A novel stimuli-synchronized alloy-treated matrix for space-defined gastrointestinal delivery of mesalamine in the Large White pig model.

PubMed

Bawa, Priya; Choonara, Yahya E; du Toit, Lisa C; Kumar, Pradeep; Ndesendo, Valence M K; Meyer, Leith C R; Pillay, Viness

2013-03-28

The study focussed on designing a Stimuli-Synchronized Matrix (SSM) for space-defined colonic delivery of the anti-inflammatory drug mesalamine. The configured matrix provided time-independent delivery and stimuli targeting. Formulations were optimized according to a Box-Behnken experimental design that constituted mesalamine-loaded BaSO4-crosslinked chitosan dispersed within a pectin, carboxymethylcellulose and xanthan gum complex. The complex was compressed into matrices and subsequently alloy-treated with pectin and ethylcellulose. In vitro drug release was determined in the presence and absence of colonic enzymes and the mean dissolution time was used for formulation optimization. To mechanistically elucidate the synchronous catalytic action of the enzymes pectinase and glucosidase on the matrix, computer-aided 3D modelling of active fractions of the enzyme-substrate complexes was generated to predict the orientation of residues affecting the substrate domain. Drug release profiles revealed distinct colonic enzyme responsiveness with fractions of 0.402 and 0.152 of mesalamine released in the presence and absence of enzymes, respectively after 24h. The commercial comparator product showed irreproducible release profiles over the same period (SD=0.550) compared to the SSM formulation (SD=0.037). FTIR spectra of alloy-treated matrices showed no peaks from 1589 to 1512cm(-1) after colonic enzyme exposure. With increasing enzyme exposure there were also no peaks between 1646 and 1132cm(-1). This indicated polymeric enzyme cleavage for controlled and space-defined release of mesalamine. Plasma concentration profiles in the Large White pig model produced a Cmax of 3.77±1.375μg/mL compared to 10.604±2.846μg/mL for the comparator formulation. The SSM formulation proved superior over the comparator product by providing superiorly controlled enzyme-responsive colonic drug delivery. Copyright © 2012 Elsevier B.V. All rights reserved.

Cell wall lipids from Mycobacterium bovis BCG are inflammatory when inoculated within a gel matrix: characterization of a new model of the granulomatous response to mycobacterial components.

PubMed

Rhoades, Elizabeth R; Geisel, Rachel E; Butcher, Barbara A; McDonough, Sean; Russell, David G

2005-05-01

The chronic inflammatory response to Mycobacterium generates complex granulomatous lesions that balance containment with destruction of infected tissues. To study the contributing factors from host and pathogen, we developed a model wherein defined mycobacterial components and leukocytes are delivered in a gel, eliciting a localized response that can be retrieved and analysed. We validated the model by comparing responses to the cell wall lipids from Mycobacterium bovis bacillus Calmette-Guerin (BCG) to reported activities in other models. BCG lipid-coated beads and bone marrow-derived macrophages (input macrophages) were injected intraperitoneally into BALB/c mice. Input macrophages and recruited peritoneal exudate cells took up fluorescently tagged BCG lipids, and matrix-associated macrophages and neutrophils produced tumor necrosis factor, interleukin-1alpha, and interleukin-6. Leukocyte numbers and cytokine levels were greater in BCG lipid-bearing matrices than matrices containing non-coated or phosphatidylglycerol-coated beads. Leukocytes arrived in successive waves of neutrophils, macrophages and eosinophils, followed by NK and T cells (CD4(+), CD8(+), or gammadelta) at 7 days and B cells within 12 days. BCG lipids also predisposed matrices for adherence and vascularization, enhancing cellular recruitment. We submit that the matrix model presents pertinent features of the murine granulomatous response that will prove to be an adaptable method for study of this complex response.

A Biofilm Matrix-Associated Protease Inhibitor Protects Pseudomonas aeruginosa from Proteolytic Attack.

PubMed

Tseng, Boo Shan; Reichhardt, Courtney; Merrihew, Gennifer E; Araujo-Hernandez, Sophia A; Harrison, Joe J; MacCoss, Michael J; Parsek, Matthew R

2018-04-10

Pseudomonas aeruginosa produces an extracellular biofilm matrix that consists of nucleic acids, exopolysaccharides, lipid vesicles, and proteins. In general, the protein component of the biofilm matrix is poorly defined and understudied relative to the other major matrix constituents. While matrix proteins have been suggested to provide many functions to the biofilm, only proteins that play a structural role have been characterized thus far. Here we identify proteins enriched in the matrix of P. aeruginosa biofilms. We then focused on a candidate matrix protein, the serine protease inhibitor ecotin (PA2755). This protein is able to inhibit neutrophil elastase, a bactericidal enzyme produced by the host immune system during P. aeruginosa biofilm infections. We show that ecotin binds to the key biofilm matrix exopolysaccharide Psl and that it can inhibit neutrophil elastase when associated with Psl. Finally, we show that ecotin protects both planktonic and biofilm P. aeruginosa cells from neutrophil elastase-mediated killing. This may represent a novel mechanism of protection for biofilms to increase their tolerance against the innate immune response. IMPORTANCE Proteins associated with the extracellular matrix of bacterial aggregates called biofilms have long been suggested to provide many important functions to the community. To date, however, only proteins that provide structural roles have been described, and few matrix-associated proteins have been identified. We developed a method to identify matrix proteins and characterized one. We show that this protein, when associated with the biofilm matrix, can inhibit a bactericidal enzyme produced by the immune system during infection and protect biofilm cells from death induced by the enzyme. This may represent a novel mechanism of protection for biofilms, further increasing their tolerance against the immune response. Together, our results are the first to show a nonstructural function for a confirmed matrix-interacting protein. Copyright © 2018 Tseng et al.

Commensal Protection of Staphylococcus aureus against Antimicrobials by Candida albicans Biofilm Matrix.

PubMed

Kong, Eric F; Tsui, Christina; Kucharíková, Sona; Andes, David; Van Dijck, Patrick; Jabra-Rizk, Mary Ann

2016-10-11

Biofilm-associated polymicrobial infections, particularly those involving fungi and bacteria, are responsible for significant morbidity and mortality and tend to be challenging to treat. Candida albicans and Staphylococcus aureus specifically are considered leading opportunistic fungal and bacterial pathogens, respectively, mainly due to their ability to form biofilms on catheters and indwelling medical devices. However, the impact of mixed-species biofilm growth on therapy remains largely understudied. In this study, we investigated the influence of C. albicans secreted cell wall polysaccharides on the response of S. aureus to antibacterial agents in biofilm. Results demonstrated significantly enhanced tolerance for S. aureus to drugs in the presence of C. albicans or its secreted cell wall polysaccharide material. Fluorescence confocal time-lapse microscopy revealed impairment of drug diffusion through the mixed biofilm matrix. Using C. albicans mutant strains with modulated cell wall polysaccharide expression, exogenous supplementation, and enzymatic degradation, the C. albicans-secreted β-1,3-glucan cell wall component was identified as the key matrix constituent providing the bacteria with enhanced drug tolerance. Further, antibody labeling demonstrated rapid coating of the bacteria by the C. albicans matrix material. Importantly, via its effect on the fungal biofilm matrix, the antifungal caspofungin sensitized the bacteria to the drugs. Understanding such symbiotic interactions with clinical relevance between microbial species in biofilms will greatly aid in overcoming the limitations of current therapies and in defining potential new targets for treating polymicrobial infections. The fungus Candida albicans and the bacterium Staphylococcus aureus are important microbial pathogens responsible for the majority of infections in hospitalized patients and are often coisolated from a host. In this study, we demonstrated that when grown together, the fungus provides the bacterium with enhanced tolerance to antimicrobial drugs. This process was mediated by polysaccharides secreted by the fungal cell into the environment. The biofilm matrix formed by these polysaccharides prevented penetration by the drugs and provided the bacteria with protection. Importantly, we show that by inhibiting the production of the fungal polysaccharides, a specific antifungal agent indirectly sensitized the bacteria to antimicrobials. Understanding the therapeutic implications of the interactions between these two diverse microbial species will aid in overcoming the limitations of current therapies and in defining new targets for treating complex polymicrobial infections. Copyright © 2016 Kong et al.

Stability and dynamical properties of material flow systems on random networks

NASA Astrophysics Data System (ADS)

Anand, K.; Galla, T.

2009-04-01

The theory of complex networks and of disordered systems is used to study the stability and dynamical properties of a simple model of material flow networks defined on random graphs. In particular we address instabilities that are characteristic of flow networks in economic, ecological and biological systems. Based on results from random matrix theory, we work out the phase diagram of such systems defined on extensively connected random graphs, and study in detail how the choice of control policies and the network structure affects stability. We also present results for more complex topologies of the underlying graph, focussing on finitely connected Erdös-Réyni graphs, Small-World Networks and Barabási-Albert scale-free networks. Results indicate that variability of input-output matrix elements, and random structures of the underlying graph tend to make the system less stable, while fast price dynamics or strong responsiveness to stock accumulation promote stability.

A photoreversible protein-patterning approach for guiding stem cell fate in three-dimensional gels

NASA Astrophysics Data System (ADS)

Deforest, Cole A.; Tirrell, David A.

2015-05-01

Although biochemically patterned hydrogels are capable of recapitulating many critical aspects of the heterogeneous cellular niche, exercising spatial and temporal control of the presentation and removal of biomolecular signalling cues in such systems has proved difficult. Here, we demonstrate a synthetic strategy that exploits two bioorthogonal photochemistries to achieve reversible immobilization of bioactive full-length proteins with good spatial and temporal control within synthetic, cell-laden biomimetic scaffolds. A photodeprotection-oxime-ligation sequence permits user-defined quantities of proteins to be anchored within distinct subvolumes of a three-dimensional matrix, and an ortho-nitrobenzyl ester photoscission reaction facilitates subsequent protein removal. By using this approach to pattern the presentation of the extracellular matrix protein vitronectin, we accomplished reversible differentiation of human mesenchymal stem cells to osteoblasts in a spatially defined manner. Our protein-patterning approach should provide further avenues to probe and direct changes in cell physiology in response to dynamic biochemical signalling.

Deconstruction of a Metastatic Tumor Microenvironment Reveals a Common Matrix Response in Human Cancers.

PubMed

Pearce, Oliver M T; Delaine-Smith, Robin M; Maniati, Eleni; Nichols, Sam; Wang, Jun; Böhm, Steffen; Rajeeve, Vinothini; Ullah, Dayem; Chakravarty, Probir; Jones, Roanne R; Montfort, Anne; Dowe, Tom; Gribben, John; Jones, J Louise; Kocher, Hemant M; Serody, Jonathan S; Vincent, Benjamin G; Connelly, John; Brenton, James D; Chelala, Claude; Cutillas, Pedro R; Lockley, Michelle; Bessant, Conrad; Knight, Martin M; Balkwill, Frances R

2018-03-01

We have profiled, for the first time, an evolving human metastatic microenvironment by measuring gene expression, matrisome proteomics, cytokine and chemokine levels, cellularity, extracellular matrix organization, and biomechanical properties, all on the same sample. Using biopsies of high-grade serous ovarian cancer metastases that ranged from minimal to extensive disease, we show how nonmalignant cell densities and cytokine networks evolve with disease progression. Multivariate integration of the different components allowed us to define, for the first time, gene and protein profiles that predict extent of disease and tissue stiffness, while also revealing the complexity and dynamic nature of matrisome remodeling during development of metastases. Although we studied a single metastatic site from one human malignancy, a pattern of expression of 22 matrisome genes distinguished patients with a shorter overall survival in ovarian and 12 other primary solid cancers, suggesting that there may be a common matrix response to human cancer. Significance: Conducting multilevel analysis with data integration on biopsies with a range of disease involvement identifies important features of the evolving tumor microenvironment. The data suggest that despite the large spectrum of genomic alterations, some human malignancies may have a common and potentially targetable matrix response that influences the course of disease. Cancer Discov; 8(3); 304-19. ©2017 AACR. This article is highlighted in the In This Issue feature, p. 253 . ©2017 American Association for Cancer Research.

Analysis of the Aspergillus fumigatus Biofilm Extracellular Matrix by Solid-State Nuclear Magnetic Resonance Spectroscopy.

PubMed

Reichhardt, Courtney; Ferreira, Jose A G; Joubert, Lydia-Marie; Clemons, Karl V; Stevens, David A; Cegelski, Lynette

2015-11-01

Aspergillus fumigatus is commonly responsible for lethal fungal infections among immunosuppressed individuals. A. fumigatus forms biofilm communities that are of increasing biomedical interest due to the association of biofilms with chronic infections and their increased resistance to antifungal agents and host immune factors. Understanding the composition of microbial biofilms and the extracellular matrix is important to understanding function and, ultimately, to developing strategies to inhibit biofilm formation. We implemented a solid-state nuclear magnetic resonance (NMR) approach to define compositional parameters of the A. fumigatus extracellular matrix (ECM) when biofilms are formed in RPMI 1640 nutrient medium. Whole biofilm and isolated matrix networks were also characterized by electron microscopy, and matrix proteins were identified through protein gel analysis. The (13)C NMR results defined and quantified the carbon contributions in the insoluble ECM, including carbonyls, aromatic carbons, polysaccharide carbons (anomeric and nonanomerics), aliphatics, etc. Additional (15)N and (31)P NMR spectra permitted more specific annotation of the carbon pools according to C-N and C-P couplings. Together these data show that the A. fumigatus ECM produced under these growth conditions contains approximately 40% protein, 43% polysaccharide, 3% aromatic-containing components, and up to 14% lipid. These fundamental chemical parameters are needed to consider the relationships between composition and function in the A. fumigatus ECM and will enable future comparisons with other organisms and with A. fumigatus grown under alternate conditions. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Model verification of mixed dynamic systems. [POGO problem in liquid propellant rockets

NASA Technical Reports Server (NTRS)

Chrostowski, J. D.; Evensen, D. A.; Hasselman, T. K.

1978-01-01

A parameter-estimation method is described for verifying the mathematical model of mixed (combined interactive components from various engineering fields) dynamic systems against pertinent experimental data. The model verification problem is divided into two separate parts: defining a proper model and evaluating the parameters of that model. The main idea is to use differences between measured and predicted behavior (response) to adjust automatically the key parameters of a model so as to minimize response differences. To achieve the goal of modeling flexibility, the method combines the convenience of automated matrix generation with the generality of direct matrix input. The equations of motion are treated in first-order form, allowing for nonsymmetric matrices, modeling of general networks, and complex-mode analysis. The effectiveness of the method is demonstrated for an example problem involving a complex hydraulic-mechanical system.

Triplex molecular layers with nonlinear nanomechanical response

NASA Astrophysics Data System (ADS)

Tsukruk, V. V.; Ahn, H.-S.; Kim, D.; Sidorenko, A.

2002-06-01

The molecular design of surface structures with built-in mechanisms for mechanical energy dissipation under nanomechanical deformation and compression resistance provided superior nanoscale wear stability. We designed robust, well-defined trilayer surface nanostructures chemically grafted to a silicon oxide surface with an effective composite modulus of about 1 GPa. The total thickness was within 20-30 nm and included an 8 nm rubber layer sandwiched between two hard layers. The rubber layer provides an effective mechanism for energy dissipation, facilitated by nonlinear, giant, reversible elastic deformations of the rubber matrix, restoring the initial status due to the presence of an effective nanodomain network and chemical grafting within the rubber matrix.

Modeling the Nonlinear, Strain Rate Dependent Deformation of Shuttle Leading Edge Materials with Hydrostatic Stress Effects Included

NASA Technical Reports Server (NTRS)

Goldberg, Robert K.; Carney, Kelly S.

2004-01-01

An analysis method based on a deformation (as opposed to damage) approach has been developed to model the strain rate dependent, nonlinear deformation of woven ceramic matrix composites, such as the Reinforced Carbon Carbon (RCC) material used on the leading edges of the Space Shuttle. In the developed model, the differences in the tension and compression deformation behaviors have also been accounted for. State variable viscoplastic equations originally developed for metals have been modified to analyze the ceramic matrix composites. To account for the tension/compression asymmetry in the material, the effective stress and effective inelastic strain definitions have been modified. The equations have also been modified to account for the fact that in an orthotropic composite the in-plane shear response is independent of the stiffness in the normal directions. The developed equations have been implemented into LS-DYNA through the use of user defined subroutines (UMATs). Several sample qualitative calculations have been conducted, which demonstrate the ability of the model to qualitatively capture the features of the deformation response present in woven ceramic matrix composites.

Host Response Signature to Staphylococcus aureus Alpha-Hemolysin Implicates Pulmonary Th17 Response

PubMed Central

Zhou, Tong; Moreno-Vinasco, Liliana; Hollett, Brian; Garcia, Joe G. N.

2012-01-01

Staphylococcus aureus pneumonia causes significant morbidity and mortality. Alpha-hemolysin (Hla), a pore-forming cytotoxin of S. aureus, has been identified through animal models of pneumonia as a critical virulence factor that induces lung injury. In spite of considerable molecular knowledge of how this cytotoxin injures the host, the precise host response to Hla in the context of infection remains poorly understood. We employed whole-genome expression profiling of infected lungs to define the host response to wild-type S. aureus compared with the response to an Hla-deficient isogenic mutant in experimental pneumonia. These data provide a complete expression profile at 4 and at 24 h postinfection, revealing a unique response to the toxin-expressing strain. Gene ontogeny analysis revealed significant differences in the extracellular matrix and cardiomyopathy pathways, both of which govern cellular interactions in the tissue microenvironment. Evaluation of individual transcript responses to Hla-secreting staphylococci was notable for upregulation of host cytokine and chemokine genes, including the p19 subunit of interleukin-23. Consistent with this observation, the cellular immune response to infection was characterized by a prominent Th17 response to the wild-type pathogen. These findings define specific host mRNA responses to Hla-producing S. aureus, coupling the pulmonary Th17 response to the secretion of this cytotoxin. Expression profiling to define the host response to a single virulence factor proved to be a valuable tool in identifying pathways for further investigation in S. aureus pneumonia. This approach may be broadly applicable to the study of bacterial toxins, defining host pathways that can be targeted to mitigate toxin-induced disease. PMID:22733574

Targeting Discoidin Domain Receptors in Prostate Cancer

DTIC Science & Technology

2016-08-01

DDRs), a set of kinase receptors that signal in response to collagen . The project’s goal is to define the expression and therapeutic potential of...antibody, which blocks receptor activation by collagen I. Mice were inoculated with PC3 cells and anti-DDR1 or control antibody treatment. The study... collagen , the major organic component of the bone extracellular matrix. Purpose: To investigate the expression, therapeutic potential, and

Influence of fiber architecture on the elastic an d inelastic response of metal matrix composites

NASA Technical Reports Server (NTRS)

Arnold, Steven M.; Pindera, Marek-Jerzy; Wilt, Thomas E.

1995-01-01

This three part paper focuses on the effect of fiber architecture (i.e., shape and distribution) on the elastic and inelastic response of metal matrix composites. The first part provides an annotative survey of the literature, presented as a historical perspective, dealing with the effects of fiber shape and distribution on the response of advanced polymeric matrix and metal matrix composites. Previous investigations dealing with both continuously and discontinuously reinforced composites are included. A summary of the state-of-the-art will assist in defining new directions in this quickly reviving area of research. The second part outlines a recently developed analytical micromechanics model that is particularly well suited for studying the influence of these effects on the response of metal matrix composites. This micromechanics model, referred to as the generalized method of cells (GMC), is capable of predicting the overall, inelastic behavior of unidirectional, multi-phased composites given the properties of the constituents. In particular, the model is sufficiently general to predict the response of unidirectional composites reinforced by either continuous or discontinuous fibers with different inclusion shapes and spatial arrangements in the presence of either perfect or imperfect interfaces and/or interfacial layers. Recent developments regarding this promising model, as well as directions for future enhancements of the model's predictive capability, are included. Finally, the third pan provides qualitative results generated using GMC for a representative titanium matix composite system, SCS-6/TlMETAL 21S. Results are presented that correctly demonstrate the relative effects of fiber arrangement and shape on the longitudinal and transverse stress-strain and creep response, with both strong and weak fiber/matrix interfacial bonds. The fiber arrangements include square, square diagonal, hexagonal and rectangular periodic arrays, as well as a random array. The fiber shapes include circular, square and cross-shaped cross sections. The effect of fiber volume fraction on the observed stress-strain response is also discussed, as the thus-far poorly documented strain rate sensitivity effect. In addition to the well documented features of architecture dependent response of continuously reinforced two-phase MMC's, new results involving continuous multi-phase internal architectures are presented. Specifically, stress strain and creep response of composites with different size fibers having different internal arrangements and bond strengths are investigated with the aim of determining the feasibility of using this approach to enhance the transverse toughness and creep resistance of TMC's.

Numerical analysis for the stick-slip vibration of a transversely moving beam in contact with a frictional wall

NASA Astrophysics Data System (ADS)

Won, Hong-In; Chung, Jintai

2018-04-01

This paper presents a numerical analysis for the stick-slip vibration of a transversely moving beam, considering both stick-slip transition and friction force discontinuity. The dynamic state of the beam was separated into the stick state and the slip state, and boundary conditions were defined for both. By applying the finite element method, two matrix-vector equations were derived: one for stick state and the other for slip state. However, the equations have different degrees of freedom depending on whether the end of a beam sticks or slips, so we encountered difficulties in time integration. To overcome the difficulties, we proposed a new numerical technique to alternatively use the matrix-vector equations with different matrix sizes. In addition, to eliminate spurious high-frequency responses, we applied the generalized-α time integration method with appropriate value of high-frequency numerical dissipation. Finally, the dynamic responses of stick-slip vibration were analyzed in time and frequency domains: the dynamic behavior of the beam was explained to facilitate understanding of the stick-slip motion, and frequency characteristics of the stick-slip vibration were investigated in relation to the natural frequencies of the beam. The effects of the axial load and the moving speed upon the dynamic response were also examined.

On functions of quasi-Toeplitz matrices

NASA Astrophysics Data System (ADS)

Bini, D. A.; Massei, S.; Meini, B.

2017-11-01

Let a(z)=\\sumi\\in Za_iz^i be a complex-valued function, defined for |z|=1, such that \\sumi=-∞+∞|ia_i|<∞. Consider the semi-infinite Toeplitz matrix T(a)=(ti,j)i,j\\in Z^+ associated with the symbol a(z) such that {ti,j=aj-i}. A quasi-Toeplitz matrix associated with the symbol a(z) is a matrix of the form A=T(a)+E where E=(ei,j), \\sumi,j\\in Z^+|ei,j|<∞, and is called a {QT}-matrix. Given a function f(x) and a {QT}-matrix M, we provide conditions under which f(M) is well defined and is a {QT}-matrix. Moreover, we introduce a parametrization of {QT}-matrices and algorithms for the computation of f(M). We treat the case where f(x) is given in terms of power series and the case where f(x) is defined in terms of a Cauchy integral. This analysis is also applied to finite matrices which can be written as the sum of a Toeplitz matrix and a low rank correction. Bibliography: 27 titles.

Commensal Protection of Staphylococcus aureus against Antimicrobials by Candida albicans Biofilm Matrix

PubMed Central

Kong, Eric F.; Tsui, Christina; Kucharíková, Sona; Andes, David

2016-01-01

ABSTRACT Biofilm-associated polymicrobial infections, particularly those involving fungi and bacteria, are responsible for significant morbidity and mortality and tend to be challenging to treat. Candida albicans and Staphylococcus aureus specifically are considered leading opportunistic fungal and bacterial pathogens, respectively, mainly due to their ability to form biofilms on catheters and indwelling medical devices. However, the impact of mixed-species biofilm growth on therapy remains largely understudied. In this study, we investigated the influence of C. albicans secreted cell wall polysaccharides on the response of S. aureus to antibacterial agents in biofilm. Results demonstrated significantly enhanced tolerance for S. aureus to drugs in the presence of C. albicans or its secreted cell wall polysaccharide material. Fluorescence confocal time-lapse microscopy revealed impairment of drug diffusion through the mixed biofilm matrix. Using C. albicans mutant strains with modulated cell wall polysaccharide expression, exogenous supplementation, and enzymatic degradation, the C. albicans-secreted β-1,3-glucan cell wall component was identified as the key matrix constituent providing the bacteria with enhanced drug tolerance. Further, antibody labeling demonstrated rapid coating of the bacteria by the C. albicans matrix material. Importantly, via its effect on the fungal biofilm matrix, the antifungal caspofungin sensitized the bacteria to the drugs. Understanding such symbiotic interactions with clinical relevance between microbial species in biofilms will greatly aid in overcoming the limitations of current therapies and in defining potential new targets for treating polymicrobial infections. PMID:27729510

Response of a Rotating Propeller to Aerodynamic Excitation

NASA Technical Reports Server (NTRS)

Arnoldi, Walter E.

1949-01-01

The flexural vibration of a rotating propeller blade with clamped shank is analyzed with the object of presenting, in matrix form, equations for the elastic bending moments in forced vibration resulting from aerodynamic forces applied at a fixed multiple of rotational speed. Matrix equations are also derived which define the critical speeds end mode shapes for any excitation order and the relation between critical speed and blade angle. Reference is given to standard works on the numerical solution of matrix equations of the forms derived. The use of a segmented blade as an approximation to a continuous blade provides a simple means for obtaining the matrix solution from the integral equation of equilibrium, so that, in the numerical application of the method presented, the several matrix arrays of the basic physical characteristics of the propeller blade are of simple form, end their simplicity is preserved until, with the solution in sight, numerical manipulations well-known in matrix algebra yield the desired critical speeds and mode shapes frame which the vibration at any operating condition may be synthesized. A close correspondence between the familiar Stodola method and the matrix method is pointed out, indicating that any features of novelty are characteristic not of the analytical procedure but only of the abbreviation, condensation, and efficient organization of the numerical procedure made possible by the use of classical matrix theory.

Examining the concept of convenient collection: an application to extended producer responsibility and product stewardship frameworks.

PubMed

Wagner, Travis P

2013-03-01

Increasingly, Extended Producer Responsibility (EPR) and Product Stewardship (PS) frameworks are being adopted as a preferred policy approach to promote cost-effective diversion and recovery of post-consumer solid waste. Because the application of EPR/PS generally requires the creation of a separate and often parallel collection and/or management system, key to increasing the amount of waste recovered is to maximize the convenience of the collection system to maximize consumer participation. Convenient collection is often mandated in EPR/PS laws, however it is not defined. Convenience is a subjective construct rendering it extremely difficult to define. However, based on a dissection of post-consumer collection efforts under a generic EPR/PS system, this paper identifies and examines five categories of convenience - knowledge requirements, proximity to a collection site, opportunity to drop-off materials, the draw of the collection site, and the ease of the process-and the various factors of convenience within each of these categories. By using a simplified multiple criteria decision analysis, this paper proposes a performance matrix of criteria of convenience. Stakeholders can use this matrix to assist in the design, assessment, and/or implementation of a convenient post-consumer collection system under an EPR/PS framework. Copyright © 2012 Elsevier Ltd. All rights reserved.

Strain Rate Dependent Deformation and Strength Modeling of a Polymer Matrix Composite Utilizing a Micromechanics Approach. Degree awarded by Cincinnati Univ.

NASA Technical Reports Server (NTRS)

Goldberg, Robert K.

1999-01-01

Potential gas turbine applications will expose polymer matrix composites to very high strain rate loading conditions, requiring an ability to understand and predict the material behavior under extreme conditions. Specifically, analytical methods designed for these applications must have the capability of properly capturing the strain rate sensitivities and nonlinearities that are present in the material response. The Ramaswamy-Stouffer constitutive equations, originally developed to analyze the viscoplastic deformation of metals, have been modified to simulate the nonlinear deformation response of ductile, crystalline polymers. The constitutive model is characterized and correlated for two representative ductile polymers. Fiberite 977-2 and PEEK, and the computed results correlate well with experimental values. The polymer constitutive equations are implemented in a mechanics of materials based composite micromechanics model to predict the nonlinear, rate dependent deformation response of a composite ply. Uniform stress and uniform strain assumptions are applied to compute the effective stresses of a composite unit cell from the applied strains. The micromechanics equations are successfully verified for two polymer matrix composites. IM7/977-2 and AS4/PEEK. The ultimate strength of a composite ply is predicted with the Hashin failure criteria that were implemented in the composite micromechanics model. The failure stresses of the two composite material systems are accurately predicted for a variety of fiber orientations and strain rates. The composite deformation model is implemented in LS-DYNA, a commercially available transient dynamic explicit finite element code. The matrix constitutive equations are converted into an incremental form, and the model is implemented into LS-DYNA through the use of a user defined material subroutine. The deformation response of a bulk polymer and a polymer matrix composite are predicted by finite element analyses. The results compare reasonably well to experimental values, with some discrepancies. The discrepancies are at least partially caused by the method used to integrate the rate equations in the polymer constitutive model.

Genetic Response of Rat Supraspinatus Tendon and Muscle to Exercise

PubMed Central

Rooney, Sarah Ilkhanipour; Tobias, John W.; Bhatt, Pankti R.; Kuntz, Andrew F.; Soslowsky, Louis J.

2015-01-01

Inflammation is a complex, biologic event that aims to protect and repair tissue. Previous studies suggest that inflammation is critical to induce a healing response following acute injury; however, whether similar inflammatory responses occur as a result of beneficial, non-injurious loading is unknown. The objective of this study was to screen for alterations in a subset of inflammatory and extracellular matrix genes to identify the responses of rat supraspinatus tendon and muscle to a known, non-injurious loading condition. We sought to define how a subset of genes representative of specific inflammation and matrix turnover pathways is altered in supraspinatus tendon and muscle 1) acutely following a single loading bout and 2) chronically following repeated loading bouts. In this study, Sprague-Dawley rats in the acute group ran a single bout of non-injurious exercise on a flat treadmill (10 m/min, 1 hour) and were sacrificed 12 or 24 hours after. Rats in the chronic group ran 5 days/wk for 1 or 8 weeks. A control group maintained normal cage activity. Supraspinatus muscle and tendon were harvested for RNA extractions, and a custom Panomics QuantiGene 2.0 multiplex assay was used to detect 48 target and 3 housekeeping genes. Muscle/tendon and acute/chronic groups had distinct gene expression. Components of the arachidonic acid cascade and matrix metalloproteinases and their inhibitors were altered with acute and chronic exercise. Collagen expression increased. Using a previously validated model of non-injurious exercise, we have shown that supraspinatus tendon and muscle respond to acute and chronic exercise by regulating inflammatory- and matrix turnover-related genes, suggesting that these pathways are involved in the beneficial adaptations to exercise. PMID:26447778

E-O Sensor Signal Recognition Simulation: Computer Code SPOT I.

DTIC Science & Technology

1978-10-01

scattering phase function PDCO , defined at the specified wavelength, given for each of the scattering angles defined. Currently, a maximum of sixty-four...PHASE MATRIX DATA IS DEFINED PDCO AVERAGE PROBABILITY FOR PHASE MATRIX DEFINITION NPROB PROBLEM NUMBER 54 Fig. 12. FLOWCHART for the SPOT Computer Code...El0.1 WLAM(N) Wavelength at which the aerosol single-scattering phase function set is defined (microns) 3 8El0.1 PDCO (N,I) Average probability for

DCE-MRI defined subvolumes of a brain metastatic lesion by principle component analysis and fuzzy-c-means clustering for response assessment of radiation therapy

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

Farjam, Reza; Tsien, Christina I.; Lawrence, Theodore S.

Purpose: To develop a pharmacokinetic modelfree framework to analyze the dynamic contrast enhanced magnetic resonance imaging (DCE-MRI) data for assessment of response of brain metastases to radiation therapy. Methods: Twenty patients with 45 analyzable brain metastases had MRI scans prior to whole brain radiation therapy (WBRT) and at the end of the 2-week therapy. The volumetric DCE images covering the whole brain were acquired on a 3T scanner with approximately 5 s temporal resolution and a total scan time of about 3 min. DCE curves from all voxels of the 45 brain metastases were normalized and then temporally aligned. Amore » DCE matrix that is constructed from the aligned DCE curves of all voxels of the 45 lesions obtained prior to WBRT is processed by principal component analysis to generate the principal components (PCs). Then, the projection coefficient maps prior to and at the end of WBRT are created for each lesion. Next, a pattern recognition technique, based upon fuzzy-c-means clustering, is used to delineate the tumor subvolumes relating to the value of the significant projection coefficients. The relationship between changes in different tumor subvolumes and treatment response was evaluated to differentiate responsive from stable and progressive tumors. Performance of the PC-defined tumor subvolume was also evaluated by receiver operating characteristic (ROC) analysis in prediction of nonresponsive lesions and compared with physiological-defined tumor subvolumes. Results: The projection coefficient maps of the first three PCs contain almost all response-related information in DCE curves of brain metastases. The first projection coefficient, related to the area under DCE curves, is the major component to determine response while the third one has a complimentary role. In ROC analysis, the area under curve of 0.88 ± 0.05 and 0.86 ± 0.06 were achieved for the PC-defined and physiological-defined tumor subvolume in response assessment. Conclusions: The PC-defined subvolume of a brain metastasis could predict tumor response to therapy similar to the physiological-defined one, while the former is determined more rapidly for clinical decision-making support.« less

DCE-MRI defined subvolumes of a brain metastatic lesion by principle component analysis and fuzzy-c-means clustering for response assessment of radiation therapy

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

Farjam, Reza; Tsien, Christina I.; Lawrence, Theodore S.

2014-01-15

Purpose: To develop a pharmacokinetic modelfree framework to analyze the dynamic contrast enhanced magnetic resonance imaging (DCE-MRI) data for assessment of response of brain metastases to radiation therapy. Methods: Twenty patients with 45 analyzable brain metastases had MRI scans prior to whole brain radiation therapy (WBRT) and at the end of the 2-week therapy. The volumetric DCE images covering the whole brain were acquired on a 3T scanner with approximately 5 s temporal resolution and a total scan time of about 3 min. DCE curves from all voxels of the 45 brain metastases were normalized and then temporally aligned. Amore » DCE matrix that is constructed from the aligned DCE curves of all voxels of the 45 lesions obtained prior to WBRT is processed by principal component analysis to generate the principal components (PCs). Then, the projection coefficient maps prior to and at the end of WBRT are created for each lesion. Next, a pattern recognition technique, based upon fuzzy-c-means clustering, is used to delineate the tumor subvolumes relating to the value of the significant projection coefficients. The relationship between changes in different tumor subvolumes and treatment response was evaluated to differentiate responsive from stable and progressive tumors. Performance of the PC-defined tumor subvolume was also evaluated by receiver operating characteristic (ROC) analysis in prediction of nonresponsive lesions and compared with physiological-defined tumor subvolumes. Results: The projection coefficient maps of the first three PCs contain almost all response-related information in DCE curves of brain metastases. The first projection coefficient, related to the area under DCE curves, is the major component to determine response while the third one has a complimentary role. In ROC analysis, the area under curve of 0.88 ± 0.05 and 0.86 ± 0.06 were achieved for the PC-defined and physiological-defined tumor subvolume in response assessment. Conclusions: The PC-defined subvolume of a brain metastasis could predict tumor response to therapy similar to the physiological-defined one, while the former is determined more rapidly for clinical decision-making support.« less

Estimation of ion competition via correlated responsivity offset in linear ion trap mass spectrometry analysis: theory and practical use in the analysis of cyanobacterial hepatotoxin microcystin-LR in extracts of food additives.

PubMed

Urban, Jan; Hrouzek, Pavel; Stys, Dalibor; Martens, Harald

2013-01-01

Responsivity is a conversion qualification of a measurement device given by the functional dependence between the input and output quantities. A concentration-response-dependent calibration curve represents the most simple experiment for the measurement of responsivity in mass spectrometry. The cyanobacterial hepatotoxin microcystin-LR content in complex biological matrices of food additives was chosen as a model example of a typical problem. The calibration curves for pure microcystin and its mixtures with extracts of green alga and fish meat were reconstructed from the series of measurement. A novel approach for the quantitative estimation of ion competition in ESI is proposed in this paper. We define the correlated responsivity offset in the intensity values using the approximation of minimal correlation given by the matrix to the target mass values of the analyte. The estimation of the matrix influence enables the approximation of the position of a priori unknown responsivity and was easily evaluated using a simple algorithm. The method itself is directly derived from the basic attributes of the theory of measurements. There is sufficient agreement between the theoretical and experimental values. However, some theoretical issues are discussed to avoid misinterpretations and excessive expectations.

Estimation of Ion Competition via Correlated Responsivity Offset in Linear Ion Trap Mass Spectrometry Analysis: Theory and Practical Use in the Analysis of Cyanobacterial Hepatotoxin Microcystin-LR in Extracts of Food Additives

PubMed Central

Hrouzek, Pavel; Štys, Dalibor; Martens, Harald

2013-01-01

Responsivity is a conversion qualification of a measurement device given by the functional dependence between the input and output quantities. A concentration-response-dependent calibration curve represents the most simple experiment for the measurement of responsivity in mass spectrometry. The cyanobacterial hepatotoxin microcystin-LR content in complex biological matrices of food additives was chosen as a model example of a typical problem. The calibration curves for pure microcystin and its mixtures with extracts of green alga and fish meat were reconstructed from the series of measurement. A novel approach for the quantitative estimation of ion competition in ESI is proposed in this paper. We define the correlated responsivity offset in the intensity values using the approximation of minimal correlation given by the matrix to the target mass values of the analyte. The estimation of the matrix influence enables the approximation of the position of a priori unknown responsivity and was easily evaluated using a simple algorithm. The method itself is directly derived from the basic attributes of the theory of measurements. There is sufficient agreement between the theoretical and experimental values. However, some theoretical issues are discussed to avoid misinterpretations and excessive expectations. PMID:23586036

Method and apparatus for optimized processing of sparse matrices

DOEpatents

Taylor, Valerie E.

1993-01-01

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

The Preparation and Characterization of INTEC HAW Phase I Composition Variation Study Glasses

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

Musick, C. A.; Peeler, D. K.; Piepel, G. F.

1999-03-01

A glass composition variation study (CVS) is in progress to define formulations for the vitrification of high activity waste (HAW) proposed to be separated from dissolved calcine stored at the Idaho National Engineering and Environmental Laboratory (INEEL). Estimates of calcine and HAW compositions prepared in FY97 were used to define test matrix glasses. The HAW composition is of particular interest because high aluminum, zirconium, phosphorous and potassium, and low iron and sodium content places it outside the realm of vitrification experience in the Department of Energy (DOE) complex. Through application of statistical techniques, a test matrix was defined for Phasemore » 1 of the CVS. From this matrix, formulations were systematically selected for preparation and characterization with respect to homogeneity, viscosity, liquidus temperature (TL), and leaching response when subjected to the Product Consistency Test (PCT). Based on the properties determined, certain formulations appear suitable for further development including use in planning Phase 2 of the study. It is recommended that glasses to be investigated in Phase 2 be limited to 3-5 wt % phosphate. The results of characterizing the Phase 1 glasses are presented in this document. A full analysis of the composition-property relationships of glasses being developed for immobilizing HAWs will be performing at the completion of CVS phases. This analysis will be needed for the optimization of the glass formulations of vitrifying HAW. Contributions were made to this document by personnel working at the INEEL, Pacific Northwest National Laboratories (PNNL), and the Savannah River Technology Center (SRTC).« less

Study of the validity of a job-exposure matrix for psychosocial work factors: results from the national French SUMER survey.

PubMed

Niedhammer, Isabelle; Chastang, Jean-François; Levy, David; David, Simone; Degioanni, Stéphanie; Theorell, Töres

2008-10-01

To construct and evaluate the validity of a job-exposure matrix (JEM) for psychosocial work factors defined by Karasek's model using national representative data of the French working population. National sample of 24,486 men and women who filled in the Job Content Questionnaire (JCQ) by Karasek measuring the scores of psychological demands, decision latitude, and social support (individual scores) in 2003 (response rate 96.5%). Median values of the three scores in the total sample of men and women were used to define high demands, low latitude, and low support (individual binary exposures). Job title was defined by both occupation and economic activity that were coded using detailed national classifications (PCS and NAF/NACE). Two JEM measures were calculated from the individual scores of demands, latitude and support for each job title: JEM scores (mean of the individual score) and JEM binary exposures (JEM score dichotomized at the median). The analysis of the variance of the individual scores of demands, latitude, and support explained by occupations and economic activities, of the correlation and agreement between individual measures and JEM measures, and of the sensitivity and specificity of JEM exposures, as well as the study of the associations with self-reported health showed a low validity of JEM measures for psychological demands and social support, and a relatively higher validity for decision latitude compared with individual measures. Job-exposure matrix measure for decision latitude might be used as a complementary exposure assessment. Further research is needed to evaluate the validity of JEM for psychosocial work factors.

Cardiac mitochondrial matrix and respiratory complex protein phosphorylation

PubMed Central

Covian, Raul

2012-01-01

It has become appreciated over the last several years that protein phosphorylation within the cardiac mitochondrial matrix and respiratory complexes is extensive. Given the importance of oxidative phosphorylation and the balance of energy metabolism in the heart, the potential regulatory effect of these classical signaling events on mitochondrial function is of interest. However, the functional impact of protein phosphorylation and the kinase/phosphatase system responsible for it are relatively unknown. Exceptions include the well-characterized pyruvate dehydrogenase and branched chain α-ketoacid dehydrogenase regulatory system. The first task of this review is to update the current status of protein phosphorylation detection primarily in the matrix and evaluate evidence linking these events with enzymatic function or protein processing. To manage the scope of this effort, we have focused on the pathways involved in energy metabolism. The high sensitivity of modern methods of detecting protein phosphorylation and the low specificity of many kinases suggests that detection of protein phosphorylation sites without information on the mole fraction of phosphorylation is difficult to interpret, especially in metabolic enzymes, and is likely irrelevant to function. However, several systems including protein translocation, adenine nucleotide translocase, cytochrome c, and complex IV protein phosphorylation have been well correlated with enzymatic function along with the classical dehydrogenase systems. The second task is to review the current understanding of the kinase/phosphatase system within the matrix. Though it is clear that protein phosphorylation occurs within the matrix, based on 32P incorporation and quantitative mass spectrometry measures, the kinase/phosphatase system responsible for this process is ill-defined. An argument is presented that remnants of the much more labile bacterial protein phosphoryl transfer system may be present in the matrix and that the evaluation of this possibility will require the application of approaches developed for bacterial cell signaling to the mitochondria. PMID:22886415

Distinct presynaptic regulation of dopamine release through NMDA receptors in striosome- and matrix-enriched areas of the rat striatum

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

Krebs, M.O.; Trovero, F.; Desban, M.

1991-05-01

Striosome- and matrix-enriched striatal zones were defined in coronal and sagittal brain sections of the rat, on the basis of {sup 3}H-naloxone binding to mu-opiate receptors (a striosome-specific marker). Then, using a new in vitro microsuperfusion device, the NMDA (50 microM)-evoked release of newly synthesized {sup 3}H-dopamine ({sup 3}H-DA) was examined in these four striatal areas under Mg(2+)-free conditions. The amplitudes of the responses were different in striosomal (171 +/- 6% and 161 +/- 5% of the spontaneous release) than in matrix areas (223 +/- 6% and 248 +/- 12%), even when glycine (1 or 100 microM) was coapplied (inmore » the presence of 1 microM strychnine). In the four areas, the NMDA-evoked release of {sup 3}H-DA was blocked completely by Mg{sup 2}{sup +} (1 mM) or (+)-5-methyl-10,11-dihydro-5H-dibenzo(a,d)cyclohepten-5,10-imine maleate (MK-801; 1 microM) and almost totally abolished by kynurenate (100 microM). Because the tetrodotoxin (TTX)-resistant NMDA-evoked release of {sup 3}H-DA was similar in striosome- (148 +/- 5% and 152 +/- 6%) or matrix-enriched (161 +/- 5% and 156 +/- 7%) areas, the indirect (TTX-sensitive) component of NMDA-evoked responses, which involves striatal neurons and/or afferent fibers, seems more important in the matrix- than in the striosome-enriched areas. The modulation of DA release by cortical glutamate and/or aspartate-containing inputs through NMDA receptors in the matrix appears thus to be partly distinct from that observed in the striosomes, providing some functional basis for the histochemical striatal heterogeneity.« less

Polarization-interference Jones-matrix mapping of biological crystal networks

NASA Astrophysics Data System (ADS)

Ushenko, O. G.; Dubolazov, O. V.; Pidkamin, L. Y.; Sidor, M. I.; Pavlyukovich, N.; Pavlyukovich, O.

2018-01-01

The paper consists of two parts. The first part presents short theoretical basics of the method of Jones-matrix mapping with the help of reference wave. It was provided experimentally measured coordinate distributions of modulus of Jones-matrix elements of polycrystalline film of bile. It was defined the values and ranges of changing of statistic moments, which characterize such distributions. The second part presents the data of statistic analysis of the distributions of matrix elements of polycrystalline film of urine of donors and patients with albuminuria. It was defined the objective criteria of differentiation of albuminuria.

Novel image analysis methods for quantification of in situ 3-D tendon cell and matrix strain.

PubMed

Fung, Ashley K; Paredes, J J; Andarawis-Puri, Nelly

2018-01-23

Macroscopic tendon loads modulate the cellular microenvironment leading to biological outcomes such as degeneration or repair. Previous studies have shown that damage accumulation and the phases of tendon healing are marked by significant changes in the extracellular matrix, but it remains unknown how mechanical forces of the extracellular matrix are translated to mechanotransduction pathways that ultimately drive the biological response. Our overarching hypothesis is that the unique relationship between extracellular matrix strain and cell deformation will dictate biological outcomes, prompting the need for quantitative methods to characterize the local strain environment. While 2-D methods have successfully calculated matrix strain and cell deformation, 3-D methods are necessary to capture the increased complexity that can arise due to high levels of anisotropy and out-of-plane motion, particularly in the disorganized, highly cellular, injured state. In this study, we validated the use of digital volume correlation methods to quantify 3-D matrix strain using images of naïve tendon cells, the collagen fiber matrix, and injured tendon cells. Additionally, naïve tendon cell images were used to develop novel methods for 3-D cell deformation and 3-D cell-matrix strain, which is defined as a quantitative measure of the relationship between matrix strain and cell deformation. The results support that these methods can be used to detect strains with high accuracy and can be further extended to an in vivo setting for observing temporal changes in cell and matrix mechanics during degeneration and healing. Copyright © 2017. Published by Elsevier Ltd.

PEG-chitosan hydrogel with tunable stiffness for study of drug response of breast cancer cells

PubMed Central

Chang, Fei-Chien; Tsao, Ching-Ting; Lin, Anqi; Zhang, Mengying; Levengood, Sheeny Lan; Zhang, Miqin

2016-01-01

Mechanical properties of the extracellular matrix have a profound effect on the behavior of anchorage-dependent cells. However, the mechanisms that define the effects of matrix stiffness on cell behavior remains unclear. Therefore, the development and fabrication of synthetic matrices with well-defined stiffness is invaluable for studying the interactions of cells with their biophysical microenvironment in vitro. We demonstrate a methoxypolyethylene glycol (mPEG)-modified chitosan hydrogel network where hydrogel stiffness can be easily modulated under physiological conditions by adjusting the degree of mPEG grafting onto chitosan (PEGylation). We show that the storage modulus of the hydrogel increases as PEGylation decreases and the gels exhibit instant self-recovery after deformation. Breast cancer cells cultured on the stiffest hydrogels adopt a more malignant phenotype with increased resistance to doxorubicin as compared with cells cultured on tissue culture polystyrene or Matrigel. This work demonstrates the utility of mPEG-modified chitosan hydrogel, with tunable mechanical properties, as an improved replacement of conventional culture system for in vitro characterization of breast cancer cell phenotype and evaluation of cancer therapies. PMID:27595012

Open and Filled Hole Static Tensile Strength Characterization of Metal Matrix Composite SCS-9/Beta21s.

DTIC Science & Technology

1992-12-01

Augmentation Program (28) state that for filled hole tensile testing of MMCs the tolerance between the pin diameter and hole diameter must not exceed .0254...Acetate replication, metallography, and fractography will be used in conjunction with analytical methods to define the aforementioned material... fractography that this bi-linear response is due to the release of residual stresses and interfacial failures of the off-axis plies and not micro

Molecular basis for endothelial lumen formation and tubulogenesis during vasculogenesis and angiogenic sprouting

PubMed Central

Davis, George E.; Stratman, Amber N.; Sacharidou, Anastasia; Koh, Wonshill

2013-01-01

Many studies reveal a fundamental role for extracellular matrix-mediated signaling through integrins and Rho GTPases as well as matrix metalloproteinases (MMPs) in the molecular control of vascular tube morphogenesis in three-dimensional (3D) tissue environments. Recent work has defined an EC lumen signaling complex of proteins that controls these vascular morphogenic events. These findings reveal a signaling interdependence between Cdc42 and MT1-MMP to control the 3D matrix-specific process of EC tubulogenesis. The EC tube formation process results in the creation of a network of proteolytically-generated vascular guidance tunnels in 3D matrices that are utilized to remodel EC-lined tubes through EC motility and could facilitate processes such as flow-induced remodeling and arteriovenous EC sorting and differentiation. Within vascular guidance tunnels, key dynamic interactions occur between endothelial cells (ECs) and pericytes to affect vessel remodeling, diameter, and vascular basement membrane matrix assembly, a fundamental process necessary for endothelial tube maturation and stabilization. Thus, the EC lumen and tube formation mechanism coordinates the concomitant establishment of a network of vascular tubes within tunnel spaces to allow for flow responsiveness, EC-mural cell interactions, and vascular extracellular matrix assembly to control the development of the functional microcirculation. PMID:21482411

Mueller matrix mapping of biological polycrystalline layers using reference wave

NASA Astrophysics Data System (ADS)

Dubolazov, A.; Ushenko, O. G.; Ushenko, Yu. O.; Pidkamin, L. Y.; Sidor, M. I.; Grytsyuk, M.; Prysyazhnyuk, P. V.

2018-01-01

The paper consists of two parts. The first part is devoted to the short theoretical basics of the method of differential Mueller-matrix description of properties of partially depolarizing layers. It was provided the experimentally measured maps of differential matrix of the 1st order of polycrystalline structure of the histological section of brain tissue. It was defined the statistical moments of the 1st-4th orders, which characterize the distribution of matrix elements. In the second part of the paper it was provided the data of statistic analysis of birefringence and dichroism of the histological sections of mice liver tissue (normal and with diabetes). It were defined the objective criteria of differential diagnostics of diabetes.

On the differentiation matrix for Daubechies-based wavelets on an interval

NASA Technical Reports Server (NTRS)

Jameson, Leland

1993-01-01

The differentiation matrix for a Daubechies-based wavlet basis defined on an interval will be constructed. It will be shown that the differentiation matrix based on the currently available boundary constructions does not maintain the superconvergence encountered under periodic boundary conditions.

Study of modal coupling procedures for the shuttle: A matrix method for damping synthesis

NASA Technical Reports Server (NTRS)

Hasselman, T. K.

1972-01-01

The damping method was applied successfully to real structures as well as analytical models. It depends on the ability to determine an appropriate modal damping matrix for each substructure. In the past, modal damping matrices were assumed diagonal for lack of being able to determine the coupling terms which are significant in the general case of nonproportional damping. This problem was overcome by formulating the damped equations of motion as a linear perturbation of the undamped equations for light structural damping. Damped modes are defined as complex vectors derived from the complex frequency response vectors of each substructure and are obtained directly from sinusoidal vibration tests. The damped modes are used to compute first order approximations to the modal damping matrices. The perturbation approach avoids ever having to solve a complex eigenvalue problem.

Disentangling giant component and finite cluster contributions in sparse random matrix spectra.

PubMed

Kühn, Reimer

2016-04-01

We describe a method for disentangling giant component and finite cluster contributions to sparse random matrix spectra, using sparse symmetric random matrices defined on Erdős-Rényi graphs as an example and test bed. Our methods apply to sparse matrices defined in terms of arbitrary graphs in the configuration model class, as long as they have finite mean degree.

RBAC-Matrix-based EMR right management system to improve HIPAA compliance.

PubMed

Lee, Hung-Chang; Chang, Shih-Hsin

2012-10-01

Security control of Electronic Medical Record (EMR) is a mechanism used to manage electronic medical records files and protect sensitive medical records document from information leakage. Researches proposed the Role-Based Access Control(RBAC). However, with the increasing scale of medical institutions, the access control behavior is difficult to have a detailed declaration among roles in RBAC. Furthermore, with the stringent specifications such as the U.S. HIPAA and Canada PIPEDA etc., patients are encouraged to have the right in regulating the access control of his EMR. In response to these problems, we propose an EMR digital rights management system, which is a RBAC-based extension to a matrix organization of medical institutions, known as RBAC-Matrix. With the aim of authorizing the EMR among roles in the organization, RBAC-Matrix also allow patients to be involved in defining access rights of his records. RBAC-Matrix authorizes access control declaration among matrix organizations of medical institutions by using XrML file in association with each EMR. It processes XrML rights declaration file-based authorization of behavior in the two-stage design, called master & servant stage, thus makes the associated EMR to be better protected. RBAC-Matrix will also make medical record file and its associated XrML declaration to two different EMRA(EMR Authorization)roles, namely, the medical records Document Creator (DC) and the medical records Document Right Setting (DRS). Access right setting, determined by the DRS, is cosigned by the patient, thus make the declaration of rights and the use of EMR to comply with HIPAA specifications.

Cinematic camera emulation using two-dimensional color transforms

NASA Astrophysics Data System (ADS)

McElvain, Jon S.; Gish, Walter

2015-02-01

For cinematic and episodic productions, on-set look management is an important component of the creative process, and involves iterative adjustments of the set, actors, lighting and camera configuration. Instead of using the professional motion capture device to establish a particular look, the use of a smaller form factor DSLR is considered for this purpose due to its increased agility. Because the spectral response characteristics will be different between the two camera systems, a camera emulation transform is needed to approximate the behavior of the destination camera. Recently, twodimensional transforms have been shown to provide high-accuracy conversion of raw camera signals to a defined colorimetric state. In this study, the same formalism is used for camera emulation, whereby a Canon 5D Mark III DSLR is used to approximate the behavior a Red Epic cinematic camera. The spectral response characteristics for both cameras were measured and used to build 2D as well as 3x3 matrix emulation transforms. When tested on multispectral image databases, the 2D emulation transforms outperform their matrix counterparts, particularly for images containing highly chromatic content.

Optical and mechanical response of high temperature optical fiber sensors

NASA Technical Reports Server (NTRS)

Sirkis, Jim

1991-01-01

The National Aerospace Plane (NASP) will experience temperatures as high as 2500 F at critical locations in its structure. Optical fiber sensors were proposed as a means of monitoring the temperature in these critical regions by either bonding the optical fiber to, or embedding the optical fiber in, metal matrix composite (MMC) components. Unfortunately, the anticipated NASP temperature ranges exceed the glass transition region of the optical fiber glass. The attempt is made to define the operating temperature range of optical fiber sensors from both optical and mechanical perspectives. A full non-linear optical analysis was performed by modeling the optical response of an isolated sensor cyclically driven through the glass transition region.

Osteoblast fibronectin mRNA, protein synthesis, and matrix are unchanged after exposure to microgravity

NASA Technical Reports Server (NTRS)

Hughes-Fulford, M.; Gilbertson, V.

1999-01-01

The well-defined osteoblast line, MC3T3-E1 was used to examine fibronectin (FN) mRNA levels, protein synthesis, and extracellular FN matrix accumulation after growth activation in spaceflight. These osteoblasts produce FN extracellular matrix (ECM) known to regulate adhesion, differentiation, and function in adherent cells. Changes in bone ECM and osteoblast cell shape occur in spaceflight. To determine whether altered FN matrix is a factor in causing these changes in spaceflight, quiescent osteoblasts were launched into microgravity and were then sera activated with and without a 1-gravity field. Synthesis of FN mRNA, protein, and matrix were measured after activation in microgravity. FN mRNA synthesis is significantly reduced in microgravity (0-G) when compared to ground (GR) osteoblasts flown in a centrifuge simulating earth's gravity (1-G) field 2.5 h after activation. However, 27.5 h after activation there were no significant differences in mRNA synthesis. A small but significant reduction of FN protein was found in the 0-G samples 2.5 h after activation. Total FN protein 27.5 h after activation showed no significant difference between any of the gravity conditions, however, there was a fourfold increase in absolute amount of protein synthesized during the incubation. Using immunofluorescence, we found no significant differences in the amount or in the orientation of the FN matrix after 27.5 h in microgravity. These results demonstrate that FN is made by sera-activated osteoblasts even during exposure to microgravity. These data also suggest that after a total period of 43 h of spaceflight FN transcription, translation, or altered matrix assembly is not responsible for the altered cell shape or altered matrix formation of osteoblasts.

Robustness of Synchrony in Complex Networks and Generalized Kirchhoff Indices

NASA Astrophysics Data System (ADS)

Tyloo, M.; Coletta, T.; Jacquod, Ph.

2018-02-01

In network theory, a question of prime importance is how to assess network vulnerability in a fast and reliable manner. With this issue in mind, we investigate the response to external perturbations of coupled dynamical systems on complex networks. We find that for specific, nonaveraged perturbations, the response of synchronous states depends on the eigenvalues of the stability matrix of the unperturbed dynamics, as well as on its eigenmodes via their overlap with the perturbation vector. Once averaged over properly defined ensembles of perturbations, the response is given by new graph topological indices, which we introduce as generalized Kirchhoff indices. These findings allow for a fast and reliable method for assessing the specific or average vulnerability of a network against changing operational conditions, faults, or external attacks.

Differential 3D Mueller-matrix mapping of optically anisotropic depolarizing biological layers

NASA Astrophysics Data System (ADS)

Ushenko, O. G.; Grytsyuk, M.; Ushenko, V. O.; Bodnar, G. B.; Vanchulyak, O.; Meglinskiy, I.

2018-01-01

The paper consists of two parts. The first part is devoted to the short theoretical basics of the method of differential Mueller-matrix description of properties of partially depolarizing layers. It was provided the experimentally measured maps of differential matrix of the 2nd order of polycrystalline structure of the histological section of rectum wall tissue. It was defined the values of statistical moments of the1st-4th orders, which characterize the distribution of matrix elements. In the second part of the paper it was provided the data of statistic analysis of birefringence and dichroism of the histological sections of connecting component of vagina wall tissue (normal and with prolapse). It were defined the objective criteria of differential diagnostics of pathologies of vagina wall.

Extracellular Matrix and Liver Disease

PubMed Central

Arriazu, Elena; Ruiz de Galarreta, Marina; Cubero, Francisco Javier; Varela-Rey, Marta; Pérez de Obanos, María Pilar; Leung, Tung Ming; Lopategi, Aritz; Benedicto, Aitor; Abraham-Enachescu, Ioana

2014-01-01

Abstract Significance: The extracellular matrix (ECM) is a dynamic microenvironment that undergoes continuous remodeling, particularly during injury and wound healing. Chronic liver injury of many different etiologies such as viral hepatitis, alcohol abuse, drug-induced liver injury, obesity and insulin resistance, metabolic disorders, and autoimmune disease is characterized by excessive deposition of ECM proteins in response to persistent liver damage. Critical Issues: This review describes the main collagenous and noncollagenous components from the ECM that play a significant role in pathological matrix deposition during liver disease. We define how increased myofibroblasts (MF) from different origins are at the forefront of liver fibrosis and how liver cell-specific regulation of the complex scarring process occurs. Recent Advances: Particular attention is paid to the role of cytokines, growth factors, reactive oxygen species, and newly identified matricellular proteins in the regulation of fibrillar type I collagen, a field to which our laboratory has significantly contributed over the years. We compile data from recent literature on the potential mechanisms driving fibrosis resolution such as MF’ apoptosis, senescence, and reversal to quiescence. Future Directions: We conclude with a brief description of how epigenetics, an evolving field, can regulate the behavior of MF and of how new “omics” tools may advance our understanding of the mechanisms by which the fibrogenic response to liver injury occurs. Antioxid. Redox Signal. 21, 1078–1097. PMID:24219114

A design of experiments test to define critical spray cleaning parameters for Brulin 815 GD and Jettacin cleaners

NASA Technical Reports Server (NTRS)

Keen, Jill M.; Evans, Kurt B.; Schiffman, Robert L.; Deweese, C. Darrell; Prince, Michael E.

1995-01-01

Experimental design testing was conducted to identify critical parameters of an aqueous spray process intended for cleaning solid rocket motor metal components (steel and aluminum). A two-level, six-parameter, fractional factorial matrix was constructed and conducted for two cleaners, Brulin 815 GD and Diversey Jettacin. The matrix parameters included cleaner temperature and concentration, wash density, wash pressure, rinse pressure, and dishwasher type. Other spray parameters: nozzle stand-off, rinse water temperature, wash and rinse time, dry conditions, and type of rinse water (deionized) were held constant. Matrix response testing utilized discriminating bond specimens (fracture energy and tensile adhesion strength) which represent critical production bond lines. Overall, Jettacin spray cleaning was insensitive to the range of conditions tested for all parameters and exhibited bond strengths significantly above the TCA test baseline for all bond lines tested. Brulin 815 was sensitive to cleaning temperature, but produced bond strengths above the TCA test baseline even at the lower temperatures. Ultimately, the experimental design database was utilized to recommend process parameter settings for future aqueous spray cleaning characterization work.

Role of proteoglycans in neuro-inflammation and central nervous system fibrosis.

PubMed

Heindryckx, Femke; Li, Jin-Ping

2018-01-31

Fibrosis is defined as the thickening and scarring of connective tissue, usually as a consequence of tissue damage. The central nervous system (CNS) is special in the sense that fibrogenic cells are restricted to vascular and meningeal areas. Inflammation and the disruption of the blood-brain barrier can lead to the infiltration of fibroblasts and trigger fibrotic response. While the initial function of the fibrotic tissue is to restore the blood-brain barrier and to limit the site of injury, it also demolishes the structure of extracellular matrix and impedes the healing process by producing inhibitory molecules and forming a physical and biochemical barrier that prevents axon regeneration. As a major constituent in the extracellular matrix, proteoglycans participate in the neuro-inflammation, modulating the fibrotic process. In this review, we will discuss the pathophysiology of fibrosis during acute injuries of the CNS, as well as during chronic neurodegenerative conditions such as Alzheimer's disease, Parkinson's disease, multiple sclerosis and age-related neurodegeneration with focus on the functional roles of proteoglycans. Copyright © 2017 International Society of Matrix Biology. Published by Elsevier B.V. All rights reserved.

Optimization of Residual Stresses in MMC's Using Compensating/Compliant Interfacial Layers. Part 2: OPTCOMP User's Guide

NASA Technical Reports Server (NTRS)

Pindera, Marek-Jerzy; Salzar, Robert S.; Williams, Todd O.

1994-01-01

A user's guide for the computer program OPTCOMP is presented in this report. This program provides a capability to optimize the fabrication or service-induced residual stresses in uni-directional metal matrix composites subjected to combined thermo-mechanical axisymmetric loading using compensating or compliant layers at the fiber/matrix interface. The user specifies the architecture and the initial material parameters of the interfacial region, which can be either elastic or elastoplastic, and defines the design variables, together with the objective function, the associated constraints and the loading history through a user-friendly data input interface. The optimization procedure is based on an efficient solution methodology for the elastoplastic response of an arbitrarily layered multiple concentric cylinder model that is coupled to the commercial optimization package DOT. The solution methodology for the arbitrarily layered cylinder is based on the local-global stiffness matrix formulation and Mendelson's iterative technique of successive elastic solutions developed for elastoplastic boundary-value problems. The optimization algorithm employed in DOT is based on the method of feasible directions.

Gene evolution and functions of extracellular matrix proteins in teeth

PubMed Central

Yoshizaki, Keigo; Yamada, Yoshihiko

2013-01-01

The extracellular matrix (ECM) not only provides physical support for tissues, but it is also critical for tissue development, homeostasis and disease. Over 300 ECM molecules have been defined as comprising the “core matrisome” in mammals through the analysis of whole genome sequences. During tooth development, the structure and functions of the ECM dynamically change. In the early stages, basement membranes (BMs) separate two cell layers of the dental epithelium and the mesenchyme. Later in the differentiation stages, the BM layer is replaced with the enamel matrix and the dentin matrix, which are secreted by ameloblasts and odontoblasts, respectively. The enamel matrix genes and the dentin matrix genes are each clustered in two closed regions located on human chromosome 4 (mouse chromosome 5), except for the gene coded for amelogenin, the major enamel matrix protein, which is located on the sex chromosomes. These genes for enamel and dentin matrix proteins are derived from a common ancestral gene, but as a result of evolution, they diverged in terms of their specific functions. These matrix proteins play important roles in cell adhesion, polarity, and differentiation and mineralization of enamel and dentin matrices. Mutations of these genes cause diseases such as odontogenesis imperfect (OI) and amelogenesis imperfect (AI). In this review, we discuss the recently defined terms matrisome and matrixome for ECMs, as well as focus on genes and functions of enamel and dentin matrix proteins. PMID:23539364

Efficient Algorithms for Estimating the Absorption Spectrum within Linear Response TDDFT

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

Brabec, Jiri; Lin, Lin; Shao, Meiyue

We present two iterative algorithms for approximating the absorption spectrum of molecules within linear response of time-dependent density functional theory (TDDFT) framework. These methods do not attempt to compute eigenvalues or eigenvectors of the linear response matrix. They are designed to approximate the absorption spectrum as a function directly. They take advantage of the special structure of the linear response matrix. Neither method requires the linear response matrix to be constructed explicitly. They only require a procedure that performs the multiplication of the linear response matrix with a vector. These methods can also be easily modified to efficiently estimate themore » density of states (DOS) of the linear response matrix without computing the eigenvalues of this matrix. We show by computational experiments that the methods proposed in this paper can be much more efficient than methods that are based on the exact diagonalization of the linear response matrix. We show that they can also be more efficient than real-time TDDFT simulations. We compare the pros and cons of these methods in terms of their accuracy as well as their computational and storage cost.« less

Making maxillary barbels with a proximal-distal gradient of Wnt signals in matrix-bound mesenchymal cells

PubMed Central

Figueroa, Francisco; Singer, Susan S.; LeClair, Elizabeth E.

2015-01-01

The evolution of specific appendages is made possible by the ontogenetic deployment of general cell signaling pathways. Many fishes, amphibians and reptiles have unique skin appendages known as barbels, which are poorly understood at the cellular and molecular level. In this study, we examine the cell arrangements, cell division patterns, and gene expression profiles associated with the zebrafish maxillary barbel, or ZMB. The earliest cellular organization of the ZMB is an internal whorl of mesenchymal cells in the dermis of the maxilla; there is no epithelial placode, nor any axially-elongated epithelial cells as expected of an apical ectodermal ridge (AER). As the ZMB develops, cells in S-phase are at first distributed randomly throughout the appendage, gradually transitioning to a proliferative population concentrated at the distal end. By observing ZMB ontogenetic stages in a Wnt-responsive transgenic reporter line, TCFsiam, we identified a strongly fluorescent mesenchymal cell layer within these developing appendages. Using an in vitro explant culture technique on developing barbel tissues, we co-localized the fluorescent label in these cells with the mitotic marker EdU. Surprisingly, TCF+ cells showed little proliferation, indicating a slow-cycling subpopulation. Transmission electron microscopy of the ZMB located the TCF+ cells in a single, circumferential layer within the barbel’s matrix core. Morphologically, these cells resemble fibroblasts or osteoblasts; in addition to their matrix-bound location, they are identified by their pancake-shaped nuclei, abundant rough endoplasmic reticulum, and cytoplasmic extensions into the surrounding extracellular matrix. Taken together, these features define a novel mesenchymal cell population in zebrafish, the ‘TCF+ core cells.’ A working model of barbel development is proposed, in which these minimally mitotic mesodermal cells produce collagenous matrix in response to ectodermally-derived Wnt signals deployed in a proximal-distal gradient along the appendage. This documents a novel mechanism of vertebrate appendage outgrowth. Similar genetic signals and cell behaviors may be responsible for the independent and repeated evolution of barbel structures in other fish species. PMID:26492827

Sensitivity of corneal biomechanical and optical behavior to material parameters using design of experiments method.

PubMed

Xu, Mengchen; Lerner, Amy L; Funkenbusch, Paul D; Richhariya, Ashutosh; Yoon, Geunyoung

2018-02-01

The optical performance of the human cornea under intraocular pressure (IOP) is the result of complex material properties and their interactions. The measurement of the numerous material parameters that define this material behavior may be key in the refinement of patient-specific models. The goal of this study was to investigate the relative contribution of these parameters to the biomechanical and optical responses of human cornea predicted by a widely accepted anisotropic hyperelastic finite element model, with regional variations in the alignment of fibers. Design of experiments methods were used to quantify the relative importance of material properties including matrix stiffness, fiber stiffness, fiber nonlinearity and fiber dispersion under physiological IOP. Our sensitivity results showed that corneal apical displacement was influenced nearly evenly by matrix stiffness, fiber stiffness and nonlinearity. However, the variations in corneal optical aberrations (refractive power and spherical aberration) were primarily dependent on the value of the matrix stiffness. The optical aberrations predicted by variations in this material parameter were sufficiently large to predict clinically important changes in retinal image quality. Therefore, well-characterized individual variations in matrix stiffness could be critical in cornea modeling in order to reliably predict optical behavior under different IOPs or after corneal surgery.

Matrix heat exchanger including a liquid, thermal couplant

DOEpatents

Fewell, Thomas E.; Ward, Charles T.

1976-01-01

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

Predicting clinical response to anticancer drugs using an ex vivo platform that captures tumour heterogeneity.

PubMed

Majumder, Biswanath; Baraneedharan, Ulaganathan; Thiyagarajan, Saravanan; Radhakrishnan, Padhma; Narasimhan, Harikrishna; Dhandapani, Muthu; Brijwani, Nilesh; Pinto, Dency D; Prasath, Arun; Shanthappa, Basavaraja U; Thayakumar, Allen; Surendran, Rajagopalan; Babu, Govind K; Shenoy, Ashok M; Kuriakose, Moni A; Bergthold, Guillaume; Horowitz, Peleg; Loda, Massimo; Beroukhim, Rameen; Agarwal, Shivani; Sengupta, Shiladitya; Sundaram, Mallikarjun; Majumder, Pradip K

2015-02-27

Predicting clinical response to anticancer drugs remains a major challenge in cancer treatment. Emerging reports indicate that the tumour microenvironment and heterogeneity can limit the predictive power of current biomarker-guided strategies for chemotherapy. Here we report the engineering of personalized tumour ecosystems that contextually conserve the tumour heterogeneity, and phenocopy the tumour microenvironment using tumour explants maintained in defined tumour grade-matched matrix support and autologous patient serum. The functional response of tumour ecosystems, engineered from 109 patients, to anticancer drugs, together with the corresponding clinical outcomes, is used to train a machine learning algorithm; the learned model is then applied to predict the clinical response in an independent validation group of 55 patients, where we achieve 100% sensitivity in predictions while keeping specificity in a desired high range. The tumour ecosystem and algorithm, together termed the CANScript technology, can emerge as a powerful platform for enabling personalized medicine.

Innate Immune Cytokines, Fibroblast Phenotypes, and Regulation of Extracellular Matrix in Lung.

PubMed

Richards, Carl D

2017-02-01

Chronic inflammation can be caused by adaptive immune responses in autoimmune and allergic conditions, driven by a T lymphocyte subset balance (TH1, TH2, Th17, Th22, and/or Treg) and skewed cellular profiles in an antigen-specific manner. However, several chronic inflammatory diseases have no clearly defined adaptive immune mechanisms that drive chronicity. These conditions include those that affect the lung such as nonatopic asthma or idiopathic pulmonary fibrosis comprising significant health problems. The remodeling of extracellular matrix (ECM) causes organ dysfunction, and it is largely generated by fibroblasts as the major cell controlling net ECM. As such, these are potential targets of treatment approaches in the context of ECM pathology. Fibroblast phenotypes contribute to ECM and inflammatory cell accumulation, and they are integrated into chronic disease mechanisms including cancer. Evidence suggests that innate cytokine responses may be critical in nonallergic/nonautoimmune disease, and they enable environmental agent exposure mechanisms that are independent of adaptive immunity. Innate immune cytokines derived from macrophage subsets (M1/M2) and innate lymphoid cell (ILC) subsets can directly regulate fibroblast function. We also suggest that STAT3-activating gp130 cytokines can sensitize fibroblasts to the innate cytokine milieu to drive phenotypes and exacerbate existing adaptive responses. Here, we review evidence exploring innate cytokine regulation of fibroblast behavior.

The matrix exponential in transient structural analysis

NASA Technical Reports Server (NTRS)

Minnetyan, Levon

1987-01-01

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

Matrix control of pancreatic cancer: New insights into fibronectin signaling.

PubMed

Topalovski, Mary; Brekken, Rolf A

2016-10-10

Pancreatic ductal adenocarcinoma (PDA) is a highly metastatic disease that resists most current therapies. A defining characteristic of PDA is an intense fibrotic response that promotes tumor cell invasion and chemoresistance. Efforts to understand the complex relationship between the tumor and its extracellular network and to therapeutically perturb tumor-stroma interactions are ongoing. Fibronectin (FN), a provisional matrix protein abundant in PDA stroma but not normal tissues, supports metastatic spread and chemoresistance of this deadly disease. FN also supports angiogenesis, which is required for even hypovascular tumors such as PDA to develop and progress. Targeting components of the tumor stroma, such as FN, can effectively reduce tumor growth and spread while also enhancing delivery of chemotherapy. Here, we review the molecular mechanisms by which FN drives angiogenesis, metastasis and chemoresistance in PDA. In light of these new findings, we also discuss therapeutic strategies to inhibit FN signaling. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

NAD+ Biosynthesis Ameliorates a Zebrafish Model of Muscular Dystrophy

PubMed Central

Goody, Michelle F.; Kelly, Meghan W.; Reynolds, Christine J.; Khalil, Andre; Crawford, Bryan D.; Henry, Clarissa A.

2012-01-01

Muscular dystrophies are common, currently incurable diseases. A subset of dystrophies result from genetic disruptions in complexes that attach muscle fibers to their surrounding extracellular matrix microenvironment. Cell-matrix adhesions are exquisite sensors of physiological conditions and mediate responses that allow cells to adapt to changing conditions. Thus, one approach towards finding targets for future therapeutic applications is to identify cell adhesion pathways that mediate these dynamic, adaptive responses in vivo. We find that nicotinamide riboside kinase 2b-mediated NAD+ biosynthesis, which functions as a small molecule agonist of muscle fiber-extracellular matrix adhesion, corrects dystrophic phenotypes in zebrafish lacking either a primary component of the dystrophin-glycoprotein complex or integrin alpha7. Exogenous NAD+ or a vitamin precursor to NAD+ reduces muscle fiber degeneration and results in significantly faster escape responses in dystrophic embryos. Overexpression of paxillin, a cell adhesion protein downstream of NAD+ in this novel cell adhesion pathway, reduces muscle degeneration in zebrafish with intact integrin receptors but does not improve motility. Activation of this pathway significantly increases organization of laminin, a major component of the extracellular matrix basement membrane. Our results indicate that the primary protective effects of NAD+ result from changes to the basement membrane, as a wild-type basement membrane is sufficient to increase resilience of dystrophic muscle fibers to damage. The surprising result that NAD+ supplementation ameliorates dystrophy in dystrophin-glycoprotein complex– or integrin alpha7–deficient zebrafish suggests the existence of an additional laminin receptor complex that anchors muscle fibers to the basement membrane. We find that integrin alpha6 participates in this pathway, but either integrin alpha7 or the dystrophin-glycoprotein complex is required in conjunction with integrin alpha6 to reduce muscle degeneration. Taken together, these results define a novel cell adhesion pathway that may have future therapeutic relevance for a broad spectrum of muscular dystrophies. PMID:23109907

Inelastic response of metal matrix composites under biaxial loading

NASA Technical Reports Server (NTRS)

Mirzadeh, F.; Pindera, Marek-Jerzy; Herakovich, Carl T.

1990-01-01

Elements of the analytical/experimental program to characterize the response of silicon carbide titanium (SCS-6/Ti-15-3) composite tubes under biaxial loading are outlined. The analytical program comprises prediction of initial yielding and subsequent inelastic response of unidirectional and angle-ply silicon carbide titanium tubes using a combined micromechanics approach and laminate analysis. The micromechanics approach is based on the method of cells model and has the capability of generating the effective thermomechanical response of metal matrix composites in the linear and inelastic region in the presence of temperature and time-dependent properties of the individual constituents and imperfect bonding on the initial yield surfaces and inelastic response of (0) and (+ or - 45)sub s SCS-6/Ti-15-3 laminates loaded by different combinations of stresses. The generated analytical predictions will be compared with the experimental results. The experimental program comprises generation of initial yield surfaces, subsequent stress-strain curves and determination of failure loads of the SCS-6/Ti-15-3 tubes under selected loading conditions. The results of the analytical investigation are employed to define the actual loading paths for the experimental program. A brief overview of the experimental methodology is given. This includes the test capabilities of the Composite Mechanics Laboratory at the University of Virginia, the SCS-6/Ti-15-3 composite tubes secured from McDonnell Douglas Corporation, a text fixture specifically developed for combined axial-torsional loading, and the MTS combined axial-torsion loader that will be employed in the actual testing.

Aligned Carbon Nanotube Tape for Sensor Applications

NASA Technical Reports Server (NTRS)

Tucker, Dennis S.

2013-01-01

For this effort, will concentrate on three applications: Vibration Gyroscope utilizes piezoelectric properties of the tape and Coriolis effect Accelerometer utilizes the piezoresistive property Strain Gauge utilizes piezoresistive property Accelerometer and Strain Gauge can also utilize piezoelectric effect Test piezoelectric properties using facilities at the Microfabrication Laboratory (AMRDEC) . Enhance piezoelectric effect using polyvinylidine fluoride and P(VDF ]TrFE) which is readily polarizable .Spray matrix solution while winding fiber; Sandwich of CNT tape and PVDF film (DOE .Two Level) . Construct and test prototype vibration gyroscope . Construct and test prototype accelerometer using cantilever design . Test strain sensitivity of CNT tape against industrial strain gauge . Embed CNT tape in composite samples as well as on surface and test to failure (4 ]point bend) A piezoelectric device exhibits an electrical response from a mechanical applied stress. . A piezoelectric device has both capacitance and resistance properties in which by applying an electric field from a waveform will exert a mechanical stress that can be monitored for a response. . The typical waveform applied is a sinusoidal waveform of a defined voltage for a defined period. The defined voltage is driven from 0 volts to the positive defined volts then back to 0 and driven to negative defined volts then back to 0. . Example. Vmax set to 10V and period set to 10 ms. . Voltage will start at zero, go to 10 volts, return to zero, go to ]10 volts and return to zero during 10 ms. . Applying this electrical field to a DUT, the capacitance response and resistance response can be observed. CNT tape is easier to manufacture and cheaper than micromachining silicon or other ceramic piezoelectric used in gyroscopes and accelerometers CNT tape properties can be modified during manufacture for specific application CNT tape has enhanced mechanical and thermal properties in addition to unique electrical properties CNT tape as a strain gauge in Structural Health Monitoring will provide an excellent material to embed within composite structures

Mechanisms of fibrosis: therapeutic translation for fibrotic disease

PubMed Central

Wynn, Thomas A; Ramalingam, Thirumalai R

2012-01-01

Fibrosis is a pathological feature of most chronic inflammatory diseases. Fibrosis, or scarring, is defined by the accumulation of excess extracellular matrix components. If highly progressive, the fibrotic process eventually leads to organ malfunction and death. Fibrosis affects nearly every tissue in the body. Here we discuss how key components of the innate and adaptive immune response contribute to the pathogenesis of fibrosis. We also describe how cell-intrinsic changes in important structural cells can perpetuate the fibrotic response by regulating the differentiation, recruitment, proliferation and activation of extracellular matrix–producing myofibroblasts. Finally, we highlight some of the key mechanisms and pathways of fibrosis that are being targeted as potential therapies for a variety of important human diseases. PMID:22772564

Using Item Data for Evaluating Criterion Reference Measures with an Empirical Investigation of Index Consistency.

ERIC Educational Resources Information Center

Meredith, Keith E.; Sabers, Darrell L.

Data required for evaluating a Criterion Referenced Measurement (CRM) is described with a matrix. The information within the matrix consists of the "pass-fail" decisions of two CRMs. By differentially defining these two CRMs, different concepts of reliability and validity can be examined. Indices suggested for analyzing the matrix are listed with…

Hacking the Matrix.

PubMed

Czerwinski, Michael; Spence, Jason R

2017-01-05

Recently in Nature, Gjorevski et al. (2016) describe a fully defined synthetic hydrogel that mimics the extracellular matrix to support in vitro growth of intestinal stem cells and organoids. The hydrogel allows exquisite control over the chemical and physical in vitro niche and enables identification of regulatory properties of the matrix. Copyright © 2017 Elsevier Inc. All rights reserved.

A generalized graph-theoretical matrix of heterosystems and its application to the VMV procedure.

PubMed

Mozrzymas, Anna

2011-12-14

The extensions of generalized (molecular) graph-theoretical matrix and vector-matrix-vector procedure are considered. The elements of the generalized matrix are redefined in order to describe molecules containing heteroatoms and multiple bonds. The adjacency, distance, detour and reciprocal distance matrices of heterosystems, and corresponding vectors are derived from newly defined generalized graph matrix. The topological indices, which are most widely used in predicting physicochemical and biological properties/activities of various compounds, can be calculated from the new generalized vector-matrix-vector invariant. Copyright © 2011 Elsevier Ltd. All rights reserved.

The association between patient-therapist MATRIX congruence and treatment outcome.

PubMed

Mendlovic, Shlomo; Saad, Amit; Roll, Uri; Ben Yehuda, Ariel; Tuval-Mashiah, Rivka; Atzil-Slonim, Dana

2018-03-14

The present study aimed to examine the association between patient-therapist micro-level congruence/incongruence ratio and psychotherapeutic outcome. Nine good- and nine poor-outcome psychodynamic treatments (segregated by comparing pre- and post-treatment BDI-II) were analyzed (N = 18) moment by moment using the MATRIX (total number of MATRIX codes analyzed = 11,125). MATRIX congruence was defined as similar adjacent MATRIX codes. the congruence/incongruence ratio tended to increase as the treatment progressed only in good-outcome treatments. Progression of MATRIX codes' congruence/incongruence ratio is associated with good outcome of psychotherapy.

A novel manifold-manifold distance index applied to looseness state assessment of viscoelastic sandwich structures

NASA Astrophysics Data System (ADS)

Sun, Chuang; Zhang, Zhousuo; Guo, Ting; Luo, Xue; Qu, Jinxiu; Zhang, Chenxuan; Cheng, Wei; Li, Bing

2014-06-01

Viscoelastic sandwich structures (VSS) are widely used in mechanical equipment; their state assessment is necessary to detect structural states and to keep equipment running with high reliability. This paper proposes a novel manifold-manifold distance-based assessment (M2DBA) method for assessing the looseness state in VSSs. In the M2DBA method, a manifold-manifold distance is viewed as a health index. To design the index, response signals from the structure are firstly acquired by condition monitoring technology and a Hankel matrix is constructed by using the response signals to describe state patterns of the VSS. Thereafter, a subspace analysis method, that is, principal component analysis (PCA), is performed to extract the condition subspace hidden in the Hankel matrix. From the subspace, pattern changes in dynamic structural properties are characterized. Further, a Grassmann manifold (GM) is formed by organizing a set of subspaces. The manifold is mapped to a reproducing kernel Hilbert space (RKHS), where support vector data description (SVDD) is used to model the manifold as a hypersphere. Finally, a health index is defined as the cosine of the angle between the hypersphere centers corresponding to the structural baseline state and the looseness state. The defined health index contains similarity information existing in the two structural states, so structural looseness states can be effectively identified. Moreover, the health index is derived by analysis of the global properties of subspace sets, which is different from traditional subspace analysis methods. The effectiveness of the health index for state assessment is validated by test data collected from a VSS subjected to different degrees of looseness. The results show that the health index is a very effective metric for detecting the occurrence and extension of structural looseness. Comparison results indicate that the defined index outperforms some existing state-of-the-art ones.

Mesenchymal Stem Cells Sense Three Dimensional Type I Collagen through Discoidin Domain Receptor 1.

PubMed

Lund, A W; Stegemann, J P; Plopper, G E

2009-01-01

The extracellular matrix provides structural and organizational cues for tissue development and defines and maintains cellular phenotype during cell fate determination. Multipotent mesenchymal stem cells use this matrix to tightly regulate the balance between their differentiation potential and self-renewal in the native niche. When understood, the mechanisms that govern cell-matrix crosstalk during differentiation will allow for efficient engineering of natural and synthetic matrices to specifically direct and maintain stem cell phenotype. This work identifies the discoidin domain receptor 1 (DDR1), a collagen activated receptor tyrosine kinase, as a potential link through which stem cells sense and respond to the 3D organization of their extracellular matrix microenvironment. DDR1 is dependent upon both the structure and proteolytic state of its collagen ligand and is specifically expressed and localized in three dimensional type I collagen culture. Inhibition of DDR1 expression results in decreased osteogenic potential, increased cell spreading, stress fiber formation and ERK1/2 phosphorylation. Additionally, loss of DDR1 activity alters the cell-mediated organization of the naïve type I collagen matrix. Taken together, these results demonstrate a role for DDR1 in the stem cell response to and interaction with three dimensional type I collagen. Dynamic changes in cell shape in 3D culture and the tuning of the local ECM microstructure, directs crosstalk between DDR1 and two dimensional mechanisms of osteogenesis that can alter their traditional roles.

Response of human macrophages to wound matrices in vitro.

PubMed

Witherel, Claire E; Graney, Pamela L; Freytes, Donald O; Weingarten, Michael S; Spiller, Kara L

2016-05-01

Chronic wounds remain a major burden to the global healthcare system. Myriad wound matrices are commercially available but their mechanisms of action are poorly understood. Recent studies have shown that macrophages are highly influenced by their microenvironment, but it is not known how different biomaterials affect this interaction. Here, it was hypothesized that human macrophages respond differently to changes in biomaterial properties in vitro with respect to phenotype, including pro-inflammatory M1, anti-inflammatory M2a, known for facilitating extracellular matrix deposition and proliferation, and M2c, which has recently been associated with tissue remodeling. Using multiple donors, it was found that collagen scaffolds cross-linked with 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide and N-hydroxysuccinimide (EDC/NHS) promoted the least inflammatory phenotype in primary human macrophages compared with scaffolds cross-linked with formaldehyde or glutaraldehyde. Importantly, gene expression analysis trends were largely conserved between donors, especially TNFa (M1), CCL22 (M2a), and MRC1 (M2a). Then the response of primary and THP1 monocyte-derived macrophages to four commercially available wound matrices were compared-Integra Dermal Regeneration Template (Integra), PriMatrix Dermal Repair Scaffold (PriMatrix), AlloMend Acellular Dermal Matrix (AlloMend), and Oasis Wound Matrix (Oasis). Gene expression trends were different between primary and THP1 monocyte-derived macrophages for all six genes analyzed in this study. Finally, the behavior of primary macrophages cultured onto the wound matrices over time was analyzed. Integra and Oasis caused down-regulation of M2a markers CCL22 and TIMP3. PriMatrix caused up-regulation of TNFa (M1) and CD163 (M2c) and down-regulation of CCL22 and TIMP3 (both M2a). AlloMend caused up-regulation in CD163 (M2c). Lastly, Oasis promoted the largest increase in the combinatorial M1/M2 score, defined as the sum of M1 genes divided by the sum of M2 genes. This preliminary study suggested that biomaterials influenced the wound microenvironment to affect macrophage phenotype. © 2016 by the Wound Healing Society.

Bayes Factor Covariance Testing in Item Response Models.

PubMed

Fox, Jean-Paul; Mulder, Joris; Sinharay, Sandip

2017-12-01

Two marginal one-parameter item response theory models are introduced, by integrating out the latent variable or random item parameter. It is shown that both marginal response models are multivariate (probit) models with a compound symmetry covariance structure. Several common hypotheses concerning the underlying covariance structure are evaluated using (fractional) Bayes factor tests. The support for a unidimensional factor (i.e., assumption of local independence) and differential item functioning are evaluated by testing the covariance components. The posterior distribution of common covariance components is obtained in closed form by transforming latent responses with an orthogonal (Helmert) matrix. This posterior distribution is defined as a shifted-inverse-gamma, thereby introducing a default prior and a balanced prior distribution. Based on that, an MCMC algorithm is described to estimate all model parameters and to compute (fractional) Bayes factor tests. Simulation studies are used to show that the (fractional) Bayes factor tests have good properties for testing the underlying covariance structure of binary response data. The method is illustrated with two real data studies.

Deciphering the Combinatorial Roles of Geometric, Mechanical, and Adhesion Cues in Regulation of Cell Spreading

PubMed Central

Harris, Greg M.; Shazly, Tarek; Jabbarzadeh, Ehsan

2013-01-01

Significant effort has gone towards parsing out the effects of surrounding microenvironment on macroscopic behavior of stem cells. Many of the microenvironmental cues, however, are intertwined, and thus, further studies are warranted to identify the intricate interplay among the conflicting downstream signaling pathways that ultimately guide a cell response. In this contribution, by patterning adhesive PEG (polyethylene glycol) hydrogels using Dip Pen Nanolithography (DPN), we demonstrate that substrate elasticity, subcellular elasticity, ligand density, and topography ultimately define mesenchymal stem cells (MSCs) spreading and shape. Physical characteristics are parsed individually with 7 kilopascal (kPa) hydrogel islands leading to smaller, spindle shaped cells and 105 kPa hydrogel islands leading to larger, polygonal cell shapes. In a parallel effort, a finite element model was constructed to characterize and confirm experimental findings and aid as a predictive tool in modeling cell microenvironments. Signaling pathway inhibition studies suggested that RhoA is a key regulator of cell response to the cooperative effect of the tunable substrate variables. These results are significant for the engineering of cell-extra cellular matrix interfaces and ultimately decoupling matrix bound cues presented to cells in a tissue microenvironment for regenerative medicine. PMID:24282570

A numerical method of detecting singularity

NASA Technical Reports Server (NTRS)

Laporte, M.; Vignes, J.

1978-01-01

A numerical method is reported which determines a value C for the degree of conditioning of a matrix. This value is C = 0 for a singular matrix and has progressively larger values for matrices which are increasingly well-conditioned. This value is C sub = C max sub max (C defined by the precision of the computer) when the matrix is perfectly well conditioned.

Efficient sparse matrix-matrix multiplication for computing periodic responses by shooting method on Intel Xeon Phi

NASA Astrophysics Data System (ADS)

Stoykov, S.; Atanassov, E.; Margenov, S.

2016-10-01

Many of the scientific applications involve sparse or dense matrix operations, such as solving linear systems, matrix-matrix products, eigensolvers, etc. In what concerns structural nonlinear dynamics, the computations of periodic responses and the determination of stability of the solution are of primary interest. Shooting method iswidely used for obtaining periodic responses of nonlinear systems. The method involves simultaneously operations with sparse and dense matrices. One of the computationally expensive operations in the method is multiplication of sparse by dense matrices. In the current work, a new algorithm for sparse matrix by dense matrix products is presented. The algorithm takes into account the structure of the sparse matrix, which is obtained by space discretization of the nonlinear Mindlin's plate equation of motion by the finite element method. The algorithm is developed to use the vector engine of Intel Xeon Phi coprocessors. It is compared with the standard sparse matrix by dense matrix algorithm and the one developed by Intel MKL and it is shown that by considering the properties of the sparse matrix better algorithms can be developed.

3D Mueller-matrix mapping of biological optically anisotropic networks

NASA Astrophysics Data System (ADS)

Ushenko, O. G.; Ushenko, V. O.; Bodnar, G. B.; Zhytaryuk, V. G.; Prydiy, O. G.; Koval, G.; Lukashevich, I.; Vanchuliak, O.

2018-01-01

The paper consists of two parts. The first part presents short theoretical basics of the method of azimuthally-invariant Mueller-matrix description of optical anisotropy of biological tissues. It was provided experimentally measured coordinate distributions of Mueller-matrix invariants (MMI) of linear and circular birefringences of skeletal muscle tissue. It was defined the values of statistic moments, which characterize the distributions of amplitudes of wavelet coefficients of MMI at different scales of scanning. The second part presents the data of statistic analysis of the distributions of amplitude of wavelet coefficients of the distributions of linear birefringence of myocardium tissue died after the infarction and ischemic heart disease. It was defined the objective criteria of differentiation of the cause of death.

Engineering a Biocompatible Scaffold with Either Micrometre or Nanometre Scale Surface Topography for Promoting Protein Adsorption and Cellular Response

PubMed Central

Le, Xuan; Poinern, Gérrard Eddy Jai; Ali, Nurshahidah; Berry, Cassandra M.; Fawcett, Derek

2013-01-01

Surface topographical features on biomaterials, both at the submicrometre and nanometre scales, are known to influence the physicochemical interactions between biological processes involving proteins and cells. The nanometre-structured surface features tend to resemble the extracellular matrix, the natural environment in which cells live, communicate, and work together. It is believed that by engineering a well-defined nanometre scale surface topography, it should be possible to induce appropriate surface signals that can be used to manipulate cell function in a similar manner to the extracellular matrix. Therefore, there is a need to investigate, understand, and ultimately have the ability to produce tailor-made nanometre scale surface topographies with suitable surface chemistry to promote favourable biological interactions similar to those of the extracellular matrix. Recent advances in nanoscience and nanotechnology have produced many new nanomaterials and numerous manufacturing techniques that have the potential to significantly improve several fields such as biological sensing, cell culture technology, surgical implants, and medical devices. For these fields to progress, there is a definite need to develop a detailed understanding of the interaction between biological systems and fabricated surface structures at both the micrometre and nanometre scales. PMID:23533416

Tagging and tracking individual networks within a complex mitochondrial web with photoactivatable GFP.

PubMed

Twig, Gilad; Graf, Solomon A; Wikstrom, Jakob D; Mohamed, Hibo; Haigh, Sarah E; Elorza, Alvaro; Deutsch, Motti; Zurgil, Naomi; Reynolds, Nicole; Shirihai, Orian S

2006-07-01

Assembly of mitochondria into networks supports fuel metabolism and calcium transport and is involved in the cellular response to apoptotic stimuli. A mitochondrial network is defined as a continuous matrix lumen whose boundaries limit molecular diffusion. Observation of individual networks has proven challenging in live cells that possess dense populations of mitochondria. Investigation into the electrical and morphological properties of mitochondrial networks has therefore not yielded consistent conclusions. In this study we used matrix-targeted, photoactivatable green fluorescent protein to tag single mitochondrial networks. This approach, coupled with real-time monitoring of mitochondrial membrane potential, permitted the examination of matrix lumen continuity and fusion and fission events over time. We found that adjacent and intertwined mitochondrial structures often represent a collection of distinct networks. We additionally found that all areas of a single network are invariably equipotential, suggesting that a heterogeneous pattern of membrane potential within a cell's mitochondria represents differences between discrete networks. Interestingly, fission events frequently occurred without any gross morphological changes and particularly without fragmentation. These events, which are invisible under standard confocal microscopy, redefine the mitochondrial network boundaries and result in electrically disconnected daughter units.

Complex mode indication function and its applications to spatial domain parameter estimation

NASA Astrophysics Data System (ADS)

Shih, C. Y.; Tsuei, Y. G.; Allemang, R. J.; Brown, D. L.

1988-10-01

This paper introduces the concept of the Complex Mode Indication Function (CMIF) and its application in spatial domain parameter estimation. The concept of CMIF is developed by performing singular value decomposition (SVD) of the Frequency Response Function (FRF) matrix at each spectral line. The CMIF is defined as the eigenvalues, which are the square of the singular values, solved from the normal matrix formed from the FRF matrix, [ H( jω)] H[ H( jω)], at each spectral line. The CMIF appears to be a simple and efficient method for identifying the modes of the complex system. The CMIF identifies modes by showing the physical magnitude of each mode and the damped natural frequency for each root. Since multiple reference data is applied in CMIF, repeated roots can be detected. The CMIF also gives global modal parameters, such as damped natural frequencies, mode shapes and modal participation vectors. Since CMIF works in the spatial domain, uneven frequency spacing data such as data from spatial sine testing can be used. A second-stage procedure for accurate damped natural frequency and damping estimation as well as mode shape scaling is also discussed in this paper.

Developing defined substrates for stem cell culture and differentiation.

PubMed

Hagbard, Louise; Cameron, Katherine; August, Paul; Penton, Christopher; Parmar, Malin; Hay, David C; Kallur, Therése

2018-07-05

Over the past few decades, a variety of different reagents for stem cell maintenance and differentiation have been commercialized. These reagents share a common goal in facilitating the manufacture of products suitable for cell therapy while reducing the amount of non-defined components. Lessons from developmental biology have identified signalling molecules that can guide the differentiation process in vitro , but less attention has been paid to the extracellular matrix used. With the introduction of more biologically relevant and defined matrices, that better mimic specific cell niches, researchers now have powerful resources to fine-tune their in vitro differentiation systems, which may allow the manufacture of therapeutically relevant cell types. In this review article, we revisit the basics of the extracellular matrix, and explore the important role of the cell-matrix interaction. We focus on laminin proteins because they help to maintain pluripotency and drive cell fate specification.This article is part of the theme issue 'Designer human tissue: coming to a lab near you'. © 2018 The Authors.

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.

NLTE steady-state response matrix method.

NASA Astrophysics Data System (ADS)

Faussurier, G.; More, R. M.

2000-05-01

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

Stimuli Responsive Ionogels for Sensing Applications—An Overview

PubMed Central

Kavanagh, Andrew; Byrne, Robert; Diamond, Dermot; Fraser, Kevin J.

2012-01-01

This overview aims to summarize the existing potential of “Ionogels” as a platform to develop stimuli responsive materials. Ionogels are a class of materials that contain an Ionic Liquid (IL) confined within a polymer matrix. Recently defined as “a solid interconnected network spreading throughout a liquid phase”, the ionogel therefore combines the properties of both its solid and liquid components. ILs are low melting salts that exist as liquids composed entirely of cations and anions at or around 100 °C. Important physical properties of these liquids such as viscosity, density, melting point and conductivity can be altered to suit a purpose by choice of the cation/anion. Here we provide an overview to highlight the literature thus far, detailing the encapsulation of IL and responsive materials within these polymeric structures. Exciting applications in the areas of optical and electrochemical sensing, solid state electrolytes and actuating materials shall be discussed. PMID:24957961

Hysteresis in the Cell Response to Time-Dependent Substrate Stiffness

PubMed Central

Besser, Achim; Schwarz, Ulrich S.

2010-01-01

Abstract Mechanical cues like the rigidity of the substrate are main determinants for the decision-making of adherent cells. Here we use a mechano-chemical model to predict the cellular response to varying substrate stiffnesses. The model equations combine the mechanics of contractile actin filament bundles with a model for the Rho-signaling pathway triggered by forces at cell-matrix contacts. A bifurcation analysis of cellular contractility as a function of substrate stiffness reveals a bistable response, thus defining a lower threshold of stiffness, below which cells are not able to build up contractile forces, and an upper threshold of stiffness, above which cells are always in a strongly contracted state. Using the full dynamical model, we predict that rate-dependent hysteresis will occur in the cellular traction forces when cells are exposed to substrates of time-dependent stiffness. PMID:20655823

Hydrocortisone and triiodothyronine regulate hyaluronate synthesis in a tissue-engineered human dermal equivalent through independent pathways.

PubMed

Deshpande, Madhura; Papp, Suzanne; Schaffer, Lana; Pouyani, Tara

2015-02-01

Hydrocortisone (HC) and triiodothyronine (T3) have both been shown to be capable of independently inhibiting hyaluronate (HA, hyaluronic acid) synthesis in a self-assembled human dermal equivalent (human dermal matrix). We sought to investigate the action of these two hormones in concert on extracellular matrix formation and HA inhibition in the tissue engineered human dermal matrix. To this end, neonatal human dermal fibroblasts were cultured in defined serum-free medium for 21 days in the presence of each hormone alone, or in combination, in varying concentrations. Through a process of self-assembly, a substantial dermal extracellular matrix formed that was characterized. The results of these studies demonstrate that combinations of the hormones T3 and hydrocortisone showed significantly higher levels of hyaluronate inhibition as compared to each hormone alone in the human dermal matrix. In order to gain preliminary insight into the genes regulating HA synthesis in this system, a differential gene array analysis was conducted in which the construct prepared in the presence of 200 μg/mL HC and 0.2 nM T3 was compared to the normal construct (0.4 μg/mL HC and 20 pM T3). Using a GLYCOv4 gene chip containing approximately 1260 human genes, we observed differential expression of 131 genes. These data suggest that when these two hormones are used in concert a different mechanism of inhibition prevails and a combination of degradation and inhibition of HA synthesis may be responsible for HA regulation in the human dermal matrix. Copyright © 2014 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

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.

Use of Multiple Isotopic Systems to Interpret Ecosystem Processes in Hawaii

NASA Astrophysics Data System (ADS)

Chadwick, O.; Derry, L.; Vitousek, P.

2007-12-01

The Hawaiian Islands are an excellent natural laboratory for studying the way in which ecosystems develop and function under varying climates. The mantle-derived basalt parent material provides a constant reaction matrix, the trade winds provide an asymmetric climate pattern that means that the same-age lava flows can be studied under different forcing factors, the relatively few plant species that made it to Hawaii provide a simplified biotic influence on substrate. In essence, we find that the geochemical evolution of basalt weathering provides shifting boundary conditions that constrain ecosystem potentialities, and allows us to apply a number of isotopic systems to enhance the specificity of our interpretation of ecosystem processes. We have applied the following isotopes to assist us in understanding the processes that impact ecosystems: O, C, Sr, Ca, N, Si and Be, and are presently exploring the use of S and Mg. We use these isotopic systems within a matrix of controls that allows us to focus on specific questions. The isotopic signatures from different isotopic systems can define climate- response patterns that are non-linear with each defining different threshold and plateau in rainfall space. Measurement of these isotopic systems allows us to evaluate multiple chemical behaviors at once and to evaluate expected responses to perturbations to any of these tracers in response to past or future changes in climate or other ecosystem drives such as land cover change. For instance, based on deep-soil samples, the plants that grew before humans reached Hawaii have C13 values that drop from -14 per mil to -26 per mil as rainfall increases from 200 mm to 3000 mm. Today the surface-soil values remain close to -14 per mil throughout the rainfall gradient due to the introduction of C4 grasses for pasture. Along the same rainfall gradient, Sr isotopes demonstrate that as C3 plants began to predominate there was a fundmental shift in nutrients supplied from rocks to those supplied by rainfall.

Analysis of structural response data using discrete modal filters. M.S. Thesis

NASA Technical Reports Server (NTRS)

Freudinger, Lawrence C.

1991-01-01

The application of reciprocal modal vectors to the analysis of structural response data is described. Reciprocal modal vectors are constructed using an existing experimental modal model and an existing frequency response matrix of a structure, and can be assembled into a matrix that effectively transforms the data from the physical space to a modal space within a particular frequency range. In other words, the weighting matrix necessary for modal vector orthogonality (typically the mass matrix) is contained within the reciprocal model matrix. The underlying goal of this work is mostly directed toward observing the modal state responses in the presence of unknown, possibly closed loop forcing functions, thus having an impact on both operating data analysis techniques and independent modal space control techniques. This study investigates the behavior of reciprocol modal vectors as modal filters with respect to certain calculation parameters and their performance with perturbed system frequency response data.

Bisphenol A Alters Autonomic Tone and Extracellular Matrix Structure and Induces Sex-Specific Effects on Cardiovascular Function in Male and Female CD-1 Mice

PubMed Central

Gear, Robin B.; Kendig, Eric L.

2015-01-01

The aim of this study was to determine whether bisphenol A (BPA) has adverse effects on cardiovascular functions in CD-1 mice and define sex-specific modes of BPA action in the heart. Dams and analyzed progeny were maintained on a defined diet containing BPA (0.03, 0.3, 3, 30, or 300 ppm) that resulted in BPA exposures from 4–5 to approximately 5000 μg/kg · d or a diet containing 17α-ethinyl estradiol (EE; ∼0.02, 0.2, and 0.15 μg/kg · d) as an oral bioavailable estrogen control. Assessment of electrocardiogram parameters using noninvasive methods found that ventricular functions in both male and female mice were not altered by either BPA or EE. However, exposure-related changes in the rates of ventricular contraction, suggestive of a shift in sympathovagal balance of heart rate control toward increased parasympathetic activity, were detected in males. Decreased systolic blood pressure was observed in males exposed to BPA above 5 μg/kg · d and in females from the highest BPA exposure group. Morphometric histological measures revealed sexually dimorphic changes in the composition of the cardiac collagen extracellular matrix, increases in fibrosis, and evidence of modest exposure-related remodeling. Experiments using the α-selective adrenergic agonist phenylephrine found that BPA enhanced reflex bradycardia in females, but not males, revealed that BPA and EE exposure sex specifically altered the sympathetic regulation of the baroreflex circuits. Increased sensitivity to the cardiotoxic effects of the β-adrenergic agonist isoproterenol was observed in BPA- and EE-exposed females. This effect was not observed in males, in which BPA or EE exposures were protective of isoproterenol-induced ischemic damage and hypertrophy. The results of RNA sequence analysis identified significant sex-specific changes in gene expression in response to BPA that were consistent with the observed exposure-related phenotypic changes in the collagenous and noncollagenous extracellular matrix, cardiac remodeling, altered autonomic responses, changes in ion channel and transporter functions, and altered glycolytic and lipid metabolism. PMID:25594700

Role of Recurrent Hypoxia-Ischemia in Preterm White Matter Injury Severity

PubMed Central

Hagen, Matthew W.; Riddle, Art; McClendon, Evelyn; Gong, Xi; Shaver, Daniel; Srivastava, Taasin; Dean, Justin M.; Bai, Ji-Zhong; Fowke, Tania M.; Gunn, Alistair J.; Jones, Daniel F.; Sherman, Larry S.; Grafe, Marjorie R.; Hohimer, A. Roger; Back, Stephen A.

2014-01-01

Objective Although the spectrum of white matter injury (WMI) in preterm infants is shifting from cystic necrotic lesions to milder forms, the factors that contribute to this changing spectrum are unclear. We hypothesized that recurrent hypoxia-ischemia (rHI) will exacerbate the spectrum of WMI defined by markers of inflammation and molecules related to the extracellular matrix (hyaluronan (HA) and the PH20 hyaluronidase) that regulate maturation of the oligodendrocyte (OL) lineage after WMI. Methods We employed a preterm fetal sheep model of in utero moderate hypoxemia and global severe but not complete cerebral ischemia that reproduces the spectrum of human WMI. The response to rHI was compared against corresponding early or later single episodes of HI. An ordinal rating scale of WMI was compared against an unbiased quantitative image analysis protocol that provided continuous histo-pathological outcome measures for astrogliosis and microglial activation. Late oligodendrocyte progenitors (preOLs) were quantified by stereology. Analysis of hyaluronan and the hyaluronidase PH20 defined the progressive response of the extracellular matrix to WMI. Results rHI resulted in a more severe spectrum of WMI with a greater burden of necrosis, but an expanded population of preOLs that displayed reduced susceptibility to cell death. WMI from single episodes of HI or rHI was accompanied by elevated HA levels and increased labeling for PH20. Expression of PH20 in fetal ovine WMI was confirmed by RT-PCR and RNA-sequencing. Conclusions rHI is associated with an increased risk for more severe WMI with necrosis, but reduced risk for preOL degeneration compared to single episodes of HI. Expansion of the preOL pool may be linked to elevated hyaluronan and PH20. PMID:25390897

An analytical X-ray CdTe detector response matrix for incomplete charge collection correction for photon energies up to 300 keV

NASA Astrophysics Data System (ADS)

Kurková, Dana; Judas, Libor

2018-05-01

Gamma and X-ray energy spectra measured with semiconductor detectors suffer from various distortions, one of them being so-called "tailing" caused by an incomplete charge collection. Using the Hecht equation, a response matrix of size 321 × 321 was constructed which was used to correct the effect of incomplete charge collection. The correction matrix was constructed analytically for an arbitrary energy bin and the size of the energy bin thus defines the width of the spectral window. The correction matrix can be applied separately from other possible spectral corrections or it can be incorporated into an already existing response matrix of the detector. The correction was tested and its adjustable parameters were optimized on the line spectra of 57Co measured with a cadmium telluride (CdTe) detector in a spectral range from 0 up to 160 keV. The best results were obtained when the values of the free path of holes were spread over a range from 0.4 to 1.0 cm and weighted by a Gauss function. The model with the optimized parameter values was then used to correct the line spectra of 152Eu in a spectral range from 0 up to 530 keV. An improvement in the energy resolution at full width at half maximum from 2.40 % ± 0.28 % to 0.96 % ± 0.28 % was achieved at 344.27 keV. Spectra of "narrow spectrum series" beams, N120, N150, N200, N250 and N300, generated with tube voltages of 120 kV, 150 kV, 200 kV, 250 kV and 300 kV respectively, and measured with the CdTe detector, were corrected in the spectral range from 0 to 160 keV (N120 and N150) and from 0 to 530 keV (N200, N250, N300). All the measured spectra correspond both qualitatively and quantitatively to the available reference data after the correction. To obtain better correspondence between N150, N200, N250 and N300 spectra and the reference data, lower values of the free paths of holes (range from 0.16 to 0.65 cm) were used for X-ray spectra correction, which suggests energy dependence of the phenomenon.

An ESS maximum principle for matrix games.

PubMed

Vincent, T L; Cressman, R

2000-11-01

Previous work has demonstrated that for games defined by differential or difference equations with a continuum of strategies, there exists a G-function, related to individual fitness, that must take on a maximum with respect to a virtual variable v whenever v is one of the vectors in the coalition of vectors which make up the evolutionarily stable strategy (ESS). This result, called the ESS maximum principle, is quite useful in determining candidates for an ESS. This principle is reformulated here, so that it may be conveniently applied to matrix games. In particular, we define a matrix game to be one in which fitness is expressed in terms of strategy frequencies and a matrix of expected payoffs. It is shown that the G-function in the matrix game setting must again take on a maximum value at all the strategies which make up the ESS coalition vector. The reformulated maximum principle is applicable to both bilinear and nonlinear matrix games. One advantage in employing this principle to solve the traditional bilinear matrix game is that the same G-function is used to find both pure and mixed strategy solutions by simply specifying an appropriate strategy space. Furthermore we show how the theory may be used to solve matrix games which are not in the usual bilinear form. We examine in detail two nonlinear matrix games: the game between relatives and the sex ratio game. In both of these games an ESS solution is determined. These examples not only illustrate the usefulness of this approach to finding solutions to an expanded class of matrix games, but aids in understanding the nature of the ESS as well.

Selective small-molecule inhibitors as chemical tools to define the roles of matrix metalloproteinases in disease.

PubMed

Meisel, Jayda E; Chang, Mayland

2017-11-01

The focus of this article is to highlight novel inhibitors and current examples where the use of selective small-molecule inhibitors has been critical in defining the roles of matrix metalloproteinases (MMPs) in disease. Selective small-molecule inhibitors are surgical chemical tools that can inhibit the targeted enzyme; they are the method of choice to ascertain the roles of MMPs and complement studies with knockout animals. This strategy can identify targets for therapeutic development as exemplified by the use of selective small-molecule MMP inhibitors in diabetic wound healing, spinal cord injury, stroke, traumatic brain injury, cancer metastasis, and viral infection. This article is part of a Special Issue entitled: Matrix Metalloproteinases edited by Rafael Fridman. Copyright © 2017 Elsevier B.V. All rights reserved.

[Psychodynamics in organisation and cooperation of child and adolescents institutions].

PubMed

Fliedl, Rainer; Sevecke, Kathrin

2017-09-01

According to underlying law (Krankenanstaltengesetz) the internal structure of Departments of Child and Adolescent Psychiatry (CAP) represents a matrix structure, defining formal roles and tasks of the personel. In contrast, external cooperation is defined in several different laws. Furthermore, patients and their systems are exhibiting a high tensional potential. These different influences can cause more or less severe enmeshments. Thus, during the treatment of this patients it is necessary to take into account the possibility of these enmeshments. It should be answered by special forms of care of the relationship between professionals and families. These special forms of relational care can be delivered by clear organizational structures and must undergo reflective processes on a regular basis. The planning and delivery of those structures is clearly seen as a central responsibility of the management of a CAP-Department.

High Strain Rate Deformation Modeling of a Polymer Matrix Composite. Part 1; Matrix Constitutive Equations

NASA Technical Reports Server (NTRS)

Goldberg, Robert K.; Stouffer, Donald C.

1998-01-01

Recently applications have exposed polymer matrix composite materials to very high strain rate loading conditions, requiring an ability to understand and predict the material behavior under these extreme conditions. In this first paper of a two part report, background information is presented, along with the constitutive equations which will be used to model the rate dependent nonlinear deformation response of the polymer matrix. Strain rate dependent inelastic constitutive models which were originally developed to model the viscoplastic deformation of metals have been adapted to model the nonlinear viscoelastic deformation of polymers. The modified equations were correlated by analyzing the tensile/ compressive response of both 977-2 toughened epoxy matrix and PEEK thermoplastic matrix over a variety of strain rates. For the cases examined, the modified constitutive equations appear to do an adequate job of modeling the polymer deformation response. A second follow-up paper will describe the implementation of the polymer deformation model into a composite micromechanical model, to allow for the modeling of the nonlinear, rate dependent deformation response of polymer matrix composites.

Thermo-mechanical response predictions for metal matrix composite laminates

NASA Technical Reports Server (NTRS)

Aboudi, J.; Hidde, J. S.; Herakovich, C. T.

1991-01-01

An analytical micromechanical model is employed for prediction of the stress-strain response of metal matrix composite laminates subjected to thermomechanical loading. The predicted behavior of laminates is based upon knowledge of the thermomechanical response of the transversely isotropic, elastic fibers and the elastic-viscoplastic, work-hardening matrix. The method is applied to study the behavior of silicon carbide/titanium metal matrix composite laminates. The response of laminates is compared with that of unidirectional lamina. The results demonstrate the effect of cooling from a stress-free temperature and the mismatch of thermal and mechanical properties of the constituent phases on the laminate's subsequent mechanical response. Typical results are presented for a variety of laminates subjected to monotonic tension, monotonic shear and cyclic tensile/compressive loadings.

Defining the Role of Solid Stress and Matrix Stiffness in Cancer Cell Proliferation and Metastasis

PubMed Central

Kalli, Maria; Stylianopoulos, Triantafyllos

2018-01-01

Solid tumors are characterized by an abnormal stroma that contributes to the development of biomechanical abnormalities in the tumor microenvironment. In particular, these abnormalities include an increase in matrix stiffness and an accumulation of solid stress in the tumor interior. So far, it is not clearly defined whether matrix stiffness and solid stress are strongly related to each other or they have distinct roles in tumor progression. Moreover, while the effects of stiffness on tumor progression are extensively studied compared to the contribution of solid stress, it is important to ascertain the biological outcomes of both abnormalities in tumorigenesis and metastasis. In this review, we discuss how each of these parameters is evolved during tumor growth and how these parameters are influenced by each other. We further review the effects of matrix stiffness and solid stress on the proliferative and metastatic potential of cancer and stromal cells and summarize the in vitro experimental setups that have been designed to study the individual contribution of these parameters. PMID:29594037

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

The Mastery Matrix for Integration Praxis: The development of a rubric for integration practice in addressing weight-related public health problems.

PubMed

Berge, Jerica M; Adamek, Margaret; Caspi, Caitlin; Grannon, Katherine Y; Loth, Katie A; Trofholz, Amanda; Nanney, Marilyn S

2018-06-01

In response to the limitations of siloed weight-related intervention approaches, scholars have called for greater integration that is intentional, strategic, and thoughtful between researchers, health care clinicians, community members, and policy makers as a way to more effectively address weight and weight-related (e.g., obesity, diabetes, cardiovascular disease, cancer) public health problems. The Mastery Matrix for Integration Praxis was developed by the Healthy Eating and Activity across the Lifespan (HEAL) team in 2017 to advance the science and praxis of integration across the domains of research, clinical practice, community, and policy to address weight-related public health problems. Integrator functions were identified and developmental stages were created to generate a rubric for measuring mastery of integration. Creating a means to systematically define and evaluate integration praxis and expertise will allow for more individuals and teams to master integration in order to work towards promoting a culture of health. Copyright © 2018 Elsevier Inc. All rights reserved.

Platform technology for scalable assembly of instantaneously functional mosaic tissues

PubMed Central

Zhang, Boyang; Montgomery, Miles; Davenport-Huyer, Locke; Korolj, Anastasia; Radisic, Milica

2015-01-01

Engineering mature tissues requires a guided assembly of cells into organized three-dimensional (3D) structures with multiple cell types. Guidance is usually achieved by microtopographical scaffold cues or by cell-gel compaction. The assembly of individual units into functional 3D tissues is often time-consuming, relying on cell ingrowth and matrix remodeling, whereas disassembly requires an invasive method that includes either matrix dissolution or mechanical cutting. We invented Tissue-Velcro, a bio-scaffold with a microfabricated hook and loop system. The assembly of Tissue-Velcro preserved the guided cell alignment realized by the topographical features in the 2D scaffold mesh and allowed for the instant establishment of coculture conditions by spatially defined stacking of cardiac cell layers or through endothelial cell coating. The assembled cardiac 3D tissue constructs were immediately functional as measured by their ability to contract in response to electrical field stimulation. Facile, on-demand tissue disassembly was demonstrated while preserving the structure, physical integrity, and beating function of individual layers. PMID:26601234

Effects of mistuning and matrix structure on the topology of frequency response curves

NASA Technical Reports Server (NTRS)

Afolabi, Dare

1989-01-01

The stability of a frequency response curve under mild perturbations of the system's matrix is investigated. Using recent developments in the theory of singularities of differentiable maps, it is shown that the stability of a response curve depends on the structure of the system's matrix. In particular, the frequency response curves of a cylic system are shown to be unstable. Consequently, slight parameter variations engendered by mistuning will induce a significant difference in the topology of the forced response curves, if the mistuning transformation crosses the bifurcation set.

Definition of Systematic, Approximately Separable, and Modular Internal Coordinates (SASMIC) for macromolecular simulation.

PubMed

Echenique, Pablo; Alonso, J L

2006-07-30

A set of rules is defined to systematically number the groups and the atoms of polypeptides in a modular manner. Supported by this numeration, a set of internal coordinates is defined. These coordinates (termed Systematic, Approximately Separable, and Modular Internal Coordinates--SASMIC) are straightforwardly written in Z-matrix form and may be directly implemented in typical Quantum Chemistry packages. A number of Perl scripts that automatically generate the Z-matrix files are provided as supplementary material. The main difference with most Z-matrix-like coordinates normally used in the literature is that normal dihedral angles ("principal dihedrals" in this work) are only used to fix the orientation of whole groups and a different type of dihedrals, termed "phase dihedrals," are used to describe the covalent structure inside the groups. This physical approach allows to approximately separate soft and hard movements of the molecule using only topological information and to directly implement constraints. As an application, we use the coordinates defined and ab initio quantum mechanical calculations to assess the commonly assumed approximation of the free energy, obtained from "integrating out" the side chain degree of freedom chi, by the Potential Energy Surface (PES) in the protected dipeptide HCO-L-Ala-NH2. We also present a subbox of the Hessian matrix in two different sets of coordinates to illustrate the approximate separation of soft and hard movements when the coordinates defined in this work are used. (PACS: 87.14.Ee, 87.15.-v, 87.15.Aa, 87.15.Cc) 2006 Wiley Periodicals, Inc.

Ancylostoma ceylanicum Excretory-Secretory Protein 2 Adopts a Netrin-Like Fold and Defines a Novel Family of Nematode Proteins

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

K Kucera; L Harrison; M Cappello

2011-12-31

Hookworms are human parasites that have devastating effects on global health, particularly in underdeveloped countries. Ancylostoma ceylanicum infects humans and animals, making it a useful model organism to study disease pathogenesis. A. ceylanicum excretory-secretory protein 2 (AceES-2), a highly immunoreactive molecule secreted by adult worms at the site of intestinal attachment, is partially protective when administered as a mucosal vaccine against hookworm anemia. The crystal structure of AceES-2 determined at 1.75 {angstrom} resolution shows that it adopts a netrin-like fold similar to that found in tissue inhibitors of matrix metalloproteases (TIMPs) and in complement factors C3 and C5. However, recombinantmore » AceES-2 does not significantly inhibit the 10 most abundant human matrix metalloproteases or complement-mediated cell lysis. The presence of a highly acidic surface on AceES-2 suggests that it may function as a cytokine decoy receptor. Several small nematode proteins that have been annotated as TIMPs or netrin-domain-containing proteins display sequence homology in structurally important regions of AceES-2's netrin-likefold. Together, our results suggest that AceES-2 defines a novel family of nematode netrin-like proteins, which may function to modulate the host immune response to hookworm and other parasites.« less

Extracellular matrix regenerative graft attenuates the negative impact of polypropylene prolapse mesh on vagina in rhesus macaque.

PubMed

Liang, Rui; Knight, Katrina; Barone, William; Powers, Robert W; Nolfi, Alexis; Palcsey, Stacy; Abramowitch, Steven; Moalli, Pamela A

2017-02-01

The use of wide pore lightweight polypropylene mesh to improve anatomical outcomes in the surgical repair of prolapse has been hampered by mesh complications. One of the prototype prolapse meshes has been found to negatively impact the vagina by inducing a decrease in smooth muscle volume and contractility and the degradation of key structural proteins (collagen and elastin), resulting in vaginal degeneration. Recently, bioscaffolds derived from extracellular matrix have been used to mediate tissue regeneration and have been widely adopted in tissue engineering applications. Here we aimed to: (1) define whether augmentation of a polypropylene prolapse mesh with an extracellular matrix regenerative graft in a primate sacrocolpopexy model could mitigate the degenerative changes; and (2) determine the impact of the extracellular matrix graft on vagina when implanted alone. A polypropylene-extracellular matrix composite graft (n = 9) and a 6-layered extracellular matrix graft alone (n = 8) were implanted in 17 middle-aged parous rhesus macaques via sacrocolpopexy and compared to historical data obtained from sham (n = 12) and the polypropylene mesh (n = 12) implanted by the same method. Vaginal function was measured in passive (ball-burst test) and active (smooth muscle contractility) mechanical tests. Vaginal histomorphologic/biochemical assessments included hematoxylin-eosin and trichrome staining, immunofluorescent labeling of α-smooth muscle actin and apoptotic cells, measurement of total collagen, collagen subtypes (ratio III/I), mature elastin, and sulfated glycosaminoglycans. Statistical analyses included 1-way analysis of variance, Kruskal-Wallis, and appropriate post-hoc tests. The host inflammatory response in the composite mesh-implanted vagina was reduced compared to that following implantation with the polypropylene mesh alone. The increase in apoptotic cells observed with the polypropylene mesh was blunted in the composite (overall P < .001). Passive mechanical testing showed inferior parameters for both polypropylene mesh alone and the composite compared to sham whereas the contractility and thickness of smooth muscle layer in the composite were improved with a value similar to sham, which was distinct from the decreases observed with polypropylene mesh alone. Biochemically, the composite had similar mature elastin content, sulfated glycosaminoglycan content, and collagen subtype III/I ratio but lower total collagen content when compared to sham (P = .011). Multilayered extracellular matrix graft alone showed overall comparable values to sham in aspects of the biomechanical, histomorphologic, or biochemical endpoints of the vagina. The increased collagen subtype ratio III/I with the extracellular matrix graft alone (P = .033 compared to sham) is consistent with an ongoing active remodeling response. Mesh augmentation with a regenerative extracellular matrix graft attenuated the negative impact of polypropylene mesh on the vagina. Application of the extracellular matrix graft alone had no measurable negative effects suggesting that the benefits of this extracellular matrix graft occur when used without a permanent material. Future studies will focus on understanding mechanisms. Copyright © 2016. Published by Elsevier Inc.

Extracellular matrix regenerative graft attenuates the negative impact of polypropylene prolapse mesh on vagina in rhesus macaque

PubMed Central

Liang, Rui; Knight, Katrina; Barone, William; Powers, Robert W.; Nolfi, Alexis; Palcsey, Stacy; Abramowitch, Steven; Moalli, Pamela A.

2016-01-01

BACKGROUND The use of wide pore lightweight polypropylene mesh to improve anatomical outcomes in the surgical repair of prolapse has been hampered by mesh complications. One of the prototype prolapse meshes has been found to negatively impact the vagina by inducing a decrease in smooth muscle volume and contractility and the degradation of key structural proteins (collagen and elastin), resulting in vaginal degeneration. Recently, bioscaffolds derived from extracellular matrix have been used to mediate tissue regeneration and have been widely adopted in tissue engineering applications. OBJECTIVE Here we aimed to: (1) define whether augmentation of a polypropylene prolapse mesh with an extracellular matrix regenerative graft in a primate sacrocolpopexy model could mitigate the degenerative changes; and (2) determine the impact of the extracellular matrix graft on vagina when implanted alone. STUDY DESIGN A polypropylene-extracellular matrix composite graft (n = 9) and a 6-layered extracellular matrix graft alone (n = 8) were implanted in 17 middle-aged parous rhesus macaques via sacrocolpopexy and compared to historical data obtained from sham (n = 12) and the polypropylene mesh (n = 12) implanted by the same method. Vaginal function was measured in passive (ball-burst test) and active (smooth muscle contractility) mechanical tests. Vaginal histomorphologic/ biochemical assessments included hematoxylin-eosin and trichrome staining, immunofluorescent labeling of α-smooth muscle actin and apoptotic cells, measurement of total collagen, collagen subtypes (ratio III/ I), mature elastin, and sulfated glycosaminoglycans. Statistical analyses included 1-way analysis of variance, Kruskal-Wallis, and appropriate posthoc tests. RESULTS The host inflammatory response in the composite mesh-implanted vagina was reduced compared to that following implantation with the polypropylene mesh alone. The increase in apoptotic cells observed with the polypropylene mesh was blunted in the composite (overall P < .001). Passive mechanical testing showed inferior parameters for both polypropylene mesh alone and the composite compared to sham whereas the contractility and thickness of smooth muscle layer in the composite were improved with a value similar to sham, which was distinct from the decreases observed with polypropylene mesh alone. Biochemically, the composite had similar mature elastin content, sulfated glycosaminoglycan content, and collagen subtype III/I ratio but lower total collagen content when compared to sham (P = .011). Multilayered extracellular matrix graft alone showed overall comparable values to sham in aspects of the biomechanical, histomorphologic, or biochemical end-points of the vagina. The increased collagen subtype ratio III/I with the extracellular matrix graft alone (P = .033 compared to sham) is consistent with an ongoing active remodeling response. CONCLUSION Mesh augmentation with a regenerative extracellular matrix graft attenuated the negative impact of polypropylene mesh on the vagina. Application of the extracellular matrix graft alone had no measurable negative effects suggesting that the benefits of this extra-cellular matrix graft occur when used without a permanent material. Future studies will focus on understanding mechanisms. PMID:27615441

Realistic simplified gaugino-higgsino models in the MSSM

NASA Astrophysics Data System (ADS)

Fuks, Benjamin; Klasen, Michael; Schmiemann, Saskia; Sunder, Marthijn

2018-03-01

We present simplified MSSM models for light neutralinos and charginos with realistic mass spectra and realistic gaugino-higgsino mixing, that can be used in experimental searches at the LHC. The formerly used naive approach of defining mass spectra and mixing matrix elements manually and independently of each other does not yield genuine MSSM benchmarks. We suggest the use of less simplified, but realistic MSSM models, whose mass spectra and mixing matrix elements are the result of a proper matrix diagonalisation. We propose a novel strategy targeting the design of such benchmark scenarios, accounting for user-defined constraints in terms of masses and particle mixing. We apply it to the higgsino case and implement a scan in the four relevant underlying parameters {μ , tan β , M1, M2} for a given set of light neutralino and chargino masses. We define a measure for the quality of the obtained benchmarks, that also includes criteria to assess the higgsino content of the resulting charginos and neutralinos. We finally discuss the distribution of the resulting models in the MSSM parameter space as well as their implications for supersymmetric dark matter phenomenology.

An Efficient Scheme of Quantum Wireless Multi-hop Communication using Coefficient Matrix

NASA Astrophysics Data System (ADS)

Zhao, Bei; Zha, Xin-Wei; Duan, Ya-Jun; Sun, Xin-Mei

2015-08-01

By defining the coefficient matrix, a new quantum teleportation scheme in quantum wireless multi-hop network is proposed. With the help of intermediate nodes, an unknown qubit state can be teleported between two distant nodes which do not share entanglement in advance. Arbitrary Bell pairs and entanglement swapping are utilized for establishing quantum channel among intermediate nodes. Using collapsed matrix, the initial quantum state can be perfectly recovered at the destination.

FEAMAC/CARES Stochastic-Strength-Based Damage Simulation Tool for Ceramic Matrix Composites

NASA Technical Reports Server (NTRS)

Nemeth, Noel; Bednarcyk, Brett; Pineda, Evan; Arnold, Steven; Mital, Subodh; Murthy, Pappu; Bhatt, Ramakrishna

2016-01-01

Reported here is a coupling of two NASA developed codes: CARES (Ceramics Analysis and Reliability Evaluation of Structures) with the MAC/GMC (Micromechanics Analysis Code/ Generalized Method of Cells) composite material analysis code. The resulting code is called FEAMAC/CARES and is constructed as an Abaqus finite element analysis UMAT (user defined material). Here we describe the FEAMAC/CARES code and an example problem (taken from the open literature) of a laminated CMC in off-axis loading is shown. FEAMAC/CARES performs stochastic-strength-based damage simulation response of a CMC under multiaxial loading using elastic stiffness reduction of the failed elements.

Stochastic-Strength-Based Damage Simulation Tool for Ceramic Matrix Composite

NASA Technical Reports Server (NTRS)

Nemeth, Noel; Bednarcyk, Brett; Pineda, Evan; Arnold, Steven; Mital, Subodh; Murthy, Pappu

2015-01-01

Reported here is a coupling of two NASA developed codes: CARES (Ceramics Analysis and Reliability Evaluation of Structures) with the MAC/GMC (Micromechanics Analysis Code/ Generalized Method of Cells) composite material analysis code. The resulting code is called FEAMAC/CARES and is constructed as an Abaqus finite element analysis UMAT (user defined material). Here we describe the FEAMAC/CARES code and an example problem (taken from the open literature) of a laminated CMC in off-axis loading is shown. FEAMAC/CARES performs stochastic-strength-based damage simulation response of a CMC under multiaxial loading using elastic stiffness reduction of the failed elements.

Rotations with Rodrigues' Vector

ERIC Educational Resources Information Center

Pina, E.

2011-01-01

The rotational dynamics was studied from the point of view of Rodrigues' vector. This vector is defined here by its connection with other forms of parametrization of the rotation matrix. The rotation matrix was expressed in terms of this vector. The angular velocity was computed using the components of Rodrigues' vector as coordinates. It appears…

Definition of a parametric form of nonsingular Mueller matrices.

PubMed

Devlaminck, Vincent; Terrier, Patrick

2008-11-01

The goal of this paper is to propose a mathematical framework to define and analyze a general parametric form of an arbitrary nonsingular Mueller matrix. Starting from previous results about nondepolarizing matrices, we generalize the method to any nonsingular Mueller matrix. We address this problem in a six-dimensional space in order to introduce a transformation group with the same number of degrees of freedom and explain why subsets of O(5,1), the orthogonal group associated with six-dimensional Minkowski space, is a physically admissible solution to this question. Generators of this group are used to define possible expressions of an arbitrary nonsingular Mueller matrix. Ultimately, the problem of decomposition of these matrices is addressed, and we point out that the "reverse" and "forward" decomposition concepts recently introduced may be inferred from the formalism we propose.

Bottom-Up and Top-Down Solid-State NMR Approaches for Bacterial Biofilm Matrix Composition

PubMed Central

Cegelski, Lynette

2015-01-01

The genomics and proteomics revolutions have been enormously successful in providing crucial “parts lists” for biological systems. Yet, formidable challenges exist in generating complete descriptions of how the parts function and assemble into macromolecular complexes and whole-cell assemblies. Bacterial biofilms are complex multicellular bacterial communities protected by a slime-like extracellular matrix that confers protection to environmental stress and enhances resistance to antibiotics and host defenses. As a non-crystalline, insoluble, heterogeneous assembly, the biofilm extracellular matrix poses a challenge to compositional analysis by conventional methods. In this Perspective, bottom-up and top-down solid-state NMR approaches are described for defining chemical composition in complex macrosystems. The “sum-of-theparts” bottom-up approach was introduced to examine the amyloid-integrated biofilms formed by E. coli and permitted the first determination of the composition of the intact extracellular matrix from a bacterial biofilm. An alternative top-down approach was developed to define composition in V. cholerae biofilms and relied on an extensive panel of NMR measurements to tease out specific carbon pools from a single sample of the intact extracellular matrix. These two approaches are widely applicable to other heterogeneous assemblies. For bacterial biofilms, quantitative parameters of matrix composition are needed to understand how biofilms are assembled, to improve the development of biofilm inhibitors, and to dissect inhibitor modes of action. Solid-state NMR approaches will also be invaluable in obtaining parameters of matrix architecture. PMID:25797008

Bottom-up and top-down solid-state NMR approaches for bacterial biofilm matrix composition.

PubMed

Cegelski, Lynette

2015-04-01

The genomics and proteomics revolutions have been enormously successful in providing crucial "parts lists" for biological systems. Yet, formidable challenges exist in generating complete descriptions of how the parts function and assemble into macromolecular complexes and whole-cell assemblies. Bacterial biofilms are complex multicellular bacterial communities protected by a slime-like extracellular matrix that confers protection to environmental stress and enhances resistance to antibiotics and host defenses. As a non-crystalline, insoluble, heterogeneous assembly, the biofilm extracellular matrix poses a challenge to compositional analysis by conventional methods. In this perspective, bottom-up and top-down solid-state NMR approaches are described for defining chemical composition in complex macrosystems. The "sum-of-the-parts" bottom-up approach was introduced to examine the amyloid-integrated biofilms formed by Escherichia coli and permitted the first determination of the composition of the intact extracellular matrix from a bacterial biofilm. An alternative top-down approach was developed to define composition in Vibrio cholerae biofilms and relied on an extensive panel of NMR measurements to tease out specific carbon pools from a single sample of the intact extracellular matrix. These two approaches are widely applicable to other heterogeneous assemblies. For bacterial biofilms, quantitative parameters of matrix composition are needed to understand how biofilms are assembled, to improve the development of biofilm inhibitors, and to dissect inhibitor modes of action. Solid-state NMR approaches will also be invaluable in obtaining parameters of matrix architecture. Copyright © 2015 Elsevier Inc. All rights reserved.

Bottom-up and top-down solid-state NMR approaches for bacterial biofilm matrix composition

NASA Astrophysics Data System (ADS)

Cegelski, Lynette

2015-04-01

The genomics and proteomics revolutions have been enormously successful in providing crucial "parts lists" for biological systems. Yet, formidable challenges exist in generating complete descriptions of how the parts function and assemble into macromolecular complexes and whole-cell assemblies. Bacterial biofilms are complex multicellular bacterial communities protected by a slime-like extracellular matrix that confers protection to environmental stress and enhances resistance to antibiotics and host defenses. As a non-crystalline, insoluble, heterogeneous assembly, the biofilm extracellular matrix poses a challenge to compositional analysis by conventional methods. In this perspective, bottom-up and top-down solid-state NMR approaches are described for defining chemical composition in complex macrosystems. The "sum-of-the-parts" bottom-up approach was introduced to examine the amyloid-integrated biofilms formed by Escherichia coli and permitted the first determination of the composition of the intact extracellular matrix from a bacterial biofilm. An alternative top-down approach was developed to define composition in Vibrio cholerae biofilms and relied on an extensive panel of NMR measurements to tease out specific carbon pools from a single sample of the intact extracellular matrix. These two approaches are widely applicable to other heterogeneous assemblies. For bacterial biofilms, quantitative parameters of matrix composition are needed to understand how biofilms are assembled, to improve the development of biofilm inhibitors, and to dissect inhibitor modes of action. Solid-state NMR approaches will also be invaluable in obtaining parameters of matrix architecture.

Multiscale Modeling of Ceramic Matrix Composites

NASA Technical Reports Server (NTRS)

Bednarcyk, Brett A.; Mital, Subodh K.; Pineda, Evan J.; Arnold, Steven M.

2015-01-01

Results of multiscale modeling simulations of the nonlinear response of SiC/SiC ceramic matrix composites are reported, wherein the microstructure of the ceramic matrix is captured. This micro scale architecture, which contains free Si material as well as the SiC ceramic, is responsible for residual stresses that play an important role in the subsequent thermo-mechanical behavior of the SiC/SiC composite. Using the novel Multiscale Generalized Method of Cells recursive micromechanics theory, the microstructure of the matrix, as well as the microstructure of the composite (fiber and matrix) can be captured.

Deep data analysis via physically constrained linear unmixing: universal framework, domain examples, and a community-wide platform.

PubMed

Kannan, R; Ievlev, A V; Laanait, N; Ziatdinov, M A; Vasudevan, R K; Jesse, S; Kalinin, S V

2018-01-01

Many spectral responses in materials science, physics, and chemistry experiments can be characterized as resulting from the superposition of a number of more basic individual spectra. In this context, unmixing is defined as the problem of determining the individual spectra, given measurements of multiple spectra that are spatially resolved across samples, as well as the determination of the corresponding abundance maps indicating the local weighting of each individual spectrum. Matrix factorization is a popular linear unmixing technique that considers that the mixture model between the individual spectra and the spatial maps is linear. Here, we present a tutorial paper targeted at domain scientists to introduce linear unmixing techniques, to facilitate greater understanding of spectroscopic imaging data. We detail a matrix factorization framework that can incorporate different domain information through various parameters of the matrix factorization method. We demonstrate many domain-specific examples to explain the expressivity of the matrix factorization framework and show how the appropriate use of domain-specific constraints such as non-negativity and sum-to-one abundance result in physically meaningful spectral decompositions that are more readily interpretable. Our aim is not only to explain the off-the-shelf available tools, but to add additional constraints when ready-made algorithms are unavailable for the task. All examples use the scalable open source implementation from https://github.com/ramkikannan/nmflibrary that can run from small laptops to supercomputers, creating a user-wide platform for rapid dissemination and adoption across scientific disciplines.

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

PubMed

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

2011-01-01

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

Removal of antibiotics in a parallel-plate thin-film-photocatalytic reactor: Process modeling and evolution of transformation by-products and toxicity.

PubMed

Özkal, Can Burak; Frontistis, Zacharias; Antonopoulou, Maria; Konstantinou, Ioannis; Mantzavinos, Dionissios; Meriç, Süreyya

2017-10-01

Photocatalytic degradation of sulfamethoxazole (SMX) antibiotic has been studied under recycling batch and homogeneous flow conditions in a thin-film coated immobilized system namely parallel-plate (PPL) reactor. Experimentally designed, statistically evaluated with a factorial design (FD) approach with intent to provide a mathematical model takes into account the parameters influencing process performance. Initial antibiotic concentration, UV energy level, irradiated surface area, water matrix (ultrapure and secondary treated wastewater) and time, were defined as model parameters. A full of 2 5 experimental design was consisted of 32 random experiments. PPL reactor test experiments were carried out in order to set boundary levels for hydraulic, volumetric and defined defined process parameters. TTIP based thin-film with polyethylene glycol+TiO 2 additives were fabricated according to pre-described methodology. Antibiotic degradation was monitored by High Performance Liquid Chromatography analysis while the degradation products were specified by LC-TOF-MS analysis. Acute toxicity of untreated and treated SMX solutions was tested by standard Daphnia magna method. Based on the obtained mathematical model, the response of the immobilized PC system is described with a polynomial equation. The statistically significant positive effects are initial SMX concentration, process time and the combined effect of both, while combined effect of water matrix and irradiated surface area displays an adverse effect on the rate of antibiotic degradation by photocatalytic oxidation. Process efficiency and the validity of the acquired mathematical model was also verified for levofloxacin and cefaclor antibiotics. Immobilized PC degradation in PPL reactor configuration was found capable of providing reduced effluent toxicity by simultaneous degradation of SMX parent compound and TBPs. Copyright © 2017. Published by Elsevier B.V.

Predicting neo-adjuvant chemotherapy response and progression-free survival of locally advanced breast cancer using textural features of intratumoral heterogeneity on F-18 FDG PET/CT and diffusion-weighted MR imaging.

PubMed

Yoon, Hai-Jeon; Kim, Yemi; Chung, Jin; Kim, Bom Sahn

2018-03-30

Predicting response to neo-adjuvant chemotherapy (NAC) and survival in locally advanced breast cancer (LABC) is important. This study investigated the prognostic value of tumor heterogeneity evaluated with textural analysis through F-18 fluorodeoxyglucose (FDG) positron emission tomography (PET) and diffusion-weighted imaging (DWI). We enrolled 83 patients with LABC who had completed NAC and curative surgery. Tumor texture indices from pretreatment FDG PET and DWI were extracted from histogram analysis and 7 different parent matrices: co-occurrence matrix, the voxel-alignment matrix, neighborhood intensity difference matrix, intensity size-zone matrix (ISZM), normalized gray-level co-occurrence matrix (NGLCM), neighboring gray-level dependence matrix (NGLDM), and texture spectrum matrix. The predictive values of textural features were tested regarding both pathologic NAC response and progression-free survival. Among 83 patients, 46 were pathologic responders, while 37 were nonresponders. The PET texture indices from 7 parent matrices, DWI texture indices from histogram, and 1 parent matrix (NGLCM) showed significant differences according to NAC response. On multivariable analysis, number nonuniformity of PET extracted from the NGLDM was an independent predictor of pathologic response (P = .009). During a median follow-up period of 17.3 months, 14 patients experienced recurrence. High-intensity zone emphasis (HIZE) and high-intensity short-zone emphasis (HISZE) from PET extracted from ISZM were significant textural predictors (P = .011 and P = .033). On Cox regression analysis, only HIZE was a significant predictor of recurrence (P = .027), while HISZE showed borderline significance (P = .107). Tumor texture indices are useful for NAC response prediction in LABC. Moreover, PET texture indices can help to predict disease recurrence. © 2018 Wiley Periodicals, Inc.

Matrix Interdiction Problem

NASA Astrophysics Data System (ADS)

Kasiviswanathan, Shiva Prasad; Pan, Feng

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

Invertible flexible matrices

NASA Astrophysics Data System (ADS)

Justino, Júlia

2017-06-01

Matrices with coefficients having uncertainties of type o (.) or O (.), called flexible matrices, are studied from the point of view of nonstandard analysis. The uncertainties of the afore-mentioned kind will be given in the form of the so-called neutrices, for instance the set of all infinitesimals. Since flexible matrices have uncertainties in their coefficients, it is not possible to define the identity matrix in an unique way and so the notion of spectral identity matrix arises. Not all nonsingular flexible matrices can be turned into a spectral identity matrix using Gauss-Jordan elimination method, implying that that not all nonsingular flexible matrices have the inverse matrix. Under certain conditions upon the size of the uncertainties appearing in a nonsingular flexible matrix, a general theorem concerning the boundaries of its minors is presented which guarantees the existence of the inverse matrix of a nonsingular flexible matrix.

Dental Enamel: Genes Define Biomechanics

PubMed Central

Rauth, Rick J.; Potter, Karen S.; Ngan, Amanda Y.-W.; Saad, Deema M.; Mehr, Rana; Luong, Vivian Q.; Schuetter, Verna L.; Miklus, Vetea G.; Chang, PeiPei; Paine, Michael L.; Lacruz, Rodrigo S.; Snead, Malcolm L.; White, Shane N.

2010-01-01

Regulated gene expression assembles an extracellular proteinaceous matrix to control biomineralization and the resultant biomechanical function of tooth enamel. The importance of the dominant enamel matrix protein, amelogenin (Amel); a minor transiently expressed protein, dentin sialoprotein (Dsp); an electrogenic sodium bicarbonate cotransporter (NBCe1); the timely removal of the proteinaceous matrix by a serine protease, Kallikrein-4 (Klk4); and the late-stage expression of Amelotin (Amtn) on enamel biomechanical function were demonstrated and measured using mouse models. PMID:20066874

The mesangial matrix in the normal and sclerotic glomerulus.

PubMed

Rosenblum, N D

1994-02-01

Mesangial sclerosis is a final common pathway to glomerular destruction in a variety of glomerular diseases. The expression of several classes of extracellular matrix (ECM) molecules has been defined in the normal and diseased mesangial matrix (MM). However, the manner in which these ECM components determine the three dimensional structure and function of the MM remains to be defined. Structural studies of the MM suggest that its constituent molecules are regionally organized into subcompartments with different three dimensional structures. The diversity of matrix molecules expressed within the MM as well as the organization of these components in nonrenal ECM's, such as the cornea, provides further support for this organizational model. The study of the cornea has also revealed that novel short chain collagenous proteins partially determine the three dimensional structure of the matrix. Recently, a novel collagen, type VIII collagen, has been described in mesangial cells and in the intact glomerulus. It is hypothesized that type VIII collagen is expressed both as a polymer and as a monomer within the glomerulus, and depending on its conformation, may serve unique functions. In the chronically diseased MM, normal MM components are overexpressed and fibrillar collagens are expressed de novo in a delayed fashion. Enhanced proteoglycan expression, observed early in disease, may determine increased volume of the mesangium. This, in turn, may stimulate the production of fibrillar collagens by mesangial cells resulting in a fibrillar noncompliant mesangial matrix.

Quantum Double of Yangian of strange Lie superalgebra Qn and multiplicative formula for universal R-matrix

NASA Astrophysics Data System (ADS)

Stukopin, Vladimir

2018-02-01

Main result is the multiplicative formula for universal R-matrix for Quantum Double of Yangian of strange Lie superalgebra Qn type. We introduce the Quantum Double of the Yangian of the strange Lie superalgebra Qn and define its PBW basis. We compute the Hopf pairing for the generators of the Yangian Double. From the Hopf pairing formulas we derive a factorized multiplicative formula for the universal R-matrix of the Yangian Double of the Lie superalgebra Qn . After them we obtain coefficients in this multiplicative formula for universal R-matrix.

AESOP- INTERACTIVE DESIGN OF LINEAR QUADRATIC REGULATORS AND KALMAN FILTERS

NASA Technical Reports Server (NTRS)

Lehtinen, B.

1994-01-01

AESOP was developed to solve a number of problems associated with the design of controls and state estimators for linear time-invariant systems. The systems considered are modeled in state-variable form by a set of linear differential and algebraic equations with constant coefficients. Two key problems solved by AESOP are the linear quadratic regulator (LQR) design problem and the steady-state Kalman filter design problem. AESOP is designed to be used in an interactive manner. The user can solve design problems and analyze the solutions in a single interactive session. Both numerical and graphical information are available to the user during the session. The AESOP program is structured around a list of predefined functions. Each function performs a single computation associated with control, estimation, or system response determination. AESOP contains over sixty functions and permits the easy inclusion of user defined functions. The user accesses these functions either by inputting a list of desired functions in the order they are to be performed, or by specifying a single function to be performed. The latter case is used when the choice of function and function order depends on the results of previous functions. The available AESOP functions are divided into several general areas including: 1) program control, 2) matrix input and revision, 3) matrix formation, 4) open-loop system analysis, 5) frequency response, 6) transient response, 7) transient function zeros, 8) LQR and Kalman filter design, 9) eigenvalues and eigenvectors, 10) covariances, and 11) user-defined functions. The most important functions are those that design linear quadratic regulators and Kalman filters. The user interacts with AESOP when using these functions by inputting design weighting parameters and by viewing displays of designed system response. Support functions obtain system transient and frequency responses, transfer functions, and covariance matrices. AESOP can also provide the user with open-loop system information including stability, controllability, and observability. The AESOP program is written in FORTRAN IV for interactive execution and has been implemented on an IBM 3033 computer using TSS 370. As currently configured, AESOP has a central memory requirement of approximately 2 Megs of 8 bit bytes. Memory requirements can be reduced by redimensioning arrays in the AESOP program. Graphical output requires adaptation of the AESOP plot routines to whatever device is available. The AESOP program was developed in 1984.

An improved V-Lambda solution of the matrix Riccati equation

NASA Technical Reports Server (NTRS)

Bar-Itzhack, Itzhack Y.; Markley, F. Landis

1988-01-01

The authors present an improved algorithm for computing the V-Lambda solution of the matrix Riccati equation. The improvement is in the reduction of the computational load, results from the orthogonality of the eigenvector matrix that has to be solved for. The orthogonality constraint reduces the number of independent parameters which define the matrix from n-squared to n (n - 1)/2. The authors show how to specify the parameters, how to solve for them and how to form from them the needed eigenvector matrix. In the search for suitable parameters, the analogy between the present problem and the problem of attitude determination is exploited, resulting in the choice of Rodrigues parameters.

Characterization of matrix effects in developing rugged high-throughput LC-MS/MS methods for bioanalysis.

PubMed

Li, Fumin; Wang, Jun; Jenkins, Rand

2016-05-01

There is an ever-increasing demand for high-throughput LC-MS/MS bioanalytical assays to support drug discovery and development. Matrix effects of sofosbuvir (protonated) and paclitaxel (sodiated) were thoroughly evaluated using high-throughput chromatography (defined as having a run time ≤1 min) under 14 elution conditions with extracts from protein precipitation, liquid-liquid extraction and solid-phase extraction. A slight separation, in terms of retention time, between underlying matrix components and sofosbuvir/paclitaxel can greatly alleviate matrix effects. High-throughput chromatography, with proper optimization, can provide rapid and effective chromatographic separation under 1 min to alleviate matrix effects and enhance assay ruggedness for regulated bioanalysis.

Structure and function of yeast glutaredoxin 2 depend on postranslational processing and are related to subcellular distribution.

PubMed

Porras, Pablo; McDonagh, Brian; Pedrajas, Jose Rafael; Bárcena, J Antonio; Padilla, C Alicia

2010-04-01

We have previously shown that glutaredoxin 2 (Grx2) from Saccharomyces cerevisiae localizes at 3 different subcellular compartments, cytosol, mitochondrial matrix and outer membrane, as the result of different postranslational processing of one single gene. Having set the mechanism responsible for this remarkable phenomenon, we have now aimed at defining whether this diversity of subcellular localizations correlates with differences in structure and function of the Grx2 isoforms. We have determined the N-terminal sequence of the soluble mitochondrial matrix Grx2 by mass spectrometry and have determined the exact cleavage site by Mitochondrial Processing Peptidase (MPP). As a consequence of this cleavage, the mitochondrial matrix Grx2 isoform possesses a basic tetrapeptide extension at the N-terminus compared to the cytosolic form. A functional relationship to this structural difference is that mitochondrial Grx2 displays a markedly higher activity in the catalysis of GSSG reduction by the mitochondrial dithiol dihydrolipoamide. We have prepared Grx2 mutants affected on key residues inside the presequence to direct the protein to one single cellular compartment; either the cytosol, the mitochondrial membrane or the matrix and have analyzed their functional phenotypes. Strains expressing Grx2 only in the cytosol are equally sensitive to H(2)O(2) as strains lacking the gene, whereas those expressing Grx2 exclusively in the mitochondrial matrix are more resistant. Mutations on key basic residues drastically affect the cellular fate of the protein, showing that evolutionary diversification of Grx2 structural and functional properties are strictly dependent on the sequence of the targeting signal peptide. Copyright 2009 Elsevier B.V. All rights reserved.

Derive Workshop Matrix Algebra and Linear Algebra.

ERIC Educational Resources Information Center

Townsley Kulich, Lisa; Victor, Barbara

This document presents the course content for a workshop that integrates the use of the computer algebra system Derive with topics in matrix and linear algebra. The first section is a guide to using Derive that provides information on how to write algebraic expressions, make graphs, save files, edit, define functions, differentiate expressions,…

The Approximation of Two-Mode Proximity Matrices by Sums of Order-Constrained Matrices.

ERIC Educational Resources Information Center

Hubert, Lawrence; Arabie, Phipps

1995-01-01

A least-squares strategy is proposed for representing a two-mode proximity matrix as an approximate sum of a small number of matrices that satisfy certain simple order constraints on their entries. The primary class of constraints considered defines Q-forms for particular conditions in a two-mode matrix. (SLD)

Eigenvector dynamics: General theory and some applications

NASA Astrophysics Data System (ADS)

Allez, Romain; Bouchaud, Jean-Philippe

2012-10-01

We propose a general framework to study the stability of the subspace spanned by P consecutive eigenvectors of a generic symmetric matrix H0 when a small perturbation is added. This problem is relevant in various contexts, including quantum dissipation (H0 is then the Hamiltonian) and financial risk control (in which case H0 is the assets' return covariance matrix). We argue that the problem can be formulated in terms of the singular values of an overlap matrix, which allows one to define an overlap distance. We specialize our results for the case of a Gaussian orthogonal H0, for which the full spectrum of singular values can be explicitly computed. We also consider the case when H0 is a covariance matrix and illustrate the usefulness of our results using financial data. The special case where the top eigenvalue is much larger than all the other ones can be investigated in full detail. In particular, the dynamics of the angle made by the top eigenvector and its true direction defines an interesting class of random processes.

The controversial nuclear matrix: a balanced point of view.

PubMed

Martelli, A M; Falcieri, E; Zweyer, M; Bortul, R; Tabellini, G; Cappellini, A; Cocco, L; Manzoli, L

2002-10-01

The nuclear matrix is defined as the residual framework after the removal of the nuclear envelope, chromatin, and soluble components by sequential extractions. According to several investigators the nuclear matrix provides the structural basis for intranuclear order. However, the existence itself and the nature of this structure is still uncertain. Although the techniques used for the visualization of the nuclear matrix have improved over the years, it is still unclear to what extent the isolated nuclear matrix corresponds to an in vivo existing structure. Therefore, considerable skepticism continues to surround the nuclear matrix fraction as an accurate representation of the situation in living cells. Here, we summarize the experimental evidence in favor of, or against, the presence of a diffuse nucleoskeleton as a facilitating organizational nonchromatin structure of the nucleus.

SMOS L1PP Performance Analysis from Commissioning Phase - Improved Algorithms and Major Results

NASA Astrophysics Data System (ADS)

Castro, Rita; Oliva, Roger; Gutiérrez, Antonio; Barbosa, José; Catarino, Nuno; Martin-Neira, Manuel; Zundo, Michele; Cabot, François

2010-05-01

Following the Soil Moisture and Ocean Salinity (SMOS) launch in November 2009, a Commissioning Phase has taken place for six months, having Deimos closely cooperated with the European Space Agency's (ESA) Level 1 team. During these six months several studies have been conducted on calibration optimization, image reconstruction improvement, geolocation assessment and the impact on scientific results, in particular to insure optimal input to Level 2 Soil Moisture and Ocean Salinity retrieval. In parallel with the scientific studies, some new algorithms/mitigation techniques had to be developed, tested and implemented during the Commissioning Phase. Prior to launch, the Level 1 Prototype Processor (L1PP) included already several experimental algorithms different from the ones existent in the operational chain. These algorithms were tested during Commissioning and some were included in the final processing baseline as a result of the planned studies. Some unforeseen algorithms had to be defined, implemented and tested during the Commissioning Phase itself and these will also be described below. In L1a, for example, the calibration of the Power Measuring Systems (PMS) can be done using a cold target as reference, i.e., the Sky at ~3 K. This has been extensively analyzed and the results will be presented here. At least two linearity corrections to the PMS response function have been tested and compared. The deflection method was selected for inclusion on the operational chain and the results leading to this decision will be also presented. In Level 1B, all the foreign sources algorithms have been tested and validated using real data. The System Response Function (G-matrix) computed for different events has been analyzed and criteria for validation of its pseudo inverse, the J+ matrix, have been defined during the Commissioning Phase. The impact of errors in the J+ matrix has been studied and well characterized. The effects of the Flat Target Response (FTR) have also been addressed and the criteria for an acceptable Flat Target Transformation auxiliary data file have been assessed and implemented during the Commissioning Phase. In L1c, the performance of L1PP's geolocation routines has been analyzed by comparing the estimated and real positions of known land features. An important activity during the Commissioning Phase was the study and impact of Radio Frequency Interference (RFI) sources in the final reconstructed image. The quantity of expected RFIs has been under-estimated and, therefore, error mitigation techniques had to be developed to overcome these unwanted sources of errors. In this presentation the latest news and results for this issue will be presented.

Benchmark matrix and guide: Part III.

PubMed

1992-01-01

The final article in the "Benchmark Matrix and Guide" series developed by Headquarters Air Force Logistics Command completes the discussion of the last three categories that are essential ingredients of a successful total quality management (TQM) program. Detailed behavioral objectives are listed in the areas of recognition, process improvement, and customer focus. These vertical categories are meant to be applied to the levels of the matrix that define the progressive stages of the TQM: business as usual, initiation, implementation, expansion, and integration. By charting the horizontal progress level and the vertical TQM category, the quality management professional can evaluate the current state of TQM in any given organization. As each category is completed, new goals can be defined in order to advance to a higher level. The benchmarking process is integral to quality improvement efforts because it focuses on the highest possible standards to evaluate quality programs.

Container and method for absorbing and reducing hydrogen concentration

DOEpatents

Wicks, George G.; Lee, Myung W.; Heung, Leung K.

2001-01-01

A method for absorbing hydrogen from an enclosed environment comprising providing a vessel; providing a hydrogen storage composition in communication with a vessel, the hydrogen storage composition further comprising a matrix defining a pore size which permits the passage of hydrogen gas while blocking the passage of gaseous poisons; placing a material within the vessel, the material evolving hydrogen gas; sealing the vessel; and absorbing the hydrogen gas released into the vessel by the hydrogen storage composition. A container for absorbing evolved hydrogen gas comprising: a vessel having an interior and adapted for receiving materials which release hydrogen gas; a hydrogen absorbing composition in communication with the interior, the composition defining a matrix surrounding a hydrogen absorber, the matrix permitting the passage of hydrogen gas while excluding gaseous poisons; wherein, when the vessel is sealed, hydrogen gas, which is released into the vessel interior, is absorbed by the hydrogen absorbing composition.

Matrix Training of Receptive Language Skills with a Toddler with Autism Spectrum Disorder: A Case Study

ERIC Educational Resources Information Center

Curiel, Emily S. L.; Sainato, Diane M.; Goldstein, Howard

2016-01-01

Matrix training is a systematic teaching approach that can facilitate generalized language. Specific responses are taught that result in the emergence of untrained responses. This type of training facilitates the use of generalized language in children with autism spectrum disorder (ASD). This study used a matrix training procedure with a toddler…

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.

Toughening of a Particulate-Reinforced/Ceramic-Matrix Composite

DTIC Science & Technology

1989-09-01

where two inhomogeneities (Q1X,2), with the misfit strains defined by eqs. (2) and (3) are replaced by the inclusions with eigenstrains of 9 1 in al...and *2 in C2. The thermal stresses in a composite can then be solved in terms of the eigenstrains . Detailed formulation for the thermal stresses in a...is a domain surrounded by the matrix and possesses the same properties as the matrix and also an eigenstrain 9* which is an inelastic strain.24 Thus

Adomian decomposition

NASA Astrophysics Data System (ADS)

Daftardar-Gejji, Varsha; Jafari, Hossein

2005-01-01

Adomian decomposition method has been employed to obtain solutions of a system of fractional differential equations. Convergence of the method has been discussed with some illustrative examples. In particular, for the initial value problem: where A=[aij] is a real square matrix, the solution turns out to be , where E([alpha]1,...,[alpha]n),1 denotes multivariate Mittag-Leffler function defined for matrix arguments and Ai is the matrix having ith row as [ai1...ain], and all other entries are zero. Fractional oscillation and Bagley-Torvik equations are solved as illustrative examples.

Considerations concerning fatigue life of metal matrix composites

NASA Technical Reports Server (NTRS)

Radhakrishnan, V. M.; Bartolotta, Paul A.

1993-01-01

Since metal matrix composites (MMC) are composed from two very distinct materials each having their own physical and mechanical properties, it is feasible that the fatigue resistance depends on the strength of the weaker constituent. Based on this assumption, isothermal fatigue lives of several MMC's were analyzed utilizing a fatigue life diagram approach. For each MMC, the fatigue life diagram was quantified using the mechanical properties of its constituents. The fatigue life regions controlled by fiber fracture and matrix were also quantitatively defined.

Using the laws of thermodynamics to understand how matrix metalloproteinases coordinate the myocardial response to injury.

PubMed

Iyer, Rugmani Padmanabhan; Jung, Mira; Lindsey, Merry L

Following myocardial infarction (MI), the left ventricle (LV) undergoes a series of molecular, cellular, and functional alterations that are both part of the wound healing response to form a scar in the infarct region and the consequence of that response. Using the laws of thermodynamics as an analogy, we present here three laws for categorizing the post-MI LV remodeling process. The first law is that the LV will attempt to maintain equilibrium and compensate as a way to maximize function, the second law is that remodeling is progressive and unidirectional, and the third law is that the final goal is (ideally, but not always achievable) a stable, equilibrated scar. This comparison helps to define the boundaries of the system, whether it be the infarct zone, the LV, the heart, or the entire body. This review provides an overview for those not directly in the field and establishes a framework to help prioritize future research directions.

Using the laws of thermodynamics to understand how matrix metalloproteinases coordinate the myocardial response to injury

PubMed Central

Iyer, Rugmani Padmanabhan; Jung, Mira; Lindsey, Merry L

2016-01-01

Following myocardial infarction (MI), the left ventricle (LV) undergoes a series of molecular, cellular, and functional alterations that are both part of the wound healing response to form a scar in the infarct region and the consequence of that response. Using the laws of thermodynamics as an analogy, we present here three laws for categorizing the post-MI LV remodeling process. The first law is that the LV will attempt to maintain equilibrium and compensate as a way to maximize function, the second law is that remodeling is progressive and unidirectional, and the third law is that the final goal is (ideally, but not always achievable) a stable, equilibrated scar. This comparison helps to define the boundaries of the system, whether it be the infarct zone, the LV, the heart, or the entire body. This review provides an overview for those not directly in the field and establishes a framework to help prioritize future research directions. PMID:27376092

CD47 Receptor Globally Regulates Metabolic Pathways That Control Resistance to Ionizing Radiation*

PubMed Central

Miller, Thomas W.; Soto-Pantoja, David R.; Schwartz, Anthony L.; Sipes, John M.; DeGraff, William G.; Ridnour, Lisa A.; Wink, David A.; Roberts, David D.

2015-01-01

Modulating tissue responses to stress is an important therapeutic objective. Oxidative and genotoxic stresses caused by ionizing radiation are detrimental to healthy tissues but beneficial for treatment of cancer. CD47 is a signaling receptor for thrombospondin-1 and an attractive therapeutic target because blocking CD47 signaling protects normal tissues while sensitizing tumors to ionizing radiation. Here we utilized a metabolomic approach to define molecular mechanisms underlying this radioprotective activity. CD47-deficient cells and cd47-null mice exhibited global advantages in preserving metabolite levels after irradiation. Metabolic pathways required for controlling oxidative stress and mediating DNA repair were enhanced. Some cellular energetics pathways differed basally in CD47-deficient cells, and the global declines in the glycolytic and tricarboxylic acid cycle metabolites characteristic of normal cell and tissue responses to irradiation were prevented in the absence of CD47. Thus, CD47 mediates signaling from the extracellular matrix that coordinately regulates basal metabolism and cytoprotective responses to radiation injury. PMID:26311851

System identification for Space Station Freedom using observer/Kalman filter Markov parameters. M.S. Thesis

NASA Technical Reports Server (NTRS)

Papadopoulos, Michael; Tolson, Robert H.

1993-01-01

The Modal Identification Experiment (MIE) is a proposed experiment to define the dynamic characteristics of Space Station Freedom. Previous studies emphasized free-decay modal identification. The feasibility of using a forced response method (Observer/Kalman Filter Identification (OKID)) is addressed. The interest in using OKID is to determine the input mode shape matrix which can be used for controller design or control-structure interaction analysis, and investigate if forced response methods may aid in separating closely spaced modes. A model of the SC-7 configuration of Space Station Freedom was excited using simulated control system thrusters to obtain acceleration output. It is shown that an 'optimum' number of outputs exists for OKID. To recover global mode shapes, a modified method called Global-Local OKID was developed. This study shows that using data from a long forced response followed by free-decay leads to the 'best' modal identification. Twelve out of the thirteen target modes were identified for such an output.

Themes in fibrosis and gastrointestinal inflammation

PubMed Central

Lund, P. Kay

2011-01-01

Wound healing is an appropriate response to inflammation and tissue injury in the gastrointestinal tract. If wound healing responses are excessive, perpetuated, or prolonged, they lead to fibrosis, distortion of tissue architecture, and loss of function. This introductory editorial and the minireviews or reviews in this themes series highlight the diversity in severity and location of fibrosis in response to gastrointestinal inflammation. The multiplicity of cellular and molecular mediators and new players, including stem cells or extracellular matrix-producing cells derived from nonmesenchymal cell types, is reviewed. Comparisons of inflammation-induced fibrosis across organ systems and the need for integrated and systems-based molecular approaches, new imaging modalities, well-characterized animal models, cell culture models, and improved diagnostic or predictive markers are reviewed. To date, intestinal fibrosis has received much less attention than inflammation in terms of defining mechanisms and underlying causes. This themes series aims to illustrate the importance of research in this area in gastrointestinal health and disease. PMID:21415411

Cellular Response to a Novel Fetal Acellular Collagen Matrix: Implications for Tissue Regeneration

PubMed Central

Rennert, Robert C.; Garg, Ravi K.; Gurtner, Geoffrey C.

2013-01-01

Introduction. PriMatrix (TEI Biosciences Inc., Boston, MA, USA) is a novel acellular collagen matrix derived from fetal bovine dermis that is designed for use in partial- and full-thickness wounds. This study analyzes the cellular response to PriMatrix in vivo, as well as the ability of this matrix to facilitate normal tissue regeneration. Methods. Five by five mm squares of rehydrated PriMatrix were implanted in a subcutaneous fashion on the dorsum of wild-type mice. Implant site tissue was harvested for histology, immunohistochemistry (IHC), and flow cytometric analyses at multiple time points until day 28. Results. PriMatrix implants were found to go through a biological progression initiated by a transient infiltrate of inflammatory cells, followed by mesenchymal cell recruitment and vascular development. IHC analysis revealed that the majority of the implanted fetal dermal collagen fibers persisted through day 28 but underwent remodeling and cellular repopulation to form tissue with a density and morphology consistent with healthy dermis. Conclusions. PriMatrix implants undergo progressive in vivo remodeling, facilitating the regeneration of histologically normal tissue through a mild inflammatory and progenitor cell response. Regeneration of normal tissue is especially important in a wound environment, and these findings warrant further investigation of PriMatrix in this setting. PMID:23970899

Cellular response to a novel fetal acellular collagen matrix: implications for tissue regeneration.

PubMed

Rennert, Robert C; Sorkin, Michael; Garg, Ravi K; Januszyk, Michael; Gurtner, Geoffrey C

2013-01-01

Introduction. PriMatrix (TEI Biosciences Inc., Boston, MA, USA) is a novel acellular collagen matrix derived from fetal bovine dermis that is designed for use in partial- and full-thickness wounds. This study analyzes the cellular response to PriMatrix in vivo, as well as the ability of this matrix to facilitate normal tissue regeneration. Methods. Five by five mm squares of rehydrated PriMatrix were implanted in a subcutaneous fashion on the dorsum of wild-type mice. Implant site tissue was harvested for histology, immunohistochemistry (IHC), and flow cytometric analyses at multiple time points until day 28. Results. PriMatrix implants were found to go through a biological progression initiated by a transient infiltrate of inflammatory cells, followed by mesenchymal cell recruitment and vascular development. IHC analysis revealed that the majority of the implanted fetal dermal collagen fibers persisted through day 28 but underwent remodeling and cellular repopulation to form tissue with a density and morphology consistent with healthy dermis. Conclusions. PriMatrix implants undergo progressive in vivo remodeling, facilitating the regeneration of histologically normal tissue through a mild inflammatory and progenitor cell response. Regeneration of normal tissue is especially important in a wound environment, and these findings warrant further investigation of PriMatrix in this setting.

Mapping of Mechanical Strains and Stresses around Quiescent Engineered Three-Dimensional Epithelial Tissues

PubMed Central

Gjorevski, Nikolce; Nelson, Celeste M.

2012-01-01

Understanding how physical signals guide biological processes requires qualitative and quantitative knowledge of the mechanical forces generated and sensed by cells in a physiologically realistic three-dimensional (3D) context. Here, we used computational modeling and engineered epithelial tissues of precise geometry to define the experimental parameters that are required to measure directly the mechanical stress profile of 3D tissues embedded within native type I collagen. We found that to calculate the stresses accurately in these settings, we had to account for mechanical heterogeneities within the matrix, which we visualized and quantified using confocal reflectance and atomic force microscopy. Using this technique, we were able to obtain traction forces at the epithelium-matrix interface, and to resolve and quantify patterns of mechanical stress throughout the surrounding matrix. We discovered that whereas single cells generate tension by contracting and pulling on the matrix, the contraction of multicellular tissues can also push against the matrix, causing emergent compression. Furthermore, tissue geometry defines the spatial distribution of mechanical stress across the epithelium, which communicates mechanically over distances spanning hundreds of micrometers. Spatially resolved mechanical maps can provide insight into the types and magnitudes of physical parameters that are sensed and interpreted by multicellular tissues during normal and pathological processes. PMID:22828342

Peptide assemblies: from cell scaffolds to immune adjuvants

NASA Astrophysics Data System (ADS)

Collier, Joel

2011-03-01

This talk will discuss two interrelated aspects of peptide self-assemblies in biological applications: their use as matrices for regenerative medicine, and their use as chemically defined adjuvants for directing immune responses against engineered antigens. In the first half of the presentation, the design of peptide self-assemblies as analogues for the extracellular matrix will be described, with a focus on self-assemblies displaying multiple different cell-binding peptides. We conducted multi-factorial investigations of peptide co-assemblies containing several different ligand-bearing peptides using statistical ``design of experiments'' (DoE). Using the DoE techniques of factorial experimentation and response surface modeling, we systematically explored how precise combinations of ligand-bearing peptides modulated endothelial cell growth, in the process finding interactions between ligands not previously appreciated. By investigating immune responses against the materials intended for tissue engineering applications, we discovered that the basic self-assembling peptides were minimally immunogenic or non-immunogenic, even when delivered in strong adjuvants. -But when they were appended to an appropriately restricted epitope peptide, these materials raised strong and persistent antibody responses. These responses were dependent on covalent conjugation between the epitope and self-assembling domains of the peptides, were mediated by T cells, and could be directed towards both peptide epitopes and conjugated protein antigens. In addition to their demonstrated utility as scaffolds for regenerative medicine, peptide self-assemblies may also be useful as chemically defined adjuvants for vaccines and immunotherapies. This work was funded by NIH/NIDCR (1 R21 DE017703-03), NIH/NIBIB (1 R01 EB009701-01), and NSF (CHE-0802286).

Temperature dependent nonlinear metal matrix laminae behavior

NASA Technical Reports Server (NTRS)

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

1986-01-01

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

A local complement response by RPE causes early-stage macular degeneration

PubMed Central

Fernandez-Godino, Rosario; Garland, Donita L.; Pierce, Eric A.

2015-01-01

Inherited and age-related macular degenerations (AMDs) are important causes of vision loss. An early hallmark of these disorders is the formation of sub-retinal pigment epithelium (RPE) basal deposits. A role for the complement system in MDs was suggested by genetic association studies, but direct functional connections between alterations in the complement system and the pathogenesis of MD remain to be defined. We used primary RPE cells from a mouse model of inherited MD due to a p.R345W mutation in EGF-containing fibulin-like extracellular matrix protein 1 (EFEMP1) to investigate the role of the RPE in early MD pathogenesis. Efemp1R345W RPE cells recapitulate the basal deposit formation observed in vivo by producing sub-RPE deposits in vitro. The deposits share features with basal deposits, and their formation was mediated by EFEMP1R345W or complement component 3a (C3a), but not by complement component 5a (C5a). Increased activation of complement appears to occur in response to an abnormal extracellular matrix (ECM), generated by the mutant EFEMP1R345W protein and reduced ECM turnover due to inhibition of matrix metalloproteinase 2 by EFEMP1R345W and C3a. Increased production of C3a also stimulated the release of cytokines such as interleukin (IL)-6 and IL-1B, which appear to have a role in deposit formation, albeit downstream of C3a. These studies provide the first direct indication that complement components produced locally by the RPE are involved in the formation of basal deposits. Furthermore, these results suggest that C3a generated by RPE is a potential therapeutic target for the treatment of EFEMP1-associated MD as well as AMD. PMID:26199322

Axisymmetric micromechanics of elastic-perfectly plastic fibrous composites under uniaxial tension loading

NASA Technical Reports Server (NTRS)

Lee, Jong-Won; Allen, David H.

1993-01-01

The uniaxial response of a continuous fiber elastic-perfectly plastic composite is modeled herein as a two-element composite cylinder. An axisymmetric analytical micromechanics solution is obtained for the rate-independent elastic-plastic response of the two-element composite cylinder subjected to tensile loading in the fiber direction for the case wherein the core fiber is assumed to be a transversely isotropic elastic-plastic material obeying the Tsai-Hill yield criterion, with yielding simulating fiber failure. The matrix is assumed to be an isotropic elastic-plastic material obeying the Tresca yield criterion. It is found that there are three different circumstances that depend on the fiber and matrix properties: fiber yield, followed by matrix yielding; complete matrix yield, followed by fiber yielding; and partial matrix yield, followed by fiber yielding, followed by complete matrix yield. The order in which these phenomena occur is shown to have a pronounced effect on the predicted uniaxial effective composite response.

Detecting and Responding to a Dengue Outbreak: Evaluation of Existing Strategies in Country Outbreak Response Planning

PubMed Central

Kroeger, Axel; Runge-Ranzinger, Silvia; O'Dempsey, Tim

2013-01-01

Background. Dengue outbreaks are occurring with increasing frequency and intensity. Evidence-based epidemic preparedness and effective response are now a matter of urgency. Therefore, we have analysed national and municipal dengue outbreak response plans. Methods. Thirteen country plans from Asia, Latin America and Australia, and one international plan were obtained from the World Health Organization. The information was transferred to a data analysis matrix where information was extracted according to predefined and emerging themes and analysed for scope, inconsistencies, omissions, and usefulness. Findings. Outbreak response planning currently has a considerable number of flaws. Outbreak governance was weak with a lack of clarity of stakeholder roles. Late timing of responses due to poor surveillance, a lack of combining routine data with additional alerts, and lack of triggers for initiating the response weakened the functionality of plans. Frequently an outbreak was not defined, and early response mechanisms based on alert signals were neglected. There was a distinct lack of consideration of contextual influences which can affect how an outbreak detection and response is managed. Conclusion. A model contingency plan for dengue outbreak prediction, detection, and response may help national disease control authorities to develop their own more detailed and functional context specific plans. PMID:24222774

Wood composites

Treesearch

Lars Berglund; Roger M. Rowell

2005-01-01

A composite can be defined as two or more elements held together by a matrix. By this definition, what we call “solid wood” is a composite. Solid wood is a three-dimensional composite composed of cellulose, hemicelluloses and lignin (with smaller amounts of inorganics and extractives), held together by a lignin matrix. The advantages of developing wood composites are (...

Modeling and parameter identification of impulse response matrix of mechanical systems

NASA Astrophysics Data System (ADS)

Bordatchev, Evgueni V.

1998-12-01

A method for studying the problem of modeling, identification and analysis of mechanical system dynamic characteristic in view of the impulse response matrix for the purpose of adaptive control is developed here. Two types of the impulse response matrices are considered: (i) on displacement, which describes the space-coupled relationship between vectors of the force and simulated displacement, which describes the space-coupled relationship between vectors of the force and simulated displacement and (ii) on acceleration, which also describes the space-coupled relationship between the vectors of the force and measured acceleration. The idea of identification consists of: (a) the practical obtaining of the impulse response matrix on acceleration by 'impact-response' technique; (b) the modeling and parameter estimation of the each impulse response function on acceleration through the fundamental representation of the impulse response function on displacement as a sum of the damped sine curves applying linear and non-linear least square methods; (c) simulating the impulse provides the additional possibility to calculate masses, damper and spring constants. The damped natural frequencies are used as a priori information and are found through the standard FFT analysis. The problem of double numerical integration is avoided by taking two derivations of the fundamental dynamic model of a mechanical system as linear combination of the mass-damper-spring subsystems. The identified impulse response matrix on displacement represents the dynamic properties of the mechanical system. From the engineering point of view, this matrix can be also understood as a 'dynamic passport' of the mechanical system and can be used for dynamic certification and analysis of the dynamic quality. In addition, the suggested approach mathematically reproduces amplitude-frequency response matrix in a low-frequency band and on zero frequency. This allows the possibility of determining the matrix of the static stiffness due to dynamic testing over the time of 10- 15 minutes. As a practical example, the dynamic properties in view of the impulse and frequency response matrices of the lathe spindle are obtained, identified and investigated. The developed approach for modeling and parameter identification appears promising for a wide range o industrial applications; for example, rotary systems.

Describing Self-Care Self-Efficacy: Definition, Measurement, Outcomes, and Implications.

PubMed

Eller, Lucille S; Lev, Elise L; Yuan, Changrong; Watkins, Ann Vreeland

2018-01-01

The pragmatic utility method of concept analysis was used to explore the usefulness of the concept self-care self-efficacy. Empirical studies across disciplines published between 1996 and 2015 were used as data. A data matrix was developed. Analytical questions and responses were derived from the data to understand patterns, develop new knowledge and achieve synthesis. Usefulness of the concept is contingent on how it is defined and measured. Self-care self-efficacy is associated with performance of self-care activities and positive health outcomes in diverse populations. Research can guide development of targeted interventions to increase patients' self-care self-efficacy, thus reducing costs, and assisting people to achieve optimal health. © 2016 NANDA International, Inc.

Quantifiable Assessment of SWNT Dispersion in Polymer Composites

NASA Technical Reports Server (NTRS)

Park, Cheol; Kim, Jae-Woo; Wise, Kristopher E.; Working, Dennis; Siochi, Mia; Harrison, Joycelyn; Gibbons, Luke; Siochi, Emilie J.; Lillehei, Peter T.; Cantrell, Sean;

Computer access security code system

NASA Technical Reports Server (NTRS)

Collins, Earl R., Jr. (Inventor)

1990-01-01

A security code system for controlling access to computer and computer-controlled entry situations comprises a plurality of subsets of alpha-numeric characters disposed in random order in matrices of at least two dimensions forming theoretical rectangles, cubes, etc., such that when access is desired, at least one pair of previously unused character subsets not found in the same row or column of the matrix is chosen at random and transmitted by the computer. The proper response to gain access is transmittal of subsets which complete the rectangle, and/or a parallelepiped whose opposite corners were defined by first groups of code. Once used, subsets are not used again to absolutely defeat unauthorized access by eavesdropping, and the like.

Dynamic Reciprocity in the Wound Microenvironment

PubMed Central

Schultz, Gregory S.; Davidson, Jeffrey M.; Kirsner, Robert S.; Bornstein, Paul; Herman, Ira M.

2011-01-01

Here, we define dynamic reciprocity (DR) as an ongoing, bidirectional interaction amongst cells and their surrounding microenvironment. In the review, we posit that DR is especially meaningful during wound healing as the DR-driven biochemical, biophysical and cellular responses to injury play pivotal roles in regulating tissue regenerative responses. Such cell-extracellular matrix interactions not only guide and regulate cellular morphology, but cellular differentiation, migration, proliferation, and survival during tissue development, including e.g. embryogenesis, angiogenesis, as well as during pathologic processes including cancer diabetes, hypertension and chronic wound healing. Herein, we examine DR within the wound microenvironment while considering specific examples across acute and chronic wound healing. This review also considers how a number of hypotheses that attempt to explain chronic wound pathophysiology, which may be understood within the DR framework. The implications of applying the principles of dynamic reciprocity to optimize wound care practice and future development of innovative wound healing therapeutics are also briefly considered. PMID:21362080

Diagnosis of middle atmosphere chemistry-dynamics interactions

NASA Astrophysics Data System (ADS)

Zhu, X.; Swartz, W. H.; Garcia, R. R.; Chartier, A.; Yee, J. H.; Yue, J.

2017-12-01

We apply the recently developed middle atmosphere climate feedback-response analysis method (MCFRAM) to diagnosing the temperature variations associated with chemistry-dynamics interactions in the middle atmosphere. By using output fields from the Whole Atmosphere Community Climate Model (WACCM) coupled with the measurements, we identify and isolate the distinctive characteristics of different components in the observed temperature variations. Both the temperature trends associated with the anthropogenic forcing and temperature changes associated with natural and internal feedback processes are quantified based on MCFRAM defined partial temperature changes corresponding to localized radiative heating, non-localized chemical heating, eddy transport, and transport by the mean meridional circulation of energy and chemical species. In addition, the temperature responses to variations of CO2, O3, and solar flux have distinctly different spatial structures that can be systematically categorized by the eigenmodes of the generalized damping matrix derived from MCFRAM.

Responsibility modulates pain-matrix activation elicited by the expressions of others in pain

PubMed Central

Cui, Fang; Abdelgabar, Abdel-Rahman; Keysers, Christian; Gazzola, Valeria

2015-01-01

Here we examine whether brain responses to dynamic facial expressions of pain are influenced by our responsibility for the observed pain. Participants played a flanker task with a confederate. Whenever either erred, the confederate was seen to receive a noxious shock. Using functional magnetic resonance imaging, we found that regions of the functionally localized pain-matrix of the participants (the anterior insula in particular) were activated most strongly when seeing the confederate receive a noxious shock when only the participant had erred (and hence had full responsibility). When both or only the confederate had erred (i.e. participant's shared or no responsibility), significantly weaker vicarious pain-matrix activations were measured. PMID:25800210

On the Theory of Reactive Mixtures for Modeling Biological Growth

PubMed Central

Ateshian, Gerard A.

2013-01-01

Mixture theory, which can combine continuum theories for the motion and deformation of solids and fluids with general principles of chemistry, is well suited for modeling the complex responses of biological tissues, including tissue growth and remodeling, tissue engineering, mechanobiology of cells and a variety of other active processes. A comprehensive presentation of the equations of reactive mixtures of charged solid and fluid constituents is lacking in the biomechanics literature. This study provides the conservation laws and entropy inequality, as well as interface jump conditions, for reactive mixtures consisting of a constrained solid mixture and multiple fluid constituents. The constituents are intrinsically incompressible and may carry an electrical charge. The interface jump condition on the mass flux of individual constituents is shown to define a surface growth equation, which predicts deposition or removal of material points from the solid matrix, complementing the description of volume growth described by the conservation of mass. A formu-lation is proposed for the reference configuration of a body whose material point set varies with time. State variables are defined which can account for solid matrix volume growth and remodeling. Constitutive constraints are provided on the stresses and momentum supplies of the various constituents, as well as the interface jump conditions for the electrochem cal potential of the fluids. Simplifications appropriate for biological tissues are also proposed, which help reduce the governing equations into a more practical format. It is shown that explicit mechanisms of growth-induced residual stresses can be predicted in this framework. PMID:17206407

Simulation of the neutron response matrix of an EJ309 liquid scintillator

NASA Astrophysics Data System (ADS)

Bai, Huaiyong; Wang, Zhimin; Zhang, Luyu; Jiang, Haoyu; Lu, Yi; Chen, Jinxiang; Zhang, Guohui

2018-04-01

The neutron response matrix is the basis for measuring the neutron energy spectrum through unfolding the pulse height spectrum detected with a liquid scintillator. Based on the light output of the EJ309 liquid scintillator and the related reaction cross sections, a Monte Carlo code is developed to obtain the neutron response matrix. The effects of the related reactions, the contributions of different number of neutron interactions and the wall effect of the recoil proton are discussed. With the obtained neutron response matrix and the GRAVEL iterative unfolding method, the neutron energy spectra of the 252Cf and the 241AmBe neutron sources are measured, and the results are respectively compared with the theoretical prediction of the 252Cf neutron energy spectrum and the previous results of the 241AmBe neutron energy spectra.

A major protein component of the Bacillus subtilis biofilm matrix.

PubMed

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

2006-02-01

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

Defined Engineered Human Myocardium with Advanced Maturation for Applications in Heart Failure Modelling and Repair

PubMed Central

Tiburcy, Malte; Hudson, James E.; Balfanz, Paul; Schlick, Susanne; Meyer, Tim; Liao, Mei-Ling Chang; Levent, Elif; Raad, Farah; Zeidler, Sebastian; Wingender, Edgar; Riegler, Johannes; Wang, Mouer; Gold, Joseph D.; Kehat, Izhak; Wettwer, Erich; Ravens, Ursula; Dierickx, Pieterjan; van Laake, Linda W.; Goumans, Marie Jose; Khadjeh, Sara; Toischer, Karl; Hasenfuss, Gerd; Couture, Larry A.; Unger, Andreas; Linke, Wolfgang A.; Araki, Toshiyuki; Neel, Benjamin; Keller, Gordon; Gepstein, Lior; Wu, Joseph C.; Zimmermann, Wolfram-Hubertus

2017-01-01

Background Advancing structural and functional maturation of stem cell-derived cardiomyocytes remains a key challenge for applications in disease modelling, drug screening, and heart repair. Here, we sought to advance cardiomyocyte maturation in engineered human myocardium (EHM) towards an adult phenotype under defined conditions. Methods We systematically investigated cell composition, matrix and media conditions to generate EHM from embryonic and induced pluripotent stem cell-derived cardiomyocytes and fibroblasts with organotypic functionality under serum-free conditions. We employed morphological, functional, and transcriptome analyses to benchmark maturation of EHM. Results EHM demonstrated important structural and functional properties of postnatal myocardium, including: (1) rod-shaped cardiomyocytes with M-bands assembled as a functional syncytium; (2) systolic twitch forces at a similar level as observed in bona fide postnatal myocardium; (3) a positive force-frequency-response; (4) inotropic responses to β-adrenergic stimulation mediated via canonical β1- and β2-adrenoceptor signaling pathways; and (5) evidence for advanced molecular maturation by transcriptome profiling. EHM responded to chronic catecholamine toxicity with contractile dysfunction, cardiomyocyte hypertrophy, cardiomyocyte death, and NT-proBNP release; all are classical hallmarks of heart failure. Additionally, we demonstrate scalability of EHM according to anticipated clinical demands for cardiac repair. Conclusions We provide proof-of-concept for a universally applicable technology for the engineering of macro-scale human myocardium for disease modelling and heart repair from embryonic and induced pluripotent stem cell-derived cardiomyocytes under defined, serum-free conditions. PMID:28167635

Defined Engineered Human Myocardium With Advanced Maturation for Applications in Heart Failure Modeling and Repair.

PubMed

Tiburcy, Malte; Hudson, James E; Balfanz, Paul; Schlick, Susanne; Meyer, Tim; Chang Liao, Mei-Ling; Levent, Elif; Raad, Farah; Zeidler, Sebastian; Wingender, Edgar; Riegler, Johannes; Wang, Mouer; Gold, Joseph D; Kehat, Izhak; Wettwer, Erich; Ravens, Ursula; Dierickx, Pieterjan; van Laake, Linda W; Goumans, Marie Jose; Khadjeh, Sara; Toischer, Karl; Hasenfuss, Gerd; Couture, Larry A; Unger, Andreas; Linke, Wolfgang A; Araki, Toshiyuki; Neel, Benjamin; Keller, Gordon; Gepstein, Lior; Wu, Joseph C; Zimmermann, Wolfram-Hubertus

2017-05-09

Advancing structural and functional maturation of stem cell-derived cardiomyocytes remains a key challenge for applications in disease modeling, drug screening, and heart repair. Here, we sought to advance cardiomyocyte maturation in engineered human myocardium (EHM) toward an adult phenotype under defined conditions. We systematically investigated cell composition, matrix, and media conditions to generate EHM from embryonic and induced pluripotent stem cell-derived cardiomyocytes and fibroblasts with organotypic functionality under serum-free conditions. We used morphological, functional, and transcriptome analyses to benchmark maturation of EHM. EHM demonstrated important structural and functional properties of postnatal myocardium, including: (1) rod-shaped cardiomyocytes with M bands assembled as a functional syncytium; (2) systolic twitch forces at a similar level as observed in bona fide postnatal myocardium; (3) a positive force-frequency response; (4) inotropic responses to β-adrenergic stimulation mediated via canonical β 1 - and β 2 -adrenoceptor signaling pathways; and (5) evidence for advanced molecular maturation by transcriptome profiling. EHM responded to chronic catecholamine toxicity with contractile dysfunction, cardiomyocyte hypertrophy, cardiomyocyte death, and N-terminal pro B-type natriuretic peptide release; all are classical hallmarks of heart failure. In addition, we demonstrate the scalability of EHM according to anticipated clinical demands for cardiac repair. We provide proof-of-concept for a universally applicable technology for the engineering of macroscale human myocardium for disease modeling and heart repair from embryonic and induced pluripotent stem cell-derived cardiomyocytes under defined, serum-free conditions. © 2017 American Heart Association, Inc.

Thermo- and pH-responsive polymer brushes-grafted gigaporous polystyrene microspheres as a high-speed protein chromatography matrix.

PubMed

Qu, Jian-Bo; Xu, Yu-Liang; Liu, Jun-Yi; Zeng, Jing-Bin; Chen, Yan-Li; Zhou, Wei-Qing; Liu, Jian-Guo

2016-04-08

Dual thermo- and pH-responsive chromatography has been proposed using poly(N-isopropylacrylamide-co-butyl methacrylate-co-N,N-dimethylaminopropyl acrylamide) (P(NIPAM-co-BMA-co-DMAPAAM)) brushes grafted gigaporous polystyrene microspheres (GPM) as matrix. Atom transfer radical polymerization (ATRP) initiator was first coupled onto GPM through Friedel-Crafts acylation with 2-bromoisobutyryl bromide. The dual-responsive polymer brushes were then grafted onto GPM via surface-initiated ATRP. The surface composition, gigaporous structure, protein adsorption and dual-responsive chromatographic properties of the matrix (GPM-P(NIPAM-co-BMA-co-DMAPAAM) were characterized in detail. Results showed that GPM were successfully grafted with thermoresponsive cationic polymer brushes and that the gigaporous structure was well maintained. A column packed with GPM-P(NIPAM-co-BMA-co-DMAPAAM presented low backpressure, good permeability and appreciable thermo-responsibility. By changing pH of the mobile phase and temperature of the column in turn, the column can separate three model proteins at the mobile phase velocity up to 2528cmh(-1). A separation mechanism of this matrix was also proposed. All results indicate that the dual thermo- and pH-responsive chromatography matrix has great potentials in 'green' high-speed protein chromatography. Copyright © 2016 Elsevier B.V. All rights reserved.

Dynamically Tunable Cell Culture Platforms for Tissue Engineering and Mechanobiology

PubMed Central

Uto, Koichiro; Tsui, Jonathan H.; DeForest, Cole A.; Kim, Deok-Ho

2016-01-01

Human tissues are sophisticated ensembles of many distinct cell types embedded in the complex, but well-defined, structures of the extracellular matrix (ECM). Dynamic biochemical, physicochemical, and mechano-structural changes in the ECM define and regulate tissue-specific cell behaviors. To recapitulate this complex environment in vitro, dynamic polymer-based biomaterials have emerged as powerful tools to probe and direct active changes in cell function. The rapid evolution of polymerization chemistries, structural modulation, and processing technologies, as well as the incorporation of stimuli-responsiveness, now permit synthetic microenvironments to capture much of the dynamic complexity of native tissue. These platforms are comprised not only of natural polymers chemically and molecularly similar to ECM, but those fully synthetic in origin. Here, we review recent in vitro efforts to mimic the dynamic microenvironment comprising native tissue ECM from the viewpoint of material design. We also discuss how these dynamic polymer-based biomaterials are being used in fundamental cell mechanobiology studies, as well as towards efforts in tissue engineering and regenerative medicine. PMID:28522885

A robust computational technique for model order reduction of two-time-scale discrete systems via genetic algorithms.

PubMed

Alsmadi, Othman M K; Abo-Hammour, Zaer S

2015-01-01

A robust computational technique for model order reduction (MOR) of multi-time-scale discrete systems (single input single output (SISO) and multi-input multioutput (MIMO)) is presented in this paper. This work is motivated by the singular perturbation of multi-time-scale systems where some specific dynamics may not have significant influence on the overall system behavior. The new approach is proposed using genetic algorithms (GA) with the advantage of obtaining a reduced order model, maintaining the exact dominant dynamics in the reduced order, and minimizing the steady state error. The reduction process is performed by obtaining an upper triangular transformed matrix of the system state matrix defined in state space representation along with the elements of B, C, and D matrices. The GA computational procedure is based on maximizing the fitness function corresponding to the response deviation between the full and reduced order models. The proposed computational intelligence MOR method is compared to recently published work on MOR techniques where simulation results show the potential and advantages of the new approach.

Delamination micromechanics analysis

NASA Technical Reports Server (NTRS)

Adams, D. F.; Mahishi, J. M.

1985-01-01

A three-dimensional finite element analysis was developed which includes elastoplastic, orthotropic material response, and fracture initiation and propagation. Energy absorption due to physical failure processes characteristic of the heterogeneous and anisotropic nature of composite materials is modeled. A local energy release rate in the presence of plasticity was defined and used as a criterion to predict the onset and growth of cracks in both micromechanics and macromechanics analyses. This crack growth simulation technique is based upon a virtual crack extension method. A three-dimensional finite element micromechanics model is used to study the effects of broken fibers, cracked matrix and fiber-matrix debond on the fracture toughness of the unidirectional composite. The energy release rates at the onset of unstable crack growth in the micromechanics analyses are used as critical energy release rates in the macromechanics analysis. This integrated micromechanical and macromechanical fracture criterion is shown to be very effective in predicting the onset and growth of cracks in general multilayered composite laminates by applying the criterion to a single-edge notched graphite/epoxy laminate subjected to implane tension normal to the notch.

Geyser periodicity and the response of geysers to deformation

USGS Publications Warehouse

Ingebritsen, S.E.; Rojstaczer, S.A.

1996-01-01

Numerical simulations of multiphase fluid and heat transport through a porous medium define combinations of rock properties and boundary conditions which lead to geyser-like periodic discharge. Within the rather narrow range of conditions that allow geyser-like behavior, eruption frequency and discharge are highly sensitive to the intrinsic permeabilities of the geyser conduit and the surrounding rock matrix, to the relative permeability functions assumed, and to pressure gradients in the matrix. In theory, heats pipes (concomitant upward flow of steam and downward flow of liquid) can exist under similar conditions, but our simulations suggest that the periodic solution is more stable. Simulated time series of geyser discharge are chaotic, but integrated quantities such as eruption frequency and mass discharge per eruption are free of chaos. These results may explain the observed sensitivity of natural geysers to small strains such as those caused by remote earthquakes, if ground motion is sufficient to induce permeability changes. Changes in geyser behavior caused by minor preseismic deformation, periodic surface loading, and Earth tides are more difficult to explain in the context of our current model. Copyright 1996 by the American Geophysical Union.

Cytotoxicity screening of 23 engineered nanomaterials using a test matrix of ten cell lines and three different assays

PubMed Central

2011-01-01

Background Engineered nanomaterials display unique properties that may have impact on human health, and thus require a reliable evaluation of their potential toxicity. Here, we performed a standardized in vitro screening of 23 engineered nanomaterials. We thoroughly characterized the physicochemical properties of the nanomaterials and adapted three classical in vitro toxicity assays to eliminate nanomaterial interference. Nanomaterial toxicity was assessed in ten representative cell lines. Results Six nanomaterials induced oxidative cell stress while only a single nanomaterial reduced cellular metabolic activity and none of the particles affected cell viability. Results from heterogeneous and chemically identical particles suggested that surface chemistry, surface coating and chemical composition are likely determinants of nanomaterial toxicity. Individual cell lines differed significantly in their response, dependent on the particle type and the toxicity endpoint measured. Conclusion In vitro toxicity of the analyzed engineered nanomaterials cannot be attributed to a defined physicochemical property. Therefore, the accurate identification of nanomaterial cytotoxicity requires a matrix based on a set of sensitive cell lines and in vitro assays measuring different cytotoxicity endpoints. PMID:21345205

Unexpected role of the IMD pathway in Drosophila gut defense against Staphylococcus aureus.

PubMed

Hori, Aki; Kurata, Shoichiro; Kuraishi, Takayuki

2018-01-01

In this study, fruit fly of the genus Drosophila is utilized as a suitable model animal to investigate the molecular mechanisms of innate immunity. To combat orally transmitted pathogenic Gram-negative bacteria, the Drosophila gut is armed with the peritrophic matrix, which is a physical barrier composed of chitin and glycoproteins: the Duox system that produces reactive oxygen species (ROS), which in turn sterilize infected microbes, and the IMD pathway that regulates the expression of antimicrobial peptides (AMPs), which in turn control ROS-resistant pathogens. However, little is known about the defense mechanisms against Gram-positive bacteria in the fly gut. Here, we show that the peritrophic matrix protects Drosophila against Gram-positive bacteria S. aureus. We also define the few roles of ROS in response to the infection and show that the IMD pathway is required for the clearance of ingested microbes, possibly independently from AMP expression. These findings provide a new aspect of the gut defense system of Drosophila, and helps to elucidate the processes of gut-microbe symbiosis and pathogenesis. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Generalized Reich-Moore R-matrix approximation

NASA Astrophysics Data System (ADS)

Arbanas, Goran; Sobes, Vladimir; Holcomb, Andrew; Ducru, Pablo; Pigni, Marco; Wiarda, Dorothea

2017-09-01

A conventional Reich-Moore approximation (RMA) of R-matrix is generalized into a manifestly unitary form by introducing a set of resonant capture channels treated explicitly in a generalized, reduced R-matrix. A dramatic reduction of channel space witnessed in conventional RMA, from Nc × Nc full R-matrix to Np × Np reduced R-matrix, where Nc = Np + Nγ, Np and Nγ denoting the number of particle and γ-ray channels, respectively, is due to Np < Nγ. A corresponding reduction of channel space in generalized RMA (GRMA) is from Nc × Nc full R-matrix to N × N, where N = Np + N, and where N is the number of capture channels defined in GRMA. We show that N = Nλ where Nλ is the number of R-matrix levels. This reduction in channel space, although not as dramatic as in the conventional RMA, could be significant for medium and heavy nuclides where N < Nγ. The resonant capture channels defined by GRMA accommodate level-level interference (via capture channels) neglected in conventional RMA. The expression for total capture cross section in GRMA is formally equal to that of the full Nc × NcR-matrix. This suggests that GRMA could yield improved nuclear data evaluations in the resolved resonance range at a cost of introducing N(N - 1)/2 resonant capture width parameters relative to conventional RMA. Manifest unitarity of GRMA justifies a method advocated by Fröhner and implemented in the SAMMY nuclear data evaluation code for enforcing unitarity of conventional RMA. Capture widths of GRMA are exactly convertible into alternative R-matrix parameters via Brune tranform. Application of idealized statistical methods to GRMA shows that variance among conventional RMA capture widths in extant RMA evaluations could be used to estimate variance among off-diagonal elements neglected by conventional RMA. Significant departure of capture widths from an idealized distribution may indicate the presence of underlying doorway states.

Uncertainty of relative sensitivity factors in glow discharge mass spectrometry

NASA Astrophysics Data System (ADS)

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

2017-10-01

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

Occupancy dynamics in a tropical bird community: unexpectedly high forest use by birds classified as non-forest species

USGS Publications Warehouse

Ruiz-Gutierrez, Viviana; Zipkin, Elise F.; Dhondt, Andre A.

2010-01-01

1. Worldwide loss of biodiversity necessitates a clear understanding of the factors driving population declines as well as informed predictions about which species and populations are at greatest risk. The biggest threat to the long-term persistence of populations is the reduction and changes in configuration of their natural habitat. 2. Inconsistencies have been noted in the responses of populations to the combined effects of habitat loss and fragmentation. These have been widely attributed to the effects of the matrix habitats in which remnant focal habitats are typically embedded. 3. We quantified the potential effects of the inter-patch matrix by estimating occupancy and colonization of forest and surrounding non-forest matrix (NF). We estimated species-specific parameters using a dynamic, multi-species hierarchical model on a bird community in southwestern Costa Rica. 4. Overall, we found higher probabilities of occupancy and colonization of forest relative to the NF across bird species, including those previously categorized as open habitat generalists not needing forest to persist. Forest dependency was a poor predictor of occupancy dynamics in our study region, largely predicting occupancy and colonization of only non-forest habitats. 5. Our results indicate that the protection of remnant forest habitats is key for the long-term persistence of all members of the bird community in this fragmented landscape, including species typically associated with open, non-forest habitats. 6.Synthesis and applications. We identified 39 bird species of conservation concern defined by having high estimates of forest occupancy, and low estimates of occupancy and colonization of non-forest. These species survive in forest but are unlikely to venture out into open, non-forested habitats, therefore, they are vulnerable to the effects of habitat loss and fragmentation. Our hierarchical community-level model can be used to estimate species-specific occupancy dynamics for focal and inter-patch matrix habitats to identify which species within a community are likely to be impacted most by habitat loss and fragmentation. This model can be applied to other taxa (i.e. amphibians, mammals and insects) to estimate species and community occurrence dynamics in response to current environmental conditions and to make predictions in response to future changes in habitat configurations.

Jones matrix polarization-correlation mapping of biological crystals networks

NASA Astrophysics Data System (ADS)

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

2017-08-01

It has been proposed the optical model of Jones-matrix description of mechanisms of optical anisotropy of polycrystalline films of human bile, namely optical activity and birefringence. The algorithm of reconstruction of distributions of parameters - optical rotation angles and phase shifts of the indicated anisotropy types has been elaborated. The objective criteria of differentiation of bile films taken from healthy donors and patients with cholelithiasis by means of statistic analysis of such distributions have been determined. The operational characteristics (sensitivity, specificity and accuracy) of Jones-matrix reconstruction method of optical anisotropy parameters were defined.

Fabrication of all-inorganic nanocrystal solids through matrix encapsulation of nanocrystal arrays.

PubMed

Kinder, Erich; Moroz, Pavel; Diederich, Geoffrey; Johnson, Alexa; Kirsanova, Maria; Nemchinov, Alexander; O'Connor, Timothy; Roth, Dan; Zamkov, Mikhail

2011-12-21

A general strategy for low-temperature processing of colloidal nanocrystals into all-inorganic films is reported. The present methodology goes beyond the traditional ligand-interlinking scheme and relies on encapsulation of morphologically defined nanocrystal arrays into a matrix of a wide-band gap semiconductor, which preserves optoelectronic properties of individual nanoparticles while rendering the nanocrystal film photoconductive. Fabricated solids exhibit excellent thermal stability, which is attributed to the heteroepitaxial structure of nanocrystal-matrix interfaces, and show compelling light-harvesting performance in prototype solar cells. © 2011 American Chemical Society

Development and application of a density dependent matrix ...

EPA Pesticide Factsheets

Ranging along the Atlantic coast from US Florida to the Maritime Provinces of Canada, the Atlantic killifish (Fundulus heteroclitus) is an important and well-studied model organism for understanding the effects of pollutants and other stressors in estuarine and marine ecosystems. Matrix population models are useful tools for ecological risk assessment because they integrate effects across the life cycle, provide a linkage between endpoints observed in the individual and ecological risk to the population as a whole, and project outcomes for many generations in the future. We developed a density dependent matrix population model for Atlantic killifish by modifying a model developed for fathead minnow (Pimephales promelas) that has proved to be extremely useful, e.g. to incorporate data from laboratory studies and project effects of endocrine disrupting chemicals. We developed a size-structured model (as opposed to one that is based upon developmental stages or age class structure) so that we could readily incorporate output from a Dynamic Energy Budget (DEB) model, currently under development. Due to a lack of sufficient data to accurately define killifish responses to density dependence, we tested a number of scenarios realistic for other fish species in order to demonstrate the outcome of including this ecologically important factor. We applied the model using published data for killifish exposed to dioxin-like compounds, and compared our results to those using

Due diligence in the characterization of matrix effects in a total IL-13 Singulex™ method.

PubMed

Fraser, Stephanie; Soderstrom, Catherine

2014-04-01

After obtaining her PhD in Cellular and Molecular biology from the University of Nevada, Reno, Stephanie has spent the last 15 years in the field of bioanalysis. She has held positions in academia, biotech, contract research and large pharma where she has managed ligand binding assay (discovery to Phase IIb clinical) and flow cytometry (preclinical) laboratories as well as taken the lead on implementing new/emergent technologies. Currently Stephanie leads Pfizer's Regulated Bioanalysis Ligand Binding Assay group, focusing on early clinical biomarker support. Interleukin (IL)-13, a Th2 cytokine, drives a range of physiological responses associated with the induction of allergic airway diseases and inflammatory bowel diseases. Analysis of IL-13 as a biomarker has provided insight into its role in disease mechanisms and progression. Serum IL-13 concentrations are often too low to be measured by standard enzyme-linked immunosorbent assay techniques, necessitating the implementation of a highly sensitive assay. Previously, the validation of a Singulex™ Erenna(®) assay for the quantitation of IL-13 was reported. Herein we describe refinement of this validation; defining the impact of matrix interference on the lower limit of quantification, adding spiked matrix QC samples, and extending endogenous IL-13 stability. A fit-for-purpose validation was conducted and the assay was used to support a Phase II clinical trial.

Predicting the shock compression response of heterogeneous powder mixtures

NASA Astrophysics Data System (ADS)

Fredenburg, D. A.; Thadhani, N. N.

2013-06-01

A model framework for predicting the dynamic shock-compression response of heterogeneous powder mixtures using readily obtained measurements from quasi-static tests is presented. Low-strain-rate compression data are first analyzed to determine the region of the bulk response over which particle rearrangement does not contribute to compaction. This region is then fit to determine the densification modulus of the mixture, σD, an newly defined parameter describing the resistance of the mixture to yielding. The measured densification modulus, reflective of the diverse yielding phenomena that occur at the meso-scale, is implemented into a rate-independent formulation of the P-α model, which is combined with an isobaric equation of state to predict the low and high stress dynamic compression response of heterogeneous powder mixtures. The framework is applied to two metal + metal-oxide (thermite) powder mixtures, and good agreement between the model and experiment is obtained for all mixtures at stresses near and above those required to reach full density. At lower stresses, rate-dependencies of the constituents, and specifically those of the matrix constituent, determine the ability of the model to predict the measured response in the incomplete compaction regime.

Electron-shuttling antibiotics structure bacterial communities by modulating cellular levels of c-di-GMP

PubMed Central

Okegbe, Chinweike; Fields, Blanche L.; Cole, Stephanie J.; Beierschmitt, Christopher; Morgan, Chase J.; Price-Whelan, Alexa; Stewart, Richard C.; Lee, Vincent T.; Dietrich, Lars E. P.

2017-01-01

Diverse organisms secrete redox-active antibiotics, which can be used as extracellular electron shuttles by resistant microbes. Shuttle-mediated metabolism can support survival when substrates are available not locally but rather at a distance. Such conditions arise in multicellular communities, where the formation of chemical gradients leads to resource limitation for cells at depth. In the pathogenic bacterium Pseudomonas aeruginosa PA14, antibiotics called phenazines act as oxidants to balance the intracellular redox state of cells in anoxic biofilm subzones. PA14 colony biofilms show a profound morphogenic response to phenazines resulting from electron acceptor-dependent inhibition of ECM production. This effect is reminiscent of the developmental responses of some eukaryotic systems to redox control, but for bacterial systems its mechanistic basis has not been well defined. Here, we identify the regulatory protein RmcA and show that it links redox conditions to PA14 colony morphogenesis by modulating levels of bis-(3′,5′)-cyclic-dimeric-guanosine (c-di-GMP), a second messenger that stimulates matrix production, in response to phenazine availability. RmcA contains four Per-Arnt-Sim (PAS) domains and domains with the potential to catalyze the synthesis and degradation of c-di-GMP. Our results suggest that phenazine production modulates RmcA activity such that the protein degrades c-di-GMP and thereby inhibits matrix production during oxidizing conditions. RmcA thus forms a mechanistic link between cellular redox sensing and community morphogenesis analogous to the functions performed by PAS-domain–containing regulatory proteins found in complex eukaryotes. PMID:28607054

Inelastic response of metal matrix composites under biaxial loading

NASA Technical Reports Server (NTRS)

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

1991-01-01

Theoretical predictions and experimental results were obtained for inelastic response of unidirectional and angle ply composite tubes subjected to axial and torsional loading. The composite material consist of silicon carbide fibers in a titanium alloy matrix. This material is known to be susceptible to fiber matrix interfacial damage. A method to distinguish between matrix yielding and fiber matrix interfacial damage is suggested. Biaxial tests were conducted on the two different layup configurations using an MTS Axial/Torsional load frame with a PC based data acquisition system. The experimentally determined elastic moduli of the SiC/Ti system are compared with those predicted by a micromechanics model. The test results indicate that fiber matrix interfacial damage occurs at relatively low load levels and is a local phenomenon. The micromechanics model used is the method of cells originally proposed by Aboudi. Finite element models using the ABACUS finite element program were used to study end effects and fixture specimen interactions. The results to date have shown good correlation between theory and experiment for response prior to damage initiation.

Matrix De Rham Complex and Quantum A-infinity algebras

NASA Astrophysics Data System (ADS)

Barannikov, S.

2014-04-01

I establish the relation of the non-commutative BV-formalism with super-invariant matrix integration. In particular, the non-commutative BV-equation, defining the quantum A ∞-algebras, introduced in Barannikov (Modular operads and non-commutative Batalin-Vilkovisky geometry. IMRN, vol. 2007, rnm075. Max Planck Institute for Mathematics 2006-48, 2007), is represented via de Rham differential acting on the supermatrix spaces related with Bernstein-Leites simple associative algebras with odd trace q( N), and gl( N| N). I also show that the matrix Lagrangians from Barannikov (Noncommutative Batalin-Vilkovisky geometry and matrix integrals. Isaac Newton Institute for Mathematical Sciences, Cambridge University, 2006) are represented by equivariantly closed differential forms.

Linking matrices in systems with periodic boundary conditions

NASA Astrophysics Data System (ADS)

Panagiotou, Eleni; Millett, Kenneth C.

2018-06-01

We study the linking matrix, a measure of entanglement for a collection of closed or open chains in 3-space based on the Gauss linking number. Periodic boundary conditions (PBC) are often used in the simulation of physical systems of filaments. To measure entanglement of closed or open chains in systems employing PBC we use the periodic linking matrix, based on the periodic linking number, defined in Panagiotou (2015 J. Comput. Phys. 300 533–73). We study the properties of the periodic linking matrix as a function of cell size. We provide analytical results concerning the eigenvalues of the periodic linking matrix and show that some of them are invariant of cell-size.

Non-Abelian integrable hierarchies: matrix biorthogonal polynomials and perturbations

NASA Astrophysics Data System (ADS)

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

2018-05-01

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

Quantum Markov chains

NASA Astrophysics Data System (ADS)

Gudder, Stanley

2008-07-01

A new approach to quantum Markov chains is presented. We first define a transition operation matrix (TOM) as a matrix whose entries are completely positive maps whose column sums form a quantum operation. A quantum Markov chain is defined to be a pair (G,E) where G is a directed graph and E =[Eij] is a TOM whose entry Eij labels the edge from vertex j to vertex i. We think of the vertices of G as sites that a quantum system can occupy and Eij is the transition operation from site j to site i in one time step. The discrete dynamics of the system is obtained by iterating the TOM E. We next consider a special type of TOM called a transition effect matrix. In this case, there are two types of dynamics, a state dynamics and an operator dynamics. Although these two types are not identical, they are statistically equivalent. We next give examples that illustrate various properties of quantum Markov chains. We conclude by showing that our formalism generalizes the usual framework for quantum random walks.

Plastic scintillator with effective pulse shape discrimination for neutron and gamma detection

DOEpatents

Zaitseva, Natalia P.; Carman, M Leslie; Cherepy, Nerine; Glenn, Andrew M.; Hamel, Sebastien; Payne, Stephen A.; Rupert, Benjamin L.

2016-04-12

In one embodiment, a scintillator material includes a polymer matrix; and a primary dye in the polymer matrix, the primary dye being a fluorescent dye, the primary dye being present in an amount of 5 wt % or more; wherein the scintillator material exhibits an optical response signature for neutrons that is different than an optical response signature for gamma rays. In another embodiment, a scintillator material includes a polymer matrix; and a primary dye in the polymer matrix, the primary dye being a fluorescent dye, the primary dye being present in an amount greater than 10 wt %.

An Initial Non-Equilibrium Porous-Media Model for CFD Simulation of Stirling Regenerators

NASA Technical Reports Server (NTRS)

Tew, Roy C.; Simon, Terry; Gedeon, David; Ibrahim, Mounir; Rong, Wei

2006-01-01

The objective of this paper is to define empirical parameters for an initial thermal non-equilibrium porous-media model for use in Computational Fluid Dynamics (CFD) codes for simulation of Stirling regenerators. The two codes currently used at Glenn Research Center for Stirling modeling are Fluent and CFD-ACE. The codes porous-media models are equilibrium models, which assume solid matrix and fluid are in thermal equilibrium. This is believed to be a poor assumption for Stirling regenerators; Stirling 1-D regenerator models, used in Stirling design, use non-equilibrium regenerator models and suggest regenerator matrix and gas average temperatures can differ by several degrees at a given axial location and time during the cycle. Experimentally based information was used to define: hydrodynamic dispersion, permeability, inertial coefficient, fluid effective thermal conductivity, and fluid-solid heat transfer coefficient. Solid effective thermal conductivity was also estimated. Determination of model parameters was based on planned use in a CFD model of Infinia's Stirling Technology Demonstration Converter (TDC), which uses a random-fiber regenerator matrix. Emphasis is on use of available data to define empirical parameters needed in a thermal non-equilibrium porous media model for Stirling regenerator simulation. Such a model has not yet been implemented by the authors or their associates.

Random walks with long-range steps generated by functions of Laplacian matrices

NASA Astrophysics Data System (ADS)

Riascos, A. P.; Michelitsch, T. M.; Collet, B. A.; Nowakowski, A. F.; Nicolleau, F. C. G. A.

2018-04-01

In this paper, we explore different Markovian random walk strategies on networks with transition probabilities between nodes defined in terms of functions of the Laplacian matrix. We generalize random walk strategies with local information in the Laplacian matrix, that describes the connections of a network, to a dynamic determined by functions of this matrix. The resulting processes are non-local allowing transitions of the random walker from one node to nodes beyond its nearest neighbors. We find that only two types of Laplacian functions are admissible with distinct behaviors for long-range steps in the infinite network limit: type (i) functions generate Brownian motions, type (ii) functions Lévy flights. For this asymptotic long-range step behavior only the lowest non-vanishing order of the Laplacian function is relevant, namely first order for type (i), and fractional order for type (ii) functions. In the first part, we discuss spectral properties of the Laplacian matrix and a series of relations that are maintained by a particular type of functions that allow to define random walks on any type of undirected connected networks. Once described general properties, we explore characteristics of random walk strategies that emerge from particular cases with functions defined in terms of exponentials, logarithms and powers of the Laplacian as well as relations of these dynamics with non-local strategies like Lévy flights and fractional transport. Finally, we analyze the global capacity of these random walk strategies to explore networks like lattices and trees and different types of random and complex networks.

A new response matrix for a 6LiI scintillator BSS system

NASA Astrophysics Data System (ADS)

Lacerda, M. A. S.; Méndez-Villafañe, R.; Lorente, A.; Ibañez, S.; Gallego, E.; Vega-Carrillo, H. R.

2017-10-01

A new response matrix was calculated for a Bonner Sphere Spectrometer (BSS) with a 6 LiI(Eu) scintillator, using the Monte Carlo N-Particle radiation transport code MCNPX. Responses were calculated for 6 spheres and the bare detector, for energies varying from 1.059E(-9) MeV to 105.9 MeV, with 20 equal-log(E)-width bins per energy decade, totalizing 221 energy groups. A comparison was done among the responses obtained in this work and other published elsewhere, for the same detector model. The calculated response functions were inserted in the response input file of the MAXED code and used to unfold the total and direct neutron spectra generated by the 241Am-Be source of the Universidad Politécnica de Madrid (UPM). These spectra were compared with those obtained using the same unfolding code with the Mares and Schraube matrix response.

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

NASA Technical Reports Server (NTRS)

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

2010-01-01

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

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

PubMed

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

2011-01-01

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

The structure of cell-matrix adhesions: the new frontier.

PubMed

Hanein, Dorit; Horwitz, Alan Rick

2012-02-01

Adhesions between the cell and the extracellular matrix (ECM) are mechanosensitive multi-protein assemblies that transmit force across the cell membrane and regulate biochemical signals in response to the chemical and mechanical environment. These combined functions in force transduction, signaling and mechanosensing contribute to cellular phenotypes that span development, homeostasis and disease. These adhesions form, mature and disassemble in response to actin organization and physical forces that originate from endogenous myosin activity or external forces by the extracellular matrix. Despite advances in our understanding of the protein composition, interactions and regulation, our understanding of matrix adhesion structure and organization, how forces affect this organization, and how these changes dictate specific signaling events is limited. Insights across multiple structural levels are acutely needed to elucidate adhesion structure and ultimately the molecular basis of signaling and mechanotransduction. Here we describe the challenges and recent advances and prospects for unraveling the structure of cell-matrix adhesions and their response to force. Copyright © 2011 Elsevier Ltd. All rights reserved.

Past matrix stiffness primes epithelial cells and regulates their future collective migration through a mechanical memory.

PubMed

Nasrollahi, Samila; Walter, Christopher; Loza, Andrew J; Schimizzi, Gregory V; Longmore, Gregory D; Pathak, Amit

2017-11-01

During morphogenesis and cancer metastasis, grouped cells migrate through tissues of dissimilar stiffness. Although the influence of matrix stiffness on cellular mechanosensitivity and motility are well-recognized, it remains unknown whether these matrix-dependent cellular features persist after cells move to a new microenvironment. Here, we interrogate whether priming of epithelial cells by a given matrix stiffness influences their future collective migration on a different matrix - a property we refer to as the 'mechanical memory' of migratory cells. To prime cells on a defined matrix and track their collective migration onto an adjoining secondary matrix of dissimilar stiffness, we develop a modular polyacrylamide substrate through step-by-step polymerization of different PA compositions. We report that epithelial cells primed on a stiff matrix migrate faster, display higher actomyosin expression, form larger focal adhesions, and retain nuclear YAP even after arriving onto a soft secondary matrix, as compared to their control behavior on a homogeneously soft matrix. Priming on a soft ECM causes a reverse effect. The depletion of YAP dramatically reduces this memory-dependent migration. Our results present a previously unidentified regulation of mechanosensitive collective cell migration by past matrix stiffness, in which mechanical memory depends on YAP activity. Copyright © 2017 Elsevier Ltd. All rights reserved.

Damping mathematical modelling and dynamic responses for FRP laminated composite plates with polymer matrix

NASA Astrophysics Data System (ADS)

Liu, Qimao

2018-02-01

This paper proposes an assumption that the fibre is elastic material and polymer matrix is viscoelastic material so that the energy dissipation depends only on the polymer matrix in dynamic response process. The damping force vectors in frequency and time domains, of FRP (Fibre-Reinforced Polymer matrix) laminated composite plates, are derived based on this assumption. The governing equations of FRP laminated composite plates are formulated in both frequency and time domains. The direct inversion method and direct time integration method for nonviscously damped systems are employed to solve the governing equations and achieve the dynamic responses in frequency and time domains, respectively. The computational procedure is given in detail. Finally, dynamic responses (frequency responses with nonzero and zero initial conditions, free vibration, forced vibrations with nonzero and zero initial conditions) of a FRP laminated composite plate are computed using the proposed methodology. The proposed methodology in this paper is easy to be inserted into the commercial finite element analysis software. The proposed assumption, based on the theory of material mechanics, needs to be further proved by experiment technique in the future.

The isothermal fatigue behavior of a unidirectional SiC/Ti composite and the Ti alloy matrix

NASA Technical Reports Server (NTRS)

Gayda, John, Jr.; Gabb, Timothy P.; Freed, Alan D.

1989-01-01

The high temperature fatigue behavior of a metal matrix composite (MMC) consisting of Ti-15V-3Cr-3Al-3Sn (Ti-15-3) matrix reinforced by 33 vol percent of continuous unidirectional SiC fibers was experimentally and analytically evaluated. Isothermal MMC fatigue tests with constant amplitude loading parallel to the fiber direction were performed at 300 and 550 C. Comparative fatigue tests of the Ti-15-3 matrix alloy were also conducted. Composite fatigue behavior and the in-situ stress state of the fiber and matrix were analyzed with a micromechanical model, the Concentric Cylinder Model (CCM). The cyclic stress-strain response of the composite was stable at 300 C. However, an increase in cyclic mean strain foreshortened MMC fatigue life at high strain ranges at 550 C. Fatigue tests of the matrix alloy and CCM analyses indicated this response was associated with stress relaxation of the matrix in the composite.

Understanding Key Mechanisms of Exercise-Induced Cardiac Protection to Mitigate Disease: Current Knowledge and Emerging Concepts.

PubMed

Bernardo, Bianca C; Ooi, Jenny Y Y; Weeks, Kate L; Patterson, Natalie L; McMullen, Julie R

2018-01-01

The benefits of exercise on the heart are well recognized, and clinical studies have demonstrated that exercise is an intervention that can improve cardiac function in heart failure patients. This has led to significant research into understanding the key mechanisms responsible for exercise-induced cardiac protection. Here, we summarize molecular mechanisms that regulate exercise-induced cardiac myocyte growth and proliferation. We discuss in detail the effects of exercise on other cardiac cells, organelles, and systems that have received less or little attention and require further investigation. This includes cardiac excitation and contraction, mitochondrial adaptations, cellular stress responses to promote survival (heat shock response, ubiquitin-proteasome system, autophagy-lysosomal system, endoplasmic reticulum unfolded protein response, DNA damage response), extracellular matrix, inflammatory response, and organ-to-organ crosstalk. We summarize therapeutic strategies targeting known regulators of exercise-induced protection and the challenges translating findings from bench to bedside. We conclude that technological advancements that allow for in-depth profiling of the genome, transcriptome, proteome and metabolome, combined with animal and human studies, provide new opportunities for comprehensively defining the signaling and regulatory aspects of cell/organelle functions that underpin the protective properties of exercise. This is likely to lead to the identification of novel biomarkers and therapeutic targets for heart disease.

Transverse thermal expansion of carbon fiber/epoxy matrix composites

NASA Technical Reports Server (NTRS)

Helmer, J. F.; Diefendorf, R. J.

1983-01-01

Thermal expansion coefficients and moduli of elasticity have been determined experimentally for a series of epoxy-matrix composites reinforced with carbon and Kevlar fibers. It is found that in the transverse direction the difference between the properties of the fiber and the matrix is not as pronounced as in the longitudinal direction, where the composite properties are fiber-dominated. Therefore, the pattern of fiber packing tends to affect transverse composite properties. The transverse properties of the composites tested are examined from the standpoint of the concept of homogeneity defined as the variation of packing (or lack thereof) throughout a sample.

Matrix addressable vertical cavity surface emitting laser array

NASA Astrophysics Data System (ADS)

Orenstein, M.; von Lehmen, A. C.; Chang-Hasnain, C.; Stoffel, N. G.; Harbison, J. P.

1991-02-01

The design, fabrication and characterization of 1024-element matrix-addressable vertical-cavity surface-emitting laser (VCSEL) arrays are described. A strained InGaAs quantum-well VCSEL structure was grown by MBE, and an array of 32 x 32 lasers was defined using a proton implantation process. A matrix addressing architecture was employed, which enables the individual addressing of each of the 1024 lasers using only 64 electrical contacts. All the lasers in the array, measured after the laser definition step, were operating with fairly homogeneous characteristics; threshold current of 6.8 mA and output quantum differential efficiency of about 8 percent.

The mecillinam resistome reveals a role for peptidoglycan endopeptidases in stimulating cell wall synthesis in Escherichia coli.

PubMed

Lai, Ghee Chuan; Cho, Hongbaek; Bernhardt, Thomas G

2017-07-01

Bacterial cells are typically surrounded by an net-like macromolecule called the cell wall constructed from the heteropolymer peptidoglycan (PG). Biogenesis of this matrix is the target of penicillin and related beta-lactams. These drugs inhibit the transpeptidase activity of PG synthases called penicillin-binding proteins (PBPs), preventing the crosslinking of nascent wall material into the existing network. The beta-lactam mecillinam specifically targets the PBP2 enzyme in the cell elongation machinery of Escherichia coli. Low-throughput selections for mecillinam resistance have historically been useful in defining mechanisms involved in cell wall biogenesis and the killing activity of beta-lactam antibiotics. Here, we used transposon-sequencing (Tn-Seq) as a high-throughput method to identify nearly all mecillinam resistance loci in the E. coli genome, providing a comprehensive resource for uncovering new mechanisms underlying PG assembly and drug resistance. Induction of the stringent response or the Rcs envelope stress response has been previously implicated in mecillinam resistance. We therefore also performed the Tn-Seq analysis in mutants defective for these responses in addition to wild-type cells. Thus, the utility of the dataset was greatly enhanced by determining the stress response dependence of each resistance locus in the resistome. Reasoning that stress response-independent resistance loci are those most likely to identify direct modulators of cell wall biogenesis, we focused our downstream analysis on this subset of the resistome. Characterization of one of these alleles led to the surprising discovery that the overproduction of endopeptidase enzymes that cleave crosslinks in the cell wall promotes mecillinam resistance by stimulating PG synthesis by a subset of PBPs. Our analysis of this activation mechanism suggests that, contrary to the prevailing view in the field, PG synthases and PG cleaving enzymes need not function in multi-enzyme complexes to expand the cell wall matrix.

Multiscale polarization diagnostics of birefringent networks in problems of necrotic changes diagnostics

NASA Astrophysics Data System (ADS)

Sakhnovskiy, M. Yu.; Ushenko, Yu. O.; Ushenko, V. O.; Besaha, R. N.; Pavlyukovich, N.; Pavlyukovich, O.

2018-01-01

The paper consists of two parts. The first part presents short theoretical basics of the method of azimuthally-invariant Mueller-matrix description of optical anisotropy of biological tissues. It was provided experimentally measured coordinate distributions of Mueller-matrix invariants (MMI) of linear and circular birefringences of skeletal muscle tissue. It was defined the values of statistic moments, which characterize the distributions of amplitudes of wavelet coefficients of MMI at different scales of scanning. The second part presents the data of statistic analysis of the distributions of amplitude of wavelet coefficients of the distributions of linear birefringence of myocardium tissue died after the infarction and ischemic heart disease. It was defined the objective criteria of differentiation of the cause of death.

Wavelet analysis of birefringence images of myocardium tissue

NASA Astrophysics Data System (ADS)

Sakhnovskiy, M. Yu.; Ushenko, Yu. O.; Kushnerik, L.; Soltys, I. V.; Pavlyukovich, N.; Pavlyukovich, O.

2018-01-01

The paper consists of two parts. The first part presents short theoretical basics of the method of azimuthally-invariant Mueller-matrix description of optical anisotropy of biological tissues. It was provided experimentally measured coordinate distributions of Mueller-matrix invariants (MMI) of linear and circular birefringences of skeletal muscle tissue. It was defined the values of statistic moments, which characterize the distributions of amplitudes of wavelet coefficients of MMI at different scales of scanning. The second part presents the data of statistic analysis of the distributions of amplitude of wavelet coefficients of the distributions of linear birefringence of myocardium tissue died after the infarction and ischemic heart disease. It was defined the objective criteria of differentiation of the cause of death.

Isolation and Identification of Proteins Secreted by Cells Cultured within Synthetic Hydrogel-Based Matrices

PubMed Central

2018-01-01

Cells interact with and remodel their microenvironment, degrading large extracellular matrix (ECM) proteins (e.g., fibronectin, collagens) and secreting new ECM proteins and small soluble factors (e.g., growth factors, cytokines). Synthetic mimics of the ECM have been developed as controlled cell culture platforms for use in both fundamental and applied studies. However, how cells broadly remodel these initially well-defined matrices remains poorly understood and difficult to probe. In this work, we have established methods for widely examining both large and small proteins that are secreted by cells within synthetic matrices. Specifically, human mesenchymal stem cells (hMSCs), a model primary cell type, were cultured within well-defined poly(ethylene glycol) (PEG)-peptide hydrogels, and these cell-matrix constructs were decellularized and degraded for subsequent isolation and analysis of deposited proteins. Shotgun proteomics using liquid chromatography and mass spectrometry identified a variety of proteins, including the large ECM proteins fibronectin and collagen VI. Immunostaining and confocal imaging confirmed these results and provided visualization of protein organization within the synthetic matrices. Additionally, culture medium was collected from the encapsulated hMSCs, and a Luminex assay was performed to identify secreted soluble factors, including vascular endothelial growth factor (VEGF), endothelial growth factor (EGF), basic fibroblast growth factor (FGF-2), interleukin 8 (IL-8), and tumor necrosis factor alpha (TNF-α). Together, these methods provide a unique approach for studying dynamic reciprocity between cells and synthetic microenvironments and have the potential to provide new biological insights into cell responses during three-dimensional (3D) controlled cell culture. PMID:29552635

Engineering large cartilage tissues using dynamic bioreactor culture at defined oxygen conditions.

PubMed

Daly, Andrew C; Sathy, Binulal N; Kelly, Daniel J

2018-01-01

Mesenchymal stem cells maintained in appropriate culture conditions are capable of producing robust cartilage tissue. However, gradients in nutrient availability that arise during three-dimensional culture can result in the development of spatially inhomogeneous cartilage tissues with core regions devoid of matrix. Previous attempts at developing dynamic culture systems to overcome these limitations have reported suppression of mesenchymal stem cell chondrogenesis compared to static conditions. We hypothesize that by modulating oxygen availability during bioreactor culture, it is possible to engineer cartilage tissues of scale. The objective of this study was to determine whether dynamic bioreactor culture, at defined oxygen conditions, could facilitate the development of large, spatially homogeneous cartilage tissues using mesenchymal stem cell laden hydrogels. A dynamic culture regime was directly compared to static conditions for its capacity to support chondrogenesis of mesenchymal stem cells in both small and large alginate hydrogels. The influence of external oxygen tension on the response to the dynamic culture conditions was explored by performing the experiment at 20% O 2 and 3% O 2 . At 20% O 2 , dynamic culture significantly suppressed chondrogenesis in engineered tissues of all sizes. In contrast, at 3% O 2 dynamic culture significantly enhanced the distribution and amount of cartilage matrix components (sulphated glycosaminoglycan and collagen II) in larger constructs compared to static conditions. Taken together, these results demonstrate that dynamic culture regimes that provide adequate nutrient availability and a low oxygen environment can be employed to engineer large homogeneous cartilage tissues. Such culture systems could facilitate the scaling up of cartilage tissue engineering strategies towards clinically relevant dimensions.

Isolation and Identification of Proteins Secreted by Cells Cultured within Synthetic Hydrogel-Based Matrices.

PubMed

Sawicki, Lisa A; Choe, Leila H; Wiley, Katherine L; Lee, Kelvin H; Kloxin, April M

2018-03-12

Cells interact with and remodel their microenvironment, degrading large extracellular matrix (ECM) proteins (e.g., fibronectin, collagens) and secreting new ECM proteins and small soluble factors (e.g., growth factors, cytokines). Synthetic mimics of the ECM have been developed as controlled cell culture platforms for use in both fundamental and applied studies. However, how cells broadly remodel these initially well-defined matrices remains poorly understood and difficult to probe. In this work, we have established methods for widely examining both large and small proteins that are secreted by cells within synthetic matrices. Specifically, human mesenchymal stem cells (hMSCs), a model primary cell type, were cultured within well-defined poly(ethylene glycol) (PEG)-peptide hydrogels, and these cell-matrix constructs were decellularized and degraded for subsequent isolation and analysis of deposited proteins. Shotgun proteomics using liquid chromatography and mass spectrometry identified a variety of proteins, including the large ECM proteins fibronectin and collagen VI. Immunostaining and confocal imaging confirmed these results and provided visualization of protein organization within the synthetic matrices. Additionally, culture medium was collected from the encapsulated hMSCs, and a Luminex assay was performed to identify secreted soluble factors, including vascular endothelial growth factor (VEGF), endothelial growth factor (EGF), basic fibroblast growth factor (FGF-2), interleukin 8 (IL-8), and tumor necrosis factor alpha (TNF-α). Together, these methods provide a unique approach for studying dynamic reciprocity between cells and synthetic microenvironments and have the potential to provide new biological insights into cell responses during three-dimensional (3D) controlled cell culture.

Regulation of Cellular Redox Signaling by Matricellular Proteins in Vascular Biology, Immunology, and Cancer.

PubMed

Roberts, David D; Kaur, Sukhbir; Isenberg, Jeffrey S

2017-10-20

In contrast to structural elements of the extracellular matrix, matricellular proteins appear transiently during development and injury responses, but their sustained expression can contribute to chronic disease. Through interactions with other matrix components and specific cell surface receptors, matricellular proteins regulate multiple signaling pathways, including those mediated by reactive oxygen and nitrogen species and H 2 S. Dysregulation of matricellular proteins contributes to the pathogenesis of vascular diseases and cancer. Defining the molecular mechanisms and receptors involved is revealing new therapeutic opportunities. Recent Advances: Thrombospondin-1 (TSP1) regulates NO, H 2 S, and superoxide production and signaling in several cell types. The TSP1 receptor CD47 plays a central role in inhibition of NO signaling, but other TSP1 receptors also modulate redox signaling. The matricellular protein CCN1 engages some of the same receptors to regulate redox signaling, and ADAMTS1 regulates NO signaling in Marfan syndrome. In addition to mediating matricellular protein signaling, redox signaling is emerging as an important pathway that controls the expression of several matricellular proteins. Redox signaling remains unexplored for many matricellular proteins. Their interactions with multiple cellular receptors remains an obstacle to defining signaling mechanisms, but improved transgenic models could overcome this barrier. Therapeutics targeting the TSP1 receptor CD47 may have beneficial effects for treating cardiovascular disease and cancer and have recently entered clinical trials. Biomarkers are needed to assess their effects on redox signaling in patients and to evaluate how these contribute to their therapeutic efficacy and potential side effects. Antioxid. Redox Signal. 27, 874-911.

C-Terminal DxD-Containing Sequences within Paramyxovirus Nucleocapsid Proteins Determine Matrix Protein Compatibility and Can Direct Foreign Proteins into Budding Particles

PubMed Central

Ray, Greeshma; Schmitt, Phuong Tieu

2016-01-01

ABSTRACT Paramyxovirus particles are formed by a budding process coordinated by viral matrix (M) proteins. M proteins coalesce at sites underlying infected cell membranes and induce other viral components, including viral glycoproteins and viral ribonucleoprotein complexes (vRNPs), to assemble at these locations from which particles bud. M proteins interact with the nucleocapsid (NP or N) components of vRNPs, and these interactions enable production of infectious, genome-containing virions. For the paramyxoviruses parainfluenza virus 5 (PIV5) and mumps virus, M-NP interaction also contributes to efficient production of virus-like particles (VLPs) in transfected cells. A DLD sequence near the C-terminal end of PIV5 NP protein was previously found to be necessary for M-NP interaction and efficient VLP production. Here, we demonstrate that 15-residue-long, DLD-containing sequences derived from either the PIV5 or Nipah virus nucleocapsid protein C-terminal ends are sufficient to direct packaging of a foreign protein, Renilla luciferase, into budding VLPs. Mumps virus NP protein harbors DWD in place of the DLD sequence found in PIV5 NP protein, and consequently, PIV5 NP protein is incompatible with mumps virus M protein. A single amino acid change converting DLD to DWD within PIV5 NP protein induced compatibility between these proteins and allowed efficient production of mumps VLPs. Our data suggest a model in which paramyxoviruses share an overall common strategy for directing M-NP interactions but with important variations contained within DLD-like sequences that play key roles in defining M/NP protein compatibilities. IMPORTANCE Paramyxoviruses are responsible for a wide range of diseases that affect both humans and animals. Paramyxovirus pathogens include measles virus, mumps virus, human respiratory syncytial virus, and the zoonotic paramyxoviruses Nipah virus and Hendra virus. Infectivity of paramyxovirus particles depends on matrix-nucleocapsid protein interactions which enable efficient packaging of encapsidated viral RNA genomes into budding virions. In this study, we have defined regions near the C-terminal ends of paramyxovirus nucleocapsid proteins that are important for matrix protein interaction and that are sufficient to direct a foreign protein into budding particles. These results advance our basic understanding of paramyxovirus genome packaging interactions and also have implications for the potential use of virus-like particles as protein delivery tools. PMID:26792745

C-Terminal DxD-Containing Sequences within Paramyxovirus Nucleocapsid Proteins Determine Matrix Protein Compatibility and Can Direct Foreign Proteins into Budding Particles.

PubMed

Ray, Greeshma; Schmitt, Phuong Tieu; Schmitt, Anthony P

2016-01-20

Paramyxovirus particles are formed by a budding process coordinated by viral matrix (M) proteins. M proteins coalesce at sites underlying infected cell membranes and induce other viral components, including viral glycoproteins and viral ribonucleoprotein complexes (vRNPs), to assemble at these locations from which particles bud. M proteins interact with the nucleocapsid (NP or N) components of vRNPs, and these interactions enable production of infectious, genome-containing virions. For the paramyxoviruses parainfluenza virus 5 (PIV5) and mumps virus, M-NP interaction also contributes to efficient production of virus-like particles (VLPs) in transfected cells. A DLD sequence near the C-terminal end of PIV5 NP protein was previously found to be necessary for M-NP interaction and efficient VLP production. Here, we demonstrate that 15-residue-long, DLD-containing sequences derived from either the PIV5 or Nipah virus nucleocapsid protein C-terminal ends are sufficient to direct packaging of a foreign protein, Renilla luciferase, into budding VLPs. Mumps virus NP protein harbors DWD in place of the DLD sequence found in PIV5 NP protein, and consequently, PIV5 NP protein is incompatible with mumps virus M protein. A single amino acid change converting DLD to DWD within PIV5 NP protein induced compatibility between these proteins and allowed efficient production of mumps VLPs. Our data suggest a model in which paramyxoviruses share an overall common strategy for directing M-NP interactions but with important variations contained within DLD-like sequences that play key roles in defining M/NP protein compatibilities. Paramyxoviruses are responsible for a wide range of diseases that affect both humans and animals. Paramyxovirus pathogens include measles virus, mumps virus, human respiratory syncytial virus, and the zoonotic paramyxoviruses Nipah virus and Hendra virus. Infectivity of paramyxovirus particles depends on matrix-nucleocapsid protein interactions which enable efficient packaging of encapsidated viral RNA genomes into budding virions. In this study, we have defined regions near the C-terminal ends of paramyxovirus nucleocapsid proteins that are important for matrix protein interaction and that are sufficient to direct a foreign protein into budding particles. These results advance our basic understanding of paramyxovirus genome packaging interactions and also have implications for the potential use of virus-like particles as protein delivery tools. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Project - line interaction implementing projects in JPL's Matrix

NASA Technical Reports Server (NTRS)

Baroff, Lynn E.

2006-01-01

Can programmatic and line organizations really work interdependently, to accomplish their work as a community? Does the matrix produce a culture in which individuals take personal responsibility for both immediate mission success and long-term growth? What is the secret to making a matrix enterprise actually work? This paper will consider those questions, and propose that developing an effective project-line partnership demands primary attention to personal interactions among people. Many potential problems can be addressed by careful definition of roles, responsibilities, and work processes for both parts of the matrix -- and by deliberate and clear communication between project and line organizations and individuals.

Nonlinear behavior of matrix-inclusion composites under high confining pressure: application to concrete and mortar

NASA Astrophysics Data System (ADS)

Le, Tuan Hung; Dormieux, Luc; Jeannin, Laurent; Burlion, Nicolas; Barthélémy, Jean-François

2008-08-01

This paper is devoted to a micromechanics-based simulation of the response of concrete to hydrostatic and oedometric compressions. Concrete is described as a composite made up of a cement matrix in which rigid inclusions are embedded. The focus is put on the role of the interface between matrix and inclusion which represent the interfacial transition zone (ITZ). A plastic behavior is considered for both the matrix and the interfaces. The effective response of the composite is derived from the modified secant method adapted to the situation of imperfect interfaces. To cite this article: T.H. Le et al., C. R. Mecanique 336 (2008).

Impulsive response of an automatic transmission system with multiple clearances: Formulation, simulation and experiment

NASA Astrophysics Data System (ADS)

Crowther, Ashley R.; Singh, Rajendra; Zhang, Nong; Chapman, Chris

2007-10-01

Impulsive responses in geared systems with multiple clearances are studied when the mean torque excitation and system load change abruptly, with application to a vehicle driveline with an automatic transmission. First, torsional lumped-mass models of the planetary and differential gear sets are formulated using matrix elements. The model is then reduced to address tractable nonlinear problems while successfully retaining the main modes of interest. Second, numerical simulations for the nonlinear model are performed for transient conditions and a typical driving situation that induces an impulsive behaviour simulated. However, initial conditions and excitation and load profiles have to be carefully defined before the model can be numerically solved. It is shown that the impacts within the planetary or differential gears may occur under combinations of engine, braking and vehicle load transients. Our analysis shows that the shaping of the engine transient by the torque converter before reaching the clearance locations is more critical. Third, a free vibration experiment is developed for an analogous driveline with multiple clearances and three experiments that excite different response regimes have been carried out. Good correlations validate the proposed methodology.

Immobilization of mercury and zinc in an alkali-activated slag matrix.

PubMed

Qian, Guangren; Sun, Darren Delai; Tay, Joo Hwa

2003-07-04

The behavior of heavy metals mercury and zinc immobilized in an alkali-activated slag (AAS) matrix has been evaluated using physical property tests, pore structure analysis and XRD, TG-DTG, FTIR and TCLP analysis. Low concentrations (0.5%) of mercury and zinc ions had only a slight affect on compressive strength, pore structure and hydration of AAS matrixes. The addition of 2% Hg ions to the AAS matrix resulted in a reduction in early compressive strength but no negative effects were noticed after 28 days of hydration. Meanwhile, 2% Hg ions can be effectively immobilized in the AAS matrix with the leachate meeting the USEPA TCLP mercury limit. For a 2% Zn-doped AAS matrix, the hydration of the AAS paste was greatly retarded and the zinc concentration in the leachate from this matrix was higher than 5mg/l even at 28 days. Based on these results, we conclude that the physical encapsulation and chemical fixation mechanisms were likely to be responsible for the immobilization of Hg ions in the AAS matrix while only chemical fixation mechanisms were responsible for the immobilization of Zn ions in the AAS matrix.

Assessment of Myocardial Remodeling Using an Elastin/Tropoelastin Specific Agent with High Field Magnetic Resonance Imaging (MRI).

PubMed

Protti, Andrea; Lavin, Begoña; Dong, Xuebin; Lorrio, Silvia; Robinson, Simon; Onthank, David; Shah, Ajay M; Botnar, Rene M

2015-08-13

Well-defined inflammation, proliferation, and maturation phases orchestrate the remodeling of the injured myocardium after myocardial infarction (MI) by controlling the formation of new extracellular matrix. The extracellular matrix consists mainly of collagen but also fractions of elastin. It is thought that elastin is responsible for maintaining elastic properties of the myocardium, thus reducing the risk of premature rupture. An elastin/tropoelastin-specific contrast agent (Gd-ESMA) was used to image tropoelastin and mature elastin fibers for in vivo assessment of extracellular matrix remodeling post-MI. Gd-ESMA enhancement was studied in a mouse model of myocardial infarction using a 7 T MRI scanner and results were compared to those achieved after injection of a nonspecific control contrast agent, gadolinium-diethylenetriamine pentaacetic acid (Gd-DTPA). In the infarcted tissue, Gd-ESMA uptake (measured as R1 relaxation rate) steadily increased from day 3 to day 21 as a result of the synthesis of elastin/tropoelastin. R1 values were in good agreement with histological findings. A similar R1 behavior was observed in the remote myocardium. No mature cross-linked elastin was found at any time point. In contrast, Gd-DTPA uptake was only observed in the infarct with no changes in R1 values between 3 and 21 days post-MI. We demonstrate the feasibility of in vivo imaging of extracellular matrix remodeling post-MI using a tropoelastin/elastin binding MR contrast agent, Gd-ESMA. We found that tropoelastin is the main contributor to the increased MRI signal at late stages of MI where its augmentation in areas of infarction was in good agreement with the R1 increase. © 2015 The Authors. Published on behalf of the American Heart Association, Inc., by Wiley Blackwell.

Functional cartilage repair capacity of de-differentiated, chondrocyte- and mesenchymal stem cell-laden hydrogels in vitro

PubMed Central

Rackwitz, Lars; Djouad, Farida; Janjanin, Sasa; Nöth, Ulrich; Tuan, Rocky S.

2017-01-01

Objective The long-term performance of cell seeded matrix based cartilage constructs depends on (1) the development of sufficient biomechanical properties, and (2) lateral integration with host tissues, both of which require cartilage specific matrix deposition within the scaffold. In this study, we have examined the potential of tissue-engineered cartilage analogs developed using different cell types, i.e., MSCs versus chondrocytes and de-differentiated chondrocytes, in an established “construct in cartilage ring” model. Design Cell-laden constructs of differentiated chondrocytes, de-differentiated chondrocytes after 2, 5 or 8 population doublings, and MSCs were either implanted into a native cartilage ring immediately after fabrication (immature group) or pretreated for 21 days in a transforming growth factor-β3 (TGF-β3) containing medium prior to implantation. After additional culture for 28 days in a serum-free, chemically defined medium, the extent of lateral integration, and biochemical and biomechanical characteristics of the implants as hybrid constructs were assessed. Results The quality of integration, the amount of accumulated cartilage-specific matrix components and associated biomechanical properties were found to be highest when using differentiated chondrocytes. De-differentiation of chondrocytes negatively impacted the properties of the implants, as even two population doublings of the chondrocytes in culture significantly lowered cartilage repair capacity. In contrast, MSCs showed chondrogenic differentiation with TGF-β3 pre-treatment and superior integrational behavior. Conclusions Chondrocyte expansion and de-differentiation impaired the cell response, resulting in inferior cartilage repair in vitro. With TGF-β3 pre-treatment, MSCs were able to undergo sustained chondrogenic differentiation and exhibited superior matrix deposition and integration compared to de-differentiated chondrocytes. PMID:24887551

Dimensional analysis using toric ideals: primitive invariants.

PubMed

Atherton, Mark A; Bates, Ronald A; Wynn, Henry P

2014-01-01

Classical dimensional analysis in its original form starts by expressing the units for derived quantities, such as force, in terms of power products of basic units [Formula: see text] etc. This suggests the use of toric ideal theory from algebraic geometry. Within this the Graver basis provides a unique primitive basis in a well-defined sense, which typically has more terms than the standard Buckingham approach. Some textbook examples are revisited and the full set of primitive invariants found. First, a worked example based on convection is introduced to recall the Buckingham method, but using computer algebra to obtain an integer [Formula: see text] matrix from the initial integer [Formula: see text] matrix holding the exponents for the derived quantities. The [Formula: see text] matrix defines the dimensionless variables. But, rather than this integer linear algebra approach it is shown how, by staying with the power product representation, the full set of invariants (dimensionless groups) is obtained directly from the toric ideal defined by [Formula: see text]. One candidate for the set of invariants is a simple basis of the toric ideal. This, although larger than the rank of [Formula: see text], is typically not unique. However, the alternative Graver basis is unique and defines a maximal set of invariants, which are primitive in a simple sense. In addition to the running example four examples are taken from: a windmill, convection, electrodynamics and the hydrogen atom. The method reveals some named invariants. A selection of computer algebra packages is used to show the considerable ease with which both a simple basis and a Graver basis can be found.

Theory of Electronic, Atomic and Molecular Collisions.

DTIC Science & Technology

1983-09-01

coordinate in a reactive collision. Dynamical entropy Is defined as a statistical property of a dynamical scattering matrix, indexed by internal states of a...matrix U by enforcing certain internal symmetries that are a property of canonical transformation matrices (FCANON algorithm: Section IV...channels are present in Eq. (12). This low of accuracy is a property of the system of coupled differential equations, not of any particular method of

Asymptotic states and the definition of the S-matrix in quantum gravity

NASA Astrophysics Data System (ADS)

Wiesendanger, C.

2013-04-01

Viewing gravitational energy-momentum p_G^\\mu as equal by observation, but different in essence from inertial energy-momentum p_I^\\mu naturally leads to the gauge theory of volume-preserving diffeomorphisms of an inner Minkowski space M4. The generalized asymptotic free scalar, Dirac and gauge fields in that theory are canonically quantized, the Fock spaces of stationary states are constructed and the gravitational limit—mapping the gravitational energy-momentum onto the inertial energy-momentum to account for their observed equality—is introduced. Next the S-matrix in quantum gravity is defined as the gravitational limit of the transition amplitudes of asymptotic in- to out-states in the gauge theory of volume-preserving diffeomorphisms. The so-defined S-matrix relates in- and out-states of observable particles carrying gravitational equal to inertial energy-momentum. Finally, generalized Lehmann-Symanzik-Zimmermann reduction formulae for scalar, Dirac and gauge fields are established which allow us to express S-matrix elements as the gravitational limit of truncated Fourier-transformed vacuum expectation values of time-ordered products of field operators of the interacting theory. Together with the generating functional of the latter established in Wiesendanger (2011 arXiv:1103.1012) any transition amplitude can in principle be computed consistently to any order in perturbative quantum gravity.

Kinetic damping in the spectra of the spherical impedance probe

NASA Astrophysics Data System (ADS)

Oberrath, J.

2018-04-01

The impedance probe is a measurement device to measure plasma parameters, such as electron density. It consists of one electrode connected to a network analyzer via a coaxial cable and is immersed into a plasma. A bias potential superposed with an alternating potential is applied to the electrode and the response of the plasma is measured. Its dynamical interaction with the plasma in an electrostatic, kinetic description can be modeled in an abstract notation based on functional analytic methods. These methods provide the opportunity to derive a general solution, which is given as the response function of the probe–plasma system. It is defined by the matrix elements of the resolvent of an appropriate dynamical operator. Based on the general solution, a residual damping for vanishing pressure can be predicted and can only be explained by kinetic effects. In this paper, an explicit response function of the spherical impedance probe is derived. Therefore, the resolvent is determined by its algebraic representation based on an expansion in orthogonal basis functions. This allows one to compute an approximated response function and its corresponding spectra. These spectra show additional damping due to kinetic effects and are in good agreement with former kinetically determined spectra.

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.

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

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

PubMed Central

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

2009-01-01

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

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

PubMed

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

2009-07-27

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

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.

Performance evaluation of matrix gradient coils.

PubMed

Jia, Feng; Schultz, Gerrit; Testud, Frederik; Welz, Anna Masako; Weber, Hans; Littin, Sebastian; Yu, Huijun; Hennig, Jürgen; Zaitsev, Maxim

2016-02-01

In this paper, we present a new performance measure of a matrix coil (also known as multi-coil) from the perspective of efficient, local, non-linear encoding without explicitly considering target encoding fields. An optimization problem based on a joint optimization for the non-linear encoding fields is formulated. Based on the derived objective function, a figure of merit of a matrix coil is defined, which is a generalization of a previously known resistive figure of merit for traditional gradient coils. A cylindrical matrix coil design with a high number of elements is used to illustrate the proposed performance measure. The results are analyzed to reveal novel features of matrix coil designs, which allowed us to optimize coil parameters, such as number of coil elements. A comparison to a scaled, existing multi-coil is also provided to demonstrate the use of the proposed performance parameter. The assessment of a matrix gradient coil profits from using a single performance parameter that takes the local encoding performance of the coil into account in relation to the dissipated power.

Assessing Fit of Item Response Models Using the Information Matrix Test

ERIC Educational Resources Information Center

Ranger, Jochen; Kuhn, Jorg-Tobias

2012-01-01

The information matrix can equivalently be determined via the expectation of the Hessian matrix or the expectation of the outer product of the score vector. The identity of these two matrices, however, is only valid in case of a correctly specified model. Therefore, differences between the two versions of the observed information matrix indicate…

A Generalized Orthotropic Elasto-Plastic Material Model for Impact Analysis

NASA Astrophysics Data System (ADS)

Hoffarth, Canio

Composite materials are now beginning to provide uses hitherto reserved for metals in structural systems such as airframes and engine containment systems, wraps for repair and rehabilitation, and ballistic/blast mitigation systems. These structural systems are often subjected to impact loads and there is a pressing need for accurate prediction of deformation, damage and failure. There are numerous material models that have been developed to analyze the dynamic impact response of polymer matrix composites. However, there are key features that are missing in those models that prevent them from providing accurate predictive capabilities. In this dissertation, a general purpose orthotropic elasto-plastic computational constitutive material model has been developed to predict the response of composites subjected to high velocity impacts. The constitutive model is divided into three components - deformation model, damage model and failure model, with failure to be added at a later date. The deformation model generalizes the Tsai-Wu failure criteria and extends it using a strain-hardening-based orthotropic yield function with a non-associative flow rule. A strain equivalent formulation is utilized in the damage model that permits plastic and damage calculations to be uncoupled and capture the nonlinear unloading and local softening of the stress-strain response. A diagonal damage tensor is defined to account for the directionally dependent variation of damage. However, in composites it has been found that loading in one direction can lead to damage in multiple coordinate directions. To account for this phenomena, the terms in the damage matrix are semi-coupled such that the damage in a particular coordinate direction is a function of the stresses and plastic strains in all of the coordinate directions. The overall framework is driven by experimental tabulated temperature and rate-dependent stress-strain data as well as data that characterizes the damage matrix and failure. The developed theory has been implemented in a commercial explicit finite element analysis code, LS-DYNARTM, as MAT213. Several verification and validation tests using a commonly available carbon-fiber composite, Toyobo's T800/F3900, have been carried and the results show that the theory and implementation are efficient, robust and accurate.

A novel method for morphological pleomorphism and heterogeneity quantitative measurement: Named cell feature level co-occurrence matrix.

PubMed

Saito, Akira; Numata, Yasushi; Hamada, Takuya; Horisawa, Tomoyoshi; Cosatto, Eric; Graf, Hans-Peter; Kuroda, Masahiko; Yamamoto, Yoichiro

2016-01-01

Recent developments in molecular pathology and genetic/epigenetic analysis of cancer tissue have resulted in a marked increase in objective and measurable data. In comparison, the traditional morphological analysis approach to pathology diagnosis, which can connect these molecular data and clinical diagnosis, is still mostly subjective. Even though the advent and popularization of digital pathology has provided a boost to computer-aided diagnosis, some important pathological concepts still remain largely non-quantitative and their associated data measurements depend on the pathologist's sense and experience. Such features include pleomorphism and heterogeneity. In this paper, we propose a method for the objective measurement of pleomorphism and heterogeneity, using the cell-level co-occurrence matrix. Our method is based on the widely used Gray-level co-occurrence matrix (GLCM), where relations between neighboring pixel intensity levels are captured into a co-occurrence matrix, followed by the application of analysis functions such as Haralick features. In the pathological tissue image, through image processing techniques, each nucleus can be measured and each nucleus has its own measureable features like nucleus size, roundness, contour length, intra-nucleus texture data (GLCM is one of the methods). In GLCM each nucleus in the tissue image corresponds to one pixel. In this approach the most important point is how to define the neighborhood of each nucleus. We define three types of neighborhoods of a nucleus, then create the co-occurrence matrix and apply Haralick feature functions. In each image pleomorphism and heterogeneity are then determined quantitatively. For our method, one pixel corresponds to one nucleus feature, and we therefore named our method Cell Feature Level Co-occurrence Matrix (CFLCM). We tested this method for several nucleus features. CFLCM is showed as a useful quantitative method for pleomorphism and heterogeneity on histopathological image analysis.

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.

A Kalman filter for a two-dimensional shallow-water model

NASA Technical Reports Server (NTRS)

Parrish, D. F.; Cohn, S. E.

1985-01-01

A two-dimensional Kalman filter is described for data assimilation for making weather forecasts. The filter is regarded as superior to the optimal interpolation method because the filter determines the forecast error covariance matrix exactly instead of using an approximation. A generalized time step is defined which includes expressions for one time step of the forecast model, the error covariance matrix, the gain matrix, and the evolution of the covariance matrix. Subsequent time steps are achieved by quantifying the forecast variables or employing a linear extrapolation from a current variable set, assuming the forecast dynamics are linear. Calculations for the evolution of the error covariance matrix are banded, i.e., are performed only with the elements significantly different from zero. Experimental results are provided from an application of the filter to a shallow-water simulation covering a 6000 x 6000 km grid.

Growth of cultured corneal endothelial cells onto a vitreous carbon matrix.

PubMed

Wickham, M G; Cleveland, P H; Binder, P S; Akers, P H

1983-01-01

Fourth passage cells of a rabbit corneal endothelial line were grown for 1 week in flasks containing pieces of a reticulated vitreous carbon matrix. The rate of cell growth in flasks containing the matrix was consistent with that in control flasks. Small fragments of the vitreous carbon material lying on the flask floor were covered by the monolayers as the cells grew to confluency. Vertical growth of cells onto larger pieces of the matrix proceeded in a staged fashion with maximum cell density on pieces of the matrix closest to the floor of the flask. As defined by scanning electron microscopy, cell growth occurred to a level at least 600 microns above the floor of the flask and the confluent monolayer. This novel culture procedure should be a model situation for study of many different aspects of the in vitro capabilities of corneal endothelial cells.

Performance analysis of landslide early warning systems at regional scale: the EDuMaP method

NASA Astrophysics Data System (ADS)

Piciullo, Luca; Calvello, Michele

2016-04-01

Landslide early warning systems (LEWSs) reduce landslide risk by disseminating timely and meaningful warnings when the level of risk is judged intolerably high. Two categories of LEWSs, can be defined on the basis of their scale of analysis: "local" systems and "regional" systems. LEWSs at regional scale (ReLEWSs) are used to assess the probability of occurrence of landslides over appropriately-defined homogeneous warning zones of relevant extension, typically through the prediction and monitoring of meteorological variables, in order to give generalized warnings to the public. Despite many studies on ReLEWSs, no standard requirements exist for assessing their performance. Empirical evaluations are often carried out by simply analysing the time frames during which significant high-consequence landslides occurred in the test area. Alternatively, the performance evaluation is based on 2x2 contingency tables computed for the joint frequency distribution of landslides and alerts, both considered as dichotomous variables. In all these cases, model performance is assessed neglecting some important aspects which are peculiar to ReLEWSs, among which: the possible occurrence of multiple landslides in the warning zone; the duration of the warnings in relation to the time of occurrence of the landslides; the level of the warning issued in relation to the landslide spatial density in the warning zone; the relative importance system managers attribute to different types of errors. An original approach, called EDuMaP method, is proposed to assess the performance of landslide early warning models operating at regional scale. The method is composed by three main phases: Events analysis, Duration Matrix, Performance analysis. The events analysis phase focuses on the definition of landslide (LEs) and warning events (WEs), which are derived from available landslides and warnings databases according to their spatial and temporal characteristics by means of ten input parameters. The evaluation of time associated with the occurrence of landslide events (LE) in relation to the occurrence of warning events (WE) in their respective classes is a fundamental step to determine the duration matrix elements. On the other hand the classification of LEs and WEs establishes the structure of the duration matrix. Indeed, the number of rows and columns of the matrix is equal to the number of classes defined for the warning and landslide events, respectively. Thus the matrix is not expressed as a 2x2 contingency and LEs and WEs are not expressed as dichotomous variables. The final phase of the method is the evaluation of the duration matrix based on a set of performance criteria assigning a performance meaning to the element of the matrix. To this aim different criteria can be defined, for instance employing an alert classification scheme derived from 2x2 contingency tables or assigning a colour code to the elements of the matrix in relation to their grade of correctness. Finally, performance indicators can be derived from the performance criteria to quantify successes and errors of the early warning models. EDuMaP has been already applied to different real case studies, highlighting the adaptability of the method to analyse the performance of structurally different ReLEWSs.

Extra-fibrillar matrix mechanics of annulus fibrosus in tension and compression.

PubMed

Cortes, Daniel H; Elliott, Dawn M

2012-07-01

The annulus fibrosus (AF) of the disk is a highly nonlinear and anisotropic material that undergoes a complex combination of loads in multiple orientations. The tensile mechanical behavior of AF in the lamellar plane is dominated by collagen fibers and has been accurately modeled using exponential functions. On the other hand, AF mechanics perpendicular to the lamella, in the radial direction, depend on the properties of the ground matrix with little to no fiber contribution. The ground matrix is mainly composed of proteoglycans (PG), which are negatively charged macromolecules that maintain the tissue hydration via osmotic pressure. The mechanical response of the ground matrix can be divided in the contribution of osmotic pressure and an elastic solid part known as extra-fibrillar matrix (EFM). Mechanical properties of the ground matrix have been measured using tensile and confined compression tests. However, EFM mechanics have not been measured directly. The objective of this study was to measure AF nonlinear mechanics of the EFM in tension and compression. To accomplish this, a combination of osmotic swelling and confined compression in disk radial direction, perpendicular to the lamella, was used. For this type of analysis, it was necessary to define a stress-free reference configuration. Thus, a brief analysis on residual stress in the disk and a procedure to estimate the reference configuration are presented. The proposed method was able to predict similar swelling deformations when using different loading protocols and models for the EFM, demonstrating its robustness. The stress-stretch curve of the EFM was linear in the range 0.9 < λ₃ < 1.3 with an aggregate modulus of 10.18±3.32 kPa; however, a significant nonlinearity was observed for compression below 0.8. The contribution of the EFM to the total aggregate modulus of the AF decreased from 70 to 30% for an applied compression of 50% of the initial thickness. The properties obtained in this study are essential for constitutive and finite element models of the AF and disk and can be applied to differentiate between functional degeneration effects such as PG loss and stiffening due to cross-linking.

In vitro study of the impact of mechanical tension on the dermal fibroblast phenotype in the context of skin wound healing.

PubMed

Rolin, Gwenae L; Binda, Delphine; Tissot, Marion; Viennet, Céline; Saas, Philippe; Muret, Patrice; Humbert, Philippe

2014-11-07

Skin wound healing is finely regulated by both matrix synthesis and degradation which are governed by dermal fibroblast activity. Actually, fibroblasts synthesize numerous extracellular matrix proteins (i.e., collagens), remodeling enzymes and their inhibitors. Moreover, they differentiate into myofibroblasts and are able to develop endogenous forces at the wound site. Such forces are crucial during skin wound healing and have been widely investigated. However, few studies have focused on the effect of exogenous mechanical tension on the dermal fibroblast phenotype, which is the objective of the present paper. To this end, an exogenous, defined, cyclic and uniaxial mechanical strain was applied to fibroblasts cultured as scratch-wounded monolayers. Results showed that fibroblasts' response was characterized by both an increase in procollagen type-I and TIMP-1 synthesis, and a decrease in MMP-1 synthesis. The monitoring of scratch-wounded monolayers did not show any decrease in kinetics of the filling up when mechanical tension was applied. Additional results obtained with proliferating fibroblasts and confluent monolayer indicated that mechanical tension-induced response of fibroblasts depends on their culture conditions. In conclusion, mechanical tension leads to the differentiation of dermal fibroblasts and may increase their wound-healing capacities. So, the exogenous uniaxial and cyclic mechanical tension reported in the present study may be considered in order to improve skin wound healing. Copyright © 2014 Elsevier Ltd. All rights reserved.

Rigidity-patterned polyelectrolyte films to control myoblast cell adhesion and spatial organization

PubMed Central

Monge, Claire; Saha, Naresh; Boudou, Thomas; Pózos-Vásquez, Cuauhtemoc; Dulong, Virginie; Glinel, Karine; Picart, Catherine

2014-01-01

In vivo, cells are sensitive to the stiffness of their micro-environment and especially to the spatial organization of the stiffness. In vitro studies of this phenomenon can help to better understand the mechanisms of the cell response to spatial variations of the matrix stiffness. In this work, we design polelyelectrolyte multilayer films made of poly(L-lysine) and a photo-reactive hyaluronan derivative. These films can be photo-crosslinked through a photomask to create spatial patterns of rigidity. Quartz substrates incorporating a chromium mask are prepared to expose selectively the film to UV light (in a physiological buffer), without any direct contact between the photomask and the soft film. We show that these micropatterns are chemically homogeneous and flat, without any preferential adsorption of adhesive proteins. Three groups of pattern geometries differing by their shape (circles or lines), size (form 2 to 100 μm) or interspacing distance between the motifs are used to study the adhesion and spatial organization of myoblast cells. On large circular micropatterns, the cells form large assemblies that are confined to the stiffest parts. Conversely, when the size of the rigidity patterns is subcellular, the cells respond by forming protrusions. Finally, on linear micropatterns of rigidity, myoblasts align and their nuclei drastically elongate in specific conditions. These results pave the way for the study of the different steps of myoblast fusion in response to matrix rigidity in well-defined geometrical conditions. PMID:25100929

A Higher Harmonic Optimal Controller to Optimise Rotorcraft Aeromechanical Behaviour

NASA Technical Reports Server (NTRS)

Leyland, Jane Anne

1996-01-01

Three methods to optimize rotorcraft aeromechanical behavior for those cases where the rotorcraft plant can be adequately represented by a linear model system matrix were identified and implemented in a stand-alone code. These methods determine the optimal control vector which minimizes the vibration metric subject to constraints at discrete time points, and differ from the commonly used non-optimal constraint penalty methods such as those employed by conventional controllers in that the constraints are handled as actual constraints to an optimization problem rather than as just additional terms in the performance index. The first method is to use a Non-linear Programming algorithm to solve the problem directly. The second method is to solve the full set of non-linear equations which define the necessary conditions for optimality. The third method is to solve each of the possible reduced sets of equations defining the necessary conditions for optimality when the constraints are pre-selected to be either active or inactive, and then to simply select the best solution. The effects of maneuvers and aeroelasticity on the systems matrix are modelled by using a pseudo-random pseudo-row-dependency scheme to define the systems matrix. Cases run to date indicate that the first method of solution is reliable, robust, and easiest to use, and that it was superior to the conventional controllers which were considered.

The current matrix elements from HAL QCD method

NASA Astrophysics Data System (ADS)

Watanabe, Kai; Ishii, Noriyoshi

2018-03-01

HAL QCD method is a method to construct a potential (HAL QCD potential) that reproduces the NN scattering phase shift faithful to the QCD. The HAL QCD potential is obtained from QCD by eliminating the degrees of freedom of quarks and gluons and leaving only two particular hadrons. Therefor, in the effective quantum mechanics of two nucleons defined by HAL QCD potential, the conserved current consists not only of the nucleon current but also an extra current originating from the potential (two-body current). Though the form of the two-body current is closely related to the potential, it is not straight forward to extract the former from the latter. In this work, we derive the the current matrix element formula in the quantum mechanics defined by the HAL QCD potential. As a first step, we focus on the non-relativistic case. To give an explicit example, we consider a second quantized non-relativistic two-channel coupling model which we refer to as the original model. From the original model, the HAL QCD potential for the open channel is constructed by eliminating the closed channel in the elastic two-particle scattering region. The current matrix element formula is derived by demanding the effective quantum mechanics defined by the HAL QCD potential to respond to the external field in the same way as the original two-channel coupling model.

Defining the light emitting area for displays in the unipolar regime of highly efficient light emitting transistors

PubMed Central

Ullah, Mujeeb; Armin, Ardalan; Tandy, Kristen; Yambem, Soniya D.; Burn, Paul L.; Meredith, Paul; Namdas, Ebinazar B.

2015-01-01

Light-emitting field effect transistors (LEFETs) are an emerging class of multifunctional optoelectronic devices. It combines the light emitting function of an OLED with the switching function of a transistor in a single device architecture. The dual functionality of LEFETs has the potential applications in active matrix displays. However, the key problem of existing LEFETs thus far has been their low EQEs at high brightness, poor ON/OFF and poorly defined light emitting area - a thin emissive zone at the edge of the electrodes. Here we report heterostructure LEFETs based on solution processed unipolar charge transport and an emissive polymer that have an EQE of up to 1% at a brightness of 1350 cd/m2, ON/OFF ratio > 104 and a well-defined light emitting zone suitable for display pixel design. We show that a non-planar hole-injecting electrode combined with a semi-transparent electron-injecting electrode enables to achieve high EQE at high brightness and high ON/OFF ratio. Furthermore, we demonstrate that heterostructure LEFETs have a better frequency response (fcut-off = 2.6 kHz) compared to single layer LEFETs. The results presented here therefore are a major step along the pathway towards the realization of LEFETs for display applications. PMID:25743444

Bile Salt-induced Biofilm Formation in Enteric Pathogens: Techniques for Identification and Quantification.

PubMed

Nickerson, Kourtney P; Faherty, Christina S

2018-05-06

Biofilm formation is a dynamic, multistage process that occurs in bacteria under harsh environmental conditions or times of stress. For enteric pathogens, a significant stress response is induced during gastrointestinal transit and upon bile exposure, a normal component of human digestion. To overcome the bactericidal effects of bile, many enteric pathogens form a biofilm hypothesized to permit survival when transiting through the small intestine. Here we present methodologies to define biofilm formation through solid-phase adherence assays as well as extracellular polymeric substance (EPS) matrix detection and visualization. Furthermore, biofilm dispersion assessment is presented to mimic the analysis of events triggering release of bacteria during the infection process. Crystal violet staining is used to detect adherent bacteria in a high-throughput 96-well plate adherence assay. EPS production assessment is determined by two assays, namely microscopy staining of the EPS matrix and semi-quantitative analysis with a fluorescently-conjugated polysaccharide binding lectin. Finally, biofilm dispersion is measured through colony counts and plating. Positive data from multiple assays support the characterization of biofilms and can be utilized to identify bile salt-induced biofilm formation in other bacterial strains.

Hesitant Fuzzy Thermodynamic Method for Emergency Decision Making Based on Prospect Theory.

PubMed

Ren, Peijia; Xu, Zeshui; Hao, Zhinan

2017-09-01

Due to the timeliness of emergency response and much unknown information in emergency situations, this paper proposes a method to deal with the emergency decision making, which can comprehensively reflect the emergency decision making process. By utilizing the hesitant fuzzy elements to represent the fuzziness of the objects and the hesitant thought of the experts, this paper introduces the negative exponential function into the prospect theory so as to portray the psychological behaviors of the experts, which transforms the hesitant fuzzy decision matrix into the hesitant fuzzy prospect decision matrix (HFPDM) according to the expectation-levels. Then, this paper applies the energy and the entropy in thermodynamics to take the quantity and the quality of the decision values into account, and defines the thermodynamic decision making parameters based on the HFPDM. Accordingly, a whole procedure for emergency decision making is conducted. What is more, some experiments are designed to demonstrate and improve the validation of the emergency decision making procedure. Last but not the least, this paper makes a case study about the emergency decision making in the firing and exploding at Port Group in Tianjin Binhai New Area, which manifests the effectiveness and practicability of the proposed method.

Defining the extracellular matrix using proteomics

PubMed Central

Byron, Adam; Humphries, Jonathan D; Humphries, Martin J

2013-01-01

The cell microenvironment has a profound influence on the behaviour, growth and survival of cells. The extracellular matrix (ECM) provides not only mechanical and structural support to cells and tissues but also binds soluble ligands and transmembrane receptors to provide spatial coordination of signalling processes. The ability of cells to sense the chemical, mechanical and topographical features of the ECM enables them to integrate complex, multiparametric information into a coherent response to the surrounding microenvironment. Consequently, dysregulation or mutation of ECM components results in a broad range of pathological conditions. Characterization of the composition of ECM derived from various cells has begun to reveal insights into ECM structure and function, and mechanisms of disease. Proteomic methodologies permit the global analysis of subcellular systems, but extracellular and transmembrane proteins present analytical difficulties to proteomic strategies owing to the particular biochemical properties of these molecules. Here, we review advances in proteomic approaches that have been applied to furthering our understanding of the ECM microenvironment. We survey recent studies that have addressed challenges in the analysis of ECM and discuss major outcomes in the context of health and disease. In addition, we summarize efforts to progress towards a systems-level understanding of ECM biology. PMID:23419153

CELLULAR CONTROL OF CONNECTIVE TISSUE MATRIX TENSION†

PubMed Central

Langevin, Helene M.; Nedergaard, Maiken; Howe, Alan

2013-01-01

The biomechanical behavior of connective tissue in response to stretching is generally attributed to the molecular composition and organization of its extracellular matrix. It also is becoming apparent that fibroblasts play an active role in regulating connective tissue tension. In response to static stretching of the tissue, fibroblasts expand within minutes by actively remodeling their cytoskeleton. This dynamic change in fibroblast shape contributes to the drop in tissue tension that occurs during viscoelastic relaxation. We propose that this response of fibroblasts plays a role in regulating extracellular fluid flow into the tissue, and protects against swelling when the matrix is stretched. This article reviews the evidence supporting possible mechanisms underlying this response including autocrine purinergic signaling. We also discuss fibroblast regulation of connective tissue tension with respect to lymphatic flow, immune function and cancer. PMID:23444198

Reconstructing source terms from atmospheric concentration measurements: Optimality analysis of an inversion technique

NASA Astrophysics Data System (ADS)

Turbelin, Grégory; Singh, Sarvesh Kumar; Issartel, Jean-Pierre

2014-12-01

In the event of an accidental or intentional contaminant release in the atmosphere, it is imperative, for managing emergency response, to diagnose the release parameters of the source from measured data. Reconstruction of the source information exploiting measured data is called an inverse problem. To solve such a problem, several techniques are currently being developed. The first part of this paper provides a detailed description of one of them, known as the renormalization method. This technique, proposed by Issartel (2005), has been derived using an approach different from that of standard inversion methods and gives a linear solution to the continuous Source Term Estimation (STE) problem. In the second part of this paper, the discrete counterpart of this method is presented. By using matrix notation, common in data assimilation and suitable for numerical computing, it is shown that the discrete renormalized solution belongs to a family of well-known inverse solutions (minimum weighted norm solutions), which can be computed by using the concept of generalized inverse operator. It is shown that, when the weight matrix satisfies the renormalization condition, this operator satisfies the criteria used in geophysics to define good inverses. Notably, by means of the Model Resolution Matrix (MRM) formalism, we demonstrate that the renormalized solution fulfils optimal properties for the localization of single point sources. Throughout the article, the main concepts are illustrated with data from a wind tunnel experiment conducted at the Environmental Flow Research Centre at the University of Surrey, UK.

Nitric oxide regulates tumor cell cross-talk with stromal cells in the tumor microenvironment of the liver.

PubMed

Decker, Ningling Kang; Abdelmoneim, Soha S; Yaqoob, Usman; Hendrickson, Helen; Hormes, Joe; Bentley, Mike; Pitot, Henry; Urrutia, Raul; Gores, Greg J; Shah, Vijay H

2008-10-01

Tumor progression is regulated through paracrine interactions between tumor cells and stromal cells in the microenvironment, including endothelial cells and myofibroblasts. Nitric oxide (NO) is a key molecule in the regulation of tumor-microenvironment interactions, although its precise role is incompletely defined. By using complementary in vitro and in vivo approaches, we studied the effect of endothelial NO synthase (eNOS)-derived NO on liver tumor growth and metastasis in relation to adjacent stromal myofibroblasts and matrix because liver tumors maintain a rich, vascular stromal network enriched with phenotypically heterogeneous myofibroblasts. Mice with an eNOS deficiency developed liver tumors more frequently in response to carcinogens compared with control animals. In a surgical model of pancreatic cancer liver metastasis, eNOS overexpression in the tumor microenvironment attenuated both the number and size of tumor implants. NO promoted anoikis of tumor cells in vitro and limited their invasive capacity. Because tumor cell anoikis and invasion are both regulated by myofibroblast-derived matrix, we explored the effect of NO on tumor cell protease expression. Both microarray and Western blot analysis revealed eNOS-dependent down-regulation of the matrix protease cathepsin B within tumor cells, and silencing of cathepsin B attenuated tumor cell invasive capacity in a similar manner to that observed with eNOS overexpression. Thus, a NO gradient within the tumor microenvironment influences tumor progression through orchestrated molecular interactions between tumor cells and stroma.

MT4-MMP and EGFR expression levels are key biomarkers for breast cancer patient response to chemotherapy and erlotinib

PubMed Central

Yip, Cassandre; Foidart, Pierre; Somja, Joan; Truong, Alice; Lienard, Mehdi; Feyereisen, Emilie; Schroeder, Hélène; Gofflot, Stéphanie; Donneau, Anne-Françoise; Collignon, Joëlle; Delvenne, Philippe; Sounni, Nor Eddine; Jerusalem, Guy; Noël, Agnès

2017-01-01

Background: Triple-negative breast cancers (TNBC) are heterogeneous cancers with poor prognosis. We aimed to determine the clinical relevance of membrane type-4 matrix metalloproteinase (MT4-MMP), a membrane type matrix metalloproteinase that interacts with epidermal growth factor receptor (EGFR) overexpressed in >50% of TNBC. Methods: We conducted a retrospective immunohistochemical analysis on human TNBC samples (n=81) and validated our findings in in vitro and in vivo assays. Results: Membrane type-4 matrix metalloproteinase and EGFR are produced in 72.5% of TNBC samples, whereas those proteins are faintly produced by healthy tissues. Unexpectedly, tumour relapse after chemotherapy was reduced in samples highly positive for MT4-MMP. Mechanistically, this is ascribed to a higher sensitivity of MT4-MMP-producing cells to alkylating or intercalating chemotherapeutic agents, as assessed in vitro. In sharp contrast, MT4-MMP expression did not affect tumour cell sensitivity to paclitaxel that interferes with protease trafficking. Importantly, MT4-MMP expression sensitised cancer cells to erlotinib, a tyrosine kinase EGFR inhibitor. In a pre-clinical model, the growth of MT4-MMP overexpressing xenografts, but not of control ones, was reduced by epirubicin or erlotinib. The combination of suboptimal drug doses blocked drastically the growth of MT4-MMP-producing tumours. Conclusions: We demonstrate that MT4-MMP defines a sub-population of TNBC sensitive to a combination of DNA-targeting chemotherapeutic agents and anti-EGFR drugs. PMID:28196064

Defining the role of mesenchymal stromal cells on the regulation of matrix metalloproteinases in skeletal muscle cells

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

Sassoli, Chiara; Nosi, Daniele; Tani, Alessia

Recent studies indicate that mesenchymal stromal cell (MSC) transplantation improves healing of injured and diseased skeletal muscle, although the mechanisms of benefit are poorly understood. In the present study, we investigated whether MSCs and/or their trophic factors were able to regulate matrix metalloproteinase (MMP) expression and activity in different cells of the muscle tissue. MSCs in co-culture with C2C12 cells or their conditioned medium (MSC-CM) up-regulated MMP-2 and MMP-9 expression and function in the myoblastic cells; these effects were concomitant with the down-regulation of the tissue inhibitor of metalloproteinases (TIMP)-1 and -2 and with increased cell motility. In the singlemore » muscle fiber experiments, MSC-CM administration increased MMP-2/9 expression in Pax-7{sup +} satellite cells and stimulated their mobilization, differentiation and fusion. The anti-fibrotic properties of MSC-CM involved also the regulation of MMPs by skeletal fibroblasts and the inhibition of their differentiation into myofibroblasts. The treatment with SB-3CT, a potent MMP inhibitor, prevented in these cells, the decrease of α-smooth actin and type-I collagen expression induced by MSC-CM, suggesting that MSC-CM could attenuate the fibrogenic response through mechanisms mediated by MMPs. Our results indicate that growth factors and cytokines released by these cells may modulate the fibrotic response and improve the endogenous mechanisms of muscle repair/regeneration. - Highlights: • MSC-CM contains paracrine factors that up-regulate MMP expression and function in different skeletal muscle cells. • MSC-CM promotes myoblast and satellite cell migration, proliferation and differentiation. • MSC-CM negatively interferes with fibroblast-myoblast transition in primary skeletal fibroblasts. • Paracrine factors from MSCs modulate the fibrotic response and improve the endogenous mechanisms of muscle regeneration.« less

Le Châtelier reciprocal relations and the mechanical analog

NASA Astrophysics Data System (ADS)

Gilmore, Robert

1983-08-01

Le Châtelier's principle is discussed carefully in terms of two sets of simple thermodynamic examples. The principle is then formulated quantitatively for general thermodynamic systems. The formulation is in terms of a perturbation-response matrix, the Le Châtelier matrix [L]. Le Châtelier's principle is contained in the diagonal elements of this matrix, all of which exceed one. These matrix elements describe the response of a system to a perturbation of either its extensive or intensive variables. These response ratios are inverses of each other. The Le Châtelier matrix is symmetric, so that a new set of thermodynamic reciprocal relations is derived. This quantitative formulation is illustrated by a single simple example which includes the original examples and shows the reciprocities among them. The assumptions underlying this new quantitative formulation of Le Châtelier's principle are general and applicable to a wide variety of nonthermodynamic systems. Le Châtelier's principle is formulated quantitatively for mechanical systems in static equilibrium, and mechanical examples of this formulation are given.

On the role of particle cracking in flow and fracture of metal matrix composites

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

Brockenbrough, J.R.; Zok, F.W.

1995-01-01

The flow response of particle-reinforced metal matrix composites is studied using finite element methods. Unit cells containing either intact or cracked particles in a power law hardening matrix are used to determine the corresponding asymptotic flow strengths. The effects of the hardening exponent and the elastic mismatch between the particles and the matrix on the flow response are examined. For comparison, the flow response of power law hardening solids containing penny-shaped cracks is also evaluated. The latter results are found to be in reasonable agreement with those corresponding to composites that contain low volume fractions of cracked particles. The asymptoticmore » results are used to develop a one-dimensional constitutive law for composites which undergo progressive damage during tensile straining. This law is used to evaluate the strain at the onset of plastic instability. It is proposed that the instability strain be used as a measure of tensile ductility when the particle content is low and the particles are uniformly distributed through the matrix.« less

Finding a Hadamard matrix by simulated annealing of spin vectors

NASA Astrophysics Data System (ADS)

Bayu Suksmono, Andriyan

2017-05-01

Reformulation of a combinatorial problem into optimization of a statistical-mechanics system enables finding a better solution using heuristics derived from a physical process, such as by the simulated annealing (SA). In this paper, we present a Hadamard matrix (H-matrix) searching method based on the SA on an Ising model. By equivalence, an H-matrix can be converted into a seminormalized Hadamard (SH) matrix, whose first column is unit vector and the rest ones are vectors with equal number of -1 and +1 called SH-vectors. We define SH spin vectors as representation of the SH vectors, which play a similar role as the spins on Ising model. The topology of the lattice is generalized into a graph, whose edges represent orthogonality relationship among the SH spin vectors. Starting from a randomly generated quasi H-matrix Q, which is a matrix similar to the SH-matrix without imposing orthogonality, we perform the SA. The transitions of Q are conducted by random exchange of {+, -} spin-pair within the SH-spin vectors that follow the Metropolis update rule. Upon transition toward zeroth energy, the Q-matrix is evolved following a Markov chain toward an orthogonal matrix, at which the H-matrix is said to be found. We demonstrate the capability of the proposed method to find some low-order H-matrices, including the ones that cannot trivially be constructed by the Sylvester method.

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.

Nonharmonicity in vibrated granular solids

NASA Astrophysics Data System (ADS)

Schreck, Carl

2012-02-01

We have shown that granular packings composed of frictionless particles with repulsive contact interactions are strongly nonharmonic. When infinitesimally perturbed along linear response eigenmodes of the static packing, energy leaks from the original mode of vibration to a continuum of frequencies due solely to contact breaking even when the system is under significant compression. Further, vibrated packings possess well-defined equilibrium positions that are different than those of the unperturbed packing. The vibrational density of states obtained using the displacement matrix and velocity autocorrelation function methods exhibit an increase in the number of low-frequency modes over that obtained from linear response of the static packing. The form of the density of states in vibrated granular packings is reminiscent of the low-frequency behavior of the vibrational density of states in fluid systems. We also investigate the effects of inter-particle friction, dissipation, particle shape, and degree of positional order on the density of states and thermal transport properties in driven granular packings.

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

PubMed Central

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

2001-01-01

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

Renal Tubule Repair: Is Wnt/β-Catenin a Friend or Foe?

PubMed

Gewin, Leslie S

2018-01-24

Wnt/β-catenin signaling is extremely important for proper kidney development. This pathway is also upregulated in injured renal tubular epithelia, both in acute kidney injury and chronic kidney disease. The renal tubular epithelium is an important target of kidney injury, and its response (repair versus persistent injury) is critical for determining whether tubulointerstitial fibrosis, the hallmark of chronic kidney disease, develops. This review discusses how Wnt/β-catenin signaling in the injured tubular epithelia promotes either repair or fibrosis after kidney injury. There is data suggesting that epithelial Wnt/β-catenin signaling is beneficial in acute kidney injury and important in tubular progenitors responsible for epithelial repair. The role of Wnt/β-catenin signaling in chronically injured epithelia is less clear. There is convincing data that Wnt/β-catenin signaling in interstitial fibroblasts and pericytes contributes to the extracellular matrix accumulation that defines fibrosis. However, some recent studies question whether Wnt/β-catenin signaling in chronically injured epithelia actually promotes fibrosis or repair.

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

PubMed

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

2003-12-01

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

Micromechanical modeling of damage growth in titanium based metal-matrix composites

NASA Technical Reports Server (NTRS)

Sherwood, James A.; Quimby, Howard M.

1994-01-01

The thermomechanical behavior of continuous-fiber reinforced titanium based metal-matrix composites (MMC) is studied using the finite element method. A thermoviscoplastic unified state variable constitutive theory is employed to capture inelastic and strain-rate sensitive behavior in the Timetal-21s matrix. The SCS-6 fibers are modeled as thermoplastic. The effects of residual stresses generated during the consolidation process on the tensile response of the composites are investigated. Unidirectional and cross-ply geometries are considered. Differences between the tensile responses in composites with perfectly bonded and completely debonded fiber/matrix interfaces are discussed. Model simulations for the completely debonded-interface condition are shown to correlate well with experimental results.

Combinatorial Discovery of Defined Substrates That Promote a Stem Cell State in Malignant Melanoma

PubMed Central

2017-01-01

The tumor microenvironment is implicated in orchestrating cancer cell transformation and metastasis. However, specific cell–ligand interactions between cancer cells and the extracellular matrix are difficult to decipher due to a dynamic and multivariate presentation of many signaling molecules. Here we report a versatile peptide microarray platform that is capable of screening for cancer cell phenotypic changes in response to ligand–receptor interactions. Using a screen of 78 peptide combinations derived from proteins present in the melanoma microenvironment, we identify a proteoglycan binding and bone morphogenic protein 7 (BMP7) derived sequence that selectively promotes the expression of several putative melanoma initiating cell markers. We characterize signaling associated with each of these peptides in the activation of melanoma pro-tumorigenic signaling and reveal a role for proteoglycan mediated adhesion and signaling through Smad 2/3. A defined substratum that controls the state of malignant melanoma may prove useful in spatially normalizing a heterogeneous population of tumor cells for discovery of therapeutics that target a specific state and for identifying new drug targets and reagents for intervention. PMID:28573199

A Rapid Method of Genomic Array Analysis of Scaffold/Matrix Attachment Regions (S/MARs) Identifies a 2.5-Mb Region of Enhanced Scaffold/Matrix Attachment at a Human Neocentromere

PubMed Central

Sumer, Huseyin; Craig, Jeffrey M.; Sibson, Mandy; Choo, K.H. Andy

2003-01-01

Human neocentromeres are fully functional centromeres that arise at previously noncentromeric regions of the genome. We have tested a rapid procedure of genomic array analysis of chromosome scaffold/matrix attachment regions (S/MARs), involving the isolation of S/MAR DNA and hybridization of this DNA to a genomic BAC/PAC array. Using this procedure, we have defined a 2.5-Mb domain of S/MAR-enriched chromatin that fully encompasses a previously mapped centromere protein-A (CENP-A)-associated domain at a human neocentromere. We have independently verified this procedure using a previously established fluorescence in situ hybridization method on salt-treated metaphase chromosomes. In silico sequence analysis of the S/MAR-enriched and surrounding regions has revealed no outstanding sequence-related predisposition. This study defines the S/MAR-enriched domain of a higher eukaryotic centromere and provides a method that has broad application for the mapping of S/MAR attachment sites over large genomic regions or throughout a genome. PMID:12840048

Recurrent Neural Network for Computing the Drazin Inverse.

PubMed

Stanimirović, Predrag S; Zivković, Ivan S; Wei, Yimin

2015-11-01

This paper presents a recurrent neural network (RNN) for computing the Drazin inverse of a real matrix in real time. This recurrent neural network (RNN) is composed of n independent parts (subnetworks), where n is the order of the input matrix. These subnetworks can operate concurrently, so parallel and distributed processing can be achieved. In this way, the computational advantages over the existing sequential algorithms can be attained in real-time applications. The RNN defined in this paper is convenient for an implementation in an electronic circuit. The number of neurons in the neural network is the same as the number of elements in the output matrix, which represents the Drazin inverse. The difference between the proposed RNN and the existing ones for the Drazin inverse computation lies in their network architecture and dynamics. The conditions that ensure the stability of the defined RNN as well as its convergence toward the Drazin inverse are considered. In addition, illustrative examples and examples of application to the practical engineering problems are discussed to show the efficacy of the proposed neural network.

A reporter mouse model for in vivo tracing and in vitro molecular studies of melanocytic lineage cells and their diseases.

PubMed

Crawford, Melissa; Leclerc, Valerie; Dagnino, Lina

2017-08-15

Alterations in melanocytic lineage cells give rise to a plethora of distinct human diseases, including neurocristopathies, cutaneous pigmentation disorders, loss of vision and hearing, and melanoma. Understanding the ontogeny and biology of melanocytic cells, as well as how they interact with their surrounding environment, are key steps in the development of therapies for diseases that involve this cell lineage. Efforts to culture and characterize primary melanocytes from normal or genetically engineered mouse models have at times yielded contrasting observations. This is due, in part, to differences in the conditions used to isolate, purify and culture these cells in individual studies. By breeding ROSA mT/mG and Tyr::CreER T2 mice, we generated animals in which melanocytic lineage cells are identified through expression of green fluorescent protein. We also used defined conditions to systematically investigate the proliferation and migration responses of primary melanocytes on various extracellular matrix (ECM) substrates. Under our culture conditions, mouse melanocytes exhibit doubling times in the range of 10 days, and retain exponential proliferative capacity for 50-60 days. In culture, these melanocytes showed distinct responses to different ECM substrates. Specifically, laminin-332 promoted cell spreading, formation of dendrites, random motility and directional migration. In contrast, low or intermediate concentrations of collagen I promoted adhesion and acquisition of a bipolar morphology, and interfered with melanocyte forward movements. Our systematic evaluation of primary melanocyte responses emphasizes the importance of clearly defining culture conditions for these cells. This, in turn, is essential for the interpretation of melanocyte responses to extracellular cues and to understand the molecular basis of disorders involving the melanocytic cell lineage. © 2017. Published by The Company of Biologists Ltd.

A reporter mouse model for in vivo tracing and in vitro molecular studies of melanocytic lineage cells and their diseases

PubMed Central

Crawford, Melissa; Leclerc, Valerie

2017-01-01

ABSTRACT Alterations in melanocytic lineage cells give rise to a plethora of distinct human diseases, including neurocristopathies, cutaneous pigmentation disorders, loss of vision and hearing, and melanoma. Understanding the ontogeny and biology of melanocytic cells, as well as how they interact with their surrounding environment, are key steps in the development of therapies for diseases that involve this cell lineage. Efforts to culture and characterize primary melanocytes from normal or genetically engineered mouse models have at times yielded contrasting observations. This is due, in part, to differences in the conditions used to isolate, purify and culture these cells in individual studies. By breeding ROSAmT/mG and Tyr::CreERT2 mice, we generated animals in which melanocytic lineage cells are identified through expression of green fluorescent protein. We also used defined conditions to systematically investigate the proliferation and migration responses of primary melanocytes on various extracellular matrix (ECM) substrates. Under our culture conditions, mouse melanocytes exhibit doubling times in the range of 10 days, and retain exponential proliferative capacity for 50-60 days. In culture, these melanocytes showed distinct responses to different ECM substrates. Specifically, laminin-332 promoted cell spreading, formation of dendrites, random motility and directional migration. In contrast, low or intermediate concentrations of collagen I promoted adhesion and acquisition of a bipolar morphology, and interfered with melanocyte forward movements. Our systematic evaluation of primary melanocyte responses emphasizes the importance of clearly defining culture conditions for these cells. This, in turn, is essential for the interpretation of melanocyte responses to extracellular cues and to understand the molecular basis of disorders involving the melanocytic cell lineage. PMID:28642245

Matrix quality and disturbance frequency drive evolution of species behavior at habitat boundaries.

PubMed

Martin, Amanda E; Fahrig, Lenore

2015-12-01

Previous theoretical studies suggest that a species' landscape should influence the evolution of its dispersal characteristics, because landscape structure affects the costs and benefits of dispersal. However, these studies have not considered the evolution of boundary crossing, that is, the tendency of animals to cross from habitat to nonhabitat ("matrix"). It is important to understand this dispersal behavior, because of its effects on the probability of population persistence. Boundary-crossing behavior drives the rate of interaction with matrix, and thus, it influences the rate of movement among populations and the risk of dispersal mortality. We used an individual-based, spatially explicit model to simulate the evolution of boundary crossing in response to landscape structure. Our simulations predict higher evolved probabilities of boundary crossing in landscapes with more habitat, less fragmented habitat, higher-quality matrix, and more frequent disturbances (i.e., fewer generations between local population extinction events). Unexpectedly, our simulations also suggest that matrix quality and disturbance frequency have much stronger effects on the evolution of boundary crossing than either habitat amount or habitat fragmentation. Our results suggest that boundary-crossing responses are most affected by the costs of dispersal through matrix and the benefits of escaping local extinction events. Evolution of optimal behavior at habitat boundaries in response to the landscape may have implications for species in human-altered landscapes, because this behavior may become suboptimal if the landscape changes faster than the species' evolutionary response to that change. Understanding how matrix quality and habitat disturbance drive evolution of behavior at boundaries, and how this in turn influences the extinction risk of species in human-altered landscapes should help us identify species of conservation concern and target them for management.

Pointwise influence matrices for functional-response regression.

PubMed

Reiss, Philip T; Huang, Lei; Wu, Pei-Shien; Chen, Huaihou; Colcombe, Stan

2017-12-01

We extend the notion of an influence or hat matrix to regression with functional responses and scalar predictors. For responses depending linearly on a set of predictors, our definition is shown to reduce to the conventional influence matrix for linear models. The pointwise degrees of freedom, the trace of the pointwise influence matrix, are shown to have an adaptivity property that motivates a two-step bivariate smoother for modeling nonlinear dependence on a single predictor. This procedure adapts to varying complexity of the nonlinear model at different locations along the function, and thereby achieves better performance than competing tensor product smoothers in an analysis of the development of white matter microstructure in the brain. © 2017, The International Biometric Society.

Vortex manipulation in a superconducting matrix with view on applications

NASA Astrophysics Data System (ADS)

Milošević, M. V.; Peeters, F. M.

2010-05-01

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

Electrical and structural properties of ZnO synthesized via infiltration of lithographically defined polymer templates

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

Chang-Yong Nam; Stein, Aaron; Kisslinger, Kim

We investigate the electrical and structural properties of infiltration-synthesized ZnO. In-plane ZnO nanowire arrays with prescribed positional registrations are generated by infiltrating diethlyzinc and water vapor into lithographically defined SU-8 polymer templates and removing organic matrix by oxygen plasma ashing. Transmission electron microscopy reveals that homogeneously amorphous as-infiltrated polymer templates transform into highly nanocrystalline ZnO upon removal of organic matrix. Field-effect transistor device measurements show that the synthesized ZnO after thermal annealing displays a typical n-type behavior, ~1019 cm -3 carrier density, and ~0.1 cm 2 V -1 s -1 electron mobility, reflecting highly nanocrystalline internal structure. The results demonstratemore » the potential application of infiltration synthesis in fabricating metal oxide electronic devices.« less

Electrical and structural properties of ZnO synthesized via infiltration of lithographically defined polymer templates

DOE PAGES

Chang-Yong Nam; Stein, Aaron; Kisslinger, Kim; ...

2015-11-17

We investigate the electrical and structural properties of infiltration-synthesized ZnO. In-plane ZnO nanowire arrays with prescribed positional registrations are generated by infiltrating diethlyzinc and water vapor into lithographically defined SU-8 polymer templates and removing organic matrix by oxygen plasma ashing. Transmission electron microscopy reveals that homogeneously amorphous as-infiltrated polymer templates transform into highly nanocrystalline ZnO upon removal of organic matrix. Field-effect transistor device measurements show that the synthesized ZnO after thermal annealing displays a typical n-type behavior, ~1019 cm -3 carrier density, and ~0.1 cm 2 V -1 s -1 electron mobility, reflecting highly nanocrystalline internal structure. The results demonstratemore » the potential application of infiltration synthesis in fabricating metal oxide electronic devices.« less

Methods and means of 3D diffuse Mueller-matrix tomography of depolarizing optically anisotropic biological layers

NASA Astrophysics Data System (ADS)

Dubolazov, O. V.; Ushenko, V. O.; Trifoniuk, L.; Ushenko, Yu. O.; Zhytaryuk, V. G.; Prydiy, O. G.; Grytsyuk, M.; Kushnerik, L.; Meglinskiy, I.

2017-09-01

A new technique of Mueller-matrix mapping of polycrystalline structure of histological sections of biological tissues is suggested. The algorithms of reconstruction of distribution of parameters of linear and circular birefringence of prostate histological sections are found. The interconnections between such distributions and parameters of linear and circular birefringence of prostate tissue histological sections are defined. The comparative investigations of coordinate distributions of phase anisotropy parameters formed by fibrillar networks of prostate tissues of different pathological states (adenoma and carcinoma) are performed. The values and ranges of change of the statistical (moments of the 1st - 4th order) parameters of coordinate distributions of the value of linear and circular birefringence are defined. The objective criteria of cause of Benign and malignant conditions differentiation are determined.

The noncommutative family Atiyah-Patodi-Singer index theorem

NASA Astrophysics Data System (ADS)

Wang, Yong

2016-12-01

In this paper, we define the eta cochain form and prove its regularity when the kernel of a family of Dirac operators is a vector bundle. We decompose the eta form as a pairing of the eta cochain form with the Chern character of an idempotent matrix and we also decompose the Chern character of the index bundle for a fibration with boundary as a pairing of the family Chern-Connes character for a manifold with boundary with the Chern character of an idempotent matrix. We define the family b-Chern-Connes character and then we prove that it is entire and give its variation formula. By this variation formula, we prove another noncommutative family Atiyah-Patodi-Singer index theorem. Thus, we extend the results of Getzler and Wu to the family case.

Cytoskeletal remodeling of connective tissue fibroblasts in response to static stretch is dependent on matrix material properties

PubMed Central

Abbott, Rosalyn D; Koptiuch, Cathryn; Iatridis, James C; Howe, Alan K; Badger, Gary J; Langevin, Helene M

2012-01-01

In areolar “loose” connective tissue, fibroblasts remodel their cytoskeleton within minutes in response to static stretch resulting in increased cell body cross-sectional area that relaxes the tissue to a lower state of resting tension. It remains unknown whether the loosely arranged collagen matrix, characteristic of areolar connective tissue, is required for this cytoskeletal response to occur. The purpose of this study was to evaluate cytoskeletal remodeling of fibroblasts in and dissociated from areolar and dense connective tissue in response to 2 hours of static stretch in both native tissue and collagen gels of varying crosslinking. Rheometric testing indicated that the areolar connective tissue had a lower dynamic modulus and was more viscous than the dense connective tissue. In response to stretch, cells within the more compliant areolar connective tissue adopted a large “sheet-like” morphology that was in contrast to the smaller dendritic morphology in the dense connective tissue. By adjusting the in vitro collagen crosslinking, and the resulting dynamic modulus, it was demonstrated that cells dissociated from dense connective tissue are capable of responding when seeded into a compliant matrix, while cells dissociated from areolar connective tissue can lose their ability to respond when their matrix becomes stiffer. This set of experiments indicated stretch-induced fibroblast expansion was dependent on the distinct matrix material properties of areolar connective tissues as opposed to the cells’ tissue of origin. These results also suggest that disease and pathological processes with increased crosslinks, such as diabetes and fibrosis, could impair fibroblast responsiveness in connective tissues. PMID:22552950

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

Mechanical tension as a driver of connective tissue growth in vitro.

PubMed

Wilson, Cameron J; Pearcy, Mark J; Epari, Devakara R

2014-07-01

We propose the progressive mechanical expansion of cell-derived tissue analogues as a novel, growth-based approach to in vitro tissue engineering. The prevailing approach to producing tissue in vitro is to culture cells in an exogenous "scaffold" that provides a basic structure and mechanical support. This necessarily pre-defines the final size of the implantable material, and specific signals must be provided to stimulate appropriate cell growth, differentiation and matrix formation. In contrast, surgical skin expansion, driven by increments of stretch, produces increasing quantities of tissue without trauma or inflammation. This suggests that connective tissue cells have the innate ability to produce growth in response to elevated tension. We posit that this capacity is maintained in vitro, and that order-of-magnitude growth may be similarly attained in self-assembling cultures of cells and their own extracellular matrix. The hypothesis that growth of connective tissue analogues can be induced by mechanical expansion in vitro may be divided into three components: (1) tension stimulates cell proliferation and extracellular matrix synthesis; (2) the corresponding volume increase will relax the tension imparted by a fixed displacement; (3) the repeated application of static stretch will produce sustained growth and a tissue structure adapted to the tensile loading. Connective tissues exist in a state of residual tension, which is actively maintained by resident cells such as fibroblasts. Studies in vitro and in vivo have demonstrated that cellular survival, reproduction, and matrix synthesis and degradation are regulated by the mechanical environment. Order-of-magnitude increases in both bone and skin volume have been achieved clinically through staged expansion protocols, demonstrating that tension-driven growth can be sustained over prolonged periods. Furthermore, cell-derived tissue analogues have demonstrated mechanically advantageous structural adaptation in response to applied loading. Together, these data suggest that a program of incremental stretch constitutes an appealing way to replicate tissue growth in cell culture, by harnessing the constituent cells' innate mechanical responsiveness. In addition to offering a platform to study the growth and structural adaptation of connective tissues, tension-driven growth presents a novel approach to in vitro tissue engineering. Because the supporting structure is secreted and organised by the cells themselves, growth is not restricted by a "scaffold" of fixed size. This also minimises potential adverse reactions to exogenous materials upon implantation. Most importantly, we posit that the growth induced by progressive stretch will allow substantial volumes of connective tissue to be produced from relatively small initial cell numbers. Copyright © 2014 Elsevier Ltd. All rights reserved.

HBV-specific and global T-cell dysfunction in chronic hepatitis B

PubMed Central

Park, Jang-June; Wong, David K.; Wahed, Abdus S.; Lee, William M.; Feld, Jordan J.; Terrault, Norah; Khalili, Mandana; Sterling, Richard K.; Kowdley, Kris V.; Bzowej, Natalie; Lau, Daryl T.; Kim, W. Ray; Smith, Coleman; Carithers, Robert L.; Torrey, Keith W.; Keith, James W.; Levine, Danielle L.; Traum, Daniel; Ho, Suzanne; Valiga, Mary E.; Johnson, Geoffrey S.; Doo, Edward; Lok, Anna S. F.; Chang, Kyong-Mi

2015-01-01

Background & Aims T cells play a critical role in in viral infection. We examined whether T-cell effector and regulatory responses can define clinical stages of chronic hepatitis B (CHB). Methods We enrolled 200 adults with CHB who participated in the NIH-supported Hepatitis B Research Network from 2011 through 2013 and 20 uninfected individuals (controls). Peripheral blood lymphocytes from these subjects were analyzed for T-cell responses (proliferation and production of interferon-γ and interleukin-10) to overlapping hepatitis B virus (HBV) peptides (preS, S, preC, core, and reverse transcriptase), influenza matrix peptides, and lipopolysaccharide. T-cell expression of regulatory markers FOXP3, programmed death-1 (PD1), and cytotoxic T lymphocyte-associated antigen-4 (CTLA4) was examined by flow cytometry. Immune measures were compared with clinical parameters, including physician-defined immune-active, immune-tolerant, or inactive CHB phenotypes, in a blinded fashion. Results Compared to controls, patients with CHB had weak T-cell proliferative, interferon-γ, and interleukin-10 responses to HBV, with increased frequency of circulating FOXP3+CD127− regulatory T cells and CD4+ T-cell expression of PD1 and CTLA4. T-cell measures did not clearly distinguish between clinical CHB phenotypes, although the HBV core-specific T-cell response was weaker in HBeAg+ than HBeAg− patients (% responders: 3% vs 23%, P=.00008). Although in vitro blockade of PD1 or CTLA4 increased T-cell responses to HBV, the effect was weaker in HBeAg+ than HBeAg− patients. Furthermore, T-cell responses to influenza and lipopolysaccharide were weaker in CHB patients than controls. Conclusion HBV persists with virus-specific and global T-cell dysfunction mediated by multiple regulatory mechanisms including circulating HBeAg, but without distinct T-cell–based immune signatures for clinical phenotypes. These findings suggest additional T-cell independent or regulatory mechanisms of CHB pathogenesis that warrant further investigation. PMID:26684441

Density matrix perturbation theory for magneto-optical response of periodic insulators

NASA Astrophysics Data System (ADS)

Lebedeva, Irina; Tokatly, Ilya; Rubio, Angel

2015-03-01

Density matrix perturbation theory offers an ideal theoretical framework for the description of response of solids to arbitrary electromagnetic fields. In particular, it allows to consider perturbations introduced by uniform electric and magnetic fields under periodic boundary conditions, though the corresponding potentials break the translational invariance of the Hamiltonian. We have implemented the density matrix perturbation theory in the open-source Octopus code on the basis of the efficient Sternheimer approach. The procedures for responses of different order to electromagnetic fields, including electric polarizability, orbital magnetic susceptibility and magneto-optical response, have been developed and tested by comparison with the results for finite systems and for wavefunction-based perturbation theory, which is already available in the code. Additional analysis of the orbital magneto-optical response is performed on the basis of analytical models. Symmetry limitations to observation of the magneto-optical response are discussed. The financial support from the Marie Curie Fellowship PIIF-GA-2012-326435 (RespSpatDisp) is gratefully acknowledged.

Role of redoximiRs in fibrogenesis.

PubMed

Fierro-Fernández, Marta; Miguel, Verónica; Lamas, Santiago

2016-04-01

Fibrosis can be defined as an excessive accumulation of extracellular matrix (ECM) components, ultimately leading to stiffness, scarring and devitalized tissue. MicroRNAs (miRNAs) are short, 19-25 nucleotides (nt), non-coding RNAs involved in the post-transcriptional regulation of gene expression. Recently, miRNAs have also emerged as powerful regulators of fibrotic processes and have been termed "fibromiRs". Oxidative stress represents a self-perpetuating mechanism in fibrogenesis. MiRNAs can also influence the expression of genes responsible for the generation of reactive oxygen species (ROS) and antioxidant defence and are termed "redoximiRs". Here, we review the current knowledge of mechanisms by which "redoximiRs" regulate fibrogenesis. This new set of miRNAs may be called "redoxifibromiRs". Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

Early local differentiation of the cell wall matrix defines the contact sites in lobed mesophyll cells of Zea mays.

PubMed

Giannoutsou, E; Sotiriou, P; Apostolakos, P; Galatis, B

2013-10-01

The morphogenesis of lobed mesophyll cells (MCs) is highly controlled and coupled with intercellular space formation. Cortical microtubule rings define the number and the position of MC isthmi. This work investigated early events of MC morphogenesis, especially the mechanism defining the position of contacts between MCs. The distributions of plasmodesmata, the hemicelluloses callose and (1 → 3,1 → 4)-β-d-glucans (MLGs) and the pectin epitopes recognized by the 2F4, JIM5, JIM7 and LM6 antibodies were studied in the cell walls of Zea mays MCs. Matrix cell wall polysaccharides were immunolocalized in hand-made sections and in sections of material embedded in LR White resin. Callose was also localized using aniline blue in hand-made sections. Plasmodesmata distribution was examined by transmission electron microscopy. Before reorganization of the dispersed cortical microtubules into microtubule rings, particular bands of the longitudinal MC walls, where the MC contacts will form, locally differentiate by selective (1) deposition of callose and the pectin epitopes recognized by the 2F4, LM6, JIM5 and JIM7 antibodies, (2) degradation of MLGs and (3) formation of secondary plasmodesmata clusterings. This cell wall matrix differentiation persists in cell contacts of mature MCs. Simultaneously, the wall bands between those of future cell contacts differentiate with (1) deposition of local cell wall thickenings including cellulose microfibrils, (2) preferential presence of MLGs, (3) absence of callose and (4) transient presence of the pectins identified by the JIM5 and JIM7 antibodies. The wall areas between cell contacts expand determinately to form the cell isthmi and the cell lobes. The morphogenesis of lobed MCs is characterized by the early patterned differentiation of two distinct cell wall subdomains, defining the sites of the future MC contacts and of the future MC isthmi respectively. This patterned cell wall differentiation precedes cortical microtubule reorganization and may define microtubule ring disposition.

High Strain Rate Deformation Modeling of a Polymer Matrix Composite. Part 2; Composite Micromechanical Model

NASA Technical Reports Server (NTRS)

Goldberg, Robert K.; Stouffer, Donald C.

1998-01-01

Recently applications have exposed polymer matrix composite materials to very high strain rate loading conditions, requiring an ability to understand and predict the material behavior under these extreme conditions. In this second paper of a two part report, a three-dimensional composite micromechanical model is described which allows for the analysis of the rate dependent, nonlinear deformation response of a polymer matrix composite. Strain rate dependent inelastic constitutive equations utilized to model the deformation response of a polymer are implemented within the micromechanics method. The deformation response of two representative laminated carbon fiber reinforced composite materials with varying fiber orientation has been predicted using the described technique. The predicted results compare favorably to both experimental values and the response predicted by the Generalized Method of Cells, a well-established micromechanics analysis method.

Cellular control of connective tissue matrix tension.

PubMed

Langevin, Helene M; Nedergaard, Maiken; Howe, Alan K

2013-08-01

The biomechanical behavior of connective tissue in response to stretching is generally attributed to the molecular composition and organization of its extracellular matrix. It also is becoming apparent that fibroblasts play an active role in regulating connective tissue tension. In response to static stretching of the tissue, fibroblasts expand within minutes by actively remodeling their cytoskeleton. This dynamic change in fibroblast shape contributes to the drop in tissue tension that occurs during viscoelastic relaxation. We propose that this response of fibroblasts plays a role in regulating extracellular fluid flow into the tissue, and protects against swelling when the matrix is stretched. This article reviews the evidence supporting possible mechanisms underlying this response including autocrine purinergic signaling. We also discuss fibroblast regulation of connective tissue tension with respect to lymphatic flow, immune function, and cancer. Copyright © 2013 Wiley Periodicals, Inc.

Critique of Macro Flow/Damage Surface Representations for Metal Matrix Composites Using Micromechanics

NASA Technical Reports Server (NTRS)

Lissenden, Cliff J.; Arnold, Steven M.

1996-01-01

Guidance for the formulation of robust, multiaxial, constitutive models for advanced materials is provided by addressing theoretical and experimental issues using micromechanics. The multiaxial response of metal matrix composites, depicted in terms of macro flow/damage surfaces, is predicted at room and elevated temperatures using an analytical micromechanical model that includes viscoplastic matrix response as well as fiber-matrix debonding. Macro flow/damage surfaces (i.e., debonding envelopes, matrix threshold surfaces, macro 'yield' surfaces, surfaces of constant inelastic strain rate, and surfaces of constant dissipation rate) are determined for silicon carbide/titanium in three stress spaces. Residual stresses are shown to offset the centers of the flow/damage surfaces from the origin and their shape is significantly altered by debonding. The results indicate which type of flow/damage surfaces should be characterized and what loadings applied to provide the most meaningful experimental data for guiding theoretical model development and verification.

Development of 10×10 Matrix-anode MCP-PMT

NASA Astrophysics Data System (ADS)

Yang, Jie; Li, Yongbin; Xu, Pengxiao; Zhao, Wenjin

2018-02-01

10×10 matrix-anode is developed by high-temperature co-fired ceramics (HTCC) technology. Based on the new matrix-anode, a new kind of photon counting imaging detector - 10×10 matrix-anode MCP-PMT is developed, and its performance parameters are tested. HTCC technology is suitable for the MCP-PMT's air impermeability and its baking process. Its response uniformity is better than the metal-ceramic or metal-glass sealing anode, and it is also a promising method to realize a higher density matrix-anode.

Toric Networks, Geometric R-Matrices and Generalized Discrete Toda Lattices

NASA Astrophysics Data System (ADS)

Inoue, Rei; Lam, Thomas; Pylyavskyy, Pavlo

2016-11-01

We use the combinatorics of toric networks and the double affine geometric R-matrix to define a three-parameter family of generalizations of the discrete Toda lattice. We construct the integrals of motion and a spectral map for this system. The family of commuting time evolutions arising from the action of the R-matrix is explicitly linearized on the Jacobian of the spectral curve. The solution to the initial value problem is constructed using Riemann theta functions.

Comparison of clast and matrix dispersal in till: Charlo-Atholville area, north-central New Brunswick

USGS Publications Warehouse

Dickson, M.L.; Broster, B.E.; Parkhill, M.A.

2004-01-01

Striations and dispersal patterns for till clasts and matrix geochemistry are used to define flow directions of glacial transport across an area of about 800km2 in the Charlo-Atholville area of north-central New Brunswick. A total of 170 clast samples and 328 till matrix samples collected for geochemical analysis across the region, were analyzed for a total of 39 elements. Major lithologic contacts used here to delineate till clast provenance were based on recent bedrock mapping. Eleven known mineral occurrences and a gossan are used to define point source targets for matrix geochemical dispersal trains and to estimate probable distance and direction of transport from unknown sources. Clast trains are traceable for distances of approximately 10 km, whereas till geochemical dispersal patterns are commonly lost within 5 km of transport. Most dispersal patterns reflect more than a single direction of glacial transport. These data indicate that a single till sheet, 1-4 m thick, was deposited as the dominant ice-flow direction fluctuated between southeastward, eastward, and northward over the study area. Directions of early flow represent changes in ice sheet dominance, first from the northwest and then from the west. Locally, eastward and northward flow represent the maximum erosive phases. The last directions of flow are likely due to late glacial ice sheet drawdown towards the valley outlet at Baie des Chaleurs.

Configuration control of seven-degree-of-freedom arms

NASA Technical Reports Server (NTRS)

Seraji, Homayoun (Inventor); Long, Mark K. (Inventor); Lee, Thomas S. (Inventor)

1992-01-01

A seven degree of freedom robot arm with a six degree of freedom end effector is controlled by a processor employing a 6 by 7 Jacobian matrix for defining location and orientation of the end effector in terms of the rotation angles of the joints, a 1 (or more) by 7 Jacobian matrix for defining 1 (or more) user specified kinematic functions constraining location or movement of selected portions of the arm in terms of the joint angles, the processor combining the two Jacobian matrices to produce an augmented 7 (or more) by 7 Jacobian matrix, the processor effecting control by computing in accordance with forward kinematics from the augmented 7 by 7 Jacobian matrix and from the seven joint angles of the arm a set of seven desired joint angles for transmittal to the joint servo loops of the arm. One of the kinematic functions constraints the orientation of the elbow plane of the arm. Another one of the kinematic functions minimizes a sum of gravitational torques on the joints. Still another kinematic function constrains the location of the arm to perform collision avoidance. Generically, one kinematic function minimizes a sum of selected mechanical parameters of at least some of the joints associated with weighting coefficients which may be changed during arm movement. The mechanical parameters may be velocity errors or gravity torques associated with individual joints.

Configuration control of seven degree of freedom arms

NASA Technical Reports Server (NTRS)

Seraji, Homayoun (Inventor)

1995-01-01

A seven-degree-of-freedom robot arm with a six-degree-of-freedom end effector is controlled by a processor employing a 6-by-7 Jacobian matrix for defining location and orientation of the end effector in terms of the rotation angles of the joints, a 1 (or more)-by-7 Jacobian matrix for defining 1 (or more) user-specified kinematic functions constraining location or movement of selected portions of the arm in terms of the joint angles, the processor combining the two Jacobian matrices to produce an augmented 7 (or more)-by-7 Jacobian matrix, the processor effecting control by computing in accordance with forward kinematics from the augmented 7-by-7 Jacobian matrix and from the seven joint angles of the arm a set of seven desired joint angles for transmittal to the joint servo loops of the arms. One of the kinematic functions constrains the orientation of the elbow plane of the arm. Another one of the kinematic functions minimizing a sum of gravitational torques on the joints. Still another one of the kinematic functions constrains the location of the arm to perform collision avoidance. Generically, one of the kinematic functions minimizes a sum of selected mechanical parameters of at least some of the joints associated with weighting coefficients which may be changed during arm movement. The mechanical parameters may be velocity errors or position errors or gravity torques associated with individual joints.

A SIMPLE AND RAPID MATRIX-ASSISTED LASER DESORPTION/IONIZATION TIME OF FLIGHT MASS SPECTROMETRY METHOD TO SCREEN FISH PLASMA SAMPLES FOR ESTROGEN-RESPONSIVE BIOMARKERS

EPA Science Inventory

In this study, we describe and evaluate the performance of a simple and rapid mass spectral method for screening fish plasma for estrogen-responsive biomarkers using matrix assisted laster desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS) couopled with a short...

Elastic-plastic finite element analyses of an unidirectional, 9 vol percent tungsten fiber reinforced copper matrix composite

NASA Technical Reports Server (NTRS)

Sanfeliz, Jose G.

1993-01-01

Micromechanical modeling via elastic-plastic finite element analyses were performed to investigate the effects that the residual stresses and the degree of matrix work hardening (i.e., cold-worked, annealed) have upon the behavior of a 9 vol percent, unidirectional W/Cu composite, undergoing tensile loading. The inclusion of the residual stress-containing state as well as the simulated matrix material conditions proved to be significant since the Cu matrix material exhibited plastic deformation, which affected the subsequent tensile response of the composite system. The stresses generated during cooldown to room temperature from the manufacturing temperature were more of a factor on the annealed-matrix composite, since they induced the softened matrix to plastically flow. This event limited the total load-carrying capacity of this matrix-dominated, ductile-ductile type material system. Plastic deformation of the hardened-matrix composite during the thermal cooldown stage was not considerable, therefore, the composite was able to sustain a higher stress before showing any appreciable matrix plasticity. The predicted room temperature, stress-strain response, and deformation stages under both material conditions represented upper and lower bounds characteristic of the composite's tensile behavior. The initial deformation stage for the hardened material condition showed negligible matrix plastic deformation while for the annealed state, its initial deformation stage showed extensive matrix plasticity. Both material conditions exhibited a final deformation stage where the fiber and matrix were straining plastically. The predicted stress-strain results were compared to the experimental, room temperature, tensile stress-strain curve generated from this particular composite system. The analyses indicated that the actual thermal-mechanical state of the composite's Cu matrix, represented by the experimental data, followed the annealed material condition.

Biglycan, a danger signal that activates the NLRP3 inflammasome via toll-like and P2X receptors.

PubMed

Babelova, Andrea; Moreth, Kristin; Tsalastra-Greul, Wasiliki; Zeng-Brouwers, Jinyang; Eickelberg, Oliver; Young, Marian F; Bruckner, Peter; Pfeilschifter, Josef; Schaefer, Roland M; Gröne, Hermann-Josef; Schaefer, Liliana

2009-09-04

The role of endogenous inducers of inflammation is poorly understood. To produce the proinflammatory master cytokine interleukin (IL)-1beta, macrophages need double stimulation with ligands to both Toll-like receptors (TLRs) for IL-1beta gene transcription and nucleotide-binding oligomerization domain-like receptors for activation of the inflammasome. It is particularly intriguing to define how this complex regulation is mediated in the absence of an infectious trigger. Biglycan, a ubiquitous leucine-rich repeat proteoglycan of the extracellular matrix, interacts with TLR2/4 on macrophages. The objective of this study was to define the role of biglycan in the synthesis and activation of IL-1beta. Here we show that in macrophages, soluble biglycan induces the NLRP3/ASC inflammasome, activating caspase-1 and releasing mature IL-1beta without the need for additional costimulatory factors. This is brought about by the interaction of biglycan with TLR2/4 and purinergic P2X(4)/P2X(7) receptors, which induces receptor cooperativity. Furthermore, reactive oxygen species formation is involved in biglycan-mediated activation of the inflammasome. By signaling through TLR2/4, biglycan stimulates the expression of NLRP3 and pro-IL-1beta mRNA. Both in a model of non-infectious inflammatory renal injury (unilateral ureteral obstruction) and in lipopolysaccharide-induced sepsis, biglycan-deficient mice displayed lower levels of active caspase-1 and mature IL-1beta in the kidney, lung, and circulation. Our results provide evidence for direct activation of the NLRP3 inflammasome by biglycan and describe a fundamental paradigm of how tissue stress or injury is monitored by innate immune receptors detecting the release of the extracellular matrix components and turning such a signal into a robust inflammatory response.

Regulation of Cellular Redox Signaling by Matricellular Proteins in Vascular Biology, Immunology, and Cancer

PubMed Central

Kaur, Sukhbir

2017-01-01

Abstract Significance: In contrast to structural elements of the extracellular matrix, matricellular proteins appear transiently during development and injury responses, but their sustained expression can contribute to chronic disease. Through interactions with other matrix components and specific cell surface receptors, matricellular proteins regulate multiple signaling pathways, including those mediated by reactive oxygen and nitrogen species and H2S. Dysregulation of matricellular proteins contributes to the pathogenesis of vascular diseases and cancer. Defining the molecular mechanisms and receptors involved is revealing new therapeutic opportunities. Recent Advances: Thrombospondin-1 (TSP1) regulates NO, H2S, and superoxide production and signaling in several cell types. The TSP1 receptor CD47 plays a central role in inhibition of NO signaling, but other TSP1 receptors also modulate redox signaling. The matricellular protein CCN1 engages some of the same receptors to regulate redox signaling, and ADAMTS1 regulates NO signaling in Marfan syndrome. In addition to mediating matricellular protein signaling, redox signaling is emerging as an important pathway that controls the expression of several matricellular proteins. Critical Issues: Redox signaling remains unexplored for many matricellular proteins. Their interactions with multiple cellular receptors remains an obstacle to defining signaling mechanisms, but improved transgenic models could overcome this barrier. Future Directions: Therapeutics targeting the TSP1 receptor CD47 may have beneficial effects for treating cardiovascular disease and cancer and have recently entered clinical trials. Biomarkers are needed to assess their effects on redox signaling in patients and to evaluate how these contribute to their therapeutic efficacy and potential side effects. Antioxid. Redox Signal. 27, 874–911. PMID:28712304

Extracellular matrix structure governs invasion resistance in bacterial biofilms.

PubMed

Nadell, Carey D; Drescher, Knut; Wingreen, Ned S; Bassler, Bonnie L

2015-08-01

Many bacteria are highly adapted for life in communities, or biofilms. A defining feature of biofilms is the production of extracellular matrix that binds cells together. The biofilm matrix provides numerous fitness benefits, including protection from environmental stresses and enhanced nutrient availability. Here we investigate defense against biofilm invasion using the model bacterium Vibrio cholerae. We demonstrate that immotile cells, including those identical to the biofilm resident strain, are completely excluded from entry into resident biofilms. Motile cells can colonize and grow on the biofilm exterior, but are readily removed by shear forces. Protection from invasion into the biofilm interior is mediated by the secreted protein RbmA, which binds mother-daughter cell pairs to each other and to polysaccharide components of the matrix. RbmA, and the invasion protection it confers, strongly localize to the cell lineages that produce it.

Oxygen Diffusion and Reaction Kinetics in Continuous Fiber Ceramic Matrix Composites

NASA Technical Reports Server (NTRS)

Halbig, Michael C.; Eckel, Andrew J.; Cawley, James D.

1999-01-01

Previous stressed oxidation tests of C/SiC composites at elevated temperatures (350 C to 1500 C) and sustained stresses (69 MPa and 172 MPa) have led to the development of a finite difference cracked matrix model. The times to failure in the samples suggest oxidation occurred in two kinetic regimes defined by the rate controlling mechanisms (i.e. diffusion controlled and reaction controlled kinetics). Microstructural analysis revealed preferential oxidation along as-fabricated, matrix microcracks and also suggested two regimes of oxidation kinetics dependent on the oxidation temperature. Based on experimental results, observation, and theory, a finite difference model was developed. The model simulates the diffusion of oxygen into a matrix crack bridged by carbon fibers. The model facilitates the study of the relative importance of temperature, the reaction rate constant, and the diffusion coefficient on the overall oxidation kinetics.

Simple and practical approach for computing the ray Hessian matrix in geometrical optics.

PubMed

Lin, Psang Dain

2018-02-01

A method is proposed for simplifying the computation of the ray Hessian matrix in geometrical optics by replacing the angular variables in the system variable vector with their equivalent cosine and sine functions. The variable vector of a boundary surface is similarly defined in such a way as to exclude any angular variables. It is shown that the proposed formulations reduce the computation time of the Hessian matrix by around 10 times compared to the previous method reported by the current group in Advanced Geometrical Optics (2016). Notably, the method proposed in this study involves only polynomial differentiation, i.e., trigonometric function calls are not required. As a consequence, the computation complexity is significantly reduced. Five illustrative examples are given. The first three examples show that the proposed method is applicable to the determination of the Hessian matrix for any pose matrix, irrespective of the order in which the rotation and translation motions are specified. The last two examples demonstrate the use of the proposed Hessian matrix in determining the axial and lateral chromatic aberrations of a typical optical system.

Polar decomposition for attitude determination from vector observations

NASA Technical Reports Server (NTRS)

Bar-Itzhack, Itzhack Y.

1993-01-01

This work treats the problem of weighted least squares fitting of a 3D Euclidean-coordinate transformation matrix to a set of unit vectors measured in the reference and transformed coordinates. A closed-form analytic solution to the problem is re-derived. The fact that the solution is the closest orthogonal matrix to some matrix defined on the measured vectors and their weights is clearly demonstrated. Several known algorithms for computing the analytic closed form solution are considered. An algorithm is discussed which is based on the polar decomposition of matrices into the closest unitary matrix to the decomposed matrix and a Hermitian matrix. A somewhat longer improved algorithm is suggested too. A comparison of several algorithms is carried out using simulated data as well as real data from the Upper Atmosphere Research Satellite. The comparison is based on accuracy and time consumption. It is concluded that the algorithms based on polar decomposition yield a simple although somewhat less accurate solution. The precision of the latter algorithms increase with the number of the measured vectors and with the accuracy of their measurement.

Intrinsically disordered proteins drive enamel formation via an evolutionarily conserved self-assembly motif.

PubMed

Wald, Tomas; Spoutil, Frantisek; Osickova, Adriana; Prochazkova, Michaela; Benada, Oldrich; Kasparek, Petr; Bumba, Ladislav; Klein, Ophir D; Sedlacek, Radislav; Sebo, Peter; Prochazka, Jan; Osicka, Radim

2017-02-28

The formation of mineralized tissues is governed by extracellular matrix proteins that assemble into a 3D organic matrix directing the deposition of hydroxyapatite. Although the formation of bones and dentin depends on the self-assembly of type I collagen via the Gly-X-Y motif, the molecular mechanism by which enamel matrix proteins (EMPs) assemble into the organic matrix remains poorly understood. Here we identified a Y/F-x-x-Y/L/F-x-Y/F motif, evolutionarily conserved from the first tetrapods to man, that is crucial for higher order structure self-assembly of the key intrinsically disordered EMPs, ameloblastin and amelogenin. Using targeted mutations in mice and high-resolution imaging, we show that impairment of ameloblastin self-assembly causes disorganization of the enamel organic matrix and yields enamel with disordered hydroxyapatite crystallites. These findings define a paradigm for the molecular mechanism by which the EMPs self-assemble into supramolecular structures and demonstrate that this process is crucial for organization of the organic matrix and formation of properly structured enamel.

Systems and methods for deactivating a matrix converter

DOEpatents

Ransom, Ray M.

2013-04-02

Systems and methods are provided for deactivating a matrix conversion module. An electrical system comprises an alternating current (AC) interface, a matrix conversion module coupled to the AC interface, an inductive element coupled between the AC interface and the matrix conversion module, and a control module. The control module is coupled to the matrix conversion module, and in response to a shutdown condition, the control module is configured to operate the matrix conversion module to deactivate the first conversion module when a magnitude of a current through the inductive element is less than a threshold value.

Role of integrin-linked kinase in regulating phosphorylation of Akt and fibroblast survival in type I collagen matrices through a beta1 integrin viability signaling pathway.

PubMed

Nho, Richard Seonghun; Xia, Hong; Kahm, Judy; Kleidon, Jill; Diebold, Deanna; Henke, Craig A

2005-07-15

A beta1 integrin phosphatidylinositol 3-kinase/Akt pathway regulates fibroblast survival in collagen matrices. When fibroblasts attach to collagen, Akt becomes phosphorylated, providing a survival signal. In contrast, in response to mechanical forces generated during collagen contraction, Akt is dephosphorylated and fibroblasts undergo apoptosis. The kinase(s) responsible for regulating Akt phosphorylation in response to matrix-derived mechanical signals are unclear. Integrin-linked kinase (ILK) is associated with the beta1 integrin in the focal adhesion complex and as such is a candidate kinase that may regulate Akt phosphorylation and fibroblast viability. Nevertheless, there is no direct evidence that matrix-derived mechanical forces regulate cell viability by modulating ILK activity. Here, we show that ILK activity decreased in response to collagen matrix contraction, which correlated with Akt dephosphorylation and induction of fibroblast apoptosis. In contrast, enforced activation of beta1 integrin by activating antibody preserved ILK and Akt activity during collagen matrix contraction, and this is associated with protection from collagen contraction-induced apoptosis. Knock-down of ILK by small, interfering RNA (siRNA) attenuated Akt phosphorylation in response to ligation of beta1 integrin by collagen or activating antibody and enhanced fibroblast apoptosis in response to collagen contraction. Kinase dead ILK attenuated Akt phosphorylation and enhanced fibroblast apoptosis, whereas hyperactive and wild type ILK augmented Akt phosphorylation and protected fibroblasts from apoptosis. Constitutively active Akt preserved Akt activity and rescued ILK siRNA-treated fibroblasts from collagen contraction-induced apoptosis. These data establish that matrix-derived mechanical forces sensed by beta1 integrin are capable of modulating ILK activity which regulates fibroblast viability via an Akt-dependent mechanism.

Interaction of electromagnetic fields with chondrocytes in gel culture

NASA Astrophysics Data System (ADS)

Grodzinsky, Alan J.; Buschmann, Michael D.; Gluzband, Yehezkiel A.

1992-01-01

The specific objectives of this research period were: (1) to quantify the effect of applied electric fields on chondrocyte metabolism, using a range of stimulation frequencies and amplitudes; (2) to compare the chondrocyte biosynthetic response to applied fields at early times in agarose gel culture before an extracellular matrix has accumulated and at later times after significant deposition of matrix around and between the cells; and (3) to begin to interpret the biosynthetic response to applied fields in terms of models of physical mechanisms. The results of these studies suggest that electric fields applied to chondrocytes in agarose can modulate the synthesis of proteoglycans and protein constituents. Biosynthesis may be inhibited or stimulated depending on the amplitude of the applied current density. In addition, the presence of extracellular matrix may enhance the ability of normal chondrocytes and cells in intact cartilage to respond to electric fields, although the presence of matrix was not required for the stimulatory response to be observed with Swarm rat chondrosarcoma cells.

The neurovascular unit, matrix proteases, and innate inflammation.

PubMed

del Zoppo, Gregory J

2010-10-01

In the central nervous system, microvessel-neuron interactions appear highly coordinated. The rapid simultaneous responses of the microvasculature, neurons, and glia to focal ischemia in experimental ischemic stroke suggest that these responses could be viewed in a unitary fashion, rather than as individual components. The "neurovascular unit" consists of microvessels (endothelial cells-basal lamina matrix-astrocyte end-feet [and pericytes]), astrocytes, neurons and their axons, and other supporting cells that are likely to modulate the function of the "unit." Each cell component generates an inflammatory response to ischemia. Matrix metalloproteinase (MMP)-9 was first associated with hemorrhagic transformation following focal ischemia in an experimental model. A series of studies of ischemic stroke patients also suggests a relationship between MMP-9 levels and several consequences of ischemic injury, including hemorrhagic transformation. Recent experimental work suggests specific cell sources for MMP-9 generation and for matrix proteases from four distinct families that could impact neurovascular unit integrity. © 2010 New York Academy of Sciences.

Tissue matrix arrays for high throughput screening and systems analysis of cell function

PubMed Central

Beachley, Vince Z.; Wolf, Matthew T.; Sadtler, Kaitlyn; Manda, Srikanth S.; Jacobs, Heather; Blatchley, Michael; Bader, Joel S.; Pandey, Akhilesh; Pardoll, Drew; Elisseeff, Jennifer H.

2015-01-01

Cell and protein arrays have demonstrated remarkable utility in the high-throughput evaluation of biological responses; however, they lack the complexity of native tissue and organs. Here, we describe tissue extracellular matrix (ECM) arrays for screening biological outputs and systems analysis. We spotted processed tissue ECM particles as two-dimensional arrays or incorporated them with cells to generate three-dimensional cell-matrix microtissue arrays. We then investigated the response of human stem, cancer, and immune cells to tissue ECM arrays originating from 11 different tissues, and validated the 2D and 3D arrays as representative of the in vivo microenvironment through quantitative analysis of tissue-specific cellular responses, including matrix production, adhesion and proliferation, and morphological changes following culture. The biological outputs correlated with tissue proteomics, and network analysis identified several proteins linked to cell function. Our methodology enables broad screening of ECMs to connect tissue-specific composition with biological activity, providing a new resource for biomaterials research and translation. PMID:26480475

Optimizing dentin bond durability: strategies to prevent hydrolytic degradation of the hybrid layer

PubMed Central

Tjäderhane, Leo; Nascimento, Fabio D.; Breschi, Lorenzo; Mazzoni, Annalisa; Tersariol, Ivarne L.S.; Geraldeli, Saulo; Tezvergil-Mutluay, Arzu; Carrilho, Marcela; Carvalho, Ricardo M.; Tay, Franklin R.; Pashley, David H.

2014-01-01

Objectives Endogenous dentin collagenolytic enzymes, matrix metalloproteinases (MMPs) and cysteine cathepsins, are responsible for the time-related hydrolysis of collagen matrix of the hybrid layers. As the integrity of the collagen matrix is essential for the preservation of long-term dentin bond strength, inhibition or inactivation of endogenous dentin proteases is necessary for durable resin-bonded composite resin restorations. Methods Dentin contains collagenolytic enzymes, matrix metalloproteinases (MMPs) and cysteine cathepsins, which are responsible for the hydrolytic degradation of collagen matrix in the bonded interface. Several tentative approaches to prevent enzyme function either directly or indirectly have been proposed in the literature. Results Chlorhexidine, a general inhibitor of both MMPs and cysteine cathepsins, applied before primer/adhesive application is the most tested method. In general, these experiments have shown that enzyme inhibition is a promising scheme to improve hybrid layer preservation and bond strength durability. Other enzyme inhibitors, e.g. enzyme-inhibiting monomers and antimicrobial compounds, may be considered promising alternatives that would allow more simple clinical application than chlorhexidine. Cross-linking collagen and/or dentin organic matrix-bound enzymes could render hybrid layer organic matrix resistant to degradation, and complete removal of water from the hybrid layer with ethanol wet bonding or biomimetic remineralization should eliminate hydrolysis of both collagen and resin components. Significance Identification of the enzymes responsible for the hydrolysis of hybrid layer collagen and understanding their function has prompted several innovative approaches to retain the hybrid layer integrity and strong dentin bonding. The ultimate goal, prevention of collagen matrix degradation with techniques and commercially available materials that are simple and effective in clinical settings may be achievable in several ways, and will likely become reality in the near future. PMID:23953737

Silencing by nuclear matrix attachment distinguishes cell-type specificity: association with increased proliferation capacity.

PubMed

Linnemann, Amelia K; Krawetz, Stephen A

2009-05-01

DNA loop organization by nuclear scaffold/matrix attachment is a key regulator of gene expression that may provide a means to modulate phenotype. We have previously shown that attachment of genes to the NaCl-isolated nuclear matrix correlates with their silencing in HeLa cells. In contrast, expressed genes were associated with the lithium 3,5-diiodosalicylate (LIS)-isolated nuclear scaffold. To define their role in determining phenotype matrix attached regions (MARs) on human chromosomes 14-18 were identified as a function of expression in a primary cell line. The locations of MARs in aortic adventitial fibroblast (AoAF) cells were very stable (r = 0.909) and 96% of genes attached at MARs are silent (P < 0.001). Approximately one-third of the genes uniquely expressed in AoAF cells were associated with the HeLa cell nuclear matrix and silenced. Comparatively, 81% were associated with the AoAF cell nuclear scaffold (P < 0.001) and expressed. This suggests that nuclear scaffold/matrix association mediates a portion of cell type-specific gene expression thereby modulating phenotype. Interestingly, nuclear matrix attachment and thus silencing of specific genes that regulate proliferation and maintain the integrity of the HeLa cell genome suggests that transformation may at least in part be achieved through aberrant nuclear matrix attachment.

Preconditioned Alternating Projection Algorithms for Maximum a Posteriori ECT Reconstruction

PubMed Central

Krol, Andrzej; Li, Si; Shen, Lixin; Xu, Yuesheng

2012-01-01

We propose a preconditioned alternating projection algorithm (PAPA) for solving the maximum a posteriori (MAP) emission computed tomography (ECT) reconstruction problem. Specifically, we formulate the reconstruction problem as a constrained convex optimization problem with the total variation (TV) regularization. We then characterize the solution of the constrained convex optimization problem and show that it satisfies a system of fixed-point equations defined in terms of two proximity operators raised from the convex functions that define the TV-norm and the constrain involved in the problem. The characterization (of the solution) via the proximity operators that define two projection operators naturally leads to an alternating projection algorithm for finding the solution. For efficient numerical computation, we introduce to the alternating projection algorithm a preconditioning matrix (the EM-preconditioner) for the dense system matrix involved in the optimization problem. We prove theoretically convergence of the preconditioned alternating projection algorithm. In numerical experiments, performance of our algorithms, with an appropriately selected preconditioning matrix, is compared with performance of the conventional MAP expectation-maximization (MAP-EM) algorithm with TV regularizer (EM-TV) and that of the recently developed nested EM-TV algorithm for ECT reconstruction. Based on the numerical experiments performed in this work, we observe that the alternating projection algorithm with the EM-preconditioner outperforms significantly the EM-TV in all aspects including the convergence speed, the noise in the reconstructed images and the image quality. It also outperforms the nested EM-TV in the convergence speed while providing comparable image quality. PMID:23271835

Preconditioned alternating projection algorithms for maximum a posteriori ECT reconstruction

NASA Astrophysics Data System (ADS)

Krol, Andrzej; Li, Si; Shen, Lixin; Xu, Yuesheng

2012-11-01

We propose a preconditioned alternating projection algorithm (PAPA) for solving the maximum a posteriori (MAP) emission computed tomography (ECT) reconstruction problem. Specifically, we formulate the reconstruction problem as a constrained convex optimization problem with the total variation (TV) regularization. We then characterize the solution of the constrained convex optimization problem and show that it satisfies a system of fixed-point equations defined in terms of two proximity operators raised from the convex functions that define the TV-norm and the constraint involved in the problem. The characterization (of the solution) via the proximity operators that define two projection operators naturally leads to an alternating projection algorithm for finding the solution. For efficient numerical computation, we introduce to the alternating projection algorithm a preconditioning matrix (the EM-preconditioner) for the dense system matrix involved in the optimization problem. We prove theoretically convergence of the PAPA. In numerical experiments, performance of our algorithms, with an appropriately selected preconditioning matrix, is compared with performance of the conventional MAP expectation-maximization (MAP-EM) algorithm with TV regularizer (EM-TV) and that of the recently developed nested EM-TV algorithm for ECT reconstruction. Based on the numerical experiments performed in this work, we observe that the alternating projection algorithm with the EM-preconditioner outperforms significantly the EM-TV in all aspects including the convergence speed, the noise in the reconstructed images and the image quality. It also outperforms the nested EM-TV in the convergence speed while providing comparable image quality.

Temperature Dependence of Electrical Resistance of Woven Melt-Infiltrated SiCf/SiC Ceramic Matrix Composites

NASA Technical Reports Server (NTRS)

Appleby, Matthew P.; Morscher, Gregory N.; Zhu, Dongming

2016-01-01

Recent studies have successfully shown the use of electrical resistance (ER)measurements to monitor room temperature damage accumulation in SiC fiber reinforced SiC matrix composites (SiCf/SiC) Ceramic Matrix Composites (CMCs). In order to determine the feasibility of resistance monitoring at elevated temperatures, the present work investigates the temperature dependent electrical response of various MI (Melt Infiltrated)-CVI (Chemical Vapor Infiltrated) SiC/SiC composites containing Hi-Nicalon Type S, Tyranno ZMI and SA reinforcing fibers. Test were conducted using a commercially available isothermal testing apparatus as well as a novel, laser-based heating approach developed to more accurately simulate thermomechanical testing of CMCs. Secondly, a post-test inspection technique is demonstrated to show the effect of high-temperature exposure on electrical properties. Analysis was performed to determine the respective contribution of the fiber and matrix to the overall composite conductivity at elevated temperatures. It was concluded that because the silicon-rich matrix material dominates the electrical response at high temperature, ER monitoring would continue to be a feasible method for monitoring stress dependent matrix cracking of melt-infiltrated SiC/SiC composites under high temperature mechanical testing conditions. Finally, the effect of thermal gradients generated during localized heating of tensile coupons on overall electrical response of the composite is determined.

Inelastic deformation of metal matrix composites

NASA Technical Reports Server (NTRS)

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

1993-01-01

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

Stability of the matrix model in operator interpretation

NASA Astrophysics Data System (ADS)

Sakai, Katsuta

2017-12-01

The IIB matrix model is one of the candidates for nonperturbative formulation of string theory, and it is believed that the model contains gravitational degrees of freedom in some manner. In some preceding works, it was proposed that the matrix model describes the curved space where the matrices represent differential operators that are defined on a principal bundle. In this paper, we study the dynamics of the model in this interpretation, and point out the necessity of the principal bundle from the viewpoint of the stability and diffeomorphism invariance. We also compute the one-loop correction which yields a mass term for each field due to the principal bundle. We find that the stability is not violated.

Numerical modeling of thermal conductive heating in fractured bedrock.

PubMed

Baston, Daniel P; Falta, Ronald W; Kueper, Bernard H

2010-01-01

Numerical modeling was employed to study the performance of thermal conductive heating (TCH) in fractured shale under a variety of hydrogeological conditions. Model results show that groundwater flow in fractures does not significantly affect the minimum treatment zone temperature, except near the beginning of heating or when groundwater influx is high. However, fracture and rock matrix properties can significantly influence the time necessary to remove all liquid water (i.e., reach superheated steam conditions) in the treatment area. Low matrix permeability, high matrix porosity, and wide fracture spacing can contribute to boiling point elevation in the rock matrix. Consequently, knowledge of these properties is important for the estimation of treatment times. Because of the variability in boiling point throughout a fractured rock treatment zone and the absence of a well-defined constant temperature boiling plateau in the rock matrix, it may be difficult to monitor the progress of thermal treatment using temperature measurements alone. Copyright © 2010 The Author(s). Journal compilation © 2010 National Ground Water Association.

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

PubMed

Ippolito, Adelaide; Viggiani, Vincenzo

2014-01-01

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

Inspiration from heart development: Biomimetic development of functional human cardiac organoids.

PubMed

Richards, Dylan J; Coyle, Robert C; Tan, Yu; Jia, Jia; Wong, Kerri; Toomer, Katelynn; Menick, Donald R; Mei, Ying

2017-10-01

Recent progress in human organoids has provided 3D tissue systems to model human development, diseases, as well as develop cell delivery systems for regenerative therapies. While direct differentiation of human embryoid bodies holds great promise for cardiac organoid production, intramyocardial cell organization during heart development provides biological foundation to fabricate human cardiac organoids with defined cell types. Inspired by the intramyocardial organization events in coronary vasculogenesis, where a diverse, yet defined, mixture of cardiac cell types self-organizes into functional myocardium in the absence of blood flow, we have developed a defined method to produce scaffold-free human cardiac organoids that structurally and functionally resembled the lumenized vascular network in the developing myocardium, supported hiPSC-CM development and possessed fundamental cardiac tissue-level functions. In particular, this development-driven strategy offers a robust, tunable system to examine the contributions of individual cell types, matrix materials and additional factors for developmental insight, biomimetic matrix composition to advance biomaterial design, tissue/organ-level drug screening, and cell therapy for heart repair. Copyright © 2017 Elsevier Ltd. All rights reserved.

Spectral properties of Google matrix of Wikipedia and other networks

NASA Astrophysics Data System (ADS)

Ermann, Leonardo; Frahm, Klaus M.; Shepelyansky, Dima L.

2013-05-01

We study the properties of eigenvalues and eigenvectors of the Google matrix of the Wikipedia articles hyperlink network and other real networks. With the help of the Arnoldi method, we analyze the distribution of eigenvalues in the complex plane and show that eigenstates with significant eigenvalue modulus are located on well defined network communities. We also show that the correlator between PageRank and CheiRank vectors distinguishes different organizations of information flow on BBC and Le Monde web sites.

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.

Micromechanics and effective elastoplastic behavior of two-phase metal matrix composites

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

Ju, J.W.; Chen, T.M.

A micromechanical framework is presented to predict effective (overall) elasto-(visco-)plastic behavior of two-phase particle-reinforced metal matrix composites (PRMMC). In particular, the inclusion phase (particle) is assumed to be elastic and the matrix material is elasto-(visco-)plastic. Emanating from Ju and Chen's (1994a,b) work on effective elastic properties of composites containing many randomly dispersed inhomogeneities, effective elastoplastic deformations and responses of PRMMC are estimated by means of the effective yield criterion'' derived micromechanically by considering effects due to elastic particles embedded in the elastoplastic matrix. The matrix material is elastic or plastic, depending on local stress and deformation, and obeys general plasticmore » flow rule and hardening law. Arbitrary (general) loadings and unloadings are permitted in the framework through the elastic predictor-plastic corrector two-step operator splitting methodology. The proposed combined micromechanical and computational approach allows one to estimate overall elastoplastic responses of PRMMCs by accounting for the microstructural information (such as the spatial distribution and micro-geometry of particles), elastic properties of constituent phases, and the plastic behavior of the matrix-only materials.« less

A general theoretical framework for interpreting patient-reported outcomes estimated from ordinally scaled item responses.

PubMed

Massof, Robert W

2014-10-01

A simple theoretical framework explains patient responses to items in rating scale questionnaires. Fixed latent variables position each patient and each item on the same linear scale. Item responses are governed by a set of fixed category thresholds, one for each ordinal response category. A patient's item responses are magnitude estimates of the difference between the patient variable and the patient's estimate of the item variable, relative to his/her personally defined response category thresholds. Differences between patients in their personal estimates of the item variable and in their personal choices of category thresholds are represented by random variables added to the corresponding fixed variables. Effects of intervention correspond to changes in the patient variable, the patient's response bias, and/or latent item variables for a subset of items. Intervention effects on patients' item responses were simulated by assuming the random variables are normally distributed with a constant scalar covariance matrix. Rasch analysis was used to estimate latent variables from the simulated responses. The simulations demonstrate that changes in the patient variable and changes in response bias produce indistinguishable effects on item responses and manifest as changes only in the estimated patient variable. Changes in a subset of item variables manifest as intervention-specific differential item functioning and as changes in the estimated person variable that equals the average of changes in the item variables. Simulations demonstrate that intervention-specific differential item functioning produces inefficiencies and inaccuracies in computer adaptive testing. © The Author(s) 2013 Reprints and permissions: sagepub.co.uk/journalsPermissions.nav.

Numerical Differentiation Methods for Computing Error Covariance Matrices in Item Response Theory Modeling: An Evaluation and a New Proposal

ERIC Educational Resources Information Center

Tian, Wei; Cai, Li; Thissen, David; Xin, Tao

2013-01-01

In item response theory (IRT) modeling, the item parameter error covariance matrix plays a critical role in statistical inference procedures. When item parameters are estimated using the EM algorithm, the parameter error covariance matrix is not an automatic by-product of item calibration. Cai proposed the use of Supplemented EM algorithm for…

Visualizing phase transition behavior of dilute stimuli responsive polymer solutions via Mueller matrix polarimetry.

PubMed

Narayanan, Amal; Chandel, Shubham; Ghosh, Nirmalya; De, Priyadarsi

2015-09-15

Probing volume phase transition behavior of superdiluted polymer solutions both micro- and macroscopically still persists as an outstanding challenge. In this regard, we have explored 4 × 4 spectral Mueller matrix measurement and its inverse analysis for excavating the microarchitectural facts about stimuli responsiveness of "smart" polymers. Phase separation behavior of thermoresponsive poly(N-isopropylacrylamide) (PNIPAM) and pH responsive poly(N,N-(dimethylamino)ethyl methacrylate) (PDMAEMA) and their copolymers were analyzed in terms of Mueller matrix derived polarization parameters, namely, depolarization (Δ), diattenuation (d), and linear retardance (δ). The Δ, d, and δ parameters provided useful information on both macro- and microstructural alterations during the phase separation. Additionally, the two step action ((i) breakage of polymer-water hydrogen bonding and (ii) polymer-polymer aggregation) at the molecular microenvironment during the cloud point generation was successfully probed via these parameters. It is demonstrated that, in comparison to the present techniques available for assessing the hydrophobic-hydrophilic switch over of simple stimuli-responsive polymers, Mueller matrix polarimetry offers an important advantage requiring a few hundred times dilute polymer solution (0.01 mg/mL, 1.1-1.4 μM) at a low-volume format.

Multi-fracture response of cross-ply ceramic composites

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

Erdman, D.L.; Weitsman, Y.J.

1996-12-31

Ceramic matrix composites are candidate materials for high temperature applications due to their ability to retain mechanical properties. However, in view of the relatively low transverse strength and ductility associated with unidirectional ceramic matrix lay-ups, it is necessary to consider multi-directional reinforcement for any practical structural application. The simplest laminate that would provide multi-directional toughness would be the cross-ply lay-up. Although there are numerous publications concerned with modeling of the stress-strain response of unidirectional ceramic matrix laminates, there are relatively few investigations in the current literature which deal with laminates such as the cross-ply lay-up. Additionally, the aforementioned publications aremore » often incomplete since they fail to address the failure mechanisms associated with this lay-up in a comprehensive manner and consequently have limited success in correlating experimental stress-strain response with mechanical test results. Furthermore, many current experimental investigations fail to report the details of damage evolution and stress-strain response which are required for correlation with analyses. This investigation presents a comprehensive extended shear-lag type analysis that considers transverse matrix cracking in the 90{degree} plies, the non-linearity of the 0{degree} plies, and slip at the 0/90 ply interface.« less

Modelling and Optimization of Polycaprolactone Ultrafine-Fibres Electrospinning Process Using Response Surface Methodology

PubMed Central

Ruys, Andrew J.

2018-01-01

Electrospun fibres have gained broad interest in biomedical applications, including tissue engineering scaffolds, due to their potential in mimicking extracellular matrix and producing structures favourable for cell and tissue growth. The development of scaffolds often involves multivariate production parameters and multiple output characteristics to define product quality. In this study on electrospinning of polycaprolactone (PCL), response surface methodology (RSM) was applied to investigate the determining parameters and find optimal settings to achieve the desired properties of fibrous scaffold for acetabular labrum implant. The results showed that solution concentration influenced fibre diameter, while elastic modulus was determined by solution concentration, flow rate, temperature, collector rotation speed, and interaction between concentration and temperature. Relationships between these variables and outputs were modelled, followed by an optimization procedure. Using the optimized setting (solution concentration of 10% w/v, flow rate of 4.5 mL/h, temperature of 45 °C, and collector rotation speed of 1500 RPM), a target elastic modulus of 25 MPa could be achieved at a minimum possible fibre diameter (1.39 ± 0.20 µm). This work demonstrated that multivariate factors of production parameters and multiple responses can be investigated, modelled, and optimized using RSM. PMID:29562614

Nano- and microstructured materials for in vitro studies of the physiology of vascular cells

PubMed Central

Chen, Hao; Biela, Sarah A; Kaufmann, Dieter

2016-01-01

The extracellular environment of vascular cells in vivo is complex in its chemical composition, physical properties, and architecture. Consequently, it has been a great challenge to study vascular cell responses in vitro, either to understand their interaction with their native environment or to investigate their interaction with artificial structures such as implant surfaces. New procedures and techniques from materials science to fabricate bio-scaffolds and surfaces have enabled novel studies of vascular cell responses under well-defined, controllable culture conditions. These advancements are paving the way for a deeper understanding of vascular cell biology and materials–cell interaction. Here, we review previous work focusing on the interaction of vascular smooth muscle cells (SMCs) and endothelial cells (ECs) with materials having micro- and nanostructured surfaces. We summarize fabrication techniques for surface topographies, materials, geometries, biochemical functionalization, and mechanical properties of such materials. Furthermore, various studies on vascular cell behavior and their biological responses to micro- and nanostructured surfaces are reviewed. Emphasis is given to studies of cell morphology and motility, cell proliferation, the cytoskeleton and cell-matrix adhesions, and signal transduction pathways of vascular cells. We finalize with a short outlook on potential interesting future studies. PMID:28144512

Biofilm matrix exoproteins induce a protective immune response against Staphylococcus aureus biofilm infection.

PubMed

Gil, Carmen; Solano, Cristina; Burgui, Saioa; Latasa, Cristina; García, Begoña; Toledo-Arana, Alejandro; Lasa, Iñigo; Valle, Jaione

2014-03-01

The Staphylococcus aureus biofilm mode of growth is associated with several chronic infections that are very difficult to treat due to the recalcitrant nature of biofilms to clearance by antimicrobials. Accordingly, there is an increasing interest in preventing the formation of S. aureus biofilms and developing efficient antibiofilm vaccines. Given the fact that during a biofilm-associated infection, the first primary interface between the host and the bacteria is the self-produced extracellular matrix, in this study we analyzed the potential of extracellular proteins found in the biofilm matrix to induce a protective immune response against S. aureus infections. By using proteomic approaches, we characterized the exoproteomes of exopolysaccharide-based and protein-based biofilm matrices produced by two clinical S. aureus strains. Remarkably, results showed that independently of the nature of the biofilm matrix, a common core of secreted proteins is contained in both types of exoproteomes. Intradermal administration of an exoproteome extract of an exopolysaccharide-dependent biofilm induced a humoral immune response and elicited the production of interleukin 10 (IL-10) and IL-17 in mice. Antibodies against such an extract promoted opsonophagocytosis and killing of S. aureus. Immunization with the biofilm matrix exoproteome significantly reduced the number of bacterial cells inside a biofilm and on the surrounding tissue, using an in vivo model of mesh-associated biofilm infection. Furthermore, immunized mice also showed limited organ colonization by bacteria released from the matrix at the dispersive stage of the biofilm cycle. Altogether, these data illustrate the potential of biofilm matrix exoproteins as a promising candidate multivalent vaccine against S. aureus biofilm-associated infections.

Distribution of Schmidt-like eigenvalues for Gaussian ensembles of the random matrix theory

NASA Astrophysics Data System (ADS)

Pato, Mauricio P.; Oshanin, Gleb

2013-03-01

We study the probability distribution function P(β)n(w) of the Schmidt-like random variable w = x21/(∑j = 1nx2j/n), where xj, (j = 1, 2, …, n), are unordered eigenvalues of a given n × n β-Gaussian random matrix, β being the Dyson symmetry index. This variable, by definition, can be considered as a measure of how any individual (randomly chosen) eigenvalue deviates from the arithmetic mean value of all eigenvalues of a given random matrix, and its distribution is calculated with respect to the ensemble of such β-Gaussian random matrices. We show that in the asymptotic limit n → ∞ and for arbitrary β the distribution P(β)n(w) converges to the Marčenko-Pastur form, i.e. is defined as P_{n}^{( \\beta )}(w) \\sim \\sqrt{(4 - w)/w} for w ∈ [0, 4] and equals zero outside of the support, despite the fact that formally w is defined on the interval [0, n]. Furthermore, for Gaussian unitary ensembles (β = 2) we present exact explicit expressions for P(β = 2)n(w) which are valid for arbitrary n and analyse their behaviour.

Breeding Guild Determines Frog Distributions in Response to Edge Effects and Habitat Conversion in the Brazil's Atlantic Forest.

PubMed

Ferreira, Rodrigo B; Beard, Karen H; Crump, Martha L

2016-01-01

Understanding the response of species with differing life-history traits to habitat edges and habitat conversion helps predict their likelihood of persistence across changing landscape. In Brazil's Atlantic Forest, we evaluated frog richness and abundance by breeding guild at four distances from the edge of a reserve: i) 200 m inside the forest, ii) 50 m inside the forest, iii) at the forest edge, and iv) 50 m inside three different converted habitats (coffee plantation, non-native Eucalyptus plantation, and abandoned pastures, hereafter matrix types). By sampling a dry and a wet season, we recorded 622 individual frogs representing 29 species, of which three were undescribed. Breeding guild (i.e. bromeliad, leaf-litter, and water-body breeders) was the most important variable explaining frog distributions in relation to edge effects and matrix types. Leaf-litter and bromeliad breeders decreased in richness and abundance from the forest interior toward the matrix habitats. Water-body breeders increased in richness toward the matrix and remained relatively stable in abundance across distances. Number of large trees (i.e. DBH > 15 cm) and bromeliads best explained frog richness and abundance across distances. Twenty species found in the interior of the forest were not found in any matrix habitat. Richness and abundance across breeding guilds were higher in the rainy season but frog distributions were similar across the four distances in the two seasons. Across matrix types, leaf-litter species primarily used Eucalyptus plantations, whereas water-body species primarily used coffee plantations. Bromeliad breeders were not found inside any matrix habitat. Our study highlights the importance of primary forest for bromeliad and leaf-litter breeders. We propose that water-body breeders use edge and matrix habitats to reach breeding habitats along the valleys. Including life-history characteristics, such as breeding guild, can improve predictions of frog distributions in response to edge effect and matrix types, and can guide more effective management and conservation actions.

Breeding Guild Determines Frog Distributions in Response to Edge Effects and Habitat Conversion in the Brazil’s Atlantic Forest

PubMed Central

Ferreira, Rodrigo B.; Beard, Karen H.; Crump, Martha L.

2016-01-01

Understanding the response of species with differing life-history traits to habitat edges and habitat conversion helps predict their likelihood of persistence across changing landscape. In Brazil’s Atlantic Forest, we evaluated frog richness and abundance by breeding guild at four distances from the edge of a reserve: i) 200 m inside the forest, ii) 50 m inside the forest, iii) at the forest edge, and iv) 50 m inside three different converted habitats (coffee plantation, non-native Eucalyptus plantation, and abandoned pastures, hereafter matrix types). By sampling a dry and a wet season, we recorded 622 individual frogs representing 29 species, of which three were undescribed. Breeding guild (i.e. bromeliad, leaf-litter, and water-body breeders) was the most important variable explaining frog distributions in relation to edge effects and matrix types. Leaf-litter and bromeliad breeders decreased in richness and abundance from the forest interior toward the matrix habitats. Water-body breeders increased in richness toward the matrix and remained relatively stable in abundance across distances. Number of large trees (i.e. DBH > 15 cm) and bromeliads best explained frog richness and abundance across distances. Twenty species found in the interior of the forest were not found in any matrix habitat. Richness and abundance across breeding guilds were higher in the rainy season but frog distributions were similar across the four distances in the two seasons. Across matrix types, leaf-litter species primarily used Eucalyptus plantations, whereas water-body species primarily used coffee plantations. Bromeliad breeders were not found inside any matrix habitat. Our study highlights the importance of primary forest for bromeliad and leaf-litter breeders. We propose that water-body breeders use edge and matrix habitats to reach breeding habitats along the valleys. Including life-history characteristics, such as breeding guild, can improve predictions of frog distributions in response to edge effect and matrix types, and can guide more effective management and conservation actions. PMID:27272328

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

PubMed Central

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

1993-01-01

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

Micromechanical Modeling of Woven Metal Matrix Composites

NASA Technical Reports Server (NTRS)

Bednarcyk, Brett A.; Pindera, Marek-Jerzy

1997-01-01

This report presents the results of an extensive micromechanical modeling effort for woven metal matrix composites. The model is employed to predict the mechanical response of 8-harness (8H) satin weave carbon/copper (C/Cu) composites. Experimental mechanical results for this novel high thermal conductivity material were recently reported by Bednarcyk et al. along with preliminary model results. The micromechanics model developed herein is based on an embedded approach. A micromechanics model for the local (micro-scale) behavior of the woven composite, the original method of cells (Aboudi), is embedded in a global (macro-scale) micromechanics model (the three-dimensional generalized method of cells (GMC-3D) (Aboudi). This approach allows representation of true repeating unit cells for woven metal matrix composites via GMC-3D, and representation of local effects, such as matrix plasticity, yarn porosity, and imperfect fiber-matrix bonding. In addition, the equations of GMC-3D were reformulated to significantly reduce the number of unknown quantities that characterize the deformation fields at the microlevel in order to make possible the analysis of actual microstructures of woven composites. The resulting micromechanical model (WCGMC) provides an intermediate level of geometric representation, versatility, and computational efficiency with respect to previous analytical and numerical models for woven composites, but surpasses all previous modeling work by allowing the mechanical response of a woven metal matrix composite, with an elastoplastic matrix, to be examined for the first time. WCGMC is employed to examine the effects of composite microstructure, porosity, residual stresses, and imperfect fiber-matrix bonding on the predicted mechanical response of 8H satin C/Cu. The previously reported experimental results are summarized, and the model predictions are compared to monotonic and cyclic tensile and shear test data. By considering appropriate levels of porosity, residual stresses, and imperfect fiber-matrix debonding, reasonably good qualitative and quantitative correlation is achieved between model and experiment.

Neutrino nuclear responses for double beta decays and astro neutrinos by charge exchange reactions

NASA Astrophysics Data System (ADS)

Ejiri, Hiroyasu

2014-09-01

Neutrino nuclear responses are crucial for neutrino studies in nuclei. Charge exchange reactions (CER) are shown to be used to study charged current neutrino nuclear responses associated with double beta decays(DBD)and astro neutrino interactions. CERs to be used are high energy-resolution (He3 ,t) reactions at RCNP, photonuclear reactions via IAR at NewSUBARU and muon capture reactions at MUSIC RCNP and MLF J-PARC. The Gamow Teller (GT) strengths studied by CERs reproduce the observed 2 neutrino DBD matrix elements. The GT and spin dipole (SD) matrix elements are found to be reduced much due to the nucleon spin isospin correlations and the non-nucleonic (delta isobar) nuclear medium effects. Impacts of the reductions on the DBD matrix elements and astro neutrino interactions are discussed.

Cartilage regeneration for treatment of osteoarthritis: a paradigm for nonsurgical intervention

PubMed Central

Sabaawy, Hatem E.

2015-01-01

Osteoarthritis (OA) is associated with articular cartilage abnormalities and affects people of older age: preventative or therapeutic treatment measures for OA and related articular cartilage disorders remain challenging. In this perspective review, we have integrated multiple biological, morphological, developmental, stem cell and homeostasis concepts of articular cartilage to develop a paradigm for cartilage regeneration. OA is conceptually defined as an injury of cartilage that initiates chondrocyte activation, expression of proteases and growth factor release from the matrix. This regenerative process results in the local activation of inflammatory response genes in cartilage without migration of inflammatory cells or angiogenesis. The end results are catabolic and anabolic responses, and it is the balance between these two outcomes that controls remodelling of the matrix and regeneration. A tantalizing clinical clue for cartilage regrowth in OA joints has been observed in surgically created joint distraction. We hypothesize that cartilage growth in these distracted joints may have a biological connection with the size of organs and regeneration. Therefore we propose a novel, practical and nonsurgical intervention to validate the role of distraction in cartilage regeneration in OA. The approach permits normal wake-up activity while during sleep; the index knee is subjected to distraction with a pull traction device. Comparison of follow-up magnetic resonance imaging (MRI) at 3 and 6 months of therapy to those taken before therapy will provide much-needed objective evidence for the use of this mode of therapy for OA. We suggest that the paradigm presented here merits investigation for treatment of OA in knee joints. PMID:26029269

Novel entries in a fungal biofilm matrix encyclopedia.

PubMed

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

2014-08-05

Virulence of Candida is linked with its ability to form biofilms. Once established, biofilm infections are nearly impossible to eradicate. Biofilm cells live immersed in a self-produced matrix, a blend of extracellular biopolymers, many of which are uncharacterized. In this study, we provide a comprehensive analysis of the matrix manufactured by Candida albicans both in vitro and in a clinical niche animal model. We further explore the function of matrix components, including the impact on drug resistance. We uncovered components from each of the macromolecular classes (55% protein, 25% carbohydrate, 15% lipid, and 5% nucleic acid) in the C. albicans biofilm matrix. Three individual polysaccharides were identified and were suggested to interact physically. Surprisingly, a previously identified polysaccharide of functional importance, β-1,3-glucan, comprised only a small portion of the total matrix carbohydrate. Newly described, more abundant polysaccharides included α-1,2 branched α-1,6-mannans (87%) associated with unbranched β-1,6-glucans (13%) in an apparent mannan-glucan complex (MGCx). Functional matrix proteomic analysis revealed 458 distinct activities. The matrix lipids consisted of neutral glycerolipids (89.1%), polar glycerolipids (10.4%), and sphingolipids (0.5%). Examination of matrix nucleic acid identified DNA, primarily noncoding sequences. Several of the in vitro matrix components, including proteins and each of the polysaccharides, were also present in the matrix of a clinically relevant in vivo biofilm. Nuclear magnetic resonance (NMR) analysis demonstrated interaction of aggregate matrix with the antifungal fluconazole, consistent with a role in drug impedance and contribution of multiple matrix components. Importance: This report is the first to decipher the complex and unique macromolecular composition of the Candida biofilm matrix, demonstrate the clinical relevance of matrix components, and show that multiple matrix components are needed for protection from antifungal drugs. The availability of these biochemical analyses provides a unique resource for further functional investigation of the biofilm matrix, a defining trait of this lifestyle. Copyright © 2014 Zarnowski et al.

Assembly and Development of the Pseudomonas aeruginosa Biofilm Matrix

PubMed Central

Ma, Luyan; Conover, Matthew; Lu, Haiping; Parsek, Matthew R.; Bayles, Kenneth; Wozniak, Daniel J.

2009-01-01

Virtually all cells living in multicellular structures such as tissues and organs are encased in an extracellular matrix. One of the most important features of a biofilm is the extracellular polymeric substance that functions as a matrix, holding bacterial cells together. Yet very little is known about how the matrix forms or how matrix components encase bacteria during biofilm development. Pseudomonas aeruginosa forms environmentally and clinically relevant biofilms and is a paradigm organism for the study of biofilms. The extracellular polymeric substance of P. aeruginosa biofilms is an ill-defined mix of polysaccharides, nucleic acids, and proteins. Here, we directly visualize the product of the polysaccharide synthesis locus (Psl exopolysaccharide) at different stages of biofilm development. During attachment, Psl is anchored on the cell surface in a helical pattern. This promotes cell–cell interactions and assembly of a matrix, which holds bacteria in the biofilm and on the surface. Chemical dissociation of Psl from the bacterial surface disrupted the Psl matrix as well as the biofilm structure. During biofilm maturation, Psl accumulates on the periphery of 3-D-structured microcolonies, resulting in a Psl matrix-free cavity in the microcolony center. At the dispersion stage, swimming cells appear in this matrix cavity. Dead cells and extracellular DNA (eDNA) are also concentrated in the Psl matrix-free area. Deletion of genes that control cell death and autolysis affects the formation of the matrix cavity and microcolony dispersion. These data provide a mechanism for how P. aeruginosa builds a matrix and subsequently a cavity to free a portion of cells for seeding dispersal. Direct visualization reveals that Psl is a key scaffolding matrix component and opens up avenues for therapeutics of biofilm-related complications. PMID:19325879

Assembly and development of the Pseudomonas aeruginosa biofilm matrix.

PubMed

Ma, Luyan; Conover, Matthew; Lu, Haiping; Parsek, Matthew R; Bayles, Kenneth; Wozniak, Daniel J

2009-03-01

Virtually all cells living in multicellular structures such as tissues and organs are encased in an extracellular matrix. One of the most important features of a biofilm is the extracellular polymeric substance that functions as a matrix, holding bacterial cells together. Yet very little is known about how the matrix forms or how matrix components encase bacteria during biofilm development. Pseudomonas aeruginosa forms environmentally and clinically relevant biofilms and is a paradigm organism for the study of biofilms. The extracellular polymeric substance of P. aeruginosa biofilms is an ill-defined mix of polysaccharides, nucleic acids, and proteins. Here, we directly visualize the product of the polysaccharide synthesis locus (Psl exopolysaccharide) at different stages of biofilm development. During attachment, Psl is anchored on the cell surface in a helical pattern. This promotes cell-cell interactions and assembly of a matrix, which holds bacteria in the biofilm and on the surface. Chemical dissociation of Psl from the bacterial surface disrupted the Psl matrix as well as the biofilm structure. During biofilm maturation, Psl accumulates on the periphery of 3-D-structured microcolonies, resulting in a Psl matrix-free cavity in the microcolony center. At the dispersion stage, swimming cells appear in this matrix cavity. Dead cells and extracellular DNA (eDNA) are also concentrated in the Psl matrix-free area. Deletion of genes that control cell death and autolysis affects the formation of the matrix cavity and microcolony dispersion. These data provide a mechanism for how P. aeruginosa builds a matrix and subsequently a cavity to free a portion of cells for seeding dispersal. Direct visualization reveals that Psl is a key scaffolding matrix component and opens up avenues for therapeutics of biofilm-related complications.

Dioptric power: its nature and its representation in three- and four-dimensional space.

PubMed

Harris, W F

1997-06-01

Dioptric power expressed in the familiar three-component form of sphere, cylinder, and axis is unsuited to mathematical and statistical treatments; there is a particular class of power that cannot be represented in the familiar form; and it is possible that sphere, cylinder, and axis will prove inadequate in future clinical and research applications in optometry and ophthalmology. Dioptric power expressed as the four-component dioptric power matrix, however, overcomes these shortcomings. The intention in this paper is to provide a definitive statement on the nature, function, and mathematical representation of dioptric power in terms of the matrix and within the limitations of paraxial or linear optics. The approach is universal in the sense that its point of departure is not power of the familiar form (that is, of thin systems) but of systems in general (thick or thin). Familiar types of power are then seen within the context of power in general. Dioptric power is defined, for systems that may be thick and astigmatic, in terms of the ray transfer matrix. A functional definition is presented for dioptric power and its components: it defines the additive contribution of incident position to emergent direction of a ray passing through the system. For systems that are thin (or thin-equivalent) it becomes possible to describe an alternative and more familiar function; for such systems dioptric power can be regarded as the increase in reduced surface curvature of a wavefront brought about by the system as the wavefront passes through it. The curvital and torsional components of the power are explored in some detail. Dioptric power, at its most general, defines a four-dimensional inner product space called dioptric power space. The familiar types of power define a three-dimensional subspace called symmetric dioptric power space. For completeness a one-dimensional antisymmetric power space is also defined: it is orthogonal in four dimensions to symmetric dioptric power space. Various bases are defined for the spaces as are coordinate vectors with respect to them. Vectorial representations of power in the literature apply only to thin systems and are not obviously generalizable to systems in general. They are shown to be merely different coordinate representations of the same subspace, the space of symmetric powers. Some of the uses and disadvantages of the different representations are described. None of the coordinate vectors fully represent, by themselves, the essential character of dioptric power. Their use is limited to applications, such as finding a mean, where addition and scalar multiplication are involved. The full character of power is represented by the dioptric power matrix; it is in this form that power is appropriate for all mathematical relationships.

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.

Fine-granularity inference and estimations to network traffic for SDN.

PubMed

Jiang, Dingde; Huo, Liuwei; Li, Ya

2018-01-01

An end-to-end network traffic matrix is significantly helpful for network management and for Software Defined Networks (SDN). However, the end-to-end network traffic matrix's inferences and estimations are a challenging problem. Moreover, attaining the traffic matrix in high-speed networks for SDN is a prohibitive challenge. This paper investigates how to estimate and recover the end-to-end network traffic matrix in fine time granularity from the sampled traffic traces, which is a hard inverse problem. Different from previous methods, the fractal interpolation is used to reconstruct the finer-granularity network traffic. Then, the cubic spline interpolation method is used to obtain the smooth reconstruction values. To attain an accurate the end-to-end network traffic in fine time granularity, we perform a weighted-geometric-average process for two interpolation results that are obtained. The simulation results show that our approaches are feasible and effective.

Fine-granularity inference and estimations to network traffic for SDN

PubMed Central

Huo, Liuwei; Li, Ya

2018-01-01

An end-to-end network traffic matrix is significantly helpful for network management and for Software Defined Networks (SDN). However, the end-to-end network traffic matrix's inferences and estimations are a challenging problem. Moreover, attaining the traffic matrix in high-speed networks for SDN is a prohibitive challenge. This paper investigates how to estimate and recover the end-to-end network traffic matrix in fine time granularity from the sampled traffic traces, which is a hard inverse problem. Different from previous methods, the fractal interpolation is used to reconstruct the finer-granularity network traffic. Then, the cubic spline interpolation method is used to obtain the smooth reconstruction values. To attain an accurate the end-to-end network traffic in fine time granularity, we perform a weighted-geometric-average process for two interpolation results that are obtained. The simulation results show that our approaches are feasible and effective. PMID:29718913

Mueller-matrix of laser-induced autofluorescence of polycrystalline films of dried peritoneal fluid in diagnostics of endometriosis

NASA Astrophysics Data System (ADS)

Ushenko, Yuriy A.; Koval, Galina D.; Ushenko, Alexander G.; Dubolazov, Olexander V.; Ushenko, Vladimir A.; Novakovskaia, Olga Yu.

2016-07-01

This research presents investigation results of the diagnostic efficiency of an azimuthally stable Mueller-matrix method of analysis of laser autofluorescence of polycrystalline films of dried uterine cavity peritoneal fluid. A model of the generalized optical anisotropy of films of dried peritoneal fluid is proposed in order to define the processes of laser autofluorescence. The influence of complex mechanisms of both phase (linear and circular birefringence) and amplitude (linear and circular dichroism) anisotropies is taken into consideration. The interconnections between the azimuthally stable Mueller-matrix elements characterizing laser autofluorescence and different mechanisms of optical anisotropy are determined. The statistical analysis of coordinate distributions of such Mueller-matrix rotation invariants is proposed. Thereupon the quantitative criteria (statistic moments of the first to the fourth order) of differentiation of polycrystalline films of dried peritoneal fluid, group 1 (healthy donors) and group 2 (uterus endometriosis patients), are determined.

Cannibalism enhances biofilm development in Bacillus subtilis.

PubMed

López, Daniel; Vlamakis, Hera; Losick, Richard; Kolter, Roberto

2009-11-01

Cannibalism is a mechanism to delay sporulation in Bacillus subtilis. Cannibal cells express the skf and sdp toxin systems to lyse a fraction of their sensitive siblings. The lysed cells release nutrients that serve to feed the community, effectively delaying spore formation. Here we provide evidence that the subpopulation of cells that differentiates into cannibals is the same subpopulation that produces the extracellular matrix that holds cells together in biofilms. Cannibalism and matrix formation are both triggered in response to the signalling molecule surfactin. Nutrients released by the cannibalized cells are preferentially used by matrix-producing cells, as they are the only cells expressing resistance to the Skf and Sdp toxins. As a result this subpopulation increases in number and matrix production is enhanced when cannibalism toxins are produced. The cannibal/matrix-producing subpopulation is also generated in response to antimicrobials produced by other microorganisms and may thus constitute a defense mechanism to protect B. subtilis from the action of antibiotics in natural settings.

Two-photon imaging in mice shows striosomes and matrix have overlapping but differential reinforcement-related responses

PubMed Central

Sur, Mriganka

2017-01-01

Striosomes were discovered several decades ago as neurochemically identified zones in the striatum, yet technical hurdles have hampered the study of the functions of these striatal compartments. Here we used 2-photon calcium imaging in neuronal birthdate-labeled Mash1-CreER;Ai14 mice to image simultaneously the activity of striosomal and matrix neurons as mice performed an auditory conditioning task. With this method, we identified circumscribed zones of tdTomato-labeled neuropil that correspond to striosomes as verified immunohistochemically. Neurons in both striosomes and matrix responded to reward-predicting cues and were active during or after consummatory licking. However, we found quantitative differences in response strength: striosomal neurons fired more to reward-predicting cues and encoded more information about expected outcome as mice learned the task, whereas matrix neurons were more strongly modulated by recent reward history. These findings open the possibility of harnessing in vivo imaging to determine the contributions of striosomes and matrix to striatal circuit function. PMID:29251596

Epigenetic regulation of cardiac fibrosis

PubMed Central

Stratton, Matthew S.; McKinsey, Timothy A.

2016-01-01

Fibrosis is defined as excess deposition of extracellular matrix (ECM), resulting in tissue scarring and organ dysfunction. In the heart, fibrosis may be reparative, replacing areas of myocyte loss with a structural scar following infarction, or reactive, which is triggered in the absence of cell death and involves interstitial ECM deposition in response to long-lasting stress. Interstitial fibrosis can increase the passive stiffness of the myocardium, resulting in impaired relaxation and diastolic dysfunction. Additionally, fibrosis can lead to disruption of electrical conduction in the heart, causing arrhythmias, and can limit myocyte oxygen availability and thus exacerbate myocardial ischemia. Here, we review recent studies that have illustrated key roles for epigenetic events in the control of pro-fibrotic gene expression, and highlight the potential of small molecules that target epigenetic regulators as a means of treating fibrotic cardiac diseases. PMID:26876451

The extracellular matrix of Staphylococcus aureus biofilms comprises cytoplasmic proteins that associate with the cell surface in response to decreasing pH.

PubMed

Foulston, Lucy; Elsholz, Alexander K W; DeFrancesco, Alicia S; Losick, Richard

2014-09-02

Biofilm formation by Staphylococcus aureus involves the formation of an extracellular matrix, but the composition of this matrix has been uncertain. Here we report that the matrix is largely composed of cytoplasmic proteins that reversibly associate with the cell surface in a manner that depends on pH. We propose a model for biofilm formation in which cytoplasmic proteins are released from cells in stationary phase. These proteins associate with the cell surface in response to decreasing pH during biofilm formation. Rather than utilizing a dedicated matrix protein, S. aureus appears to recycle cytoplasmic proteins that moonlight as components of the extracellular matrix. Staphylococcus aureus is a leading cause of multiantibiotic-resistant nosocomial infections and is often found growing as a biofilm in catheters and chronic wounds. Biofilm formation is an important pathogenicity strategy that enhances resistance to antimicrobials, thereby limiting treatment options and ultimately contributing to increased morbidity and mortality. Cells in a biofilm are held together by an extracellular matrix that consists in whole or in part of protein, but the nature of the proteins in the S. aureus matrix is not well understood. Here we postulate that S. aureus recycles proteins from the cytoplasm to form the extracellular matrix. This strategy, of cytoplasmic proteins moonlighting as matrix proteins, could allow enhanced flexibility and adaptability for S. aureus in forming biofilms under infection conditions and could promote the formation of mixed-species biofilms in chronic wounds. Copyright © 2014 Foulston et al.

Influence of surface morphology and UFG on damping and mechanical properties of composite reinforced with spinel MgAl{sub 2}O{sub 4}-SiC core-shell microcomposites

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

Singh, Subhash; Pal, Kaushik, E-mail: pl_kshk@yaho

Interface between ceramic particulate and matrix is known to control the response of the materials and functionality of the composite. Among numerous physical properties, grain structure of the materials has also played a significant role in defining the behaviour of metal matrix composites. Usually, silicon carbide (SiC) particles show poor interfacial wettability in aluminium melt. Herein, we were successfully synthesized magnesium oxide (MgO) and nanocrystalline magnesium aluminate (MgAl{sub 2}O{sub 4}) spinel coated silicon carbide (SiC) core-shell micro-composites through sol-gel technique to improve the wettability of dispersoids. Core-shell structures of submicron size were thoroughly investigated by various characterization techniques. Further, aluminiummore » matrix composites incorporated with pristine SiC, MgO grafted SiC and MgAl{sub 2}O{sub 4} grafted SiC particles were fabricated by stir casting technique, respectively. Additionally, as-cast composites were processed via friction stir processing (FSP) technique to observe the influence of grain refinement on mechanical and damping properties. Electron back scattered diffraction (EBSD), Field emission scanning electron microscopy (FE-SEM) and X-ray energy dispersion spectroscopy (EDX) analysis were conducted for investigating grain size refinement, adequate dispersion, stability and de-agglomeration of encapsulated SiC particles in aluminium matrix. The mechanical as well as thermal cyclic (from − 100 to 400 °C) damping performance of the as-cast and friction stir processed composites were studied, respectively. Finally, the enhanced properties were attributable to reduced agglomeration, stabilization and proper dispersion of the tailored SiC particles Al matrix. - Highlights: •Synthesizing a novel coating layer of MgO and MgAl{sub 2}O{sub 4} spinel onto SiC particles •Significant improvement in UTS and hardness by reinforcing tailored SiC in Al •Significant grain refinements were obtained through FSP •SiC/MgAl{sub 2}O{sub 4}/Al exhibits ~ 61% higher storage modulus as compare to pure Al after FSP.« less

The Effect of Oral Vaccination with Mycobacterium bovis BCG on the Development of Tuberculosis in Captive European Badgers (Meles meles).

PubMed

Chambers, Mark A; Aldwell, Frank; Williams, Gareth A; Palmer, Si; Gowtage, Sonya; Ashford, Roland; Dalley, Deanna J; Davé, Dipesh; Weyer, Ute; Salguero, Francisco J; Nunez, Alejandro; Nadian, Allan K; Crawshaw, Timothy; Corner, Leigh A L; Lesellier, Sandrine

2017-01-01

The European badger ( Meles meles ) is a reservoir host of Mycobacterium bovis and responsible for a proportion of the tuberculosis (TB) cases seen in cattle in the United Kingdom and Republic of Ireland. An injectable preparation of the bacillus Calmette-Guérin (BCG) vaccine is licensed for use in badgers in the UK and its use forms part of the bovine TB eradication plans of England and Wales. However, there are practical limitations to the widespread application of an injectable vaccine for badgers and a research priority is the development of an oral vaccine deliverable to badgers in bait. Previous studies reported the successful vaccination of badgers with oral preparations of 10 8 colony forming units (CFU) of both Pasteur and Danish strains of BCG contained within a lipid matrix composed of triglycerides of fatty acids. Protection against TB in these studies was expressed as a reduction in the number and apparent progression of visible lesions, and reductions in the bacterial load and dissemination of infection. To reduce the cost of an oral vaccine and reduce the potential for environmental contamination with BCG, it is necessary to define the minimal efficacious dose of oral BCG for badgers. The objectives of the two studies reported here were to compare the efficacy of BCG Danish strain in a lipid matrix with unformulated BCG given orally, and to evaluate the efficacy of BCG Danish in a lipid matrix at a 10-fold lower dose than previously evaluated in badgers. In the first study, both BCG unformulated and in a lipid matrix reduced the number and apparent progression of visible lesions and the dissemination of infection from the lung. In the second study, vaccination with BCG in the lipid matrix at a 10-fold lower dose produced a similar outcome, but with greater intra-group variability than seen with the higher dose in the first study. Further research is needed before we are able to recommend a final dose of BCG for oral vaccination of badgers against TB or to know whether oral vaccination of wild badgers with BCG will significantly reduce transmission of the disease.

The Effect of Oral Vaccination with Mycobacterium bovis BCG on the Development of Tuberculosis in Captive European Badgers (Meles meles)

PubMed Central

Chambers, Mark A.; Aldwell, Frank; Williams, Gareth A.; Palmer, Si; Gowtage, Sonya; Ashford, Roland; Dalley, Deanna J.; Davé, Dipesh; Weyer, Ute; Salguero, Francisco J.; Nunez, Alejandro; Nadian, Allan K.; Crawshaw, Timothy; Corner, Leigh A. L.; Lesellier, Sandrine

2017-01-01

The European badger (Meles meles) is a reservoir host of Mycobacterium bovis and responsible for a proportion of the tuberculosis (TB) cases seen in cattle in the United Kingdom and Republic of Ireland. An injectable preparation of the bacillus Calmette-Guérin (BCG) vaccine is licensed for use in badgers in the UK and its use forms part of the bovine TB eradication plans of England and Wales. However, there are practical limitations to the widespread application of an injectable vaccine for badgers and a research priority is the development of an oral vaccine deliverable to badgers in bait. Previous studies reported the successful vaccination of badgers with oral preparations of 108 colony forming units (CFU) of both Pasteur and Danish strains of BCG contained within a lipid matrix composed of triglycerides of fatty acids. Protection against TB in these studies was expressed as a reduction in the number and apparent progression of visible lesions, and reductions in the bacterial load and dissemination of infection. To reduce the cost of an oral vaccine and reduce the potential for environmental contamination with BCG, it is necessary to define the minimal efficacious dose of oral BCG for badgers. The objectives of the two studies reported here were to compare the efficacy of BCG Danish strain in a lipid matrix with unformulated BCG given orally, and to evaluate the efficacy of BCG Danish in a lipid matrix at a 10-fold lower dose than previously evaluated in badgers. In the first study, both BCG unformulated and in a lipid matrix reduced the number and apparent progression of visible lesions and the dissemination of infection from the lung. In the second study, vaccination with BCG in the lipid matrix at a 10-fold lower dose produced a similar outcome, but with greater intra-group variability than seen with the higher dose in the first study. Further research is needed before we are able to recommend a final dose of BCG for oral vaccination of badgers against TB or to know whether oral vaccination of wild badgers with BCG will significantly reduce transmission of the disease. PMID:28174695

Practical implementation of tetrahedral mesh reconstruction in emission tomography

PubMed Central

Boutchko, R.; Sitek, A.; Gullberg, G. T.

2014-01-01

This paper presents a practical implementation of image reconstruction on tetrahedral meshes optimized for emission computed tomography with parallel beam geometry. Tetrahedral mesh built on a point cloud is a convenient image representation method, intrinsically three-dimensional and with a multi-level resolution property. Image intensities are defined at the mesh nodes and linearly interpolated inside each tetrahedron. For the given mesh geometry, the intensities can be computed directly from tomographic projections using iterative reconstruction algorithms with a system matrix calculated using an exact analytical formula. The mesh geometry is optimized for a specific patient using a two stage process. First, a noisy image is reconstructed on a finely-spaced uniform cloud. Then, the geometry of the representation is adaptively transformed through boundary-preserving node motion and elimination. Nodes are removed in constant intensity regions, merged along the boundaries, and moved in the direction of the mean local intensity gradient in order to provide higher node density in the boundary regions. Attenuation correction and detector geometric response are included in the system matrix. Once the mesh geometry is optimized, it is used to generate the final system matrix for ML-EM reconstruction of node intensities and for visualization of the reconstructed images. In dynamic PET or SPECT imaging, the system matrix generation procedure is performed using a quasi-static sinogram, generated by summing projection data from multiple time frames. This system matrix is then used to reconstruct the individual time frame projections. Performance of the new method is evaluated by reconstructing simulated projections of the NCAT phantom and the method is then applied to dynamic SPECT phantom and patient studies and to a dynamic microPET rat study. Tetrahedral mesh-based images are compared to the standard voxel-based reconstruction for both high and low signal-to-noise ratio projection datasets. The results demonstrate that the reconstructed images represented as tetrahedral meshes based on point clouds offer image quality comparable to that achievable using a standard voxel grid while allowing substantial reduction in the number of unknown intensities to be reconstructed and reducing the noise. PMID:23588373

Practical implementation of tetrahedral mesh reconstruction in emission tomography

NASA Astrophysics Data System (ADS)

Boutchko, R.; Sitek, A.; Gullberg, G. T.

2013-05-01

This paper presents a practical implementation of image reconstruction on tetrahedral meshes optimized for emission computed tomography with parallel beam geometry. Tetrahedral mesh built on a point cloud is a convenient image representation method, intrinsically three-dimensional and with a multi-level resolution property. Image intensities are defined at the mesh nodes and linearly interpolated inside each tetrahedron. For the given mesh geometry, the intensities can be computed directly from tomographic projections using iterative reconstruction algorithms with a system matrix calculated using an exact analytical formula. The mesh geometry is optimized for a specific patient using a two stage process. First, a noisy image is reconstructed on a finely-spaced uniform cloud. Then, the geometry of the representation is adaptively transformed through boundary-preserving node motion and elimination. Nodes are removed in constant intensity regions, merged along the boundaries, and moved in the direction of the mean local intensity gradient in order to provide higher node density in the boundary regions. Attenuation correction and detector geometric response are included in the system matrix. Once the mesh geometry is optimized, it is used to generate the final system matrix for ML-EM reconstruction of node intensities and for visualization of the reconstructed images. In dynamic PET or SPECT imaging, the system matrix generation procedure is performed using a quasi-static sinogram, generated by summing projection data from multiple time frames. This system matrix is then used to reconstruct the individual time frame projections. Performance of the new method is evaluated by reconstructing simulated projections of the NCAT phantom and the method is then applied to dynamic SPECT phantom and patient studies and to a dynamic microPET rat study. Tetrahedral mesh-based images are compared to the standard voxel-based reconstruction for both high and low signal-to-noise ratio projection datasets. The results demonstrate that the reconstructed images represented as tetrahedral meshes based on point clouds offer image quality comparable to that achievable using a standard voxel grid while allowing substantial reduction in the number of unknown intensities to be reconstructed and reducing the noise.

In vitro model to study the effects of matrix stiffening on Ca2+ handling and myofilament function in isolated adult rat cardiomyocytes

PubMed Central

Najafi, Aref; Fontoura, Dulce; Valent, Erik; Goebel, Max; Kardux, Kim; Falcão‐Pires, Inês; van der Velden, Jolanda

2017-01-01

Key points This paper describes a novel model that allows exploration of matrix‐induced cardiomyocyte adaptations independent of the passive effect of matrix rigidity on cardiomyocyte function.Detachment of adult cardiomyocytes from the matrix enables the study of matrix effects on cell shortening, Ca2+ handling and myofilament function.Cell shortening and Ca2+ handling are altered in cardiomyocytes cultured for 24 h on a stiff matrix.Matrix stiffness‐impaired cardiomyocyte contractility is reversed upon normalization of extracellular stiffness.Matrix stiffness‐induced reduction in unloaded shortening is more pronounced in cardiomyocytes isolated from obese ZSF1 rats with heart failure with preserved ejection fraction compared to lean ZSF1 rats. Abstract Extracellular matrix (ECM) stiffening is a key element of cardiac disease. Increased rigidity of the ECM passively inhibits cardiac contraction, but if and how matrix stiffening also actively alters cardiomyocyte contractility is incompletely understood. In vitro models designed to study cardiomyocyte–matrix interaction lack the possibility to separate passive inhibition by a stiff matrix from active matrix‐induced alterations of cardiomyocyte properties. Here we introduce a novel experimental model that allows exploration of cardiomyocyte functional alterations in response to matrix stiffening. Adult rat cardiomyocytes were cultured for 24 h on matrices of tuneable stiffness representing the healthy and the diseased heart and detached from their matrix before functional measurements. We demonstrate that matrix stiffening, independent of passive inhibition, reduces cell shortening and Ca2+ handling but does not alter myofilament‐generated force. Additionally, detachment of adult cultured cardiomyocytes allowed the transfer of cells from one matrix to another. This revealed that stiffness‐induced cardiomyocyte changes are reversed when matrix stiffness is normalized. These matrix stiffness‐induced changes in cardiomyocyte function could not be explained by adaptation in the microtubules. Additionally, cardiomyocytes isolated from stiff hearts of the obese ZSF1 rat model of heart failure with preserved ejection fraction show more pronounced reduction in unloaded shortening in response to matrix stiffening. Taken together, we introduce a method that allows evaluation of the influence of ECM properties on cardiomyocyte function separate from the passive inhibitory component of a stiff matrix. As such, it adds an important and physiologically relevant tool to investigate the functional consequences of cardiomyocyte–matrix interactions. PMID:28485491

Electrostatic interactions and binding orientation of HIV-1 matrix studied by neutron reflectivity.

PubMed

Nanda, Hirsh; Datta, Siddhartha A K; Heinrich, Frank; Lösche, Mathias; Rein, Alan; Krueger, Susan; Curtis, Joseph E

2010-10-20

The N-terminal matrix (MA) domain of the HIV-1 Gag protein is responsible for binding to the plasma membrane of host cells during viral assembly. The putative membrane-binding interface of MA was previously mapped by means of mutagenesis and analysis of its trimeric crystal structure. However, the orientation of MA on membranes has not been directly determined by experimental measurements. We present neutron reflectivity measurements that resolve the one-dimensional scattering length density profile of MA bound to a biomimetic of the native viral membrane. A molecular refinement procedure was developed using atomic structures of MA to determine the orientation of the protein on the membrane. The orientation defines a lipid-binding interface consistent with previous mutagenesis results. The MA protein maintains this orientation without the presence of a myristate group, driven only by electrostatic interactions. Furthermore, MA is found to penetrate the membrane headgroup region peripherally such that only the side chains of specific Lys and Arg residues interact with the surface. The results suggest that electrostatic interactions are sufficient to favorably orient MA on viral membrane mimics. The spatial determination of the membrane-bound protein demonstrates the ability of neutron reflectivity to discern orientation and penetration under physiologically relevant conditions. Copyright © 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Novel, Starch-Like Polysaccharides Are Synthesized by an Unbound Form of Granule-Bound Starch Synthase in Glycogen-Accumulating Mutants of Chlamydomonas reinhardtii1

PubMed Central

Dauvillée, David; Colleoni, Christophe; Shaw, Eudean; Mouille, Gregory; D'Hulst, Christophe; Morell, Matthew; Samuel, Michael S.; Bouchet, Brigitte; Gallant, Daniel J.; Sinskey, Anthony; Ball, Steven

1999-01-01

In vascular plants, mutations leading to a defect in debranching enzyme lead to the simultaneous synthesis of glycogen-like material and normal starch. In Chlamydomonas reinhardtii comparable defects lead to the replacement of starch by phytoglycogen. Therefore, debranching was proposed to define a mandatory step for starch biosynthesis. We now report the characterization of small amounts of an insoluble, amylose-like material found in the mutant algae. This novel, starch-like material was shown to be entirely dependent on the presence of granule-bound starch synthase (GBSSI), the enzyme responsible for amylose synthesis in plants. However, enzyme activity assays, solubilization of proteins from the granule, and western blots all failed to detect GBSSI within the insoluble polysaccharide matrix. The glycogen-like polysaccharides produced in the absence of GBSSI were proved to be qualitatively and quantitatively identical to those produced in its presence. Therefore, we propose that GBSSI requires the presence of crystalline amylopectin for granule binding and that the synthesis of amylose-like material can proceed at low levels without the binding of GBSSI to the polysaccharide matrix. Our results confirm that amylopectin synthesis is completely blocked in debranching-enzyme-defective mutants of C. reinhardtii. PMID:9880375

Individual movement behavior, matrix heterogeneity, and the dynamics of spatially structured populations.

PubMed

Revilla, Eloy; Wiegand, Thorsten

2008-12-09

The dynamics of spatially structured populations is characterized by within- and between-patch processes. The available theory describes the latter with simple distance-dependent functions that depend on landscape properties such as interpatch distance or patch size. Despite its potential role, we lack a good mechanistic understanding of how the movement of individuals between patches affects the dynamics of these populations. We used the theoretical framework provided by movement ecology to make a direct representation of the processes determining how individuals connect local populations in a spatially structured population of Iberian lynx. Interpatch processes depended on the heterogeneity of the matrix where patches are embedded and the parameters defining individual movement behavior. They were also very sensitive to the dynamic demographic variables limiting the time moving, the within-patch dynamics of available settlement sites (both spatiotemporally heterogeneous) and the response of individuals to the perceived risk while moving. These context-dependent dynamic factors are an inherent part of the movement process, producing connectivities and dispersal kernels whose variability is affected by other demographic processes. Mechanistic representations of interpatch movements, such as the one provided by the movement-ecology framework, permit the dynamic interaction of birth-death processes and individual movement behavior, thus improving our understanding of stochastic spatially structured populations.

Optical properties of metal nanoparticles embedded in amorphous silicon analysed using discrete dipole approximation

NASA Astrophysics Data System (ADS)

Fantoni, Alessandro; Fernandes, Miguel; Vygranenko, Yuri; Vieira, Manuela; Oliveira-Silva, Rui P.; Prazeres, D. M. F.; Ribeiro, Ana P. C.; Alegria, Elisabete C. B. A.

2018-02-01

Localized surface plasmons (LSP) can be excited in metal nanoparticles (NP) by UV, visible or NIR light and are described as coherent oscillation of conduction electrons. Taking advantage of the tunable optical properties of NPs, we propose the realization of a plasmonic structure, based on the LSP interaction of NP with an embedding matrix of amorphous silicon. This study is directed to define the characteristics of NP and substrate necessary to the development of a LSP proteomics sensor that, once provided immobilized antibodies on its surface, will screen the concentration of selected antigens through the determination of LSPR spectra and peaks of light absorption. Metals of interest for NP composition are: Aluminium and Gold. Recent advances in nanoparticle production techniques allow almost full control over shapes and size, permitting full control over their optical and plasmonic properties and, above all, over their responsive spectra. Analytical solution is only possible for simple NP geometries, therefore our analysis, is realized recurring to computer simulation using the Discrete Dipole Approximation method (DDA). In this work we use the free software DDSCAT to study the optical properties of metal nanoparticles embedded in an amorphous silicon matrix, as a function of size, shape, aspect-ratio and metal type. Experimental measurements realized with arrays of metal nanoparticles are compared with the simulations.

Immunomodulatory effects of amniotic membrane matrix incorporated into collagen scaffolds.

PubMed

Hortensius, Rebecca A; Ebens, Jill H; Harley, Brendan A C

2016-06-01

Adult tendon wound repair is characterized by the formation of disorganized collagen matrix which leads to decreases in mechanical properties and scar formation. Studies have linked this scar formation to the inflammatory phase of wound healing. Instructive biomaterials designed for tendon regeneration are often designed to provide both structural and cellular support. In order to facilitate regeneration, success may be found by tempering the body's inflammatory response. This work combines collagen-glycosaminoglycan scaffolds, previously developed for tissue regeneration, with matrix materials (hyaluronic acid and amniotic membrane) that have been shown to promote healing and decreased scar formation in skin studies. The results presented show that scaffolds containing amniotic membrane matrix have significantly increased mechanical properties and that tendon cells within these scaffolds have increased metabolic activity even when the media is supplemented with the pro-inflammatory cytokine interleukin-1 beta. Collagen scaffolds containing hyaluronic acid or amniotic membrane also temper the expression of genes associated with the inflammatory response in normal tendon healing (TNF-α, COLI, MMP-3). These results suggest that alterations to scaffold composition, to include matrix known to decrease scar formation in vivo, can modify the inflammatory response in tenocytes. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 104A: 1332-1342, 2016. © 2016 Wiley Periodicals, Inc.

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

Photon polarization version of the GHz-Mermin Gedanken

NASA Technical Reports Server (NTRS)

Kiess, Thomas E.

1992-01-01

We have defined a photon polarization analog of the Greenberger, Horne, and Zeilinger (GHZ) experiment that was initially proposed for spin-1/2 quanta. Analogs of the ket states and Pauli spin matrix operators are presented.

Quantitative characterization of microstructure of asphalt mixtures

DOT National Transportation Integrated Search

2010-10-01

The microstructure of the fine aggregate matrix has a significant influence on the : mechanical properties and evolution of damage in an asphalt mixture. However, very little : work has been done to define and quantitatively characterize the microstr...

Comparison of three controllers applied to helicopter vibration

NASA Technical Reports Server (NTRS)

Leyland, Jane A.

1992-01-01

A comparison was made of the applicability and suitability of the deterministic controller, the cautious controller, and the dual controller for the reduction of helicopter vibration by using higher harmonic blade pitch control. A randomly generated linear plant model was assumed and the performance index was defined to be a quadratic output metric of this linear plant. A computer code, designed to check out and evaluate these controllers, was implemented and used to accomplish this comparison. The effects of random measurement noise, the initial estimate of the plant matrix, and the plant matrix propagation rate were determined for each of the controllers. With few exceptions, the deterministic controller yielded the greatest vibration reduction (as characterized by the quadratic output metric) and operated with the greatest reliability. Theoretical limitations of these controllers were defined and appropriate candidate alternative methods, including one method particularly suitable to the cockpit, were identified.

VizieR Online Data Catalog: Outliers and similarity in APOGEE (Reis+, 2018)

NASA Astrophysics Data System (ADS)

Reis, I.; Poznanski, D.; Baron, D.; Zasowski, G.; Shahaf, S.

2017-11-01

t-SNE is a dimensionality reduction algorithm that is particularly well suited for the visualization of high-dimensional datasets. We use t-SNE to visualize our distance matrix. A-priori, these distances could define a space with almost as many dimensions as objects, i.e., tens of thousand of dimensions. Obviously, since many stars are quite similar, and their spectra are defined by a few physical parameters, the minimal spanning space might be smaller. By using t-SNE we can examine the structure of our sample projected into 2D. We use our distance matrix as input to the t-SNE algorithm and in return get a 2D map of the objects in our dataset. For each star in a sample of 183232 APOGEE stars, the APOGEE IDs of the 99 stars with most similar spectra (according to the method described in paper), ordered by similarity. (3 data files).

Azimuthally invariant Mueller-matrix mapping of biological optically anisotropic network

NASA Astrophysics Data System (ADS)

Ushenko, Yu. O.; Vanchuliak, O.; Bodnar, G. B.; Ushenko, V. O.; Grytsyuk, M.; Pavlyukovich, N.; Pavlyukovich, O. V.; Antonyuk, O.

2017-09-01

A new technique of Mueller-matrix mapping of polycrystalline structure of histological sections of biological tissues is suggested. The algorithms of reconstruction of distribution of parameters of linear and circular dichroism of histological sections liver tissue of mice with different degrees of severity of diabetes are found. The interconnections between such distributions and parameters of linear and circular dichroism of liver of mice tissue histological sections are defined. The comparative investigations of coordinate distributions of parameters of amplitude anisotropy formed by Liver tissue with varying severity of diabetes (10 days and 24 days) are performed. The values and ranges of change of the statistical (moments of the 1st - 4th order) parameters of coordinate distributions of the value of linear and circular dichroism are defined. The objective criteria of cause of the degree of severity of the diabetes differentiation are determined.

Lax representations for matrix short pulse equations

NASA Astrophysics Data System (ADS)

Popowicz, Z.

2017-10-01

The Lax representation for different matrix generalizations of Short Pulse Equations (SPEs) is considered. The four-dimensional Lax representations of four-component Matsuno, Feng, and Dimakis-Müller-Hoissen-Matsuno equations are obtained. The four-component Feng system is defined by generalization of the two-dimensional Lax representation to the four-component case. This system reduces to the original Feng equation, to the two-component Matsuno equation, or to the Yao-Zang equation. The three-component version of the Feng equation is presented. The four-component version of the Matsuno equation with its Lax representation is given. This equation reduces the new two-component Feng system. The two-component Dimakis-Müller-Hoissen-Matsuno equations are generalized to the four-parameter family of the four-component SPE. The bi-Hamiltonian structure of this generalization, for special values of parameters, is defined. This four-component SPE in special cases reduces to the new two-component SPE.

Tumor morphology and phenotypic evolution driven by selective pressure from the microenvironment.

PubMed

Anderson, Alexander R A; Weaver, Alissa M; Cummings, Peter T; Quaranta, Vito

2006-12-01

Emergence of invasive behavior in cancer is life-threatening, yet ill-defined due to its multifactorial nature. We present a multiscale mathematical model of cancer invasion, which considers cellular and microenvironmental factors simultaneously and interactively. Unexpectedly, the model simulations predict that harsh tumor microenvironment conditions (e.g., hypoxia, heterogenous extracellular matrix) exert a dramatic selective force on the tumor, which grows as an invasive mass with fingering margins, dominated by a few clones with aggressive traits. In contrast, mild microenvironment conditions (e.g., normoxia, homogeneous matrix) allow clones with similar aggressive traits to coexist with less aggressive phenotypes in a heterogeneous tumor mass with smooth, noninvasive margins. Thus, the genetic make-up of a cancer cell may realize its invasive potential through a clonal evolution process driven by definable microenvironmental selective forces. Our mathematical model provides a theoretical/experimental framework to quantitatively characterize this selective pressure for invasion and test ways to eliminate it.

Electrical and structural properties of ZnO synthesized via infiltration of lithographically defined polymer templates

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

Nam, Chang-Yong, E-mail: cynam@bnl.gov; Stein, Aaron; Kisslinger, Kim

We investigate the electrical and structural properties of infiltration-synthesized ZnO. In-plane ZnO nanowire arrays with prescribed positional registrations are generated by infiltrating diethlyzinc and water vapor into lithographically defined SU-8 polymer templates and removing organic matrix by oxygen plasma ashing. Transmission electron microscopy reveals that homogeneously amorphous as-infiltrated polymer templates transform into highly nanocrystalline ZnO upon removal of organic matrix. Field-effect transistor device measurements show that the synthesized ZnO after thermal annealing displays a typical n-type behavior, ∼10{sup 19 }cm{sup −3} carrier density, and ∼0.1 cm{sup 2} V{sup −1} s{sup −1} electron mobility, reflecting highly nanocrystalline internal structure. The results demonstrate themore » potential application of infiltration synthesis in fabricating metal oxide electronic devices.« less

The Ablowitz–Ladik system on a finite set of integers

NASA Astrophysics Data System (ADS)

Xia, Baoqiang

2018-07-01

We show how to solve initial-boundary value problems for integrable nonlinear differential–difference equations on a finite set of integers. The method we employ is the discrete analogue of the unified transform (Fokas method). The implementation of this method to the Ablowitz–Ladik system yields the solution in terms of the unique solution of a matrix Riemann–Hilbert problem, which has a jump matrix with explicit -dependence involving certain functions referred to as spectral functions. Some of these functions are defined in terms of the initial value, while the remaining spectral functions are defined in terms of two sets of boundary values. These spectral functions are not independent but satisfy an algebraic relation called global relation. We analyze the global relation to characterize the unknown boundary values in terms of the given initial and boundary values. We also discuss the linearizable boundary conditions.

Multi-indexed Meixner and little q-Jacobi (Laguerre) polynomials

NASA Astrophysics Data System (ADS)

Odake, Satoru; Sasaki, Ryu

2017-04-01

As the fourth stage of the project multi-indexed orthogonal polynomials, we present the multi-indexed Meixner and little q-Jacobi (Laguerre) polynomials in the framework of ‘discrete quantum mechanics’ with real shifts defined on the semi-infinite lattice in one dimension. They are obtained, in a similar way to the multi-indexed Laguerre and Jacobi polynomials reported earlier, from the quantum mechanical systems corresponding to the original orthogonal polynomials by multiple application of the discrete analogue of the Darboux transformations or the Crum-Krein-Adler deletion of virtual state vectors. The virtual state vectors are the solutions of the matrix Schrödinger equation on all the lattice points having negative energies and infinite norm. This is in good contrast to the (q-)Racah systems defined on a finite lattice, in which the ‘virtual state’ vectors satisfy the matrix Schrödinger equation except for one of the two boundary points.

Depressed immune surveillance against cancer: role of deficient T cell: extracellular matrix interactions.

PubMed

Górski, A; Castronovo, V; Stepień-Sopniewska, B; Grieb, P; Ryba, M; Mrowiec, T; Korczak-Kowalska, G; Wierzbicki, P; Matysiak, W; Dybowska, B

1994-07-01

Although T cells infiltrate malignant tumors, the local immune response is usually inefficient and tumors escape destruction. While extracellular matrix proteins strongly costimulate T cell responses in normal individuals, our studies indicate that peripheral blood T cells from cancer patients and tumor infiltrating cells respond poorly or are resistant to stimulative signals mediated by collagen I and IV and fibronectin. Moreover, the adhesive properties of cancer T cells are markedly depressed. Those functional deficiencies are paralleled by variable deficits in integrin and non-integrin T cell receptors for extracellular matrix. Immunotherapy with BCG causes a dramatic but transient increase in T cell: ECM interactions.

Acoustic response of a rectangular levitator with orifices

NASA Technical Reports Server (NTRS)

El-Raheb, Michael; Wagner, Paul

1990-01-01

The acoustic response of a rectangular cavity to speaker-generated excitation through waveguides terminating at orifices in the cavity walls is analyzed. To find the effects of orifices, acoustic pressure is expressed by eigenfunctions satisfying Neumann boundary conditions as well as by those satisfying Dirichlet ones. Some of the excess unknowns can be eliminated by point constraints set over the boundary, by appeal to Lagrange undetermined multipliers. The resulting transfer matrix must be further reduced by partial condensation to the order of a matrix describing unmixed boundary conditions. If the cavity is subjected to an axial temperature dependence, the transfer matrix is determined numerically.

Continuous-Time Bilinear System Identification

NASA Technical Reports Server (NTRS)

Juang, Jer-Nan

2003-01-01

The objective of this paper is to describe a new method for identification of a continuous-time multi-input and multi-output bilinear system. The approach is to make judicious use of the linear-model properties of the bilinear system when subjected to a constant input. Two steps are required in the identification process. The first step is to use a set of pulse responses resulting from a constant input of one sample period to identify the state matrix, the output matrix, and the direct transmission matrix. The second step is to use another set of pulse responses with the same constant input over multiple sample periods to identify the input matrix and the coefficient matrices associated with the coupling terms between the state and the inputs. Numerical examples are given to illustrate the concept and the computational algorithm for the identification method.

Binary blend of glyceryl monooleate and glyceryl monostearate for magnetically induced thermo-responsive local drug delivery system.

PubMed

Mengesha, Abebe E; Wydra, Robert J; Hilt, J Zach; Bummer, Paul M

2013-12-01

To develop a novel monoglycerides-based thermal-sensitive drug delivery system, specifically for local intracavitary chemotherapy. Lipid matrices containing mixtures of glyceryl monooleate (GMO) and glyceryl monostearate (GMS) were evaluated for their potential application as magnetically induced thermo-responsive local drug delivery systems using a poorly water-soluble model drug, nifedipine (NF). Oleic acid-modified iron oxide (OA-Fe3O4) nanoparticles were embedded into the GMO-GMS matrix for remote activation of the drug release using an alternating magnetic field (AMF). The crystallization behavior of binary blends of GMO and GMS as characterized by DSC did show temperature dependent phase transition. GMO-GMS (75:25 wt%) blend showed a melting (T m ) and crystallization (T c ) points at 42°C and 37°C, respectively indicating the potential of the matrix to act as an 'on-demand' drug release. The matrix released only 35% of the loaded drug slowly in 10 days at 37°C whereas 96% release was obtained at 42°C. A concentration of 0.5% OA-Fe3O4 heated the matrix to 42.3 and 45.5°C within 5 min and 10 min of AMF exposure, respectively. The in vitro NF release profiles form the monoglycerides matrix containing 0.5% OA-Fe3O4 nanoparticles after AMF activation confirmed the thermo-responsive nature of the matrix that could provide pulsatile drug release 'on-demand'.

MATRIX DISCRIMINANT ANALYSIS WITH APPLICATION TO COLORIMETRIC SENSOR ARRAY DATA

PubMed Central

Suslick, Kenneth S.

2014-01-01

With the rapid development of nano-technology, a “colorimetric sensor array” (CSA) which is referred to as an optical electronic nose has been developed for the identification of toxicants. Unlike traditional sensors which rely on a single chemical interaction, CSA can measure multiple chemical interactions by using chemo-responsive dyes. The color changes of the chemo-responsive dyes are recorded before and after exposure to toxicants and serve as a template for classification. The color changes are digitalized in the form of a matrix with rows representing dye effects and columns representing the spectrum of colors. Thus, matrix-classification methods are highly desirable. In this article, we develop a novel classification method, matrix discriminant analysis (MDA), which is a generalization of linear discriminant analysis (LDA) for the data in matrix form. By incorporating the intrinsic matrix-structure of the data in discriminant analysis, the proposed method can improve CSA’s sensitivity and more importantly, specificity. A penalized MDA method, PMDA, is also introduced to further incorporate sparsity structure in discriminant function. Numerical studies suggest that the proposed MDA and PMDA methods outperform LDA and other competing discriminant methods for matrix predictors. The asymptotic consistency of MDA is also established. R code and data are available online as supplementary material. PMID:26783371

Osteoblast Differentiation and Bone Matrix Formation In Vivo and In Vitro.

PubMed

Blair, Harry C; Larrouture, Quitterie C; Li, Yanan; Lin, Hang; Beer-Stoltz, Donna; Liu, Li; Tuan, Rocky S; Robinson, Lisa J; Schlesinger, Paul H; Nelson, Deborah J

2017-06-01

We review the characteristics of osteoblast differentiation and bone matrix synthesis. Bone in air breathing vertebrates is a specialized tissue that developmentally replaces simpler solid tissues, usually cartilage. Bone is a living organ bounded by a layer of osteoblasts that, because of transport and compartmentalization requirements, produce bone matrix exclusively as an organized tight epithelium. With matrix growth, osteoblasts are reorganized and incorporated into the matrix as living cells, osteocytes, which communicate with each other and surface epithelium by cell processes within canaliculi in the matrix. The osteoblasts secrete the organic matrix, which are dense collagen layers that alternate parallel and orthogonal to the axis of stress loading. Into this matrix is deposited extremely dense hydroxyapatite-based mineral driven by both active and passive transport and pH control. As the matrix matures, hydroxyapatite microcrystals are organized into a sophisticated composite in the collagen layer by nucleation in the protein lattice. Recent studies on differentiating osteoblast precursors revealed a sophisticated proton export network driving mineralization, a gene expression program organized with the compartmentalization of the osteoblast epithelium that produces the mature bone matrix composite, despite varying serum calcium and phosphate. Key issues not well defined include how new osteoblasts are incorporated in the epithelial layer, replacing those incorporated in the accumulating matrix. Development of bone in vitro is the subject of numerous projects using various matrices and mesenchymal stem cell-derived preparations in bioreactors. These preparations reflect the structure of bone to variable extents, and include cells at many different stages of differentiation. Major challenges are production of bone matrix approaching the in vivo density and support for trabecular bone formation. In vitro differentiation is limited by the organization and density of osteoblasts and by endogenous and exogenous inhibitors.

Osteoblast Differentiation and Bone Matrix Formation In Vivo and In Vitro

PubMed Central

Larrouture, Quitterie C.; Li, Yanan; Lin, Hang; Beer-Stoltz, Donna; Liu, Li; Tuan, Rocky S.; Robinson, Lisa J.; Schlesinger, Paul H.; Nelson, Deborah J.

2017-01-01

We review the characteristics of osteoblast differentiation and bone matrix synthesis. Bone in air breathing vertebrates is a specialized tissue that developmentally replaces simpler solid tissues, usually cartilage. Bone is a living organ bounded by a layer of osteoblasts that, because of transport and compartmentalization requirements, produce bone matrix exclusively as an organized tight epithelium. With matrix growth, osteoblasts are reorganized and incorporated into the matrix as living cells, osteocytes, which communicate with each other and surface epithelium by cell processes within canaliculi in the matrix. The osteoblasts secrete the organic matrix, which are dense collagen layers that alternate parallel and orthogonal to the axis of stress loading. Into this matrix is deposited extremely dense hydroxyapatite-based mineral driven by both active and passive transport and pH control. As the matrix matures, hydroxyapatite microcrystals are organized into a sophisticated composite in the collagen layer by nucleation in the protein lattice. Recent studies on differentiating osteoblast precursors revealed a sophisticated proton export network driving mineralization, a gene expression program organized with the compartmentalization of the osteoblast epithelium that produces the mature bone matrix composite, despite varying serum calcium and phosphate. Key issues not well defined include how new osteoblasts are incorporated in the epithelial layer, replacing those incorporated in the accumulating matrix. Development of bone in vitro is the subject of numerous projects using various matrices and mesenchymal stem cell-derived preparations in bioreactors. These preparations reflect the structure of bone to variable extents, and include cells at many different stages of differentiation. Major challenges are production of bone matrix approaching the in vivo density and support for trabecular bone formation. In vitro differentiation is limited by the organization and density of osteoblasts and by endogenous and exogenous inhibitors. PMID:27846781

Multiscale Static Analysis of Notched and Unnotched Laminates Using the Generalized Method of Cells

NASA Technical Reports Server (NTRS)

Naghipour Ghezeljeh, Paria; Arnold, Steven M.; Pineda, Evan J.; Stier, Bertram; Hansen, Lucas; Bednarcyk, Brett A.; Waas, Anthony M.

2016-01-01

The generalized method of cells (GMC) is demonstrated to be a viable micromechanics tool for predicting the deformation and failure response of laminated composites, with and without notches, subjected to tensile and compressive static loading. Given the axial [0], transverse [90], and shear [+45/-45] response of a carbon/epoxy (IM7/977-3) system, the unnotched and notched behavior of three multidirectional layups (Layup 1: [0,45,90,-45](sub 2S), Layup 2: [0,60,0](sub 3S), and Layup 3: [30,60,90,-30, -60](sub 2S)) are predicted under both tensile and compressive static loading. Matrix nonlinearity is modeled in two ways. The first assumes all nonlinearity is due to anisotropic progressive damage of the matrix only, which is modeled, using the multiaxial mixed-mode continuum damage model (MMCDM) within GMC. The second utilizes matrix plasticity coupled with brittle final failure based on the maximum principle strain criteria to account for matrix nonlinearity and failure within the Finite Element Analysis--Micromechanics Analysis Code (FEAMAC) software multiscale framework. Both MMCDM and plasticity models incorporate brittle strain- and stress-based failure criteria for the fiber. Upon satisfaction of these criteria, the fiber properties are immediately reduced to a nominal value. The constitutive response for each constituent (fiber and matrix) is characterized using a combination of vendor data and the axial, transverse, and shear responses of unnotched laminates. Then, the capability of the multiscale methodology is assessed by performing blind predictions of the mentioned notched and unnotched composite laminates response under tensile and compressive loading. Tabulated data along with the detailed results (i.e., stress-strain curves as well as damage evolution states at various ratios of strain to failure) for all laminates are presented.

High-temperature durability considerations for HSCT combustor

NASA Technical Reports Server (NTRS)

Jacobson, Nathan S.

1992-01-01

The novel combustor designs for the High Speed Civil Transport will require high temperature materials with long term environmental stability. Higher liner temperatures than in conventional combustors and the need for reduced weight necessitates the use of advanced ceramic matrix composites. The combustor environment is defined at the current state of design, the major degradation routes are discussed for each candidate ceramic material, and where possible, the maximum use temperatures are defined for these candidate ceramics.

A generalized Lyapunov theory for robust root clustering of linear state space models with real parameter uncertainty

NASA Technical Reports Server (NTRS)

Yedavalli, R. K.

1992-01-01

The problem of analyzing and designing controllers for linear systems subject to real parameter uncertainty is considered. An elegant, unified theory for robust eigenvalue placement is presented for a class of D-regions defined by algebraic inequalities by extending the nominal matrix root clustering theory of Gutman and Jury (1981) to linear uncertain time systems. The author presents explicit conditions for matrix root clustering for different D-regions and establishes the relationship between the eigenvalue migration range and the parameter range. The bounds are all obtained by one-shot computation in the matrix domain and do not need any frequency sweeping or parameter gridding. The method uses the generalized Lyapunov theory for getting the bounds.

Filamin A Mediates Wound Closure by Promoting Elastic Deformation and Maintenance of Tension in the Collagen Matrix

PubMed Central

Mohammadi, Hamid; Pinto, Vanessa I.; Wang, Yongqiang; Hinz, Boris; Janmey, Paul A.; McCulloch, Christopher A.

2016-01-01

Cell-mediated remodeling and wound closure are critical for efficient wound healing, but the contribution of actin-binding proteins to contraction of the extracellular matrix is not defined. We examined the role of filamin A (FLNa), an actin filament cross-linking protein, in wound contraction and maintenance of matrix tension. Conditional deletion of FLNa in fibroblasts in mice was associated with ~ 4 day delay of full-thickness skin wound contraction compared with wild-type (WT) mice. We modeled the healing wound matrix using cultured fibroblasts plated on grid-supported collagen gels that create lateral boundaries, which are analogues to wound margins. In contrast to WT cells, FLNa knockdown (KD) cells could not completely maintain tension when matrix compaction was resisted by boundaries, which manifested as relaxed matrix tension. Similarly, WT cells on cross-linked collagen, which requires higher levels of sustained tension, exhibited approximately fivefold larger deformation fields and approximately twofold greater fiber alignment compared with FLNa KD cells. Maintenance of boundary-resisted tension markedly influenced the elongation of cell extensions: in WT cells, the number (~50%) and length (~300%) of cell extensions were greater than FLNa KD cells. We conclude that FLNa is required for wound contraction, in part by enabling elastic deformation and maintenance of tension in the matrix. PMID:26134946

On the selection of user-defined parameters in data-driven stochastic subspace identification

NASA Astrophysics Data System (ADS)

Priori, C.; De Angelis, M.; Betti, R.

2018-02-01

The paper focuses on the time domain output-only technique called Data-Driven Stochastic Subspace Identification (DD-SSI); in order to identify modal models (frequencies, damping ratios and mode shapes), the role of its user-defined parameters is studied, and rules to determine their minimum values are proposed. Such investigation is carried out using, first, the time histories of structural responses to stationary excitations, with a large number of samples, satisfying the hypothesis on the input imposed by DD-SSI. Then, the case of non-stationary seismic excitations with a reduced number of samples is considered. In this paper, partitions of the data matrix different from the one proposed in the SSI literature are investigated, together with the influence of different choices of the weighting matrices. The study is carried out considering two different applications: (1) data obtained from vibration tests on a scaled structure and (2) in-situ tests on a reinforced concrete building. Referring to the former, the identification of a steel frame structure tested on a shaking table is performed using its responses in terms of absolute accelerations to a stationary (white noise) base excitation and to non-stationary seismic excitations of low intensity. Black-box and modal models are identified in both cases and the results are compared with those from an input-output subspace technique. With regards to the latter, the identification of a complex hospital building is conducted using data obtained from ambient vibration tests.

Silencing by nuclear matrix attachment distinguishes cell-type specificity: association with increased proliferation capacity

PubMed Central

Linnemann, Amelia K.; Krawetz, Stephen A.

2009-01-01

DNA loop organization by nuclear scaffold/matrix attachment is a key regulator of gene expression that may provide a means to modulate phenotype. We have previously shown that attachment of genes to the NaCl-isolated nuclear matrix correlates with their silencing in HeLa cells. In contrast, expressed genes were associated with the lithium 3,5-diiodosalicylate (LIS)-isolated nuclear scaffold. To define their role in determining phenotype matrix attached regions (MARs) on human chromosomes 14–18 were identified as a function of expression in a primary cell line. The locations of MARs in aortic adventitial fibroblast (AoAF) cells were very stable (r = 0.909) and 96% of genes attached at MARs are silent (P < 0.001). Approximately one-third of the genes uniquely expressed in AoAF cells were associated with the HeLa cell nuclear matrix and silenced. Comparatively, 81% were associated with the AoAF cell nuclear scaffold (P < 0.001) and expressed. This suggests that nuclear scaffold/matrix association mediates a portion of cell type-specific gene expression thereby modulating phenotype. Interestingly, nuclear matrix attachment and thus silencing of specific genes that regulate proliferation and maintain the integrity of the HeLa cell genome suggests that transformation may at least in part be achieved through aberrant nuclear matrix attachment. PMID:19276204

Formulation development and optimization of sustained release matrix tablet of Itopride HCl by response surface methodology and its evaluation of release kinetics

PubMed Central

Bose, Anirbandeep; Wong, Tin Wui; Singh, Navjot

2012-01-01

The objective of this present investigation was to develop and formulate sustained release (SR) matrix tablets of Itopride HCl, by using different polymer combinations and fillers, to optimize by Central Composite Design response surface methodology for different drug release variables and to evaluate drug release pattern of the optimized product. Sustained release matrix tablets of various combinations were prepared with cellulose-based polymers: hydroxy propyl methyl cellulose (HPMC) and polyvinyl pyrolidine (pvp) and lactose as fillers. Study of pre-compression and post-compression parameters facilitated the screening of a formulation with best characteristics that underwent here optimization study by response surface methodology (Central Composite Design). The optimized tablet was further subjected to scanning electron microscopy to reveal its release pattern. The in vitro study revealed that combining of HPMC K100M (24.65 MG) with pvp(20 mg)and use of LACTOSE as filler sustained the action more than 12 h. The developed sustained release matrix tablet of improved efficacy can perform therapeutically better than a conventional tablet. PMID:23960836

Formulation development and optimization of sustained release matrix tablet of Itopride HCl by response surface methodology and its evaluation of release kinetics.

PubMed

Bose, Anirbandeep; Wong, Tin Wui; Singh, Navjot

2013-04-01

The objective of this present investigation was to develop and formulate sustained release (SR) matrix tablets of Itopride HCl, by using different polymer combinations and fillers, to optimize by Central Composite Design response surface methodology for different drug release variables and to evaluate drug release pattern of the optimized product. Sustained release matrix tablets of various combinations were prepared with cellulose-based polymers: hydroxy propyl methyl cellulose (HPMC) and polyvinyl pyrolidine (pvp) and lactose as fillers. Study of pre-compression and post-compression parameters facilitated the screening of a formulation with best characteristics that underwent here optimization study by response surface methodology (Central Composite Design). The optimized tablet was further subjected to scanning electron microscopy to reveal its release pattern. The in vitro study revealed that combining of HPMC K100M (24.65 MG) with pvp(20 mg)and use of LACTOSE as filler sustained the action more than 12 h. The developed sustained release matrix tablet of improved efficacy can perform therapeutically better than a conventional tablet.

Limits of linearity and detection for some drugs of abuse.

PubMed

Needleman, S B; Romberg, R W

1990-01-01

The limits of linearity (LOL) and detection (LOD) are important factors in establishing the reliability of an analytical procedure for accurately assaying drug concentrations in urine specimens. Multiple analyses of analyte over an extended range of concentrations provide a measure of the ability of the analytical procedure to correctly identify known quantities of drug in a biofluid matrix. Each of the seven drugs of abuse gives linear analytical responses from concentrations at or near their LOD to concentrations several-fold higher than those generally encountered in the drug screening laboratory. The upper LOL exceeds the Department of Navy (DON) cutoff values by factors of approximately 2 to 160. The LOD varies from 0.4 to 5.0% of the DON cutoff value for each drug. The limit of quantitation (LOQ) is calculated as the LOD + 7 SD. The range for LOL is greater for drugs analyzed with deuterated internal standards compared with those using conventional internal standards. For THC acid, cocaine, PCP, and morphine, LOLs are 8 to 160-fold greater than the defined cutoff concentrations. For the other drugs, the LOL's are only 2 to 4-fold greater than the defined cutoff concentrations.

Rock Physics and Petrographic Parameters Relationship Within Siliciclastic Rocks: Quartz Sandstone Outcrop Study Case

NASA Astrophysics Data System (ADS)

Syafriyono, S.; Caesario, D.; Swastika, A.; Adlan, Q.; Syafri, I.; Abdurrokhim, A.; Mardiana, U.; Mohamad, F.; Alfadli, M. K.; Sari, V. M.

2018-03-01

Rock physical parameters value (Vp and Vs) is one of fundamental aspects in reservoir characterization as a tool to detect rock heterogenity. Its response is depend on several reservoir conditions such as lithology, pressure and reservoir fluids. The value of Vp and Vs is controlled by grain contact and contact stiffness, a function of clay mineral content and porosity also affected by mineral composition. The study about Vp and Vs response within sandstone and its relationship with petrographic parameters has become important to define anisotrophy of reservoir characteristics distribution and could give a better understanding about local diagenesis that influence clastic reservoir properties. Petrographic analysis and Vp-Vs calculation was carried out to 12 core sample which is obtained by hand-drilling of the outcrop in Sukabumi area, West Java as a part of Bayah Formation. Data processing and interpretation of sedimentary vertical succession showing that this outcrop comprises of 3 major sandstone layers indicating fluvial depositional environment. As stated before, there are 4 petrographic parameters (sorting, roundness, clay mineral content, and grain contact) which are responsible to the differences of shear wave and compressional wave value in this outcrop. Lithology with poor-sorted and well- roundness has Vp value lower than well-sorted and poor-roundness (sub-angular) grain. For the sample with high clay content, Vp value is ranging from 1681 to 2000 m/s and could be getting high until 2190 to 2714 m/s in low clay content sample even though the presence of clay minerals cannot be defined neither as matrix nor cement. The whole sample have suture grain contact indicating telogenesis regime whereas facies has no relationship with Vp and Vs value because of the different type of facies show similar petrographic parameters after diagenesis.

Decomposition of the Multistatic Response Matrix and Target Characterization

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

Chambers, D H

2008-02-14

Decomposition of the time-reversal operator for an array, or equivalently the singular value decomposition of the multistatic response matrix, has been used to improve imaging and localization of targets in complicated media. Typically, each singular value is associated with one scatterer even though it has been shown in several cases that a single scatterer can generate several singular values. In this paper we review the analysis of the time-reversal operator (TRO), or equivalently the multistatic response matrix (MRM), of an array system and a small target. We begin with two-dimensional scattering from a small cylinder then show the results formore » a small non-spherical target in three dimensions. We show that the number and magnitudes of the singular values contain information about target composition, shape, and orientation.« less

System and plastic scintillator for discrimination of thermal neutron, fast neutron, and gamma radiation

DOEpatents

Zaitseva, Natalia P.; Carman, M. Leslie; Faust, Michelle A.; Glenn, Andrew M.; Martinez, H. Paul; Pawelczak, Iwona A.; Payne, Stephen A.

2017-05-16

A scintillator material according to one embodiment includes a polymer matrix; a primary dye in the polymer matrix, the primary dye being a fluorescent dye, the primary dye being present in an amount of 3 wt % or more; and at least one component in the polymer matrix, the component being selected from a group consisting of B, Li, Gd, a B-containing compound, a Li-containing compound and a Gd-containing compound, wherein the scintillator material exhibits an optical response signature for thermal neutrons that is different than an optical response signature for fast neutrons and gamma rays. A system according to one embodiment includes a scintillator material as disclosed herein and a photodetector for detecting the response of the material to fast neutron, thermal neutron and gamma ray irradiation.

Dissecting the Impact of Matrix Anchorage and Elasticity in Cell Adhesion

PubMed Central

Pompe, Tilo; Glorius, Stefan; Bischoff, Thomas; Uhlmann, Ina; Kaufmann, Martin; Brenner, Sebastian; Werner, Carsten

2009-01-01

Abstract Extracellular matrices determine cellular fate decisions through the regulation of intracellular force and stress. Previous studies suggest that matrix stiffness and ligand anchorage cause distinct signaling effects. We show herein how defined noncovalent anchorage of adhesion ligands to elastic substrates allows for dissection of intracellular adhesion signaling pathways related to matrix stiffness and receptor forces. Quantitative analysis of the mechanical balance in cell adhesion using traction force microscopy revealed distinct scalings of the strain energy imparted by the cells on the substrates dependent either on matrix stiffness or on receptor force. Those scalings suggested the applicability of a linear elastic theoretical framework for the description of cell adhesion in a certain parameter range, which is cell-type-dependent. Besides the deconvolution of biophysical adhesion signaling, site-specific phosphorylation of focal adhesion kinase, dependent either on matrix stiffness or on receptor force, also demonstrated the dissection of biochemical signaling events in our approach. Moreover, the net contractile moment of the adherent cells and their strain energy exerted on the elastic substrate was found to be a robust measure of cell adhesion with a unifying power-law scaling exponent of 1.5 independent of matrix stiffness. PMID:19843448

IOL calculation using paraxial matrix optics.

PubMed

Haigis, Wolfgang

2009-07-01

Matrix methods have a long tradition in paraxial physiological optics. They are especially suited to describe and handle optical systems in a simple and intuitive manner. While these methods are more and more applied to calculate the refractive power(s) of toric intraocular lenses (IOL), they are hardly used in routine IOL power calculations for cataract and refractive surgery, where analytical formulae are commonly utilized. Since these algorithms are also based on paraxial optics, matrix optics can offer rewarding approaches to standard IOL calculation tasks, as will be shown here. Some basic concepts of matrix optics are introduced and the system matrix for the eye is defined, and its application in typical IOL calculation problems is illustrated. Explicit expressions are derived to determine: predicted refraction for a given IOL power; necessary IOL power for a given target refraction; refractive power for a phakic IOL (PIOL); predicted refraction for a thick lens system. Numerical examples with typical clinical values are given for each of these expressions. It is shown that matrix optics can be applied in a straightforward and intuitive way to most problems of modern routine IOL calculation, in thick or thin lens approximation, for aphakic or phakic eyes.

Analysis of modified SMI method for adaptive array weight control

NASA Technical Reports Server (NTRS)

Dilsavor, R. L.; Moses, R. L.

1989-01-01

An adaptive array is applied to the problem of receiving a desired signal in the presence of weak interference signals which need to be suppressed. A modification, suggested by Gupta, of the sample matrix inversion (SMI) algorithm controls the array weights. In the modified SMI algorithm, interference suppression is increased by subtracting a fraction F of the noise power from the diagonal elements of the estimated covariance matrix. Given the true covariance matrix and the desired signal direction, the modified algorithm is shown to maximize a well-defined, intuitive output power ratio criterion. Expressions are derived for the expected value and variance of the array weights and output powers as a function of the fraction F and the number of snapshots used in the covariance matrix estimate. These expressions are compared with computer simulation and good agreement is found. A trade-off is found to exist between the desired level of interference suppression and the number of snapshots required in order to achieve that level with some certainty. The removal of noise eigenvectors from the covariance matrix inverse is also discussed with respect to this application. Finally, the type and severity of errors which occur in the covariance matrix estimate are characterized through simulation.

The Use of Task-based Cognitive Tests for Defining Vocational Aptness of Individuals with Disabilities.

PubMed

Kwon, Jae-Sung; Oh, Duck-Won

2015-06-01

The purpose of this study was to demonstrate the use of task-based cognitive tests to detect potential problems in the assessment of work training for vocational rehabilitation. Eleven participants with a normal range of cognitive functioning scores were recruited for this study. Participants were all trainees who participated in a vocational training program. The Rey Complex Figure Test and the Allen Cognitive Level Screen were randomly administered to all participants. Responses to the tests were qualitatively analyzed with matrix and scatter charts. Observational outcomes derived from the tests indicated that response errors, distortions, and behavioral problems occurred in most participants. These factors may impede occupational performance despite normal cognitive function. These findings suggest that the use of task-based tests may be beneficial for detecting potential problems associated with the work performance of people with disabilities. Specific analysis using the task-based tests may be necessary to complete the decision-making process for vocational aptness. Furthermore, testing should be led by professionals with a higher specialization in this field.

Sample size determination for GEE analyses of stepped wedge cluster randomized trials.

PubMed

Li, Fan; Turner, Elizabeth L; Preisser, John S

2018-06-19

In stepped wedge cluster randomized trials, intact clusters of individuals switch from control to intervention from a randomly assigned period onwards. Such trials are becoming increasingly popular in health services research. When a closed cohort is recruited from each cluster for longitudinal follow-up, proper sample size calculation should account for three distinct types of intraclass correlations: the within-period, the inter-period, and the within-individual correlations. Setting the latter two correlation parameters to be equal accommodates cross-sectional designs. We propose sample size procedures for continuous and binary responses within the framework of generalized estimating equations that employ a block exchangeable within-cluster correlation structure defined from the distinct correlation types. For continuous responses, we show that the intraclass correlations affect power only through two eigenvalues of the correlation matrix. We demonstrate that analytical power agrees well with simulated power for as few as eight clusters, when data are analyzed using bias-corrected estimating equations for the correlation parameters concurrently with a bias-corrected sandwich variance estimator. © 2018, The International Biometric Society.

Hitting a Moving Target: Basic Mechanisms of Recovery from Acquired Developmental Brain Injury

PubMed Central

Giza, Christopher C.; Kolb, Bryan; Harris, Neil G.; Asarnow, Robert F.; Prins, Mayumi L.

2009-01-01

Acquired brain injuries represent a major cause of disability in the pediatric population. Understanding responses to developmental acquired brain injuries requires knowledge of the neurobiology of normal development, age-at-injury effects and experience-dependent neuroplasticity. In the developing brain, full recovery cannot be considered as a return to the premorbid baseline, since ongoing maturation means that cerebral functioning in normal individuals will continue to advance. Thus, the recovering immature brain has to ‘hit a moving target’ to achieve full functional recovery, defined as parity with age-matched uninjured peers. This review will discuss the consequences of developmental injuries such as focal lesions, diffuse hypoxia and traumatic brain injury (TBI). Underlying cellular and physiological mechanisms relevant to age-at-injury effects will be described in considerable detail, including but not limited to alterations in neurotransmission, connectivity/network functioning, the extracellular matrix, response to oxidative stress and changes in cerebral metabolism. Finally, mechanisms of experience-dependent plasticity will be reviewed in conjunction with their effects on neural repair and recovery. PMID:19956795

In vitro model to study the effects of matrix stiffening on Ca2+ handling and myofilament function in isolated adult rat cardiomyocytes.

PubMed

van Deel, Elza D; Najafi, Aref; Fontoura, Dulce; Valent, Erik; Goebel, Max; Kardux, Kim; Falcão-Pires, Inês; van der Velden, Jolanda

2017-07-15

This paper describes a novel model that allows exploration of matrix-induced cardiomyocyte adaptations independent of the passive effect of matrix rigidity on cardiomyocyte function. Detachment of adult cardiomyocytes from the matrix enables the study of matrix effects on cell shortening, Ca 2+ handling and myofilament function. Cell shortening and Ca 2+ handling are altered in cardiomyocytes cultured for 24 h on a stiff matrix. Matrix stiffness-impaired cardiomyocyte contractility is reversed upon normalization of extracellular stiffness. Matrix stiffness-induced reduction in unloaded shortening is more pronounced in cardiomyocytes isolated from obese ZSF1 rats with heart failure with preserved ejection fraction compared to lean ZSF1 rats. Extracellular matrix (ECM) stiffening is a key element of cardiac disease. Increased rigidity of the ECM passively inhibits cardiac contraction, but if and how matrix stiffening also actively alters cardiomyocyte contractility is incompletely understood. In vitro models designed to study cardiomyocyte-matrix interaction lack the possibility to separate passive inhibition by a stiff matrix from active matrix-induced alterations of cardiomyocyte properties. Here we introduce a novel experimental model that allows exploration of cardiomyocyte functional alterations in response to matrix stiffening. Adult rat cardiomyocytes were cultured for 24 h on matrices of tuneable stiffness representing the healthy and the diseased heart and detached from their matrix before functional measurements. We demonstrate that matrix stiffening, independent of passive inhibition, reduces cell shortening and Ca 2+ handling but does not alter myofilament-generated force. Additionally, detachment of adult cultured cardiomyocytes allowed the transfer of cells from one matrix to another. This revealed that stiffness-induced cardiomyocyte changes are reversed when matrix stiffness is normalized. These matrix stiffness-induced changes in cardiomyocyte function could not be explained by adaptation in the microtubules. Additionally, cardiomyocytes isolated from stiff hearts of the obese ZSF1 rat model of heart failure with preserved ejection fraction show more pronounced reduction in unloaded shortening in response to matrix stiffening. Taken together, we introduce a method that allows evaluation of the influence of ECM properties on cardiomyocyte function separate from the passive inhibitory component of a stiff matrix. As such, it adds an important and physiologically relevant tool to investigate the functional consequences of cardiomyocyte-matrix interactions. © 2017 The Authors. The Journal of Physiology published by John Wiley & Sons Ltd on behalf of The Physiological Society.

An analytical solution for the elastoplastic response of a continuous fiber composite under uniaxial loading

NASA Technical Reports Server (NTRS)

Lee, Jong-Won; Allen, David H.

1990-01-01

A continuous fiber composite is modelled by a two-element composite cylinder in order to predict the elastoplastic response of the composite under a monotonically increasing tensile loading parallel to fibers. The fibers and matrix are assumed to be elastic-perfectly plastic materials obeying Hill's and Tresca's yield criteria, respectively. Here, the composite behavior when the fibers yield prior to the matrix is investigated.

Impact of Material and Architecture Model Parameters on the Failure of Woven Ceramic Matrix Composites (CMCs) via the Multiscale Generalized Method of Cells

NASA Technical Reports Server (NTRS)

Liu, Kuang C.; Arnold, Steven M.

2011-01-01

It is well known that failure of a material is a locally driven event. In the case of ceramic matrix composites (CMCs), significant variations in the microstructure of the composite exist and their significance on both deformation and life response need to be assessed. Examples of these variations include changes in the fiber tow shape, tow shifting/nesting and voids within and between tows. In the present work, the effects of many of these architectural parameters and material scatter of woven ceramic composite properties at the macroscale (woven RUC) will be studied to assess their sensitivity. The recently developed Multiscale Generalized Method of Cells methodology is used to determine the overall deformation response, proportional elastic limit (first matrix cracking), and failure under tensile loading conditions. The macroscale responses investigated illustrate the effect of architectural and material parameters on a single RUC representing a five harness satin weave fabric. Results shows that the most critical architectural parameter is weave void shape and content with other parameters being less in severity. Variation of the matrix material properties was also studied to illustrate the influence of the material variability on the overall features of the composite stress-strain response.

Estimation and Control with Relative Measurements: Algorithms and Scaling Laws

DTIC Science & Technology

2007-09-01

eigenvector of L −1 corre- sponding to its largest eigenvalue. Since L−1 is a positive matrix, Perron - Frobenius theory tells us that |u1| := {|u11...the Frobenius norm of a matrix, and a linear vector space SV as the space of all bounded node-functions with respect to the above defined 144 norm...je‖2F where Eu is the set edges in E that are incident on u. It can be shown from the relationship between the Frobenius norm and the singular

Handling of computational in vitro/in vivo correlation problems by Microsoft Excel: IV. Generalized matrix analysis of linear compartment systems.

PubMed

Langenbucher, Frieder

2005-01-01

A linear system comprising n compartments is completely defined by the rate constants between any of the compartments and the initial condition in which compartment(s) the drug is present at the beginning. The generalized solution is the time profiles of drug amount in each compartment, described by polyexponential equations. Based on standard matrix operations, an Excel worksheet computes the rate constants and the coefficients, finally the full time profiles for a specified range of time values.

Transactions of the Conference on Applied Mathematics and Computing (9th) Held in Minneapolis, Minnesota on 18-21 June 1991

DTIC Science & Technology

1992-03-01

the ith row of I<. The preconditioned matrix K is thus a stochastic matrix, and by the Perron - Frobenius theorem (e.g., Horn and Johnson, 1989), K...now be determined. For equations (10) and (11) to be real, the radical must be nonnegative . This condition on d defines the index zero threshold...ddhsi: sfl] [r;I,r;I] . Since h/lh is positive-definite, (3.2) shows that a , and 13, are nonnegative . This fact can be used t~ test a candidates

Newest Developments in the German Explosive Safety Quantitative Risk Analysis Software (ESQRA-GE)

DTIC Science & Technology

2010-07-01

Joule is shown if the density exceeds one over 56 m ². For both densities the fragments are considered that pass through a specified volume element. An...maximum velocity for each angle interval: ( , )fragN f m and 0 max ( ).fragv f  (5) We use a barrel filled with water to determine the...matrix. We employ characteristic quantities as mass, momentum and energy of the fragment matrix defined as , ijfm r c M m  , (6) , ij ifm r

The topological particle and Morse theory

NASA Astrophysics Data System (ADS)

Rogers, Alice

2000-09-01

Canonical BRST quantization of the topological particle defined by a Morse function h is described. Stochastic calculus, using Brownian paths which implement the WKB method in a new way providing rigorous tunnelling results even in curved space, is used to give an explicit and simple expression for the matrix elements of the evolution operator for the BRST Hamiltonian. These matrix elements lead to a representation of the manifold cohomology in terms of critical points of h along lines developed by Witten (Witten E 1982 J. Diff. Geom. 17 661-92).

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

Mathematical foundations of the GraphBLAS

DOE PAGES

Kepner, Jeremy; Aaltonen, Peter; Bader, David; ...

2016-12-01

The GraphBLAS standard (GraphBlas.org) is being developed to bring the potential of matrix-based graph algorithms to the broadest possible audience. Mathematically, the GraphBLAS defines a core set of matrix-based graph operations that can be used to implement a wide class of graph algorithms in a wide range of programming environments. This study provides an introduction to the mathematics of the GraphBLAS. Graphs represent connections between vertices with edges. Matrices can represent a wide range of graphs using adjacency matrices or incidence matrices. Adjacency matrices are often easier to analyze while incidence matrices are often better for representing data. Fortunately, themore » two are easily connected by matrix multiplication. A key feature of matrix mathematics is that a very small number of matrix operations can be used to manipulate a very wide range of graphs. This composability of a small number of operations is the foundation of the GraphBLAS. A standard such as the GraphBLAS can only be effective if it has low performance overhead. Finally, performance measurements of prototype GraphBLAS implementations indicate that the overhead is low.« less

Thermal and mechanical behavior of metal matrix and ceramic matrix composites

NASA Technical Reports Server (NTRS)

Kennedy, John M. (Editor); Moeller, Helen H. (Editor); Johnson, W. S. (Editor)

1990-01-01

The present conference discusses local stresses in metal-matrix composites (MMCs) subjected to thermal and mechanical loads, the computational simulation of high-temperature MMCs' cyclic behavior, an analysis of a ceramic-matrix composite (CMC) flexure specimen, and a plasticity analysis of fibrous composite laminates under thermomechanical loads. Also discussed are a comparison of methods for determining the fiber-matrix interface frictional stresses of CMCs, the monotonic and cyclic behavior of an SiC/calcium aluminosilicate CMC, the mechanical and thermal properties of an SiC particle-reinforced Al alloy MMC, the temperature-dependent tensile and shear response of a graphite-reinforced 6061 Al-alloy MMC, the fiber/matrix interface bonding strength of MMCs, and fatigue crack growth in an Al2O3 short fiber-reinforced Al-2Mg matrix MMC.

Three-dimensional finite element modeling of pericellular matrix and cell mechanics in the nucleus pulposus of the intervertebral disk based on in situ morphology.

PubMed

Cao, Li; Guilak, Farshid; Setton, Lori A

2011-02-01

Nucleus pulposus (NP) cells of the intervertebral disk (IVD) have unique morphological characteristics and biologic responses to mechanical stimuli that may regulate maintenance and health of the IVD. NP cells reside as single cell, paired or multiple cells in a contiguous pericellular matrix (PCM), whose structure and properties may significantly influence cell and extracellular matrix mechanics. In this study, a computational model was developed to predict the stress-strain, fluid pressure and flow fields for cells and their surrounding PCM in the NP using three-dimensional (3D) finite element models based on the in situ morphology of cell-PCM regions of the mature rat NP, measured using confocal microscopy. Three-dimensional geometries of the extracellular matrix and representative cell-matrix units were used to construct 3D finite element models of the structures as isotropic and biphasic materials. In response to compressive strain of the extracellular matrix, NP cells and PCM regions were predicted to experience volumetric strains that were 1.9-3.7 and 1.4-2.1 times greater than the extracellular matrix, respectively. Volumetric and deviatoric strain concentrations were generally found at the cell/PCM interface, while von Mises stress concentrations were associated with the PCM/extracellular matrix interface. Cell-matrix units containing greater cell numbers were associated with higher peak cell strains and lower rates of fluid pressurization upon loading. These studies provide new model predictions for micromechanics of NP cells that can contribute to an understanding of mechanotransduction in the IVD and its changes with aging and degeneration.

The fundamental role of mechanical properties in the progression of cancer disease and inflammation

NASA Astrophysics Data System (ADS)

Mierke, Claudia Tanja

2014-07-01

The role of mechanical properties in cancer disease and inflammation is still underinvestigated and even ignored in many oncological and immunological reviews. In particular, eight classical hallmarks of cancer have been proposed, but they still ignore the mechanics behind the processes that facilitate cancer progression. To define the malignant transformation of neoplasms and finally reveal the functional pathway that enables cancer cells to promote cancer progression, these classical hallmarks of cancer require the inclusion of specific mechanical properties of cancer cells and their microenvironment such as the extracellular matrix as well as embedded cells such as fibroblasts, macrophages or endothelial cells. Thus, this review will present current cancer research from a biophysical point of view and will therefore focus on novel physical aspects and biophysical methods to investigate the aggressiveness of cancer cells and the process of inflammation. As cancer or immune cells are embedded in a certain microenvironment such as the extracellular matrix, the mechanical properties of this microenvironment cannot be neglected, and alterations of the microenvironment may have an impact on the mechanical properties of the cancer or immune cells. Here, it is highlighted how biophysical approaches, both experimental and theoretical, have an impact on the classical hallmarks of cancer and inflammation. It is even pointed out how these biophysical approaches contribute to the understanding of the regulation of cancer disease and inflammatory responses after tissue injury through physical microenvironmental property sensing mechanisms. The recognized physical signals are transduced into biochemical signaling events that guide cellular responses, such as malignant tumor progression, after the transition of cancer cells from an epithelial to a mesenchymal phenotype or an inflammatory response due to tissue injury. Moreover, cell adaptation to mechanical alterations, in particular the understanding of mechano-coupling and mechano-regulating functions in cell invasion, appears as an important step in cancer progression and inflammatory response to injuries. This may lead to novel insights into cancer disease and inflammatory diseases and will overcome classical views on cancer and inflammation. In addition, this review will discuss how the physics of cancer and inflammation can help to reveal whether cancer cells will invade connective tissue and metastasize or how leukocytes extravasate and migrate through the tissue. In this review, the physical concepts of cancer progression, including the tissue basement membrane a cancer cell is crossing, its invasion and transendothelial migration as well as the basic physical concepts of inflammatory processes and the cellular responses to the mechanical stress of the microenvironment such as external forces and matrix stiffness, are presented and discussed. In conclusion, this review will finally show how physical measurements can improve classical approaches that investigate cancer and inflammatory diseases, and how these physical insights can be integrated into classical tumor biological approaches.

Hierarchical Simulation of Hot Composite Structures

NASA Technical Reports Server (NTRS)

Chamis, C. C.; Murthy, P. L. N.; Singhal, S. N.

1993-01-01

Computational procedures are described to simulate the thermal and mechanical behavior of high temperature metal matrix composites (HT-MMC) in the following three broad areas: (1) Behavior of HT-MMC's from micromechanics to laminate via Metal Matrix Composite Analyzer (METCAN), (2) tailoring of HT-MMC behavior for optimum specific performance via Metal Matrix Laminate Tailoring (MMLT), and (3) HT-MMC structural response for hot structural components via High Temperature Composite Analyzer (HITCAN). Representative results from each area are presented to illustrate the effectiveness of computational simulation procedures. The sample case results show that METCAN can be used to simulate material behavior such as strength, stress-strain response, and cyclic life in HTMMC's; MMLT can be used to tailor the fabrication process for optimum performance such as that for in-service load carrying capacity of HT-MMC's; and HITCAN can be used to evaluate static fracture and fatigue life of hot pressurized metal matrix composite rings.

Damage evolution and mechanical response of cross-ply ceramic composite laminates

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

Weitsman, Y.; Yu, N.; Zhu, H.

1995-12-31

A mechanistic model for the damage evolution and mechanical response of cross-ply ceramic composite laminates under monotonically increasing uniaxial tension is presented. The model accounts for a variety of damage mechanisms evolving in cross-ply ceramic composite laminates, such as fiber-bridged matrix cracks in 0{degrees}-plies, transversely oriented matrix cracks in 90{degrees}-plies, and slips at 0{degrees}/90{degrees} ply interfaces as well as at the fiber/matrix interfaces. Energy criteria are developed to determine the creation and progression of matrix cracks and slip zones. The model predicts that the crack density in 0{degrees}-plies becomes higher than that within the 90{degrees}-plies as the applied load ismore » incrementally increased, which agrees with the experimental observation. It is also shown that the model provides a reasonable prediction for the nonlinear stress-strain behavior of crossply SiC/CAS ceramic composites.« less

Tissue specificity of the hormonal response in sex accessory tissues is associated with nuclear matrix protein patterns.

PubMed

Getzenberg, R H; Coffey, D S

1990-09-01

The DNA of interphase nuclei have very specific three-dimensional organizations that are different in different cell types, and it is possible that this varying DNA organization is responsible for the tissue specificity of gene expression. The nuclear matrix organizes the three-dimensional structure of the DNA and is believed to be involved in the control of gene expression. This study compares the nuclear structural proteins between two sex accessory tissues in the same animal responding to the same androgen stimulation by the differential expression of major tissue-specific secretory proteins. We demonstrate here that the nuclear matrix is tissue specific in the rat ventral prostate and seminal vesicle, and undergoes characteristic alterations in its protein composition upon androgen withdrawal. Three types of nuclear matrix proteins were observed: 1) nuclear matrix proteins that are different and tissue specific in the rat ventral prostate and seminal vesicle, 2) a set of nuclear matrix proteins that either appear or disappear upon androgen withdrawal, and 3) a set of proteins that are common to both the ventral prostate and seminal vesicle and do not change with the hormonal state of the animal. Since the nuclear matrix is known to bind androgen receptors in a tissue- and steroid-specific manner, we propose that the tissue specificity of the nuclear matrix arranges the DNA in a unique conformation, which may be involved in the specific interaction of transcription factors with DNA sequences, resulting in tissue-specific patterns of secretory protein expression.

Algebraic approach to small-world network models

NASA Astrophysics Data System (ADS)

Rudolph-Lilith, Michelle; Muller, Lyle E.

2014-01-01

We introduce an analytic model for directed Watts-Strogatz small-world graphs and deduce an algebraic expression of its defining adjacency matrix. The latter is then used to calculate the small-world digraph's asymmetry index and clustering coefficient in an analytically exact fashion, valid nonasymptotically for all graph sizes. The proposed approach is general and can be applied to all algebraically well-defined graph-theoretical measures, thus allowing for an analytical investigation of finite-size small-world graphs.

Responses in large-scale structure

NASA Astrophysics Data System (ADS)

Barreira, Alexandre; Schmidt, Fabian

2017-06-01

We introduce a rigorous definition of general power-spectrum responses as resummed vertices with two hard and n soft momenta in cosmological perturbation theory. These responses measure the impact of long-wavelength perturbations on the local small-scale power spectrum. The kinematic structure of the responses (i.e., their angular dependence) can be decomposed unambiguously through a ``bias'' expansion of the local power spectrum, with a fixed number of physical response coefficients, which are only a function of the hard wavenumber k. Further, the responses up to n-th order completely describe the (n+2)-point function in the squeezed limit, i.e. with two hard and n soft modes, which one can use to derive the response coefficients. This generalizes previous results, which relate the angle-averaged squeezed limit to isotropic response coefficients. We derive the complete expression of first- and second-order responses at leading order in perturbation theory, and present extrapolations to nonlinear scales based on simulation measurements of the isotropic response coefficients. As an application, we use these results to predict the non-Gaussian part of the angle-averaged matter power spectrum covariance CovNGl=0(k1,k2), in the limit where one of the modes, say k2, is much smaller than the other. Without any free parameters, our model results are in very good agreement with simulations for k2 lesssim 0.06 h Mpc-1, and for any k1 gtrsim 2k2. The well-defined kinematic structure of the power spectrum response also permits a quick evaluation of the angular dependence of the covariance matrix. While we focus on the matter density field, the formalism presented here can be generalized to generic tracers such as galaxies.

METCAN: The metal matrix composite analyzer

NASA Technical Reports Server (NTRS)

Hopkins, Dale A.; Murthy, Pappu L. N.

1988-01-01

Metal matrix composites (MMC) are the subject of intensive study and are receiving serious consideration for critical structural applications in advanced aerospace systems. MMC structural analysis and design methodologies are studied. Predicting the mechanical and thermal behavior and the structural response of components fabricated from MMC requires the use of a variety of mathematical models. These models relate stresses to applied forces, stress intensities at the tips of cracks to nominal stresses, buckling resistance to applied force, or vibration response to excitation forces. The extensive research in computational mechanics methods for predicting the nonlinear behavior of MMC are described. This research has culminated in the development of the METCAN (METal Matrix Composite ANalyzer) computer code.

A frequency domain global parameter estimation method for multiple reference frequency response measurements

NASA Astrophysics Data System (ADS)

Shih, C. Y.; Tsuei, Y. G.; Allemang, R. J.; Brown, D. L.

1988-10-01

A method of using the matrix Auto-Regressive Moving Average (ARMA) model in the Laplace domain for multiple-reference global parameter identification is presented. This method is particularly applicable to the area of modal analysis where high modal density exists. The method is also applicable when multiple reference frequency response functions are used to characterise linear systems. In order to facilitate the mathematical solution, the Forsythe orthogonal polynomial is used to reduce the ill-conditioning of the formulated equations and to decouple the normal matrix into two reduced matrix blocks. A Complex Mode Indicator Function (CMIF) is introduced, which can be used to determine the proper order of the rational polynomials.

Modeling damage evolution in a hybrid ceramic matrix composite under static tensile load

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

Bonora, N.; Newaz, G.

In this investigation, damage evolution in a unidirectional hybrid ceramic composite made from Nicalon and SiC fibers in a Lithium Aluminosilicate (LAS) glass matrix was studied. The static stress-strain response of the composite exhibited a linear response followed by load drop in a progressive manner. Careful experiments were conducted stopping the tests at various strain levels and using replication technique, scanning and optical microscopy to monitor the evolution of damage in these composites. It was observed that the constituents of the composite failed in a sequential manner at increasing strain levels. The matrix cracks were followed by SiC fiber failuresmore » near ultimate tensile stress. After that, the load drop was associated with progressive failure of the Nicalon fibers. Identification of these failure modes were critical to the development of a concentric cylinder model representing all three constituent phases to predict the constitutive response of the CMC computationally. The strain-to-failure of the matrix and fibers were used to progressively fail the constituents in the model and the overall experimental constitutive response of the CMC was recovered. A strain based analytical representation was developed relating stiffness loss to applied strain. Based on this formulation, damage evolution and its consequence on tensile stress-strain response was predicted for room temperature behavior of hybrid CMCs. The contribution of the current work is that the proposed strain-damage phenomenological model can capture the damage evolution and the corresponding material response for continuous fiber-reinforced CMCs. The modeling approach shows much promise for the complex damage processes observed in hybrid CMCs.« less

Quantitative analysis of eyes and other optical systems in linear optics.

PubMed

Harris, William F; Evans, Tanya; van Gool, Radboud D

2017-05-01

To show that 14-dimensional spaces of augmented point P and angle Q characteristics, matrices obtained from the ray transference, are suitable for quantitative analysis although only the latter define an inner-product space and only on it can one define distances and angles. The paper examines the nature of the spaces and their relationships to other spaces including symmetric dioptric power space. The paper makes use of linear optics, a three-dimensional generalization of Gaussian optics. Symmetric 2 × 2 dioptric power matrices F define a three-dimensional inner-product space which provides a sound basis for quantitative analysis (calculation of changes, arithmetic means, etc.) of refractive errors and thin systems. For general systems the optical character is defined by the dimensionally-heterogeneous 4 × 4 symplectic matrix S, the transference, or if explicit allowance is made for heterocentricity, the 5 × 5 augmented symplectic matrix T. Ordinary quantitative analysis cannot be performed on them because matrices of neither of these types constitute vector spaces. Suitable transformations have been proposed but because the transforms are dimensionally heterogeneous the spaces are not naturally inner-product spaces. The paper obtains 14-dimensional spaces of augmented point P and angle Q characteristics. The 14-dimensional space defined by the augmented angle characteristics Q is dimensionally homogenous and an inner-product space. A 10-dimensional subspace of the space of augmented point characteristics P is also an inner-product space. The spaces are suitable for quantitative analysis of the optical character of eyes and many other systems. Distances and angles can be defined in the inner-product spaces. The optical systems may have multiple separated astigmatic and decentred refracting elements. © 2017 The Authors Ophthalmic & Physiological Optics © 2017 The College of Optometrists.

Nonlinear mechanical response of the extracellular matrix: learning from articular cartilage

NASA Astrophysics Data System (ADS)

Kearns, Sarah; Das, Moumita

2015-03-01

We study the mechanical structure-function relations in the extracellular matrix (ECM) with focus on nonlinear shear and compression response. As a model system, our study focuses on the ECM in articular cartilage tissue which has two major mechanobiological components: a network of the biopolymer collagen that acts as a stiff, reinforcing matrix, and a flexible aggrecan network that facilitates deformability. We model this system as a double network hydrogel made of interpenetrating networks of stiff and flexible biopolymers respectively. We study the linear and nonlinear mechanical response of the model ECM to shear and compression forces using a combination of rigidity percolation theory and energy minimization approaches. Our results may provide useful insights into the design principles of the ECM as well as biomimetic hydrogels that are mechanically robust and can, at the same time, easily adapt to cues in their surroundings.

Computational Simulation of the High Strain Rate Tensile Response of Polymer Matrix Composites

NASA Technical Reports Server (NTRS)

Goldberg, Robert K.

2002-01-01

A research program is underway to develop strain rate dependent deformation and failure models for the analysis of polymer matrix composites subject to high strain rate impact loads. Under these types of loading conditions, the material response can be highly strain rate dependent and nonlinear. State variable constitutive equations based on a viscoplasticity approach have been developed to model the deformation of the polymer matrix. The constitutive equations are then combined with a mechanics of materials based micromechanics model which utilizes fiber substructuring to predict the effective mechanical and thermal response of the composite. To verify the analytical model, tensile stress-strain curves are predicted for a representative composite over strain rates ranging from around 1 x 10(exp -5)/sec to approximately 400/sec. The analytical predictions compare favorably to experimentally obtained values both qualitatively and quantitatively. Effective elastic and thermal constants are predicted for another composite, and compared to finite element results.

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.

Non-Abelian Geometric Phases Carried by the Quantum Noise Matrix

NASA Astrophysics Data System (ADS)

Bharath, H. M.; Boguslawski, Matthew; Barrios, Maryrose; Chapman, Michael

2017-04-01

Topological phases of matter are characterized by topological order parameters that are built using Berry's geometric phase. Berry's phase is the geometric information stored in the overall phase of a quantum state. We show that geometric information is also stored in the second and higher order spin moments of a quantum spin system, captured by a non-abelian geometric phase. The quantum state of a spin-S system is uniquely characterized by its spin moments up to order 2S. The first-order spin moment is the spin vector, and the second-order spin moment represents the spin fluctuation tensor, i.e., the quantum noise matrix. When the spin vector is transported along a loop in the Bloch ball, we show that the quantum noise matrix picks up a geometric phase. Considering spin-1 systems, we formulate this geometric phase as an SO(3) operator. Geometric phases are usually interpreted in terms of the solid angle subtended by the loop at the center. However, solid angles are not well defined for loops that pass through the center. Here, we introduce a generalized solid angle which is well defined for all loops inside the Bloch ball, in terms of which, we interpret the SO(3) geometric phase. This geometric phase can be used to characterize topological spin textures in cold atomic clouds.

A Comprehensive Evaluation of Nasal and Bronchial Cytokines and Chemokines Following Experimental Rhinovirus Infection in Allergic Asthma: Increased Interferons (IFN-γ and IFN-λ) and Type 2 Inflammation (IL-5 and IL-13).

PubMed

Hansel, Trevor T; Tunstall, Tanushree; Trujillo-Torralbo, Maria-Belen; Shamji, Betty; Del-Rosario, Ajerico; Dhariwal, Jaideep; Kirk, Paul D W; Stumpf, Michael P H; Koopmann, Jens; Telcian, Aurica; Aniscenko, Julia; Gogsadze, Leila; Bakhsoliani, Eteri; Stanciu, Luminita; Bartlett, Nathan; Edwards, Michael; Walton, Ross; Mallia, Patrick; Hunt, Toby M; Hunt, Trevor L; Hunt, Duncan G; Westwick, John; Edwards, Matthew; Kon, Onn Min; Jackson, David J; Johnston, Sebastian L

2017-05-01

Rhinovirus infection is a major cause of asthma exacerbations. We studied nasal and bronchial mucosal inflammatory responses during experimental rhinovirus-induced asthma exacerbations. We used nasosorption on days 0, 2-5 and 7 and bronchosorption at baseline and day 4 to sample mucosal lining fluid to investigate airway mucosal responses to rhinovirus infection in patients with allergic asthma (n=28) and healthy non-atopic controls (n=11), by using a synthetic absorptive matrix and measuring levels of 34 cytokines and chemokines using a sensitive multiplex assay. Following rhinovirus infection asthmatics developed more upper and lower respiratory symptoms and lower peak expiratory flows compared to controls (all P<0.05). Asthmatics also developed higher nasal lining fluid levels of an anti-viral pathway (including IFN-γ, IFN-λ/IL-29, CXCL11/ITAC, CXCL10/IP10 and IL-15) and a type 2 inflammatory pathway (IL-4, IL-5, IL-13, CCL17/TARC, CCL11/eotaxin, CCL26/eotaxin-3) (area under curve day 0-7, all P<0.05). Nasal IL-5 and IL-13 were higher in asthmatics at day 0 (P<0.01) and levels increased by days 3 and 4 (P<0.01). A hierarchical correlation matrix of 24 nasal lining fluid cytokine and chemokine levels over 7days demonstrated expression of distinct interferon-related and type 2 pathways in asthmatics. In asthmatics IFN-γ, CXCL10/IP10, CXCL11/ITAC, IL-15 and IL-5 increased in bronchial lining fluid following viral infection (all P<0.05). Precision sampling of mucosal lining fluid identifies robust interferon and type 2 responses in the upper and lower airways of asthmatics during an asthma exacerbation. Nasosorption and bronchosorption have potential to define asthma endotypes in stable disease and at exacerbation. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Frequency domain system identification methods - Matrix fraction description approach

NASA Technical Reports Server (NTRS)

Horta, Luca G.; Juang, Jer-Nan

1993-01-01

This paper presents the use of matrix fraction descriptions for least-squares curve fitting of the frequency spectra to compute two matrix polynomials. The matrix polynomials are intermediate step to obtain a linearized representation of the experimental transfer function. Two approaches are presented: first, the matrix polynomials are identified using an estimated transfer function; second, the matrix polynomials are identified directly from the cross/auto spectra of the input and output signals. A set of Markov parameters are computed from the polynomials and subsequently realization theory is used to recover a minimum order state space model. Unevenly spaced frequency response functions may be used. Results from a simple numerical example and an experiment are discussed to highlight some of the important aspect of the algorithm.

Singular value description of a digital radiographic detector: Theory and measurements

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

Kyprianou, Iacovos S.; Badano, Aldo; Gallas, Brandon D.

The H operator represents the deterministic performance of any imaging system. For a linear, digital imaging system, this system operator can be written in terms of a matrix, H, that describes the deterministic response of the system to a set of point objects. A singular value decomposition of this matrix results in a set of orthogonal functions (singular vectors) that form the system basis. A linear combination of these vectors completely describes the transfer of objects through the linear system, where the respective singular values associated with each singular vector describe the magnitude with which that contribution to the objectmore » is transferred through the system. This paper is focused on the measurement, analysis, and interpretation of the H matrix for digital x-ray detectors. A key ingredient in the measurement of the H matrix is the detector response to a single x ray (or infinitestimal x-ray beam). The authors have developed a method to estimate the 2D detector shift-variant, asymmetric ray response function (RRF) from multiple measured line response functions (LRFs) using a modified edge technique. The RRF measurements cover a range of x-ray incident angles from 0 deg. (equivalent location at the detector center) to 30 deg. (equivalent location at the detector edge) for a standard radiographic or cone-beam CT geometric setup. To demonstrate the method, three beam qualities were tested using the inherent, Lu/Er, and Yb beam filtration. The authors show that measures using the LRF, derived from an edge measurement, underestimate the system's performance when compared with the H matrix derived using the RRF. Furthermore, the authors show that edge measurements must be performed at multiple directions in order to capture rotational asymmetries of the RRF. The authors interpret the results of the H matrix SVD and provide correlations with the familiar MTF methodology. Discussion is made about the benefits of the H matrix technique with regards to signal detection theory, and the characterization of shift-variant imaging systems.« less

Design for the fabrication of high efficiency solar cells

DOEpatents

Simmons, Joseph H.

1998-01-01

A method and apparatus for a photo-active region for generation of free carriers when a first surface is exposed to optical radiation. The photo-active region includes a conducting transparent matrix and clusters of semiconductor materials embedded within the conducting transparent matrix. The clusters are arranged in the matrix material so as to define at least a first distribution of cluster sizes ranging from those with the highest bandgap energy near a light incident surface of the photo-active region to those with the smallest bandgap energy near an opposite second surface of the photo-active region. Also disclosed is a method and apparatus for a solar cell. The solar cell includes a photo-active region containing a plurality of semiconductor clusters of varying sizes as described.

Research of ceramic matrix for a safe immobilization of radioactive sludge waste

NASA Astrophysics Data System (ADS)

Dorofeeva, Ludmila; Orekhov, Dmitry

2018-03-01

The research and improvement of the existing method for radioactive waste hardening by fixation in a ceramic matrix was carried out. For the samples covered with the sodium silicate and tested after the storage on the air the speed of a radionuclides leaching was determined. The properties of a clay ceramics and the optimum conditions of sintering were defined. The experimental data about the influence of a temperature mode sintering, water quantities, sludge and additives in the samples on their mechanical durability and a water resistance were obtained. The comparative analysis of the conducted research is aimed at improvement of the existing method of the hardening radioactive waste by inclusion in a ceramic matrix and reveals the advantages of the received results over analogs.

On the role of the transformation eigenstrain in the growth or shrinkage of spheroidal isotropic precipitations

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

Fischer, F.D.; Boehm, H.J.

The jumps of the strain and stress tensors on the surface of elastic homogeneous or inhomogeneous ellipsoidal inclusions embedded in an elastic matrix are obtained from results reported in the literature. They are used to derive closed-form expressions for the thermodynamic force in such matrix-inclusion systems that are subjected to a generally defined homogeneous transformation eigenstrain. A detailed study is presented for an isotropic spheroidal inclusion in an isotropic matrix in which the most important parameters are the inclusion's aspect ratio {alpha} and an eigenstrain triaxiality parameter d-bar. The fluctuations of the thermodynamic force are investigated for a set ofmore » specific transformation eigenstrain tensors and are presented for inclusion shapes ranging from disk-like to fiber-like spheroids.« less

Equiangular tight frames and unistochastic matrices

NASA Astrophysics Data System (ADS)

Goyeneche, Dardo; Turek, Ondřej

2017-06-01

We demonstrate that a complex equiangular tight frame composed of N vectors in dimension d, denoted ETF (d, N), exists if and only if a certain bistochastic matrix, univocally determined by N and d, belongs to a special class of unistochastic matrices. This connection allows us to find new complex ETFs in infinitely many dimensions and to derive a method to introduce non-trivial free parameters in ETFs. We present an explicit six-parametric family of complex ETF(6,16), which defines a family of symmetric POVMs. Minimal and maximal possible average entanglement of the vectors within this qubit-qutrit family are described. Furthermore, we propose an efficient numerical procedure to compute the unitary matrix underlying a unistochastic matrix, which we apply to find all existing classes of complex ETFs containing up to 20 vectors.

Generating Nonnormal Multivariate Data Using Copulas: Applications to SEM.

PubMed

Mair, Patrick; Satorra, Albert; Bentler, Peter M

2012-07-01

This article develops a procedure based on copulas to simulate multivariate nonnormal data that satisfy a prespecified variance-covariance matrix. The covariance matrix used can comply with a specific moment structure form (e.g., a factor analysis or a general structural equation model). Thus, the method is particularly useful for Monte Carlo evaluation of structural equation models within the context of nonnormal data. The new procedure for nonnormal data simulation is theoretically described and also implemented in the widely used R environment. The quality of the method is assessed by Monte Carlo simulations. A 1-sample test on the observed covariance matrix based on the copula methodology is proposed. This new test for evaluating the quality of a simulation is defined through a particular structural model specification and is robust against normality violations.

General practitioners’ justifications for therapeutic inertia in cardiovascular prevention: an empirically grounded typology

PubMed Central

Lebeau, Jean-Pierre; Cadwallader, Jean-Sébastien; Vaillant-Roussel, Hélène; Pouchain, Denis; Yaouanc, Virginie; Aubin-Auger, Isabelle; Mercier, Alain; Rusch, Emmanuel; Remmen, Roy; Vermeire, Etienne; Hendrickx, Kristin

2016-01-01

Objective To construct a typology of general practitioners’ (GPs) responses regarding their justification of therapeutic inertia in cardiovascular primary prevention for high-risk patients with hypertension. Design Empirically grounded construction of typology. Types were defined by attributes derived from the qualitative analysis of GPs’ reported reasons for inaction. Participants 256 GPs randomised in the intervention group of a cluster randomised controlled trial. Setting GPs members of 23 French Regional Colleges of Teachers in General Practice, included in the EffectS of a multifaceted intervention on CArdiovascular risk factors in high-risk hyPErtensive patients (ESCAPE) trial. Data collection and analysis The database consisted of 2638 written responses given by the GPs to an open-ended question asking for the reasons why drug treatment was not changed as suggested by the national guidelines. All answers were coded using constant comparison analysis. A matrix analysis of codes per GP allowed the construction of a response typology, where types were defined by codes as attributes. Initial coding and definition of types were performed independently by two teams. Results Initial coding resulted in a list of 69 codes in the final codebook, representing 4764 coded references in the question responses. A typology including seven types was constructed. 100 GPs were allocated to one and only one of these types, while 25 GPs did not provide enough data to allow classification. Types (numbers of GPs allocated) were: ‘optimists’ (28), ‘negotiators’ (20), ‘checkers’ (15), ‘contextualisers’ (13), ‘cautious’ (11), ‘rounders’ (8) and ‘scientists’ (5). For the 36 GPs that provided 50 or more coded references, analysis of the code evolution over time and across patients showed a consistent belonging to the initial type for any given GP. Conclusion This typology could provide GPs with some insight into their general ways of considering changes in the treatment/management of cardiovascular risk factors and guide design of specific physician-centred interventions to reduce inappropriate inaction. Trial registration number NCT00348855. PMID:27178974

High performance volume-of-intersection projectors for 3D-PET image reconstruction based on polar symmetries and SIMD vectorisation.

PubMed

Scheins, J J; Vahedipour, K; Pietrzyk, U; Shah, N J

2015-12-21

For high-resolution, iterative 3D PET image reconstruction the efficient implementation of forward-backward projectors is essential to minimise the calculation time. Mathematically, the projectors are summarised as a system response matrix (SRM) whose elements define the contribution of image voxels to lines-of-response (LORs). In fact, the SRM easily comprises billions of non-zero matrix elements to evaluate the tremendous number of LORs as provided by state-of-the-art PET scanners. Hence, the performance of iterative algorithms, e.g. maximum-likelihood-expectation-maximisation (MLEM), suffers from severe computational problems due to the intensive memory access and huge number of floating point operations. Here, symmetries occupy a key role in terms of efficient implementation. They reduce the amount of independent SRM elements, thus allowing for a significant matrix compression according to the number of exploitable symmetries. With our previous work, the PET REconstruction Software TOolkit (PRESTO), very high compression factors (>300) are demonstrated by using specific non-Cartesian voxel patterns involving discrete polar symmetries. In this way, a pre-calculated memory-resident SRM using complex volume-of-intersection calculations can be achieved. However, our original ray-driven implementation suffers from addressing voxels, projection data and SRM elements in disfavoured memory access patterns. As a consequence, a rather limited numerical throughput is observed due to the massive waste of memory bandwidth and inefficient usage of cache respectively. In this work, an advantageous symmetry-driven evaluation of the forward-backward projectors is proposed to overcome these inefficiencies. The polar symmetries applied in PRESTO suggest a novel organisation of image data and LOR projection data in memory to enable an efficient single instruction multiple data vectorisation, i.e. simultaneous use of any SRM element for symmetric LORs. In addition, the calculation time is further reduced by using simultaneous multi-threading (SMT). A global speedup factor of 11 without SMT and above 100 with SMT has been achieved for the improved CPU-based implementation while obtaining equivalent numerical results.

Using multiple climate projections for assessing hydrological response to climate change in the Thukela River Basin, South Africa

NASA Astrophysics Data System (ADS)

Graham, L. Phil; Andersson, Lotta; Horan, Mark; Kunz, Richard; Lumsden, Trevor; Schulze, Roland; Warburton, Michele; Wilk, Julie; Yang, Wei

This study used climate change projections from different regional approaches to assess hydrological effects on the Thukela River Basin in KwaZulu-Natal, South Africa. Projecting impacts of future climate change onto hydrological systems can be undertaken in different ways and a variety of effects can be expected. Although simulation results from global climate models (GCMs) are typically used to project future climate, different outcomes from these projections may be obtained depending on the GCMs themselves and how they are applied, including different ways of downscaling from global to regional scales. Projections of climate change from different downscaling methods, different global climate models and different future emissions scenarios were used as input to simulations in a hydrological model to assess climate change impacts on hydrology. A total of 10 hydrological change simulations were made, resulting in a matrix of hydrological response results. This matrix included results from dynamically downscaled climate change projections from the same regional climate model (RCM) using an ensemble of three GCMs and three global emissions scenarios, and from statistically downscaled projections using results from five GCMs with the same emissions scenario. Although the matrix of results does not provide complete and consistent coverage of potential uncertainties from the different methods, some robust results were identified. In some regards, the results were in agreement and consistent for the different simulations. For others, particularly rainfall, the simulations showed divergence. For example, all of the statistically downscaled simulations showed an annual increase in precipitation and corresponding increase in river runoff, while the RCM downscaled simulations showed both increases and decreases in runoff. According to the two projections that best represent runoff for the observed climate, increased runoff would generally be expected for this basin in the future. Dealing with such variability in results is not atypical for assessing climate change impacts in Africa and practitioners are faced with how to interpret them. This work highlights the need for additional, well-coordinated regional climate downscaling for the region to further define the range of uncertainties involved.

Global Gene Expression Profiling in PAI-1 Knockout Murine Heart and Kidney: Molecular Basis of Cardiac-Selective Fibrosis

PubMed Central

Ghosh, Asish K.; Murphy, Sheila B.; Kishore, Raj; Vaughan, Douglas E.

2013-01-01

Fibrosis is defined as an abnormal matrix remodeling due to excessive synthesis and accumulation of extracellular matrix proteins in tissues during wound healing or in response to chemical, mechanical and immunological stresses. At present, there is no effective therapy for organ fibrosis. Previous studies demonstrated that aged plasminogen activator inhibitor-1(PAI-1) knockout mice develop spontaneously cardiac-selective fibrosis without affecting any other organs. We hypothesized that differential expressions of profibrotic and antifibrotic genes in PAI-1 knockout hearts and unaffected organs lead to cardiac selective fibrosis. In order to address this prediction, we have used a genome-wide gene expression profiling of transcripts derived from aged PAI-1 knockout hearts and kidneys. The variations of global gene expression profiling were compared within four groups: wildtype heart vs. knockout heart; wildtype kidney vs. knockout kidney; knockout heart vs. knockout kidney and wildtype heart vs. wildtype kidney. Analysis of illumina-based microarray data revealed that several genes involved in different biological processes such as immune system processing, response to stress, cytokine signaling, cell proliferation, adhesion, migration, matrix organization and transcriptional regulation were affected in hearts and kidneys by the absence of PAI-1, a potent inhibitor of urokinase and tissue-type plasminogen activator. Importantly, the expressions of a number of genes, involved in profibrotic pathways including Ankrd1, Pi16, Egr1, Scx, Timp1, Timp2, Klf6, Loxl1 and Klotho, were deregulated in PAI-1 knockout hearts compared to wildtype hearts and PAI-1 knockout kidneys. While the levels of Ankrd1, Pi16 and Timp1 proteins were elevated during EndMT, the level of Timp4 protein was decreased. To our knowledge, this is the first comprehensive report on the influence of PAI-1 on global gene expression profiling in the heart and kidney and its implication in fibrogenesis and several other biological processes. The significance of these observations in the light of heart-specific profibrotic signaling and fibrogenesis are discussed. PMID:23724005

High performance volume-of-intersection projectors for 3D-PET image reconstruction based on polar symmetries and SIMD vectorisation

NASA Astrophysics Data System (ADS)

Scheins, J. J.; Vahedipour, K.; Pietrzyk, U.; Shah, N. J.

2015-12-01

For high-resolution, iterative 3D PET image reconstruction the efficient implementation of forward-backward projectors is essential to minimise the calculation time. Mathematically, the projectors are summarised as a system response matrix (SRM) whose elements define the contribution of image voxels to lines-of-response (LORs). In fact, the SRM easily comprises billions of non-zero matrix elements to evaluate the tremendous number of LORs as provided by state-of-the-art PET scanners. Hence, the performance of iterative algorithms, e.g. maximum-likelihood-expectation-maximisation (MLEM), suffers from severe computational problems due to the intensive memory access and huge number of floating point operations. Here, symmetries occupy a key role in terms of efficient implementation. They reduce the amount of independent SRM elements, thus allowing for a significant matrix compression according to the number of exploitable symmetries. With our previous work, the PET REconstruction Software TOolkit (PRESTO), very high compression factors (>300) are demonstrated by using specific non-Cartesian voxel patterns involving discrete polar symmetries. In this way, a pre-calculated memory-resident SRM using complex volume-of-intersection calculations can be achieved. However, our original ray-driven implementation suffers from addressing voxels, projection data and SRM elements in disfavoured memory access patterns. As a consequence, a rather limited numerical throughput is observed due to the massive waste of memory bandwidth and inefficient usage of cache respectively. In this work, an advantageous symmetry-driven evaluation of the forward-backward projectors is proposed to overcome these inefficiencies. The polar symmetries applied in PRESTO suggest a novel organisation of image data and LOR projection data in memory to enable an efficient single instruction multiple data vectorisation, i.e. simultaneous use of any SRM element for symmetric LORs. In addition, the calculation time is further reduced by using simultaneous multi-threading (SMT). A global speedup factor of 11 without SMT and above 100 with SMT has been achieved for the improved CPU-based implementation while obtaining equivalent numerical results.

Tenascin-C in the extracellular matrix promotes the selection of highly proliferative and tubulogenesis-defective endothelial cells

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

Alves, Tercia Rodrigues; Universidade Federal do Rio de Janeiro; Carvalho da Fonseca, Anna Carolina

2011-09-10

The extracellular matrix (ECM) contains important cues for tissue homeostasis and morphogenesis. The matricellular protein tenascin-C (TN-C) is overexpressed in remodeling tissues and cancer. In the present work, we studied the effect of different ECM-which exhibited a significant diversity in their TN-C content-in endothelial survival, proliferation and tubulogenic differentiation: autologous (endothelial) ECM devoid of TN-C, but bearing large amounts of FN; fibroblast ECM, bearing both high TN-C and FN contents; and finally, glioma-derived matrices, usually poor in FN, but very rich in TN-C. HUVECs initially adhered to the immobilized matrix produced by U373 MG glioma cells, but significantly detached andmore » died by anoikis (50 to 80%) after 24 h, as compared with cells incubated with endothelial and fibroblast matrices. Surviving endothelial cells (20 to 50%) became up to 6-fold more proliferative and formed 74-97% less tube-like structures in vitro than cells grown on non-tumoral matrices. An antibody against the EGF-like repeats of tenascin-C (TN-C) partially rescued cells from the tubulogenic defect, indicating that this molecule is responsible for the selection of highly proliferative and tubulogenic defective endothelial cells. Interestingly, by using defined substrata, in conditions that mimic glioma and normal cell ECM composition, we observed that fibronectin (FN) modulates the TN-C-induced selection of endothelial cells. Our data show that TN-C is able to modulate endothelial branching morphogenesis in vitro and, since it is prevalent in matrices of injured and tumor tissues, also suggest a role for this protein in vascular morphogenesis, in these physiological contexts.« less

The paradox of managing a project-oriented matrix: establishing coherence within chaos.

PubMed

Greiner, L E; Schein, V E

1981-01-01

Projects that require the flexible coordination of multidisciplinary teams have tended to adopt a matrix structure to accomplish complex tasks. Yet these project-oriented matrix structures themselves require careful coordination if they are to realize the objectives set for them. The authors identify the basic organizational questions that project-oriented matrix organizations must face. They examine the relationship between responsibility and authority; the tradeoffs between economic efficiency and the technical quality of the work produced; and the sensitive issues of managing individualistic, highly trained professionals while also maintaining group cohesiveness.

Modeling State-Space Aeroelastic Systems Using a Simple Matrix Polynomial Approach for the Unsteady Aerodynamics

NASA Technical Reports Server (NTRS)

Pototzky, Anthony S.

2008-01-01

A simple matrix polynomial approach is introduced for approximating unsteady aerodynamics in the s-plane and ultimately, after combining matrix polynomial coefficients with matrices defining the structure, a matrix polynomial of the flutter equations of motion (EOM) is formed. A technique of recasting the matrix-polynomial form of the flutter EOM into a first order form is also presented that can be used to determine the eigenvalues near the origin and everywhere on the complex plane. An aeroservoelastic (ASE) EOM have been generalized to include the gust terms on the right-hand side. The reasons for developing the new matrix polynomial approach are also presented, which are the following: first, the "workhorse" methods such as the NASTRAN flutter analysis lack the capability to consistently find roots near the origin, along the real axis or accurately find roots farther away from the imaginary axis of the complex plane; and, second, the existing s-plane methods, such as the Roger s s-plane approximation method as implemented in ISAC, do not always give suitable fits of some tabular data of the unsteady aerodynamics. A method available in MATLAB is introduced that will accurately fit generalized aerodynamic force (GAF) coefficients in a tabular data form into the coefficients of a matrix polynomial form. The root-locus results from the NASTRAN pknl flutter analysis, the ISAC-Roger's s-plane method and the present matrix polynomial method are presented and compared for accuracy and for the number and locations of roots.

The effects of isotope-labeled analogs on the LC-IDMS measurement by comparison of ESI responses and matrix effect of melamine, 13C3-melamine, 13C3+15N3-melamine, and 15N3-melamine.

PubMed

Li, Xiu Qin; Zhang, Qing He; Yang, Zong; Li, Hong Mei; Huang, Dong Feng

2017-05-01

In this paper, the effect of isotope-labeled analogs on the liquid chromatography-isotope dilution mass spectrometry (LC-IDMS) measurement was evaluated based on the comparison research of electrospray ionization responses (ESI) and matrix effect of melamine, 13 C 3 -melamine, 13 C 3 + 15 N 3 -melamine, and 15 N 3 -melamine. The isotope-labeled melamines had similar ionization efficiency with melamine in the electrospray ionization source, but the intensity of corresponding quantitative fragment ions had distinctive differences. Based on the density functional theory at the B3LYP/6-311+G** level, this phenomenon was explained very well. The rare cleavage pathways of melamine, which just could be exactly identified by 15 N-labeled melamines, resulted in the difference of quantitative fragment ions between 15 N-labeled melamines and melamine. The interaction of ESI response between melamine and isotope-labeled melamines was investigated using MRM monitor mode. 15 N-labeled melamine had significant ion inter-suppression effect on melamine, while 13 C-labeled melamine had little influence on melamine. Finally, the influence of different isotope-labeled melamines on the LC-IDMS result was evaluated using the IDMS correction factor (θ). Taking the determination of melamine in milk powder as an example, the matrix effects of different isotope-labeled melamines and melamine had notable difference and the impact of this difference on the measurement results depended on the concentrations of analyte and matrix solution. It was worth noting that 15 N 3 -melamine exhibited significant ion suppression to melamine in matrix solution. The deviation of the results from IDMS method might reach 59% using 15 N 3 -melamine as internal standard in special matrix solution. Graphical Abstract The comparison of ESI responses of melamine, 13 C 3 -melamine, 13 C 3 + 15 N 3 -melamine and 15 N 3 -melamine.

Deformation and Failure of a Multi-Wall Carbon Nanotube Yarn Composite

NASA Technical Reports Server (NTRS)

Gates, Thomas S.; Jefferson, Gail D.; Frankland, Sarah-Jane V.

2008-01-01

Forests of multi-walled carbon nanotubes can be twisted and manipulated into continuous fibers or yarns that exhibit many of the characteristics of traditional textiles. Macro-scale analysis and test may provide strength and stiffness predictions for a composite composed of a polymer matrix and low-volume fraction yarns. However, due to the nano-scale of the carbon nanotubes, it is desirable to use atomistic calculations to consider tube-tube interactions and the influence of simulated twist on the effective friction coefficient. This paper reports laboratory test data on the mechanical response of a multi-walled, carbon nanotube yarn/polymer composite from both dynamic and quasi-static tensile tests. Macroscale and nano-scale analysis methods are explored and used to define some of the key structure-property relationships. The measured influence of hot-wet aging on the tensile properties is also reported.

Noise Response Data Reveal Novel Controllability Gramian for Nonlinear Network Dynamics

PubMed Central

Kashima, Kenji

2016-01-01

Control of nonlinear large-scale dynamical networks, e.g., collective behavior of agents interacting via a scale-free connection topology, is a central problem in many scientific and engineering fields. For the linear version of this problem, the so-called controllability Gramian has played an important role to quantify how effectively the dynamical states are reachable by a suitable driving input. In this paper, we first extend the notion of the controllability Gramian to nonlinear dynamics in terms of the Gibbs distribution. Next, we show that, when the networks are open to environmental noise, the newly defined Gramian is equal to the covariance matrix associated with randomly excited, but uncontrolled, dynamical state trajectories. This fact theoretically justifies a simple Monte Carlo simulation that can extract effectively controllable subdynamics in nonlinear complex networks. In addition, the result provides a novel insight into the relationship between controllability and statistical mechanics. PMID:27264780

Rapid analysis of clenbuterol, salbutamol, procaterol, and fenoterol in pharmaceuticals and human urine by capillary electrophoresis.

PubMed

Sirichai, Somsak; Khanatharana, Proespichaya

2008-09-15

Capillary electrophoresis (CE) with UV detection for the simultaneous and short-time analysis of clenbuterol, salbutamol, procaterol, fenoterol is described and validated. Optimized conditions were found to be a 10 mmoll(-1) borate buffer (pH 10.0), an separation voltage of 19 kV, and a separation temperature of 32 degrees C. Detection was set at 205 nm. Under the optimized conditions, analyses of the four analytes in pharmaceutical and human urine samples were carried out in approximately 1 min. The interference of the sample matrix was not observed. The LOD (limits of detection) defined at S/N of 3:1 was found between 0.5 and 2.0 mgl(-1) for the analytes. The linearity of the detector response was within the range from 2.0 to 30 mgl(-1) with correlation coefficient >0.996.

Engineered Models of Confined Cell Migration

PubMed Central

Paul, Colin D.; Hung, Wei-Chien; Wirtz, Denis; Konstantopoulos, Konstantinos

2017-01-01

Cells in the body are physically confined by neighboring cells, tissues, and the extracellular matrix. Although physical confinement modulates intracellular signaling and the underlying mechanisms of cell migration, it is difficult to study in vivo. Furthermore, traditional two-dimensional cell migration assays do not recapitulate the complex topographies found in the body. Therefore, a number of experimental in vitro models that confine and impose forces on cells in well-defined microenvironments have been engineered. We describe the design and use of microfluidic microchannel devices, grooved substrates, micropatterned lines, vertical confinement devices, patterned hydrogels, and micropipette aspiration assays for studying cell responses to confinement. Use of these devices has enabled the delineation of changes in cytoskeletal reorganization, cell–substrate adhesions, intracellular signaling, nuclear shape, and gene expression that result from physical confinement. These assays and the physiologically relevant signaling pathways that have been elucidated are beginning to have a translational and clinical impact. PMID:27420571

Proteomic Definitions of Mesenchymal Stem Cells

PubMed Central

Maurer, Martin H.

2011-01-01

Mesenchymal stem cells (MSCs) are pluripotent cells isolated from the bone marrow and various other organs. They are able to proliferate and self-renew, as well as to give rise to progeny of at least the osteogenic, chondrogenic, and adipogenic lineages. Despite this functional definition, MSCs can also be defined by their expression of a distinct set of cell surface markers. In the current paper, studies investigating the proteome of human MSCs are reviewed with the aim to identify common protein markers of MSCs. The proteomic analysis of MSCs revealed a distinct set of proteins representing the basic molecular inventory, including proteins for (i) cell surface markers, (ii) the responsiveness to growth factors, (iii) the reuse of developmental signaling cascades in adult stem cells, (iv) the interaction with molecules of the extracellular matrix, (v) the expression of genes regulating transcription and translation, (vi) the control of the cell number, and (vii) the protection against cellular stress. PMID:21437194

Research on Rigid Body Motion Tracing in Space based on NX MCD

NASA Astrophysics Data System (ADS)

Wang, Junjie; Dai, Chunxiang; Shi, Karen; Qin, Rongkang

2018-03-01

In the use of MCD (Mechatronics Concept Designer) which is a module belong to SIEMENS Ltd industrial design software UG (Unigraphics NX), user can define rigid body and kinematic joint to make objects move according to the existing plan in simulation. At this stage, user may have the desire to see the path of some points in the moving object intuitively. In response to this requirement, this paper will compute the pose through the transformation matrix which can be available from the solver engine, and then fit these sampling points through B-spline curve. Meanwhile, combined with the actual constraints of rigid bodies, the traditional equal interval sampling strategy was optimized. The result shown that this method could satisfy the demand and make up for the deficiency in traditional sampling method. User can still edit and model on this 3D curve. Expected result has been achieved.

Data-Driven Learning of Q-Matrix

PubMed Central

Liu, Jingchen; Xu, Gongjun; Ying, Zhiliang

2013-01-01

The recent surge of interests in cognitive assessment has led to developments of novel statistical models for diagnostic classification. Central to many such models is the well-known Q-matrix, which specifies the item–attribute relationships. This article proposes a data-driven approach to identification of the Q-matrix and estimation of related model parameters. A key ingredient is a flexible T-matrix that relates the Q-matrix to response patterns. The flexibility of the T-matrix allows the construction of a natural criterion function as well as a computationally amenable algorithm. Simulations results are presented to demonstrate usefulness and applicability of the proposed method. Extension to handling of the Q-matrix with partial information is presented. The proposed method also provides a platform on which important statistical issues, such as hypothesis testing and model selection, may be formally addressed. PMID:23926363

Integrated genome-wide DNA copy number and expression analysis identifies distinct mechanisms of primary chemoresistance in ovarian carcinomas.

PubMed

Etemadmoghadam, Dariush; deFazio, Anna; Beroukhim, Rameen; Mermel, Craig; George, Joshy; Getz, Gad; Tothill, Richard; Okamoto, Aikou; Raeder, Maria B; Harnett, Paul; Lade, Stephen; Akslen, Lars A; Tinker, Anna V; Locandro, Bianca; Alsop, Kathryn; Chiew, Yoke-Eng; Traficante, Nadia; Fereday, Sian; Johnson, Daryl; Fox, Stephen; Sellers, William; Urashima, Mitsuyoshi; Salvesen, Helga B; Meyerson, Matthew; Bowtell, David

2009-02-15

A significant number of women with serous ovarian cancer are intrinsically refractory to platinum-based treatment. We analyzed somatic DNA copy number variation and gene expression data to identify key mechanisms associated with primary resistance in advanced-stage serous cancers. Genome-wide copy number variation was measured in 118 ovarian tumors using high-resolution oligonucleotide microarrays. A well-defined subset of 85 advanced-stage serous tumors was then used to relate copy number variation to primary resistance to treatment. The discovery-based approach was complemented by quantitative-PCR copy number analysis of 12 candidate genes as independent validation of previously reported associations with clinical outcome. Likely copy number variation targets and tumor molecular subtypes were further characterized by gene expression profiling. Amplification of 19q12, containing cyclin E (CCNE1), and 20q11.22-q13.12, mapping immediately adjacent to the steroid receptor coactivator NCOA3, was significantly associated with poor response to primary treatment. Other genes previously associated with copy number variation and clinical outcome in ovarian cancer were not associated with primary treatment resistance. Chemoresistant tumors with high CCNE1 copy number and protein expression were associated with increased cellular proliferation but so too was a subset of treatment-responsive patients, suggesting a cell-cycle independent role for CCNE1 in modulating chemoresponse. Patients with a poor clinical outcome without CCNE1 amplification overexpressed genes involved in extracellular matrix deposition. We have identified two distinct mechanisms of primary treatment failure in serous ovarian cancer, involving CCNE1 amplification and enhanced extracellular matrix deposition. CCNE1 copy number is validated as a dominant marker of patient outcome in ovarian cancer.

Machine Learning Classification of Heterogeneous Fields to Estimate Physical Responses

NASA Astrophysics Data System (ADS)

McKenna, S. A.; Akhriev, A.; Alzate, C.; Zhuk, S.

2017-12-01

The promise of machine learning to enhance physics-based simulation is examined here using the transient pressure response to a pumping well in a heterogeneous aquifer. 10,000 random fields of log10 hydraulic conductivity (K) are created and conditioned on a single K measurement at the pumping well. Each K-field is used as input to a forward simulation of drawdown (pressure decline). The differential equations governing groundwater flow to the well serve as a non-linear transform of the input K-field to an output drawdown field. The results are stored and the data set is split into training and testing sets for classification. A Euclidean distance measure between any two fields is calculated and the resulting distances between all pairs of fields define a similarity matrix. Similarity matrices are calculated for both input K-fields and the resulting drawdown fields at the end of the simulation. The similarity matrices are then used as input to spectral clustering to determine groupings of similar input and output fields. Additionally, the similarity matrix is used as input to multi-dimensional scaling to visualize the clustering of fields in lower dimensional spaces. We examine the ability to cluster both input K-fields and output drawdown fields separately with the goal of identifying K-fields that create similar drawdowns and, conversely, given a set of simulated drawdown fields, identify meaningful clusters of input K-fields. Feature extraction based on statistical parametric mapping provides insight into what features of the fields drive the classification results. The final goal is to successfully classify input K-fields into the correct output class, and also, given an output drawdown field, be able to infer the correct class of input field that created it.

Influence of Renal Sympathetic Denervation on Cardiac Extracellular Matrix Turnover and Cardiac Fibrosis.

PubMed

Dörr, Oliver; Liebetrau, Christoph; Möllmann, Helge; Gaede, Luise; Troidl, Christian; Morczeck, Kareen; Wiebe, Jens; Hoffmann, Jedrzej; Voss, Sandra; Bauer, Timm; Hamm, Christian; Nef, Holger

2015-10-01

Renal sympathetic denervation (RSD) represents an effective treatment option for patients with resistant arterial hypertension (HT). Extracellular matrix (ECM) turnover and deposition are essential processes in HT-related cardiovascular remodeling, fibrosis, and cardiac hypertrophy and contribute to hypertensive heart disease. The primary aim of the present study was to examine the effect of RSD on increased collagen turnover as reflected by serum levels of amino-terminal pro-peptides (PINP, PIIINP) and a carboxyl-terminal pro-peptide (PICP), specific biomarkers for cardiac ECM turnover and cardiovascular fibrosis. A total of 100 consecutive patients (mean age: 65.9±10.1 years) undergoing RSD were included in this study. A therapeutic response was defined as an office systolic blood pressure (SBP) reduction of >10mm Hg 6 months after RSD. Venous serum samples for measurement of PICP, PINP, and PIIINP were collected prior to and 6 months after RSD. A significant reduction in the office SBP of 24.3 mm Hg (SBP baseline: 166.9±14.3 mm Hg (P < 0.001) was documented 6 months after RSD. At this time point, the serum levels of PICP, PINP, and PIIINP (P < 0.01) were significantly decreased compared to baseline values in patients with an increased collagen turnover, showing significant differences comparing BP responders and nonresponders. In addition to the effective blood pressure reduction in response to RSD, this study demonstrates a positive effect of RSD on biomarkers reflecting cardiovascular ECM turnover and deposition. These results suggest a beneficial effect of RSD on cardiovascular fibrosis, hypertensive heart disease, and end-organ damage in high-risk patients. © American Journal of Hypertension, Ltd 2015. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Conjunctive management of multi-reservoir network system and groundwater system

NASA Astrophysics Data System (ADS)

Mani, A.; Tsai, F. T. C.

2015-12-01

This study develops a successive mixed-integer linear fractional programming (successive MILFP) method to conjunctively manage water resources provided by a multi-reservoir network system and a groundwater system. The conjunctive management objectives are to maximize groundwater withdrawals and maximize reservoir storages while satisfying water demands and raising groundwater level to a target level. The decision variables in the management problem are reservoir releases and spills, network flows and groundwater pumping rates. Using the fractional programming approach, the objective function is defined as a ratio of total groundwater withdraws to total reservoir storage deficits from the maximum storages. Maximizing this ratio function tends to maximizing groundwater use and minimizing surface water use. This study introduces a conditional constraint on groundwater head in order to sustain aquifers from overpumping: if current groundwater level is less than a target level, groundwater head at the next time period has to be raised; otherwise, it is allowed to decrease up to a certain extent. This conditional constraint is formulated into a set of mixed binary nonlinear constraints and results in a mixed-integer nonlinear fractional programming (MINLFP) problem. To solve the MINLFP problem, we first use the response matrix approach to linearize groundwater head with respect to pumping rate and reduce the problem to an MILFP problem. Using the Charnes-Cooper transformation, the MILFP is transformed to an equivalent mixed-integer linear programming (MILP). The solution of the MILP is successively updated by updating the response matrix in every iteration. The study uses IBM CPLEX to solve the MILP problem. The methodology is applied to water resources management in northern Louisiana. This conjunctive management approach aims to recover the declining groundwater level of the stressed Sparta aquifer by using surface water from a network of four reservoirs as an alternative source of supply.

An analysis of thermal response factors and how to reduce their computational time requirement

NASA Technical Reports Server (NTRS)

Wiese, M. R.

1982-01-01

Te RESFAC2 version of the Thermal Response Factor Program (RESFAC) is the result of numerous modifications and additions to the original RESFAC. These modifications and additions have significantly reduced the program's computational time requirement. As a result of this work, the program is more efficient and its code is both readable and understandable. This report describes what a thermal response factor is; analyzes the original matrix algebra calculations and root finding techniques; presents a new root finding technique and streamlined matrix algebra; supplies ten validation cases and their results.

A proteomic study of the arabidopsis nuclear matrix.

PubMed

Calikowski, Tomasz T; Meulia, Tea; Meier, Iris

2003-10-01

The eukaryotic nucleus has been proposed to be organized by two interdependent nucleoprotein structures, the DNA-based chromatin and the RNA-dependent nuclear matrix. The functional composition and molecular organization of the second component have not yet been resolved. Here, we describe the isolation of the nuclear matrix from the model plant Arabidopsis, its initial characterization by confocal and electron microscopy, and the identification of 36 proteins by mass spectrometry. Electron microscopy of resinless samples confirmed a structure very similar to that described for the animal nuclear matrix. Two-dimensional gel electrophoresis resolved approximately 300 protein spots. Proteins were identified in batches by ESI tandem mass spectrometry after resolution by 1D SDS-PAGE. Among the identified proteins were a number of demonstrated or predicted Arabidopsis homologs of nucleolar proteins such as IMP4, Nop56, Nop58, fibrillarins, nucleolin, as well as ribosomal components and a putative histone deacetylase. Others included homologs of eEF-1, HSP/HSC70, and DnaJ, which have also been identified in the nucleolus or nuclear matrix of human cells, as well as a number of novel proteins with unknown function. This study is the first proteomic approach towards the characterization of a higher plant nuclear matrix. It demonstrates the striking similarities both in structure and protein composition of the operationally defined nuclear matrix across kingdoms whose unicellular ancestors have separated more than one billion years ago. Copyright 2003 Wiley-Liss, Inc.

Regulation of Extracellular Matrix Synthesis by Shell Extracts from the Marine Bivalve Pecten maximus in Human Articular Chondrocytes- Application for Cartilage Engineering.

PubMed

Bouyoucef, Mouloud; Rakic, Rodolphe; Gómez-Leduc, Tangni; Latire, Thomas; Marin, Frédéric; Leclercq, Sylvain; Carreiras, Franck; Serpentini, Antoine; Lebel, Jean-Marc; Galéra, Philippe; Legendre, Florence

2018-04-07

The shells of the bivalve mollusks are organo-mineral structures predominantly composed of calcium carbonate, but also of a minor organic matrix, a mixture of proteins, glycoproteins, and polysaccharides. These proteins are involved in mineral deposition and, more generally, in the spatial organization of the shell crystallites in well-defined microstructures. In this work, we extracted different organic shell extracts (acid-soluble matrix, acid-insoluble matrix, water-soluble matrix, guanidine HCl/EDTA-extracted matrix, referred as ASM, AIM, WSM, and EDTAM, respectively) from the shell of the scallop Pecten maximus and studied their biological activities on human articular chondrocytes (HACs). We found that these extracts differentially modulate the biological activities of HACs, depending on the type of extraction and the concentration used. Furthermore, we showed that, unlike ASM and AIM, WSM promotes maintenance of the chondrocyte phenotype in monolayer culture. WSM increased the expression of chondrocyte-specific markers (aggrecan and type II collagen), without enhancing that of the main chondrocyte dedifferentiation marker (type I collagen). We also demonstrated that WSM could favor redifferentiation of chondrocyte in collagen sponge scaffold in hypoxia. Thus, this study suggests that the organic matrix of Pecten maximus, particularly WSM, may contain interesting molecules with chondrogenic effects. Our research emphasizes the potential use of WSM of Pecten maximus for cell therapy of cartilage.

Metal matrix composite micromechanics: In-situ behavior influence on composite properties

NASA Technical Reports Server (NTRS)

Murthy, P. L. N.; Hopkins, D. A.; Chamis, C. C.

1989-01-01

Recent efforts in computational mechanics methods for simulating the nonlinear behavior of metal matrix composites have culminated in the implementation of the Metal Matrix Composite Analyzer (METCAN) computer code. In METCAN material nonlinearity is treated at the constituent (fiber, matrix, and interphase) level where the current material model describes a time-temperature-stress dependency of the constituent properties in a material behavior space. The composite properties are synthesized from the constituent instantaneous properties by virtue of composite micromechanics and macromechanics models. The behavior of metal matrix composites depends on fabrication process variables, in situ fiber and matrix properties, bonding between the fiber and matrix, and/or the properties of an interphase between the fiber and matrix. Specifically, the influence of in situ matrix strength and the interphase degradation on the unidirectional composite stress-strain behavior is examined. These types of studies provide insight into micromechanical behavior that may be helpful in resolving discrepancies between experimentally observed composite behavior and predicted response.

Incorporation of Mean Stress Effects into the Micromechanical Analysis of the High Strain Rate Response of Polymer Matrix Composites

NASA Technical Reports Server (NTRS)

Goldberg, Robert K.; Roberts, Gary D.; Gilat, Amos

2002-01-01

The results presented here are part of an ongoing research program, to develop strain rate dependent deformation and failure models for the analysis of polymer matrix composites subject to high strain rate impact loads. A micromechanics approach is employed in this work, in which state variable constitutive equations originally developed for metals have been modified to model the deformation of the polymer matrix, and a strength of materials based micromechanics method is used to predict the effective response of the composite. In the analysis of the inelastic deformation of the polymer matrix, the definitions of the effective stress and effective inelastic strain have been modified in order to account for the effect of hydrostatic stresses, which are significant in polymers. Two representative polymers, a toughened epoxy and a brittle epoxy, are characterized through the use of data from tensile and shear tests across a variety of strain rates. Results computed by using the developed constitutive equations correlate well with data generated via experiments. The procedure used to incorporate the constitutive equations within a micromechanics method is presented, and sample calculations of the deformation response of a composite for various fiber orientations and strain rates are discussed.

Distinguishing dose, focus, and blur for lithography characterization and control

NASA Astrophysics Data System (ADS)

Ausschnitt, Christopher P.; Brunner, Timothy A.

2007-03-01

We derive a physical model to describe the dependence of pattern dimensions on dose, defocus and blur. The coefficients of our model are constants of a given lithographic process. Model inversion applied to dimensional measurements then determines effective dose, defocus and blur for wafers patterned with the same process. In practice, our approach entails the measurement of proximate grating targets of differing dose and focus sensitivity. In our embodiment, the measured attribute of one target is exclusively sensitive to dose, whereas the measured attributes of a second target are distinctly sensitive to defocus and blur. On step-and-scan exposure tools, z-blur is varied in a controlled manner by adjusting the across slit tilt of the image plane. The effects of z-blur and x,y-blur are shown to be equivalent. Furthermore, the exposure slit width is shown to determine the tilt response of the grating attributes. Thus, the response of the measured attributes can be characterized by a conventional focus-exposure matrix (FEM), over which the exposure tool settings are intentionally changed. The model coefficients are determined by a fit to the measured FEM response. The model then fully defines the response for wafers processed under "fixed" dose, focus and blur conditions. Model inversion applied to measurements from the same targets on all such wafers enables the simultaneous determination of effective dose and focus/tilt (DaFT) at each measurement site.

STABILITY AND CHANGE IN ESTUARINE BIOFILM BACTERIAL COMMUNITY DIVERSITY

EPA Science Inventory

Biofilms develop on all surfaces in aquatic environments and are defined as matrix-enclosed microbial populations adherent to each other and/or surfaces (1, 31). A substantial part of the microbial activity in nature is associated with surfaces (12). Surface association (biofou...

ERK-regulated αB-crystallin induction by matrix detachment inhibits anoikis and promotes lung metastasis in vivo.

PubMed

Malin, D; Strekalova, E; Petrovic, V; Rajanala, H; Sharma, B; Ugolkov, A; Gradishar, W J; Cryns, V L

2015-11-05

Evasion of extracellular matrix detachment-induced apoptosis ('anoikis') is a defining characteristic of metastatic tumor cells. The ability of metastatic carcinoma cells to survive matrix detachment and escape anoikis enables them to disseminate as viable circulating tumor cells and seed distant organs. Here we report that αB-crystallin, an antiapoptotic molecular chaperone implicated in the pathogenesis of diverse poor-prognosis solid tumors, is induced by matrix detachment and confers anoikis resistance. Specifically, we demonstrate that matrix detachment downregulates extracellular signal-regulated kinase (ERK) activity and increases αB-crystallin protein and messenger RNA (mRNA) levels. Moreover, we show that ERK inhibition in adherent cancer cells mimics matrix detachment by increasing αB-crystallin protein and mRNA levels, whereas constitutive ERK activation suppresses αB-crystallin induction during matrix detachment. These findings indicate that ERK inhibition is both necessary and sufficient for αB-crystallin induction by matrix detachment. To examine the functional consequences of αB-crystallin induction in anoikis, we stably silenced αB-crystallin in two different metastatic carcinoma cell lines. Strikingly, silencing αB-crystallin increased matrix detachment-induced caspase activation and apoptosis but did not affect cell viability of adherent cancer cells. In addition, silencing αB-crystallin in metastatic carcinoma cells reduced the number of viable circulating tumor cells and inhibited lung metastasis in two orthotopic models, but had little or no effect on primary tumor growth. Taken together, our findings point to αB-crystallin as a novel regulator of anoikis resistance that is induced by matrix detachment-mediated suppression of ERK signaling and promotes lung metastasis. Our results also suggest that αB-crystallin represents a promising molecular target for antimetastatic therapies.

Spectrum of walk matrix for Koch network and its application

NASA Astrophysics Data System (ADS)

Xie, Pinchen; Lin, Yuan; Zhang, Zhongzhi

2015-06-01

Various structural and dynamical properties of a network are encoded in the eigenvalues of walk matrix describing random walks on the network. In this paper, we study the spectra of walk matrix of the Koch network, which displays the prominent scale-free and small-world features. Utilizing the particular architecture of the network, we obtain all the eigenvalues and their corresponding multiplicities. Based on the link between the eigenvalues of walk matrix and random target access time defined as the expected time for a walker going from an arbitrary node to another one selected randomly according to the steady-state distribution, we then derive an explicit solution to the random target access time for random walks on the Koch network. Finally, we corroborate our computation for the eigenvalues by enumerating spanning trees in the Koch network, using the connection governing eigenvalues and spanning trees, where a spanning tree of a network is a subgraph of the network, that is, a tree containing all the nodes.

Evolutionary stability for matrix games under time constraints.

PubMed

Garay, József; Csiszár, Villő; Móri, Tamás F

2017-02-21

Game theory focuses on payoffs and typically ignores time constraints that play an important role in evolutionary processes where the repetition of games can depend on the strategies, too. We introduce a matrix game under time constraints, where each pairwise interaction has two consequences: both players receive a payoff and they cannot play the next game for a specified time duration. Thus our model is defined by two matrices: a payoff matrix and an average time duration matrix. Maynard Smith's concept of evolutionary stability is extended to this class of games. We illustrate the effect of time constraints by the well-known prisoner's dilemma game, where additional time constraints can ensure the existence of unique evolutionary stable strategies (ESS), both pure and mixed, or the coexistence of two pure ESS. Our general results may be useful in several fields of biology where evolutionary game theory is applied, principally in ecological games, where time constraints play an inevitable role. Copyright © 2016 Elsevier Ltd. All rights reserved.

Microengineering as a tool to study substratum modulation and cell behaviour.

PubMed

Keatch, R P; Armoogum, K; Schor, S L; Pridham, M S; Banks, K; Khor, T Y; Matthew, C

2002-01-01

This research is an investigation of the means by which geometrical parameters (e.g. area and shape) and various surface attributes (materials and surface finish) of microengineered structures can modulate cellular response. This is based on biological observations indicating that: (i) the response of tissue cells to injury is determined by the net signal transduction response elicited by soluble regulatory molecules (e.g. cytokines), (ii) common matrix constituents (e.g. collagen) directly affect cell behaviour by the same signal transduction mechanisms mediating cytokine bioactivity, (iii) cellular response to cytokines is modulated by the precise nature of the extracellular matrix to which the target cells are adherent, including its biochemical composition and physical structure.

High-Strain-Rate Constitutive Characterization and Modeling of Metal Matrix Composites

DTIC Science & Technology

2014-03-07

protective coatings. Even though most MMCs studied to date are aluminum matrix composites, magnesium and its alloys have also been considered to be... plastic response of the matrix. Based on a simple analysis of the effect of misalignments of microscale kinks, Argon estimated that the compressive... deformations ; if the fibers break into small enough pieces, their stiffening effect could be reduced. We are examining both possibilities to explain

Non-Immunogenic Structurally and Biologically Intact Tissue Matrix Grafts for the Immediate Repair of Ballistic-Induced Vascular and Nerve Tissue Injury in Combat Casualty Care

DTIC Science & Technology

2005-07-01

as an access graft is addressed using statistical methods below. Graft consistency can be defined statistically as the variance associated with the...addressed using statistical methods below. Graft consistency can be defined statistically as the variance associated with the sample of grafts tested in...measured using a refractometer (Brix % method). The equilibration data are shown in Graph 1. The results suggest the following equilibration scheme: 40% v/v

Matrix Metalloproteinase 9 Displays a Particular Time Response to Acute Stress: Variation in Its Levels and Activity Distribution in Rat Hippocampus.

PubMed

Aguayo, Felipe I; Pacheco, Aníbal A; García-Rojo, Gonzalo J; Pizarro-Bauerle, Javier A; Doberti, Ana V; Tejos, Macarena; García-Pérez, María A; Rojas, Paulina S; Fiedler, Jenny L

2018-05-16

A single stress exposure facilitates memory formation through neuroplastic processes that reshape excitatory synapses in the hippocampus, probably requiring changes in extracellular matrix components. We tested the hypothesis that matrix metalloproteinase 9 (MMP-9), an enzyme that degrades components of extracellular matrix and synaptic proteins such as β-dystroglycan (β-DG 43 ), changes their activity and distribution in rat hippocampus during the acute stress response. After 2.5 h of restraint stress, we found (i) increased MMP-9 levels and potential activity in whole hippocampal extracts, accompanied by β-DG 43 cleavage, and (ii) a significant enhancement of MMP-9 immunoreactivity in dendritic fields such as stratum radiatum and the molecular layer of hippocampus. After 24 h of stress, we found that (i) MMP-9 net activity rises at somatic field, i.e., stratum pyramidale and granule cell layers, and also at synaptic field, mainly stratum radiatum and the molecular layer of hippocampus, and (ii) hippocampal synaptoneurosome fractions are enriched with MMP-9, without variation of its potential enzymatic activity, in accordance with the constant level of cleaved β-DG 43 . These findings indicate that stress triggers a peculiar timing response in the MMP-9 levels, net activity, and subcellular distribution in the hippocampus, suggesting its involvement in the processing of substrates during the stress response.

The methyltransferase SET9 regulates TGFB1 activation of renal fibroblasts via interaction with SMAD3.

PubMed

Shuttleworth, Victoria G; Gaughan, Luke; Nawafa, Lotfia; Mooney, Caitlin A; Cobb, Steven L; Sheerin, Neil S; Logan, Ian R

2018-01-08

Chronic kidney disease (CKD) is a global socioeconomic problem. It is characterised by the presence of differentiated myofibroblasts, which cause tissue fibrosis in response to TGFB1, leading to renal failure. Here, we define a novel interaction between the SET9 lysine methyltransferase (also known as SETD7) and SMAD3, the principal mediator of TGFB1 signalling in myofibroblasts. We show that SET9-deficient fibroblasts exhibit globally altered gene expression profiles in response to TGFB1, whilst overexpression of SET9 enhances SMAD3 transcriptional activity. We also show that SET9 facilitates nuclear import of SMAD3 and controls SMAD3 protein degradation via ubiquitylation. On a cellular level, we demonstrate that SET9 is broadly required for the effects of TGFB1 in diseased primary renal fibroblasts; SET9 promotes fibroblast migration into wounds, expression of extracellular matrix proteins, collagen contractility and myofibroblast differentiation. Finally, we demonstrate that SET9 is recruited to the α-smooth muscle actin gene in response to TGFB1, providing a mechanism by which SET9 regulates myofibroblast contractility and differentiation. Together with previous studies, we make the case for SET9 inhibition in the treatment of progressive CKD. © 2018. Published by The Company of Biologists Ltd.

Data-driven fault detection, isolation and estimation of aircraft gas turbine engine actuator and sensors

NASA Astrophysics Data System (ADS)

Naderi, E.; Khorasani, K.

2018-02-01

In this work, a data-driven fault detection, isolation, and estimation (FDI&E) methodology is proposed and developed specifically for monitoring the aircraft gas turbine engine actuator and sensors. The proposed FDI&E filters are directly constructed by using only the available system I/O data at each operating point of the engine. The healthy gas turbine engine is stimulated by a sinusoidal input containing a limited number of frequencies. First, the associated system Markov parameters are estimated by using the FFT of the input and output signals to obtain the frequency response of the gas turbine engine. These data are then used for direct design and realization of the fault detection, isolation and estimation filters. Our proposed scheme therefore does not require any a priori knowledge of the system linear model or its number of poles and zeros at each operating point. We have investigated the effects of the size of the frequency response data on the performance of our proposed schemes. We have shown through comprehensive case studies simulations that desirable fault detection, isolation and estimation performance metrics defined in terms of the confusion matrix criterion can be achieved by having access to only the frequency response of the system at only a limited number of frequencies.

Complex changes in the apoptotic and cell differentiation programs during initiation of the hair follicle response to chemotherapy.

PubMed

Sharova, Tatyana Y; Poterlowicz, Krzysztof; Botchkareva, Natalia V; Kondratiev, Nikita A; Aziz, Ahmar; Spiegel, Jeffrey H; Botchkarev, Vladimir A; Sharov, Andrey A

2014-12-01

Chemotherapy has severe side effects in normal rapidly proliferating organs, such as hair follicles, and causes massive apoptosis in hair matrix keratinocytes followed by hair loss. To define the molecular signature of hair follicle response to chemotherapy, human scalp hair follicles cultured ex vivo were treated with doxorubicin (DXR), and global microarray analysis was performed 3 hours after treatment. Microarray data revealed changes in expression of 504 genes in DXR-treated hair follicles versus controls. Among these genes, upregulations of several tumor necrosis factor family of apoptotic receptors (FAS, TRAIL (tumor necrosis factor-related apoptosis-inducing ligand) receptors 1/2), as well as of a large number of keratin-associated protein genes, were seen after DXR treatment. Hair follicle apoptosis induced by DXR was significantly inhibited by either TRAIL-neutralizing antibody or caspase-8 inhibitor, thus suggesting a previously unreported role for TRAIL receptor signaling in mediating DXR-induced hair loss. These data demonstrate that the early phase of the hair follicle response to DXR includes upregulation of apoptosis-associated markers, as well as substantial reorganization of the terminal differentiation programs in hair follicle keratinocytes. These data provide an important platform for further studies toward the design of effective approaches for the management of chemotherapy-induced hair loss.

Complex changes in the apoptotic and cell differentiation programs during initiation of the hair follicle response to chemotherapy

PubMed Central

Sharova, Tatyana Y.; Poterlowicz, Krzysztof; Botchkareva, Natalia V.; Kondratiev, Nikita A.; Aziz, Ahmar; Spiegel, Jeffrey H.; Botchkarev, Vladimir A.; Sharov, Andrey A.

2014-01-01

Chemotherapy has severe side-effects for normal rapidly proliferating organs, such as hair follicle, and causes massive apoptosis in hair matrix keratinocytes followed by hair loss. To define the molecular signature of hair follicle response to chemotherapy, human scalp hair follicles cultured ex vivo were treated with doxorubicin and global microarray analysis was performed 3 hours after treatment. Microarray data revealed changes in expression of 504 genes in doxorubicin-treated hair follicles versus the controls. Among these genes, upregulations of several tumor necrosis factor family of apoptotic receptors (FAS, TRAIL receptors 1/2), as well as of a large number of the keratin-associated protein genes were seen after doxorubicin treatment. Hair follicle apoptosis induced by doxorubicin was significantly inhibited by either TRAIL neutralizing antibody or caspase 8 inhibitor, thus suggesting a novel role for TRAIL receptor signaling in mediating doxorubicin-induced hair loss. These data demonstrate that the early phase of the hair follicle response to doxorubicin includes upregulation of apoptosis-associated markers, as well as substantial re-organization of the terminal differentiation programs in hair follicle keratinocytes. These data provide an important platform for further studies towards the design of novel approaches for management of chemotherapy-induced hair loss. PMID:24999588

The choice of the source space and the Laplacian matrix in LORETA and the spatio-temporal Kalman filter EEG inverse methods.

PubMed

Habboush, Nawar; Hamid, Laith; Japaridze, Natia; Wiegand, Gert; Heute, Ulrich; Stephani, Ulrich; Galka, Andreas; Siniatchkin, Michael

2015-08-01

The discretization of the brain and the definition of the Laplacian matrix influence the results of methods based on spatial and spatio-temporal smoothness, since the Laplacian operator is used to define the smoothness based on the neighborhood of each grid point. In this paper, the results of low resolution electromagnetic tomography (LORETA) and the spatiotemporal Kalman filter (STKF) are computed using, first, a greymatter source space with the standard definition of the Laplacian matrix and, second, using a whole-brain source space and a modified definition of the Laplacian matrix. Electroencephalographic (EEG) source imaging results of five inter-ictal spikes from a pre-surgical patient with epilepsy are used to validate the two aforementioned approaches. The results using the whole-brain source space and the modified definition of the Laplacian matrix were concentrated in a single source activation, stable, and concordant with the location of the focal cortical dysplasia (FCD) in the patient's brain compared with the results which use a grey-matter grid and the classical definition of the Laplacian matrix. This proof-of-concept study demonstrates a substantial improvement of source localization with both LORETA and STKF and constitutes a basis for further research in a large population of patients with epilepsy.

Reversed headspace analysis for characterization, identification, and analysis of solid and liquid matrices: Part I.

PubMed

Markelov, M; Bershevits, O

2006-03-01

This paper offers a methodology of an experimentally simple reversed headspace (RHS) analysis for measuring of matrix effects and their use for identification and characterization of condensed matrices such as pharmaceuticals, polymers, chromatographic packing, etc. applicable for both quality control monitoring and research and development investigation. In RHS methods, the matrix is spiked and equilibrated with a mixture of volatile chemicals containing various functional groups (molecular sensor array or MSA mixture). Headspace chromatograms of the same spikes of a sample and an empty vial are compared. Examination of basic headspace theory shows that matrix specific constants (M), rather than partition coefficients (K), can be calculated from the headspace chromatograms and M=(K-1)xbeta, where beta is a degree of matrix volume change during equilibration. Matrix specific constants can be plotted against any property of chemicals (polarity, dielectric constant, solubility parameter, vapor pressure, etc.) or just against a set of consecutive numbers, each representing a chemical in MSA. This plot is, in a sense, a molecular affinity spectrum (MAS) specific for a given matrix at a given temperature and is independent of an instrument. Changes in MAS that correspond to chemicals with a particular functional group give an insight to the type of differences between matrices and may quantitatively define them.

Multi-allelic haplotype model based on genetic partition for genomic prediction and variance component estimation using SNP markers.

PubMed

Da, Yang

2015-12-18

The amount of functional genomic information has been growing rapidly but remains largely unused in genomic selection. Genomic prediction and estimation using haplotypes in genome regions with functional elements such as all genes of the genome can be an approach to integrate functional and structural genomic information for genomic selection. Towards this goal, this article develops a new haplotype approach for genomic prediction and estimation. A multi-allelic haplotype model treating each haplotype as an 'allele' was developed for genomic prediction and estimation based on the partition of a multi-allelic genotypic value into additive and dominance values. Each additive value is expressed as a function of h - 1 additive effects, where h = number of alleles or haplotypes, and each dominance value is expressed as a function of h(h - 1)/2 dominance effects. For a sample of q individuals, the limit number of effects is 2q - 1 for additive effects and is the number of heterozygous genotypes for dominance effects. Additive values are factorized as a product between the additive model matrix and the h - 1 additive effects, and dominance values are factorized as a product between the dominance model matrix and the h(h - 1)/2 dominance effects. Genomic additive relationship matrix is defined as a function of the haplotype model matrix for additive effects, and genomic dominance relationship matrix is defined as a function of the haplotype model matrix for dominance effects. Based on these results, a mixed model implementation for genomic prediction and variance component estimation that jointly use haplotypes and single markers is established, including two computing strategies for genomic prediction and variance component estimation with identical results. The multi-allelic genetic partition fills a theoretical gap in genetic partition by providing general formulations for partitioning multi-allelic genotypic values and provides a haplotype method based on the quantitative genetics model towards the utilization of functional and structural genomic information for genomic prediction and estimation.

Vibrational response and mechanical properties characterization of aluminium alloy 6061/Sic composite

NASA Astrophysics Data System (ADS)

Kumbhar, A. P.; Vyavahare, R. T.; Kulkarni, S. G.

2018-05-01

Aluminium alloy based metal matrix composites (AAMMC) are mainly used in sliding wear application, automobile, Aircraft and aerospace components, Marine fittings, Transport and other industry are becoming highly advantageous due to their excellent wear resistance, lighter weight, higher strength and durability. In this paper the effect of reinforcement percentage on vibration response and mechanical properties of metal matrix composite has been investigated. Composite material was prepared by varying Sic (0, 3, 6, and 9 wt. %) by stir casting method. Natural frequency, tensile strength, rockwell hardness and compressive strength were analyzed. The result shows that, addition of sic in aluminium matrix increases natural frequency, hardness, tensile strength, compressive strength and 9 wt. % showed maximum natural frequency, hardness, tensile strength, compressive strength.

Characterizing species interactions to understand press perturbations: What is the community matrix?

USGS Publications Warehouse

Novak, Mark; Yeakel, Justin D.; Noble, Andrew E.; Doak, Daniel F.; Emmerson, Mark; Estes, James A.; Jacob, Ute; Tinker, M. Tim; Wootton, J. Timothy

2016-01-01

The community matrix is among ecology's most important mathematical abstractions, formally encapsulating the interconnected network of effects that species have on one another's populations. Despite its importance, the term `community matrix' has been applied to matrices having differing interpretations. This has hindered the application of theory for understanding community structure and perturbation responses, particularly in the contexts of ecosystem-based management and conservation. Here we clarify the correspondence and distinctions between the Interaction matrix, the Alpha matrix and the Jacobian matrix, terms which are frequently used interchangeably and have numerous synonyms, including the term Community matrix. We illustrate how these matrices correspond to different ways of characterizing interaction strengths, how they permit insights regarding different types of press perturbations of species growth rates or abundances, and how these are related by a simple scaling relationship. Connections to additional interaction strength characterizations encapsulated by the Beta matrix, the Gamma matrix, and the Removal matrix are also discussed. Our synthesis highlights the empirical challenges that remain in using these mathematical tools to understand actual communities.

Nonlinearity and Strain-Rate Dependence in the Deformation Response of Polymer Matrix Composites Modeled

NASA Technical Reports Server (NTRS)

Goldberg, Robert K.

2000-01-01

There has been no accurate procedure for modeling the high-speed impact of composite materials, but such an analytical capability will be required in designing reliable lightweight engine-containment systems. The majority of the models in use assume a linear elastic material response that does not vary with strain rate. However, for containment systems, polymer matrix composites incorporating ductile polymers are likely to be used. For such a material, the deformation response is likely to be nonlinear and to vary with strain rate. An analytical model has been developed at the NASA Glenn Research Center at Lewis Field that incorporates both of these features. A set of constitutive equations that was originally developed to analyze the viscoplastic deformation of metals (Ramaswamy-Stouffer equations) was modified to simulate the nonlinear, rate-dependent deformation of polymers. Specifically, the effects of hydrostatic stresses on the inelastic response, which can be significant in polymers, were accounted for by a modification of the definition of the effective stress. The constitutive equations were then incorporated into a composite micromechanics model based on the mechanics of materials theory. This theory predicts the deformation response of a composite material from the properties and behavior of the individual constituents. In this manner, the nonlinear, rate-dependent deformation response of a polymer matrix composite can be predicted.

Apparent mass matrix of standing subjects exposed to multi-axial whole-body vibration.

PubMed

Tarabini, Marco; Solbiati, Stefano; Saggin, Bortolino; Scaccabarozzi, Diego

2016-08-01

This paper describes the experimental characterisation of the apparent mass matrix of eight male subjects in standing position and the identification of nonlinearities under both mono-axial and dual-axis whole-body vibration. The nonlinear behaviour of the response was studied using the conditioned response techniques considering models of increasing complexity. Results showed that the cross-axis terms are comparable to the diagonal terms. The contribution of the nonlinear effects are minor and can be endorsed to the change of modal parameters during the tests. The nonlinearity generated by the vibration magnitude is more evident in the subject response, since magnitude-dependent effects in the population are overlaid by the scatter in the subjects' biometric data. The biodynamic response is influenced by the addition of a secondary vibration axis and, in case of dual-axis vibrations, the overall magnitude has a marginal contribution. Practitioner Summary: We have measured both the diagonal and cross-axis elements of the apparent mass matrix. The effect of nonlinearities and the simultaneous presence of vibration along two axes are smaller than the inter-subject variability.

Nipah virus matrix protein: expert hacker of cellular machines.

PubMed

Watkinson, Ruth E; Lee, Benhur

2016-08-01

Nipah virus (NiV, Henipavirus) is a highly lethal emergent zoonotic paramyxovirus responsible for repeated human outbreaks of encephalitis in South East Asia. There are no approved vaccines or treatments, thus improved understanding of NiV biology is imperative. NiV matrix protein recruits a plethora of cellular machinery to scaffold and coordinate virion budding. Intriguingly, matrix also hijacks cellular trafficking and ubiquitination pathways to facilitate transient nuclear localization. While the biological significance of matrix nuclear localization for an otherwise cytoplasmic virus remains enigmatic, the molecular details have begun to be characterized, and are conserved among matrix proteins from divergent paramyxoviruses. Matrix protein appropriation of cellular machinery will be discussed in terms of its early nuclear targeting and later role in virion assembly. © 2016 Federation of European Biochemical Societies.

Public data mining plus domestic experimental study defined involvement of the old-yet-uncharacterized gene matrix-remodeling associated 7 (MXRA7) in physiopathology of the eye.

PubMed

Jia, Changkai; Zhang, Feng; Zhu, Ying; Qi, Xia; Wang, Yiqiang

2017-10-20

Matrix-remodeling associated 7 (MXRA7) gene was first reported in 2002 and named so for its co-expression with several genes known to relate with matrix-remodeling. However, not any studies had been intentionally performed to characterize this gene. We started defining the functions of MXRA7 by integrating bioinformatics analysis and experimental study. Data mining of MXRA7 expression in BioGPS, Gene Expression Omnibus and EurExpress platforms highlighted high level expression of Mxra7 in murine ocular tissues. Real-time PCR was employed to measure Mxra7 mRNA in tissues of adult C57BL/6 mice and demonstrated that Mxra7 was preferentially expressed at higher level in retina, corneas and lens than in other tissues. Then the inflammatory corneal neovascularization (CorNV) model and fungal corneal infections were induced in Balb/c mice, and mRNA levels of Mxra7 as well as several matrix-remodeling related genes (Mmp3, Mmp13, Ecm1, Timp1) were monitored with RT-PCR. The results demonstrated a time-dependent Mxra7 under-expression pattern (U-shape curve along timeline), while all other matrix-remodeling related genes manifested an opposite changes pattern (dome-shape curve). When limited data from BioGPS concerning human MXRA7 gene expression in human tissues were looked at, it was found that ocular tissue was also the one expressing highest level of MXRA7. To conclude, integrative assay of MXRA7 gene expression in public databank as well as domestic animal models revealed a selective high expression MXRA7 in murine and human ocular tissues, and its change patterns in two corneal disease models implied that MXRA7 might play a role in pathological processes or diseases involving injury, neovascularization and would healing. Copyright © 2017 Elsevier B.V. All rights reserved.

The neuroscience of body memory: From the self through the space to the others.

PubMed

Riva, Giuseppe

2017-07-25

Our experience of the body is not direct; rather, it is mediated by perceptual information, influenced by internal information, and recalibrated through stored implicit and explicit body representation (body memory). This paper presents an overview of the current investigations related to body memory by bringing together recent studies from neuropsychology, neuroscience, and evolutionary and cognitive psychology. To do so, in the paper, I explore the origin of representations of human body to elucidate their developmental process and, in particular, their relationship with more explicit concepts of self. First, it is suggested that our bodily experience is constructed from early development through the continuous integration of sensory and cultural data from six different representations of the body, i.e., the Sentient Body (Minimal Selfhood), the Spatial Body (Self Location), the Active Body (Agency), the Personal Body (Whole Body Ownership - Me); the Objectified Body (Objectified Self - Mine), and the Social Body (Body Satisfaction - Ideal Me). Then, it is suggested that these six representations can be combined in a coherent supramodal representation, i.e. the "body matrix", through a predictive, multisensory processing activated by central, top-down, attentional processes. From an evolutionary perspective, the main goal of the body matrix is to allow the self to protect and extend its boundaries at both the homeostatic and psychological levels. From one perspective, the self extends its boundaries (peripersonal space) through the enactment and recognition of motor schemas. From another perspective, the body matrix, by defining the boundaries of the body, also defines where the self is present, i.e., in the body that is processed by the body matrix as the most likely to be its one, and in the space surrounding it. In the paper I also introduce and discuss the concept of "embodied medicine": the use of advanced technology for altering the body matrix with the goal of improving our health and well-being. Copyright © 2017 The Author(s). Published by Elsevier Ltd.. All rights reserved.

Swimming of an assembly of rigid spheres at low Reynolds number.

PubMed

Felderhof, B U

2014-11-01

A matrix formulation is derived for the calculation of the swimming speed and the power required for swimming of an assembly of rigid spheres immersed in a viscous fluid of infinite extent. The spheres may have arbitrary radii and may interact with elastic forces. The analysis is based on the Stokes mobility matrix of the set of spheres, defined in low Reynolds number hydrodynamics. For small amplitude, swimming optimization of the swimming speed at given power leads to an eigenvalue problem. The method allows straightforward calculation of the swimming performance of structures modeled as assemblies of interacting rigid spheres.

Fluorescence excitation-emission matrix spectroscopy for degradation monitoring of machinery lubricants

NASA Astrophysics Data System (ADS)

Sosnovski, Oleg; Suresh, Pooja; Dudelzak, Alexander E.; Green, Benjamin

2018-02-01

Lubrication oil is a vital component of heavy rotating machinery defining the machine's health, operational safety and effectiveness. Recently, the focus has been on developing sensors that provide real-time/online monitoring of oil condition/lubricity. Industrial practices and standards for assessing oil condition involve various analytical methods. Most these techniques are unsuitable for online applications. The paper presents the results of studying degradation of antioxidant additives in machinery lubricants using Fluorescence Excitation-Emission Matrix (EEM) Spectroscopy and Machine Learning techniques. EEM Spectroscopy is capable of rapid and even standoff sensing; it is potentially applicable to real-time online monitoring.

On Poisson's ratio for metal matrix composite laminates. [aluminum boron composites

NASA Technical Reports Server (NTRS)

Herakovich, C. T.; Shuart, M. J.

1978-01-01

The definition of Poisson's ratio for nonlinear behavior of metal matrix composite laminates is discussed and experimental results for tensile and compressive loading of five different boron-aluminum laminates are presented. It is shown that there may be considerable difference in the value of Poisson's ratio as defined by a total strain or an incremental strain definition. It is argued that the incremental definition is more appropriate for nonlinear material behavior. Results from a (0) laminate indicate that the incremental definition provides a precursor to failure which is not evident if the total strain definition is used.

Simulating Initial and Progressive Failure of Open-Hole Composite Laminates under Tension

NASA Astrophysics Data System (ADS)

Guo, Zhangxin; Zhu, Hao; Li, Yongcun; Han, Xiaoping; Wang, Zhihua

2016-12-01

A finite element (FE) model is developed for the progressive failure analysis of fiber reinforced polymer laminates. The failure criterion for fiber and matrix failure is implemented in the FE code Abaqus using user-defined material subroutine UMAT. The gradual degradation of the material properties is controlled by the individual fracture energies of fiber and matrix. The failure and damage in composite laminates containing a central hole subjected to uniaxial tension are simulated. The numerical results show that the damage model can be used to accurately predicte the progressive failure behaviour both qualitatively and quantitatively.

Efficient propagation of the hierarchical equations of motion using the matrix product state method

NASA Astrophysics Data System (ADS)

Shi, Qiang; Xu, Yang; Yan, Yaming; Xu, Meng

2018-05-01

We apply the matrix product state (MPS) method to propagate the hierarchical equations of motion (HEOM). It is shown that the MPS approximation works well in different type of problems, including boson and fermion baths. The MPS method based on the time-dependent variational principle is also found to be applicable to HEOM with over one thousand effective modes. Combining the flexibility of the HEOM in defining the effective modes and the efficiency of the MPS method thus may provide a promising tool in simulating quantum dynamics in condensed phases.

On using the Hilbert transform for blind identification of complex modes: A practical approach

NASA Astrophysics Data System (ADS)

Antunes, Jose; Debut, Vincent; Piteau, Pilippe; Delaune, Xavier; Borsoi, Laurent

2018-01-01

The modal identification of dynamical systems under operational conditions, when subjected to wide-band unmeasured excitations, is today a viable alternative to more traditional modal identification approaches based on processing sets of measured FRFs or impulse responses. Among current techniques for performing operational modal identification, the so-called blind identification methods are the subject of considerable investigation. In particular, the SOBI (Second-Order Blind Identification) method was found to be quite efficient. SOBI was originally developed for systems with normal modes. To address systems with complex modes, various extension approaches have been proposed, in particular: (a) Using a first-order state-space formulation for the system dynamics; (b) Building complex analytic signals from the measured responses using the Hilbert transform. In this paper we further explore the latter option, which is conceptually interesting while preserving the model order and size. Focus is on applicability of the SOBI technique for extracting the modal responses from analytic signals built from a set of vibratory responses. The novelty of this work is to propose a straightforward computational procedure for obtaining the complex cross-correlation response matrix to be used for the modal identification procedure. After clarifying subtle aspects of the general theoretical framework, we demonstrate that the correlation matrix of the analytic responses can be computed through a Hilbert transform of the real correlation matrix, so that the actual time-domain responses are no longer required for modal identification purposes. The numerical validation of the proposed technique is presented based on time-domain simulations of a conceptual physical multi-modal system, designed to display modes ranging from normal to highly complex, while keeping modal damping low and nearly independent of the modal complexity, and which can prove very interesting in test bench applications. Numerical results for complex modal identifications are presented, and the quality of the identified modal matrix and modal responses, extracted using the complex SOBI technique and implementing the proposed formulation, is assessed.

Double-scaling limits of random matrices and minimal (2m, 1) models: the merging of two cuts in a degenerate case

NASA Astrophysics Data System (ADS)

Marchal, O.; Cafasso, M.

2011-04-01

In this paper, we show that the double-scaling-limit correlation functions of a random matrix model when two cuts merge with degeneracy 2m (i.e. when y ~ x2m for arbitrary values of the integer m) are the same as the determinantal formulae defined by conformal (2m, 1) models. Our approach follows the one developed by Bergère and Eynard in (2009 arXiv:0909.0854) and uses a Lax pair representation of the conformal (2m, 1) models (giving a Painlevé II integrable hierarchy) as suggested by Bleher and Eynard in (2003 J. Phys. A: Math. Gen. 36 3085). In particular we define Baker-Akhiezer functions associated with the Lax pair in order to construct a kernel which is then used to compute determinantal formulae giving the correlation functions of the double-scaling limit of a matrix model near the merging of two cuts.

On the inversion of geodetic integrals defined over the sphere using 1-D FFT

NASA Astrophysics Data System (ADS)

García, R. V.; Alejo, C. A.

2005-08-01

An iterative method is presented which performs inversion of integrals defined over the sphere. The method is based on one-dimensional fast Fourier transform (1-D FFT) inversion and is implemented with the projected Landweber technique, which is used to solve constrained least-squares problems reducing the associated 1-D cyclic-convolution error. The results obtained are as precise as the direct matrix inversion approach, but with better computational efficiency. A case study uses the inversion of Hotine’s integral to obtain gravity disturbances from geoid undulations. Numerical convergence is also analyzed and comparisons with respect to the direct matrix inversion method using conjugate gradient (CG) iteration are presented. Like the CG method, the number of iterations needed to get the optimum (i.e., small) error decreases as the measurement noise increases. Nevertheless, for discrete data given over a whole parallel band, the method can be applied directly without implementing the projected Landweber method, since no cyclic convolution error exists.

Manifold learning-based subspace distance for machinery damage assessment

NASA Astrophysics Data System (ADS)

Sun, Chuang; Zhang, Zhousuo; He, Zhengjia; Shen, Zhongjie; Chen, Binqiang

2016-03-01

Damage assessment is very meaningful to keep safety and reliability of machinery components, and vibration analysis is an effective way to carry out the damage assessment. In this paper, a damage index is designed by performing manifold distance analysis on vibration signal. To calculate the index, vibration signal is collected firstly, and feature extraction is carried out to obtain statistical features that can capture signal characteristics comprehensively. Then, manifold learning algorithm is utilized to decompose feature matrix to be a subspace, that is, manifold subspace. The manifold learning algorithm seeks to keep local relationship of the feature matrix, which is more meaningful for damage assessment. Finally, Grassmann distance between manifold subspaces is defined as a damage index. The Grassmann distance reflecting manifold structure is a suitable metric to measure distance between subspaces in the manifold. The defined damage index is applied to damage assessment of a rotor and the bearing, and the result validates its effectiveness for damage assessment of machinery component.

Evaluation of entropy and JM-distance criterions as features selection methods using spectral and spatial features derived from LANDSAT images

NASA Technical Reports Server (NTRS)

Parada, N. D. J. (Principal Investigator); Dutra, L. V.; Mascarenhas, N. D. A.; Mitsuo, Fernando Augusta, II

1984-01-01

A study area near Ribeirao Preto in Sao Paulo state was selected, with predominance in sugar cane. Eight features were extracted from the 4 original bands of LANDSAT image, using low-pass and high-pass filtering to obtain spatial features. There were 5 training sites in order to acquire the necessary parameters. Two groups of four channels were selected from 12 channels using JM-distance and entropy criterions. The number of selected channels was defined by physical restrictions of the image analyzer and computacional costs. The evaluation was performed by extracting the confusion matrix for training and tests areas, with a maximum likelihood classifier, and by defining performance indexes based on those matrixes for each group of channels. Results show that in spatial features and supervised classification, the entropy criterion is better in the sense that allows a more accurate and generalized definition of class signature. On the other hand, JM-distance criterion strongly reduces the misclassification within training areas.

Calibration of the ROSAT HRI Spectral Response

NASA Technical Reports Server (NTRS)

Prestwich, Andrea

1998-01-01

The ROSAT High Resolution Imager has a limited (2-band) spectral response. This spectral capability can give X-ray hardness ratios on spatial scales of 5 arcseconds. The spectral response of the center of the detector was calibrated before the launch of ROSAT, but the gain decreases-with time and also is a function of position on the detector. To complicate matters further, the satellite is "wobbled", possibly moving a source across several spatial gain states. These difficulties have prevented the spectral response of the ROSAT HRI from being used for scientific measurements. We have used Bright Earth data and in-flight calibration sources to map the spatial and temporal gain changes, and written software which will allow ROSAT users to generate a calibrated XSPEC response matrix and hence determine a calibrated hardness ratio. In this report, we describe the calibration procedure and show how to obtain a response matrix. In Section 2 we give an overview of the calibration procedure, in Section 3 we give a summary of HRI spatial and temporal gain variations. Section 4 describes the routines used to determine the gain distribution of a source. In Sections 5 and 6, we describe in detail how the Bright Earth database and calibration sources are used to derive a corrected response matrix for a given observation. Finally, Section 7 describes how to use the software.

Calibration of the ROSAT HRI Spectral Response

NASA Technical Reports Server (NTRS)

Prestwich, Andrea H.; Silverman, John; McDowell, Jonathan; Callanan, Paul; Snowden, Steve

2000-01-01

The ROSAT High Resolution Imager has a limited (2-band) spectral response. This spectral capability can give X-ray hardness ratios on spatial scales of 5 arcseconds. The spectral response of the center of the detector was calibrated before the launch of ROSAT, but the gain decreases with time and also is a function of position on the detector. To complicate matters further, the satellite is 'wobbled', possibly moving a source across several spatial gain states. These difficulties have prevented the spectral response of the ROSAT High Resolution Imager (HRI) from being used for scientific measurements. We have used Bright Earth data and in-flight calibration sources to map the spatial and temporal gain changes, and written software which will allow ROSAT users to generate a calibrated XSPEC (an x ray spectral fitting package) response matrix and hence determine a calibrated hardness ratio. In this report, we describe the calibration procedure and show how to obtain a response matrix. In Section 2 we give an overview of the calibration procedure, in Section 3 we give a summary of HRI spatial and temporal gain variations. Section 4 describes the routines used to determine the gain distribution of a source. In Sections 5 and 6, we describe in detail how, the Bright Earth database and calibration sources are used to derive a corrected response matrix for a given observation. Finally, Section 7 describes how to use the software.

Linear spin-2 fields in most general backgrounds

NASA Astrophysics Data System (ADS)

Bernard, Laura; Deffayet, Cédric; Schmidt-May, Angnis; von Strauss, Mikael

2016-04-01

We derive the full perturbative equations of motion for the most general background solutions in ghost-free bimetric theory in its metric formulation. Clever field redefinitions at the level of fluctuations enable us to circumvent the problem of varying a square-root matrix appearing in the theory. This greatly simplifies the expressions for the linear variation of the bimetric interaction terms. We show that these field redefinitions exist and are uniquely invertible if and only if the variation of the square-root matrix itself has a unique solution, which is a requirement for the linearized theory to be well defined. As an application of our results we examine the constraint structure of ghost-free bimetric theory at the level of linear equations of motion for the first time. We identify a scalar combination of equations which is responsible for the absence of the Boulware-Deser ghost mode in the theory. The bimetric scalar constraint is in general not manifestly covariant in its nature. However, in the massive gravity limit the constraint assumes a covariant form when one of the interaction parameters is set to zero. For that case our analysis provides an alternative and almost trivial proof of the absence of the Boulware-Deser ghost. Our findings generalize previous results in the metric formulation of massive gravity and also agree with studies of its vielbein version.

Tendon exhibits complex poroelastic behavior at the nanoscale as revealed by high-frequency AFM-based rheology.

PubMed

Connizzo, Brianne K; Grodzinsky, Alan J

2017-03-21

Tendons transmit load from muscle to bone by utilizing their unique static and viscoelastic tensile properties. These properties are highly dependent on the composition and structure of the tissue matrix, including the collagen I hierarchy, proteoglycans, and water. While the role of matrix constituents in the tensile response has been studied, their role in compression, particularly in matrix pressurization via regulation of fluid flow, is not well understood. Injured or diseased tendons and tendon regions that naturally experience compression are known to have alterations in glycosaminoglycan content, which could modulate fluid flow and ultimately mechanical function. While recent theoretical studies have predicted tendon mechanics using poroelastic theory, no experimental data have directly demonstrated such behavior. In this study, we use high-bandwidth AFM-based rheology to determine the dynamic response of tendons to compressive loading at the nanoscale and to determine the presence of poroelastic behavior. Tendons are found to have significant characteristic dynamic relaxation behavior occurring at both low and high frequencies. Classic poroelastic behavior is observed, although we hypothesize that the full dynamic response is caused by a combination of flow-dependent poroelasticity as well as flow-independent viscoelasticity. Tendons also demonstrate regional dependence in their dynamic response, particularly near the junction of tendon and bone, suggesting that the structural and compositional heterogeneity in tendon may be responsible for regional poroelastic behavior. Overall, these experiments provide the foundation for understanding fluid-flow-dependent poroelastic mechanics of tendon, and the methodology is valuable for assessing changes in tendon matrix compressive behavior at the nanoscale. Copyright © 2017 Elsevier Ltd. All rights reserved.