nancy

2014-01-10

Plasma fibronectin is a vital component of the fibrin clot; however its role on clot structure is not clearly understood. The goal of this study was to examine the influence of fibronectin on the kinetics of formation, structural characteristics and composition of reconstituted fibrin clots or fibrin matrices. Fibrin matrices were formed by adding thrombin to 1, 2 or 4 mg/ml fibrinogen supplemented with 0-0.4 mg/ml fibronectin. The rate of fibrin matrix formation was then monitored by measuring light absorbance properties at different time points. Confocal microscopy of fluorescein conjugated fibrinogen was used to visualize the structural characteristics of fibrin matrices. The amount of fibronectin in fibrin matrices was determined through electrophoresis and immunoblotting of solubilized matrices. Fibronectin concentration positively correlated with the initial rate of fibrin matrix formation and with steady state light absorbance values of fibrin matrices. An increase in fibronectin concentration resulted in thinner and denser fibers in the fibrin matrices. Electrophoresis and immunoblotting showed that fibronectin was covalently and non-covalently bound to fibrin matrices and in the form of high molecular weight multimers. The formation of fibronectin multimers was attributed to cross-linking of fibronectin by trace amounts Factor XIIIa. These findings are novel because they link results from light absorbance studies to microcopy analyses and demonstrate an influence of fibronectin on fibrin matrix structural characteristics. This data is important in developing therapies that destabilize fibrin clots. Copyright © 2014. Published by Elsevier Inc.

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.

Tumor grade and matrix metalloproteinase 2 expression in stromal fibroblasts help to stratify the high-risk group of patients with early breast cancer identified on the basis of st Gallen recommendations.

PubMed

Niemiec, Joanna; Adamczyk, Agnieszka; Małecki, Krzysztof; Ambicka, Aleksandra; Ryś, Janusz

2013-04-01

It is still being discussed if the assessment of basal markers or if adhesion molecules expression contributes additional prognostic information to the classic prognostic factors and hence should be included into standard morphologic reports. The aim of the study was to assess the prognostic significance of: (i) classification recommended by St Gallen experts (ii) tumor grade, expression of (iii) basal markers, (iv) adhesion molecules, and (v) matrix metalloproteinase 2 (MMP-2) in patients with T1-T2 N0M0 chemotherapy-naive ductal breast cancer. In 79 patients with tumors characterized by estrogen receptor (ER) and progesterone receptor (PgR) positive, human epidermal growth factor receptor 2 negative (HER2) phenotype and MIB-1 labeling index (MIB-l) LI ≤ 15% (low-risk group) cumulative 17-year breast cancer-specific survival probability was 100% and was significantly higher than in 95 patients from the high-risk group (ER(-)/PgR(-)/HER2(-) or HER2(+) or MIB-1 LI > 15%) (72.5%). We found that MMP-2 fibroblast expression indicated 2 subgroups with significantly different survival rates in women with grade 3 tumor (88.9% for MMP-2 positivity and 56.0% for negativity). Cox multivariate analysis revealed that both grade 3 combined with stromal fibroblast MMP-2(-) and a high-risk group according to St Gallen recommendations are independent negative prognostic factors that influence survival of patients with breast cancer. To the best of our knowledge, we have shown for the first time that MMP-2(-) in stromal fibroblasts might indicate poor survivors in the group of patients with grade 3 tumors and that the cumulative effect of both above-mentioned parameters might be helpful in selecting the high-risk individuals from the group of patients with luminal B subtype/HER2(+)/triple negative phenotype identified according to St Gallen recommendations. Copyright © 2013 Elsevier Inc. All rights reserved.

Comparative gene expression profiling of ADAMs, MMPs, TIMPs, EMMPRIN, EGF-R and VEGFA in low grade meningioma.

PubMed

Rooprai, Harcharan K; Martin, Andrew J; King, Andrew; Appadu, Usha D; Jones, Huw; Selway, Richard P; Gullan, Richard W; Pilkington, Geoffrey J

2016-12-01

MMPs (matrix metalloproteinases), ADAMs (a disintegrin and metalloproteinase) and TIMPs (tissue inhibitors of metalloproteinases) are implicated in invasion and angiogenesis: both are tissue remodeling processes involving regulated proteolysis of the extracellular matrix, growth factors and their receptors. The expression of these three groups and their correlations with clinical behaviour has been reported in gliomas but a similar comprehensive study in meningiomas is lacking. In this study, we aimed to evaluate the patterns of expression of 23 MMPs, 4 TIMPs, 8 ADAMs, selective growth factors and their receptors in 17 benign meningiomas using a quantitative real-time polymerase chain reaction (qPCR). Results indicated very high gene expression of 13 proteases, inhibitors and growth factors studied: MMP2 and MMP14, TIMP-1, -2 and -3, ADAM9, 10, 12, 15 and 17, EGF-R, EMMPRIN and VEGF-A, in almost every meningioma. Expression pattern analysis showed several positive correlations between MMPs, ADAMs, TIMPs and growth factors. Furthermore, our findings suggest that expression of MMP14, ADAM9, 10, 12, 15 and 17, TIMP-2, EGF-R and EMMPRIN reflects histological subtype of meningioma such that fibroblastic subtype had the highest mRNA expression, transitional subtype was intermediate and meningothelial type had the lowest expression. In conclusion, this is the first comprehensive study characterizing gene expression of 8 ADAMs in meningiomas. These neoplasms, although by histological definition benign, have invasive potential. Taken together, the selected elevated gene expression pattern may serve to identify targets for therapeutic intervention or indicators of biological progression and recurrence.

Modeling analysis on germination and seedling growth using ultrasound seed pretreatment in switchgrass.

PubMed

Wang, Quanzhen; Chen, Guo; Yersaiyiti, Hayixia; Liu, Yuan; Cui, Jian; Wu, Chunhui; Zhang, Yunwei; He, Xueqing

2012-01-01

Switchgrass is a perennial C4 plant with great potential as a bioenergy source and, thus, a high demand for establishment from seed. This research investigated the effects of ultrasound treatment on germination and seedling growth in switchgrass. Using an orthogonal matrix design, conditions for the ultrasound pretreatment in switchgrass seed, including sonication time (factor A), sonication temperature (factor B) and ultrasound output power (factor C), were optimized for germinating and stimulating seedling growth (indicated as plumular and radicular lengths) through modeling analysis. The results indicate that sonication temperature (B) was the most effective factor for germination, whereas output power (C) had the largest effect on seedling growth when ultrasound treatment was used. Combined with the analyses of range, variance and models, the final optimal ultrasonic treatment conditions were sonication for 22.5 min at 39.7°C and at an output power of 348 W, which provided the greatest germination percentage and best seedling growth. For this study, the orthogonal matrix design was an efficient method for optimizing the conditions of ultrasound seed treatment on switchgrass. The electrical conductivity of seed leachates in three experimental groups (control, soaked in water only, and ultrasound treatment) was determined to investigate the effects of ultrasound on seeds and eliminate the effect of water in the ultrasound treatments. The results showed that the electrical conductivity of seed leachates during either ultrasound treatment or water bath treatment was significantly higher than that of the control, and that the ultrasound treatment had positive effects on switchgrass seeds.

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.

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.

2010-04-01

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 found to be responsible for 97% of total vehicular emissions of CO, 22% of NOx, 95-97% of each aromatic species, 72-85% of each carbonyl species, 74% of ammonia, negligible amounts of particle number, 26% of PM2.5, and 2% of BC; diesel-powered vehicles account for the balance. Because the mobile lab spent 17% of its time waiting at stoplights, the results may overemphasize idling conditions, possibly resulting in an underestimate of NOx and overestimate of CO emissions. On the other hand, estimates of the inventory that do not correctly account for emissions during idling are likely to produce bias in the opposite direction.The resulting fuel-based estimates of emissions are lower than in the official inventory for CO and NOx and higher for VOCs. For NOx, the fuel-based estimates are lower for gasoline-powered vehicles but higher for diesel-powered ones compared to the official inventory. While conclusions regarding the inventory should be interpreted with care because of the small sample size, 3.5 h of driving, the discrepancies with the official inventory agree with those reported in other studies.

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.

Receptor control in mesenchymal stem cell engineering

NASA Astrophysics Data System (ADS)

Dalby, Matthew J.; García, Andrés J.; Salmeron-Sanchez, Manuel

2018-03-01

Materials science offers a powerful tool to control mesenchymal stem cell (MSC) growth and differentiation into functional phenotypes. A complex interplay between the extracellular matrix and growth factors guides MSC phenotypes in vivo. In this Review, we discuss materials-based bioengineering approaches to direct MSC fate in vitro and in vivo, mimicking cell-matrix-growth factor crosstalk. We first scrutinize MSC-matrix interactions and how the properties of a material can be tailored to support MSC growth and differentiation in vitro, with an emphasis on MSC self-renewal mechanisms. We then highlight important growth factor signalling pathways and investigate various materials-based strategies for growth factor presentation and delivery. Integrin-growth factor crosstalk in the context of MSC engineering is introduced, and bioinspired material designs with the potential to control the MSC niche phenotype are considered. Finally, we summarize important milestones on the road to MSC engineering for regenerative medicine.

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.

Factors associated with smoking in Asian American adults: a systematic review.

PubMed

Zhang, Jing; Wang, Zhongmiao

2008-05-01

This review systematically examined the factors associated with smoking in Asian American adults (aged > or =17 years). A total of 21 quantitative studies published in peer-reviewed journals from 1997 to 2006 were reviewed and abstracted using the matrix method. Statistically significant factors reported by the studies were summarized. Methodological quality of the studies also was assessed (maximum possible score = 10). Acculturation and education were the most frequently reported factors (n = 10, 47.6%). Acculturation was negatively associated with men's smoking but was positively associated with women's smoking. Education was uniformly found to be negatively related to smoking. Age was reported to have either a positive or a negative relationship with smoking (n = 9, 42.9%). Men were more likely to smoke than women (n = 7, 33.3%). The mean methodological score of the reviewed studies was 4.14 (on a scale of 1-10 points; SD = 1.62; range = 2-8). Health promotion professionals need to consider the summarized factors associated with Asian American adults' smoking behavior when planning smoking prevention programs and when recruiting participants for smoking cessation programs. When addressing acculturation, program planners should design different health education materials and use different strategies for men and women. To identify, understand, and incorporate essential factors into effective interventions, future studies should aim at higher methodological quality by using longitudinal design and increasing the use of theory, the test of data validity and reliability, and the report of effect sizes.

Influencing Factors on Choosing Psychiatry as a Career: An Exploration in Chinese University Students.

PubMed

Zhong, Jiawei; Zheng, Luna; Chen, Xiaoling; Gao, Qianqian; Zhang, Bingren; Wang, Wei

2016-12-01

There is a consistent need of psychiatric professionals in the world including China, and a consistent challenge to recruit more medical students into the psychiatric careers. We aimed to look for factors which have an impact on career-choosing of psychiatry in Chinese university students. We invited 508 non-medical students (NM), 304 medical students without (MO) and 123 medical students with clinical internship experience (MW), to answer a matrix of 43 questions regarding factors influencing career-choosing of psychiatry. Answers to these questions were analyzed through exploratory and confirmatory factor analyses, once the latent factors were identified and structurally-validated, their mean scores in three groups of students were calculated. Five factors with five items each were identified, namely social status inferiority, career importance, practice reward, career preference, and practice stress. NM scored lower than MO and MW did on Social Status Inferiority; NM group scored higher than MO and MW groups did on Career Importance; MW scored lower than NM and MO did on Practice Reward and on Career Preference; Regarding Practice Stress, NM scored higher than MO did, who then in turn, scored higher than MW did. In addition, Practice Stress was positively correlated with advice of the medical educators; and Social Status Inferiority and Career Preference were positively correlated with the psychiatry teaching of the medical educators. Raising career rewards, improving social status, and reinforcing psychiatric education might help to recruit more medical students to specialize in psychiatry practicing.

High VEGF-D and Low MMP-2 Serum Levels Predict Nodal-Positive Disease in Invasive Bladder Cancer

PubMed Central

Benoit, Tobias; Keller, Etienne X.; Wolfsgruber, Pirmin; Hermanns, Thomas; Günthart, Michele; Banzola, Irina; Sulser, Tullio; Provenzano, Maurizio; Poyet, Cédric

2015-01-01

Background To investigate stromal variables including angiogenesis, lymphangiogenesis, and matrix metalloproteinase (MMP) in the serum of patients with urothelial carcinoma of the bladder (UCB) and to evaluate their association with histopathological characteristics and clinical outcome. Material/Methods Protein levels of vascular endothelial growth factors-A, -C, -D (VEGF-A/-C/-D), their receptors- VEGF-R2 and -R3 (VEGF-R2/-R3), and matrix metalloproteinases 2, -3, and -7 (MMP-2, MMP-3, MMP-7) were quantified in the blood serum samples of 71 patients with UCB before radical cystectomy (RC). Samples of patients with non-invasive UCB or no history of UCB were investigated as controls (n=20). Protein levels in the serum were measured using a flow cytometric cytokine assay. Results A positive association for VEGF-D (p<0.001) and an inverse association for MMP-2 (p=0.017) were observed in patients with positive lymph node (LN) status at the time of RC. VEGF-A (p<0.001), VEGF-C (p<0.001), MMP-2 (p<0.001), and MMP-7 (p=0.005) serum levels were different in serum of patients with invasive UCB compared with non-invasive UCB or healthy individuals. None of the serum markers were associated with disease progression. Conclusions High VEGF-D and low MMP-2 serum levels predict LN metastasis in patients with UCB at the time of RC. VEGF-A, VEGF-C, MMP-2, and MMP-7 serum levels varied significantly between invasive and non-invasive disease as well as in comparison with healthy individuals. Clinical implementation of these marker serum measurements may be valuable to select high-risk patients with more invasive or nodal-positive disease. PMID:26241709

Verb and auxiliary movement in agrammatic Broca’s aphasia

PubMed Central

Bastiaanse, Roelien; Thompson, Cynthia K.

2011-01-01

Verb production in agrammatic Broca’s aphasia has repeatedly been shown to be impaired by a number of investigators. Not only is the number of verbs produced often significantly reduced, but verb inflections and auxiliaries are often omitted as well (e.g., Bastiaanse, Jonkers, & Moltmaker-Osinga, 1996; Saffran, Berndt, & Schwartz, 1989; Thompson, Shapiro, Li, & Schendel, 1994, 1997). It has been suggested that these problems are, in part, caused by the fact that finite verbs need to be moved from their base-generated position to inflectional nodes in the syntactic tree (e.g., Bastiaanse & Van Zonneveld, 1998). Others have suggested that production deficits in agrammatism can be predicted based on the position that certain structures take in the syntactic tree (Friedmann & Grodzinsky, 1997; Hagiwara, 1995). If the former theory is correct, several predictions can be made. First of all, the discrepancy between production of finite verbs in the matrix and embedded clause that has been found for Dutch (Bastiaanse & Van Zonneveld, 1998) should not be observed in English, since the word order of the matrix and embedded clause are the same in the latter language. Second, if verb movement (including movement of auxiliaries) is problematic for speakers with agrammatic aphasia, then a hierarchy in the production of auxiliaries in yes/no questions, auxiliaries, and finite verbs in declarative sentences in English would be expected, since the former has been moved and the two latter are in base-generated position. In the present paper, these hypotheses were tested in a cross-linguistic study of Dutch and English. Results showed the position in the syntactic tree does not predict deficit patterns; rather the critical factor appears to relate to whether or not verb or auxiliary movement is required. PMID:12590917

A plasma-based biomatrix mixed with endothelial progenitor cells and keratinocytes promotes matrix formation, angiogenesis, and reepithelialization in full-thickness wounds.

PubMed

Vermeulen, Pieter; Dickens, Stijn; Degezelle, Karlien; Van den Berge, Stefaan; Hendrickx, Benoit; Vranckx, Jan Jeroen

2009-07-01

In search of an autologous vascularized skin substitute, we treated full-thickness wounds (FTWs) with autologous platelet-rich plasma gel (APG) in which we embedded endothelial progenitor cells (EPCs) and basal cell keratinocytes (KCs). We cultivated autologous KCs in low-serum conditions and expanded autologous EPCs from venous blood. FTWs (n = 55) were created on the backs of four pigs, covered with wound chambers, and randomly assigned to the following treatments: (1) APG, (2) APG + KCs, (3) APG + EPCs, (4) APG + KCs + EPCs, and (5) saline. All wounds were biopsied to measure neovascularization (lectin Bandeiraea Simplicifolia-1 (BS-1), alpha smooth muscle actin [alphaSMA], and membrane type 1 matrix metalloproteinase (MT1-MMP)), matrix deposition (fibronectin, collagen type I/III, and alphavbeta3), and reepithelialization. Wound fluids were analyzed for protein expression. All APG-treated wounds showed more vascular structures (p < 0.001), and the addition of EPCs further improved neovascularization, as confirmed by higher lectin, alphaSMA, and MT1-MMP. APG groups had higher collagen I/III (p < 0.05), alphavbeta3, and fibronectin content (p < 0.001), and they exhibited higher concentrations of platelet-derived growth factor subunit bb, basic fibroblast growth factor, hepatocyte growth factor, insulin growth factor-1, transforming growth factor-beta1 and -beta3, matrix metalloproteinase-1 and -z9, and tissue-inhibiting matrix metalloproteinase-1 and -2. Applying APG + KCs resulted in the highest reepithelialization rates (p < 0.001). No differences were found for wound contraction by planimetry. In this porcine FTW model, APG acts as a supportive biomatrix that, along with the embedded cells, improves extracellular matrix organization, promotes angiogenesis, and accelerates reepithelialization.

Robust Adaptive Beamforming with Sensor Position Errors Using Weighted Subspace Fitting-Based Covariance Matrix Reconstruction.

PubMed

Chen, Peng; Yang, Yixin; Wang, Yong; Ma, Yuanliang

2018-05-08

When sensor position errors exist, the performance of recently proposed interference-plus-noise covariance matrix (INCM)-based adaptive beamformers may be severely degraded. In this paper, we propose a weighted subspace fitting-based INCM reconstruction algorithm to overcome sensor displacement for linear arrays. By estimating the rough signal directions, we construct a novel possible mismatched steering vector (SV) set. We analyze the proximity of the signal subspace from the sample covariance matrix (SCM) and the space spanned by the possible mismatched SV set. After solving an iterative optimization problem, we reconstruct the INCM using the estimated sensor position errors. Then we estimate the SV of the desired signal by solving an optimization problem with the reconstructed INCM. The main advantage of the proposed algorithm is its robustness against SV mismatches dominated by unknown sensor position errors. Numerical examples show that even if the position errors are up to half of the assumed sensor spacing, the output signal-to-interference-plus-noise ratio is only reduced by 4 dB. Beam patterns plotted using experiment data show that the interference suppression capability of the proposed beamformer outperforms other tested beamformers.

Diagnosing and Correcting Mass Accuracy and Signal Intensity Error Due to Initial Ion Position Variations in a MALDI TOFMS

NASA Astrophysics Data System (ADS)

Malys, Brian J.; Piotrowski, Michelle L.; Owens, Kevin G.

2018-02-01

Frustrated by worse than expected error for both peak area and time-of-flight (TOF) in matrix assisted laser desorption ionization (MALDI) experiments using samples prepared by electrospray deposition, it was finally determined that there was a correlation between sample location on the target plate and the measured TOF/peak area. Variations in both TOF and peak area were found to be due to small differences in the initial position of ions formed in the source region of the TOF mass spectrometer. These differences arise largely from misalignment of the instrument sample stage, with a smaller contribution arising from the non-ideal shape of the target plates used. By physically measuring the target plates used and comparing TOF data collected from three different instruments, an estimate of the magnitude and direction of the sample stage misalignment was determined for each of the instruments. A correction method was developed to correct the TOFs and peak areas obtained for a given combination of target plate and instrument. Two correction factors are determined, one by initially collecting spectra from each sample position used and another by using spectra from a single position for each set of samples on a target plate. For TOF and mass values, use of the correction factor reduced the error by a factor of 4, with the relative standard deviation (RSD) of the corrected masses being reduced to 12-24 ppm. For the peak areas, the RSD was reduced from 28% to 16% for samples deposited twice onto two target plates over two days.

Diagnosing and Correcting Mass Accuracy and Signal Intensity Error Due to Initial Ion Position Variations in a MALDI TOFMS

NASA Astrophysics Data System (ADS)

Malys, Brian J.; Piotrowski, Michelle L.; Owens, Kevin G.

2017-12-01

Frustrated by worse than expected error for both peak area and time-of-flight (TOF) in matrix assisted laser desorption ionization (MALDI) experiments using samples prepared by electrospray deposition, it was finally determined that there was a correlation between sample location on the target plate and the measured TOF/peak area. Variations in both TOF and peak area were found to be due to small differences in the initial position of ions formed in the source region of the TOF mass spectrometer. These differences arise largely from misalignment of the instrument sample stage, with a smaller contribution arising from the non-ideal shape of the target plates used. By physically measuring the target plates used and comparing TOF data collected from three different instruments, an estimate of the magnitude and direction of the sample stage misalignment was determined for each of the instruments. A correction method was developed to correct the TOFs and peak areas obtained for a given combination of target plate and instrument. Two correction factors are determined, one by initially collecting spectra from each sample position used and another by using spectra from a single position for each set of samples on a target plate. For TOF and mass values, use of the correction factor reduced the error by a factor of 4, with the relative standard deviation (RSD) of the corrected masses being reduced to 12-24 ppm. For the peak areas, the RSD was reduced from 28% to 16% for samples deposited twice onto two target plates over two days. [Figure not available: see fulltext.

Accuracy limitations of hyperbolic multilateration systems

DOT National Transportation Integrated Search

1973-03-22

The report is an analysis of the accuracy limitations of hyperbolic multilateration systems. A central result is a demonstration that the inverse of the covariance matrix for positional errors corresponds to the moment of inertia matrix of a simple m...

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.

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

High-temperature asymptotics of supersymmetric partition functions

DOE PAGES

Ardehali, Arash Arabi

2016-07-05

We study the supersymmetric partition function of 4d supersymmetric gauge theories with a U(1) R-symmetry on Euclidean S 3 × S β 1, with S 3 the unit-radius squashed three-sphere, and β the circumference of the circle. For superconformal theories, this partition function coincides (up to a Casimir energy factor) with the 4d superconformal index. The partition function can be computed exactly using the supersymmetric localization of the gauge theory path-integral. It takes the form of an elliptic hypergeometric integral, which may be viewed as a matrix-integral over the moduli space of the holonomies of the gauge fields around Smore » β 1. At high temperatures (β → 0, corresponding to the hyperbolic limit of the elliptic hypergeometric integral) we obtain from the matrix-integral a quantum effective potential for the holonomies. The effective potential is proportional to the temperature. Therefore the high-temperature limit further localizes the matrix-integral to the locus of the minima of the potential. If the effective potential is positive semi-definite, the leading high-temperature asymptotics of the partition function is given by the formula of Di Pietro and Komargodski, and the subleading asymptotics is connected to the Coulomb branch dynamics on R 3 × S 1. In theories where the effective potential is not positive semi-definite, the Di Pietro-Komargodski formula needs to be modified. In particular, this modification occurs in the SU(2) theory of Intriligator-Seiberg-Shenker, and the SO(N) theory of Brodie-Cho-Intriligator, both believed to exhibit “misleading” anomaly matchings, and both believed to yield interacting superconformal field theories with c < a. Lastly, two new simple tests for dualities between 4d supersymmetric gauge theories emerge as byproducts of our analysis.« less

Expression of hLAMP-1-Positive Particles During Early Heart Development in the Chick.

PubMed

Abd-Elhamid, T H; Conway, M L; Sinning, A R

2017-10-01

Heart development requires coordinated activity of various factors, the disturbance of which can lead to congenital heart defects. Heart lectin-associated matrix protein-1 (hLAMP-1) is a matrix protein expressed within Hensen's node at Hamburger-Hamilton (HH) stage 4, in the lateral mesoderm by HH stages 5-6 and enhanced within the left pre-cardiac field at HH stage 7. At HH stages 15-16, hLAMP-1 expression is observed in the atrioventricular canal and the outflow tract. Also, the role of hLAMP-1 in induction of mesenchyme formation in chick heart has been well documented. To further elucidate the role of this molecule in heart development, we examined its expression patterns during HH stages 8-14 in the chick. In this regard, we immunostained sections of the heart during HH stages 8-14 with antibodies specific to hLAMP-1. Our results showed prominent expression of hLAMP-1-positive particles in the extracellular matrix associated with the pre-cardiac mesoderm, the endoderm, ectoderm as well as neuroectoderm at HH stages 8-9. After formation of the linear heart tube at HH stage 10, the expression of hLAMP-1-stained particles disappears in those regions of original contact between the endoderm and heart forming fields due to rupture of the dorsal mesocardium while their expression becomes confined to the arterial and venous poles of the heart tube. This expression pattern is maintained until HH stage 14. This expression pattern suggests that hLAMP-1 may be involved in the formation of the endocardial tube. © 2017 Blackwell Verlag GmbH.

PDGF-regulated rab4-dependent recycling of alphavbeta3 integrin from early endosomes is necessary for cell adhesion and spreading.

PubMed

Roberts, M; Barry, S; Woods, A; van der Sluijs, P; Norman, J

2001-09-18

It has been postulated that the regulation of integrin vesicular traffic facilitates cell migration by internalizing integrins at the rear of the cell and transporting them forward within vesicles for exocytosis at the leading edge to form new contacts with the extracellular matrix. The rab family of GTPases control key targeting events in the endo/exocytic pathway; therefore, these GTPases may be involved in the regulation of cell-matrix contact assembly. The endo/exocytic cycle of alphavbeta3 and alpha5beta1 integrins was studied using mouse 3T3 fibroblast cell lines. In serum-starved cells, internalized integrins were transported through rab4-positive, early endosomes and arrived at the rab11-positive, perinuclear recycling compartment approximately 30 min after endocytosis. From the recycling compartment, integrins were recycled to the plasma membrane in a rab11-dependent fashion. Following treatment with PDGF, alphavbeta3 integrin, but not alpha5beta1, was rapidly recycled directly back to the plasma membrane from the early endosomes via a rab4-dependent mechanism without the involvement of rab11. This rapid recycling pathway directed alphavbeta3 to numerous small puncta distributed evenly across the dorsal surface of the cell, and the integrin only became localized into focal complexes at later times following PDGF addition. Interestingly, inhibition of PDGF-stimulated alphavbeta3 recycling using dominant-negative rab4 mutants compromised cell adhesion and spreading on vitronectin (a ligand for alphavbeta3), but adhesion to fibronectin (a ligand for alpha5beta1 and alphavbeta3) was unchanged. We propose that growth factor-regulated, rab4-dependent recycling of alphavbeta3 integrin from early endosomes to the plasma membrane is a critical upstream event in the assembly of cell-matrix contacts.

Trabecular meshwork ECM remodeling in glaucoma: could RAS be a target?

PubMed

Agarwal, Puneet; Agarwal, Renu

2018-06-14

Disturbances of extracellular matrix (ECM) homeostasis in trabecular meshwork (TM) cause increased aqueous outflow resistance leading to elevated intraocular pressure (IOP) in glaucomatous eyes. Therefore, restoration of ECM homeostasis is a rational approach to prevent disease progression. Since renin-angiotensin system (RAS) inhibition positively alters ECM homeostasis in cardiovascular pathologies involving pressure and volume overload, it is likely that RAS inhibitors reduce IOP primarily by restoring ECM homeostasis. Areas covered: Current evidence showing the presence of RAS components in ocular tissue and its role in regulating aqueous humor dynamics is briefly summarized. The role of RAS in ECM remodeling is discussed both in terms of its effects on ECM synthesis and its breakdown. The mechanisms of ECM remodeling involving interactions of RAS with transforming growth factor-β, Wnt/β-catenin signaling, bone morphogenic proteins, connective tissue growth factor, and matrix metalloproteinases in ocular tissue are discussed. Expert opinion: Current literature strongly indicates a significant role of RAS in ECM remodeling in TM of hypertensive eyes. Hence, IOP-lowering effect of RAS inhibitors may primarily be attributed to restoration of ECM homeostasis in aqueous outflow pathways rather than its vascular effects. However, the mechanistic targets for RAS inhibitors have much wider distribution and consequences, which remain relatively unexplored in TM.

Physical and Chemical Factors Influencing the Transport and Fate of Microorganisms in Soils with Preferential Flow

NASA Astrophysics Data System (ADS)

Wang, Y.; Bradford, S. A.; Simunek, J.

2011-12-01

Laboratory and numerical studies were conducted to investigate the influence of physical and chemical factors on the transport of E.coli O157:H7 and coliphage φX174 through preferential flow systems. Preferential flow systems were created in 13.2 cm diameter and 20 cm length columns by embedding sand lens of various grain size, length, and vertical position into finer textured matrix sand. Tracer solutions containing bromide and microbes were prepared at different ionic strength (IS) and sprayed onto the surface of the columns at desired steady rates using a rain simulator to achieve saturated or unsaturated conditions. Effluents were collected at the column bottom continuously and analyzed for concentrations of bromide, φX174, and E.coli. Complementary numerical simulations were conducted using the HYDRUS 2D code over a wider range of physical and chemical conditions, and to analyze bromide and microbe transport in the columns. Results indicated that preferential transport of the microbes was dependent on the hydraulic contrasts between the matrix and lens, the length of the lens, the size of microorganism, and the water saturation. The IS also influenced the preferential transport of microbes. In particular, increasing retention with IS decreased the overall microbe transport but increased the relative importance of preferential flow.

Matched field localization based on CS-MUSIC algorithm

NASA Astrophysics Data System (ADS)

Guo, Shuangle; Tang, Ruichun; Peng, Linhui; Ji, Xiaopeng

2016-04-01

The problem caused by shortness or excessiveness of snapshots and by coherent sources in underwater acoustic positioning is considered. A matched field localization algorithm based on CS-MUSIC (Compressive Sensing Multiple Signal Classification) is proposed based on the sparse mathematical model of the underwater positioning. The signal matrix is calculated through the SVD (Singular Value Decomposition) of the observation matrix. The observation matrix in the sparse mathematical model is replaced by the signal matrix, and a new concise sparse mathematical model is obtained, which means not only the scale of the localization problem but also the noise level is reduced; then the new sparse mathematical model is solved by the CS-MUSIC algorithm which is a combination of CS (Compressive Sensing) method and MUSIC (Multiple Signal Classification) method. The algorithm proposed in this paper can overcome effectively the difficulties caused by correlated sources and shortness of snapshots, and it can also reduce the time complexity and noise level of the localization problem by using the SVD of the observation matrix when the number of snapshots is large, which will be proved in this paper.

Multichannel Compressive Sensing MRI Using Noiselet Encoding

PubMed Central

Pawar, Kamlesh; Egan, Gary; Zhang, Jingxin

2015-01-01

The incoherence between measurement and sparsifying transform matrices and the restricted isometry property (RIP) of measurement matrix are two of the key factors in determining the performance of compressive sensing (CS). In CS-MRI, the randomly under-sampled Fourier matrix is used as the measurement matrix and the wavelet transform is usually used as sparsifying transform matrix. However, the incoherence between the randomly under-sampled Fourier matrix and the wavelet matrix is not optimal, which can deteriorate the performance of CS-MRI. Using the mathematical result that noiselets are maximally incoherent with wavelets, this paper introduces the noiselet unitary bases as the measurement matrix to improve the incoherence and RIP in CS-MRI. Based on an empirical RIP analysis that compares the multichannel noiselet and multichannel Fourier measurement matrices in CS-MRI, we propose a multichannel compressive sensing (MCS) framework to take the advantage of multichannel data acquisition used in MRI scanners. Simulations are presented in the MCS framework to compare the performance of noiselet encoding reconstructions and Fourier encoding reconstructions at different acceleration factors. The comparisons indicate that multichannel noiselet measurement matrix has better RIP than that of its Fourier counterpart, and that noiselet encoded MCS-MRI outperforms Fourier encoded MCS-MRI in preserving image resolution and can achieve higher acceleration factors. To demonstrate the feasibility of the proposed noiselet encoding scheme, a pulse sequences with tailored spatially selective RF excitation pulses was designed and implemented on a 3T scanner to acquire the data in the noiselet domain from a phantom and a human brain. The results indicate that noislet encoding preserves image resolution better than Fouirer encoding. PMID:25965548

System and method for object localization

NASA Technical Reports Server (NTRS)

Kelly, Alonzo J. (Inventor); Zhong, Yu (Inventor)

2005-01-01

A computer-assisted method for localizing a rack, including sensing an image of the rack, detecting line segments in the sensed image, recognizing a candidate arrangement of line segments in the sensed image indicative of a predetermined feature of the rack, generating a matrix of correspondence between the candidate arrangement of line segments and an expected position and orientation of the predetermined feature of the rack, and estimating a position and orientation of the rack based on the matrix of correspondence.

A New Measure of Wireless Network Connectivity

DTIC Science & Technology

2014-10-31

matrix QG. From Lemma 1, QG is a non-zero nonnegative matrix. Thus from the Perron - Frobenius Theorem, [24], its largest magni- tude eigenvalue, known as...the Perron - Frobenius eigenvalue is real and positive. Further as QG is symmetric, all its eigenval- ues are real, and its largest magnitude...eigenvalue λmax(QG) is also its largest singular value. Also from the Perron - Frobenius Theorem, should the network be connected, i.e. QG is positive as opposed

Matrix-assisted laser desorption ionization-time of flight mass spectrometry for direct bacterial identification from positive blood culture pellets.

PubMed

Prod'hom, Guy; Bizzini, Alain; Durussel, Christian; Bille, Jacques; Greub, Gilbert

2010-04-01

An ammonium chloride erythrocyte-lysing procedure was used to prepare a bacterial pellet from positive blood cultures for direct matrix-assisted laser desorption-ionization time of flight (MALDI-TOF) mass spectrometry analysis. Identification was obtained for 78.7% of the pellets tested. Moreover, 99% of the MALDI-TOF identifications were congruent at the species level when considering valid scores. This fast and accurate method is promising.

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.

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

Metabolic rate associates with, but does not generate covariation between, behaviours in western stutter-trilling crickets, Gryllus integer.

PubMed

Krams, Indrikis A; Niemelä, Petri T; Trakimas, Giedrius; Krams, Ronalds; Burghardt, Gordon M; Krama, Tatjana; Kuusik, Aare; Mänd, Marika; Rantala, Markus J; Mänd, Raivo; Kekäläinen, Jukka; Sirkka, Ilkka; Luoto, Severi; Kortet, Raine

2017-03-29

The causes and consequences of among-individual variation and covariation in behaviours are of substantial interest to behavioural ecology, but the proximate mechanisms underpinning this (co)variation are still unclear. Previous research suggests metabolic rate as a potential proximate mechanism to explain behavioural covariation. We measured the resting metabolic rate (RMR), boldness and exploration in western stutter-trilling crickets, Gryllus integer , selected differentially for short and fast development over two generations. After applying mixed-effects models to reveal the sign of the covariation, we applied structural equation models to an individual-level covariance matrix to examine whether the RMR generates covariation between the measured behaviours. All traits showed among-individual variation and covariation: RMR and boldness were positively correlated, RMR and exploration were negatively correlated, and boldness and exploration were negatively correlated. However, the RMR was not a causal factor generating covariation between boldness and exploration. Instead, the covariation between all three traits was explained by another, unmeasured mechanism. The selection lines differed from each other in all measured traits and significantly affected the covariance matrix structure between the traits, suggesting that there is a genetic component in the trait integration. Our results emphasize that interpretations made solely from the correlation matrix might be misleading. © 2017 The Author(s).

Metabolic rate associates with, but does not generate covariation between, behaviours in western stutter-trilling crickets, Gryllus integer

PubMed Central

Trakimas, Giedrius; Krams, Ronalds; Burghardt, Gordon M.; Krama, Tatjana; Kuusik, Aare; Mänd, Marika; Rantala, Markus J.; Mänd, Raivo; Sirkka, Ilkka; Luoto, Severi; Kortet, Raine

2017-01-01

The causes and consequences of among-individual variation and covariation in behaviours are of substantial interest to behavioural ecology, but the proximate mechanisms underpinning this (co)variation are still unclear. Previous research suggests metabolic rate as a potential proximate mechanism to explain behavioural covariation. We measured the resting metabolic rate (RMR), boldness and exploration in western stutter-trilling crickets, Gryllus integer, selected differentially for short and fast development over two generations. After applying mixed-effects models to reveal the sign of the covariation, we applied structural equation models to an individual-level covariance matrix to examine whether the RMR generates covariation between the measured behaviours. All traits showed among-individual variation and covariation: RMR and boldness were positively correlated, RMR and exploration were negatively correlated, and boldness and exploration were negatively correlated. However, the RMR was not a causal factor generating covariation between boldness and exploration. Instead, the covariation between all three traits was explained by another, unmeasured mechanism. The selection lines differed from each other in all measured traits and significantly affected the covariance matrix structure between the traits, suggesting that there is a genetic component in the trait integration. Our results emphasize that interpretations made solely from the correlation matrix might be misleading. PMID:28330918

Environmental Impact Assessment of the Industrial Estate Development Plan with the Geographical Information System and Matrix Methods

PubMed Central

Ghasemian, Mohammad; Poursafa, Parinaz; Amin, Mohammad Mehdi; Ziarati, Mohammad; Ghoddousi, Hamid; Momeni, Seyyed Alireza; Rezaei, Amir Hossein

2012-01-01

Background. The purpose of this study is environmental impact assessment of the industrial estate development planning. Methods. This cross-sectional study was conducted in 2010 in Isfahan province, Iran. GIS and matrix methods were applied. Data analysis was done to identify the current situation of the region, zoning vulnerable areas, and scoping the region. Quantitative evaluation was done by using matrix of Wooten and Rau. Results. The net score for impact of industrial units operation on air quality of the project area was (−3). According to the transition of industrial estate pollutants, residential places located in the radius of 2500 meters of the city were expected to be affected more. The net score for impact of construction of industrial units on plant species of the project area was (−2). Environmental protected areas were not affected by the air and soil pollutants because of their distance from industrial estate. Conclusion. Positive effects of project activities outweigh the drawbacks and the sum scores allocated to the project activities on environmental factor was (+37). Totally it does not have detrimental effects on the environment and residential neighborhood. EIA should be considered as an anticipatory, participatory environmental management tool before determining a plan application. PMID:22272210

Effects of chitosan-coated fibers as a scaffold for three-dimensional cultures of rabbit fibroblasts for ligament tissue engineering.

PubMed

Sarukawa, Junichiro; Takahashi, Masaaki; Abe, Masashi; Suzuki, Daisuke; Tokura, Seiichi; Furuike, Tetsuya; Tamura, Hiroshi

2011-01-01

Material selection in tissue-engineering scaffolds is one of the primary factors defining cellular response and matrix formation. In this study, we fabricated chitosan-coated poly(lactic acid) (PLA) fiber scaffolds to test our hypothesis that PLA fibers coated with chitosan highly promoted cell supporting properties compared to those without chitosan. Both PLA fibers (PLA group) and chitosan-coated PLA fibers (PLA-chitosan group) were fabricated for this study. Anterior cruciate ligament (ACL) fibroblasts were isolated from Japanese white rabbits and cultured on scaffolds consisting of each type of fiber. The effects of cell adhesivity, proliferation, and synthesis of the extracellular matrix (ECM) for each fiber were analyzed by cell counting, hydroxyproline assay, scanning electron microscopy and quantitative RT-PCR. Cell adhesivity, proliferation, hydroxyproline content and the expression of type-I collagen mRNA were significantly higher in the PLA-chitosan group than in the PLA group. Scanning electron microscopic observation showed that fibroblasts proliferated with a high level of ECM synthesis around the cells. Chitosan coating improved ACL fibroblast adhesion and proliferation, and had a positive effect on matrix production. Thus, the advantages of chitosan-coated PLA fibers show them to be a suitable biomaterial for ACL tissue-engineering scaffolds.

Extracellular Hsp70 Enhances Mesoangioblast Migration via an Autocrine Signaling Pathway.

PubMed

Barreca, Maria M; Spinello, Walter; Cavalieri, Vincenzo; Turturici, Giuseppina; Sconzo, Gabriella; Kaur, Punit; Tinnirello, Rosaria; Asea, Alexzander A A; Geraci, Fabiana

2017-07-01

Mouse mesoangioblasts are vessel-associated progenitor stem cells endowed with the ability of multipotent mesoderm differentiation. Therefore, they represent a promising tool in the regeneration of injured tissues. Several studies have demonstrated that homing of mesoangioblasts into blood and injured tissues are mainly controlled by cytokines/chemokines and other inflammatory factors. However, little is known about the molecular mechanisms regulating their ability to traverse the extracellular matrix (ECM). Here, we demonstrate that membrane vesicles released by mesoangioblasts contain Hsp70, and that the released Hsp70 is able to interact by an autocrine mechanism with Toll-like receptor 4 (TLR4) and CD91 to stimulate migration. We further demonstrate that Hsp70 has a positive role in regulating matrix metalloproteinase 2 (MMP2) and MMP9 expression and that MMP2 has a more pronounced effect on cell migration, as compared to MMP9. In addition, the analysis of the intracellular pathways implicated in Hsp70 regulated signal transduction showed the involvement of both PI3K/AKT and NF-κB. Taken together, our findings present a paradigm shift in our understanding of the molecular mechanisms that regulate mesoangioblast stem cells ability to traverse the extracellular matrix (ECM). J. Cell. Physiol. 232: 1845-1861, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Kinematic equations for control of the redundant eight-degree-of-freedom advanced research manipulator 2

NASA Technical Reports Server (NTRS)

Williams, Robert L., II

1992-01-01

The forward position and velocity kinematics for the redundant eight-degree-of-freedom Advanced Research Manipulator 2 (ARM2) are presented. Inverse position and velocity kinematic solutions are also presented. The approach in this paper is to specify two of the unknowns and solve for the remaining six unknowns. Two unknowns can be specified with two restrictions. First, the elbow joint angle and rate cannot be specified because they are known from the end-effector position and velocity. Second, one unknown must be specified from the four-jointed wrist, and the second from joints that translate the wrist, elbow joint excluded. There are eight solutions to the inverse position problem. The inverse velocity solution is unique, assuming the Jacobian matrix is not singular. A discussion of singularities is based on specifying two joint rates and analyzing the reduced Jacobian matrix. When this matrix is singular, the generalized inverse may be used as an alternate solution. Computer simulations were developed to verify the equations. Examples demonstrate agreement between forward and inverse solutions.

Source contributions to total concentrations and carcinogenic potencies of polychlorinated dibenzo-p-dioxins and polychlorinated dibenzofurans (PCDD/Fs) in ambient air: a case study in Suzhou City, China.

PubMed

Xuan, Zhiqiang; Bi, Chenglu; Li, Jiafu; Nie, Jihua; Chen, Zhihai

2017-10-01

The potential source categories and source contributions of polychlorinated dibenzo-p-dioxins and polychlorinated dibenzofurans (PCDD/Fs) in ambient air from Suzhou City, China, were performed by principal component analysis-multiple linear regression (PCA-MLR) and positive matrix factorization (PMF). The carcinogenic potencies of PCDD/Fs were quantitatively apportioned based on the positive matrix factorization-toxic equivalent concentration (PMF-TEQ) method. The results of the present study were summarized as follows. (1) The total concentrations and toxic equivalent concentrations of PCDD/Fs (∑PCDD/Fs and TEQ) in ambient air from Suzhou City were 1.34-42.80 pg N m -3 and 0.081-1.22 pg I-TEQ N m -3 , respectively. (2) PCA-MLR suggested that industrial combustion (IC), electric arc furnaces (EAFs) and secondary aluminum smelters (ALSs), unleaded gas-fueled vehicle sources (UGFVs), ALSs, and hazardous solid waste incinerators (HSWIs) could be the primary PCDD/F contributors, accounting for 13.2, 16.7, 35.5, 19.4, and 15.2% of ∑PCDD/Fs, respectively. (3) PMF and PMF-TEQ indicated that EAFs (carbon steel), UGFVs, IC, ALSs, municipal solid waste incinerators (MSWIs) and hospital waste incinerators (HWIs), and HSWIs contributed 10.9, 10.9, 42.8, 11.3, 10.7, and 13.4% to ∑PCDD/Fs, but contributed 8.3, 12.3, 50.3, 12.7, 6.0, and 10.4% to carcinogenic potencies of PCDD/Fs. This study was the first attempt to quantitatively apportion the source-specific carcinogenic potencies of PCDD/Fs in ambient air.

Protective role of Smad6 in inflammation-induced valvular cell calcification

PubMed Central

Li, Xin; Lim, Jina J.; Lu, Jinxiu; Pedego, Taylor M.; Demer, Linda; Tintut, Yin

2016-01-01

Calcific aortic vascular and valvular disease (CAVD) is associated with hyperlipidemia, the effects of which occur through chronic inflammation. Evidence suggests that inhibitory small mothers against decapentaplegic (I-Smads; Smad6 and 7) regulate valve embryogenesis and may serve as a mitigating factor in CAVD. However, whether I-Smads regulate inflammation-induced calcific vasculopathy is not clear. Therefore, we investigated the role of I-Smads in atherosclerotic calcification. Results showed that expression of Smad6, but not Smad7, was reduced in aortic and valve tissues of hyperlipidemic compared with normolipemic mice, while expression of tumor necrosis factor alpha (TNF-a) was upregulated. To test whether the effects are in response to inflammatory cytokines, we isolated murine aortic valve leaflets and cultured valvular interstitial cells (mVIC) from the normolipemic mice. By immunochemistry, mVICs were strongly positive for vimentin, weakly positive for smooth muscle alpha actin, and negative for an endothelial cell marker. TNF-a upregulated alkaline phosphatase (ALP) activity and matrix mineralization in mVICs. By gene expression analysis, TNF-a significantly upregulated bone morphogenetic protein 2 (BMP-2) expression while downregulating Smad6 expression. Smad7 expression was not significantly affected. To further test the role of Smad6 on TNF-a-induced valvular cell calcification, we knocked down Smad6 expression using lentiviral transfection. In cells transfected with Smad6 shRNA, TNF-a further augmented ALP activity, expression of BMP-2, Wnt- and redox-regulated genes, and matrix mineralization compared with the control cells. These findings suggest that TNF-a induces valvular and vascular cell calcification, in part, by specifically reducing the expression of a BMP-2 signaling inhibitor, Smad6. PMID:25864564

Protective Role of Smad6 in Inflammation-Induced Valvular Cell Calcification.

PubMed

Li, Xin; Lim, Jina; Lu, Jinxiu; Pedego, Taylor M; Demer, Linda; Tintut, Yin

2015-10-01

Calcific aortic vascular and valvular disease (CAVD) is associated with hyperlipidemia, the effects of which occur through chronic inflammation. Evidence suggests that inhibitory small mothers against decapentaplegic (I-Smads; Smad6 and 7) regulate valve embryogenesis and may serve as a mitigating factor in CAVD. However, whether I-Smads regulate inflammation-induced calcific vasculopathy is not clear. Therefore, we investigated the role of I-Smads in atherosclerotic calcification. Results showed that expression of Smad6, but not Smad7, was reduced in aortic and valve tissues of hyperlipidemic compared with normolipemic mice, while expression of tumor necrosis factor alpha (TNF-α) was upregulated. To test whether the effects are in response to inflammatory cytokines, we isolated murine aortic valve leaflets and cultured valvular interstitial cells (mVIC) from the normolipemic mice. By immunochemistry, mVICs were strongly positive for vimentin, weakly positive for smooth muscle α actin, and negative for an endothelial cell marker. TNF-α upregulated alkaline phosphatase (ALP) activity and matrix mineralization in mVICs. By gene expression analysis, TNF-α significantly upregulated bone morphogenetic protein 2 (BMP-2) expression while downregulating Smad6 expression. Smad7 expression was not significantly affected. To further test the role of Smad6 on TNF-α-induced valvular cell calcification, we knocked down Smad6 expression using lentiviral transfection. In cells transfected with Smad6 shRNA, TNF-α further augmented ALP activity, expression of BMP-2, Wnt- and redox-regulated genes, and matrix mineralization compared with the control cells. These findings suggest that TNF-α induces valvular and vascular cell calcification, in part, by specifically reducing the expression of a BMP-2 signaling inhibitor, Smad6. © 2015 Wiley Periodicals, Inc.

Matrix metalloproteinase-14 is a biomarker of angiogenic activity in proliferative diabetic retinopathy

PubMed Central

Mohammad, Ghulam; Allegaert, Eef; Ahmad, Ajmal; Siddiquei, Mohammad Mairaj; Alam, Kaiser; Gikandi, Priscilla W.; De Hertogh, Gert; Opdenakker, Ghislain

2018-01-01

Purpose Matrix metalloproteinase-14 (MMP-14) is a transmembrane MMP that plays a critical role in promoting angiogenesis. We investigated the expression levels of MMP-14 and correlated the levels with clinical disease activity and with the levels of the angiogenic factors vascular endothelial growth factor (VEGF) and MMP-9 in proliferative diabetic retinopathy (PDR). To reinforce the findings at the functional level, we examined the expression of MMP-14 in the retinas of diabetic rats. Methods Vitreous samples from 34 patients with PDR and 18 nondiabetic patients and epiretinal membranes from 13 patients with PDR and the retinas of rats were studied with enzyme-linked immunosorbent assay, immunohistochemistry, western blotting, and real-time reverse transcription PCR (RT–PCR). Results The MMP-14, VEGF, and MMP-9 levels were statistically significantly higher in the vitreous samples from patients with PDR than in the samples from the nondiabetic controls (p<0.001 for all comparisons). The MMP-14 levels in patients with PDR with active neovascularization were statistically significantly higher than those in patients with inactive PDR (p<0.001). There were statistically significant positive correlations between levels of MMP-14 and levels of VEGF (r = 0.3; p = 0.032) and MMP-9 (r = 0.54; p<0.001). In the epiretinal membranes, MMP-14 was expressed in vascular endothelial cells, leukocytes, and myofibroblasts. Statistically significant positive correlations were detected between the numbers of blood vessels expressing CD31 and the numbers of blood vessels (r = 0.74; p = 0.004) and stromal cells (r = 0.72; p = 0.005) expressing MMP-14. Statistically significant increases of MMP-14 mRNA and protein were detected in rat retinas after induction of diabetes. Conclusions These results suggest that MMP-14 is involved in PDR angiogenesis. PMID:29853773

Generalized probabilistic theories and conic extensions of polytopes

NASA Astrophysics Data System (ADS)

Fiorini, Samuel; Massar, Serge; Patra, Manas K.; Tiwary, Hans Raj

2015-01-01

Generalized probabilistic theories (GPT) provide a general framework that includes classical and quantum theories. It is described by a cone C and its dual C*. We show that whether some one-way communication complexity problems can be solved within a GPT is equivalent to the recently introduced cone factorization of the corresponding communication matrix M. We also prove an analogue of Holevo's theorem: when the cone C is contained in {{{R}}n}, the classical capacity of the channel realized by sending GPT states and measuring them is bounded by log n. Polytopes and optimising functions over polytopes arise in many areas of discrete mathematics. A conic extension of a polytope is the intersection of a cone C with an affine subspace whose projection onto the original space yields the desired polytope. Extensions of polytopes can sometimes be much simpler geometric objects than the polytope itself. The existence of a conic extension of a polytope is equivalent to that of a cone factorization of the slack matrix of the polytope, on the same cone. We show that all 0/1 polytopes whose vertices can be recognized by a polynomial size circuit, which includes as a special case the travelling salesman polytope and many other polytopes from combinatorial optimization, have small conic extension complexity when the cone is the completely positive cone. Using recent exponential lower bounds on the linear extension complexity of polytopes, this provides an exponential gap between the communication complexity of GPT based on the completely positive cone and classical communication complexity, and a conjectured exponential gap with quantum communication complexity. Our work thus relates the communication complexity of generalizations of quantum theory to questions of mainstream interest in the area of combinatorial optimization.

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

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.

Structure of four executive functioning tests in healthy older adults.

PubMed

de Frias, Cindy M; Dixon, Roger A; Strauss, Esther

2006-03-01

The authors examined the factor structure of 4 indicators of executive functioning derived from 2 new (i.e., Hayling and Brixton) and 2 traditional (i.e., Stroop and Color Trails) tests. Data were from a cross-sectional sample of 55- to 85-year-old healthy adults (N=427) from the Victoria Longitudinal Study. Confirmatory factor analysis (LISREL 8.52) tested both a 2-factor model of Inhibition (Hayling, Stroop) and Shifting (Brixton, Color Trails) and a single-factor model. The 2-factor model did not fit the data because the covariance matrix of the factors was not positive definite. The single-factor model fit the data well, chi(2)(2, N=427)=0.32, p=.85, root-mean-square error of approximation (RMSEA)=.00, comparative fit index (CFI)=1.00, goodness-of-fit index (GFI)=1.00. Moreover, the single-factor structure of executive functioning was invariant (configural and metric) across gender, and invariant (configural with limited metric) across age. Structural relations showed that poorer executive functioning performance was related to older age and lower fluid intelligence, chi(2)(11, N=418)=23.04, p=.02, RMSEA=.05, CFI=.97, GFI=.98.

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

NASA Astrophysics Data System (ADS)

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

2014-09-01

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

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 matrix degrading and anabolic matrix regenerating activities.

Abnormalities in the Regulators of Angiogenesis in Patients with Scleroderma

PubMed Central

HUMMERS, LAURA K.; HALL, AMY; WIGLEY, FREDRICK M.; SIMONS, MICHAEL

2014-01-01

Objective To determine plasma levels of regulators of angiogenesis in patients with scleroderma and to correlate those levels with manifestations of scleroderma-related vascular disease. Methods Plasma levels of vascular endothelial growth factor (VEGF), platelet-derived growth factor (PDGF), fibroblast growth factor-2 (FGF-2), matrix metalloproteinase-9 (MMP-9), endostatin, pro-MMP-1, hepatocyte growth factor (HGF), placental growth factor (PlGF), and FGF-4 were examined by ELISA in a cross-sectional study of 113 patients with scleroderma and 27 healthy controls. Simple and multivariate regression models were used to look for associations between factor levels and clinical disease characteristics. Results There were marked differences in the levels of pro-angiogenic growth factors between patients with scleroderma and controls, with significant elevations of VEGF, PDGF, FGF-2, and PlGF among patients with scleroderma (p < 0.0001). Levels of MMP were also higher in scleroderma patients compared to controls (MMP-9 and pro-MMP-1) (p < 0.0001). Levels of the pro-angiogenic and anti-fibrotic factor, HGF, were noted to be lower in patients with scleroderma, but had a positive correlation with right ventricular systolic pressure (RVSP) as measured by echocardiogram (p < 0.0001) and the Raynaud Severity Score (p = 0.05). Endostatin (an anti-angiogenic factor) was notably higher in patients with scleroderma (p < 0.0001) and also correlated positively with RVSP (p = 0.023). Conclusion These results demonstrate striking abnormalities in the circulating regulators of angiogenesis in patients with scleroderma. The levels of some factors correlate with measures of vascular disease among patients with scleroderma. Dysregulated angiogenesis may play a role in the development of scleroderma vascular disease. PMID:19228661

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

Thermal form-factor approach to dynamical correlation functions of integrable lattice models

NASA Astrophysics Data System (ADS)

Göhmann, Frank; Karbach, Michael; Klümper, Andreas; Kozlowski, Karol K.; Suzuki, Junji

2017-11-01

We propose a method for calculating dynamical correlation functions at finite temperature in integrable lattice models of Yang-Baxter type. The method is based on an expansion of the correlation functions as a series over matrix elements of a time-dependent quantum transfer matrix rather than the Hamiltonian. In the infinite Trotter-number limit the matrix elements become time independent and turn into the thermal form factors studied previously in the context of static correlation functions. We make this explicit with the example of the XXZ model. We show how the form factors can be summed utilizing certain auxiliary functions solving finite sets of nonlinear integral equations. The case of the XX model is worked out in more detail leading to a novel form-factor series representation of the dynamical transverse two-point function.

[Preparation of hydrophilic matrix sustained release tablets of total lactones from Andrographis paniculata and study on its in vitro release mechanism].

PubMed

Xu, Fang-Fang; Shi, Wei; Zhang, Hui; Guo, Qing-Ming; Wang Zhen-Zhong; Bi, Yu-An; Wang, Zhi-Min; Xiao, Wei

2015-01-01

In this study, hydrophilic matrix sustained release tablets of total lactones from Andrographis paniculata were prepared and the in vitro release behavior were also evaluated. The optimal prescription was achieved by studying the main factor of the type and amount of hydroxypropyl methylcellulose (HPMC) using single factor test and evaluating through cumulative release of three lactones. No burst drug release from the obtained matrix tablets was observed. Drug release sustained to 14 h. The release mechanism of three lactones from A. paniculata was accessed by zero-order, first-order, Higuchi and Peppas equation. The release behavior of total lactones from A. paniculata was better agreed with Higuchi model and the drug release from the tablets was controlled by degradation of the matrix. The preparation of hydrophilic matrix sustained release tablets of total lactones from A. paniculata with good performance of drug release was simple.

Carcinogenesis: alterations in reciprocal interactions of normal functional structure of biologic systems.

PubMed

Davydyan, Garri

2015-12-01

The evolution of biologic systems (BS) includes functional mechanisms that in some conditions may lead to the development of cancer. Using mathematical group theory and matrix analysis, previously, it was shown that normally functioning BS are steady functional structures regulated by three basis regulatory components: reciprocal links (RL), negative feedback (NFB) and positive feedback (PFB). Together, they form an integrative unit maintaining system's autonomy and functional stability. It is proposed that phylogenetic development of different species is implemented by the splitting of "rudimentary" characters into two relatively independent functional parts that become encoded in chromosomes. The functional correlate of splitting mechanisms is RL. Inversion of phylogenetic mechanisms during ontogenetic development leads cell differentiation until cells reach mature states. Deterioration of reciprocal structure in the genome during ontogenesis gives rise of pathological conditions characterized by unsteadiness of the system. Uncontrollable cell proliferation and invasive cell growth are the leading features of the functional outcomes of malfunctioning systems. The regulatory element responsible for these changes is RL. In matrix language, pathological regulation is represented by matrices having positive values of diagonal elements ( TrA  > 0) and also positive values of matrix determinant ( detA  > 0). Regulatory structures of that kind can be obtained if the negative entry of the matrix corresponding to RL is replaced with the positive one. To describe not only normal but also pathological states of BS, a unit matrix should be added to the basis matrices representing RL, NFB and PFB. A mathematical structure corresponding to the set of these four basis functional patterns (matrices) is a split quaternion (coquaternion). The structure and specific role of basis elements comprising four-dimensional linear space of split quaternions help to understand what changes in mechanism of cell differentiation may lead to cancer development.

Harmonic elastic inclusions in the presence of point moment

NASA Astrophysics Data System (ADS)

Wang, Xu; Schiavone, Peter

2017-12-01

We employ conformal mapping techniques to design harmonic elastic inclusions when the surrounding matrix is simultaneously subjected to remote uniform stresses and a point moment located at an arbitrary position in the matrix. Our analysis indicates that the uniform and hydrostatic stress field inside the inclusion as well as the constant hoop stress along the entire inclusion-matrix interface (on the matrix side) are independent of the action of the point moment. In contrast, the non-elliptical shape of the harmonic inclusion depends on both the remote uniform stresses and the point moment.

Extended Krylov subspaces approximations of matrix functions. Application to computational electromagnetics

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

Druskin, V.; Lee, Ping; Knizhnerman, L.

There is now a growing interest in the area of using Krylov subspace approximations to compute the actions of matrix functions. The main application of this approach is the solution of ODE systems, obtained after discretization of partial differential equations by method of lines. In the event that the cost of computing the matrix inverse is relatively inexpensive, it is sometimes attractive to solve the ODE using the extended Krylov subspaces, originated by actions of both positive and negative matrix powers. Examples of such problems can be found frequently in computational electromagnetics.

Control of electrolyte fill to fuel cell stack

DOEpatents

Pollack, William

1982-01-01

A fuel cell stack which can be operated with cells in a horizontal position so that the fuel cell stack does not have to be taken out of operation when adding an electrolyte such as an acid. Acid is supplied to each matrix in a stack of fuel cells at a uniform, low pressure so that the matrix can either be filled initially or replenished with acid lost in operation of the cell, without exceeding the bubble pressure of the matrix or the flooding pressure of the electrodes on either side of the matrix. Acid control to each cell is achieved by restricting and offsetting the opening of electrolyte fill holes in the matrix relative to openings in the plates which sandwich the matrix and electrodes therebetween.

Platelet lysate and chondroitin sulfate loaded contact lenses to heal corneal lesions.

PubMed

Sandri, Giuseppina; Bonferoni, Maria Cristina; Rossi, Silvia; Delfino, Alessio; Riva, Federica; Icaro Cornaglia, Antonia; Marrubini, Giorgio; Musitelli, Giorgio; Del Fante, Claudia; Perotti, Cesare; Caramella, Carla; Ferrari, Franca

2016-07-25

Hemoderivative tear substitutes contain various ephiteliotrophic factors, such as growth factors (GF), involved in ocular surface homeostasis without immunogenic properties. The aim of the present work was the loading of platelet lysate into contact lenses to improve the precorneal permanence of platelet lysate growth factors on the ocular surface to enhance the treatment of corneal lesions. To this purpose, chondroitin sulfate, a sulfated glycosaminoglycan, which is normally present in the extracellular matrix, was associated with platelet lysate. In fact, chondroitin sulfate is capable of electrostatic interaction with positively charged growth factors, in particular, with bFGF, IGF, VEGF, PDGF and TGF-β, resulting in their stabilization and reduced degradation in solution. In the present work, various types of commercially available contact lenses have been loaded with chondroitin sulfate or chondroitin sulfate in association with platelet lysate to achieve a release of growth factors directly onto the corneal surface lesions. One type of contact lenses (PureVision(®)) showed in vitro good proliferation properties towards corneal cells and were able to enhance cut closure in cornea constructs. Copyright © 2016 Elsevier B.V. All rights reserved.

Effect of platelet lysate on human cells involved in different phases of wound healing.

PubMed

Barsotti, Maria Chiara; Chiara Barsotti, Maria; Losi, Paola; Briganti, Enrica; Sanguinetti, Elena; Magera, Angela; Al Kayal, Tamer; Feriani, Roberto; Di Stefano, Rossella; Soldani, Giorgio

2013-01-01

Platelets are rich in mediators able to positively affect cell activity in wound healing. Aim of this study was to characterize the effect of different concentrations of human pooled allogeneic platelet lysate on human cells involved in the different phases of wound healing (inflammatory phase, angiogenesis, extracellular matrix secretion and epithelialization). Platelet lysate effect was studied on endothelial cells, monocytes, fibroblasts and keratinocytes, in terms of viability and proliferation, migration, angiogenesis, tissue repair pathway activation (ERK1/2) and inflammatory response evaluation (NFκB). Results were compared both with basal medium and with a positive control containing serum and growth factors. Platelet lysate induced viability and proliferation at the highest concentrations tested (10% and 20% v/v). Whereas both platelet lysate concentrations increased cell migration, only 20% platelet lysate was able to significantly promote angiogenic activity (p<0.05 vs. control), comparably to the positive control. Both platelet lysate concentrations activated important inflammatory pathways such as ERK1/2 and NFκB with the same early kinetics, whereas the effect was different for later time-points. These data suggest the possibility of using allogeneic platelet lysate as both an alternative to growth factors commonly used for cell culture and as a tool for clinical regenerative application for wound healing.

Effect of Platelet Lysate on Human Cells Involved in Different Phases of Wound Healing

PubMed Central

Briganti, Enrica; Sanguinetti, Elena; Magera, Angela; Al Kayal, Tamer; Feriani, Roberto; Di Stefano, Rossella; Soldani, Giorgio

2013-01-01

Background Platelets are rich in mediators able to positively affect cell activity in wound healing. Aim of this study was to characterize the effect of different concentrations of human pooled allogeneic platelet lysate on human cells involved in the different phases of wound healing (inflammatory phase, angiogenesis, extracellular matrix secretion and epithelialization). Methodology/Principal Findings Platelet lysate effect was studied on endothelial cells, monocytes, fibroblasts and keratinocytes, in terms of viability and proliferation, migration, angiogenesis, tissue repair pathway activation (ERK1/2) and inflammatory response evaluation (NFκB). Results were compared both with basal medium and with a positive control containing serum and growth factors. Platelet lysate induced viability and proliferation at the highest concentrations tested (10% and 20% v/v). Whereas both platelet lysate concentrations increased cell migration, only 20% platelet lysate was able to significantly promote angiogenic activity (p<0.05 vs. control), comparably to the positive control. Both platelet lysate concentrations activated important inflammatory pathways such as ERK1/2 and NFκB with the same early kinetics, whereas the effect was different for later time-points. Conclusion/Significance These data suggest the possibility of using allogeneic platelet lysate as both an alternative to growth factors commonly used for cell culture and as a tool for clinical regenerative application for wound healing. PMID:24386412

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...

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),…

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…

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.

Optimizing indomethacin-loaded chitosan nanoparticle size, encapsulation, and release using Box-Behnken experimental design.

PubMed

Abul Kalam, Mohd; Khan, Abdul Arif; Khan, Shahanavaj; Almalik, Abdulaziz; Alshamsan, Aws

2016-06-01

Indomethacin chitosan nanoparticles (NPs) were developed by ionotropic gelation and optimized by concentrations of chitosan and tripolyphosphate (TPP) and stirring time by 3-factor 3-level Box-Behnken experimental design. Optimal concentration of chitosan (A) and TPP (B) were found 0.6mg/mL and 0.4mg/mL with 120min stirring time (C), with applied constraints of minimizing particle size (R1) and maximizing encapsulation efficiency (R2) and drug release (R3). Based on obtained 3D response surface plots, factors A, B and C were found to give synergistic effect on R1, while factor A has a negative impact on R2 and R3. Interaction of AB was negative on R1 and R2 but positive on R3. The factor AC was having synergistic effect on R1 and on R3, while the same combination had a negative effect on R2. The interaction BC was positive on the all responses. NPs were found in the size range of 321-675nm with zeta potentials (+25 to +32mV) after 6 months storage. Encapsulation, drug release, and content were in the range of 56-79%, 48-73% and 98-99%, respectively. In vitro drug release data were fitted in different kinetic models and pattern of drug release followed Higuchi-matrix type. Copyright © 2016 Elsevier B.V. All rights reserved.

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.

The Compact and Biologically Relevant Structure of Inter-α-inhibitor Is Maintained by the Chondroitin Sulfate Chain and Divalent Cations.

PubMed

Scavenius, Carsten; Nikolajsen, Camilla Lund; Stenvang, Marcel; Thøgersen, Ida B; Wyrożemski, Łukasz; Wisniewski, Hans-Georg; Otzen, Daniel E; Sanggaard, Kristian W; Enghild, Jan J

2016-02-26

Inter-α-inhibitor is a proteoglycan of unique structure. The protein consists of three subunits, heavy chain 1, heavy chain 2, and bikunin covalently joined by a chondroitin sulfate chain originating at Ser-10 of bikunin. Inter-α-inhibitor interacts with an inflammation-associated protein, tumor necrosis factor-inducible gene 6 protein, in the extracellular matrix. This interaction leads to transfer of the heavy chains from the chondroitin sulfate of inter-α-inhibitor to hyaluronan and consequently to matrix stabilization. Divalent cations and heavy chain 2 are essential co-factors in this transfer reaction. In the present study, we have investigated how divalent cations in concert with the chondroitin sulfate chain influence the structure and stability of inter-α-inhibitor. The results showed that Mg(2+) or Mn(2+), but not Ca(2+), induced a conformational change in inter-α-inhibitor as evidenced by a decrease in the Stokes radius and a bikunin chondroitin sulfate-dependent increase of the thermodynamic stability. This structure was shown to be essential for the ability of inter-α-inhibitor to participate in extracellular matrix stabilization. In addition, the data revealed that bikunin was positioned adjacent to both heavy chains and that the two heavy chains also were in close proximity. The chondroitin sulfate chain interacted with all protein components and inter-α-inhibitor dissociated when it was degraded. Conventional purification protocols result in the removal of the Mg(2+) found in plasma and because divalent cations influence the conformation and affect function it is important to consider this when characterizing the biological activity of inter-α-inhibitor. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Nanoparticulate delivery of agents for induced elastogenesis in three-dimensional collagenous matrices.

PubMed

Venkataraman, Lavanya; Sivaraman, Balakrishnan; Vaidya, Pratik; Ramamurthi, Anand

2016-12-01

The degradation of elastic matrix in the infrarenal aortic wall is a critical parameter underlying the formation and progression of abdominal aortic aneurysms. It is mediated by the chronic overexpression of matrix metalloprotease (MMP)-2 and MMP-9, leading to a progressive loss of elasticity and weakening of the aortic wall. Delivery of therapeutic agents to inhibit MMPs, while concurrently coaxing cell-based regenerative repair of the elastic matrix represents a potential strategy for slowing or arresting abdominal aortic aneurysm growth. Previous studies have demonstrated elastogenic induction of healthy and aneurysmal aortic smooth muscle cells and inhibition of MMPs, following exogenous delivery of elastogenic factors such as transforming growth factor (TGF)-β1, as well as MMP-inhibitors such as doxycycline (DOX) in two-dimensional culture. Based on these findings, and others that demonstrated elastogenic benefits of nanoparticulate delivery of these agents in two-dimensional culture, poly(lactide-co-glycolide) nanoparticles were developed for localized, controlled and sustained delivery of DOX and TGF-β1 to human aortic smooth muscle cells within a three-dimensional gels of type I collagen, which closely simulate the arterial tissue microenvironment. DOX and TGF-β1 released from these nanoparticles influenced elastogenic outcomes positively within the collagen constructs over 21 days of culture, which were comparable to that induced by exogenous supplementation of DOX and TGF-β1 within the culture medium. However, this was accomplished at doses ~20-fold lower than the exogenous dosages of the agents, illustrating that their localized, controlled and sustained delivery from nanoparticles embedded within a three-dimensional scaffold is an efficient strategy for directed elastogenesis. Copyright © 2014 John Wiley & Sons, Ltd. Copyright © 2014 John Wiley & Sons, Ltd.

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.

Matrix Metallopeptidase 14 Plays an Important Role in Regulating Tumorigenic Gene Expression and Invasion Ability of HeLa Cells.

PubMed

Zhang, Ying-Hui; Wang, Juan-Juan; Li, Min; Zheng, Han-Xi; Xu, Lan; Chen, You-Guo

2016-03-01

The objectives of this study were to investigate the functional effect of matrix metallopeptidase 14 (MMP14) on cell invasion in cervical cancer cells (HeLa line) and to study the underlying molecular mechanisms. Expression vector of short hairpin RNA targeting MMP14 was treated in HeLa cells, and then, transfection efficiency was verified by a florescence microscope. Transwell assay was used to investigate cell invasion ability in HeLa cells. Quantitative polymerase chain reaction and Western blotting analysis were used to detect the expression of MMP14 and relative factors in messenger RNA and protein levels, respectively. Matrix metallopeptidase 14 short hairpin RNA expression vector transfection obviously decreased MMP14 expression in messenger RNA and protein levels. Down-regulation of MMP14 suppressed invasion ability of HeLa cells and reduced transforming growth factor β1 and vascular endothelial growth factor B expressions. Furthermore, MMP14 knockdown decreased bone sialoprotein and enhanced forkhead box protein L2 expression in both RNA and protein levels. Matrix metallopeptidase 14 plays an important role in regulating invasion of HeLa cells. Matrix metallopeptidase 14 knockdown contributes to attenuating the malignant phenotype of cervical cancer cell.

Dimensions of postconcussive symptoms in children with mild traumatic brain injuries.

PubMed

Ayr, Lauren K; Yeates, Keith Owen; Taylor, H Gerry; Browne, Michael

2009-01-01

The dimensions of postconcussive symptoms (PCS) were examined in a prospective, longitudinal study of 186 8 to 15 year old children with mild traumatic brain injuries (TBI). Parents and children completed a 50-item questionnaire within 2 weeks of injury and again at 3 months after injury, rating the frequency of PCS on a 4-point scale. Common factor analysis with target rotation was used to rotate the ratings to four hypothesized dimensions, representing cognitive, somatic, emotional, and behavioral symptoms. The rotated factor matrix for baseline parent ratings was consistent with the target matrix. The rotated matrix for baseline child ratings was consistent with the target matrix for cognitive and somatic symptoms but not for emotional and behavioral symptoms. The rotated matrices for ratings obtained 3 months after injury were largely consistent with the target matrix derived from analyses of baseline ratings, except that parent ratings of behavioral symptoms did not cluster as before. Parent and child ratings of PCS following mild TBI yield consistent factors reflecting cognitive and somatic symptom dimensions, but dimensions of emotional and behavioral symptoms are less robust across time and raters. (JINS, 2009, 15, 19-30.).

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.

Movement behaviour within and beyond perceptual ranges in three small mammals: effects of matrix type and body mass.

PubMed

Prevedello, Jayme Augusto; Forero-Medina, Germán; Vieira, Marcus Vinícius

2010-11-01

1. For animal species inhabiting heterogeneous landscapes, the tortuosity of the dispersal path is a key determinant of the success in locating habitat patches. Path tortuosity within and beyond perceptual range must differ, and may be differently affected by intrinsic attributes of individuals and extrinsic environmental factors. Understanding how these factors interact to determine path tortuosity allows more accurate inference of successful movements between habitat patches. 2. We experimentally determined the effects of intrinsic (body mass and species identity) and extrinsic factors (distance to nearest forest fragment and matrix type) on the tortuosity of movements of three forest-dwelling didelphid marsupials, in a fragmented landscape of the Atlantic Forest, Brazil. 3. A total of 202 individuals were captured in forest fragments and released in three unsuitable matrix types (mowed pasture, abandoned pasture and manioc plantation), carrying spool-and-line devices. 4. Twenty-four models were formulated representing a priori hypotheses of major determinants of path tortuosity, grouped in three scenarios (only intrinsic factors, only extrinsic factors and models with combinations of both), and compared using a model selection approach. Models were tested separately for individuals released within the perceptual range of the species, and for individuals released beyond the perceptual range. 5. Matrix type strongly affected path tortuosity, with more obstructed matrix types hampering displacement of animals. Body mass was more important than species identity to determine path tortuosity, with larger animals moving more linearly. Increased distance to the fragment resulted in more tortuous paths, but actually reflects a threshold in perceptual range: linear paths within perceptual range, tortuous paths beyond. 6. The variables tested explained successfully path tortuosity, but only for animals released within the perceptual range. Other factors, such as wind intensity and direction of plantation rows, may be more important for individuals beyond their perceptual range. 7. Simplistic scenarios considering only intrinsic or extrinsic factors are inadequate to predict path tortuosity, and to infer dispersal success in heterogeneous landscapes. Perceptual range represents a fundamental threshold where the effects of matrix type, body mass and individual behaviour change drastically. © 2010 The Authors. Journal compilation © 2010 British Ecological Society.

The AdS{sub 5}xS{sup 5} superstring worldsheet S matrix and crossing symmetry

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

Janik, Romuald A.

2006-04-15

An S matrix satisfying the Yang-Baxter equation with symmetries relevant to the AdS{sub 5}xS{sup 5} superstring recently has been determined up to an unknown scalar factor. Such scalar factors are typically fixed using crossing relations; however, due to the lack of conventional relativistic invariance, in this case its determination remained an open problem. In this paper we propose an algebraic way to implement crossing relations for the AdS{sub 5}xS{sup 5} superstring worldsheet S matrix. We base our construction on a Hopf-algebraic formulation of crossing in terms of the antipode and introduce generalized rapidities living on the universal cover of themore » parameter space which is constructed through an auxillary, coupling-constant dependent, elliptic curve. We determine the crossing transformation and write functional equations for the scalar factor of the S matrix in the generalized rapidity plane.« less

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.

Tuning the Fano factor of graphene via Fermi velocity modulation

NASA Astrophysics Data System (ADS)

Lima, Jonas R. F.; Barbosa, Anderson L. R.; Bezerra, C. G.; Pereira, Luiz Felipe C.

2018-03-01

In this work we investigate the influence of a Fermi velocity modulation on the Fano factor of periodic and quasi-periodic graphene superlattices. We consider the continuum model and use the transfer matrix method to solve the Dirac-like equation for graphene where the electrostatic potential, energy gap and Fermi velocity are piecewise constant functions of the position x. We found that in the presence of an energy gap, it is possible to tune the energy of the Fano factor peak and consequently the location of the Dirac point, by a modulation in the Fermi velocity. Hence, the peak of the Fano factor can be used experimentally to identify the Dirac point. We show that for higher values of the Fermi velocity the Fano factor goes below 1/3 at the Dirac point. Furthermore, we show that in periodic superlattices the location of Fano factor peaks is symmetric when the Fermi velocity vA and vB is exchanged, however by introducing quasi-periodicity the symmetry is lost. The Fano factor usually holds a universal value for a specific transport regime, which reveals that the possibility of controlling it in graphene is a notable result.

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.

Monocyte activation by smooth muscle cell-derived matrices.

PubMed

Kaufmann, J; Jorgensen, R W; Martin, B M; Franzblau, C

1990-12-01

Mononuclear phagocytes adhere to and penetrate the vessel wall endothelium and contact the subendothelial space prior to the development of the atherosclerotic plaque. In an attempt to model the early events of plaque development we used an elastin-rich, multicomponent, cell-derived matrix from neonatal rat aortic smooth muscle cells as a substratum for monocytes. Using this model, we show that human monocyte morphology and metabolism are markedly altered by the matrix substratum. When a mixed mononuclear cell population is seeded on matrix or plastic, only monocytes adhere to the matrix surface. In contrast, lymphocytes as well as monocytes adhere to the plastic surface. The matrix-adherent monocytes develop large intracellular granules and form extensive clusters of individual cells. Metabolically, these cells develop sodium fluoride resistant non-specific esterase activity and their media contain more growth factor activity and PGE2. Although total protein synthesis is equivalent in both cultures, the matrix contact induces an increase in specific proteins in the media. We also show that a purified alpha-elastin substratum induces some, but not all, of the monocyte changes seen when using the matrix substratum. Using the alpha-elastin substratum, there is selective adhesion of monocytes and increased growth factor activity, however, the cells are morphologically different from the matrix-adherent cells. Thus, the use of the smooth muscle cell-derived matrix, in conjunction with purified matrix components, serves as a model that can provide insight into the mechanisms of monocyte adhesion and stimulation by the matrix environment that exists in vivo. Such mechanisms may be particularly important in atherogenesis.

Access of Hydrogen-Radicals to the Peptide-Backbone as a Measure for Estimating the Flexibility of Proteins Using Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry

PubMed Central

Takayama, Mitsuo; Nagoshi, Keishiro; Iimuro, Ryunosuke; Inatomi, Kazuma

2014-01-01

A factor for estimating the flexibility of proteins is described that uses a cleavage method of “in-source decay (ISD)” coupled with matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS). The MALDI-ISD spectra of bovine serum albumin (BSA), myoglobin and thioredoxin show discontinuous intense ion peaks originating from one-side preferential cleavage at the N-Cα bond of Xxx-Asp, Xxx-Asn, Xxx-Cys and Gly-Xxx residues. Consistent with these observations, Asp, Asn and Gly residues are also identified by other flexibility measures such as B-factor, turn preference, protection and fluorescence decay factors, while Asp, Asn, Cys and Gly residues are identified by turn preference factor based on X-ray crystallography. The results suggest that protein molecules embedded in/on MALDI matrix crystals partly maintain α-helix and that the reason some of the residues are more susceptible to ISD (Asp, Asn, Cys and Gly) and others less so (Ile and Val) is because of accessibility of the peptide backbone to hydrogen-radicals from matrix molecules. The hydrogen-radical accessibility in MALDI-ISD could therefore be adopted as a factor for measuring protein flexibility. PMID:24828203

Matrix isolation technique for the study of some factors affecting the partitioning of trace elements. [using vibrational spectroscopy

NASA Technical Reports Server (NTRS)

Grzybowski, J. M.; Allen, R. O.

1974-01-01

The factors that affect the preferred positions of cations in ionic solid solutions were investigated utilizing vibrational spectroscopy. Solid solutions of the sulfate and chromate ions codoped with La(+3) and Ca(+2) in a KBr host lattice were examined as a function of the polyvalent cation concentration. The cation-anion pairing process was found to be random for Ca(+2), whereas the formation of La(+3)-SO4(-2) ion pairs with a C2 sub v bonding geometry is highly preferential to any type of La(+3)-CrO4(-2) ion pair formation. The relative populations of ion pair site configurations are discussed in terms of an energy-entropy competition model which can be applied to the partition of trace elements during magmatic processes.

Enhancing Three-dimensional Movement Control System for Assemblies of Machine-Building Facilities

NASA Astrophysics Data System (ADS)

Kuzyakov, O. N.; Andreeva, M. A.

2018-01-01

Aspects of enhancing three-dimensional movement control system are given in the paper. Such system is to be used while controlling assemblies of machine-building facilities, which is a relevant issue. The base of the system known is three-dimensional movement control device with optical principle of action. The device consists of multi point light emitter and light receiver matrix. The processing of signals is enhanced to increase accuracy of measurements by switching from discrete to analog signals. Light receiver matrix is divided into four areas, and the output value of each light emitter in each matrix area is proportional to its luminance level. Thus, determing output electric signal value of each light emitter in corresponding area leads to determing position of multipoint light emitter and position of object tracked. This is done by using Case-based reasoning method, the precedent in which is described as integral signal value of each matrix area, coordinates of light receivers, which luminance level is high, and decision to be made in this situation.

The Effect of Multi Wall Carbon Nanotubes on Some Physical Properties of Epoxy Matrix

NASA Astrophysics Data System (ADS)

Al-Saadi, Tagreed M.; hammed Aleabi, Suad; Al-Obodi, Entisar E.; Abdul-Jabbar Abbas, Hadeel

2018-05-01

This research involves using epoxy resin as a matrix for making a composite material, while the multi wall carbon nanotubes (MWNCTs) is used as a reinforcing material with different fractions (0.0,0.02, 0.04, 0.06) of the matrix weight. The mechanical ( hardness ), electrical ( dielectric constant, dielectric loss factor, dielectric strength, electrical conductivity ), and thermal properties (thermal conductivity ) were studied. The results showed the increase of hardness, thermal conductivity, electrical conductivity and break down strength with the increase of MWCNT concentration, but the behavior of dielectric loss factor and dielectric constant is opposite that.

Chaos and random matrices in supersymmetric SYK

NASA Astrophysics Data System (ADS)

Hunter-Jones, Nicholas; Liu, Junyu

2018-05-01

We use random matrix theory to explore late-time chaos in supersymmetric quantum mechanical systems. Motivated by the recent study of supersymmetric SYK models and their random matrix classification, we consider the Wishart-Laguerre unitary ensemble and compute the spectral form factors and frame potentials to quantify chaos and randomness. Compared to the Gaussian ensembles, we observe the absence of a dip regime in the form factor and a slower approach to Haar-random dynamics. We find agreement between our random matrix analysis and predictions from the supersymmetric SYK model, and discuss the implications for supersymmetric chaotic systems.

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.

Large-region acoustic source mapping using a movable array and sparse covariance fitting.

PubMed

Zhao, Shengkui; Tuna, Cagdas; Nguyen, Thi Ngoc Tho; Jones, Douglas L

2017-01-01

Large-region acoustic source mapping is important for city-scale noise monitoring. Approaches using a single-position measurement scheme to scan large regions using small arrays cannot provide clean acoustic source maps, while deploying large arrays spanning the entire region of interest is prohibitively expensive. A multiple-position measurement scheme is applied to scan large regions at multiple spatial positions using a movable array of small size. Based on the multiple-position measurement scheme, a sparse-constrained multiple-position vectorized covariance matrix fitting approach is presented. In the proposed approach, the overall sample covariance matrix of the incoherent virtual array is first estimated using the multiple-position array data and then vectorized using the Khatri-Rao (KR) product. A linear model is then constructed for fitting the vectorized covariance matrix and a sparse-constrained reconstruction algorithm is proposed for recovering source powers from the model. The user parameter settings are discussed. The proposed approach is tested on a 30 m × 40 m region and a 60 m × 40 m region using simulated and measured data. Much cleaner acoustic source maps and lower sound pressure level errors are obtained compared to the beamforming approaches and the previous sparse approach [Zhao, Tuna, Nguyen, and Jones, Proc. IEEE Intl. Conf. on Acoustics, Speech and Signal Processing (ICASSP) (2016)].

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.

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…

UB Matrix Implementation for Inelastic Neutron Scattering Experiments

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

Lumsden, Mark D; Robertson, Lee; Yethiraj, Mohana

The UB matrix approach has been extended to handle inelastic neutron scattering experiments with differing k{sub i} and k{sub f}. We have considered the typical goniometer employed on triple-axis and time-of-flight spectrometers. Expressions are derived to allow for calculation of the UB matrix and for converting from observables to Q-energy space. In addition, we have developed appropriate modes for calculation of angles for a specified Q-energy position.

Active subspace: toward scalable low-rank learning.

PubMed

Liu, Guangcan; Yan, Shuicheng

2012-12-01

We address the scalability issues in low-rank matrix learning problems. Usually these problems resort to solving nuclear norm regularized optimization problems (NNROPs), which often suffer from high computational complexities if based on existing solvers, especially in large-scale settings. Based on the fact that the optimal solution matrix to an NNROP is often low rank, we revisit the classic mechanism of low-rank matrix factorization, based on which we present an active subspace algorithm for efficiently solving NNROPs by transforming large-scale NNROPs into small-scale problems. The transformation is achieved by factorizing the large solution matrix into the product of a small orthonormal matrix (active subspace) and another small matrix. Although such a transformation generally leads to nonconvex problems, we show that a suboptimal solution can be found by the augmented Lagrange alternating direction method. For the robust PCA (RPCA) (Candès, Li, Ma, & Wright, 2009 ) problem, a typical example of NNROPs, theoretical results verify the suboptimality of the solution produced by our algorithm. For the general NNROPs, we empirically show that our algorithm significantly reduces the computational complexity without loss of optimality.

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.

Weighted Geometric Dilution of Precision Calculations with Matrix Multiplication

PubMed Central

Chen, Chien-Sheng

2015-01-01

To enhance the performance of location estimation in wireless positioning systems, the geometric dilution of precision (GDOP) is widely used as a criterion for selecting measurement units. Since GDOP represents the geometric effect on the relationship between measurement error and positioning determination error, the smallest GDOP of the measurement unit subset is usually chosen for positioning. The conventional GDOP calculation using matrix inversion method requires many operations. Because more and more measurement units can be chosen nowadays, an efficient calculation should be designed to decrease the complexity. Since the performance of each measurement unit is different, the weighted GDOP (WGDOP), instead of GDOP, is used to select the measurement units to improve the accuracy of location. To calculate WGDOP effectively and efficiently, the closed-form solution for WGDOP calculation is proposed when more than four measurements are available. In this paper, an efficient WGDOP calculation method applying matrix multiplication that is easy for hardware implementation is proposed. In addition, the proposed method can be used when more than exactly four measurements are available. Even when using all-in-view method for positioning, the proposed method still can reduce the computational overhead. The proposed WGDOP methods with less computation are compatible with global positioning system (GPS), wireless sensor networks (WSN) and cellular communication systems. PMID:25569755

Spatiotemporal distribution of extracellular matrix changes during mouse duodenojejunal flexure formation.

PubMed

Onouchi, Sawa; Ichii, Osamu; Nakamura, Teppei; Elewa, Yaser Hosny Ali; Kon, Yasuhiro

2016-08-01

Although gut flexures characterize gut morphology, the mechanisms underlying flexure formation remain obscure. Previously, we analyzed the mouse duodenojejunal flexure (DJF) as a model for its formation and reported asymmetric morphologies between the inner and outer bending sides of the fetal mouse DJF, implying their contribution to DJF formation. We now present the extracellular matrix (ECM) as an important factor for gut morphogenesis. We investigate ECM distribution during mouse DJF formation by histological techniques. In the intercellular space of the gut wall, high Alcian-Blue positivity for proteoglycans shifted from the outer to the inner side of the gut wall during DJF formation. Immunopositivity for fibronectin, collagen I, or pan-tenascin was higher at the inner than at the outer side. Collagen IV and laminins localized to the epithelial basement membrane. Beneath the mesothelium at the pre-formation stage, collagen IV and laminin immunopositivity showed inverse results, corresponding to the different cellular characteristics at this site. At the post-formation stage, however, laminin positivity beneath the mesothelium was the reverse of that observed during the pre-formation stage. High immunopositivity for collagen IV and laminins at the inner gut wall mesenchyme of the post-formation DJF implied a different blood vessel distribution. We conclude that ECM distribution changes spatiotemporally during mouse DJF formation, indicating ECM association with the establishment of asymmetric morphologies during this process.

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 novel measurement techniques for PM-bound metals, which could enhance our understanding of the sources of atmospheric aerosols by providing us with measurements with finer time resolutions that otherwise would not have been possible using traditional filter-based measurement techniques.

A Note on Alternating Minimization Algorithm for the Matrix Completion Problem

DOE PAGES

Gamarnik, David; Misra, Sidhant

2016-06-06

Here, we consider the problem of reconstructing a low-rank matrix from a subset of its entries and analyze two variants of the so-called alternating minimization algorithm, which has been proposed in the past.We establish that when the underlying matrix has rank one, has positive bounded entries, and the graph underlying the revealed entries has diameter which is logarithmic in the size of the matrix, both algorithms succeed in reconstructing the matrix approximately in polynomial time starting from an arbitrary initialization.We further provide simulation results which suggest that the second variant which is based on the message passing type updates performsmore » significantly better.« less

A study of blood contamination of Siqveland matrix bands.

PubMed

Lowe, A H; Bagg, J; Burke, F J T; MacKenzie, D; McHugh, S

2002-01-12

AIMS To use a sensitive forensic test to measure blood contamination of used Siqveland matrix bands following routine cleaning and sterilisation procedures in general dental practice. Sixteen general dental practices in the West of Scotland participated. Details of instrument cleaning procedures were recorded for each practice. A total of 133 Siqveland matrix bands were recovered following cleaning and sterilisation and were examined for residual blood contamination by the Kastle-Meyer test, a well-recognised forensic technique. Ultrasonic baths were used for the cleaning of 62 (47%) bands and retainers and the remainder (53%) were hand scrubbed prior to autoclaving. Overall, 21% of the matrix bands and 19% of the retainers gave a positive Kastle-Meyer test, indicative of residual blood contamination, following cleaning and sterilisation. In relation to cleaning method, 34% of hand-scrubbed bands and 32% of hand-scrubbed retainers were positive for residual blood by the Kastle-Meyer test compared with 6% and 3% respectively of ultrasonically cleaned bands and retainers (P < 0.001). If Siqveland matrix bands are re-processed in the assembled state, then adequate pre-sterilisation cleaning cannot be achieved reliably. Ultrasonic baths are significantly more effective than hand cleaning for these items of equipment.

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.

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.

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.

Structural characterization of phospholipids by matrix-assisted laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry.

PubMed

Marto, J A; White, F M; Seldomridge, S; Marshall, A G

1995-11-01

Matrix-assisted laser desorption/ionization (MALDI) Fourier transform ion cyclotron resonance mass spectrometry provides for structural analysis of the principal biological phospholipids: glycerophosphatidylcholine, -ethanolamine, -serine, and -inositol. Both positive and negative molecular or quasimolecular ions are generated in high abundance. Isolated molecular ions may be collisionally activated in the source side of a dual trap mass analyzer, yielding fragments serving to identify the polar head group (positive ion mode) and fatty acid side chains (negative ion mode). Azimuthal quadrupolar excitation following collisionally activated dissociation refocuses productions close to the solenoid axis; subsequent transfer of product ions to the analyzer ion trap allows for high-resolution mass analysis. Cyro-cooling of the sample probe with liquid nitrogen greatly reduces matrix adduction encountered in the negative ion mode.

Differential modulation of degradative and repair responses of interleukin-1-treated chondrocytes by platelet-derived growth factor.

PubMed Central

Harvey, A K; Stack, S T; Chandrasekhar, S

1993-01-01

Interleukin 1 (IL-1) plays a dual role in cartilage matrix degeneration by promoting extracellular proteinase action such as the matrix metalloproteinases (increased degradation) and by suppressing the synthesis of extracellular matrix molecules (inhibition of repair). Platelet-derived growth factor (PDGF) is a wound-healing hormone which is released along with IL-1 during the inflammatory response. Since previous studies have shown that PDGF enhances IL-1 alpha effects on metalloproteinase activity, in this report, we have examined whether PDGF modifies IL-1 beta effects on cartilage proteoglycan synthesis. Initially, we confirmed that rabbit articular chondrocytes treated with IL-1 beta + PDGF induced higher proteinase activity, in comparison with IL-1-treated cells. We further observed that the increased proteinase activity correlated with an increase in the synthesis of collagenase/stromelysin proteins and a corresponding increase in the steady-state mRNA levels for both the enzymes. Studies on IL-1 receptor expression suggested that PDGF caused an increase in IL-1 receptor expression which, by augmenting the IL-1 response, may have led to the increase in proteinase induction. Analysis of proteoglycan synthesis confirmed that IL-1 reduced the incorporation of sulphated proteoglycan, aggrecan, into the extracellular matrix of chondrocytes, whereas PDGF stimulated it. However, cells treated with IL-1 + PDGF synthesized normal levels of aggrecan. This is in contrast with cells treated with IL-1 + fibroblast growth factor, in which case only proteinase activity was potentiated. The results allow us to conclude that (a) the two effector functions that play a role in matrix remodelling, namely matrix lysis (proteinase induction) and matrix repair (proteoglycan synthesis), occur via distinct pathways and (b) PDGF may play a crucial role in cartilage repair by initially causing matrix degradation followed by promoting new matrix synthesis. Images Figure 1 Figure 2 Figure 5 Figure 6 PMID:8503839

[Special application of matrix-assisted laser desorption ionization time-of-flight mass spectrometry in clinical microbiological diagnostics].

PubMed

Nagy, Erzsébet; Abrók, Marianna; Bartha, Noémi; Bereczki, László; Juhász, Emese; Kardos, Gábor; Kristóf, Katalin; Miszti, Cecilia; Urbán, Edit

2014-09-21

Matrix-assisted laser desorption ionization time-of-flight mass spectrometry as a new possibility for rapid identification of bacteria and fungi revolutionized the clinical microbiological diagnostics. It has an extreme importance in the routine microbiological laboratories, as identification of the pathogenic species rapidly will influence antibiotic selection before the final determination of antibiotic resistance of the isolate. The classical methods for identification of bacteria or fungi, based on biochemical tests, are influenced by many environmental factors. The matrix-assisted laser desorption ionization time-of-flight mass spectrometry is a rapid method which is able to identify a great variety of the isolated bacteria and fungi based on the composition of conserved ribosomal proteins. Recently several other applications of the method have also been investigated such as direct identification of pathogens from the positive blood cultures. There are possibilities to identify bacteria from the urine samples in urinary tract infection or from other sterile body fluids. Using selective enrichment broth Salmonella sp from the stool samples can be identified more rapidly, too. The extended spectrum beta-lactamase or carbapenemase production of the isolated bacteria can be also detected by this method helping the antibiotic selection in some cases. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry based methods are suitable to investigate changes in deoxyribonucleic acid or ribonucleic acid, to carry out rapid antibiotic resistance determination or other proteomic analysis. The aim of this paper is to give an overview about present possibilities of using this technique in the clinical microbiological routine procedures.

Association between matrix metalloproteinase-10 concentration and smoking in individuals without cardiovascular disease.

PubMed

Páramo, José A; Beloqui, Oscar; Rodríguez, José A; Diez, Javier; Orbe, Josune

2008-12-01

Smoking is an important cardiovascular risk factor whose underlying mechanism is incompletely understood. However, it has been suggested that alterations in the balance between synthesis and degradation of the extracellular matrix (ECM) may play a role. The aim of this study was to determine whether there is an independent association between smoking and the concentration of circulating metalloproteinases (MMPs) in individuals without cardiovascular disease. Metabolic parameters, the carotid intima-media thickness (IMT), inflammatory markers (fibrinogen, C-reactive protein and interleukin-6), markers of endothelial damage (e.g., von Willebrand factor), and the concentration of MMP-1, -9 and -10 and tissue inhibitor of metalloproteinase-1 (TIMP-1) were assessed in 400 asymptomatic individuals with cardiovascular risk factors. Subjects were divided into non-smokers (n=195), smokers (n=118) and former smokers (n=87). In addition, global cardiovascular risk was determined from PROCAM and REGICOR scores. Both MMP-1 and MMP-10 concentrations were significantly higher in smokers than non-smokers (P< .05 and P< .001, respectively), though there was no difference in the levels of MMP-9, TIMP-1, IMT and other inflammatory parameters. There were positive correlations between the MMP-10 concentration and PROCAM and REGICOR scores (P< .001). Multivariate analysis showed that there was still an association between smoking and the MMP-10 concentration after adjustment for age, sex and other cardiovascular risk factors (P< .001). Multiple regression analysis showed that smoking accounted for 28% of the variability in the MMP-10 concentration. There was an independent association between smoking and the MMP-10 concentration in asymptomatic individuals. This relationship between MMP-10 and the ECM may indicate a mechanism through which this MMP contributes to smoking-related atherosclerosis.

M2 macrophages induce ovarian cancer cell proliferation via a heparin binding epidermal growth factor/matrix metalloproteinase 9 intercellular feedback loop.

PubMed

Carroll, Molly J; Kapur, Arvinder; Felder, Mildred; Patankar, Manish S; Kreeger, Pamela K

2016-12-27

In ovarian cancer, a high ratio of anti-inflammatory M2 to pro-inflammatory M1 macrophages correlates with poor patient prognosis. The mechanisms driving poor tumor outcome as a result of the presence of M2 macrophages in the tumor microenvironment remain unclear and are challenging to study with current techniques. Therefore, in this study we utilized a micro-culture device previously developed by our lab to model concentrated paracrine signaling in order to address our hypothesis that interactions between M2 macrophages and ovarian cancer cells induce tumor cell proliferation. Using the micro-culture device, we determined that co-culture with M2-differentiated primary macrophages or THP-1 increased OVCA433 proliferation by 10-12%. This effect was eliminated with epidermal growth factor receptor (EGFR) or heparin-bound epidermal growth factor (HB-EGF) neutralizing antibodies and HBEGF expression in peripheral blood mononuclear cells from ovarian cancer patients was 9-fold higher than healthy individuals, suggesting a role for HB-EGF in tumor progression. However, addition of HB-EGF at levels secreted by macrophages or macrophage-conditioned media did not induce proliferation to the same extent, indicating a role for other factors in this process. Matrix metalloproteinase-9, MMP-9, which cleaves membrane-bound HB-EGF, was elevated in co-culture and its inhibition decreased proliferation. Utilizing inhibitors and siRNA against MMP9 in each population, we determined that macrophage-secreted MMP-9 released HB-EGF from macrophages, which increased MMP9 in OVCA433, resulting in a positive feedback loop to drive HB-EGF release and increase proliferation in co-culture. Identification of multi-cellular interactions such as this may provide insight into how to most effectively control ovarian cancer progression.

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

Zhang, Yaping; Williams, Brent J.; Goldstein, Allen H.

Here, we present a rapid method for apportioning the sources of atmospheric organic aerosol composition measured by gas chromatography–mass spectrometry methods. Here, we specifically apply this new analysis method to data acquired on a thermal desorption aerosol gas chromatograph (TAG) system. Gas chromatograms are divided by retention time into evenly spaced bins, within which the mass spectra are summed. A previous chromatogram binning method was introduced for the purpose of chromatogram structure deconvolution (e.g., major compound classes) (Zhang et al., 2014). Here we extend the method development for the specific purpose of determining aerosol samples' sources. Chromatogram bins are arrangedmore » into an input data matrix for positive matrix factorization (PMF), where the sample number is the row dimension and the mass-spectra-resolved eluting time intervals (bins) are the column dimension. Then two-dimensional PMF can effectively do three-dimensional factorization on the three-dimensional TAG mass spectra data. The retention time shift of the chromatogram is corrected by applying the median values of the different peaks' shifts. Bin width affects chemical resolution but does not affect PMF retrieval of the sources' time variations for low-factor solutions. A bin width smaller than the maximum retention shift among all samples requires retention time shift correction. A six-factor PMF comparison among aerosol mass spectrometry (AMS), TAG binning, and conventional TAG compound integration methods shows that the TAG binning method performs similarly to the integration method. However, the new binning method incorporates the entirety of the data set and requires significantly less pre-processing of the data than conventional single compound identification and integration. In addition, while a fraction of the most oxygenated aerosol does not elute through an underivatized TAG analysis, the TAG binning method does have the ability to achieve molecular level resolution on other bulk aerosol components commonly observed by the AMS.« less

Wintertime aerosol chemical composition and source apportionment of the organic fraction across Ireland

NASA Astrophysics Data System (ADS)

Ovadnevaite, J.; Lin, C.; Ceburnis, D.; Huang, R. J. J.; O'Dowd, C. D. D.

2017-12-01

A national wide characterization of PM1 was studied for the first time using a high-time resolution Aerosol Chemical Speciation Monitor (ACSM) and Aethalometer in Ireland during the heating season. Dublin, the capital of Ireland, is the most polluted area with an average PM1 of 7.6 μg/m3, with frequent occurrence of peak concentration over 200 μg/m3 primarily due to solid fuels burning, while Mace Head, in the west coast, is least polluted with an average PM1 of 0.8 μg/m3 due to the distance from the emission sources. The organic aerosol is the most dominant species across Ireland, contributing 65%, 58%, 32%, 33% to total PM1 mass in Dublin, Birr, Carnsore Point, and Mace Head, respectively. Birr, a small town in the midland of Ireland, has comparable PM1 levels (4.8 μg/m3) and similar chemical compositions with that in Dublin. Carnsore Point, on the southeast coast, has similar composition with that at Mace Head, but nearly 3 times the levels of PM1 mass due to its relative closeness to other European countries. Positive matrix factorization (PMF) with the multi-linear engine (ME-2) was performed on the organic matrix to quantify the contribution of factor candidates. Peat burning was found to be the dominant factor across Ireland, contributing more than 40% of the total organic mass in Dublin and Birr while OOA is dominant at rural Carnsore Point and Mace Head. Possible geographic origins of PM1 species and organic factors using polar plots were explored. The findings of solid fuels burning (primarily peat burning) driving the pollution episodes suggest an elimination or controlled emission of solid fuels burning would reduce PM1 by at least 50%.

Factorization in large-scale many-body calculations

DOE PAGES

Johnson, Calvin W.; Ormand, W. Erich; Krastev, Plamen G.

2013-08-07

One approach for solving interacting many-fermion systems is the configuration-interaction method, also sometimes called the interacting shell model, where one finds eigenvalues of the Hamiltonian in a many-body basis of Slater determinants (antisymmetrized products of single-particle wavefunctions). The resulting Hamiltonian matrix is typically very sparse, but for large systems the nonzero matrix elements can nonetheless require terabytes or more of storage. An alternate algorithm, applicable to a broad class of systems with symmetry, in our case rotational invariance, is to exactly factorize both the basis and the interaction using additive/multiplicative quantum numbers; such an algorithm recreates the many-body matrix elementsmore » on the fly and can reduce the storage requirements by an order of magnitude or more. Here, we discuss factorization in general and introduce a novel, generalized factorization method, essentially a ‘double-factorization’ which speeds up basis generation and set-up of required arrays. Although we emphasize techniques, we also place factorization in the context of a specific (unpublished) configuration-interaction code, BIGSTICK, which runs both on serial and parallel machines, and discuss the savings in memory due to factorization.« less

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.

Role of G protein-coupled estrogen receptor-1, matrix metalloproteinases 2 and 9, and heparin binding epidermal growth factor-like growth factor in estradiol-17β-stimulated bovine satellite cell proliferation.

PubMed

Kamanga-Sollo, E; Thornton, K J; White, M E; Dayton, W R

2014-10-01

In feedlot steers, estradiol-17β (E2) and combined E2 and trenbolone acetate (a testosterone analog) implants enhance rate and efficiency of muscle growth; and, consequently, these compounds are widely used as growth promoters. Although the positive effects of E2 on rate and efficiency of bovine muscle growth are well established, the mechanisms involved in these effects are not well understood. Combined E2 and trenbolone acetate implants result in significantly increased muscle satellite cell number in feedlot steers. Additionally, E2 treatment stimulates proliferation of cultured bovine satellite cells (BSC). Studies in nonmuscle cells have shown that binding of E2 to G protein-coupled estrogen receptor (GPER)-1 results in activation of matrix metalloproteinases 2 and 9 (MMP2/9) resulting in proteolytic release of heparin binding epidermal growth factor-like growth factor (hbEGF) from the cell surface. Released hbEGF binds to and activates the epidermal growth factor receptor resulting in increased proliferation. To assess if GPER-1, MMP2/9, and/or hbEGF are involved in the mechanism of E2-stimulated BSC proliferation, we have examined the effects of G36 (a specific inhibitor of GPER-1), CRM197 (a specific inhibitor of hbEGF), and MMP-2/MMP-9 Inhibitor II (an inhibitor of MMP2/9 activity) on E2-stimulated BSC proliferation. Inhibition of GPER-1, MMP2/9, or hbEGF suppresses E2-stimulated BSC proliferation (P < 0.001) suggesting that all these are required in order for E2 to stimulate BSC proliferation. These results strongly suggest that E2 may stimulate BSC proliferation by binding to GPER-1 resulting in MMP2/9-catalyzed release of cell membrane-bound hbEGF and subsequent activation of epidermal growth factor receptor by binding of released hbEGF. Copyright © 2014 Elsevier Inc. All rights reserved.

Long-term measurements of submicrometer aerosol chemistry at the Southern Great Plains (SGP) using an Aerosol Chemical Speciation Monitor (ACSM)

DOE PAGES

Parworth, Caroline; Tilp, Alison; Fast, Jerome; ...

2015-04-01

In this study the long-term trends of non-refractory submicrometer aerosol (NR-PM1) composition and mass concentration measured by an Aerosol Chemical Speciation Monitor (ACSM) at the Atmospheric Radiation Measurement (ARM) program's Southern Great Plains (SGP) site are discussed. NR-PM1 data was recorded at ~30 min intervals over a period of 19 months between November 2010 and June 2012. Positive Matrix Factorization (PMF) was performed on the measured organic mass spectral matrix using a rolling window technique to derive factors associated with distinct sources, evolution processes, and physiochemical properties. The rolling window approach also allows us to capture the dynamic variations ofmore » the chemical properties in the organic aerosol (OA) factors over time. Three OA factors were obtained including two oxygenated OA (OOA) factors, differing in degrees of oxidation, and a biomass burning OA (BBOA) factor. Back trajectory analyses were performed to investigate possible sources of major NR-PM1 species at the SGP site. Organics dominated NR-PM1 mass concentration for the majority of the study with the exception of winter, when ammonium nitrate increases due to transport of precursor species from surrounding urban and agricultural areas and also due to cooler temperatures. Sulfate mass concentrations have little seasonal variation with mixed regional and local sources. In the spring BBOA emissions increase and are mainly associated with local fires. Isoprene and carbon monoxide emission rates were obtained by the Model of Emissions of Gases and Aerosols from Nature (MEGAN) and the 2011 U.S. National Emissions Inventory to represent the spatial distribution of biogenic and anthropogenic sources, respectively. The combined spatial distribution of isoprene emissions and air mass trajectories suggest that biogenic emissions from the southeast contribute to SOA formation at the SGP site during the summer.« less

An Upper Bound on High Speed Satellite Collision Probability When Only One Object has Position Uncertainty Information

NASA Technical Reports Server (NTRS)

Frisbee, Joseph H., Jr.

2015-01-01

Upper bounds on high speed satellite collision probability, PC †, have been investigated. Previous methods assume an individual position error covariance matrix is available for each object. The two matrices being combined into a single, relative position error covariance matrix. Components of the combined error covariance are then varied to obtain a maximum PC. If error covariance information for only one of the two objects was available, either some default shape has been used or nothing could be done. An alternative is presented that uses the known covariance information along with a critical value of the missing covariance to obtain an approximate but potentially useful Pc upper bound.

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.

Active tissue stiffness modulation controls valve interstitial cell phenotype and osteogenic potential in 3D culture.

PubMed

Duan, Bin; Yin, Ziying; Hockaday Kang, Laura; Magin, Richard L; Butcher, Jonathan T

2016-05-01

Calcific aortic valve disease (CAVD) progression is a highly dynamic process whereby normally fibroblastic valve interstitial cells (VIC) undergo osteogenic differentiation, maladaptive extracellular matrix (ECM) composition, structural remodeling, and tissue matrix stiffening. However, how VIC with different phenotypes dynamically affect matrix properties and how the altered matrix further affects VIC phenotypes in response to physiological and pathological conditions have not yet been determined. In this study, we develop 3D hydrogels with tunable matrix stiffness to investigate the dynamic interplay between VIC phenotypes and matrix biomechanics. We find that VIC populated within hydrogels with valve leaflet like stiffness differentiate towards myofibroblasts in osteogenic media, but surprisingly undergo osteogenic differentiation when cultured within lower initial stiffness hydrogels. VIC differentiation progressively stiffens the hydrogel microenvironment, which further upregulates both early and late osteogenic markers. These findings identify a dynamic positive feedback loop that governs acceleration of VIC calcification. Temporal stiffening of pathologically lower stiffness matrix back to normal level, or blocking the mechanosensitive RhoA/ROCK signaling pathway, delays the osteogenic differentiation process. Therefore, direct ECM biomechanical modulation can affect VIC phenotypes towards and against osteogenic differentiation in 3D culture. These findings highlight the importance of the homeostatic maintenance of matrix stiffness to restrict pathological VIC differentiation. We implement 3D hydrogels with tunable matrix stiffness to investigate the dynamic interaction between valve interstitial cells (VIC, major cell population in heart valve) and matrix biomechanics. This work focuses on how human VIC responses to changing 3D culture environments. Our findings identify a dynamic positive feedback loop that governs acceleration of VIC calcification, which is the hallmark of calcific aortic valve disease. Temporal stiffening of pathologically lower stiffness matrix back to normal level, or blocking the mechanosensitive signaling pathway, delays VIC osteogenic differentiation. Our findings provide an improved understanding of VIC-matrix interactions to aid in interpretation of VIC calcification studies in vitro and suggest that ECM disruption resulting in local tissue stiffness decreases may promote calcific aortic valve disease. Copyright © 2016 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Modeling invasive breast cancer: growth factors propel progression of HER2-positive premalignant lesions

PubMed Central

Pradeep, C-R; Zeisel, A; Köstler, WJ; Lauriola, M; Jacob-Hirsch, J; Haibe-Kains, B; Amariglio, N; Ben-Chetrit, N; Emde, A; Solomonov, I; Neufeld, G; Piccart, M; Sagi, I; Sotiriou, C; Rechavi, G; Domany, E; Desmedt, C; Yarden, Y

2013-01-01

The HER2/neu oncogene encodes a receptor-like tyrosine kinase whose overexpression in breast cancer predicts poor prognosis and resistance to conventional therapies. However, the mechanisms underlying aggressiveness of HER2 (human epidermal growth factor receptor 2)-overexpressing tumors remain incompletely understood. Because it assists epidermal growth factor (EGF) and neuregulin receptors, we overexpressed HER2 in MCF10A mammary cells and applied growth factors. HER2-overexpressing cells grown in extracellular matrix formed filled spheroids, which protruded outgrowths upon growth factor stimulation. Our transcriptome analyses imply a two-hit model for invasive growth: HER2-induced proliferation and evasion from anoikis generate filled structures, which are morphologically and transcriptionally analogous to preinvasive patients’ lesions. In the second hit, EGF escalates signaling and transcriptional responses leading to invasive growth. Consistent with clinical relevance, a gene expression signature based on the HER2/EGF-activated transcriptional program can predict poorer prognosis of a subgroup of HER2-overexpressing patients. In conclusion, the integration of a three-dimensional cellular model and clinical data attributes progression of HER2-overexpressing lesions to EGF-like growth factors acting in the context of the tumor's microenvironment. PMID:22139081

Source Apportionment of Atmospheric Polychlorinated Biphenyls in New Jersey 1997-2011.

PubMed

Praipipat, Pornsawai; Meng, Qingyu; Miskewitz, Robert J; Rodenburg, Lisa A

2017-02-07

Concentrations of polychlorinated biphenyls (PCBs) in the Delaware River currently exceed the Water Quality Criteria of 16 pg/L for the sum of PCBs due in part to atmospheric deposition. The purpose of this work was to use a source apportionment tool called Positive Matrix Factorization (PMF) to identify the sources of PCBs to the atmosphere in this area and determine whether their concentrations are declining over time. The data set was compiled by the Delaware Atmospheric Deposition Network (DADN) from samples taken in Camden, NJ from 1999 to 2011 and New Brunswick, NJ from 1997 to 2011. The PMF analysis revealed four resolved factors at each site. The factors that dominate the PCB burden in the atmosphere at both Camden and New Brunswick resemble Aroclor 1242. These factors declined in concentration during some portions of the monitoring period, but this decline slowed or stopped during 2003-2011. None of the factors displayed consistent declines in concentration throughout the monitoring periods, and some factors actually increased in concentration during some periods. This suggests natural attenuation alone will not control atmospheric PCB concentrations, and additional efforts are needed to control PCB atmospheric emissions as well as the numerous other sources of PCBs to the estuary.

IL-17s adopt a cystine knot fold: structure and activity of a novel cytokine, IL-17F, and implications for receptor binding

PubMed Central

Hymowitz, Sarah G.; Filvaroff, Ellen H.; Yin, JianPing; Lee, James; Cai, Liping; Risser, Philip; Maruoka, Miko; Mao, Weiguang; Foster, Jessica; Kelley, Robert F.; Pan, Guohua; Gurney, Austin L.; de Vos, Abraham M.; Starovasnik, Melissa A.

2001-01-01

The proinflammatory cytokine interleukin 17 (IL-17) is the founding member of a family of secreted proteins that elicit potent cellular responses. We report a novel human IL-17 homolog, IL-17F, and show that it is expressed by activated T cells, can stimulate production of other cytokines such as IL-6, IL-8 and granulocyte colony-stimulating factor, and can regulate cartilage matrix turnover. Unexpectedly, the crystal structure of IL-17F reveals that IL-17 family members adopt a monomer fold typical of cystine knot growth factors, despite lacking the disulfide responsible for defining the canonical ‘knot’ structure. IL-17F dimerizes in a parallel manner like neurotrophins, and features an unusually large cavity on its surface. Remarkably, this cavity is located in precisely the same position where nerve growth factor binds its high affinity receptor, TrkA, suggesting further parallels between IL-17s and neurotrophins with respect to receptor recognition. PMID:11574464

Surface water polycyclic aromatic hydrocarbons (PAH) in urban areas of Nanjing, China.

PubMed

Wang, Chunhui; Zhou, Shenglu; Wu, Shaohua; Song, Jing; Shi, Yaxing; Li, Baojie; Chen, Hao

2017-10-01

The concentration, sources and environmental risks of polycyclic aromatic hydrocarbons (PAHs) in surface water in urban areas of Nanjing were investigated. The range of ∑ 16 PAHs concentration is between 4,076 and 29,455 ng/L, with a mean of 17,212 ng/L. The composition of PAHs indicated that 2- and 3-ring PAHs have the highest proportion in all PAHs, while the 5- and 6-ring PAHs were the least in proportion. By diagnostic ratio analysis, combustion and petroleum were a mixture input that contributed to the water PAH in urban areas of Nanjing. Positive matrix factorization quantitatively identified four factors, including coke oven, coal combustion, oil source, and vehicle emission, as the main sources. Toxic equivalency factors of BaP (BaP eq ) evaluate the environmental risks of PAHs and indicate the PAH concentration in surface water in urban areas of Nanjing had been polluted and might cause potential environmental risks. Therefore, the PAH contamination in surface water in urban areas of Nanjing should draw considerable attention.

Inhibition of Osteoclast Differentiation and Bone Resorption by N-Methylpyrrolidone*

PubMed Central

Ghayor, Chafik; Correro, Rita M.; Lange, Katrin; Karfeld-Sulzer, Lindsay S.; Grätz, Klaus W.; Weber, Franz E.

2011-01-01

Regulation of RANKL (receptor activator of nuclear factor κB ligand)-induced osteoclast differentiation is of current interest in the development of antiresorptive agents. Osteoclasts are multinucleated cells that play a crucial role in bone resorption. In this study, we investigated the effects of N-methylpyrrolidone (NMP) on the regulation of RANKL-induced osteoclastogenesis. NMP inhibited RANKL-induced tartrate-resistant acid phosphatase activity and the formation of tartrate-resistant acid phosphatase-positive multinucleated cells. The RANKL-induced expression of NFATc1 (nuclear factor of activated T cells, cytoplasmic 1) and c-Fos, which are key transcription factors for osteoclastogenesis, was also reduced by treatment with NMP. Furthermore, NMP induced disruption of the actin rings and decreased the mRNAs of cathepsin K and MMP-9 (matrix metalloproteinase-9), both involved in bone resorption. Taken together, these results suggest that NMP inhibits osteoclast differentiation and attenuates bone resorption. Therefore, NMP could prove useful for the treatment of osteoporosis or other bone diseases associated with excessive bone resorption. PMID:21613210

Source apportionment of exposures to volatile organic compounds. I. Evaluation of receptor models using simulated exposure data

NASA Astrophysics Data System (ADS)

Miller, Shelly L.; Anderson, Melissa J.; Daly, Eileen P.; Milford, Jana B.

Four receptor-oriented source apportionment models were evaluated by applying them to simulated personal exposure data for select volatile organic compounds (VOCs) that were generated by Monte Carlo sampling from known source contributions and profiles. The exposure sources modeled are environmental tobacco smoke, paint emissions, cleaning and/or pesticide products, gasoline vapors, automobile exhaust, and wastewater treatment plant emissions. The receptor models analyzed are chemical mass balance, principal component analysis/absolute principal component scores, positive matrix factorization (PMF), and graphical ratio analysis for composition estimates/source apportionment by factors with explicit restriction, incorporated in the UNMIX model. All models identified only the major contributors to total exposure concentrations. PMF extracted factor profiles that most closely represented the major sources used to generate the simulated data. None of the models were able to distinguish between sources with similar chemical profiles. Sources that contributed <5% to the average total VOC exposure were not identified.

Heavy metals in particulate and colloidal matter from atmospheric deposition of urban Guangzhou, South China.

PubMed

Huang, Wen; Duan, Dandan; Zhang, Yulong; Cheng, Hefa; Ran, Yong

2014-08-30

Suspended particulate matter (SPM) and colloidal matter (COM) in annual dry and wet deposition samples in urban Guangzhou were for the first time collected, and their trace metals were investigated by using inductively coupled plasma mass spectrometry (ICP-MS). The deposition flux of SPM and of metal elements varied largely among the investigated seasons, and reached the maximum in spring. The correlation analysis indicated that significant correlations existed among some of the metal elements in the deposition samples. The enrichment factors (EF) of metals in COM in the deposition ranging from 79.66 to 130,000 were much higher than those of SPM ranging from 1.65 to 286.48, indicating the important role of COM. The factor analysis showed that emissions from street dust, non-ferrous metal production, and heavy fuel oil were major sources of the trace metals. Positive matrix factorization (PMF) model was used to quantitatively estimate anthropogenic source. Copyright © 2013 Elsevier Ltd. All rights reserved.

Phospho-ubiquitin: upending the PINK–Parkin–ubiquitin cascade

PubMed Central

Matsuda, Noriyuki

2016-01-01

Mitochondria with decreased membrane potential are characterized by defects in protein import into the matrix and impairments in high-efficiency synthesis of ATP. These low-quality mitochondria are marked with ubiquitin for selective degradation. Key factors in this mechanism are PTEN-induced putative kinase 1 (PINK1, a mitochondrial kinase) and Parkin (a ubiquitin ligase), disruption of which has been implicated in predisposition to Parkinson’s disease. Previously, the clearance of damaged mitochondria had been thought to be the end result of a simple cascading reaction of PINK1–Parkin–ubiquitin. However, in the past year, several research groups including ours unexpectedly revealed that Parkin regulation is mediated by PINK1-dependent phosphorylation of ubiquitin. These results overturned the simple hierarchy that posited PINK1 and ubiquitin as the upstream and downstream factors of Parkin, respectively. Although ubiquitylation is well-known as a post-translational modification, it has recently become clear that ubiquitin itself can be modified, and that this modification unexpectedly converts ubiquitin to a factor that functions in retrograde signalling. PMID:26839319

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.

Aging Effects in Polymer Composites

NASA Technical Reports Server (NTRS)

Chamis, Chistos C.; McManus, Hugh L.

1999-01-01

Simulation of composites degradation due to aging are described. Laminate geometry, material properties, and matrix degradation states are specified as functions of position and time. Matrix shrinkage and property changes are modeled as functions of the degradation states. Aging effects at the laminate, ply, and micro levels are evaluated, to determine failure of any kind. The results obtained show substantial ply stress built up as a result of aging accompanied by comparable laminate strength degradation in matrix dominated composite strengths.

Design and characterization of a plastic optical fiber pH sensor

NASA Astrophysics Data System (ADS)

Ferreira, Licínio; Simões, Pedro; Carvalho, Rui S.; Lopes, Paulo; Ferreira, Mário

2013-11-01

In this paper are present the design and characterization of a pH sensor using plastic optical fiber (POF) technology and a material produced by the sol-gel process with TEOS (tetraethyl orthosilicate) to immobilize universal indicator of pH (comprised of Thymol Blue, Methyl Red, Bromothymol Blue and Phenolphthalein) inside the silica matrix. This matrix is positioned between two extensions of plastic optical fiber tightly positioned at each side with both fibers aligned and sharing a common optical axis. This set will work as a pH sensor since the matrix embedded with indicator and in the presence of a solution (basic or acid solution) will change the optical transmittance properties. The optical source is a superluminescent white LED and the receiver is a photodiode having a good and linear responsivity in the visible spectrum. This pH sensitive matrix has large pores which allow the diffusion of the surrounding fluid molecules into the matrix and thus the close contact of these to the indicator molecules. This contact causes the change of color of the whole matrix allowing proper colorimetric detection by the photodiode. This variation of color associated with the detector wavelength linear response is the base of operation of the proposed device. This pH sensor presents many advantages over the standard and commercial pH meters namely, lightweight, portability and a low cost.

Multifunctional and biologically active matrices from multicomponent polymeric solutions

NASA Technical Reports Server (NTRS)

Kiick, Kristi L. (Inventor); Yamaguchi, Nori (Inventor); Rabolt, John (Inventor); Casper, Cheryl (Inventor)

2012-01-01

A functionalized electrospun matrix for the controlled-release of biologically active agents, such as growth factors, is presented. The functionalized matrix comprises a matrix polymer, a compatibilizing polymer and a biomolecule or other small functioning molecule. In certain aspects the electrospun polymer fibers comprise at least one biologically active molecule functionalized with low molecular weight heparin.

Sparse Covariance Matrix Estimation With Eigenvalue Constraints

PubMed Central

LIU, Han; WANG, Lie; ZHAO, Tuo

2014-01-01

We propose a new approach for estimating high-dimensional, positive-definite covariance matrices. Our method extends the generalized thresholding operator by adding an explicit eigenvalue constraint. The estimated covariance matrix simultaneously achieves sparsity and positive definiteness. The estimator is rate optimal in the minimax sense and we develop an efficient iterative soft-thresholding and projection algorithm based on the alternating direction method of multipliers. Empirically, we conduct thorough numerical experiments on simulated datasets as well as real data examples to illustrate the usefulness of our method. Supplementary materials for the article are available online. PMID:25620866

Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for Use with Positive Blood Cultures: Methodology, Performance, and Optimization.

PubMed

Faron, Matthew L; Buchan, Blake W; Ledeboer, Nathan A

2017-12-01

Early initiation of effective antibiotics for septic patients is essential for patient survival. Matrix-assisted desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has revolutionized clinical microbiology for isolate identification and has the possibility to impact how blood culture testing is performed. This review discusses the various uses of MALDI-TOF MS for the identification and susceptibility testing of positive blood cultures, the performance of these methods, and the outcomes involved with its implementation. Copyright © 2017 American Society for Microbiology.

A major protein component of the Bacillus subtilis biofilm matrix.

PubMed

Branda, Steven S; Chu, Frances; Kearns, Daniel B; Losick, Richard; Kolter, Roberto

2006-02-01

Microbes construct structurally complex multicellular communities (biofilms) through production of an extracellular matrix. Here we present evidence from scanning electron microscopy showing that a wild strain of the Gram positive bacterium Bacillus subtilis builds such a matrix. Genetic, biochemical and cytological evidence indicates that the matrix is composed predominantly of a protein component, TasA, and an exopolysaccharide component. The absence of TasA or the exopolysaccharide resulted in a residual matrix, while the absence of both components led to complete failure to form complex multicellular communities. Extracellular complementation experiments revealed that a functional matrix can be assembled even when TasA and the exopolysaccharide are produced by different cells, reinforcing the view that the components contribute to matrix formation in an extracellular manner. Having defined the major components of the biofilm matrix and the control of their synthesis by the global regulator SinR, we present a working model for how B. subtilis switches between nomadic and sedentary lifestyles.

Induction of fibroblast senescence generates a non-fibrogenic myofibroblast phenotype that differentially impacts on cancer prognosis

PubMed Central

Thirdborough, Steve; Mellows, Toby; Garcia, Edwin; Woo, Jeongmin; Tod, Joanne; Frampton, Steve; Jenei, Veronika; Moutasim, Karwan A.; Kabir, Tasnuva D.; Brennan, Peter A; Venturi, Giulia; Ford, Kirsty; Herranz, Nicolas; Lim, Kue Peng; Clarke, James; Lambert, Daniel W.; Prime, Stephen S.; Underwood, Timothy J.; Vijayanand, Pandurangan; Eliceiri, Kevin W.; Woelk, Christopher; King, Emma V.; Gil, Jesus; Ottensmeier, Christian H.; Thomas, Gareth J.

2017-01-01

Cancer-associated fibroblasts (CAF) remain a poorly characterized, heterogeneous cell population. Here we characterized two previously described tumor-promoting CAF sub-types, smooth muscle actin (SMA)-positive myofibroblasts and senescent fibroblasts, identifying a novel link between the two. Analysis of CAF cultured ex vivo, showed that senescent CAF are predominantly SMA-positive; this was confirmed by immunochemistry in head & neck (HNSCC) and esophageal (EAC) cancers. In vitro, we found that fibroblasts induced to senesce develop molecular, ultrastructural and contractile features typical of myofibroblasts and this is dependent on canonical TGF-β signaling. Similar to TGF-β1-generated myofibroblasts, these cells secrete soluble factors that promote tumor cell motility. However, RNA-sequencing revealed significant transcriptomic differences between the two SMA-positive CAF groups, particularly in genes associated with extracellular matrix (ECM) deposition and organization, which differentially promote tumor cell invasion. Notably, second harmonic generation imaging and bioinformatic analysis of SMA-positive human HNSCC and EAC showed that collagen fiber organization correlates with poor prognosis, indicating that heterogeneity within the SMA-positive CAF population differentially impacts on survival. These results show that non-fibrogenic, SMA-positive myofibroblasts can be directly generated through induction of fibroblast senescence and suggest that senescence and myofibroblast differentiation are closely linked processes. PMID:27992856

Induction of fibroblast senescence generates a non-fibrogenic myofibroblast phenotype that differentially impacts on cancer prognosis.

PubMed

Mellone, Massimiliano; Hanley, Christopher J; Thirdborough, Steve; Mellows, Toby; Garcia, Edwin; Woo, Jeongmin; Tod, Joanne; Frampton, Steve; Jenei, Veronika; Moutasim, Karwan A; Kabir, Tasnuva D; Brennan, Peter A; Venturi, Giulia; Ford, Kirsty; Herranz, Nicolas; Lim, Kue Peng; Clarke, James; Lambert, Daniel W; Prime, Stephen S; Underwood, Timothy J; Vijayanand, Pandurangan; Eliceiri, Kevin W; Woelk, Christopher; King, Emma V; Gil, Jesus; Ottensmeier, Christian H; Thomas, Gareth J

2016-12-15

Cancer-associated fibroblasts (CAF) remain a poorly characterized, heterogeneous cell population. Here we characterized two previously described tumor-promoting CAF sub-types, smooth muscle actin (SMA)-positive myofibroblasts and senescent fibroblasts, identifying a novel link between the two. Analysis of CAF cultured ex vivo , showed that senescent CAF are predominantly SMA-positive; this was confirmed by immunochemistry in head & neck (HNSCC) and esophageal (EAC) cancers. In vitro , we found that fibroblasts induced to senesce develop molecular, ultrastructural and contractile features typical of myofibroblasts and this is dependent on canonical TGF-β signaling. Similar to TGF-β1-generated myofibroblasts, these cells secrete soluble factors that promote tumor cell motility. However, RNA-sequencing revealed significant transcriptomic differences between the two SMA-positive CAF groups, particularly in genes associated with extracellular matrix (ECM) deposition and organization, which differentially promote tumor cell invasion. Notably, second harmonic generation imaging and bioinformatic analysis of SMA-positive human HNSCC and EAC showed that collagen fiber organization correlates with poor prognosis, indicating that heterogeneity within the SMA-positive CAF population differentially impacts on survival. These results show that non-fibrogenic, SMA-positive myofibroblasts can be directly generated through induction of fibroblast senescence and suggest that senescence and myofibroblast differentiation are closely linked processes.

Associations between knee structural measures, circulating inflammatory factors and MMP13 in patients with knee osteoarthritis.

PubMed

Ruan, G; Xu, J; Wang, K; Wu, J; Zhu, Q; Ren, J; Bian, F; Chang, B; Bai, X; Han, W; Ding, C

2018-05-22

To investigate cross-sectional associations between serum level of Matrix metalloproteinase (MMP)13 and knee structural measures and circulating inflammatory factors in patients with symptomatic knee osteoarthritis (OA). A total of 149 subjects with symptomatic knee OA were included. Magnetic resonance imaging was used to measure infrapatellar fat pad (IPFP) volume, IPFP signal intensity alternation, cartilage volume and cartilage defects. Knee radiography was used to assess radiographic OA using the Kellgren-Lawrence (K-L) grading system. Enzyme-linked immunosorbent assay was used to measure the serum levels of inflammatory factors and MMP13. In multivariable analyses, serum MMP13 was negatively associated with cartilage volume at patellar site (β: -32.94 mm 3 per 10 ng/ml, P < 0.05), and positively associated with cartilage defect at medial femoral site (OR: 1.13 per 10 ng/ml, P < 0.05). Also, MMP13 was positively associated with K-L grading and IPFP signal intensity alteration (OR: 1.14 and 1.15 per 10 ng/ml, respectively, both P < 0.05), and negatively associated with IPFP volume (β: -0.34 cm 3 per 10 ng/ml, P < 0.05). Furthermore, serum level of adiponectin was negatively associated serum MMP13 quartiles (OR: 0.66 per 10 μg/ml, P < 0.05), and serum levels of tumor necrosis factor (TNF)-α, interleukin (IL)-8 and IL-18 were positively associated with serum MMP13 quartiles (ORs: 1.01-1.18 per 10 pg/ml, all P < 0.05). Serum level of MMP13 was associated with knee structural abnormalities as well as serum inflammatory factors. These suggest that systemic MMP13 may play a role in knee OA, and could be regulated by inflammatory factors. Copyright © 2018 Osteoarthritis Research Society International. Published by Elsevier Ltd. All rights reserved.

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.

Institutional and matrix support and its relationship with primary healthcare

PubMed Central

dos Santos, Alaneir de Fátima; Machado, Antônio Thomaz Gonzaga da Matta; dos Reis, Clarice Magalhães Rodrigues; Abreu, Daisy Maria Xavier; de Araújo, Lucas Henrique Lobato; Rodrigues, Simone Cristina; de Lima, Ângela Maria de Lourdes Dayrell; Jorge, Alzira de Oliveira; Fonseca, Délcio

2015-01-01

OBJECTIVE To analyze whether the level of institutional and matrix support is associated with better certification of primary healthcare teams. METHODS In this cross-sectional study, we evaluated two kinds of primary healthcare support – 14,489 teams received institutional support and 14,306 teams received matrix support. Logistic regression models were applied. In the institutional support model, the independent variable was “level of support” (as calculated by the sum of supporting activities for both modalities). In the matrix support model, in turn, the independent variables were the supporting activities. The multivariate analysis has considered variables with p < 0.20. The model was adjusted by the Hosmer-Lemeshow test. RESULTS The teams had institutional and matrix supporting activities (84.0% and 85.0%), respectively, with 55.0% of them performing between six and eight activities. For the institutional support, we have observed 1.96 and 3.77 chances for teams who had medium and high levels of support to have very good or good certification, respectively. For the matrix support, the chances of their having very good or good certification were 1.79 and 3.29, respectively. Regarding to the association between institutional support activities and the certification, the very good or good certification was positively associated with self-assessment (OR = 1.95), permanent education (OR = 1.43), shared evaluation (OR = 1.40), and supervision and evaluation of indicators (OR = 1.37). In regards to the matrix support, the very good or good certification was positively associated with permanent education (OR = 1.50), interventions in the territory (OR = 1.30), and discussion in the work processes (OR = 1.23). CONCLUSIONS In Brazil, supporting activities are being incorporated in primary healthcare, and there is an association between the level of support, both matrix and institutional, and the certification result. PMID:26274872

Tensor-GMRES method for large sparse systems of nonlinear equations

NASA Technical Reports Server (NTRS)

Feng, Dan; Pulliam, Thomas H.

1994-01-01

This paper introduces a tensor-Krylov method, the tensor-GMRES method, for large sparse systems of nonlinear equations. This method is a coupling of tensor model formation and solution techniques for nonlinear equations with Krylov subspace projection techniques for unsymmetric systems of linear equations. Traditional tensor methods for nonlinear equations are based on a quadratic model of the nonlinear function, a standard linear model augmented by a simple second order term. These methods are shown to be significantly more efficient than standard methods both on nonsingular problems and on problems where the Jacobian matrix at the solution is singular. A major disadvantage of the traditional tensor methods is that the solution of the tensor model requires the factorization of the Jacobian matrix, which may not be suitable for problems where the Jacobian matrix is large and has a 'bad' sparsity structure for an efficient factorization. We overcome this difficulty by forming and solving the tensor model using an extension of a Newton-GMRES scheme. Like traditional tensor methods, we show that the new tensor method has significant computational advantages over the analogous Newton counterpart. Consistent with Krylov subspace based methods, the new tensor method does not depend on the factorization of the Jacobian matrix. As a matter of fact, the Jacobian matrix is never needed explicitly.

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.

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.

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

Time-oriented experimental design method to optimize hydrophilic matrix formulations with gelation kinetics and drug release profiles.

PubMed

Shin, Sangmun; Choi, Du Hyung; Truong, Nguyen Khoa Viet; Kim, Nam Ah; Chu, Kyung Rok; Jeong, Seong Hoon

2011-04-04

A new experimental design methodology was developed by integrating the response surface methodology and the time series modeling. The major purposes were to identify significant factors in determining swelling and release rate from matrix tablets and their relative factor levels for optimizing the experimental responses. Properties of tablet swelling and drug release were assessed with ten factors and two default factors, a hydrophilic model drug (terazosin) and magnesium stearate, and compared with target values. The selected input control factors were arranged in a mixture simplex lattice design with 21 experimental runs. The obtained optimal settings for gelation were PEO, LH-11, Syloid, and Pharmacoat with weight ratios of 215.33 (88.50%), 5.68 (2.33%), 19.27 (7.92%), and 3.04 (1.25%), respectively. The optimal settings for drug release were PEO and citric acid with weight ratios of 191.99 (78.91%) and 51.32 (21.09%), respectively. Based on the results of matrix swelling and drug release, the optimal solutions, target values, and validation experiment results over time were similar and showed consistent patterns with very small biases. The experimental design methodology could be a very promising experimental design method to obtain maximum information with limited time and resources. It could also be very useful in formulation studies by providing a systematic and reliable screening method to characterize significant factors in the sustained release matrix tablet. Copyright © 2011 Elsevier B.V. All rights reserved.

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

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.

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.

Tissue architecture and breast cancer: the role of extracellular matrix and steroid hormones

PubMed Central

Hansen, R K; Bissell, M J

2010-01-01

The changes in tissue architecture that accompany the development of breast cancer have been the focus of investigations aimed at developing new cancer therapeutics. As we learn more about the normal mammary gland, we have begun to understand the complex signaling pathways underlying the dramatic shifts in the structure and function of breast tissue. Integrin-, growth factor-, and steroid hormone-signaling pathways all play an important part in maintaining tissue architecture; disruption of the delicate balance of signaling results in dramatic changes in the way cells interact with each other and with the extracellular matrix, leading to breast cancer. The extracellular matrix itself plays a central role in coordinating these signaling processes. In this review, we consider the interrelationships between the extracellular matrix, integrins, growth factors, and steroid hormones in mammary gland development and function. PMID:10903527

Dynamic stabilization of the magnetic field surrounding the neutron electric dipole moment spectrometer at the Paul Scherrer Institute

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

Afach, S.; Fertl, M.; Franke, B., E-mail: beatrice.franke@psi.ch, E-mail: bernhard.lauss@psi.ch

The Surrounding Field Compensation (SFC) system described in this work is installed around the four-layer Mu-metal magnetic shield of the neutron electric dipole moment spectrometer located at the Paul Scherrer Institute. The SFC system reduces the DC component of the external magnetic field by a factor of about 20. Within a control volume of approximately 2.5 m × 2.5 m × 3 m, disturbances of the magnetic field are attenuated by factors of 5–50 at a bandwidth from 10{sup −3} Hz up to 0.5 Hz, which corresponds to integration times longer than several hundreds of seconds and represent the important timescale for the neutron electric dipole moment measurement.more » These shielding factors apply to random environmental noise from arbitrary sources. This is achieved via a proportional-integral feedback stabilization system that includes a regularized pseudoinverse matrix of proportionality factors which correlates magnetic field changes at all sensor positions to current changes in the SFC coils.« less

Formation of bone-like mineralized matrix by periodontal ligament cells in vivo: a morphological study in rats.

PubMed

Hiraga, Toru; Ninomiya, Tadashi; Hosoya, Akihiro; Takahashi, Masafumi; Nakamura, Hiroaki

2009-01-01

Periodontal ligament (PDL) is a unique connective tissue that not only connects cementum and alveolar bone to support teeth, but also plays an important role in reconstructing periodontal tissues. Previous studies have suggested that PDL cells have osteogenic potential; however, they lack precise histological examinations. Here, we studied bone-like matrix formation by PDL cells in rats using morphological techniques. Rat and human PDL cells exhibited substantial alkaline phosphatase activity and induced mineralization in vitro. RT-PCR analyses showed that PDL cells expressed the osteoblast markers, Runx2, osterix, and osteocalcin. These results suggest that PDL cells share similar phenotypes with osteoblasts. To examine the bone-like matrix formation in vivo, PDL cells isolated from green fluorescent protein (GFP)-transgenic rats were inoculated with hydroxyapatite (HA) disks into wild-type rats. Five weeks after the implantation, the pores in HA disks were occupied by GFP-positive cells. Mineralized matrix formation was also found on the surface of HA pores. At 12 weeks, some of the pores were filled with bone-like mineralized matrices (BLMM), which were positive for the bone matrix proteins, osteopontin, bone sialoprotein, and osteocalcin. Immunohistochemical examination revealed that most of the osteoblast- and osteocyte-like cells on or in the BLMM were GFP-positive, suggesting that the BLMM were directly formed by the inoculated PDL cells. On the pore surfaces, Sharpey's fiber-like structures embedded in cementum-like mineralized layers were also observed. These results collectively suggest that PDL cells have the ability to form periodontal tissues and could be a useful source for regenerative therapies of periodontal diseases.

Joint release rate estimation and measurement-by-measurement model correction for atmospheric radionuclide emission in nuclear accidents: An application to wind tunnel experiments.

PubMed

Li, Xinpeng; Li, Hong; Liu, Yun; Xiong, Wei; Fang, Sheng

2018-03-05

The release rate of atmospheric radionuclide emissions is a critical factor in the emergency response to nuclear accidents. However, there are unavoidable biases in radionuclide transport models, leading to inaccurate estimates. In this study, a method that simultaneously corrects these biases and estimates the release rate is developed. Our approach provides a more complete measurement-by-measurement correction of the biases with a coefficient matrix that considers both deterministic and stochastic deviations. This matrix and the release rate are jointly solved by the alternating minimization algorithm. The proposed method is generic because it does not rely on specific features of transport models or scenarios. It is validated against wind tunnel experiments that simulate accidental releases in a heterogonous and densely built nuclear power plant site. The sensitivities to the position, number, and quality of measurements and extendibility of the method are also investigated. The results demonstrate that this method effectively corrects the model biases, and therefore outperforms Tikhonov's method in both release rate estimation and model prediction. The proposed approach is robust to uncertainties and extendible with various center estimators, thus providing a flexible framework for robust source inversion in real accidents, even if large uncertainties exist in multiple factors. Copyright © 2017 Elsevier B.V. All rights reserved.

Perceived barriers to medical-error reporting: an exploratory investigation.

PubMed

Uribe, Claudia L; Schweikhart, Sharon B; Pathak, Dev S; Dow, Merrell; Marsh, Gail B

2002-01-01

Medical-error reporting is an essential component for patient safety enhancement. Unfortunately, medical errors are largely underreported across healthcare institutions. This problem can be attributed to different factors and barriers present at organizational and individual levels that ultimately prevent individuals from generating the report. This study explored the factors that affect medical-error reporting among physicians and nurses at a large academic medical center located in the midwest United States. A nominal group session was conducted to identify the most relevant factors that act as barriers for error reporting. These factors were then used to design a questionnaire that explored the likelihood of the factors to act as barriers and their likelihood to be modified. Using these two parameters, the results were analyzed and combined into a Factor Relevance Matrix. The matrix identifies the factors for which immediate actions should be undertaken to improve medical-error reporting (immediate action factors). It also identifies factors that require long-term strategies (long-term strategy factors) as well as factors that the organization should be aware of but that are of lower priority (awareness factors). The strategies outlined in this study may assist healthcare organizations in improving medical-error reporting, as part of the efforts toward patient-safety enhancement. Although factors affecting medical-error reporting may vary between different organizations, the process used in identifying the factors and the Factor Relevance Matrix developed in this study are easily adaptable to any organizational setting.

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.

A Plant Proteinase Inhibitor from Enterolobium contortisiliquum Attenuates Pulmonary Mechanics, Inflammation and Remodeling Induced by Elastase in Mice

PubMed Central

Theodoro-Júnior, Osmar Aparecido; Righetti, Renato Fraga; Almeida-Reis, Rafael; Martins-Oliveira, Bruno Tadeu; Oliva, Leandro Vilela; Prado, Carla Máximo; Saraiva-Romanholo, Beatriz Mangueira; Leick, Edna Aparecida; Pinheiro, Nathalia Montouro; Lobo, Yara Aparecida; Martins, Mílton de Arruda; Oliva, Maria Luiza Vilela; Tibério, Iolanda de Fátima Lopes Calvo

2017-01-01

Proteinase inhibitors have been associated with anti-inflammatory and antioxidant activities and may represent a potential therapeutic treatment for emphysema. Our aim was to evaluate the effects of a plant Kunitz proteinase inhibitor, Enterolobium contortisiliquum trypsin inhibitor (EcTI), on several aspects of experimental elastase-induced pulmonary inflammation in mice. C57/Bl6 mice were intratracheally administered elastase (ELA) or saline (SAL) and were treated intraperitoneally with EcTI (ELA-EcTI, SAL-EcTI) on days 1, 14 and 21. On day 28, pulmonary mechanics, exhaled nitric oxide (ENO) and number leucocytes in the bronchoalveolar lavage fluid (BALF) were evaluated. Subsequently, lung immunohistochemical staining was submitted to morphometry. EcTI treatment reduced responses of the mechanical respiratory system, number of cells in the BALF, and reduced tumor necrosis factor-α (TNF-α), matrix metalloproteinase-9 (MMP-9), matrix metalloproteinase-12 (MMP-12), tissue inhibitor of matrix metalloproteinase (TIMP-1), endothelial nitric oxide synthase (eNOS) and inducible nitric oxide synthase (iNOS)-positive cells and volume proportion of isoprostane, collagen and elastic fibers in the airways and alveolar walls compared with the ELA group. EcTI treatment reduced elastase induced pulmonary inflammation, remodeling, oxidative stress and mechanical alterations, suggesting that this inhibitor may be a potential therapeutic tool for chronic obstructive pulmonary disease (COPD) management. PMID:28216579

Increased shedding of microvesicles from intimal smooth muscle cells in athero-prone areas of the human aorta: implications for understanding of the predisease stage.

PubMed

Bobryshev, Yuri V; Killingsworth, Murray C; Orekhov, Alexander N

2013-01-01

This study evaluated whether a change in the content of matrix microvesicles might occur at the preatherosclerotic stage. Applying quantitative electron microscopic and immunohistochemical analyses, two areas of grossly normal segments of the thoracic aorta were compared: atherosclerosis-prone (AP) areas, situated at the dorsal aspect of the aorta along the rows of intercostal branch origins, and atherosclerosis-resistant (AR) areas, situated at the corresponding sites of the ventral aspect of the aorta. The electron microscopic analysis showed that there were 1.4 times more microvesicles in AP areas than AR areas (p = 0.019). It was found that matrix microvesicles originated as a result of blebbing and shedding of surface membranes of smooth muscle cells. A quantitative analysis of the expression of ADP-ribosylation factor 6 (ARF6), which is known to be involved in membrane trafficking and microvesicle formation, showed that ARF6 expression was 1.3 times higher in AP areas than that in AR areas (p = 0.006). There was a positive correlation between the content of matrix microparticles and the expression of ARF6 by intimal smooth muscle cells (r = 0.61; p < 0.0001). The present study supports the concept that alterations of the arterial intima occur at the predisease stage. Copyright © 2012 S. Karger AG, Basel.

Cross-correlation matrix analysis of Chinese and American bank stocks in subprime crisis

NASA Astrophysics Data System (ADS)

Zhu, Shi-Zhao; Li, Xin-Li; Nie, Sen; Zhang, Wen-Qing; Yu, Gao-Feng; Han, Xiao-Pu; Wang, Bing-Hong

2015-05-01

In order to study the universality of the interactions among different markets, we analyze the cross-correlation matrix of the price of the Chinese and American bank stocks. We then find that the stock prices of the emerging market are more correlated than that of the developed market. Considering that the values of the components for the eigenvector may be positive or negative, we analyze the differences between two markets in combination with the endogenous and exogenous events which influence the financial markets. We find that the sparse pattern of components of eigenvectors out of the threshold value has no change in American bank stocks before and after the subprime crisis. However, it changes from sparse to dense for Chinese bank stocks. By using the threshold value to exclude the external factors, we simulate the interactions in financial markets. Project supported by the National Natural Science Foundation of China (Grant Nos. 11275186, 91024026, and FOM2014OF001) and the University of Shanghai for Science and Technology (USST) of Humanities and Social Sciences, China (Grant Nos. USST13XSZ05 and 11YJA790231).

Effect of the Microstructure on the Fracture Mode of Short-Fiber Reinforced Plastic Composites

NASA Astrophysics Data System (ADS)

Nishikawa, Masaaki; Okabe, Tomonaga; Takeda, Nobuo

A numerical simulation was presented to discuss the microscopic damage and its influence on the strength and energy-absorbing capability of short-fiber reinforced plastic composites. The dominant damage includes matrix crack and/or interfacial debonding, when the fibers are shorter than the critical length for fiber breakage. The simulation addressed the matrix crack with a continuum damage mechanics (CDM) model and the interfacial debonding with an embedded process zone (EPZ) model. Fictitious free-edge effects on the fracture modes were successfully eliminated with the periodic-cell simulation. The advantage of our simulation was pointed out by demonstrating that the simulation with edge effects significantly overestimates the dissipative energy of the composites. We then investigated the effect of the material microstructure on the fracture modes in the composites. The simulated results clarified that the inter-fiber distance affects the breaking strain of the composites and the fiber-orientation angle affects the position of the damage initiation. These factors influence the strength and energy-absorbing capability of short fiber-reinforced composites.

A novel three-dimensional bone chip organ culture.

PubMed

Kuttenberger, Johannes; Polska, Elzbieta; Schaefer, Birgit M

2013-07-01

The objective of this study was to develop a 3D bone chip organ culture model. We aimed to collect in vitro evidence of the ability of vital bone chips to promote new bone formation. We developed a 3D in vitro hypoxic bone chip organ culture model. Histology of the bone chips was performed before and after culture and immunohistochemistry after 3-week culture. The 3D culture supernatants were tested for the presence of pro-angiogenic growth factors, TGFβ1, GADPH, bone alkaline phosphatase, osteocalcin, osteonectin, osteopontin, bone sialoprotein and collagen type I. Histology after culture revealed bone chips in a matrix of fibrin remnants and a fibrous-appearing matter. Collagen type I- and IV-positive structures were also identified. Cells could be seen on the surface of the bone chips, with spindle-shaped cells bridging the bone chip particles. Pro-angiogenic growth factors and TGFβ1were detected in the 3D cell culture supernatants. The transcripts for osteocalcin, bone sialoprotein and collagen type I were revealed only via PCR. Our results indicate that bone chips in our 3D organ culture remain vital and may stimulate the growth of a bone-forming matrix. The use of autogenous bone chips for oral and maxillofacial bone augmentation procedures is widespread in clinical practice. The rationale for this is that if bone chips remain vital in vivo, they could provide an environment promoting new bone formation through growth factors and cells. This 3D culture method is an essential tool for investigating the behaviour of bone chips.

Matrix Metalloproteinase-9 Is a Predictive Factor for Systematic Hypertension and Heart Dysfunction in Patients with Obstructive Sleep Apnea Syndrome

PubMed Central

Wang, Shuhui; Li, Shisheng; Wang, Bin; Liu, Jiajia

2018-01-01

Patients with obstructive sleep apnea syndrome (OSAS) showed higher prevalence in cardiovascular diseases due to aberrant hypoxia and oxidative stress. However, not all OSAS patients end up with cardiovascular disorders, and identification of novel biomarker will be invaluable for differentiating patients at risk. Here we tested the serum matrix metalloproteinase-9 (MMP-9) levels in 47 untreated OSAS patients and found that the MMP-9 level was positively correlated with severity of OSAS, which was consistent with hypoxia degree and duration. Besides, the MMP-9 level was higher in patients complicated with systematic hypertension (P < 0.001). Furthermore, we selected those OSAS patients without any cardiovascular dysfunction (n = 35) and followed up for up to five years. By the end of follow-up, 12 patients had hypertension onset and 3 patients had left ventricular hypertrophy. By analyzing the clinical outcomes with MMP-9 expression, we demonstrated that high serum MMP-9 in OSAS patients was a risk factor for occurrence of cardiovascular diseases. In addition, we cultured the vascular endothelial cells (VEC) from rat aorta in hypoxia condition to investigate whether MMP-9 was elevated due to hypoxia in OSAS patients. Cellular results revealed that the expression, secretion, and activity of MMP-9 were all upregulated by hypoxia and can cleave the beta2-adrenergic receptor (β2AR) on VEC surface. Our results not only determined MMP-9 as a risk factor for cardiovascular diseases in OSAS patients, but also showed the possible involvement of hypoxia-MMP-9-β2AR signaling axis. PMID:29693002

Pentraxin 3 in serum and synovial fluid of patients with rheumatoid arthritis with and without autoantibodies.

PubMed

Weitoft, T; Larsson, A; Saxne, T; Manivel, V A; Lysholm, J; Knight, A; Rönnelid, J

2017-09-01

Pentraxin 3 (PTX3) is a locally produced multifunctional protein involved in inflammation, matrix deposition, and immunity. As patients with seropositive rheumatoid arthritis (RA) have a more severe disease course and higher risk of joint destruction than seronegative patients, the aim of the present study was to examine differences in PTX3 in synovial fluid (SF) (and serum) in seropositive compared to seronegative RA, and other local markers of inflammation and destruction. Ninety-seven RA patients with knee effusion were included. Serum and SF levels of PTX3, as well as serum levels of anti-citrullinated protein antibody and rheumatoid factor of immunoglobulin A and M subclasses, and markers of inflammation and potential destruction in SF: white blood cell counts, tumour necrosis factor, interleukin-6, vascular endothelial growth factor, metalloproteinase 3, and cartilage oligomeric matrix protein, were analysed. In addition, a radiographic knee examination was performed. Seropositive patients had significantly higher PTX3 levels in SF than seronegative patients, whereas there was no difference for serum levels. SF-PTX3 levels correlated with disease activity and with local inflammatory markers, especially polymorphonuclear cells, and with autoantibody levels. There was no correlation between PTX3 levels in serum and SF. The correlation of disease activity and autoantibody levels with SF-PTX3 levels in antibody-positive patients suggests a role for PTX3 in the inflammatory process specifically in seropositive RA joints, and supports the hypothesis that seropositive and seronegative RA are different disease entities. Polymorphonuclear granulocytes may be an important source of PTX3 in RA SF.

Infrared spectroscopy of polycyclic aromatic hydrocarbon cations. 1: Matrix-isolated naphthalene and perdeuterated naphthalene

NASA Technical Reports Server (NTRS)

Hudgins, D. M.; Sandford, S. A.; Allamandola, Louis J.

1994-01-01

Ionized polycyclic aromatic hydrocarbons (PAHs) are thought to constitute an important component of the interstellar medium. Despite this fact, the infrared spectroscopic properties of ionized PAHs are almost unknown. The results we present here derive from our ongoing spectroscopic study of matrix isolated PAH ions and include the spectra of the naphthalene cation, C10H8(+), and its fully deuterated analog, C10D8(+), between 4000 and 200/cm. Ions are generated by in situ Lyman-alpha photoionization of the neutral precursor. Bands of the C10H8(+) ion are observed at 1525.7, 1518.8, 1400.9, 1218.0, 1216.9, 1214.9, 1023.2, and 758.7/cm. Positions and relative intensities of these bands agree well with those in the available literature. The 758.7/cm band has not previously been reported. C10D8(+) ion bands appear at 1466.2, 1463.8, 1379.4, 1373.8, 1077.3, 1075.4, and 1063.1/cm. Compared to the analogous modes in the neutral molecule, the intensities of the cation's CC modes are enhanced by an order of magnitude, while CH modes are depressed by this same factor. Integrated absorption intensities are calculated for the strongest bands of C10H8 and for the observed bands of C10H8(+). Absolute intensities derived for the naphthalene cation differ from earlier experimental results by a factor of approximately 50, and from theoretical predictions by a factor of approximately 300. Reasons for these discrepancies and from the astronomical implications of PAH cation spectra are discussed.

Heparin-induced conformational changes of fibronectin within the extracellular matrix promote hMSC osteogenic differentiation.

PubMed

Li, Bojun; Lin, Zhe; Mitsi, Maria; Zhang, Yang; Vogel, Viola

2015-01-01

An increasing body of evidence suggests important roles of extracellular matrix (ECM) in regulating stem cell fate. This knowledge can be exploited in tissue engineering applications for the design of ECM scaffolds appropriate to direct stem cell differentiation. By probing the conformation of fibronectin (Fn) using fluorescence resonance energy transfer (FRET), we show here that heparin treatment of the fibroblast-derived ECM scaffolds resulted in more extended conformations of fibrillar Fn in ECM. Since heparin is a highly negatively charged molecule while fibronectin contains segments of positively charged modules, including FnIII13, electrostatic interactions between Fn and heparin might interfere with residual quaternary structure in relaxed fibronectin fibers thereby opening up buried sites. The conformation of modules FnIII12-14 in particular, which contain one of the heparin binding sites as well as binding sites for many growth factors, may be activated by heparin, resulting in alterations in growth factor binding to Fn. Indeed, upregulated osteogenic differentiation was observed when hMSCs were seeded on ECM scaffolds that had been treated with heparin and were subsequently chemically fixed. In contrast, either rigidifying relaxed fibers by fixation alone, or heparin treatment without fixation had no effect. We hypothesize that fibronectin's conformations within the ECM are activated by heparin such as to coordinate with other factors to upregulate hMSC osteogenic differentiation. Thus, the conformational changes of fibronectin within the ECM could serve as a 'converter' to tune hMSC differentiation in extracellular matrices. This knowledge could also be exploited to promote osteogenic stem cell differentiation on biomedical surfaces.

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

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.

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.

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.

Global Radius of Curvature Estimation and Control System for Segmented Mirrors

NASA Technical Reports Server (NTRS)

Rakoczy, John M. (Inventor)

2006-01-01

An apparatus controls positions of plural mirror segments in a segmented mirror with an edge sensor system and a controller. Current mirror segment edge sensor measurements and edge sensor reference measurements are compared with calculated edge sensor bias measurements representing a global radius of curvature. Accumulated prior actuator commands output from an edge sensor control unit are combined with an estimator matrix to form the edge sensor bias measurements. An optimal control matrix unit then accumulates the plurality of edge sensor error signals calculated by the summation unit and outputs the corresponding plurality of actuator commands. The plural mirror actuators respond to the actuator commands by moving respective positions of the mixor segments. A predetermined number of boundary conditions, corresponding to a plurality of hexagonal mirror locations, are removed to afford mathematical matrix calculation.

Expression of CD44v6 as matrix-associated ectodomain in the bone development.

PubMed

Nakajima, Kosei; Taniguchi, Kazumi; Mutoh, Ken-ichiro

2010-08-01

This study describes the expression of CD44v6 in the bone development and is the first study of its kind to the authors' best knowledge. The CD44 family is a family of transmembrane glycoproteins that acts as cell adhesion molecules binding cells to other cells as well as cells to the extracellular matrix. It has been suggested that the CD44v6, a family member of CD44, is closely related to the osteosarcoma metastasis. In general, when cancer cells metastasize, they revert to their immature forms. In the present study, therefore, we have investigated CD44v6 and the standard form of CD44 (CD44st) in two types of immature forms of bone tissues: developmentally immature stages from fetuses to adults as well as experimentally immature stages using fracture models. CD44st expression was identified in osteoblasts, osteocytes, and in the peripheral portion of the bone matrix from the fetal to young ages of rats. Many more intense reactions for CD44v6 were observed in the bone matrix than CD44st in fetal stages. In experimental fracture models, positive immunoreactions to CD44st were clearly observed in the osteoblasts and osteocytes. CD44v6-positive immunoreactivity, however, was not detected in either osteoblasts or the bone matrix. In conclusion, CD44v6 is expressed in the embryonic stages and may be involved in the bone matrix formation as a matrix-associated ectodomain during normal ontogenetic development but not involved in the process of fracture healing.

Non-Linear Optimization Applied to Angle-of-Arrival Satellite-Based Geolocation with Correlated Measurements

DTIC Science & Technology

2015-03-01

General covariance intersection covariance matrix Σ1 Measurement 1’s covariance matrix I(X) Fisher information matrix g Confidence region L Lower... information in this chapter will discuss the motivation and background of the geolocation algorithm with the scope of the applications for this research. The...algorithm is able to produce the best description of an object given the information from a set of measurements. Determining a position requires the use of a

Source apportionment of aerosol particles at a European air pollution hot spot using particle number size distributions and chemical composition.

PubMed

Leoni, Cecilia; Pokorná, Petra; Hovorka, Jan; Masiol, Mauro; Topinka, Jan; Zhao, Yongjing; Křůmal, Kamil; Cliff, Steven; Mikuška, Pavel; Hopke, Philip K

2018-03-01

Ostrava in the Moravian-Silesian region (Czech Republic) is a European air pollution hot spot for airborne particulate matter (PM), polycyclic aromatic hydrocarbons (PAHs), and ultrafine particles (UFPs). Air pollution source apportionment is essential for implementation of successful abatement strategies. UFPs or nanoparticles of diameter <100 nm exhibit the highest deposition efficiency in human lungs. To permit apportionment of PM sources at the hot-spot including nanoparticles, Positive Matrix Factorization (PMF) was applied to highly time resolved particle number size distributions (NSD, 14 nm-10 μm) and PM 0.09-1.15 chemical composition. Diurnal patterns, meteorological variables, gaseous pollutants, organic markers, and associations between the NSD factors and chemical composition factors were used to identify the pollution sources. The PMF on the NSD reveals two factors in the ultrafine size range: industrial UFPs (28%, number mode diameter - NMD 45 nm), industrial/fresh road traffic nanoparticles (26%, NMD 26 nm); three factors in the accumulation size range: urban background (24%, NMD 93 nm), coal burning (14%, volume mode diameter - VMD 0.5 μm), regional pollution (3%, VMD 0.8 μm) and one factor in the coarse size range: industrial coarse particles/road dust (2%, VMD 5 μm). The PMF analysis of PM 0.09-1.15 revealed four factors: SIA/CC/BB (52%), road dust (18%), sinter/steel (16%), iron production (16%). The factors in the ultrafine size range resolved with NSD have a positive correlation with sinter/steel production and iron production factors resolved with chemical composition. Coal combustion factor resolved with NSD has moderate correlation with SIA/CC/BB factor. The organic markers homohopanes correlate with coal combustion and the levoglucosan correlates with urban background. The PMF applications to NSD and chemical composition datasets are complementary. PAHs in PM 1 were found to be associated with coal combustion factor. Copyright © 2017 Elsevier Ltd. All rights reserved.

Generating false negatives and false positives for As and Mo concentrations in groundwater due to well installation.

PubMed

Wallis, Ilka; Pichler, Thomas

2018-08-01

Groundwater monitoring relies on the acquisition of 'representative' groundwater samples, which should reflect the ambient water quality at a given location. However, drilling of a monitoring well for sample acquisition has the potential to perturb groundwater conditions to a point that may prove to be detrimental to the monitoring objective. Following installation of 20 monitoring wells in close geographic proximity in central Florida, opposing concentration trends for As and Mo were observed. In the first year after well installation As and Mo concentrations increased in some wells by a factor of 2, while in others As and Mo concentrations decreased by a factor of up to 100. Given this relatively short period of time, a natural change in groundwater composition of such magnitude is not expected, leaving well installation itself as the likely cause for the observed concentration changes. Hence, initial concentrations were identified as 'false negatives' if concentrations increased with time or as 'false positives' if concentrations decreased. False negatives were observed if concentrations were already high, i.e., the As or Mo were present at the time of drilling. False positives were observed if concentrations were relatively lower, i.e., As or Mo were present at low concentrations of approximately 1 to 2μg/L before drilling, but then released from the aquifer matrix as a result of drilling. Generally, As and Mo were present in the aquifer matrix in either pyrite or organic matter, both of which are susceptible to dissolution if redox conditions change due to the addition of oxygen. Thus, introduction of an oxidant into an anoxic aquifer through use of an oxygen saturated drilling fluid served as the conceptual model for the trends where concentrations decreased with time. Mixing between drilling fluid and groundwater (i.e., dilution) was used as the conceptual model for scenarios where increasing trends were observed. Conceptual models were successfully tested through formulation and application of data-driven reactive transport models, using the USGS code MODFLOW in conjunction with the reactive multicomponent transport code PHT3D. Copyright © 2018 Elsevier B.V. All rights reserved.

Three dimensional time reversal optical tomography

NASA Astrophysics Data System (ADS)

Wu, Binlin; Cai, W.; Alrubaiee, M.; Xu, M.; Gayen, S. K.

2011-03-01

Time reversal optical tomography (TROT) approach is used to detect and locate absorptive targets embedded in a highly scattering turbid medium to assess its potential in breast cancer detection. TROT experimental arrangement uses multi-source probing and multi-detector signal acquisition and Multiple-Signal-Classification (MUSIC) algorithm for target location retrieval. Light transport from multiple sources through the intervening medium with embedded targets to the detectors is represented by a response matrix constructed using experimental data. A TR matrix is formed by multiplying the response matrix by its transpose. The eigenvectors with leading non-zero eigenvalues of the TR matrix correspond to embedded objects. The approach was used to: (a) obtain the location and spatial resolution of an absorptive target as a function of its axial position between the source and detector planes; and (b) study variation in spatial resolution of two targets at the same axial position but different lateral positions. The target(s) were glass sphere(s) of diameter ~9 mm filled with ink (absorber) embedded in a 60 mm-thick slab of Intralipid-20% suspension in water with an absorption coefficient μa ~ 0.003 mm-1 and a transport mean free path lt ~ 1 mm at 790 nm, which emulate the average values of those parameters for human breast tissue. The spatial resolution and accuracy of target location depended on axial position, and target contrast relative to the background. Both the targets could be resolved and located even when they were only 4-mm apart. The TROT approach is fast, accurate, and has the potential to be useful in breast cancer detection and localization.

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.

Grapevine tissues and phenology differentially affect soluble carbohydrates determination by capillary electrophoresis.

PubMed

Moreno, Daniela; Berli, Federico; Bottini, Rubén; Piccoli, Patricia N; Silva, María F

2017-09-01

Soluble carbohydrates distribution depends on plant physiology and, among other important factors, determines fruit yield and quality. In plant biology, the analysis of sugars is useful for many purposes, including metabolic studies. Capillary electrophoresis (CE) proved to be a powerful green separation technique with minimal sample preparation, even in complex plant tissues, that can provide high-resolution efficiency. Matrix effect refers to alterations in the analytical response caused by components of a sample other than the analyte of interest. Thus, the assessment and reduction of the matrix factor is fundamental for metabolic studies in different matrices. The present study evaluated the source and levels of matrix effects in the determination of most abundant sugars in grapevine tissues (mature and young leaves, berries and roots) at two phenological growth stages. Sucrose was the sugar that showed the least matrix effects, while fructose was the most affected analyte. Based on plant tissues, young leaves presented the smaller matrix effects, irrespectively of the phenology. These changes may be attributed to considerable differences at chemical composition of grapevine tissues with plant development. Therefore, matrix effect should be an important concern for plant metabolomics. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

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.

Using RSAT to scan genome sequences for transcription factor binding sites and cis-regulatory modules.

PubMed

Turatsinze, Jean-Valery; Thomas-Chollier, Morgane; Defrance, Matthieu; van Helden, Jacques

2008-01-01

This protocol shows how to detect putative cis-regulatory elements and regions enriched in such elements with the regulatory sequence analysis tools (RSAT) web server (http://rsat.ulb.ac.be/rsat/). The approach applies to known transcription factors, whose binding specificity is represented by position-specific scoring matrices, using the program matrix-scan. The detection of individual binding sites is known to return many false predictions. However, results can be strongly improved by estimating P value, and by searching for combinations of sites (homotypic and heterotypic models). We illustrate the detection of sites and enriched regions with a study case, the upstream sequence of the Drosophila melanogaster gene even-skipped. This protocol is also tested on random control sequences to evaluate the reliability of the predictions. Each task requires a few minutes of computation time on the server. The complete protocol can be executed in about one hour.

Tissue factor pathway inhibitor 2 is found in skin and its C-terminal region encodes for antibacterial activity.

PubMed

Papareddy, Praveen; Kalle, Martina; Sørensen, Ole E; Lundqvist, Katarina; Mörgelin, Matthias; Malmsten, Martin; Schmidtchen, Artur

2012-01-01

Tissue factor pathway inhibitor 2 (TFPI-2) is a matrix-associated serine protease inhibitor with an enigmatic function in vivo. Here, we describe that TFPI-2 is present in fibrin of wounds and also expressed in skin, where it is up-regulated upon wounding. Neutrophil elastase cleaved TFPI-2, and a C-terminal fragment was found to bind to bacteria. Similarly, a prototypic peptide representing this C-terminal part, EDC34, bound to bacteria and bacterial lipopolysaccharide, and induced bacterial permeabilization. The peptide also induced leakage in artificial liposomes, and displayed a random coil conformation upon interactions with liposomes as well as lipopolysaccharide. EDC34 was antibacterial against both Gram-negative and Gram-positive bacteria in physiological buffer conditions. The results demonstrate that the C-terminus of TFPI-2 encodes for antimicrobial activity, and may be released during wounding.

Elastic interactions between single microcrack and single osteon microstructure of human femur cortical bone

NASA Astrophysics Data System (ADS)

Mansor, N. N.; Daud, R.; Basaruddin, K. S.; Mat, F.; Bajuri, Y.; Ariffin, A. K.

2017-09-01

Inmultiscale Haversian system of cortical bone fracture, a homogenous bone modeling consideration is limited to only one Young modulus was significant for each cortex without having any constituents in that bone. A two dimension model of human femur cortical bone is presented by considering the anatomical positions of four cortices, e.g anterior, posterior, medial and lateral. The Haversian system is modeled under tensile loading by considering the interstitial matrix, osteon and cement line mechanical properties. The interaction between single microcrack and single osteon is evaluated using linear elastic fracture mechanics theory, and was determined using of stress intensity factor, strain energy release rate, and the critical stress intensity factor and critical strain energy release rate parameter. The results indicate that the medial cortex has the highest SIFs while the lowest was posterior cortex. The Young modulus of material was greatly influence the fracture parameters. More stiff the material, the SIF was reduced.

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

Zhou, Dan, E-mail: danzhou@is.mpg.de; Sigle, Wilfried; Wang, Yi

We studied ZrO{sub 2} − La{sub 2/3}Sr{sub 1/3}MnO{sub 3} pillar–matrix thin films which were found to show anomalous magnetic and electron transport properties. With the application of an aberration-corrected transmission electron microscope, interfacial chemistry, and atomic-arrangement of the system, especially of the pillar–matrix interface were revealed at atomic resolution. Minor amounts of Zr were found to occupy Mn positions within the matrix. The Zr concentration reaches a minimum near the pillar–matrix interface accompanied by oxygen vacancies. La and Mn diffusion into the pillar was revealed at atomic resolution and a concomitant change of the Mn valence state was observed.

Position Error Covariance Matrix Validation and Correction

NASA Technical Reports Server (NTRS)

Frisbee, Joe, Jr.

2016-01-01

In order to calculate operationally accurate collision probabilities, the position error covariance matrices predicted at times of closest approach must be sufficiently accurate representations of the position uncertainties. This presentation will discuss why the Gaussian distribution is a reasonable expectation for the position uncertainty and how this assumed distribution type is used in the validation and correction of position error covariance matrices.

Peptide-Modified Chitosan Hydrogels Accelerate Skin Wound Healing by Promoting Fibroblast Proliferation, Migration, and Secretion

PubMed Central

Chen, Xionglin; Zhang, Min; Chen, Shixuan; Wang, Xueer; Tian, Zhihui; Chen, Yinghua; Xu, Pengcheng; Zhang, Lei

2017-01-01

Skin wound healing is a complicated process that involves a variety of cells and cytokines. Fibroblasts play an important role in this process and participate in transformation into myofibroblasts, the synthesis of extracellular matrix (ECM) and fibers, and the secretion of a variety of growth factors. This study assessed the effects of peptide Ser-Ile-Lys-Val-Ala-Val (SIKVAV)--modified chitosan hydrogels on skin wound healing. We investigated the capability of peptide SIKVAV to promote cell proliferation and migration, the synthesis of collagen, and the secretion of a variety of growth factors using fibroblasts in vitro. We also treated skin wounds established in mice using peptide SIKVAV-modified chitosan hydrogels. Hematoxylin and eosin staining showed that peptide-modified chitosan hydrogels enhanced the reepithelialization of wounds compared with negative and positive controls. Masson’s trichrome staining demonstrated that more collagen fibers were deposited in the wounds treated with peptide-modified chitosan hydrogels compared with the negative and positive controls. Immunohistochemistry revealed that the peptide-modified chitosan hydrogels promoted angiogenesis in the skin wound. Taken together, these results suggest that peptide SIKVAV-modified chitosan hydrogels may be useful in wound dressing and the treatment of skin wounds. PMID:28901187

Mind the gap—deficits in our knowledge of aspects impacting the bioavailability of phytochemicals and their metabolites—a position paper focusing on carotenoids and polyphenols

PubMed Central

McDougall, Gordon J.; Alegría, Amparo; Alminger, Marie; Arrigoni, Eva; Aura, Anna‐Marja; Brito, Catarina; Cilla, Antonio; El, Sedef N.; Karakaya, Sibel; Martínez‐Cuesta, Marie C.; Santos, Claudia N.

2015-01-01

Various secondary plant metabolites or phytochemicals, including polyphenols and carotenoids, have been associated with a variety of health benefits, such as reduced incidence of type 2 diabetes, cardiovascular diseases, and several types of cancer, most likely due to their involvement in ameliorating inflammation and oxidative stress. However, discrepancies exist between their putative effects when comparing observational and intervention studies, especially when using pure compounds. These discrepancies may in part be explained by differences in intake levels and their bioavailability. Prior to exerting their bioactivity, these compounds must be made bioavailable, and considerable differences may arise due to their matrix release, changes during digestion, uptake, metabolism, and biodistribution, even before considering dose‐ and host‐related factors. Though many insights have been gained on factors affecting secondary plant metabolite bioavailability, many gaps still exist in our knowledge. In this position paper, we highlight several major gaps in our understanding of phytochemical bioavailability, including effects of food processing, changes during digestion, involvement of cellular transporters in influx/efflux through the gastrointestinal epithelium, changes during colonic fermentation, and their phase I and phase II metabolism following absorption. PMID:25988374

A theory of planned behaviour-based analysis of TIMSS 2011 to determine factors influencing inquiry teaching practices in high-performing countries

NASA Astrophysics Data System (ADS)

Pongsophon, Pongprapan; Herman, Benjamin C.

2017-07-01

Given the abundance of literature describing the strong relationship between inquiry-based teaching and student achievement, more should be known about the factors impacting science teachers' classroom inquiry implementation. This study utilises the theory of planned behaviour to propose and validate a causal model of inquiry-based teaching through analysing data relating to high-performing countries retrieved from the 2011 Trends in International Mathematics and Science Study assessments. Data analysis was completed through structural equation modelling using a polychoric correlation matrix for data input and diagonally weighted least squares estimation. Adequate fit of the full model to the empirical data was realised. The model demonstrates that the extent the teachers participated in academic collaborations was positively related to their occupational satisfaction, confidence in teaching inquiry, and classroom inquiry practices. Furthermore, the teachers' confidence with implementing inquiry was positively related to their classroom inquiry implementation and occupational satisfaction. However, perceived student-generated constraints demonstrated a negative relationship with the teachers' confidence with implementing inquiry and occupational satisfaction. Implications from this study include supporting teachers through promoting collaborative opportunities that facilitate inquiry-based practices and occupational satisfaction.

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

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...

eMBI: Boosting Gene Expression-based Clustering for Cancer Subtypes.

PubMed

Chang, Zheng; Wang, Zhenjia; Ashby, Cody; Zhou, Chuan; Li, Guojun; Zhang, Shuzhong; Huang, Xiuzhen

2014-01-01

Identifying clinically relevant subtypes of a cancer using gene expression data is a challenging and important problem in medicine, and is a necessary premise to provide specific and efficient treatments for patients of different subtypes. Matrix factorization provides a solution by finding checker-board patterns in the matrices of gene expression data. In the context of gene expression profiles of cancer patients, these checkerboard patterns correspond to genes that are up- or down-regulated in patients with particular cancer subtypes. Recently, a new matrix factorization framework for biclustering called Maximum Block Improvement (MBI) is proposed; however, it still suffers several problems when applied to cancer gene expression data analysis. In this study, we developed many effective strategies to improve MBI and designed a new program called enhanced MBI (eMBI), which is more effective and efficient to identify cancer subtypes. Our tests on several gene expression profiling datasets of cancer patients consistently indicate that eMBI achieves significant improvements in comparison with MBI, in terms of cancer subtype prediction accuracy, robustness, and running time. In addition, the performance of eMBI is much better than another widely used matrix factorization method called nonnegative matrix factorization (NMF) and the method of hierarchical clustering, which is often the first choice of clinical analysts in practice.

eMBI: Boosting Gene Expression-based Clustering for Cancer Subtypes

PubMed Central

Chang, Zheng; Wang, Zhenjia; Ashby, Cody; Zhou, Chuan; Li, Guojun; Zhang, Shuzhong; Huang, Xiuzhen

2014-01-01

Identifying clinically relevant subtypes of a cancer using gene expression data is a challenging and important problem in medicine, and is a necessary premise to provide specific and efficient treatments for patients of different subtypes. Matrix factorization provides a solution by finding checker-board patterns in the matrices of gene expression data. In the context of gene expression profiles of cancer patients, these checkerboard patterns correspond to genes that are up- or down-regulated in patients with particular cancer subtypes. Recently, a new matrix factorization framework for biclustering called Maximum Block Improvement (MBI) is proposed; however, it still suffers several problems when applied to cancer gene expression data analysis. In this study, we developed many effective strategies to improve MBI and designed a new program called enhanced MBI (eMBI), which is more effective and efficient to identify cancer subtypes. Our tests on several gene expression profiling datasets of cancer patients consistently indicate that eMBI achieves significant improvements in comparison with MBI, in terms of cancer subtype prediction accuracy, robustness, and running time. In addition, the performance of eMBI is much better than another widely used matrix factorization method called nonnegative matrix factorization (NMF) and the method of hierarchical clustering, which is often the first choice of clinical analysts in practice. PMID:25374455

More efficient parameter estimates for factor analysis of ordinal variables by ridge generalized least squares.

PubMed

Yuan, Ke-Hai; Jiang, Ge; Cheng, Ying

2017-11-01

Data in psychology are often collected using Likert-type scales, and it has been shown that factor analysis of Likert-type data is better performed on the polychoric correlation matrix than on the product-moment covariance matrix, especially when the distributions of the observed variables are skewed. In theory, factor analysis of the polychoric correlation matrix is best conducted using generalized least squares with an asymptotically correct weight matrix (AGLS). However, simulation studies showed that both least squares (LS) and diagonally weighted least squares (DWLS) perform better than AGLS, and thus LS or DWLS is routinely used in practice. In either LS or DWLS, the associations among the polychoric correlation coefficients are completely ignored. To mend such a gap between statistical theory and empirical work, this paper proposes new methods, called ridge GLS, for factor analysis of ordinal data. Monte Carlo results show that, for a wide range of sample sizes, ridge GLS methods yield uniformly more accurate parameter estimates than existing methods (LS, DWLS, AGLS). A real-data example indicates that estimates by ridge GLS are 9-20% more efficient than those by existing methods. Rescaled and adjusted test statistics as well as sandwich-type standard errors following the ridge GLS methods also perform reasonably well. © 2017 The British Psychological Society.

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

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

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

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

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.

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.

An Alternating Least Squares Method for the Weighted Approximation of a Symmetric Matrix.

ERIC Educational Resources Information Center

ten Berge, Jos M. F.; Kiers, Henk A. L.

1993-01-01

R. A. Bailey and J. C. Gower explored approximating a symmetric matrix "B" by another, "C," in the least squares sense when the squared discrepancies for diagonal elements receive specific nonunit weights. A solution is proposed where "C" is constrained to be positive semidefinite and of a fixed rank. (SLD)

Effect of inclusions on heterogeneous crack nucleation in nanocomposites

NASA Astrophysics Data System (ADS)

Gutkin, M. Yu.; Ovid'Ko, I. A.; Skiba, N. V.

2007-02-01

A two-dimensional theoretical model is proposed for the heterogeneous nucleation of a grain-boundary nanocrack in a nanocomposite consisting of a nanocrystalline matrix and nanoinclusions whose elastic moduli are identical to those of the matrix. The inclusions have the form of rods with a rectangular cross section and undergo dilatation eigenstrain induced by the differences in the lattice parameters and thermal expansion coefficients of the matrix and inclusions. In terms of the model, a mode-I-II nanocrack nucleates at the negative disclination of a biaxial dipole consisting of wedge grain-boundary (or junction) disclinations; then, the nanocrack opens along a grain boundary and reaches an inclusion boundary. Depending on the relative positions and orientations of the initial segment of the nanocrack and the inclusion, the nanocrack can either penetrate into the inclusion or bypass it along the matrix-inclusion interface. The nanocrack nucleation probability increases near an inclusion with negative (compressive) dilatation eigenstrain. A decrease in the inclusion size decreases (increases) the probability of a crack opening along the interface if the dilatation eigenstrain is negative (positive).