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

Improved Estimation and Interpretation of Correlations in Neural Circuits

PubMed Central

Yatsenko, Dimitri; Josić, Krešimir; Ecker, Alexander S.; Froudarakis, Emmanouil; Cotton, R. James; Tolias, Andreas S.

2015-01-01

Ambitious projects aim to record the activity of ever larger and denser neuronal populations in vivo. Correlations in neural activity measured in such recordings can reveal important aspects of neural circuit organization. However, estimating and interpreting large correlation matrices is statistically challenging. Estimation can be improved by regularization, i.e. by imposing a structure on the estimate. The amount of improvement depends on how closely the assumed structure represents dependencies in the data. Therefore, the selection of the most efficient correlation matrix estimator for a given neural circuit must be determined empirically. Importantly, the identity and structure of the most efficient estimator informs about the types of dominant dependencies governing the system. We sought statistically efficient estimators of neural correlation matrices in recordings from large, dense groups of cortical neurons. Using fast 3D random-access laser scanning microscopy of calcium signals, we recorded the activity of nearly every neuron in volumes 200 μm wide and 100 μm deep (150–350 cells) in mouse visual cortex. We hypothesized that in these densely sampled recordings, the correlation matrix should be best modeled as the combination of a sparse graph of pairwise partial correlations representing local interactions and a low-rank component representing common fluctuations and external inputs. Indeed, in cross-validation tests, the covariance matrix estimator with this structure consistently outperformed other regularized estimators. The sparse component of the estimate defined a graph of interactions. These interactions reflected the physical distances and orientation tuning properties of cells: The density of positive ‘excitatory’ interactions decreased rapidly with geometric distances and with differences in orientation preference whereas negative ‘inhibitory’ interactions were less selective. Because of its superior performance, this ‘sparse+latent’ estimator likely provides a more physiologically relevant representation of the functional connectivity in densely sampled recordings than the sample correlation matrix. PMID:25826696

Analysis of cross-correlations between financial markets after the 2008 crisis

NASA Astrophysics Data System (ADS)

Sensoy, A.; Yuksel, S.; Erturk, M.

2013-10-01

We analyze the cross-correlation matrix C of the index returns of the main financial markets after the 2008 crisis using methods of random matrix theory. We test the eigenvalues of C for universal properties of random matrices and find that the majority of the cross-correlation coefficients arise from randomness. We show that the eigenvector of the largest deviating eigenvalue of C represents a global market itself. We reveal that high volatility of financial markets is observed at the same times with high correlations between them which lowers the risk diversification potential even if one constructs a widely internationally diversified portfolio of stocks. We identify and compare the connection and cluster structure of markets before and after the crisis using minimal spanning and ultrametric hierarchical trees. We find that after the crisis, the co-movement degree of the markets increases. We also highlight the key financial markets of pre and post crisis using main centrality measures and analyze the changes. We repeat the study using rank correlation and compare the differences. Further implications are discussed.

Towards a nondestructive chemical characterization of biofilm matrix by Raman microscopy.

PubMed

Ivleva, Natalia P; Wagner, Michael; Horn, Harald; Niessner, Reinhard; Haisch, Christoph

2009-01-01

In this study, the applicability of Raman microscopy (RM) for nondestructive chemical analysis of biofilm matrix, including microbial constituents and extracellular polymeric substances (EPS), has been assessed. The examination of a wide range of reference samples such as biofilm-specific polysaccharides, proteins, microorganisms, and encapsulated bacteria revealed characteristic frequency regions and specific marker bands for different biofilm constituents. Based on received data, the assignment of Raman bands in spectra of multispecies biofilms was performed. The study of different multispecies biofilms showed that RM can correlate various structural appearances within the biofilm to variations in their chemical composition and provide chemical information about a complex biofilm matrix. The results of RM analysis of biofilms are in good agreement with data obtained by confocal laser scanning microscopy (CLSM). Thus, RM is a promising tool for a label-free chemical characterization of different biofilm constituents. Moreover, the combination of RM with CLSM analysis for the study of biofilms grown under different environmental conditions can provide new insights into the complex structure/function correlations in biofilms.

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.

The Extracellular Matrix of Candida albicans Biofilms Impairs Formation of Neutrophil Extracellular Traps.

PubMed

Johnson, Chad J; Cabezas-Olcoz, Jonathan; Kernien, John F; Wang, Steven X; Beebe, David J; Huttenlocher, Anna; Ansari, Hamayail; Nett, Jeniel E

2016-09-01

Neutrophils release extracellular traps (NETs) in response to planktonic C. albicans. These complexes composed of DNA, histones, and proteins inhibit Candida growth and dissemination. Considering the resilience of Candida biofilms to host defenses, we examined the neutrophil response to C. albicans during biofilm growth. In contrast to planktonic C. albicans, biofilms triggered negligible release of NETs. Time lapse imaging confirmed the impairment in NET release and revealed neutrophils adhering to hyphae and migrating on the biofilm. NET inhibition depended on an intact extracellular biofilm matrix as physical or genetic disruption of this component resulted in NET release. Biofilm inhibition of NETosis could not be overcome by protein kinase C activation via phorbol myristate acetate (PMA) and was associated with suppression of neutrophil reactive oxygen species (ROS) production. The degree of impaired NET release correlated with resistance to neutrophil attack. The clinical relevance of the role for extracellular matrix in diminishing NET production was corroborated in vivo using a rat catheter model. The C. albicans pmr1Δ/Δ, defective in production of matrix mannan, appeared to elicit a greater abundance of NETs by scanning electron microscopy imaging, which correlated with a decreased fungal burden. Together, these findings show that C. albicans biofilms impair neutrophil response through an inhibitory pathway induced by the extracellular matrix.

The Extracellular Matrix of Candida albicans Biofilms Impairs Formation of Neutrophil Extracellular Traps

PubMed Central

Cabezas-Olcoz, Jonathan; Wang, Steven X.; Huttenlocher, Anna; Ansari, Hamayail; Nett, Jeniel E.

2016-01-01

Neutrophils release extracellular traps (NETs) in response to planktonic C. albicans. These complexes composed of DNA, histones, and proteins inhibit Candida growth and dissemination. Considering the resilience of Candida biofilms to host defenses, we examined the neutrophil response to C. albicans during biofilm growth. In contrast to planktonic C. albicans, biofilms triggered negligible release of NETs. Time lapse imaging confirmed the impairment in NET release and revealed neutrophils adhering to hyphae and migrating on the biofilm. NET inhibition depended on an intact extracellular biofilm matrix as physical or genetic disruption of this component resulted in NET release. Biofilm inhibition of NETosis could not be overcome by protein kinase C activation via phorbol myristate acetate (PMA) and was associated with suppression of neutrophil reactive oxygen species (ROS) production. The degree of impaired NET release correlated with resistance to neutrophil attack. The clinical relevance of the role for extracellular matrix in diminishing NET production was corroborated in vivo using a rat catheter model. The C. albicans pmr1Δ/Δ, defective in production of matrix mannan, appeared to elicit a greater abundance of NETs by scanning electron microscopy imaging, which correlated with a decreased fungal burden. Together, these findings show that C. albicans biofilms impair neutrophil response through an inhibitory pathway induced by the extracellular matrix. PMID:27622514

Different matrix micro-environments in colon cancer and diverticular disease.

PubMed

Klinge, U; Rosch, R; Junge, K; Krones, C J; Stumpf, M; Lynen-Jansen, P; Mertens, P R; Schumpelick, V

2007-05-01

The extracellular matrix and the interactive signalling between its components are thought to play a pivotal role for tumour development and metastasis formation. An altered matrix composition as potential underlying pathology for the development of colorectal cancer was hypothesized. In a retrospective study of patients with colon cancer, the extracellular matrix in tumour-free bowel specimen was investigated in comparison with non-infected bowel specimen from patients operated on for colonic diverticulosis. The following matrix parameters with known associations to tumour formation, cell proliferation, invasion and metastasis were analysed by immunohistochemistry and quantified by a scoring system: VEGF, TGF-beta, ESDN, CD117, c-erb-2, cyclin D1, p53, p27, COX-2, YB-1, collagen I/III, MMP-13, PAI and uPAR. Expression profiles and correlations were calculated. The comparison of the two groups revealed a significantly decreased immunostaining for CD117 and TGF-beta in the cancer group (8.5+/-2.6 vs 10.3+/-2,1 and 4.9+/-1.5 vs 8.1+/-3, respectively), whereas PAI scores were significantly higher than in patients with diverticular disease (8.1+/-1.6 vs 6.2+/-0.9). Overall correlation patterns of matrix parameters indicated pronounced differences between tumour-free tissue in cancer patients compared with patients with diverticular disease. Our results indicate distinct differences in the colonic tissue architecture between cancer patients and patients with diverticulitis that support the notion of an altered matrix composition predisposing to the development of colon cancer.

Fluctuation-dissipation theory of input-output interindustrial relations

NASA Astrophysics Data System (ADS)

Iyetomi, Hiroshi; Nakayama, Yasuhiro; Aoyama, Hideaki; Fujiwara, Yoshi; Ikeda, Yuichi; Souma, Wataru

2011-01-01

In this study, the fluctuation-dissipation theory is invoked to shed light on input-output interindustrial relations at a macroscopic level by its application to indices of industrial production (IIP) data for Japan. Statistical noise arising from finiteness of the time series data is carefully removed by making use of the random matrix theory in an eigenvalue analysis of the correlation matrix; as a result, two dominant eigenmodes are detected. Our previous study successfully used these two modes to demonstrate the existence of intrinsic business cycles. Here a correlation matrix constructed from the two modes describes genuine interindustrial correlations in a statistically meaningful way. Furthermore, it enables us to quantitatively discuss the relationship between shipments of final demand goods and production of intermediate goods in a linear response framework. We also investigate distinctive external stimuli for the Japanese economy exerted by the current global economic crisis. These stimuli are derived from residuals of moving-average fluctuations of the IIP remaining after subtracting the long-period components arising from inherent business cycles. The observation reveals that the fluctuation-dissipation theory is applicable to an economic system that is supposed to be far from physical equilibrium.

Least-Squares Approximation of an Improper Correlation Matrix by a Proper One.

ERIC Educational Resources Information Center

Knol, Dirk L.; ten Berge, Jos M. F.

1989-01-01

An algorithm, based on a solution for C. I. Mosier's oblique Procrustes rotation problem, is presented for the best least-squares fitting correlation matrix approximating a given missing value or improper correlation matrix. Results are of interest for missing value and tetrachoric correlation, indefinite matrix correlation, and constrained…

Statistical analysis of latent generalized correlation matrix estimation in transelliptical distribution.

PubMed

Han, Fang; Liu, Han

2017-02-01

Correlation matrix plays a key role in many multivariate methods (e.g., graphical model estimation and factor analysis). The current state-of-the-art in estimating large correlation matrices focuses on the use of Pearson's sample correlation matrix. Although Pearson's sample correlation matrix enjoys various good properties under Gaussian models, its not an effective estimator when facing heavy-tail distributions with possible outliers. As a robust alternative, Han and Liu (2013b) advocated the use of a transformed version of the Kendall's tau sample correlation matrix in estimating high dimensional latent generalized correlation matrix under the transelliptical distribution family (or elliptical copula). The transelliptical family assumes that after unspecified marginal monotone transformations, the data follow an elliptical distribution. In this paper, we study the theoretical properties of the Kendall's tau sample correlation matrix and its transformed version proposed in Han and Liu (2013b) for estimating the population Kendall's tau correlation matrix and the latent Pearson's correlation matrix under both spectral and restricted spectral norms. With regard to the spectral norm, we highlight the role of "effective rank" in quantifying the rate of convergence. With regard to the restricted spectral norm, we for the first time present a "sign subgaussian condition" which is sufficient to guarantee that the rank-based correlation matrix estimator attains the optimal rate of convergence. In both cases, we do not need any moment condition.

Atomic-scale investigation and magnetic properties of Cu80Co20 nanowires

NASA Astrophysics Data System (ADS)

Hannour, A.; Lardé, R.; Jean, M.; Bran, J.; Pareige, P.; Le Breton, J. M.

2011-09-01

Cu80Co20 granular alloy nanowires were synthesized by electrodeposition method and investigated by x-ray diffraction (XRD), Laser Assisted Wide Angle Tomographic Atom Probe (LAWATAP), and SQUID magnetometry. XRD results reveal the existence of a fcc Cu matrix and fcc Co-rich nanograins, with a preferred orientation along the [200] direction (perpendicular to the substrate surface). The Co-rich nanograins could be coherent with the Cu matrix. 3D reconstructions of a nano-sized volume, obtained by LAWATAP, reveal the heterogeneous aspect of the Cu80Co20 nanowires: Co-rich nanoclusters with size between 2 and 10 nm are detected, and the presence of Cu and Co oxides is evidenced. Magnetization measurements indicate that the Co-rich nanoclusters are superparamagnetic, with a blocking temperature that extends up to, at least, room temperature. The presence of ferromagnetic domains at room temperature indicates that some Co-rich nanoclusters are correlated within a volume that corresponds to a so-called interacting superparamagnetic phase. As a matter of fact, by LAWATAP atomic-scale analysis, a very good correlation is obtained between microstructure and magnetic properties.

Reliability, validity and feasibility of nail ultrasonography in psoriatic arthritis.

PubMed

Arbault, Anaïs; Devilliers, Hervé; Laroche, Davy; Cayot, Audrey; Vabres, Pierre; Maillefert, Jean-Francis; Ornetti, Paul

2016-10-01

To determine the feasibility, reliability and validity of nails ultrasonography in psoriatic arthritis as an outcome measure. Pilot prospective single-centre study of eight ultrasonography parameters in B mode and power Doppler concerning the distal interphalangeal (DIP) joint, the matrix, the bed and nail plate. Intra-observer and inter-observer reliability was evaluated for the seven quantitative parameters (ICC and kappa). Correlations between ultrasonography and clinical variables were searched to assess external validity. Feasibility was assessed by the time to carry out the examination and the percentage of missing data. Twenty-seven patients with psoriatic arthritis (age 55.0±16.2 years, disease duration 13.4±9.4 years) were included. Of these, 67% presented nail involvement on ultrasonography vs 37% on physical examination (P<0.05). Reliability was good (ICC and weighted kappa>0.75) for the seven quantitative parameters, except for synovitis of the DIP joint in B mode. The synovitis of the DIP joint revealed by ultrasonography correlated with the total number of clinical synovitis and Doppler US of the nail (matrix and bed). Doppler US of the matrix correlated with VAS pain but not with the ASDAS-CRP or with clinical enthesitis. No significant correlation was found with US nail thickness. The feasibility and reliability of ultrasonography of the nail in psoriatic arthritis appear to be satisfactory. Among the eight parameters evaluated, power Doppler of the matrix which correlated with local inflammation (DIP joint and bed) and with VAS pain could become an interesting outcome measure, provided that it is also sensitive to change. Copyright © 2015 Société française de rhumatologie. Published by Elsevier SAS. All rights reserved.

Correlated matrix-fluctuation-mediated activated transport of dilute penetrants in glass-forming liquids and suspensions

NASA Astrophysics Data System (ADS)

Zhang, Rui; Schweizer, Kenneth S.

2017-05-01

We formulate a microscopic, force-level statistical mechanical theory for the activated diffusion of dilute penetrants in dense liquids, colloidal suspensions, and glasses. The approach explicitly and self-consistently accounts for coupling between penetrant hopping and matrix dynamic displacements that actively facilitate the hopping event. The key new ideas involve two mechanistically (at a stochastic trajectory level) coupled dynamic free energy functions for the matrix and spherical penetrant particles. A single dynamic coupling parameter quantifies how much the matrix displaces relative to the penetrant when the latter reaches its transition state which is determined via the enforcement of a temporal causality or coincidence condition. The theory is implemented for dilute penetrants smaller than the matrix particles, with or without penetrant-matrix attractive forces. Model calculations reveal a rich dependence of the penetrant diffusion constant and degree of dynamic coupling on size ratio, volume fraction, and attraction strength. In the absence of attractions, a near exponential decrease of penetrant diffusivity with size ratio over an intermediate range is predicted, in contrast to the much steeper, non-exponential variation if one assumes local matrix dynamical fluctuations are not correlated with penetrant motion. For sticky penetrants, the relative and absolute influence of caging versus physical bond formation is studied. The conditions for a dynamic crossover from the case where a time scale separation between penetrant and matrix activated hopping exists to a "slaved" or "constraint release" fully coupled regime are determined. The particle mixture model is mapped to treat experimental thermal systems and applied to make predictions for the diffusivity of water, toluene, methanol, and oxygen in polyvinylacetate liquids and glasses. The theory agrees well with experiment with values of the penetrant-matrix size ratio close to their chemically intuitive values.

Correlated matrix-fluctuation-mediated activated transport of dilute penetrants in glass-forming liquids and suspensions

PubMed Central

Schweizer, Kenneth S.

2017-01-01

We formulate a microscopic, force-level statistical mechanical theory for the activated diffusion of dilute penetrants in dense liquids, colloidal suspensions, and glasses. The approach explicitly and self-consistently accounts for coupling between penetrant hopping and matrix dynamic displacements that actively facilitate the hopping event. The key new ideas involve two mechanistically (at a stochastic trajectory level) coupled dynamic free energy functions for the matrix and spherical penetrant particles. A single dynamic coupling parameter quantifies how much the matrix displaces relative to the penetrant when the latter reaches its transition state which is determined via the enforcement of a temporal causality or coincidence condition. The theory is implemented for dilute penetrants smaller than the matrix particles, with or without penetrant-matrix attractive forces. Model calculations reveal a rich dependence of the penetrant diffusion constant and degree of dynamic coupling on size ratio, volume fraction, and attraction strength. In the absence of attractions, a near exponential decrease of penetrant diffusivity with size ratio over an intermediate range is predicted, in contrast to the much steeper, non-exponential variation if one assumes local matrix dynamical fluctuations are not correlated with penetrant motion. For sticky penetrants, the relative and absolute influence of caging versus physical bond formation is studied. The conditions for a dynamic crossover from the case where a time scale separation between penetrant and matrix activated hopping exists to a “slaved” or “constraint release” fully coupled regime are determined. The particle mixture model is mapped to treat experimental thermal systems and applied to make predictions for the diffusivity of water, toluene, methanol, and oxygen in polyvinylacetate liquids and glasses. The theory agrees well with experiment with values of the penetrant-matrix size ratio close to their chemically intuitive values. PMID:28527449

Nondestructive evaluation of a new hydrolytically degradable and photo-clickable PEG hydrogel for cartilage tissue engineering.

PubMed

Neumann, Alexander J; Quinn, Timothy; Bryant, Stephanie J

2016-07-15

Photopolymerizable and hydrolytically labile poly(ethylene glycol) (PEG) hydrogels formed from photo-clickable reactions were investigated as cell delivery platforms for cartilage tissue engineering (TE). PEG hydrogels were formed from thiol-norbornene PEG macromers whereby the crosslinks contained caprolactone segments with hydrolytically labile ester linkages. Juvenile bovine chondrocytes encapsulated in the hydrogels were cultured for up to four weeks and assessed biochemically and histologically, using standard destructive assays, and for mechanical and ultrasound properties, as nondestructive assays. Bulk degradation of acellular hydrogels was confirmed by a decrease in compressive modulus and an increase in mass swelling ratio over time. Chondrocytes deposited increasing amounts of sulfated glycosaminoglycans and collagens in the hydrogels with time. Spatially, collagen type II and aggrecan were present in the neotissue with formation of a territorial matrix beginning at day 21. Nondestructive measurements revealed an 8-fold increase in compressive modulus from days 7 to 28, which correlated with total collagen content. Ultrasound measurements revealed changes in the constructs over time, which differed from the mechanical properties, and appeared to correlate with ECM structure and organization shown by immunohistochemical analysis. Overall, non-destructive and destructive measurements show that this new hydrolytically degradable PEG hydrogel is promising for cartilage TE. Designing synthetic hydrogels whose degradation matches tissue growth is critical to maintaining mechanical integrity as the hydrogel degrades and new tissue forms, but is challenging due to the nature of the hydrogel crosslinks that inhibit diffusion of tissue matrix molecules. This study details a promising, new, photo-clickable and synthetic hydrogel whose degradation supports cartilaginous tissue matrix growth leading to the formation of a territorial matrix, concomitant with an increase in mechanical properties. Nondestructive assays based on mechanical and ultrasonic properties were also investigated using a novel instrument and found to correlate with matrix deposition and evolution. In sum, this study presents a new hydrogel platform combined with nondestructive assessments, which together have potential for in vitro cartilage tissue engineering. Copyright © 2016 Acta Materialia Inc. All rights reserved.

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

PubMed

Abdel-Latif, Mohamed S

2015-01-01

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

Statistical analysis of latent generalized correlation matrix estimation in transelliptical distribution

PubMed Central

Han, Fang; Liu, Han

2016-01-01

Correlation matrix plays a key role in many multivariate methods (e.g., graphical model estimation and factor analysis). The current state-of-the-art in estimating large correlation matrices focuses on the use of Pearson’s sample correlation matrix. Although Pearson’s sample correlation matrix enjoys various good properties under Gaussian models, its not an effective estimator when facing heavy-tail distributions with possible outliers. As a robust alternative, Han and Liu (2013b) advocated the use of a transformed version of the Kendall’s tau sample correlation matrix in estimating high dimensional latent generalized correlation matrix under the transelliptical distribution family (or elliptical copula). The transelliptical family assumes that after unspecified marginal monotone transformations, the data follow an elliptical distribution. In this paper, we study the theoretical properties of the Kendall’s tau sample correlation matrix and its transformed version proposed in Han and Liu (2013b) for estimating the population Kendall’s tau correlation matrix and the latent Pearson’s correlation matrix under both spectral and restricted spectral norms. With regard to the spectral norm, we highlight the role of “effective rank” in quantifying the rate of convergence. With regard to the restricted spectral norm, we for the first time present a “sign subgaussian condition” which is sufficient to guarantee that the rank-based correlation matrix estimator attains the optimal rate of convergence. In both cases, we do not need any moment condition. PMID:28337068

State-Space System Realization with Input- and Output-Data Correlation

NASA Technical Reports Server (NTRS)

Juang, Jer-Nan

1997-01-01

This paper introduces a general version of the information matrix consisting of the autocorrelation and cross-correlation matrices of the shifted input and output data. Based on the concept of data correlation, a new system realization algorithm is developed to create a model directly from input and output data. The algorithm starts by computing a special type of correlation matrix derived from the information matrix. The special correlation matrix provides information on the system-observability matrix and the state-vector correlation. A system model is then developed from the observability matrix in conjunction with other algebraic manipulations. This approach leads to several different algorithms for computing system matrices for use in representing the system model. The relationship of the new algorithms with other realization algorithms in the time and frequency domains is established with matrix factorization of the information matrix. Several examples are given to illustrate the validity and usefulness of these new algorithms.

Monitoring damage growth in titanium matrix composites using acoustic emission

NASA Technical Reports Server (NTRS)

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

1993-01-01

The application of the acoustic emission (AE) technique to locate and monitor damage growth in titanium matrix composites (TMC) was investigated. Damage growth was studied using several optical techniques including a long focal length, high magnification microscope system with image acquisition capabilities. Fracture surface examinations were conducted using a scanning electron microscope (SEM). The AE technique was used to locate damage based on the arrival times of AE events between two sensors. Using model specimens exhibiting a dominant failure mechanism, correlations were established between the observed damage growth mechanisms and the AE results in terms of the events amplitude. These correlations were used to monitor the damage growth process in laminates exhibiting multiple modes of damage. Results revealed that the AE technique is a viable and effective tool to monitor damage growth in TMC.

Genomic and protein expression profiling identifies CDK6 as novel independent prognostic marker in medulloblastoma.

PubMed

Mendrzyk, Frank; Radlwimmer, Bernhard; Joos, Stefan; Kokocinski, Felix; Benner, Axel; Stange, Daniel E; Neben, Kai; Fiegler, Heike; Carter, Nigel P; Reifenberger, Guido; Korshunov, Andrey; Lichter, Peter

2005-12-01

Medulloblastoma is the most common malignant brain tumor in children. Despite multimodal aggressive treatment, nearly half of the patients die as a result of this tumor. Identification of molecular markers for prognosis and development of novel pathogenesis-based therapies depends crucially on a better understanding of medulloblastoma pathomechanisms. We performed genome-wide analysis of DNA copy number imbalances in 47 medulloblastomas using comparative genomic hybridization to large insert DNA microarrays (matrix-CGH). The expression of selected candidate genes identified by matrix-CGH was analyzed immunohistochemically on tissue microarrays representing medulloblastomas from 189 clinically well-documented patients. To identify novel prognostic markers, genomic findings and protein expression data were correlated to patient survival. Matrix-CGH analysis revealed frequent DNA copy number alterations of several novel candidate regions. Among these, gains at 17q23.2-qter (P < .01) and losses at 17p13.1 to 17p13.3 (P = .04) were significantly correlated to poor prognosis. Within 17q23.2-qter and 7q21.2, two of the most frequently gained chromosomal regions, confined amplicons were identified that contained the PPM1D and CDK6 genes, respectively. Immunohistochemistry revealed strong expression of PPM1D in 148 (88%) of 168 and CDK6 in 50 (30%) of 169 medulloblastomas. Overexpression of CDK6 correlated significantly with poor prognosis (P < .01) and represented an independent prognostic marker of overall survival on multivariate analysis (P = .02). We identified CDK6 as a novel molecular marker that can be determined by immunohistochemistry on routinely processed tissue specimens and may facilitate the prognostic assessment of medulloblastoma patients. Furthermore, increased protein-levels of PPM1D and CDK6 may link the TP53 and RB1 tumor suppressor pathways to medulloblastoma pathomechanisms.

Coexistence of two electronic phases in LaTiO3+δ (0.01⩽δ⩽0.12) and their evolution with δ

NASA Astrophysics Data System (ADS)

Zhou, H. D.; Goodenough, J. B.

2005-04-01

Although LaTiO3+δ(0.01⩽δ⩽0.12) is single-phase to powder x-ray diffraction, its properties reveal that a hole-poor strongly correlated electronic phase coexists with a hole-rich itinerant-electron phase. With δ⩽0.03 , the hole-rich phase exists as a minority phase of isolated, mobile itinerant-electron clusters embedded in the hole-poor phase. With δ⩾0.08 , isolated hole-poor clusters are embedded in an itinerant-electron matrix. As δ>0.08 increases, the hole-poor clusters become smaller and more isolated until they are reduced to superparamagnetic strong-correlation fluctuations by δ=0.12 . This behavior is consistent with prediction from the virial theorem of a first-order phase change at the crossover from localized (or strongly correlated) to itinerant electronic behavior, a smaller equilibrium (Ti-O) bond length being in the itinerant-electron phase. Accordingly, the variation of volume with oxidation state does not obey Végard’s law; the itinerant-electron minority phase exerts a compressive force on the hole-poor matrix, and the hole-poor minority phase exerts a tensile stress on the hole-rich matrix.

An Efficient Local Correlation Matrix Decomposition Approach for the Localization Implementation of Ensemble-Based Assimilation Methods

NASA Astrophysics Data System (ADS)

Zhang, Hongqin; Tian, Xiangjun

2018-04-01

Ensemble-based data assimilation methods often use the so-called localization scheme to improve the representation of the ensemble background error covariance (Be). Extensive research has been undertaken to reduce the computational cost of these methods by using the localized ensemble samples to localize Be by means of a direct decomposition of the local correlation matrix C. However, the computational costs of the direct decomposition of the local correlation matrix C are still extremely high due to its high dimension. In this paper, we propose an efficient local correlation matrix decomposition approach based on the concept of alternating directions. This approach is intended to avoid direct decomposition of the correlation matrix. Instead, we first decompose the correlation matrix into 1-D correlation matrices in the three coordinate directions, then construct their empirical orthogonal function decomposition at low resolution. This procedure is followed by the 1-D spline interpolation process to transform the above decompositions to the high-resolution grid. Finally, an efficient correlation matrix decomposition is achieved by computing the very similar Kronecker product. We conducted a series of comparison experiments to illustrate the validity and accuracy of the proposed local correlation matrix decomposition approach. The effectiveness of the proposed correlation matrix decomposition approach and its efficient localization implementation of the nonlinear least-squares four-dimensional variational assimilation are further demonstrated by several groups of numerical experiments based on the Advanced Research Weather Research and Forecasting model.

Sapphire reinforced alumina matrix composites

NASA Technical Reports Server (NTRS)

Jaskowiak, Martha H.; Setlock, John A.

1994-01-01

Unidirectionally reinforced A1203 matrix composites have been fabricated by hot pressing. Approximately 30 volume % of either coated or uncoated sapphire fiber was used as reinforcement. Unstabilized ZrO2 was applied as the fiber coating. Composite mechanical behavior was analyzed both after fabrication and after additional heat treatment. The results of composite tensile tests were correlated with fiber-matrix interfacial shear strengths determined from fiber push-out tests. Substantially higher strength and greater fiber pull-out were observed for the coated fiber composites for all processing conditions studied. The coated fiber composites retained up to 95% and 87% of their as-fabricated strength when heat treated at 14000C for 8 or 24 hours, respectively. Electron microscopy analysis of the fracture surfaces revealed extensive fiber pull-out both before and after heat treatment.

Rich structure in the correlation matrix spectra in non-equilibrium steady states

NASA Astrophysics Data System (ADS)

Biswas, Soham; Leyvraz, Francois; Monroy Castillero, Paulino; Seligman, Thomas H.

2017-01-01

It has been shown that, if a model displays long-range (power-law) spatial correlations, its equal-time correlation matrix will also have a power law tail in the distribution of its high-lying eigenvalues. The purpose of this paper is to show that the converse is generally incorrect: a power-law tail in the high-lying eigenvalues of the correlation matrix may exist even in the absence of equal-time power law correlations in the initial model. We may therefore view the study of the eigenvalue distribution of the correlation matrix as a more powerful tool than the study of spatial Correlations, one which may in fact uncover structure, that would otherwise not be apparent. Specifically, we show that in the Totally Asymmetric Simple Exclusion Process, whereas there are no clearly visible correlations in the steady state, the eigenvalues of its correlation matrix exhibit a rich structure which we describe in detail.

Rich structure in the correlation matrix spectra in non-equilibrium steady states.

PubMed

Biswas, Soham; Leyvraz, Francois; Monroy Castillero, Paulino; Seligman, Thomas H

2017-01-17

It has been shown that, if a model displays long-range (power-law) spatial correlations, its equal-time correlation matrix will also have a power law tail in the distribution of its high-lying eigenvalues. The purpose of this paper is to show that the converse is generally incorrect: a power-law tail in the high-lying eigenvalues of the correlation matrix may exist even in the absence of equal-time power law correlations in the initial model. We may therefore view the study of the eigenvalue distribution of the correlation matrix as a more powerful tool than the study of spatial Correlations, one which may in fact uncover structure, that would otherwise not be apparent. Specifically, we show that in the Totally Asymmetric Simple Exclusion Process, whereas there are no clearly visible correlations in the steady state, the eigenvalues of its correlation matrix exhibit a rich structure which we describe in detail.

Repeated decompositions reveal the stability of infomax decomposition of fMRI data

PubMed Central

Duann, Jeng-Ren; Jung, Tzyy-Ping; Sejnowski, Terrence J.; Makeig, Scott

2010-01-01

In this study, we decomposed 12 fMRI data sets from six subjects each 101 times using the infomax algorithm. The first decomposition was taken as a reference decomposition; the others were used to form a component matrix of 100 by 100 components. Equivalence relations between components in this matrix, defined as maximum spatial correlations to the components of the reference decomposition, were found by the Hungarian sorting method and used to form 100 equivalence classes for each data set. We then tested the reproducibility of the matched components in the equivalence classes using uncertainty measures based on component distributions, time courses, and ROC curves. Infomax ICA rarely failed to derive nearly the same components in different decompositions. Very few components per data set were poorly reproduced, even using vector angle uncertainty measures stricter than correlation and detection theory measures. PMID:17281453

Robust validation of approximate 1-matrix functionals with few-electron harmonium atoms

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

Cioslowski, Jerzy, E-mail: jerzy@wmf.univ.szczecin.pl; Piris, Mario; Matito, Eduard

2015-12-07

A simple comparison between the exact and approximate correlation components U of the electron-electron repulsion energy of several states of few-electron harmonium atoms with varying confinement strengths provides a stringent validation tool for 1-matrix functionals. The robustness of this tool is clearly demonstrated in a survey of 14 known functionals, which reveals their substandard performance within different electron correlation regimes. Unlike spot-testing that employs dissociation curves of diatomic molecules or more extensive benchmarking against experimental atomization energies of molecules comprising some standard set, the present approach not only uncovers the flaws and patent failures of the functionals but, even moremore » importantly, also allows for pinpointing their root causes. Since the approximate values of U are computed at exact 1-densities, the testing requires minimal programming and thus is particularly suitable for rapid screening of new functionals.« less

Pre-Processed Recursive Lattice Reduction for Complexity Reduction in Spatially and Temporally Correlated MIMO Channels

NASA Astrophysics Data System (ADS)

An, Chan-Ho; Yang, Janghoon; Jang, Seunghun; Kim, Dong Ku

In this letter, a pre-processed lattice reduction (PLR) scheme is developed for the lattice reduction aided (LRA) detection of multiple input multiple-output (MIMO) systems in spatially correlated channel. The PLR computes the LLL-reduced matrix of the equivalent matrix, which is the product of the present channel matrix and unimodular transformation matrix for LR of spatial correlation matrix, rather than the present channel matrix itself. In conjunction with PLR followed by recursive lattice reduction (RLR) scheme [7], pre-processed RLR (PRLR) is shown to efficiently carry out the LR of the channel matrix, especially for the burst packet message in spatially and temporally correlated channel while matching the performance of conventional LRA detection.

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.

Characteristics of global organic matrix in normal and pimpled chicken eggshells.

PubMed

Liu, Z; Song, L; Zhang, F; He, W; Linhardt, R J

2017-10-01

The organic matrix from normal and pimpled calcified chicken eggshells were dissociated into acid-insoluble, water-insoluble, and facultative-soluble (both acid- and water-soluble) components, to understand the influence of shell matrix on eggshell qualities. A linear correlation was shown among these 3 matrix components in normal eggshells but was not observed in pimpled eggshells. In pimpled eggshells, the percentage contents of all 4 groups of matrix (the total matrix, acid-insoluble matrix, water-insoluble matrix, and facultative-soluble matrix) were significantly higher than that in normal eggshells. The amounts of both total matrix and acid-insoluble matrix in individual pimpled calcified shells were high, even though their weight was much lower than a normal eggshell. In both normal and pimpled eggshells, the calcified eggshell weight and shell thickness significantly and positively correlated with the amounts of all 4 groups of matrix in an individual calcified shell. In normal eggshells, the calcified shell thickness and shell breaking strength showed no significant correlations with the percentage contents of all 4 groups of matrix. In normal eggshells, only the shell membrane weight significantly correlated with the constituent ratios of both acid-insoluble matrix and facultative-soluble matrix in the whole matrix. In pimpled eggshells, 3 variables (calcified shell weight, shell thickness, and breaking strength) were significantly correlated with the constituent proportions of both acid-insoluble matrix and facultative-matrix. This study suggests that mechanical properties of normal eggshells may not linearly depend on the organic matrix content in the calcified eggshells and that pimpled eggshells might result by the disequilibrium enrichment of some proteins with negative effects. © 2017 Poultry Science Association Inc.

On base station cooperation using statistical CSI in jointly correlated MIMO downlink channels

NASA Astrophysics Data System (ADS)

Zhang, Jun; Jiang, Bin; Jin, Shi; Gao, Xiqi; Wong, Kai-Kit

2012-12-01

This article studies the transmission of a single cell-edge user's signal using statistical channel state information at cooperative base stations (BSs) with a general jointly correlated multiple-input multiple-output (MIMO) channel model. We first present an optimal scheme to maximize the ergodic sum capacity with per-BS power constraints, revealing that the transmitted signals of all BSs are mutually independent and the optimum transmit directions for each BS align with the eigenvectors of the BS's own transmit correlation matrix of the channel. Then, we employ matrix permanents to derive a closed-form tight upper bound for the ergodic sum capacity. Based on these results, we develop a low-complexity power allocation solution using convex optimization techniques and a simple iterative water-filling algorithm (IWFA) for power allocation. Finally, we derive a necessary and sufficient condition for which a beamforming approach achieves capacity for all BSs. Simulation results demonstrate that the upper bound of ergodic sum capacity is tight and the proposed cooperative transmission scheme increases the downlink system sum capacity considerably.

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.

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.

Market Correlation Structure Changes Around the Great Crash: A Random Matrix Theory Analysis of the Chinese Stock Market

NASA Astrophysics Data System (ADS)

Han, Rui-Qi; Xie, Wen-Jie; Xiong, Xiong; Zhang, Wei; Zhou, Wei-Xing

The correlation structure of a stock market contains important financial contents, which may change remarkably due to the occurrence of financial crisis. We perform a comparative analysis of the Chinese stock market around the occurrence of the 2008 crisis based on the random matrix analysis of high-frequency stock returns of 1228 Chinese stocks. Both raw correlation matrix and partial correlation matrix with respect to the market index in two time periods of one year are investigated. We find that the Chinese stocks have stronger average correlation and partial correlation in 2008 than in 2007 and the average partial correlation is significantly weaker than the average correlation in each period. Accordingly, the largest eigenvalue of the correlation matrix is remarkably greater than that of the partial correlation matrix in each period. Moreover, each largest eigenvalue and its eigenvector reflect an evident market effect, while other deviating eigenvalues do not. We find no evidence that deviating eigenvalues contain industrial sectorial information. Surprisingly, the eigenvectors of the second largest eigenvalues in 2007 and of the third largest eigenvalues in 2008 are able to distinguish the stocks from the two exchanges. We also find that the component magnitudes of the some largest eigenvectors are proportional to the stocks’ capitalizations.

Actomyosin tension as a determinant of metastatic cancer mechanical tropism

NASA Astrophysics Data System (ADS)

McGrail, Daniel J.; Kieu, Quang Minh N.; Iandoli, Jason A.; Dawson, Michelle R.

2015-04-01

Despite major advances in the characterization of molecular regulators of cancer growth and metastasis, patient survival rates have largely stagnated. Recent studies have shown that mechanical cues from the extracellular matrix can drive the transition to a malignant phenotype. Moreover, it is also known that the metastatic process, which results in over 90% of cancer-related deaths, is governed by intracellular mechanical forces. To better understand these processes, we identified metastatic tumor cells originating from different locations which undergo inverse responses to altered matrix elasticity: MDA-MB-231 breast cancer cells that prefer rigid matrices and SKOV-3 ovarian cancer cells that prefer compliant matrices as characterized by parameters such as tumor cell proliferation, chemoresistance, and migration. Transcriptomic analysis revealed higher expression of genes associated with cytoskeletal tension and contractility in cells that prefer stiff environments, both when comparing MDA-MB-231 to SKOV-3 cells as well as when comparing bone-metastatic to lung-metastatic MDA-MB-231 subclones. Using small molecule inhibitors, we found that blocking the activity of these pathways mitigated rigidity-dependent behavior in both cell lines. Probing the physical forces exerted by cells on the underlying substrates revealed that though force magnitude may not directly correlate with functional outcomes, other parameters such as force polarization do correlate directly with cell motility. Finally, this biophysical analysis demonstrates that intrinsic levels of cell contractility determine the matrix rigidity for maximal cell function, possibly influencing tissue sites for metastatic cancer cell engraftment during dissemination. By increasing our understanding of the physical interactions of cancer cells with their microenvironment, these studies may help develop novel therapeutic strategies.

A generalization of random matrix theory and its application to statistical physics.

PubMed

Wang, Duan; Zhang, Xin; Horvatic, Davor; Podobnik, Boris; Eugene Stanley, H

2017-02-01

To study the statistical structure of crosscorrelations in empirical data, we generalize random matrix theory and propose a new method of cross-correlation analysis, known as autoregressive random matrix theory (ARRMT). ARRMT takes into account the influence of auto-correlations in the study of cross-correlations in multiple time series. We first analytically and numerically determine how auto-correlations affect the eigenvalue distribution of the correlation matrix. Then we introduce ARRMT with a detailed procedure of how to implement the method. Finally, we illustrate the method using two examples taken from inflation rates for air pressure data for 95 US cities.

Nuclear Matrix Association: Switching to the Invasive Cytotrophoblast

PubMed Central

Drennan, Kathryn J.; Linnemann, Amelia K.; Platts, Adrian E.; Heng, Henry H.; Armant, D. Randall; Krawetz, Stephen A.

2010-01-01

Abnormal trophoblast invasion is associated with the most common and most severe complications of human pregnancy. The biology of invasion, as well as the etiology of abnormal invasion remains poorly understood. The aim of this study was to characterize the transcriptome of the HTR-8/SVneo human cytotrophoblast cell line which displays well characterized invasive and non-invasive behavior, and to correlate the activity of the transcriptome with nuclear matrix attachment and cell phenotype. Comparison of the invasive to non-invasive HTR transcriptomes was unremarkable. In contrast, comparison of the MARs on chromosomes 14–18 revealed an increased number of MARs associated with the invasive phenotype. These attachment areas were more likely to be associated with silent rather than actively transcribed genes. This study supports that view that that nuclear matrix attachment may play an important role in cytotrophoblast invasion by ensuring specific silencing that facilitates invasion. PMID:20346505

Asymmetric correlation matrices: an analysis of financial data

NASA Astrophysics Data System (ADS)

Livan, G.; Rebecchi, L.

2012-06-01

We analyse the spectral properties of correlation matrices between distinct statistical systems. Such matrices are intrinsically non-symmetric, and lend themselves to extend the spectral analyses usually performed on standard Pearson correlation matrices to the realm of complex eigenvalues. We employ some recent random matrix theory results on the average eigenvalue density of this type of matrix to distinguish between noise and non-trivial correlation structures, and we focus on financial data as a case study. Namely, we employ daily prices of stocks belonging to the American and British stock exchanges, and look for the emergence of correlations between two such markets in the eigenvalue spectrum of their non-symmetric correlation matrix. We find several non trivial results when considering time-lagged correlations over short lags, and we corroborate our findings by additionally studying the asymmetric correlation matrix of the principal components of our datasets.

Matrix density alters zyxin phosphorylation, which limits peripheral process formation and extension in endothelial cells invading 3D collagen matrices.

PubMed

Abbey, Colette A; Bayless, Kayla J

2014-09-01

This study was designed to determine the optimal conditions required for known pro-angiogenic stimuli to elicit successful endothelial sprouting responses. We used an established, quantifiable model of endothelial cell (EC) sprout initiation where ECs were tested for invasion in low (1 mg/mL) and high density (5 mg/mL) 3D collagen matrices. Sphingosine 1-phosphate (S1P) alone, or S1P combined with stromal derived factor-1α (SDF) and phorbol ester (TPA), elicited robust sprouting responses. The ability of these factors to stimulate sprouting was more effective in higher density collagen matrices. S1P stimulation resulted in a significant increase in invasion distance, and with the exception of treatment groups containing phorbol ester, invasion distance was longer in 1mg/mL compared to 5mg/mL collagen matrices. Closer examination of cell morphology revealed that increasing matrix density and supplementing with SDF and TPA enhanced the formation of multicellular structures more closely resembling capillaries. TPA enhanced the frequency and size of lumen formation and correlated with a robust increase in phosphorylation of p42/p44 Erk kinase, while S1P and SDF did not. Also, a higher number of significantly longer extended processes formed in 5mg/mL compared to 1mg/mL collagen matrices. Because collagen matrices at higher density have been reported to be stiffer, we tested for changes in the mechanosensitive protein, zyxin. Interestingly, zyxin phosphorylation levels inversely correlated with matrix density, while levels of total zyxin did not change significantly. Immunofluorescence and localization studies revealed that total zyxin was distributed evenly throughout invading structures, while phosphorylated zyxin was slightly more intense in extended peripheral processes. Silencing zyxin expression increased extended process length and number of processes, while increasing zyxin levels decreased extended process length. Altogether these data indicate that ECs integrate signals from multiple exogenous factors, including changes in matrix density, to accomplish successful sprouting responses. We show here for the first time that zyxin limited the formation and extension of fine peripheral processes used by ECs for matrix interrogation, providing a molecular explanation for altered EC responses to high and low density collagen matrices. Copyright © 2014 International Society of Matrix Biology. Published by Elsevier B.V. All rights reserved.

Structure and Self-Assembly of the Calcium Binding Matrix Protein of Human Metapneumovirus

PubMed Central

Leyrat, Cedric; Renner, Max; Harlos, Karl; Huiskonen, Juha T.; Grimes, Jonathan M.

2014-01-01

Summary The matrix protein (M) of paramyxoviruses plays a key role in determining virion morphology by directing viral assembly and budding. Here, we report the crystal structure of the human metapneumovirus M at 2.8 Å resolution in its native dimeric state. The structure reveals the presence of a high-affinity Ca2+ binding site. Molecular dynamics simulations (MDS) predict a secondary lower-affinity site that correlates well with data from fluorescence-based thermal shift assays. By combining small-angle X-ray scattering with MDS and ensemble analysis, we captured the structure and dynamics of M in solution. Our analysis reveals a large positively charged patch on the protein surface that is involved in membrane interaction. Structural analysis of DOPC-induced polymerization of M into helical filaments using electron microscopy leads to a model of M self-assembly. The conservation of the Ca2+ binding sites suggests a role for calcium in the replication and morphogenesis of pneumoviruses. PMID:24316400

Experimental investigation of the ordering pathway in a Ni-33 at.%Cr alloy

DOE PAGES

Gwalani, B.; Alam, T.; Miller, C.; ...

2016-06-17

The present study involves a detailed experimental investigation of the concurrent compositional clustering and long-range ordering tendencies in a Ni-33 at.%Cr alloy, carried out by coupling synchrotron-based X-ray diffraction (XRD), transmission electron microscopy (TEM), and atom probe tomography (APT). Synchrotron-based XRD results clearly exhibited progressively increasing lattice contraction in the matrix with increasing isothermal aging time, at 475 degrees C, eventually leading to the development of long-range ordering (LRO) of the Pt2Mo-type. Detailed TEM and APT investigations revealed that this LRO in the matrix is manifested in the form of nanometer-scale ordered domains, and the spatial distribution, size, morphology andmore » compositional evolution of these domains have been carefully investigated. Here, the APT results also revealed the early stages of compositional clustering prior to the onset of long-range ordering in this alloy and such compositional clustering can potentially be correlated to the lattice contraction and previously proposed short-range ordering tendencies.« less

Covariance, correlation matrix, and the multiscale community structure of networks.

PubMed

Shen, Hua-Wei; Cheng, Xue-Qi; Fang, Bin-Xing

2010-07-01

Empirical studies show that real world networks often exhibit multiple scales of topological descriptions. However, it is still an open problem how to identify the intrinsic multiple scales of networks. In this paper, we consider detecting the multiscale community structure of network from the perspective of dimension reduction. According to this perspective, a covariance matrix of network is defined to uncover the multiscale community structure through the translation and rotation transformations. It is proved that the covariance matrix is the unbiased version of the well-known modularity matrix. We then point out that the translation and rotation transformations fail to deal with the heterogeneous network, which is very common in nature and society. To address this problem, a correlation matrix is proposed through introducing the rescaling transformation into the covariance matrix. Extensive tests on real world and artificial networks demonstrate that the correlation matrix significantly outperforms the covariance matrix, identically the modularity matrix, as regards identifying the multiscale community structure of network. This work provides a novel perspective to the identification of community structure and thus various dimension reduction methods might be used for the identification of community structure. Through introducing the correlation matrix, we further conclude that the rescaling transformation is crucial to identify the multiscale community structure of network, as well as the translation and rotation transformations.

Exploring Market State and Stock Interactions on the Minute Timescale

PubMed Central

Tan, Lei; Chen, Jun-Jie; Zheng, Bo; Ouyang, Fang-Yan

2016-01-01

A stock market is a non-stationary complex system. The stock interactions are important for understanding the state of the market. However, our knowledge on the stock interactions on the minute timescale is limited. Here we apply the random matrix theory and methods in complex networks to study the stock interactions and sector interactions. Further, we construct a new kind of cross-correlation matrix to investigate the correlation between the stock interactions at different minutes within one trading day. Based on 50 million minute-to-minute price data in the Shanghai stock market, we discover that the market states in the morning and afternoon are significantly different. The differences mainly exist in three aspects, i.e. the co-movement of stock prices, interactions of sectors and correlation between the stock interactions at different minutes. In the afternoon, the component stocks of sectors are more robust and the structure of sectors is firmer. Therefore, the market state in the afternoon is more stable. Furthermore, we reveal that the information of the sector interactions can indicate the financial crisis in the market, and the indicator based on the empirical data in the afternoon is more effective. PMID:26900948

Exploring Market State and Stock Interactions on the Minute Timescale.

PubMed

Tan, Lei; Chen, Jun-Jie; Zheng, Bo; Ouyang, Fang-Yan

2016-01-01

A stock market is a non-stationary complex system. The stock interactions are important for understanding the state of the market. However, our knowledge on the stock interactions on the minute timescale is limited. Here we apply the random matrix theory and methods in complex networks to study the stock interactions and sector interactions. Further, we construct a new kind of cross-correlation matrix to investigate the correlation between the stock interactions at different minutes within one trading day. Based on 50 million minute-to-minute price data in the Shanghai stock market, we discover that the market states in the morning and afternoon are significantly different. The differences mainly exist in three aspects, i.e. the co-movement of stock prices, interactions of sectors and correlation between the stock interactions at different minutes. In the afternoon, the component stocks of sectors are more robust and the structure of sectors is firmer. Therefore, the market state in the afternoon is more stable. Furthermore, we reveal that the information of the sector interactions can indicate the financial crisis in the market, and the indicator based on the empirical data in the afternoon is more effective.

Carbon matrix based magnetic nanocomposites for potential biomedical applications.

PubMed

Izydorzak-Wozniak, M; Leonowicz, M

2014-03-01

It was found that by varying the pyrolysis temperature of the polymeric precursor, carbon matrix magnetic nanocomposites with different constitution and fractions of magnetic component were made. X-ray diffraction, transmission electron microscopy and Raman spectroscopy revealed the presence of nanocrystallites (NCs) of Co, Fe3C and Ni embedded in porous, partially-graphitized carbon matrix. Vibrating sample magnetometer measurements enabled to determine the correlation between NCs size distribution and magnetic properties. The magnetic studies confirmed that the coercivity, saturation and remanent magnetizations, as well as fraction of the magnetic component depend on the pyrolysis temperature. The Co#C and Fe3C#C composites exhibited ferromagnetic behavior with a remanent to saturation magnetization (M(R)/M(S)) ratio ranging from 0.25 to 0.3, whereas in the Ni containing samples a relatively small M(R)/M(S) ratio point to significant contribution of superparamagnetic interactions. As the carbon matrix magnetic nanocomposites are proposed for biomedical application the basic cytotoxicity test were performed to evaluate a potential toxic effect of the materials on MG-63 cells line.

Psychometric evaluation of the Shared Decision-Making Instrument--Revised.

PubMed

Bartlett, Jacqueline A; Peterson, Jane A

2013-02-01

The purpose of this study was to evaluate the psychometric properties of the Shared Decision-Making Inventory-Revised (SDMI-R) to measure four constructs (knowledge, attitudes, self-efficacy, and intent) theoretically defined as vital in discussing the human papillomavirus (HPV) disease and vaccine with clients. The SDMI-R was distributed to a sample (N = 1,525) of school nurses. Correlational matrixes denoted moderate to strong correlations, indicating adequate internal reliability. Reliability for the total instrument was satisfactory (α = .874) along with Attitude, Self-Efficacy and Intent subscales .828, .917, .891, respectively. Exploratory factor analysis revealed five components that explained 75.96% of the variance.

What affects the predictability of evolutionary constraints using a G-matrix? The relative effects of modular pleiotropy and mutational correlation.

PubMed

Chebib, Jobran; Guillaume, Frédéric

2017-10-01

Phenotypic traits do not always respond to selection independently from each other and often show correlated responses to selection. The structure of a genotype-phenotype map (GP map) determines trait covariation, which involves variation in the degree and strength of the pleiotropic effects of the underlying genes. It is still unclear, and debated, how much of that structure can be deduced from variational properties of quantitative traits that are inferred from their genetic (co) variance matrix (G-matrix). Here we aim to clarify how the extent of pleiotropy and the correlation among the pleiotropic effects of mutations differentially affect the structure of a G-matrix and our ability to detect genetic constraints from its eigen decomposition. We show that the eigenvectors of a G-matrix can be predictive of evolutionary constraints when they map to underlying pleiotropic modules with correlated mutational effects. Without mutational correlation, evolutionary constraints caused by the fitness costs associated with increased pleiotropy are harder to infer from evolutionary metrics based on a G-matrix's geometric properties because uncorrelated pleiotropic effects do not affect traits' genetic correlations. Correlational selection induces much weaker modular partitioning of traits' genetic correlations in absence then in presence of underlying modular pleiotropy. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

EMMPRIN expression positively correlates with WHO grades of astrocytomas and meningiomas.

PubMed

Tsai, Wen-Chiuan; Chen, Ying; Huang, Li-Chun; Lee, Herng-Sheng; Ma, Hsin-I; Huang, Shih-Ming; Sytwu, Huey-Kang; Hueng, Dueng-Yuan

2013-09-01

High-grade primary brain tumors possessed poor outcome due to invasiveness. Extracellular matrix metalloproteinase inducer (EMMPRIN) stimulates peri-tumoral fibroblasts to secrete matrix metalloproteinase and promote invasiveness. This study hypothesized that high-grade brain tumors overexpress EMMPRIN. Analyzing the public delinked database from the Gene Expression Omnibus profile, the results showed that the EMMPRIN mRNA level was higher in WHO grade IV (n = 81) than in grade III (n = 19, p < 0.0005) astrocytomas and non-tumor brain tissue controls (n = 23, p < 0.00001). The results of tissue microarray-based immunohistochemical (IHC) staining revealed that EMMPRIN levels positively correlated with WHO grades for astrocytomas (p = 0.008) and meningiomas (p = 0.048). EMMPRIN mRNA levels in conventional glioma cell lines (n = 36) was not less than those in glioma primary culture cells (n = 27) and glioblastoma stem-like cells (n = 12). The GBM8401, U87MG, and LN229 human glioma cell lines also overexpressed EMMPRIN. Hematoxylin and eosin, IHC, and immunofluorescence staining of xenografts confirmed that high-grade brain tumors overexpressed EMMPRIN. Lastly, Kaplan-Meier analysis revealed poorer survival in WHO grade IV (n = 56) than in grade III astrocytomas (n = 21, by log-rank test; p = 0.0001, 95 % CI: 1.842-3.053). However, in high-grade astrocytomas, there was no difference in survival between high and low EMMPRIN mRNA levels. Thus, this study identified that high-grade brain tumors overexpress EMMPRIN, which positively correlates with WHO grades in human astrocytomas and meningiomas, and suggests that EMMPRIN may be a therapeutic target of brain tumor.

Protein structure similarity from Principle Component Correlation analysis.

PubMed

Zhou, Xiaobo; Chou, James; Wong, Stephen T C

2006-01-25

Owing to rapid expansion of protein structure databases in recent years, methods of structure comparison are becoming increasingly effective and important in revealing novel information on functional properties of proteins and their roles in the grand scheme of evolutionary biology. Currently, the structural similarity between two proteins is measured by the root-mean-square-deviation (RMSD) in their best-superimposed atomic coordinates. RMSD is the golden rule of measuring structural similarity when the structures are nearly identical; it, however, fails to detect the higher order topological similarities in proteins evolved into different shapes. We propose new algorithms for extracting geometrical invariants of proteins that can be effectively used to identify homologous protein structures or topologies in order to quantify both close and remote structural similarities. We measure structural similarity between proteins by correlating the principle components of their secondary structure interaction matrix. In our approach, the Principle Component Correlation (PCC) analysis, a symmetric interaction matrix for a protein structure is constructed with relationship parameters between secondary elements that can take the form of distance, orientation, or other relevant structural invariants. When using a distance-based construction in the presence or absence of encoded N to C terminal sense, there are strong correlations between the principle components of interaction matrices of structurally or topologically similar proteins. The PCC method is extensively tested for protein structures that belong to the same topological class but are significantly different by RMSD measure. The PCC analysis can also differentiate proteins having similar shapes but different topological arrangements. Additionally, we demonstrate that when using two independently defined interaction matrices, comparison of their maximum eigenvalues can be highly effective in clustering structurally or topologically similar proteins. We believe that the PCC analysis of interaction matrix is highly flexible in adopting various structural parameters for protein structure comparison.

Genetic diversity and gene differentiation among ten species of Zingiberaceae from Eastern India.

PubMed

Mohanty, Sujata; Panda, Manoj Kumar; Acharya, Laxmikanta; Nayak, Sanghamitra

2014-08-01

In the present study, genetic fingerprints of ten species of Zingiberaceae from eastern India were developed using PCR-based markers. 19 RAPD (Rapid Amplified polymorphic DNA), 8 ISSR (Inter Simple Sequence Repeats) and 8 SSR (Simple Sequence Repeats) primers were used to elucidate genetic diversity important for utilization, management and conservation. These primers produced 789 loci, out of which 773 loci were polymorphic (including 220 unique loci) and 16 monomorphic loci. Highest number of bands amplified (263) in Curcuma caesia whereas lowest (209) in Zingiber cassumunar. Though all the markers discriminated the species effectively, analysis of combined data of all markers resulted in better distinction of individual species. Highest number of loci was amplified with SSR primers with resolving power in a range of 17.4-39. Dendrogram based on three molecular data using unweighted pair group method with arithmetic mean classified all the species into two clusters. Mantle matrix correspondence test revealed high matrix correlation in all the cases. Correlation values for RAPD, ISSR and SSR were 0.797, 0.84 and 0.8, respectively, with combined data. In both the genera wild and cultivated species were completely separated from each other at genomic level. It also revealed distinct genetic identity between species of Curcuma and Zingiber. High genetic diversity documented in the present study provides a baseline data for optimization of conservation and breeding programme of the studied zingiberacious species.

ppcor: An R Package for a Fast Calculation to Semi-partial Correlation Coefficients.

PubMed

Kim, Seongho

2015-11-01

Lack of a general matrix formula hampers implementation of the semi-partial correlation, also known as part correlation, to the higher-order coefficient. This is because the higher-order semi-partial correlation calculation using a recursive formula requires an enormous number of recursive calculations to obtain the correlation coefficients. To resolve this difficulty, we derive a general matrix formula of the semi-partial correlation for fast computation. The semi-partial correlations are then implemented on an R package ppcor along with the partial correlation. Owing to the general matrix formulas, users can readily calculate the coefficients of both partial and semi-partial correlations without computational burden. The package ppcor further provides users with the level of the statistical significance with its test statistic.

Least-Squares Approximation of an Improper by a Proper Correlation Matrix Using a Semi-Infinite Convex Program. Research Report 87-7.

ERIC Educational Resources Information Center

Knol, Dirk L.; ten Berge, Jos M. F.

An algorithm is presented for the best least-squares fitting correlation matrix approximating a given missing value or improper correlation matrix. The proposed algorithm is based on a solution for C. I. Mosier's oblique Procrustes rotation problem offered by J. M. F. ten Berge and K. Nevels (1977). It is shown that the minimization problem…

Quantum Femtosecond Magnetism: Phase Transition in Step with Light in a Strongly Correlated Manganese Oxide

NASA Astrophysics Data System (ADS)

Wang, Jigang

2014-03-01

Research of non-equilibrium phase transitions of strongly correlated electrons is built around addressing an outstanding challenge: how to achieve ultrafast manipulation of competing magnetic/electronic phases and reveal thermodynamically hidden orders at highly non-thermal, femtosecond timescales? Recently we reveal a new paradigm called quantum femtosecond magnetism-photoinduced femtosecond magnetic phase transitions driven by quantum spin flip fluctuations correlated with laser-excited inter-atomic coherent bonding. We demonstrate an antiferromagnetic (AFM) to ferromagnetic (FM) switching during about 100 fs laser pulses in a colossal magneto-resistive manganese oxide. Our results show a huge photoinduced femtosecond spin generation, measured by magnetic circular dichroism, with photo-excitation threshold behavior absent in the picosecond dynamics. This reveals an initial quantum coherent regime of magnetism, while the optical polarization/coherence still interacts with the spins to initiate local FM correlations that compete with the surrounding AFM matrix. Our results thus provide a framework that explores quantum non-equilibrium kinetics to drive phase transitions between exotic ground states in strongly correlated elecrons, and raise fundamental questions regarding some accepted rules, such as free energy and adiabatic potential surface. This work is in collaboration with Tianqi Li, Aaron Patz, Leonidas Mouchliadis, Jiaqiang Yan, Thomas A. Lograsso, Ilias E. Perakis. This work was supported by the National Science Foundation (contract no. DMR-1055352). Material synthesis at the Ames Laboratory was supported by the US Department of Energy-Basic Energy Sciences (contract no. DE-AC02-7CH11358).

Investigating Einstein-Podolsky-Rosen steering of continuous-variable bipartite states by non-Gaussian pseudospin measurements

NASA Astrophysics Data System (ADS)

Xiang, Yu; Xu, Buqing; Mišta, Ladislav; Tufarelli, Tommaso; He, Qiongyi; Adesso, Gerardo

2017-10-01

Einstein-Podolsky-Rosen (EPR) steering is an asymmetric form of correlations which is intermediate between quantum entanglement and Bell nonlocality, and can be exploited as a resource for quantum communication with one untrusted party. In particular, steering of continuous-variable Gaussian states has been extensively studied theoretically and experimentally, as a fundamental manifestation of the EPR paradox. While most of these studies focused on quadrature measurements for steering detection, two recent works revealed that there exist Gaussian states which are only steerable by suitable non-Gaussian measurements. In this paper we perform a systematic investigation of EPR steering of bipartite Gaussian states by pseudospin measurements, complementing and extending previous findings. We first derive the density-matrix elements of two-mode squeezed thermal Gaussian states in the Fock basis, which may be of independent interest. We then use such a representation to investigate steering of these states as detected by a simple nonlinear criterion, based on second moments of the correlation matrix constructed from pseudospin operators. This analysis reveals previously unexplored regimes where non-Gaussian measurements are shown to be more effective than Gaussian ones to witness steering of Gaussian states in the presence of local noise. We further consider an alternative set of pseudospin observables, whose expectation value can be expressed more compactly in terms of Wigner functions for all two-mode Gaussian states. However, according to the adopted criterion, these observables are found to be always less sensitive than conventional Gaussian observables for steering detection. Finally, we investigate continuous-variable Werner states, which are non-Gaussian mixtures of Gaussian states, and find that pseudospin measurements are always more effective than Gaussian ones to reveal their steerability. Our results provide useful insights on the role of non-Gaussian measurements in characterizing quantum correlations of Gaussian and non-Gaussian states of continuous-variable quantum systems.

Direct Preparation of Few Layer Graphene Epoxy Nanocomposites from Untreated Flake Graphite.

PubMed

Throckmorton, James; Palmese, Giuseppe

2015-07-15

The natural availability of flake graphite and the exceptional properties of graphene and graphene-polymer composites create a demand for simple, cost-effective, and scalable methods for top-down graphite exfoliation. This work presents a novel method of few layer graphite nanocomposite preparation directly from untreated flake graphite using a room temperature ionic liquid and laminar shear processing regimen. The ionic liquid serves both as a solvent and initiator for epoxy polymerization and is incorporated chemically into the matrix. This nanocomposite shows low electrical percolation (0.005 v/v) and low thickness (1-3 layers) graphite/graphene flakes by TEM. Additionally, the effect of processing conditions by rheometry and comparison with solvent-free conditions reveal the interactions between processing and matrix properties and provide insight into the theory of the chemical and physical exfoliation of graphite crystals and the resulting polymer matrix dispersion. An interaction model that correlates the interlayer shear physics of graphite flakes and processing parameters is proposed and tested.

Direct determination of neonicotinoid insecticides in an analytically challenging crop such as Chinese chives using selective ELISAs.

PubMed

Watanabe, Eiki; Miyake, Shiro

2018-06-05

Easy-to-use commercial kit-based enzyme-linked immunosorbent assays (ELISAs) have been used to detect neonicotinoid dinotefuran, clothianidin and imidacloprid in Chinese chives, which are considered a troublesome matrix for chromatographic techniques. Based on their high water solubility, water was used as an extractant. Matrix interference could be avoided substantially just diluting sample extracts. Average recoveries of insecticides from spiked samples were 85-113%, with relative standard deviation of <15%. The concentrations of insecticides detected from the spiked samples with the proposed ELISA methods correlated well with those by the reference high-performance liquid chromatography (HPLC) method. The residues analyzed by the ELISA methods were consistently 1.24 times that found by the HPLC method, attributable to loss of analyte during sample clean-up for HPLC analyses. It was revealed that the ELISA methods can be applied easily to pesticide residue analysis in troublesome matrix such as Chinese chives.

Efficient estimation of three-dimensional covariance and its application in the analysis of heterogeneous samples in cryo-electron microscopy

PubMed Central

Liao, Hstau Y.; Hashem, Yaser; Frank, Joachim

2015-01-01

Summary Single-particle cryogenic electron microscopy (cryo-EM) is a powerful tool for the study of macromolecular structures at high resolution. Classification allows multiple structural states to be extracted and reconstructed from the same sample. One classification approach is via the covariance matrix, which captures the correlation between every pair of voxels. Earlier approaches employ computing-intensive resampling and estimate only the eigenvectors of the matrix, which are then used in a separate fast classification step. We propose an iterative scheme to explicitly estimate the covariance matrix in its entirety. In our approach, the flexibility in choosing the solution domain allows us to examine a part of the molecule in greater detail. 3D covariance maps obtained in this way from experimental data (cryo-EM images of the eukaryotic pre-initiation complex) prove to be in excellent agreement with conclusions derived by using traditional approaches, revealing in addition the interdependencies of ligand bindings and structural changes. PMID:25982529

Efficient estimation of three-dimensional covariance and its application in the analysis of heterogeneous samples in cryo-electron microscopy.

PubMed

Liao, Hstau Y; Hashem, Yaser; Frank, Joachim

2015-06-02

Single-particle cryogenic electron microscopy (cryo-EM) is a powerful tool for the study of macromolecular structures at high resolution. Classification allows multiple structural states to be extracted and reconstructed from the same sample. One classification approach is via the covariance matrix, which captures the correlation between every pair of voxels. Earlier approaches employ computing-intensive resampling and estimate only the eigenvectors of the matrix, which are then used in a separate fast classification step. We propose an iterative scheme to explicitly estimate the covariance matrix in its entirety. In our approach, the flexibility in choosing the solution domain allows us to examine a part of the molecule in greater detail. Three-dimensional covariance maps obtained in this way from experimental data (cryo-EM images of the eukaryotic pre-initiation complex) prove to be in excellent agreement with conclusions derived by using traditional approaches, revealing in addition the interdependencies of ligand bindings and structural changes. Copyright © 2015 Elsevier Ltd. All rights reserved.

Characteristic analysis on UAV-MIMO channel based on normalized correlation matrix.

PubMed

Gao, Xi jun; Chen, Zi li; Hu, Yong Jiang

2014-01-01

Based on the three-dimensional GBSBCM (geometrically based double bounce cylinder model) channel model of MIMO for unmanned aerial vehicle (UAV), the simple form of UAV space-time-frequency channel correlation function which includes the LOS, SPE, and DIF components is presented. By the methods of channel matrix decomposition and coefficient normalization, the analytic formula of UAV-MIMO normalized correlation matrix is deduced. This formula can be used directly to analyze the condition number of UAV-MIMO channel matrix, the channel capacity, and other characteristic parameters. The simulation results show that this channel correlation matrix can be applied to describe the changes of UAV-MIMO channel characteristics under different parameter settings comprehensively. This analysis method provides a theoretical basis for improving the transmission performance of UAV-MIMO channel. The development of MIMO technology shows practical application value in the field of UAV communication.

Characteristic Analysis on UAV-MIMO Channel Based on Normalized Correlation Matrix

PubMed Central

Xi jun, Gao; Zi li, Chen; Yong Jiang, Hu

2014-01-01

Based on the three-dimensional GBSBCM (geometrically based double bounce cylinder model) channel model of MIMO for unmanned aerial vehicle (UAV), the simple form of UAV space-time-frequency channel correlation function which includes the LOS, SPE, and DIF components is presented. By the methods of channel matrix decomposition and coefficient normalization, the analytic formula of UAV-MIMO normalized correlation matrix is deduced. This formula can be used directly to analyze the condition number of UAV-MIMO channel matrix, the channel capacity, and other characteristic parameters. The simulation results show that this channel correlation matrix can be applied to describe the changes of UAV-MIMO channel characteristics under different parameter settings comprehensively. This analysis method provides a theoretical basis for improving the transmission performance of UAV-MIMO channel. The development of MIMO technology shows practical application value in the field of UAV communication. PMID:24977185

Revealing Slip Bands In A Metal-Matrix/Fiber Composite

NASA Technical Reports Server (NTRS)

Lerch, Bradley A.

1995-01-01

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

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

Techniques for Fault Detection and Visualization of Telemetry Dependence Relationships for Root Cause Fault Analysis in Complex Systems

NASA Astrophysics Data System (ADS)

Guy, Nathaniel

This thesis explores new ways of looking at telemetry data, from a time-correlative perspective, in order to see patterns within the data that may suggest root causes of system faults. It was thought initially that visualizing an animated Pearson Correlation Coefficient (PCC) matrix for telemetry channels would be sufficient to give new understanding; however, testing showed that the high dimensionality and inability to easily look at change over time in this approach impeded understanding. Different correlative techniques, combined with the time curve visualization proposed by Bach et al (2015), were adapted to visualize both raw telemetry and telemetry data correlations. Review revealed that these new techniques give insights into the data, and an intuitive grasp of data families, which show the effectiveness of this approach for enhancing system understanding and assisting with root cause analysis for complex aerospace systems.

Three-dimensional matrix fiber alignment modulates cell migration and MT1-MMP utility by spatially and temporally directing protrusions

NASA Astrophysics Data System (ADS)

Fraley, Stephanie I.; Wu, Pei-Hsun; He, Lijuan; Feng, Yunfeng; Krisnamurthy, Ranjini; Longmore, Gregory D.; Wirtz, Denis

2015-10-01

Multiple attributes of the three-dimensional (3D) extracellular matrix (ECM) have been independently implicated as regulators of cell motility, including pore size, crosslink density, structural organization, and stiffness. However, these parameters cannot be independently varied within a complex 3D ECM protein network. We present an integrated, quantitative study of these parameters across a broad range of complex matrix configurations using self-assembling 3D collagen and show how each parameter relates to the others and to cell motility. Increasing collagen density resulted in a decrease and then an increase in both pore size and fiber alignment, which both correlated significantly with cell motility but not bulk matrix stiffness within the range tested. However, using the crosslinking enzyme Transglutaminase II to alter microstructure independently of density revealed that motility is most significantly predicted by fiber alignment. Cellular protrusion rate, protrusion orientation, speed of migration, and invasion distance showed coupled biphasic responses to increasing collagen density not predicted by 2D models or by stiffness, but instead by fiber alignment. The requirement of matrix metalloproteinase (MMP) activity was also observed to depend on microstructure, and a threshold of MMP utility was identified. Our results suggest that fiber topography guides protrusions and thereby MMP activity and motility.

Extension of latin hypercube samples with correlated variables.

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

Hora, Stephen Curtis; Helton, Jon Craig; Sallaberry, Cedric J. PhD.

2006-11-01

A procedure for extending the size of a Latin hypercube sample (LHS) with rank correlated variables is described and illustrated. The extension procedure starts with an LHS of size m and associated rank correlation matrix C and constructs a new LHS of size 2m that contains the elements of the original LHS and has a rank correlation matrix that is close to the original rank correlation matrix C. The procedure is intended for use in conjunction with uncertainty and sensitivity analysis of computationally demanding models in which it is important to make efficient use of a necessarily limited number ofmore » model evaluations.« less

Robust Image Regression Based on the Extended Matrix Variate Power Exponential Distribution of Dependent Noise.

PubMed

Luo, Lei; Yang, Jian; Qian, Jianjun; Tai, Ying; Lu, Gui-Fu

2017-09-01

Dealing with partial occlusion or illumination is one of the most challenging problems in image representation and classification. In this problem, the characterization of the representation error plays a crucial role. In most current approaches, the error matrix needs to be stretched into a vector and each element is assumed to be independently corrupted. This ignores the dependence between the elements of error. In this paper, it is assumed that the error image caused by partial occlusion or illumination changes is a random matrix variate and follows the extended matrix variate power exponential distribution. This has the heavy tailed regions and can be used to describe a matrix pattern of l×m dimensional observations that are not independent. This paper reveals the essence of the proposed distribution: it actually alleviates the correlations between pixels in an error matrix E and makes E approximately Gaussian. On the basis of this distribution, we derive a Schatten p -norm-based matrix regression model with L q regularization. Alternating direction method of multipliers is applied to solve this model. To get a closed-form solution in each step of the algorithm, two singular value function thresholding operators are introduced. In addition, the extended Schatten p -norm is utilized to characterize the distance between the test samples and classes in the design of the classifier. Extensive experimental results for image reconstruction and classification with structural noise demonstrate that the proposed algorithm works much more robustly than some existing regression-based methods.

The search for Pleiades in trait constellations: functional integration and phenotypic selection in the complex flowers of Morrenia brachystephana (Apocynaceae).

PubMed

Baranzelli, M C; Sérsic, A N; Cocucci, A A

2014-04-01

Pollinator-mediated natural selection on single traits, such as corolla tube or spur length, has been well documented. However, flower phenotypes are usually complex, and selection is expected to act on several traits that functionally interact rather than on a single isolated trait. Despite the fact that selection on complex phenotypes is expectedly widespread, multivariate selection modelling on such phenotypes still remains under-explored in plants. Species of the subfamily Asclepiadoideae (Apocynaceae) provide an opportunity to study such complex flower contrivances integrated by fine-scaled organs from disparate developmental origin. We studied the correlation structure among linear floral traits (i) by testing a priori morphological, functional or developmental hypotheses among traits and (ii) by exploring the organization of flower covariation, considering alternative expectations of modular organization or whole flower integration through conditional dependence analysis (CDA) and integration matrices. The phenotypic selection approach was applied to determine whether floral traits involved in the functioning of the pollination mechanism were affected by natural selection. Floral integration was low, suggesting that flowers are organized in more than just one correlation pleiad; our hypothetical functional correlation matrix was significantly correlated with the empirical matrix, and the CDA revealed three putative modules. Analyses of phenotypic selection showed significant linear and correlational gradients, lending support to expectations of functional interactions between floral traits. Significant correlational selection gradients found involved traits of different floral whorls, providing evidence for the existence of functional integration across developmental domains. © 2014 The Authors. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

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

Exploring multicollinearity using a random matrix theory approach.

PubMed

Feher, Kristen; Whelan, James; Müller, Samuel

2012-01-01

Clustering of gene expression data is often done with the latent aim of dimension reduction, by finding groups of genes that have a common response to potentially unknown stimuli. However, what is poorly understood to date is the behaviour of a low dimensional signal embedded in high dimensions. This paper introduces a multicollinear model which is based on random matrix theory results, and shows potential for the characterisation of a gene cluster's correlation matrix. This model projects a one dimensional signal into many dimensions and is based on the spiked covariance model, but rather characterises the behaviour of the corresponding correlation matrix. The eigenspectrum of the correlation matrix is empirically examined by simulation, under the addition of noise to the original signal. The simulation results are then used to propose a dimension estimation procedure of clusters from data. Moreover, the simulation results warn against considering pairwise correlations in isolation, as the model provides a mechanism whereby a pair of genes with `low' correlation may simply be due to the interaction of high dimension and noise. Instead, collective information about all the variables is given by the eigenspectrum.

Neutrinoless ββ decay mediated by the exchange of light and heavy neutrinos: the role of nuclear structure correlations

NASA Astrophysics Data System (ADS)

Menéndez, J.

2018-01-01

Neutrinoless β β decay nuclear matrix elements calculated with the shell model and energy-density functional theory typically disagree by more than a factor of two in the standard scenario of light-neutrino exchange. In contrast, for a decay mediated by sterile heavy neutrinos the deviations are reduced to about 50%, an uncertainty similar to the one due to short-range effects. We compare matrix elements in the light- and heavy-neutrino-exchange channels, exploring the radial, momentum transfer and angular momentum-parity matrix element distributions, and considering transitions that involve correlated and uncorrelated nuclear states. We argue that the shorter-range heavy-neutrino exchange is less sensitive to collective nuclear correlations, and that discrepancies in matrix elements are mostly due to the treatment of long-range correlations in many-body calculations. Our analysis supports previous studies suggesting that isoscalar pairing correlations, which affect mostly the longer-range part of the neutrinoless β β decay operator, are partially responsible for the differences between nuclear matrix elements in the standard light-neutrino-exchange mechanism.

Structure and self-assembly of the calcium binding matrix protein of human metapneumovirus.

PubMed

Leyrat, Cedric; Renner, Max; Harlos, Karl; Huiskonen, Juha T; Grimes, Jonathan M

2014-01-07

The matrix protein (M) of paramyxoviruses plays a key role in determining virion morphology by directing viral assembly and budding. Here, we report the crystal structure of the human metapneumovirus M at 2.8 Å resolution in its native dimeric state. The structure reveals the presence of a high-affinity Ca²⁺ binding site. Molecular dynamics simulations (MDS) predict a secondary lower-affinity site that correlates well with data from fluorescence-based thermal shift assays. By combining small-angle X-ray scattering with MDS and ensemble analysis, we captured the structure and dynamics of M in solution. Our analysis reveals a large positively charged patch on the protein surface that is involved in membrane interaction. Structural analysis of DOPC-induced polymerization of M into helical filaments using electron microscopy leads to a model of M self-assembly. The conservation of the Ca²⁺ binding sites suggests a role for calcium in the replication and morphogenesis of pneumoviruses. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

Eigenvalue density of cross-correlations in Sri Lankan financial market

NASA Astrophysics Data System (ADS)

Nilantha, K. G. D. R.; Ranasinghe; Malmini, P. K. C.

2007-05-01

We apply the universal properties with Gaussian orthogonal ensemble (GOE) of random matrices namely spectral properties, distribution of eigenvalues, eigenvalue spacing predicted by random matrix theory (RMT) to compare cross-correlation matrix estimators from emerging market data. The daily stock prices of the Sri Lankan All share price index and Milanka price index from August 2004 to March 2005 were analyzed. Most eigenvalues in the spectrum of the cross-correlation matrix of stock price changes agree with the universal predictions of RMT. We find that the cross-correlation matrix satisfies the universal properties of the GOE of real symmetric random matrices. The eigen distribution follows the RMT predictions in the bulk but there are some deviations at the large eigenvalues. The nearest-neighbor spacing and the next nearest-neighbor spacing of the eigenvalues were examined and found that they follow the universality of GOE. RMT with deterministic correlations found that each eigenvalue from deterministic correlations is observed at values, which are repelled from the bulk distribution.

Aortic Wall Extracellular Matrix Proteins Correlate with Syntax Score in Patients Undergoing Coronary Artery Bypass Surgery

PubMed Central

Chiong, Terri; Cheow, Esther S. H.; Woo, Chin C.; Lin, Xiao Y.; Khin, Lay W.; Lee, Chuen N.; Hartman, Mikael; Sze, Siu K.; Sorokin, Vitaly A.

2016-01-01

Aims: The SYNTAX score correlate with major cardiovascular events post-revascularization, although the histopathological basis is unclear. We aim to evaluate the association between syntax score and extracellular matrix histological characteristics of aortic punch tissue obtained during coronary artery bypass surgery (CABG). This analysis compares coronary artery bypass surgery patients with High and Low syntax score which were followed up for one year period. Methods and Results: Patients with High (score ≥ 33, (n=77)) and Low Syntax Scores (score ≤ 22, (n=71)) undergoing elective CABG were recruited prospectively. Baseline clinical characteristics and surgical risks were well matched. At 1 year, EMACCE (Sum of cardiovascular death, stroke, congestive cardiac failure, and limb, gut and myocardial ischemia) was significantly elevated in the High syntax group (P=0.022). Mass spectrometry (MS)-based quantitative iTRAQ proteomic results validated on independent cohort by immunohistochemistry (IHC) revealed that the High syntax group had significantly upraised Collagen I (P<0.0001) and Elastin (P<0.0001) content in ascending aortic wall. Conclusion: This study shows that aortic extracellular matrix (ECM) differ between High and Low syntax groups with up-regulation of Collagen I and Elastin level in High Syntax Score group. This identifies aortic punches collected during CABG as another biomarker source related with atherosclerosis severity and possible clinical outcome. PMID:27347220

Redistribution of Sr and rare earth elements in the matrices of CV3 carbonaceous chondrites during aqueous alteration in their parent body

NASA Astrophysics Data System (ADS)

Jogo, Kaori; Ito, Motoo; Nakamura, Tomoki; Kobayashi, Sachio; Lee, Jong Ik

2018-03-01

We measured the abundances of Sr and rare earth elements (REEs) in the matrices of five CV3 carbonaceous chondrites: Meteorite Hills (MET) 00430, MET 01070, La Paz ice field (LAP) 02206, Asuka (A) 881317 and Roberts Massif (RBT) 04143. In the MET 00430 and MET 01074 matrices, the Sr/CI and light REE (LREE, La-Nd)/CI ratios positively correlate with the amounts of Ca-rich secondary minerals, which formed during aqueous alteration in the CV3 chondrite parent body. In contrast, in the LAP 02206 and RBT 04143 matrices, although the Sr/CI ratios correlate with the amounts of Ca-rich secondary minerals, the LREE/CI ratios vary independently from the amounts of any secondary minerals. This suggests that the LREE/CI ratios in these matrices were produced prior to the parent body alteration, probably in the solar nebula. The LREE/CI ratios of the LAP 02206 and RBT 04143 matrices reveal the mixing process of matrix minerals prior to the accretion of the CV3 chondrite parent body. The mixing degrees of matrix minerals might be different between these two matrices. Because solid materials would be mixed over time according to the radial diffusion model of a turbulent disk, the matrix minerals consisting of LAP 02206 and RBT 04143 matrices might be incorporated into their parent body with different timing.

Inactivation kinetics of various chemical disinfectants on Aeromonas hydrophila planktonic cells and biofilms.

PubMed

Jahid, Iqbal Kabir; Ha, Sang-Do

2014-05-01

The present article focuses on the inactivation kinetics of various disinfectants including ethanol, sodium hypochlorite, hydrogen peroxide, peracetic acid, and benzalkonium chloride against Aeromonas hydrophila biofilms and planktonic cells. Efficacy was determined by viable plate count and compared using a modified Weibull model. The removal of the biofilms matrix was determined by the crystal violet assay and was confirmed by field-emission scanning electron microscope. The results revealed that all the experimental data and calculated Weibull α (scale) and β (shape) parameters had a good fit, as the R(2) values were between 0.88 and 0.99. Biofilms are more resistant to disinfectants than planktonic cells. Ethanol (70%) was the most effective in killing cells in the biofilms and significantly reduced (p<0.05) the biofilms matrix. The Weibull parameter b-value correlated (R(2)=0.6835) with the biofilms matrix removal. The present findings deduce that the Weibull model is suitable to determine biofilms matrix reduction as well as the effectiveness of chemical disinfectants on biofilms. The study showed that the Weibull model could successfully be used on food and food contact surfaces to determine the exact contact time for killing biofilms-forming foodborne pathogens.

Stromal matrix metalloproteinase 2 regulates collagen expression and promotes the outgrowth of experimental metastases.

PubMed

Bates, Andreia L; Pickup, Michael W; Hallett, Miranda A; Dozier, E Ashley; Thomas, Stacy; Fingleton, Barbara

2015-04-01

Breast cancer survival rates decrease from 99% for patients with local disease to 25% for those with distant metastases. Matrix metalloproteinases (MMPs), including MMP2, are associated with metastatic progression. We found that loss of host MMP2 reduces the proliferation of experimental metastases in the lungs and identified fibroblasts in tumour-bearing lungs as the major source of MMP2. In vitro, spheroidal mammary tumour growth was increased by co-culture with control fibroblasts isolated from tumour-bearing lungs, but not when fibroblasts with stable Mmp2 knockdown were used. This result prompted us to assess whether MMP2 was responsible for a tumour-proliferative, activated fibroblast phenotype. To test this, we evaluated: (a) fibroblasts from wild-type tumour-bearing lungs, with or without shRNA-mediated MMP2 knockdown; and (b) normal, quiescent fibroblasts isolated from either WT or Mmp2(-/-) mice. Quantitative PCR revealed that Mmp2 knockdown attenuated expression of two markers of activation (α-smooth muscle actin and vimentin), but there was minimal expression in quiescent WT or Mmp2(-/-) fibroblasts, as expected. Placing quiescent fibroblasts under activating conditions led to increases in activation-associated transcripts in WT but not Mmp2(-/-) fibroblasts. Additionally, Mmp2 knockdown fibroblasts showed significantly decreased expression of the matrix transcripts collagen I, collagen IV and fibronectin. Addition of active TGFβ was sufficient to rescue the MMP2-dependent collagen I and IV expression, while MMP2-induced collagen expression was blocked by the addition of TGFβ1-neutralizing antibody. Gene expression data in stromal cells of human breast cancers reveal that MMP2 expression is also positively correlated with activation and matrix transcripts. Thus, we present a model whereby MMP2 production in tumour fibroblasts is important for TGFβ1 activity and subsequent activation of fibroblasts to a matrix-producing, proliferation-supportive phenotype. Overall, our results reveal a previously undefined role for MMP2 in metastatic outgrowth mediated by fibroblasts, and extend the mechanisms by which MMPs contribute to tumour progression. Copyright © 2014 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

Robust and sparse correlation matrix estimation for the analysis of high-dimensional genomics data.

PubMed

Serra, Angela; Coretto, Pietro; Fratello, Michele; Tagliaferri, Roberto; Stegle, Oliver

2018-02-15

Microarray technology can be used to study the expression of thousands of genes across a number of different experimental conditions, usually hundreds. The underlying principle is that genes sharing similar expression patterns, across different samples, can be part of the same co-expression system, or they may share the same biological functions. Groups of genes are usually identified based on cluster analysis. Clustering methods rely on the similarity matrix between genes. A common choice to measure similarity is to compute the sample correlation matrix. Dimensionality reduction is another popular data analysis task which is also based on covariance/correlation matrix estimates. Unfortunately, covariance/correlation matrix estimation suffers from the intrinsic noise present in high-dimensional data. Sources of noise are: sampling variations, presents of outlying sample units, and the fact that in most cases the number of units is much larger than the number of genes. In this paper, we propose a robust correlation matrix estimator that is regularized based on adaptive thresholding. The resulting method jointly tames the effects of the high-dimensionality, and data contamination. Computations are easy to implement and do not require hand tunings. Both simulated and real data are analyzed. A Monte Carlo experiment shows that the proposed method is capable of remarkable performances. Our correlation metric is more robust to outliers compared with the existing alternatives in two gene expression datasets. It is also shown how the regularization allows to automatically detect and filter spurious correlations. The same regularization is also extended to other less robust correlation measures. Finally, we apply the ARACNE algorithm on the SyNTreN gene expression data. Sensitivity and specificity of the reconstructed network is compared with the gold standard. We show that ARACNE performs better when it takes the proposed correlation matrix estimator as input. The R software is available at https://github.com/angy89/RobustSparseCorrelation. aserra@unisa.it or robtag@unisa.it. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Repeated short climatic change affects the epidermal differentiation program and leads to matrix remodeling in a human organotypic skin model.

PubMed

Boutrand, Laetitia-Barbollat; Thépot, Amélie; Muther, Charlotte; Boher, Aurélie; Robic, Julie; Guéré, Christelle; Vié, Katell; Damour, Odile; Lamartine, Jérôme

2017-01-01

Human skin is subject to frequent changes in ambient temperature and humidity and needs to cope with these environmental modifications. To decipher the molecular response of human skin to repeated climatic change, a versatile model of skin equivalent subject to "hot-wet" (40°C, 80% relative humidity [RH]) or "cold-dry" (10°C, 40% RH) climatic stress repeated daily was used. To obtain an exhaustive view of the molecular mechanisms elicited by climatic change, large-scale gene expression DNA microarray analysis was performed and modulated function was determined by bioinformatic annotation. This analysis revealed several functions, including epidermal differentiation and extracellular matrix, impacted by repeated variations in climatic conditions. Some of these molecular changes were confirmed by histological examination and protein expression. Both treatments (hot-wet and cold-dry) reduced the expression of genes encoding collagens, laminin, and proteoglycans, suggesting a profound remodeling of the extracellular matrix. Strong induction of the entire family of late cornified envelope genes after cold-dry exposure, confirmed at protein level, was also observed. These changes correlated with an increase in epidermal differentiation markers such as corneodesmosin and a thickening of the stratum corneum, indicating possible implementation of defense mechanisms against dehydration. This study for the first time reveals the complex pattern of molecular response allowing adaption of human skin to repeated change in its climatic environment.

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…

Volatility and correlation-based systemic risk measures in the US market

NASA Astrophysics Data System (ADS)

Civitarese, Jamil

2016-10-01

This paper deals with the problem of how to use simple systemic risk measures to assess portfolio risk characteristics. Using three simple examples taken from previous literature, one based on raw and partial correlations, another based on the eigenvalue decomposition of the covariance matrix and the last one based on an eigenvalue entropy, a Granger-causation analysis revealed some of them are not always a good measure of risk in the S&P 500 and in the VIX. The measures selected do not Granger-cause the VIX index in all windows selected; therefore, in the sense of risk as volatility, the indicators are not always suitable. Nevertheless, their results towards returns are similar to previous works that accept them. A deeper analysis has shown that any symmetric measure based on eigenvalue decomposition of correlation matrices, however, is not useful as a measure of "correlation" risk. The empirical counterpart analysis of this proposition stated that negative correlations are usually small and, therefore, do not heavily distort the behavior of the indicator.

Curcuminoids-loaded lipid nanoparticles: novel approach towards malaria treatment.

PubMed

Nayak, Aditya P; Tiyaboonchai, Waree; Patankar, Swati; Madhusudhan, Basavaraj; Souto, Eliana B

2010-11-01

In the present work, curcuminoids-loaded lipid nanoparticles for parenteral administration were successfully prepared by a nanoemulsion technique employing high-speed homogenizer and ultrasonic probe. For the production of nanoparticles, trimyristin, tristerin and glyceryl monostearate were selected as solid lipids and medium chain triglyceride (MCT) as liquid lipid. Scanning electron microscopy (SEM) revealed the spherical nature of the particles with sizes ranging between 120 and 250 nm measured by photon correlation spectroscopy (PCS). The zeta potential of the particles ranged between -28 and -45 mV depending on the nature of the lipid matrix produced, which also influenced the entrapment efficiency (EE) and drug loading capacity (LC) found to be in the range of 80-94% and 1.62-3.27%, respectively. The LC increased reciprocally on increasing the amount of MCT as confirmed by differential scanning calorimetry (DSC). DSC analyses revealed that increasing imperfections within the lipid matrix allowed for increasing encapsulation parameters. Nanoparticles were further sterilized by filtration process which was found to be superior over autoclaving in preventing thermal degradation of thermo-sensitive curcuminoids. The in vivo pharmacodynamic activity revealed 2-fold increase in antimalarial activity of curcuminoids entrapped in lipid nanoparticles when compared to free curcuminoids at the tested dosage level. Copyright (c) 2010 Elsevier B.V. All rights reserved.

Deformation mechanisms of idealised cermets under multi-axial loading

NASA Astrophysics Data System (ADS)

Bele, E.; Goel, A.; Pickering, E. G.; Borstnar, G.; Katsamenis, O. L.; Pierron, F.; Danas, K.; Deshpande, V. S.

2017-05-01

The response of idealised cermets comprising approximately 60% by volume steel spheres in a Sn/Pb solder matrix is investigated under a range of axisymmetric compressive stress states. Digital volume correlation (DVC) anal`ysis of X-ray micro-computed tomography scans (μ-CT), and the measured macroscopic stress-strain curves of the specimens revealed two deformation mechanisms. At low triaxialities the deformation is granular in nature, with dilation occurring within shear bands. Under higher imposed hydrostatic pressures, the deformation mechanism transitions to a more homogeneous incompressible mode. However, DVC analyses revealed that under all triaxialities there are regions with local dilatory and compaction responses, with the magnitude of dilation and the number of zones wherein dilation occurs decreasing with increasing triaxiality. Two numerical models are presented in order to clarify these mechanisms: (i) a periodic unit cell model comprising nearly rigid spherical particles in a porous metal matrix and (ii) a discrete element model comprising a large random aggregate of spheres connected by non-linear normal and tangential "springs". The periodic unit cell model captured the measured stress-strain response with reasonable accuracy but under-predicted the observed dilation at the lower triaxialities, because the kinematic constraints imposed by the skeleton of rigid particles were not accurately accounted for in this model. By contrast, the discrete element model captured the kinematics and predicted both the overall levels of dilation and the simultaneous presence of both local compaction and dilatory regions with the specimens. However, the levels of dilation in this model are dependent on the assumed contact law between the spheres. Moreover, since the matrix is not explicitly included in the analysis, this model cannot be used to predict the stress-strain responses. These analyses have revealed that the complete constitutive response of cermets depends both on the kinematic constraints imposed by the particle aggregate skeleton, and the constraints imposed by the metal matrix filling the interstitial spaces in that skeleton.

Correlating PMC-MMC Bonded Joint 3D FEA with Test

NASA Technical Reports Server (NTRS)

Jacobson, Mindy; Rodini, Benjamin; Chen, Wayne C.; Flom, Yury A.; Posey, Alan J.

2005-01-01

A viewgraph presentation on the correlation of Polymer Matrix Composites (PMC) and Metal Matrix Composites (MMC) bonded joints using three dimensional finite element analyses with materials tests is shown.

Linking pain and the body: neural correlates of visually induced analgesia.

PubMed

Longo, Matthew R; Iannetti, Gian Domenico; Mancini, Flavia; Driver, Jon; Haggard, Patrick

2012-02-22

The visual context of seeing the body can reduce the experience of acute pain, producing a multisensory analgesia. Here we investigated the neural correlates of this "visually induced analgesia" using fMRI. We induced acute pain with an infrared laser while human participants looked either at their stimulated right hand or at another object. Behavioral results confirmed the expected analgesic effect of seeing the body, while fMRI results revealed an associated reduction of laser-induced activity in ipsilateral primary somatosensory cortex (SI) and contralateral operculoinsular cortex during the visual context of seeing the body. We further identified two known cortical networks activated by sensory stimulation: (1) a set of brain areas consistently activated by painful stimuli (the so-called "pain matrix"), and (2) an extensive set of posterior brain areas activated by the visual perception of the body ("visual body network"). Connectivity analyses via psychophysiological interactions revealed that the visual context of seeing the body increased effective connectivity (i.e., functional coupling) between posterior parietal nodes of the visual body network and the purported pain matrix. Increased connectivity with these posterior parietal nodes was seen for several pain-related regions, including somatosensory area SII, anterior and posterior insula, and anterior cingulate cortex. These findings suggest that visually induced analgesia does not involve an overall reduction of the cortical response elicited by laser stimulation, but is consequent to the interplay between the brain's pain network and a posterior network for body perception, resulting in modulation of the experience of pain.

Performance analysis of structured gradient algorithm. [for adaptive beamforming linear arrays

NASA Technical Reports Server (NTRS)

Godara, Lal C.

1990-01-01

The structured gradient algorithm uses a structured estimate of the array correlation matrix (ACM) to estimate the gradient required for the constrained least-mean-square (LMS) algorithm. This structure reflects the structure of the exact array correlation matrix for an equispaced linear array and is obtained by spatial averaging of the elements of the noisy correlation matrix. In its standard form the LMS algorithm does not exploit the structure of the array correlation matrix. The gradient is estimated by multiplying the array output with the receiver outputs. An analysis of the two algorithms is presented to show that the covariance of the gradient estimated by the structured method is less sensitive to the look direction signal than that estimated by the standard method. The effect of the number of elements on the signal sensitivity of the two algorithms is studied.

Group identification in Indonesian stock market

NASA Astrophysics Data System (ADS)

Nurriyadi Suparno, Ervano; Jo, Sung Kyun; Lim, Kyuseong; Purqon, Acep; Kim, Soo Yong

2016-08-01

The characteristic of Indonesian stock market is interesting especially because it represents developing countries. We investigate the dynamics and structures by using Random Matrix Theory (RMT). Here, we analyze the cross-correlation of the fluctuations of the daily closing price of stocks from the Indonesian Stock Exchange (IDX) between January 1, 2007, and October 28, 2014. The eigenvalue distribution of the correlation matrix consists of noise which is filtered out using the random matrix as a control. The bulk of the eigenvalue distribution conforms to the random matrix, allowing the separation of random noise from original data which is the deviating eigenvalues. From the deviating eigenvalues and the corresponding eigenvectors, we identify the intrinsic normal modes of the system and interpret their meaning based on qualitative and quantitative approach. The results show that the largest eigenvector represents the market-wide effect which has a predominantly common influence toward all stocks. The other eigenvectors represent highly correlated groups within the system. Furthermore, identification of the largest components of the eigenvectors shows the sector or background of the correlated groups. Interestingly, the result shows that there are mainly two clusters within IDX, natural and non-natural resource companies. We then decompose the correlation matrix to investigate the contribution of the correlated groups to the total correlation, and we find that IDX is still driven mainly by the market-wide effect.

Dry sliding wear system response of ferritic and tempered martensitic ductile iron

NASA Astrophysics Data System (ADS)

Jha, V. K.; Mozumder, Y. H.; Shama, S.; Behera, R. K.; Pattaniak, A.; P, Sindhoora L.; Mishra, S. C.; Sen, S.

2015-02-01

Spheroidal graphite cast iron (SG iron) is the most preferable member of cast iron family due to its strength and toughness along with good tribological properties. SG iron specimens with annealed and martensitic matrix were subjected to dry sliding wear condition and the system response was correlated to matrix microstructure. Respective microstructure was obtained by annealing and quench and tempering heat treatment process for an austenitizing temperature of 1000°C. Specimens were subjected to Ball on plate wear tester under 40N, 50N, 60N load for a sliding distance of 7.54m. Except for quench and tempered specimen at 50N, weight loss was observed in every condition. The wear surface under optical microscope reveals adhesive mechanism for as-cast and annealed specimen whereas delaminated wear track feature was observed for quench and tempered specimen.

Statistics of time delay and scattering correlation functions in chaotic systems. I. Random matrix theory

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

Novaes, Marcel

2015-06-15

We consider the statistics of time delay in a chaotic cavity having M open channels, in the absence of time-reversal invariance. In the random matrix theory approach, we compute the average value of polynomial functions of the time delay matrix Q = − iħS{sup †}dS/dE, where S is the scattering matrix. Our results do not assume M to be large. In a companion paper, we develop a semiclassical approximation to S-matrix correlation functions, from which the statistics of Q can also be derived. Together, these papers contribute to establishing the conjectured equivalence between the random matrix and the semiclassical approaches.

Sulfites and the wine metabolome.

PubMed

Roullier-Gall, Chloé; Hemmler, Daniel; Gonsior, Michael; Li, Yan; Nikolantonaki, Maria; Aron, Alissa; Coelho, Christian; Gougeon, Régis D; Schmitt-Kopplin, Philippe

2017-12-15

In a context of societal concern about food preservation, the reduction of sulfite input plays a major role in the wine industry. To improve the understanding of the chemistry involved in the SO 2 protection, a series of bottle aged Chardonnay wines made from the same must, but with different concentrations of SO 2 added at pressing were analyzed by ultrahigh resolution mass spectrometry (FT-ICR-MS) and excitation emission matrix fluorescence (EEMF). Metabolic fingerprints from FT-ICR-MS data could discriminate wines according to the added concentration to the must but they also revealed chemistry-related differences according to the type of stopper, providing a wine metabolomics picture of the impact of distinct stopping strategies. Spearman rank correlation was applied to link the statistically modeled EEMF components (parallel factor analysis (PARAFAC)) and the exact mass information from FT-ICR-MS, and thus revealing the extent of sulfur-containing compounds which could show some correlation with fluorescence fingerprints. Copyright © 2017 Elsevier Ltd. All rights reserved.

Comparative Controller Design for a Marine Gas Turbine Propulsion Plant

DTIC Science & Technology

1988-09-01

ADDRESS (City State, and ZIP Code) ,onterey, California 93943-5000 Monterey, California 93943-5000 Sa. NAME OF FUNDING/SPONSORING 8b OFFICE SYMBOL 9 ...155 7. A21 MATRIX COEFFICIENT CORRELATION DATA ----------- 156 8. A22 MATRIX COEFFICIENT CORRELATION DATA ----------- 157 9 . A23 MATRIX...Flowchart of VRD Algorithm ----------------------- 29 8. Steady State Convergence Map --------------------- 34 9 . Smoothed Dynamic Transition Map

POLYMAT-C: a comprehensive SPSS program for computing the polychoric correlation matrix.

PubMed

Lorenzo-Seva, Urbano; Ferrando, Pere J

2015-09-01

We provide a free noncommercial SPSS program that implements procedures for (a) obtaining the polychoric correlation matrix between a set of ordered categorical measures, so that it can be used as input for the SPSS factor analysis (FA) program; (b) testing the null hypothesis of zero population correlation for each element of the matrix by using appropriate simulation procedures; (c) obtaining valid and accurate confidence intervals via bootstrap resampling for those correlations found to be significant; and (d) performing, if necessary, a smoothing procedure that makes the matrix amenable to any FA estimation procedure. For the main purpose (a), the program uses a robust unified procedure that allows four different types of estimates to be obtained at the user's choice. Overall, we hope the program will be a very useful tool for the applied researcher, not only because it provides an appropriate input matrix for FA, but also because it allows the researcher to carefully check the appropriateness of the matrix for this purpose. The SPSS syntax, a short manual, and data files related to this article are available as Supplemental materials that are available for download with this article.

A Method of Q-Matrix Validation for the Linear Logistic Test Model

PubMed Central

Baghaei, Purya; Hohensinn, Christine

2017-01-01

The linear logistic test model (LLTM) is a well-recognized psychometric model for examining the components of difficulty in cognitive tests and validating construct theories. The plausibility of the construct model, summarized in a matrix of weights, known as the Q-matrix or weight matrix, is tested by (1) comparing the fit of LLTM with the fit of the Rasch model (RM) using the likelihood ratio (LR) test and (2) by examining the correlation between the Rasch model item parameters and LLTM reconstructed item parameters. The problem with the LR test is that it is almost always significant and, consequently, LLTM is rejected. The drawback of examining the correlation coefficient is that there is no cut-off value or lower bound for the magnitude of the correlation coefficient. In this article we suggest a simulation method to set a minimum benchmark for the correlation between item parameters from the Rasch model and those reconstructed by the LLTM. If the cognitive model is valid then the correlation coefficient between the RM-based item parameters and the LLTM-reconstructed item parameters derived from the theoretical weight matrix should be greater than those derived from the simulated matrices. PMID:28611721

Information loss in effective field theory: Entanglement and thermal entropies

NASA Astrophysics Data System (ADS)

Boyanovsky, Daniel

2018-03-01

Integrating out high energy degrees of freedom to yield a low energy effective field theory leads to a loss of information with a concomitant increase in entropy. We obtain the effective field theory of a light scalar field interacting with heavy fields after tracing out the heavy degrees of freedom from the time evolved density matrix. The initial density matrix describes the light field in its ground state and the heavy fields in equilibrium at a common temperature T . For T =0 , we obtain the reduced density matrix in a perturbative expansion; it reveals an emergent mixed state as a consequence of the entanglement between light and heavy fields. We obtain the effective action that determines the time evolution of the reduced density matrix for the light field in a nonperturbative Dyson resummation of one-loop correlations of the heavy fields. The Von-Neumann entanglement entropy associated with the reduced density matrix is obtained for the nonresonant and resonant cases in the asymptotic long time limit. In the nonresonant case the reduced density matrix displays an incipient thermalization albeit with a wave-vector, time and coupling dependent effective temperature as a consequence of memory of initial conditions. The entanglement entropy is time independent and is the thermal entropy for this effective, nonequilibrium temperature. In the resonant case the light field fully thermalizes with the heavy fields, the reduced density matrix loses memory of the initial conditions and the entanglement entropy becomes the thermal entropy of the light field. We discuss the relation between the entanglement entropy ultraviolet divergences and renormalization.

Modeling the two-way feedback between contractility and matrix realignment reveals a nonlinear mode of cancer cell invasion

PubMed Central

Ahmadzadeh, Hossein; Webster, Marie R.; Behera, Reeti; Jimenez Valencia, Angela M.; Wirtz, Denis; Weeraratna, Ashani T.; Shenoy, Vivek B.

2017-01-01

Cancer cell invasion from primary tumors is mediated by a complex interplay between cellular adhesions, actomyosin-driven contractility, and the physical characteristics of the extracellular matrix (ECM). Here, we incorporate a mechanochemical free-energy–based approach to elucidate how the two-way feedback loop between cell contractility (induced by the activity of chemomechanical interactions such as Ca2+ and Rho signaling pathways) and matrix fiber realignment and strain stiffening enables the cells to polarize and develop contractile forces to break free from the tumor spheroids and invade into the ECM. Interestingly, through this computational model, we are able to identify a critical stiffness that is required by the matrix to break intercellular adhesions and initiate cell invasion. Also, by considering the kinetics of the cell movement, our model predicts a biphasic invasiveness with respect to the stiffness of the matrix. These predictions are validated by analyzing the invasion of melanoma cells in collagen matrices of varying concentration. Our model also predicts a positive correlation between the elongated morphology of the invading cells and the alignment of fibers in the matrix, suggesting that cell polarization is directly proportional to the stiffness and alignment of the matrix. In contrast, cells in nonfibrous matrices are found to be rounded and not polarized, underscoring the key role played by the nonlinear mechanics of fibrous matrices. Importantly, our model shows that mechanical principles mediated by the contractility of the cells and the nonlinearity of the ECM behavior play a crucial role in determining the phenotype of the cell invasion. PMID:28196892

Statistical properties of cross-correlation in the Korean stock market

NASA Astrophysics Data System (ADS)

Oh, G.; Eom, C.; Wang, F.; Jung, W.-S.; Stanley, H. E.; Kim, S.

2011-01-01

We investigate the statistical properties of the cross-correlation matrix between individual stocks traded in the Korean stock market using the random matrix theory (RMT) and observe how these affect the portfolio weights in the Markowitz portfolio theory. We find that the distribution of the cross-correlation matrix is positively skewed and changes over time. We find that the eigenvalue distribution of original cross-correlation matrix deviates from the eigenvalues predicted by the RMT, and the largest eigenvalue is 52 times larger than the maximum value among the eigenvalues predicted by the RMT. The β_{473} coefficient, which reflect the largest eigenvalue property, is 0.8, while one of the eigenvalues in the RMT is approximately zero. Notably, we show that the entropy function E(σ) with the portfolio risk σ for the original and filtered cross-correlation matrices are consistent with a power-law function, E( σ) σ^{-γ}, with the exponent γ 2.92 and those for Asian currency crisis decreases significantly.

Correlation of lung surface area to apoptosis and proliferation in human emphysema.

PubMed

Imai, K; Mercer, B A; Schulman, L L; Sonett, J R; D'Armiento, J M

2005-02-01

Pulmonary emphysema is associated with alterations in matrix proteins and protease activity. These alterations may be linked to programmed cell death by apoptosis, potentially influencing lung architecture and lung function. To evaluate apoptosis in emphysema, lung tissue was analysed from 10 emphysema patients and six individuals without emphysema (normal). Morphological analysis revealed alveolar cells in emphysematous lungs with convoluted nuclei characteristic of apoptosis. DNA fragmentation was detected using terminal deoxynucleotide transferase-mediated dUTP nick-end labelling (TUNEL) and gel electrophoresis. TUNEL revealed higher apoptosis in emphysematous than normal lungs. Markers of apoptosis, including active caspase-3, proteolytic fragment of poly (ADP-ribose) polymerase, Bax and Bad, were detected in emphysematous lungs. Linear regression showed that apoptosis was inversely correlated with surface area. Emphysematous lungs demonstrated lower surface areas and increased cell proliferation. There was no correlation between apoptosis and proliferation, suggesting that, although both events increase during emphysema, they are not in equilibrium, potentially contributing to reduced lung surface area. In summary, cell-based mechanisms associated with emphysematous parenchymal damage include increased apoptosis and cell proliferation. Apoptosis correlated with airspace enlargement, supporting epidemiological evidence of the progressive nature of emphysema. These data extend the understanding of cell dynamics and structural changes within the lung during emphysema pathogenesis.

A bias correction for covariance estimators to improve inference with generalized estimating equations that use an unstructured correlation matrix.

PubMed

Westgate, Philip M

2013-07-20

Generalized estimating equations (GEEs) are routinely used for the marginal analysis of correlated data. The efficiency of GEE depends on how closely the working covariance structure resembles the true structure, and therefore accurate modeling of the working correlation of the data is important. A popular approach is the use of an unstructured working correlation matrix, as it is not as restrictive as simpler structures such as exchangeable and AR-1 and thus can theoretically improve efficiency. However, because of the potential for having to estimate a large number of correlation parameters, variances of regression parameter estimates can be larger than theoretically expected when utilizing the unstructured working correlation matrix. Therefore, standard error estimates can be negatively biased. To account for this additional finite-sample variability, we derive a bias correction that can be applied to typical estimators of the covariance matrix of parameter estimates. Via simulation and in application to a longitudinal study, we show that our proposed correction improves standard error estimation and statistical inference. Copyright © 2012 John Wiley & Sons, Ltd.

An attempt to determine the effect of increase of observation correlations on detectability and identifiability of a single gross error

NASA Astrophysics Data System (ADS)

Prószyński, Witold; Kwaśniak, Mieczysław

2016-12-01

The paper presents the results of investigating the effect of increase of observation correlations on detectability and identifiability of a single gross error, the outlier test sensitivity and also the response-based measures of internal reliability of networks. To reduce in a research a practically incomputable number of possible test options when considering all the non-diagonal elements of the correlation matrix as variables, its simplest representation was used being a matrix with all non-diagonal elements of equal values, termed uniform correlation. By raising the common correlation value incrementally, a sequence of matrix configurations could be obtained corresponding to the increasing level of observation correlations. For each of the measures characterizing the above mentioned features of network reliability the effect is presented in a diagram form as a function of the increasing level of observation correlations. The influence of observation correlations on sensitivity of the w-test for correlated observations (Förstner 1983, Teunissen 2006) is investigated in comparison with the original Baarda's w-test designated for uncorrelated observations, to determine the character of expected sensitivity degradation of the latter when used for correlated observations. The correlation effects obtained for different reliability measures exhibit mutual consistency in a satisfactory extent. As a by-product of the analyses, a simple formula valid for any arbitrary correlation matrix is proposed for transforming the Baarda's w-test statistics into the w-test statistics for correlated observations.

A versatile setup for ultrafast broadband optical spectroscopy of coherent collective modes in strongly correlated quantum systems

PubMed Central

Baldini, Edoardo; Mann, Andreas; Borroni, Simone; Arrell, Christopher; van Mourik, Frank; Carbone, Fabrizio

2016-01-01

A femtosecond pump-probe setup is described that is optimised for broadband transient reflectivity experiments on solid samples over a wide temperature range. By combining high temporal resolution and a broad detection window, this apparatus can investigate the interplay between coherent collective modes and high-energy electronic excitations, which is a distinctive characteristic of correlated electron systems. Using a single-shot readout array detector at frame rates of 10 kHz allows resolving coherent oscillations with amplitudes <10−4. We demonstrate its operation on the charge-transfer insulator La2CuO4, revealing coherent phonons with frequencies up to 13 THz and providing access into their Raman matrix elements. PMID:27990455

EMMPRIN and its ligand cyclophilin A as novel diagnostic markers in inflammatory cardiomyopathy.

PubMed

Seizer, Peter; Geisler, Tobias; Bigalke, Boris; Schneider, Martin; Klingel, Karin; Kandolf, Reinhard; Stellos, Konstantinos; Schreieck, Jürgen; Gawaz, Meinrad; May, Andreas E

2013-03-10

During inflammatory cardiomyopathy matrix metalloproteinases are crucially involved in cardiac remodeling. The aim of the present study was to investigate whether the "extracellular matrix metalloproteinase inducer" EMMPRIN (CD147) and its ligand Cyclophilin A (CyPA) are upregulated in inflammatory cardiomyopathy and may serve as diagnostic markers. Therefore, a series of 102 human endomyocardial biopsies were analyzed for the expression of EMMPRIN and CyPA and correlated with histological and immunohistological findings. Endomyocardial biopsies were stained for EMMPRIN and CyPA in addition to standard histology (HE, Trichrom) and immunohistological stainings (MHC-II, CD68, CD3). 39 (38.2%) biopsies met the immunohistological criteria of an inflammatory cardiomyopathy. EMMPRIN, which was predominantly expressed on cardiomyocytes, was slightly (but significantly) upregulated in non inflammatory cardiomyopathies compared to normal histopathological findings and highly upregulated in inflammatory cardiomyopathy compared to both non inflammatory cardiomyopathy and normal histopathology. In contrast, CyPA reveals no enhanced expression in non inflammatory cardiomyopathies and a highly enhanced expression in inflammatory cardiomyopathy, where it is closely associated with leucocytes infiltrates. We found a strong correlation between both EMMPRIN and CyPA with the expression of MHC-II molecules (correlation coefficient 0.475 and 0.527, p<0.05). Moreover, we found a correlation for both EMMPRIN and CyPA with CD68 (correlation coefficient 0.393 and 0.387, p<0.05) and CD3 (correlation coefficient 0.360 and 0.235, p<0.05). EMMPRIN is enhanced in both inflammatory and non inflammatory cardiomyopathies and can serve as a marker of myocardial remodeling. CyPA may represent a novel and specific marker for cardiac inflammation. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

ChromAlign: A two-step algorithmic procedure for time alignment of three-dimensional LC-MS chromatographic surfaces.

PubMed

Sadygov, Rovshan G; Maroto, Fernando Martin; Hühmer, Andreas F R

2006-12-15

We present an algorithmic approach to align three-dimensional chromatographic surfaces of LC-MS data of complex mixture samples. The approach consists of two steps. In the first step, we prealign chromatographic profiles: two-dimensional projections of chromatographic surfaces. This is accomplished by correlation analysis using fast Fourier transforms. In this step, a temporal offset that maximizes the overlap and dot product between two chromatographic profiles is determined. In the second step, the algorithm generates correlation matrix elements between full mass scans of the reference and sample chromatographic surfaces. The temporal offset from the first step indicates a range of the mass scans that are possibly correlated, then the correlation matrix is calculated only for these mass scans. The correlation matrix carries information on highly correlated scans, but it does not itself determine the scan or time alignment. Alignment is determined as a path in the correlation matrix that maximizes the sum of the correlation matrix elements. The computational complexity of the optimal path generation problem is reduced by the use of dynamic programming. The program produces time-aligned surfaces. The use of the temporal offset from the first step in the second step reduces the computation time for generating the correlation matrix and speeds up the process. The algorithm has been implemented in a program, ChromAlign, developed in C++ language for the .NET2 environment in WINDOWS XP. In this work, we demonstrate the applications of ChromAlign to alignment of LC-MS surfaces of several datasets: a mixture of known proteins, samples from digests of surface proteins of T-cells, and samples prepared from digests of cerebrospinal fluid. ChromAlign accurately aligns the LC-MS surfaces we studied. In these examples, we discuss various aspects of the alignment by ChromAlign, such as constant time axis shifts and warping of chromatographic surfaces.

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

PubMed

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

2007-08-15

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

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

NASA Astrophysics Data System (ADS)

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

2007-08-01

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

Exploration of CdTe quantum dots as mesoscale pressure sensors via time-resolved shock-compression photoluminescent emission spectroscopy

NASA Astrophysics Data System (ADS)

Kang, Zhitao; Banishev, Alexandr A.; Lee, Gyuhyon; Scripka, David A.; Breidenich, Jennifer; Xiao, Pan; Christensen, James; Zhou, Min; Summers, Christopher J.; Dlott, Dana D.; Thadhani, Naresh N.

2016-07-01

The nanometer size of CdTe quantum dots (QDs) and their unique optical properties, including size-tunable narrow photoluminescent emission, broad absorption, fast photoluminescence decay, and negligible light scattering, are ideal features for spectrally tagging the shock response of localized regions in highly heterogeneous materials such as particulate media. In this work, the time-resolved laser-excited photoluminescence response of QDs to shock-compression was investigated to explore their utilization as mesoscale sensors for pressure measurements and in situ diagnostics during shock loading experiments. Laser-driven shock-compression experiments with steady-state shock pressures ranging from 2.0 to 13 GPa were performed on nanocomposite films of CdTe QDs dispersed in a soft polyvinyl alcohol polymer matrix and in a hard inorganic sodium silicate glass matrix. Time-resolved photoluminescent emission spectroscopy was used to correlate photoluminescence changes with the history of shock pressure and the dynamics of the matrix material surrounding the QDs. The results revealed pressure-induced blueshifts in emitted wavelength, decreases in photoluminescent emission intensity, reductions in peak width, and matrix-dependent response times. Data obtained for these QD response characteristics serve as indicators for their use as possible time-resolved diagnostics of the dynamic shock-compression response of matrix materials in which such QDs are embedded as in situ sensors.

Aggrecan-based extracellular matrix shows unique cortical features and conserved subcortical principles of mammalian brain organization in the Madagascan lesser hedgehog tenrec (Echinops telfairi Martin, 1838).

PubMed

Morawski, M; Brückner, G; Jäger, C; Seeger, G; Künzle, H; Arendt, T

2010-02-03

The Madagascan tenrecs (Afrotheria), an ancient mammalian clade, are characterized by unique brain anatomy. Striking features are an expanded paleocortex but a small and poorly differentiated neocortex devoid of a distinct granular layer IV. To investigate the organization of cortical areas we analyzed extracellular matrix components in perineuronal nets (PNs) using antibodies to aggrecan, lectin staining and hyaluronan-binding protein. Selected subcortical regions were studied to correlate the cortical patterns with features in evolutionary conserved systems. In the neocortex, paleocortex and hippocampus PNs were associated with nonpyramidal neurons. Quantitative analysis in the cerebral cortex revealed area-specific proportions and laminar distribution patterns of neurons ensheathed by PNs. Cortical PNs showed divergent structural phenotypes. Diffuse PNs forming a cotton wool-like perisomatic rim were characteristic of the paleocortex. These PNs were associated with a dense pericellular plexus of calretinin-immunoreactive fibres. Clearly contoured PNs were devoid of a calretinin-positive plexus and predominated in the neocortex and hippocampus. The organization of the extracellular matrix in subcortical nuclei followed the widely distributed mammalian type. We conclude that molecular properties of the aggrecan-based extracellular matrix are conserved during evolution of mammals; however, the matrix scaffold is adapted to specific wiring patterns of cortical and subcortical neuronal networks. Copyright 2010 IBRO. Published by Elsevier Ltd. All rights reserved.

Exploration of CdTe quantum dots as mesoscale pressure sensors via time-resolved shock-compression photoluminescent emission spectroscopy

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

Kang, Zhitao; School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0245; Banishev, Alexandr A.

The nanometer size of CdTe quantum dots (QDs) and their unique optical properties, including size-tunable narrow photoluminescent emission, broad absorption, fast photoluminescence decay, and negligible light scattering, are ideal features for spectrally tagging the shock response of localized regions in highly heterogeneous materials such as particulate media. In this work, the time-resolved laser-excited photoluminescence response of QDs to shock-compression was investigated to explore their utilization as mesoscale sensors for pressure measurements and in situ diagnostics during shock loading experiments. Laser-driven shock-compression experiments with steady-state shock pressures ranging from 2.0 to 13 GPa were performed on nanocomposite films of CdTe QDs dispersedmore » in a soft polyvinyl alcohol polymer matrix and in a hard inorganic sodium silicate glass matrix. Time-resolved photoluminescent emission spectroscopy was used to correlate photoluminescence changes with the history of shock pressure and the dynamics of the matrix material surrounding the QDs. The results revealed pressure-induced blueshifts in emitted wavelength, decreases in photoluminescent emission intensity, reductions in peak width, and matrix-dependent response times. Data obtained for these QD response characteristics serve as indicators for their use as possible time-resolved diagnostics of the dynamic shock-compression response of matrix materials in which such QDs are embedded as in situ sensors.« less

Tumor image signatures and habitats: a processing pipeline of multimodality metabolic and physiological images.

PubMed

You, Daekeun; Kim, Michelle M; Aryal, Madhava P; Parmar, Hemant; Piert, Morand; Lawrence, Theodore S; Cao, Yue

2018-01-01

To create tumor "habitats" from the "signatures" discovered from multimodality metabolic and physiological images, we developed a framework of a processing pipeline. The processing pipeline consists of six major steps: (1) creating superpixels as a spatial unit in a tumor volume; (2) forming a data matrix [Formula: see text] containing all multimodality image parameters at superpixels; (3) forming and clustering a covariance or correlation matrix [Formula: see text] of the image parameters to discover major image "signatures;" (4) clustering the superpixels and organizing the parameter order of the [Formula: see text] matrix according to the one found in step 3; (5) creating "habitats" in the image space from the superpixels associated with the "signatures;" and (6) pooling and clustering a matrix consisting of correlation coefficients of each pair of image parameters from all patients to discover subgroup patterns of the tumors. The pipeline was applied to a dataset of multimodality images in glioblastoma (GBM) first, which consisted of 10 image parameters. Three major image "signatures" were identified. The three major "habitats" plus their overlaps were created. To test generalizability of the processing pipeline, a second image dataset from GBM, acquired on the scanners different from the first one, was processed. Also, to demonstrate the clinical association of image-defined "signatures" and "habitats," the patterns of recurrence of the patients were analyzed together with image parameters acquired prechemoradiation therapy. An association of the recurrence patterns with image-defined "signatures" and "habitats" was revealed. These image-defined "signatures" and "habitats" can be used to guide stereotactic tissue biopsy for genetic and mutation status analysis and to analyze for prediction of treatment outcomes, e.g., patterns of failure.

The link between employee attitudes and employee effectiveness: Data matrix of meta-analytic estimates based on 1161 unique correlations.

PubMed

Mackay, Michael M

2016-09-01

This article offers a correlation matrix of meta-analytic estimates between various employee job attitudes (i.e., Employee engagement, job satisfaction, job involvement, and organizational commitment) and indicators of employee effectiveness (i.e., Focal performance, contextual performance, turnover intention, and absenteeism). The meta-analytic correlations in the matrix are based on over 1100 individual studies representing over 340,000 employees. Data was collected worldwide via employee self-report surveys. Structural path analyses based on the matrix, and the interpretation of the data, can be found in "Investigating the incremental validity of employee engagement in the prediction of employee effectiveness: a meta-analytic path analysis" (Mackay et al., 2016) [1].

Estimation of Covariance Matrix on Bi-Response Longitudinal Data Analysis with Penalized Spline Regression

NASA Astrophysics Data System (ADS)

Islamiyati, A.; Fatmawati; Chamidah, N.

2018-03-01

The correlation assumption of the longitudinal data with bi-response occurs on the measurement between the subjects of observation and the response. It causes the auto-correlation of error, and this can be overcome by using a covariance matrix. In this article, we estimate the covariance matrix based on the penalized spline regression model. Penalized spline involves knot points and smoothing parameters simultaneously in controlling the smoothness of the curve. Based on our simulation study, the estimated regression model of the weighted penalized spline with covariance matrix gives a smaller error value compared to the error of the model without covariance matrix.

Nanoscale Origins of the Size Effect in the Compression Response of Single Crystal Ni-Base Superalloy Micro-Pillars

PubMed Central

Ying, Siqi; Ma, Lifeng; Papadaki, Chrysanthi; Romano Brandt, Leon; Zhang, Hongjia

2018-01-01

Nickel superalloys play a pivotal role in enabling power-generation devices on land, sea, and in the air. They derive their strength from coherent cuboidal precipitates of the ordered γ’ phase that is different from the γ matrix in composition, structure and properties. In order to reveal the correlation between elemental distribution, dislocation glide and the plastic deformation of micro- and nano-sized volumes of a nickel superalloy, a combined in situ nanoindentation compression study was carried out with a scanning electron microscope (SEM) on micro- and nano-pillars fabricated by focused ion beam (FIB) milling of Ni-base superalloy CMSX4. The observed mechanical response (hardening followed by softening) was correlated with the progression of crystal slip that was revealed using FIB nano-tomography and energy-dispersive spectroscopy (EDS) elemental mapping. A hypothesis was put forward that the dependence of material strength on the size of the sample (micropillar diameter) is correlated with the characteristic dimension of the structural units (γ’ precipitates). By proposing two new dislocation-based models, the results were found to be described well by a new parameter-free Hall–Petch equation. PMID:29621189

Nondestructive evaluation of ceramic matrix composite combustor components.

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

Sun, J. G.; Verrilli, M. J.; Stephan, R.

Combustor liners fabricated from a SiC/SiC composite were nondestructively interrogated before and after combustion rig testing. The combustor liners were inspected by X-ray, ultrasonic and thermographic techniques. In addition, mechanical test results were obtained from witness coupons, representing the as-manufactured liners, and from coupons machined from the components after combustion exposure. Thermography indications were found to correlate with reduced material properties obtained after rig testing. Microstructural examination of the SiC/SiC liners revealed the thermography indications to be delaminations and damaged fiber tows.

Lung tissue remodelling in MCT-induced pulmonary hypertension: a proposal for a novel scoring system and changes in extracellular matrix and fibrosis associated gene expression.

PubMed

Franz, Marcus; Grün, Katja; Betge, Stefan; Rohm, Ilonka; Ndongson-Dongmo, Bernadin; Bauer, Reinhard; Schulze, P Christian; Lichtenauer, Michael; Petersen, Iver; Neri, Dario; Berndt, Alexander; Jung, Christian

2016-12-06

Pulmonary hypertension (PH) is associated with vasoconstriction and remodelling. We studied lung tissue remodelling in a rat model of PH with special focus on histology and extracellular matrix (ECM) remodelling. After induction of PH by monocrotaline, lung tissue was analysed histologically, by gene expression analysis and immunofluorescence labelling of ED-A domain containing fibronectin (ED-A+ Fn), B domain containing tenascin-C (B+ Tn-C) as well as alpha-smooth muscle actin (α-SMA). Serum concentrations of ED-A+ Fn were determined by ELISA. Systolic right ventricular pressure (RVPsys) values were significantly elevated in PH (n = 18; 75 ± 26.4 mmHg) compared to controls (n = 10; 29 ± 19.3 mmHg; p = 0.015). The histological sum-score was significantly increased in PH (8.0 ± 2.2) compared to controls (2.5 ± 1.6; p < 0.001). Gene expression analysis revealed relevant induction of several key genes of extracellular matrix remodelling. Increased protein deposition of ED-A+ Fn but not of B+ Tn-C and α-SMA in lung tissue was found in PH (2.88 ± 3.19 area%) compared to controls (1.32 ± 0.16 area%; p = 0.030). Serum levels of ED-A+ Fn were significantly higher in PH (p = 0.007) positively correlating with RVPsys (r = 0.618, p = 0.019). We here present a novel histological scoring system to assess lung tissue remodelling in PH. Gene expression analysis revealed induction of candidate genes involved in collagen matrix turnover, fibrosis and vascular remodelling. The stable increased tissue deposition of ED-A+ Fn in PH as well as its dynamics in serum suggests a role as a promising novel biomarker and potential therapeutic target.

Heavy metal concentration in groundwater from Besant Nagar to Sathankuppam, South Chennai, Tamil Nadu, India

NASA Astrophysics Data System (ADS)

Sridhar, S. G. D.; Sakthivel, A. M.; Sangunathan, U.; Balasubramanian, M.; Jenefer, S.; Mohamed Rafik, M.; Kanagaraj, G.

2017-12-01

The assessment of groundwater quality is an obligatory pre-requisite to developing countries like India with rural-based economy. Heavy metal concentration in groundwater from Besant Nagar to Sathankuppam, South Chennai was analyzed to assess the acquisition process. The study area has rapid urbanization since few decades, which deteriorated the condition of the aquifer of the area. Totally 30 groundwater samples were collected during pre-monsoon (June 2014) and post-monsoon (January 2015) from the same aquifer to assess the heavy metal concentration in groundwater. Groundwater samples were analyzed for heavy metals such as Fe, Pb, Zn, Cu, Ni, Cr, Co and Mn using atomic absorption spectrophotometry (AAS). Correlation matrix revealed that there is no significant correlation between heavy metals and other parameters during pre-monsoon except EC with Cr but Fe and Zn have good positive correlation during post-monsoon.

Strong correlation induced charge localization in antiferromagnets

PubMed Central

Zhu, Zheng; Jiang, Hong-Chen; Qi, Yang; Tian, Chushun; Weng, Zheng-Yu

2013-01-01

The fate of a hole injected in an antiferromagnet is an outstanding issue of strongly correlated physics. It provides important insights into doped Mott insulators closely related to high-temperature superconductivity. Here, we report a systematic numerical study of t-J ladder systems based on the density matrix renormalization group. It reveals a surprising result for the single hole's motion in an otherwise well-understood undoped system. Specifically, we find that the common belief of quasiparticle picture is invalidated by the self-localization of the doped hole. In contrast to Anderson localization caused by disorders, the charge localization discovered here is an entirely new phenomenon purely of strong correlation origin. It results from destructive quantum interference of novel signs picked up by the hole, and since the same effect is of a generic feature of doped Mott physics, our findings unveil a new paradigm which may go beyond the single hole doped system. PMID:24002668

A covariance correction that accounts for correlation estimation to improve finite-sample inference with generalized estimating equations: A study on its applicability with structured correlation matrices

PubMed Central

Westgate, Philip M.

2016-01-01

When generalized estimating equations (GEE) incorporate an unstructured working correlation matrix, the variances of regression parameter estimates can inflate due to the estimation of the correlation parameters. In previous work, an approximation for this inflation that results in a corrected version of the sandwich formula for the covariance matrix of regression parameter estimates was derived. Use of this correction for correlation structure selection also reduces the over-selection of the unstructured working correlation matrix. In this manuscript, we conduct a simulation study to demonstrate that an increase in variances of regression parameter estimates can occur when GEE incorporates structured working correlation matrices as well. Correspondingly, we show the ability of the corrected version of the sandwich formula to improve the validity of inference and correlation structure selection. We also study the relative influences of two popular corrections to a different source of bias in the empirical sandwich covariance estimator. PMID:27818539

A covariance correction that accounts for correlation estimation to improve finite-sample inference with generalized estimating equations: A study on its applicability with structured correlation matrices.

PubMed

Westgate, Philip M

2016-01-01

When generalized estimating equations (GEE) incorporate an unstructured working correlation matrix, the variances of regression parameter estimates can inflate due to the estimation of the correlation parameters. In previous work, an approximation for this inflation that results in a corrected version of the sandwich formula for the covariance matrix of regression parameter estimates was derived. Use of this correction for correlation structure selection also reduces the over-selection of the unstructured working correlation matrix. In this manuscript, we conduct a simulation study to demonstrate that an increase in variances of regression parameter estimates can occur when GEE incorporates structured working correlation matrices as well. Correspondingly, we show the ability of the corrected version of the sandwich formula to improve the validity of inference and correlation structure selection. We also study the relative influences of two popular corrections to a different source of bias in the empirical sandwich covariance estimator.

Distributed Storage Algorithm for Geospatial Image Data Based on Data Access Patterns.

PubMed

Pan, Shaoming; Li, Yongkai; Xu, Zhengquan; Chong, Yanwen

2015-01-01

Declustering techniques are widely used in distributed environments to reduce query response time through parallel I/O by splitting large files into several small blocks and then distributing those blocks among multiple storage nodes. Unfortunately, however, many small geospatial image data files cannot be further split for distributed storage. In this paper, we propose a complete theoretical system for the distributed storage of small geospatial image data files based on mining the access patterns of geospatial image data using their historical access log information. First, an algorithm is developed to construct an access correlation matrix based on the analysis of the log information, which reveals the patterns of access to the geospatial image data. Then, a practical heuristic algorithm is developed to determine a reasonable solution based on the access correlation matrix. Finally, a number of comparative experiments are presented, demonstrating that our algorithm displays a higher total parallel access probability than those of other algorithms by approximately 10-15% and that the performance can be further improved by more than 20% by simultaneously applying a copy storage strategy. These experiments show that the algorithm can be applied in distributed environments to help realize parallel I/O and thereby improve system performance.

Collective behavior of stock price movements in an emerging market

NASA Astrophysics Data System (ADS)

Pan, Raj Kumar; Sinha, Sitabhra

2007-10-01

To investigate the universality of the structure of interactions in different markets, we analyze the cross-correlation matrix C of stock price fluctuations in the National Stock Exchange (NSE) of India. We find that this emerging market exhibits strong correlations in the movement of stock prices compared to developed markets, such as the New York Stock Exchange (NYSE). This is shown to be due to the dominant influence of a common market mode on the stock prices. By comparison, interactions between related stocks, e.g., those belonging to the same business sector, are much weaker. This lack of distinct sector identity in emerging markets is explicitly shown by reconstructing the network of mutually interacting stocks. Spectral analysis of C for NSE reveals that, the few largest eigenvalues deviate from the bulk of the spectrum predicted by random matrix theory, but they are far fewer in number compared to, e.g., NYSE. We show this to be due to the relative weakness of intrasector interactions between stocks, compared to the market mode, by modeling stock price dynamics with a two-factor model. Our results suggest that the emergence of an internal structure comprising multiple groups of strongly coupled components is a signature of market development.

Minimum number of measurements for evaluating Bertholletia excelsa.

PubMed

Baldoni, A B; Tonini, H; Tardin, F D; Botelho, S C C; Teodoro, P E

2017-09-27

Repeatability studies on fruit species are of great importance to identify the minimum number of measurements necessary to accurately select superior genotypes. This study aimed to identify the most efficient method to estimate the repeatability coefficient (r) and predict the minimum number of measurements needed for a more accurate evaluation of Brazil nut tree (Bertholletia excelsa) genotypes based on fruit yield. For this, we assessed the number of fruits and dry mass of seeds of 75 Brazil nut genotypes, from native forest, located in the municipality of Itaúba, MT, for 5 years. To better estimate r, four procedures were used: analysis of variance (ANOVA), principal component analysis based on the correlation matrix (CPCOR), principal component analysis based on the phenotypic variance and covariance matrix (CPCOV), and structural analysis based on the correlation matrix (mean r - AECOR). There was a significant effect of genotypes and measurements, which reveals the need to study the minimum number of measurements for selecting superior Brazil nut genotypes for a production increase. Estimates of r by ANOVA were lower than those observed with the principal component methodology and close to AECOR. The CPCOV methodology provided the highest estimate of r, which resulted in a lower number of measurements needed to identify superior Brazil nut genotypes for the number of fruits and dry mass of seeds. Based on this methodology, three measurements are necessary to predict the true value of the Brazil nut genotypes with a minimum accuracy of 85%.

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.

Plant-derived micronutrients suppress monocyte adhesion to cultured human aortic endothelial cell layer by modulating its extracellular matrix composition.

PubMed

Ivanov, Vadim; Ivanova, Svetlana; Kalinovsky, Tatiana; Niedzwiecki, Aleksandra; Rath, Matthias

2008-07-01

Monocyte adhesion to endothelium plays an important role in atherosclerosis. We investigated the effects of micronutrients on monocyte-binding properties of extracellular matrix (ECM) produced by human aortic endothelial cells (AoEC). Confluent cultures of AoEC were exposed to ascorbic acid, quercetin, gotu kola extract (10% asiatic acid), green tea extract (40% epigallocatechin gallate), or a mixture of these micronutrients for 48 hours. AoEC-produced ECM was exposed by differential treatment. U937 monocyte adhesion was assayed by fluorescence. ECM composition was assayed immunochemically and with radiolabeled metabolic precursors. AoEC exposure to micronutrients reduced ECM capacity to bind monocytes in a dose-dependent manner. This effect was accompanied by profound changes in the ECM composition. Correlation analysis revealed that changes in monocyte adhesion to ECM had the strongest positive correlation with ECM content for laminin (CC = 0.9681, P < 0.01), followed by fibronectin, collagens type III, I, and IV, biglycan, heparan sulfate, and elastin. The strongest negative correlation was with chondroitin sulfate (CC = -0.9623, P < 0.01), followed by perlecan and versican. Individual micronutrients had diverse effects on ECM composition and binding properties, and their mixture was the most effective treatment. In conclusion, micronutrient-dependent reduction of monocyte adhesion to endothelium is partly mediated through specific modulation of ECM composition and properties.

Partial covariance based functional connectivity computation using Ledoit-Wolf covariance regularization.

PubMed

Brier, Matthew R; Mitra, Anish; McCarthy, John E; Ances, Beau M; Snyder, Abraham Z

2015-11-01

Functional connectivity refers to shared signals among brain regions and is typically assessed in a task free state. Functional connectivity commonly is quantified between signal pairs using Pearson correlation. However, resting-state fMRI is a multivariate process exhibiting a complicated covariance structure. Partial covariance assesses the unique variance shared between two brain regions excluding any widely shared variance, hence is appropriate for the analysis of multivariate fMRI datasets. However, calculation of partial covariance requires inversion of the covariance matrix, which, in most functional connectivity studies, is not invertible owing to rank deficiency. Here we apply Ledoit-Wolf shrinkage (L2 regularization) to invert the high dimensional BOLD covariance matrix. We investigate the network organization and brain-state dependence of partial covariance-based functional connectivity. Although RSNs are conventionally defined in terms of shared variance, removal of widely shared variance, surprisingly, improved the separation of RSNs in a spring embedded graphical model. This result suggests that pair-wise unique shared variance plays a heretofore unrecognized role in RSN covariance organization. In addition, application of partial correlation to fMRI data acquired in the eyes open vs. eyes closed states revealed focal changes in uniquely shared variance between the thalamus and visual cortices. This result suggests that partial correlation of resting state BOLD time series reflect functional processes in addition to structural connectivity. Copyright © 2015 Elsevier Inc. All rights reserved.

Partial covariance based functional connectivity computation using Ledoit-Wolf covariance regularization

PubMed Central

Brier, Matthew R.; Mitra, Anish; McCarthy, John E.; Ances, Beau M.; Snyder, Abraham Z.

2015-01-01

Functional connectivity refers to shared signals among brain regions and is typically assessed in a task free state. Functional connectivity commonly is quantified between signal pairs using Pearson correlation. However, resting-state fMRI is a multivariate process exhibiting a complicated covariance structure. Partial covariance assesses the unique variance shared between two brain regions excluding any widely shared variance, hence is appropriate for the analysis of multivariate fMRI datasets. However, calculation of partial covariance requires inversion of the covariance matrix, which, in most functional connectivity studies, is not invertible owing to rank deficiency. Here we apply Ledoit-Wolf shrinkage (L2 regularization) to invert the high dimensional BOLD covariance matrix. We investigate the network organization and brain-state dependence of partial covariance-based functional connectivity. Although RSNs are conventionally defined in terms of shared variance, removal of widely shared variance, surprisingly, improved the separation of RSNs in a spring embedded graphical model. This result suggests that pair-wise unique shared variance plays a heretofore unrecognized role in RSN covariance organization. In addition, application of partial correlation to fMRI data acquired in the eyes open vs. eyes closed states revealed focal changes in uniquely shared variance between the thalamus and visual cortices. This result suggests that partial correlation of resting state BOLD time series reflect functional processes in addition to structural connectivity. PMID:26208872

Effective Perron-Frobenius eigenvalue for a correlated random map

NASA Astrophysics Data System (ADS)

Pool, Roman R.; Cáceres, Manuel O.

2010-09-01

We investigate the evolution of random positive linear maps with various type of disorder by analytic perturbation and direct simulation. Our theoretical result indicates that the statistics of a random linear map can be successfully described for long time by the mean-value vector state. The growth rate can be characterized by an effective Perron-Frobenius eigenvalue that strongly depends on the type of correlation between the elements of the projection matrix. We apply this approach to an age-structured population dynamics model. We show that the asymptotic mean-value vector state characterizes the population growth rate when the age-structured model has random vital parameters. In this case our approach reveals the nontrivial dependence of the effective growth rate with cross correlations. The problem was reduced to the calculation of the smallest positive root of a secular polynomial, which can be obtained by perturbations in terms of Green’s function diagrammatic technique built with noncommutative cumulants for arbitrary n -point correlations.

One-electron reduced density matrices of strongly correlated harmonium atoms.

PubMed

Cioslowski, Jerzy

2015-03-21

Explicit asymptotic expressions are derived for the reduced one-electron density matrices (the 1-matrices) of strongly correlated two- and three-electron harmonium atoms in the ground and first excited states. These expressions, which are valid at the limit of small confinement strength ω, yield electron densities and kinetic energies in agreement with the published values. In addition, they reveal the ω(5/6) asymptotic scaling of the exchange components of the electron-electron repulsion energies that differs from the ω(2/3) scaling of their Coulomb and correlation counterparts. The natural orbitals of the totally symmetric ground state of the two-electron harmonium atom are found to possess collective occupancies that follow a mixed power/Gaussian dependence on the angular momentum in variance with the simple power-law prediction of Hill's asymptotics. Providing rigorous constraints on energies as functionals of 1-matrices, these results are expected to facilitate development of approximate implementations of the density matrix functional theory and ensure their proper description of strongly correlated systems.

Comparison of Plasma, Saliva, and Hair Levetiracetam Concentrations.

PubMed

Karaś-Ruszczyk, Katarzyna; Kuczyńska, Julita; Sienkiewicz-Jarosz, Halina; Kurkowska-Jastrzębska, Iwona; Bienkowski, Przemyslaw; Restel, Magdalena; Samochowiec, Jerzy; Mierzejewski, Pawel

2017-06-01

Previous findings revealed high correlations between serum/plasma and saliva levetiracetam concentrations, indicating saliva as an alternative matrix for monitoring levetiracetam therapy. Levetiracetam concentration in the hair, which could reflect long-term drug exposure and patients' compliance, has not been systematically tested, as yet. The aim of this study was to determine the correlation between plasma, saliva, and hair levetiracetam concentrations in 47 patients with epilepsy. Plasma, saliva, and hair levetiracetam concentrations were measured by liquid chromatography-tandem mass spectrometry with positive ionization. Levetiracetam saliva and plasma concentrations were highly correlated (r = 0.93). Plasma concentrations were not influenced by sex, age, and other concomitant antiepileptic drugs. Levetiracetam hair concentrations correlated with plasma concentrations (r = 0.36) but not daily dose (mg/kg). Drug hair concentrations were not influenced by hair color or treatment (dyed). The results tend to indicate that saliva may be a reliable alternative to plasma for monitoring levetiracetam concentrations. Levetiracetam can also be detected in human hair.

Random matrix theory and portfolio optimization in Moroccan stock exchange

NASA Astrophysics Data System (ADS)

El Alaoui, Marwane

2015-09-01

In this work, we use random matrix theory to analyze eigenvalues and see if there is a presence of pertinent information by using Marčenko-Pastur distribution. Thus, we study cross-correlation among stocks of Casablanca Stock Exchange. Moreover, we clean correlation matrix from noisy elements to see if the gap between predicted risk and realized risk would be reduced. We also analyze eigenvectors components distributions and their degree of deviations by computing the inverse participation ratio. This analysis is a way to understand the correlation structure among stocks of Casablanca Stock Exchange portfolio.

Alteration of matrix metalloproteinase-3 O-glycan structure as a biomarker for disease activity of rheumatoid arthritis.

PubMed

Takeshita, Masaru; Kuno, Atsushi; Suzuki, Katsuya; Matsuda, Atsushi; Shimazaki, Hiroko; Nakagawa, Tomomi; Otomo, Yuki; Kabe, Yasuaki; Suematsu, Makoto; Narimatsu, Hisashi; Takeuchi, Tsutomu

2016-05-21

Nearly all secreted proteins are glycosylated, and serum glycoproteins that exhibit disease-associated glycosylation changes have potential to be biomarkers. In rheumatoid arthritis (RA), C-reactive protein (CRP), and matrix metalloproteinase-3 (MMP-3) are widely used as serologic biomarkers, but they lack sufficient specificity or precision. We performed comparative glycosylation profiling of MMP-3 using a recently developed antibody-overlay lectin microarray technology that allows semicomprehensive and quantitative analysis of specific protein glycosylation to develop an RA-specific disease activity biomarker. Serum was taken from patients with RA (n = 24) whose disease activity was scored using composite measures, and MMP-3 was immunoprecipitated and subjected to lectin microarray analysis. A disease activity index (DAI) based on lectin signal was developed and validated using another cohort (n = 60). Synovial fluid MMP-3 in patients with RA and patients with osteoarthritis (OA) was also analyzed. Intense signals were observed on a sialic acid-binding lectin (Agrocybe cylindracea galectin [ACG]) and O-glycan-binding lectins (Jacalin, Agaricus bisporus agglutinin [ABA], and Amaranthus caudatus agglutinin [ACA]) by applying subnanogram levels of serum MMP-3. ACG, ABA, and ACA revealed differences in MMP-3 quantity, and Jacalin revealed differences in MMP-3 quality. The resultant index, ACG/Jacalin, correlated well with disease activity. Further validation using another cohort confirmed that this index correlated well with several DAIs and their components, and reflected DAI changes following RA treatment, with correlations greater than those for MMP-3 and CRP. Furthermore, MMP-3, which generated a high ACG/Jacalin score, accumulated in synovial fluid of patients with RA but not in that of patients with OA. Sialidase digestion revealed that the difference in quality was derived from O-glycan α-2,6-sialylation. This is the first report of a glycoprotein biomarker using glycan change at a local lesion to assess disease activity in autoimmune diseases. Differences in the degree of serum MMP-3 α-2,6-sialylation may be a useful index for estimating disease activity.

The Pathway Coexpression Network: Revealing pathway relationships

PubMed Central

Tanzi, Rudolph E.

2018-01-01

A goal of genomics is to understand the relationships between biological processes. Pathways contribute to functional interplay within biological processes through complex but poorly understood interactions. However, limited functional references for global pathway relationships exist. Pathways from databases such as KEGG and Reactome provide discrete annotations of biological processes. Their relationships are currently either inferred from gene set enrichment within specific experiments, or by simple overlap, linking pathway annotations that have genes in common. Here, we provide a unifying interpretation of functional interaction between pathways by systematically quantifying coexpression between 1,330 canonical pathways from the Molecular Signatures Database (MSigDB) to establish the Pathway Coexpression Network (PCxN). We estimated the correlation between canonical pathways valid in a broad context using a curated collection of 3,207 microarrays from 72 normal human tissues. PCxN accounts for shared genes between annotations to estimate significant correlations between pathways with related functions rather than with similar annotations. We demonstrate that PCxN provides novel insight into mechanisms of complex diseases using an Alzheimer’s Disease (AD) case study. PCxN retrieved pathways significantly correlated with an expert curated AD gene list. These pathways have known associations with AD and were significantly enriched for genes independently associated with AD. As a further step, we show how PCxN complements the results of gene set enrichment methods by revealing relationships between enriched pathways, and by identifying additional highly correlated pathways. PCxN revealed that correlated pathways from an AD expression profiling study include functional clusters involved in cell adhesion and oxidative stress. PCxN provides expanded connections to pathways from the extracellular matrix. PCxN provides a powerful new framework for interrogation of global pathway relationships. Comprehensive exploration of PCxN can be performed at http://pcxn.org/. PMID:29554099

Collagenolytic Matrix Metalloproteinase Structure-Function Relationships: Insights From Molecular Dynamics Studies.

PubMed

Karabencheva-Christova, Tatyana G; Christov, Christo Z; Fields, Gregg B

2017-01-01

Several members of the zinc-dependent matrix metalloproteinase (MMP) family catalyze collagen degradation. Experimental data reveal a collaboration between different MMP domains in order to achieve efficient collagenolysis. Molecular dynamics (MD) simulations have been utilized to provide atomistic details of the collagenolytic process. The triple-helical structure of collagen exhibits local regions of flexibility, with modulation of interchain salt bridges and water bridges contributing to accessibility of individual chains by the enzyme. In turn, the hemopexin-like (HPX) domain of the MMP initially binds the triple helix and facilitates the presentation of individual strands to active site in the catalytic (CAT) domain. Extensive positive and negative correlated motions are observed between the CAT and HPX domains when collagen is bound. Ultimately, the MD simulation studies have complemented structural (NMR spectroscopy, X-ray crystallography) and kinetic analyses to provide a more detailed mechanistic view of MMP-catalyzed collagenolysis. © 2017 Elsevier Inc. All rights reserved.

0{nu}{beta}{beta}-decay nuclear matrix elements with self-consistent short-range correlations

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

Simkovic, Fedor; Bogoliubov Laboratory of Theoretical Physics, JINR, RU-141 980 Dubna, Moscow region; Department of Nuclear Physics, Comenius University, Mlynska dolina F1, SK-842 15 Bratislava

A self-consistent calculation of nuclear matrix elements of the neutrinoless double-beta decays (0{nu}{beta}{beta}) of {sup 76}Ge, {sup 82}Se, {sup 96}Zr, {sup 100}Mo, {sup 116}Cd, {sup 128}Te, {sup 130}Te, and {sup 136}Xe is presented in the framework of the renormalized quasiparticle random phase approximation (RQRPA) and the standard QRPA. The pairing and residual interactions as well as the two-nucleon short-range correlations are for the first time derived from the same modern realistic nucleon-nucleon potentials, namely, from the charge-dependent Bonn potential (CD-Bonn) and the Argonne V18 potential. In a comparison with the traditional approach of using the Miller-Spencer Jastrow correlations, matrix elementsmore » for the 0{nu}{beta}{beta} decay are obtained that are larger in magnitude. We analyze the differences among various two-nucleon correlations including those of the unitary correlation operator method (UCOM) and quantify the uncertainties in the calculated 0{nu}{beta}{beta}-decay matrix elements.« less

Distribution of the Determinant of the Sample Correlation Matrix: Monte Carlo Type One Error Rates.

ERIC Educational Resources Information Center

Reddon, John R.; And Others

1985-01-01

Computer sampling from a multivariate normal spherical population was used to evaluate the type one error rates for a test of sphericity based on the distribution of the determinant of the sample correlation matrix. (Author/LMO)

Matrix viscoplasticity and its shielding by active mechanics in microtissue models: experiments and mathematical modeling

NASA Astrophysics Data System (ADS)

Liu, Alan S.; Wang, Hailong; Copeland, Craig R.; Chen, Christopher S.; Shenoy, Vivek B.; Reich, Daniel H.

2016-09-01

The biomechanical behavior of tissues under mechanical stimulation is critically important to physiological function. We report a combined experimental and modeling study of bioengineered 3D smooth muscle microtissues that reveals a previously unappreciated interaction between active cell mechanics and the viscoplastic properties of the extracellular matrix. The microtissues’ response to stretch/unstretch actuations, as probed by microcantilever force sensors, was dominated by cellular actomyosin dynamics. However, cell lysis revealed a viscoplastic response of the underlying model collagen/fibrin matrix. A model coupling Hill-type actomyosin dynamics with a plastic perfectly viscoplastic description of the matrix quantitatively accounts for the microtissue dynamics, including notably the cells’ shielding of the matrix plasticity. Stretch measurements of single cells confirmed the active cell dynamics, and were well described by a single-cell version of our model. These results reveal the need for new focus on matrix plasticity and its interactions with active cell mechanics in describing tissue dynamics.

Matrix viscoplasticity and its shielding by active mechanics in microtissue models: experiments and mathematical modeling

PubMed Central

Liu, Alan S.; Wang, Hailong; Copeland, Craig R.; Chen, Christopher S.; Shenoy, Vivek B.; Reich, Daniel H.

2016-01-01

The biomechanical behavior of tissues under mechanical stimulation is critically important to physiological function. We report a combined experimental and modeling study of bioengineered 3D smooth muscle microtissues that reveals a previously unappreciated interaction between active cell mechanics and the viscoplastic properties of the extracellular matrix. The microtissues’ response to stretch/unstretch actuations, as probed by microcantilever force sensors, was dominated by cellular actomyosin dynamics. However, cell lysis revealed a viscoplastic response of the underlying model collagen/fibrin matrix. A model coupling Hill-type actomyosin dynamics with a plastic perfectly viscoplastic description of the matrix quantitatively accounts for the microtissue dynamics, including notably the cells’ shielding of the matrix plasticity. Stretch measurements of single cells confirmed the active cell dynamics, and were well described by a single-cell version of our model. These results reveal the need for new focus on matrix plasticity and its interactions with active cell mechanics in describing tissue dynamics. PMID:27671239

Global Gene Expression Analysis in PKCα-/- Mouse Skin Reveals Structural Changes in the Dermis and Defective Wound Granulation Tissue.

PubMed

Cooper, Nichola H; Balachandra, Jeya P; Hardman, Matthew J

2015-12-01

The skin's mechanical integrity is maintained by an organized and robust dermal extracellular matrix (ECM). Resistance to mechanical disruption hinges primarily on homeostasis of the dermal collagen fibril architecture, which is regulated, at least in part, by members of the small leucine-rich proteoglycan (SLRP) family. Here we present data linking protein kinase C alpha (PKCα) to the regulated expression of multiple ECM components including SLRPs. Global microarray profiling reveals deficiencies in ECM gene expression in PKCα-/- skin correlating with abnormal collagen fibril morphology, disorganized dermal architecture, and reduced skin strength. Detailed analysis of the skin and wounds from wild-type and PKCα-/- mice reveals a failure to upregulate collagen and other ECM components in response to injury, resulting in delayed granulation tissue deposition in PKCα-/- wounds. Thus, our data reveal a previously unappreciated role for PKCα in the regulation of ECM structure and deposition during skin wound healing.

Immunohistochemical expression of TGF-β1 and MMP-9 in periapical lesions.

PubMed

Álvares, Pâmella Recco; Arruda, José Alcides Almeida de; Silva, Leorik Pereira da; Nascimento, George João Ferreira do; Silveira, Maria Fonseca da; Sobral, Ana Paula Veras

2017-07-03

The objective of this study was to evaluate the expression of matrix metalloproteinase 9 (MMP-9) and transforming growth factor beta (TGF-β1) in periapical lesion samples correlated with the intensity of the inflammatory infiltrate and thickness of the epithelial lining. Forty-five cases of periapical lesions (23 periapical granulomas and 22 radicular cysts) were subjected to morphological and immunohistochemical analyses using anti-MMP-9 and anti-TGF-β1 antibodies. The data were analyzed using the following tests: non-parametric Mann-Whitney, chi-square, Fisher's exact test and Spearman's correlation test (P<0.05). Analysis of inflammatory infiltrate revealed that 78% of periapical granulomas presented infiltrate grade III, in contrast with 32% of radicular cysts (P<0.001). Morphological evaluation of the epithelial thickness in radicular cysts revealed the presence of atrophic epithelium in 86% of the cysts. The immunostaining of MMP-9 was score 2 in 67% of the granulomas and 77% of the cysts. Both lesions were predominantly score 1 for TGF-β1. Significant differences were confirmed between the expression scores of TGF-β1 and MMP-9 in periapical granulomas (p = 0.004) and in radicular cysts (p < 0.001). Expression of TGF-β1 was different for periapical granulomas and radicular cysts. This immunoregulatory cytokine seems more representative in asymptomatic lesions. The extracellular matrix remodeling process dependent on MMP-9 seems to be similar for both periapical granulomas and radicular cysts. TGF-β1 and MMP-9 may play an important role in the maintenance of periapical lesions.

A determinant-based criterion for working correlation structure selection in generalized estimating equations.

PubMed

Jaman, Ajmery; Latif, Mahbub A H M; Bari, Wasimul; Wahed, Abdus S

2016-05-20

In generalized estimating equations (GEE), the correlation between the repeated observations on a subject is specified with a working correlation matrix. Correct specification of the working correlation structure ensures efficient estimators of the regression coefficients. Among the criteria used, in practice, for selecting working correlation structure, Rotnitzky-Jewell, Quasi Information Criterion (QIC) and Correlation Information Criterion (CIC) are based on the fact that if the assumed working correlation structure is correct then the model-based (naive) and the sandwich (robust) covariance estimators of the regression coefficient estimators should be close to each other. The sandwich covariance estimator, used in defining the Rotnitzky-Jewell, QIC and CIC criteria, is biased downward and has a larger variability than the corresponding model-based covariance estimator. Motivated by this fact, a new criterion is proposed in this paper based on the bias-corrected sandwich covariance estimator for selecting an appropriate working correlation structure in GEE. A comparison of the proposed and the competing criteria is shown using simulation studies with correlated binary responses. The results revealed that the proposed criterion generally performs better than the competing criteria. An example of selecting the appropriate working correlation structure has also been shown using the data from Madras Schizophrenia Study. Copyright © 2015 John Wiley & Sons, Ltd.

Network analysis of a financial market based on genuine correlation and threshold method

NASA Astrophysics Data System (ADS)

Namaki, A.; Shirazi, A. H.; Raei, R.; Jafari, G. R.

2011-10-01

A financial market is an example of an adaptive complex network consisting of many interacting units. This network reflects market’s behavior. In this paper, we use Random Matrix Theory (RMT) notion for specifying the largest eigenvector of correlation matrix as the market mode of stock network. For a better risk management, we clean the correlation matrix by removing the market mode from data and then construct this matrix based on the residuals. We show that this technique has an important effect on correlation coefficient distribution by applying it for Dow Jones Industrial Average (DJIA). To study the topological structure of a network we apply the removing market mode technique and the threshold method to Tehran Stock Exchange (TSE) as an example. We show that this network follows a power-law model in certain intervals. We also show the behavior of clustering coefficients and component numbers of this network for different thresholds. These outputs are useful for both theoretical and practical purposes such as asset allocation and risk management.

The static structure and dynamics of cadmium sulfide nanoparticles within poly(styrene- block-isoprene) diblock copolymer melts

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

Jang, Woo -Sik; Koo, Peter; Bryson, Kyle

Here, the static structure and dynamic behavior of cadmium sulfide nanoparticles suspended in block copolymer matrix are investigated using transmission electron microscopy, small-angle X-ray scattering, and X-ray photon correlation spectroscopy. The transmission electron micro- scopy study shows that cadmium sulfide nanoparticles are preferentially segregated within the polyisoprene domain of a poly(styrene- block-isoprene) diblock copolymer. For the dynamics study, X-ray photon correlation spectroscopy captures the relaxation process of cadmium sulfide nanoparticles. The measured characteristic relaxation time reveals that the observed dynamics are hyperdiffusive. The characteristic velocity and corresponding activation energy, which are hallmarks of a hyperdiffusive system, are determined from themore » relationship between the characteristic relaxation time and the wavevector.« less

The static structure and dynamics of cadmium sulfide nanoparticles within poly(styrene- block-isoprene) diblock copolymer melts

DOE PAGES

Jang, Woo -Sik; Koo, Peter; Bryson, Kyle; ...

2015-12-20

Here, the static structure and dynamic behavior of cadmium sulfide nanoparticles suspended in block copolymer matrix are investigated using transmission electron microscopy, small-angle X-ray scattering, and X-ray photon correlation spectroscopy. The transmission electron micro- scopy study shows that cadmium sulfide nanoparticles are preferentially segregated within the polyisoprene domain of a poly(styrene- block-isoprene) diblock copolymer. For the dynamics study, X-ray photon correlation spectroscopy captures the relaxation process of cadmium sulfide nanoparticles. The measured characteristic relaxation time reveals that the observed dynamics are hyperdiffusive. The characteristic velocity and corresponding activation energy, which are hallmarks of a hyperdiffusive system, are determined from themore » relationship between the characteristic relaxation time and the wavevector.« less

Quantum Dynamics of Solitons in Strongly Interacting Systems on Optical Lattices

NASA Astrophysics Data System (ADS)

Rubbo, Chester; Balakrishnan, Radha; Reinhardt, William; Satija, Indubala; Rey, Ana; Manmana, Salvatore

2012-06-01

We present results of the quantum dynamics of solitons in XXZ spin-1/2 systems which in general can be derived from a system of spinless fermions or hard-core bosons (HCB) with nearest neighbor interaction on a lattice. A mean-field treatment using spin-coherent states revealed analytic solutions of both bright and dark solitons [1]. We take these solutions and apply a full quantum evolution using the adaptive time-dependent density matrix renormalization group method (adaptive t-DMRG), which takes into account the effect of strong correlations. We use local spin observables, correlations functions, and entanglement entropies as measures for the stability of these soliton solutions over the simulation times. [4pt] [1] R. Balakrishnan, I.I. Satija, and C.W. Clark, Phys. Rev. Lett. 103, 230403 (2009).

A random matrix approach to credit risk.

PubMed

Münnix, Michael C; Schäfer, Rudi; Guhr, Thomas

2014-01-01

We estimate generic statistical properties of a structural credit risk model by considering an ensemble of correlation matrices. This ensemble is set up by Random Matrix Theory. We demonstrate analytically that the presence of correlations severely limits the effect of diversification in a credit portfolio if the correlations are not identically zero. The existence of correlations alters the tails of the loss distribution considerably, even if their average is zero. Under the assumption of randomly fluctuating correlations, a lower bound for the estimation of the loss distribution is provided.

A Random Matrix Approach to Credit Risk

PubMed Central

Guhr, Thomas

2014-01-01

We estimate generic statistical properties of a structural credit risk model by considering an ensemble of correlation matrices. This ensemble is set up by Random Matrix Theory. We demonstrate analytically that the presence of correlations severely limits the effect of diversification in a credit portfolio if the correlations are not identically zero. The existence of correlations alters the tails of the loss distribution considerably, even if their average is zero. Under the assumption of randomly fluctuating correlations, a lower bound for the estimation of the loss distribution is provided. PMID:24853864

LC-MS/MS signal suppression effects in the analysis of pesticides in complex environmental matrices.

PubMed

Choi, B K; Hercules, D M; Gusev, A I

2001-02-01

The application of LC separation and mobile phase additives in addressing LC-MS/MS matrix signal suppression effects for the analysis of pesticides in a complex environmental matrix was investigated. It was shown that signal suppression is most significant for analytes eluting early in the LC-MS analysis. Introduction of different buffers (e.g. ammonium formate, ammonium hydroxide, formic acid) into the LC mobile phase was effective in improving signal correlation between the matrix and standard samples. The signal improvement is dependent on buffer concentration as well as LC separation of the matrix components. The application of LC separation alone was not effective in addressing suppression effects when characterizing complex matrix samples. Overloading of the LC column by matrix components was found to significantly contribute to analyte-matrix co-elution and suppression of signal. This signal suppression effect can be efficiently compensated by 2D LC (LC-LC) separation techniques. The effectiveness of buffers and LC separation in improving signal correlation between standard and matrix samples is discussed.

Separable decompositions of bipartite mixed states

NASA Astrophysics Data System (ADS)

Li, Jun-Li; Qiao, Cong-Feng

2018-04-01

We present a practical scheme for the decomposition of a bipartite mixed state into a sum of direct products of local density matrices, using the technique developed in Li and Qiao (Sci. Rep. 8:1442, 2018). In the scheme, the correlation matrix which characterizes the bipartite entanglement is first decomposed into two matrices composed of the Bloch vectors of local states. Then, we show that the symmetries of Bloch vectors are consistent with that of the correlation matrix, and the magnitudes of the local Bloch vectors are lower bounded by the correlation matrix. Concrete examples for the separable decompositions of bipartite mixed states are presented for illustration.

Surface characterization of LDEF carbon fiber/polymer matrix composites

NASA Technical Reports Server (NTRS)

Grammer, Holly L.; Wightman, James P.; Young, Philip R.; Slemp, Wayne S.

1995-01-01

XPS (x-ray photoelectron spectroscopy) and SEM (scanning electron microscopy) analysis of both carbon fiber/epoxy matrix and carbon fiber/polysulfone matrix composites revealed significant changes in the surface composition as a result of exposure to low-earth orbit. The carbon 1s curve fit XPS analysis in conjunction with the SEM photomicrographs revealed significant erosion of the polymer matrix resins by atomic oxygen to expose the carbon fibers of the composite samples. This erosion effect on the composites was seen after 10 months in orbit and was even more obvious after 69 months.

Testing Pattern Hypotheses for Correlation Matrices

ERIC Educational Resources Information Center

McDonald, Roderick P.

1975-01-01

The treatment of covariance matrices given by McDonald (1974) can be readily modified to cover hypotheses prescribing zeros and equalities in the correlation matrix rather than the covariance matrix, still with the convenience of the closed-form Least Squares solution and the classical Newton method. (Author/RC)

Structure-function correlations in glaucoma using matrix and standard automated perimetry versus time-domain and spectral-domain OCT devices.

PubMed

Pinto, Luciano Moreira; Costa, Elaine Fiod; Melo, Luiz Alberto S; Gross, Paula Blasco; Sato, Eduardo Toshio; Almeida, Andrea Pereira; Maia, Andre; Paranhos, Augusto

2014-04-10

We examined the structure-function relationship between two perimetric tests, the frequency doubling technology (FDT) matrix and standard automated perimetry (SAP), and two optical coherence tomography (OCT) devices (time-domain and spectral-domain). This cross-sectional study included 97 eyes from 29 healthy individuals, and 68 individuals with early, moderate, or advanced primary open-angle glaucoma. The correlations between overall and sectorial parameters of retinal nerve fiber layer thickness (RNFL) measured with Stratus and Spectralis OCT, and the visual field sensitivity obtained with FDT matrix and SAP were assessed. The relationship also was evaluated using a previously described linear model. The correlation coefficients for the threshold sensitivity measured with SAP and Stratus OCT ranged from 0.44 to 0.79, and those for Spectralis OCT ranged from 0.30 to 0.75. Regarding FDT matrix, the correlation ranged from 0.40 to 0.79 with Stratus OCT and from 0.39 to 0.79 with Spectralis OCT. Stronger correlations were found in the overall measurements and the arcuate sectors for both visual fields and OCT devices. A linear relationship was observed between FDT matrix sensitivity and the OCT devices. The previously described linear model fit the data from SAP and the OCT devices well, particularly in the inferotemporal sector. The FDT matrix and SAP visual sensitivities were related strongly to the RNFL thickness measured with the Stratus and Spectralis OCT devices, particularly in the overall and arcuate sectors. Copyright 2014 The Association for Research in Vision and Ophthalmology, Inc.

Extension of the spatial autocorrelation (SPAC) method to mixed-component correlations of surface waves

USGS Publications Warehouse

Haney, Matthew M.; Mikesell, T. Dylan; van Wijk, Kasper; Nakahara, Hisashi

2012-01-01

Using ambient seismic noise for imaging subsurface structure dates back to the development of the spatial autocorrelation (SPAC) method in the 1950s. We present a theoretical analysis of the SPAC method for multicomponent recordings of surface waves to determine the complete 3 × 3 matrix of correlations between all pairs of three-component motions, called the correlation matrix. In the case of isotropic incidence, when either Rayleigh or Love waves arrive from all directions with equal power, the only non-zero off-diagonal terms in the matrix are the vertical–radial (ZR) and radial–vertical (RZ) correlations in the presence of Rayleigh waves. Such combinations were not considered in the development of the SPAC method. The method originally addressed the vertical–vertical (ZZ), RR and TT correlations, hence the name spatial autocorrelation. The theoretical expressions we derive for the ZR and RZ correlations offer additional ways to measure Rayleigh wave dispersion within the SPAC framework. Expanding on the results for isotropic incidence, we derive the complete correlation matrix in the case of generally anisotropic incidence. We show that the ZR and RZ correlations have advantageous properties in the presence of an out-of-plane directional wavefield compared to ZZ and RR correlations. We apply the results for mixed-component correlations to a data set from Akutan Volcano, Alaska and find consistent estimates of Rayleigh wave phase velocity from ZR compared to ZZ correlations. This work together with the recently discovered connections between the SPAC method and time-domain correlations of ambient noise provide further insights into the retrieval of surface wave Green’s functions from seismic noise.

Nonlinear optical microscopy reveals invading endothelial cells anisotropically alter three-dimensional collagen matrices

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

Lee, P.-F.; Yeh, Alvin T.; Bayless, Kayla J.

The interactions between endothelial cells (ECs) and the extracellular matrix (ECM) are fundamental in mediating various steps of angiogenesis, including cell adhesion, migration and sprout formation. Here, we used a noninvasive and non-destructive nonlinear optical microscopy (NLOM) technique to optically image endothelial sprouting morphogenesis in three-dimensional (3D) collagen matrices. We simultaneously captured signals from collagen fibers and endothelial cells using second harmonic generation (SHG) and two-photon excited fluorescence (TPF), respectively. Dynamic 3D imaging revealed EC interactions with collagen fibers along with quantifiable alterations in collagen matrix density elicited by EC movement through and morphogenesis within the matrix. Specifically, we observedmore » increased collagen density in the area between bifurcation points of sprouting structures and anisotropic increases in collagen density around the perimeter of lumenal structures, but not advancing sprout tips. Proteinase inhibition studies revealed membrane-associated matrix metalloproteinase were utilized for sprout advancement and lumen expansion. Rho-associated kinase (p160ROCK) inhibition demonstrated that the generation of cell tension increased collagen matrix alterations. This study followed sprouting ECs within a 3D matrix and revealed that the advancing structures recognize and significantly alter their extracellular environment at the periphery of lumens as they progress.« less

Mitochondrial unfolded protein response controls matrix pre-RNA processing and translation.

PubMed

Münch, Christian; Harper, J Wade

2016-06-30

The mitochondrial matrix is unique in that it must integrate the folding and assembly of proteins derived from the nuclear and mitochondrial genomes. In Caenorhabditis elegans, the mitochondrial unfolded protein response (UPRmt) senses matrix protein misfolding and induces a program of nuclear gene expression, including mitochondrial chaperonins, to promote mitochondrial proteostasis. While misfolded mitochondrial-matrix-localized ornithine transcarbamylase induces chaperonin expression, our understanding of mammalian UPRmt is rudimentary, reflecting a lack of acute triggers for UPRmt activation. This limitation has prevented analysis of the cellular responses to matrix protein misfolding and the effects of UPRmt on mitochondrial translation to control protein folding loads. Here we combine pharmacological inhibitors of matrix-localized HSP90/TRAP1 (ref. 8) or LON protease, which promote chaperonin expression, with global transcriptional and proteomic analysis to reveal an extensive and acute response of human cells to UPRmt. This response encompasses widespread induction of nuclear genes, including matrix-localized proteins involved in folding, pre-RNA processing and translation. Functional studies revealed rapid but reversible translation inhibition in mitochondria occurring concurrently with defects in pre-RNA processing caused by transcriptional repression and LON-dependent turnover of the mitochondrial pre-RNA processing nuclease MRPP3 (ref. 10). This study reveals that acute mitochondrial protein folding stress activates both increased chaperone availability within the matrix and reduced matrix-localized protein synthesis through translational inhibition, and provides a framework for further dissection of mammalian UPRmt.

Density matrix renormalization group with efficient dynamical electron correlation through range separation

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

Hedegård, Erik Donovan, E-mail: erik.hedegard@phys.chem.ethz.ch; Knecht, Stefan; Reiher, Markus, E-mail: markus.reiher@phys.chem.ethz.ch

2015-06-14

We present a new hybrid multiconfigurational method based on the concept of range-separation that combines the density matrix renormalization group approach with density functional theory. This new method is designed for the simultaneous description of dynamical and static electron-correlation effects in multiconfigurational electronic structure problems.

Determining the Number of Components from the Matrix of Partial Correlations

ERIC Educational Resources Information Center

Velicer, Wayne F.

1976-01-01

A method is presented for determining the number of components to retain in a principal components or image components analysis which utilizes a matrix of partial correlations. Advantages and uses of the method are discussed and a comparison of the proposed method with existing methods is presented. (JKS)

Asymptotic coincidence of the statistics for degenerate and non-degenerate correlated real Wishart ensembles

NASA Astrophysics Data System (ADS)

Wirtz, Tim; Kieburg, Mario; Guhr, Thomas

2017-06-01

The correlated Wishart model provides the standard benchmark when analyzing time series of any kind. Unfortunately, the real case, which is the most relevant one in applications, poses serious challenges for analytical calculations. Often these challenges are due to square root singularities which cannot be handled using common random matrix techniques. We present a new way to tackle this issue. Using supersymmetry, we carry out an anlaytical study which we support by numerical simulations. For large but finite matrix dimensions, we show that statistical properties of the fully correlated real Wishart model generically approach those of a correlated real Wishart model with doubled matrix dimensions and doubly degenerate empirical eigenvalues. This holds for the local and global spectral statistics. With Monte Carlo simulations we show that this is even approximately true for small matrix dimensions. We explicitly investigate the k-point correlation function as well as the distribution of the largest eigenvalue for which we find a surprisingly compact formula in the doubly degenerate case. Moreover we show that on the local scale the k-point correlation function exhibits the sine and the Airy kernel in the bulk and at the soft edges, respectively. We also address the positions and the fluctuations of the possible outliers in the data.

Anatomical relationships between serotonin 5-HT2A and dopamine D2 receptors in living human brain.

PubMed

Ishii, Tatsuya; Kimura, Yasuyuki; Ichise, Masanori; Takahata, Keisuke; Kitamura, Soichiro; Moriguchi, Sho; Kubota, Manabu; Zhang, Ming-Rong; Yamada, Makiko; Higuchi, Makoto; Okubo, Yoshinori; Suhara, Tetsuya

2017-01-01

Seven healthy volunteers underwent PET scans with [18F]altanserin and [11C]FLB 457 for 5-HT2A and D2 receptors, respectively. As a measure of receptor density, a binding potential (BP) was calculated from PET data for 76 cerebral cortical regions. A correlation matrix was calculated between the binding potentials of [18F]altanserin and [11C]FLB 457 for those regions. The regional relationships were investigated using a bicluster analysis of the correlation matrix with an iterative signature algorithm. We identified two clusters of regions. The first cluster identified a distinct profile of correlation coefficients between 5-HT2A and D2 receptors, with the former in regions related to sensorimotor integration (supplementary motor area, superior parietal gyrus, and paracentral lobule) and the latter in most cortical regions. The second cluster identified another distinct profile of correlation coefficients between 5-HT2A receptors in the bilateral hippocampi and D2 receptors in most cortical regions. The observation of two distinct clusters in the correlation matrix suggests regional interactions between 5-HT2A and D2 receptors in sensorimotor integration and hippocampal function. A bicluster analysis of the correlation matrix of these neuroreceptors may be beneficial in understanding molecular networks in the human brain.

Density matrix embedding in an antisymmetrized geminal power bath

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

Tsuchimochi, Takashi; Welborn, Matthew; Van Voorhis, Troy, E-mail: tvan@mit.edu

2015-07-14

Density matrix embedding theory (DMET) has emerged as a powerful tool for performing wave function-in-wave function embedding for strongly correlated systems. In traditional DMET, an accurate calculation is performed on a small impurity embedded in a mean field bath. Here, we extend the original DMET equations to account for correlation in the bath via an antisymmetrized geminal power (AGP) wave function. The resulting formalism has a number of advantages. First, it allows one to properly treat the weak correlation limit of independent pairs, which DMET is unable to do with a mean-field bath. Second, it associates a size extensive correlationmore » energy with a given density matrix (for the models tested), which AGP by itself is incapable of providing. Third, it provides a reasonable description of charge redistribution in strongly correlated but non-periodic systems. Thus, AGP-DMET appears to be a good starting point for describing electron correlation in molecules, which are aperiodic and possess both strong and weak electron correlation.« less

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.

Quantitative proteomics reveals altered expression of extracellular matrix related proteins of human primary dermal fibroblasts in response to sulfated hyaluronan and collagen applied as artificial extracellular matrix.

PubMed

Müller, Stephan A; van der Smissen, Anja; von Feilitzsch, Margarete; Anderegg, Ulf; Kalkhof, Stefan; von Bergen, Martin

2012-12-01

Fibroblasts are the main matrix producing cells of the dermis and are also strongly regulated by their matrix environment which can be used to improve and guide skin wound healing processes. Here, we systematically investigated the molecular effects on primary dermal fibroblasts in response to high-sulfated hyaluronan [HA] (hsHA) by quantitative proteomics. The comparison of non- and high-sulfated HA revealed regulation of 84 of more than 1,200 quantified proteins. Based on gene enrichment we found that sulfation of HA alters extracellular matrix remodeling. The collagen degrading enzymes cathepsin K, matrix metalloproteinases-2 and -14 were found to be down-regulated on hsHA. Additionally protein expression of thrombospondin-1, decorin, collagen types I and XII were reduced, whereas the expression of trophoblast glycoprotein and collagen type VI were slightly increased. This study demonstrates that global proteomics provides a valuable tool for revealing proteins involved in molecular effects of growth substrates for further material optimization.

Integrative analysis of gut microbiota composition, host colonic gene expression and intraluminal metabolites in aging C57BL/6J mice.

PubMed

van der Lugt, Benthe; Rusli, Fenni; Lute, Carolien; Lamprakis, Andreas; Salazar, Ethel; Boekschoten, Mark V; Hooiveld, Guido J; Müller, Michael; Vervoort, Jacques; Kersten, Sander; Belzer, Clara; Kok, Dieuwertje E G; Steegenga, Wilma T

2018-05-16

The aging process is associated with diminished colonic health. In this study, we applied an integrative approach to reveal potential interactions between determinants of colonic health in aging C57BL/6J mice. Analysis of gut microbiota composition revealed an enrichment of various potential pathobionts, including Desulfovibrio spp . , and a decline of the health-promoting Akkermansia spp . and Lactobacillus spp. during aging. Intraluminal concentrations of various metabolites varied between ages and we found evidence for an increased gut permeability at higher age. Colonic gene expression analysis suggested that during the early phase of aging (between 6 and 12 months), expression of genes involved in epithelial-to-mesenchymal transition and (re)organization of the extracellular matrix were increased. Differential expression of these genes was strongly correlated with Bifidobacterium spp. During the later phase of aging (between 12 and 28 months), gene expression profiles pointed towards a diminished antimicrobial defense and were correlated with an uncultured Gastranaerophilales spp. This study demonstrates that aging is associated with pronounced changes in gut microbiota composition and colonic gene expression. Furthermore, the strong correlations between specific bacterial genera and host gene expression may imply that orchestrated interactions take place in the vicinity of the colonic wall and potentially mediate colonic health during aging.

Ethylene Glycol - Polyethylene Glycol (EG-PEG) Mixtures: Infrared Spectra Wavelet Cross-Correlation Analysis.

PubMed

Caccamo, Maria Teresa; Magazù, Salvatore

2017-03-01

Infrared spectra were collected on mixtures of ethylene glycol (EG) and polyethylene glycol 600 (PEG600) as a function of weight fraction from pure EG to pure PEG600. In this paper, it will be shown that while the OH vibrational contribution drastically reduces its center frequency from 3450 cm -1 to 3300 cm -1 in the weight fraction range 0-25%, the displacement of the mixture spectral features of the mixtures from ideal behavior, i.e., in the absence of interaction, shows the presence of a non-ideal mixing process. Furthermore, wavelet cross-correlation analysis of the registered pairs of spectra and of the intramolecular O-H stretching contributions reveals how the addition of a small amount of pure EG to PEG600 dramatically influences the structural properties of the polymeric matrix, owing to an increase the intermolecular connectivity. In particular, the wavelet cross-correlation parameters, evaluated between each pair of the registered data as a function of weight fraction, in a linear-logarithmic plot, reveals an inflection point for a weight fraction of about 25% of EG, which confirms that, within the three-dimensional networks of hydrogen-bonded EG-PEG600 molecules, a key role is played by EG in determining an increase in the hydrogen-bond network density.

Cytoskeletal filament assembly and the control of cell spreading and function by extracellular matrix

NASA Technical Reports Server (NTRS)

Mooney, D. J.; Langer, R.; Ingber, D. E.

1995-01-01

This study was undertaken to analyze how cell binding to extracellular matrix produces changes in cell shape. We focused on the initial process of cell spreading that follows cell attachment to matrix and, thus, cell 'shape' changes are defined here in terms of alterations in projected cell areas, as determined by computerized image analysis. Cell spreading kinetics and changes in microtubule and actin microfilament mass were simultaneously quantitated in hepatocytes plated on different extracellular matrix substrata. The initial rate of cell spreading was highly dependent on the matrix coating density and decreased from 740 microns 2/h to 50 microns 2/h as the coating density was lowered from 1000 to 1 ng/cm2. At approximately 4 to 6 hours after plating, this initial rapid spreading rate slowed and became independent of the matrix density regardless of whether laminin, fibronectin, type I collagen or type IV collagen was used for cell attachment. Analysis of F-actin mass revealed that cell adhesion to extracellular matrix resulted in a 20-fold increase in polymerized actin within 30 minutes after plating, before any significant change in cell shape was observed. This was followed by a phase of actin microfilament disassembly which correlated with the most rapid phase of cell extension and ended at about 6 hours; F-actin mass remained relatively constant during the slow matrix-independent spreading phase. Microtubule mass increased more slowly in spreading cells, peaking at 4 hours, the time at which the transition between rapid and slow spreading rates was observed. However, inhibition of this early rise in microtubule mass using either nocodazole or cycloheximide did not prevent this transition. Use of cytochalasin D revealed that microfilament integrity was absolutely required for hepatocyte spreading whereas interference with microtubule assembly (using nocodazole or taxol) or protein synthesis (using cycloheximide) only partially suppressed cell extension. In contrast, cell spreading could be completely inhibited by combining suboptimal doses of cytochalasin D and nocodazole, suggesting that intact microtubules can stabilize cell form when the microfilament lattice is partially compromised. The physiological relevance of the cytoskeleton and cell shape in hepatocyte physiology was highlighted by the finding that a short exposure (6 hour) of cells to nocodazole resulted in production of smaller cells 42 hours later that exhibited enhanced production of a liver-specific product (albumin). These data demonstrate that spreading and flattening of the entire cell body is not driven directly by net polymerization of either microfilaments or microtubules.(ABSTRACT TRUNCATED AT 400 WORDS).

Optimizing the calcium content of a copolymer acrylamide gel matrix for dark-grown seedlings

NASA Technical Reports Server (NTRS)

Myers, P. N.; Mitchell, C. A.

1998-01-01

A copolymer acrylamide acrylate gel was investigated as the sole root matrix for dark-grown seedlings of soybean (Glycine max Merr. 'Century 84'). Increasing Ca2+ in the hydrating solution of the hydrogel from 1 to 10 mM decreased its water-holding capacity from 97 to 46 mL g-1, yet water potential of the medium remained high, sufficient for normal plant growth at all Ca2+ concentrations tested. Elongation rate of dark-grown soybean seedlings over a 54-hour period was 0.9, 1.5, and 1.8 mm h-1 with 1.0, 2.5, or 5.0 mM Ca2+, respectively, but did not increase with further increases in Ca2+ concentration. Further study revealed that Na+ was released from the hydrogel medium and was taken up by the seedlings as Ca2+ increased in the medium. In dry hypocotyl tissue, sodium content correlated negatively with calcium content. Despite the presence of Na+ in the hydrogel, seedling growth was normal when adequate Ca2+ was added in the hydrating solution. Acrylamide hydrogels hold good potential as a sole growth matrix for short-term experiments with dark-grown seedlings without irrigation.

T Lymphocytes Influence the Mineralization Process of Bone

PubMed Central

El Khassawna, Thaqif; Serra, Alessandro; Bucher, Christian H.; Petersen, Ansgar; Schlundt, Claudia; Könnecke, Ireen; Malhan, Deeksha; Wendler, Sebastian; Schell, Hanna; Volk, Hans-Dieter; Schmidt-Bleek, Katharina; Duda, Georg N.

2017-01-01

Bone is a unique organ able to regenerate itself after injuries. This regeneration requires the local interplay between different biological systems such as inflammation and matrix formation. Structural reconstitution is initiated by an inflammatory response orchestrated by the host immune system. However, the individual role of T cells and B cells in regeneration and their relationship to bone tissue reconstitution remain unknown. Comparing bone and fracture healing in animals with and without mature T and B cells revealed the essential role of these immune cells in determining the tissue mineralization and thus the bone quality. Bone without mature T and B cells is stiffer when compared to wild-type bone thus lacking the elasticity that helps to absorb forces, thus preventing fractures. In-depth analysis showed dysregulations in collagen deposition and osteoblast distribution upon lack of mature T and B cells. These changes in matrix deposition have been correlated with T cells rather than B cells within this study. This work presents, for the first time, a direct link between immune cells and matrix formation during bone healing after fracture. It illustrates specifically the role of T cells in the collagen organization process and the lack thereof in the absence of T cells. PMID:28596766

Magnetic properties of the Bled El Hadba phosphate-bearing formation (Djebel Onk, Algeria): Consequences of the enrichment of the phosphate ore deposit

NASA Astrophysics Data System (ADS)

Bezzi, Nacer; Aïfa, Tahar; Merabet, Djoudi; Pivan, Jean-Yves

2008-02-01

To improve the enrichment of the Thanetian marine phosphate ore deposit from the quarry of Bled El Hadba (Djebel Onk, Algeria) before its exploitation, we first conducted a joint study using different techniques for comparison. These studies reveal that magnetic minerals play a significant role within the matrix of the central productive unit which is squeezed between two other units. Magnetic separation procedures show that there are some positive correlations between magnetic susceptibility and grain size fraction (80-250 μm). These dolomite-rich fractions are more clearly separated. Different tools were used to characterize the magnetic minerals (X-ray, microprobe, differential scanning calorimetry, thermogravimetric and thermomagnetic analyses). They show correlations between magnetic phases and the presence of associated magnetic minerals within the matrix or included in the phosphate ore deposit. They enabled us to distinguish a series of magnetic minerals (magnetite, hematite, maghemite, goethite, ilmenite, pyrite, iron-titanium oxide and titanium oxide sulphate) and to determine that Fe and Ti are prevalent in the separated fractions, following the same variation as Mg. The phosphorous (phosphate) rate is higher in the non-magnetic material, especially in the layers that are rich in dolomitic carbonates (upper and lower units), which could be trapped within the dolomitic matrix, while Magnesium (dolomite) is more important in the magnetic fraction. The separation of phosphate elements and dolomite carbonates is effective and therefore the ore can be enriched through magnetic procedures. Comparison between products enriched by magnetic separation, flotation and calcination showed important differences, chemically, economically and technically speaking.

Commander and User Perceptions of the Army’s Intransit Visibility (ITV) Architecture

DTIC Science & Technology

2007-03-01

covariance matrix; (c) Bartlett’s test of Sphericity; and (d) Kaiser-Meyer- Olkin ( KMO ) measure of sampling adequacy. The inter-item correlation matrix...001), and all diagonal terms had a value of 1 while off-diagonal terms were 0. The KMO measure of sampling adequacy reflects the homogeneity...amongst the variables and serves as an index for comparing the magnitudes of correlation coefficients to partial correlation coefficients. KMO values at

Multivariate analysis of fears in dental phobic patients according to a reduced FSS-II scale.

PubMed

Hakeberg, M; Gustafsson, J E; Berggren, U; Carlsson, S G

1995-10-01

This study analyzed and assessed dimensions of a questionnaire developed to measure general fears and phobias. A previous factor analysis among 109 dental phobics had revealed a five-factor structure with 22 items and an explained total variance of 54%. The present study analyzed the same material using a multivariate statistical procedure (LISREL) to reveal structural latent variables. The LISREL analysis, based on the correlation matrix, yielded a chi-square of 216.6 with 195 degrees of freedom (P = 0.138) and showed a model with seven latent variables. One was a general fear factor correlated to all 22 items. The other six factors concerned "Illness & Death" (5 items), "Failures & Embarrassment" (5 items), "Social situations" (5 items), "Physical injuries" (4 items), "Animals & Natural phenomena" (4 items). One item (opposite sex) was included in both "Failures & Embarrassment" and "Social situations". The last factor, "Social interaction", combined all the items in "Failures & Embarrassment" and "Social situations" (9 items). In conclusion, this multivariate statistical analysis (LISREL) revealed and confirmed a factor structure similar to our previous study, but added two important dimensions not shown with a traditional factor analysis. This reduced FSS-II version measures general fears and phobias and may be used on a routine clinical basis as well as in dental phobia research.

The roles of MMP-9/TIMP-1 in cerebral edema following experimental acute cerebral infarction in rats.

PubMed

Li, Dan-Dong; Song, Jin-Ning; Huang, Huan; Guo, Xiao-Ye; An, Ji-Yang; Zhang, Ming; Li, Yu; Sun, Peng; Pang, Hong-Gang; Zhao, Yong-Lin; Wang, Jun-Feng

2013-08-29

Matrix metalloproteinases 9 (MMP-9) and its endogenous inhibitor, tissue inhibitor of metalloproteinases 1 (TIMP-1), regulate homeostasis and turnover of the extra cellular matrix (ECM). They play important roles in acute cerebral infarction (ACI). The contributions of MMP-9 and TIMP-1 to the early stages of ACI are not completely understood. This study investigates the time course of MMP-9 and TIMP-1 and their relations to edema after ACI in rats. Serum concentrations of MMP-9 and TIMP-1 protein were measured using ELISA and mRNA level were measured using real-time PCR. Brain samples were harvested and the brain water content (BWC) was measured. Results revealed that MMP-9 concentration increased fast during the first 12 h after ACI, while after 12 h the increase was much slower. The MMP-9 protein concentration was elevated earlier than the mRNA level. BWC increased starting at 6 h after ACI to reach a peak at 12 h and decreased back to normal levels at 72 h. Both the MMP-9 protein and its mRNA were positively correlated with BWC, however no correlation was found between TIMP-1 levels and BWC. The MMP-9/TIMP-1 protein ratio was more closely correlated with BWC than the MMP-9 concentration. These results indicate that brain edema induced by ACI is associated with increased MMP-9 levels and MMP-9/TIMP-1 ratio in serum. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

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.

Scale Free Reduced Rank Image Analysis.

ERIC Educational Resources Information Center

Horst, Paul

In the traditional Guttman-Harris type image analysis, a transformation is applied to the data matrix such that each column of the transformed data matrix is the best least squares estimate of the corresponding column of the data matrix from the remaining columns. The model is scale free. However, it assumes (1) that the correlation matrix is…

The nuclear matrix prepared by amine modification

PubMed Central

Wan, Katherine M.; Nickerson, Jeffrey A.; Krockmalnic, Gabriela; Penman, Sheldon

1999-01-01

The nucleus is spatially ordered by attachments to a nonchromatin nuclear structure, the nuclear matrix. The nuclear matrix and chromatin are intimately connected and integrated structures, and so a major technical challenge in nuclear matrix research has been to remove chromatin while retaining a native nuclear matrix. Most methods for removing chromatin require first a nuclease digestion and then a salt extraction to remove cut chromatin. We have hypothesized that cut chromatin is held in place by charge interactions involving nucleosomal amino groups. We have tested this hypothesis by chemically modifying amino groups after nuclease digestion. By using this protocol, chromatin could be effectively removed at physiological ionic strength. We compared the ultrastructure and composition of this nuclear matrix preparation with the traditional high-salt nuclear matrix and with the third nuclear matrix preparation that we have developed from which chromatin is removed after extensive crosslinking. All three matrix preparations reveal internal nuclear matrix structures that are built on a network of branched filaments of about 10 nm diameter. That such different chromatin-removal protocols reveal similar principles of nuclear matrix construction increases our confidence that we are observing important architectural elements of the native structure in the living cell. PMID:9927671

Muscle synergies during bench press are reliable across days.

PubMed

Kristiansen, Mathias; Samani, Afshin; Madeleine, Pascal; Hansen, Ernst Albin

2016-10-01

Muscle synergies have been investigated during different types of human movement using nonnegative matrix factorization. However, there are not any reports available on the reliability of the method. To evaluate between-day reliability, 21 subjects performed bench press, in two test sessions separated by approximately 7days. The movement consisted of 3 sets of 8 repetitions at 60% of the three repetition maximum in bench press. Muscle synergies were extracted from electromyography data of 13 muscles, using nonnegative matrix factorization. To evaluate between-day reliability, we performed a cross-correlation analysis and a cross-validation analysis, in which the synergy components extracted in the first test session were recomputed, using the fixed synergy components from the second test session. Two muscle synergies accounted for >90% of the total variance, and reflected the concentric and eccentric phase, respectively. The cross-correlation values were strong to very strong (r-values between 0.58 and 0.89), while the cross-validation values ranged from substantial to almost perfect (ICC3, 1 values between 0.70 and 0.95). The present findings revealed that the same general structure of the muscle synergies was present across days and the extraction of muscle synergies is thus deemed reliable. Copyright © 2016 Elsevier Ltd. All rights reserved.

Analysis of some metallic elements and metalloids composition and relationships in parasol mushroom Macrolepiota procera.

PubMed

Falandysz, Jerzy; Sapkota, Atindra; Dryżałowska, Anna; Mędyk, Małgorzata; Feng, Xinbin

2017-06-01

The aim of the study was to characterise the multi-elemental composition and associations between a group of 32 elements and 16 rare earth elements collected by mycelium from growing substrates and accumulated in fruiting bodies of Macrolepiota procera from 16 sites from the lowland areas of Poland. The elements were quantified by inductively coupled plasma quadrupole mass spectrometry using validated method. The correlation matrix obtained from a possible 48 × 16 data matrix has been used to examine if any association exits between 48 elements in mushrooms foraged from 16 sampling localizations by multivariate approach using principal component (PC) analysis. The model could explain up to 93% variability by eight factors for which an eigenvalue value was ≥1. Absolute values of the correlation coefficient were above 0.72 (significance at p < 0.05) for 43 elements. From a point of view by consumer, the absolute content of Cd, Hg, Pb in caps of M. procera collected from background (unpolluted) areas could be considered elevated while sporadic/occasional ingestion of this mushroom is considered safe. The multivariate functional analysis revealed on associated accumulation of many elements in this mushroom. M. procera seem to possess some features of a bio-indicative species for anthropogenic Pb but also for some geogenic metals.

Relationship between second-generation frequency doubling technology and standard automated perimetry in patients with glaucoma.

PubMed

Zarkovic, Andrea; Mora, Justin; McKelvie, James; Gamble, Greg

2007-12-01

The aim of the study was to establish the correlation between visual filed loss as shown by second-generation Frequency Doubling Technology (Humphrey Matrix) and Standard Automated Perimetry (Humphrey Field Analyser) in patients with glaucoma. Also, compared were the test duration and reliability. Forty right eyes from glaucoma patients from a private ophthalmology practice were included in this prospective study. All participants had tests within an 8-month period. Pattern deviation plots and mean deviation were compared to establish the correlation between the two perimetry tests. Overall correlation and correlation between hemifields, quadrants and individual test locations were assessed. Humphrey Field Analyser tests were slightly more reliable (37/40 vs. 34/40 for Matrix)) but overall of longer duration. There was good correlation (0.69) between mean deviations. Superior hemifields and superonasal quadrants had the highest correlation (0.88 [95% CI 0.79, 0.94]). Correlation between individual points was independent of distance from the macula. Generally, the Matrix and Humphrey Field Analyser perimetry correlate well; however, each machine utilizes a different method of analysing data and thus the direct comparison should be made with caution.

Interactions between Skeletal Muscle Myoblasts and their Extracellular Matrix Revealed by a Serum Free Culture System.

PubMed

Chaturvedi, Vishal; Dye, Danielle E; Kinnear, Beverley F; van Kuppevelt, Toin H; Grounds, Miranda D; Coombe, Deirdre R

2015-01-01

Decellularisation of skeletal muscle provides a system to study the interactions of myoblasts with muscle extracellular matrix (ECM). This study describes the efficient decellularisation of quadriceps muscle with the retention of matrix components and the use of this matrix for myoblast proliferation and differentiation under serum free culture conditions. Three decellularisation approaches were examined; the most effective was phospholipase A2 treatment, which removed cellular material while maximizing the retention of ECM components. Decellularised muscle matrices were then solubilized and used as substrates for C2C12 mouse myoblast serum free cultures. The muscle matrix supported myoblast proliferation and differentiation equally as well as collagen and fibronectin. Immunofluorescence analyses revealed that myoblasts seeded on muscle matrix and fibronectin differentiated to form long, well-aligned myotubes, while myoblasts seeded on collagen were less organized. qPCR analyses showed a time dependent increase in genes involved in skeletal muscle differentiation and suggested that muscle-derived matrix may stimulate an increased rate of differentiation compared to collagen and fibronectin. Decellularized whole muscle three-dimensional scaffolds also supported cell adhesion and spreading, with myoblasts aligning along specific tracts of matrix proteins within the scaffolds. Thus, under serum free conditions, intact acellular muscle matrices provided cues to direct myoblast adhesion and migration. In addition, myoblasts were shown to rapidly secrete and organise their own matrix glycoproteins to create a localized ECM microenvironment. This serum free culture system has revealed that the correct muscle ECM facilitates more rapid cell organisation and differentiation than single matrix glycoprotein substrates.

DBDA as a Novel Matrix for the Analyses of Small Molecules and Quantification of Fatty Acids by Negative Ion MALDI-TOF MS.

PubMed

Ling, Ling; Li, Ying; Wang, Sheng; Guo, Liming; Xiao, Chunsheng; Chen, Xuesi; Guo, Xinhua

2018-04-01

Matrix interference ions in low mass range has always been a concern when using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to analyze small molecules (<500 Da). In this work, a novel matrix, N1,N4-dibenzylidenebenzene-1,4-diamine (DBDA) was synthesized for the analyses of small molecules by negative ion MALDI-TOF MS. Notably, only neat ions ([M-H] - ) of fatty acids without matrix interference appeared in the mass spectra and the limit of detection (LOD) reached 0.3 fmol. DBDA also has great performance towards other small molecules such as amino acids, peptides, and nucleotide. Furthermore, with this novel matrix, the free fatty acids in serum were quantitatively analyzed based on the correlation curves with correlation coefficient of 0.99. In addition, UV-Vis experiments and molecular orbital calculations were performed to explore mechanism about DBDA used as matrix in the negative ion mode. The present work shows that the DBDA matrix is a highly sensitive matrix with few interference ions for analysis of small molecules. Meanwhile, DBDA is able to precisely quantify the fatty acids in real biological samples. Graphical Abstract ᅟ.

A test of the hypothesis that correlational selection generates genetic correlations.

PubMed

Roff, Derek A; Fairbairn, Daphne J

2012-09-01

Theory predicts that correlational selection on two traits will cause the major axis of the bivariate G matrix to orient itself in the same direction as the correlational selection gradient. Two testable predictions follow from this: for a given pair of traits, (1) the sign of correlational selection gradient should be the same as that of the genetic correlation, and (2) the correlational selection gradient should be positively correlated with the value of the genetic correlation. We test this hypothesis with a meta-analysis utilizing empirical estimates of correlational selection gradients and measures of the correlation between the two focal traits. Our results are consistent with both predictions and hence support the underlying hypothesis that correlational selection generates a genetic correlation between the two traits and hence orients the bivariate G matrix. © 2012 The Author(s). Evolution© 2012 The Society for the Study of Evolution.

Extraction of extracellular polymeric substances from aerobic granule with compact interior structure.

PubMed

Adav, Sunil S; Lee, Duu-Jong

2008-06-15

Extracellular polymeric substances (EPS) were extracted from aerobic granules of compact interior structure using seven extraction methods. Ultrasound followed by the chemical reagents formamide and NaOH outperformed other methods in extracting EPS from aerobic granules of compact interior. The collected EPS revealed no contamination by intracellular substances and consisted mainly of proteins, polysaccharides, humic substances and lipids. The quantity of extracted proteins exhibited a weak correlation with quantity of extracted carbohydrates but no correlation with quantity of extracted humic substances. The total polysaccharides/total proteins (PN/PS) ratios for sludge flocs were approximately 0.9 regardless of extraction method. Protein content was significantly enriched in the granules, producing a PN/PS ratio of 3.4-6.2. This experimental result correlated with observations using excitation-emission matrix (EEM) and confocal laser scanning microscope technique. However, detailed study disproved the use of EEM results as a quantitative index of extracted EPS from sludge flocs or from granules.

Static properties of ferromagnetic quantum chains: Numerical results and experimental data on two S=1/2 systems (invited)

NASA Astrophysics Data System (ADS)

Kopinga, K.; Delica, T.; Leschke, H.

1990-05-01

New results of a variant of the numerically exact quantum transfer matrix method have been compared with experimental data on the static properties of [C6H11NH3]CuBr3(CHAB), a ferromagnetic system with about 5% easy-plane anisotropy. Above T=3.5 K, the available data on the zero-field heat capacity, the excess heat capacity ΔC=C(B)-C(B=0), and the magnetization are described with an accuracy comparable to the experimental error. Calculations of the spin-spin correlation functions reveal that the good description of the experimental correlation length in CHAB by a classical spin model is largely accidental. The zero-field susceptibility, which can be deduced from these correlation functions, is in fair agreement with the reported experimental data between 4 and 100 K. The method also seems to yield accurate results for the chlorine isomorph, CHAC, a system with about 2% uniaxial anisotropy.

Multi-population Genomic Relationships for Estimating Current Genetic Variances Within and Genetic Correlations Between Populations.

PubMed

Wientjes, Yvonne C J; Bijma, Piter; Vandenplas, Jérémie; Calus, Mario P L

2017-10-01

Different methods are available to calculate multi-population genomic relationship matrices. Since those matrices differ in base population, it is anticipated that the method used to calculate genomic relationships affects the estimate of genetic variances, covariances, and correlations. The aim of this article is to define the multi-population genomic relationship matrix to estimate current genetic variances within and genetic correlations between populations. The genomic relationship matrix containing two populations consists of four blocks, one block for population 1, one block for population 2, and two blocks for relationships between the populations. It is known, based on literature, that by using current allele frequencies to calculate genomic relationships within a population, current genetic variances are estimated. In this article, we theoretically derived the properties of the genomic relationship matrix to estimate genetic correlations between populations and validated it using simulations. When the scaling factor of across-population genomic relationships is equal to the product of the square roots of the scaling factors for within-population genomic relationships, the genetic correlation is estimated unbiasedly even though estimated genetic variances do not necessarily refer to the current population. When this property is not met, the correlation based on estimated variances should be multiplied by a correction factor based on the scaling factors. In this study, we present a genomic relationship matrix which directly estimates current genetic variances as well as genetic correlations between populations. Copyright © 2017 by the Genetics Society of America.

Simulation of speckle patterns with pre-defined correlation distributions.

PubMed

Song, Lipei; Zhou, Zhen; Wang, Xueyan; Zhao, Xing; Elson, Daniel S

2016-03-01

We put forward a method to easily generate a single or a sequence of fully developed speckle patterns with pre-defined correlation distribution by utilizing the principle of coherent imaging. The few-to-one mapping between the input correlation matrix and the correlation distribution between simulated speckle patterns is realized and there is a simple square relationship between the values of these two correlation coefficient sets. This method is demonstrated both theoretically and experimentally. The square relationship enables easy conversion from any desired correlation distribution. Since the input correlation distribution can be defined by a digital matrix or a gray-scale image acquired experimentally, this method provides a convenient way to simulate real speckle-related experiments and to evaluate data processing techniques.

Simulation of speckle patterns with pre-defined correlation distributions

PubMed Central

Song, Lipei; Zhou, Zhen; Wang, Xueyan; Zhao, Xing; Elson, Daniel S.

2016-01-01

We put forward a method to easily generate a single or a sequence of fully developed speckle patterns with pre-defined correlation distribution by utilizing the principle of coherent imaging. The few-to-one mapping between the input correlation matrix and the correlation distribution between simulated speckle patterns is realized and there is a simple square relationship between the values of these two correlation coefficient sets. This method is demonstrated both theoretically and experimentally. The square relationship enables easy conversion from any desired correlation distribution. Since the input correlation distribution can be defined by a digital matrix or a gray-scale image acquired experimentally, this method provides a convenient way to simulate real speckle-related experiments and to evaluate data processing techniques. PMID:27231589

Noise-immune complex correlation for vasculature imaging based on standard and Jones-matrix optical coherence tomography

NASA Astrophysics Data System (ADS)

Makita, Shuichi; Kurokawa, Kazuhiro; Hong, Young-Joo; Li, En; Miura, Masahiro; Yasuno, Yoshiaki

2016-03-01

A new optical coherence angiography (OCA) method, called correlation mapping OCA (cmOCA), is presented by using the SNR-corrected complex correlation. An SNR-correction theory for the complex correlation calculation is presented. The method also integrates a motion-artifact-removal method for the sample motion induced decorrelation artifact. The theory is further extended to compute more reliable correlation by using multi- channel OCT systems, such as Jones-matrix OCT. The high contrast vasculature imaging of in vivo human posterior eye has been obtained. Composite imaging of cmOCA and degree of polarization uniformity indicates abnormalities of vasculature and pigmented tissues simultaneously.

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.

Multireference quantum chemistry through a joint density matrix renormalization group and canonical transformation theory.

PubMed

Yanai, Takeshi; Kurashige, Yuki; Neuscamman, Eric; Chan, Garnet Kin-Lic

2010-01-14

We describe the joint application of the density matrix renormalization group and canonical transformation theory to multireference quantum chemistry. The density matrix renormalization group provides the ability to describe static correlation in large active spaces, while the canonical transformation theory provides a high-order description of the dynamic correlation effects. We demonstrate the joint theory in two benchmark systems designed to test the dynamic and static correlation capabilities of the methods, namely, (i) total correlation energies in long polyenes and (ii) the isomerization curve of the [Cu(2)O(2)](2+) core. The largest complete active spaces and atomic orbital basis sets treated by the joint DMRG-CT theory in these systems correspond to a (24e,24o) active space and 268 atomic orbitals in the polyenes and a (28e,32o) active space and 278 atomic orbitals in [Cu(2)O(2)](2+).

Model correlation and damage location for large space truss structures: Secant method development and evaluation

NASA Technical Reports Server (NTRS)

Smith, Suzanne Weaver; Beattie, Christopher A.

1991-01-01

On-orbit testing of a large space structure will be required to complete the certification of any mathematical model for the structure dynamic response. The process of establishing a mathematical model that matches measured structure response is referred to as model correlation. Most model correlation approaches have an identification technique to determine structural characteristics from the measurements of the structure response. This problem is approached with one particular class of identification techniques - matrix adjustment methods - which use measured data to produce an optimal update of the structure property matrix, often the stiffness matrix. New methods were developed for identification to handle problems of the size and complexity expected for large space structures. Further development and refinement of these secant-method identification algorithms were undertaken. Also, evaluation of these techniques is an approach for model correlation and damage location was initiated.

Fibronectin gene expression, synthesis and accumulation during in vitro differentiation of chicken osteoblasts

NASA Technical Reports Server (NTRS)

Winnard, R. G.; Gerstenfeld, L. C.; Toma, C. D.; Franceschi, R. T.; Landis, W. J. (Principal Investigator)

1995-01-01

A well-defined chicken osteoblast culture system(18) has been used to examine fibronectin (FN) mRNA levels, synthesis, and accumulation during in vitro differentiation and matrix mineralization. Immunofluorescent staining of cells after 6 or 18 days in culture revealed that FN was initially associated with the cell surface and in partial coalignment with cytoskeletal elements while at the latter time most FN was associated with the extracellular matrix as a ubiquitous fibrillar network. Western blot analysis of total cell-associated proteins also detected FN at all culture times. However, when results were normalized to cellular DNA, FN levels increased until 12-16 and remained relatively constant thereafter. Similarly, FN synthesis as measured by [35S]-methionine labeling, and immunoprecipitation was greatest in early cultures (culture day 3) and then declined such that synthesis decreased 60% at day 18 and 94% after 24-31 days. FN mRNA levels as measured by Northern blot analysis were well correlated with FN synthesis. These results clearly show that FN is made by primary osteoblasts during their in vitro maturation. In contrast to other osteoblast markers such as alkaline phosphatase, osteocalcin, and osteopontin, whose expression increases as cells differentiate, FN accumulates in the matrix during periods of early cell growth and attachment and then remains proportional to cell number. Results with FN differ from those obtained with collagen which continues to accumulate in the extracellular matrix during osteoblast maturation. These results are consistent with FN being important for the initial attachment of early osteoblasts or osteoblast precursors to the pericellular matrix.

Cross-section fluctuations in chaotic scattering systems.

PubMed

Ericson, Torleif E O; Dietz, Barbara; Richter, Achim

2016-10-01

Exact analytical expressions for the cross-section correlation functions of chaotic scattering systems have hitherto been derived only under special conditions. The objective of the present article is to provide expressions that are applicable beyond these restrictions. The derivation is based on a statistical model of Breit-Wigner type for chaotic scattering amplitudes which has been shown to describe the exact analytical results for the scattering (S)-matrix correlation functions accurately. Our results are given in the energy and in the time representations and apply in the whole range from isolated to overlapping resonances. The S-matrix contributions to the cross-section correlations are obtained in terms of explicit irreducible and reducible correlation functions. Consequently, the model can be used for a detailed exploration of the key features of the cross-section correlations and the underlying physical mechanisms. In the region of isolated resonances, the cross-section correlations contain a dominant contribution from the self-correlation term. For narrow states the self-correlations originate predominantly from widely spaced states with exceptionally large partial width. In the asymptotic region of well-overlapping resonances, the cross-section autocorrelation functions are given in terms of the S-matrix autocorrelation functions. For inelastic correlations, in particular, the Ericson fluctuations rapidly dominate in that region. Agreement with known analytical and experimental results is excellent.

Aggregation of carbon dioxide sequestration storage assessment units

USGS Publications Warehouse

Blondes, Madalyn S.; Schuenemeyer, John H.; Olea, Ricardo A.; Drew, Lawrence J.

2013-01-01

The U.S. Geological Survey is currently conducting a national assessment of carbon dioxide (CO2) storage resources, mandated by the Energy Independence and Security Act of 2007. Pre-emission capture and storage of CO2 in subsurface saline formations is one potential method to reduce greenhouse gas emissions and the negative impact of global climate change. Like many large-scale resource assessments, the area under investigation is split into smaller, more manageable storage assessment units (SAUs), which must be aggregated with correctly propagated uncertainty to the basin, regional, and national scales. The aggregation methodology requires two types of data: marginal probability distributions of storage resource for each SAU, and a correlation matrix obtained by expert elicitation describing interdependencies between pairs of SAUs. Dependencies arise because geologic analogs, assessment methods, and assessors often overlap. The correlation matrix is used to induce rank correlation, using a Cholesky decomposition, among the empirical marginal distributions representing individually assessed SAUs. This manuscript presents a probabilistic aggregation method tailored to the correlations and dependencies inherent to a CO2 storage assessment. Aggregation results must be presented at the basin, regional, and national scales. A single stage approach, in which one large correlation matrix is defined and subsets are used for different scales, is compared to a multiple stage approach, in which new correlation matrices are created to aggregate intermediate results. Although the single-stage approach requires determination of significantly more correlation coefficients, it captures geologic dependencies among similar units in different basins and it is less sensitive to fluctuations in low correlation coefficients than the multiple stage approach. Thus, subsets of one single-stage correlation matrix are used to aggregate to basin, regional, and national scales.

Groundwater quality characterization around Jawaharnagar open dumpsite, Telangana State

NASA Astrophysics Data System (ADS)

Unnisa, Syeda Azeem; Zainab Bi, Shaik

2017-11-01

In the present work groundwater samples were collected from ten different data points in and around Jawaharnagar municipal dumpsite, Telangana State Hyderabad city from May 2015 to May 2016 on monthly basis for groundwater quality characterization. Pearson's correlation coefficient ( r) value was determined using correlation matrix to identify the highly correlated and interrelated water quality standards issued by Bureau of Indian Standard (IS-10500:2012). It is found that most of the groundwater samples are above acceptable limits and are not potable. The chemical analysis results revealed that pH range from 7.2 to 7.8, TA 222 to 427 mg/l, TDS 512 to 854 mg/l, TH 420 to 584 mg/l, Calcium 115 to 140 mg/l, Magnesium 55 to 115 mg/l, Chlorides 202 to 290 mg/l, Sulphates 170 to 250 mg/l, Nitrates 6.5 to 11.3 mg/l, and Fluoride 0.9 to 1.7 mg/l. All samples showed higher range of physicochemical parameters except nitrate content which was lower than permissible limit. Highly positive correlation was observed between pH-TH ( r = 0.5063), TA-Cl- ( r = 0.5896), TDS-SO4 - ( r = 0.5125), Mg2+-NO3 - ( r = 0.5543) and Cl--F- ( r = 0.7786). The groundwater samples in and around Jawaharnagar municipal dumpsite implies that groundwater samples were contaminated by municipal leachate migration from open dumpsite. The results revealed that the systematic calculations of correlation coefficient between water parameters and regression analysis provide qualitative and rapid monitoring of groundwater quality.

Nanoscale protein architecture of the kidney glomerular basement membrane

PubMed Central

Suleiman, Hani; Zhang, Lei; Roth, Robyn; Heuser, John E; Miner, Jeffrey H; Shaw, Andrey S; Dani, Adish

2013-01-01

In multicellular organisms, proteins of the extracellular matrix (ECM) play structural and functional roles in essentially all organs, so understanding ECM protein organization in health and disease remains an important goal. Here, we used sub-diffraction resolution stochastic optical reconstruction microscopy (STORM) to resolve the in situ molecular organization of proteins within the kidney glomerular basement membrane (GBM), an essential mediator of glomerular ultrafiltration. Using multichannel STORM and STORM-electron microscopy correlation, we constructed a molecular reference frame that revealed a laminar organization of ECM proteins within the GBM. Separate analyses of domains near the N- and C-termini of agrin, laminin, and collagen IV in mouse and human GBM revealed a highly oriented macromolecular organization. Our analysis also revealed disruptions in this GBM architecture in a mouse model of Alport syndrome. These results provide the first nanoscopic glimpse into the organization of a complex ECM. DOI: http://dx.doi.org/10.7554/eLife.01149.001 PMID:24137544

Genetic Markers Analyses and Bioinformatic Approaches to Distinguish Between Olive Tree (Olea europaea L.) Cultivars.

PubMed

Ben Ayed, Rayda; Ben Hassen, Hanen; Ennouri, Karim; Rebai, Ahmed

2016-12-01

The genetic diversity of 22 olive tree cultivars (Olea europaea L.) sampled from different Mediterranean countries was assessed using 5 SNP markers (FAD2.1; FAD2.3; CALC; SOD and ANTHO3) located in four different genes. The genotyping analysis of the 22 cultivars with 5 SNP loci revealed 11 alleles (average 2.2 per allele). The dendrogram based on cultivar genotypes revealed three clusters consistent with the cultivars classification. Besides, the results obtained with the five SNPs were compared to those obtained with the SSR markers using bioinformatic analyses and by computing a cophenetic correlation coefficient, indicating the usefulness of the UPGMA method for clustering plant genotypes. Based on principal coordinate analysis using a similarity matrix, the first two coordinates, revealed 54.94 % of the total variance. This work provides a more comprehensive explanation of the diversity available in Tunisia olive cultivars, and an important contribution for olive breeding and olive oil authenticity.

Bioinspired active whisker sensor for robotic vibrissal tactile sensing

NASA Astrophysics Data System (ADS)

Ju, Feng; Ling, Shih-Fu

2014-12-01

A whisker transducer (WT) inspired by rat’s vibrissal tactile perception is proposed based on a transduction matrix model characterizing the electro-mechanical transduction process in both forward and backward directions. It is capable of acting as an actuator to sweep the whisker and simultaneously as a sensor to sense the force, motion, and mechanical impedance at whisker tip. Its validity is confirmed by numerical simulation using a finite element model. A prototype is then fabricated and its transduction matrix is determined by parameter identification. The calibrated WT can accurately sense mechanical impedance which is directly related to stiffness, mass and damping. Subsequent vibrissal tactile sensing of sandpaper texture reveals that the real part of mechanical impedance sensed by WT is correlated with sandpaper roughness. Texture discrimination is successfully achieved by inputting the real part to a k-means clustering algorithm. The mechanical impedance sensing ability as well as other features of the WT such as simultaneous-actuation-and-sensing makes it a good solution to robotic tactile sensing.

Influence of heat treatment on microstructure and hot crack susceptibility of laser-drilled turbine blades made from Rene 80

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

Osterle, W.; Krause, S.; Moelders, T.

2008-11-15

Turbine components from conventionally cast nickel-base alloy Rene 80 show different hot cracking susceptibilities depending on their heat treatment conditions leading to slightly different microstructures. Electron probe micro-analysis, focused ion beam technique and analytical transmission electron microscopy were applied to reveal and identify grain boundary precipitates and the {gamma}-{gamma}'-microstructure. The distribution of borides along grain boundaries was evaluated statistically by quantitative metallography. The following features could be correlated with an increase of cracking susceptibility: i) Increasing grain size, ii) increasing fraction of grain boundaries with densely spaced borides, iii) lack of secondary {gamma}'-particles in matrix channels between the coarse cuboidalmore » {gamma}'-precipitates. The latter feature seems to be responsible for linking-up of cracked grain boundary precipitates which occurred as an additional cracking mechanism after one heat treatment, whereas decohesion at the boride-matrix-interface in the heat affected zone of laser-drilled holes was observed for both heat treatments.« less

Efficient tomography of a quantum many-body system

NASA Astrophysics Data System (ADS)

Lanyon, B. P.; Maier, C.; Holzäpfel, M.; Baumgratz, T.; Hempel, C.; Jurcevic, P.; Dhand, I.; Buyskikh, A. S.; Daley, A. J.; Cramer, M.; Plenio, M. B.; Blatt, R.; Roos, C. F.

2017-12-01

Quantum state tomography is the standard technique for estimating the quantum state of small systems. But its application to larger systems soon becomes impractical as the required resources scale exponentially with the size. Therefore, considerable effort is dedicated to the development of new characterization tools for quantum many-body states. Here we demonstrate matrix product state tomography, which is theoretically proven to allow for the efficient and accurate estimation of a broad class of quantum states. We use this technique to reconstruct the dynamical state of a trapped-ion quantum simulator comprising up to 14 entangled and individually controlled spins: a size far beyond the practical limits of quantum state tomography. Our results reveal the dynamical growth of entanglement and describe its complexity as correlations spread out during a quench: a necessary condition for future demonstrations of better-than-classical performance. Matrix product state tomography should therefore find widespread use in the study of large quantum many-body systems and the benchmarking and verification of quantum simulators and computers.

Network trending; leadership, followership and neutrality among companies: A random matrix approach

NASA Astrophysics Data System (ADS)

Mobarhan, N. S. Safavi; Saeedi, A.; Roodposhti, F. Rahnamay; Jafari, G. R.

2016-11-01

In this article, we analyze the cross-correlation between returns of different stocks to answer the following important questions. The first one is: If there exists collective behavior in a financial market, how could we detect it? And the second question is: Is there a particular company among the companies of a market as the leader of the collective behavior? Or is there no specified leadership governing the system similar to some complex systems? We use the method of random matrix theory to answer the mentioned questions. Cross-correlation matrix of index returns of four different markets is analyzed. The participation ratio quantity related to each matrices' eigenvectors and the eigenvalue spectrum is calculated. We introduce shuffled-matrix created of cross correlation matrix in such a way that the elements of the later one are displaced randomly. Comparing the participation ratio quantities obtained from a correlation matrix of a market and its related shuffled-one, on the bulk distribution region of the eigenvalues, we detect a meaningful deviation between the mentioned quantities indicating the collective behavior of the companies forming the market. By calculating the relative deviation of participation ratios, we obtain a measure to compare the markets according to their collective behavior. Answering the second question, we show there are three groups of companies: The first group having higher impact on the market trend called leaders, the second group is followers and the third one is the companies who have not a considerable role in the trend. The results can be utilized in portfolio construction.

Isolation and characterization of chicken bile matrix metalloproteinase

USDA-ARS?s Scientific Manuscript database

Avian bile is rich in matrix metalloproteinases (MMP), the enzymes that cleave extracellular matrix (ECM) proteins such as collagens and proteoglycans. Changes in bile MMP expression have been correlated with hepatic and gall bladder pathologies but the significance of their expression in normal, he...

Decay of correlations between cross-polarized electromagnetic waves in a two-dimensional random medium.

PubMed

Gorodnichev, E E

2018-04-01

The problem of multiple scattering of polarized light in a two-dimensional medium composed of fiberlike inhomogeneities is studied. The attenuation lengths for the density matrix elements are calculated. For a highly absorbing medium it is found that, as the sample thickness increases, the intensity of waves polarized along the fibers decays faster than the other density matrix elements. With further increase in the sample thickness, the off-diagonal elements which are responsible for correlations between the cross-polarized waves disappear. In the asymptotic limit of very thick samples the scattered light proves to be polarized perpendicular to the fibers. The difference in the attenuation lengths between the density matrix elements results in a nonmonotonic depth dependence of the degree of polarization. In the opposite case of a weakly absorbing medium, the off-diagonal element of the density matrix and, correspondingly, the correlations between the cross-polarized fields are shown to decay faster than the intensity of waves polarized along and perpendicular to the fibers.

Matrix elements of N-particle explicitly correlated Gaussian basis functions with complex exponential parameters

NASA Astrophysics Data System (ADS)

Bubin, Sergiy; Adamowicz, Ludwik

2006-06-01

In this work we present analytical expressions for Hamiltonian matrix elements with spherically symmetric, explicitly correlated Gaussian basis functions with complex exponential parameters for an arbitrary number of particles. The expressions are derived using the formalism of matrix differential calculus. In addition, we present expressions for the energy gradient that includes derivatives of the Hamiltonian integrals with respect to the exponential parameters. The gradient is used in the variational optimization of the parameters. All the expressions are presented in the matrix form suitable for both numerical implementation and theoretical analysis. The energy and gradient formulas have been programed and used to calculate ground and excited states of the He atom using an approach that does not involve the Born-Oppenheimer approximation.

Matrix elements of N-particle explicitly correlated Gaussian basis functions with complex exponential parameters.

PubMed

Bubin, Sergiy; Adamowicz, Ludwik

2006-06-14

In this work we present analytical expressions for Hamiltonian matrix elements with spherically symmetric, explicitly correlated Gaussian basis functions with complex exponential parameters for an arbitrary number of particles. The expressions are derived using the formalism of matrix differential calculus. In addition, we present expressions for the energy gradient that includes derivatives of the Hamiltonian integrals with respect to the exponential parameters. The gradient is used in the variational optimization of the parameters. All the expressions are presented in the matrix form suitable for both numerical implementation and theoretical analysis. The energy and gradient formulas have been programmed and used to calculate ground and excited states of the He atom using an approach that does not involve the Born-Oppenheimer approximation.

System of multifunctional Jones matrix tomography of phase anisotropy in diagnostics of endometriosis

NASA Astrophysics Data System (ADS)

Ushenko, V. O.; Koval, G. D.; Ushenko, Yu. O.; Pidkamin, L. Y.; Sidor, M. I.; Vanchuliak, O.; Motrich, A. V.; Gorsky, M. P.; Meglinskiy, I.

2017-09-01

The paper presents the results of Jones-matrix mapping of uterine wall histological sections with second-degree and third-degree endometriosis. The technique of experimental measurement of coordinate distributions of the modulus and phase values of Jones matrix elements is suggested. Within the statistical and cross-correlation approaches the modulus and phase maps of Jones matrix images of optically thin biological layers of polycrystalline films of plasma and cerebrospinal fluid are analyzed. A set of objective parameters (statistical and generalized correlation moments), which are the most sensitive to changes in the phase of anisotropy, associated with the features of polycrystalline structure of uterine wall histological sections with second-degree and third-degree endometriosis are determined.

Dynamic evolution of cross-correlations in the Chinese stock market.

PubMed

Ren, Fei; Zhou, Wei-Xing

2014-01-01

The analysis of cross-correlations is extensively applied for the understanding of interconnections in stock markets and the portfolio risk estimation. Current studies of correlations in Chinese market mainly focus on the static correlations between return series, and this calls for an urgent need to investigate their dynamic correlations. Our study aims to reveal the dynamic evolution of cross-correlations in the Chinese stock market, and offer an exact interpretation for the evolution behavior. The correlation matrices constructed from the return series of 367 A-share stocks traded on the Shanghai Stock Exchange from January 4, 1999 to December 30, 2011 are calculated over a moving window with a size of 400 days. The evolutions of the statistical properties of the correlation coefficients, eigenvalues, and eigenvectors of the correlation matrices are carefully analyzed. We find that the stock correlations are significantly increased in the periods of two market crashes in 2001 and 2008, during which only five eigenvalues significantly deviate from the random correlation matrix, and the systemic risk is higher in these volatile periods than calm periods. By investigating the significant contributors of the deviating eigenvectors in different time periods, we observe a dynamic evolution behavior in business sectors such as IT, electronics, and real estate, which lead the rise (drop) before (after) the crashes. Our results provide new perspectives for the understanding of the dynamic evolution of cross-correlations in the Chines stock markets, and the result of risk estimation is valuable for the application of risk management.

Dynamic Evolution of Cross-Correlations in the Chinese Stock Market

PubMed Central

Ren, Fei; Zhou, Wei-Xing

2014-01-01

The analysis of cross-correlations is extensively applied for the understanding of interconnections in stock markets and the portfolio risk estimation. Current studies of correlations in Chinese market mainly focus on the static correlations between return series, and this calls for an urgent need to investigate their dynamic correlations. Our study aims to reveal the dynamic evolution of cross-correlations in the Chinese stock market, and offer an exact interpretation for the evolution behavior. The correlation matrices constructed from the return series of 367 A-share stocks traded on the Shanghai Stock Exchange from January 4, 1999 to December 30, 2011 are calculated over a moving window with a size of 400 days. The evolutions of the statistical properties of the correlation coefficients, eigenvalues, and eigenvectors of the correlation matrices are carefully analyzed. We find that the stock correlations are significantly increased in the periods of two market crashes in 2001 and 2008, during which only five eigenvalues significantly deviate from the random correlation matrix, and the systemic risk is higher in these volatile periods than calm periods. By investigating the significant contributors of the deviating eigenvectors in different time periods, we observe a dynamic evolution behavior in business sectors such as IT, electronics, and real estate, which lead the rise (drop) before (after) the crashes. Our results provide new perspectives for the understanding of the dynamic evolution of cross-correlations in the Chines stock markets, and the result of risk estimation is valuable for the application of risk management. PMID:24867071

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

PubMed Central

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

2017-01-01

The present study aims to investigate the association of transforming growth factor-β2 (TGF-β2) and matrix metalloproteinases (MMPs), MMP-2 and MMP-3, and tissue inhibitors of matrix metalloproteinases (TIMPs), TIMP-1, TIMP-2 and TIMP-3 in the aqueous humor of patients with high myopia or cataracts. The levels of TGF-β2 and MMPs/TIMPs were measured with the Luminex xMAP Technology using commercially available Milliplex xMAP kits. The association between TGF-β2 and MMPs/TIMPs levels was analyzed using the Spearmans correlation test. The levels of TGF-β2 were identified to be positively correlated with the levels of TIMP-1 and TIMP-3 (TIMP-1: r=0.334; P=0.007; TIMP-3: r=0.309; P=0.012). The levels of MMP-2, MMP-3 and TIMP-2 did not significantly correlate with TGF-β2 levels (P>0.05). A positive correlation was identified between TGF-β2 and TIMPs in the aqueous humor of human eyes with elongated axial length. It appears that TGF-β2 stimulates the expression of TIMPs as a compensatory reaction to the development of high myopia. PMID:29188062

Brueckner G -matrix approach for neutron-proton pairing correlations in the deformed BCS approach

NASA Astrophysics Data System (ADS)

Ha, Eunja; Cheoun, Myung-Ki; Šimkovic, F.

2015-10-01

Ground states of even-even Ge isotopes with mass number A =64 -76 have been studied in the deformed Bardeen-Cooper-Schrieffer (BCS) theory by taking neutron-proton (n p ) pairing correlations as well as neutron-neutron (n n ) and proton-proton (p p ) pairing correlations. The n p pairing has two different modes J =0 ,T =1 (isotriplet) and J =1 ,T =0 (isosinglet). In this work, the Brueckner G matrix, based on the CD-Bonn potential, has been exploited to reduce the ambiguity regarding nucleon-nucleon interactions inside nuclei compared to the results by a simple schematic phenomenological force. We found that the G matrix plays important roles to obtain reasonable descriptions of even-even nuclei compared to the schematic force. The n p pairing strength has been shown to have a clear correlation with quadrupole deformation parameter β2 for the isotopes, and affects the smearing of the Fermi surfaces of not only N =Z nuclei but also N ≠Z nuclei. In particular, the coexistence of the like particle (n n and p p ) and the n p pairing modes was found to become more salient by the G -matrix approach than by the schematic force approach.

Investigation of damage mechanisms in a cross-ply metal-matrix composite under thermomechanical loading. Master's thesis

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

Schubbe, J.J.

1990-12-01

Metal matrix composites (MMCs) are rapidly becoming strong candidates for high temperature and high stiffness structural applications such as the Advanced Tactical Fighter (ATF). This study systematically investigated the failure modes and associated damage in a cross-ply, (0/90)2s SCS6/Ti-15-3 metal matrix composite under in-phase and out-of-phase thermomechanic fatigue. Initiation and progression of fatigue damage were recorded and correlated to changes in Young's Modulus of the composite material. Experimental results show an internal stabilization of reaction zone size but degradation and separation from constituent materials under extended cyclic thermal loading. Critical to damage were transverse cracks initiating in the 90 degreesmore » plies, growing and coalescing from fiber/matrix interfaces internal to the specimen, progressing outward through the 0 degree plies before failure. Maximum mechanical strain at failure was determined to be approximately 0.0075 mm/mm. A correlation was made relating maximum matrix stress to failure life, resulting in a fatigue threshold limit of 280 MPa. An attempt was made to correlate the degradation in Young's Modulus (Damage=1-E/Eo) with the applied life cycles from different TMF tests.« less

Nurse staffing levels and outcomes - mining the UK national data sets for insight.

PubMed

Leary, Alison; Tomai, Barbara; Swift, Adrian; Woodward, Andrew; Hurst, Keith

2017-04-18

Purpose Despite the generation of mass data by the nursing workforce, determining the impact of the contribution to patient safety remains challenging. Several cross-sectional studies have indicated a relationship between staffing and safety. The purpose of this paper is to uncover possible associations and explore if a deeper understanding of relationships between staffing and other factors such as safety could be revealed within routinely collected national data sets. Design/methodology/approach Two longitudinal routinely collected data sets consisting of 30 years of UK nurse staffing data and seven years of National Health Service (NHS) benchmark data such as survey results, safety and other indicators were used. A correlation matrix was built and a linear correlation operation was applied (Pearson product-moment correlation coefficient). Findings A number of associations were revealed within both the UK staffing data set and the NHS benchmarking data set. However, the challenges of using these data sets soon became apparent. Practical implications Staff time and effort are required to collect these data. The limitations of these data sets include inconsistent data collection and quality. The mode of data collection and the itemset collected should be reviewed to generate a data set with robust clinical application. Originality/value This paper revealed that relationships are likely to be complex and non-linear; however, the main contribution of the paper is the identification of the limitations of routinely collected data. Much time and effort is expended in collecting this data; however, its validity, usefulness and method of routine national data collection appear to require re-examination.

DBDA as a Novel Matrix for the Analyses of Small Molecules and Quantification of Fatty Acids by Negative Ion MALDI-TOF MS

NASA Astrophysics Data System (ADS)

Ling, Ling; Li, Ying; Wang, Sheng; Guo, Liming; Xiao, Chunsheng; Chen, Xuesi; Guo, Xinhua

2018-01-01

Matrix interference ions in low mass range has always been a concern when using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to analyze small molecules (<500 Da). In this work, a novel matrix, N1,N4-dibenzylidenebenzene-1,4-diamine (DBDA) was synthesized for the analyses of small molecules by negative ion MALDI-TOF MS. Notably, only neat ions ([M-H]-) of fatty acids without matrix interference appeared in the mass spectra and the limit of detection (LOD) reached 0.3 fmol. DBDA also has great performance towards other small molecules such as amino acids, peptides, and nucleotide. Furthermore, with this novel matrix, the free fatty acids in serum were quantitatively analyzed based on the correlation curves with correlation coefficient of 0.99. In addition, UV-Vis experiments and molecular orbital calculations were performed to explore mechanism about DBDA used as matrix in the negative ion mode. The present work shows that the DBDA matrix is a highly sensitive matrix with few interference ions for analysis of small molecules. Meanwhile, DBDA is able to precisely quantify the fatty acids in real biological samples. [Figure not available: see fulltext.

On-line observation of cell growth in a three-dimensional matrix on surface-modified microelectrode arrays.

PubMed

Lin, Shu-Ping; Kyriakides, Themis R; Chen, Jia-Jin J

2009-06-01

Despite many successful applications of microelectrode arrays (MEAs), typical two-dimensional in-vitro cultures do not project the full scale of the cell growth environment in the three-dimensional (3D) in-vivo setting. This study aims to on-line monitor in-vitro cell growth in a 3D matrix on the surface-modified MEAs with a dynamic perfusion culture system. A 3D matrix consisting of poly(ethylene glycol) hydrogel supplemented with poly-D-lysine was subsequently synthesized in situ on the self-assembled monolayer modified MEAs. FTIR spectrum analysis revealed a peak at 2100 cm(-1) due to the degradation of the structure of the 3D matrix. After 2 wks, microscopic examination revealed that the non-degraded area was around 1500 microm(2) and provided enough space for cell growth. Fluorescence microscopy revealed that the degraded 3D matrix was non-cytotoxic allowing the growth of NIH3T3 fibroblasts and cortical neurons in vitro. Time-course changes of total impedance including resistance and reactance were recorded for 8 days to evaluate the cell growth in the 3D matrix on the MEA. A consistent trend reflecting changes of reactance and total impedance was observed. These in-vitro assays demonstrate that our 3D matrix can construct a biomimetic system for cell growth and analysis of cell surface interactions.

The G matrix under fluctuating correlational mutation and selection.

PubMed

Revell, Liam J

2007-08-01

Theoretical quantitative genetics provides a framework for reconstructing past selection and predicting future patterns of phenotypic differentiation. However, the usefulness of the equations of quantitative genetics for evolutionary inference relies on the evolutionary stability of the additive genetic variance-covariance matrix (G matrix). A fruitful new approach for exploring the evolutionary dynamics of G involves the use of individual-based computer simulations. Previous studies have focused on the evolution of the eigenstructure of G. An alternative approach employed in this paper uses the multivariate response-to-selection equation to evaluate the stability of G. In this approach, I measure similarity by the correlation between response-to-selection vectors due to random selection gradients. I analyze the dynamics of G under several conditions of correlational mutation and selection. As found in a previous study, the eigenstructure of G is stabilized by correlational mutation and selection. However, over broad conditions, instability of G did not result in a decreased consistency of the response to selection. I also analyze the stability of G when the correlation coefficients of correlational mutation and selection and the effective population size change through time. To my knowledge, no prior study has used computer simulations to investigate the stability of G when correlational mutation and selection fluctuate. Under these conditions, the eigenstructure of G is unstable under some simulation conditions. Different results are obtained if G matrix stability is assessed by eigenanalysis or by the response to random selection gradients. In this case, the response to selection is most consistent when certain aspects of the eigenstructure of G are least stable and vice versa.

Combined infrared and ultraviolet-visible spectroscopy matrix-isolated carbon vapor

NASA Technical Reports Server (NTRS)

Kurtz, Joe; Huffman, Donald R.

1990-01-01

Infrared and UV-visible absorption spectra have been measured on the same sample of matrix-isolated carbon vapor in order to establish correlations between absorption intensities of vibrational and electronic transitions as a function of sample annealing. A high degree of correlation has been found between the IR feature at 1998/cm recently assigned to C8 and a UV absorption feature at about 3100 A. Thus, for the first time, direct evidence is given for the assignment of one of the unknown UV-visible features of the long-studied matrix-isolated carbon vapor spectrum.

Fabrication and characterization of novel polymer-matrix nanocomposites and their constituents

NASA Astrophysics Data System (ADS)

Ding, Rui

Two main issues for the wide application of polymer-matrix nanocomposites need to be addressed: cost-effective processing of high-performance nanomaterials, and fundamental understanding of the nanofiller-polymer interaction related to property changes of nanocomposites. To fabricate inexpensive and robust carbon nanofibers (CNFs) by the electrospinning technique, an organosolv lignin for replacing polyacrylonitrile (PAN) precursor was investigated in this work. Modification of lignin to its butyl ester alters the electrospinnability and the thermal mobility of the lignin/PAN blend precursor fibers, which further affect the thermostabilization and carbonization processes of CNFs. The micromorphology, carbon structure, and mechanical properties of resultant CNFs were evaluated in detail. Lignin butyration reveals a new approach to controlling inter-fiber bonding of CNFs which efficiently increases the tensile strength and modulus of nonwoven mats. A commercial vapor-grown CNF reinforcing of room-temperature-vulcanized (RTV) polysiloxane foam has potential impact on the residual tin catalyst in composites and consequently the aging and the long-term performance of the materials. Elemental spectra and mapping were employed to analyze the distribution and the composition of tin catalyst residues in the CNF/polysiloxane composites. Thermal analysis revealed a significant increase of thermal stability for CNF-filled composites. Further, the glass transition properties of polysiloxane are not evidently influenced by the physical interaction between CNF filler and polysiloxane matrix. Nanocomposites consisting of anthracene, a model polycyclic aromatic hydrocarbon (PAH) compound, and a thermosetting epoxy was matrix was studied to interpret the reinforcing effect on the glass transition temperature ( Tg) by different routes: physical dispersion and/or covalent modification. The molecular dynamics of the relaxation processes were analyzed by broadband dielectric spectroscopy (BDS). By parametric fitting using the Havriliak-Negami (HN) function, the Arrhenius diagram was obtained to evaluate the temperature dependence of the relaxation processes at different length scales for the nanocomposites. The segmental alpha relaxation was strongly affected by the reinforcing approaches and the correlation of T g-scaled fragility to molecular structures provides the explanation for the mechanisms of the nanofiller-polymer interaction. In addition, the accelerated chemical aging of nylon 6 polymer, a common material for wire insulations, was monitored by a nondestructive dielectric/capacitive method. The correlation between dielectric properties and electrical breakdown strength was found dependent on the polarity of the aircraft fluids to which nylon 6 was exposed. It was concluded that permittivity/capacitance measurement offers a feasible nondestructive method for diagnosing the breakdown strength of chemically immersed nylon 6.

Variability of protein content in calcium oxalate monohydrate stones.

PubMed

Williams, James C; Zarse, Chad A; Jackson, Molly E; Witzmann, Frank A; McAteer, James A

2006-08-01

Urinary stones are heterogeneous in their fragility to lithotripter shockwaves. As a first step in gaining a better understanding of the role of matrix in stone fragility, we measured extractible protein in calcium oxalate monohydrate (COM) stones that were extensively characterized by micro-computed tomography (micro CT). Stones were scanned using micro CT (Scanco mCT20, 34 microm). They were ground, and the protein extracted using four methods: 0.25M EDTA, 2% SDS reducing buffer, 9M urea buffer, and 10% acetic acid. Protein was measured using NanoOrange. The SDS extracts were also examined using polyacrylamide electrophoresis (PAGE). Extracted protein was highest with the SDS or urea methods (0.28% +/- 0.13% and 0.24% +/- 0.11%, respectively) and lower using the EDTA method (0.17% +/- 0.05%; P < 0.02). Acetic acid extracted little protein (0.006 +/- 0.002%; P < 0.001). Individual stones were significantly different in extractability of protein by the different methods, and SDS-PAGE revealed different protein patterns for individual stones. Extracted protein did not correlate with X-ray-lucent void percentage, which ranged from 0.06% to 2.8% of stone volume, or with apatite content. Extractible stone-matrix protein differs for individual COM stones, and yield is dependent on the extraction method. The presence of X-ray-lucent voids or minor amounts of apatite in stones did not correlate with protein content. The amounts of protein recovered were much lower than reported by Boyce, showing that these methods extracted only a fraction of the protein bound up in the stones. The results suggest that none of the methods tested will be useful for helping to answer the question of whether matrix content differs among stones of differing fragility to lithotripter shockwaves.

Extracellular matrix proteins matrix metallopeptidase 9 (MMP9) and soluble intercellular adhesion molecule 1 (sICAM-1) and correlations with clinical staging in euthymic bipolar disorder.

PubMed

Reininghaus, Eva Z; Lackner, Nina; Birner, Armin; Bengesser, Susanne; Fellendorf, Frederike T; Platzer, Martina; Rieger, Alexandra; Queissner, Robert; Kainzbauer, Nora; Reininghaus, Bernd; McIntyre, Roger S; Mangge, Harald; Zelzer, Sieglinde; Fuchs, Dietmar; Dejonge, Silvia; Müller, Norbert

2016-03-01

Matrix metallopeptidase 9 (MMP9) and soluble intercellular adhesion molecule 1 (sICAM-1) are both involved in the restructuring of connective tissues. Evidence also implicates MMP9 and sICAM in cardiovascular and neoplastic diseases, where blood levels may be a marker of disease severity or prognosis. In individuals with bipolar disorder (BD), higher risk for cardiovascular illness has been extensively reported. The aim of this investigation was to measure and compare peripheral levels of serum MMP9 and sICAM in adults with euthymic BD and healthy controls (HC). Furthermore, we focussed on correlations with illness severity and metabolic parameters. MMP9 levels among the BD sample (n = 112) were significantly higher than among the HC (n = 80) (MMP9: F = 9.885, p = 0.002, η(2)  = 0.058) after controlling for confounding factors. Patients with BD in a later, progressive stage of disease showed significantly higher MMP9 as well as sICAM-1 levels compared to patients with BD in an earlier stage of disease (MMP9: F = 5.8, p = 0.018, η(2)  = 0.054; sICAM-1: F = 5.6, p = 0.020, η(2)  = 0.052). Correlation analyses of cognitive measures revealed a negative association between performance on the d2 Test of Attention and MMP9 (r = -0.287, p = 0.018) in the BD sample. Despite the sample being euthymic (i.e., according to conventional criteria) at the time of analysis, we found significant correlations between MMP9 as well as sICAM-1 and subthreshold depressive/hypomanic symptoms. A collection of disparate findings herein point to a role of MMP9 and cICAM-1 in the patho-progressive process of BD: the increased levels of serum MMP9 and sICAM-1, the correlation between higher levels of these parameters, progressive stage, and cognitive dysfunction in BD, and the positive correlation with subthreshold symptoms. As sICAM-1 and MMP9 are reliable biomarkers of inflammatory and early atherosclerotic disease, these markers may provide indications of the presence of occult cardiovascular disease in this highly at-risk population. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Community Detection for Correlation Matrices

NASA Astrophysics Data System (ADS)

MacMahon, Mel; Garlaschelli, Diego

2015-04-01

A challenging problem in the study of complex systems is that of resolving, without prior information, the emergent, mesoscopic organization determined by groups of units whose dynamical activity is more strongly correlated internally than with the rest of the system. The existing techniques to filter correlations are not explicitly oriented towards identifying such modules and can suffer from an unavoidable information loss. A promising alternative is that of employing community detection techniques developed in network theory. Unfortunately, this approach has focused predominantly on replacing network data with correlation matrices, a procedure that we show to be intrinsically biased because of its inconsistency with the null hypotheses underlying the existing algorithms. Here, we introduce, via a consistent redefinition of null models based on random matrix theory, the appropriate correlation-based counterparts of the most popular community detection techniques. Our methods can filter out both unit-specific noise and system-wide dependencies, and the resulting communities are internally correlated and mutually anticorrelated. We also implement multiresolution and multifrequency approaches revealing hierarchically nested subcommunities with "hard" cores and "soft" peripheries. We apply our techniques to several financial time series and identify mesoscopic groups of stocks which are irreducible to a standard, sectorial taxonomy; detect "soft stocks" that alternate between communities; and discuss implications for portfolio optimization and risk management.

Dynamic multifactor clustering of financial networks

NASA Astrophysics Data System (ADS)

Ross, Gordon J.

2014-02-01

We investigate the tendency for financial instruments to form clusters when there are multiple factors influencing the correlation structure. Specifically, we consider a stock portfolio which contains companies from different industrial sectors, located in several different countries. Both sector membership and geography combine to create a complex clustering structure where companies seem to first be divided based on sector, with geographical subclusters emerging within each industrial sector. We argue that standard techniques for detecting overlapping clusters and communities are not able to capture this type of structure and show how robust regression techniques can instead be used to remove the influence of both sector and geography from the correlation matrix separately. Our analysis reveals that prior to the 2008 financial crisis, companies did not tend to form clusters based on geography. This changed immediately following the crisis, with geography becoming a more important determinant of clustering structure.

Keratin 17 null mice exhibit age- and strain-dependent alopecia.

PubMed

McGowan, Kevin M; Tong, Xuemei; Colucci-Guyon, Emma; Langa, Francina; Babinet, Charles; Coulombe, Pierre A

2002-06-01

Onset of type I keratin 17 (K17) synthesis marks the adoption of an appendageal fate within embryonic ectoderm, and its expression persists in specific cell types within mature hair, glands, and nail. We report that K17 null mice develop severe alopecia during the first week postbirth, correlating with hair fragility, alterations in follicular histology, and apoptosis in matrix cells. These alterations are incompletely penetrant and normalize starting with the first postnatal cycle. Absence of a hair phenotype correlates with a genetic strain-dependent compensation by related keratins, including K16. These findings reveal a crucial role for K17 in the structural integrity of the first hair produced and the survival of hair-producing cells. Given that identical inherited mutations in this gene can cause either pachyonychia congenita or steatocystoma multiplex, the features of this mouse model suggest that this clinical heterogeneity arises from a cell type-specific, genetically determined compensation by related keratins.

Raman and Fourier Transform Infrared (FT-IR) Mineral to Matrix Ratios Correlate with Physical Chemical Properties of Model Compounds and Native Bone Tissue.

PubMed

Taylor, Erik A; Lloyd, Ashley A; Salazar-Lara, Carolina; Donnelly, Eve

2017-10-01

Raman and Fourier transform infrared (FT-IR) spectroscopic imaging techniques can be used to characterize bone composition. In this study, our objective was to validate the Raman mineral:matrix ratios (ν 1 PO 4 :amide III, ν 1 PO 4 :amide I, ν 1 PO 4 :Proline + hydroxyproline, ν 1 PO 4 :Phenylalanine, ν 1 PO 4 :δ CH 2 peak area ratios) by correlating them to ash fraction and the IR mineral:matrix ratio (ν 3 PO 4 :amide I peak area ratio) in chemical standards and native bone tissue. Chemical standards consisting of varying ratios of synthetic hydroxyapatite (HA) and collagen, as well as bone tissue from humans, sheep, and mice, were characterized with confocal Raman spectroscopy and FT-IR spectroscopy and gravimetric analysis. Raman and IR mineral:matrix ratio values from chemical standards increased reciprocally with ash fraction (Raman ν 1 PO 4 /Amide III: P < 0.01, R 2  = 0.966; Raman ν 1 PO 4 /Amide I: P < 0.01, R 2  = 0.919; Raman ν 1 PO 4 /Proline + Hydroxyproline: P < 0.01, R 2  = 0.976; Raman ν 1 PO 4 /Phenylalanine: P < 0.01, R 2  = 0.911; Raman ν 1 PO 4 /δ CH 2 : P < 0.01, R 2  = 0.894; IR P < 0.01, R 2  = 0.91). Fourier transform infrared mineral:matrix ratio values from native bone tissue were also similar to theoretical mineral:matrix ratio values for a given ash fraction. Raman and IR mineral:matrix ratio values were strongly correlated ( P < 0.01, R 2  = 0.82). These results were confirmed by calculating the mineral:matrix ratio for theoretical IR spectra, developed by applying the Beer-Lambert law to calculate the relative extinction coefficients of HA and collagen over the same range of wavenumbers (800-1800 cm -1 ). The results confirm that the Raman mineral:matrix bone composition parameter correlates strongly to ash fraction and to its IR counterpart. Finally, the mineral:matrix ratio values of the native bone tissue are similar to those of both chemical standards and theoretical values, confirming the biological relevance of the chemical standards and the characterization techniques.

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

PubMed

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

2017-01-01

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

Exploratory factor analysis of the Oral Health Impact Profile.

PubMed

John, M T; Reissmann, D R; Feuerstahler, L; Waller, N; Baba, K; Larsson, P; Celebić, A; Szabo, G; Rener-Sitar, K

2014-09-01

Although oral health-related quality of life (OHRQoL) as measured by the Oral Health Impact Profile (OHIP) is thought to be multidimensional, the nature of these dimensions is not known. The aim of this report was to explore the dimensionality of the OHIP using the Dimensions of OHRQoL (DOQ) Project, an international study of general population subjects and prosthodontic patients. Using the project's Learning Sample (n = 5173), we conducted an exploratory factor analysis on the 46 OHIP items not specifically referring to dentures for 5146 subjects with sufficiently complete data. The first eigenvalue (27·0) of the polychoric correlation matrix was more than ten times larger than the second eigenvalue (2·6), suggesting the presence of a dominant, higher-order general factor. Follow-up analyses with Horn's parallel analysis revealed a viable second-order, four-factor solution. An oblique rotation of this solution revealed four highly correlated factors that we named Oral Function, Oro-facial Pain, Oro-facial Appearance and Psychosocial Impact. These four dimensions and the strong general factor are two viable hypotheses for the factor structure of the OHIP. © 2014 John Wiley & Sons Ltd.

Polarization effects in cutaneous autofluorescent spectra

NASA Astrophysics Data System (ADS)

Borisova, E.; Angelova, L.; Jeliazkova, Al.; Genova, Ts.; Pavlova, E.; Troyanova, P.; Avramov, L.

2014-05-01

Used polarized light for fluorescence excitation one could obtain response related to the anisotropy features of extracellular matrix. The fluorophore anisotropy is attenuated during lesions' growth and level of such decrease could be correlated with the stage of tumor development. Our preliminary investigations are based on in vivo point-by-point measurements of excitation-emission matrices (EEM) from healthy volunteers skin on different ages and from different anatomical places using linear polarizer and analyzer for excitation and emission light detected. Measurements were made using spectrofluorimeter FluoroLog 3 (HORIBA Jobin Yvon, France) with fiber-optic probe in steady-state regime using excitation in the region of 280-440 nm. Three different situations were evaluated and corresponding excitation-emission matrices were developed - with parallel and perpendicular positions for linear polarizer and analyzer, and without polarization of excitation and fluorescence light detected from a forearm skin surface. The fluorescence spectra obtained reveal differences in spectral intensity, related to general attenuation, due to filtering effects of used polarizer/analyzer couple. Significant spectral shape changes were observed for the complex autofluorescence signal detected, which correlated with collagen and protein cross-links fluorescence, that could be addressed to the tissue extracellular matrix and general condition of the skin investigated, due to morphological destruction during lesions' growth. A correlation between volunteers' age and the fluorescence spectra detected was observed during our measurements. Our next step is to increase developed initial database and to evaluate all sources of intrinsic fluorescent polarization effects and found if they are significantly altered from normal skin to cancerous state of the tissue, this way to develop a non-invasive diagnostic tool for dermatological practice.

Wip1 is associated with tumorigenity and metastasis through MMP-2 in human intrahepatic cholangiocarcinoma

PubMed Central

Liu, Sulai; Jiang, Bo; Li, Hao; He, Zili; Lv, Pin; Peng, Chuang; Wang, Yonggang; Cheng, Wei; Xu, Zhengquan; Chen, Wei; Liu, Zhengkai; Zhang, Bao; Shen, Shengqian; Xiang, Shuanglin

2017-01-01

Wip1 has been shown to correlate with the metastasis/invasion of several tumors. This study was designed to investigate the clinical significance and biological function of Wip1 in intrahepatic cholangiocarcinoma (ICC). The expression of Wip1 was investigated in sixty human ICC biopsy samples by immunohistochemistry. Transient and stable knockdown of Wip1 in two human ICC cells (ICC-9810 and SSP25) were established using short hairpin RNA expression vector. Immunohistochemistry revealed that Wip1 was up-regulated in human ICC tissues (47/60, 78.3%). High levels of Wip1 in human ICC correlated with metastasis to the lymph metastasis (P=0.022). Genetic depletion of Wip1 in ICC cells resulted in significantly inhibited proliferation and invasion compared with controls. Most importantly, Wip1 down-regulation impaired tumor migration capacity of ICC cells in vivo. Subsequent investigations revealed that matrix metalloproteinase-2 (MMP-2) is an important target of Wip1. Consistently, in human ICC tissues, Wip1 level was positively correlated with MMP-2 expression. Taken together, our founding indicates that Wip1 may be a crucial regulator in the tumorigenicity and invasion of human ICC, Wip1 exerts its pro-invasion function at least in part through the MMP-2 signaling pathway, suggesting Wip1 as a potential therapeutic target for ICC. PMID:28915621

Robust alignment of chromatograms by statistically analyzing the shifts matrix generated by moving window fast Fourier transform cross-correlation.

PubMed

Zhang, Mingjing; Wen, Ming; Zhang, Zhi-Min; Lu, Hongmei; Liang, Yizeng; Zhan, Dejian

2015-03-01

Retention time shift is one of the most challenging problems during the preprocessing of massive chromatographic datasets. Here, an improved version of the moving window fast Fourier transform cross-correlation algorithm is presented to perform nonlinear and robust alignment of chromatograms by analyzing the shifts matrix generated by moving window procedure. The shifts matrix in retention time can be estimated by fast Fourier transform cross-correlation with a moving window procedure. The refined shift of each scan point can be obtained by calculating the mode of corresponding column of the shifts matrix. This version is simple, but more effective and robust than the previously published moving window fast Fourier transform cross-correlation method. It can handle nonlinear retention time shift robustly if proper window size has been selected. The window size is the only one parameter needed to adjust and optimize. The properties of the proposed method are investigated by comparison with the previous moving window fast Fourier transform cross-correlation and recursive alignment by fast Fourier transform using chromatographic datasets. The pattern recognition results of a gas chromatography mass spectrometry dataset of metabolic syndrome can be improved significantly after preprocessing by this method. Furthermore, the proposed method is available as an open source package at https://github.com/zmzhang/MWFFT2. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Cancer associated fibroblasts (CAFs) are activated in cutaneous basal cell carcinoma and in the peritumoural skin.

PubMed

Omland, Silje Haukali; Wettergren, Erika Elgstrand; Mollerup, Sarah; Asplund, Maria; Mourier, Tobias; Hansen, Anders Johannes; Gniadecki, Robert

2017-10-07

Cutaneous basal cell carcinoma (BCC) is the commonest cancer worldwide. BCC is locally invasive and the surrounding stromal microenvironment is pivotal for tumourigenesis. Cancer associated fibroblasts (CAFs) in the microenvironment are essential for tumour growth in a variety of neoplasms but their role in BCC is poorly understood. Material included facial BCC and control skin from the peritumoural area and from the buttocks. With next-generation sequencing (NGS) we compared mRNA expression between BCC and peritumoural skin. qRT-PCR, immunohistochemical and immunofluorescent staining were performed to validate the NGS results and to investigate CAF-related cyto-and chemokines. NGS revealed upregulation of 65 genes in BCC coding for extracellular matrix components pointing at CAF-related matrix remodeling. qRT-PCR showed increased mRNA expression of CAF markers FAP-α, PDGFR-β and prolyl-4-hydroxylase in BCC. Peritumoural skin (but not buttock skin) also exhibited high expression of PDGFR-β and prolyl-4-hydroxylase but not FAP-α. We found a similar pattern for the CAF-associated chemokines CCL17, CCL18, CCL22, CCL25, CXCL12 and IL6 with high expression in BCC and peritumoural skin but absence in buttock skin. Immunofluorescence revealed correlation between FAP-α and PDGFR-β and CXCL12 and CCL17. Matrix remodeling is the most prominent molecular feature of BCC. CAFs are present within BCC stroma and associated with increased expression of chemokines involved in tumour progression and immunosuppression (CXCL12, CCL17). Fibroblasts from chronically sun-exposed skin near tumours show gene expression patterns resembling that of CAFs, indicating that stromal fibroblasts in cancer-free surgical BCC margins exhibit a tumour promoting phenotype.

Compositional depth profiles of the type 316 stainless steel undergone the corrosion in liquid lithium using laser-induced breakdown spectroscopy

NASA Astrophysics Data System (ADS)

Li, Ying; Ke, Chuan; Liu, Xiang; Gou, Fujun; Duan, Xuru; Zhao, Yong

2017-12-01

Liquid metal lithium cause severe corrosion on the surface of metal structure material that used in the blanket and first wall of fusion device. Fast and accurate compositional depth profile measurement for the boundary layer of the corroded specimen will reveal the clues for the understanding and evaluation of the liquid lithium corrosion process as well as the involved corrosion mechanism. In this work, the feasibility of laser-induced breakdown spectroscopy for the compositional depth profile analysis of type 316 stainless steel which was corroded by liquid lithium in certain conditions was demonstrated. High sensitivity of LIBS was revealed especially for the corrosion medium Li in addition to the matrix elements of Fe, Cr, Ni and Mn by the spectral analysis of the plasma emission. Compositional depth profile analysis for the concerned elements which related to corrosion was carried out on the surface of the corroded specimen. Based on the verified local thermodynamic equilibrium shot-by-shot along the depth profile, the matrix effect was evaluated as negligible by the extracted physical parameter of the plasmas generated by each laser pulse in the longitudinal depth profile. In addition, the emission line intensity ratios were introduced to further reduce the impact on the emission line intensity variations arise from the strong inhomogeneities on the corroded surface. Compositional depth profiles for the matrix elements of Fe, Cr, Ni, Mn and the corrosion medium Li were constructed with their measured relative emission line intensities. The distribution and correlations of the concerned elements in depth profile may indicate the clues to the complicated process of composition diffusion and mass transfer. The results obtained demonstrate the potentiality of LIBS as an effective technique to perform spectrochemical measurement in the research fields of liquid metal lithium corrosion.

Five- and six-electron harmonium atoms: Highly accurate electronic properties and their application to benchmarking of approximate 1-matrix functionals

NASA Astrophysics Data System (ADS)

Cioslowski, Jerzy; Strasburger, Krzysztof

2018-04-01

Electronic properties of several states of the five- and six-electron harmonium atoms are obtained from large-scale calculations employing explicitly correlated basis functions. The high accuracy of the computed energies (including their components), natural spinorbitals, and their occupation numbers makes them suitable for testing, calibration, and benchmarking of approximate formalisms of quantum chemistry and solid state physics. In the case of the five-electron species, the availability of the new data for a wide range of the confinement strengths ω allows for confirmation and generalization of the previously reached conclusions concerning the performance of the presently known approximations for the electron-electron repulsion energy in terms of the 1-matrix that are at heart of the density matrix functional theory (DMFT). On the other hand, the properties of the three low-lying states of the six-electron harmonium atom, computed at ω = 500 and ω = 1000, uncover deficiencies of the 1-matrix functionals not revealed by previous studies. In general, the previously published assessment of the present implementations of DMFT being of poor accuracy is found to hold. Extending the present work to harmonically confined systems with even more electrons is most likely counterproductive as the steep increase in computational cost required to maintain sufficient accuracy of the calculated properties is not expected to be matched by the benefits of additional information gathered from the resulting benchmarks.

Matrix-assisted laser desorption/ionization imaging mass spectrometry for direct measurement of clozapine in rat brain tissue.

PubMed

Hsieh, Yunsheng; Casale, Roger; Fukuda, Elaine; Chen, Jiwen; Knemeyer, Ian; Wingate, Julia; Morrison, Richard; Korfmacher, Walter

2006-01-01

Matrix-assisted laser desorption/ionization hyphenated with quadrupole time-of-flight (QTOF) mass spectrometry (MS) has been used to directly determine the distribution of pharmaceuticals in rat brain tissue slices which might unravel their disposition for new drug development. Clozapine, an antipsychotic drug, and norclozapine were used as model compounds to investigate fundamental parameters such as matrix and solvent effects and irradiance dependence on MALDI intensity but also to address the issues with direct tissue imaging MS technique such as (1) uniform coating by the matrix, (2) linearity of MALDI signals, and (3) redistribution of surface analytes. The tissue sections were coated with various matrices on MALDI plates by airspray deposition prior to MS detection. MALDI signals of analytes were detected by monitoring the dissociation of the individual protonated molecules to their predominant MS/MS product ions. The matrices were chosen for tissue applications based on their ability to form a homogeneous coating of dense crystals and to yield greater sensitivity. Images revealing the spatial localization in tissue sections using MALDI-QTOF following a direct infusion of (3)H-clozapine into rat brain were found to be in good correlation with those using a radioautographic approach. The density of clozapine and its major metabolites from whole brain homogenates was further confirmed using fast high-performance liquid chromatography/tandem mass spectrometry (HPLC-MS/MS) procedures. Copyright (c) 2006 John Wiley & Sons, Ltd.

Microstructure and wear characterization of aluminum matrix composites reinforced with industrial waste fly ash particulates synthesized by friction stir processing

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

Dinaharan, I., E-mail: dinaweld2009@gmail.com

Fly ash (FA) is a waste product of coal combustion in thermal power plants which is available in massive quantities all over the world causing land pollution. This paper reports the characterization of AA6061 aluminum matrix composites (AMCs) reinforced with FA particles synthesized using friction stir processing (FSP). The volume fraction of FA particles was varied from 0 to 18 in steps of 6. The prepared AMCs were characterized using optical microscopy (OM), scanning electron microscopy (SEM) and electron backscattered diagram (EBSD). The wear rate was estimated using a pin-on-disc wear apparatus. FA particles were observed to be distributed homogeneouslymore » in the AMC irrespective of the location within the stir zone. The EBSD micrographs revealed remarkable grain refinement in the AMC. The incorporation of FA particles enhanced the microhardness and wear resistance of the AMC. The strengthening mechanisms of the AMC were discussed and correlated to the observed microstructures. The wear mechanisms were identified by characterizing the wear debris and worn surfaces. - Highlights: •Industrial waste fly ash was used to produce aluminum matrix composites. •Friction stir processing was used to produce AA6061/Fly Ash composite. •Fly ash particles refined the grains of aluminum matrix. •Fly ash particles enhanced the hardness and wear resistance. •Successful utilization of fly ash to make aluminum composites reduces land pollution.« less

Towards the development of new phosphors with reduced content of rare earth elements: Structural and optical characterization of Ce:Tb: Al{sub 2}SiO{sub 5}

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

Chiriu, D.; Stagi, L.; Carbonaro, C.M.

2016-05-15

Highlights: • A new promising inert matrix as host of luminescent ions is proposed. • Al2SiO5 matrix is free from Rare earths (critical raw materials). • Doping the matrix with Ce and Tb we obtain an efficient green emitter. • Cerium acts as sensitizer for Terbium emission. - Abstract: A new promising inert matrix as host of luminescent ions is proposed. Al2SiO5 samples, doped with rare earths (Ce, Tb single doped and co-doped) are proposed as good prospect for the development of new UV–vis converter with reduced content of rare earths elements. Structural characterization by Raman, XRD spectroscopy and TEMmore » imaging reveals the sillimanite phase and nano sized dimension of the investigated powders. Optical characterization by steady time and time resolved emission spectroscopy for the single doped and co-doped samples allows to identify an efficient energy transfer from Ce to Tb ions under near UV excitation wavelength. The intense green emission observed in the Ce:Tb co-doped Al2SiO5 system suggests its potential application as efficient blue pumped green emitter phosphor to be exploited for white LED: to this purpose we tested the compound in combination with a red emitting doping ion recording for Ce:Tb:Cr:ASO system a correlated color temperature of 6720 K.« less

Matrix elements of explicitly correlated Gaussian basis functions with arbitrary angular momentum

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

Joyce, Tennesse; Varga, Kálmán

2016-05-14

A new algorithm for calculating the Hamiltonian matrix elements with all-electron explicitly correlated Gaussian functions for quantum-mechanical calculations of atoms with arbitrary angular momentum is presented. The calculations are checked on several excited states of three and four electron systems. The presented formalism can be used as unified framework for high accuracy calculations of properties of small atoms and molecules.

Targeting invadopodia-mediated breast cancer metastasis by using ABL kinase inhibitors

PubMed Central

Meirson, Tomer; Genna, Alessandro; Lukic, Nikola; Makhnii, Tetiana; Alter, Joel; Sharma, Ved P.; Wang, Yarong; Samson, Abraham O.; Condeelis, John S.; Gil-Henn, Hava

2018-01-01

Metastatic dissemination of cancer cells from the primary tumor and their spread to distant sites in the body is the leading cause of mortality in breast cancer patients. While researchers have identified treatments that shrink or slow metastatic tumors, no treatment that permanently eradicates metastasis exists at present. Here, we show that the ABL kinase inhibitors imatinib, nilotinib, and GNF-5 impede invadopodium precursor formation and cortactin-phosphorylation dependent invadopodium maturation, leading to decreased actin polymerization in invadopodia, reduced extracellular matrix degradation, and impaired matrix proteolysis-dependent invasion. Using a mouse xenograft model we demonstrate that, while primary tumor size is not affected by ABL kinase inhibitors, the in vivo matrix metalloproteinase (MMP) activity, tumor cell invasion, and consequent spontaneous metastasis to lungs are significantly impaired in inhibitor-treated mice. Further proteogenomic analysis of breast cancer patient databases revealed co-expression of the Abl-related gene (Arg) and cortactin across all hormone- and human epidermal growth factor receptor 2 (HER2)-receptor status tumors, which correlates synergistically with distant metastasis and poor patient prognosis. Our findings establish a prognostic value for Arg and cortactin as predictors of metastatic dissemination and suggest that therapeutic inhibition of ABL kinases may be used for blocking breast cancer metastasis. PMID:29774130

Effective correlator for RadioAstron project

NASA Astrophysics Data System (ADS)

Sergeev, Sergey

This paper presents the implementation of programme FX-correlator for Very Long Baseline Interferometry, adapted for the project "RadioAstron". Software correlator implemented for heterogeneous computing systems using graphics accelerators. It is shown that for the task interferometry implementation of the graphics hardware has a high efficiency. The host processor of heterogeneous computing system, performs the function of forming the data flow for graphics accelerators, the number of which corresponds to the number of frequency channels. So, for the Radioastron project, such channels is seven. Each accelerator is perform correlation matrix for all bases for a single frequency channel. Initial data is converted to the floating-point format, is correction for the corresponding delay function and computes the entire correlation matrix simultaneously. Calculation of the correlation matrix is performed using the sliding Fourier transform. Thus, thanks to the compliance of a solved problem for architecture graphics accelerators, managed to get a performance for one processor platform Kepler, which corresponds to the performance of this task, the computing cluster platforms Intel on four nodes. This task successfully scaled not only on a large number of graphics accelerators, but also on a large number of nodes with multiple accelerators.

Exchange-correlation approximations for reduced-density-matrix-functional theory at finite temperature: Capturing magnetic phase transitions in the homogeneous electron gas

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

Baldsiefen, Tim; Cangi, Attila; Eich, F. G.

Here, we derive an intrinsically temperature-dependent approximation to the correlation grand potential for many-electron systems in thermodynamical equilibrium in the context of finite-temperature reduced-density-matrix-functional theory (FT-RDMFT). We demonstrate its accuracy by calculating the magnetic phase diagram of the homogeneous electron gas. We compare it to known limits from highly accurate quantum Monte Carlo calculations as well as to phase diagrams obtained within existing exchange-correlation approximations from density functional theory and zero-temperature RDMFT.

Exchange-correlation approximations for reduced-density-matrix-functional theory at finite temperature: Capturing magnetic phase transitions in the homogeneous electron gas

DOE PAGES

Baldsiefen, Tim; Cangi, Attila; Eich, F. G.; ...

2017-12-18

Here, we derive an intrinsically temperature-dependent approximation to the correlation grand potential for many-electron systems in thermodynamical equilibrium in the context of finite-temperature reduced-density-matrix-functional theory (FT-RDMFT). We demonstrate its accuracy by calculating the magnetic phase diagram of the homogeneous electron gas. We compare it to known limits from highly accurate quantum Monte Carlo calculations as well as to phase diagrams obtained within existing exchange-correlation approximations from density functional theory and zero-temperature RDMFT.

Correlation, Cost Risk, and Geometry

NASA Technical Reports Server (NTRS)

Dean, Edwin B.

1992-01-01

The geometric viewpoint identifies the choice of a correlation matrix for the simulation of cost risk with the pairwise choice of data vectors corresponding to the parameters used to obtain cost risk. The correlation coefficient is the cosine of the angle between the data vectors after translation to an origin at the mean and normalization for magnitude. Thus correlation is equivalent to expressing the data in terms of a non orthogonal basis. To understand the many resulting phenomena requires the use of the tensor concept of raising the index to transform the measured and observed covariant components into contravariant components before vector addition can be applied. The geometric viewpoint also demonstrates that correlation and covariance are geometric properties, as opposed to purely statistical properties, of the variates. Thus, variates from different distributions may be correlated, as desired, after selection from independent distributions. By determining the principal components of the correlation matrix, variates with the desired mean, magnitude, and correlation can be generated through linear transforms which include the eigenvalues and the eigenvectors of the correlation matrix. The conversion of the data to a non orthogonal basis uses a compound linear transformation which distorts or stretches the data space. Hence, the correlated data does not have the same properties as the uncorrelated data used to generate it. This phenomena is responsible for seemingly strange observations such as the fact that the marginal distributions of the correlated data can be quite different from the distributions used to generate the data. The joint effect of statistical distributions and correlation remains a fertile area for further research. In terms of application to cost estimating, the geometric approach demonstrates that the estimator must have data and must understand that data in order to properly choose the correlation matrix appropriate for a given estimate. There is a general feeling by employers and managers that the field of cost requires little technical or mathematical background. Contrary to that opinion, this paper demonstrates that a background in mathematics equivalent to that needed for typical engineering and scientific disciplines at the masters or doctorate level is appropriate within the field of cost risk.

Visualization of newt aragonitic otoconial matrices using transmission electron microscopy

NASA Technical Reports Server (NTRS)

Steyger, P. S.; Wiederhold, M. L.

1995-01-01

Otoconia are calcified protein matrices within the gravity-sensing organs of the vertebrate vestibular system. These protein matrices are thought to originate from the supporting or hair cells in the macula during development. Previous studies of mammalian calcitic, barrel-shaped otoconia revealed an organized protein matrix consisting of a thin peripheral layer, a well-defined organic core and a flocculent matrix inbetween. No studies have reported the microscopic organization of the aragonitic otoconial matrix, despite its protein characterization. Pote et al. (1993b) used densitometric methods and inferred that prismatic (aragonitic) otoconia have a peripheral protein distribution, compared to that described for the barrel-shaped, calcitic otoconia of birds, mammals, and the amphibian utricle. By using tannic acid as a negative stain, we observed three kinds of organic matrices in preparations of fixed, decalcified saccular otoconia from the adult newt: (1) fusiform shapes with a homogenous electron-dense matrix; (2) singular and multiple strands of matrix; and (3) more significantly, prismatic shapes outlined by a peripheral organic matrix. These prismatic shapes remain following removal of the gelatinous matrix, revealing an internal array of organic matter. We conclude that prismatic otoconia have a largely peripheral otoconial matrix, as inferred by densitometry.

Random matrix theory for analyzing the brain functional network in attention deficit hyperactivity disorder

NASA Astrophysics Data System (ADS)

Wang, Rong; Wang, Li; Yang, Yong; Li, Jiajia; Wu, Ying; Lin, Pan

2016-11-01

Attention deficit hyperactivity disorder (ADHD) is the most common childhood neuropsychiatric disorder and affects approximately 6 -7 % of children worldwide. Here, we investigate the statistical properties of undirected and directed brain functional networks in ADHD patients based on random matrix theory (RMT), in which the undirected functional connectivity is constructed based on correlation coefficient and the directed functional connectivity is measured based on cross-correlation coefficient and mutual information. We first analyze the functional connectivity and the eigenvalues of the brain functional network. We find that ADHD patients have increased undirected functional connectivity, reflecting a higher degree of linear dependence between regions, and increased directed functional connectivity, indicating stronger causality and more transmission of information among brain regions. More importantly, we explore the randomness of the undirected and directed functional networks using RMT. We find that for ADHD patients, the undirected functional network is more orderly than that for normal subjects, which indicates an abnormal increase in undirected functional connectivity. In addition, we find that the directed functional networks are more random, which reveals greater disorder in causality and more chaotic information flow among brain regions in ADHD patients. Our results not only further confirm the efficacy of RMT in characterizing the intrinsic properties of brain functional networks but also provide insights into the possibilities RMT offers for improving clinical diagnoses and treatment evaluations for ADHD patients.

A preliminary evaluation of myoelectrical energy distribution of the front neck muscles in pharyngeal phase during normal swallowing.

PubMed

Mingxing Zhu; Wanzhang Yang; Samuel, Oluwarotimi Williams; Yun Xiang; Jianping Huang; Haiqing Zou; Guanglin Li

2016-08-01

Pharyngeal phase is a central hub of swallowing in which food bolus pass through from the oral cavity to the esophageal. Proper understanding of the muscular activities in the pharyngeal phase is useful for assessing swallowing function and the occurrence of dysphagia in humans. In this study, high-density (HD) surface electromyography (sEMG) was used to study the muscular activities in the pharyngeal phase during swallowing tasks involving three healthy male subjects. The root mean square (RMS) of the HD sEMG data was computed by using a series of segmented windows as myoelectrical energy. And the RMS of each window covering all channels (16×5) formed a matrix. During the pharyngeal phase of swallowing, three of the matrixes were chosen and normalized to obtain the HD energy maps and the statistical parameter. The maps across different viscosity levels offered the energy distribution which showed the muscular activities of the left and right sides of the front neck muscles. In addition, the normalized average RMS (NARE) across different viscosity levels revealed a left-right significant correlation (r=0.868±0.629, p<;0.01) quantitatively, while it showed even stronger correlation when swallowing water. This pilot study suggests that HD sEMG would be a potential tool to evaluate muscular activities in pharyngeal phase during normal swallowing. Also, it might provide useful information for dysphagia diagnosis.

In vitro culture increases mechanical stability of human tissue engineered cartilage constructs by prevention of microscale scaffold buckling.

PubMed

Middendorf, Jill M; Shortkroff, Sonya; Dugopolski, Caroline; Kennedy, Stephen; Siemiatkoski, Joseph; Bartell, Lena R; Cohen, Itai; Bonassar, Lawrence J

2017-11-07

Many studies have measured the global compressive properties of tissue engineered (TE) cartilage grown on porous scaffolds. Such scaffolds are known to exhibit strain softening due to local buckling under loading. As matrix is deposited onto these scaffolds, the global compressive properties increase. However the relationship between the amount and distribution of matrix in the scaffold and local buckling is unknown. To address this knowledge gap, we studied how local strain and construct buckling in human TE constructs changes over culture times and GAG content. Confocal elastography techniques and digital image correlation (DIC) were used to measure and record buckling modes and local strains. Receiver operating characteristic (ROC) curves were used to quantify construct buckling. The results from the ROC analysis were placed into Kaplan-Meier survival function curves to establish the probability that any point in a construct buckled. These analysis techniques revealed the presence of buckling at early time points, but bending at later time points. An inverse correlation was observed between the probability of buckling and the total GAG content of each construct. This data suggests that increased GAG content prevents the onset of construct buckling and improves the microscale compressive tissue properties. This increase in GAG deposition leads to enhanced global compressive properties by prevention of microscale buckling. Copyright © 2017 Elsevier Ltd. All rights reserved.

Matrix isolation studies of hydrogen bonding - An historical perspective

NASA Astrophysics Data System (ADS)

Barnes, Austin J.

2018-07-01

An historical introduction sets matrix isolation in perspective with other spectroscopic techniques for studying hydrogen-bonded complexes. This is followed by detailed accounts of various aspects of hydrogen-bonded complexes that have been studied using matrix isolation spectroscopy: Matrix effects: stabilisation of complexes. Strongly hydrogen-bonded molecular complexes: the vibrational correlation diagram. Anomalous spectra: the Ratajczak-Yaremko model. Metastable complexes. Csbnd H hydrogen bonding and blue shifting hydrogen bonds.

Structure-performance relationships of phenyl cinnamic acid derivatives as MALDI-MS matrices for sulfatide detection.

PubMed

Tambe, Suparna; Blott, Henning; Fülöp, Annabelle; Spang, Nils; Flottmann, Dirk; Bräse, Stefan; Hopf, Carsten; Junker, Hans-Dieter

2017-02-01

A key aspect for the further development of matrix-assisted laser desorption ionization (MALDI)-mass spectrometry (MS) is a better understanding of the working principles of MALDI matrices. To address this issue, a chemical compound library of 59 structurally related cinnamic acid derivatives was synthesized. Potential MALDI matrices were evaluated with sulfatides, a class of anionic lipids which are abundant in complex brain lipid mixtures. For each matrix relative mean S/N ratios of sulfatides were determined against 9-aminoacridine as a reference matrix using negative ion mass spectrometry with 355 and 337 nm laser systems. The comparison of matrix features with their corresponding relative mean S/N ratios for sulfatide detection identified correlations between matrix substitution patterns, their chemical functionality, and their MALDI-MS performance. Crystal structures of six selected matrices provided structural insight in hydrogen bond interactions in the solid state. Principal component analysis allowed the additional identification of correlation trends between structural and physical matrix properties like number of exchangeable protons at the head group, MW, logP, UV-Vis, and sulfatide detection sensitivity. Graphical abstract Design, synthesis and mass spectrometric evaluation of MALDI-MS matrix compound libraries allows the identification of matrix structure - MALDI-MS performance relationships using multivariate statistics as a tool.

Combining Correlation Matrices: Simulation Analysis of Improved Fixed-Effects Methods

ERIC Educational Resources Information Center

Hafdahl, Adam R.

2007-01-01

The originally proposed multivariate meta-analysis approach for correlation matrices--analyze Pearson correlations, with each study's observed correlations replacing their population counterparts in its conditional-covariance matrix--performs poorly. Two refinements are considered: Analyze Fisher Z-transformed correlations, and substitute better…

Random matrix theory analysis of cross-correlations in the US stock market: Evidence from Pearson’s correlation coefficient and detrended cross-correlation coefficient

NASA Astrophysics Data System (ADS)

Wang, Gang-Jin; Xie, Chi; Chen, Shou; Yang, Jiao-Jiao; Yang, Ming-Yan

2013-09-01

In this study, we first build two empirical cross-correlation matrices in the US stock market by two different methods, namely the Pearson’s correlation coefficient and the detrended cross-correlation coefficient (DCCA coefficient). Then, combining the two matrices with the method of random matrix theory (RMT), we mainly investigate the statistical properties of cross-correlations in the US stock market. We choose the daily closing prices of 462 constituent stocks of S&P 500 index as the research objects and select the sample data from January 3, 2005 to August 31, 2012. In the empirical analysis, we examine the statistical properties of cross-correlation coefficients, the distribution of eigenvalues, the distribution of eigenvector components, and the inverse participation ratio. From the two methods, we find some new results of the cross-correlations in the US stock market in our study, which are different from the conclusions reached by previous studies. The empirical cross-correlation matrices constructed by the DCCA coefficient show several interesting properties at different time scales in the US stock market, which are useful to the risk management and optimal portfolio selection, especially to the diversity of the asset portfolio. It will be an interesting and meaningful work to find the theoretical eigenvalue distribution of a completely random matrix R for the DCCA coefficient because it does not obey the Marčenko-Pastur distribution.

Empirical data and the variance-covariance matrix for the 1969 Smithsonian Standard Earth (2)

NASA Technical Reports Server (NTRS)

Gaposchkin, E. M.

1972-01-01

The empirical data used in the 1969 Smithsonian Standard Earth (2) are presented. The variance-covariance matrix, or the normal equations, used for correlation analysis, are considered. The format and contents of the matrix, available on magnetic tape, are described and a sample printout is given.

Regulation of matrix metalloproteinases (MMPs) expression and secretion in MDA-MB-231 breast cancer cells by LIM and SH3 protein 1 (LASP1).

PubMed

Endres, Marcel; Kneitz, Susanne; Orth, Martin F; Perera, Ruwan K; Zernecke, Alma; Butt, Elke

2016-09-27

The process of tumor invasion requires degradation of extracellular matrix by proteolytic enzymes. Cancer cells form protrusive invadopodia, which produce and release matrix metalloproteinases (MMPs) to degrade the basement membrane thereby enabling metastasis. We investigated the effect of LASP1, a newly identified protein in invadopodia, on expression, secretion and activation of MMPs in invasive breast tumor cell lines.By analyzing microarray data of in-house generated control and LASP1-depleted MDA-MB-231 breast cancer cells, we observed downregulation of MMP1, -3 and -9 upon LASP1 depletion. This was confirmed by Western blot analysis. Conversely, rescue experiments restored in part MMP expression and secretion. The regulatory effect of LASP1 on MMP expression was also observed in BT-20 breast cancer cells as well as in prostate and bladder cancer cell lines.In line with bioinformatic FunRich analysis of our data, which mapped a high regulation of transcription factors by LASP1, public microarray data analysis detected a correlation between high LASP1 expression and enhanced c-Fos levels, a protein that is part of the transcription factor AP-1 and known to regulate MMP expression. Compatibly, in luciferase reporter assays, AP-1 showed a decreased transcriptional activity after LASP1 knockdown.Zymography assays and Western blot analysis revealed an additional promotion of MMP secretion into the extracellular matrix by LASP1, thus, most likely, altering the microenvironment during cancer progression.The newly identified role of LASP1 in regulating matrix degradation by affecting MMP transcription and secretion elucidated the migratory potential of LASP1 overexpressing aggressive tumor cells in earlier studies.

Matrix Rigidity Regulates Cancer Cell Growth and Cellular Phenotype

PubMed Central

Tilghman, Robert W.; Cowan, Catharine R.; Mih, Justin D.; Koryakina, Yulia; Gioeli, Daniel; Slack-Davis, Jill K.; Blackman, Brett R.; Tschumperlin, Daniel J.; Parsons, J. Thomas

2010-01-01

Background The mechanical properties of the extracellular matrix have an important role in cell growth and differentiation. However, it is unclear as to what extent cancer cells respond to changes in the mechanical properties (rigidity/stiffness) of the microenvironment and how this response varies among cancer cell lines. Methodology/Principal Findings In this study we used a recently developed 96-well plate system that arrays extracellular matrix-conjugated polyacrylamide gels that increase in stiffness by at least 50-fold across the plate. This plate was used to determine how changes in the rigidity of the extracellular matrix modulate the biological properties of tumor cells. The cell lines tested fall into one of two categories based on their proliferation on substrates of differing stiffness: “rigidity dependent” (those which show an increase in cell growth as extracellular rigidity is increased), and “rigidity independent” (those which grow equally on both soft and stiff substrates). Cells which grew poorly on soft gels also showed decreased spreading and migration under these conditions. More importantly, seeding the cell lines into the lungs of nude mice revealed that the ability of cells to grow on soft gels in vitro correlated with their ability to grow in a soft tissue environment in vivo. The lung carcinoma line A549 responded to culture on soft gels by expressing the differentiated epithelial marker E-cadherin and decreasing the expression of the mesenchymal transcription factor Slug. Conclusions/Significance These observations suggest that the mechanical properties of the matrix environment play a significant role in regulating the proliferation and the morphological properties of cancer cells. Further, the multiwell format of the soft-plate assay is a useful and effective adjunct to established 3-dimensional cell culture models. PMID:20886123

Low-temperature matrix effects on orientational motion of Methyl radical trapped in gas solids: Angular tunneling vs. libration

NASA Astrophysics Data System (ADS)

Dmitriev, Yurij A.; Zelenetckii, Ilia A.; Benetis, Nikolas P.

2018-05-01

EPR investigation of the lineshape of matrix -isolated methyl radical, CH3, spectra recorded in solid N2O and CO2 was carried out. Reversible temperature-dependent line width anisotropy was observed in both matrices. This effect is a fingerprint of the extra-slow radical rotation about the in-plane C2 axes. The rotation was found to be anisotropic and closely correlated to the orientational dynamics of the matrix molecules. It was suggested that a recently discovered "hoping precession" effect of matrix molecules in solid CO2 is a common feature of matrices of the linear molecules CO, N2O, and CO2. A new low-temperature matrix effect, referred to as "libration trap", was proposed which accounts for the changing CH3 reorientational motion about the radical C3-axis from rotation to libration. Temperature dependence of the intensity of the EPR satellites produced by these nonrotating-but librating methyls was presented. This allowed for a rough estimation of the rotation hindering potential due to correlation mismatch between the radical and the nearest matrix molecules' librations.

S-matrix analysis of the baryon electric charge correlation

NASA Astrophysics Data System (ADS)

Lo, Pok Man; Friman, Bengt; Redlich, Krzysztof; Sasaki, Chihiro

2018-03-01

We compute the correlation of the net baryon number with the electric charge (χBQ) for an interacting hadron gas using the S-matrix formulation of statistical mechanics. The observable χBQ is particularly sensitive to the details of the pion-nucleon interaction, which are consistently incorporated in the current scheme via the empirical scattering phase shifts. Comparing to the recent lattice QCD studies in the (2 + 1)-flavor system, we find that the natural implementation of interactions and the proper treatment of resonances in the S-matrix approach lead to an improved description of the lattice data over that obtained in the hadron resonance gas model.

Efficient Storage Scheme of Covariance Matrix during Inverse Modeling

NASA Astrophysics Data System (ADS)

Mao, D.; Yeh, T. J.

2013-12-01

During stochastic inverse modeling, the covariance matrix of geostatistical based methods carries the information about the geologic structure. Its update during iterations reflects the decrease of uncertainty with the incorporation of observed data. For large scale problem, its storage and update cost too much memory and computational resources. In this study, we propose a new efficient storage scheme for storage and update. Compressed Sparse Column (CSC) format is utilized to storage the covariance matrix, and users can assign how many data they prefer to store based on correlation scales since the data beyond several correlation scales are usually not very informative for inverse modeling. After every iteration, only the diagonal terms of the covariance matrix are updated. The off diagonal terms are calculated and updated based on shortened correlation scales with a pre-assigned exponential model. The correlation scales are shortened by a coefficient, i.e. 0.95, every iteration to show the decrease of uncertainty. There is no universal coefficient for all the problems and users are encouraged to try several times. This new scheme is tested with 1D examples first. The estimated results and uncertainty are compared with the traditional full storage method. In the end, a large scale numerical model is utilized to validate this new scheme.

Tensor models, Kronecker coefficients and permutation centralizer algebras

NASA Astrophysics Data System (ADS)

Geloun, Joseph Ben; Ramgoolam, Sanjaye

2017-11-01

We show that the counting of observables and correlators for a 3-index tensor model are organized by the structure of a family of permutation centralizer algebras. These algebras are shown to be semi-simple and their Wedderburn-Artin decompositions into matrix blocks are given in terms of Clebsch-Gordan coefficients of symmetric groups. The matrix basis for the algebras also gives an orthogonal basis for the tensor observables which diagonalizes the Gaussian two-point functions. The centres of the algebras are associated with correlators which are expressible in terms of Kronecker coefficients (Clebsch-Gordan multiplicities of symmetric groups). The color-exchange symmetry present in the Gaussian model, as well as a large class of interacting models, is used to refine the description of the permutation centralizer algebras. This discussion is extended to a general number of colors d: it is used to prove the integrality of an infinite family of number sequences related to color-symmetrizations of colored graphs, and expressible in terms of symmetric group representation theory data. Generalizing a connection between matrix models and Belyi maps, correlators in Gaussian tensor models are interpreted in terms of covers of singular 2-complexes. There is an intriguing difference, between matrix and higher rank tensor models, in the computational complexity of superficially comparable correlators of observables parametrized by Young diagrams.

Imaging of downward-looking linear array SAR using three-dimensional spatial smoothing MUSIC algorithm

NASA Astrophysics Data System (ADS)

Zhang, Siqian; Kuang, Gangyao

2014-10-01

In this paper, a novel three-dimensional imaging algorithm of downward-looking linear array SAR is presented. To improve the resolution, multiple signal classification (MUSIC) algorithm has been used. However, since the scattering centers are always correlated in real SAR system, the estimated covariance matrix becomes singular. To address the problem, a three-dimensional spatial smoothing method is proposed in this paper to restore the singular covariance matrix to a full-rank one. The three-dimensional signal matrix can be divided into a set of orthogonal three-dimensional subspaces. The main idea of the method is based on extracting the array correlation matrix as the average of all correlation matrices from the subspaces. In addition, the spectral height of the peaks contains no information with regard to the scattering intensity of the different scattering centers, thus it is difficulty to reconstruct the backscattering information. The least square strategy is used to estimate the amplitude of the scattering center in this paper. The above results of the theoretical analysis are verified by 3-D scene simulations and experiments on real data.

On the Feynman-Hellmann theorem in quantum field theory and the calculation of matrix elements

DOE PAGES

Bouchard, Chris; Chang, Chia Cheng; Kurth, Thorsten; ...

2017-07-12

In this paper, the Feynman-Hellmann theorem can be derived from the long Euclidean-time limit of correlation functions determined with functional derivatives of the partition function. Using this insight, we fully develop an improved method for computing matrix elements of external currents utilizing only two-point correlation functions. Our method applies to matrix elements of any external bilinear current, including nonzero momentum transfer, flavor-changing, and two or more current insertion matrix elements. The ability to identify and control all the systematic uncertainties in the analysis of the correlation functions stems from the unique time dependence of the ground-state matrix elements and the fact that all excited states and contact terms are Euclidean-time dependent. We demonstrate the utility of our method with a calculation of the nucleon axial charge using gradient-flowed domain-wall valence quarks on themore » $$N_f=2+1+1$$ MILC highly improved staggered quark ensemble with lattice spacing and pion mass of approximately 0.15 fm and 310 MeV respectively. We show full control over excited-state systematics with the new method and obtain a value of $$g_A = 1.213(26)$$ with a quark-mass-dependent renormalization coefficient.« less

Development and experimental design of a novel controlled-release matrix tablet formulation for indapamide hemihydrate.

PubMed

Antovska, Packa; Ugarkovic, Sonja; Petruševski, Gjorgji; Stefanova, Bosilka; Manchevska, Blagica; Petkovska, Rumenka; Makreski, Petre

2017-11-01

Development, experimental design and in vitro in vivo correlation (IVIVC) of controlled-release matrix formulation. Development of novel oral controlled delivery system for indapamide hemihydrate, optimization of the formulation by experimental design and evaluation regarding IVIVC on a pilot scale batch as a confirmation of a well-established formulation. In vitro dissolution profiles of controlled-release tablets of indapamide hemihydrate from four different matrices had been evaluated in comparison to the originator's product Natrilix (Servier) as a direction for further development and optimization of a hydroxyethylcellulose-based matrix controlled-release formulation. A central composite factorial design had been applied for the optimization of a chosen controlled-release tablet formulation. The controlled-release tablets with appropriate physical and technological properties had been obtained with a matrix: binder concentration variations in the range: 20-40w/w% for the matrix and 1-3w/w% for the binder. The experimental design had defined the design space for the formulation and was prerequisite for extraction of a particular formulation that would be a subject for transfer on pilot scale and IVIV correlation. The release model of the optimized formulation has shown best fit to the zero order kinetics depicted with the Hixson-Crowell erosion-dependent mechanism of release. Level A correlation was obtained.

Development of extracellular matrix in chick paravertebral sympathetic ganglia.

PubMed

Luckenbill-Edds, L

1986-08-01

Alcian blue staining coupled with enzyme digestion or critical electrolyte staining revealed differences in the development of extracellular matrix (ECM) within sympathetic ganglia compared with the surrounding capsule. On day 5 of chick development (Hamburger-Hamilton stage 26) only hyaluronic acid (HA) could be detected in the ECM surrounding condensing primary ganglia. By day 7 (st 30) the ganglionic capsule contained HA, as well as sulfated glycosaminoglycans (GAGs), and this pattern continued into the adult stage. During the later stages of embryonic life (st 41-45) satellite cells appear, showing fine structural characteristics that point to their role in the secretion of intraganglionic ECM. Only during these stages could ECM be detected histochemically within ganglia, the same stages (days 15-19) when routine electron microscopic methods reveal collagen fibrils embedded in a granular ground substance. Thus, the intraganglionic environment appears as a separate compartment free of detectable amounts of GAG until late embryonic stages when ECM is secreted around satellite cells. This developmental pattern could represent a role of ECM in the histological stabilization of ganglia during the late stages of differentiation, since the appearance of intraganglionic ECM is correlated with the appearance of small dense-cored vesicles characteristic of adult neurons. The developmental pattern of ECM in differentiating sympathetic ganglia is compared with that of other tissues that undergo condensation and morphogenesis.

Detection of altered extracellular matrix in surface layers of unstable carotid plaque: an optical spectroscopy, birefringence and microarray genetic analysis.

PubMed

Korol, Renee M; Canham, Peter B; Liu, Li; Viswanathan, Kasinath; Ferguson, Gary G; Hammond, Rob R; Finlay, Helen M; Baker, Henry V; Lopez, Cecilia; Lucas, Alexandra R

2011-01-01

Erosion and rupture of surface layers in atherosclerotic plaque can cause heart attack and stroke; however, changes in luminal surface composition are incompletely defined. Laser-induced fluorescence spectroscopy (LIFS), with limited tissue penetration, was used to investigate the surface of unstable carotid plaque and correlated with microscopy, birefringence and gene expression. Arterial matrix collagens I, III and elastin were assessed in unstable plaques (n = 25) and reference left internal mammary arteries (LIMA, n = 10). LIFS in addition to selective histological staining with picrosirius red, Movat pentachrome and immunostaining revealed decreased elastin and increased collagen I and III (P < 0.05) in carotid plaque when compared with LIMA. Within plaque, collagen I was elevated in the internal carotid region versus the common carotid region. Polarized light microscopy detected layers of aligned collagen and associated mechanical rigidity of the fibrous cap. Microarray analysis of three carotid and three LIMA specimens confirmed up-regulation of collagen I, III and IV, lysyl oxidase and MMP-12. In conclusion, LIFS analysis coupled with microscopy revealed marked regional differences in collagen I, III and elastin in surface layers of carotid plaque; indicative of plaque instability. Birefringence measurements demonstrated mechanical rigidity and weakening of the fibrous cap with complementary changes in ECM gene expression. © 2011 The Authors. Photochemistry and Photobiology © 2011 The American Society of Photobiology.

Characterization of cancer and normal tissue fluorescence through wavelet transform and singular value decomposition

NASA Astrophysics Data System (ADS)

Gharekhan, Anita H.; Biswal, Nrusingh C.; Gupta, Sharad; Pradhan, Asima; Sureshkumar, M. B.; Panigrahi, Prasanta K.

2008-02-01

The statistical and characteristic features of the polarized fluorescence spectra from cancer, normal and benign human breast tissues are studied through wavelet transform and singular value decomposition. The discrete wavelets enabled one to isolate high and low frequency spectral fluctuations, which revealed substantial randomization in the cancerous tissues, not present in the normal cases. In particular, the fluctuations fitted well with a Gaussian distribution for the cancerous tissues in the perpendicular component. One finds non-Gaussian behavior for normal and benign tissues' spectral variations. The study of the difference of intensities in parallel and perpendicular channels, which is free from the diffusive component, revealed weak fluorescence activity in the 630nm domain, for the cancerous tissues. This may be ascribable to porphyrin emission. The role of both scatterers and fluorophores in the observed minor intensity peak for the cancer case is experimentally confirmed through tissue-phantom experiments. Continuous Morlet wavelet also highlighted this domain for the cancerous tissue fluorescence spectra. Correlation in the spectral fluctuation is further studied in different tissue types through singular value decomposition. Apart from identifying different domains of spectral activity for diseased and non-diseased tissues, we found random matrix support for the spectral fluctuations. The small eigenvalues of the perpendicular polarized fluorescence spectra of cancerous tissues fitted remarkably well with random matrix prediction for Gaussian random variables, confirming our observations about spectral fluctuations in the wavelet domain.

Prognostic impact of a compartment-specific angiogenic marker profile in patients with pancreatic cancer.

PubMed

Kahlert, Christoph; Fiala, Maria; Musso, Gabriel; Halama, Niels; Keim, Sophia; Mazzone, Massimiliano; Lasitschka, Felix; Pecqueux, Mathieu; Klupp, Fee; Schmidt, Thomas; Rahbari, Nuh; Schölch, Sebastian; Pilarsky, Christian; Ulrich, Alexis; Schneider, Martin; Weitz, Juergen; Koch, Moritz

2014-12-30

Pancreatic cancer consists of a heterogenous bulk of tumor cells and stroma cells which contribute to tumor progression by releasing angiogenic factors. Those factors can be detected as circulating serum factors. We performed a compartment-specific analysis of tumor-derived and stroma-derived angiogenic factors to identify biomarkers and molecular targets for the treatment of pancreatic cancer. Kryo-frozen tissue from primary ductal adenocarcinomas (n = 51) was laser-microdissected to isolate tumor and stroma tissue. Expression of 17 angiogenic factors (angiopoietin-2, follistatin, GCSF, HGF, interleukin-8, leptin, PDGF-BB, PECAM-1, VEGF, matrix metalloproteinase -1, -2, -3, -7, -9, -10, -12, and -13) was analyzed using a multiplex elisa assay for tissue-derived proteins and corresponding serum. Our study reveals a compartment-specific expression profile for several angiogenic factors and matrix metalloproteinases. ROC analysis of corresponding serum samples reveals MMP-7 and MMP-12 as strong classifiers for the diagnosis of patients with pancreatic cancer vs. healthy control donors. High expression of tumor-derived PDGF-BB and MMP-1 correlates with prolonged survival in univariate and multivariate analysis. In conclusion, a distinct expression patterns for angiogenic cytokines and MMPs in pancreatic cancer and surrounding stroma may implicate them as novel targets for cancer treatment. Tumor-derived PDGF-BB and MMP-1 are significant and independent prognostic markers for poor survival.

Sequential Dictionary Learning From Correlated Data: Application to fMRI Data Analysis.

PubMed

Seghouane, Abd-Krim; Iqbal, Asif

2017-03-22

Sequential dictionary learning via the K-SVD algorithm has been revealed as a successful alternative to conventional data driven methods such as independent component analysis (ICA) for functional magnetic resonance imaging (fMRI) data analysis. fMRI datasets are however structured data matrices with notions of spatio-temporal correlation and temporal smoothness. This prior information has not been included in the K-SVD algorithm when applied to fMRI data analysis. In this paper we propose three variants of the K-SVD algorithm dedicated to fMRI data analysis by accounting for this prior information. The proposed algorithms differ from the K-SVD in their sparse coding and dictionary update stages. The first two algorithms account for the known correlation structure in the fMRI data by using the squared Q, R-norm instead of the Frobenius norm for matrix approximation. The third and last algorithm account for both the known correlation structure in the fMRI data and the temporal smoothness. The temporal smoothness is incorporated in the dictionary update stage via regularization of the dictionary atoms obtained with penalization. The performance of the proposed dictionary learning algorithms are illustrated through simulations and applications on real fMRI data.

Optimal portfolio strategy with cross-correlation matrix composed by DCCA coefficients: Evidence from the Chinese stock market

NASA Astrophysics Data System (ADS)

Sun, Xuelian; Liu, Zixian

2016-02-01

In this paper, a new estimator of correlation matrix is proposed, which is composed of the detrended cross-correlation coefficients (DCCA coefficients), to improve portfolio optimization. In contrast to Pearson's correlation coefficients (PCC), DCCA coefficients acquired by the detrended cross-correlation analysis (DCCA) method can describe the nonlinear correlation between assets, and can be decomposed in different time scales. These properties of DCCA make it possible to improve the investment effect and more valuable to investigate the scale behaviors of portfolios. The minimum variance portfolio (MVP) model and the Mean-Variance (MV) model are used to evaluate the effectiveness of this improvement. Stability analysis shows the effect of two kinds of correlation matrices on the estimation error of portfolio weights. The observed scale behaviors are significant to risk management and could be used to optimize the portfolio selection.

What is the difference in organic matrix of aragonite vs. vaterite polymorph in natural shell and pearl? Study of the pearl-forming freshwater bivalve mollusc Hyriopsis cumingii.

PubMed

Ma, Yufei; Berland, Sophie; Andrieu, Jean-Pierre; Feng, Qingling; Bédouet, Laurent

2013-04-01

Aragonite pearl, vaterite pearl and shell nacre of the freshwater mollusc Hyriopsis cumingii (Zhejiang province, China) were chosen to analyze microstructure and organic composition in the different habits of calcium carbonate. SEM and TEM were used to reveal the microstructure and mineralogical phase. We found that tablets in vaterite exhibited more irregular texture and were packaged with more organic matrices than in aragonite forms. Then a peculiar method was introduced to extract water soluble matrix (WSM), acid soluble matrix (ASM) and acid insoluble matrix (AIM) from the three samples, and biochemical analysis of these organic matrixes involved in crystal formation and polymorph selection was carried out. High performance liquid chromatography (HPLC) confirms the hydrophobic pattern of the organic matrix intermingled with mineral, the opposite of the early mobilizable water soluble fraction. Amino acid composition confirms hydrophobic residues as major components of all the extracts, but it reveals an imbalance in acidic residues rates in WSM vs. ASM and in aragonite vs. vaterite. Electrophoresis gives evidence for signatures in proteins with a 140 kDa material specific for aragonite in WSM. Conversely all ASM extracts reveal the presence of about 55 kDa components, including a discrete band in vaterite extract. Copyright © 2012 Elsevier B.V. All rights reserved.

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…

Human mesenchymal stem cells cultured on silk hydrogels with variable stiffness and growth factor differentiate into mature smooth muscle cell phenotype.

PubMed

Floren, Michael; Bonani, Walter; Dharmarajan, Anirudh; Motta, Antonella; Migliaresi, Claudio; Tan, Wei

2016-02-01

Cell-matrix and cell-biomolecule interactions play critical roles in a diversity of biological events including cell adhesion, growth, differentiation, and apoptosis. Evidence suggests that a concise crosstalk of these environmental factors may be required to direct stem cell differentiation toward matured cell type and function. However, the culmination of these complex interactions to direct stem cells into highly specific phenotypes in vitro is still widely unknown, particularly in the context of implantable biomaterials. In this study, we utilized tunable hydrogels based on a simple high pressure CO2 method and silk fibroin (SF) the structural protein of Bombyx mori silk fibers. Modification of SF protein starting water solution concentration results in hydrogels of variable stiffness while retaining key structural parameters such as matrix pore size and β-sheet crystallinity. To further resolve the complex crosstalk of chemical signals with matrix properties, we chose to investigate the role of 3D hydrogel stiffness and transforming growth factor (TGF-β1), with the aim of correlating the effects on the vascular commitment of human mesenchymal stem cells. Our data revealed the potential to upregulate matured vascular smooth muscle cell phenotype (myosin heavy chain expression) of hMSCs by employing appropriate matrix stiffness and growth factor (within 72h). Overall, our observations suggest that chemical and physical stimuli within the cellular microenvironment are tightly coupled systems involved in the fate decisions of hMSCs. The production of tunable scaffold materials that are biocompatible and further specialized to mimic tissue-specific niche environments will be of considerable value to future tissue engineering platforms. This article investigates the role of silk fibroin hydrogel stiffness and transforming growth factor (TGF-β1), with the aim of correlating the effects on the vascular commitment of human mesenchymal stem cells. Specifically, we demonstrate the upregulation of mature vascular smooth muscle cell phenotype (myosin heavy chain expression) of hMSCs by employing appropriate matrix stiffness and growth factor (within 72h). Moreover, we demonstrate the potential to direct specialized hMSC differentiation by modulating stiffness and growth factor using silk fibroin, a well-tolerated and -defined biomaterial with an impressive portfolio of tissue engineering applications. Altogether, our study reinforce the fact that complex differentiation protocols may be simplified by engineering the cellular microenvironment on multiple scales, i.e. matrix stiffness with growth factor. Crown Copyright © 2015. Published by Elsevier Ltd. All rights reserved.

Noise sensitivity of portfolio selection in constant conditional correlation GARCH models

NASA Astrophysics Data System (ADS)

Varga-Haszonits, I.; Kondor, I.

2007-11-01

This paper investigates the efficiency of minimum variance portfolio optimization for stock price movements following the Constant Conditional Correlation GARCH process proposed by Bollerslev. Simulations show that the quality of portfolio selection can be improved substantially by computing optimal portfolio weights from conditional covariances instead of unconditional ones. Measurement noise can be further reduced by applying some filtering method on the conditional correlation matrix (such as Random Matrix Theory based filtering). As an empirical support for the simulation results, the analysis is also carried out for a time series of S&P500 stock prices.

Critical behavior of dissipative two-dimensional spin lattices

NASA Astrophysics Data System (ADS)

Rota, R.; Storme, F.; Bartolo, N.; Fazio, R.; Ciuti, C.

2017-04-01

We explore critical properties of two-dimensional lattices of spins interacting via an anisotropic Heisenberg Hamiltonian that are subject to incoherent spin flips. We determine the steady-state solution of the master equation for the density matrix via the corner-space renormalization method. We investigate the finite-size scaling and critical exponent of the magnetic linear susceptibility associated with a dissipative ferromagnetic transition. We show that the von Neumann entropy increases across the critical point, revealing a strongly mixed character of the ferromagnetic phase. Entanglement is witnessed by the quantum Fisher information, which exhibits a critical behavior at the transition point, showing that quantum correlations play a crucial role in the transition.

Stable-unstable transition for a Bose-Hubbard chain coupled to an environment

NASA Astrophysics Data System (ADS)

Guo, Chu; de Vega, Ines; Schollwöck, Ulrich; Poletti, Dario

2018-05-01

Interactions in quantum systems may induce transitions to exotic correlated phases of matter which can be vulnerable to coupling to an environment. Here, we study the stability of a Bose-Hubbard chain coupled to a bosonic bath at zero and nonzero temperature. We show that only above a critical interaction the chain loses bosons and its properties are significantly affected. The transition is of a different nature than the superfluid-Mott-insulator transition and occurs at a different critical interaction. We explain such a stable-unstable transition by the opening of a global charge gap. The comparison of accurate matrix product state simulations to approximative approaches that miss this transition reveals its many-body origin.

Estimating and Identifying Unspecified Correlation Structure for Longitudinal Data

PubMed Central

Hu, Jianhua; Wang, Peng; Qu, Annie

2014-01-01

Identifying correlation structure is important to achieving estimation efficiency in analyzing longitudinal data, and is also crucial for drawing valid statistical inference for large size clustered data. In this paper, we propose a nonparametric method to estimate the correlation structure, which is applicable for discrete longitudinal data. We utilize eigenvector-based basis matrices to approximate the inverse of the empirical correlation matrix and determine the number of basis matrices via model selection. A penalized objective function based on the difference between the empirical and model approximation of the correlation matrices is adopted to select an informative structure for the correlation matrix. The eigenvector representation of the correlation estimation is capable of reducing the risk of model misspecification, and also provides useful information on the specific within-cluster correlation pattern of the data. We show that the proposed method possesses the oracle property and selects the true correlation structure consistently. The proposed method is illustrated through simulations and two data examples on air pollution and sonar signal studies. PMID:26361433

Quantitative image analysis for investigating cell-matrix interactions

NASA Astrophysics Data System (ADS)

Burkel, Brian; Notbohm, Jacob

2017-07-01

The extracellular matrix provides both chemical and physical cues that control cellular processes such as migration, division, differentiation, and cancer progression. Cells can mechanically alter the matrix by applying forces that result in matrix displacements, which in turn may localize to form dense bands along which cells may migrate. To quantify the displacements, we use confocal microscopy and fluorescent labeling to acquire high-contrast images of the fibrous material. Using a technique for quantitative image analysis called digital volume correlation, we then compute the matrix displacements. Our experimental technology offers a means to quantify matrix mechanics and cell-matrix interactions. We are now using these experimental tools to modulate mechanical properties of the matrix to study cell contraction and migration.

Assessment of the Speech Intelligibility Performance of Post Lingual Cochlear Implant Users at Different Signal-to-Noise Ratios Using the Turkish Matrix Test.

PubMed

Polat, Zahra; Bulut, Erdoğan; Ataş, Ahmet

2016-09-01

Spoken word recognition and speech perception tests in quiet are being used as a routine in assessment of the benefit which children and adult cochlear implant users receive from their devices. Cochlear implant users generally demonstrate high level performances in these test materials as they are able to achieve high level speech perception ability in quiet situations. Although these test materials provide valuable information regarding Cochlear Implant (CI) users' performances in optimal listening conditions, they do not give realistic information regarding performances in adverse listening conditions, which is the case in the everyday environment. The aim of this study was to assess the speech intelligibility performance of post lingual CI users in the presence of noise at different signal-to-noise ratio with the Matrix Test developed for Turkish language. Cross-sectional study. The thirty post lingual implant user adult subjects, who had been using implants for a minimum of one year, were evaluated with Turkish Matrix test. Subjects' speech intelligibility was measured using the adaptive and non-adaptive Matrix Test in quiet and noisy environments. The results of the study show a correlation between Pure Tone Average (PTA) values of the subjects and Matrix test Speech Reception Threshold (SRT) values in the quiet. Hence, it is possible to asses PTA values of CI users using the Matrix Test also. However, no correlations were found between Matrix SRT values in the quiet and Matrix SRT values in noise. Similarly, the correlation between PTA values and intelligibility scores in noise was also not significant. Therefore, it may not be possible to assess the intelligibility performance of CI users using test batteries performed in quiet conditions. The Matrix Test can be used to assess the benefit of CI users from their systems in everyday life, since it is possible to perform intelligibility test with the Matrix test using a material that CI users experience in their everyday life and it is possible to assess their difficulty in speech discrimination in noisy conditions they have to cope with.

Raman Spectroscopy Reveals New Insights into the Zonal Organization of Native and Tissue-Engineered Articular Cartilage

PubMed Central

2016-01-01

Tissue architecture is intimately linked with its functions, and loss of tissue organization is often associated with pathologies. The intricate depth-dependent extracellular matrix (ECM) arrangement in articular cartilage is critical to its biomechanical functions. In this study, we developed a Raman spectroscopic imaging approach to gain new insight into the depth-dependent arrangement of native and tissue-engineered articular cartilage using bovine tissues and cells. Our results revealed previously unreported tissue complexity into at least six zones above the tidemark based on a principal component analysis and k-means clustering analysis of the distribution and orientation of the main ECM components. Correlation of nanoindentation and Raman spectroscopic data suggested that the biomechanics across the tissue depth are influenced by ECM microstructure rather than composition. Further, Raman spectroscopy together with multivariate analysis revealed changes in the collagen, glycosaminoglycan, and water distributions in tissue-engineered constructs over time. These changes were assessed using simple metrics that promise to instruct efforts toward the regeneration of a broad range of tissues with native zonal complexity and functional performance. PMID:28058277

Dysregulated miR-127-5p contributes to type II collagen degradation by targeting matrix metalloproteinase-13 in human intervertebral disc degeneration.

PubMed

Hua, Wen-Bin; Wu, Xing-Huo; Zhang, Yu-Kun; Song, Yu; Tu, Ji; Kang, Liang; Zhao, Kang-Cheng; Li, Shuai; Wang, Kun; Liu, Wei; Shao, Zeng-Wu; Yang, Shu-Hua; Yang, Cao

2017-08-01

Intervertebral disc degeneration (IDD) is a chronic disease associated with the degradation of extracellular matrix (ECM). Matrix metalloproteinase (MMP)-13 is a major enzyme that mediates the degradation of ECM components. MMP-13 has been predicted to be a potential target of miR-127-5p. However, the exact function of miR-127-5p in IDD is still unclear. We designed this study to evaluate the correlation between miR-127-5p level and the degeneration of human intervertebral discs and explore the potential mechanisms. miR-127-5p levels and MMP-13 mRNA levels were detected by quantitative real-time polymerase chain reaction (qPCR). To determine whether MMP-13 is a target of miR-127-5p, dual luciferase reporter assays were performed. miR-127-5p mimic and miR-127-5p inhibitor were used to overexpress or downregulate miR-127-5p expression in human NP cells, respectively. Small interfering RNA (siRNA) was used to knock down MMP-13 expression in human NP cells. Type II collagen expression in human NP cells was detected by qPCR, western blotting, and immunofluorescence staining. We confirmed that miR-127-5p was significantly downregulated in nucleus pulposus (NP) tissue of degenerative discs and its expression was inversely correlated with MMP-13 mRNA levels. We reveal that MMP-13 may act as a target of miR-127-5p. Expression of miR-127-5p was inversely correlated with type II collagen expression in human NP cells. Moreover, suppression of MMP-13 expression by siRNA blocked downstream signaling and increased type II collagen expression. Dysregulated miR-127-5p contributed to the degradation of type II collagen by targeting MMP-13 in human IDD. Our findings highlight that miR-127-5p may serve as a new therapeutic target in IDD. Copyright © 2017 Elsevier B.V. and Société Française de Biochimie et Biologie Moléculaire (SFBBM). All rights reserved.

Detection of Matrix Crack Density of CFRP using an Electrical Potential Change Method with Multiple Probes

NASA Astrophysics Data System (ADS)

Todoroki, Akira; Omagari, Kazuomi

Carbon Fiber Reinforced Plastic (CFRP) laminates are adopted for fuel tank structures of next generation space rockets or automobiles. Matrix cracks may cause fuel leak or trigger fatigue damage. A monitoring system of the matrix crack density is required. The authors have developed an electrical resistance change method for the monitoring of delamination cracks in CFRP laminates. Reinforcement fibers are used as a self-sensing system. In the present study, the electric potential method is adopted for matrix crack density monitoring. Finite element analysis (FEA) was performed to investigate the possibility of monitoring matrix crack density using multiple electrodes mounted on a single surface of a specimen. The FEA reveals the matrix crack density increases electrical resistance for a target segment between electrodes. Experimental confirmation was also performed using cross-ply laminates. Eight electrodes were mounted on a single surface of a specimen using silver paste after polishing of the specimen surface with sandpaper. The two outermost electrodes applied electrical current, and the inner electrodes measured electric voltage changes. The slope of electrical resistance during reloading is revealed to be an appropriate index for the detection of matrix crack density.

Comparing the structure of an emerging market with a mature one under global perturbation

NASA Astrophysics Data System (ADS)

Namaki, A.; Jafari, G. R.; Raei, R.

2011-09-01

In this paper we investigate the Tehran stock exchange (TSE) and Dow Jones Industrial Average (DJIA) in terms of perturbed correlation matrices. To perturb a stock market, there are two methods, namely local and global perturbation. In the local method, we replace a correlation coefficient of the cross-correlation matrix with one calculated from two Gaussian-distributed time series, whereas in the global method, we reconstruct the correlation matrix after replacing the original return series with Gaussian-distributed time series. The local perturbation is just a technical study. We analyze these markets through two statistical approaches, random matrix theory (RMT) and the correlation coefficient distribution. By using RMT, we find that the largest eigenvalue is an influence that is common to all stocks and this eigenvalue has a peak during financial shocks. We find there are a few correlated stocks that make the essential robustness of the stock market but we see that by replacing these return time series with Gaussian-distributed time series, the mean values of correlation coefficients, the largest eigenvalues of the stock markets and the fraction of eigenvalues that deviate from the RMT prediction fall sharply in both markets. By comparing these two markets, we can see that the DJIA is more sensitive to global perturbations. These findings are crucial for risk management and portfolio selection.

Failure prediction in ceramic composites using acoustic emission and digital image correlation

NASA Astrophysics Data System (ADS)

Whitlow, Travis; Jones, Eric; Przybyla, Craig

2016-02-01

The objective of the work performed here was to develop a methodology for linking in-situ detection of localized matrix cracking to the final failure location in continuous fiber reinforced CMCs. First, the initiation and growth of matrix cracking are measured and triangulated via acoustic emission (AE) detection. High amplitude events at relatively low static loads can be associated with initiation of large matrix cracks. When there is a localization of high amplitude events, a measurable effect on the strain field can be observed. Full field surface strain measurements were obtained using digital image correlation (DIC). An analysis using the combination of the AE and DIC data was able to predict the final failure location.

Contractile recovery of microtissues after giant shear events

NASA Astrophysics Data System (ADS)

Morley, Cameron; Bhattacharjee, Tapomoy; Ellison, Sarah; Sawyer, W.; Angelini, Thomas

Cells are often dispersed in extracellular matrix (ECM) gels like collagen and Matrigel as minimal tissue models. Generally, large-scale contraction of these constructs is observed, in which the degree of contraction of the entire system correlates with cell density and ECM concentration. The freedom to perform diverse mechanical experiments on these contracting constructs is limited by the challenges of handling and supporting these delicate samples. Here, we present a method to create simple cell-ECM constructs that can be manipulated with significantly reduced experimental limitations. We 3D print mixtures of MCF10A cells and ECM (collagen-I and Matrigel) into a 3D growth medium made from jammed microgels. With this approach, we are able to apply shear stresses to the cell constructs times after printing and observe the collective response. Preliminary results reveal that, following shear deformations that exceed 300% and dramatically smear cells and matrix in space, the cells actively re-contract the construct toward the un-sheared construct. These results suggest that new principles of collective recovery can be employed for tissue engineering applications using jammed microgels as a re-configurable support medium.

Ground-state properties of anyons in a one-dimensional lattice

NASA Astrophysics Data System (ADS)

Tang, Guixin; Eggert, Sebastian; Pelster, Axel

2015-12-01

Using the Anyon-Hubbard Hamiltonian, we analyze the ground-state properties of anyons in a one-dimensional lattice. To this end we map the hopping dynamics of correlated anyons to an occupation-dependent hopping Bose-Hubbard model using the fractional Jordan-Wigner transformation. In particular, we calculate the quasi-momentum distribution of anyons, which interpolates between Bose-Einstein and Fermi-Dirac statistics. Analytically, we apply a modified Gutzwiller mean-field approach, which goes beyond a classical one by including the influence of the fractional phase of anyons within the many-body wavefunction. Numerically, we use the density-matrix renormalization group by relying on the ansatz of matrix product states. As a result it turns out that the anyonic quasi-momentum distribution reveals both a peak-shift and an asymmetry which mainly originates from the nonlocal string property. In addition, we determine the corresponding quasi-momentum distribution of the Jordan-Wigner transformed bosons, where, in contrast to the hard-core case, we also observe an asymmetry for the soft-core case, which strongly depends on the particle number density.

Matrix-product-state method with local basis optimization for nonequilibrium electron-phonon systems

NASA Astrophysics Data System (ADS)

Heidrich-Meisner, Fabian; Brockt, Christoph; Dorfner, Florian; Vidmar, Lev; Jeckelmann, Eric

We present a method for simulating the time evolution of quasi-one-dimensional correlated systems with strongly fluctuating bosonic degrees of freedom (e.g., phonons) using matrix product states. For this purpose we combine the time-evolving block decimation (TEBD) algorithm with a local basis optimization (LBO) approach. We discuss the performance of our approach in comparison to TEBD with a bare boson basis, exact diagonalization, and diagonalization in a limited functional space. TEBD with LBO can reduce the computational cost by orders of magnitude when boson fluctuations are large and thus it allows one to investigate problems that are out of reach of other approaches. First, we test our method on the non-equilibrium dynamics of a Holstein polaron and show that it allows us to study the regime of strong electron-phonon coupling. Second, the method is applied to the scattering of an electronic wave packet off a region with electron-phonon coupling. Our study reveals a rich physics including transient self-trapping and dissipation. Supported by Deutsche Forschungsgemeinschaft (DFG) via FOR 1807.

Emp is a component of the nuclear matrix of mammalian cells and undergoes dynamic rearrangements during cell division

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

Bala, Shashi; Kumar, Ajay; Soni, Shivani

2006-04-21

Emp, originally detected in erythroblastic islands, is expressed in numerous cell types and tissues suggesting a functionality not limited to hematopoiesis. To study the function of Emp in non-hematopoietic cells, an epitope-tagged recombinant human Emp was expressed in HEK cells. Preliminary studies revealed that Emp partitioned into both the nuclear and Triton X-100-insoluble cytoskeletal fractions in approximately a 4:1 ratio. In this study, we report investigations of Emp in the nucleus. Sequential extractions of interphase nuclei showed that recombinant Emp was present predominantly in the nuclear matrix. Immunofluorescence microscopy showed that Emp was present in typical nuclear speckles enriched withmore » the spliceosome assembly factor SC35 and partially co-localized with actin staining. Coimmunoprecipitation and GST-pull-down assays confirmed the apparent close association of Emp with nuclear actin. During mitosis, Emp was detected at the mitotic spindle/spindle poles, as well as in the contractile ring during cytokinesis. These results suggest that Emp undergoes dynamic rearrangements within the nuclear architecture that are correlated with cell division.« less

Emp is a component of the nuclear matrix of mammalian cells and undergoes dynamic rearrangements during cell division.

PubMed

Bala, Shashi; Kumar, Ajay; Soni, Shivani; Sinha, Sudha; Hanspal, Manjit

2006-04-21

Emp, originally detected in erythroblastic islands, is expressed in numerous cell types and tissues suggesting a functionality not limited to hematopoiesis. To study the function of Emp in non-hematopoietic cells, an epitope-tagged recombinant human Emp was expressed in HEK cells. Preliminary studies revealed that Emp partitioned into both the nuclear and Triton X-100-insoluble cytoskeletal fractions in approximately a 4:1 ratio. In this study, we report investigations of Emp in the nucleus. Sequential extractions of interphase nuclei showed that recombinant Emp was present predominantly in the nuclear matrix. Immunofluorescence microscopy showed that Emp was present in typical nuclear speckles enriched with the spliceosome assembly factor SC35 and partially co-localized with actin staining. Coimmunoprecipitation and GST-pull-down assays confirmed the apparent close association of Emp with nuclear actin. During mitosis, Emp was detected at the mitotic spindle/spindle poles, as well as in the contractile ring during cytokinesis. These results suggest that Emp undergoes dynamic rearrangements within the nuclear architecture that are correlated with cell division.

How to Study a Matrix

ERIC Educational Resources Information Center

Jairam, Dharmananda; Kiewra, Kenneth A.; Kauffman, Douglas F.; Zhao, Ruomeng

2012-01-01

This study investigated how best to study a matrix. Fifty-three participants studied a matrix topically (1 column at a time), categorically (1 row at a time), or in a unified way (all at once). Results revealed that categorical and unified study produced higher: (a) performance on relationship and fact tests, (b) study material satisfaction, and…

Targeting functional motifs of a protein family

NASA Astrophysics Data System (ADS)

Bhadola, Pradeep; Deo, Nivedita

2016-10-01

The structural organization of a protein family is investigated by devising a method based on the random matrix theory (RMT), which uses the physiochemical properties of the amino acid with multiple sequence alignment. A graphical method to represent protein sequences using physiochemical properties is devised that gives a fast, easy, and informative way of comparing the evolutionary distances between protein sequences. A correlation matrix associated with each property is calculated, where the noise reduction and information filtering is done using RMT involving an ensemble of Wishart matrices. The analysis of the eigenvalue statistics of the correlation matrix for the β -lactamase family shows the universal features as observed in the Gaussian orthogonal ensemble (GOE). The property-based approach captures the short- as well as the long-range correlation (approximately following GOE) between the eigenvalues, whereas the previous approach (treating amino acids as characters) gives the usual short-range correlations, while the long-range correlations are the same as that of an uncorrelated series. The distribution of the eigenvector components for the eigenvalues outside the bulk (RMT bound) deviates significantly from RMT observations and contains important information about the system. The information content of each eigenvector of the correlation matrix is quantified by introducing an entropic estimate, which shows that for the β -lactamase family the smallest eigenvectors (low eigenmodes) are highly localized as well as informative. These small eigenvectors when processed gives clusters involving positions that have well-defined biological and structural importance matching with experiments. The approach is crucial for the recognition of structural motifs as shown in β -lactamase (and other families) and selectively identifies the important positions for targets to deactivate (activate) the enzymatic actions.

Novel insights into anoxic/aerobic(1)/aerobic(2) biological fluidized-bed system for coke wastewater treatment by fluorescence excitation-emission matrix spectra coupled with parallel factor analysis.

PubMed

Ou, Hua-Se; Wei, Chao-Hai; Mo, Ce-Hui; Wu, Hai-Zhen; Ren, Yuan; Feng, Chun-Hua

2014-10-01

Fluorescence spectroscopy coupled with parallel factor analysis (PARAFAC) was applied to investigate the contaminant removal efficiency and fluorescent characteristic variations in a full scale coke wastewater (CWW) treatment plant with a novel anoxic/aerobic(1)/aerobic(2) (A/O(1)/O(2)) process, which combined with internal-loop fluidized-bed reactor. Routine monitoring results indicated that primary contaminants in CWW, such as phenols and free cyanide, were removed efficiently in A/O(1)/O(2) process (removal efficiency reached 99% and 95%, respectively). Three-dimensional excitation-emission matrix fluorescence spectroscopy and PARAFAC identified three fluorescent components, including two humic-like fluorescence components (C1 and C3) and one protein-like component (C2). Principal component analysis revealed that C1 and C2 correlated with COD (correlation coefficient (r)=0.782, p<0.01 and r=0.921, p<0.01), respectively) and phenols (r=0.796, p<0.01 and r=0.914, p<0.01, respectively), suggesting that C1 and C2 might be associated with the predominating aromatic contaminants in CWW. C3 correlated with mixed liquor suspended solids (r=0.863, p<0.01) in fluidized-bed reactors, suggesting that it might represent the biological dissolved organic matter. In A/O(1)/O(2) process, the fluorescence intensities of C1 and C2 consecutively decreased, indicating the degradation of aromatic contaminants. Correspondingly, the fluorescence intensity of C3 increased in aerobic(1) stage, suggesting an increase of biological dissolved organic matter. Copyright © 2014 Elsevier Ltd. All rights reserved.

The study of Thai stock market across the 2008 financial crisis

NASA Astrophysics Data System (ADS)

Kanjamapornkul, K.; Pinčák, Richard; Bartoš, Erik

2016-11-01

The cohomology theory for financial market can allow us to deform Kolmogorov space of time series data over time period with the explicit definition of eight market states in grand unified theory. The anti-de Sitter space induced from a coupling behavior field among traders in case of a financial market crash acts like gravitational field in financial market spacetime. Under this hybrid mathematical superstructure, we redefine a behavior matrix by using Pauli matrix and modified Wilson loop for time series data. We use it to detect the 2008 financial market crash by using a degree of cohomology group of sphere over tensor field in correlation matrix over all possible dominated stocks underlying Thai SET50 Index Futures. The empirical analysis of financial tensor network was performed with the help of empirical mode decomposition and intrinsic time scale decomposition of correlation matrix and the calculation of closeness centrality of planar graph.

Tailoring mechanical and antibacterial properties of chitosan/gelatin nanofiber membranes with Fe3O4 nanoparticles for potential wound dressing application

NASA Astrophysics Data System (ADS)

Cai, Ning; Li, Chao; Han, Chao; Luo, Xiaogang; Shen, Liang; Xue, Yanan; Yu, Faquan

2016-04-01

In this work, magnetic Fe3O4 nanoparticles (NPs) were utilized to improve the mechanical and antibacterial properties of chitosan (CS)/gelatin (GE) composite nanofiber membranes. Homogeneous Fe3O4/CS/GE nanofibers were electrospun successfully. Scanning electron microscopy (SEM) and transmission electron microscopy (TEM) images confirmed the presence of well-dispersed Fe3O4 NPs in the composite nanofibers. Fourier transform infrared spectroscopy (FTIR) spectra revealed the effective interactions of Fe3O4 NPs to the composite matrix through hydrogen bonding. The improvement on the thermal stability of the Fe3O4/CS/GE was observed by differential scanning calorimetry (DSC) and thermo gravimetric analysis (TGA), which is tightly correlated to strong filler-matrix adhesion. The incorporation of Fe3O4 NPs resulted in a substantial enhancement of mechanical properties. The optimum mechanical performance was demonstrated on 1 wt% Fe3O4/CS/GE nanofiber membranes, achieving 155% augment of Young's modulus, 128% increase of tensile strength, and 100% boost of toughness from CS/GE. The excellent mechanical enhancement can be explained by the effective dispersion of fillers and the filler-matrix interactions, which ensures the efficient load transfer from CS/GE matrix to Fe3O4 nanofillers. Moreover, zones of inhibition for Escherichia coli and Staphylococcus aureus expanded markedly with the supplement of Fe3O4 NPs. In all, nanofiber membranes made of Fe3O4/CS/GE composite with tailored mechanical and antibacterial properties appear a promising wound dressing material.

LANDSAT-D Thematic Mapper image dimensionality reduction and geometric correction accuracy. [Walnut Creek Watershed, Texas

NASA Technical Reports Server (NTRS)

Ford, G. E. (Principal Investigator)

1984-01-01

Principal components transformations was applied to a Walnut Creek, Texas subscene to reduce the dimensionality of the multispectral sensor data. This transformation was also applied to a LANDSAT 3 MSS subscene of the same area acquired in a different season and year. Results of both procedures are tabulated and allow for comparisons between TM and MSS data. The TM correlation matrix shows that visible bands 1 to 3 exhibit a high degree of correlation in the range 0.92 to 0.96. Correlation for bands 5 to 7 is 0.93. Band 4 is not highly correlated with any other band, with corrections in the range 0.13 to 0.52. The thermal band (6) is not highly correlated with other bands in the range 0.13 to 0.46. The MSS correlation matrix shows that bands 4 and 5 are highly correlated (0.96) as are bands 6 and 7 with a correlation of 0.92.

Not all that glitters is RMT in the forecasting of risk of portfolios in the Brazilian stock market

NASA Astrophysics Data System (ADS)

Sandoval, Leonidas; Bortoluzzo, Adriana Bruscato; Venezuela, Maria Kelly

2014-09-01

Using stocks of the Brazilian stock exchange (BM&F-Bovespa), we build portfolios of stocks based on Markowitz's theory and test the predicted and realized risks. This is done using the correlation matrices between stocks, and also using Random Matrix Theory in order to clean such correlation matrices from noise. We also calculate correlation matrices using a regression model in order to remove the effect of common market movements and their cleaned versions using Random Matrix Theory. This is done for years of both low and high volatility of the Brazilian stock market, from 2004 to 2012. The results show that the use of regression to subtract the market effect on returns greatly increases the accuracy of the prediction of risk, and that, although the cleaning of the correlation matrix often leads to portfolios that better predict risks, in periods of high volatility of the market this procedure may fail to do so. The results may be used in the assessment of the true risks when one builds a portfolio of stocks during periods of crisis.

Auger analysis of a fiber/matrix interface in a ceramic matrix composite

NASA Technical Reports Server (NTRS)

Honecy, Frank S.; Pepper, Stephen V.

1988-01-01

Auger electron spectroscopy (AES) depth profiling was used to characterize the fiber/matrix interface of an SiC fiber, reaction bonded Si3N4 matrix composite. Depth profiles of the as received double coated fiber revealed concentration oscillations which disappeared after annealing the fiber in the environment used to fabricate the composite. After the composite was fractured, the Auger depth profiles showed that failure occurred in neither the Beta-SiC fiber body nor in the Si3N4 matrix but, concurrently, at the fiber coating/matrix interface and within the fiber coating itself.

Quasiparticle random phase approximation uncertainties and their correlations in the analysis of 0{nu}{beta}{beta} decay

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

Faessler, Amand; Rodin, V.; Fogli, G. L.

2009-03-01

The variances and covariances associated to the nuclear matrix elements of neutrinoless double beta decay (0{nu}{beta}{beta}) are estimated within the quasiparticle random phase approximation. It is shown that correlated nuclear matrix elements uncertainties play an important role in the comparison of 0{nu}{beta}{beta} decay rates for different nuclei, and that they are degenerate with the uncertainty in the reconstructed Majorana neutrino mass.

Holographic hierarchy in the Gaussian matrix model via the fuzzy sphere

NASA Astrophysics Data System (ADS)

Garner, David; Ramgoolam, Sanjaye

2013-10-01

The Gaussian Hermitian matrix model was recently proposed to have a dual string description with worldsheets mapping to a sphere target space. The correlators were written as sums over holomorphic (Belyi) maps from worldsheets to the two-dimensional sphere, branched over three points. We express the matrix model correlators by using the fuzzy sphere construction of matrix algebras, which can be interpreted as a string field theory description of the Belyi strings. This gives the correlators in terms of trivalent ribbon graphs that represent the couplings of irreducible representations of su(2), which can be evaluated in terms of 3j and 6j symbols. The Gaussian model perturbed by a cubic potential is then recognised as a generating function for Ponzano-Regge partition functions for 3-manifolds having the worldsheet as boundary, and equipped with boundary data determined by the ribbon graphs. This can be viewed as a holographic extension of the Belyi string worldsheets to membrane worldvolumes, forming part of a holographic hierarchy linking, via the large N expansion, the zero-dimensional QFT of the Matrix model to 2D strings and 3D membranes. Note that if, after removing the white vertices, the graph contains a blue edge connecting to the same black vertex at both ends, then the triangulation generated from the black edges will contain faces that resemble cut discs. These faces are triangles with two of the edges identified.

Serum levels of matrix metalloproteinases: implications in clinical neurology.

PubMed

Romi, Fredrik; Helgeland, Geir; Gilhus, Nils Erik

2012-01-01

Matrix metalloproteinases (MMPs) are zinc-dependent enzymes involved in remodeling extracellular matrix and cell-matrix interactions. A pathogenic role of MMPs in neurological disorders is likely. This paper focuses on serological clinical aspects only. In multiple sclerosis, higher serum MMP-3 is seen during relapses. Lower serum MMP-8 and -9 levels correlate with fewer contrast-enhanced T(2)-weighted MRI lesions, and serum MMP-9 can be used in monitoring treatment. In myasthenia gravis, serum MMP-2, -3, and -9 levels are elevated in both generalized and ocular diseases. A proportion of the patients have markedly increased serum MMP-3. In acute stroke, higher serum MMP-9 correlates with larger infarct volume, stroke severity, and worse functional outcome, and serum MMP-3 is significantly lower than in several other neurological disorders and healthy controls. In amyotrophic lateral sclerosis, serum MMP-2 correlates with disease progression, and both serum MMP-1 and -2 are elevated. In Alzheimer's disease, serum MMP-3, -9, and -10 are elevated. In migraine, serum MMP-2 is elevated, and also MMP-9 in those patients with migraine without aura. MMP-9 is implicated in the pathogenesis of experimental epilepsy. A pathogenic role of MMPs in these conditions could be related to their ability to degrade extracellular matrix. MMPs may also facilitate autoimmunity. Copyright © 2012 S. Karger AG, Basel.

Thermomechanical testing of high-temperature composites - Thermomechanical fatigue (TMF) behavior of SiC(SCS-6)/Ti-15-3

NASA Technical Reports Server (NTRS)

Castelli, Michael G.; Bartolotta, Paul; Ellis, John R.

1992-01-01

Thermomechanical testing techniques recently developed for monolithic structural alloys were successfully extended to continuous fiber reinforced composite materials in plate form. The success of this adaptation was verified on a model metal matrix composite (MMC) material, namely SiC(SCS-6)/Ti-15V-3Cr-3Al-3Sn. Effects of heating system type and specimen preparation are also addressed. Cyclic lives determined under full thermomechanical conditions were shown to be significantly reduced from those obtained under comparable isothermal and in-phase bi-thermal conditions. Fractography and metallography from specimens subjected to isothermal, out-of-phase and in-phase conditions reveal distinct differences in damage-failure modes. Isothermal metallography revealed extensive matrix cracking associated with fiber damage throughout the entire cross-section of the specimen. Out-of-phase metallography revealed extensive matrix damage associated with minimal (if any) fiber cracking. However, the damage was located exclusively at surface and near-surface locations. In-phase conditions produced extensive fiber cracking throughout the entire cross-section, associated with minimal (if any) matrix damage.

Thermomechanical testing techniques for high-temparature composites: TMF behavior of SiC(SCS-6)/Ti-15-3

NASA Technical Reports Server (NTRS)

Castelli, Michael G.; Ellis, J. Rodney; Bartolotta, Paul A.

1990-01-01

Thermomechanical testing techniques recently developed for monolithic structural alloys were successfully extended to continuous fiber reinforced composite materials in plate form. The success of this adaptation was verified on a model metal matrix composite (MMC) material, namely SiC(SCS-6)/Ti-15V-3Cr-3Al-3Sn. Effects of heating system type and specimen preparation are also addressed. Cyclic lives determined under full thermo-mechanical conditions were shown to be significantly reduced from those obtained under comparable isothermal and in-phase bi-thermal conditions. Fractography and metallography from specimens subjected to isothermal, out-of-phase and in-phase conditions reveal distinct differences in damage-failure modes. Isothermal metallography revealed extensive matrix cracking associated with fiber damage throughout the entire cross-section of the specimen. Out-of-phase metallography revealed extensive matrix damage associated with minimal (if any) fiber cracking. However, the damage was located exclusively at surface and near-surface locations. In-phase conditions produced extensive fiber cracking throughout the entire cross-section, associated with minimal (if any) matrix damage.

A METHOD FOR IN-SITU CHARACTERIZATION OF RF HEATING IN PARALLEL TRANSMIT MRI

PubMed Central

Alon, Leeor; Deniz, Cem Murat; Brown, Ryan; Sodickson, Daniel K.; Zhu, Yudong

2012-01-01

In ultra high field magnetic resonance imaging, parallel radio-frequency (RF) transmission presents both opportunities and challenges for specific absorption rate (SAR) management. On one hand, parallel transmission provides flexibility in tailoring electric fields in the body while facilitating magnetization profile control. On the other hand, it increases the complexity of energy deposition as well as possibly exacerbating local SAR by improper design or delivery of RF pulses. This study shows that the information needed to characterize RF heating in parallel transmission is contained within a local power correlation matrix. Building upon a calibration scheme involving a finite number of magnetic resonance thermometry measurements, the present work establishes a way of estimating the local power correlation matrix. Determination of this matrix allows prediction of temperature change for an arbitrary parallel transmit RF pulse. In the case of a three transmit coil MR experiment in a phantom, determination and validation of the power correlation matrix was conducted in less than 200 minutes with induced temperature changes of <4 degrees C. Further optimization and adaptation are possible, and simulations evaluating potential feasibility for in vivo use are presented. The method allows general characteristics indicative of RF coil/pulse safety determined in situ. PMID:22714806

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

Bouchard, Chris; Chang, Chia Cheng; Kurth, Thorsten

In this paper, the Feynman-Hellmann theorem can be derived from the long Euclidean-time limit of correlation functions determined with functional derivatives of the partition function. Using this insight, we fully develop an improved method for computing matrix elements of external currents utilizing only two-point correlation functions. Our method applies to matrix elements of any external bilinear current, including nonzero momentum transfer, flavor-changing, and two or more current insertion matrix elements. The ability to identify and control all the systematic uncertainties in the analysis of the correlation functions stems from the unique time dependence of the ground-state matrix elements and the fact that all excited states and contact terms are Euclidean-time dependent. We demonstrate the utility of our method with a calculation of the nucleon axial charge using gradient-flowed domain-wall valence quarks on themore » $$N_f=2+1+1$$ MILC highly improved staggered quark ensemble with lattice spacing and pion mass of approximately 0.15 fm and 310 MeV respectively. We show full control over excited-state systematics with the new method and obtain a value of $$g_A = 1.213(26)$$ with a quark-mass-dependent renormalization coefficient.« less

The mechanical properties measurement of multiwall carbon nanotube reinforced nanocrystalline aluminum matrix composite

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

Sharma, Manjula, E-mail: manjula.physics@gmail.com; Pal, Hemant; Sharma, Vimal

Nanocrystalline aluminum matrix composite containing carbon nanotubes were fabricated using physical mixing method followed by cold pressing. The microstructure of the composite has been investigated using X-ray diffraction, scanning electron microscopy and energy dispersive spectroscopy techniques. These studies revealed that the carbon nanotubes were homogeneously dispersed throughout the metal matrix. The consolidated samples were pressureless sintered in inert atmosphere to further actuate a strong interface between carbon nanotubes and aluminum matrix. The nanoindentation tests carried out on considered samples showed that with the addition of 0.5 wt% carbon nanotubes, the hardness and elastic modulus of the aluminum matrix increased bymore » 21.2 % and 2 % repectively. The scratch tests revealed a decrease in the friction coefficient of the carbon nanotubes reinforced composite due to the presence of lubricating interfacial layer. The prepared composites were promising entities to be used in the field of sporting goods, construction materials and automobile industries.« less

Sequence divergence of microsatellites for phylogeographic assessment of Moroccan Medicago species.

PubMed

Zitouna, N; Marghali, S; Gharbi, M; Haddioui, A; Trifi-Farah, N

2014-03-12

Six Medicago species were investigated to characterize and valorize plant genetic resources of pastoral interest in Morocco. Samples were obtained from the core collection of the South Australian Research and Development Institute (SARDI). The transferability of single sequence repeat markers of Medicago truncatula was successful with 97.6% efficiency across the five species. A total of 283 alleles and 243 genotypes were generated using seven SSR markers, confirming the high level of polymorphism that is characteristic of the Medicago genus, despite a heterozygosity deficit (HO = 0.378; HE = 0.705). In addition, a high level of gene flow was revealed among the species analyzed with significant intra-specific variation. The unweighted pair group method with arithmetic mean dendrogram generated by the dissimilarity matrix revealed that M. polymorpha and M. orbicularis are closely related, and that M. truncatula is likely the ancestral species. The Pearson correlation index revealed no significant correlations between the geographic distribution of the Moroccan species and genetic similarities, indicating local adaptation of these species to different ecological environments independent of their topographical proximities. The substantial genetic variation observed was likely due to the predominance of selfing species, the relative proximity of prospected sites, human impacts, and the nature of the SARDI core collections, which are selected for their high genetic diversity. The results of this first report on Moroccan Medicago species will be of great interest for establishing strategies aiming at reasonable management and selection programs for local and Mediterranean germplasm in the face of increasing environmental change.

EvolQG - An R package for evolutionary quantitative genetics

PubMed Central

Melo, Diogo; Garcia, Guilherme; Hubbe, Alex; Assis, Ana Paula; Marroig, Gabriel

2016-01-01

We present an open source package for performing evolutionary quantitative genetics analyses in the R environment for statistical computing. Evolutionary theory shows that evolution depends critically on the available variation in a given population. When dealing with many quantitative traits this variation is expressed in the form of a covariance matrix, particularly the additive genetic covariance matrix or sometimes the phenotypic matrix, when the genetic matrix is unavailable and there is evidence the phenotypic matrix is sufficiently similar to the genetic matrix. Given this mathematical representation of available variation, the \\textbf{EvolQG} package provides functions for calculation of relevant evolutionary statistics; estimation of sampling error; corrections for this error; matrix comparison via correlations, distances and matrix decomposition; analysis of modularity patterns; and functions for testing evolutionary hypotheses on taxa diversification. PMID:27785352

Effect of flaw size and temperature on the matrix cracking behavior of a brittle ceramic matrix composite

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

Anandakumar, U.; Webb, J.E.; Singh, R.N.

The matrix cracking behavior of a zircon matrix - uniaxial SCS 6 fiber composite was studied as a function of initial flaw size and temperature. The composites were fabricated by a tape casting and hot pressing technique. Surface flaws of controlled size were introduced using a vicker`s indenter. The composite samples were tested in three point flexure at three different temperatures to study the non steady state and steady state matrix cracking behavior. The composite samples exhibited steady state and non steady matrix cracking behavior at all temperatures. The steady state matrix cracking stress and steady state crack size increasedmore » with increasing temperature. The results of the study correlated well with the results predicted by the matrix cracking models.« less

Co-expression Network Approach to Studying the Effects of Botulinum Neurotoxin-A.

PubMed

Mukund, Kavitha; Ward, Samuel R; Lieber, Richard L; Subramaniam, Shankar

2017-10-16

Botulinum Neurotoxin A (BoNT-A) is a potent neurotoxin with several clinical applications.The goal of this study was to utilize co-expression network theory to analyze temporal transcriptional data from skeletal muscle after BoNT-A treatment. Expression data for 2000 genes (extracted using a ranking heuristic) served as the basis for this analysis. Using weighted gene co-expression network analysis (WGCNA), we identified 19 co-expressed modules, further hierarchically clustered into 5 groups. Quantifying average expression and co-expression patterns across these groups revealed temporal aspects of muscle's response to BoNT-A. Functional analysis revealed enrichment of group 1 with metabolism; group 5 with contradictory functions of atrophy and cellular recovery; and groups 2 and 3 with extracellular matrix (ECM) and non-fast fiber isoforms. Topological positioning of two highly ranked, significantly expressed genes- Dclk1 and Ostalpha within group 5 suggested possible mechanistic roles in recovery from BoNT-A induced atrophy. Phenotypic correlations of groups with titin and myosin protein content further emphasized the effect of BoNT-A on the sarcomeric contraction machinery in early phase of chemodenervation. In summary, our approach revealed a hierarchical functional response to BoNT-A induced paralysis with early metabolic and later ECM responses and identified putative biomarkers associated with chemodenervation. Additionally, our results provide an unbiased validation of the response documented in our previous workBotulinum Neurotoxin A (BoNT-A) is a potent neurotoxin with several clinical applications.The goal of this study was to utilize co-expression network theory to analyze temporal transcriptional data from skeletal muscle after BoNT-A treatment. Expression data for 2000 genes (extracted using a ranking heuristic) served as the basis for this analysis. Using weighted gene co-expression network analysis (WGCNA), we identified 19 co-expressed modules, further hierarchically clustered into 5 groups. Quantifying average expression and co-expression patterns across these groups revealed temporal aspects of muscle's response to BoNT-A. Functional analysis revealed enrichment of group 1 with metabolism; group 5 with contradictory functions of atrophy and cellular recovery; and groups 2 and 3 with extracellular matrix (ECM) and non-fast fiber isoforms. Topological positioning of two highly ranked, significantly expressed genes- Dclk1 and Ostalpha within group 5 suggested possible mechanistic roles in recovery from BoNT-A induced atrophy. Phenotypic correlations of groups with titin and myosin protein content further emphasized the effect of BoNT-A on the sarcomeric contraction machinery in early phase of chemodenervation. In summary, our approach revealed a hierarchical functional response to BoNT-A induced paralysis with early metabolic and later ECM responses and identified putative biomarkers associated with chemodenervation. Additionally, our results provide an unbiased validation of the response documented in our previous work.

Sensitivity analysis of a sound absorption model with correlated inputs

NASA Astrophysics Data System (ADS)

Chai, W.; Christen, J.-L.; Zine, A.-M.; Ichchou, M.

2017-04-01

Sound absorption in porous media is a complex phenomenon, which is usually addressed with homogenized models, depending on macroscopic parameters. Since these parameters emerge from the structure at microscopic scale, they may be correlated. This paper deals with sensitivity analysis methods of a sound absorption model with correlated inputs. Specifically, the Johnson-Champoux-Allard model (JCA) is chosen as the objective model with correlation effects generated by a secondary micro-macro semi-empirical model. To deal with this case, a relatively new sensitivity analysis method Fourier Amplitude Sensitivity Test with Correlation design (FASTC), based on Iman's transform, is taken into application. This method requires a priori information such as variables' marginal distribution functions and their correlation matrix. The results are compared to the Correlation Ratio Method (CRM) for reference and validation. The distribution of the macroscopic variables arising from the microstructure, as well as their correlation matrix are studied. Finally the results of tests shows that the correlation has a very important impact on the results of sensitivity analysis. Assessment of correlation strength among input variables on the sensitivity analysis is also achieved.

Evolution of worldwide stock markets, correlation structure, and correlation-based graphs

NASA Astrophysics Data System (ADS)

Song, Dong-Ming; Tumminello, Michele; Zhou, Wei-Xing; Mantegna, Rosario N.

2011-08-01

We investigate the daily correlation present among market indices of stock exchanges located all over the world in the time period January 1996 to July 2009. We discover that the correlation among market indices presents both a fast and a slow dynamics. The slow dynamics reflects the development and consolidation of globalization. The fast dynamics is associated with critical events that originate in a specific country or region of the world and rapidly affect the global system. We provide evidence that the short term time scale of correlation among market indices is less than 3 trading months (about 60 trading days). The average values of the nondiagonal elements of the correlation matrix, correlation-based graphs, and the spectral properties of the largest eigenvalues and eigenvectors of the correlation matrix are carrying information about the fast and slow dynamics of the correlation of market indices. We introduce a measure of mutual information based on link co-occurrence in networks in order to detect the fast dynamics of successive changes of correlation-based graphs in a quantitative way.

Principle component analysis (PCA) for investigation of relationship between population dynamics of microbial pathogenesis, chemical and sensory characteristics in beef slices containing Tarragon essential oil.

PubMed

Alizadeh Behbahani, Behrooz; Tabatabaei Yazdi, Farideh; Shahidi, Fakhri; Mortazavi, Seyed Ali; Mohebbi, Mohebbat

2017-04-01

Principle component analysis (PCA) was employed to examine the effect of the exerted treatments on the beef shelf life as well as discovering the correlations between the studied responses. Considering the variability of the dimensions of the responses, correlation coefficients were applied to form the matrix and extract the eigenvalue. Antimicrobial effect was evaluated on 10 pathogenic microorganisms through the methods of hole-plate diffusion method, disk diffusion method, pour plate method, minimum inhibitory concentration and minimum bactericidal/fungicidal concentration. Antioxidant potential and total phenolic content were examined through the method of 2,2-diphenyl-1-picrylhydrazyl (DPPH) and Folin-Ciocalteu method, respectively. The components were identified through gas chromatography and gas chromatography/mass spectrometry. Barhang seed mucilage (BSM) based edible coating containing 0, 0.5, 1 and 1.5% (w/w) Tarragon (T) essential oil mix were applied on beef slices to control the growth of pathogenic microorganisms. Microbiological (total viable count, psychrotrophic count, Escherichia coli, Staphylococcus aureus and fungi), chemical (thiobarbituric acid, peroxide value and pH) and sensory characteristics (odor, color and overall acceptability) analysis measurements were made during the storage periodically. PCA was employed to examine the effect of the exerted treatments on the beef shelf life as well as discovering the correlations between the studied responses. Considering the variability of the dimensions of the responses, correlation coefficients were applied to form the matrix and extract the eigenvalue. The PCA showed that the properties of the uncoated meat samples on the 9th, 12th, 15th and 18th days of storage are continuously changing independent of the exerted treatments on the other samples. This reveals the effect of the exerted treatments on the samples. Copyright © 2017 Elsevier Ltd. All rights reserved.

Genetic Background is a Key Determinant of Glomerular Extracellular Matrix Composition and Organization

PubMed Central

Randles, Michael J.; Woolf, Adrian S.; Huang, Jennifer L.; Byron, Adam; Humphries, Jonathan D.; Price, Karen L.; Kolatsi-Joannou, Maria; Collinson, Sophie; Denny, Thomas; Knight, David; Mironov, Aleksandr; Starborg, Toby; Korstanje, Ron; Humphries, Martin J.; Long, David A.

2015-01-01

Glomerular disease often features altered histologic patterns of extracellular matrix (ECM). Despite this, the potential complexities of the glomerular ECM in both health and disease are poorly understood. To explore whether genetic background and sex determine glomerular ECM composition, we investigated two mouse strains, FVB and B6, using RNA microarrays of isolated glomeruli combined with proteomic glomerular ECM analyses. These studies, undertaken in healthy young adult animals, revealed unique strain- and sex-dependent glomerular ECM signatures, which correlated with variations in levels of albuminuria and known predisposition to progressive nephropathy. Among the variation, we observed changes in netrin 4, fibroblast growth factor 2, tenascin C, collagen 1, meprin 1-α, and meprin 1-β. Differences in protein abundance were validated by quantitative immunohistochemistry and Western blot analysis, and the collective differences were not explained by mutations in known ECM or glomerular disease genes. Within the distinct signatures, we discovered a core set of structural ECM proteins that form multiple protein–protein interactions and are conserved from mouse to man. Furthermore, we found striking ultrastructural changes in glomerular basement membranes in FVB mice. Pathway analysis of merged transcriptomic and proteomic datasets identified potential ECM regulatory pathways involving inhibition of matrix metalloproteases, liver X receptor/retinoid X receptor, nuclear factor erythroid 2-related factor 2, notch, and cyclin-dependent kinase 5. These pathways may therefore alter ECM and confer susceptibility to disease. PMID:25896609

Comparison of Regenerative Tissue Quality following Matrix-Associated Cell Implantation Using Amplified Chondrocytes Compared to Synovium-Derived Stem Cells in a Rabbit Model for Cartilage Lesions.

PubMed

Schmal, Hagen; Kowal, Justyna M; Kassem, Moustapha; Seidenstuecker, Michael; Bernstein, Anke; Böttiger, Katharina; Xiong, Tanshiyue; Südkamp, Norbert P; Kubosch, Eva J

2018-01-01

Known problems of the autologous chondrocyte implantation motivate the search for cellular alternatives. The aim of the study was to test the potential of synovium-derived stem cells (SMSC) to regenerate cartilage using a matrix-associated implantation. In an osteochondral defect model of the medial femoral condyle in a rabbit, a collagen membrane was seeded with either culture-expanded allogenic chondrocytes or SMSC and then transplanted into the lesion. A tailored piece synovium served as a control. Rabbit SMSC formed typical cartilage in vitro. Macroscopic evaluation of defect healing and the thickness of the regenerated tissue did not reveal a significant difference between the intervention groups. However, instantaneous and shear modulus, reflecting the biomechanical strength of the repair tissue, was superior in the implantation group using allogenic chondrocytes ( p < 0.05). This correlated with a more chondrogenic structure and higher proteoglycan expression, resulting in a lower OARSI score ( p < 0.05). The repair tissue of all groups expressed comparable amounts of the collagen types I, II, and X. Cartilage regeneration following matrix-associated implantation using allogenic undifferentiated synovium-derived stem cells in a defect model in rabbits showed similar macroscopic results and collagen composition compared to amplified chondrocytes; however, biomechanical characteristics and histological scoring were inferior.

Comparison of Regenerative Tissue Quality following Matrix-Associated Cell Implantation Using Amplified Chondrocytes Compared to Synovium-Derived Stem Cells in a Rabbit Model for Cartilage Lesions

PubMed Central

Kowal, Justyna M.; Seidenstuecker, Michael; Bernstein, Anke; Böttiger, Katharina; Xiong, Tanshiyue; Südkamp, Norbert P.

2018-01-01

Known problems of the autologous chondrocyte implantation motivate the search for cellular alternatives. The aim of the study was to test the potential of synovium-derived stem cells (SMSC) to regenerate cartilage using a matrix-associated implantation. In an osteochondral defect model of the medial femoral condyle in a rabbit, a collagen membrane was seeded with either culture-expanded allogenic chondrocytes or SMSC and then transplanted into the lesion. A tailored piece synovium served as a control. Rabbit SMSC formed typical cartilage in vitro. Macroscopic evaluation of defect healing and the thickness of the regenerated tissue did not reveal a significant difference between the intervention groups. However, instantaneous and shear modulus, reflecting the biomechanical strength of the repair tissue, was superior in the implantation group using allogenic chondrocytes (p < 0.05). This correlated with a more chondrogenic structure and higher proteoglycan expression, resulting in a lower OARSI score (p < 0.05). The repair tissue of all groups expressed comparable amounts of the collagen types I, II, and X. Cartilage regeneration following matrix-associated implantation using allogenic undifferentiated synovium-derived stem cells in a defect model in rabbits showed similar macroscopic results and collagen composition compared to amplified chondrocytes; however, biomechanical characteristics and histological scoring were inferior. PMID:29765410

Flexible regenerated cellulose/polypyrrole composite films with enhanced dielectric properties.

PubMed

Raghunathan, Sreejesh Poikavila; Narayanan, Sona; Poulose, Aby Cheruvathur; Joseph, Rani

2017-02-10

Flexible regenerated cellulose/polypyrrole (RC-PPy) conductive composite films were prepared by insitu polymerization of pyrrole on regenerated cellulose (RC) matrix using ammonium persulphate as oxidant. FTIR, XPS and XRD analysis of RC-PPy composite films revealed strong interaction between polypyrrole (PPy) and RC matrix. XRD results indicated that crystalline structure of RC matrix remains intact even after composite formation. SEM micrographs revealed the formation of a continuous conductive network of PPy particles in the RC matrix, leading to significant improvement in electrical and dielectric properties. The electrical conductivity of RC-PPy composites with 12wt% of PPy was 3.2×10 -5 S/cm, which is approximately seven fold higher than that of RC. Composites showed high dielectric constant and low dielectric loss values, which is essential in capacitor application. Copyright © 2016 Elsevier Ltd. All rights reserved.

EMMPRIN expression in oral squamous cell carcinomas: correlation with tumor proliferation and patient survival.

PubMed

Monteiro, Luís Silva; Delgado, Maria Leonor; Ricardo, Sara; Garcez, Fernanda; do Amaral, Barbas; Pacheco, José Júlio; Lopes, Carlos; Bousbaa, Hassan

2014-01-01

The aim of our study was to explore the clinicopathological and prognostic significance of extracellular matrix metalloproteinase inducer (EMMPRIN) expression in oral squamous cell carcinomas (OSCC), and its relation with the proliferative tumor status of OSCC. We examined EMMPRIN and Ki-67 proteins expression by immunohistochemistry in 74 cases with OSCC. Statistical analysis was conducted to examine their clinicopathological and prognostic significance in OSCC. EMMPRIN membrane expression was observed in all cases, with both membrane and cytoplasmic tumor expression in 61 cases (82.4%). EMMPRIN overexpression was observed in 56 cases (75.7%). Moderately or poorly differentiated tumors showed EMMPRIN overexpression more frequently than well-differentiated tumors (P = 0.002). Overexpression of EMMPRIN was correlated with high Ki-67 expression (P = 0.004). In the multivariate analysis, EMMPRIN overexpression reveals an adverse independent prognostic value for cancer-specific survival (CSS) (P = 0.034). Our results reveal that EMMPRIN protein is overexpressed in more than two-thirds of OSCC cases, especially in high proliferative and less differentiated tumors. The independent value of EMMPRIN overexpression in CSS suggests that this protein could be used as an important biological prognostic marker for patients with OSCC. Moreover, the high expression of EMMPRIN makes it a possible therapeutic target in OSCC patients.

Temporal evolution of financial-market correlations.

PubMed

Fenn, Daniel J; Porter, Mason A; Williams, Stacy; McDonald, Mark; Johnson, Neil F; Jones, Nick S

2011-08-01

We investigate financial market correlations using random matrix theory and principal component analysis. We use random matrix theory to demonstrate that correlation matrices of asset price changes contain structure that is incompatible with uncorrelated random price changes. We then identify the principal components of these correlation matrices and demonstrate that a small number of components accounts for a large proportion of the variability of the markets that we consider. We characterize the time-evolving relationships between the different assets by investigating the correlations between the asset price time series and principal components. Using this approach, we uncover notable changes that occurred in financial markets and identify the assets that were significantly affected by these changes. We show in particular that there was an increase in the strength of the relationships between several different markets following the 2007-2008 credit and liquidity crisis.

Temporal evolution of financial-market correlations

NASA Astrophysics Data System (ADS)

Fenn, Daniel J.; Porter, Mason A.; Williams, Stacy; McDonald, Mark; Johnson, Neil F.; Jones, Nick S.

2011-08-01

We investigate financial market correlations using random matrix theory and principal component analysis. We use random matrix theory to demonstrate that correlation matrices of asset price changes contain structure that is incompatible with uncorrelated random price changes. We then identify the principal components of these correlation matrices and demonstrate that a small number of components accounts for a large proportion of the variability of the markets that we consider. We characterize the time-evolving relationships between the different assets by investigating the correlations between the asset price time series and principal components. Using this approach, we uncover notable changes that occurred in financial markets and identify the assets that were significantly affected by these changes. We show in particular that there was an increase in the strength of the relationships between several different markets following the 2007-2008 credit and liquidity crisis.

Random Matrix Theory and Econophysics

NASA Astrophysics Data System (ADS)

Rosenow, Bernd

2000-03-01

Random Matrix Theory (RMT) [1] is used in many branches of physics as a ``zero information hypothesis''. It describes generic behavior of different classes of systems, while deviations from its universal predictions allow to identify system specific properties. We use methods of RMT to analyze the cross-correlation matrix C of stock price changes [2] of the largest 1000 US companies. In addition to its scientific interest, the study of correlations between the returns of different stocks is also of practical relevance in quantifying the risk of a given stock portfolio. We find [3,4] that the statistics of most of the eigenvalues of the spectrum of C agree with the predictions of RMT, while there are deviations for some of the largest eigenvalues. We interpret these deviations as a system specific property, e.g. containing genuine information about correlations in the stock market. We demonstrate that C shares universal properties with the Gaussian orthogonal ensemble of random matrices. Furthermore, we analyze the eigenvectors of C through their inverse participation ratio and find eigenvectors with large ratios at both edges of the eigenvalue spectrum - a situation reminiscent of localization theory results. This work was done in collaboration with V. Plerou, P. Gopikrishnan, T. Guhr, L.A.N. Amaral, and H.E Stanley and is related to recent work of Laloux et al.. 1. T. Guhr, A. Müller Groeling, and H.A. Weidenmüller, ``Random Matrix Theories in Quantum Physics: Common Concepts'', Phys. Rep. 299, 190 (1998). 2. See, e.g. R.N. Mantegna and H.E. Stanley, Econophysics: Correlations and Complexity in Finance (Cambridge University Press, Cambridge, England, 1999). 3. V. Plerou, P. Gopikrishnan, B. Rosenow, L.A.N. Amaral, and H.E. Stanley, ``Universal and Nonuniversal Properties of Cross Correlations in Financial Time Series'', Phys. Rev. Lett. 83, 1471 (1999). 4. V. Plerou, P. Gopikrishnan, T. Guhr, B. Rosenow, L.A.N. Amaral, and H.E. Stanley, ``Random Matrix Theory Analysis of Diffusion in Stock Price Dynamics, preprint

Covariance structure in the skull of Catarrhini: a case of pattern stasis and magnitude evolution.

PubMed

de Oliveira, Felipe Bandoni; Porto, Arthur; Marroig, Gabriel

2009-04-01

The study of the genetic variance/covariance matrix (G-matrix) is a recent and fruitful approach in evolutionary biology, providing a window of investigating for the evolution of complex characters. Although G-matrix studies were originally conducted for microevolutionary timescales, they could be extrapolated to macroevolution as long as the G-matrix remains relatively constant, or proportional, along the period of interest. A promising approach to investigating the constancy of G-matrices is to compare their phenotypic counterparts (P-matrices) in a large group of related species; if significant similarity is found among several taxa, it is very likely that the underlying G-matrices are also equivalent. Here we study the similarity of covariance and correlation structure in a broad sample of Old World monkeys and apes (Catarrhini). We made phylogenetically structured comparisons of correlation and covariance matrices derived from 39 skull traits, ranging from between species to the superfamily level. We also compared the overall magnitude of integration between skull traits (r2) for all Catarrhini genera. Our results show that P-matrices were not strictly constant among catarrhines, but the amount of divergence observed among taxa was generally low. There was significant and positive correlation between the amount of divergence in correlation and covariance patterns among the 30 genera and their phylogenetic distances derived from a recently proposed phylogenetic hypothesis. Our data demonstrate that the P-matrices remained relatively similar along the evolutionary history of catarrhines, and comparisons with the G-matrix available for a New World monkey genus (Saguinus) suggests that the same holds for all anthropoids. The magnitude of integration, in contrast, varied considerably among genera, indicating that evolution of the magnitude, rather than the pattern of inter-trait correlations, might have played an important role in the diversification of the catarrhine skull.

Fibrotic-like changes in degenerate human intervertebral discs revealed by quantitative proteomic analysis.

PubMed

Yee, A; Lam, M P Y; Tam, V; Chan, W C W; Chu, I K; Cheah, K S E; Cheung, K M C; Chan, D

2016-03-01

Intervertebral disc degeneration (IDD) can lead to symptomatic conditions including sciatica and back pain. The purpose of this study is to understand the extracellular matrix (ECM) changes in disc biology through comparative proteomic analysis of degenerated and non-degenerated human intervertebral disc (IVD) tissues of different ages. Seven non-degenerated (11-46 years of age) and seven degenerated (16-53 years of age) annulus fibrosus (AF) and nucleus pulposus (NP) samples were used. Proteins were extracted using guanidine hydrochloride, separated from large proteoglycans (PGs) by caesium chloride (CsCl) density gradient ultracentrifugation, and identified using liquid chromatography (LC) coupled with tandem mass spectrometry (MS/MS). For quantitative comparison, proteins were labeled with iTRAQ reagents. Collagen fibrils in the NP were assessed using scanning electron microscopy (SEM). In the AF, quantitative analysis revealed increased levels of HTRA1, COMP and CILP in degeneration when compared with samples from older individuals. Fibronectin showed increment with age and degeneration. In the NP, more CILP and CILP2 were present in degenerated samples of younger individuals. Reduced protein solubility was observed in degenerated and older non-degenerated samples correlated with an accumulation of type I collagen in the insoluble fibers. Characterization of collagen fibrils in the NP revealed smaller mean fibril diameters and decreased porosity in the degenerated samples. Our study identified distinct matrix changes associated with aging and degeneration in the intervertebral discs (IVDs). The nature of the ECM changes, together with observed decreased in solubility and changes in fibril diameter is consistent with a fibrotic-like environment. Copyright © 2015 Osteoarthritis Research Society International. Published by Elsevier Ltd. All rights reserved.

Application of Solid-State NMR Relaxometry for Characterization and Formulation Optimization of Grinding-Induced Drug Nanoparticle.

PubMed

Ueda, Keisuke; Higashi, Kenjirou; Moribe, Kunikazu

2016-03-07

The formation mechanism of drug nanoparticles was investigated using solid-state nuclear magnetic resonance (NMR) techniques for the efficient discovery of an optimized nanoparticle formulation. The cogrinding of nifedipine (NIF) with polymers, including hydroxypropyl methylcellulose (HPMC) and polyvinylpyrrolidone (PVP), and sodium dodecyl sulfate (SDS) was performed to prepare the NIF nanoparticle formulations. Then, solid-state NMR relaxometry was used for the nanometer-order characterization of NIF in the polymer matrix. Solid-state NMR measurements revealed that the crystal size of NIF was reduced to several tens of nanometers with amorphization of NIF by cogrinding with HPMC and SDS for 100 min. Similarly, the size of the NIF crystal was reduced to less than 90 nm in the 40 min ground mixture of NIF/PVP/SDS. Furthermore, 100 min grinding of NIF/PVP/SDS induced amorphization of almost all the NIF crystals followed by nanosizing. The hydrogen bond between NIF and PVP led to the efficient amorphization of NIF in the NIF/PVP/SDS system compared with NIF/HPMC/SDS system. The efficient nanosizing of the NIF crystal in the solid state, revealed by the solid-state NMR relaxation time measurements, enabled the formation of large amounts of NIF nanoparticles in water followed by the polymer dissolution. In contrast, excess amorphization of the NIF crystals failed to efficiently prepare the NIF nanoparticles. The solid-state characterization of the crystalline NIF revealed good correlation with the NIF nanoparticles formation during aqueous dispersion. Furthermore, the solid-state NMR measurements including relaxometry successfully elucidated the nanometer-order dispersion state of NIF in polymer matrix, leading to the discovery of optimized conditions for the preparation of suitable drug nanoparticles.

A technique for plasma velocity-space cross-correlation

NASA Astrophysics Data System (ADS)

Mattingly, Sean; Skiff, Fred

2018-05-01

An advance in experimental plasma diagnostics is presented and used to make the first measurement of a plasma velocity-space cross-correlation matrix. The velocity space correlation function can detect collective fluctuations of plasmas through a localized measurement. An empirical decomposition, singular value decomposition, is applied to this Hermitian matrix in order to obtain the plasma fluctuation eigenmode structure on the ion distribution function. A basic theory is introduced and compared to the modes obtained by the experiment. A full characterization of these modes is left for future work, but an outline of this endeavor is provided. Finally, the requirements for this experimental technique in other plasma regimes are discussed.

Role of the Euclidean signature in lattice calculations of quasidistributions and other nonlocal matrix elements

NASA Astrophysics Data System (ADS)

Briceño, Raúl A.; Hansen, Maxwell T.; Monahan, Christopher J.

2017-07-01

Lattice quantum chromodynamics (QCD) provides the only known systematic, nonperturbative method for first-principles calculations of nucleon structure. However, for quantities such as light-front parton distribution functions (PDFs) and generalized parton distributions (GPDs), the restriction to Euclidean time prevents direct calculation of the desired observable. Recently, progress has been made in relating these quantities to matrix elements of spatially nonlocal, zero-time operators, referred to as quasidistributions. Still, even for these time-independent matrix elements, potential subtleties have been identified in the role of the Euclidean signature. In this work, we investigate the analytic behavior of spatially nonlocal correlation functions and demonstrate that the matrix elements obtained from Euclidean lattice QCD are identical to those obtained using the Lehmann-Symanzik-Zimmermann reduction formula in Minkowski space. After arguing the equivalence on general grounds, we also show that it holds in a perturbative calculation, where special care is needed to identify the lattice prediction. Finally we present a proof of the uniqueness of the matrix elements obtained from Minkowski and Euclidean correlation functions to all order in perturbation theory.

Role of the Euclidean signature in lattice calculations of quasidistributions and other nonlocal matrix elements

DOE PAGES

Briceno, Raul A.; Hansen, Maxwell T.; Monahan, Christopher J.

2017-07-11

Lattice quantum chromodynamics (QCD) provides the only known systematic, nonperturbative method for first-principles calculations of nucleon structure. However, for quantities such as light-front parton distribution functions (PDFs) and generalized parton distributions (GPDs), the restriction to Euclidean time prevents direct calculation of the desired observable. Recently, progress has been made in relating these quantities to matrix elements of spatially nonlocal, zero-time operators, referred to as quasidistributions. Still, even for these time-independent matrix elements, potential subtleties have been identified in the role of the Euclidean signature. In this work, we investigate the analytic behavior of spatially nonlocal correlation functions and demonstrate thatmore » the matrix elements obtained from Euclidean lattice QCD are identical to those obtained using the Lehmann-Symanzik-Zimmermann reduction formula in Minkowski space. After arguing the equivalence on general grounds, we also show that it holds in a perturbative calculation, where special care is needed to identify the lattice prediction. Lastly, we present a proof of the uniqueness of the matrix elements obtained from Minkowski and Euclidean correlation functions to all order in perturbation theory.« less

Heterogeneous distribution of alectinib in neuroblastoma xenografts revealed by matrix-assisted laser desorption ionization mass spectrometry imaging: a pilot study.

PubMed

Ryu, Shoraku; Hayashi, Mitsuhiro; Aikawa, Hiroaki; Okamoto, Isamu; Fujiwara, Yasuhiro; Hamada, Akinobu

2018-01-01

The penetration of the anaplastic lymphoma kinase (ALK) inhibitor alectinib in neuroblastomas and the relationship between alectinib and ALK expression are unknown. The aim of this study was to perform a quantitative investigation of the inter- and intra-tumoural distribution of alectinib in different neuroblastoma xenograft models using matrix-assisted laser desorption ionization MS imaging (MALDI-MSI). The distribution of alectinib in NB1 (ALK amplification) and SK-N-FI (ALK wild-type) xenograft tissues was analysed using MALDI-MSI. The abundance of alectinib in tumours and intra-tumoural areas was quantified using ion signal intensities from MALDI-MSI after normalization by correlation with LC-MS/MS. The distribution of alectinib was heterogeneous in neuroblastomas. The penetration of alectinib was not significantly different between ALK amplification and ALK wide-type tissues using both LC-MS/MS concentrations and MSI intensities. Normalization with an internal standard increased the quantitative property of MSI by adjusting for the ion suppression effect. The distribution of alectinib in different intra-tumoural areas can alternatively be quantified from MS images by correlation with LC-MS/MS. The penetration of alectinib into tumour tissues may not be homogenous or influenced by ALK expression in the early period after single-dose administration. MALDI-MSI may prove to be a valuable pharmaceutical method for elucidating the mechanism of action of drugs by clarifying their microscopic distribution in heterogeneous tissues. © 2017 The British Pharmacological Society.

Statistics of time delay and scattering correlation functions in chaotic systems. II. Semiclassical approximation

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

Novaes, Marcel

2015-06-15

We consider S-matrix correlation functions for a chaotic cavity having M open channels, in the absence of time-reversal invariance. Relying on a semiclassical approximation, we compute the average over E of the quantities Tr[S{sup †}(E − ϵ) S(E + ϵ)]{sup n}, for general positive integer n. Our result is an infinite series in ϵ, whose coefficients are rational functions of M. From this, we extract moments of the time delay matrix Q = − iħS{sup †}dS/dE and check that the first 8 of them agree with the random matrix theory prediction from our previous paper [M. Novaes, J. Math. Phys.more » 56, 062110 (2015)].« less

A physiologically motivated sparse, compact, and smooth (SCS) approach to EEG source localization.

PubMed

Cao, Cheng; Akalin Acar, Zeynep; Kreutz-Delgado, Kenneth; Makeig, Scott

2012-01-01

Here, we introduce a novel approach to the EEG inverse problem based on the assumption that principal cortical sources of multi-channel EEG recordings may be assumed to be spatially sparse, compact, and smooth (SCS). To enforce these characteristics of solutions to the EEG inverse problem, we propose a correlation-variance model which factors a cortical source space covariance matrix into the multiplication of a pre-given correlation coefficient matrix and the square root of the diagonal variance matrix learned from the data under a Bayesian learning framework. We tested the SCS method using simulated EEG data with various SNR and applied it to a real ECOG data set. We compare the results of SCS to those of an established SBL algorithm.

Random matrix theory and cross-correlations in global financial indices and local stock market indices

NASA Astrophysics Data System (ADS)

Nobi, Ashadun; Maeng, Seong Eun; Ha, Gyeong Gyun; Lee, Jae Woo

2013-02-01

We analyzed cross-correlations between price fluctuations of global financial indices (20 daily stock indices over the world) and local indices (daily indices of 200 companies in the Korean stock market) by using random matrix theory (RMT). We compared eigenvalues and components of the largest and the second largest eigenvectors of the cross-correlation matrix before, during, and after the global financial the crisis in the year 2008. We find that the majority of its eigenvalues fall within the RMT bounds [ λ -, λ +], where λ - and λ + are the lower and the upper bounds of the eigenvalues of random correlation matrices. The components of the eigenvectors for the largest positive eigenvalues indicate the identical financial market mode dominating the global and local indices. On the other hand, the components of the eigenvector corresponding to the second largest eigenvalue are positive and negative values alternatively. The components before the crisis change sign during the crisis, and those during the crisis change sign after the crisis. The largest inverse participation ratio (IPR) corresponding to the smallest eigenvector is higher after the crisis than during any other periods in the global and local indices. During the global financial the crisis, the correlations among the global indices and among the local stock indices are perturbed significantly. However, the correlations between indices quickly recover the trends before the crisis.

Shear banding leads to accelerated aging dynamics in a metallic glass

NASA Astrophysics Data System (ADS)

Küchemann, Stefan; Liu, Chaoyang; Dufresne, Eric M.; Shin, Jeremy; Maaß, Robert

2018-01-01

Traditionally, strain localization in metallic glasses is related to the thickness of the shear defect, which is confined to the nanometer scale. Using site-specific x-ray photon correlation spectroscopy, we reveal significantly accelerated relaxation dynamics around a shear band in a metallic glass at a length scale that is orders of magnitude larger than the defect itself. The relaxation time in the shear-band vicinity is up to ten times smaller compared to the as-cast matrix, and the relaxation dynamics occurs in a characteristic three-stage aging response that manifests itself in the temperature-dependent shape parameter known from classical stretched exponential relaxation dynamics of disordered materials. We demonstrate that the time-dependent correlation functions describing the aging at different temperatures can be captured and collapsed using simple scaling functions. These insights highlight how a ubiquitous nanoscale strain-localization mechanism in metallic glasses leads to a fundamental change of the relaxation dynamics at the mesoscale.

Correlation study of nanocrystalline carbon doped thin films prepared by a thermionic vacuum arc deposition technique

NASA Astrophysics Data System (ADS)

Dinca-Balan, Virginia; Vladoiu, Rodica; Mandes, Aurelia; Prodan, Gabriel

2017-11-01

The synthesis of Ag, Mg and Si nanocrystalline, embedded in a hydrogen-free amorphous carbon (a-C) matrix, deposited by a high vacuum and free buffer gas technique, were investigated. The films with compact structures and extremely smooth surfaces were prepared using the thermionic vacuum arc method in one electron gun configuration, on glass and silicon substrates. The surface morphology and wettability of the obtained multifunctional thin films were investigated using transmission electron microscopy (TEM), scanning electron microscopy (SEM) and free surface energy (FSE) by See System. The results from the TEM measurements show how the Ag, Mg and Si interacted with carbon and the influence these materials have on the thin film structure formation and the grain size distribution. SEM correlated with EDX results reveal a very precise comparative study, regarding the quantity of the elements that morphed into carbides nanostructures. Also, the FSE results prove how different materials in combination with carbon can make changes to the surface properties.

Shear banding leads to accelerated aging dynamics in a metallic glass

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

Küchemann, Stefan; Liu, Chaoyang; Dufresne, Eric M.

Traditionally, strain localization in metallic glasses is related to the thickness of the shear defect, which is confined to the nanometer scale. In this study, using site-specific x-ray photon correlation spectroscopy (XPCS), we reveal significantly accelerated relaxation dynamics around a shear band in a metallic glass at a length scale that is orders of magnitude larger than the defect itself. The relaxation time in the shear-band vicinity is up to ten-times smaller compared to the as-cast matrix, and the relaxation dynamics occurs in a characteristic three-stage aging response that manifests itself in the temperature-dependent shape parameter known from classical stretchedmore » exponential relaxation dynamics of disordered materials. We demonstrate that the time-dependent correlation functions describing the aging at different temperatures can be captured and collapsed using simple scaling functions. Finally, these insights highlight how an ubiquitous nano-scale strain-localization mechanism in metallic glasses leads to a fundamental change of the relaxation dynamics at the mesoscale.« less

MiR-142-5p promotes bone repair by maintaining osteoblast activity.

PubMed

Tu, Manli; Tang, Juanjuan; He, Hongbo; Cheng, Peng; Chen, Chao

2017-05-01

MicroRNAs play important roles in regulating bone regeneration and remodeling. However, the pathophysiological roles of microRNAs in bone repair remain unclear. Here we identify a significant upregulation of miR-142-5p correlated with active osteoblastogenesis during the bone healing process. In vitro, miR-142-5p promoted osteoblast activity and matrix mineralization by targeting the gene encoding WW-domain-containing E3 ubiquitin protein ligase 1. We also found that the expression of miR-142-5p in the callus of aged mice was lower than that in the callus of young mice and directly correlated with the age-related delay in bone healing. Furthermore, treatment with agomir-142-5p in the fracture areas stimulated osteoblast activity which repaired the bone fractures in aged mice. Thus, our study revealed that miR-142-5p plays a crucial role in healing fractures by maintaining osteoblast activity, and provided a new molecular target therapeutic strategy for bone healing.

Shear banding leads to accelerated aging dynamics in a metallic glass

DOE PAGES

Küchemann, Stefan; Liu, Chaoyang; Dufresne, Eric M.; ...

2018-01-11

Traditionally, strain localization in metallic glasses is related to the thickness of the shear defect, which is confined to the nanometer scale. In this study, using site-specific x-ray photon correlation spectroscopy (XPCS), we reveal significantly accelerated relaxation dynamics around a shear band in a metallic glass at a length scale that is orders of magnitude larger than the defect itself. The relaxation time in the shear-band vicinity is up to ten-times smaller compared to the as-cast matrix, and the relaxation dynamics occurs in a characteristic three-stage aging response that manifests itself in the temperature-dependent shape parameter known from classical stretchedmore » exponential relaxation dynamics of disordered materials. We demonstrate that the time-dependent correlation functions describing the aging at different temperatures can be captured and collapsed using simple scaling functions. Finally, these insights highlight how an ubiquitous nano-scale strain-localization mechanism in metallic glasses leads to a fundamental change of the relaxation dynamics at the mesoscale.« less

Geochemical assessment of heavy metals pollution in surface sediments of Vellar and Coleroon estuaries, southeast coast of India.

PubMed

Nethaji, S; Kalaivanan, R; Arya Viswam; Jayaprakash, M

2017-02-15

Surface sediments were collected from Vellar and Coleroon estuaries for determine sediment texture, calcium carbonate, organic matter and heavy metals. Pollution indices such as pollution load index (PLI), contamination factor (CF), enrichment factor (EF) and geo-accumulation index (I geo ) were done for this study to know the level of heavy metals pollution in the estuarine ecosystem. Pearson correlation matrix and factor were used to assess the relationship and source of heavy metals in the estuarine sediments. The results of PLI values reveal that the study area was polluted by all the heavy metals. The calculated values of CF and I geo followed the decreasing order Cu>Ni>Pb>Co>Cr>Zn>Mn>Fe and illustrate that Cu, Ni and Pb are contaminated due to anthropogenic sources in both estuaries. Correlation and factor analysis suggest that FeMn oxyhydroxides, organic matter and fine particles are responsible for high concentration of heavy metals. Copyright © 2016 Elsevier Ltd. All rights reserved.

Keratin 17 null mice exhibit age- and strain-dependent alopecia

PubMed Central

McGowan, Kevin M.; Tong, Xuemei; Colucci-Guyon, Emma; Langa, Francina; Babinet, Charles; Coulombe, Pierre A.

2002-01-01

Onset of type I keratin 17 (K17) synthesis marks the adoption of an appendageal fate within embryonic ectoderm, and its expression persists in specific cell types within mature hair, glands, and nail. We report that K17 null mice develop severe alopecia during the first week postbirth, correlating with hair fragility, alterations in follicular histology, and apoptosis in matrix cells. These alterations are incompletely penetrant and normalize starting with the first postnatal cycle. Absence of a hair phenotype correlates with a genetic strain-dependent compensation by related keratins, including K16. These findings reveal a crucial role for K17 in the structural integrity of the first hair produced and the survival of hair-producing cells. Given that identical inherited mutations in this gene can cause either pachyonychia congenita or steatocystoma multiplex, the features of this mouse model suggest that this clinical heterogeneity arises from a cell type-specific, genetically determined compensation by related keratins. PMID:12050118

Matrix metalloproteinase processing of signaling molecules to regulate inflammation.

PubMed

Butler, Georgina S; Overall, Christopher M

2013-10-01

Inflammation is a complex and highly regulated process that facilitates the clearance of pathogens and mediates tissue repair. Failure to resolve inflammation can lead to chronic inflammatory diseases such as periodontitis. Matrix metalloproteinases are generally thought to be detrimental in disease because degradation of extracellular matrix contributes to pathology. However, proteomic techniques (degradomics) are revealing that matrix metalloproteinases process a diverse array of substrates and therefore have a broad range of functions. Many matrix metalloproteinase substrates modulate inflammation and hence, by processing these proteins, matrix metalloproteinases can orchestrate the inflammatory response. © 2013 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Collagen in the spicule organic matrix of the gorgonian Leptogorgia virgulata

NASA Technical Reports Server (NTRS)

Kingsley, R. J.; Tsuzaki, M.; Watabe, N.; Mechanic, G. L.

1990-01-01

Decalcification of the calcareous spicules from the gorgonian Leptogorgia virgulata reveals an organic matrix that may be divided into water insoluble and soluble fractions. The insoluble fraction displays characteristics typical of collagen, which is an unusual component of an invertebrate calcium carbonate structure. This matrix fraction exhibits a collagenous amino acid profile and behavior upon SDS-PAGE. Furthermore, the reducible crosslink, dihydroxylysinonorleucine (DHLNL), is detected in this fraction. The composition of the matrix varies seasonally; i.e., the collagenous composition is most prevalent in the summer. These results indicate that the insoluble matrix is a dynamic structure. Potential roles of this matrix in spicule calcification are discussed.

Negative correlation between rates of molecular evolution and flowering cycles in temperate woody bamboos revealed by plastid phylogenomics.

PubMed

Ma, Peng-Fei; Vorontsova, Maria S; Nanjarisoa, Olinirina Prisca; Razanatsoa, Jacqueline; Guo, Zhen-Hua; Haevermans, Thomas; Li, De-Zhu

2017-12-21

Heterogeneous rates of molecular evolution are universal across the tree of life, posing challenges for phylogenetic inference. The temperate woody bamboos (tribe Arundinarieae, Poaceae) are noted for their extremely slow molecular evolutionary rates, supposedly caused by their mysterious monocarpic reproduction. However, the correlation between substitution rates and flowering cycles has not been formally tested. Here we present 15 newly sequenced plastid genomes of temperate woody bamboos, including the first genomes ever sequenced from Madagascar representatives. A data matrix of 46 plastid genomes representing all 12 lineages of Arundinarieae was assembled for phylogenetic and molecular evolutionary analyses. We conducted phylogenetic analyses using different sequences (e.g., coding and noncoding) combined with different data partitioning schemes, revealing conflicting relationships involving internodes among several lineages. A great difference in branch lengths were observed among the major lineages, and topological inconsistency could be attributed to long-branch attraction (LBA). Using clock model-fitting by maximum likelihood and Bayesian approaches, we furthermore demonstrated extensive rate variation among these major lineages. Rate accelerations mainly occurred for the isolated lineages with limited species diversification, totaling 11 rate shifts during the tribe's evolution. Using linear regression analysis, we found a negative correlation between rates of molecular evolution and flowering cycles for Arundinarieae, notwithstanding that the correlation maybe insignificant when taking the phylogenetic structure into account. Using the temperate woody bamboos as an example, we found further evidence that rate heterogeneity is universal in plants, suggesting that this will pose a challenge for phylogenetic reconstruction of bamboos. The bamboos with longer flowering cycles tend to evolve more slowly than those with shorter flowering cycles, in accordance with a putative generation time effect.

Triple collocation-based estimation of spatially correlated observation error covariance in remote sensing soil moisture data assimilation

NASA Astrophysics Data System (ADS)

Wu, Kai; Shu, Hong; Nie, Lei; Jiao, Zhenhang

2018-01-01

Spatially correlated errors are typically ignored in data assimilation, thus degenerating the observation error covariance R to a diagonal matrix. We argue that a nondiagonal R carries more observation information making assimilation results more accurate. A method, denoted TC_Cov, was proposed for soil moisture data assimilation to estimate spatially correlated observation error covariance based on triple collocation (TC). Assimilation experiments were carried out to test the performance of TC_Cov. AMSR-E soil moisture was assimilated with a diagonal R matrix computed using the TC and assimilated using a nondiagonal R matrix, as estimated by proposed TC_Cov. The ensemble Kalman filter was considered as the assimilation method. Our assimilation results were validated against climate change initiative data and ground-based soil moisture measurements using the Pearson correlation coefficient and unbiased root mean square difference metrics. These experiments confirmed that deterioration of diagonal R assimilation results occurred when model simulation is more accurate than observation data. Furthermore, nondiagonal R achieved higher correlation coefficient and lower ubRMSD values over diagonal R in experiments and demonstrated the effectiveness of TC_Cov to estimate richly structuralized R in data assimilation. In sum, compared with diagonal R, nondiagonal R may relieve the detrimental effects of assimilation when simulated model results outperform observation data.

Visualization of extracellular matrix components within sectioned Salmonella biofilms on the surface of human gallstones.

PubMed

Marshall, Joanna M; Flechtner, Alan D; La Perle, Krista M; Gunn, John S

2014-01-01

Chronic carriage of Salmonella Typhi is mediated primarily through the formation of bacterial biofilms on the surface of cholesterol gallstones. Biofilms, by definition, involve the formation of a bacterial community encased within a protective macromolecular matrix. Previous work has demonstrated the composition of the biofilm matrix to be complex and highly variable in response to altered environmental conditions. Although known to play an important role in bacterial persistence in a variety of contexts, the Salmonella biofilm matrix remains largely uncharacterized under physiological conditions. Initial attempts to study matrix components and architecture of the biofilm matrix on gallstone surfaces were hindered by the auto-fluorescence of cholesterol. In this work we describe a method for sectioning and direct visualization of extracellular matrix components of the Salmonella biofilm on the surface of human cholesterol gallstones and provide a description of the major matrix components observed therein. Confocal micrographs revealed robust biofilm formation, characterized by abundant but highly heterogeneous expression of polysaccharides such as LPS, Vi and O-antigen capsule. CsgA was not observed in the biofilm matrix and flagellar expression was tightly restricted to the biofilm-cholesterol interface. Images also revealed the presence of preexisting Enterobacteriaceae encased within the structure of the gallstone. These results demonstrate the use and feasibility of this method while highlighting the importance of studying the native architecture of the gallstone biofilm. A better understanding of the contribution of individual matrix components to the overall biofilm structure will facilitate the development of more effective and specific methods to disrupt these bacterial communities.

Genetic Differentiation in the Stingless Bee, Scaptotrigona xanthotricha Moure, 1950 (Apidae, Meliponini): a Species with Wide Geographic Distribution in the Atlantic Rainforest.

PubMed

Duarte, Olívia M P; Gaiotto, Fernanda A; Costa, Marco A

2014-01-01

Stingless bees are important pollinators that are severely threatened by anthropic interference, resulting in a strong population decline. Scaptotrigona xanthotricha has a wide distribution in the Atlantic Rainforest, ranging from the northeastern state of Bahia to Santa Catarina in southern Brazil. To understand the genetic structure of S. xanthotricha, 12 species-specific microsatellite loci were analyzed in 42 colonies sampled throughout the species range. The results indicated 5 distinct clusters throughout the sampled area with high rates of genetic diversity, and the greatest diversity was found in southern Bahia. Greater differentiation was observed between samples from the extremes of the distribution, with an F ST value of 0.189 between cluster 1 and 5. The genetic differentiation analysis for all loci had an F ST value of 0.113, a result that is consistent with the analysis of molecular variance, which revealed 7.72% of the variation occurring between groups. The Mantel correlation between a genetic differentiation matrix and a geographic distance matrix (r = 0.184, P = 0.043) indicated a tendency toward increased differentiation with increased distance. This study revealed the profile of differentiation and distribution of genetic diversity in this species and indicates parameters that should be considered in future taxonomic revisions and activities for its management and conservation. © The American Genetic Association 2014. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Treating Sample Covariances for Use in Strongly Coupled Atmosphere-Ocean Data Assimilation

NASA Astrophysics Data System (ADS)

Smith, Polly J.; Lawless, Amos S.; Nichols, Nancy K.

2018-01-01

Strongly coupled data assimilation requires cross-domain forecast error covariances; information from ensembles can be used, but limited sampling means that ensemble derived error covariances are routinely rank deficient and/or ill-conditioned and marred by noise. Thus, they require modification before they can be incorporated into a standard assimilation framework. Here we compare methods for improving the rank and conditioning of multivariate sample error covariance matrices for coupled atmosphere-ocean data assimilation. The first method, reconditioning, alters the matrix eigenvalues directly; this preserves the correlation structures but does not remove sampling noise. We show that it is better to recondition the correlation matrix rather than the covariance matrix as this prevents small but dynamically important modes from being lost. The second method, model state-space localization via the Schur product, effectively removes sample noise but can dampen small cross-correlation signals. A combination that exploits the merits of each is found to offer an effective alternative.

Understanding the Relationship between Red Wine Matrix, Tannin Activity, and Sensory Properties.

PubMed

Watrelot, Aude A; Byrnes, Nadia K; Heymann, Hildegarde; Kennedy, James A

2016-11-30

One major red wine mouthfeel characteristic, astringency, is derived from grape-extracted tannins and is considered to be a result of interaction with salivary proteins and the oral mucosa. To improve our understanding of the role that the enthalpy of interaction of tannin with a hydrophobic surface (tannin activity) has in astringency perception, a chromatographic method was used to determine the tannin concentration and activity of 34 Cabernet Sauvignon wines, as well as sensory analysis done on 13 of those wines. In addition, astringency-relevant matrix parameters (pH, titratable acidity, ethanol, glucose, and fructose) were measured across all wines. Tannin activity was not significantly correlated with any matrix variables, and the perception of drying and grippy was not correlated with tannin concentration and activity. However, ethanol content was well related to mouthfeel attributes and appeared to drive perceived drying. Although fructose and glucose content were well correlated, they did not drive the perception of sweetness, which is explained by the well-known mixture suppression effect.

Sum-rule corrections: a route to error cancellations in correlation matrix renormalisation theory

NASA Astrophysics Data System (ADS)

Liu, C.; Liu, J.; Yao, Y. X.; Wang, C. Z.; Ho, K. M.

2017-03-01

We recently proposed the correlation matrix renormalisation (CMR) theory to efficiently and accurately calculate ground state total energy of molecular systems, based on the Gutzwiller variational wavefunction (GWF) to treat the electronic correlation effects. To help reduce numerical complications and better adapt the CMR to infinite lattice systems, we need to further refine the way to minimise the error originated from the approximations in the theory. This conference proceeding reports our recent progress on this key issue, namely, we obtained a simple analytical functional form for the one-electron renormalisation factors, and introduced a novel sum-rule correction for a more accurate description of the intersite electron correlations. Benchmark calculations are performed on a set of molecules to show the reasonable accuracy of the method.

Examination of the Chayes-Kruskal procedure for testing correlations between proportions

USGS Publications Warehouse

Kork, J.O.

1977-01-01

The Chayes-Kruskal procedure for testing correlations between proportions uses a linear approximation to the actual closure transformation to provide a null value, pij, against which an observed closed correlation coefficient, rij, can be tested. It has been suggested that a significant difference between pij and rij would indicate a nonzero covariance relationship between the ith and jth open variables. In this paper, the linear approximation to the closure transformation is described in terms of a matrix equation. Examination of the solution set of this equation shows that estimation of, or even the identification of, significant nonzero open correlations is essentially impossible even if the number of variables and the sample size are large. The method of solving the matrix equation is described in the appendix. ?? 1977 Plenum Publishing Corporation.

Quantum correlation properties in Matrix Product States of finite-number spin rings

NASA Astrophysics Data System (ADS)

Zhu, Jing-Min; He, Qi-Kai

2018-02-01

The organization and structure of quantum correlation (QC) of quantum spin-chains are very rich and complex. Hence the depiction and measures about the QC of finite-number spin rings deserved to be investigated intensively by using Matrix Product States(MPSs) in addition to the case with infinite-number. Here the dependencies of the geometric quantum discord(GQD) of two spin blocks on the total spin number, the spacing spin number and the environment parameter are presented in detail. We also compare the GQD with the total correlation(TC) and the classical correlation(CC) and illustrate its characteristics. Predictably, our findings may provide the potential of designing the optimal QC experimental detection proposals and pave the way for the designation of optimal quantum information processing schemes.

Noise-immune complex correlation for optical coherence angiography based on standard and Jones matrix optical coherence tomography

PubMed Central

Makita, Shuichi; Kurokawa, Kazuhiro; Hong, Young-Joo; Miura, Masahiro; Yasuno, Yoshiaki

2016-01-01

This paper describes a complex correlation mapping algorithm for optical coherence angiography (cmOCA). The proposed algorithm avoids the signal-to-noise ratio dependence and exhibits low noise in vasculature imaging. The complex correlation coefficient of the signals, rather than that of the measured data are estimated, and two-step averaging is introduced. Algorithms of motion artifact removal based on non perfusing tissue detection using correlation are developed. The algorithms are implemented with Jones-matrix OCT. Simultaneous imaging of pigmented tissue and vasculature is also achieved using degree of polarization uniformity imaging with cmOCA. An application of cmOCA to in vivo posterior human eyes is presented to demonstrate that high-contrast images of patients’ eyes can be obtained. PMID:27446673

Mechanical, structural, and dynamical modifications of cholesterol exposed porcine aortic elastin.

PubMed

Bilici, Kubra; Morgan, Steven W; Silverstein, Moshe C; Wang, Yunjie; Sun, Hyung Jin; Zhang, Yanhang; Boutis, Gregory S

2016-11-01

Elastin is a protein of the extracellular matrix that contributes significantly to the elasticity of connective tissues. In this study, we examine dynamical and structural modifications of aortic elastin exposed to cholesterol by NMR spectroscopic and relaxation methodologies. Macroscopic measurements are also presented and reveal that cholesterol treatment may cause a decrease in the stiffness of tissue. 2 H NMR relaxation techniques revealed differences between the relative populations of water that correlate with the swelling of the tissue following cholesterol exposure. 13 C magic-angle-spinning NMR spectroscopy and relaxation methods indicate that cholesterol treated aortic elastin is more mobile than control samples. Molecular dynamics simulations on a short elastin repeat VPGVG in the presence of cholesterol are used to investigate the energetic and entropic contributions to the retractive force, in comparison to the same peptide in water. Peptide stiffness is observed to reduce following cholesterol exposure due to a decrease in the entropic force. Copyright © 2016 Elsevier B.V. All rights reserved.

Mechanical, Structural, and Dynamical Modifications of Cholesterol Exposed Porcine Aortic Elastin

PubMed Central

Bilici, Kubra; Morgan, Steven W.; Silverstein, Moshe C.; Wang, Yunjie; Sun, Hyung Jin; Zhang, Katherine; Boutis, Gregory S.

2016-01-01

Elastin is a protein of the extracellular matrix that contributes significantly to the elasticity of connective tissues. In this study, we examine dynamical and structural modifications of aortic elastin exposed to cholesterol by NMR spectroscopic and relaxation methodologies. Macroscopic measurements are also presented and reveal that cholesterol treatment may cause a decrease in the stiffness of tissue. 2H NMR relaxation techniques revealed differences between the relative populations of water that correlate with the swelling of the tissue following cholesterol exposure. 13C magic-angle-spinning NMR spectroscopy and relaxation methods indicate that cholesterol treated aortic elastin appears more mobile than control samples. Molecular dynamics simulations on a short elastin repeat VPGVG in the presence of cholesterol are used to investigate the energetic and entropic contributions to the retractive force, in comparison to the same peptide in water. Peptide stiffness is observed to reduce following cholesterol exposure due to a decrease in the entropic force. PMID:27648754

Effect of lignin content on a GH11 endoxylanase acting on glucuronoarabinoxylan-lignin nanocomposites.

PubMed

Boukari, Imen; Rémond, Caroline; O'Donohue, Michael; Chabbert, Brigitte

2012-06-20

The effects of lignin content on the activity and action pattern of GH11 endoxylanase from Thermobacillus xylanilyticus were investigated using in vitro reconstituted non-covalent glucuronoarabinoxylan-model lignin (GAX-DHP) nanocomposites. Four types of nanocomposites were prepared, each displaying different lignin contents. Variations in the DHP (model lignin) polymerization process were induced by increasing the coniferyl alcohol concentration. Examination of the morphology of the nanocomposites revealed globular particles enrobed in a matrix. The size of these particles increased in line with the lignin concentration. Physicochemical characterization of the in vitro reconstituted GAX-DHPs strongly suggested that increased particle size is directly related to the solubility and reactivity of coniferyl alcohol, as reflected by changes in the amount of β-O-4 linkages. Evaluation of the impact of the GH11 endoxylanase on the GAX-DHP nanocomposites revealed a negative correlation between the proportion and organization patterns of DHP in the nanocomposites and enzyme activity. Copyright © 2012 Elsevier Ltd. All rights reserved.

Toward structural dynamics: protein motions viewed by chemical shift modulations and direct detection of C'N multiple-quantum relaxation.

PubMed

Mori, Mirko; Kateb, Fatiha; Bodenhausen, Geoffrey; Piccioli, Mario; Abergel, Daniel

2010-03-17

Multiple quantum relaxation in proteins reveals unexpected relationships between correlated or anti-correlated conformational backbone dynamics in alpha-helices or beta-sheets. The contributions of conformational exchange to the relaxation rates of C'N coherences (i.e., double- and zero-quantum coherences involving backbone carbonyl (13)C' and neighboring amide (15)N nuclei) depend on the kinetics of slow exchange processes, as well as on the populations of the conformations and chemical shift differences of (13)C' and (15)N nuclei. The relaxation rates of C'N coherences, which reflect concerted fluctuations due to slow chemical shift modulations (CSMs), were determined by direct (13)C detection in diamagnetic and paramagnetic proteins. In well-folded proteins such as lanthanide-substituted calbindin (CaLnCb), copper,zinc superoxide dismutase (Cu,Zn SOD), and matrix metalloproteinase (MMP12), slow conformational exchange occurs along the entire backbone. Our observations demonstrate that relaxation rates of C'N coherences arising from slow backbone dynamics have positive signs (characteristic of correlated fluctuations) in beta-sheets and negative signs (characteristic of anti-correlated fluctuations) in alpha-helices. This extends the prospects of structure-dynamics relationships to slow time scales that are relevant for protein function and enzymatic activity.

Evolution equation for quantum coherence

PubMed Central

Hu, Ming-Liang; Fan, Heng

2016-01-01

The estimation of the decoherence process of an open quantum system is of both theoretical significance and experimental appealing. Practically, the decoherence can be easily estimated if the coherence evolution satisfies some simple relations. We introduce a framework for studying evolution equation of coherence. Based on this framework, we prove a simple factorization relation (FR) for the l1 norm of coherence, and identified the sets of quantum channels for which this FR holds. By using this FR, we further determine condition on the transformation matrix of the quantum channel which can support permanently freezing of the l1 norm of coherence. We finally reveal the universality of this FR by showing that it holds for many other related coherence and quantum correlation measures. PMID:27382933

Molecular symmetry with quaternions.

PubMed

Fritzer, H P

2001-09-01

A new and relatively simple version of the quaternion calculus is offered which is especially suitable for applications in molecular symmetry and structure. After introducing the real quaternion algebra and its classical matrix representation in the group SO(4) the relations with vectors in 3-space and the connection with the rotation group SO(3) through automorphism properties of the algebra are discussed. The correlation of the unit quaternions with both the Cayley-Klein and the Euler parameters through the group SU(2) is presented. Besides rotations the extension of quaternions to other important symmetry operations, reflections and the spatial inversion, is given. Finally, the power of the quaternion calculus for molecular symmetry problems is revealed by treating some examples applied to icosahedral symmetry.

Coupled Cluster Method with Single and Double Excitations Tailored by Matrix Product State Wave Functions.

PubMed

Veis, Libor; Antalík, Andrej; Brabec, Jiří; Neese, Frank; Legeza, Örs; Pittner, Jiří

2016-10-03

In the past decade, the quantum chemical version of the density matrix renormalization group (DMRG) method has established itself as the method of choice for calculations of strongly correlated molecular systems. Despite its favorable scaling, it is in practice not suitable for computations of dynamic correlation. We present a novel method for accurate "post-DMRG" treatment of dynamic correlation based on the tailored coupled cluster (CC) theory in which the DMRG method is responsible for the proper description of nondynamic correlation, whereas dynamic correlation is incorporated through the framework of the CC theory. We illustrate the potential of this method on prominent multireference systems, in particular, N 2 and Cr 2 molecules and also oxo-Mn(Salen), for which we have performed the first post-DMRG computations in order to shed light on the energy ordering of the lowest spin states.

FPGA-based coprocessor for matrix algorithms implementation

NASA Astrophysics Data System (ADS)

Amira, Abbes; Bensaali, Faycal

2003-03-01

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

GAGA: a new algorithm for genomic inference of geographic ancestry reveals fine level population substructure in Europeans.

PubMed

Lao, Oscar; Liu, Fan; Wollstein, Andreas; Kayser, Manfred

2014-02-01

Attempts to detect genetic population substructure in humans are troubled by the fact that the vast majority of the total amount of observed genetic variation is present within populations rather than between populations. Here we introduce a new algorithm for transforming a genetic distance matrix that reduces the within-population variation considerably. Extensive computer simulations revealed that the transformed matrix captured the genetic population differentiation better than the original one which was based on the T1 statistic. In an empirical genomic data set comprising 2,457 individuals from 23 different European subpopulations, the proportion of individuals that were determined as a genetic neighbour to another individual from the same sampling location increased from 25% with the original matrix to 52% with the transformed matrix. Similarly, the percentage of genetic variation explained between populations by means of Analysis of Molecular Variance (AMOVA) increased from 1.62% to 7.98%. Furthermore, the first two dimensions of a classical multidimensional scaling (MDS) using the transformed matrix explained 15% of the variance, compared to 0.7% obtained with the original matrix. Application of MDS with Mclust, SPA with Mclust, and GemTools algorithms to the same dataset also showed that the transformed matrix gave a better association of the genetic clusters with the sampling locations, and particularly so when it was used in the AMOVA framework with a genetic algorithm. Overall, the new matrix transformation introduced here substantially reduces the within population genetic differentiation, and can be broadly applied to methods such as AMOVA to enhance their sensitivity to reveal population substructure. We herewith provide a publically available (http://www.erasmusmc.nl/fmb/resources/GAGA) model-free method for improved genetic population substructure detection that can be applied to human as well as any other species data in future studies relevant to evolutionary biology, behavioural ecology, medicine, and forensics.

Data mining graphene: Correlative analysis of structure and electronic degrees of freedom in graphenic monolayers with defects

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

Ziatdinov, Maxim A.; Fujii, Shintaro; Kiguchi, Manabu

The link between changes in the material crystal structure and its mechanical, electronic, magnetic, and optical functionalities known as the structure-property relationship is the cornerstone of the contemporary materials science research. The recent advances in scanning transmission electron and scanning probe microscopies (STEM and SPM) have opened an unprecedented path towards examining the materials structure property relationships on the single-impurity and atomic-configuration levels. Lacking, however, are the statistics-based approaches for cross-correlation of structure and property variables obtained in different information channels of the STEM and SPM experiments. Here we have designed an approach based on a combination of sliding windowmore » Fast Fourier Transform, Pearson correlation matrix, linear and kernel canonical correlation, to study a relationship between lattice distortions and electron scattering from the SPM data on graphene with defects. Our analysis revealed that the strength of coupling to strain is altered between different scattering channels which can explain coexistence of several quasiparticle interference patterns in the nanoscale regions of interest. In addition, the application of the kernel functions allowed us extracting a non-linear component of the relationship between the lattice strain and scattering intensity in graphene. Lastly, the outlined approach can be further utilized to analyzing correlations in various multi-modal imaging techniques where the information of interest is spatially distributed and has usually a complex multidimensional nature.« less

Data mining graphene: Correlative analysis of structure and electronic degrees of freedom in graphenic monolayers with defects

DOE PAGES

Ziatdinov, Maxim A.; Fujii, Shintaro; Kiguchi, Manabu; ...

2016-11-09

The link between changes in the material crystal structure and its mechanical, electronic, magnetic, and optical functionalities known as the structure-property relationship is the cornerstone of the contemporary materials science research. The recent advances in scanning transmission electron and scanning probe microscopies (STEM and SPM) have opened an unprecedented path towards examining the materials structure property relationships on the single-impurity and atomic-configuration levels. Lacking, however, are the statistics-based approaches for cross-correlation of structure and property variables obtained in different information channels of the STEM and SPM experiments. Here we have designed an approach based on a combination of sliding windowmore » Fast Fourier Transform, Pearson correlation matrix, linear and kernel canonical correlation, to study a relationship between lattice distortions and electron scattering from the SPM data on graphene with defects. Our analysis revealed that the strength of coupling to strain is altered between different scattering channels which can explain coexistence of several quasiparticle interference patterns in the nanoscale regions of interest. In addition, the application of the kernel functions allowed us extracting a non-linear component of the relationship between the lattice strain and scattering intensity in graphene. Lastly, the outlined approach can be further utilized to analyzing correlations in various multi-modal imaging techniques where the information of interest is spatially distributed and has usually a complex multidimensional nature.« less

Electrical condition monitoring method for polymers

DOEpatents

Watkins, Jr., Kenneth S.; Morris, Shelby J [Hampton, VA; Masakowski, Daniel D [Worcester, MA; Wong, Ching Ping [Duluth, GA; Luo, Shijian [Boise, ID

2008-08-19

An electrical condition monitoring method utilizes measurement of electrical resistivity of an age sensor made of a conductive matrix or composite disposed in a polymeric structure such as an electrical cable. The conductive matrix comprises a base polymer and conductive filler. The method includes communicating the resistivity to a measuring instrument and correlating resistivity of the conductive matrix of the polymeric structure with resistivity of an accelerated-aged conductive composite.

Project Effectiveness and the Balance of Power in Matrix Organizations: An Exploratory Study.

DTIC Science & Technology

1986-09-01

Vasconcellos , Eduardo . "A Model for a Better Understanding of the Matrix Structure." IEEE Transactions on Engineering Management, EM-26: 56-65 (August...coercive power correlated negatively with degree of support (39:219-220). Vasconcellos recognized the five common power sources referenced above and...effect. The second variable identified by Vasconcellos was used to differentiate matrix structures. He felt that it was necessary to differentiate

Procollagen III N-terminal Propeptide and Desmosine are Released by Matrix Destruction in Pulmonary Tuberculosis

PubMed Central

Seddon, Jo; Kasprowicz, Victoria; Walker, Naomi F.; Yuen, Ho Ming; Sunpath, Henry; Tezera, Liku; Meintjes, Graeme; Wilkinson, Robert J.; Bishai, William R.; Friedland, Jon S.; Elkington, Paul T.

2013-01-01

Background. Tuberculosis is transmitted by patients with pulmonary disease. Matrix metalloproteinases (MMPs) drive lung destruction in tuberculosis but the resulting matrix degradation products (MDPs) have not been studied. We investigate the hypothesis that MMP activity generates matrix turnover products as correlates of lung pathology. Methods. Induced sputum and plasma were collected prospectively from human immunodeficiency virus (HIV) positive and negative patients with pulmonary tuberculosis and controls. Concentrations of MDPs and MMPs were analyzed by ELISA and Luminex array in 2 patient cohorts. Results. Procollagen III N-terminal propeptide (PIIINP) was 3.8-fold higher in induced sputum of HIV-uninfected tuberculosis patients compared to controls and desmosine, released during elastin degradation, was 2.4-fold higher. PIIINP was elevated in plasma of tuberculosis patients. Plasma PIIINP correlated with induced sputum MMP-1 concentrations and radiological scores, demonstrating that circulating MDPs reflect lung destruction. In a second patient cohort of mixed HIV seroprevalence, plasma PIIINP concentration was increased 3.0-fold above controls (P < .001). Plasma matrix metalloproteinase-8 concentrations were also higher in tuberculosis patients (P = .001). Receiver operating characteristic analysis utilizing these 2 variables demonstrated an area under the curve of 0.832 (P < .001). Conclusions. In pulmonary tuberculosis, MMP-driven immunopathology generates matrix degradation products. PMID:23922364

Energy and energy gradient matrix elements with N-particle explicitly correlated complex Gaussian basis functions with L =1

NASA Astrophysics Data System (ADS)

Bubin, Sergiy; Adamowicz, Ludwik

2008-03-01

In this work we consider explicitly correlated complex Gaussian basis functions for expanding the wave function of an N-particle system with the L =1 total orbital angular momentum. We derive analytical expressions for various matrix elements with these basis functions including the overlap, kinetic energy, and potential energy (Coulomb interaction) matrix elements, as well as matrix elements of other quantities. The derivatives of the overlap, kinetic, and potential energy integrals with respect to the Gaussian exponential parameters are also derived and used to calculate the energy gradient. All the derivations are performed using the formalism of the matrix differential calculus that facilitates a way of expressing the integrals in an elegant matrix form, which is convenient for the theoretical analysis and the computer implementation. The new method is tested in calculations of two systems: the lowest P state of the beryllium atom and the bound P state of the positronium molecule (with the negative parity). Both calculations yielded new, lowest-to-date, variational upper bounds, while the number of basis functions used was significantly smaller than in previous studies. It was possible to accomplish this due to the use of the analytic energy gradient in the minimization of the variational energy.

Energy and energy gradient matrix elements with N-particle explicitly correlated complex Gaussian basis functions with L=1.

PubMed

Bubin, Sergiy; Adamowicz, Ludwik

2008-03-21

In this work we consider explicitly correlated complex Gaussian basis functions for expanding the wave function of an N-particle system with the L=1 total orbital angular momentum. We derive analytical expressions for various matrix elements with these basis functions including the overlap, kinetic energy, and potential energy (Coulomb interaction) matrix elements, as well as matrix elements of other quantities. The derivatives of the overlap, kinetic, and potential energy integrals with respect to the Gaussian exponential parameters are also derived and used to calculate the energy gradient. All the derivations are performed using the formalism of the matrix differential calculus that facilitates a way of expressing the integrals in an elegant matrix form, which is convenient for the theoretical analysis and the computer implementation. The new method is tested in calculations of two systems: the lowest P state of the beryllium atom and the bound P state of the positronium molecule (with the negative parity). Both calculations yielded new, lowest-to-date, variational upper bounds, while the number of basis functions used was significantly smaller than in previous studies. It was possible to accomplish this due to the use of the analytic energy gradient in the minimization of the variational energy.

Molecular spectroscopic identification of the water compartments in bone.

PubMed

Unal, Mustafa; Yang, Shan; Akkus, Ozan

2014-10-01

Matrix bound water is a correlate of bone's fracture resistance and assessment of bound water is emerging as a novel measure of bone's mechanical integrity. Raman spectroscopy is one of the few nondestructive modalities to assess the hydration status in bone; however, it has not been used to study the OH-band in bone. A sequential dehydration protocol was developed to replace unbound (heat drying) and bound (ethanol or deuterium) water in bone. Raman spectra were collected serially to track the OH-band during dehydration. Spectra of synthetic hydroxyapatite, demineralized bone and bulk water were collected to identify mineral and collagen contributions to the OH-band. Band assignments were supported by computational simulations of the molecular vibrations of Gly-Pro-Hyp amino acid sequence. Experimentally and theoretically obtained spectra were interpreted for band-assignments. Water loss was measured gravimetrically and correlated to Raman intensities. Four peaks were identified to be sensitive to dehydration: 3220cm(-1) (water), 3325cm(-1) (NH and water), 3453cm(-1) (hydroxyproline and water), and 3584cm(-1) (mineral and water). These peaks were differentially sensitive to deuterium treatment such that some water peaks were replaced with deuterium oxide faster than the rest. Specifically, the peaks at 3325 and 3584cm(-1) were more tightly bound to the matrix than the remaining bands. Comparison of dehydration in mineralized and demineralized bone revealed a volume of water that may be locked in the matrix by mineral crystals. The OH-range of bone was dominated by collagen and the water since the spectral profile of dehydrated demineralized bone was similar to that of the mineralized bone. Furthermore, water associates to bone mainly by collagen as findings of experimentally and theoretically spectra. The current work is among the first thorough analysis of the Raman OH stretch band in bone and such spectral information may be used to understand the involvement of water in the fragility of aging and in diseased bone. Published by Elsevier Inc.

Exploration of polyamide structure-property relationships by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.

PubMed

Barrère, Caroline; Rejaibi, Majed; Curat, Aurélien; Hubert-Roux, Marie; Lavanant, Hélène; Afonso, Carlos; Kebir, Nasreddine; Desilles, Nicolas; Lecamp, Laurence; Burel, Fabrice; Loutelier-Bourhis, Corinne

2014-08-15

Polyamides (PA) are among the most used classes of polymers because of their attractive properties. Depending on the nature and proportion of the co-monomers used for their synthesis, they can exhibit a very large range of melting temperatures (Tm ). This study aims at the correlation of data from mass spectrometry (MS) with differential scanning calorimetry (DSC) and X-ray diffraction analyses to relate molecular structure to physical properties such as melting temperature, enthalpy change and crystallinity rate. Six different PA copolymers with molecular weights around 3500 g mol(-1) were synthesized with varying proportions of different co-monomers (amino-acid AB/di-amine AA/di-acid BB). Their melting temperature, enthalpy change and crystallinity rate were measured by DSC and X-ray diffraction. Their structural characterization was carried out by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). Because of the poor solubility of PA, a solvent-free sample preparation strategy was used with 2,5-dihydroxybenzoic acid (2,5-DHB) as the matrix and sodium iodide as the cationizing agent. The different proportions of the repeating unit types led to the formation of PA with melting temperatures ranging from 115°C to 185°C. The structural characterization of these samples by MALDI-TOF-MS revealed a collection of different ion distributions with different sequences of repeating units (AA, BB; AB/AA, BB and AB) in different proportions according to the mixture of monomers used in the synthesis. The relative intensities of these ion distributions were related to sample complexity and structure. They were correlated to DSC and X-ray results, to explain the observed physical properties. The structural information obtained by MALDI-TOF-MS provided a better understanding of the variation of the PA melting temperature and established a structure-properties relationship. This work will allow future PA designs to be monitored. Copyright © 2014 John Wiley & Sons, Ltd.

Proceedings of the Japan - U.S. Conference on Composite Materials (6th) Held in Orlando, Florida on June 22-24, 1992

DTIC Science & Technology

1993-03-01

correlation was determined between the matrix microplastic flow and the global composite tensile stress-strain curve. Based on the knowledge of the...framentation of the elastic matrix to form remnant elastic pockets at Silw tip surrounded y the matrix plastic flow. The matrix microplasticity is also...Deformation of SiC-Al Composites.’ Mater. Sci. Engng., A131:55-68. 11. Hamann, R., P. F. Gobin, and R. Fougeres, 1990. "A Study of the Microplasticity of Some

Signatures of bifurcation on quantum correlations: Case of the quantum kicked top

NASA Astrophysics Data System (ADS)

Bhosale, Udaysinh T.; Santhanam, M. S.

2017-01-01

Quantum correlations reflect the quantumness of a system and are useful resources for quantum information and computational processes. Measures of quantum correlations do not have a classical analog and yet are influenced by classical dynamics. In this work, by modeling the quantum kicked top as a multiqubit system, the effect of classical bifurcations on measures of quantum correlations such as the quantum discord, geometric discord, and Meyer and Wallach Q measure is studied. The quantum correlation measures change rapidly in the vicinity of a classical bifurcation point. If the classical system is largely chaotic, time averages of the correlation measures are in good agreement with the values obtained by considering the appropriate random matrix ensembles. The quantum correlations scale with the total spin of the system, representing its semiclassical limit. In the vicinity of trivial fixed points of the kicked top, the scaling function decays as a power law. In the chaotic limit, for large total spin, quantum correlations saturate to a constant, which we obtain analytically, based on random matrix theory, for the Q measure. We also suggest that it can have experimental consequences.

Evaluation of the default-mode network by quantitative 15O-PET: comparative study between cerebral blood flow and oxygen consumption.

PubMed

Aoe, Jo; Watabe, Tadashi; Shimosegawa, Eku; Kato, Hiroki; Kanai, Yasukazu; Naka, Sadahiro; Matsunaga, Keiko; Isohashi, Kayako; Tatsumi, Mitsuaki; Hatazawa, Jun

2018-06-22

Resting-state functional MRI (rs-fMRI) has revealed the existence of a default-mode network (DMN) based on spontaneous oscillations of the blood oxygenation level-dependent (BOLD) signal. The BOLD signal reflects the deoxyhemoglobin concentration, which depends on the relationship between the regional cerebral blood flow (CBF) and the cerebral metabolic rate of oxygen (CMRO 2 ). However, these two factors cannot be separated in BOLD rs-fMRI. In this study, we attempted to estimate the functional correlations in the DMN by means of quantitative 15 O-labeled gases and water PET, and to compare the contribution of the CBF and CMRO 2 to the DMN. Nine healthy volunteers (5 men and 4 women; mean age, 47.0 ± 1.2 years) were studied by means of 15 O-O 2 , 15 O-CO gases and 15 O-water PET. Quantitative CBF and CMRO 2 images were generated by an autoradiographic method and transformed into MNI standardized brain template. Regions of interest were placed on normalized PET images according to the previous rs-fMRI study. For the functional correlation analysis, the intersubject Pearson's correlation coefficients (r) were calculated for all pairs in the brain regions and correlation matrices were obtained for CBF and CMRO 2 , respectively. We defined r > 0.7 as a significant positive correlation and compared the correlation matrices of CBF and CMRO 2 . Significant positive correlations (r > 0.7) were observed in 24 pairs of brain regions for the CBF and 22 pairs of brain regions for the CMRO 2 . Among them, 12 overlapping networks were observed between CBF and CMRO 2 . Correlation analysis of CBF led to the detection of more brain networks as compared to that of CMRO 2 , indicating that the CBF can capture the state of the spontaneous activity with a higher sensitivity. We estimated the functional correlations in the DMN by means of quantitative PET using 15 O-labeled gases and water. The correlation matrix derived from the CBF revealed a larger number of brain networks as compared to that derived from the CMRO 2 , indicating that contribution to the functional correlation in the DMN is higher in the blood flow more than the oxygen consumption.

Portfolio optimization and the random magnet problem

NASA Astrophysics Data System (ADS)

Rosenow, B.; Plerou, V.; Gopikrishnan, P.; Stanley, H. E.

2002-08-01

Diversification of an investment into independently fluctuating assets reduces its risk. In reality, movements of assets are mutually correlated and therefore knowledge of cross-correlations among asset price movements are of great importance. Our results support the possibility that the problem of finding an investment in stocks which exposes invested funds to a minimum level of risk is analogous to the problem of finding the magnetization of a random magnet. The interactions for this "random magnet problem" are given by the cross-correlation matrix C of stock returns. We find that random matrix theory allows us to make an estimate for C which outperforms the standard estimate in terms of constructing an investment which carries a minimum level of risk.

Statistical Analysis of Big Data on Pharmacogenomics

PubMed Central

Fan, Jianqing; Liu, Han

2013-01-01

This paper discusses statistical methods for estimating complex correlation structure from large pharmacogenomic datasets. We selectively review several prominent statistical methods for estimating large covariance matrix for understanding correlation structure, inverse covariance matrix for network modeling, large-scale simultaneous tests for selecting significantly differently expressed genes and proteins and genetic markers for complex diseases, and high dimensional variable selection for identifying important molecules for understanding molecule mechanisms in pharmacogenomics. Their applications to gene network estimation and biomarker selection are used to illustrate the methodological power. Several new challenges of Big data analysis, including complex data distribution, missing data, measurement error, spurious correlation, endogeneity, and the need for robust statistical methods, are also discussed. PMID:23602905

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

PubMed Central

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

2009-01-01

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

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

PubMed

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

2009-01-01

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

Tenascin-C levels in synovial fluid are elevated after injury to the human and canine joint and correlate with markers of inflammation and matrix degradation.

PubMed

Chockalingam, P S; Glasson, S S; Lohmander, L S

2013-02-01

We have previously shown the capacity of tenascin-C (TN-C) to induce inflammatory mediators and matrix degradation in vitro in human articular cartilage. The objective of the present study was to follow TN-C release into knee synovial fluid after acute joint injury or in joint disease, and to correlate TN-C levels with markers of cartilage matrix degradation and inflammation. Human knee synovial fluid samples (n = 164) were from a cross-sectional convenience cohort. Diagnostic groups were knee healthy reference, knee anterior cruciate ligament rupture, with or without concomitant meniscus lesions, isolated knee meniscus injury, acute inflammatory arthritis (AIA) and knee osteoarthritis (OA). TN-C was measured in synovial fluid samples using an enzyme-linked immunosorbent assay (ELISA) and results correlated to other cartilage markers. TN-C release was also monitored in joints of dogs that underwent knee instability surgery. Statistically significantly higher levels of TN-C compared to reference subjects were observed in the joint fluid of all human disease groups and in the dogs that underwent knee instability surgery. Statistically significant correlations were observed between the TN-C levels in the synovial fluid of the human patients and the levels of aggrecanase-dependent Ala-Arg-Gly-aggrecan (ARG-aggrecan) fragments and matrix metalloproteinases 1 and 3. We find highly elevated levels of TN-C in human knee joints after injury, AIA or OA that correlated with markers of cartilage degradation and inflammation. TN-C in synovial fluid may serve dual roles as a marker of joint damage and a stimulant of further joint degradation. Copyright © 2012 Osteoarthritis Research Society International. Published by Elsevier Ltd. All rights reserved.

The large-N Yang-Mills S matrix is ultraviolet finite, but the large-N QCD S matrix is only renormalizable

NASA Astrophysics Data System (ADS)

Bochicchio, Marco

2017-03-01

Yang-Mills (YM) theory and QCD are known to be renormalizable, but not ultraviolet (UV) finite, order by order, in perturbation theory. It is a fundamental question whether YM theory or QCD is UV finite, or only renormalizable, order by order, in the large-N 't Hooft or Veneziano expansions. We demonstrate that the renormalization group (RG) and asymptotic freedom imply that in 't Hooft large-N expansion the S matrix in YM theory is UV finite, while in both 't Hooft and Veneziano large-N expansions, the S matrix in confining massless QCD is renormalizable but not UV finite. By the same argument, the large-N N =1 supersymmetry (SUSY) YM S matrix is UV finite as well. Besides, we demonstrate that, in both 't Hooft and Veneziano large-N expansions, the correlators of local gauge-invariant operators, as opposed to the S matrix, are renormalizable but, in general, not UV finite, either in YM theory and N =1 SUSY YM theory or a fortiori in massless QCD. Moreover, we compute explicitly the counterterms that arise from renormalizing the 't Hooft and Veneziano expansions by deriving in confining massless QCD-like theories a low-energy theorem of the Novikov-Shifman-Vainshtein-Zakharov type that relates the log derivative with respect to the gauge coupling of a k -point correlator, or the log derivative with respect to the RG-invariant scale, to a (k +1 )-point correlator with the insertion of Tr F2 at zero momentum. Finally, we argue that similar results hold in the large-N limit of a vast class of confining massive QCD-like theories, provided a renormalization scheme exists—as, for example, MS ¯ —in which the beta function is not dependent on the masses. Specifically, in both 't Hooft and Veneziano large-N expansions, the S matrix in confining massive QCD and massive N =1 SUSY QCD is renormalizable but not UV finite.

A Generalized Method of Image Analysis from an Intercorrelation Matrix which May Be Singular.

ERIC Educational Resources Information Center

Yanai, Haruo; Mukherjee, Bishwa Nath

1987-01-01

This generalized image analysis method is applicable to singular and non-singular correlation matrices (CMs). Using the orthogonal projector and a weaker generalized inverse matrix, image and anti-image covariance matrices can be derived from a singular CM. (SLD)

Maintenance of neural progenitor cell stemness in 3D hydrogels requires matrix remodelling

NASA Astrophysics Data System (ADS)

Madl, Christopher M.; Lesavage, Bauer L.; Dewi, Ruby E.; Dinh, Cong B.; Stowers, Ryan S.; Khariton, Margarita; Lampe, Kyle J.; Nguyen, Duong; Chaudhuri, Ovijit; Enejder, Annika; Heilshorn, Sarah C.

2017-12-01

Neural progenitor cell (NPC) culture within three-dimensional (3D) hydrogels is an attractive strategy for expanding a therapeutically relevant number of stem cells. However, relatively little is known about how 3D material properties such as stiffness and degradability affect the maintenance of NPC stemness in the absence of differentiation factors. Over a physiologically relevant range of stiffness from ~0.5 to 50 kPa, stemness maintenance did not correlate with initial hydrogel stiffness. In contrast, hydrogel degradation was both correlated with, and necessary for, maintenance of NPC stemness. This requirement for degradation was independent of cytoskeletal tension generation and presentation of engineered adhesive ligands, instead relying on matrix remodelling to facilitate cadherin-mediated cell-cell contact and promote β-catenin signalling. In two additional hydrogel systems, permitting NPC-mediated matrix remodelling proved to be a generalizable strategy for stemness maintenance in 3D. Our findings have identified matrix remodelling, in the absence of cytoskeletal tension generation, as a previously unknown strategy to maintain stemness in 3D.

Maintenance of Neural Progenitor Cell Stemness in 3D Hydrogels Requires Matrix Remodeling

PubMed Central

Madl, Christopher M.; LeSavage, Bauer L.; Dewi, Ruby E.; Dinh, Cong B.; Stowers, Ryan S.; Khariton, Margarita; Lampe, Kyle J.; Nguyen, Duong; Chaudhuri, Ovijit; Enejder, Annika; Heilshorn, Sarah C.

2017-01-01

Neural progenitor cell (NPC) culture within 3D hydrogels is an attractive strategy for expanding a therapeutically-relevant number of stem cells. However, relatively little is known about how 3D material properties such as stiffness and degradability affect the maintenance of NPC stemness in the absence of differentiation factors. Over a physiologically-relevant range of stiffness from ~0.5–50 kPa, stemness maintenance did not correlate with initial hydrogel stiffness. In contrast, hydrogel degradation was both correlated with, and necessary for, maintenance of NPC stemness. This requirement for degradation was independent of cytoskeletal tension generation and presentation of engineered adhesive ligands, instead relying on matrix remodeling to facilitate cadherin-mediated cell-cell contact and promote β-catenin signaling. In two additional hydrogel systems, permitting NPC-mediated matrix remodeling proved to be a generalizable strategy for stemness maintenance in 3D. Our findings have identified matrix remodeling, in the absence of cytoskeletal tension generation, as a previously unknown strategy to maintain stemness in 3D. PMID:29115291

Complex network analysis of resting-state fMRI of the brain.

PubMed

Anwar, Abdul Rauf; Hashmy, Muhammad Yousaf; Imran, Bilal; Riaz, Muhammad Hussnain; Mehdi, Sabtain Muhammad Muntazir; Muthalib, Makii; Perrey, Stephane; Deuschl, Gunther; Groppa, Sergiu; Muthuraman, Muthuraman

2016-08-01

Due to the fact that the brain activity hardly ever diminishes in healthy individuals, analysis of resting state functionality of the brain seems pertinent. Various resting state networks are active inside the idle brain at any time. Based on various neuro-imaging studies, it is understood that various structurally distant regions of the brain could be functionally connected. Regions of the brain, that are functionally connected, during rest constitutes to the resting state network. In the present study, we employed the complex network measures to estimate the presence of community structures within a network. Such estimate is named as modularity. Instead of using a traditional correlation matrix, we used a coherence matrix taken from the causality measure between different nodes. Our results show that in prolonged resting state the modularity starts to decrease. This decrease was observed in all the resting state networks and on both sides of the brain. Our study highlights the usage of coherence matrix instead of correlation matrix for complex network analysis.

Relationships Between Abrasive Wear, Hardness, and Surface Grinding Characteristics of Titanium-Based Metal Matrix Composites

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

Blau, Peter Julian; Jolly, Brian C

2009-01-01

The objective of this work was to support the development of grinding models for titanium metal-matrix composites (MMCs) by investigating possible relationships between their indentation hardness, low-stress belt abrasion, high-stress belt abrasion, and the surface grinding characteristics. Three Ti-based particulate composites were tested and compared with the popular titanium alloy Ti-6Al-4V. The three composites were a Ti-6Al-4V-based MMC with 5% TiB{sub 2} particles, a Ti-6Al-4V MMC with 10% TiC particles, and a Ti-6Al-4V/Ti-7.5%W binary alloy matrix that contained 7.5% TiC particles. Two types of belt abrasion tests were used: (a) a modified ASTM G164 low-stress loop abrasion test, and (b)more » a higher-stress test developed to quantify the grindability of ceramics. Results were correlated with G-ratios (ratio of stock removed to abrasives consumed) obtained from an instrumented surface grinder. Brinell hardness correlated better with abrasion characteristics than microindentation or scratch hardness. Wear volumes from low-stress and high-stress abrasive belt tests were related by a second-degree polynomial. Grindability numbers correlated with hard particle content but were also matrix-dependent.« less

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.

Refractive index inversion based on Mueller matrix method

NASA Astrophysics Data System (ADS)

Fan, Huaxi; Wu, Wenyuan; Huang, Yanhua; Li, Zhaozhao

2016-03-01

Based on Stokes vector and Jones vector, the correlation between Mueller matrix elements and refractive index was studied with the result simplified, and through Mueller matrix way, the expression of refractive index inversion was deduced. The Mueller matrix elements, under different incident angle, are simulated through the expression of specular reflection so as to analyze the influence of the angle of incidence and refractive index on it, which is verified through the measure of the Mueller matrix elements of polished metal surface. Research shows that, under the condition of specular reflection, the result of Mueller matrix inversion is consistent with the experiment and can be used as an index of refraction of inversion method, and it provides a new way for target detection and recognition technology.

Screening for angiogenic inhibitors in zebrafish to evaluate a predictive model for developmental vascular toxicity.

PubMed

Tal, Tamara; Kilty, Claire; Smith, Andrew; LaLone, Carlie; Kennedy, Brendán; Tennant, Alan; McCollum, Catherine W; Bondesson, Maria; Knudsen, Thomas; Padilla, Stephanie; Kleinstreuer, Nicole

2017-06-01

Chemically-induced vascular toxicity during embryonic development may cause a wide range of adverse effects. To identify putative vascular disrupting chemicals (pVDCs), a predictive pVDC signature was constructed from 124 U.S. EPA ToxCast high-throughput screening (HTS) assays and used to rank 1060 chemicals for their potential to disrupt vascular development. Thirty-seven compounds were selected for targeted testing in transgenic Tg(kdrl:EGFP) and Tg(fli1:EGFP) zebrafish embryos to identify chemicals that impair developmental angiogenesis. We hypothesized that zebrafish angiogenesis toxicity data would correlate with human cell-based and cell-free in vitro HTS ToxCast data. Univariate statistical associations used to filter HTS data based on correlations with zebrafish angiogenic inhibition in vivo revealed 132 total significant associations, 33 of which were already captured in the pVDC signature, and 689 non-significant assay associations. Correlated assays were enriched in cytokine and extracellular matrix pathways. Taken together, the findings indicate the utility of zebrafish assays to evaluate an HTS-based predictive toxicity signature and also provide an experimental basis for expansion of the pVDC signature with novel HTS assays. Published by Elsevier Inc.

Orbital optimisation in the perfect pairing hierarchy: applications to full-valence calculations on linear polyacenes

NASA Astrophysics Data System (ADS)

Lehtola, Susi; Parkhill, John; Head-Gordon, Martin

2018-03-01

We describe the implementation of orbital optimisation for the models in the perfect pairing hierarchy. Orbital optimisation, which is generally necessary to obtain reliable results, is pursued at perfect pairing (PP) and perfect quadruples (PQ) levels of theory for applications on linear polyacenes, which are believed to exhibit strong correlation in the π space. While local minima and σ-π symmetry breaking solutions were found for PP orbitals, no such problems were encountered for PQ orbitals. The PQ orbitals are used for single-point calculations at PP, PQ and perfect hextuples (PH) levels of theory, both only in the π subspace, as well as in the full σπ valence space. It is numerically demonstrated that the inclusion of single excitations is necessary also when optimised orbitals are used. PH is found to yield good agreement with previously published density matrix renormalisation group data in the π space, capturing over 95% of the correlation energy. Full-valence calculations made possible by our novel, efficient code reveal that strong correlations are weaker when larger basis sets or active spaces are employed than in previous calculations. The largest full-valence PH calculations presented correspond to a (192e,192o) problem.

Matrix metalloproteinase 14 modulates diabetes and Alzheimer's disease cross-talk: a meta-analysis.

PubMed

Cheng, Jack; Liu, Hsin-Ping; Lee, Cheng-Chun; Chen, Mei-Ying; Lin, Wei-Yong; Tsai, Fuu-Jen

2018-02-01

Diabetes mellitus is associated with dementia, but whether diabetes is associated with Alzheimer's disease remains controversial. Alzheimer's disease is characterized by amyloid beta aggregation. We hypothesized that genes, involved in amyloid beta degradation, may be altered due to diabetes and thus participate in progression of Alzheimer's disease. Expression profiling of amyloid beta-degrading enzymes in streptozotocin-induced diabetic mice and their correlation with expression of amyloid precursor protein in hippocampus of Alzheimer's disease patients were accessed. We found that matrix metalloproteinase 14 decreased in brain but not in other tissues of streptozotocin-induced diabetic mice, and was negatively correlated with expression of amyloid precursor protein in hippocampus of Alzheimer's disease patients. These findings suggested matrix metalloproteinase 14 may link insulin-deficient diabetes to Alzheimer's disease.

Phase distribution and flow mechanism in an amphibolite facies ultramylonite

NASA Astrophysics Data System (ADS)

Kilian, Rüdiger

2014-05-01

Rocks deforming by diffusion creep, are usually characterized by a small grain size, a weak or no crystallographic preferred orientation and an anti-correlated phase distribution of which the latter gives the most revealing insight into the active deformation mechanism. The present study focuses on the phase distribution in an amphibolite facies ultramylonite from a several meters wide shear zone within the Nordmannvik Nappe of the Norwegian Caledonides. In the shear zone, a granulite facies protolith is transformed to a fine grained matrix of quartz (50%), biotite (20%), white mica (20%), oligoclase (7%) and ilmenite/titanite with grain sizes below 10 μm (eq. diameter). Large grains of garnet, white mica and plagioclase form porphyroclasts. At high matrix proportions white mica and plagioclase porphyroclasts are less abundant. The matrix shows a homogeneous fabric and shows a strong anti-correlation of phases. Quartz forms single grains or clusters, which are at most a few grains thick, with a long axis inclined at 30 - 60° to the foliation, antithetic to the sense of shear. Quartz clusters have a regular spacing of ~30 μm, separated by biotite-stacks and oligoclase. White mica forms parallel to the foliation and replaces longer biotite grains (during shearing of the mica). Concurrently new biotite grows at those quartz grain boundaries, which are oriented at a high angle to the foliation. Only adjacent to porphyroclasts, the matrix homogeneity is disturbed. Biotite and plagioclase are depleted in the compressional sector and grow in the extensional sector. Correspondingly, garnet porphyroclasts have newly grown Ca-rich rims in compressional sectors and signs of dissolution in extensional ones. Thermodynamic modeling suggests that the modal composition of the matrix and the Ca-rich garnet rims form the stable assemblage. The microstructural positions of the phases can be related to the kinematics of granular flow. The alignment of quartz grains into clusters subparallel to the inferred shortening direction can be compared to the dynamic formation of force chains permitting high and low pressure sites in the matrix, similarly observed in numerical models of granular flow (e.g. Deubelbeiss et al., 2011). Biotite + oligoclase occupy sites of locally lower pressure and garnet rims + white mica those of higher pressure. It is suggested that a cyclic reaction of garnet + white mica = plagioclase + biotite, driven by dynamically changing, local gradients, causes the distribution of phases by nucleation, growth and mutual replacement during granular flow. Additionally, straining of biotite might contribute to its replacement by white mica. Deubelbeiss, Y., B. J. P. Kaus, J. A. D. Connolly, and L. Caricchi (2011), Potential causes for the non-Newtonian rheology of crystal-bearing magmas, Geochem. Geophys. Geosyst., 12, Q05007, doi:10.1029/2010GC003485.

When do correlations increase with firing rates in recurrent networks?

PubMed Central

2017-01-01

A central question in neuroscience is to understand how noisy firing patterns are used to transmit information. Because neural spiking is noisy, spiking patterns are often quantified via pairwise correlations, or the probability that two cells will spike coincidentally, above and beyond their baseline firing rate. One observation frequently made in experiments, is that correlations can increase systematically with firing rate. Theoretical studies have determined that stimulus-dependent correlations that increase with firing rate can have beneficial effects on information coding; however, we still have an incomplete understanding of what circuit mechanisms do, or do not, produce this correlation-firing rate relationship. Here, we studied the relationship between pairwise correlations and firing rates in recurrently coupled excitatory-inhibitory spiking networks with conductance-based synapses. We found that with stronger excitatory coupling, a positive relationship emerged between pairwise correlations and firing rates. To explain these findings, we used linear response theory to predict the full correlation matrix and to decompose correlations in terms of graph motifs. We then used this decomposition to explain why covariation of correlations with firing rate—a relationship previously explained in feedforward networks driven by correlated input—emerges in some recurrent networks but not in others. Furthermore, when correlations covary with firing rate, this relationship is reflected in low-rank structure in the correlation matrix. PMID:28448499

Exchange bias of Ni nanoparticles embedded in an antiferromagnetic IrMn matrix.

PubMed

Kuerbanjiang, Balati; Wiedwald, Ulf; Haering, Felix; Biskupek, Johannes; Kaiser, Ute; Ziemann, Paul; Herr, Ulrich

2013-11-15

The magnetic properties of Ni nanoparticles (Ni-NPs) embedded in an antiferromagnetic IrMn matrix were investigated. The Ni-NPs of 8.4 nm mean diameter were synthesized by inert gas aggregation. In a second processing step, the Ni-NPs were in situ embedded in IrMn films or SiOx films under ultrahigh vacuum (UHV) conditions. Findings showed that Ni-NPs embedded in IrMn have an exchange bias field HEB = 821 Oe at 10 K, and 50 Oe at 300 K. The extracted value of the exchange energy density is 0.06 mJ m(-2) at 10 K, which is in good accordance with the results from multilayered thin film systems. The Ni-NPs embedded in SiOx did not show exchange bias. As expected for this particle size, they are superparamagnetic at T = 300 K. A direct comparison of the Ni-NPs embedded in IrMn or SiOx reveals an increase of the blocking temperature from 210 K to around 400 K. The coercivity of the Ni-NPs exchange coupled to the IrMn matrix at 10 K is 8 times larger than the value for Ni-NPs embedded in SiOx. We studied time-dependent remanent magnetization at different temperatures. The relaxation behavior is described by a magnetic viscosity model which reflects a rather flat distribution of energy barriers. Furthermore, we investigated the effects of different field cooling processes on the magnetic properties of the embedded Ni-NPs. Exchange bias values fit to model calculations which correlate the contribution of the antiferromagnetic IrMn matrix to its grain size.

High permittivity polyaniline-barium titanate nanocomposites with excellent electromagnetic interference shielding response

NASA Astrophysics Data System (ADS)

Saini, Parveen; Arora, Manju; Gupta, Govind; Gupta, Bipin Kumar; Singh, Vidya Nand; Choudhary, Veena

2013-05-01

Organic conductive polymers are at the forefront of materials science research because of their diverse applications built around their interesting and unique properties. This work reports for the first time a correlation between the structural, electrical, and electromagnetic properties of polyaniline (PANI)-tetragonal BaTiO3 (TBT) nanocomposites prepared by in-situ emulsion polymerization. XRD studies and HRTEM micrographs of these nanocomposites clearly revealed the incorporation of TBT nanoparticles in the conducting PANI matrix. EPR and XPS measurements reveal that increase in loading level of BaTiO3 results in a reduction of the doping level of PANI. The Ku-Band (12.4-18 GHz) network analysis of these composites shows exceptional microwave shielding response with absorption dominated total shielding effectiveness (SET) value of -71.5 dB (blockage of more than 99.99999% of incident radiation) which is the highest value reported in the literature. Such a high attenuation level, which critically depends on the fraction of BaTiO3 is attributed to optimized dielectric and electrical attributes. This demonstrates the possibility of using these materials in stealth technology and for making futuristic radar absorbing materials (RAMs).Organic conductive polymers are at the forefront of materials science research because of their diverse applications built around their interesting and unique properties. This work reports for the first time a correlation between the structural, electrical, and electromagnetic properties of polyaniline (PANI)-tetragonal BaTiO3 (TBT) nanocomposites prepared by in-situ emulsion polymerization. XRD studies and HRTEM micrographs of these nanocomposites clearly revealed the incorporation of TBT nanoparticles in the conducting PANI matrix. EPR and XPS measurements reveal that increase in loading level of BaTiO3 results in a reduction of the doping level of PANI. The Ku-Band (12.4-18 GHz) network analysis of these composites shows exceptional microwave shielding response with absorption dominated total shielding effectiveness (SET) value of -71.5 dB (blockage of more than 99.99999% of incident radiation) which is the highest value reported in the literature. Such a high attenuation level, which critically depends on the fraction of BaTiO3 is attributed to optimized dielectric and electrical attributes. This demonstrates the possibility of using these materials in stealth technology and for making futuristic radar absorbing materials (RAMs). Electronic supplementary information (ESI) available. See DOI: 10.1039/c3nr00634d

Thermo-Oxidative Stability of Graphite/PMR-15 Composites: Effect of Fiber Surface Modification on Composite Shear Properties

NASA Technical Reports Server (NTRS)

Madhukar, Madhu S.; Bowles, Kenneth J.; Papadopolous, Demetrios S.

1994-01-01

Experiments were conducted to establish a correlation between the weight loss of a polyimide (PMR- 15) matrix and graphite fibers and the in-plane shear properties of their unidirectional composites subjected to different isothermal aging times up to 1000 hr at 316 C. The role of fiber surface treatment on the composite degradation during the thermo-oxidative aging was investigated by using A4 graphite fibers with three surface modifications: untreated (AU-4), surface treated (AS-4), and surface treated and sized with an epoxy-compatible sizing (AS-4G). The weight loss of the matrix fibers, and composites was determined during the aging. The effect of thermal aging was seen in all the fiber samples in terms of weight loss and reduction in fiber diameter. Calculated values of weight loss fluxes for different surfaces of rectangular unidirectional composite plates showed that the largest weight loss occurred at those cut surfaces where fibers were perpendicular to the surface. Consequently, the largest amount of damage was also noted on these cut surfaces. Optical observation of the neat matrix and composite plates subjected to different aging times revealed that the degradation (such as matrix microcracking and void growth) occurred in a thin surface layer near the specimen edges. The in-plane shear modulus of the composites was unaffected by the fiber surface treatment and the thermal aging. The shear strength of the composites with the untreated fibers was the lowest and it decreased with aging. A fracture surface examination of the composites with untreated fibers suggested that the weak interface allowed the oxidation reaction to proceed along the interface and thus expose the inner material to further oxidation. The results indicated that the fiber-matrix interface affected the composite degradation process during its thermal aging and that the the weak interface accelerated the composite degradation.

Age-dependence of power spectral density and fractal dimension of bone mineralized matrix in atomic force microscope topography images: potential correlates of bone tissue age and bone fragility in female femoral neck trabeculae

PubMed Central

Milovanovic, Petar; Djuric, Marija; Rakocevic, Zlatko

2012-01-01

There is an increasing interest in bone nano-structure, the ultimate goal being to reveal the basis of age-related bone fragility. In this study, power spectral density (PSD) data and fractal dimensions of the mineralized bone matrix were extracted from atomic force microscope topography images of the femoral neck trabeculae. The aim was to evaluate age-dependent differences in the mineralized matrix of human bone and to consider whether these advanced nano-descriptors might be linked to decreased bone remodeling observed by some authors and age-related decline in bone mechanical competence. The investigated bone specimens belonged to a group of young adult women (n = 5, age: 20–40 years) and a group of elderly women (n = 5, age: 70–95 years) without bone diseases. PSD graphs showed the roughness density distribution in relation to spatial frequency. In all cases, there was a fairly linear decrease in magnitude of the power spectra with increasing spatial frequencies. The PSD slope was steeper in elderly individuals (−2.374 vs. −2.066), suggesting the dominance of larger surface morphological features. Fractal dimension of the mineralized bone matrix showed a significant negative trend with advanced age, declining from 2.467 in young individuals to 2.313 in the elderly (r = 0.65, P = 0.04). Higher fractal dimension in young women reflects domination of smaller mineral grains, which is compatible with the more freshly remodeled structure. In contrast, the surface patterns in elderly individuals were indicative of older tissue age. Lower roughness and reduced structural complexity (decreased fractal dimension) of the interfibrillar bone matrix in the elderly suggest a decline in bone toughness, which explains why aged bone is more brittle and prone to fractures. PMID:22946475

Age-dependence of power spectral density and fractal dimension of bone mineralized matrix in atomic force microscope topography images: potential correlates of bone tissue age and bone fragility in female femoral neck trabeculae.

PubMed

Milovanovic, Petar; Djuric, Marija; Rakocevic, Zlatko

2012-11-01

There is an increasing interest in bone nano-structure, the ultimate goal being to reveal the basis of age-related bone fragility. In this study, power spectral density (PSD) data and fractal dimensions of the mineralized bone matrix were extracted from atomic force microscope topography images of the femoral neck trabeculae. The aim was to evaluate age-dependent differences in the mineralized matrix of human bone and to consider whether these advanced nano-descriptors might be linked to decreased bone remodeling observed by some authors and age-related decline in bone mechanical competence. The investigated bone specimens belonged to a group of young adult women (n = 5, age: 20-40 years) and a group of elderly women (n = 5, age: 70-95 years) without bone diseases. PSD graphs showed the roughness density distribution in relation to spatial frequency. In all cases, there was a fairly linear decrease in magnitude of the power spectra with increasing spatial frequencies. The PSD slope was steeper in elderly individuals (-2.374 vs. -2.066), suggesting the dominance of larger surface morphological features. Fractal dimension of the mineralized bone matrix showed a significant negative trend with advanced age, declining from 2.467 in young individuals to 2.313 in the elderly (r = 0.65, P = 0.04). Higher fractal dimension in young women reflects domination of smaller mineral grains, which is compatible with the more freshly remodeled structure. In contrast, the surface patterns in elderly individuals were indicative of older tissue age. Lower roughness and reduced structural complexity (decreased fractal dimension) of the interfibrillar bone matrix in the elderly suggest a decline in bone toughness, which explains why aged bone is more brittle and prone to fractures. © 2012 The Authors Journal of Anatomy © 2012 Anatomical Society.

Testing of self-repairing composite airplane components by use of CAI and the release of the repair chemicals from carefully inserted small tubes

NASA Astrophysics Data System (ADS)

Dry, Carolyn

2007-04-01

The research on self repair of airplane components, under an SBIR phase II with Wright Patterson Air Force Base, has investigated the attributes and best end use applications for such a technology. These attributes include issues related to manufacturability, cost, potential benefits such as weight reduction, and cost reduction. The goal of our research has been to develop self-repairing composites with unique strength for air vehicles. Our revolutionary approach involves the autonomous release of repair chemicals from within the composite matrix itself. The repair agents are contained in hollow, structural fibers that are embedded within the matrix. Under stress, the composite senses external environmental factors and reacts by releasing the repair agents from within the hollow vessels. This autonomous response occurs wherever and whenever cracking, debonding or other matrix damage transpires. Superior performance over the life of the composite is achieved through this self-repairing mechanism. The advantages to the military would be safely executed missions, fewer repairs and eventually lighter vehicles. In particular the research has addressed the issues by correlating the impact of the various factors, such as 1) delivery vessel placement, shape/size and effect on composite strength, chemicals released and their effect on the matrix, release trigger and efficacy and any impact on matrix properties 2) impact of composite processing methods that involve heat and pressure on the repair vessels. Our self repairing system can be processed at temperatures of 300-350F, repairs in less than 30 seconds and does not damage the composite by repair fiber insertion or chemical release. Scaling up and manufacture of components has revealed that anticipating potential problems allowed us to avoid those associated with processing temperatures and pressures. The presentation will focus on compression after impact testing and the placement of repair fibers/tubes into prepreg laminates.

Controlled Breast Cancer Microarrays for the Deconvolution of Cellular Multilayering and Density Effects upon Drug Responses

PubMed Central

Håkanson, Maria; Kobel, Stefan; Lutolf, Matthias P.; Textor, Marcus; Cukierman, Edna; Charnley, Mirren

2012-01-01

Background Increasing evidence shows that the cancer microenvironment affects both tumorigenesis and the response of cancer to drug treatment. Therefore in vitro models that selectively reflect characteristics of the in vivo environment are greatly needed. Current methods allow us to screen the effect of extrinsic parameters such as matrix composition and to model the complex and three-dimensional (3D) cancer environment. However, 3D models that reflect characteristics of the in vivo environment are typically too complex and do not allow the separation of discrete extrinsic parameters. Methodology/Principal Findings In this study we used a poly(ethylene glycol) (PEG) hydrogel-based microwell array to model breast cancer cell behavior in multilayer cell clusters that allows a rigorous control of the environment. The innovative array fabrication enables different matrix proteins to be integrated into the bottom surface of microwells. Thereby, extrinsic parameters including dimensionality, type of matrix coating and the extent of cell-cell adhesion could be independently studied. Our results suggest that cell to matrix interactions and increased cell-cell adhesion, at high cell density, induce independent effects on the response to Taxol in multilayer breast cancer cell clusters. In addition, comparing the levels of apoptosis and proliferation revealed that drug resistance mediated by cell-cell adhesion can be related to altered cell cycle regulation. Conversely, the matrix-dependent response to Taxol did not correlate with proliferation changes suggesting that cell death inhibition may be responsible for this effect. Conclusions/Significance The application of the PEG hydrogel platform provided novel insight into the independent role of extrinsic parameters controlling drug response. The presented platform may not only become a useful tool for basic research related to the role of the cancer microenvironment but could also serve as a complementary platform for in vitro drug development. PMID:22792141

Matrix exponential-based closures for the turbulent subgrid-scale stress tensor.

PubMed

Li, Yi; Chevillard, Laurent; Eyink, Gregory; Meneveau, Charles

2009-01-01

Two approaches for closing the turbulence subgrid-scale stress tensor in terms of matrix exponentials are introduced and compared. The first approach is based on a formal solution of the stress transport equation in which the production terms can be integrated exactly in terms of matrix exponentials. This formal solution of the subgrid-scale stress transport equation is shown to be useful to explore special cases, such as the response to constant velocity gradient, but neglecting pressure-strain correlations and diffusion effects. The second approach is based on an Eulerian-Lagrangian change of variables, combined with the assumption of isotropy for the conditionally averaged Lagrangian velocity gradient tensor and with the recent fluid deformation approximation. It is shown that both approaches lead to the same basic closure in which the stress tensor is expressed as the matrix exponential of the resolved velocity gradient tensor multiplied by its transpose. Short-time expansions of the matrix exponentials are shown to provide an eddy-viscosity term and particular quadratic terms, and thus allow a reinterpretation of traditional eddy-viscosity and nonlinear stress closures. The basic feasibility of the matrix-exponential closure is illustrated by implementing it successfully in large eddy simulation of forced isotropic turbulence. The matrix-exponential closure employs the drastic approximation of entirely omitting the pressure-strain correlation and other nonlinear scrambling terms. But unlike eddy-viscosity closures, the matrix exponential approach provides a simple and local closure that can be derived directly from the stress transport equation with the production term, and using physically motivated assumptions about Lagrangian decorrelation and upstream isotropy.

Compressed sensing of hyperspectral images based on scrambled block Hadamard ensemble

NASA Astrophysics Data System (ADS)

Wang, Li; Feng, Yan

2016-11-01

A fast measurement matrix based on scrambled block Hadamard ensemble for compressed sensing (CS) of hyperspectral images (HSI) is investigated. The proposed measurement matrix offers several attractive features. First, the proposed measurement matrix possesses Gaussian behavior, which illustrates that the matrix is universal and requires a near-optimal number of samples for exact reconstruction. In addition, it could be easily implemented in the optical domain due to its integer-valued elements. More importantly, the measurement matrix only needs small memory for storage in the sampling process. Experimental results on HSIs reveal that the reconstruction performance of the proposed measurement matrix is comparable or better than Gaussian matrix and Bernoulli matrix using different reconstruction algorithms while consuming less computational time. The proposed matrix could be used in CS of HSI, which would save the storage memory on board, improve the sampling efficiency, and ameliorate the reconstruction quality.

Dimension-six matrix elements for meson mixing and lifetimes from sum rules

NASA Astrophysics Data System (ADS)

Kirk, M.; Lenz, A.; Rauh, T.

2017-12-01

The hadronic matrix elements of dimension-six Δ F = 0, 2 operators are crucial inputs for the theory predictions of mixing observables and lifetime ratios in the B and D system. We determine them using HQET sum rules for three-point correlators. The results of the required three-loop computation of the correlators and the one-loop computation of the QCD-HQET matching are given in analytic form. For mixing matrix elements we find very good agreement with recent lattice results and comparable theoretical uncertainties. For lifetime matrix elements we present the first ever determination in the D meson sector and the first determination of Δ B = 0 matrix elements with uncertainties under control — superseeding preliminary lattice studies stemming from 2001 and earlier. With our state-of-the-art determination of the bag parameters we predict: τ( B +)/ τ( B d 0 ) = 1.082 - 0.026 + 0.022 , τ( B s 0 )/ τ( B d 0 ) = 0.9994 ± 0.0025, τ( D +)/ τ( D 0) = 2. 7 - 0.8 + 0.7 and the mixing-observables in the B s and B d system, in good agreement with the most recent experimental averages.

Sum-rule corrections: A route to error cancellations in correlation matrix renormalisation theory

DOE PAGES

Liu, C.; Liu, J.; Yao, Y. X.; ...

2017-01-16

Here, we recently proposed the correlation matrix renormalisation (CMR) theory to efficiently and accurately calculate ground state total energy of molecular systems, based on the Gutzwiller variational wavefunction (GWF) to treat the electronic correlation effects. To help reduce numerical complications and better adapt the CMR to infinite lattice systems, we need to further refine the way to minimise the error originated from the approximations in the theory. This conference proceeding reports our recent progress on this key issue, namely, we obtained a simple analytical functional form for the one-electron renormalisation factors, and introduced a novel sum-rule correction for a moremore » accurate description of the intersite electron correlations. Benchmark calculations are performed on a set of molecules to show the reasonable accuracy of the method.« less

Sum-rule corrections: A route to error cancellations in correlation matrix renormalisation theory

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

Liu, C.; Liu, J.; Yao, Y. X.

Here, we recently proposed the correlation matrix renormalisation (CMR) theory to efficiently and accurately calculate ground state total energy of molecular systems, based on the Gutzwiller variational wavefunction (GWF) to treat the electronic correlation effects. To help reduce numerical complications and better adapt the CMR to infinite lattice systems, we need to further refine the way to minimise the error originated from the approximations in the theory. This conference proceeding reports our recent progress on this key issue, namely, we obtained a simple analytical functional form for the one-electron renormalisation factors, and introduced a novel sum-rule correction for a moremore » accurate description of the intersite electron correlations. Benchmark calculations are performed on a set of molecules to show the reasonable accuracy of the method.« less

Analysis of network clustering behavior of the Chinese stock market

NASA Astrophysics Data System (ADS)

Chen, Huan; Mai, Yong; Li, Sai-Ping

2014-11-01

Random Matrix Theory (RMT) and the decomposition of correlation matrix method are employed to analyze spatial structure of stocks interactions and collective behavior in the Shanghai and Shenzhen stock markets in China. The result shows that there exists prominent sector structures, with subsectors including the Real Estate (RE), Commercial Banks (CB), Pharmaceuticals (PH), Distillers&Vintners (DV) and Steel (ST) industries. Furthermore, the RE and CB subsectors are mostly anti-correlated. We further study the temporal behavior of the dataset and find that while the sector structures are relatively stable from 2007 through 2013, the correlation between the real estate and commercial bank stocks shows large variations. By employing the ensemble empirical mode decomposition (EEMD) method, we show that this anti-correlation behavior is closely related to the monetary and austerity policies of the Chinese government during the period of study.

Development and Preliminary Validation of the Strategic Thinking Mindset Test (STMT)

DTIC Science & Technology

2017-06-01

reliability. The test’s three subscales (intellectual flexibility, inclusiveness, and humility) each correlated significantly with alternative measures of...34 TABLE 9. STAGE 4 SAMPLE DEMOGRAPHICS ................................................................ 35 TABLE 10. INTERITEM CORRELATION ...MATRIX (ALL ITEMS) ...................................... 39 TABLE 11. ITEM-SCALE AND VALIDITY CORRELATIONS (ALL ITEMS) .................... 40

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…

Chondrogenic properties of collagen type XI, a component of cartilage extracellular matrix.

PubMed

Li, Ang; Wei, Yiyong; Hung, Clark; Vunjak-Novakovic, Gordana

2018-08-01

Cartilage extracellular matrix (ECM) has been used for promoting tissue engineering. However, the exact effects of ECM on chondrogenesis and the acting mechanisms are not well understood. In this study, we investigated the chondrogenic effects of cartilage ECM on human mesenchymal stem cells (MSCs) and identified the contributing molecular components. To this end, a preparation of articular cartilage ECM was supplemented to pellets of chondrogenically differentiating MSCs, pellets of human chondrocytes, and bovine articular cartilage explants to evaluate the effects on cell proliferation and the production of cartilaginous matrix. Selective enzymatic digestion and screening of ECM components were conducted to identify matrix molecules with chondrogenic properties. Cartilage ECM promoted MSC proliferation, production of cartilaginous matrix, and maturity of chondrogenic differentiation, and inhibited the hypertrophic differentiation of MSC-derived chondrocytes. Selective digestion of ECM components revealed a contributory role of collagens in promoting chondrogenesis. The screening of various collagen subtypes revealed strong chondrogenic effect of collagen type XI. Finally, collagen XI was found to promote production and inhibit degradation of cartilage matrix in human articular chondrocyte pellets and bovine articular cartilage explants. Our results indicate that cartilage ECM promotes chondrogenesis and inhibits hypertrophic differentiation in MSCs. Collagen type XI is the ECM component that has the strongest effects on enhancing the production and inhibiting the degradation of cartilage matrix. Copyright © 2018 Elsevier Ltd. All rights reserved.

Measuring order in disordered systems and disorder in ordered systems: Random matrix theory for isotropic and nematic liquid crystals and its perspective on pseudo-nematic domains

NASA Astrophysics Data System (ADS)

Zhao, Yan; Stratt, Richard M.

2018-05-01

Surprisingly long-ranged intermolecular correlations begin to appear in isotropic (orientationally disordered) phases of liquid crystal forming molecules when the temperature or density starts to close in on the boundary with the nematic (ordered) phase. Indeed, the presence of slowly relaxing, strongly orientationally correlated, sets of molecules under putatively disordered conditions ("pseudo-nematic domains") has been apparent for some time from light-scattering and optical-Kerr experiments. Still, a fully microscopic characterization of these domains has been lacking. We illustrate in this paper how pseudo-nematic domains can be studied in even relatively small computer simulations by looking for order-parameter tensor fluctuations much larger than one would expect from random matrix theory. To develop this idea, we show that random matrix theory offers an exact description of how the probability distribution for liquid-crystal order parameter tensors converges to its macroscopic-system limit. We then illustrate how domain properties can be inferred from finite-size-induced deviations from these random matrix predictions. A straightforward generalization of time-independent random matrix theory also allows us to prove that the analogous random matrix predictions for the time dependence of the order-parameter tensor are similarly exact in the macroscopic limit, and that relaxation behavior of the domains can be seen in the breakdown of the finite-size scaling required by that random-matrix theory.

Family Reintegration Experiences of Soldiers with Mild Traumatic Brain Injury

DTIC Science & Technology

2014-02-26

depression scores in the spouse. Weak within-couple correlation were indicated on the other measures. Table 3 presents the Spearman correlation matrix...separately. Table 2: Spearman Correlation Coefficients for Couples Spouse MAT Spouse Depression Spouse...Anxiety Soldier MAT -0.06 Soldier Depression -0.61 Soldier Anxiety -0.12 Table 3: Spearman Correlation Coefficients for Soldiers and

Improving performances of suboptimal greedy iterative biclustering heuristics via localization.

PubMed

Erten, Cesim; Sözdinler, Melih

2010-10-15

Biclustering gene expression data is the problem of extracting submatrices of genes and conditions exhibiting significant correlation across both the rows and the columns of a data matrix of expression values. Even the simplest versions of the problem are computationally hard. Most of the proposed solutions therefore employ greedy iterative heuristics that locally optimize a suitably assigned scoring function. We provide a fast and simple pre-processing algorithm called localization that reorders the rows and columns of the input data matrix in such a way as to group correlated entries in small local neighborhoods within the matrix. The proposed localization algorithm takes its roots from effective use of graph-theoretical methods applied to problems exhibiting a similar structure to that of biclustering. In order to evaluate the effectivenesss of the localization pre-processing algorithm, we focus on three representative greedy iterative heuristic methods. We show how the localization pre-processing can be incorporated into each representative algorithm to improve biclustering performance. Furthermore, we propose a simple biclustering algorithm, Random Extraction After Localization (REAL) that randomly extracts submatrices from the localization pre-processed data matrix, eliminates those with low similarity scores, and provides the rest as correlated structures representing biclusters. We compare the proposed localization pre-processing with another pre-processing alternative, non-negative matrix factorization. We show that our fast and simple localization procedure provides similar or even better results than the computationally heavy matrix factorization pre-processing with regards to H-value tests. We next demonstrate that the performances of the three representative greedy iterative heuristic methods improve with localization pre-processing when biological correlations in the form of functional enrichment and PPI verification constitute the main performance criteria. The fact that the random extraction method based on localization REAL performs better than the representative greedy heuristic methods under same criteria also confirms the effectiveness of the suggested pre-processing method. Supplementary material including code implementations in LEDA C++ library, experimental data, and the results are available at http://code.google.com/p/biclustering/ cesim@khas.edu.tr; melihsozdinler@boun.edu.tr Supplementary data are available at Bioinformatics online.

Characterizing the Joint Effect of Diverse Test-Statistic Correlation Structures and Effect Size on False Discovery Rates in a Multiple-Comparison Study of Many Outcome Measures

NASA Technical Reports Server (NTRS)

Feiveson, Alan H.; Ploutz-Snyder, Robert; Fiedler, James

2011-01-01

In their 2009 Annals of Statistics paper, Gavrilov, Benjamini, and Sarkar report the results of a simulation assessing the robustness of their adaptive step-down procedure (GBS) for controlling the false discovery rate (FDR) when normally distributed test statistics are serially correlated. In this study we extend the investigation to the case of multiple comparisons involving correlated non-central t-statistics, in particular when several treatments or time periods are being compared to a control in a repeated-measures design with many dependent outcome measures. In addition, we consider several dependence structures other than serial correlation and illustrate how the FDR depends on the interaction between effect size and the type of correlation structure as indexed by Foerstner s distance metric from an identity. The relationship between the correlation matrix R of the original dependent variables and R, the correlation matrix of associated t-statistics is also studied. In general R depends not only on R, but also on sample size and the signed effect sizes for the multiple comparisons.

Damage Characterization in SiC/SiC Composites using Electrical Resistance

NASA Technical Reports Server (NTRS)

Smith, Craig E.; Xia, Zhenhai

2011-01-01

SiC/SiC ceramic matrix composites (CMCs) under creep-rupture loading accumulate damage by means of local matrix cracks that typically form near a stress concentration, such as a 90o fiber tow or large matrix pore, and grow over time. Such damage is difficult to detect through conventional techniques. Electrical resistance changes can be correlated with matrix cracking to provide a means of damage detection. Sylramic-iBN fiber-reinforced SiC composites with both melt infiltrated (MI) and chemical vapor infiltrated (CVI) matrix types are compared here. Results for both systems exhibit an increase in resistance prior to fracture, which can be detected either in situ or post-damage.

QCD dirac operator at nonzero chemical potential: lattice data and matrix model.

PubMed

Akemann, Gernot; Wettig, Tilo

2004-03-12

Recently, a non-Hermitian chiral random matrix model was proposed to describe the eigenvalues of the QCD Dirac operator at nonzero chemical potential. This matrix model can be constructed from QCD by mapping it to an equivalent matrix model which has the same symmetries as QCD with chemical potential. Its microscopic spectral correlations are conjectured to be identical to those of the QCD Dirac operator. We investigate this conjecture by comparing large ensembles of Dirac eigenvalues in quenched SU(3) lattice QCD at a nonzero chemical potential to the analytical predictions of the matrix model. Excellent agreement is found in the two regimes of weak and strong non-Hermiticity, for several different lattice volumes.

Quantification and micron-scale imaging of spatial distribution of trace beryllium in shrapnel fragments and metallurgic samples with correlative fluorescence detection method and secondary ion mass spectrometry (SIMS)

PubMed Central

Abraham, Jerrold L.; Chandra, Subhash; Agrawal, Anoop

2014-01-01

Recently, a report raised the possibility of shrapnel-induced chronic beryllium disease (CBD) from long-term exposure to the surface of retained aluminum shrapnel fragments in the body. Since the shrapnel fragments contained trace beryllium, methodological developments were needed for beryllium quantification and to study its spatial distribution in relation to other matrix elements, such as aluminum and iron, in metallurgic samples. In this work, we developed methodology for quantification of trace beryllium in samples of shrapnel fragments and other metallurgic sample-types with main matrix of aluminum (aluminum cans from soda, beer, carbonated water, and aluminum foil). Sample preparation procedures were developed for dissolving beryllium for its quantification with the fluorescence detection method for homogenized measurements. The spatial distribution of trace beryllium on the sample surface and in 3D was imaged with a dynamic secondary ion mass spectrometry (SIMS) instrument, CAMECA IMS 3f SIMS ion microscope. The beryllium content of shrapnel (~100 ppb) was the same as the trace quantities of beryllium found in aluminum cans. The beryllium content of aluminum foil (~25 ppb) was significantly lower than cans. SIMS imaging analysis revealed beryllium to be distributed in the form of low micron-sized particles and clusters distributed randomly in X-Y-and Z dimensions, and often in association with iron, in the main aluminum matrix of cans. These observations indicate a plausible formation of Be-Fe or Al-Be alloy in the matrix of cans. Further observations were made on fluids (carbonated water) for understanding if trace beryllium in cans leached out and contaminated the food product. A direct comparison of carbonated water in aluminum cans and plastic bottles revealed that beryllium was below the detection limits of the fluorescence detection method (~0.01 ppb). These observations indicate that beryllium present in aluminum matrix was either present in an immobile form or its mobilization into the food product was prevented by a polymer coating on the inside of cans, a practice used in food industry to prevent contamination of food products. The lack of such coating in retained shrapnel fragments renders their surface a possible source of contamination for long-term exposure of tissues and fluids and induction of disease, as characterized in a recent study. Methodological developments reported here can be extended to studies of beryllium in electronics devices and components. PMID:25146877

Quantification and micron-scale imaging of spatial distribution of trace beryllium in shrapnel fragments and metallurgic samples with correlative fluorescence detection method and secondary ion mass spectrometry (SIMS).

PubMed

Abraham, J L; Chandra, S; Agrawal, A

2014-11-01

Recently, a report raised the possibility of shrapnel-induced chronic beryllium disease from long-term exposure to the surface of retained aluminum shrapnel fragments in the body. Since the shrapnel fragments contained trace beryllium, methodological developments were needed for beryllium quantification and to study its spatial distribution in relation to other matrix elements, such as aluminum and iron, in metallurgic samples. In this work, we developed methodology for quantification of trace beryllium in samples of shrapnel fragments and other metallurgic sample-types with main matrix of aluminum (aluminum cans from soda, beer, carbonated water and aluminum foil). Sample preparation procedures were developed for dissolving beryllium for its quantification with the fluorescence detection method for homogenized measurements. The spatial distribution of trace beryllium on the sample surface and in 3D was imaged with a dynamic secondary ion mass spectrometry instrument, CAMECA IMS 3f secondary ion mass spectrometry ion microscope. The beryllium content of shrapnel (∼100 ppb) was the same as the trace quantities of beryllium found in aluminum cans. The beryllium content of aluminum foil (∼25 ppb) was significantly lower than cans. SIMS imaging analysis revealed beryllium to be distributed in the form of low micron-sized particles and clusters distributed randomly in X-Y- and Z dimensions, and often in association with iron, in the main aluminum matrix of cans. These observations indicate a plausible formation of Be-Fe or Al-Be alloy in the matrix of cans. Further observations were made on fluids (carbonated water) for understanding if trace beryllium in cans leached out and contaminated the food product. A direct comparison of carbonated water in aluminum cans and plastic bottles revealed that beryllium was below the detection limits of the fluorescence detection method (∼0.01 ppb). These observations indicate that beryllium present in aluminum matrix was either present in an immobile form or its mobilization into the food product was prevented by a polymer coating on the inside of cans, a practice used in food industry to prevent contamination of food products. The lack of such coating in retained shrapnel fragments renders their surface a possible source of contamination for long-term exposure of tissues and fluids and induction of disease, as characterized in a recent study. Methodological developments reported here can be extended to studies of beryllium in electronics devices and components. © 2014 The Authors Journal of Microscopy © 2014 Royal Microscopical Society.

Computational Characterization of Type I collagen-based Extra-cellular Matrix

NASA Astrophysics Data System (ADS)

Liang, Long; Jones, Christopher Allen Rucksack; Lin, Daniel; Jiao, Yang; Sun, Bo

2015-03-01

A model of extracellular matrix (ECM) of collagen fibers has been built, in which cells could communicate with distant partners via fiber-mediated long-range-transmitted stress states. The ECM is modeled as a spring-like fiber network derived from skeletonized confocal microscopy data. Different local and global perturbations have been performed on the network, each followed by an optimized global Monte-Carlo (MC) energy minimization leading to the deformed network in response to the perturbations. In the optimization, a highly efficient local energy update procedure is employed and force-directed MC moves are used, which results in a convergence to the energy minimum state 20 times faster than the commonly used random displacement trial moves in MC. Further analysis and visualization of the distribution and correlation of the resulting force network reveal that local perturbations can give rise to global impacts: the force chains formed with a linear extent much further than the characteristic length scale associated with the perturbation sites and average fiber length. This behavior provides a strong evidence for our hypothesis of fiber-mediated long-range force transmission in ECM networks and the resulting long-range cell-cell mechanical signaling. ASU Seed Grant.

Computer-aided diagnosis in phase contrast imaging X-ray computed tomography for quantitative characterization of ex vivo human patellar cartilage.

PubMed

Nagarajan, Mahesh B; Coan, Paola; Huber, Markus B; Diemoz, Paul C; Glaser, Christian; Wismuller, Axel

2013-10-01

Visualization of ex vivo human patellar cartilage matrix through the phase contrast imaging X-ray computed tomography (PCI-CT) has been previously demonstrated. Such studies revealed osteoarthritis-induced changes to chondrocyte organization in the radial zone. This study investigates the application of texture analysis to characterizing such chondrocyte patterns in the presence and absence of osteoarthritic damage. Texture features derived from Minkowski functionals (MF) and gray-level co-occurrence matrices (GLCM) were extracted from 842 regions of interest (ROI) annotated on PCI-CT images of ex vivo human patellar cartilage specimens. These texture features were subsequently used in a machine learning task with support vector regression to classify ROIs as healthy or osteoarthritic; classification performance was evaluated using the area under the receiver operating characteristic curve (AUC). The best classification performance was observed with the MF features perimeter (AUC: 0.94 ±0.08 ) and "Euler characteristic" (AUC: 0.94 ±0.07 ), and GLCM-derived feature "Correlation" (AUC: 0.93 ±0.07). These results suggest that such texture features can provide a detailed characterization of the chondrocyte organization in the cartilage matrix, enabling classification of cartilage as healthy or osteoarthritic with high accuracy.

18F-FDG PET radiomics approaches: comparing and clustering features in cervical cancer.

PubMed

Tsujikawa, Tetsuya; Rahman, Tasmiah; Yamamoto, Makoto; Yamada, Shizuka; Tsuyoshi, Hideaki; Kiyono, Yasushi; Kimura, Hirohiko; Yoshida, Yoshio; Okazawa, Hidehiko

2017-11-01

The aims of our study were to find the textural features on 18 F-FDG PET/CT which reflect the different histological architectures between cervical cancer subtypes and to make a visual assessment of the association between 18 F-FDG PET textural features in cervical cancer. Eighty-three cervical cancer patients [62 squamous cell carcinomas (SCCs) and 21 non-SCCs (NSCCs)] who had undergone pretreatment 18 F-FDG PET/CT were enrolled. A texture analysis was performed on PET/CT images, from which 18 PET radiomics features were extracted including first-order features such as standardized uptake value (SUV), metabolic tumor volume (MTV) and total lesion glycolysis (TLG), second- and high-order textural features using SUV histogram, normalized gray-level co-occurrence matrix (NGLCM), and neighborhood gray-tone difference matrix, respectively. These features were compared between SCC and NSCC using a Bonferroni adjusted P value threshold of 0.0028 (0.05/18). To assess the association between PET features, a heat map analysis with hierarchical clustering, one of the radiomics approaches, was performed. Among 18 PET features, correlation, a second-order textural feature derived from NGLCM, was a stable parameter and it was the only feature which showed a robust trend toward significant difference between SCC and NSCC. Cervical SCC showed a higher correlation (0.70 ± 0.07) than NSCC (0.64 ± 0.07, P = 0.0030). The other PET features did not show any significant differences between SCC and NSCC. A higher correlation in SCC might reflect higher structural integrity and stronger spatial/linear relationship of cancer cells compared with NSCC. A heat map with a PET feature dendrogram clearly showed 5 distinct clusters, where correlation belonged to a cluster including MTV and TLG. However, the association between correlation and MTV/TLG was not strong. Correlation was a relatively independent PET feature in cervical cancer. 18 F-FDG PET textural features might reflect the differences in histological architecture between cervical cancer subtypes. PET radiomics approaches reveal the association between PET features and will be useful for finding a single feature or a combination of features leading to precise diagnoses, potential prognostic models, and effective therapeutic strategies.

Temporal and spatial correlation patterns of air pollutants in Chinese cities

PubMed Central

Dai, Yue-Hua

2017-01-01

As a huge threat to the public health, China’s air pollution has attracted extensive attention and continues to grow in tandem with the economy. Although the real-time air quality report can be utilized to update our knowledge on air quality, questions about how pollutants evolve across time and how pollutants are spatially correlated still remain a puzzle. In view of this point, we adopt the PMFG network method to analyze the six pollutants’ hourly data in 350 Chinese cities in an attempt to find out how these pollutants are correlated temporally and spatially. In terms of time dimension, the results indicate that, except for O3, the pollutants have a common feature of the strong intraday patterns of which the daily variations are composed of two contraction periods and two expansion periods. Besides, all the time series of the six pollutants possess strong long-term correlations, and this temporal memory effect helps to explain why smoggy days are always followed by one after another. In terms of space dimension, the correlation structure shows that O3 is characterized by the highest spatial connections. The PMFGs reveal the relationship between this spatial correlation and provincial administrative divisions by filtering the hierarchical structure in the correlation matrix and refining the cliques as the tinny spatial clusters. Finally, we check the stability of the correlation structure and conclude that, except for PM10 and O3, the other pollutants have an overall stable correlation, and all pollutants have a slight trend to become more divergent in space. These results not only enhance our understanding of the air pollutants’ evolutionary process, but also shed lights on the application of complex network methods into geographic issues. PMID:28832599

Variational optimization algorithms for uniform matrix product states

NASA Astrophysics Data System (ADS)

Zauner-Stauber, V.; Vanderstraeten, L.; Fishman, M. T.; Verstraete, F.; Haegeman, J.

2018-01-01

We combine the density matrix renormalization group (DMRG) with matrix product state tangent space concepts to construct a variational algorithm for finding ground states of one-dimensional quantum lattices in the thermodynamic limit. A careful comparison of this variational uniform matrix product state algorithm (VUMPS) with infinite density matrix renormalization group (IDMRG) and with infinite time evolving block decimation (ITEBD) reveals substantial gains in convergence speed and precision. We also demonstrate that VUMPS works very efficiently for Hamiltonians with long-range interactions and also for the simulation of two-dimensional models on infinite cylinders. The new algorithm can be conveniently implemented as an extension of an already existing DMRG implementation.

CHARACTERIZATION OF CRYPTOSPORIDIUM PARVUM BY MATRIX-ASSISTED LASER DESORPTION -- IONIZATION TIME OF FLIGHT MASS SPECTROMETRY

EPA Science Inventory

Matrix assisted laser desorption/ionization (MALDI) mass spectrometry was used to investigate whole and freeze thawed Cryptosporidium parvum oocysts. Whole oocysts revealed some mass spectral features. Reproducible patterns of spectral markers and increased sensitivity were obtai...

Differential MicroRNA Expression Profile in Myxomatous Mitral Valve Prolapse and Fibroelastic Deficiency Valves

PubMed Central

Chen, Yei-Tsung; Wang, Juan; Wee, Abby S. Y.; Yong, Quek-Wei; Tay, Edgar Lik-Wui; Woo, Chin Cheng; Sorokin, Vitaly; Richards, Arthur Mark; Ling, Lieng-Hsi

2016-01-01

Myxomatous mitral valve prolapse (MMVP) and fibroelastic deficiency (FED) are two common variants of degenerative mitral valve disease (DMVD), which is a leading cause of mitral regurgitation worldwide. While pathohistological studies have revealed differences in extracellular matrix content in MMVP and FED, the molecular mechanisms underlying these two disease entities remain to be elucidated. By using surgically removed valvular specimens from MMVP and FED patients that were categorized on the basis of echocardiographic, clinical and operative findings, a cluster of microRNAs that expressed differentially were identified. The expressions of has-miR-500, -3174, -17, -1193, -646, -1273e, -4298, -203, -505, and -939 showed significant differences between MMVP and FED after applying Bonferroni correction (p < 0.002174). The possible involvement of microRNAs in the pathogenesis of DMVD were further suggested by the presences of in silico predicted target sites on a number of genes reported to be involved in extracellular matrix homeostasis and marker genes for cellular composition of mitral valves, including decorin (DCN), aggrecan (ACAN), fibromodulin (FMOD), α actin 2 (ACTA2), extracellular matrix protein 2 (ECM2), desmin (DES), endothelial cell specific molecule 1 (ESM1), and platelet/ endothelial cell adhesion molecule 1 (PECAM1), as well as inverse correlations of selected microRNA and mRNA expression in MMVP and FED groups. Our results provide evidence that distinct molecular mechanisms underlie MMVP and FED. Moreover, the microRNAs identified may be targets for the future development of diagnostic biomarkers and therapeutics. PMID:27213335

Genetic Background is a Key Determinant of Glomerular Extracellular Matrix Composition and Organization.

PubMed

Randles, Michael J; Woolf, Adrian S; Huang, Jennifer L; Byron, Adam; Humphries, Jonathan D; Price, Karen L; Kolatsi-Joannou, Maria; Collinson, Sophie; Denny, Thomas; Knight, David; Mironov, Aleksandr; Starborg, Toby; Korstanje, Ron; Humphries, Martin J; Long, David A; Lennon, Rachel

2015-12-01

Glomerular disease often features altered histologic patterns of extracellular matrix (ECM). Despite this, the potential complexities of the glomerular ECM in both health and disease are poorly understood. To explore whether genetic background and sex determine glomerular ECM composition, we investigated two mouse strains, FVB and B6, using RNA microarrays of isolated glomeruli combined with proteomic glomerular ECM analyses. These studies, undertaken in healthy young adult animals, revealed unique strain- and sex-dependent glomerular ECM signatures, which correlated with variations in levels of albuminuria and known predisposition to progressive nephropathy. Among the variation, we observed changes in netrin 4, fibroblast growth factor 2, tenascin C, collagen 1, meprin 1-α, and meprin 1-β. Differences in protein abundance were validated by quantitative immunohistochemistry and Western blot analysis, and the collective differences were not explained by mutations in known ECM or glomerular disease genes. Within the distinct signatures, we discovered a core set of structural ECM proteins that form multiple protein-protein interactions and are conserved from mouse to man. Furthermore, we found striking ultrastructural changes in glomerular basement membranes in FVB mice. Pathway analysis of merged transcriptomic and proteomic datasets identified potential ECM regulatory pathways involving inhibition of matrix metalloproteases, liver X receptor/retinoid X receptor, nuclear factor erythroid 2-related factor 2, notch, and cyclin-dependent kinase 5. These pathways may therefore alter ECM and confer susceptibility to disease. Copyright © 2015 by the American Society of Nephrology.

A structural investigation of the alkali metal site distribution within bioactive glass using neutron diffraction and multinuclear solid state NMR.

PubMed

Martin, Richard A; Twyman, Helen L; Rees, Gregory J; Smith, Jodie M; Barney, Emma R; Smith, Mark E; Hanna, John V; Newport, Robert J

2012-09-21

The atomic-scale structure of Bioglass and the effect of substituting lithium for sodium within these glasses have been investigated using neutron diffraction and solid state magic angle spinning (MAS) NMR. Applying an effective isomorphic substitution difference function to the neutron diffraction data has enabled the Na-O and Li-O nearest-neighbour correlations to be isolated from the overlapping Ca-O, O-(P)-O and O-(Si)-O correlations. These results reveal that Na and Li behave in a similar manner within the glassy matrix and do not disrupt the short range order of the network former. Residual differences are attributed solely to the variation in ionic radius between the two species. Successful simplification of the 2 < r (Å) < 3 region via the difference method has enabled all the nearest neighbour correlations to be deconvolved. The diffraction data provides the first direct experimental evidence of split Na-O nearest-neighbour correlations in these melt quench bioactive glasses, and an analogous splitting of the Li-O correlations. The observed correlations are attributed to the metal ions bonded either to bridging or to non-bridging oxygen atoms. (23)Na triple quantum MAS (3QMAS) NMR data corroborates the split Na-O correlations. The structural sites present will be intimately related to the release properties of the glass system in physiological fluids such as plasma and saliva, and hence to the bioactivity of the material. Detailed structural knowledge is therefore a prerequisite for optimizing material design.

Making molecular balloons in laser-induced explosive boiling of polymer solutions.

PubMed

Leveugle, Elodie; Sellinger, Aaron; Fitz-Gerald, James M; Zhigilei, Leonid V

2007-05-25

The effect of the dynamic molecular rearrangements leading to compositional segregation is revealed in coarse-grained molecular dynamics simulations of short pulse laser interaction with a polymer solution in a volatile matrix. An internal release of matrix vapor at the onset of the explosive boiling of the overheated liquid is capable of pushing polymer molecules to the outskirts of a transient bubble, forming a polymer-rich surface layer enclosing the volatile matrix material. The results explain unexpected "deflated balloon" structures observed in films deposited by the matrix-assisted pulsed laser evaporation technique.

Bose-Einstein correlations: A study of an invariance group

NASA Astrophysics Data System (ADS)

Bialas, A.; Zalewski, K.

2005-08-01

A group of transformations changing the phases of the elements of the single-particle density matrix, but leaving unchanged the predictions for identical particles concerning the momentum distributions, momentum correlations etc., is identified. Its implications for the determinations of the interaction regions from studies of Bose-Einstein correlations are discussed.

Optoelectronic associative memory

NASA Technical Reports Server (NTRS)

Chao, Tien-Hsin (Inventor)

1993-01-01

An associative optical memory including an input spatial light modulator (SLM) in the form of an edge enhanced liquid crystal light valve (LCLV) and a pair of memory SLM's in the form of liquid crystal televisions (LCTV's) forms a matrix array of an input image which is cross correlated with a matrix array of stored images. The correlation product is detected and nonlinearly amplified to illuminate a replica of the stored image array to select the stored image correlating with the input image. The LCLV is edge enhanced by reducing the bias frequency and voltage and rotating its orientation. The edge enhancement and nonlinearity of the photodetection improves the orthogonality of the stored image. The illumination of the replicate stored image provides a clean stored image, uncontaminated by the image comparison process.

Simultaneous infrared and UV-visible absorption spectra of matrix-isolated carbon vapor

NASA Technical Reports Server (NTRS)

Kurtz, Joe; Huffman, Donald R.

1989-01-01

Carbon molecules were suggested as possible carriers of the diffuse interstellar bands. In particular, it was proposed that the 443 nm diffuse interstellar band is due to the same molecule which gives rise to the 447 nm absorption feature in argon matrix-isolated carbon vapor. If so, then an associated C-C stretching mode should be seen in the IR. By doing spectroscopy in both the IR and UV-visible regions on the same sample, the present work provides evidence for correlating UV-visible absorption features with those found in the IR. Early data indicates no correlation between the strongest IR feature (1997/cm) and the 447 nm band. Correlation with weaker IR features is being investigated.

A note on implementation of decaying product correlation structures for quasi-least squares.

PubMed

Shults, Justine; Guerra, Matthew W

2014-08-30

This note implements an unstructured decaying product matrix via the quasi-least squares approach for estimation of the correlation parameters in the framework of generalized estimating equations. The structure we consider is fairly general without requiring the large number of parameters that are involved in a fully unstructured matrix. It is straightforward to show that the quasi-least squares estimators of the correlation parameters yield feasible values for the unstructured decaying product structure. Furthermore, subject to conditions that are easily checked, the quasi-least squares estimators are valid for longitudinal Bernoulli data. We demonstrate implementation of the structure in a longitudinal clinical trial with both a continuous and binary outcome variable. Copyright © 2014 John Wiley & Sons, Ltd.

Computation of the soft anomalous dimension matrix in coordinate space

NASA Astrophysics Data System (ADS)

Mitov, Alexander; Sterman, George; Sung, Ilmo

2010-08-01

We complete the coordinate space calculation of the three-parton correlation in the two-loop massive soft anomalous dimension matrix. The full answer agrees with the result found previously by a different approach. The coordinate space treatment of renormalized two-loop gluon exchange diagrams exhibits their color symmetries in a transparent fashion. We compare coordinate space calculations of the soft anomalous dimension matrix with massive and massless eikonal lines and examine its nonuniform limit at absolute threshold.

Large-N and Bethe Ansatz

NASA Astrophysics Data System (ADS)

Jurčo, Branislav

We describe an integrable model, related to the Gaudin magnet, and its relation to the matrix model of Brézin, Itzykson, Parisi and Zuber. Relation is based on Bethe ansatz for the integrable model and its interpretation using orthogonal polynomials and saddle point approximation. Large-N limit of the matrix model corresponds to the thermodynamic limit of the integrable system. In this limit (functional) Bethe ansatz is the same as the generating function for correlators of the matrix models.

Photomask CD and LER characterization using Mueller matrix spectroscopic ellipsometry

NASA Astrophysics Data System (ADS)

Heinrich, A.; Dirnstorfer, I.; Bischoff, J.; Meiner, K.; Ketelsen, H.; Richter, U.; Mikolajick, T.

2014-10-01

Critical dimension and line edge roughness on photomask arrays are determined with Mueller matrix spectroscopic ellipsometry. Arrays with large sinusoidal perturbations are measured for different azimuth angels and compared with simulations based on rigorous coupled wave analysis. Experiment and simulation show that line edge roughness leads to characteristic changes in the different Mueller matrix elements. The influence of line edge roughness is interpreted as an increase of isotropic character of the sample. The changes in the Mueller matrix elements are very similar when the arrays are statistically perturbed with rms roughness values in the nanometer range suggesting that the results on the sinusoidal test structures are also relevant for "real" mask errors. Critical dimension errors and line edge roughness have similar impact on the SE MM measurement. To distinguish between both deviations, a strategy based on the calculation of sensitivities and correlation coefficients for all Mueller matrix elements is shown. The Mueller matrix elements M13/M31 and M34/M43 are the most suitable elements due to their high sensitivities to critical dimension errors and line edge roughness and, at the same time, to a low correlation coefficient between both influences. From the simulated sensitivities, it is estimated that the measurement accuracy has to be in the order of 0.01 and 0.001 for the detection of 1 nm critical dimension error and 1 nm line edge roughness, respectively.

Coil-to-coil physiological noise correlations and their impact on fMRI time-series SNR

PubMed Central

Triantafyllou, C.; Polimeni, J. R.; Keil, B.; Wald, L. L.

2017-01-01

Purpose Physiological nuisance fluctuations (“physiological noise”) are a major contribution to the time-series Signal to Noise Ratio (tSNR) of functional imaging. While thermal noise correlations between array coil elements have a well-characterized effect on the image Signal to Noise Ratio (SNR0), the element-to-element covariance matrix of the time-series fluctuations has not yet been analyzed. We examine this effect with a goal of ultimately improving the combination of multichannel array data. Theory and Methods We extend the theoretical relationship between tSNR and SNR0 to include a time-series noise covariance matrix Ψt, distinct from the thermal noise covariance matrix Ψ0, and compare its structure to Ψ0 and the signal coupling matrix SSH formed from the signal intensity vectors S. Results Inclusion of the measured time-series noise covariance matrix into the model relating tSNR and SNR0 improves the fit of experimental multichannel data and is shown to be distinct from Ψ0 or SSH. Conclusion Time-series noise covariances in array coils are found to differ from Ψ0 and more surprisingly, from the signal coupling matrix SSH. Correct characterization of the time-series noise has implications for the analysis of time-series data and for improving the coil element combination process. PMID:26756964

Ward identities and combinatorics of rainbow tensor models

NASA Astrophysics Data System (ADS)

Itoyama, H.; Mironov, A.; Morozov, A.

2017-06-01

We discuss the notion of renormalization group (RG) completion of non-Gaussian Lagrangians and its treatment within the framework of Bogoliubov-Zimmermann theory in application to the matrix and tensor models. With the example of the simplest non-trivial RGB tensor theory (Aristotelian rainbow), we introduce a few methods, which allow one to connect calculations in the tensor models to those in the matrix models. As a byproduct, we obtain some new factorization formulas and sum rules for the Gaussian correlators in the Hermitian and complex matrix theories, square and rectangular. These sum rules describe correlators as solutions to finite linear systems, which are much simpler than the bilinear Hirota equations and the infinite Virasoro recursion. Search for such relations can be a way to solving the tensor models, where an explicit integrability is still obscure.

Financial time series: A physics perspective

NASA Astrophysics Data System (ADS)

Gopikrishnan, Parameswaran; Plerou, Vasiliki; Amaral, Luis A. N.; Rosenow, Bernd; Stanley, H. Eugene

2000-06-01

Physicists in the last few years have started applying concepts and methods of statistical physics to understand economic phenomena. The word ``econophysics'' is sometimes used to refer to this work. One reason for this interest is the fact that Economic systems such as financial markets are examples of complex interacting systems for which a huge amount of data exist and it is possible that economic problems viewed from a different perspective might yield new results. This article reviews the results of a few recent phenomenological studies focused on understanding the distinctive statistical properties of financial time series. We discuss three recent results-(i) The probability distribution of stock price fluctuations: Stock price fluctuations occur in all magnitudes, in analogy to earthquakes-from tiny fluctuations to very drastic events, such as market crashes, eg., the crash of October 19th 1987, sometimes referred to as ``Black Monday''. The distribution of price fluctuations decays with a power-law tail well outside the Lévy stable regime and describes fluctuations that differ by as much as 8 orders of magnitude. In addition, this distribution preserves its functional form for fluctuations on time scales that differ by 3 orders of magnitude, from 1 min up to approximately 10 days. (ii) Correlations in financial time series: While price fluctuations themselves have rapidly decaying correlations, the magnitude of fluctuations measured by either the absolute value or the square of the price fluctuations has correlations that decay as a power-law and persist for several months. (iii) Correlations among different companies: The third result bears on the application of random matrix theory to understand the correlations among price fluctuations of any two different stocks. From a study of the eigenvalue statistics of the cross-correlation matrix constructed from price fluctuations of the leading 1000 stocks, we find that the largest 5-10% of the eigenvalues and the corresponding eigenvectors show systematic deviations from the predictions for a random matrix, whereas the rest of the eigenvalues conform to random matrix behavior-suggesting that these 5-10% of the eigenvalues contain system-specific information about correlated behavior. .

The relationship between tics, OC, ADHD and autism symptoms: A cross-disorder symptom analysis in Gilles de la Tourette syndrome patients and their family members

PubMed Central

Huisman-van Dijk, Hilde M.; van de Schoot, Rens; Rijkeboer, Marleen M.; Mathews, Carol A; Cath, Dainelle C

2016-01-01

Gilles de la Tourette’s syndrome (GTS) is a disorder in which co-morbid obsessive-compulsive (OC), Attention Deficit Hyperactivity Disorder (ADHD) and autism symptoms occur in up to 60% of patients, suggesting shared etiology. We aimed to explore the phenotypic structure underlying GTS, taking tic, OC, ADHD, and autism symptoms into account as measured by various symptom scales (YGTSS, Y-BOCS, CAARS and AQ) in 225 GTS patients and 371 family members. First, Confirmatory Factor Analyses (CFA) were performed on the symptom structure of each separate symptom scale. Second, the symptom dimensions derived from each scale were combined in one model, and correlations between them were calculated. Using the correlation matrix, Exploratory Factor Analyses (EFA) were performed on the symptom dimensions across the scales. EFA revealed a five factor structure: tic/aggression/symmetry; OC symptoms/compulsive tics/numbers and patterns; ADHD symptoms; autism symptoms; and hoarding/inattention symptoms. The symptom factors found in this study are partly in line with the traditional categorical boundaries of the symptom scales used, and partly reveal a symptom structure that cuts through the diagnostic categories. This phenotypic structure might more closely reflect underlying etiologies than a structure that classically describes GTS patients according to absence or presence of comorbid OCD, ADHD and autism, and might inform both future genetic and treatment studies. PMID:26826899

The relationship between tics, OC, ADHD and autism symptoms: A cross- disorder symptom analysis in Gilles de la Tourette syndrome patients and family-members.

PubMed

Huisman-van Dijk, Hilde M; Schoot, Rens van de; Rijkeboer, Marleen M; Mathews, Carol A; Cath, Daniëlle C

2016-03-30

Gilles de la Tourette's syndrome (GTS) is a disorder in which obsessive-compulsive (OC), Attention Deficit Hyperactivity Disorder (ADHD) and autism symptoms occur in up to 60% of patients, suggesting shared etiology. We explored the phenotypic structure of tic, OC, ADHD, and autism symptoms as measured by the YGTSS,Y-BOCS,CAARS and AQ, in 225 GTS patients and 371 family members. First, Confirmatory Factor Analyses (CFA) were performed on the symptom structure of each separate symptom scale. Second, the symptom dimensions derived from each scale were combined in one model, and correlations between them were calculated. Using the correlation matrix, Exploratory Factor Analyses (EFA) were performed on the symptom dimensions across the scales. EFA revealed a five factor structure: tic/aggression/symmetry; OC symptoms/compulsive tics/ numbers and patterns; ADHD symptoms; autism symptoms; and hoarding/inattention symptoms. The results are partly in line with the traditional categorical boundaries of the symptom scales used, and partly reveal a symptom structure that cuts through the diagnostic categories. This phenotypic structure might more closely reflect underlying etiologies than a structure that classically describes GTS patients according to absence or presence of comorbid OCD, ADHD and autism, and might inform both future genetic and treatment studies. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Sector Identification in a Set of Stock Return Time Series Traded at the London Stock Exchange

NASA Astrophysics Data System (ADS)

Coronnello, C.; Tumminello, M.; Lillo, F.; Micciche, S.; Mantegna, R. N.

2005-09-01

We compare some methods recently used in the literature to detect the existence of a certain degree of common behavior of stock returns belonging to the same economic sector. Specifically, we discuss methods based on random matrix theory and hierarchical clustering techniques. We apply these methods to a portfolio of stocks traded at the London Stock Exchange. The investigated time series are recorded both at a daily time horizon and at a 5-minute time horizon. The correlation coefficient matrix is very different at different time horizons confirming that more structured correlation coefficient matrices are observed for long time horizons. All the considered methods are able to detect economic information and the presence of clusters characterized by the economic sector of stocks. However, different methods present a different degree of sensitivity with respect to different sectors. Our comparative analysis suggests that the application of just a single method could not be able to extract all the economic information present in the correlation coefficient matrix of a stock portfolio.

Some issues on modeling atmospheric turbulence experienced by helicopter rotor blades

NASA Technical Reports Server (NTRS)

Costello, Mark; Gaonkar, G. H.; Prasad, J. V. R.; Schrage, D. P.

1992-01-01

The atmospheric turbulence velocities seen by nonrotating aircraft components and rotating blades can be substantially different. The differences are due to the spatial motion of the rotor blades, which move fore and aft through the gust waves. Body-fixed atmospheric turbulence refers to the actual atmospheric turbulence experienced by a point fixed on a nonrotating aircraft component such as the aircraft's center of gravity or the rotor hub, while blade-fixed atmospheric turbulence refers to the atmospheric turbulence experienced by an element of the rotating rotor blade. An example is presented, which, though overly simplified, shows important differences between blade- and body-fixed rotorcraft atmospheric turbulence models. All of the information necessary to develop the dynamic equations describing the atmospheric turbulence velocity field experienced by an aircraft is contained in the atmospheric turbulence velocity correlation matrix. It is for this reason that a generalized formulation of the correlation matrix describing atmospheric turbulence that a rotating blade encounters is developed. From this correlation matrix, earlier treated cases restricted to a rotor flying straight and level directly into the mean wind can be recovered as special cases.

Tracing and separating plasma components causing matrix effects in hydrophilic interaction chromatography-electrospray ionization mass spectrometry.

PubMed

Ekdahl, Anja; Johansson, Maria C; Ahnoff, Martin

2013-04-01

Matrix effects on electrospray ionization were investigated for plasma samples analysed by hydrophilic interaction chromatography (HILIC) in gradient elution mode, and HILIC columns of different chemistries were tested for separation of plasma components and model analytes. By combining mass spectral data with post-column infusion traces, the following components of protein-precipitated plasma were identified and found to have significant effect on ionization: urea, creatinine, phosphocholine, lysophosphocholine, sphingomyelin, sodium ion, chloride ion, choline and proline betaine. The observed effect on ionization was both matrix-component and analyte dependent. The separation of identified plasma components and model analytes on eight columns was compared, using pair-wise linear correlation analysis and principal component analysis (PCA). Large changes in selectivity could be obtained by change of column, while smaller changes were seen when the mobile phase buffer was changed from ammonium formate pH 3.0 to ammonium acetate pH 4.5. While results from PCA and linear correlation analysis were largely in accord, linear correlation analysis was judged to be more straight-forward in terms of conduction and interpretation.

Double Gamow-Teller Transitions and its Relation to Neutrinoless β β Decay

NASA Astrophysics Data System (ADS)

Shimizu, Noritaka; Menéndez, Javier; Yako, Kentaro

2018-04-01

We study the double Gamow-Teller (DGT) strength distribution of 48Ca with state-of-the-art large-scale nuclear shell model calculations. Our analysis shows that the centroid energy of the DGT giant resonance depends mostly on the isovector pairing interaction, while the resonance width is more sensitive to isoscalar pairing. Pairing correlations are also key in neutrinoless β β (0 ν β β ) decay. We find a simple relation between the centroid energy of the 48Ca DGT giant resonance and the 0 ν β β decay nuclear matrix element. More generally, we observe a very good linear correlation between the DGT transition to the ground state of the final nucleus and the 0 ν β β decay matrix element. The correlation, which originates on the dominant short-range character of both transitions, extends to heavier systems including several β β emitters and also holds in energy-density functional results. Our findings suggest that DGT experiments can be a very valuable tool to obtain information on the value of 0 ν β β decay nuclear matrix elements.

Distribution of erlotinib in rash and normal skin in cancer patients receiving erlotinib visualized by matrix assisted laser desorption/ionization mass spectrometry imaging.

PubMed

Nishimura, Meiko; Hayashi, Mitsuhiro; Mizutani, Yu; Takenaka, Kei; Imamura, Yoshinori; Chayahara, Naoko; Toyoda, Masanori; Kiyota, Naomi; Mukohara, Toru; Aikawa, Hiroaki; Fujiwara, Yasuhiro; Hamada, Akinobu; Minami, Hironobu

2018-04-06

The development of skin rashes is the most common adverse event observed in cancer patients treated with epidermal growth factor receptor-tyrosine kinase inhibitors such as erlotinib. However, the pharmacological evidence has not been fully revealed. Erlotinib distribution in the rashes was more heterogeneous than that in the normal skin, and the rashes contained statistically higher concentrations of erlotinib than adjacent normal skin in the superficial skin layer (229 ± 192 vs. 120 ± 103 ions/mm 2 ; P = 0.009 in paired t -test). LC-MS/MS confirmed that the concentration of erlotinib in the skin rashes was higher than that in normal skin in the superficial skin layer (1946 ± 1258 vs. 1174 ± 662 ng/cm 3 ; P = 0.028 in paired t -test). The results of MALDI-MSI and LC-MS/MS were well correlated (coefficient of correlation 0.879, P < 0.0001). Focal distribution of erlotinib in the skin tissue was visualized using non-labeled MALDI-MSI. Erlotinib concentration in the superficial layer of the skin rashes was higher than that in the adjacent normal skin. We examined patients with advanced pancreatic cancer who developed skin rashes after treatment with erlotinib and gemcitabine. We biopsied both the rash and adjacent normal skin tissues, and visualized and compared the distribution of erlotinib within the skin using matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI). The tissue concentration of erlotinib was also measured by liquid chromatography-tandem mass spectrometry (LC-MS/MS) with laser microdissection.

Distribution of erlotinib in rash and normal skin in cancer patients receiving erlotinib visualized by matrix assisted laser desorption/ionization mass spectrometry imaging

PubMed Central

Mizutani, Yu; Takenaka, Kei; Imamura, Yoshinori; Chayahara, Naoko; Toyoda, Masanori; Kiyota, Naomi; Mukohara, Toru; Aikawa, Hiroaki; Fujiwara, Yasuhiro; Hamada, Akinobu; Minami, Hironobu

2018-01-01

Background The development of skin rashes is the most common adverse event observed in cancer patients treated with epidermal growth factor receptor-tyrosine kinase inhibitors such as erlotinib. However, the pharmacological evidence has not been fully revealed. Results Erlotinib distribution in the rashes was more heterogeneous than that in the normal skin, and the rashes contained statistically higher concentrations of erlotinib than adjacent normal skin in the superficial skin layer (229 ± 192 vs. 120 ± 103 ions/mm2; P = 0.009 in paired t-test). LC-MS/MS confirmed that the concentration of erlotinib in the skin rashes was higher than that in normal skin in the superficial skin layer (1946 ± 1258 vs. 1174 ± 662 ng/cm3; P = 0.028 in paired t-test). The results of MALDI-MSI and LC-MS/MS were well correlated (coefficient of correlation 0.879, P < 0.0001). Conclusions Focal distribution of erlotinib in the skin tissue was visualized using non-labeled MALDI-MSI. Erlotinib concentration in the superficial layer of the skin rashes was higher than that in the adjacent normal skin. Methods We examined patients with advanced pancreatic cancer who developed skin rashes after treatment with erlotinib and gemcitabine. We biopsied both the rash and adjacent normal skin tissues, and visualized and compared the distribution of erlotinib within the skin using matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI). The tissue concentration of erlotinib was also measured by liquid chromatography-tandem mass spectrometry (LC–MS/MS) with laser microdissection. PMID:29719624

Quality of dissolved organic matter affects planktonic but not biofilm bacterial production in streams.

PubMed

Kamjunke, Norbert; Herzsprung, Peter; Neu, Thomas R

2015-02-15

Streams and rivers are important sites of organic carbon mineralization which is dependent on the land use within river catchments. Here we tested whether planktonic and epilithic biofilm bacteria differ in their response to the quality of dissolved organic carbon (DOC). Thus, planktonic and biofilm bacterial production was compared with patterns of DOC along a land-use gradient in the Bode catchment area (Germany). The freshness index of DOC was positively related to the proportion of agricultural area in the catchment. The humification index correlated with the proportion of forest area. Abundance and production of planktonic bacteria were lower in headwaters than at downstream sites. Planktonic production was weakly correlated to the total concentration of DOC but more strongly to quality-measures as revealed by spectra indexes, i.e. positively to the freshness index and negatively to the humification index. In contrast to planktonic bacteria, abundance and production of biofilm bacteria were independent of DOC quality. This finding may be explained by the association of biofilm bacteria with benthic algae and an extracellular matrix which represent additional substrate sources. The data show that planktonic bacteria seem to be regulated at a landscape scale controlled by land use, whereas biofilm bacteria are regulated at a biofilm matrix scale controlled by autochthonous production. Thus, the effects of catchment-scale land use changes on ecosystem processes are likely lower in small streams dominated by biofilm bacteria than in larger streams dominated by planktonic bacteria. Copyright © 2014 Elsevier B.V. All rights reserved.

Association of BCSC-1 and MMP-14 with human breast cancer.

PubMed

Di, Dalin; Chen, Lei; Guo, Yingying; Wang, Lina; Wang, Huidong; Ju, Jiyu

2018-04-01

Breast cancer suppressor candidate-1 (BCSC-1) is a candidate tumor suppressor gene that was identified recently. Decreased levels of BCSC-1 have been detected in a variety of cancer types in previous studies. Matrix metalloproteinase (MMP)-14 is a membrane-type MMP that plays an important role in tumor progression and prognosis. Previous research has indicated that MMP-14 is highly expressed in different cancer types and promotes tumor invasion or metastasis by remodeling the extracellular matrix. However, there have been few reports on BCSC-1 and MMP-14 in human breast cancer in recent years. In the present study, the association of BCSC-1 and MMP-14 with human breast cancer was investigated. The immunohistochemical analysis results revealed reduced expression of BCSC-1 and overexpression of MMP-14 in breast cancer tissues compared with adjacent normal breast tissues. Quantitative polymerase chain reaction and western blot analyses also showed that BCSC-1 was expressed at significantly lower levels, and that MMP-14 was expressed at significantly higher levels in breast cancer tissues compared with healthy breast tissue. Furthermore, decreased expression of BCSC-1 and overexpression of MMP-14 were associated with tumor cellular differentiation, lymph node metastasis and distant metastasis. A correlational analysis between BCSC-1 and MMP-14 was also conducted, and the results indicated a negative correlation between the two. In conclusion, the current findings indicate that BCSC-1 is downregulated, while MMP-14 is overexpressed in human breast cancer. These two genes may play important roles during the process of human breast cancer development.

Escherichia coli Biofilms Have an Organized and Complex Extracellular Matrix Structure

PubMed Central

Hung, Chia; Zhou, Yizhou; Pinkner, Jerome S.; Dodson, Karen W.; Crowley, Jan R.; Heuser, John; Chapman, Matthew R.; Hadjifrangiskou, Maria; Henderson, Jeffrey P.; Hultgren, Scott J.

2013-01-01

ABSTRACT Bacterial biofilms are ubiquitous in nature, and their resilience is derived in part from a complex extracellular matrix that can be tailored to meet environmental demands. Although common developmental stages leading to biofilm formation have been described, how the extracellular components are organized to allow three-dimensional biofilm development is not well understood. Here we show that uropathogenic Escherichia coli (UPEC) strains produce a biofilm with a highly ordered and complex extracellular matrix (ECM). We used electron microscopy (EM) techniques to image floating biofilms (pellicles) formed by UPEC. EM revealed intricately constructed substructures within the ECM that encase individual, spatially segregated bacteria with a distinctive morphology. Mutational and biochemical analyses of these biofilms confirmed curli as a major matrix component and revealed important roles for cellulose, flagella, and type 1 pili in pellicle integrity and ECM infrastructure. Collectively, the findings of this study elucidated that UPEC pellicles have a highly organized ultrastructure that varies spatially across the multicellular community. PMID:24023384

Levy Matrices and Financial Covariances

NASA Astrophysics Data System (ADS)

Burda, Zdzislaw; Jurkiewicz, Jerzy; Nowak, Maciej A.; Papp, Gabor; Zahed, Ismail

2003-10-01

In a given market, financial covariances capture the intra-stock correlations and can be used to address statistically the bulk nature of the market as a complex system. We provide a statistical analysis of three SP500 covariances with evidence for raw tail distributions. We study the stability of these tails against reshuffling for the SP500 data and show that the covariance with the strongest tails is robust, with a spectral density in remarkable agreement with random Lévy matrix theory. We study the inverse participation ratio for the three covariances. The strong localization observed at both ends of the spectral density is analogous to the localization exhibited in the random Lévy matrix ensemble. We discuss two competitive mechanisms responsible for the occurrence of an extensive and delocalized eigenvalue at the edge of the spectrum: (a) the Lévy character of the entries of the correlation matrix and (b) a sort of off-diagonal order induced by underlying inter-stock correlations. (b) can be destroyed by reshuffling, while (a) cannot. We show that the stocks with the largest scattering are the least susceptible to correlations, and likely candidates for the localized states. We introduce a simple model for price fluctuations which captures behavior of the SP500 covariances. It may be of importance for assets diversification.

Fourier-Legendre expansion of the one-electron density matrix of ground-state two-electron atoms.

PubMed

Ragot, Sébastien; Ruiz, María Belén

2008-09-28

The density matrix rho(r,r(')) of a spherically symmetric system can be expanded as a Fourier-Legendre series of Legendre polynomials P(l)(cos theta=rr(')rr(')). Application is here made to harmonically trapped electron pairs (i.e., Moshinsky's and Hooke's atoms), for which exact wavefunctions are known, and to the helium atom, using a near-exact wavefunction. In the present approach, generic closed form expressions are derived for the series coefficients of rho(r,r(')). The series expansions are shown to converge rapidly in each case, with respect to both the electron number and the kinetic energy. In practice, a two-term expansion accounts for most of the correlation effects, so that the correlated density matrices of the atoms at issue are essentially a linear functions of P(l)(cos theta)=cos theta. For example, in the case of Hooke's atom, a two-term expansion takes in 99.9% of the electrons and 99.6% of the kinetic energy. The correlated density matrices obtained are finally compared to their determinantal counterparts, using a simplified representation of the density matrix rho(r,r(')), suggested by the Legendre expansion. Interestingly, two-particle correlation is shown to impact the angular delocalization of each electron, in the one-particle space spanned by the r and r(') variables.

Automated vessel segmentation using cross-correlation and pooled covariance matrix analysis.

PubMed

Du, Jiang; Karimi, Afshin; Wu, Yijing; Korosec, Frank R; Grist, Thomas M; Mistretta, Charles A

2011-04-01

Time-resolved contrast-enhanced magnetic resonance angiography (CE-MRA) provides contrast dynamics in the vasculature and allows vessel segmentation based on temporal correlation analysis. Here we present an automated vessel segmentation algorithm including automated generation of regions of interest (ROIs), cross-correlation and pooled sample covariance matrix analysis. The dynamic images are divided into multiple equal-sized regions. In each region, ROIs for artery, vein and background are generated using an iterative thresholding algorithm based on the contrast arrival time map and contrast enhancement map. Region-specific multi-feature cross-correlation analysis and pooled covariance matrix analysis are performed to calculate the Mahalanobis distances (MDs), which are used to automatically separate arteries from veins. This segmentation algorithm is applied to a dual-phase dynamic imaging acquisition scheme where low-resolution time-resolved images are acquired during the dynamic phase followed by high-frequency data acquisition at the steady-state phase. The segmented low-resolution arterial and venous images are then combined with the high-frequency data in k-space and inverse Fourier transformed to form the final segmented arterial and venous images. Results from volunteer and patient studies demonstrate the advantages of this automated vessel segmentation and dual phase data acquisition technique. Copyright © 2011 Elsevier Inc. All rights reserved.

Mechanical Strains Induced in Osteoblasts by Use of Point Femtosecond Laser Targeting

PubMed Central

Bomzon, Ze'ev; Day, Daniel; Gu, Min; Cartmell, Sarah

2006-01-01

A study demonstrating how ultrafast laser radiation stimulates osteoblasts is presented. The study employed a custom made optical system that allowed for simultaneous confocal cell imaging and targeted femtosecond pulse laser irradiation. When femtosecond laser light was focused onto a single cell, a rise in intracellular Ca2+ levels was observed followed by contraction of the targeted cell. This contraction caused deformation of neighbouring cells leading to a heterogeneous strain field throughout the monolayer. Quantification of the strain fields in the monolayer using digital image correlation revealed local strains much higher than threshold values typically reported to stimulate extracellular bone matrix production in vitro. This use of point targeting with femtosecond pulse lasers could provide a new method for stimulating cell activity in orthopaedic tissue engineering. PMID:23165014

Ulex europeus agglutinin-I binding as a potential prognostic marker in ovarian cancer.

PubMed

Blonski, Katharina; Milde-Langosch, Karin; Bamberger, Ana-Maria; Osterholz, Tina; Utler, Christian; Berger, Jürgen; Löning, Thomas; Schumacher, Udo

2007-01-01

Ovarian cancer represents the malignant tumour of the female genital tract with the worst prognosis, mainly caused by early intraperitoneal spread. Cell-to-cell and cell-to-matrix interactions play a functionally important role in this spread and are both mediated by the cell membrane. Changes in the glycosylation of the cell membrane, as detected by lectin histochemistry, are sometimes associated with a poor prognosis. The expression of lectin binding of 164 ovarian cancer patients was analysed and the staining results were correlated with the clinical data of the patients. The univariate and multivariate statistical analysis revealed an independent prognostic significance for Ulex europeus agglutinin-I (UEA-I) binding. These findings indicate that UEA-I binding can serve as a prognostic factor in ovarian cancer.

Integrated optics to improve resolution on multiple configuration

NASA Astrophysics Data System (ADS)

Liu, Hua; Ding, Quanxin; Guo, Chunjie; Zhou, Liwei

2015-04-01

Inspired to in order to reveal the structure to improve imaging resolution, further technical requirement is proposed in some areas of the function and influence on the development of multiple configuration. To breakthrough diffraction limit, smart structures are recommended as the most efficient and economical method, while by used to improve the system performance, especially on signal to noise ratio and resolution. Integrated optics were considered in the selection, with which typical multiple configuration, by use the method of simulation experiment. Methodology can change traditional design concept and to develop the application space. Our calculations using multiple matrix transfer method, also the correlative algorithm and full calculations, show the expected beam shaping through system and, in particular, the experimental results will support our argument, which will be reported in the presentation.

Microstructures and magnetic properties of Co-Al-O granular thin films

NASA Astrophysics Data System (ADS)

Ohnuma, M.; Hono, K.; Onodera, H.; Ohnuma, S.; Fujimori, H.; Pedersen, J. S.

2000-01-01

The microstructures of Co-Al-O thin films of wide varieties of compositions are studied by transmission electron microscopy and small angle x-ray scattering (SAXS). In the superparamagnetic specimens, high resolution electron microscope images reveal that isolated spherical Co particles are surrounded by an amorphous aluminum oxide matrix. However, in the soft ferromagnetic films, the shape of the Co particles is prolate ellipsoidal. SAXS intensities from the soft magnetic specimens decrease inversely with the wave vector, q, in a low wave-vector region, while an interparticle interference peak is observed for the superparamagnetic specimens. The scattering profiles of the soft magnetic films imply that the Co particles have a cylindrical shape and are randomly oriented. The correlation between the magnetic properties and the microstructures is discussed.

Heat transfer and flow friction correlations for perforated plate matrix heat exchangers

NASA Astrophysics Data System (ADS)

Ratna Raju, L.; Kumar, S. Sunil; Chowdhury, K.; Nandi, T. K.

2017-02-01

Perforated plate matrix heat exchangers (MHE) are constructed of high conductivity perforated plates stacked alternately with low conductivity spacers. They are being increasingly used in many cryogenic applications including Claude cycle or Reversed Brayton cycle cryo-refrigerators and liquefiers. Design of high NTU (number of (heat) transfer unit) cryogenic MHEs requires accurate heat transfer coefficient and flow friction factor. Thermo-hydraulic behaviour of perforated plates strongly depends on the geometrical parameters. Existing correlations, however, are mostly expressed as functions of Reynolds number only. This causes, for a given configuration, significant variations in coefficients from one correlation to the other. In this paper we present heat transfer and flow friction correlations as functions of all geometrical and other controlling variables. A FluentTM based numerical model has been developed for heat transfer and pressure drop studies over a stack of alternately arranged perforated plates and spacers. The model is validated with the data from literature. Generalized correlations are obtained through regression analysis over a large number of computed data.

Modulation of Correlated Segment Fluctuations in IDPs upon Complex Formation as an Allosteric Regulatory Mechanism.

PubMed

Beier, Andreas; Schwarz, Thomas C; Kurzbach, Dennis; Platzer, Gerald; Tribuzio, Francesca; Konrat, Robert

2018-05-05

Molecular recognition of and by intrinsically disordered proteins (IDPs) is an intriguing and still largely elusive phenomenon. Typically, protein recognition involving IDPs requires either folding upon binding or, alternatively, the formation of "fuzzy complexes." Here we show via correlation analyses of paramagnetic relaxation enhancement data unprecedented and striking alterations of the concerted fluctuations within the conformational ensemble of IDPs upon ligand binding. We study the binding of α-synuclein to calmodulin, a ubiquitous calcium-binding protein, and the binding of the extracellular matrix IDP osteopontin to heparin, a mimic of the extracellular matrix ligand hyaluronic acid. In both cases, binding leads to reduction of correlated long-range motions in these two IDPs and thus indicates a loosening of structural compaction upon binding. Most importantly, however, the simultaneous presence of correlated and anti-correlated fluctuations in IDPs suggests the prevalence of "energetic frustration" and provides an explanation for the puzzling observation of disordered allostery in IDPs. Copyright © 2018. Published by Elsevier Ltd.

Overcoming multicollinearity in multiple regression using correlation coefficient

NASA Astrophysics Data System (ADS)

Zainodin, H. J.; Yap, S. J.

2013-09-01

Multicollinearity happens when there are high correlations among independent variables. In this case, it would be difficult to distinguish between the contributions of these independent variables to that of the dependent variable as they may compete to explain much of the similar variance. Besides, the problem of multicollinearity also violates the assumption of multiple regression: that there is no collinearity among the possible independent variables. Thus, an alternative approach is introduced in overcoming the multicollinearity problem in achieving a well represented model eventually. This approach is accomplished by removing the multicollinearity source variables on the basis of the correlation coefficient values based on full correlation matrix. Using the full correlation matrix can facilitate the implementation of Excel function in removing the multicollinearity source variables. It is found that this procedure is easier and time-saving especially when dealing with greater number of independent variables in a model and a large number of all possible models. Hence, in this paper detailed insight of the procedure is shown, compared and implemented.

Research on criticality analysis method of CNC machine tools components under fault rate correlation

NASA Astrophysics Data System (ADS)

Gui-xiang, Shen; Xian-zhuo, Zhao; Zhang, Ying-zhi; Chen-yu, Han

2018-02-01

In order to determine the key components of CNC machine tools under fault rate correlation, a system component criticality analysis method is proposed. Based on the fault mechanism analysis, the component fault relation is determined, and the adjacency matrix is introduced to describe it. Then, the fault structure relation is hierarchical by using the interpretive structure model (ISM). Assuming that the impact of the fault obeys the Markov process, the fault association matrix is described and transformed, and the Pagerank algorithm is used to determine the relative influence values, combined component fault rate under time correlation can obtain comprehensive fault rate. Based on the fault mode frequency and fault influence, the criticality of the components under the fault rate correlation is determined, and the key components are determined to provide the correct basis for equationting the reliability assurance measures. Finally, taking machining centers as an example, the effectiveness of the method is verified.

RETRACTED ARTICLE: Microstructure of carbide precipitates in L12-Ni3Al and L10-TiAl

NASA Astrophysics Data System (ADS)

Han, Chang Suk

2008-04-01

The crystallographic structures of carbide formed in Ni3Al- and TiAl-based intermetallics containing carbon are investigated in this study using transmission electron microscopy. In an L12-ordered Ni3Al alloy with 4 mol.% of chromium and 0.2 mol.% to 3.0 mol.% of carbon, fine octahedral precipitates of M23C6 type carbide were formed in the matrix by aging at temperatures around 973 K after solution annealing at 1423 K. TEM examination revealed that the M23C6 phase and the matrix lattices have a cube-cube orientation relationship and maintain partial atomic matching at the {111} interface. After prolonged aging or by aging at higher temperatures, the M23C6 precipitates adopt a rod-like morphology elongated parallel to the <100> directions. In L10-ordered TiAl containing from 0.1 mol.% to 2.0 mol.% carbon, TEM observations reveal that needle-like precipitates, which lie only in one direction parallel to the [001] axis of the L10 matrix appear in the matrix mainly at dislocations. Selected-area electron diffraction (SAED) patterns analyses showed that the needle-shaped precipitate is perovskite-type Ti3AlC. The orientation relationship between the Ti3AlC and the L10 matrix was found to be (001)Ti3AlC//(001)L10 matrix and [010]Ti3AlC//[010]L10 matrix. By aging at higher temperatures or for a longer period at 1073 K, plate-like precipitates of Ti2AlC with a hexagonal structure form on the {111} planes of the L10 matrix. The orientation relationship between the Ti2AlC and the L10 matrix is (0001)Ti2AlC//(111)L10 matrix and Ti2AlC//L10 matrix.

Rapid Diffusion of Green Fluorescent Protein in the Mitochondrial Matrix

PubMed Central

Partikian, Arthur; Ölveczky, Bence; Swaminathan, R.; Li, Yuxin; Verkman, A.S.

1998-01-01

Abstract. It is thought that the high protein density in the mitochondrial matrix results in severely restricted solute diffusion and metabolite channeling from one enzyme to another without free aqueous-phase diffusion. To test this hypothesis, we measured the diffusion of green fluorescent protein (GFP) expressed in the mitochondrial matrix of fibroblast, liver, skeletal muscle, and epithelial cell lines. Spot photobleaching of GFP with a 100× objective (0.8-μm spot diam) gave half-times for fluorescence recovery of 15–19 ms with >90% of the GFP mobile. As predicted for aqueous-phase diffusion in a confined compartment, fluorescence recovery was slowed or abolished by increased laser spot size or bleach time, and by paraformaldehyde fixation. Quantitative analysis of bleach data using a mathematical model of matrix diffusion gave GFP diffusion coefficients of 2–3 × 10−7 cm2/s, only three to fourfold less than that for GFP diffusion in water. In contrast, little recovery was found for bleaching of GFP in fusion with subunits of the fatty acid β-oxidation multienzyme complex that are normally present in the matrix. Measurement of the rotation of unconjugated GFP by time-resolved anisotropy gave a rotational correlation time of 23.3 ± 1 ns, similar to that of 20 ns for GFP rotation in water. A rapid rotational correlation time of 325 ps was also found for a small fluorescent probe (BCECF, ∼0.5 kD) in the matrix of isolated liver mitochondria. The rapid and unrestricted diffusion of solutes in the mitochondrial matrix suggests that metabolite channeling may not be required to overcome diffusive barriers. We propose that the clustering of matrix enzymes in membrane-associated complexes might serve to establish a relatively uncrowded aqueous space in which solutes can freely diffuse. PMID:9472034

Fibronectin Deposition Participates in Extracellular Matrix Assembly and Vascular Morphogenesis

PubMed Central

Hielscher, Abigail; Ellis, Kim; Qiu, Connie; Porterfield, Josh; Gerecht, Sharon

2016-01-01

The extracellular matrix (ECM) has been demonstrated to facilitate angiogenesis. In particular, fibronectin has been documented to activate endothelial cells, resulting in their transition from a quiescent state to an active state in which the cells exhibit enhanced migration and proliferation. The goal of this study is to examine the role of polymerized fibronectin during vascular tubulogenesis using a 3 dimensional (3D) cell-derived de-cellularized matrix. A fibronectin-rich 3D de-cellularized ECM was used as a scaffold to study vascular morphogenesis of endothelial cells (ECs). Confocal analyses of several matrix proteins reveal high intra- and extra-cellular deposition of fibronectin in formed vascular structures. Using a small peptide inhibitor of fibronectin polymerization, we demonstrate that inhibition of fibronectin fibrillogenesis in ECs cultured atop de-cellularized ECM resulted in decreased vascular morphogenesis. Further, immunofluorescence and ultrastructural analyses reveal decreased expression of stromal matrix proteins in the absence of polymerized fibronectin with high co-localization of matrix proteins found in association with polymerized fibronectin. Evaluating vascular kinetics, live cell imaging showed that migration, migration velocity, and mean square displacement, are disrupted in structures grown in the absence of polymerized fibronectin. Additionally, vascular organization failed to occur in the absence of a polymerized fibronectin matrix. Consistent with these observations, we tested vascular morphogenesis following the disruption of EC adhesion to polymerized fibronectin, demonstrating that block of integrins α5β1 and αvβ3, abrogated vascular morphogenesis. Overall, fibronectin deposition in a 3D cell-derived de-cellularized ECM appears to be imperative for matrix assembly and vascular morphogenesis. PMID:26811931

Social patterns revealed through random matrix theory

NASA Astrophysics Data System (ADS)

Sarkar, Camellia; Jalan, Sarika

2014-11-01

Despite the tremendous advancements in the field of network theory, very few studies have taken weights in the interactions into consideration that emerge naturally in all real-world systems. Using random matrix analysis of a weighted social network, we demonstrate the profound impact of weights in interactions on emerging structural properties. The analysis reveals that randomness existing in particular time frame affects the decisions of individuals rendering them more freedom of choice in situations of financial security. While the structural organization of networks remains the same throughout all datasets, random matrix theory provides insight into the interaction pattern of individuals of the society in situations of crisis. It has also been contemplated that individual accountability in terms of weighted interactions remains as a key to success unless segregation of tasks comes into play.

The correlation of low-velocity impact resistance of graphite-fiber-reinforced composites with matrix properties

NASA Technical Reports Server (NTRS)

Bowles, K. J.

1986-01-01

Summarized are basic studies that were conducted to correlate the impact resistance of graphite-fiber-reinforced composites with polymer matrix properties. Three crosslinked epoxy resins and a linear polysulfone were selected as composite matrices. As a group, these resins possess a significantly large range of mechanical properties. The mechanical properties of the resins and their respective composites were measured. Neat resin specimens and unidirectional and crossply composite specimens were impact tested with an instrumented dropweight tester. Impact resistances of the specimens were assessed on the basis of loading capability, energy absorption, and extent of damage.

Detecting Lamb waves with broadband acousto-ultrasonic signals in composite structures

NASA Technical Reports Server (NTRS)

Kautz, Harold E.

1992-01-01

Lamb waves can be produced and detected in ceramic matrix composites (CMC) and metal matrix composites (MMC) plates using the acousto-ultrasonic configuration employing broadband transducers. Experimental dispersion curves of lowest symmetric and lowest antisymmetric modes behave in a manner analogous to the graphite/polymer theoretical curves. In this study a basis has been established for analyzing Lamb wave velocities for characterizing composite plates. Lamb wave disperison curves and group velocities were correlated with variations in axial stiffness and shear stiffness in MMC and CMC. For CMCs, interfacial shear strength was also correlated with the first antisymmetric Lamb mode.

Detecting Lamb waves with broad-band acousto-ultrasonic signals in composite structures

NASA Technical Reports Server (NTRS)

Kautz, Harold E.

1992-01-01

Lamb waves can be produced and detected in ceramic matrix composites (CMC) and metal matrix composites (MMC) plates using the acousto-ultrasonic configuration employing broadband transducers. Experimental dispersion curves of lowest symmetric and antisymmetric modes behave in a manner analogous to the graphite/polymer theoretical curves. In this study a basis has been established for analyzing Lamb wave velocities for characterizing composite plates. Lamb wave dispersion curves and group velocities were correlated with variations in axial stiffness and shear stiffness in MMC and CMC. For CMC, interfacial shear strength was also correlated with the first antisymmetric Lamb mode.

Radiation-induced microcrystal shape change as a mechanism of wasteform degradation

NASA Astrophysics Data System (ADS)

Ojovan, Michael I.; Burakov, Boris E.; Lee, William E.

2018-04-01

Experiments with actinide-containing insulating wasteforms such as devitrified glasses containing 244Cm, Ti-pyrochlore, single-phase La-monazite, Pu-monazite ceramics, Eu-monazite and zircon single crystals containing 238Pu indicate that mechanical self-irradiation-induced destruction may not reveal itself for many years (even decades). The mechanisms causing these slowly-occurring changes remain unknown therefore in addition to known mechanisms of wasteform degradation such as matrix swelling and loss of solid solution we have modelled the damaging effects of electrical fields induced by the decay of radionuclides in clusters embedded in a non-conducting matrix. Three effects were important: (i) electric breakdown; (ii) cluster shape change due to dipole interaction, and (iii) cluster shape change due to polarisation interaction. We reveal a critical size of radioactive clusters in non-conducting matrices so that the matrix material can be damaged if clusters are larger than this critical size. The most important parameters that control the matrix integrity are the radioactive cluster (inhomogeneity) size, specific radioactivity, and effective matrix electrical conductivity. We conclude that the wasteform should be as homogeneous as possible and even electrically conductive to avoid potential damage caused by electrical charges induced by radioactive decay.

Methods of Technological Forecasting,

DTIC Science & Technology

1977-05-01

Trend Extrapolation Progress Curve Analogy Trend Correlation Substitution Analysis or Substitution Growth Curves Envelope Curve Advances in the State of...the Art Technological Mapping Contextual Mapping Matrix Input-Output Analysis Mathematical Models Simulation Models Dynamic Modelling. CHAPTER IV...Generation Interaction between Needs and Possibilities Map of the Technological Future — (‘ross- Impact Matri x Discovery Matrix Morphological Analysis

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…

Increased matrix metalloproteinases as possible cause of osseoarticular tissue destruction in long-term haemodialysis and beta 2-microglobulin amyloidosis.

PubMed

Ohashi, K; Kawai, R; Hara, M; Okada, Y; Tachibana, S; Ogura, Y

1996-04-01

Immunolocalization of matrix metalloproteinases (MMPs) and tissue inhibitors of matrix metalloproteinases (TIMPs) in periarticular tissues of beta 2-microglobulin amyloidosis patients was investigated. MMP-1 (interstitial collagenase) the most strongly expressed of the MMPs, was localized in the synovial lining cells, mesenchymal cells in granulation tissue and nodular amyloid deposits, and chondrocytes within areas of cartilage erosion. Expression of MMP-1 was correlated with the degree of macrophage infiltration and synovial cell hyperplasia, but it was not correlated with the degree of amyloid deposition or haemodialysis period. Expression of MMP-1 appeared more intense than that of TIMP-1 and TIMP-2 in highly inflammatory cases. MMP-2 was mildly expressed in the interstitial fibroblasts and MMP-3 was faintly stained in the extracellular matrix of the synovial membrane. MMP-9 (gelatinase B) was found to be strongly positive in the osteoclasts which increased in the progressing osteolytic lesion from the destructive arthropathy. These results suggest involvement of MMPs in inflammation with an imbalance between expression of MMPs and TIMPs being closely related to pathogenesis of the destructive arthropathy.

Joint analysis of phenotypic and molecular diversity provides new insights on the genetic variability of the Brazilian physic nut germplasm bank

PubMed Central

Alves, Alexandre Alonso; Bhering, Leonardo Lopes; Rosado, Tatiana Barbosa; Laviola, Bruno Galvêas; Formighieri, Eduardo Fernandes; Cruz, Cosme Damião

2013-01-01

The genetic variability of the Brazilian physic nut (Jatropha curcas) germplasm bank (117 accessions) was assessed using a combination of phenotypic and molecular data. The joint dissimilarity matrix showed moderate correlation with the original matrices of phenotypic and molecular data. However, the correlation between the phenotypic dissimilarity matrix and the genotypic dissimilarity matrix was low. This finding indicated that molecular markers (RAPD and SSR) did not adequately sample the genomic regions that were relevant for phenotypic differentiation of the accessions. The dissimilarity values of the joint dissimilarity matrix were used to measure phenotypic + molecular diversity. This diversity varied from 0 to 1.29 among the 117 accessions, with an average dissimilarity among genotypes of 0.51. Joint analysis of phenotypic and molecular diversity indicated that the genetic diversity of the physic nut germplasm was 156% and 64% higher than the diversity estimated from phenotypic and molecular data, respectively. These results show that Jatropha genetic variability in Brazil is not as limited as previously thought. PMID:24130445

Joint analysis of phenotypic and molecular diversity provides new insights on the genetic variability of the Brazilian physic nut germplasm bank.

PubMed

Alves, Alexandre Alonso; Bhering, Leonardo Lopes; Rosado, Tatiana Barbosa; Laviola, Bruno Galvêas; Formighieri, Eduardo Fernandes; Cruz, Cosme Damião

2013-09-01

The genetic variability of the Brazilian physic nut (Jatropha curcas) germplasm bank (117 accessions) was assessed using a combination of phenotypic and molecular data. The joint dissimilarity matrix showed moderate correlation with the original matrices of phenotypic and molecular data. However, the correlation between the phenotypic dissimilarity matrix and the genotypic dissimilarity matrix was low. This finding indicated that molecular markers (RAPD and SSR) did not adequately sample the genomic regions that were relevant for phenotypic differentiation of the accessions. The dissimilarity values of the joint dissimilarity matrix were used to measure phenotypic + molecular diversity. This diversity varied from 0 to 1.29 among the 117 accessions, with an average dissimilarity among genotypes of 0.51. Joint analysis of phenotypic and molecular diversity indicated that the genetic diversity of the physic nut germplasm was 156% and 64% higher than the diversity estimated from phenotypic and molecular data, respectively. These results show that Jatropha genetic variability in Brazil is not as limited as previously thought.

Interacting hadron resonance gas model in the K -matrix formalism

NASA Astrophysics Data System (ADS)

Dash, Ashutosh; Samanta, Subhasis; Mohanty, Bedangadas

2018-05-01

An extension of hadron resonance gas (HRG) model is constructed to include interactions using relativistic virial expansion of partition function. The noninteracting part of the expansion contains all the stable baryons and mesons and the interacting part contains all the higher mass resonances which decay into two stable hadrons. The virial coefficients are related to the phase shifts which are calculated using K -matrix formalism in the present work. We have calculated various thermodynamics quantities like pressure, energy density, and entropy density of the system. A comparison of thermodynamic quantities with noninteracting HRG model, calculated using the same number of hadrons, shows that the results of the above formalism are larger. A good agreement between equation of state calculated in K -matrix formalism and lattice QCD simulations is observed. Specifically, the lattice QCD calculated interaction measure is well described in our formalism. We have also calculated second-order fluctuations and correlations of conserved charges in K -matrix formalism. We observe a good agreement of second-order fluctuations and baryon-strangeness correlation with lattice data below the crossover temperature.

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

Briceno, Raul A.; Hansen, Maxwell T.; Monahan, Christopher J.

Lattice quantum chromodynamics (QCD) provides the only known systematic, nonperturbative method for first-principles calculations of nucleon structure. However, for quantities such as light-front parton distribution functions (PDFs) and generalized parton distributions (GPDs), the restriction to Euclidean time prevents direct calculation of the desired observable. Recently, progress has been made in relating these quantities to matrix elements of spatially nonlocal, zero-time operators, referred to as quasidistributions. Still, even for these time-independent matrix elements, potential subtleties have been identified in the role of the Euclidean signature. In this work, we investigate the analytic behavior of spatially nonlocal correlation functions and demonstrate thatmore » the matrix elements obtained from Euclidean lattice QCD are identical to those obtained using the Lehmann-Symanzik-Zimmermann reduction formula in Minkowski space. After arguing the equivalence on general grounds, we also show that it holds in a perturbative calculation, where special care is needed to identify the lattice prediction. Lastly, we present a proof of the uniqueness of the matrix elements obtained from Minkowski and Euclidean correlation functions to all order in perturbation theory.« less

Emergent causality and the N-photon scattering matrix in waveguide QED

NASA Astrophysics Data System (ADS)

Sánchez-Burillo, E.; Cadarso, A.; Martín-Moreno, L.; García-Ripoll, J. J.; Zueco, D.

2018-01-01

In this work we discuss the emergence of approximate causality in a general setup from waveguide QED—i.e. a one-dimensional propagating field interacting with a scatterer. We prove that this emergent causality translates into a structure for the N-photon scattering matrix. Our work builds on the derivation of a Lieb-Robinson-type bound for continuous models and for all coupling strengths, as well as on several intermediate results, of which we highlight: (i) the asymptotic independence of space-like separated wave packets, (ii) the proper definition of input and output scattering states, and (iii) the characterization of the ground state and correlations in the model. We illustrate our formal results by analyzing the two-photon scattering from a quantum impurity in the ultrastrong coupling regime, verifying the cluster decomposition and ground-state nature. Besides, we generalize the cluster decomposition if inelastic or Raman scattering occurs, finding the structure of the S-matrix in momentum space for linear dispersion relations. In this case, we compute the decay of the fluorescence (photon-photon correlations) caused by this S-matrix.

Matrix thermalization

NASA Astrophysics Data System (ADS)

Craps, Ben; Evnin, Oleg; Nguyen, Kévin

2017-02-01

Matrix quantum mechanics offers an attractive environment for discussing gravitational holography, in which both sides of the holographic duality are well-defined. Similarly to higher-dimensional implementations of holography, collapsing shell solutions in the gravitational bulk correspond in this setting to thermalization processes in the dual quantum mechanical theory. We construct an explicit, fully nonlinear supergravity solution describing a generic collapsing dilaton shell, specify the holographic renormalization prescriptions necessary for computing the relevant boundary observables, and apply them to evaluating thermalizing two-point correlation functions in the dual matrix theory.

Health monitoring method for composite materials

DOEpatents

Watkins, Jr., Kenneth S.; Morris, Shelby J [Hampton, VA

2011-04-12

An in-situ method for monitoring the health of a composite component utilizes a condition sensor made of electrically conductive particles dispersed in a polymeric matrix. The sensor is bonded or otherwise formed on the matrix surface of the composite material. Age-related shrinkage of the sensor matrix results in a decrease in the resistivity of the condition sensor. Correlation of measured sensor resistivity with data from aged specimens allows indirect determination of mechanical damage and remaining age of the composite component.

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

Regulated Production of Mineralization-competent Matrix Vesicles in Hypertrophic Chondrocytes

PubMed Central

Kirsch, Thorsten; Nah, Hyun-Duck; Shapiro, Irving M.; Pacifici, Maurizio

1997-01-01

Matrix vesicles have a critical role in the initiation of mineral deposition in skeletal tissues, but the ways in which they exert this key function remain poorly understood. This issue is made even more intriguing by the fact that matrix vesicles are also present in nonmineralizing tissues. Thus, we tested the novel hypothesis that matrix vesicles produced and released by mineralizing cells are structurally and functionally different from those released by nonmineralizing cells. To test this hypothesis, we made use of cultures of chick embryonic hypertrophic chondrocytes in which mineralization was triggered by treatment with vitamin C and phosphate. Ultrastructural analysis revealed that both control nonmineralizing and vitamin C/phosphatetreated mineralizing chondrocytes produced and released matrix vesicles that exhibited similar round shape, smooth contour, and average size. However, unlike control vesicles, those produced by mineralizing chondrocytes had very strong alkaline phosphatase activity and contained annexin V, a membrane-associated protein known to mediate Ca2+ influx into matrix vesicles. Strikingly, these vesicles also formed numerous apatite-like crystals upon incubation with synthetic cartilage lymph, while control vesicles failed to do so. Northern blot and immunohistochemical analyses showed that the production and release of annexin V-rich matrix vesicles by mineralizing chondrocytes were accompanied by a marked increase in annexin V expression and, interestingly, were followed by increased expression of type I collagen. Studies on embryonic cartilages demonstrated a similar sequence of phenotypic changes during the mineralization process in vivo. Thus, chondrocytes located in the hypertrophic zone of chick embryo tibial growth plate were characterized by strong annexin V expression, and those located at the chondro–osseous mineralizing border exhibited expression of both annexin V and type I collagen. These findings reveal that hypertrophic chondrocytes can qualitatively modulate their production of matrix vesicles and only when induced to initiate mineralization, will release mineralization-competent matrix vesicles rich in annexin V and alkaline phosphatase. The occurrence of type I collagen in concert with cartilage matrix calcification suggests that the protein may facilitate crystal growth after rupture of the matrix vesicle membrane; it may also offer a smooth transition from mineralized type II/type X collagen-rich cartilage matrix to type I collagen-rich bone matrix. PMID:9166414

Meta-Analytic Structural Equation Modeling: A Two-Stage Approach

ERIC Educational Resources Information Center

Cheung, Mike W. L.; Chan, Wai

2005-01-01

To synthesize studies that use structural equation modeling (SEM), researchers usually use Pearson correlations (univariate r), Fisher z scores (univariate z), or generalized least squares (GLS) to combine the correlation matrices. The pooled correlation matrix is then analyzed by the use of SEM. Questionable inferences may occur for these ad hoc…

The Robustness of LISREL Estimates in Structural Equation Models with Categorical Variables.

ERIC Educational Resources Information Center

Ethington, Corinna A.

This study examined the effect of type of correlation matrix on the robustness of LISREL maximum likelihood and unweighted least squares structural parameter estimates for models with categorical manifest variables. Two types of correlation matrices were analyzed; one containing Pearson product-moment correlations and one containing tetrachoric,…

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

PubMed

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

2017-09-21

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

Hydrophilic polyurethane matrix promotes chondrogenesis of mesenchymal stem cells☆

PubMed Central

Nalluri, Sandeep M.; Krishnan, G. Rajesh; Cheah, Calvin; Arzumand, Ayesha; Yuan, Yuan; Richardson, Caley A.; Yang, Shuying; Sarkar, Debanjan

2016-01-01

Segmental polyurethanes exhibit biphasic morphology and can control cell fate by providing distinct matrix guided signals to increase the chondrogenic potential of mesenchymal stem cells (MSCs). Polyethylene glycol (PEG) based hydrophilic polyurethanes can deliver differential signals to MSCs through their matrix phases where hard segments are cell-interactive domains and PEG based soft segments are minimally interactive with cells. These coordinated communications can modulate cell–matrix interactions to control cell shape and size for chondrogenesis. Biphasic character and hydrophilicity of polyurethanes with gel like architecture provide a synthetic matrix conducive for chondrogenesis of MSCs, as evidenced by deposition of cartilage-associated extracellular matrix. Compared to monophasic hydrogels, presence of cell interactive domains in hydrophilic polyurethanes gels can balance cell–cell and cell–matrix interactions. These results demonstrate the correlation between lineage commitment and the changes in cell shape, cell–matrix interaction, and cell–cell adhesion during chondrogenic differentiation which is regulated by polyurethane phase morphology, and thus, represent hydrophilic polyurethanes as promising synthetic matrices for cartilage regeneration. PMID:26046282

Correlated noise in the COBE DMR sky maps

NASA Technical Reports Server (NTRS)

Lineweaver, C. H.; Smoot, G. F.; Bennett, C. L.; Wright, E. L.; Tenorio, L.; Kogut, A.; Keegstra, P. B.; Hinshaw, G.; Banday, A. J.

1994-01-01

The Cosmic Background Explorer Satellite Differential Radiometer (COBE DMR) sky maps contain low-level correlated noise. We obtain estimates of the amplitude and pattern of the correlated noise from three techniques: angular averages of the covariance matrix, Monte Carlo simulations of two-point correlation functions and direct analysis of the DMR maps. The results from the three methods are mutually consistent. The noise covariance matrix of a DMR sky maps is diagonal to an accuracy of better than 1%. For a given sky pixel, the dominant noise covariance occure with the ring of pixels at an angular separation of 60 deg due to the 60 deg separation of the DMR horns. The mean covariance at 60 deg is 0.45%((sup +0.18)(sub -0.14)) of the mean variance. Additionally, the variance in a given pixel is 0.7% greater than would be expected from a single beam experiment with the same noise properties. Autocorrelation functions suffer from a approximately 1.5 sigma positive bias at 60 deg while cross-correlations have no bias. Published COBE DMR results are not significantly affected by correlated noise.

Advanced Composites: Mechanical Properties and Hardware Programs for Selected Resin Matrix Materials. [considering space shuttle applications

NASA Technical Reports Server (NTRS)

Welhart, E. K.

1976-01-01

This design note presents typical mechanical properties tabulated from industrial and governmental agencies' test programs. All data are correlated to specific products and all of the best known products are presented. The data include six epoxies, eight polyimides and one polyquinoxaline matrix material. Bron and graphite are the fiber reinforcements. Included are forty-two summaries of advanced (resin matrix) composite programs in existence in the United States. It is concluded that the selection of appropriate matrices, the geometric manner in which the fibers are incorporated in the matrix and the durability of the bond between fiber and matrix establish the end properties of the composite material and the performance of the fabricated structure.

The improved Apriori algorithm based on matrix pruning and weight analysis

NASA Astrophysics Data System (ADS)

Lang, Zhenhong

2018-04-01

This paper uses the matrix compression algorithm and weight analysis algorithm for reference and proposes an improved matrix pruning and weight analysis Apriori algorithm. After the transactional database is scanned for only once, the algorithm will construct the boolean transaction matrix. Through the calculation of one figure in the rows and columns of the matrix, the infrequent item set is pruned, and a new candidate item set is formed. Then, the item's weight and the transaction's weight as well as the weight support for items are calculated, thus the frequent item sets are gained. The experimental result shows that the improved Apriori algorithm not only reduces the number of repeated scans of the database, but also improves the efficiency of data correlation mining.

Longitudinal development of cortical thickness, folding, and fiber density networks in the first 2 years of life.

PubMed

Nie, Jingxin; Li, Gang; Wang, Li; Shi, Feng; Lin, Weili; Gilmore, John H; Shen, Dinggang

2014-08-01

Quantitatively characterizing the development of cortical anatomical networks during the early stage of life plays an important role in revealing the relationship between cortical structural connection and high-level functional development. The development of correlation networks of cortical-thickness, cortical folding, and fiber-density is systematically analyzed in this article to study the relationship between different anatomical properties during the first 2 years of life. Specifically, longitudinal MR images of 73 healthy subjects from birth to 2 year old are used. For each subject at each time point, its measures of cortical thickness, cortical folding, and fiber density are projected to its cortical surface that has been partitioned into 78 cortical regions. Then, the correlation matrices for cortical thickness, cortical folding, and fiber density at each time point can be constructed, respectively, by computing the inter-regional Pearson correlation coefficient (of any pair of ROIs) across all 73 subjects. Finally, the presence/absence pattern (i.e., binary pattern) of the connection network is constructed from each inter-regional correlation matrix, and its statistical and anatomical properties are adopted to analyze the longitudinal development of anatomical networks. The results show that the development of anatomical network could be characterized differently by using different anatomical properties (i.e., using cortical thickness, cortical folding, or fiber density). Copyright © 2013 Wiley Periodicals, Inc.

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

Expression and purification of myristoylated matrix protein of Mason-Pfizer monkey virus for NMR and MS measurements.

PubMed

Prchal, Jan; Junkova, Petra; Strmiskova, Miroslava; Lipov, Jan; Hynek, Radovan; Ruml, Tomas; Hrabal, Richard

2011-09-01

Matrix proteins play multiple roles both in early and late stages of the viral replication cycle. Their N-terminal myristoylation is important for interaction with the host cell membrane during virus budding. We used Escherichia coli, carrying N-myristoyltransferase gene, for the expression of the myristoylated His-tagged matrix protein of Mason-Pfizer monkey virus. An efficient, single-step purification procedure eliminating all contaminating proteins including, importantly, the non-myristoylated matrix protein was designed. The comparison of NMR spectra of matrix protein with its myristoylated form revealed substantial structural changes induced by this fatty acid modification. Copyright © 2011 Elsevier Inc. All rights reserved.

Effects of fiber, matrix, and interphase on carbon fiber composite compression strength

NASA Technical Reports Server (NTRS)

Nairn, John A.; Harper, Sheila I.; Bascom, Willard D.

1994-01-01

The major goal of this project was to obtain basic information on compression failure properties of carbon fiber composites. To do this, we investigated fiber effects, matrix effects, and fiber/matrix interface effects. Using each of nine fiber types, we prepared embedded single-fiber specimens, single-ply specimens, and full laminates. From the single-fiber specimens, in addition to the standard fragmentation test analysis, we were able to use the low crack density data to provide information about the distribution of fiber flaws. The single-ply specimens provided evidence of a correlation between the size of kink band zones and the quality of the interface. Results of the laminate compression experiments mostly agreed with the results from single-ply experiments, although the ultimate compression strengths of laminates were higher. Generally, these experiments showed a strong effect of interfacial properties. Matrix effects were examined using laminates subjected to precracking under mixed-mode loading conditions. A large effect of precracking conditions on the mode 1 toughness of the laminates was found. In order to control the properties of the fiber/matrix interface, we prepared composites of carbon fiber and polycarbonate and subjected these to annealing. The changes in interfacial properties directly correlated with changes in compression strength.

Partition of volatile organic compounds from air and from water into plant cuticular matrix: An LFER analysis

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

Platts, J.A.; Abraham, M.H.

The partitioning of organic compounds between air and foliage and between water and foliage is of considerable environmental interest. The purpose of this work is to show that partitioning into the cuticular matrix of one particular species can be satisfactorily modeled by general equations the authors have previously developed and, hence, that the same general equations could be used to model partitioning into other plant materials of the same or different species. The general equations are linear free energy relationships that employ descriptors for polarity/polarizability, hydrogen bond acidity and basicity, dispersive effects, and volume. They have been applied to themore » partition of 62 very varied organic compounds between cuticular matrix of the tomato fruit, Lycopersicon esculentum, and either air (MX{sub a}) or water (MX{sub w}). Values of log MX{sub a} covering a range of 12.4 log units are correlated with a standard deviation of 0.232 log unit, and values of log MX{sub w} covering a range of 7.6 log unit are correlated with an SD of 0.236 log unit. Possibilities are discussed for the prediction of new air-plant cuticular matrix and water-plant cuticular matrix partition values on the basis of the equations developed.« less

Matrix Metalloproteinases 2 and 9 Are Differentially Expressed in Patients with Indeterminate and Cardiac Clinical Forms of Chagas Disease

PubMed Central

Fares, Rafaelle Christine Gomes; Gomes, Juliana de Assis Silva; Garzoni, Luciana Ribeiro; Waghabi, Mariana Caldas; Saraiva, Roberto Magalhães; Medeiros, Nayara Ingrid; Oliveira-Prado, Roberta; Sangenis, Luiz Henrique Conde; Chambela, Mayara da Costa; de Araújo, Fernanda Fortes; Teixeira-Carvalho, Andréa; Damásio, Marcos Paulo; Valente, Vanessa Azevedo; Ferreira, Karine Silvestre; Sousa, Giovane Rodrigo; Rocha, Manoel Otávio da Costa

2013-01-01

Dilated chronic cardiomyopathy (DCC) from Chagas disease is associated with myocardial remodeling and interstitial fibrosis, resulting in extracellular matrix (ECM) changes. In this study, we characterized for the first time the serum matrix metalloproteinase 2 (MMP-2) and MMP-9 levels, as well as their main cell sources in peripheral blood mononuclear cells from patients presenting with the indeterminate (IND) or cardiac (CARD) clinical form of Chagas disease. Our results showed that serum levels of MMP-9 are associated with the severity of Chagas disease. The analysis of MMP production by T lymphocytes showed that CD8+ T cells are the main mononuclear leukocyte source of both MMP-2 and MMP-9 molecules. Using a new 3-dimensional model of fibrosis, we observed that sera from patients with Chagas disease induced an increase in the extracellular matrix components in cardiac spheroids. Furthermore, MMP-2 and MMP-9 showed different correlations with matrix proteins and inflammatory cytokines in patients with Chagas disease. Our results suggest that MMP-2 and MMP-9 show distinct activities in Chagas disease pathogenesis. While MMP-9 seems to be involved in the inflammation and cardiac remodeling of Chagas disease, MMP-2 does not correlate with inflammatory molecules. PMID:23856618

Spectral statistics of random geometric graphs

NASA Astrophysics Data System (ADS)

Dettmann, C. P.; Georgiou, O.; Knight, G.

2017-04-01

We use random matrix theory to study the spectrum of random geometric graphs, a fundamental model of spatial networks. Considering ensembles of random geometric graphs we look at short-range correlations in the level spacings of the spectrum via the nearest-neighbour and next-nearest-neighbour spacing distribution and long-range correlations via the spectral rigidity Δ3 statistic. These correlations in the level spacings give information about localisation of eigenvectors, level of community structure and the level of randomness within the networks. We find a parameter-dependent transition between Poisson and Gaussian orthogonal ensemble statistics. That is the spectral statistics of spatial random geometric graphs fits the universality of random matrix theory found in other models such as Erdős-Rényi, Barabási-Albert and Watts-Strogatz random graphs.

Scaling and correlations in foreign exchange market

NASA Astrophysics Data System (ADS)

Jiang, J.; Ma, K.; Cai, X.

2007-02-01

We observe that the distribution of the relative return, describing the variation of a certain currency, of 74 global currencies obeys a power-law. By using the random matrix theory we find that the distribution of eigenvalues of correlation matrix of relative return also follows a power-law. Using a scaled factorial moment we investigate the distribution of correlation coefficients of the relative return and observe intermittence phenomenon. Furthermore, we define the influence strength for a certain currency, which reflects the influence of its price change to the community interested. By doing that, we find that the distribution of influence strength is again a power-law. Beyond that, we compare the influence strength of Chinese Yuan (RMB) to those of other seven important currencies, which may have some interesting indications.

The failing human heart is characterized by decreased numbers of telocytes as result of apoptosis and altered extracellular matrix composition.

PubMed

Richter, Manfred; Kostin, Sawa

2015-11-01

Telocytes (TCs) are a novel type of interstitial cells only recently described. This study aimed at characterizing and quantifying TCs and telopodes (Tps) in normal and diseased hearts. We have been suggested that TCs are influenced by the extracellular matrix (ECM) composition. We used transmission electron microscopy and c-kit immunolabelling to identify and quantify TCs in explanted human hearts with heart failure (HF) because of dilated, ischemic or inflammatory cardiomyopathy. LV myectomy samples from patients with aortic stenosis with preserved ejection fraction and samples from donor hearts which could not be used for transplantation served as controls. Quantitative immunoconfocal analysis revealed that 1 mm(2) of the normal myocardium contains 14.9 ± 3.4 TCs and 41.6 ± 5.9 Tps. As compared with the control group, the number of TCs and Tps in HF decreased more than twofold. There were no differences between HF and control in the number of Ki67-positive TCs. In contrast, terminal deoxynucleotidyl transferase-mediated dUTP nick end labelling-positive TCs increased threefold in diseased hearts as compared to control. Significant inverse correlations were found between the amount of mature fibrillar collagen type I and the number of TCs (r = -0.84; P < 0.01) and Tps (r = -0.85; P < 0.01). The levels of degraded collagens showed a significant positive relationship with the TCs numbers. It is concluded that in HF the number of TCs are decreased because of higher rates of TCs apoptosis. Moreover, our results indicate that a close relationship exists between TCs and the ECM protein composition such that the number of TCs and Tps correlates negatively with the amount of mature fibrillar collagens and correlates positively with degraded collagens. © 2015 The Authors. Journal of Cellular and Molecular Medicine published by John Wiley & Sons Ltd and Foundation for Cellular and Molecular Medicine.

Correlation of spacecraft thermal mathematical models to reference data

NASA Astrophysics Data System (ADS)

Torralbo, Ignacio; Perez-Grande, Isabel; Sanz-Andres, Angel; Piqueras, Javier

2018-03-01

Model-to-test correlation is a frequent problem in spacecraft-thermal control design. The idea is to determine the values of the parameters of the thermal mathematical model (TMM) that allows reaching a good fit between the TMM results and test data, in order to reduce the uncertainty of the mathematical model. Quite often, this task is performed manually, mainly because a good engineering knowledge and experience is needed to reach a successful compromise, but the use of a mathematical tool could facilitate this work. The correlation process can be considered as the minimization of the error of the model results with regard to the reference data. In this paper, a simple method is presented suitable to solve the TMM-to-test correlation problem, using Jacobian matrix formulation and Moore-Penrose pseudo-inverse, generalized to include several load cases. Aside, in simple cases, this method also allows for analytical solutions to be obtained, which helps to analyze some problems that appear when the Jacobian matrix is singular. To show the implementation of the method, two problems have been considered, one more academic, and the other one the TMM of an electronic box of PHI instrument of ESA Solar Orbiter mission, to be flown in 2019. The use of singular value decomposition of the Jacobian matrix to analyze and reduce these models is also shown. The error in parameter space is used to assess the quality of the correlation results in both models.